PARADIGM pathway analysis of mRNASeq expression and copy number data
Brain Lower Grade Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1FN15NM
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1FN15NM
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 56 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
Ephrin A reverse signaling 87
IL23-mediated signaling events 87
Signaling mediated by p38-alpha and p38-beta 67
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 62
FOXM1 transcription factor network 62
Aurora B signaling 61
Signaling events regulated by Ret tyrosine kinase 58
IL12-mediated signaling events 56
TCR signaling in naïve CD8+ T cells 56
Syndecan-1-mediated signaling events 53
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 516 . 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 ( 516 ).

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
Ephrin A reverse signaling 0.1686 87 611 7 -0.063 0 1000 -1000 -0.007 -1000
IL23-mediated signaling events 0.1686 87 5278 60 -0.49 0.026 1000 -1000 -0.073 -1000
Signaling mediated by p38-alpha and p38-beta 0.1298 67 2948 44 -0.1 0.026 1000 -1000 -0.019 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1202 62 4227 68 -0.3 0.18 1000 -1000 -0.074 -1000
FOXM1 transcription factor network 0.1202 62 3181 51 -0.27 0.026 1000 -1000 -0.092 -1000
Aurora B signaling 0.1182 61 4090 67 -0.26 0.046 1000 -1000 -0.031 -1000
Signaling events regulated by Ret tyrosine kinase 0.1124 58 4803 82 -0.074 0.026 1000 -1000 -0.042 -1000
IL12-mediated signaling events 0.1085 56 4956 87 -0.4 0.073 1000 -1000 -0.078 -1000
TCR signaling in naïve CD8+ T cells 0.1085 56 5223 93 -0.18 0.21 1000 -1000 -0.04 -1000
Syndecan-1-mediated signaling events 0.1027 53 1819 34 -0.075 0.026 1000 -1000 -0.027 -1000
Thromboxane A2 receptor signaling 0.1008 52 5461 105 -0.13 0.034 1000 -1000 -0.032 -1000
Endothelins 0.0950 49 4725 96 -0.13 0.026 1000 -1000 -0.043 -1000
Signaling events mediated by the Hedgehog family 0.0911 47 2488 52 -0.093 0.048 1000 -1000 -0.029 -1000
Effects of Botulinum toxin 0.0911 47 1224 26 -0.088 0.026 1000 -1000 -0.001 -1000
Syndecan-4-mediated signaling events 0.0911 47 3214 67 -0.094 0.035 1000 -1000 -0.03 -1000
Reelin signaling pathway 0.0891 46 2617 56 -0.1 0.059 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 0.0891 46 371 8 -0.023 0.042 1000 -1000 -0.002 -1000
ErbB2/ErbB3 signaling events 0.0814 42 2749 65 -0.1 0.037 1000 -1000 -0.048 -1000
FOXA2 and FOXA3 transcription factor networks 0.0814 42 1933 46 -0.22 0.03 1000 -1000 -0.09 -1000
Syndecan-3-mediated signaling events 0.0795 41 1442 35 -0.061 0.063 1000 -1000 -0.018 -1000
Arf6 signaling events 0.0775 40 2490 62 -0.14 0.054 1000 -1000 -0.03 -1000
Aurora C signaling 0.0756 39 273 7 -0.072 0.011 1000 -1000 -0.015 -1000
IL4-mediated signaling events 0.0736 38 3475 91 -0.42 0.27 1000 -1000 -0.11 -1000
Visual signal transduction: Rods 0.0736 38 2025 52 -0.1 0.026 1000 -1000 -0.024 -1000
Caspase cascade in apoptosis 0.0717 37 2748 74 -0.13 0.05 1000 -1000 -0.034 -1000
HIF-1-alpha transcription factor network 0.0717 37 2839 76 -0.11 0.056 1000 -1000 -0.048 -1000
a4b1 and a4b7 Integrin signaling 0.0717 37 187 5 -0.008 0.012 1000 -1000 0.007 -1000
E-cadherin signaling events 0.0717 37 188 5 -0.046 0.026 1000 -1000 0.006 -1000
amb2 Integrin signaling 0.0698 36 2976 82 -0.15 0.028 1000 -1000 -0.024 -1000
BCR signaling pathway 0.0698 36 3648 99 -0.095 0.044 1000 -1000 -0.045 -1000
Glypican 2 network 0.0678 35 142 4 -0.002 0.004 1000 -1000 0.007 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0678 35 2646 74 -0.063 0.059 1000 -1000 -0.049 -1000
EGFR-dependent Endothelin signaling events 0.0678 35 741 21 -0.034 0.037 1000 -1000 -0.034 -1000
Ras signaling in the CD4+ TCR pathway 0.0678 35 601 17 -0.054 0.034 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 0.0659 34 4325 125 -0.073 0.063 1000 -1000 -0.046 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0659 34 1782 52 -0.15 0.067 1000 -1000 -0.031 -1000
LPA receptor mediated events 0.0659 34 3513 102 -0.1 0.03 1000 -1000 -0.067 -1000
Osteopontin-mediated events 0.0640 33 1291 38 -0.05 0.027 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 0.0640 33 1753 52 -0.075 0.036 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0620 32 2750 85 -0.17 0.038 1000 -1000 -0.036 -1000
PDGFR-alpha signaling pathway 0.0620 32 1408 44 -0.1 0.032 1000 -1000 -0.029 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0581 30 1634 54 -0.073 0.033 1000 -1000 -0.028 -1000
Glypican 1 network 0.0581 30 1450 48 -0.08 0.05 1000 -1000 -0.022 -1000
Fc-epsilon receptor I signaling in mast cells 0.0581 30 2951 97 -0.06 0.042 1000 -1000 -0.052 -1000
Ceramide signaling pathway 0.0581 30 2294 76 -0.068 0.045 1000 -1000 -0.028 -1000
Calcium signaling in the CD4+ TCR pathway 0.0581 30 951 31 -0.094 0.025 1000 -1000 -0.043 -1000
IL1-mediated signaling events 0.0562 29 1846 62 -0.073 0.045 1000 -1000 -0.025 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0562 29 2620 88 -0.087 0.029 1000 -1000 -0.059 -1000
BMP receptor signaling 0.0523 27 2226 81 -0.079 0.044 1000 -1000 -0.033 -1000
PLK1 signaling events 0.0523 27 2318 85 -0.078 0.038 1000 -1000 -0.031 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0523 27 999 37 -0.034 0.046 1000 -1000 -0.022 -1000
S1P5 pathway 0.0523 27 459 17 -0.053 0.026 1000 -1000 -0.01 -1000
Ephrin B reverse signaling 0.0523 27 1298 48 -0.027 0.027 1000 -1000 -0.017 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0504 26 907 34 -0.017 0.04 1000 -1000 -0.019 -1000
Visual signal transduction: Cones 0.0504 26 1010 38 -0.055 0.034 1000 -1000 -0.007 -1000
IL6-mediated signaling events 0.0504 26 1998 75 -0.1 0.04 1000 -1000 -0.04 -1000
Regulation of nuclear SMAD2/3 signaling 0.0484 25 3438 136 -0.18 0.16 1000 -1000 -0.037 -1000
Glucocorticoid receptor regulatory network 0.0484 25 2897 114 -0.27 0.14 1000 -1000 -0.065 -1000
Canonical Wnt signaling pathway 0.0484 25 1322 51 -0.13 0.066 1000 -1000 -0.041 -1000
JNK signaling in the CD4+ TCR pathway 0.0465 24 414 17 -0.025 0.026 1000 -1000 -0.025 -1000
Noncanonical Wnt signaling pathway 0.0465 24 626 26 -0.048 0.026 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 0.0465 24 1893 76 -0.046 0.048 1000 -1000 -0.045 -1000
Coregulation of Androgen receptor activity 0.0446 23 1753 76 -0.082 0.05 1000 -1000 -0.016 -1000
TCGA08_p53 0.0446 23 164 7 -0.017 0.025 1000 -1000 -0.011 -1000
Presenilin action in Notch and Wnt signaling 0.0426 22 1378 61 -0.13 0.063 1000 -1000 -0.036 -1000
FAS signaling pathway (CD95) 0.0426 22 1071 47 -0.099 0.039 1000 -1000 -0.038 -1000
EPHB forward signaling 0.0426 22 1890 85 -0.029 0.054 1000 -1000 -0.046 -1000
Syndecan-2-mediated signaling events 0.0407 21 1466 69 -0.061 0.038 1000 -1000 -0.029 -1000
Cellular roles of Anthrax toxin 0.0407 21 856 39 -0.13 0.029 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0407 21 1257 58 -0.088 0.051 1000 -1000 -0.05 -1000
TCGA08_rtk_signaling 0.0407 21 571 26 -0.047 0.061 1000 -1000 -0.007 -1000
Rapid glucocorticoid signaling 0.0407 21 428 20 -0.075 0.027 1000 -1000 -0.004 -1000
E-cadherin signaling in keratinocytes 0.0407 21 909 43 -0.046 0.027 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class III 0.0388 20 814 40 -0.064 0.05 1000 -1000 -0.021 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0388 20 2493 120 -0.11 0.074 1000 -1000 -0.035 -1000
IL27-mediated signaling events 0.0368 19 996 51 -0.085 0.026 1000 -1000 -0.048 -1000
S1P1 pathway 0.0349 18 680 36 -0.095 0.026 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 0.0349 18 1090 58 -0.075 0.041 1000 -1000 -0.032 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0349 18 1471 78 -0.017 0.037 1000 -1000 -0.055 -1000
Signaling events mediated by PTP1B 0.0329 17 1297 76 -0.072 0.04 1000 -1000 -0.04 -1000
EPO signaling pathway 0.0329 17 973 55 -0.029 0.07 1000 -1000 -0.034 -1000
ceramide signaling pathway 0.0329 17 840 49 -0.06 0.037 1000 -1000 -0.034 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0310 16 1403 83 -0.094 0.051 1000 -1000 -0.024 -1000
IL2 signaling events mediated by STAT5 0.0310 16 363 22 -0.028 0.027 1000 -1000 -0.04 -1000
LPA4-mediated signaling events 0.0291 15 181 12 -0.031 0.005 1000 -1000 -0.019 -1000
Paxillin-dependent events mediated by a4b1 0.0291 15 556 36 -0.038 0.047 1000 -1000 -0.027 -1000
Integrins in angiogenesis 0.0291 15 1317 84 -0.024 0.057 1000 -1000 -0.037 -1000
Wnt signaling 0.0291 15 105 7 -0.007 0.01 1000 -1000 -0.013 -1000
Plasma membrane estrogen receptor signaling 0.0291 15 1351 86 -0.039 0.038 1000 -1000 -0.04 -1000
S1P4 pathway 0.0291 15 397 25 -0.053 0.045 1000 -1000 -0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0271 14 661 45 -0.06 0.061 1000 -1000 -0.05 -1000
Signaling events mediated by PRL 0.0271 14 481 34 -0.059 0.033 1000 -1000 -0.029 -1000
Regulation of Androgen receptor activity 0.0271 14 1030 70 -0.066 0.036 1000 -1000 -0.047 -1000
BARD1 signaling events 0.0252 13 755 57 -0.041 0.051 1000 -1000 -0.033 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0252 13 387 28 -0.053 0.032 1000 -1000 -0.016 -1000
VEGFR1 specific signals 0.0252 13 749 56 -0.038 0.055 1000 -1000 -0.035 -1000
TRAIL signaling pathway 0.0233 12 615 48 -0.001 0.063 1000 -1000 -0.028 -1000
Regulation of p38-alpha and p38-beta 0.0233 12 696 54 -0.055 0.056 1000 -1000 -0.048 -1000
Class I PI3K signaling events 0.0233 12 916 73 -0.074 0.048 1000 -1000 -0.037 -1000
Regulation of Telomerase 0.0233 12 1270 102 -0.13 0.065 1000 -1000 -0.042 -1000
ErbB4 signaling events 0.0213 11 813 69 -0.071 0.045 1000 -1000 -0.032 -1000
Insulin-mediated glucose transport 0.0213 11 378 32 -0.04 0.051 1000 -1000 -0.031 -1000
IFN-gamma pathway 0.0213 11 768 68 -0.099 0.056 1000 -1000 -0.042 -1000
PDGFR-beta signaling pathway 0.0213 11 1069 97 -0.072 0.072 1000 -1000 -0.04 -1000
Atypical NF-kappaB pathway 0.0194 10 319 31 -0.019 0.038 1000 -1000 -0.016 -1000
Insulin Pathway 0.0194 10 761 74 -0.071 0.062 1000 -1000 -0.037 -1000
Aurora A signaling 0.0174 9 543 60 -0.058 0.058 1000 -1000 -0.012 -1000
Nectin adhesion pathway 0.0174 9 614 63 -0.046 0.066 1000 -1000 -0.055 -1000
Signaling mediated by p38-gamma and p38-delta 0.0174 9 146 15 -0.016 0.026 1000 -1000 -0.026 -1000
Class I PI3K signaling events mediated by Akt 0.0155 8 607 68 -0.032 0.048 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class I 0.0155 8 930 104 -0.06 0.059 1000 -1000 -0.029 -1000
Canonical NF-kappaB pathway 0.0136 7 299 39 -0.06 0.059 1000 -1000 -0.025 -1000
HIF-2-alpha transcription factor network 0.0136 7 331 43 -0.058 0.059 1000 -1000 -0.039 -1000
FoxO family signaling 0.0136 7 478 64 -0.033 0.079 1000 -1000 -0.053 -1000
IGF1 pathway 0.0136 7 425 57 -0.014 0.064 1000 -1000 -0.035 -1000
S1P3 pathway 0.0136 7 321 42 0 0.038 1000 -1000 -0.032 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0136 7 235 33 -0.029 0.065 1000 -1000 -0.033 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0116 6 797 125 -0.02 0.065 1000 -1000 -0.032 -1000
Arf6 trafficking events 0.0116 6 485 71 -0.05 0.048 1000 -1000 -0.021 -1000
Class IB PI3K non-lipid kinase events 0.0116 6 18 3 -0.02 0.02 1000 -1000 -0.008 -1000
p38 MAPK signaling pathway 0.0116 6 305 44 -0.018 0.042 1000 -1000 -0.031 -1000
Circadian rhythm pathway 0.0097 5 110 22 -0.007 0.038 1000 -1000 -0.035 -1000
Hedgehog signaling events mediated by Gli proteins 0.0097 5 367 65 -0.006 0.059 1000 -1000 -0.043 -1000
Arf6 downstream pathway 0.0097 5 254 43 -0.043 0.049 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class II 0.0078 4 357 75 -0.094 0.071 1000 -1000 -0.016 -1000
PLK2 and PLK4 events 0.0078 4 12 3 0.001 -1000 1000 -1000 -0.012 -1000
mTOR signaling pathway 0.0078 4 260 53 -0.018 0.041 1000 -1000 -0.028 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 39 23 -0.001 0.05 1000 -1000 -0.028 -1000
Arf1 pathway 0.0019 1 60 54 -0.001 0.039 1000 -1000 -0.016 -1000
Alternative NF-kappaB pathway 0.0019 1 15 13 0 0.059 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 0 0.061 1000 -1000 -0.023 -1000
Total NA 3279 188474 7203 -10 -990 131000 -131000 -4.2 -131000
Ephrin A reverse signaling

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.052 0.14 -10000 0 -0.28 126 126
EFNA5 -0.029 0.14 -10000 0 -0.43 48 48
FYN -0.056 0.13 0.18 6 -0.29 100 106
neuron projection morphogenesis -0.052 0.14 -10000 0 -0.28 126 126
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.052 0.14 -10000 0 -0.28 126 126
EPHA5 -0.063 0.16 -10000 0 -0.43 79 79
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.42 0.54 -9999 0 -1.2 132 132
IL23A -0.44 0.55 -9999 0 -1.2 140 140
NF kappa B1 p50/RelA/I kappa B alpha -0.39 0.53 -9999 0 -1.2 130 130
positive regulation of T cell mediated cytotoxicity -0.45 0.6 -9999 0 -1.3 140 140
ITGA3 -0.39 0.5 -9999 0 -1.2 121 121
IL17F -0.26 0.32 -9999 0 -0.71 130 130
IL12B -0.02 0.045 -9999 0 -0.16 5 5
STAT1 (dimer) -0.43 0.57 -9999 0 -1.2 140 140
CD4 -0.37 0.49 -9999 0 -1.1 118 118
IL23 -0.42 0.53 -9999 0 -1.2 143 143
IL23R -0.2 0.38 -9999 0 -1.1 75 75
IL1B -0.46 0.59 -9999 0 -1.3 140 140
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.38 0.49 -9999 0 -1.1 121 121
TYK2 -0.007 0.035 -9999 0 -10000 0 0
STAT4 -0.064 0.16 -9999 0 -0.26 162 162
STAT3 0.026 0.003 -9999 0 -10000 0 0
IL18RAP -0.023 0.13 -9999 0 -0.28 84 84
IL12RB1 -0.032 0.1 -9999 0 -0.37 34 34
PIK3CA 0.025 0.02 -9999 0 -0.43 1 1
IL12Rbeta1/TYK2 -0.022 0.082 -9999 0 -0.31 26 26
IL23R/JAK2 -0.19 0.36 -9999 0 -1.1 64 64
positive regulation of chronic inflammatory response -0.45 0.6 -9999 0 -1.3 140 140
natural killer cell activation 0.005 0.007 -9999 0 -10000 0 0
JAK2 -0.008 0.042 -9999 0 -10000 0 0
PIK3R1 0.026 0.003 -9999 0 -10000 0 0
NFKB1 0.024 0.005 -9999 0 -10000 0 0
RELA 0.023 0.006 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.39 0.49 -9999 0 -1.1 148 148
ALOX12B -0.45 0.55 -9999 0 -1.2 153 153
CXCL1 -0.43 0.54 -9999 0 -1.2 138 138
T cell proliferation -0.45 0.6 -9999 0 -1.3 140 140
NFKBIA 0.024 0.005 -9999 0 -10000 0 0
IL17A -0.2 0.25 -9999 0 -0.55 122 122
PI3K -0.4 0.54 -9999 0 -1.2 137 137
IFNG -0.018 0.031 -9999 0 -0.11 20 20
STAT3 (dimer) -0.38 0.51 -9999 0 -1.1 131 131
IL18R1 -0.006 0.11 -9999 0 -0.42 27 27
IL23/IL23R/JAK2/TYK2/SOCS3 -0.26 0.36 -9999 0 -0.78 112 112
IL18/IL18R -0.004 0.13 -9999 0 -0.29 76 76
macrophage activation -0.019 0.02 -9999 0 -0.044 133 133
TNF -0.46 0.59 -9999 0 -1.3 139 139
STAT3/STAT4 -0.43 0.55 -9999 0 -1.2 144 144
STAT4 (dimer) -0.45 0.58 -9999 0 -1.2 145 145
IL18 0.002 0.093 -9999 0 -0.29 39 39
IL19 -0.38 0.48 -9999 0 -1.1 121 121
STAT5A (dimer) -0.43 0.57 -9999 0 -1.2 138 138
STAT1 0.021 0.028 -9999 0 -0.13 16 16
SOCS3 -0.029 0.12 -9999 0 -0.43 30 30
CXCL9 -0.45 0.55 -9999 0 -1.2 151 151
MPO -0.45 0.56 -9999 0 -1.2 153 153
positive regulation of humoral immune response -0.45 0.6 -9999 0 -1.3 140 140
IL23/IL23R/JAK2/TYK2 -0.49 0.69 -9999 0 -1.4 136 136
IL6 -0.4 0.54 -9999 0 -1.2 125 125
STAT5A 0.016 0.066 -9999 0 -0.43 11 11
IL2 0.01 0.019 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.007 -9999 0 -10000 0 0
CD3E -0.43 0.55 -9999 0 -1.2 141 141
keratinocyte proliferation -0.45 0.6 -9999 0 -1.3 140 140
NOS2 -0.4 0.51 -9999 0 -1.2 126 126
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.33 -10000 0 -0.97 62 62
MKNK1 0.022 0.01 -10000 0 -10000 0 0
MAPK14 -0.015 0.12 -10000 0 -0.29 74 74
ATF2/c-Jun -0.021 0.1 -10000 0 -0.42 11 11
MAPK11 -0.024 0.13 -10000 0 -0.31 83 83
MITF -0.026 0.14 0.3 1 -0.33 83 84
MAPKAPK5 -0.027 0.14 -10000 0 -0.34 83 83
KRT8 -0.064 0.18 -10000 0 -0.37 114 114
MAPKAPK3 0.025 0.021 -10000 0 -0.43 1 1
MAPKAPK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.03 0.18 -10000 0 -0.42 83 83
CEBPB -0.034 0.16 -10000 0 -0.37 84 84
SLC9A1 -0.04 0.16 0.3 1 -0.39 81 82
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.023 0.15 -10000 0 -0.33 85 85
p38alpha-beta/MNK1 -0.011 0.14 -10000 0 -0.33 81 81
JUN -0.019 0.097 -10000 0 -0.42 11 11
PPARGC1A -0.04 0.17 -10000 0 -0.38 91 91
USF1 -0.025 0.14 0.3 1 -0.34 81 82
RAB5/GDP/GDI1 -0.012 0.11 -10000 0 -0.25 83 83
NOS2 -0.054 0.23 -10000 0 -0.93 24 24
DDIT3 -0.026 0.14 0.22 1 -0.34 82 83
RAB5A 0.026 0.004 -10000 0 -10000 0 0
HSPB1 0.007 0.15 0.28 68 -0.28 75 143
p38alpha-beta/HBP1 -0.008 0.14 -10000 0 -0.33 71 71
CREB1 -0.03 0.15 -10000 0 -0.36 82 82
RAB5/GDP 0.019 0.003 -10000 0 -10000 0 0
EIF4E -0.033 0.12 0.24 4 -0.3 75 79
RPS6KA4 -0.025 0.14 -10000 0 -0.34 80 80
PLA2G4A -0.04 0.13 0.2 1 -0.33 76 77
GDI1 -0.026 0.14 -10000 0 -0.34 83 83
TP53 -0.053 0.17 -10000 0 -0.42 82 82
RPS6KA5 -0.033 0.15 -10000 0 -0.35 89 89
ESR1 -0.035 0.15 -10000 0 -0.35 89 89
HBP1 0.02 0.011 -10000 0 -10000 0 0
MEF2C -0.028 0.14 -10000 0 -0.34 82 82
MEF2A -0.028 0.14 -10000 0 -0.35 82 82
EIF4EBP1 -0.034 0.15 -10000 0 -0.36 81 81
KRT19 -0.062 0.18 -10000 0 -0.37 116 116
ELK4 -0.025 0.14 0.3 1 -0.34 81 82
ATF6 -0.025 0.14 0.3 1 -0.34 81 82
ATF1 -0.033 0.15 -10000 0 -0.37 84 84
p38alpha-beta/MAPKAPK2 0 0.15 -10000 0 -0.33 81 81
p38alpha-beta/MAPKAPK3 -0.002 0.15 -10000 0 -0.34 82 82
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.004 0.075 -10000 0 -0.25 30 30
NFATC2 -0.083 0.23 -10000 0 -0.57 60 60
NFATC3 -0.036 0.11 -10000 0 -0.27 67 67
CD40LG -0.24 0.4 -10000 0 -0.94 106 106
ITCH -0.024 0.091 -10000 0 -0.22 86 86
CBLB -0.023 0.093 -10000 0 -0.44 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.36 -10000 0 -0.89 81 81
JUNB 0.007 0.072 -10000 0 -0.21 39 39
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.11 -10000 0 -0.26 87 87
T cell anergy -0.066 0.16 0.26 1 -0.39 88 89
TLE4 -0.06 0.17 -10000 0 -0.5 44 44
Jun/NFAT1-c-4/p21SNFT -0.2 0.44 -10000 0 -0.98 105 105
AP-1/NFAT1-c-4 -0.24 0.5 -10000 0 -1.1 106 106
IKZF1 -0.063 0.18 -10000 0 -0.58 39 39
T-helper 2 cell differentiation -0.14 0.28 -10000 0 -0.81 48 48
AP-1/NFAT1 -0.063 0.18 -10000 0 -0.43 67 67
CALM1 -0.01 0.072 -10000 0 -0.2 2 2
EGR2 -0.24 0.51 -10000 0 -1.1 100 100
EGR3 -0.26 0.55 -10000 0 -1.3 94 94
NFAT1/FOXP3 -0.054 0.19 -10000 0 -0.47 56 56
EGR1 -0.043 0.14 -10000 0 -0.27 111 111
JUN 0.009 0.031 -10000 0 -0.14 9 9
EGR4 -0.088 0.17 -10000 0 -0.38 108 108
mol:Ca2+ -0.025 0.06 -10000 0 -0.15 88 88
GBP3 -0.079 0.22 -10000 0 -0.62 63 63
FOSL1 -0.028 0.13 -10000 0 -0.25 97 97
NFAT1-c-4/MAF/IRF4 -0.19 0.43 -10000 0 -0.96 106 106
DGKA -0.057 0.16 -10000 0 -0.46 43 43
CREM 0.023 0.022 -10000 0 -0.43 1 1
NFAT1-c-4/PPARG -0.2 0.44 -10000 0 -0.99 106 106
CTLA4 -0.079 0.19 -10000 0 -0.52 63 63
NFAT1-c-4 (dimer)/EGR1 -0.23 0.47 -10000 0 -1.1 106 106
NFAT1-c-4 (dimer)/EGR4 -0.24 0.46 -10000 0 -1 108 108
FOS -0.041 0.14 -10000 0 -0.35 70 70
IFNG -0.1 0.21 -10000 0 -0.66 35 35
T cell activation -0.11 0.23 -10000 0 -0.69 35 35
MAF 0.024 0.035 -10000 0 -0.43 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.18 0.38 0.84 106 -10000 0 106
TNF -0.3 0.44 -10000 0 -0.99 124 124
FASLG -0.26 0.55 -10000 0 -1.3 101 101
TBX21 -0.004 0.099 -10000 0 -0.39 27 27
BATF3 0.001 0.091 -10000 0 -0.26 45 45
PRKCQ 0.015 0.061 -10000 0 -0.43 9 9
PTPN1 -0.058 0.16 -10000 0 -0.48 36 36
NFAT1-c-4/ICER1 -0.19 0.43 -10000 0 -0.97 105 105
GATA3 -0.038 0.14 -10000 0 -0.43 49 49
T-helper 1 cell differentiation -0.1 0.2 -10000 0 -0.64 37 37
IL2RA -0.17 0.32 -10000 0 -0.82 69 69
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.055 0.16 -10000 0 -0.46 41 41
E2F1 0.017 0.057 -10000 0 -0.36 8 8
PPARG 0.009 0.081 -10000 0 -0.43 16 16
SLC3A2 -0.055 0.16 -10000 0 -0.48 38 38
IRF4 -0.006 0.1 -10000 0 -0.28 53 53
PTGS2 -0.26 0.43 -10000 0 -1 109 109
CSF2 -0.24 0.39 -10000 0 -0.95 106 106
JunB/Fra1/NFAT1-c-4 -0.2 0.43 -10000 0 -0.96 105 105
IL4 -0.15 0.3 -10000 0 -0.87 46 46
IL5 -0.24 0.4 -10000 0 -0.94 106 106
IL2 -0.12 0.23 -10000 0 -0.71 33 33
IL3 -0.024 0.082 -10000 0 -0.65 4 4
RNF128 -0.085 0.2 -10000 0 -0.52 88 88
NFATC1 -0.18 0.38 -10000 0 -0.85 106 106
CDK4 0.11 0.21 0.59 47 -10000 0 47
PTPRK -0.057 0.16 -10000 0 -0.49 38 38
IL8 -0.26 0.42 -10000 0 -0.97 114 114
POU2F1 0.025 0.02 -10000 0 -0.43 1 1
FOXM1 transcription factor network

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.18 0.49 -9999 0 -1.1 84 84
PLK1 0.006 0.15 -9999 0 -1.3 6 6
BIRC5 -0.19 0.51 -9999 0 -1.4 75 75
HSPA1B -0.19 0.5 -9999 0 -1.2 83 83
MAP2K1 0.01 0.045 -9999 0 -0.18 1 1
BRCA2 -0.19 0.51 -9999 0 -1.2 83 83
FOXM1 -0.27 0.7 -9999 0 -1.7 85 85
XRCC1 -0.18 0.49 -9999 0 -1.2 77 77
FOXM1B/p19 -0.19 0.5 -9999 0 -1.2 83 83
Cyclin D1/CDK4 -0.17 0.45 -9999 0 -1 83 83
CDC2 -0.19 0.52 -9999 0 -1.2 85 85
TGFA -0.16 0.44 -9999 0 -1 86 86
SKP2 -0.19 0.5 -9999 0 -1.2 81 81
CCNE1 0.016 0.022 -9999 0 -0.14 2 2
CKS1B -0.18 0.49 -9999 0 -1.1 87 87
RB1 -0.1 0.32 -9999 0 -0.85 56 56
FOXM1C/SP1 -0.22 0.59 -9999 0 -1.4 87 87
AURKB -0.23 0.56 -9999 0 -1.4 90 90
CENPF -0.2 0.52 -9999 0 -1.3 77 77
CDK4 0.014 0.026 -9999 0 -10000 0 0
MYC -0.16 0.43 -9999 0 -0.99 88 88
CHEK2 0.004 0.066 -9999 0 -0.37 6 6
ONECUT1 -0.18 0.47 -9999 0 -1.1 85 85
CDKN2A -0.012 0.11 -9999 0 -0.3 55 55
LAMA4 -0.18 0.49 -9999 0 -1.2 79 79
FOXM1B/HNF6 -0.23 0.58 -9999 0 -1.4 85 85
FOS -0.26 0.56 -9999 0 -1.2 124 124
SP1 0.025 0.009 -9999 0 -10000 0 0
CDC25B -0.18 0.49 -9999 0 -1.2 78 78
response to radiation 0 0.026 -9999 0 -10000 0 0
CENPB -0.18 0.49 -9999 0 -1.2 79 79
CENPA -0.21 0.53 -9999 0 -1.3 84 84
NEK2 -0.23 0.56 -9999 0 -1.3 92 92
HIST1H2BA -0.18 0.48 -9999 0 -1.2 80 80
CCNA2 -0.012 0.1 -9999 0 -0.24 63 63
EP300 0.022 0.04 -9999 0 -0.43 4 4
CCNB1/CDK1 -0.22 0.59 -9999 0 -1.5 78 78
CCNB2 -0.23 0.57 -9999 0 -1.4 89 89
CCNB1 -0.19 0.52 -9999 0 -1.3 79 79
ETV5 -0.19 0.49 -9999 0 -1.2 84 84
ESR1 -0.2 0.5 -9999 0 -1.2 89 89
CCND1 -0.18 0.46 -9999 0 -1.1 84 84
GSK3A 0.012 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.012 0.091 -9999 0 -0.3 26 26
CDK2 0.014 0.049 -9999 0 -0.29 8 8
G2/M transition of mitotic cell cycle -0.003 0.03 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.2 0.55 -9999 0 -1.3 86 86
GAS1 -0.18 0.49 -9999 0 -1.2 78 78
MMP2 -0.19 0.5 -9999 0 -1.2 82 82
RB1/FOXM1C -0.19 0.48 -9999 0 -1.1 85 85
CREBBP 0.026 0.003 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.071 0.19 -10000 0 -0.41 101 101
STMN1 -0.047 0.12 0.18 3 -0.31 76 79
Aurora B/RasGAP/Survivin -0.057 0.19 -10000 0 -0.33 137 137
Chromosomal passenger complex/Cul3 protein complex -0.069 0.15 -10000 0 -0.35 87 87
BIRC5 -0.064 0.17 -10000 0 -0.43 80 80
DES -0.26 0.45 -10000 0 -0.86 167 167
Aurora C/Aurora B/INCENP -0.013 0.11 -10000 0 -0.24 94 94
Aurora B/TACC1 -0.027 0.11 -10000 0 -0.26 87 87
Aurora B/PP2A -0.034 0.13 -10000 0 -0.31 87 87
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.019 0.059 -10000 0 -0.14 92 92
mitotic metaphase/anaphase transition 0.001 0.005 -10000 0 -10000 0 0
NDC80 -0.095 0.19 0.19 6 -0.36 145 151
Cul3 protein complex 0.046 0.027 -10000 0 -0.26 2 2
KIF2C -0.093 0.25 -10000 0 -0.48 104 104
PEBP1 0.015 0.04 -10000 0 -0.44 3 3
KIF20A -0.079 0.17 -10000 0 -0.43 93 93
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.035 0.13 -10000 0 -0.31 88 88
SEPT1 0.024 0.024 -10000 0 -0.19 5 5
SMC2 0.026 0.004 -10000 0 -10000 0 0
SMC4 0.017 0.036 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.12 0.3 0.24 1 -0.76 90 91
PSMA3 0.026 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.043 0.12 0.12 1 -0.3 88 89
AURKB -0.074 0.18 -10000 0 -0.31 151 151
AURKC 0.011 0.051 -10000 0 -0.18 26 26
CDCA8 -0.01 0.075 -10000 0 -0.18 62 62
cytokinesis -0.16 0.32 0.22 2 -0.73 109 111
Aurora B/Septin1 -0.13 0.32 0.26 2 -0.7 105 107
AURKA 0.018 0.038 -10000 0 -0.15 22 22
INCENP 0.015 0.029 -10000 0 -0.44 1 1
KLHL13 0.025 0.028 -10000 0 -0.43 2 2
BUB1 -0.043 0.15 -10000 0 -0.31 97 97
hSgo1/Aurora B/Survivin -0.083 0.22 -10000 0 -0.37 161 161
EVI5 0.021 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.11 0.29 -10000 0 -0.63 103 103
SGOL1 -0.047 0.15 -10000 0 -0.28 122 122
CENPA -0.1 0.25 0.18 2 -0.56 102 104
NCAPG -0.061 0.16 -10000 0 -0.43 77 77
Aurora B/HC8 Proteasome -0.035 0.13 -10000 0 -0.31 88 88
NCAPD2 0.024 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.035 0.13 -10000 0 -0.31 88 88
RHOA 0.026 0.004 -10000 0 -10000 0 0
NCAPH -0.015 0.12 -10000 0 -0.26 73 73
NPM1 -0.083 0.2 -10000 0 -0.5 94 94
RASA1 0.026 0.003 -10000 0 -10000 0 0
KLHL9 0.024 0.008 -10000 0 -10000 0 0
mitotic prometaphase -0.004 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.13 -10000 0 -0.31 88 88
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin -0.13 0.31 0.2 1 -0.67 106 107
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
NSUN2 -0.082 0.2 -10000 0 -0.51 91 91
MYLK -0.049 0.12 -10000 0 -0.29 98 98
KIF23 -0.036 0.13 -10000 0 -0.25 108 108
VIM -0.081 0.15 0.18 6 -0.32 128 134
RACGAP1 0.017 0.022 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.085 0.21 -10000 0 -0.53 90 90
Chromosomal passenger complex -0.13 0.29 0.19 1 -0.64 107 108
Chromosomal passenger complex/EVI5 -0.043 0.19 -10000 0 -0.32 140 140
TACC1 0.025 0.005 -10000 0 -10000 0 0
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.008 0.071 -10000 0 -0.39 11 11
Crk/p130 Cas/Paxillin -0.051 0.12 -10000 0 -0.28 76 76
JUN -0.061 0.14 -10000 0 -0.27 119 119
HRAS 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.018 0.15 -10000 0 -0.28 111 111
RAP1A 0.021 0.01 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.016 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.025 0.16 -10000 0 -0.28 133 133
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.004 0.12 -10000 0 -0.26 86 86
RHOA 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.038 0.15 -10000 0 -0.26 135 135
GRB7 0.001 0.044 -10000 0 -0.13 41 41
RET51/GFRalpha1/GDNF -0.019 0.15 -10000 0 -0.28 121 121
MAPKKK cascade -0.049 0.14 -10000 0 -0.28 125 125
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.003 0.12 -10000 0 -0.26 84 84
lamellipodium assembly -0.036 0.1 -10000 0 -0.26 65 65
RET51/GFRalpha1/GDNF/SHC -0.023 0.16 -10000 0 -0.28 127 127
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC -0.003 0.12 -10000 0 -0.26 83 83
RET9/GFRalpha1/GDNF/Shank3 -0.006 0.12 -10000 0 -0.26 88 88
MAPK3 -0.074 0.12 0.17 5 -0.26 123 128
DOK1 0.025 0.021 -10000 0 -0.28 2 2
DOK6 -0.017 0.13 -10000 0 -0.43 46 46
PXN 0.026 0.004 -10000 0 -10000 0 0
neurite development -0.067 0.13 -10000 0 -0.36 52 52
DOK5 0.016 0.066 -10000 0 -0.43 11 11
GFRA1 -0.015 0.12 -10000 0 -0.31 61 61
MAPK8 -0.062 0.14 -10000 0 -0.28 133 133
HRAS/GTP -0.035 0.17 -10000 0 -0.3 132 132
tube development 0 0.12 0.2 14 -0.25 82 96
MAPK1 -0.074 0.12 0.17 5 -0.26 124 129
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.11 -10000 0 -0.25 82 82
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
PDLIM7 0.023 0.021 -10000 0 -0.13 9 9
RET51/GFRalpha1/GDNF/Dok6 -0.028 0.18 -10000 0 -0.31 133 133
SHC1 0.024 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.032 0.17 -10000 0 -0.29 138 138
RET51/GFRalpha1/GDNF/Dok5 -0.026 0.16 -10000 0 -0.28 131 131
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
CREB1 -0.041 0.14 -10000 0 -0.31 85 85
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.025 0.11 -10000 0 -0.26 81 81
RET51/GFRalpha1/GDNF/Grb7 -0.028 0.16 -10000 0 -0.28 135 135
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.044 0.15 -10000 0 -0.3 107 107
DOK4 0.012 0.079 -10000 0 -0.43 16 16
JNK cascade -0.062 0.13 0.19 1 -0.4 44 45
RET9/GFRalpha1/GDNF/FRS2 -0.004 0.12 -10000 0 -0.26 86 86
SHANK3 0.021 0.035 -10000 0 -0.19 10 10
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.1 -10000 0 -0.25 81 81
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.053 0.15 -10000 0 -0.28 130 130
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.15 -10000 0 -0.28 134 134
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.051 0.15 -10000 0 -0.28 123 123
PI3K -0.06 0.16 0.23 1 -0.38 81 82
SOS1 0.026 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.006 0.12 -10000 0 -0.25 82 82
GRB10 0.021 0.03 -10000 0 -0.43 2 2
activation of MAPKK activity -0.052 0.14 -10000 0 -0.34 85 85
RET51/GFRalpha1/GDNF/FRS2 -0.025 0.16 -10000 0 -0.28 134 134
GAB1 0.025 0.02 -10000 0 -0.43 1 1
IRS1 0.026 0.003 -10000 0 -10000 0 0
IRS2 0.024 0.021 -10000 0 -0.43 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.053 0.15 -10000 0 -0.29 123 123
RET51/GFRalpha1/GDNF/PKC alpha -0.025 0.16 -10000 0 -0.28 129 129
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GDNF -0.034 0.15 -10000 0 -0.38 73 73
RAC1 0.023 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.023 0.16 -10000 0 -0.28 131 131
Rac1/GTP -0.037 0.12 -10000 0 -0.3 63 63
RET9/GFRalpha1/GDNF -0.028 0.12 -10000 0 -0.28 86 86
GFRalpha1/GDNF -0.035 0.14 -10000 0 -0.34 86 86
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.073 0.13 -10000 0 -0.35 61 61
TBX21 -0.33 0.46 -10000 0 -1.1 121 121
B2M 0.025 0.016 -10000 0 -0.13 5 5
TYK2 -0.002 0.034 -10000 0 -10000 0 0
IL12RB1 -0.027 0.1 -10000 0 -0.37 33 33
GADD45B -0.24 0.36 -10000 0 -0.85 85 85
IL12RB2 -0.049 0.12 -10000 0 -0.28 74 74
GADD45G -0.25 0.38 -10000 0 -1 68 68
natural killer cell activation -0.012 0.02 -10000 0 -0.043 80 80
RELB 0.02 0.025 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
IL18 -0.005 0.095 -10000 0 -0.3 38 38
IL2RA -0.015 0.071 -10000 0 -0.43 8 8
IFNG -0.008 0.021 -10000 0 -0.13 5 5
STAT3 (dimer) -0.24 0.33 -10000 0 -0.73 128 128
HLA-DRB5 -0.002 0.006 -10000 0 -0.02 41 41
FASLG -0.3 0.42 -10000 0 -0.98 111 111
NF kappa B2 p52/RelB -0.29 0.43 -10000 0 -0.93 128 128
CD4 0.017 0.035 -10000 0 -0.23 6 6
SOCS1 0.008 0.068 -10000 0 -0.43 8 8
EntrezGene:6955 -0.001 0.007 -10000 0 -0.023 41 41
CD3D -0.033 0.12 -10000 0 -0.38 39 39
CD3E -0.052 0.14 -10000 0 -0.26 130 130
CD3G 0.004 0.044 -10000 0 -0.15 2 2
IL12Rbeta2/JAK2 -0.029 0.096 -10000 0 -0.28 44 44
CCL3 -0.4 0.55 -10000 0 -1.3 128 128
CCL4 -0.39 0.56 -10000 0 -1.3 124 124
HLA-A 0 0.003 -10000 0 -0.049 1 1
IL18/IL18R -0.021 0.14 -10000 0 -0.31 76 76
NOS2 -0.28 0.41 -10000 0 -0.96 103 103
IL12/IL12R/TYK2/JAK2/SPHK2 -0.067 0.13 -10000 0 -0.36 57 57
IL1R1 -0.32 0.44 -10000 0 -1 107 107
IL4 0.017 0.034 -10000 0 -10000 0 0
JAK2 -0.003 0.034 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.007 -10000 0 -0.021 40 40
TCR/CD3/MHC I/CD8 -0.046 0.12 -10000 0 -0.4 35 35
RAB7A -0.19 0.3 0.52 1 -0.74 65 66
lysosomal transport -0.18 0.28 0.51 1 -0.69 67 68
FOS -0.23 0.44 -10000 0 -1.2 70 70
STAT4 (dimer) -0.28 0.38 0.5 1 -0.83 129 130
STAT5A (dimer) -0.3 0.43 -10000 0 -0.92 135 135
GZMA -0.37 0.5 -10000 0 -1.1 133 133
GZMB -0.36 0.49 -10000 0 -1.1 127 127
HLX 0.018 0.046 -10000 0 -0.21 16 16
LCK -0.34 0.47 -10000 0 -1 135 135
TCR/CD3/MHC II/CD4 -0.038 0.1 -10000 0 -0.26 56 56
IL2/IL2R 0.002 0.11 -10000 0 -0.24 68 68
MAPK14 -0.24 0.36 -10000 0 -0.83 95 95
CCR5 -0.28 0.42 -10000 0 -1 87 87
IL1B -0.094 0.16 -10000 0 -0.28 173 173
STAT6 -0.072 0.11 -10000 0 -0.48 4 4
STAT4 -0.064 0.16 -10000 0 -0.26 162 162
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.028 -10000 0 -0.13 16 16
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.023 0.03 -10000 0 -0.33 3 3
IL12B -0.012 0.038 -10000 0 -0.15 6 6
CD8A -0.024 0.13 -10000 0 -0.29 83 83
CD8B -0.002 0.1 -10000 0 -0.32 42 42
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.073 0.13 0.35 61 -10000 0 61
IL2RB -0.028 0.13 -10000 0 -0.43 39 39
proteasomal ubiquitin-dependent protein catabolic process -0.26 0.34 0.49 1 -0.75 129 130
IL2RG 0.001 0.087 -10000 0 -0.22 52 52
IL12 -0.019 0.084 -10000 0 -0.34 22 22
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
CD247 0.008 0.065 -10000 0 -0.21 30 30
IL2 -0.014 0.009 -10000 0 -10000 0 0
SPHK2 0.021 0.01 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.024 0.1 -10000 0 -0.43 25 25
IL12/IL12R/TYK2/JAK2 -0.36 0.52 -10000 0 -1.1 134 134
MAP2K3 -0.24 0.36 -10000 0 -0.81 102 102
RIPK2 0.024 0.007 -10000 0 -10000 0 0
MAP2K6 -0.24 0.36 -10000 0 -0.8 108 108
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.007 -10000 0 -0.023 43 43
IL18RAP -0.032 0.13 -10000 0 -0.3 76 76
IL12Rbeta1/TYK2 -0.017 0.086 -10000 0 -0.33 25 25
EOMES 0.022 0.097 -10000 0 -0.8 5 5
STAT1 (dimer) -0.24 0.32 -10000 0 -0.73 120 120
T cell proliferation -0.2 0.27 0.49 1 -0.6 118 119
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.014 0.11 -10000 0 -0.41 30 30
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.23 0.3 -10000 0 -0.66 124 124
ATF2 -0.22 0.33 0.51 1 -0.76 96 97
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 -0.046 0.17 0.23 19 -0.36 78 97
FYN -0.072 0.2 0.25 18 -0.44 89 107
LAT/GRAP2/SLP76 -0.074 0.17 0.23 5 -0.39 80 85
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.057 0.15 0.22 20 -0.33 83 103
B2M 0.021 0.021 -10000 0 -0.14 5 5
IKBKG -0.013 0.051 0.092 17 -0.12 28 45
MAP3K8 0.016 0.047 -10000 0 -0.2 17 17
mol:Ca2+ -0.016 0.027 0.089 12 -0.07 40 52
integrin-mediated signaling pathway 0.022 0.039 -10000 0 -0.24 9 9
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.081 0.2 0.25 16 -0.44 88 104
TRPV6 0.21 0.52 1.1 116 -0.45 39 155
CD28 -0.023 0.12 -10000 0 -0.28 80 80
SHC1 -0.074 0.19 0.23 25 -0.4 98 123
receptor internalization -0.059 0.15 0.24 2 -0.38 67 69
PRF1 -0.11 0.33 -10000 0 -0.96 55 55
KRAS 0.025 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.043 0.13 0.21 17 -0.28 76 93
LAT -0.084 0.19 0.23 16 -0.42 96 112
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.035 0.12 -10000 0 -0.38 41 41
CD3E -0.052 0.15 -10000 0 -0.27 127 127
CD3G 0.001 0.044 -10000 0 -10000 0 0
RASGRP2 -0.003 0.019 0.13 1 -0.16 2 3
RASGRP1 -0.065 0.16 0.26 17 -0.35 86 103
HLA-A -0.002 0.006 -10000 0 -10000 0 0
RASSF5 0.016 0.062 -10000 0 -0.3 16 16
RAP1A/GTP/RAPL 0.023 0.039 -10000 0 -0.24 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.065 0.16 35 -0.12 17 52
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.038 0.067 -10000 0 -0.18 62 62
PRKCA -0.045 0.088 0.15 5 -0.22 61 66
GRAP2 -0.007 0.1 -10000 0 -0.43 25 25
mol:IP3 -0.063 0.14 0.18 18 -0.31 87 105
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.055 0.14 -10000 0 -0.36 61 61
ORAI1 -0.18 0.43 0.44 14 -0.95 114 128
CSK -0.076 0.19 0.22 18 -0.41 98 116
B7 family/CD28 -0.065 0.21 0.26 8 -0.45 87 95
CHUK 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.09 0.2 0.26 1 -0.44 100 101
PTPN6 -0.085 0.19 0.22 4 -0.42 95 99
VAV1 -0.078 0.2 0.21 24 -0.41 103 127
Monovalent TCR/CD3 -0.044 0.11 -10000 0 -0.27 88 88
CBL 0.025 0.007 -10000 0 -10000 0 0
LCK -0.089 0.22 0.25 18 -0.45 104 122
PAG1 -0.073 0.19 0.21 27 -0.41 96 123
RAP1A 0.021 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.089 0.2 0.26 1 -0.44 97 98
CD80 -0.001 0.073 -10000 0 -0.18 55 55
CD86 0 0.1 -10000 0 -0.43 25 25
PDK1/CARD11/BCL10/MALT1 -0.04 0.084 -10000 0 -0.21 66 66
HRAS 0.025 0.006 -10000 0 -10000 0 0
GO:0035030 -0.078 0.17 0.21 17 -0.38 91 108
CD8A -0.027 0.13 -10000 0 -0.29 83 83
CD8B -0.006 0.1 -10000 0 -0.33 42 42
PTPRC -0.004 0.1 -10000 0 -0.43 24 24
PDK1/PKC theta -0.065 0.18 0.29 15 -0.4 80 95
CSK/PAG1 -0.074 0.18 0.21 19 -0.4 93 112
SOS1 0.026 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.019 -10000 0 -0.091 4 4
GRAP2/SLP76 -0.073 0.19 0.23 10 -0.41 96 106
STIM1 -0.008 0.2 1.2 10 -0.89 2 12
RAS family/GTP -0.011 0.08 0.18 22 -0.17 35 57
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.063 0.16 -10000 0 -0.4 67 67
mol:DAG -0.07 0.11 0.13 2 -0.27 99 101
RAP1A/GDP 0.004 0.027 0.077 22 -0.062 5 27
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.008 0.065 -10000 0 -0.21 30 30
cytotoxic T cell degranulation -0.1 0.31 -10000 0 -0.9 56 56
RAP1A/GTP 0 0.007 -10000 0 -0.05 4 4
mol:PI-3-4-5-P3 -0.067 0.17 0.24 17 -0.38 86 103
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.078 0.17 0.22 10 -0.39 85 95
NRAS 0.021 0.01 -10000 0 -10000 0 0
ZAP70 -0.004 0.098 -10000 0 -0.43 22 22
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.087 0.16 0.2 1 -0.38 87 88
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
CD8 heterodimer -0.023 0.13 -10000 0 -0.3 81 81
CARD11 0.012 0.067 -10000 0 -0.43 11 11
PRKCB -0.053 0.093 0.15 6 -0.22 74 80
PRKCE -0.047 0.09 0.15 6 -0.22 66 72
PRKCQ -0.074 0.2 0.28 14 -0.43 86 100
LCP2 0.02 0.033 -10000 0 -0.15 15 15
BCL10 0.021 0.01 -10000 0 -10000 0 0
regulation of survival gene product expression -0.048 0.13 0.21 21 -0.29 81 102
IKK complex -0.003 0.057 0.17 20 -0.11 7 27
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.034 0.1 0.17 19 -0.22 66 85
PDPK1 -0.055 0.15 0.23 20 -0.32 81 101
TCR/CD3/MHC I/CD8/Fyn -0.09 0.22 0.23 1 -0.51 87 88
Syndecan-1-mediated 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
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CCL5 -0.025 0.12 -10000 0 -0.43 39 39
SDCBP 0.025 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.065 0.14 0.24 6 -0.31 80 86
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.056 0.14 0.2 10 -0.34 59 69
Syndecan-1/Syntenin -0.048 0.14 0.24 15 -0.34 57 72
MAPK3 -0.051 0.13 0.2 14 -0.37 40 54
HGF/MET -0.04 0.12 -10000 0 -0.28 83 83
TGFB1/TGF beta receptor Type II 0.021 0.022 -10000 0 -0.43 1 1
BSG 0.025 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.055 0.14 0.2 10 -0.34 59 69
Syndecan-1/RANTES -0.068 0.16 0.24 15 -0.38 67 82
Syndecan-1/CD147 -0.043 0.14 0.24 4 -0.37 43 47
Syndecan-1/Syntenin/PIP2 -0.047 0.14 0.24 12 -0.34 54 66
LAMA5 0.024 0.022 -10000 0 -0.28 2 2
positive regulation of cell-cell adhesion -0.047 0.14 0.23 12 -0.33 54 66
MMP7 -0.073 0.16 -10000 0 -0.29 150 150
HGF -0.009 0.091 -10000 0 -0.2 69 69
Syndecan-1/CASK -0.069 0.13 -10000 0 -0.3 81 81
Syndecan-1/HGF/MET -0.075 0.16 0.24 4 -0.35 88 92
regulation of cell adhesion -0.043 0.14 0.26 25 -0.36 39 64
HPSE -0.014 0.12 -10000 0 -0.43 39 39
positive regulation of cell migration -0.065 0.14 0.24 6 -0.31 80 86
SDC1 -0.063 0.14 0.19 2 -0.31 85 87
Syndecan-1/Collagen -0.065 0.14 0.24 6 -0.31 80 86
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET -0.047 0.14 -10000 0 -0.43 52 52
PRKACA 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.23 133 133
MAPK1 -0.051 0.13 0.2 13 -0.36 40 53
homophilic cell adhesion -0.061 0.14 0.22 15 -0.32 74 89
MMP1 -0.008 0.048 -10000 0 -0.43 1 1
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.023 0.016 -10000 0 -10000 0 0
GNB1/GNG2 -0.055 0.077 -10000 0 -0.18 125 125
AKT1 -0.032 0.12 0.3 8 -0.27 30 38
EGF -0.01 0.11 -10000 0 -0.43 33 33
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.074 0.33 18 -0.22 2 20
mol:Ca2+ -0.051 0.16 0.33 7 -0.29 127 134
LYN 0.009 0.081 0.32 19 -0.24 4 23
RhoA/GTP -0.025 0.062 -10000 0 -0.13 112 112
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.18 0.31 11 -0.35 128 139
GNG2 0.022 0.04 -10000 0 -0.43 4 4
ARRB2 0.026 0.002 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.001 0.099 -10000 0 -0.4 21 21
G beta5/gamma2 -0.065 0.1 -10000 0 -0.24 123 123
PRKCH -0.064 0.17 0.33 7 -0.34 125 132
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
TXA2/TP beta/beta Arrestin3 -0.008 0.045 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.003 0.063 -10000 0 -0.16 52 52
G12 family/GTP -0.067 0.14 -10000 0 -0.3 116 116
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
ADRBK2 0.024 0.029 -10000 0 -0.33 3 3
RhoA/GTP/ROCK1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP 0.023 0.11 0.29 21 -0.31 9 30
mol:NADP 0.017 0.034 -10000 0 -0.28 4 4
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.009 0.12 -10000 0 -0.38 43 43
mol:IP3 -0.068 0.19 0.35 7 -0.37 127 134
cell morphogenesis 0.033 0.007 -10000 0 -10000 0 0
PLCB2 -0.1 0.25 0.39 6 -0.5 126 132
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.088 0.31 16 -0.21 12 28
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.071 0.3 9 -0.25 9 18
RHOA 0.026 0.004 -10000 0 -10000 0 0
PTGIR 0.012 0.049 -10000 0 -0.19 22 22
PRKCB1 -0.07 0.18 0.33 6 -0.36 128 134
GNAQ 0.026 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.034 -10000 0 -0.28 4 4
TXA2/TXA2-R family -0.11 0.25 0.39 6 -0.52 129 135
LCK -0.001 0.085 0.34 16 -0.23 2 18
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.005 0.048 -10000 0 -0.2 9 9
TXA2-R family/G12 family/GDP/G beta/gamma -0.048 0.17 -10000 0 -0.43 80 80
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.009 0.049 -10000 0 -0.2 9 9
MAPK14 -0.041 0.12 0.26 11 -0.23 125 136
TGM2/GTP -0.081 0.2 0.38 3 -0.41 126 129
MAPK11 -0.043 0.12 0.26 11 -0.23 126 137
ARHGEF1 -0.036 0.083 0.14 1 -0.18 113 114
GNAI2 0.025 0.005 -10000 0 -10000 0 0
JNK cascade -0.076 0.19 0.35 7 -0.38 129 136
RAB11/GDP 0.026 0.006 -10000 0 -10000 0 0
ICAM1 -0.054 0.15 0.3 6 -0.28 131 137
cAMP biosynthetic process -0.066 0.18 0.35 7 -0.34 127 134
Gq family/GTP/EBP50 0.005 0.07 0.24 8 -0.22 33 41
actin cytoskeleton reorganization 0.033 0.007 -10000 0 -10000 0 0
SRC 0.004 0.063 0.3 9 -0.23 2 11
GNB5 0.026 0.003 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
EGF/EGFR -0.011 0.12 0.33 27 -0.26 33 60
VCAM1 -0.076 0.18 0.3 6 -0.36 131 137
TP beta/Gq family/GDP/G beta5/gamma2 -0.001 0.099 -10000 0 -0.4 21 21
platelet activation -0.053 0.16 0.32 12 -0.3 129 141
PGI2/IP 0.01 0.034 -10000 0 -0.12 22 22
PRKACA 0.004 0.037 -10000 0 -0.23 8 8
Gq family/GDP/G beta5/gamma2 -0.001 0.094 -10000 0 -0.37 22 22
TXA2/TP beta/beta Arrestin2 -0.021 0.12 -10000 0 -0.48 33 33
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.036 -10000 0 -0.22 9 9
mol:DAG -0.078 0.21 0.37 6 -0.4 127 133
EGFR -0.016 0.12 -10000 0 -0.4 46 46
TXA2/TP alpha -0.093 0.23 0.41 6 -0.46 126 132
Gq family/GTP -0.002 0.063 0.21 5 -0.21 35 40
YES1 0.009 0.078 0.34 16 -0.23 4 20
GNAI2/GTP 0.003 0.045 -10000 0 -0.2 9 9
PGD2/DP 0.005 0.043 -10000 0 -0.1 52 52
SLC9A3R1 0.022 0.04 -10000 0 -0.43 4 4
FYN 0.01 0.077 0.32 18 -0.22 2 20
mol:NO 0.017 0.034 -10000 0 -0.28 4 4
GNA15 0.013 0.07 -10000 0 -0.43 12 12
PGK/cGMP 0.007 0.069 -10000 0 -0.25 31 31
RhoA/GDP 0.025 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.055 -10000 0 -0.29 2 2
NOS3 0.017 0.034 -10000 0 -0.28 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.061 0.18 0.31 9 -0.34 122 131
PRKCB -0.075 0.18 0.35 5 -0.36 131 136
PRKCE -0.066 0.18 0.32 8 -0.35 124 132
PRKCD -0.077 0.2 0.32 7 -0.38 130 137
PRKCG -0.086 0.19 0.36 7 -0.38 130 137
muscle contraction -0.1 0.24 0.39 5 -0.48 131 136
PRKCZ -0.07 0.17 0.33 7 -0.34 131 138
ARR3 -0.007 0.018 -10000 0 -0.13 1 1
TXA2/TP beta 0.01 0.052 -10000 0 -0.21 11 11
PRKCQ -0.063 0.18 0.29 11 -0.35 122 133
MAPKKK cascade -0.088 0.22 0.37 6 -0.44 128 134
SELE -0.066 0.16 0.3 6 -0.32 132 138
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.053 -10000 0 -0.21 9 9
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 0.009 0.081 -10000 0 -0.34 23 23
chemotaxis -0.13 0.29 0.39 5 -0.61 131 136
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.06 -10000 0 -0.43 9 9
Rac1/GTP 0.016 0.007 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.056 0.13 0.24 1 -0.28 102 103
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
mol:Ca2+ -0.045 0.22 -10000 0 -0.76 34 34
EDN1 -0.036 0.11 0.21 1 -0.3 47 48
EDN3 0.006 0.09 -10000 0 -0.4 23 23
EDN2 -0.006 0.031 -10000 0 -0.13 20 20
HRAS/GDP -0.051 0.17 0.26 9 -0.44 47 56
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.13 -10000 0 -0.34 47 47
ADCY4 -0.069 0.14 -10000 0 -0.3 92 92
ADCY5 -0.073 0.14 -10000 0 -0.32 92 92
ADCY6 -0.067 0.13 -10000 0 -0.31 82 82
ADCY7 -0.067 0.13 -10000 0 -0.3 85 85
ADCY1 -0.072 0.14 -10000 0 -0.29 113 113
ADCY2 -0.071 0.14 -10000 0 -0.31 88 88
ADCY3 -0.067 0.13 -10000 0 -0.29 94 94
ADCY8 -0.081 0.15 -10000 0 -0.3 120 120
ADCY9 -0.067 0.14 -10000 0 -0.3 94 94
arachidonic acid secretion -0.066 0.2 0.29 10 -0.46 78 88
ETB receptor/Endothelin-1/Gq/GTP -0.026 0.12 -10000 0 -0.3 57 57
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.024 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.013 0.13 -10000 0 -0.25 103 103
ETA receptor/Endothelin-1/Gs/GTP -0.041 0.16 -10000 0 -0.26 155 155
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.099 0.2 0.23 1 -0.45 108 109
EDNRB -0.014 0.12 -10000 0 -0.42 39 39
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.065 0.16 0.24 1 -0.38 66 67
CYSLTR1 -0.064 0.15 0.24 1 -0.42 48 49
SLC9A1 -0.034 0.098 0.17 1 -0.25 61 62
mol:GDP -0.063 0.18 0.27 10 -0.47 50 60
SLC9A3 -0.074 0.25 -10000 0 -0.68 55 55
RAF1 -0.072 0.19 0.26 10 -0.45 72 82
JUN -0.037 0.19 -10000 0 -0.62 32 32
JAK2 -0.055 0.13 0.24 1 -0.27 110 111
mol:IP3 -0.042 0.14 -10000 0 -0.41 40 40
ETA receptor/Endothelin-1 -0.04 0.17 0.41 1 -0.32 116 117
PLCB1 0.01 0.081 -10000 0 -0.43 17 17
PLCB2 0.011 0.073 -10000 0 -0.36 17 17
ETA receptor/Endothelin-3 -0.018 0.11 0.17 1 -0.3 48 49
FOS -0.11 0.31 0.35 5 -0.87 65 70
Gai/GDP 0.002 0.14 -10000 0 -0.71 15 15
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca ++ -0.071 0.17 0.22 1 -0.43 62 63
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
PRKCB1 -0.042 0.14 -10000 0 -0.4 40 40
GNAQ 0.024 0.011 -10000 0 -10000 0 0
GNAZ 0.026 0.004 -10000 0 -10000 0 0
GNAL -0.028 0.15 -10000 0 -0.42 61 61
Gs family/GDP -0.073 0.18 0.26 5 -0.42 67 72
ETA receptor/Endothelin-1/Gq/GTP -0.029 0.12 0.19 1 -0.32 45 46
MAPK14 -0.033 0.12 -10000 0 -0.43 28 28
TRPC6 -0.049 0.24 -10000 0 -0.82 33 33
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.032 0.13 -10000 0 -0.39 37 37
ETB receptor/Endothelin-2 -0.004 0.09 -10000 0 -0.3 37 37
ETB receptor/Endothelin-3 -0.003 0.11 -10000 0 -0.34 49 49
ETB receptor/Endothelin-1 -0.027 0.13 -10000 0 -0.31 69 69
MAPK3 -0.1 0.27 0.33 8 -0.76 65 73
MAPK1 -0.1 0.28 0.33 8 -0.75 66 74
Rac1/GDP -0.052 0.16 0.28 2 -0.45 43 45
cAMP biosynthetic process -0.073 0.16 0.22 1 -0.37 79 80
MAPK8 -0.049 0.22 -10000 0 -0.67 40 40
SRC 0.025 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.022 0.098 0.16 1 -0.3 38 39
p130Cas/CRK/Src/PYK2 -0.049 0.18 0.32 10 -0.53 37 47
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.053 0.16 0.34 1 -0.45 44 45
COL1A2 -0.058 0.16 -10000 0 -0.46 43 43
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.018 0.089 -10000 0 -0.26 35 35
mol:DAG -0.042 0.14 -10000 0 -0.41 40 40
MAP2K2 -0.081 0.22 0.33 15 -0.57 69 84
MAP2K1 -0.089 0.23 0.27 7 -0.59 69 76
EDNRA -0.033 0.12 0.21 1 -0.32 42 43
positive regulation of muscle contraction -0.024 0.13 0.21 38 -0.3 44 82
Gq family/GDP -0.043 0.17 -10000 0 -0.48 40 40
HRAS/GTP -0.061 0.17 0.25 11 -0.44 52 63
PRKCH -0.042 0.13 -10000 0 -0.43 33 33
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA -0.039 0.14 0.23 8 -0.44 33 41
PRKCB -0.052 0.14 -10000 0 -0.44 37 37
PRKCE -0.043 0.14 0.22 1 -0.43 33 34
PRKCD -0.052 0.15 -10000 0 -0.44 45 45
PRKCG -0.075 0.15 -10000 0 -0.39 61 61
regulation of vascular smooth muscle contraction -0.13 0.36 0.39 5 -1 64 69
PRKCQ -0.035 0.15 0.22 21 -0.46 33 54
PLA2G4A -0.073 0.22 0.29 10 -0.5 78 88
GNA14 0.008 0.081 -10000 0 -0.34 23 23
GNA15 0.012 0.071 -10000 0 -0.36 16 16
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA11 0.016 0.06 -10000 0 -0.43 9 9
Rac1/GTP -0.012 0.13 -10000 0 -0.25 102 102
MMP1 0.017 0.1 0.42 12 -0.83 1 13
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.044 0.19 -10000 0 -0.58 53 53
IHH 0.012 0.056 0.18 1 -0.19 8 9
SHH Np/Cholesterol/GAS1 -0.011 0.084 0.16 12 -0.24 53 65
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.011 0.083 0.24 53 -0.15 12 65
SMO/beta Arrestin2 -0.005 0.12 -10000 0 -0.39 20 20
SMO -0.02 0.11 -10000 0 -0.37 33 33
AKT1 -0.003 0.11 -10000 0 -0.53 13 13
ARRB2 0.026 0.002 -10000 0 -10000 0 0
BOC 0.023 0.036 -10000 0 -0.43 3 3
ADRBK1 0.025 0.005 -10000 0 -10000 0 0
heart looping -0.019 0.11 -10000 0 -0.36 33 33
STIL -0.012 0.13 0.23 3 -0.28 56 59
DHH N/PTCH2 0.004 0.085 -10000 0 -0.31 31 31
DHH N/PTCH1 -0.02 0.12 -10000 0 -0.28 79 79
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DHH -0.007 0.1 -10000 0 -0.43 27 27
PTHLH -0.061 0.26 -10000 0 -0.78 53 53
determination of left/right symmetry -0.019 0.11 -10000 0 -0.36 33 33
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
skeletal system development -0.06 0.25 -10000 0 -0.77 53 53
IHH N/Hhip -0.04 0.14 -10000 0 -0.33 78 78
DHH N/Hhip -0.049 0.14 -10000 0 -0.31 101 101
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.019 0.11 -10000 0 -0.36 33 33
pancreas development -0.058 0.16 -10000 0 -0.29 135 135
HHAT 0.012 0.077 -10000 0 -0.43 15 15
PI3K 0.038 0.007 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.016 0.047 -10000 0 -0.43 3 3
somite specification -0.019 0.11 -10000 0 -0.36 33 33
SHH Np/Cholesterol/PTCH1 -0.036 0.11 -10000 0 -0.28 68 68
SHH Np/Cholesterol/PTCH2 -0.016 0.082 0.15 2 -0.24 56 58
SHH Np/Cholesterol/Megalin -0.059 0.12 0.15 8 -0.27 115 123
SHH -0.03 0.097 -10000 0 -0.31 52 52
catabolic process -0.018 0.12 -10000 0 -0.34 52 52
SMO/Vitamin D3 -0.032 0.12 0.29 2 -0.32 39 41
SHH Np/Cholesterol/Hhip -0.048 0.12 0.16 8 -0.27 98 106
LRP2 -0.093 0.18 -10000 0 -0.31 183 183
receptor-mediated endocytosis -0.066 0.14 -10000 0 -0.4 47 47
SHH Np/Cholesterol/BOC -0.014 0.08 -10000 0 -0.24 54 54
SHH Np/Cholesterol/CDO -0.02 0.089 0.17 1 -0.25 59 60
mesenchymal cell differentiation 0.048 0.12 0.27 98 -0.15 8 106
mol:Vitamin D3 -0.001 0.14 0.32 3 -0.28 68 71
IHH N/PTCH2 0.023 0.051 -10000 0 -0.33 6 6
CDON 0.001 0.095 -10000 0 -0.43 23 23
IHH N/PTCH1 -0.011 0.12 -10000 0 -0.34 52 52
Megalin/LRPAP1 -0.052 0.14 -10000 0 -0.3 108 108
PTCH2 0.016 0.048 -10000 0 -0.28 10 10
SHH Np/Cholesterol -0.019 0.075 0.2 1 -0.23 52 53
PTCH1 -0.019 0.12 -10000 0 -0.34 52 52
HHIP -0.058 0.16 -10000 0 -0.29 135 135
Effects of Botulinum toxin

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
STX1A -0.011 0.046 -10000 0 -0.1 77 77
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.019 0.12 -10000 0 -0.31 69 69
STXBP1 0.016 0.044 -10000 0 -0.16 26 26
ACh/CHRNA1 -0.042 0.11 0.13 8 -0.25 84 92
RAB3GAP2/RIMS1/UNC13B 0.01 0.11 -10000 0 -0.26 67 67
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.049 0.16 -10000 0 -0.32 112 112
mol:ACh -0.008 0.057 0.098 60 -0.11 74 134
RAB3GAP2 0.026 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.031 0.12 -10000 0 -0.25 92 92
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.042 0.11 0.13 8 -0.25 84 92
UNC13B 0.025 0.021 -10000 0 -0.43 1 1
CHRNA1 -0.065 0.15 -10000 0 -0.43 68 68
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.056 0.13 0.13 2 -0.31 90 92
SNAP25 -0.043 0.098 -10000 0 -0.26 86 86
VAMP2 0.005 0 -10000 0 -10000 0 0
SYT1 -0.088 0.17 -10000 0 -0.43 92 92
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0 0.052 -10000 0 -0.16 32 32
STX1A/SNAP25 fragment 1/VAMP2 -0.031 0.12 -10000 0 -0.25 92 92
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 0.013 0.069 0.25 1 -0.43 5 6
Syndecan-4/Syndesmos -0.059 0.2 0.32 1 -0.46 92 93
positive regulation of JNK cascade -0.053 0.2 0.31 1 -0.44 93 94
Syndecan-4/ADAM12 -0.068 0.2 0.34 1 -0.46 93 94
CCL5 -0.025 0.12 -10000 0 -0.43 39 39
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DNM2 0.025 0.006 -10000 0 -10000 0 0
ITGA5 0.017 0.043 -10000 0 -0.16 24 24
SDCBP 0.025 0.006 -10000 0 -10000 0 0
PLG 0.001 0.026 -10000 0 -0.17 1 1
ADAM12 -0.001 0.077 -10000 0 -0.18 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.033 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.079 0.22 0.32 1 -0.49 95 96
Syndecan-4/CXCL12/CXCR4 -0.056 0.21 0.32 1 -0.46 93 94
Syndecan-4/Laminin alpha3 -0.07 0.21 0.32 1 -0.48 94 95
MDK -0.002 0.097 -10000 0 -0.27 48 48
Syndecan-4/FZD7 -0.078 0.22 -10000 0 -0.5 96 96
Syndecan-4/Midkine -0.067 0.21 0.32 1 -0.47 90 91
FZD7 -0.018 0.13 -10000 0 -0.43 48 48
Syndecan-4/FGFR1/FGF -0.044 0.19 0.3 1 -0.44 85 86
THBS1 -0.018 0.1 -10000 0 -0.43 23 23
integrin-mediated signaling pathway -0.066 0.2 0.32 1 -0.46 92 93
positive regulation of MAPKKK cascade -0.053 0.2 0.31 1 -0.44 93 94
Syndecan-4/TACI -0.063 0.2 0.31 1 -0.46 93 94
CXCR4 0.012 0.072 -10000 0 -0.27 25 25
cell adhesion 0.017 0.036 0.2 14 -0.2 1 15
Syndecan-4/Dynamin -0.063 0.2 -10000 0 -0.46 93 93
Syndecan-4/TSP1 -0.071 0.21 0.32 1 -0.48 94 95
Syndecan-4/GIPC -0.063 0.2 -10000 0 -0.46 92 92
Syndecan-4/RANTES -0.077 0.21 0.32 1 -0.48 94 95
ITGB1 0.023 0.012 -10000 0 -10000 0 0
LAMA1 -0.024 0.14 -10000 0 -0.43 51 51
LAMA3 -0.004 0.1 -10000 0 -0.29 49 49
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.035 0.16 0.85 18 -0.4 1 19
Syndecan-4/alpha-Actinin -0.061 0.2 0.32 1 -0.46 93 94
TFPI -0.024 0.12 -10000 0 -0.23 99 99
F2 0.006 0.031 -10000 0 -0.14 1 1
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
positive regulation of cell adhesion -0.094 0.22 0.31 1 -0.49 103 104
ACTN1 0.014 0.044 -10000 0 -0.14 35 35
TNC -0.005 0.1 -10000 0 -0.43 24 24
Syndecan-4/CXCL12 -0.062 0.2 0.32 1 -0.46 93 94
FGF6 -0.013 0.01 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CXCL12 0.021 0.038 -10000 0 -0.24 8 8
TNFRSF13B -0.003 0.028 -10000 0 -0.13 11 11
FGF2 0.024 0.029 -10000 0 -0.43 2 2
FGFR1 0.025 0.005 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.079 0.19 -10000 0 -0.46 93 93
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.034 -10000 0 -0.16 5 5
cell migration -0.013 0.015 -10000 0 -10000 0 0
PRKCD 0.001 0.096 -10000 0 -0.41 26 26
vasculogenesis -0.068 0.2 0.32 1 -0.46 94 95
SDC4 -0.077 0.2 -10000 0 -0.48 93 93
Syndecan-4/Tenascin C -0.069 0.21 0.32 1 -0.48 92 93
Syndecan-4/PI-4-5-P2/PKC alpha -0.027 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.058 0.2 0.32 1 -0.46 89 90
MMP9 -0.045 0.13 -10000 0 -0.23 133 133
Rac1/GTP 0.017 0.036 0.2 14 -0.2 1 15
cytoskeleton organization -0.056 0.2 0.32 1 -0.44 92 93
GIPC1 0.025 0.009 -10000 0 -0.13 1 1
Syndecan-4/TFPI -0.074 0.21 0.34 1 -0.48 93 94
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.015 0.07 -10000 0 -0.3 22 22
VLDLR 0.014 0.067 -10000 0 -0.35 15 15
CRKL 0.026 0.008 -10000 0 -0.13 1 1
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
ITGA3 0.017 0.046 -10000 0 -0.43 3 3
RELN/VLDLR/Fyn 0 0.1 -10000 0 -0.26 67 67
MAPK8IP1/MKK7/MAP3K11/JNK1 0.059 0.055 -10000 0 -0.22 15 15
AKT1 -0.047 0.11 -10000 0 -0.26 98 98
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
DAB1 -0.039 0.15 -10000 0 -0.36 80 80
RELN/LRP8/DAB1 -0.024 0.12 -10000 0 -0.24 103 103
LRPAP1/LRP8 0.03 0.026 -10000 0 -0.3 2 2
RELN/LRP8/DAB1/Fyn -0.017 0.11 -10000 0 -0.23 96 96
DAB1/alpha3/beta1 Integrin -0.021 0.11 -10000 0 -0.24 78 78
long-term memory -0.1 0.17 -10000 0 -0.32 154 154
DAB1/LIS1 -0.014 0.12 -10000 0 -0.23 98 98
DAB1/CRLK/C3G -0.02 0.11 -10000 0 -0.24 81 81
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DAB1/NCK2 -0.014 0.12 -10000 0 -0.23 97 97
ARHGEF2 0.025 0.02 -10000 0 -0.43 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.071 0.17 -10000 0 -0.29 155 155
CDK5R1 0 0.1 -10000 0 -0.42 30 30
RELN -0.046 0.14 -10000 0 -0.43 58 58
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.001 0.095 -10000 0 -0.25 58 58
GRIN2A/RELN/LRP8/DAB1/Fyn -0.052 0.16 -10000 0 -0.28 134 134
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
RELN/VLDLR/DAB1 -0.031 0.12 -10000 0 -0.25 103 103
ITGB1 0.023 0.012 -10000 0 -10000 0 0
MAP1B -0.032 0.12 0.16 5 -0.25 100 105
RELN/LRP8 0.003 0.095 -10000 0 -0.25 57 57
GRIN2B/RELN/LRP8/DAB1/Fyn -0.057 0.15 -10000 0 -0.28 140 140
PI3K 0.038 0.007 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.037 -10000 0 -0.27 4 4
RAP1A -0.022 0.12 0.31 9 -0.35 14 23
PAFAH1B1 0.026 0.002 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.04 -10000 0 -0.43 4 4
CRLK/C3G 0.037 0.01 -10000 0 -10000 0 0
GRIN2B -0.077 0.16 -10000 0 -0.43 83 83
NCK2 0.026 0.002 -10000 0 -10000 0 0
neuron differentiation -0.028 0.13 -10000 0 -0.36 45 45
neuron adhesion -0.014 0.13 0.34 12 -0.37 10 22
LRP8 0.02 0.03 -10000 0 -0.43 2 2
GSK3B -0.052 0.11 -10000 0 -0.25 91 91
RELN/VLDLR/DAB1/Fyn -0.024 0.12 -10000 0 -0.24 102 102
MAP3K11 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.049 0.12 -10000 0 -0.27 103 103
CDK5 0.02 0.011 -10000 0 -10000 0 0
MAPT 0.006 0.098 0.77 6 -0.39 8 14
neuron migration -0.042 0.16 0.23 54 -0.31 94 148
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.029 0.13 -10000 0 -0.36 45 45
RELN/VLDLR 0.005 0.097 -10000 0 -0.23 66 66
TCGA08_retinoblastoma

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
CDKN2B 0.003 0.078 -10000 0 -0.31 25 25
CDKN2C 0.01 0.041 -10000 0 -0.15 10 10
CDKN2A -0.013 0.1 -10000 0 -0.28 55 55
CCND2 0.016 0.068 0.21 47 -0.19 1 48
RB1 -0.023 0.079 0.12 1 -0.24 51 52
CDK4 0.021 0.077 0.24 48 -0.17 1 49
CDK6 0.017 0.081 0.25 44 -0.16 10 54
G1/S progression 0.042 0.099 0.26 75 -0.25 3 78
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.035 0.12 -10000 0 -0.3 51 51
NFATC4 -0.057 0.089 0.22 2 -0.23 49 51
ERBB2IP 0.026 0.02 -10000 0 -0.42 1 1
HSP90 (dimer) 0.025 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.047 0.11 0.2 1 -0.24 115 116
JUN -0.022 0.083 0.2 3 -0.38 9 12
HRAS 0.024 0.006 -10000 0 -10000 0 0
DOCK7 -0.064 0.098 -10000 0 -0.24 111 111
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.034 0.13 -10000 0 -0.25 119 119
AKT1 0.003 0.007 -10000 0 -10000 0 0
BAD -0.006 0.004 -10000 0 -10000 0 0
MAPK10 -0.03 0.065 0.17 2 -0.22 7 9
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.05 0.12 0.21 1 -0.26 115 116
RAF1 -0.044 0.12 0.27 6 -0.32 45 51
ErbB2/ErbB3/neuregulin 2 -0.003 0.08 0.16 2 -0.25 40 42
STAT3 0.028 0.043 -10000 0 -0.91 1 1
cell migration -0.022 0.077 0.22 13 -0.2 11 24
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.1 0.25 0.35 2 -0.61 82 84
FOS -0.083 0.2 0.28 3 -0.41 118 121
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.047 0.11 0.2 1 -0.24 115 116
MAPK3 -0.08 0.21 0.36 2 -0.51 70 72
MAPK1 -0.083 0.21 0.36 2 -0.51 70 72
JAK2 -0.067 0.097 -10000 0 -0.24 108 108
NF2 0.005 0.033 -10000 0 -0.69 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.052 0.12 0.18 1 -0.26 116 117
NRG1 -0.081 0.18 -10000 0 -0.32 156 156
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
MAPK8 -0.053 0.12 -10000 0 -0.26 113 113
MAPK9 -0.029 0.063 0.17 3 -0.21 5 8
ERBB2 -0.022 0.017 -10000 0 -0.32 1 1
ERBB3 -0.017 0.12 -10000 0 -0.35 57 57
SHC1 0.024 0.014 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
apoptosis 0.003 0.013 -10000 0 -0.2 1 1
STAT3 (dimer) 0.029 0.042 -10000 0 -0.89 1 1
RNF41 -0.01 0.008 -10000 0 -10000 0 0
FRAP1 -0.004 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.041 0.074 -10000 0 -0.18 96 96
ErbB2/ErbB2/HSP90 (dimer) 0 0.025 -10000 0 -0.27 1 1
CHRNA1 -0.091 0.24 0.33 2 -0.63 71 73
myelination -0.054 0.089 0.23 3 -0.26 22 25
PPP3CB -0.065 0.091 -10000 0 -0.22 111 111
KRAS 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.11 -10000 0 -0.23 100 100
NRG2 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.053 0.12 0.18 1 -0.26 117 118
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.048 0.13 0.27 6 -0.34 42 48
SRC 0.025 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.068 0.097 -10000 0 -0.24 114 114
MAP2K1 -0.088 0.2 -10000 0 -0.58 38 38
heart morphogenesis -0.047 0.11 0.2 1 -0.24 115 116
RAS family/GDP -0.026 0.12 0.23 1 -0.29 48 49
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.008 0.035 -10000 0 -0.74 1 1
CHRNE -0.002 0.031 0.1 1 -0.18 9 10
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.007 -10000 0 -10000 0 0
nervous system development -0.047 0.11 0.2 1 -0.24 115 116
CDC42 0.022 0.01 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.13 0.3 -10000 0 -0.84 50 50
PCK1 -0.18 0.39 -10000 0 -1.2 50 50
HNF4A -0.15 0.33 -10000 0 -0.92 53 53
KCNJ11 -0.18 0.4 -10000 0 -1 76 76
AKT1 -0.067 0.18 -10000 0 -0.43 47 47
response to starvation -0.003 0.026 -10000 0 -0.22 4 4
DLK1 -0.16 0.35 -10000 0 -0.89 71 71
NKX2-1 -0.058 0.15 0.3 3 -0.37 47 50
ACADM -0.13 0.3 -10000 0 -0.83 51 51
TAT -0.19 0.39 -10000 0 -1.1 55 55
CEBPB 0.013 0.073 -10000 0 -0.36 17 17
CEBPA 0.015 0.05 -10000 0 -0.43 5 5
TTR -0.12 0.27 0.53 3 -0.84 38 41
PKLR -0.13 0.3 -10000 0 -0.8 58 58
APOA1 -0.18 0.4 -10000 0 -1.1 56 56
CPT1C -0.13 0.3 -10000 0 -0.84 49 49
ALAS1 -0.06 0.18 0.46 1 -0.71 4 5
TFRC -0.14 0.3 -10000 0 -0.93 38 38
FOXF1 0.019 0.042 -10000 0 -0.19 16 16
NF1 0.03 0.02 -10000 0 -0.42 1 1
HNF1A (dimer) 0.025 0.026 -10000 0 -0.44 1 1
CPT1A -0.13 0.3 -10000 0 -0.82 55 55
HMGCS1 -0.13 0.3 -10000 0 -0.82 56 56
NR3C1 -0.017 0.089 -10000 0 -0.2 85 85
CPT1B -0.15 0.32 -10000 0 -0.84 64 64
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.024 0.013 -10000 0 -10000 0 0
GCK -0.16 0.37 0.5 1 -0.9 78 79
CREB1 0.008 0.058 -10000 0 -0.18 36 36
IGFBP1 -0.22 0.48 -10000 0 -1.2 85 85
PDX1 -0.058 0.17 -10000 0 -0.57 10 10
UCP2 -0.14 0.32 -10000 0 -0.84 61 61
ALDOB -0.14 0.35 -10000 0 -0.92 56 56
AFP -0.035 0.1 -10000 0 -0.36 22 22
BDH1 -0.16 0.35 -10000 0 -0.95 62 62
HADH -0.13 0.32 -10000 0 -0.85 56 56
F2 -0.15 0.35 -10000 0 -0.99 45 45
HNF1A 0.025 0.026 -10000 0 -0.44 1 1
G6PC -0.034 0.16 -10000 0 -0.88 10 10
SLC2A2 -0.064 0.19 -10000 0 -0.54 16 16
INS 0.008 0.086 0.21 59 -0.4 4 63
FOXA1 -0.007 0.087 -10000 0 -0.28 32 32
FOXA3 -0.041 0.14 -10000 0 -0.37 61 61
FOXA2 -0.15 0.37 -10000 0 -0.92 64 64
ABCC8 -0.19 0.41 -10000 0 -0.97 88 88
ALB -0.07 0.23 -10000 0 -0.91 32 32
Syndecan-3-mediated signaling events

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
CTTN 0.025 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.012 0.14 -10000 0 -0.35 64 64
Syndecan-3/Neurocan -0.042 0.15 -10000 0 -0.37 77 77
POMC 0.015 0.063 -10000 0 -0.28 18 18
EGFR -0.016 0.12 -10000 0 -0.4 46 46
Syndecan-3/EGFR -0.051 0.15 -10000 0 -0.38 74 74
AGRP 0.012 0.024 -10000 0 -10000 0 0
NCSTN 0.026 0.004 -10000 0 -10000 0 0
PSENEN 0.022 0.01 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
NCAN -0.001 0.1 -10000 0 -0.4 31 31
long-term memory -0.013 0.14 -10000 0 -0.35 72 72
Syndecan-3/IL8 -0.054 0.16 -10000 0 -0.4 77 77
PSEN1 0.025 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.036 0.011 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
limb bud formation -0.046 0.14 -10000 0 -0.38 77 77
MC4R -0.051 0.16 -10000 0 -0.43 70 70
SRC 0.025 0.005 -10000 0 -10000 0 0
PTN 0.019 0.03 -10000 0 -0.43 2 2
FGFR/FGF/Syndecan-3 -0.046 0.14 -10000 0 -0.38 77 77
neuron projection morphogenesis -0.015 0.15 0.26 1 -0.35 65 66
Syndecan-3/AgRP -0.03 0.14 -10000 0 -0.37 77 77
Syndecan-3/AgRP/MC4R -0.045 0.16 -10000 0 -0.38 77 77
Fyn/Cortactin 0.036 0.01 -10000 0 -10000 0 0
SDC3 -0.047 0.14 -10000 0 -0.39 77 77
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.053 0.16 -10000 0 -0.39 77 77
IL8 -0.061 0.15 -10000 0 -0.25 158 158
Syndecan-3/Fyn/Cortactin -0.013 0.14 -10000 0 -0.36 72 72
Syndecan-3/CASK -0.045 0.14 -10000 0 -0.36 77 77
alpha-MSH/MC4R -0.025 0.13 -10000 0 -0.32 76 76
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.024 0.036 -10000 0 -0.26 6 6
ARNO/beta Arrestin1-2 -0.099 0.31 -10000 0 -0.8 82 82
EGFR -0.016 0.12 -10000 0 -0.4 46 46
EPHA2 0.012 0.045 -10000 0 -0.15 29 29
USP6 0.023 0.022 -10000 0 -10000 0 0
IQSEC1 0.023 0.027 -10000 0 -0.17 8 8
EGFR/EGFR/EGF/EGF -0.02 0.12 -10000 0 -0.32 69 69
ARRB2 0.011 0.007 -10000 0 -10000 0 0
mol:GTP 0.007 0.042 0.18 5 -0.17 11 16
ARRB1 0.012 0.077 -10000 0 -0.43 15 15
FBXO8 0.025 0.005 -10000 0 -10000 0 0
TSHR -0.084 0.17 -10000 0 -0.28 187 187
EGF -0.01 0.11 -10000 0 -0.43 33 33
somatostatin receptor activity 0 0 0.001 59 -0.001 26 85
ARAP2 0.012 0.079 -10000 0 -0.43 16 16
mol:GDP -0.016 0.13 0.19 45 -0.29 45 90
mol:PI-3-4-5-P3 0 0 0.001 78 -0.001 12 90
ITGA2B -0.012 0.12 -10000 0 -0.43 40 40
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.036 -10000 0 -0.25 3 3
ADAP1 0.014 0.054 -10000 0 -0.24 17 17
KIF13B 0.025 0.005 -10000 0 -10000 0 0
HGF/MET -0.04 0.12 -10000 0 -0.28 83 83
PXN 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.13 0.25 53 -0.26 32 85
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.004 0.11 -10000 0 -0.28 70 70
ADRB2 0.005 0.094 -10000 0 -0.42 24 24
receptor agonist activity 0 0 0 28 0 23 51
actin filament binding 0 0 0.001 60 0 28 88
SRC 0.025 0.005 -10000 0 -10000 0 0
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
GNAQ 0.026 0.004 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 72 -0.001 17 89
ARF6/GDP -0.026 0.14 0.23 5 -0.42 36 41
ARF6/GDP/GULP/ACAP1 -0.012 0.16 0.22 31 -0.34 52 83
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.094 -10000 0 -0.24 51 51
ACAP1 0.01 0.06 -10000 0 -0.43 5 5
ACAP2 0.026 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.023 0.007 -10000 0 -10000 0 0
EFNA1 0.024 0.014 -10000 0 -0.13 4 4
HGF -0.009 0.091 -10000 0 -0.2 69 69
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 -0.14 0.38 -10000 0 -1 81 81
NCK1 0.025 0.02 -10000 0 -0.43 1 1
fibronectin binding 0 0 0.001 64 0 25 89
endosomal lumen acidification 0 0 0.001 61 0 31 92
microtubule-based process 0 0 -10000 0 0 12 12
GULP1 -0.016 0.13 -10000 0 -0.37 55 55
GNAQ/ARNO -0.12 0.35 -10000 0 -0.93 81 81
mol:Phosphatidic acid 0 0 0 18 -10000 0 18
PIP3-E 0 0 0 39 0 14 53
MET -0.047 0.14 -10000 0 -0.43 52 52
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.43 12 12
GIT1 0.026 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 64 -0.001 20 84
GNA11 0.017 0.06 -10000 0 -0.43 9 9
LHCGR 0.009 0.031 -10000 0 -0.13 16 16
AGTR1 0.001 0.093 -10000 0 -0.29 39 39
desensitization of G-protein coupled receptor protein signaling pathway 0.023 0.007 -10000 0 -10000 0 0
IPCEF1/ARNO -0.13 0.33 -10000 0 -0.88 81 81
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.025 0.021 -9999 0 -0.43 1 1
Aurora C/Aurora B/INCENP -0.011 0.11 -9999 0 -0.23 94 94
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.007 0.031 -9999 0 -10000 0 0
AURKB -0.072 0.17 -9999 0 -0.3 152 152
AURKC 0.011 0.051 -9999 0 -0.18 26 26
IL4-mediated signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.36 -10000 0 -1.1 39 39
STAT6 (cleaved dimer) -0.28 0.39 -10000 0 -1 75 75
IGHG1 -0.1 0.2 -10000 0 -0.98 13 13
IGHG3 -0.24 0.34 -10000 0 -0.95 56 56
AKT1 -0.18 0.31 -10000 0 -0.89 58 58
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.31 -10000 0 -0.94 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.33 -10000 0 -0.94 61 61
THY1 -0.26 0.39 -10000 0 -1.2 41 41
MYB -0.016 0.12 -10000 0 -0.28 67 67
HMGA1 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.21 0.31 -10000 0 -0.81 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.2 0.33 -10000 0 -0.94 63 63
SP1 0.025 0.019 -10000 0 -0.12 1 1
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
SOCS5 0.033 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.27 0.38 -10000 0 -1 66 66
SOCS1 -0.21 0.28 -10000 0 -0.73 59 59
SOCS3 -0.23 0.36 -10000 0 -1 63 63
FCER2 -0.26 0.4 -10000 0 -1.1 54 54
PARP14 0.017 0.046 -10000 0 -0.22 13 13
CCL17 -0.25 0.36 -10000 0 -1.1 39 39
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.24 -10000 0 -0.7 49 49
T cell proliferation -0.27 0.38 -10000 0 -1.1 60 60
IL4R/JAK1 -0.25 0.36 -10000 0 -1.1 40 40
EGR2 -0.34 0.5 -10000 0 -1.3 76 76
JAK2 -0.008 0.041 -10000 0 -10000 0 0
JAK3 -0.011 0.1 -10000 0 -0.26 55 55
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.008 0.022 -10000 0 -10000 0 0
COL1A2 -0.088 0.2 -10000 0 -1.3 7 7
CCL26 -0.22 0.37 -10000 0 -1 42 42
IL4R -0.26 0.38 -10000 0 -1.1 39 39
PTPN6 0.019 0.065 -10000 0 -0.42 10 10
IL13RA2 -0.42 0.55 -10000 0 -1.3 124 124
IL13RA1 -0.013 0.071 -10000 0 -0.42 9 9
IRF4 -0.12 0.32 -10000 0 -1.3 30 30
ARG1 -0.09 0.21 -10000 0 -1 16 16
CBL -0.19 0.29 -10000 0 -0.76 71 71
GTF3A 0.003 0.052 -10000 0 -0.15 26 26
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
IL13RA1/JAK2 -0.01 0.07 -10000 0 -0.32 8 8
IRF4/BCL6 -0.099 0.3 -10000 0 -1.2 30 30
CD40LG 0.003 0.054 -10000 0 -10000 0 0
MAPK14 -0.22 0.32 -10000 0 -0.83 76 76
mitosis -0.17 0.29 -10000 0 -0.82 58 58
STAT6 -0.28 0.4 -10000 0 -1.1 53 53
SPI1 0.015 0.064 -10000 0 -0.4 10 10
RPS6KB1 -0.16 0.28 -10000 0 -0.78 58 58
STAT6 (dimer) -0.28 0.4 -10000 0 -1.1 53 53
STAT6 (dimer)/PARP14 -0.26 0.38 -10000 0 -1.1 56 56
mast cell activation 0.007 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.31 -10000 0 -0.86 60 60
FRAP1 -0.18 0.31 -10000 0 -0.89 58 58
LTA -0.28 0.42 -10000 0 -1.3 53 53
FES 0.024 0.024 -10000 0 -0.21 4 4
T-helper 1 cell differentiation 0.27 0.39 1.1 53 -10000 0 53
CCL11 -0.25 0.34 -10000 0 -1 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.3 -10000 0 -0.86 53 53
IL2RG -0.002 0.087 -10000 0 -0.22 50 50
IL10 -0.33 0.5 -10000 0 -1.3 81 81
IRS1 0.026 0.003 -10000 0 -10000 0 0
IRS2 0.024 0.021 -10000 0 -0.43 1 1
IL4 -0.064 0.12 -10000 0 -0.88 4 4
IL5 -0.25 0.36 -10000 0 -1.1 35 35
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.32 -10000 0 -0.92 43 43
COL1A1 -0.26 0.49 -10000 0 -1.4 77 77
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.36 -10000 0 -1.1 36 36
IL2R gamma/JAK3 -0.009 0.1 -10000 0 -0.27 53 53
TFF3 -0.25 0.36 -10000 0 -1.1 36 36
ALOX15 -0.26 0.36 -10000 0 -1.1 37 37
MYBL1 0.024 0.011 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.24 0.35 -10000 0 -0.92 68 68
SHC1 0.024 0.014 -10000 0 -10000 0 0
CEBPB 0.013 0.074 -10000 0 -0.34 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.33 -10000 0 -0.93 62 62
mol:PI-3-4-5-P3 -0.18 0.31 -10000 0 -0.89 58 58
PI3K -0.19 0.34 -10000 0 -0.98 58 58
DOK2 -0.016 0.11 -10000 0 -0.25 77 77
ETS1 0.022 0.052 -10000 0 -0.37 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 -10000 0 -0.67 47 47
ITGB3 -0.27 0.39 -10000 0 -1.2 49 49
PIGR -0.34 0.51 -10000 0 -1.3 81 81
IGHE 0.011 0.058 0.15 12 -0.2 14 26
MAPKKK cascade -0.13 0.22 -10000 0 -0.65 47 47
BCL6 0.027 0.006 -10000 0 -10000 0 0
OPRM1 -0.26 0.36 -10000 0 -1.1 39 39
RETNLB -0.26 0.36 -10000 0 -1.1 36 36
SELP -0.25 0.36 -10000 0 -1.1 35 35
AICDA -0.24 0.35 -10000 0 -1 38 38
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.031 -10000 0 -0.3 2 2
Metarhodopsin II/Arrestin 0.013 0.05 -10000 0 -0.26 12 12
PDE6G/GNAT1/GTP 0.009 0.07 -10000 0 -0.26 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.008 0.047 -10000 0 -0.15 31 31
GRK1 0.021 0.015 -10000 0 -0.13 1 1
CNG Channel -0.047 0.14 -10000 0 -0.25 141 141
mol:Na + -0.068 0.13 -10000 0 -0.24 159 159
mol:ADP 0.021 0.015 -10000 0 -0.13 1 1
RGS9-1/Gbeta5/R9AP 0.019 0.088 -10000 0 -0.27 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.058 0.14 -10000 0 -0.25 159 159
CNGB1 -0.072 0.14 -10000 0 -0.24 176 176
RDH5 0.016 0.038 -10000 0 -0.13 31 31
SAG -0.009 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.11 0.31 3 -0.31 46 49
Na + (4 Units) -0.079 0.12 -10000 0 -0.23 153 153
RGS9 -0.011 0.12 -10000 0 -0.39 44 44
GNB1/GNGT1 0.02 0.016 -10000 0 -10000 0 0
GNAT1/GDP 0.026 0.081 -10000 0 -0.23 40 40
GUCY2D 0.007 0.032 -10000 0 -0.13 16 16
GNGT1 -0.012 0.011 -10000 0 -10000 0 0
GUCY2F 0.011 0.024 -10000 0 -10000 0 0
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.018 0.087 0.15 2 -0.24 59 61
mol:11-cis-retinal 0.016 0.038 -10000 0 -0.13 31 31
mol:cGMP -0.006 0.11 -10000 0 -0.24 80 80
GNB1 0.022 0.01 -10000 0 -10000 0 0
Rhodopsin 0.013 0.063 -10000 0 -0.29 12 12
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 -0.018 0.12 -10000 0 -0.32 63 63
Metarhodopsin II 0.018 0.046 -10000 0 -0.23 12 12
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.003 0.12 -10000 0 -0.25 82 82
RGS9BP 0.017 0.05 -10000 0 -0.39 7 7
Metarhodopsin II/Transducin -0.001 0.043 -10000 0 -0.25 11 11
GCAP Family/Ca ++ -0.007 0.11 -10000 0 -0.23 93 93
PDE6A/B 0.001 0.095 -10000 0 -0.31 37 37
mol:Pi 0.017 0.088 -10000 0 -0.27 40 40
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.023 0.03 -10000 0 -0.18 2 2
PDE6B 0.002 0.092 -10000 0 -0.28 40 40
PDE6A 0 0.088 -10000 0 -0.43 17 17
PDE6G -0.001 0.1 -10000 0 -0.32 39 39
RHO -0.003 0.077 -10000 0 -0.21 46 46
PDE6 0.009 0.12 -10000 0 -0.24 88 88
GUCA1A -0.061 0.15 -10000 0 -0.43 68 68
GC2/GCAP Family 0.006 0.12 -10000 0 -0.25 82 82
GUCA1C -0.007 0.029 -10000 0 -0.13 16 16
GUCA1B 0.012 0.079 -10000 0 -0.41 17 17
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 -0.026 0.11 -10000 0 -0.41 18 18
ACTA1 -0.054 0.13 0.22 2 -0.33 70 72
NUMA1 -0.027 0.11 -10000 0 -0.4 19 19
SPTAN1 -0.049 0.13 0.24 3 -0.33 66 69
LIMK1 -0.028 0.14 0.22 13 -0.33 62 75
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BIRC2 0.025 0.005 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
CASP10 -0.055 0.097 0.16 1 -0.28 71 72
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
PTK2 -0.03 0.12 -10000 0 -0.34 31 31
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.048 0.13 0.24 3 -0.33 66 69
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.003 -10000 0 -10000 0 0
GSN -0.054 0.13 0.22 4 -0.33 72 76
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.13 0.29 -10000 0 -0.59 136 136
BID -0.024 0.066 0.11 1 -0.18 70 71
MAP3K1 -0.011 0.065 -10000 0 -0.44 5 5
TRADD 0.025 0.02 -10000 0 -0.43 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.016 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.048 0.13 0.18 11 -0.33 68 79
CASP9 0.022 0.012 -10000 0 -0.13 1 1
DNA repair 0.011 0.056 0.23 9 -0.15 9 18
neuron apoptosis 0.016 0.064 -10000 0 -0.62 4 4
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.037 0.13 0.22 1 -0.31 71 72
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.013 0.16 -10000 0 -0.92 12 12
TRAF2 0.026 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.046 0.13 0.31 8 -0.31 70 78
CASP7 -0.009 0.096 0.24 21 -0.26 32 53
KRT18 -0.067 0.21 -10000 0 -0.57 73 73
apoptosis -0.051 0.14 0.29 2 -0.45 32 34
DFFA -0.049 0.13 0.19 6 -0.32 70 76
DFFB -0.049 0.13 0.19 5 -0.32 70 75
PARP1 -0.011 0.056 0.15 9 -0.23 9 18
actin filament polymerization 0.025 0.13 0.31 62 -0.25 10 72
TNF -0.06 0.16 -10000 0 -0.26 151 151
CYCS -0.011 0.056 0.19 4 -0.19 12 16
SATB1 -0.014 0.16 -10000 0 -0.86 12 12
SLK -0.052 0.13 0.33 1 -0.33 70 71
p15 BID/BAX -0.011 0.063 -10000 0 -0.19 23 23
CASP2 0.024 0.11 0.21 86 -0.32 14 100
JNK cascade 0.011 0.065 0.43 5 -10000 0 5
CASP3 -0.055 0.13 0.18 3 -0.34 71 74
LMNB2 0.025 0.11 0.23 11 -0.39 14 25
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CASP4 0.016 0.044 -10000 0 -0.16 26 26
Mammalian IAPs/DIABLO 0.05 0.064 -10000 0 -0.24 23 23
negative regulation of DNA binding -0.13 0.29 -10000 0 -0.58 136 136
stress fiber formation -0.052 0.13 0.33 1 -0.32 70 71
GZMB -0.052 0.12 -10000 0 -0.28 98 98
CASP1 0.003 0.049 -10000 0 -0.29 13 13
LMNB1 0.019 0.13 0.23 11 -0.42 17 28
APP 0.016 0.065 -10000 0 -0.63 4 4
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.02 -10000 0 -0.3 1 1
VIM -0.049 0.15 0.32 1 -0.44 35 36
LMNA 0.027 0.11 0.24 6 -0.44 8 14
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.095 -10000 0 -0.34 18 18
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.059 0.13 -10000 0 -0.32 77 77
APAF-1/Caspase 9 -0.072 0.22 -10000 0 -0.62 70 70
nuclear fragmentation during apoptosis -0.026 0.11 -10000 0 -0.4 19 19
CFL2 -0.026 0.14 0.26 9 -0.31 62 71
GAS2 -0.054 0.13 0.19 1 -0.32 75 76
positive regulation of apoptosis 0.028 0.12 0.24 11 -0.39 15 26
PRF1 -0.014 0.12 -10000 0 -0.43 33 33
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.078 0.3 -10000 0 -0.75 52 52
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.041 0.34 -10000 0 -0.76 54 54
SMAD4 0.026 0.005 -10000 0 -10000 0 0
ID2 -0.065 0.31 -10000 0 -0.79 46 46
AP1 -0.011 0.1 -10000 0 -0.28 56 56
ABCG2 -0.067 0.32 -10000 0 -0.81 45 45
HIF1A 0.005 0.071 -10000 0 -0.35 2 2
TFF3 -0.069 0.32 -10000 0 -0.79 47 47
GATA2 0.014 0.066 -10000 0 -0.43 10 10
AKT1 -0.005 0.086 -10000 0 -0.23 15 15
response to hypoxia -0.021 0.075 -10000 0 -0.18 43 43
MCL1 -0.065 0.31 -10000 0 -0.8 45 45
NDRG1 -0.076 0.31 -10000 0 -0.81 46 46
SERPINE1 -0.092 0.32 -10000 0 -0.78 57 57
FECH -0.066 0.31 -10000 0 -0.8 45 45
FURIN -0.064 0.31 -10000 0 -0.8 45 45
NCOA2 -0.004 0.11 -10000 0 -0.43 34 34
EP300 -0.015 0.13 -10000 0 -0.32 54 54
HMOX1 -0.069 0.32 -10000 0 -0.8 48 48
BHLHE40 -0.07 0.32 -10000 0 -0.81 47 47
BHLHE41 -0.07 0.32 -10000 0 -0.84 47 47
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.056 0.1 -10000 0 -0.31 1 1
ENG 0.013 0.078 0.26 4 -0.29 1 5
JUN 0.018 0.024 -10000 0 -0.13 9 9
RORA -0.065 0.31 -10000 0 -0.8 46 46
ABCB1 -0.021 0.12 -10000 0 -0.69 10 10
TFRC -0.065 0.31 -10000 0 -0.8 45 45
CXCR4 -0.07 0.32 -10000 0 -0.82 47 47
TF -0.083 0.34 -10000 0 -0.83 53 53
CITED2 -0.065 0.31 -10000 0 -0.8 45 45
HIF1A/ARNT -0.034 0.39 -10000 0 -0.92 44 44
LDHA -0.012 0.14 -10000 0 -0.86 9 9
ETS1 -0.07 0.31 -10000 0 -0.8 44 44
PGK1 -0.065 0.31 -10000 0 -0.8 44 44
NOS2 -0.074 0.33 -10000 0 -0.82 48 48
ITGB2 -0.072 0.33 -10000 0 -0.85 46 46
ALDOA -0.064 0.31 -10000 0 -0.79 46 46
Cbp/p300/CITED2 -0.087 0.37 -10000 0 -0.86 58 58
FOS -0.032 0.14 -10000 0 -0.39 56 56
HK2 -0.072 0.33 -10000 0 -0.83 47 47
SP1 0.031 0.007 -10000 0 -10000 0 0
GCK -0.1 0.42 -10000 0 -1.3 50 50
HK1 -0.064 0.31 -10000 0 -0.8 45 45
NPM1 -0.064 0.31 -10000 0 -0.8 45 45
EGLN1 -0.065 0.31 -10000 0 -0.81 44 44
CREB1 0.03 0.008 -10000 0 -10000 0 0
PGM1 -0.067 0.31 -10000 0 -0.79 45 45
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.075 0.27 -10000 0 -0.83 41 41
IGFBP1 -0.099 0.33 -10000 0 -0.77 63 63
VEGFA -0.053 0.28 -10000 0 -0.66 51 51
HIF1A/JAB1 0.02 0.057 -10000 0 -0.36 1 1
CP -0.11 0.35 -10000 0 -0.84 57 57
CXCL12 -0.067 0.31 -10000 0 -0.79 47 47
COPS5 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.009 -10000 0 -10000 0 0
BNIP3 -0.066 0.31 -10000 0 -0.8 45 45
EGLN3 -0.069 0.32 -10000 0 -0.81 48 48
CA9 -0.08 0.32 -10000 0 -0.81 49 49
TERT -0.089 0.33 -10000 0 -0.81 52 52
ENO1 -0.065 0.31 -10000 0 -0.79 45 45
PFKL -0.064 0.31 -10000 0 -0.8 45 45
NCOA1 0.026 0.003 -10000 0 -10000 0 0
ADM -0.075 0.32 -10000 0 -0.79 51 51
ARNT 0.005 0.068 -10000 0 -0.27 1 1
HNF4A -0.004 0.055 -10000 0 -0.13 52 52
ADFP -0.078 0.3 -10000 0 -0.75 52 52
SLC2A1 -0.056 0.27 -10000 0 -0.65 51 51
LEP -0.067 0.29 -10000 0 -0.78 43 43
HIF1A/ARNT/Cbp/p300 -0.051 0.34 -10000 0 -0.77 57 57
EPO -0.047 0.24 -10000 0 -0.72 24 24
CREBBP -0.013 0.12 -10000 0 -0.31 52 52
HIF1A/ARNT/Cbp/p300/HDAC7 -0.038 0.34 -10000 0 -0.76 52 52
PFKFB3 -0.07 0.31 -10000 0 -0.82 43 43
NT5E -0.067 0.32 -10000 0 -0.8 47 47
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.023 0.012 -9999 0 -10000 0 0
ITGB7 0.001 0.091 -9999 0 -0.26 44 44
ITGA4 -0.008 0.1 -9999 0 -0.26 61 61
alpha4/beta7 Integrin -0.005 0.1 -9999 0 -0.28 56 56
alpha4/beta1 Integrin 0.012 0.077 -9999 0 -0.29 26 26
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.014 0.1 -9999 0 -0.26 63 63
E-cadherin/beta catenin -0.017 0.11 -9999 0 -0.3 59 59
CTNNB1 0.026 0.004 -9999 0 -10000 0 0
JUP 0.02 0.049 -9999 0 -0.39 7 7
CDH1 -0.046 0.15 -9999 0 -0.43 59 59
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.01 0.13 -10000 0 -0.33 54 54
alphaM/beta2 Integrin/GPIbA -0.011 0.12 -10000 0 -0.32 56 56
alphaM/beta2 Integrin/proMMP-9 -0.035 0.14 -10000 0 -0.3 96 96
PLAUR 0.011 0.042 -10000 0 -0.43 1 1
HMGB1 0.009 0.031 -10000 0 -0.12 1 1
alphaM/beta2 Integrin/Talin -0.003 0.12 -10000 0 -0.33 44 44
AGER -0.008 0.092 -10000 0 -0.4 22 22
RAP1A 0.021 0.01 -10000 0 -10000 0 0
SELPLG -0.001 0.1 -10000 0 -0.43 29 29
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.16 -10000 0 -0.28 131 131
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.041 0.13 -10000 0 -0.23 133 133
CYR61 -0.015 0.1 -10000 0 -0.24 71 71
TLN1 0.026 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.024 0.12 -10000 0 -0.37 30 30
RHOA 0.026 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.003 0.042 -10000 0 -10000 0 0
MYH2 -0.039 0.11 -10000 0 -0.4 24 24
MST1R 0.02 0.049 -10000 0 -0.39 7 7
leukocyte activation during inflammatory response -0.021 0.13 -10000 0 -0.3 73 73
APOB -0.025 0.13 -10000 0 -0.29 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.013 0.067 -10000 0 -0.26 24 24
JAM3 0.024 0.007 -10000 0 -10000 0 0
GP1BA 0.014 0.072 -10000 0 -0.43 13 13
alphaM/beta2 Integrin/CTGF -0.016 0.13 -10000 0 -0.34 57 57
alphaM/beta2 Integrin -0.045 0.13 -10000 0 -0.42 32 32
JAM3 homodimer 0.024 0.007 -10000 0 -10000 0 0
ICAM2 0.025 0.005 -10000 0 -10000 0 0
ICAM1 0.011 0.062 -10000 0 -0.43 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.044 0.13 -10000 0 -0.42 32 32
cell adhesion -0.011 0.12 -10000 0 -0.32 56 56
NFKB1 -0.1 0.19 -10000 0 -0.42 109 109
THY1 0.015 0.062 -10000 0 -0.43 9 9
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.005 0.083 -10000 0 -0.25 44 44
alphaM/beta2 Integrin/LRP/tPA 0.007 0.12 -10000 0 -0.34 40 40
IL6 -0.12 0.23 -10000 0 -0.52 93 93
ITGB2 -0.014 0.097 -10000 0 -0.33 33 33
elevation of cytosolic calcium ion concentration -0.008 0.12 -10000 0 -0.3 58 58
alphaM/beta2 Integrin/JAM2/JAM3 0.012 0.11 -10000 0 -0.32 39 39
JAM2 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.002 0.13 -10000 0 -0.28 73 73
alphaM/beta2 Integrin/uPA/Plg -0.012 0.12 -10000 0 -0.32 53 53
RhoA/GTP -0.037 0.12 -10000 0 -0.35 37 37
positive regulation of phagocytosis -0.04 0.14 -10000 0 -0.39 52 52
Ron/MSP 0.015 0.083 -10000 0 -0.3 31 31
alphaM/beta2 Integrin/uPAR/uPA -0.006 0.12 -10000 0 -0.3 58 58
alphaM/beta2 Integrin/uPAR -0.011 0.12 -10000 0 -0.33 46 46
PLAU -0.001 0.081 -10000 0 -0.19 64 64
PLAT 0.005 0.058 -10000 0 -0.43 2 2
actin filament polymerization -0.036 0.11 0.19 2 -0.39 23 25
MST1 0.001 0.099 -10000 0 -0.36 32 32
alphaM/beta2 Integrin/lipoprotein(a) -0.015 0.14 -10000 0 -0.3 73 73
TNF -0.15 0.27 -10000 0 -0.63 101 101
RAP1B 0.026 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.02 0.13 -10000 0 -0.31 64 64
fibrinolysis -0.013 0.12 -10000 0 -0.32 53 53
HCK 0.014 0.063 -10000 0 -0.27 19 19
dendritic cell antigen processing and presentation -0.044 0.13 -10000 0 -0.42 32 32
VTN 0.012 0.075 -10000 0 -0.35 19 19
alphaM/beta2 Integrin/CYR61 -0.03 0.13 -10000 0 -0.31 72 72
LPA 0.005 0.039 -10000 0 -10000 0 0
LRP1 0.026 0.004 -10000 0 -10000 0 0
cell migration -0.05 0.13 -10000 0 -0.29 94 94
FN1 0.021 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.007 0.12 -10000 0 -0.33 49 49
MPO -0.05 0.15 -10000 0 -0.43 64 64
KNG1 -0.009 0.032 -10000 0 -0.13 22 22
RAP1/GDP 0.028 0.015 -10000 0 -10000 0 0
ROCK1 -0.034 0.12 -10000 0 -0.4 23 23
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.01 0.019 -10000 0 -10000 0 0
CTGF 0.004 0.086 -10000 0 -0.43 17 17
alphaM/beta2 Integrin/Hck -0.009 0.14 -10000 0 -0.36 50 50
ITGAM -0.02 0.12 -10000 0 -0.41 36 36
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.005 0.15 -10000 0 -0.4 50 50
HP -0.034 0.13 -10000 0 -0.24 113 113
leukocyte adhesion -0.031 0.14 -10000 0 -0.35 57 57
SELP 0.003 0.042 -10000 0 -10000 0 0
BCR signaling 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
JUN -0.058 0.18 0.26 9 -0.41 83 92
IKBKB 0.015 0.09 0.24 21 -0.31 3 24
AKT1 -0.022 0.1 0.26 24 -0.22 33 57
IKBKG 0.004 0.093 0.24 14 -0.27 14 28
CALM1 -0.04 0.14 0.24 2 -0.46 36 38
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
MAP3K1 -0.033 0.18 0.3 17 -0.48 50 67
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.15 0.22 4 -0.4 56 60
DOK1 0.025 0.021 -10000 0 -0.28 2 2
AP-1 -0.044 0.12 0.22 4 -0.27 74 78
LYN 0.021 0.035 -10000 0 -0.43 2 2
BLNK -0.021 0.13 -10000 0 -0.43 49 49
SHC1 0.024 0.014 -10000 0 -10000 0 0
BCR complex -0.006 0.096 -10000 0 -0.27 51 51
CD22 -0.065 0.15 -10000 0 -0.43 53 53
CAMK2G -0.037 0.14 0.26 4 -0.44 34 38
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
SHC/GRB2/SOS1 -0.027 0.11 -10000 0 -0.25 68 68
GO:0007205 -0.042 0.16 0.22 3 -0.41 55 58
SYK 0.009 0.083 -10000 0 -0.35 23 23
ELK1 -0.039 0.15 0.22 2 -0.47 37 39
NFATC1 -0.043 0.14 0.27 6 -0.42 49 55
B-cell antigen/BCR complex -0.006 0.096 -10000 0 -0.27 51 51
PAG1/CSK 0.036 0.01 -10000 0 -10000 0 0
NFKBIB 0.017 0.046 0.13 23 -0.13 13 36
HRAS -0.031 0.14 0.26 6 -0.44 31 37
NFKBIA 0.016 0.047 0.12 26 -0.13 13 39
NF-kappa-B/RelA/I kappa B beta 0.022 0.041 0.13 23 -10000 0 23
RasGAP/Csk -0.002 0.12 -10000 0 -0.24 96 96
mol:GDP -0.037 0.15 0.22 3 -0.44 45 48
PTEN 0.025 0.006 -10000 0 -10000 0 0
CD79B -0.005 0.099 -10000 0 -0.26 54 54
NF-kappa-B/RelA/I kappa B alpha 0.022 0.041 0.13 23 -10000 0 23
GRB2 0.025 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.059 0.18 0.34 4 -0.51 50 54
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.044 0.16 0.22 3 -0.41 58 61
CSK 0.026 0.003 -10000 0 -10000 0 0
FOS -0.059 0.16 0.22 2 -0.45 44 46
CHUK -0.006 0.098 0.24 12 -0.3 18 30
IBTK 0.026 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.002 0.15 0.24 12 -0.46 28 40
PTPN6 -0.068 0.15 0.22 2 -0.45 52 54
RELA 0.025 0.005 -10000 0 -10000 0 0
BCL2A1 0.007 0.038 0.12 5 -0.12 2 7
VAV2 -0.053 0.15 0.23 1 -0.47 47 48
ubiquitin-dependent protein catabolic process 0.019 0.046 0.13 24 -0.13 13 37
BTK -0.018 0.21 -10000 0 -1.1 18 18
CD19 -0.056 0.14 -10000 0 -0.39 60 60
MAP4K1 0.013 0.061 -10000 0 -0.34 13 13
CD72 0.017 0.048 -10000 0 -0.43 4 4
PAG1 0.025 0.006 -10000 0 -10000 0 0
MAPK14 -0.026 0.16 0.27 19 -0.41 49 68
SH3BP5 0.024 0.029 -10000 0 -0.43 2 2
PIK3AP1 -0.041 0.16 -10000 0 -0.47 46 46
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.06 0.23 -10000 0 -0.66 46 46
RAF1 -0.028 0.13 0.26 5 -0.42 29 34
RasGAP/p62DOK/SHIP -0.002 0.12 -10000 0 -0.23 98 98
CD79A -0.001 0.086 -10000 0 -0.25 42 42
re-entry into mitotic cell cycle -0.044 0.11 0.22 4 -0.27 74 78
RASA1 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.024 0.11 0.24 6 -0.41 20 26
MAPK1 -0.023 0.11 0.23 6 -0.41 19 25
CD72/SHP1 -0.056 0.16 0.27 12 -0.43 51 63
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.031 0.16 0.28 17 -0.41 52 69
actin cytoskeleton organization -0.027 0.15 0.3 19 -0.41 43 62
NF-kappa-B/RelA 0.044 0.079 0.24 18 -0.21 8 26
Calcineurin -0.011 0.13 0.22 1 -0.43 29 30
PI3K -0.067 0.13 -10000 0 -0.37 56 56
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.043 0.17 -10000 0 -0.44 56 56
SOS1 0.026 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.068 0.27 -10000 0 -0.8 55 55
DAPP1 -0.095 0.31 -10000 0 -0.92 55 55
cytokine secretion -0.04 0.14 0.26 6 -0.39 49 55
mol:DAG -0.044 0.16 0.22 3 -0.41 58 61
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
MAP2K1 -0.026 0.12 0.24 6 -0.43 22 28
B-cell antigen/BCR complex/FcgammaRIIB -0.028 0.13 -10000 0 -0.25 115 115
mol:PI-3-4-5-P3 -0.056 0.094 0.18 1 -0.29 46 47
ETS1 -0.026 0.13 0.26 9 -0.41 32 41
B-cell antigen/BCR complex/LYN/SYK/BLNK 0 0.13 -10000 0 -0.26 89 89
B-cell antigen/BCR complex/LYN -0.048 0.15 -10000 0 -0.42 56 56
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 -0.033 0.15 0.28 15 -0.44 42 57
B-cell antigen/BCR complex/LYN/SYK -0.049 0.17 0.27 1 -0.43 61 62
CARD11 -0.022 0.18 0.25 23 -0.51 36 59
FCGR2B -0.05 0.15 -10000 0 -0.26 135 135
PPP3CA 0.025 0.011 -10000 0 -0.13 2 2
BCL10 0.021 0.01 -10000 0 -10000 0 0
IKK complex 0.01 0.05 0.14 25 -0.12 5 30
PTPRC -0.003 0.1 -10000 0 -0.43 24 24
PDPK1 -0.034 0.079 0.2 14 -0.21 36 50
PPP3CB 0.024 0.013 -10000 0 -10000 0 0
PPP3CC 0.025 0.005 -10000 0 -10000 0 0
POU2F2 0.021 0.033 0.15 18 -10000 0 18
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.002 0.097 -9999 0 -0.27 48 48
GPC2 0.004 0.084 -9999 0 -0.37 22 22
GPC2/Midkine 0.002 0.091 -9999 0 -0.31 36 36
neuron projection morphogenesis 0.002 0.09 -9999 0 -0.31 36 36
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.084 -10000 0 -0.23 62 62
epithelial cell differentiation 0.024 0.086 -10000 0 -0.22 55 55
CYFIP2 0.022 0.037 -10000 0 -0.28 6 6
ENAH -0.024 0.061 0.27 3 -10000 0 3
EGFR -0.016 0.12 -10000 0 -0.4 46 46
EPHA2 0.012 0.045 -10000 0 -0.15 29 29
MYO6 -0.014 0.08 0.18 21 -0.21 55 76
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.045 0.028 -10000 0 -0.23 3 3
AQP5 -0.063 0.16 -10000 0 -0.44 69 69
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.077 0.18 18 -0.21 51 69
regulation of calcium-dependent cell-cell adhesion -0.015 0.081 0.18 19 -0.21 57 76
EGF -0.01 0.11 -10000 0 -0.43 33 33
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
AQP3 -0.019 0.1 -10000 0 -0.46 16 16
cortical microtubule organization 0.024 0.086 -10000 0 -0.22 55 55
GO:0000145 -0.026 0.07 0.16 20 -0.2 51 71
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.088 -10000 0 -0.22 55 55
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
ARF6/GDP -0.038 0.056 -10000 0 -0.2 35 35
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.054 0.036 -10000 0 -0.25 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.027 0.085 -10000 0 -0.34 18 18
PVRL2 0.02 0.023 -10000 0 -0.43 1 1
ZYX -0.013 0.069 0.18 11 -0.21 44 55
ARF6/GTP 0.059 0.038 -10000 0 -0.24 3 3
CDH1 -0.046 0.15 -10000 0 -0.43 59 59
EGFR/EGFR/EGF/EGF -0.02 0.12 -10000 0 -0.24 105 105
RhoA/GDP 0.026 0.083 -10000 0 -0.21 55 55
actin cytoskeleton organization -0.028 0.075 0.17 21 -0.21 49 70
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
IGF1R 0.026 0.004 -10000 0 -10000 0 0
IGF1 0.012 0.076 -10000 0 -0.34 20 20
DIAPH1 0.02 0.12 -10000 0 -0.6 8 8
Wnt receptor signaling pathway -0.024 0.086 0.22 55 -10000 0 55
RHOA 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.038 0.056 -10000 0 -0.2 35 35
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.029 0.077 0.17 21 -0.22 49 70
EFNA1 0.024 0.014 -10000 0 -0.13 4 4
LPP -0.036 0.077 0.17 19 -0.21 61 80
Ephrin A1/EPHA2 0.013 0.079 -10000 0 -0.2 54 54
SEC6/SEC8 -0.015 0.06 -10000 0 -0.21 26 26
MGAT3 -0.016 0.082 0.18 19 -0.21 57 76
HGF/MET -0.025 0.12 -10000 0 -0.25 95 95
HGF -0.009 0.091 -10000 0 -0.2 69 69
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.085 -10000 0 -0.23 62 62
actin cable formation -0.004 0.096 0.32 13 -0.26 11 24
KIAA1543 -0.032 0.076 0.17 13 -0.22 55 68
KIFC3 -0.016 0.079 0.18 16 -0.21 55 71
NCK1 0.025 0.02 -10000 0 -0.43 1 1
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ACTN1 -0.019 0.08 0.18 19 -0.21 56 75
NCK1/GIT1 0.038 0.016 -10000 0 -0.3 1 1
mol:GDP 0.024 0.086 -10000 0 -0.22 55 55
EXOC4 0.02 0.011 -10000 0 -10000 0 0
STX4 -0.014 0.079 0.18 19 -0.21 53 72
PIP5K1C -0.013 0.078 0.18 18 -0.21 51 69
LIMA1 0.019 0.056 -10000 0 -0.43 8 8
ABI1 0.023 0.008 -10000 0 -10000 0 0
ROCK1 -0.021 0.082 0.4 6 -10000 0 6
adherens junction assembly -0.01 0.089 0.27 10 -0.38 6 16
IGF-1R heterotetramer/IGF1 0.014 0.09 -10000 0 -0.22 62 62
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
MET -0.047 0.14 -10000 0 -0.43 52 52
PLEKHA7 -0.019 0.085 0.19 1 -0.23 55 56
mol:GTP 0.052 0.036 -10000 0 -0.25 3 3
establishment of epithelial cell apical/basal polarity 0.02 0.12 0.33 27 -0.37 1 28
cortical actin cytoskeleton stabilization -0.01 0.084 -10000 0 -0.23 62 62
regulation of cell-cell adhesion -0.028 0.075 0.17 21 -0.21 49 70
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.085 -10000 0 -0.23 62 62
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.4 46 46
EGF/EGFR -0.008 0.11 -10000 0 -0.24 88 88
EGF/EGFR dimer/SHC/GRB2/SOS1 0.022 0.1 -10000 0 -0.24 64 64
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.006 0.083 -10000 0 -0.28 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.01 0.11 -10000 0 -0.43 33 33
EGF/EGFR dimer/SHC 0 0.11 -10000 0 -0.27 67 67
mol:GDP 0.016 0.1 -10000 0 -0.23 64 64
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.002 0.086 -10000 0 -0.23 47 47
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.087 -10000 0 -0.22 63 63
SHC1 0.024 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.096 -10000 0 -0.22 63 63
FRAP1 -0.034 0.075 0.11 7 -0.22 64 71
EGF/EGFR dimer -0.02 0.12 -10000 0 -0.32 69 69
SOS1 0.026 0.002 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.005 0.088 -10000 0 -0.3 34 34
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.042 0.2 -9999 0 -0.47 69 69
MAP3K8 0.015 0.047 -9999 0 -0.2 17 17
FOS -0.041 0.18 -9999 0 -0.44 70 70
PRKCA 0.02 0.024 -9999 0 -0.43 1 1
PTPN7 -0.054 0.15 -9999 0 -0.29 122 122
HRAS 0.024 0.006 -9999 0 -10000 0 0
PRKCB -0.011 0.098 -9999 0 -0.22 68 68
NRAS 0.021 0.01 -9999 0 -10000 0 0
RAS family/GTP 0.034 0.026 -9999 0 -10000 0 0
MAPK3 -0.032 0.16 -9999 0 -0.43 66 66
MAP2K1 0.003 0.1 -9999 0 -0.44 20 20
ELK1 0.021 0.017 -9999 0 -10000 0 0
BRAF -0.005 0.083 -9999 0 -0.39 21 21
mol:GTP 0 0.001 -9999 0 -0.004 59 59
MAPK1 -0.035 0.17 -9999 0 -0.43 69 69
RAF1 -0.001 0.086 -9999 0 -0.41 19 19
KRAS 0.025 0.005 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.029 0.025 -10000 0 -0.28 2 2
Necdin/E2F1 0.013 0.082 -10000 0 -0.31 29 29
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.015 0.11 -10000 0 -0.24 73 73
NGF (dimer)/p75(NTR)/BEX1 -0.018 0.13 -10000 0 -0.28 91 91
NT-4/5 (dimer)/p75(NTR) -0.005 0.089 -10000 0 -0.29 40 40
IKBKB 0.025 0.005 -10000 0 -10000 0 0
AKT1 -0.029 0.092 0.18 9 -0.24 71 80
IKBKG 0.026 0.003 -10000 0 -10000 0 0
BDNF -0.01 0.089 -10000 0 -0.43 14 14
MGDIs/NGR/p75(NTR)/LINGO1 -0.002 0.13 -10000 0 -0.3 78 78
FURIN 0.026 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.01 0.098 -10000 0 -0.26 53 53
LINGO1 0.001 0.1 -10000 0 -0.43 28 28
Sortilin/TRAF6/NRIF 0.025 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.01 0.089 -10000 0 -0.43 14 14
NTRK1 0.016 0.055 -10000 0 -0.22 20 20
RTN4R -0.006 0.11 -10000 0 -0.43 31 31
neuron apoptosis -0.066 0.16 0.29 9 -0.45 38 47
IRAK1 0.026 0.003 -10000 0 -10000 0 0
SHC1 -0.038 0.1 0.19 1 -0.28 73 74
ARHGDIA 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.001 0.12 -10000 0 -0.25 78 78
MAGEH1 0.018 0.06 -10000 0 -0.43 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.14 -10000 0 -0.27 98 98
Mammalian IAPs/DIABLO 0.05 0.064 -10000 0 -0.24 23 23
proNGF (dimer) -0.025 0.13 -10000 0 -0.43 46 46
MAGED1 0.026 0.002 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.16 12 12
ZNF274 0.021 0.01 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.017 0.094 -10000 0 -0.24 69 69
NGF -0.025 0.13 -10000 0 -0.43 46 46
cell cycle arrest -0.037 0.089 0.26 10 -0.21 71 81
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.021 0.099 -10000 0 -0.25 71 71
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.012 0.081 -10000 0 -0.24 40 40
NCSTN 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.017 0.12 -10000 0 -0.28 73 73
PSENEN 0.022 0.01 -10000 0 -10000 0 0
mol:ceramide -0.032 0.097 0.18 7 -0.25 73 80
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.021 0.094 -10000 0 -0.31 23 23
p75(NTR)/beta APP 0.005 0.09 -10000 0 -0.3 35 35
BEX1 0.01 0.084 -10000 0 -0.43 18 18
mol:GDP -0.044 0.1 -10000 0 -0.27 76 76
NGF (dimer) -0.025 0.13 -10000 0 -0.25 117 117
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.013 0.12 -10000 0 -0.27 76 76
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RAC1/GTP -0.006 0.094 -10000 0 -0.23 67 67
MYD88 0.019 0.054 -10000 0 -0.43 7 7
CHUK 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.007 0.12 -10000 0 -0.27 76 76
RHOB 0.025 0.012 -10000 0 -0.13 3 3
RHOA 0.026 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.028 0.044 -10000 0 -0.3 6 6
NT3 (dimer) 0.006 0.032 -10000 0 -10000 0 0
TP53 -0.021 0.1 0.22 32 -0.24 49 81
PRDM4 -0.032 0.099 0.18 7 -0.25 74 81
BDNF (dimer) -0.017 0.12 -10000 0 -0.26 93 93
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
SORT1 0.02 0.022 -10000 0 -0.43 1 1
activation of caspase activity 0.011 0.11 -10000 0 -0.24 73 73
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.005 0.11 -10000 0 -0.25 74 74
RHOC 0.02 0.023 -10000 0 -0.28 2 2
XIAP 0.026 0.001 -10000 0 -10000 0 0
MAPK10 -0.017 0.13 0.3 25 -0.32 39 64
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.032 0.098 0.18 7 -0.25 73 80
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.007 0.12 -10000 0 -0.27 77 77
PSEN1 0.025 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.032 0.016 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.002 0.091 -10000 0 -0.3 38 38
MAPK8 -0.026 0.13 0.31 14 -0.32 40 54
MAPK9 -0.015 0.13 0.3 26 -0.33 36 62
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 0.006 0.032 -10000 0 -10000 0 0
NTF4 -0.003 0.033 -10000 0 -0.16 12 12
NDN -0.003 0.11 -10000 0 -0.43 33 33
RAC1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.011 0.1 -10000 0 -0.22 72 72
p75 CTF/Sortilin/TRAF6/NRIF 0.044 0.045 -10000 0 -0.24 6 6
RhoA-B-C/GTP -0.017 0.12 -10000 0 -0.28 73 73
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.026 0.095 -10000 0 -0.24 46 46
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.097 -10000 0 -0.25 47 47
PRKACB 0.021 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.007 0.077 -10000 0 -0.32 18 18
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BIRC2 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.05 0.1 0.14 7 -0.27 77 84
BAD -0.018 0.14 0.29 28 -0.33 36 64
RIPK2 0.024 0.007 -10000 0 -10000 0 0
NGFR -0.017 0.12 -10000 0 -0.28 72 72
CYCS -0.026 0.09 0.22 8 -0.24 61 69
ADAM17 0.022 0.045 -10000 0 -0.43 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.005 0.11 -10000 0 -0.25 66 66
BCL2L11 -0.021 0.13 0.28 25 -0.33 37 62
BDNF (dimer)/p75(NTR) -0.02 0.11 -10000 0 -0.3 53 53
PI3K 0.007 0.11 -10000 0 -0.25 72 72
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.006 0.11 -10000 0 -0.25 74 74
NDNL2 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.026 0.002 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.034 0.13 -10000 0 -0.32 77 77
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.006 0.11 -10000 0 -0.25 73 73
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
PLG -0.01 0.019 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.044 0.11 0.24 2 -0.28 81 83
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
NGFRAP1 0.026 0.002 -10000 0 -10000 0 0
CASP3 -0.018 0.13 0.28 26 -0.32 38 64
E2F1 0.014 0.056 -10000 0 -0.21 24 24
CASP9 0.022 0.012 -10000 0 -0.13 1 1
IKK complex -0.021 0.13 -10000 0 -0.31 43 43
NGF (dimer)/TRKA -0.012 0.1 -10000 0 -0.3 53 53
MMP7 -0.073 0.16 -10000 0 -0.29 150 150
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.012 0.11 -10000 0 -0.24 71 71
MMP3 -0.005 0.047 -10000 0 -0.43 1 1
APAF-1/Caspase 9 -0.029 0.082 -10000 0 -0.3 15 15
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.008 0.17 0.36 11 -1.1 9 20
VDR -0.014 0.11 -10000 0 -0.26 71 71
FAM120B 0.025 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.15 -10000 0 -0.32 96 96
RXRs/LXRs/DNA/Oxysterols -0.073 0.21 -10000 0 -0.47 97 97
MED1 0.026 0.003 -10000 0 -10000 0 0
mol:9cRA -0.006 0.02 -10000 0 -0.098 1 1
RARs/THRs/DNA/Src-1 0.023 0.041 -10000 0 -0.22 14 14
RXRs/NUR77 0.011 0.11 -10000 0 -0.25 59 59
RXRs/PPAR -0.013 0.098 -10000 0 -0.26 58 58
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.29 33 33
RARs/VDR/DNA/Vit D3 0.042 0.071 -10000 0 -0.22 32 32
RARA 0.026 0.003 -10000 0 -10000 0 0
NCOA1 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.014 0.11 -10000 0 -0.26 71 71
RARs/RARs/DNA/9cRA 0.035 0.032 -10000 0 -0.22 3 3
RARG 0.025 0.008 -10000 0 -10000 0 0
RPS6KB1 0.028 0.12 0.58 17 -0.43 9 26
RARs/THRs/DNA/SMRT 0.022 0.041 -10000 0 -0.22 14 14
THRA 0.023 0.035 -10000 0 -0.43 3 3
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.009 0.08 -10000 0 -0.29 33 33
RXRs/PPAR/9cRA/PGJ2/DNA -0.004 0.11 -10000 0 -0.2 95 95
NR1H4 -0.042 0.13 -10000 0 -0.24 128 128
RXRs/LXRs/DNA 0.011 0.12 -10000 0 -0.23 83 83
NR1H2 0.015 0.026 -10000 0 -10000 0 0
NR1H3 0.015 0.031 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.003 0.12 -10000 0 -0.24 79 79
NR4A1 0.012 0.062 -10000 0 -0.43 7 7
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.037 0.11 -10000 0 -0.25 85 85
RXRG -0.036 0.14 -10000 0 -0.4 63 63
RXR alpha/CCPG 0.027 0.028 -10000 0 -10000 0 0
RXRA 0.015 0.029 -10000 0 -10000 0 0
RXRB 0.015 0.031 -10000 0 -0.1 1 1
THRB 0.015 0.059 -10000 0 -0.23 22 22
PPARG 0.009 0.081 -10000 0 -0.43 16 16
PPARD 0.026 0.003 -10000 0 -10000 0 0
TNF -0.15 0.37 -10000 0 -0.96 81 81
mol:Oxysterols -0.006 0.019 -10000 0 -10000 0 0
cholesterol transport -0.072 0.21 -10000 0 -0.46 97 97
PPARA 0.026 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.035 -10000 0 -0.43 3 3
RXRs/NUR77/BCL2 -0.016 0.094 -10000 0 -0.25 59 59
SREBF1 -0.085 0.24 -10000 0 -0.87 30 30
RXRs/RXRs/DNA/9cRA -0.004 0.11 -10000 0 -0.2 97 97
ABCA1 -0.086 0.24 -10000 0 -0.55 84 84
RARs/THRs 0.067 0.05 -10000 0 -0.22 13 13
RXRs/FXR -0.01 0.14 -10000 0 -0.26 103 103
BCL2 0.021 0.045 -10000 0 -0.43 5 5
LPA receptor mediated 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
GNB1/GNG2 0.013 0.089 -10000 0 -0.22 61 61
NF kappa B1 p50/RelA/I kappa B alpha 0 0.11 0.24 15 -0.31 33 48
AP1 -0.03 0.1 -10000 0 -0.23 92 92
mol:PIP3 -0.036 0.088 -10000 0 -0.24 60 60
AKT1 0.001 0.1 0.27 17 -0.34 5 22
PTK2B -0.005 0.09 0.17 14 -0.22 49 63
RHOA 0.004 0.079 0.22 17 -0.36 7 24
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.071 0.21 22 -0.28 10 32
MAGI3 0.02 0.022 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
apoptosis -0.021 0.087 -10000 0 -0.27 52 52
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.088 0.21 8 -0.26 20 28
NF kappa B1 p50/RelA -0.023 0.11 -10000 0 -0.32 37 37
endothelial cell migration -0.022 0.11 -10000 0 -0.3 57 57
ADCY4 -0.014 0.12 -10000 0 -0.35 52 52
ADCY5 -0.015 0.12 -10000 0 -0.34 52 52
ADCY6 -0.013 0.12 -10000 0 -0.34 52 52
ADCY7 -0.014 0.12 -10000 0 -0.34 52 52
ADCY1 -0.032 0.12 -10000 0 -0.36 50 50
ADCY2 -0.018 0.12 -10000 0 -0.35 54 54
ADCY3 -0.013 0.12 -10000 0 -0.34 52 52
ADCY8 -0.035 0.14 -10000 0 -0.39 59 59
ADCY9 -0.014 0.12 -10000 0 -0.34 52 52
GSK3B -0.006 0.087 0.18 9 -0.25 24 33
arachidonic acid secretion -0.02 0.12 -10000 0 -0.32 60 60
GNG2 0.022 0.04 -10000 0 -0.43 4 4
TRIP6 0.013 0.031 -10000 0 -0.21 7 7
GNAO1 -0.018 0.089 -10000 0 -0.25 61 61
HRAS 0.025 0.006 -10000 0 -10000 0 0
NFKBIA -0.018 0.12 0.24 17 -0.34 35 52
GAB1 0.025 0.02 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.11 -10000 0 -0.84 7 7
JUN 0.019 0.023 -10000 0 -0.13 9 9
LPA/LPA2/NHERF2 0.028 0.039 -10000 0 -0.25 7 7
TIAM1 0.017 0.13 -10000 0 -1 7 7
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
mol:IP3 -0.008 0.066 0.2 15 -0.29 10 25
PLCB3 0.017 0.048 0.18 23 -0.23 7 30
FOS -0.031 0.14 -10000 0 -0.43 48 48
positive regulation of mitosis -0.02 0.12 -10000 0 -0.32 60 60
LPA/LPA1-2-3 0.007 0.094 -10000 0 -0.23 63 63
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
stress fiber formation 0.002 0.097 0.2 10 -0.32 11 21
GNAZ -0.014 0.084 -10000 0 -0.25 54 54
EGFR/PI3K-beta/Gab1 -0.03 0.095 -10000 0 -0.24 60 60
positive regulation of dendritic cell cytokine production 0.006 0.093 -10000 0 -0.23 63 63
LPA/LPA2/MAGI-3 0.021 0.042 -10000 0 -0.25 8 8
ARHGEF1 0.015 0.097 0.2 60 -0.2 48 108
GNAI2 -0.015 0.085 -10000 0 -0.25 55 55
GNAI3 -0.003 0.062 -10000 0 -0.26 26 26
GNAI1 -0.015 0.083 -10000 0 -0.25 53 53
LPA/LPA3 0.002 0.036 -10000 0 -0.17 9 9
LPA/LPA2 0.013 0.042 -10000 0 -0.2 15 15
LPA/LPA1 -0.017 0.1 -10000 0 -0.3 57 57
HB-EGF/EGFR -0.035 0.11 -10000 0 -0.26 84 84
HBEGF -0.033 0.09 -10000 0 -0.29 48 48
mol:DAG -0.008 0.066 0.2 15 -0.29 10 25
cAMP biosynthetic process -0.016 0.14 0.3 10 -0.34 59 69
NFKB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
LYN -0.015 0.12 0.24 19 -0.36 31 50
GNAQ 0.002 0.037 -10000 0 -0.25 7 7
LPAR2 0.018 0.054 -10000 0 -0.34 10 10
LPAR3 -0.009 0.043 -10000 0 -10000 0 0
LPAR1 -0.025 0.14 -10000 0 -0.39 57 57
IL8 -0.1 0.21 0.33 11 -0.44 110 121
PTK2 -0.014 0.09 0.19 25 -0.22 60 85
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
CASP3 -0.021 0.087 -10000 0 -0.27 52 52
EGFR -0.017 0.12 -10000 0 -0.4 46 46
PLCG1 -0.013 0.059 0.15 6 -0.22 23 29
PLD2 -0.013 0.094 0.19 29 -0.22 63 92
G12/G13 0.018 0.084 -10000 0 -0.23 48 48
PI3K-beta -0.022 0.085 -10000 0 -0.27 30 30
cell migration 0.009 0.052 0.24 1 -0.24 5 6
SLC9A3R2 0.025 0.01 -10000 0 -0.13 2 2
PXN 0.002 0.098 0.2 8 -0.33 11 19
HRAS/GTP -0.02 0.12 -10000 0 -0.33 60 60
RAC1 0.023 0.009 -10000 0 -10000 0 0
MMP9 -0.042 0.13 -10000 0 -0.23 133 133
PRKCE 0.022 0.034 -10000 0 -0.2 9 9
PRKCD -0.009 0.096 0.22 30 -0.29 27 57
Gi(beta/gamma) -0.019 0.13 -10000 0 -0.35 59 59
mol:LPA -0.001 0.022 -10000 0 -0.16 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.094 0.33 1 -0.35 9 10
MAPKKK cascade -0.02 0.12 -10000 0 -0.32 60 60
contractile ring contraction involved in cytokinesis 0.001 0.087 0.22 21 -0.35 9 30
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.007 0.06 0.12 1 -0.26 23 24
GNA15 -0.005 0.057 -10000 0 -0.27 19 19
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.008 0.09 0.21 8 -0.27 20 28
GNA11 -0.002 0.049 -10000 0 -0.25 15 15
Rac1/GTP 0.03 0.11 -10000 0 -0.9 7 7
MMP2 -0.023 0.11 -10000 0 -0.3 57 57
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.006 0.085 0.19 4 -0.21 52 56
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.092 0.3 5 -0.27 10 15
alphaV/beta3 Integrin/Osteopontin/Src 0.002 0.095 -10000 0 -0.3 39 39
AP1 -0.023 0.12 -10000 0 -0.36 24 24
ILK -0.015 0.08 -10000 0 -0.22 47 47
bone resorption -0.032 0.13 0.32 2 -0.35 43 45
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
PYK2/p130Cas 0.02 0.11 -10000 0 -0.25 55 55
ITGAV 0.027 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.005 0.11 -10000 0 -0.31 53 53
alphaV/beta3 Integrin/Osteopontin 0.018 0.1 -10000 0 -0.24 55 55
MAP3K1 -0.018 0.083 0.19 6 -0.22 51 57
JUN 0.019 0.023 -10000 0 -0.13 9 9
MAPK3 -0.026 0.081 0.19 4 -0.21 62 66
MAPK1 -0.026 0.079 0.19 3 -0.21 61 64
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.029 0.084 0.19 4 -0.23 54 58
ITGB3 0 0.082 -10000 0 -0.19 64 64
NFKBIA -0.025 0.08 0.19 2 -0.27 15 17
FOS -0.031 0.14 -10000 0 -0.33 72 72
CD44 -0.015 0.12 -10000 0 -0.31 62 62
CHUK 0.025 0.005 -10000 0 -10000 0 0
PLAU -0.044 0.18 -10000 0 -1.1 12 12
NF kappa B1 p50/RelA 0.004 0.098 -10000 0 -0.34 11 11
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
RELA 0.025 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.02 0.064 -10000 0 -0.3 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.025 0.1 0.19 7 -0.27 57 64
VAV3 -0.05 0.098 0.19 4 -0.24 79 83
MAP3K14 -0.019 0.084 0.19 4 -0.22 52 56
ROCK2 0.008 0.088 -10000 0 -0.43 20 20
SPP1 -0.023 0.12 -10000 0 -0.31 65 65
RAC1 0.023 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.092 0.18 3 -0.23 60 63
MMP2 -0.046 0.11 -10000 0 -0.4 24 24
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.004 0.097 -10000 0 -0.22 75 75
regulation of S phase of mitotic cell cycle -0.01 0.083 -10000 0 -0.22 69 69
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.024 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.012 0.036 -10000 0 -0.25 9 9
PELP1 0.026 0.002 -10000 0 -10000 0 0
AKT1 0.007 0.001 -10000 0 -10000 0 0
MAP2K1 -0.035 0.096 0.18 27 -0.29 18 45
T-DHT/AR -0.033 0.11 -10000 0 -0.23 104 104
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 55 55
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
mol:GDP -0.05 0.13 -10000 0 -0.38 71 71
cell proliferation -0.043 0.16 0.29 7 -0.42 53 60
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
FOS -0.075 0.26 0.27 1 -0.78 56 57
mol:Ca2+ -0.007 0.019 -10000 0 -0.054 50 50
MAPK3 -0.036 0.13 0.27 8 -0.32 51 59
MAPK1 -0.015 0.089 0.22 1 -0.3 17 18
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 55 55
cAMP biosynthetic process -0.001 0.036 0.23 1 -0.24 9 10
GNG2 0.022 0.04 -10000 0 -0.43 4 4
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 55 55
HRAS/GTP 0 0.095 -10000 0 -0.22 70 70
actin cytoskeleton reorganization 0.029 0.019 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 55 55
PI3K 0.035 0.007 -10000 0 -10000 0 0
apoptosis 0.033 0.15 0.42 55 -0.24 6 61
T-DHT/AR/PELP1 -0.014 0.1 -10000 0 -0.26 71 71
HRAS/GDP -0.036 0.13 -10000 0 -0.36 71 71
CREB1 -0.037 0.16 0.25 6 -0.45 55 61
RAC1-CDC42/GTP 0.036 0.024 -10000 0 -10000 0 0
AR -0.048 0.16 -10000 0 -0.34 104 104
GNB1 0.022 0.01 -10000 0 -10000 0 0
RAF1 -0.02 0.098 0.19 15 -0.22 69 84
RAC1-CDC42/GDP -0.021 0.13 -10000 0 -0.34 67 67
T-DHT/AR/PELP1/Src 0.006 0.099 -10000 0 -0.24 71 71
MAP2K2 -0.036 0.092 0.18 23 -0.29 16 39
T-DHT/AR/PELP1/Src/PI3K -0.011 0.084 -10000 0 -0.22 69 69
GNAZ 0.026 0.004 -10000 0 -10000 0 0
SHBG 0.017 0.06 -10000 0 -0.43 9 9
Gi family/GNB1/GNG2/GDP -0.03 0.12 -10000 0 -0.35 37 37
mol:T-DHT 0 0.001 -10000 0 -0.002 36 36
RAC1 0.023 0.009 -10000 0 -10000 0 0
GNRH1 0.002 0.035 -10000 0 -0.3 6 6
Gi family/GTP -0.021 0.068 -10000 0 -0.2 37 37
CDC42 0.022 0.01 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.022 0.1 -10000 0 -0.3 52 52
CRKL 0.011 0.14 0.29 9 -0.46 20 29
mol:PIP3 0.001 0.039 -10000 0 -0.84 1 1
AKT1 -0.003 0.043 0.28 1 -0.73 1 2
PTK2B 0.018 0.032 -10000 0 -0.13 22 22
RAPGEF1 0.014 0.14 0.3 12 -0.44 20 32
RANBP10 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
HGF/MET/SHIP2 -0.004 0.11 -10000 0 -0.24 81 81
MAP3K5 -0.008 0.16 0.28 11 -0.47 29 40
HGF/MET/CIN85/CBL/ENDOPHILINS 0.007 0.11 -10000 0 -0.26 55 55
AP1 -0.01 0.1 0.15 4 -0.24 55 59
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -10000 0 0
apoptosis -0.17 0.38 -10000 0 -0.8 130 130
STAT3 (dimer) -0.006 0.09 0.22 4 -0.41 7 11
GAB1/CRKL/SHP2/PI3K 0.038 0.14 0.29 5 -0.43 19 24
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
CBL/CRK 0.02 0.14 0.29 8 -0.44 20 28
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
ELK1 0.038 0.16 0.31 119 -0.27 2 121
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.066 -10000 0 -0.3 12 12
PAK1 -0.004 0.059 -10000 0 -0.7 1 1
HGF/MET/RANBP10 -0.004 0.11 -10000 0 -0.24 83 83
HRAS -0.047 0.2 -10000 0 -0.6 53 53
DOCK1 0.008 0.14 0.28 10 -0.44 20 30
GAB1 0 0.14 0.26 2 -0.49 19 21
CRK 0.01 0.14 0.3 10 -0.46 20 30
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.045 0.19 -10000 0 -0.53 63 63
JUN 0.019 0.023 -10000 0 -0.13 9 9
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.082 -10000 0 -0.24 60 60
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell morphogenesis 0.019 0.14 0.31 29 -0.45 11 40
GRB2/SHC 0.005 0.088 0.19 8 -0.22 51 59
FOS -0.031 0.14 -10000 0 -0.43 48 48
GLMN 0.003 0.002 -10000 0 -10000 0 0
cell motility 0.037 0.16 0.31 119 -0.27 2 121
HGF/MET/MUC20 -0.032 0.1 -10000 0 -0.24 83 83
cell migration 0.005 0.087 0.19 8 -0.22 51 59
GRB2 0.025 0.006 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.022 0.1 -10000 0 -0.3 52 52
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.014 0.084 -10000 0 -0.24 53 53
MET/MUC20 -0.031 0.097 -10000 0 -0.3 52 52
RAP1B 0.015 0.14 0.3 15 -0.41 20 35
RAP1A 0.013 0.13 0.3 14 -0.4 20 34
HGF/MET/RANBP9 -0.004 0.11 -10000 0 -0.24 83 83
RAF1 -0.024 0.2 0.35 2 -0.56 53 55
STAT3 -0.006 0.09 0.22 4 -0.41 7 11
cell proliferation 0.001 0.15 0.3 13 -0.36 54 67
RPS6KB1 -0.005 0.043 -10000 0 -0.17 17 17
MAPK3 0.025 0.15 0.52 7 -10000 0 7
MAPK1 0.031 0.16 0.58 12 -10000 0 12
RANBP9 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.01 0.15 0.3 6 -0.46 26 32
SRC -0.018 0.078 0.16 1 -0.23 53 54
PI3K 0.005 0.09 0.19 9 -0.22 59 68
MET/Glomulin -0.038 0.092 -10000 0 -0.28 52 52
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K1 -0.021 0.19 0.33 4 -0.52 53 57
MET -0.047 0.14 -10000 0 -0.43 52 52
MAP4K1 -0.006 0.17 0.28 12 -0.48 29 41
PTK2 0.023 0.008 -10000 0 -10000 0 0
MAP2K2 -0.015 0.2 0.33 17 -0.52 53 70
BAD 0 0.051 -10000 0 -0.7 1 1
MAP2K4 -0.006 0.15 0.29 11 -0.43 28 39
SHP2/GRB2/SOS1/GAB1 -0.006 0.13 -10000 0 -0.35 51 51
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PXN 0.026 0.004 -10000 0 -10000 0 0
SH3KBP1 0.026 0.003 -10000 0 -10000 0 0
HGS -0.025 0.074 0.17 2 -0.22 57 59
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.009 0.091 -10000 0 -0.2 69 69
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.005 0.094 0.19 10 -0.22 62 72
PDPK1 -0.002 0.045 0.32 1 -0.78 1 2
HGF/MET/SHIP -0.007 0.11 -10000 0 -0.24 86 86
PDGFR-alpha signaling pathway

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
PDGFRA -0.028 0.14 -10000 0 -0.41 55 55
PDGF/PDGFRA/CRKL -0.003 0.099 -10000 0 -0.3 50 50
positive regulation of JUN kinase activity 0.03 0.084 -10000 0 -0.23 46 46
CRKL 0.026 0.008 -10000 0 -0.13 1 1
PDGF/PDGFRA/Caveolin-3 -0.009 0.1 -10000 0 -0.3 52 52
AP1 -0.094 0.25 -10000 0 -0.79 54 54
mol:IP3 -0.024 0.091 -10000 0 -0.31 44 44
PLCG1 -0.024 0.092 -10000 0 -0.31 44 44
PDGF/PDGFRA/alphaV Integrin -0.003 0.1 -10000 0 -0.3 51 51
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.091 -10000 0 -0.31 44 44
CAV3 0.002 0.031 -10000 0 -0.13 14 14
CAV1 0.006 0.051 -10000 0 -0.43 2 2
SHC/Grb2/SOS1 0.032 0.085 -10000 0 -0.23 46 46
PDGF/PDGFRA/Shf -0.005 0.11 -10000 0 -0.31 53 53
FOS -0.1 0.25 0.31 2 -0.78 54 56
JUN -0.02 0.025 0.16 1 -10000 0 1
oligodendrocyte development -0.003 0.1 -10000 0 -0.3 51 51
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:DAG -0.024 0.091 -10000 0 -0.31 44 44
PDGF/PDGFRA -0.028 0.14 -10000 0 -0.41 55 55
actin cytoskeleton reorganization -0.003 0.099 -10000 0 -0.29 51 51
SRF 0.014 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -10000 0 0
PI3K 0.019 0.088 -10000 0 -0.25 48 48
PDGF/PDGFRA/Crk/C3G 0.017 0.09 -10000 0 -0.25 51 51
JAK1 -0.021 0.088 -10000 0 -0.3 46 46
ELK1/SRF -0.011 0.081 0.15 28 -0.25 41 69
SHB 0.026 0.004 -10000 0 -10000 0 0
SHF 0.022 0.04 -10000 0 -0.43 4 4
CSNK2A1 0.029 0.018 -10000 0 -10000 0 0
GO:0007205 -0.028 0.1 0.23 6 -0.34 43 49
SOS1 0.026 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.03 0.084 -10000 0 -0.23 46 46
PDGF/PDGFRA/SHB -0.003 0.099 -10000 0 -0.29 51 51
PDGF/PDGFRA/Caveolin-1 -0.005 0.085 -10000 0 -0.31 31 31
ITGAV 0.026 0.002 -10000 0 -10000 0 0
ELK1 -0.034 0.087 0.2 5 -0.3 43 48
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PDGF/PDGFRA/Crk -0.003 0.1 -10000 0 -0.3 51 51
JAK-STAT cascade -0.021 0.088 -10000 0 -0.3 46 46
cell proliferation -0.005 0.11 -10000 0 -0.31 53 53
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.025 0.005 -10000 0 -10000 0 0
VLDLR 0.014 0.067 -10000 0 -0.35 15 15
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
NUDC 0.022 0.01 -10000 0 -10000 0 0
RELN/LRP8 0.003 0.095 -10000 0 -0.25 57 57
CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
KATNA1 0.025 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.007 0.11 0.18 82 -0.23 53 135
IQGAP1/CaM 0.033 0.033 -10000 0 -0.28 4 4
DAB1 -0.039 0.15 -10000 0 -0.36 80 80
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
PLA2G7 -0.004 0.11 -10000 0 -0.31 46 46
CALM1 0.025 0.009 -10000 0 -0.13 1 1
DYNLT1 0.024 0.029 -10000 0 -0.43 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.03 0.026 -10000 0 -0.3 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.004 -10000 0 -10000 0 0
CDK5R1 0 0.1 -10000 0 -0.42 30 30
LIS1/Poliovirus Protein 3A 0.01 0.002 -10000 0 -10000 0 0
CDK5R2 -0.05 0.16 -10000 0 -0.36 102 102
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.035 0.13 -10000 0 -0.27 109 109
YWHAE 0.026 0.002 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.014 0.18 0.32 79 -0.42 31 110
MAP1B 0.005 0.012 -10000 0 -0.26 1 1
RAC1 0.011 0.016 -10000 0 -10000 0 0
p35/CDK5 -0.021 0.092 0.18 8 -0.23 66 74
RELN -0.046 0.14 -10000 0 -0.43 58 58
PAFAH/LIS1 0.011 0.064 0.17 1 -0.26 25 26
LIS1/CLIP170 0.028 0.007 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.03 0.11 -10000 0 -0.36 28 28
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.073 0.16 -10000 0 -0.3 132 132
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.037 0.14 0.29 19 -0.43 32 51
LIS1/IQGAP1 0.025 0.029 0.17 2 -0.26 4 6
RHOA 0.012 0.016 -10000 0 -0.15 4 4
PAFAH1B1 0.013 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.022 0.01 -10000 0 -10000 0 0
PAFAH1B2 0.012 0.074 -10000 0 -0.43 14 14
MAP1B/LIS1/Dynein heavy chain 0.025 0.019 -10000 0 -0.17 1 1
NDEL1/Katanin 60/Dynein heavy chain 0.019 0.18 0.32 78 -0.4 31 109
LRP8 0.02 0.03 -10000 0 -0.43 2 2
NDEL1/Katanin 60 0.013 0.18 0.32 80 -0.42 31 111
P39/CDK5 -0.037 0.11 0.21 11 -0.26 72 83
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.012 -10000 0 -10000 0 0
CDK5 -0.029 0.072 0.18 9 -0.22 52 61
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.006 -10000 0 -10000 0 0
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.024 0.12 -10000 0 -0.24 100 100
RELN/VLDLR 0.005 0.097 -10000 0 -0.23 66 66
CDC42 0.008 0.042 -10000 0 -0.46 4 4
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.025 -10000 0 -0.26 2 2
fibroblast growth factor receptor signaling pathway 0.046 0.027 -10000 0 -0.26 2 2
LAMA1 -0.024 0.14 -10000 0 -0.43 51 51
PRNP 0.025 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.016 0.11 -10000 0 -0.3 56 56
SMAD2 0.018 0.032 0.18 14 -0.23 1 15
GPC1/PrPc/Cu2+ 0.032 0.013 -10000 0 -10000 0 0
GPC1/Laminin alpha1 -0.001 0.1 -10000 0 -0.3 51 51
TDGF1 -0.029 0.14 -10000 0 -0.34 75 75
CRIPTO/GPC1 -0.005 0.11 -10000 0 -0.31 54 54
APP/GPC1 0.036 0.014 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.088 -10000 0 -0.27 53 53
FLT1 0.024 0.021 -10000 0 -0.43 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.022 -10000 0 -0.2 2 2
SERPINC1 0.015 0.029 -10000 0 -0.13 14 14
FYN -0.016 0.083 -10000 0 -0.26 51 51
FGR -0.013 0.076 -10000 0 -0.26 42 42
positive regulation of MAPKKK cascade -0.051 0.15 0.32 5 -0.4 55 60
SLIT2 -0.044 0.14 -10000 0 -0.27 122 122
GPC1/NRG -0.043 0.13 -10000 0 -0.3 99 99
NRG1 -0.08 0.18 -10000 0 -0.32 156 156
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.018 -10000 0 -10000 0 0
LYN -0.019 0.087 -10000 0 -0.26 54 54
mol:Spermine 0.006 0.008 -10000 0 -10000 0 0
cell growth 0.046 0.027 -10000 0 -0.26 2 2
BMP signaling pathway -0.024 0.015 -10000 0 -10000 0 0
SRC -0.014 0.081 -10000 0 -0.26 48 48
TGFBR1 0.024 0.022 -10000 0 -0.28 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.032 0.087 -10000 0 -0.19 84 84
GPC1 0.024 0.015 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.024 0.022 -10000 0 -0.28 2 2
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
BLK -0.048 0.11 -10000 0 -0.28 76 76
HCK -0.021 0.092 -10000 0 -0.28 53 53
FGF2 0.024 0.029 -10000 0 -0.43 2 2
FGFR1 0.025 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer 0.024 0.021 -10000 0 -0.43 1 1
TGFBR2 0.024 0.016 -10000 0 -0.13 5 5
cell death 0.036 0.014 -10000 0 -10000 0 0
ATIII/GPC1 0.032 0.023 -10000 0 -10000 0 0
PLA2G2A/GPC1 0 0.07 -10000 0 -0.28 20 20
LCK -0.037 0.1 -10000 0 -0.28 69 69
neuron differentiation -0.043 0.13 -10000 0 -0.3 99 99
PrPc/Cu2+ 0.019 0.004 -10000 0 -10000 0 0
APP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.016 -10000 0 -0.13 5 5
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.008 -10000 0 -10000 0 0
LAT2 -0.023 0.12 0.17 4 -0.44 24 28
AP1 -0.015 0.17 -10000 0 -0.56 28 28
mol:PIP3 -0.009 0.17 0.3 37 -0.48 28 65
IKBKB 0.005 0.11 0.24 38 -0.27 20 58
AKT1 -0.03 0.11 0.31 22 -0.34 9 31
IKBKG 0.001 0.1 0.23 28 -0.27 20 48
MS4A2 -0.006 0.037 -10000 0 -0.14 24 24
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
MAP3K1 -0.007 0.13 0.32 10 -0.48 23 33
mol:Ca2+ -0.001 0.14 0.27 38 -0.37 25 63
LYN 0.021 0.036 -10000 0 -0.45 2 2
CBLB -0.019 0.1 -10000 0 -0.4 21 21
SHC1 0.024 0.014 -10000 0 -10000 0 0
RasGAP/p62DOK 0.042 0.047 -10000 0 -0.23 14 14
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
PLD2 -0.041 0.1 0.26 18 -0.24 73 91
PTPN13 -0.007 0.13 -10000 0 -0.54 16 16
PTPN11 0.021 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.005 0.1 0.26 22 -0.31 15 37
SYK 0.009 0.085 -10000 0 -0.38 21 21
GRB2 0.025 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.029 0.14 0.21 6 -0.48 28 34
LAT -0.029 0.11 -10000 0 -0.37 29 29
PAK2 -0.009 0.15 0.3 9 -0.54 23 32
NFATC2 -0.051 0.15 -10000 0 -0.53 43 43
HRAS -0.014 0.16 0.26 8 -0.6 23 31
GAB2 0.025 0.005 -10000 0 -10000 0 0
PLA2G1B 0.025 0.094 -10000 0 -0.82 5 5
Fc epsilon R1 -0.016 0.13 -10000 0 -0.28 86 86
Antigen/IgE/Fc epsilon R1 -0.008 0.12 -10000 0 -0.25 86 86
mol:GDP -0.016 0.16 0.25 3 -0.61 26 29
JUN 0.019 0.023 -10000 0 -0.13 9 9
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
FOS -0.031 0.14 -10000 0 -0.43 48 48
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.38 25 25
CHUK 0 0.1 0.22 31 -0.27 21 52
KLRG1 -0.023 0.098 0.16 3 -0.34 25 28
VAV1 -0.026 0.13 0.17 2 -0.47 26 28
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.018 0.1 0.18 4 -0.4 21 25
negative regulation of mast cell degranulation -0.003 0.11 0.19 15 -0.42 17 32
BTK -0.022 0.17 -10000 0 -0.68 25 25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.051 0.14 -10000 0 -0.29 110 110
GAB2/PI3K/SHP2 -0.046 0.081 -10000 0 -0.24 61 61
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 0.19 1 -0.26 75 76
RAF1 0.02 0.099 -10000 0 -0.93 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.02 0.16 -10000 0 -0.28 122 122
FCER1G 0.006 0.09 -10000 0 -0.44 19 19
FCER1A -0.06 0.15 -10000 0 -0.28 137 137
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.11 -10000 0 -0.24 76 76
MAPK3 0.024 0.093 -10000 0 -0.82 5 5
MAPK1 0.023 0.096 -10000 0 -0.85 5 5
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.003 0.14 -10000 0 -0.54 25 25
DUSP1 0.008 0.077 -10000 0 -0.25 32 32
NF-kappa-B/RelA 0.004 0.059 0.13 15 -0.17 16 31
actin cytoskeleton reorganization -0.005 0.13 -10000 0 -0.53 16 16
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.006 0.14 0.26 3 -0.54 22 25
FER -0.026 0.11 -10000 0 -0.34 36 36
RELA 0.025 0.005 -10000 0 -10000 0 0
ITK -0.024 0.092 -10000 0 -0.35 35 35
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG1 -0.007 0.17 0.29 17 -0.64 23 40
cytokine secretion -0.002 0.038 -10000 0 -0.15 4 4
SPHK1 -0.028 0.12 0.2 1 -0.42 25 26
PTK2 -0.006 0.13 -10000 0 -0.58 13 13
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.017 0.15 0.25 10 -0.53 26 36
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.004 0.16 0.3 30 -0.5 23 53
MAP2K2 0.023 0.098 -10000 0 -0.82 5 5
MAP2K1 0.015 0.092 -10000 0 -0.87 5 5
MAP2K7 0.025 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.007 0.1 0.18 21 -0.34 20 41
MAP2K4 0.032 0.063 -10000 0 -1.4 1 1
Fc epsilon R1/FcgammaRIIB -0.031 0.16 -10000 0 -0.29 121 121
mol:Choline -0.041 0.1 0.26 18 -0.23 73 91
SHC/Grb2/SOS1 0.019 0.12 -10000 0 -0.41 17 17
FYN 0.025 0.005 -10000 0 -10000 0 0
DOK1 0.025 0.021 -10000 0 -0.28 2 2
PXN -0.004 0.12 -10000 0 -0.54 13 13
HCLS1 -0.026 0.12 -10000 0 -0.44 26 26
PRKCB -0.005 0.13 0.26 28 -0.36 24 52
FCGR2B -0.05 0.15 -10000 0 -0.26 135 135
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.003 0.11 0.2 10 -0.42 17 27
LCP2 0.021 0.033 -10000 0 -0.15 14 14
PLA2G4A -0.027 0.12 -10000 0 -0.38 34 34
RASA1 0.026 0.003 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.041 0.1 0.26 18 -0.23 73 91
IKK complex 0.009 0.092 0.22 39 -0.22 15 54
WIPF1 0.026 0.002 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.005 0.023 -10000 0 -0.3 1 1
MAP4K4 -0.01 0.094 -10000 0 -0.37 16 16
BAG4 0.014 0.071 -10000 0 -0.43 13 13
PKC zeta/ceramide -0.032 0.13 0.14 1 -0.29 74 75
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BAX -0.063 0.14 -10000 0 -0.35 93 93
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AKT1 0.003 0.046 0.68 2 -10000 0 2
BAD -0.036 0.12 0.19 12 -0.27 70 82
SMPD1 -0.009 0.076 0.16 7 -0.17 66 73
RB1 -0.041 0.12 0.18 1 -0.27 71 72
FADD/Caspase 8 -0.003 0.091 -10000 0 -0.38 13 13
MAP2K4 -0.04 0.11 0.24 1 -0.27 64 65
NSMAF 0.025 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.038 0.11 0.18 6 -0.32 43 49
EGF -0.01 0.11 -10000 0 -0.43 33 33
mol:ceramide -0.042 0.12 0.14 1 -0.28 73 74
MADD 0.025 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.007 0.024 -10000 0 -0.3 1 1
ASAH1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.12 0.18 1 -0.26 71 72
cell proliferation -0.02 0.11 -10000 0 -0.32 40 40
BID -0.006 0.11 -10000 0 -0.64 7 7
MAP3K1 -0.041 0.12 0.25 1 -0.27 70 71
EIF2A -0.04 0.11 0.25 2 -0.34 33 35
TRADD 0.025 0.02 -10000 0 -0.43 1 1
CRADD 0.026 0.003 -10000 0 -10000 0 0
MAPK3 -0.029 0.093 0.17 6 -0.43 16 22
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.03 0.093 0.17 6 -0.43 16 22
Cathepsin D/ceramide -0.028 0.12 0.14 1 -0.27 71 72
FADD -0.01 0.091 -10000 0 -0.36 15 15
KSR1 -0.041 0.12 -10000 0 -0.27 69 69
MAPK8 -0.068 0.16 -10000 0 -0.38 59 59
PRKRA -0.041 0.12 0.13 1 -0.27 71 72
PDGFA 0.016 0.036 -10000 0 -0.43 1 1
TRAF2 0.026 0.005 -10000 0 -10000 0 0
IGF1 0.012 0.076 -10000 0 -0.34 20 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.042 0.12 0.14 1 -0.28 73 74
CTSD 0.025 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.037 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.021 0.12 -10000 0 -0.34 40 40
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.007 0.024 -10000 0 -0.3 1 1
RelA/NF kappa B1 0.037 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.003 0.087 -10000 0 -0.25 44 44
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.096 -10000 0 -0.34 21 21
TNFR1A/BAG4/TNF-alpha 0 0.12 -10000 0 -0.27 77 77
mol:Sphingosine-1-phosphate 0.005 0.023 -10000 0 -0.3 1 1
MAP2K1 -0.037 0.11 0.18 6 -0.54 15 21
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
CYCS -0.033 0.084 -10000 0 -0.21 82 82
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.023 0.063 -10000 0 -0.31 17 17
EIF2AK2 -0.041 0.11 0.16 3 -0.27 67 70
TNF-alpha/TNFR1A/FAN 0.008 0.11 -10000 0 -0.27 66 66
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.079 -10000 0 -0.51 6 6
MAP2K2 -0.032 0.088 0.17 6 -0.41 15 21
SMPD3 -0.02 0.1 0.19 1 -0.29 39 40
TNF -0.06 0.16 -10000 0 -0.26 151 151
PKC zeta/PAR4 0.004 0.085 -10000 0 -0.31 31 31
mol:PHOSPHOCHOLINE -0.009 0.089 0.2 33 -0.19 50 83
NF kappa B1/RelA/I kappa B alpha 0.045 0.073 -10000 0 -0.22 29 29
AIFM1 -0.044 0.095 -10000 0 -0.22 82 82
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.009 0.057 -10000 0 -0.25 22 22
NFATC2 -0.022 0.075 -10000 0 -0.26 40 40
NFATC3 0.002 0.023 -10000 0 -0.14 1 1
CD40LG -0.073 0.14 0.31 3 -0.38 51 54
PTGS2 -0.094 0.18 0.36 1 -0.46 74 75
JUNB 0.007 0.072 -10000 0 -0.21 39 39
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.018 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.018 -10000 0 -10000 0 0
CALM1 0.021 0.016 -10000 0 -0.14 1 1
JUN 0.015 0.025 -10000 0 -0.14 9 9
mol:Ca2+ -0.003 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.005 -10000 0 -10000 0 0
FOSL1 -0.028 0.13 -10000 0 -0.25 97 97
CREM 0.023 0.022 -10000 0 -0.43 1 1
Jun/NFAT1-c-4/p21SNFT -0.029 0.12 -10000 0 -0.35 34 34
FOS -0.036 0.14 -10000 0 -0.37 62 62
IFNG -0.072 0.14 0.31 1 -0.38 49 50
AP-1/NFAT1-c-4 -0.057 0.17 -10000 0 -0.42 50 50
FASLG -0.073 0.14 0.36 1 -0.38 50 51
NFAT1-c-4/ICER1 -0.024 0.097 0.18 1 -0.25 56 57
IL2RA -0.074 0.15 0.31 3 -0.39 55 58
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.072 0.14 0.33 2 -0.38 45 47
JunB/Fra1/NFAT1-c-4 -0.039 0.13 0.19 2 -0.27 90 92
IL4 -0.071 0.14 0.33 2 -0.38 46 48
IL2 -0.011 0.14 -10000 0 -0.93 12 12
IL3 0.009 0.069 -10000 0 -0.66 5 5
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
BATF3 0.001 0.091 -10000 0 -0.26 45 45
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.02 -10000 0 -0.43 1 1
IL1-mediated signaling events

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
UBC13/UEV1A 0.019 0.002 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.024 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.098 -10000 0 -0.32 34 34
IRAK/TOLLIP 0.028 0.008 -10000 0 -10000 0 0
IKBKB 0.025 0.005 -10000 0 -10000 0 0
IKBKG 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.056 0.14 -10000 0 -0.31 101 101
IL1A -0.033 0.14 -10000 0 -0.28 97 97
IL1B -0.057 0.12 -10000 0 -0.32 76 76
IRAK/TRAF6/p62/Atypical PKCs 0.045 0.052 -10000 0 -0.2 15 15
IL1R2 -0.045 0.14 -10000 0 -0.25 127 127
IL1R1 0.006 0.077 -10000 0 -0.43 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.093 -10000 0 -0.34 23 23
TOLLIP 0.025 0.006 -10000 0 -10000 0 0
TICAM2 0.016 0.064 -10000 0 -0.38 12 12
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.03 0.049 -10000 0 -10000 0 0
JUN -0.009 0.036 0.16 6 -0.22 10 16
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.017 0.12 -10000 0 -0.25 82 82
IL1 alpha/IL1R1/IL1RAP/MYD88 0.02 0.12 -10000 0 -0.26 66 66
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.029 0.12 -10000 0 -0.24 66 66
IL1 beta fragment/IL1R1/IL1RAP -0.044 0.12 0.17 1 -0.26 90 91
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.009 0.042 0.17 10 -0.21 13 23
IRAK1 0.014 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.12 -10000 0 -0.28 69 69
IRAK4 0.026 0.004 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.025 0.11 -10000 0 -0.36 30 30
CHUK 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.044 0.12 0.17 1 -0.26 90 91
IL1 beta/IL1R2 -0.073 0.14 -10000 0 -0.26 144 144
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.015 -10000 0 -0.2 1 1
NF kappa B1 p50/RelA -0.023 0.11 -10000 0 -0.35 18 18
IRAK3 0.022 0.041 -10000 0 -0.33 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.023 0.13 -10000 0 -0.26 89 89
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.099 -10000 0 -0.25 65 65
IL1 alpha/IL1R1/IL1RAP 0.009 0.11 -10000 0 -0.28 62 62
RELA 0.025 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
MYD88 0.019 0.054 -10000 0 -0.43 7 7
IRAK/TRAF6/MEKK3 0.042 0.018 -10000 0 -0.22 1 1
IL1RAP 0.007 0.067 -10000 0 -0.43 7 7
UBE2N 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.04 0.1 -10000 0 -0.32 28 28
CASP1 0.01 0.071 -10000 0 -0.43 11 11
IL1RN/IL1R2 -0.056 0.14 -10000 0 -0.29 114 114
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.028 0.13 -10000 0 -0.26 87 87
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.1 -10000 0 -0.36 28 28
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
IL1RN -0.035 0.13 -10000 0 -0.24 117 117
TRAF6/TAK1/TAB1/TAB2 0.036 0.015 -10000 0 -0.21 1 1
MAP2K6 0.015 0.028 0.18 11 -0.2 2 13
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.06 0.25 -10000 0 -0.85 38 38
NCK1/PAK1/Dok-R -0.056 0.12 -10000 0 -0.41 39 39
NCK1/Dok-R -0.057 0.28 -10000 0 -1 36 36
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
mol:beta2-estradiol 0.011 0.058 0.23 31 -10000 0 31
RELA 0.025 0.005 -10000 0 -10000 0 0
SHC1 0.024 0.015 -10000 0 -10000 0 0
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
F2 0.012 0.064 0.25 27 -10000 0 27
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.03 0.27 -10000 0 -0.96 36 36
FN1 0.021 0.029 -10000 0 -10000 0 0
PLD2 -0.064 0.28 -10000 0 -1.1 36 36
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 -0.071 0.16 -10000 0 -0.25 180 180
ELK1 -0.057 0.26 -10000 0 -0.95 36 36
GRB7 0.001 0.044 -10000 0 -0.13 41 41
PAK1 0.008 0.061 -10000 0 -0.43 5 5
Tie2/Ang1/alpha5/beta1 Integrin -0.036 0.28 -10000 0 -0.99 36 36
CDKN1A -0.069 0.24 -10000 0 -0.67 61 61
ITGA5 0.017 0.043 -10000 0 -0.16 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.057 0.28 -10000 0 -1 36 36
CRK 0.026 0.002 -10000 0 -10000 0 0
mol:NO -0.01 0.21 -10000 0 -0.6 38 38
PLG -0.068 0.28 -10000 0 -1.1 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.052 0.23 -10000 0 -0.81 37 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
ANGPT2 -0.066 0.24 -10000 0 -0.87 31 31
BMX -0.072 0.28 -10000 0 -1.1 36 36
ANGPT1 -0.083 0.3 -10000 0 -1.2 32 32
tube development -0.063 0.22 -10000 0 -0.66 53 53
ANGPT4 -0.008 0.1 -10000 0 -0.27 53 53
response to hypoxia -0.006 0.018 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.086 0.31 -10000 0 -1.2 36 36
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
FGF2 0.024 0.03 -10000 0 -0.43 2 2
STAT5A (dimer) -0.073 0.28 -10000 0 -0.73 66 66
mol:L-citrulline -0.01 0.21 -10000 0 -0.6 38 38
AGTR1 0 0.094 -10000 0 -0.29 39 39
MAPK14 -0.059 0.28 -10000 0 -1 37 37
Tie2/SHP2 -0.019 0.2 -10000 0 -1.1 14 14
TEK -0.022 0.21 -10000 0 -1.2 14 14
RPS6KB1 -0.047 0.24 -10000 0 -0.81 37 37
Angiotensin II/AT1 0 0.067 -10000 0 -0.24 30 30
Tie2/Ang1/GRB2 -0.056 0.29 -10000 0 -1.1 36 36
MAPK3 -0.061 0.26 -10000 0 -0.98 36 36
MAPK1 -0.061 0.26 -10000 0 -0.97 36 36
Tie2/Ang1/GRB7 -0.06 0.3 -10000 0 -1.1 36 36
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.068 0.29 -10000 0 -1.1 36 36
PI3K -0.063 0.28 -10000 0 -0.97 37 37
FES -0.062 0.29 -10000 0 -1 37 37
Crk/Dok-R -0.057 0.28 -10000 0 -1 36 36
Tie2/Ang1/ABIN2 -0.056 0.3 -10000 0 -1.1 36 36
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.052 0.23 -10000 0 -0.76 38 38
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.038 0.25 -10000 0 -0.81 37 37
Tie2/Ang2 -0.087 0.3 -10000 0 -0.9 53 53
Tie2/Ang1 -0.065 0.3 -10000 0 -1.1 36 36
FOXO1 -0.059 0.24 -10000 0 -0.72 53 53
ELF1 0.026 0.022 -10000 0 -10000 0 0
ELF2 -0.06 0.28 -10000 0 -1 36 36
mol:Choline -0.061 0.27 -10000 0 -1 36 36
cell migration -0.029 0.066 -10000 0 -0.23 39 39
FYN -0.074 0.25 -10000 0 -0.76 53 53
DOK2 -0.016 0.11 -10000 0 -0.25 77 77
negative regulation of cell cycle -0.06 0.22 -10000 0 -0.59 66 66
ETS1 0.003 0.082 -10000 0 -0.28 35 35
PXN -0.023 0.22 0.41 3 -0.67 37 40
ITGB1 0.023 0.012 -10000 0 -10000 0 0
NOS3 -0.02 0.23 -10000 0 -0.69 38 38
RAC1 0.023 0.009 -10000 0 -10000 0 0
TNF -0.074 0.17 -10000 0 -0.41 91 91
MAPKKK cascade -0.061 0.27 -10000 0 -1 36 36
RASA1 0.026 0.003 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.058 0.3 -10000 0 -1.1 36 36
NCK1 0.025 0.02 -10000 0 -0.43 1 1
vasculogenesis -0.005 0.19 0.34 2 -0.54 38 40
mol:Phosphatidic acid -0.061 0.27 -10000 0 -1 36 36
mol:Angiotensin II -0.001 0.006 -10000 0 -10000 0 0
mol:NADP -0.01 0.21 -10000 0 -0.6 38 38
Rac1/GTP -0.044 0.22 -10000 0 -0.75 37 37
MMP2 -0.07 0.28 -10000 0 -1.1 36 36
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.034 0.1 -10000 0 -0.23 61 61
SMAD6-7/SMURF1 0.039 0.03 -10000 0 -0.26 2 2
NOG -0.029 0.14 -10000 0 -0.39 67 67
SMAD9 -0.047 0.18 -10000 0 -0.49 61 61
SMAD4 0.026 0.004 -10000 0 -10000 0 0
SMAD5 -0.022 0.11 0.19 1 -0.39 22 23
BMP7/USAG1 -0.009 0.093 -10000 0 -0.3 37 37
SMAD5/SKI -0.013 0.11 -10000 0 -0.37 24 24
SMAD1 0.019 0.05 -10000 0 -0.42 2 2
BMP2 -0.033 0.15 -10000 0 -0.43 66 66
SMAD1/SMAD1/SMAD4 0.022 0.053 -10000 0 -0.31 3 3
BMPR1A 0.025 0.005 -10000 0 -10000 0 0
BMPR1B 0.003 0.1 -10000 0 -0.43 26 26
BMPR1A-1B/BAMBI 0.031 0.069 -10000 0 -0.26 24 24
AHSG -0.029 0.14 -10000 0 -0.43 49 49
CER1 -0.001 0.033 -10000 0 -10000 0 0
BMP2-4/CER1 -0.005 0.13 -10000 0 -0.31 69 69
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.033 0.13 -10000 0 -0.42 35 35
BMP2-4 (homodimer) -0.017 0.14 -10000 0 -0.36 69 69
RGMB 0.02 0.047 -10000 0 -0.3 9 9
BMP6/BMPR2/BMPR1A-1B 0.044 0.074 -10000 0 -0.24 29 29
RGMA 0.016 0.066 -10000 0 -0.43 11 11
SMURF1 0.021 0.011 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.025 0.12 -10000 0 -0.39 38 38
BMP2-4/USAG1 -0.011 0.13 -10000 0 -0.3 82 82
SMAD6/SMURF1/SMAD5 -0.011 0.1 -10000 0 -0.38 20 20
SOSTDC1 -0.028 0.12 -10000 0 -0.23 102 102
BMP7/BMPR2/BMPR1A-1B 0.043 0.072 -10000 0 -0.23 30 30
SKI 0.022 0.01 -10000 0 -10000 0 0
BMP6 (homodimer) 0.017 0.054 -10000 0 -0.24 17 17
HFE2 0.012 0.025 -10000 0 -0.13 8 8
ZFYVE16 0.026 0.003 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD -0.001 0.13 -10000 0 -0.3 72 72
SMAD5/SMAD5/SMAD4 -0.015 0.11 -10000 0 -0.36 26 26
MAPK1 0.026 0.003 -10000 0 -10000 0 0
TAK1/TAB family -0.011 0.1 -10000 0 -0.36 24 24
BMP7 (homodimer) 0.02 0.049 -10000 0 -0.43 6 6
NUP214 0.025 0.005 -10000 0 -10000 0 0
BMP6/FETUA -0.008 0.11 -10000 0 -0.32 52 52
SMAD1/SKI 0.025 0.057 -10000 0 -0.37 3 3
SMAD6 0.022 0.041 -10000 0 -0.43 4 4
CTDSP2 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA -0.023 0.15 -10000 0 -0.32 101 101
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.079 0.17 -10000 0 -0.3 162 162
BMPR2 (homodimer) 0.026 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.042 0.023 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.02 0.074 -10000 0 -0.3 25 25
CHRDL1 -0.036 0.15 -10000 0 -0.43 65 65
ENDOFIN/SMAD1 0.03 0.06 0.3 1 -0.37 3 4
SMAD6-7/SMURF1/SMAD1 0.036 0.064 -10000 0 -0.35 4 4
SMAD6/SMURF1 0.021 0.011 -10000 0 -10000 0 0
BAMBI 0.022 0.019 -10000 0 -0.13 6 6
SMURF2 0.024 0.029 -10000 0 -0.43 2 2
BMP2-4/CHRDL1 -0.036 0.16 -10000 0 -0.3 125 125
BMP2-4/GREM1 -0.054 0.17 -10000 0 -0.3 153 153
SMAD7 0.026 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.038 0.18 -10000 0 -0.47 61 61
SMAD1/SMAD6 0.021 0.055 -10000 0 -0.36 3 3
TAK1/SMAD6 0.03 0.017 -10000 0 -10000 0 0
BMP7 0.02 0.049 -10000 0 -0.43 6 6
BMP6 0.017 0.054 -10000 0 -0.24 17 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.029 0.11 -10000 0 -0.35 37 37
PPM1A 0.025 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.029 0.061 0.3 1 -0.36 3 4
SMAD7/SMURF1 0.03 0.016 -10000 0 -10000 0 0
CTDSPL 0.025 0.02 -10000 0 -0.43 1 1
PPP1CA 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.001 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
PPP1R15A 0.019 0.021 -10000 0 -0.13 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.049 0.14 -10000 0 -0.42 46 46
CHRD 0.021 0.045 -10000 0 -0.43 5 5
BMPR2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.032 0.13 -10000 0 -0.41 40 40
BMP4 0.007 0.088 -10000 0 -0.4 22 22
FST -0.016 0.12 -10000 0 -0.27 71 71
BMP2-4/NOG -0.024 0.17 -10000 0 -0.39 83 83
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.044 0.069 -10000 0 -0.22 25 25
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.023 0.076 0.22 66 -0.092 6 72
BUB1B -0.03 0.1 0.12 2 -0.27 71 73
PLK1 0.003 0.031 0.093 11 -0.12 9 20
PLK1S1 0.007 0.029 0.11 3 -0.16 6 9
KIF2A 0 0.039 0.21 5 -0.19 6 11
regulation of mitotic centrosome separation 0.003 0.031 0.093 11 -0.12 9 20
GOLGA2 0.025 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.034 0.14 -10000 0 -0.29 100 100
WEE1 -0.003 0.084 -10000 0 -0.35 25 25
cytokinesis -0.067 0.16 0.23 1 -0.39 97 98
PP2A-alpha B56 -0.031 0.22 -10000 0 -0.63 62 62
AURKA 0.008 0.025 0.11 1 -0.34 1 2
PICH/PLK1 -0.008 0.062 0.16 6 -0.22 24 30
CENPE -0.018 0.061 0.11 1 -0.24 28 29
RhoA/GTP 0.019 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.001 0.039 0.21 5 -0.18 6 11
PPP2CA 0.026 0.003 -10000 0 -10000 0 0
FZR1 0.025 0.006 -10000 0 -10000 0 0
TPX2 -0.006 0.071 0.11 11 -0.27 31 42
PAK1 0.009 0.061 -10000 0 -0.44 5 5
SPC24 -0.044 0.14 -10000 0 -0.43 55 55
FBXW11 0.026 0.004 -10000 0 -10000 0 0
CLSPN -0.05 0.12 0.12 3 -0.26 119 122
GORASP1 0.026 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.017 3 -0.017 5 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.001 0.017 0.051 15 -0.065 8 23
G2 phase of mitotic cell cycle 0 0.002 0.014 2 -0.01 1 3
STAG2 0.026 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.013 0.072 -10000 0 -0.52 9 9
spindle elongation 0.003 0.031 0.093 11 -0.12 9 20
ODF2 0.026 0.005 -10000 0 -10000 0 0
BUB1 -0.052 0.23 -10000 0 -0.68 61 61
TPT1 0 0.043 -10000 0 -0.18 22 22
CDC25C -0.028 0.12 0.15 1 -0.36 56 57
CDC25B 0.026 0.006 -10000 0 -10000 0 0
SGOL1 -0.023 0.076 0.092 6 -0.22 66 72
RHOA 0.026 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.041 -10000 0 -0.23 5 5
CDC14B 0.006 0.002 -10000 0 -10000 0 0
CDC20 -0.028 0.12 -10000 0 -0.25 93 93
PLK1/PBIP1 -0.013 0.06 0.087 1 -0.22 33 34
mitosis -0.002 0.004 0.023 2 -10000 0 2
FBXO5 0 0.03 0.097 5 -0.14 6 11
CDC2 0.001 0.002 0.011 1 -0.014 1 2
NDC80 -0.056 0.16 -10000 0 -0.43 73 73
metaphase plate congression -0.024 0.089 -10000 0 -0.23 76 76
ERCC6L -0.003 0.063 0.26 1 -0.22 24 25
NLP/gamma Tubulin 0.003 0.02 0.069 8 -0.087 6 14
microtubule cytoskeleton organization 0 0.043 -10000 0 -0.18 22 22
G2/M transition DNA damage checkpoint 0 0.002 0.016 1 -10000 0 1
PPP1R12A 0.026 0.02 -10000 0 -0.43 1 1
interphase 0 0.002 0.016 1 -10000 0 1
PLK1/PRC1-2 -0.016 0.11 0.14 1 -0.22 97 98
GRASP65/GM130/RAB1/GTP/PLK1 0.037 0.035 -10000 0 -0.17 1 1
RAB1A 0.026 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.004 0.026 0.078 25 -0.13 3 28
mitotic prometaphase 0.002 0.007 0.018 76 -0.012 3 79
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.06 0.21 1 -0.48 2 3
microtubule-based process -0.032 0.1 0.12 2 -0.24 95 97
Golgi organization 0.003 0.031 0.093 11 -0.12 9 20
Cohesin/SA2 0.017 0.028 0.1 1 -0.12 5 6
PPP1CB/MYPT1 0.038 0.016 -10000 0 -0.31 1 1
KIF20A -0.078 0.17 -10000 0 -0.43 93 93
APC/C/CDC20 -0.004 0.074 0.12 2 -0.23 40 42
PPP2R1A 0.022 0.01 -10000 0 -10000 0 0
chromosome segregation -0.013 0.06 0.086 1 -0.22 33 34
PRC1 0.019 0.032 -10000 0 -0.13 21 21
ECT2 0.001 0.038 0.22 6 -0.17 3 9
C13orf34 0.003 0.026 0.073 22 -0.1 8 30
NUDC -0.024 0.089 -10000 0 -0.23 76 76
regulation of attachment of spindle microtubules to kinetochore -0.029 0.099 0.12 2 -0.26 71 73
spindle assembly 0.002 0.027 0.084 11 -0.1 8 19
spindle stabilization 0.007 0.029 0.11 3 -0.16 6 9
APC/C/HCDH1 0.023 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 -0.033 0.1 0.12 2 -0.24 95 97
CCNB1 0.017 0.038 -10000 0 -0.14 2 2
PPP1CB 0.027 0.002 -10000 0 -10000 0 0
BTRC 0.025 0.005 -10000 0 -10000 0 0
ROCK2 -0.004 0.085 -10000 0 -0.39 22 22
TUBG1 0.008 0.021 -10000 0 -0.24 1 1
G2/M transition of mitotic cell cycle -0.003 0.034 -10000 0 -0.23 5 5
MLF1IP -0.018 0.076 -10000 0 -0.31 30 30
INCENP 0.024 0.021 -10000 0 -0.44 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.011 0.086 -10000 0 -0.29 41 41
CRKL 0.026 0.008 -10000 0 -0.13 1 1
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.008 0.1 -10000 0 -0.26 61 61
alpha4/beta7 Integrin/MAdCAM1 0.01 0.12 -10000 0 -0.24 90 90
EPO 0.013 0.03 -10000 0 -0.18 7 7
alpha4/beta7 Integrin -0.005 0.1 -10000 0 -0.28 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.012 0.077 -10000 0 -0.29 26 26
EPO/EPOR (dimer) 0.027 0.025 -10000 0 -0.3 1 1
lamellipodium assembly 0.014 0.035 -10000 0 -0.26 4 4
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
JAK2 0.006 0.051 -10000 0 -0.22 22 22
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
MADCAM1 -0.034 0.13 -10000 0 -0.24 111 111
cell adhesion 0.008 0.12 -10000 0 -0.24 90 90
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
ITGB1 0.023 0.012 -10000 0 -10000 0 0
SRC -0.024 0.099 0.18 29 -0.24 67 96
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.009 0.11 -10000 0 -0.26 74 74
p130Cas/Crk/Dock1 -0.007 0.099 0.35 1 -0.22 63 64
VCAM1 -0.033 0.13 -10000 0 -0.3 85 85
RHOA 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.046 0.066 -10000 0 -0.23 23 23
BCAR1 -0.034 0.092 0.19 28 -0.23 67 95
EPOR 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.036 -10000 0 -0.27 4 4
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.01 0.096 0.22 66 -10000 0 66
GNAI2 0.025 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.016 0.094 -10000 0 -0.26 61 61
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
RhoA/GTP -0.009 0.097 -10000 0 -0.22 66 66
negative regulation of cAMP metabolic process -0.018 0.099 -10000 0 -0.24 67 67
GNAZ 0.026 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNA12 0.022 0.009 -10000 0 -10000 0 0
S1PR5 -0.053 0.16 -10000 0 -0.3 124 124
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.019 0.1 -10000 0 -0.24 67 67
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
Ephrin B reverse signaling

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
EFNB2 0.022 0.029 -10000 0 -0.16 10 10
EPHB2 0.017 0.04 -10000 0 -0.43 3 3
EFNB1 -0.023 0.082 -10000 0 -0.31 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0 0.095 -10000 0 -0.25 46 46
Ephrin B2/EPHB1-2 0.016 0.082 -10000 0 -0.25 41 41
neuron projection morphogenesis -0.009 0.085 -10000 0 -0.24 46 46
Ephrin B1/EPHB1-2/Tiam1 -0.008 0.11 -10000 0 -0.26 61 61
DNM1 -0.027 0.12 -10000 0 -0.22 107 107
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.009 0.085 0.21 2 -0.51 13 15
YES1 -0.005 0.13 -10000 0 -0.77 13 13
Ephrin B1/EPHB1-2/NCK2 -0.008 0.11 -10000 0 -0.26 62 62
PI3K 0.027 0.091 -10000 0 -0.52 13 13
mol:GDP -0.009 0.1 -10000 0 -0.26 61 61
ITGA2B -0.012 0.12 -10000 0 -0.43 40 40
endothelial cell proliferation 0.025 0.022 -10000 0 -0.26 1 1
FYN -0.003 0.12 -10000 0 -0.75 13 13
MAP3K7 -0.01 0.089 0.22 1 -0.54 13 14
FGR -0.008 0.13 -10000 0 -0.76 13 13
TIAM1 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
RGS3 0.025 0.013 -10000 0 -0.13 3 3
cell adhesion -0.012 0.11 -10000 0 -0.4 21 21
LYN -0.002 0.12 -10000 0 -0.75 13 13
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.11 -10000 0 -0.69 13 13
Ephrin B1/EPHB1-2 -0.01 0.095 -10000 0 -0.58 13 13
SRC -0.004 0.12 -10000 0 -0.74 13 13
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
EPHB1 -0.009 0.12 -10000 0 -0.43 39 39
EPHB4 0.021 0.011 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
BLK -0.01 0.13 -10000 0 -0.74 13 13
HCK -0.004 0.13 -10000 0 -0.76 13 13
regulation of stress fiber formation 0.009 0.1 0.26 62 -10000 0 62
MAPK8 -0.014 0.09 -10000 0 -0.5 13 13
Ephrin B1/EPHB1-2/RGS3 -0.008 0.11 -10000 0 -0.26 62 62
endothelial cell migration 0.026 0.11 0.19 96 -0.41 13 109
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTPN13 0.023 0.052 -10000 0 -0.47 5 5
regulation of focal adhesion formation 0.009 0.1 0.26 62 -10000 0 62
chemotaxis 0.009 0.11 0.26 62 -10000 0 62
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.004 0.09 -10000 0 -0.24 46 46
angiogenesis -0.009 0.095 -10000 0 -0.58 13 13
LCK -0.019 0.13 -10000 0 -0.76 13 13
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.003 0.095 0.32 38 -10000 0 38
KIRREL -0.009 0.12 -10000 0 -0.42 40 40
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.003 0.095 -10000 0 -0.32 38 38
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.002 -10000 0 -10000 0 0
WASL 0.02 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.029 0.08 -10000 0 -0.24 38 38
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.003 0.069 -10000 0 -0.24 32 32
FYN -0.009 0.076 0.18 22 -0.22 39 61
mol:Ca2+ 0.026 0.08 -10000 0 -0.24 39 39
mol:DAG 0.027 0.081 -10000 0 -0.24 39 39
NPHS2 0.001 0.033 -10000 0 -0.44 1 1
mol:IP3 0.027 0.081 -10000 0 -0.24 39 39
regulation of endocytosis 0.023 0.072 -10000 0 -0.21 39 39
Nephrin/NEPH1/podocin/Cholesterol 0.016 0.076 -10000 0 -0.24 39 39
establishment of cell polarity -0.003 0.095 -10000 0 -0.32 38 38
Nephrin/NEPH1/podocin/NCK1-2 0.04 0.082 -10000 0 -0.22 38 38
Nephrin/NEPH1/beta Arrestin2 0.025 0.074 -10000 0 -0.22 39 39
NPHS1 -0.001 0.053 -10000 0 -0.15 40 40
Nephrin/NEPH1/podocin 0.018 0.073 -10000 0 -0.23 39 39
TJP1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
NCK2 0.026 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.081 -10000 0 -0.24 39 39
CD2AP 0.026 0.002 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.027 0.08 -10000 0 -0.24 38 38
GRB2 0.025 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.014 0.087 0.19 26 -0.23 46 72
cytoskeleton organization -0.017 0.083 0.2 12 -0.27 32 44
Nephrin/NEPH1 0.009 0.067 -10000 0 -0.22 38 38
Nephrin/NEPH1/ZO-1 0.021 0.081 -10000 0 -0.25 38 38
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.008 0.077 -10000 0 -0.22 50 50
RGS9BP 0.017 0.05 -10000 0 -0.39 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.021 0.015 -10000 0 -0.13 1 1
mol:Na + -0.019 0.088 -10000 0 -0.25 51 51
mol:ADP 0.005 0.016 -10000 0 -10000 0 0
GNAT2 0.015 0.018 -10000 0 -0.13 2 2
RGS9-1/Gbeta5/R9AP 0.019 0.088 -10000 0 -0.27 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.02 0.025 -10000 0 -0.13 1 1
GRK7 0.017 0.023 -10000 0 -0.13 6 6
CNGB3 0.004 0.032 -10000 0 -0.13 16 16
Cone Metarhodopsin II/X-Arrestin 0.013 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.11 0.18 18 -0.26 94 112
Cone PDE6 0.034 0.086 -10000 0 -0.23 40 40
Cone Metarhodopsin II 0.029 0.013 -10000 0 -10000 0 0
Na + (4 Units) -0.025 0.12 -10000 0 -0.24 109 109
GNAT2/GDP 0.024 0.078 -10000 0 -0.22 40 40
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.004 0.03 0.18 8 -10000 0 8
Cone Transducin 0.009 0.083 -10000 0 -0.23 50 50
SLC24A2 -0.042 0.15 -10000 0 -0.43 59 59
GNB3/GNGT2 -0.001 0.1 -10000 0 -0.31 51 51
GNB3 -0.007 0.12 -10000 0 -0.4 38 38
GNAT2/GTP 0.014 0.01 -10000 0 -10000 0 0
CNGA3 -0.049 0.14 -10000 0 -0.43 54 54
ARR3 -0.007 0.018 -10000 0 -0.13 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.019 0.089 -10000 0 -0.26 51 51
mol:Pi 0.017 0.088 -10000 0 -0.27 40 40
Cone CNG Channel 0.009 0.082 -10000 0 -0.21 47 47
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.042 0.15 -10000 0 -0.43 59 59
RGS9 -0.011 0.12 -10000 0 -0.39 44 44
PDE6C 0.004 0.025 -10000 0 -0.13 5 5
GNGT2 0.008 0.082 -10000 0 -0.3 28 28
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.005 0.036 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.009 0.2 0.48 7 -0.66 17 24
CRP -0.016 0.2 0.59 5 -0.67 17 22
cell cycle arrest -0.021 0.22 0.49 3 -0.66 29 32
TIMP1 -0.013 0.2 0.46 2 -0.68 20 22
IL6ST -0.008 0.11 -10000 0 -0.43 32 32
Rac1/GDP -0.05 0.16 -10000 0 -0.42 59 59
AP1 0.033 0.1 -10000 0 -0.58 2 2
GAB2 0.026 0.005 -10000 0 -10000 0 0
TNFSF11 -0.018 0.2 0.5 2 -0.69 15 17
HSP90B1 0.012 0.16 -10000 0 -0.91 14 14
GAB1 0.025 0.021 -10000 0 -0.43 1 1
MAPK14 -0.073 0.19 -10000 0 -0.54 56 56
AKT1 0.035 0.049 -10000 0 -0.7 1 1
FOXO1 0.035 0.051 -10000 0 -0.66 1 1
MAP2K6 -0.059 0.16 0.2 2 -0.45 59 61
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.049 0.17 0.29 3 -0.44 53 56
MITF -0.05 0.15 -10000 0 -0.41 56 56
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.006 -10000 0 -10000 0 0
A2M 0.017 0.082 -10000 0 -1.2 2 2
CEBPB 0.017 0.073 -10000 0 -0.36 17 17
GRB2/SOS1/GAB family/SHP2 0.007 0.081 -10000 0 -0.43 6 6
STAT3 -0.028 0.24 0.5 3 -0.7 30 33
STAT1 0.017 0.045 -10000 0 -0.9 1 1
CEBPD -0.044 0.3 0.49 4 -1 35 39
PIK3CA 0.026 0.02 -10000 0 -0.43 1 1
PI3K 0.04 0.007 -10000 0 -10000 0 0
JUN 0.019 0.023 -10000 0 -0.13 9 9
PIAS3/MITF -0.032 0.16 -10000 0 -0.41 50 50
MAPK11 -0.076 0.19 -10000 0 -0.56 54 54
STAT3 (dimer)/FOXO1 -0.007 0.17 -10000 0 -0.56 18 18
GRB2/SOS1/GAB family -0.012 0.15 -10000 0 -0.42 34 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.046 0.15 -10000 0 -0.34 83 83
GRB2 0.025 0.006 -10000 0 -10000 0 0
JAK2 0.025 0.006 -10000 0 -10000 0 0
LBP 0.001 0.19 0.44 8 -0.6 22 30
PIK3R1 0.027 0.003 -10000 0 -10000 0 0
JAK1 0.019 0.016 -10000 0 -10000 0 0
MYC -0.022 0.28 0.49 4 -0.87 36 40
FGG -0.02 0.2 0.5 2 -0.67 17 19
macrophage differentiation -0.021 0.22 0.49 3 -0.66 29 32
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.003 0.12 -10000 0 -0.27 61 61
JUNB -0.021 0.24 0.45 10 -0.81 22 32
FOS -0.031 0.14 -10000 0 -0.43 48 48
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.051 0.16 0.23 1 -0.41 62 63
STAT1/PIAS1 -0.022 0.16 0.24 1 -0.4 48 49
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.049 -10000 0 -0.34 6 6
STAT3 (dimer) -0.025 0.24 0.5 3 -0.7 29 32
PRKCD -0.026 0.23 0.41 28 -0.55 50 78
IL6R 0.005 0.082 -10000 0 -0.35 22 22
SOCS3 -0.094 0.3 0.39 2 -1.1 38 40
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.078 -10000 0 -0.24 32 32
Rac1/GTP -0.05 0.17 -10000 0 -0.43 59 59
HCK 0.014 0.063 -10000 0 -0.27 19 19
MAPKKK cascade 0.032 0.08 -10000 0 -0.96 1 1
bone resorption -0.016 0.19 0.5 2 -0.63 17 19
IRF1 -0.015 0.2 0.51 3 -0.69 15 18
mol:GDP -0.058 0.16 0.2 1 -0.43 62 63
SOS1 0.026 0.002 -10000 0 -10000 0 0
VAV1 -0.058 0.16 0.2 1 -0.44 62 63
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.25 -10000 0 -0.49 111 111
PTPN11 0.009 0.079 -10000 0 -0.69 6 6
IL6/IL6RA -0.024 0.11 -10000 0 -0.32 51 51
gp130 (dimer)/TYK2/TYK2/LMO4 0.021 0.074 -10000 0 -0.25 30 30
gp130 (dimer)/JAK2/JAK2/LMO4 0.02 0.075 -10000 0 -0.25 31 31
IL6 -0.038 0.12 -10000 0 -0.41 40 40
PIAS3 0.024 0.008 -10000 0 -10000 0 0
PTPRE 0.023 0.024 -10000 0 -0.43 1 1
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
RAC1 0.023 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.035 0.12 0.21 1 -0.31 65 66
LMO4 0.018 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.028 0.22 -10000 0 -0.67 28 28
MCL1 0.039 0.057 -10000 0 -0.62 1 1
Regulation of nuclear SMAD2/3 signaling

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.017 0.048 -10000 0 -0.43 4 4
HSPA8 0.023 0.022 -10000 0 -0.43 1 1
SMAD3/SMAD4/ER alpha 0.017 0.092 0.21 2 -0.27 20 22
AKT1 0.015 0.034 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 71 71
NKX2-5 0 0.005 -10000 0 -10000 0 0
muscle cell differentiation 0.062 0.17 0.36 100 -10000 0 100
SMAD2-3/SMAD4/SP1 0.02 0.12 -10000 0 -0.27 34 34
SMAD4 -0.009 0.069 -10000 0 -0.23 13 13
CBFB 0.026 0.002 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.028 0.08 -10000 0 -0.26 23 23
SMAD3/SMAD4/VDR 0.037 0.11 -10000 0 -0.24 35 35
MYC 0.009 0.087 -10000 0 -0.38 22 22
CDKN2B -0.18 0.49 -10000 0 -1.5 60 60
AP1 0.001 0.092 -10000 0 -0.26 30 30
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.004 0.083 -10000 0 -0.31 17 17
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.037 0.14 -10000 0 -0.37 62 62
SP3 0.027 0.01 -10000 0 -10000 0 0
CREB1 0.026 0.002 -10000 0 -10000 0 0
FOXH1 -0.003 0.076 -10000 0 -0.42 10 10
SMAD3/SMAD4/GR 0.039 0.084 -10000 0 -0.24 6 6
GATA3 -0.053 0.14 -10000 0 -0.44 53 53
SKI/SIN3/HDAC complex/NCoR1 0.014 0.061 -10000 0 -0.3 15 15
MEF2C/TIF2 -0.02 0.13 0.29 4 -0.29 48 52
endothelial cell migration 0.16 0.46 1.3 73 -10000 0 73
MAX 0.032 0.019 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.021 0.022 -10000 0 -0.43 1 1
RUNX2 0.017 0.057 -10000 0 -0.25 18 18
RUNX3 -0.001 0.091 -10000 0 -0.3 36 36
RUNX1 -0.007 0.1 -10000 0 -0.24 62 62
CTBP1 0.026 0.005 -10000 0 -10000 0 0
NR3C1 0.033 0.019 -10000 0 -10000 0 0
VDR -0.014 0.11 -10000 0 -0.26 71 71
CDKN1A -0.041 0.25 -10000 0 -1.3 20 20
KAT2B 0.021 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.011 0.13 -10000 0 -0.3 71 71
DCP1A 0.026 0.004 -10000 0 -10000 0 0
SKI 0.022 0.01 -10000 0 -10000 0 0
SERPINE1 -0.17 0.47 -10000 0 -1.3 73 73
SMAD3/SMAD4/ATF2 0.019 0.086 -10000 0 -0.24 20 20
SMAD3/SMAD4/ATF3 0.014 0.091 -10000 0 -0.28 15 15
SAP30 0.025 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.041 0.061 0.19 6 -0.26 4 10
JUN -0.014 0.082 -10000 0 -0.27 25 25
SMAD3/SMAD4/IRF7 0.019 0.084 -10000 0 -0.26 12 12
TFE3 0.014 0.035 -10000 0 -10000 0 0
COL1A2 0.005 0.093 -10000 0 -0.88 5 5
mesenchymal cell differentiation -0.02 0.087 0.28 15 -10000 0 15
DLX1 -0.066 0.16 -10000 0 -0.43 76 76
TCF3 0.023 0.029 -10000 0 -0.43 2 2
FOS -0.03 0.14 -10000 0 -0.39 57 57
SMAD3/SMAD4/Max 0.039 0.084 0.2 6 -0.22 10 16
Cbp/p300/SNIP1 0.036 0.043 -10000 0 -0.26 4 4
ZBTB17 0.023 0.014 -10000 0 -10000 0 0
LAMC1 -0.01 0.061 0.21 1 -0.31 2 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.024 0.082 -10000 0 -0.26 14 14
IRF7 0.016 0.052 -10000 0 -0.21 20 20
ESR1 0.009 0.071 -10000 0 -0.27 25 25
HNF4A -0.007 0.042 -10000 0 -0.13 40 40
MEF2C -0.01 0.12 0.21 36 -0.28 51 87
SMAD2-3/SMAD4 0.008 0.1 -10000 0 -0.24 32 32
Cbp/p300/Src-1 0.043 0.049 -10000 0 -0.26 4 4
IGHV3OR16-13 0.001 0.023 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.02 0.045 -10000 0 -0.38 6 6
CREBBP 0.021 0.023 -10000 0 -10000 0 0
SKIL 0.021 0.049 -10000 0 -0.43 6 6
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
SNIP1 0.022 0.011 -10000 0 -10000 0 0
GCN5L2 0 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.019 0.083 -10000 0 -0.23 8 8
MSG1/HSC70 0.015 0.072 -10000 0 -0.3 20 20
SMAD2 0 0.059 -10000 0 -0.14 55 55
SMAD3 0.006 0.056 -10000 0 -0.21 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.06 -10000 0 -0.25 14 14
SMAD2/SMAD2/SMAD4 -0.005 0.043 -10000 0 -0.25 1 1
NCOR1 0.024 0.028 -10000 0 -0.43 2 2
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
NCOA1 0.026 0.003 -10000 0 -10000 0 0
MYOD/E2A -0.045 0.13 -10000 0 -0.3 91 91
SMAD2-3/SMAD4/SP1/MIZ-1 0.02 0.12 -10000 0 -0.27 36 36
IFNB1 -0.01 0.06 0.19 1 -0.3 5 6
SMAD3/SMAD4/MEF2C 0.005 0.13 -10000 0 -0.31 36 36
CITED1 -0.001 0.093 -10000 0 -0.24 52 52
SMAD2-3/SMAD4/ARC105 0.023 0.1 -10000 0 -0.23 25 25
RBL1 0.012 0.077 -10000 0 -0.41 16 16
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.049 0.19 -10000 0 -0.54 60 60
RUNX1-3/PEBPB2 0.02 0.087 -10000 0 -0.24 48 48
SMAD7 -0.016 0.11 -10000 0 -0.38 22 22
MYC/MIZ-1 0.02 0.067 0.18 7 -0.29 18 25
SMAD3/SMAD4 -0.023 0.18 0.27 43 -0.43 67 110
IL10 -0.062 0.19 0.21 18 -0.48 68 86
PIASy/HDAC complex 0.022 0.023 -10000 0 -10000 0 0
PIAS3 0.02 0.017 -10000 0 -10000 0 0
CDK2 0.015 0.049 -10000 0 -0.44 4 4
IL5 -0.039 0.13 0.24 1 -0.38 32 33
CDK4 0.02 0.024 -10000 0 -10000 0 0
PIAS4 0.022 0.023 -10000 0 -10000 0 0
ATF3 0.006 0.072 -10000 0 -0.43 9 9
SMAD3/SMAD4/SP1 0.024 0.099 -10000 0 -0.25 22 22
FOXG1 -0.001 0.11 -10000 0 -0.43 30 30
FOXO3 0.002 0.037 -10000 0 -10000 0 0
FOXO1 0.002 0.038 -10000 0 -0.3 1 1
FOXO4 0.001 0.041 -10000 0 -0.27 2 2
heart looping -0.01 0.12 0.21 36 -0.28 51 87
CEBPB 0.007 0.076 -10000 0 -0.36 17 17
SMAD3/SMAD4/DLX1 -0.026 0.14 -10000 0 -0.28 84 84
MYOD1 -0.09 0.17 -10000 0 -0.43 95 95
SMAD3/SMAD4/HNF4 0.021 0.079 -10000 0 -0.22 12 12
SMAD3/SMAD4/GATA3 -0.026 0.15 -10000 0 -0.32 83 83
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.049 -10000 0 -0.43 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.017 0.11 -10000 0 -0.25 38 38
SMAD3/SMAD4/SP1-3 0.043 0.096 -10000 0 -0.27 12 12
MED15 0.026 0.004 -10000 0 -10000 0 0
SP1 0.013 0.038 -10000 0 -0.16 3 3
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.006 0.12 -10000 0 -0.26 74 74
ITGB5 -0.007 0.08 -10000 0 -0.44 7 7
TGIF/SIN3/HDAC complex/CtBP 0.012 0.074 -10000 0 -0.46 10 10
SMAD3/SMAD4/AR -0.019 0.13 -10000 0 -0.29 76 76
AR -0.047 0.16 -10000 0 -0.33 104 104
negative regulation of cell growth -0.002 0.094 -10000 0 -0.38 18 18
SMAD3/SMAD4/MYOD -0.037 0.14 -10000 0 -0.29 102 102
E2F5 0.023 0.029 -10000 0 -0.43 2 2
E2F4 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.11 -10000 0 -0.22 72 72
SMAD2-3/SMAD4/FOXO1-3a-4 -0.028 0.14 -10000 0 -0.4 55 55
TFDP1 0.025 0.021 -10000 0 -0.43 1 1
SMAD3/SMAD4/AP1 0.022 0.1 -10000 0 -0.26 30 30
SMAD3/SMAD4/RUNX2 0.021 0.087 -10000 0 -0.28 15 15
TGIF2 0.021 0.045 -10000 0 -0.38 6 6
TGIF1 0.016 0.06 -10000 0 -0.27 17 17
ATF2 0.016 0.069 -10000 0 -0.43 12 12
Glucocorticoid receptor regulatory network

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
PCK2 0.047 0.09 -10000 0 -0.84 3 3
SMARCC2 0.024 0.017 -10000 0 -10000 0 0
SMARCC1 0.024 0.017 -10000 0 -10000 0 0
TBX21 -0.067 0.17 -10000 0 -0.67 32 32
SUMO2 0.023 0.016 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.033 -10000 0 -0.16 10 10
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 -0.037 0.15 -10000 0 -0.34 89 89
GR alpha/HSP90/FKBP51/HSP90 0.049 0.12 0.26 20 -0.23 48 68
PRL -0.034 0.068 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.11 0.19 0.48 54 -0.33 2 56
RELA -0.032 0.092 -10000 0 -0.26 23 23
FGG 0.09 0.14 0.4 43 -10000 0 43
GR beta/TIF2 0.056 0.12 0.28 26 -0.29 31 57
IFNG -0.13 0.18 -10000 0 -0.58 27 27
apoptosis 0.014 0.17 0.57 19 -0.47 11 30
CREB1 0.026 0.009 -10000 0 -10000 0 0
histone acetylation -0.048 0.1 -10000 0 -0.33 35 35
BGLAP -0.039 0.097 -10000 0 -0.78 2 2
GR/PKAc 0.076 0.068 0.28 10 -10000 0 10
NF kappa B1 p50/RelA -0.05 0.15 -10000 0 -0.31 108 108
SMARCD1 0.024 0.017 -10000 0 -10000 0 0
MDM2 0.047 0.063 0.2 44 -10000 0 44
GATA3 -0.032 0.14 -10000 0 -0.42 49 49
AKT1 0.022 0.013 0.18 2 -10000 0 2
CSF2 -0.056 0.084 -10000 0 -10000 0 0
GSK3B 0.023 0.026 -10000 0 -0.43 1 1
NR1I3 0.021 0.17 0.55 19 -0.53 6 25
CSN2 0.074 0.12 0.34 33 -10000 0 33
BRG1/BAF155/BAF170/BAF60A 0.06 0.047 -10000 0 -0.22 11 11
NFATC1 0.005 0.095 -10000 0 -0.43 23 23
POU2F1 0.025 0.021 -10000 0 -0.43 1 1
CDKN1A -0.044 0.28 -10000 0 -1.4 20 20
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.01 -10000 0 -10000 0 0
SFN -0.023 0.11 -10000 0 -0.22 90 90
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.032 0.12 0.27 12 -0.23 58 70
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.04 0.27 0.54 16 -0.76 54 70
JUN -0.078 0.13 0.27 2 -0.38 43 45
IL4 -0.062 0.12 -10000 0 -0.52 14 14
CDK5R1 0 0.1 -10000 0 -0.42 30 30
PRKACA 0.025 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.092 0.1 -10000 0 -0.32 53 53
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.051 0.11 0.28 11 -0.21 44 55
cortisol/GR alpha (monomer) 0.14 0.19 0.54 56 -10000 0 56
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.071 0.14 -10000 0 -0.42 57 57
AP-1/NFAT1-c-4 -0.17 0.23 -10000 0 -0.55 87 87
AFP -0.077 0.12 -10000 0 -0.5 5 5
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.084 0.096 0.39 12 -10000 0 12
TP53 0.004 0.12 -10000 0 -0.47 32 32
PPP5C 0.022 0.01 -10000 0 -10000 0 0
KRT17 -0.27 0.42 -10000 0 -1.1 98 98
KRT14 -0.057 0.086 -10000 0 -10000 0 0
TBP 0.03 0.016 -10000 0 -0.29 1 1
CREBBP 0.025 0.046 -10000 0 -0.25 14 14
HDAC1 0.02 0.009 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
AP-1 -0.17 0.23 -10000 0 -0.55 89 89
MAPK14 0.024 0.015 -10000 0 -10000 0 0
MAPK10 0.021 0.038 -10000 0 -0.43 3 3
MAPK11 0.016 0.058 -10000 0 -0.43 8 8
KRT5 -0.24 0.39 -10000 0 -1.1 84 84
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.027 0.009 -10000 0 -10000 0 0
STAT1 0.024 0.033 -10000 0 -0.16 10 10
CGA -0.048 0.085 -10000 0 -0.4 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.044 0.09 0.31 8 -0.38 4 12
MAPK3 0.024 0.016 -10000 0 -10000 0 0
MAPK1 0.024 0.015 -10000 0 -10000 0 0
ICAM1 -0.098 0.19 -10000 0 -0.64 31 31
NFKB1 -0.031 0.089 -10000 0 -0.22 34 34
MAPK8 -0.079 0.12 0.31 1 -0.35 51 52
MAPK9 0.023 0.015 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.012 0.18 0.57 19 -0.48 13 32
BAX -0.024 0.11 -10000 0 -0.6 1 1
POMC -0.086 0.22 -10000 0 -1.5 9 9
EP300 0.021 0.061 -10000 0 -0.29 18 18
cortisol/GR alpha (dimer)/p53 0.12 0.18 0.49 47 -0.46 1 48
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.053 0.19 18 -10000 0 18
SGK1 0.002 0.24 -10000 0 -1.4 14 14
IL13 -0.13 0.19 -10000 0 -0.68 19 19
IL6 -0.14 0.29 -10000 0 -0.89 52 52
PRKACG 0.01 0.024 -10000 0 -10000 0 0
IL5 -0.1 0.15 -10000 0 -0.69 4 4
IL2 -0.13 0.18 -10000 0 -0.6 21 21
CDK5 0.02 0.012 -10000 0 -10000 0 0
PRKACB 0.021 0.01 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
IL8 -0.19 0.35 -10000 0 -0.9 86 86
CDK5R1/CDK5 0.015 0.071 -10000 0 -0.3 22 22
NF kappa B1 p50/RelA/PKAc -0.007 0.12 -10000 0 -0.3 24 24
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.45 52 -10000 0 52
SMARCA4 0.024 0.016 -10000 0 -10000 0 0
chromatin remodeling 0.079 0.12 0.34 28 -0.37 6 34
NF kappa B1 p50/RelA/Cbp -0.014 0.15 -10000 0 -0.38 34 34
JUN (dimer) -0.077 0.13 0.27 2 -0.38 43 45
YWHAH 0.019 0.033 -10000 0 -10000 0 0
VIPR1 -0.071 0.18 -10000 0 -0.67 35 35
NR3C1 0.083 0.12 0.35 44 -10000 0 44
NR4A1 0.008 0.087 -10000 0 -0.45 15 15
TIF2/SUV420H1 0.015 0.083 -10000 0 -0.3 32 32
MAPKKK cascade 0.014 0.17 0.57 19 -0.47 11 30
cortisol/GR alpha (dimer)/Src-1 0.14 0.17 0.48 55 -10000 0 55
PBX1 0.025 0.021 -10000 0 -0.43 1 1
POU1F1 0 0.021 -10000 0 -10000 0 0
SELE -0.15 0.28 -10000 0 -0.81 63 63
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.078 0.12 0.35 27 -0.37 6 33
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.16 0.45 52 -10000 0 52
mol:cortisol 0.066 0.11 0.31 53 -10000 0 53
MMP1 -0.041 0.09 -10000 0 -0.94 2 2
Canonical Wnt signaling pathway

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
HDAC1 0.024 0.024 0.19 4 -10000 0 4
AES 0.026 0.019 0.17 3 -10000 0 3
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.03 0.017 -10000 0 -10000 0 0
SMAD4 0.026 0.004 -10000 0 -10000 0 0
DKK2 -0.039 0.14 -10000 0 -0.26 112 112
TLE1 0.025 0.035 0.18 4 -0.43 2 6
MACF1 0.022 0.01 -10000 0 -10000 0 0
CTNNB1 0.044 0.099 0.28 30 -0.3 5 35
WIF1 -0.13 0.18 -10000 0 -0.27 266 266
beta catenin/RanBP3 0.016 0.1 0.4 27 -0.3 1 28
KREMEN2 -0.007 0.1 -10000 0 -0.24 63 63
DKK1 -0.035 0.13 -10000 0 -0.25 112 112
beta catenin/beta TrCP1 0.053 0.097 0.28 27 -0.28 4 31
FZD1 0.021 0.01 -10000 0 -10000 0 0
AXIN2 0.003 0.16 0.58 18 -0.89 5 23
AXIN1 0.027 0.002 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.075 -10000 0 -0.53 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.066 0.09 0.3 15 -0.58 3 18
Axin1/APC/GSK3 0.03 0.073 0.24 13 -0.25 2 15
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.075 0.24 15 -0.42 2 17
HNF1A 0.027 0.029 0.19 4 -0.43 1 5
CTBP1 0.027 0.021 0.19 4 -10000 0 4
MYC 0.008 0.36 0.55 64 -1.5 21 85
RANBP3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0 0.11 -10000 0 -0.27 68 68
NKD1 0.016 0.059 -10000 0 -0.28 16 16
TCF4 0.026 0.027 0.18 4 -0.38 1 5
TCF3 0.025 0.032 0.18 3 -0.37 2 5
WNT1/LRP6/FZD1/Axin1 0.052 0.03 -10000 0 -10000 0 0
Ran/GTP 0.019 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.13 0.5 29 -0.36 1 30
LEF1 0.026 0.026 0.18 4 -0.14 5 9
DVL1 0.027 0.037 -10000 0 -0.26 1 1
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.062 0.11 0.3 16 -0.73 3 19
DKK1/LRP6/Kremen 2 0.002 0.11 -10000 0 -0.25 71 71
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.028 0.022 0.19 4 -10000 0 4
NLK 0.024 0.013 -10000 0 -0.16 1 1
CCND1 -0.018 0.25 0.56 19 -1.5 11 30
WNT1 0.01 0.04 -10000 0 -0.13 33 33
GSK3A 0.022 0.01 -10000 0 -10000 0 0
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
FRAT1 0.023 0.03 -10000 0 -0.43 2 2
PPP2R5D 0.026 0.057 0.28 8 -0.28 2 10
APC 0.038 0.079 0.19 101 -10000 0 101
WNT1/LRP6/FZD1 0.042 0.079 0.2 75 -0.2 2 77
CREBBP 0.028 0.021 0.19 4 -10000 0 4
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.018 0.1 -10000 0 -0.25 53 53
MAP4K1 0.013 0.061 -10000 0 -0.34 13 13
MAP3K8 0.016 0.047 -10000 0 -0.2 17 17
PRKCB -0.007 0.098 -10000 0 -0.22 68 68
DBNL 0.023 0.009 -10000 0 -10000 0 0
CRKL 0.026 0.008 -10000 0 -0.13 1 1
MAP3K1 -0.007 0.082 0.17 1 -0.36 10 11
JUN -0.025 0.17 -10000 0 -0.57 42 42
MAP3K7 -0.007 0.081 -10000 0 -0.36 10 10
GRAP2 -0.007 0.1 -10000 0 -0.43 25 25
CRK 0.026 0.002 -10000 0 -10000 0 0
MAP2K4 -0.002 0.092 0.26 4 -0.35 12 16
LAT 0.003 0.1 -10000 0 -0.43 26 26
LCP2 0.02 0.033 -10000 0 -0.15 15 15
MAPK8 -0.023 0.18 -10000 0 -0.6 43 43
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.002 0.089 -10000 0 -0.28 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55 0.022 0.098 -10000 0 -0.24 48 48
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.023 0.13 -10000 0 -0.32 71 71
GNB1/GNG2 0.021 0.097 -10000 0 -0.28 28 28
mol:DAG 0.003 0.089 0.21 13 -0.26 25 38
PLCG1 0.003 0.091 0.21 13 -0.27 25 38
YES1 -0.013 0.082 -10000 0 -0.27 40 40
FZD3 0.023 0.035 -10000 0 -0.43 3 3
FZD6 0.015 0.04 -10000 0 -0.43 1 1
G protein 0.025 0.1 0.26 3 -0.27 26 29
MAP3K7 -0.048 0.1 0.28 6 -0.3 24 30
mol:Ca2+ 0.003 0.087 0.21 13 -0.26 25 38
mol:IP3 0.003 0.089 0.21 13 -0.26 25 38
NLK 0.01 0.044 -10000 0 -0.95 1 1
GNB1 0.022 0.01 -10000 0 -10000 0 0
CAMK2A -0.048 0.11 0.21 13 -0.29 35 48
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.007 0.087 -10000 0 -0.27 44 44
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
GNAS -0.013 0.079 0.16 1 -0.26 41 42
GO:0007205 -0.005 0.088 0.21 13 -0.27 25 38
WNT6 0.003 0.087 -10000 0 -0.43 17 17
WNT4 0.008 0.057 -10000 0 -0.43 5 5
NFAT1/CK1 alpha -0.002 0.12 0.33 3 -0.32 27 30
GNG2 0.022 0.04 -10000 0 -0.43 4 4
WNT5A 0.01 0.078 -10000 0 -0.33 22 22
WNT11 0.009 0.075 -10000 0 -0.43 13 13
CDC42 0.001 0.064 -10000 0 -0.32 8 8
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.028 0.14 -10000 0 -0.42 55 55
KLHL20 0.011 0.07 0.16 6 -0.22 6 12
CYFIP2 0.022 0.037 -10000 0 -0.28 6 6
Rac1/GDP -0.004 0.095 0.26 4 -0.26 47 51
ENAH -0.032 0.14 -10000 0 -0.42 62 62
AP1M1 0.025 0.006 -10000 0 -10000 0 0
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.004 0.065 -10000 0 -0.24 1 1
ABI1/Sra1/Nap1 -0.014 0.035 -10000 0 -0.15 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.021 0.12 -10000 0 -0.26 70 70
RAPGEF1 -0.019 0.14 0.24 5 -0.37 55 60
CTNND1 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.028 0.15 -10000 0 -0.43 62 62
CRK -0.03 0.14 0.22 1 -0.4 57 58
E-cadherin/gamma catenin/alpha catenin 0.014 0.1 -10000 0 -0.26 63 63
alphaE/beta7 Integrin 0.019 0.069 -10000 0 -0.3 19 19
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.23 1 1
DLG1 -0.031 0.14 -10000 0 -0.42 61 61
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.044 -10000 0 -0.18 1 1
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
ARF6/GTP/NME1/Tiam1 0.048 0.012 -10000 0 -10000 0 0
PI3K -0.015 0.057 -10000 0 -0.23 1 1
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.02 0.12 -10000 0 -0.31 63 63
TIAM1 0.026 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.029 0.088 -10000 0 -0.22 55 55
AKT1 -0.003 0.043 0.12 2 -10000 0 2
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.046 0.15 -10000 0 -0.43 59 59
RhoA/GDP 0.004 0.1 0.26 8 -0.26 52 60
actin cytoskeleton organization 0.014 0.06 0.16 19 -0.16 6 25
CDC42/GDP 0 0.1 0.25 5 -0.25 51 56
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.079 -10000 0 -0.22 61 61
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
RAC1 0.023 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.031 0.095 -10000 0 -0.23 55 55
E-cadherin/Ca2+/beta catenin/alpha catenin 0.015 0.085 -10000 0 -0.22 59 59
mol:GDP -0.011 0.11 0.26 9 -0.3 52 61
CDC42/GTP/IQGAP1 0.027 0.028 -10000 0 -0.23 4 4
JUP 0.02 0.049 -10000 0 -0.39 7 7
p120 catenin/RhoA/GDP 0.009 0.1 0.26 6 -0.26 51 57
RAC1/GTP/IQGAP1 0.027 0.029 -10000 0 -0.26 4 4
PIP5K1C/AP1M1 0.037 0.009 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.051 0.14 19 -0.17 14 33
NME1 0.026 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.031 0.15 -10000 0 -0.42 62 62
regulation of cell-cell adhesion -0.009 0.055 -10000 0 -0.21 1 1
WASF2 0.009 0.029 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.082 0.24 2 -0.26 1 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.12 -10000 0 -0.25 74 74
CCND1 0.012 0.06 0.16 15 -0.2 14 29
VAV2 -0.013 0.15 -10000 0 -0.44 26 26
RAP1/GDP 0.004 0.091 0.27 4 -0.25 7 11
adherens junction assembly -0.03 0.14 -10000 0 -0.4 62 62
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.023 0.008 -10000 0 -10000 0 0
PIP5K1C 0.025 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.016 0.11 -10000 0 -0.24 74 74
E-cadherin/beta catenin -0.028 0.1 -10000 0 -0.32 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.032 0.14 -10000 0 -0.42 60 60
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
Rac1/GTP -0.016 0.084 -10000 0 -0.34 7 7
E-cadherin/beta catenin/alpha catenin 0.016 0.1 -10000 0 -0.26 59 59
ITGAE 0.026 0.002 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.028 0.15 -10000 0 -0.44 62 62
Coregulation of Androgen receptor activity

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
NRIP1 0.026 0.004 -9999 0 -10000 0 0
SVIL 0.015 0.042 -9999 0 -0.16 23 23
ZNF318 0.026 0.003 -9999 0 -10000 0 0
JMJD2C 0 0.005 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.02 0.11 -9999 0 -0.26 77 77
CARM1 0.025 0.006 -9999 0 -10000 0 0
PRDX1 0.012 0.066 -9999 0 -0.43 11 11
PELP1 0.026 0.002 -9999 0 -10000 0 0
CTNNB1 0.026 0.004 -9999 0 -10000 0 0
AKT1 0.025 0.005 -9999 0 -10000 0 0
PTK2B 0.018 0.032 -9999 0 -0.13 22 22
MED1 0.026 0.003 -9999 0 -10000 0 0
MAK 0.007 0.063 -9999 0 -0.16 51 51
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.011 0.069 -9999 0 -0.43 12 12
GSN 0.017 0.06 -9999 0 -0.37 11 11
NCOA2 -0.005 0.11 -9999 0 -0.43 34 34
NCOA6 0.025 0.005 -9999 0 -10000 0 0
DNA-PK 0.05 0.014 -9999 0 -10000 0 0
NCOA4 0.025 0.005 -9999 0 -10000 0 0
PIAS3 0.023 0.008 -9999 0 -10000 0 0
cell proliferation -0.005 0.079 -9999 0 -0.52 10 10
XRCC5 0.026 0.003 -9999 0 -10000 0 0
UBE3A 0.026 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.03 0.12 -9999 0 -0.27 92 92
FHL2 -0.02 0.16 -9999 0 -0.98 12 12
RANBP9 0.026 0.003 -9999 0 -10000 0 0
JMJD1A -0.009 0.038 -9999 0 -0.13 42 42
CDK6 0.004 0.083 -9999 0 -0.43 17 17
TGFB1I1 0.022 0.039 -9999 0 -0.23 9 9
T-DHT/AR/CyclinD1 -0.029 0.12 -9999 0 -0.27 87 87
XRCC6 0.026 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.026 0.12 -9999 0 -0.25 107 107
CTDSP1 0.026 0.003 -9999 0 -10000 0 0
CTDSP2 0.025 0.006 -9999 0 -10000 0 0
BRCA1 0.025 0.012 -9999 0 -0.13 3 3
TCF4 0.025 0.02 -9999 0 -0.43 1 1
CDKN2A -0.012 0.11 -9999 0 -0.3 55 55
SRF 0.024 0.027 -9999 0 -10000 0 0
NKX3-1 -0.035 0.077 -9999 0 -0.17 105 105
KLK3 0.003 0.046 -9999 0 -10000 0 0
TMF1 0.025 0.02 -9999 0 -0.43 1 1
HNRNPA1 0.026 0.004 -9999 0 -10000 0 0
AOF2 0 0.001 -9999 0 -10000 0 0
APPL1 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.024 0.11 -9999 0 -0.26 80 80
AR -0.056 0.16 -9999 0 -0.34 104 104
UBA3 0.026 0.004 -9999 0 -10000 0 0
PATZ1 0.026 0.004 -9999 0 -10000 0 0
PAWR 0.003 0.087 -9999 0 -0.25 44 44
PRKDC 0.025 0.005 -9999 0 -10000 0 0
PA2G4 0.026 0.003 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.017 0.099 -9999 0 -0.23 77 77
RPS6KA3 0.025 0.02 -9999 0 -0.43 1 1
T-DHT/AR/ARA70 -0.021 0.11 -9999 0 -0.26 78 78
LATS2 0.018 0.046 -9999 0 -0.21 15 15
T-DHT/AR/PRX1 -0.026 0.1 -9999 0 -0.24 86 86
Cyclin D3/CDK11 p58 0.019 0.005 -9999 0 -10000 0 0
VAV3 -0.031 0.11 -9999 0 -0.2 115 115
KLK2 -0.044 0.12 -9999 0 -0.41 40 40
CASP8 0.021 0.033 -9999 0 -0.23 3 3
T-DHT/AR/TIF2/CARM1 -0.017 0.12 -9999 0 -0.27 87 87
TMPRSS2 -0.082 0.25 -9999 0 -0.89 43 43
CCND1 0.011 0.07 -9999 0 -0.26 25 25
PIAS1 0.022 0.04 -9999 0 -0.43 4 4
mol:T-DHT -0.006 0.019 -9999 0 -0.064 42 42
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.025 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.029 0.12 -9999 0 -0.28 79 79
CMTM2 0.013 0.073 -9999 0 -0.43 13 13
SNURF 0.011 0.079 -9999 0 -0.4 18 18
ZMIZ1 0.016 0.029 -9999 0 -10000 0 0
CCND3 0.026 0.007 -9999 0 -10000 0 0
TGIF1 0.016 0.06 -9999 0 -0.27 17 17
FKBP4 0.024 0.007 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.017 0.075 -10000 0 -0.21 55 55
TP53 -0.015 0.07 -10000 0 -0.29 25 25
Senescence -0.015 0.07 -10000 0 -0.29 25 25
Apoptosis -0.015 0.07 -10000 0 -0.29 25 25
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.01 0.056 0.21 34 -10000 0 34
MDM4 0.025 0.006 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.14 -10000 0 -0.55 26 26
HDAC1 0.022 0.014 -10000 0 -10000 0 0
AES 0.025 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
DTX1 0.019 0.053 -10000 0 -0.39 8 8
LRP6/FZD1 0.03 0.017 -10000 0 -10000 0 0
TLE1 0.024 0.029 -10000 0 -0.43 2 2
AP1 -0.027 0.091 -10000 0 -0.25 60 60
NCSTN 0.026 0.004 -10000 0 -10000 0 0
ADAM10 0.015 0.069 -10000 0 -0.43 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.065 -10000 0 -10000 0 0
NICD/RBPSUH 0.016 0.12 -10000 0 -0.49 26 26
WIF1 -0.13 0.18 -10000 0 -0.27 266 266
NOTCH1 0 0.12 -10000 0 -0.52 26 26
PSENEN 0.022 0.01 -10000 0 -10000 0 0
KREMEN2 -0.007 0.1 -10000 0 -0.24 63 63
DKK1 -0.035 0.13 -10000 0 -0.25 112 112
beta catenin/beta TrCP1 0.011 0.072 0.28 6 -0.31 2 8
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.004 -10000 0 -10000 0 0
AXIN1 0.007 0.049 0.34 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.02 0.049 0.29 4 -0.26 3 7
PSEN1 0.025 0.005 -10000 0 -10000 0 0
FOS -0.031 0.14 -10000 0 -0.43 48 48
JUN 0.019 0.023 -10000 0 -0.13 9 9
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
CTNNB1 0.002 0.072 0.29 7 -0.33 2 9
MAPK3 0.026 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.007 0.11 -10000 0 -0.27 68 68
HNF1A 0.025 0.021 -10000 0 -0.43 1 1
CTBP1 0.026 0.006 -10000 0 -10000 0 0
MYC -0.033 0.28 -10000 0 -1.4 21 21
NKD1 0.016 0.059 -10000 0 -0.28 16 16
FZD1 0.021 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.013 0.12 -10000 0 -0.5 26 26
apoptosis -0.027 0.09 -10000 0 -0.25 60 60
Delta 1/NOTCHprecursor -0.001 0.14 -10000 0 -0.55 26 26
DLL1 -0.008 0.12 -10000 0 -0.43 38 38
PPARD 0.022 0.058 -10000 0 -1.1 1 1
Gamma Secretase 0.063 0.032 -10000 0 -10000 0 0
APC 0.003 0.069 0.34 1 -0.47 4 5
DVL1 -0.012 0.07 -10000 0 -0.26 32 32
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.007 0.11 -10000 0 -0.25 71 71
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.004 -10000 0 -10000 0 0
NLK 0.014 0.011 -10000 0 -10000 0 0
CCND1 -0.01 0.21 -10000 0 -1.3 13 13
WNT1 0.007 0.04 -10000 0 -0.13 33 33
Axin1/APC/beta catenin 0.004 0.094 0.3 6 -0.42 3 9
DKK2 -0.039 0.14 -10000 0 -0.26 112 112
NOTCH1 precursor/DVL1 -0.019 0.14 -10000 0 -0.53 24 24
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
FRAT1 0.023 0.03 -10000 0 -0.43 2 2
NOTCH/Deltex homolog 1 0.015 0.13 -10000 0 -0.51 26 26
PPP2R5D 0.01 0.052 0.25 8 -0.3 4 12
MAPK1 0.026 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.011 0.12 -10000 0 -0.24 98 98
RBPJ 0.026 0.004 -10000 0 -10000 0 0
CREBBP 0.027 0.007 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.052 0.2 30 -0.2 2 32
RFC1 0 0.037 0.18 18 -0.2 2 20
PRKDC 0.007 0.054 0.2 35 -0.2 2 37
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CASP7 -0.016 0.14 -10000 0 -0.57 29 29
FASLG/FAS/FADD/FAF1 0.003 0.054 0.19 14 -0.25 9 23
MAP2K4 -0.028 0.11 0.22 1 -0.33 38 39
mol:ceramide 0.003 0.068 -10000 0 -0.26 18 18
GSN -0.001 0.062 0.19 26 -0.3 9 35
FASLG/FAS/FADD/FAF1/Caspase 8 0.004 0.055 -10000 0 -0.26 6 6
FAS 0.011 0.064 -10000 0 -0.28 18 18
BID -0.01 0.052 0.26 17 -10000 0 17
MAP3K1 -0.024 0.11 0.22 1 -0.35 33 34
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
RB1 0.001 0.039 0.18 19 -0.2 2 21
CFLAR 0.026 0.008 -10000 0 -10000 0 0
HGF/MET -0.006 0.12 -10000 0 -0.24 86 86
ARHGDIB 0.006 0.052 0.2 32 -0.22 1 33
FADD 0.022 0.014 -10000 0 -10000 0 0
actin filament polymerization 0.004 0.067 0.24 19 -0.19 26 45
NFKB1 -0.011 0.12 -10000 0 -0.75 11 11
MAPK8 -0.045 0.15 -10000 0 -0.47 43 43
DFFA 0 0.034 0.17 16 -0.2 2 18
DNA fragmentation during apoptosis -0.003 0.045 0.18 17 -0.18 12 29
FAS/FADD/MET -0.004 0.1 -10000 0 -0.26 57 57
CFLAR/RIP1 0.039 0.009 -10000 0 -10000 0 0
FAIM3 0.004 0.088 -10000 0 -0.43 18 18
FAF1 0.019 0.016 -10000 0 -10000 0 0
PARP1 0.001 0.039 0.18 19 -0.2 2 21
DFFB 0 0.034 0.17 16 -0.2 2 18
CHUK -0.011 0.11 -10000 0 -0.71 10 10
FASLG 0.007 0.04 -10000 0 -0.13 32 32
FAS/FADD 0.024 0.049 -10000 0 -0.31 8 8
HGF -0.009 0.091 -10000 0 -0.2 69 69
LMNA -0.001 0.047 0.2 12 -0.21 1 13
CASP6 0.001 0.041 0.19 18 -0.22 3 21
CASP10 0.022 0.015 -10000 0 -0.13 1 1
CASP3 0.003 0.046 0.22 18 -0.22 2 20
PTPN13 0.022 0.041 -10000 0 -0.37 5 5
CASP8 -0.01 0.066 0.34 17 -10000 0 17
IL6 -0.099 0.36 -10000 0 -1.2 47 47
MET -0.047 0.14 -10000 0 -0.43 52 52
ICAD/CAD 0.001 0.044 0.3 6 -0.21 1 7
FASLG/FAS/FADD/FAF1/Caspase 10 0.003 0.069 -10000 0 -0.27 17 17
activation of caspase activity by cytochrome c -0.01 0.051 0.26 17 -10000 0 17
PAK2 0.002 0.041 0.19 21 -0.22 1 22
BCL2 0.021 0.045 -10000 0 -0.43 5 5
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.007 0.089 -10000 0 -0.26 49 49
cell-cell adhesion 0.02 0.05 0.22 25 -10000 0 25
Ephrin B/EPHB2/RasGAP 0.054 0.058 -10000 0 -0.24 12 12
ITSN1 0.026 0.003 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
SHC1 0.024 0.014 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.012 0.077 -10000 0 -0.26 38 38
HRAS/GDP 0.018 0.064 -10000 0 -0.27 10 10
Ephrin B/EPHB1/GRB7 0.042 0.098 -10000 0 -0.26 45 45
Endophilin/SYNJ1 0.012 0.056 0.18 26 -0.22 13 39
KRAS 0.025 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.045 0.088 -10000 0 -0.24 38 38
endothelial cell migration 0.042 0.028 -10000 0 -0.22 1 1
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.001 0.044 -10000 0 -0.13 41 41
PAK1 -0.012 0.065 0.29 3 -0.23 14 17
HRAS 0.025 0.006 -10000 0 -10000 0 0
RRAS 0.01 0.054 0.18 22 -0.23 11 33
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.005 0.08 0.19 17 -0.23 45 62
lamellipodium assembly -0.02 0.05 -10000 0 -0.22 25 25
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.011 0.074 -10000 0 -0.3 10 10
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPHB2 0.017 0.04 -10000 0 -0.43 3 3
EPHB3 0.025 0.011 -10000 0 -0.13 2 2
EPHB1 -0.009 0.12 -10000 0 -0.43 39 39
EPHB4 0.021 0.011 -10000 0 -10000 0 0
mol:GDP -0.002 0.057 0.23 3 -0.3 7 10
Ephrin B/EPHB2 0.042 0.053 -10000 0 -0.24 13 13
Ephrin B/EPHB3 0.052 0.045 -10000 0 -0.23 11 11
JNK cascade -0.003 0.078 0.45 2 -0.23 39 41
Ephrin B/EPHB1 0.031 0.089 -10000 0 -0.24 45 45
RAP1/GDP 0.044 0.095 0.23 64 -0.28 8 72
EFNB2 0.022 0.029 -10000 0 -0.16 10 10
EFNB3 0.016 0.064 -10000 0 -0.36 13 13
EFNB1 0.025 0.012 -10000 0 -0.13 3 3
Ephrin B2/EPHB1-2 0.017 0.082 -10000 0 -0.25 41 41
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.077 -10000 0 -0.32 11 11
Rap1/GTP -0.001 0.073 -10000 0 -0.29 12 12
axon guidance -0.007 0.088 -10000 0 -0.26 49 49
MAPK3 0.002 0.066 0.19 1 -0.29 8 9
MAPK1 0.002 0.066 0.19 1 -0.29 8 9
Rac1/GDP 0.024 0.084 0.23 40 -0.28 8 48
actin cytoskeleton reorganization -0.004 0.047 -10000 0 -0.27 7 7
CDC42/GDP 0.04 0.098 0.23 69 -0.28 8 77
PI3K 0.046 0.03 -10000 0 -0.22 1 1
EFNA5 -0.029 0.14 -10000 0 -0.43 48 48
Ephrin B2/EPHB4 0.025 0.022 -10000 0 -0.26 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.014 0.045 -10000 0 -0.29 8 8
CDC42 0.022 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.07 -10000 0 -0.29 11 11
PTK2 0.054 0.16 0.54 52 -10000 0 52
MAP4K4 -0.003 0.079 0.46 2 -0.23 39 41
SRC 0.025 0.005 -10000 0 -10000 0 0
KALRN 0.02 0.038 -10000 0 -0.17 16 16
Intersectin/N-WASP 0.03 0.017 -10000 0 -10000 0 0
neuron projection morphogenesis 0.032 0.12 0.3 69 -0.34 4 73
MAP2K1 0.005 0.069 -10000 0 -0.3 9 9
WASL 0.02 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.03 0.086 -10000 0 -0.25 40 40
cell migration 0.004 0.087 0.39 1 -0.36 8 9
NRAS 0.021 0.01 -10000 0 -10000 0 0
SYNJ1 0.012 0.056 0.18 24 -0.22 13 37
PXN 0.026 0.004 -10000 0 -10000 0 0
TF -0.022 0.075 0.17 20 -0.24 33 53
HRAS/GTP 0.016 0.082 -10000 0 -0.23 43 43
Ephrin B1/EPHB1-2 0.018 0.08 -10000 0 -0.24 39 39
cell adhesion mediated by integrin 0.002 0.048 0.21 11 -0.19 16 27
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0.02 0.087 -10000 0 -0.24 45 45
RAC1-CDC42/GTP -0.004 0.059 -10000 0 -0.3 8 8
RASA1 0.026 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.03 0.08 0.23 35 -0.29 6 41
ruffle organization 0.039 0.13 0.35 52 -0.42 3 55
NCK1 0.025 0.02 -10000 0 -0.43 1 1
receptor internalization -0.024 0.075 0.17 20 -0.24 31 51
Ephrin B/EPHB2/KALRN 0.053 0.061 -10000 0 -0.24 14 14
ROCK1 0.02 0.031 0.18 17 -10000 0 17
RAS family/GDP -0.007 0.044 -10000 0 -0.28 7 7
Rac1/GTP -0.001 0.058 -10000 0 -0.23 25 25
Ephrin B/EPHB1/Src/Paxillin 0.006 0.074 -10000 0 -0.24 39 39
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.015 0.048 0.16 1 -0.25 13 14
EPHB2 0.017 0.04 -10000 0 -0.43 3 3
Syndecan-2/TACI 0.012 0.046 -10000 0 -0.24 14 14
LAMA1 -0.024 0.14 -10000 0 -0.43 51 51
Syndecan-2/alpha2 ITGB1 0.021 0.093 -10000 0 -0.26 43 43
HRAS 0.025 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.001 0.041 -10000 0 -0.25 13 13
ITGA5 0.017 0.043 -10000 0 -0.16 24 24
BAX -0.001 0.037 -10000 0 -10000 0 0
EPB41 0.021 0.023 -10000 0 -0.28 2 2
positive regulation of cell-cell adhesion 0.016 0.04 -10000 0 -0.22 13 13
LAMA3 -0.004 0.1 -10000 0 -0.29 49 49
EZR 0.017 0.06 -10000 0 -0.43 9 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.013 0.041 -10000 0 -0.43 2 2
Syndecan-2/MMP2 0.01 0.06 -10000 0 -0.25 24 24
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.017 0.068 -10000 0 -0.3 19 19
dendrite morphogenesis 0.011 0.049 -10000 0 -0.24 16 16
Syndecan-2/GM-CSF 0.011 0.044 -10000 0 -0.25 13 13
determination of left/right symmetry 0.002 0.049 -10000 0 -0.3 13 13
Syndecan-2/PKC delta 0.005 0.081 -10000 0 -0.29 32 32
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.02 0.066 0.19 49 -0.23 13 62
MAPK1 0.02 0.063 0.19 46 -0.23 11 57
Syndecan-2/RACK1 0.028 0.043 -10000 0 -0.21 13 13
NF1 0.025 0.02 -10000 0 -0.43 1 1
FGFR/FGF/Syndecan-2 0.002 0.049 -10000 0 -0.3 13 13
ITGA2 0.002 0.09 -10000 0 -0.43 19 19
MAPK8 -0.003 0.056 -10000 0 -0.25 25 25
Syndecan-2/alpha2/beta1 Integrin 0.008 0.11 0.19 1 -0.26 62 63
Syndecan-2/Kininogen 0.009 0.047 -10000 0 -0.25 13 13
ITGB1 0.023 0.012 -10000 0 -10000 0 0
SRC 0.025 0.064 0.19 50 -0.2 13 63
Syndecan-2/CASK/Protein 4.1 0.012 0.041 -10000 0 -0.21 15 15
extracellular matrix organization 0.013 0.045 -10000 0 -0.24 14 14
actin cytoskeleton reorganization 0.015 0.048 0.16 1 -0.25 13 14
Syndecan-2/Caveolin-2/Ras 0.023 0.046 -10000 0 -0.23 13 13
Syndecan-2/Laminin alpha3 0.002 0.077 0.16 1 -0.28 31 32
Syndecan-2/RasGAP 0.038 0.045 -10000 0 -0.2 13 13
alpha5/beta1 Integrin 0.029 0.034 -10000 0 -0.26 3 3
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
Syndecan-2 dimer 0.011 0.049 -10000 0 -0.24 16 16
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.045 0.18 9 -0.2 11 20
RHOA 0.026 0.004 -10000 0 -10000 0 0
SDCBP 0.025 0.006 -10000 0 -10000 0 0
TNFRSF13B -0.003 0.028 -10000 0 -0.13 11 11
RASA1 0.026 0.003 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.017 0.068 -10000 0 -0.3 19 19
Syndecan-2/Synbindin 0.016 0.045 -10000 0 -0.25 13 13
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CASP3 0.013 0.089 0.19 46 -0.27 30 76
FN1 0.021 0.029 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.028 0.099 0.17 4 -0.26 70 74
SDC2 0.002 0.049 -10000 0 -0.3 13 13
KNG1 -0.009 0.032 -10000 0 -0.13 22 22
Syndecan-2/Neurofibromin 0.018 0.045 -10000 0 -0.25 13 13
TRAPPC4 0.025 0.007 -10000 0 -10000 0 0
CSF2 -0.014 0.009 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.013 0.045 -10000 0 -0.24 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.041 -10000 0 -0.23 13 13
Syndecan-2/Ezrin 0.026 0.063 -10000 0 -0.29 17 17
PRKACA 0.025 0.066 0.19 48 -0.23 13 61
angiogenesis -0.028 0.099 0.17 4 -0.26 70 74
MMP2 0.013 0.067 -10000 0 -0.26 24 24
IL8 -0.061 0.15 -10000 0 -0.25 158 158
calcineurin-NFAT signaling pathway 0.012 0.046 -10000 0 -0.24 14 14
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.04 -10000 0 -0.43 4 4
ANTXR2 0.021 0.035 -10000 0 -0.19 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.006 -10000 0 -0.058 6 6
monocyte activation -0.13 0.23 -10000 0 -0.42 176 176
MAP2K2 0.013 0.039 -10000 0 -0.61 2 2
MAP2K1 -0.003 0.007 -10000 0 -0.11 1 1
MAP2K7 -0.003 0.006 -10000 0 -10000 0 0
MAP2K6 -0.003 0.011 -10000 0 -0.22 1 1
CYAA -0.007 0.023 -10000 0 -0.21 6 6
MAP2K4 -0.003 0.008 -10000 0 -0.11 2 2
IL1B -0.043 0.079 0.17 2 -0.22 76 78
Channel 0.028 0.031 -10000 0 -0.23 6 6
NLRP1 -0.004 0.014 -10000 0 -0.22 2 2
CALM1 0.025 0.009 -10000 0 -0.13 1 1
negative regulation of phagocytosis -0.004 0.078 -10000 0 -0.39 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.006 0.058 6 -10000 0 6
MAPK3 -0.003 0.006 -10000 0 -10000 0 0
MAPK1 -0.003 0.006 -10000 0 -10000 0 0
PGR -0.022 0.061 -10000 0 -0.21 47 47
PA/Cellular Receptors 0.029 0.034 -10000 0 -0.25 6 6
apoptosis -0.001 0.006 -10000 0 -0.058 6 6
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.029 0.027 -10000 0 -0.22 6 6
macrophage activation -0.005 0.005 -10000 0 -10000 0 0
TNF -0.06 0.16 -10000 0 -0.26 151 151
VCAM1 -0.13 0.23 -10000 0 -0.43 174 174
platelet activation -0.004 0.078 -10000 0 -0.39 20 20
MAPKKK cascade -0.005 0.024 0.091 1 -0.077 42 43
IL18 -0.012 0.051 0.16 3 -0.23 22 25
negative regulation of macrophage activation -0.001 0.006 -10000 0 -0.058 6 6
LEF -0.001 0.006 -10000 0 -0.058 6 6
CASP1 -0.001 0.018 -10000 0 -0.098 12 12
mol:cAMP -0.005 0.079 -10000 0 -0.39 20 20
necrosis -0.001 0.006 -10000 0 -0.058 6 6
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.028 0.029 -10000 0 -0.21 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR -0.014 0.11 -10000 0 -0.26 71 71
Cbp/p300/PCAF 0.048 0.03 -10000 0 -0.26 4 4
EP300 0.022 0.04 -10000 0 -0.43 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.073 -10000 0 -0.37 10 10
KAT2B 0.025 0.008 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.012 0.075 0.2 6 -0.39 7 13
RAR alpha/9cRA/Cyclin H -0.008 0.11 0.22 1 -0.38 11 12
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.062 0.18 1 -0.31 10 11
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.026 0.1 -10000 0 -0.4 18 18
NCOR2 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.009 0.08 -10000 0 -0.29 33 33
RXRs/RARs/NRIP1/9cRA -0.075 0.19 -10000 0 -0.56 32 32
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
NCOA3 0.025 0.005 -10000 0 -10000 0 0
NCOA1 0.026 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA -0.014 0.11 -10000 0 -0.26 71 71
RARG 0.026 0.008 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.009 -10000 0 -10000 0 0
MAPK3 0.027 0.002 -10000 0 -10000 0 0
MAPK1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.087 0.2 -10000 0 -0.45 90 90
RARA -0.026 0.097 -10000 0 -0.24 75 75
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.012 0.089 0.18 1 -0.34 20 21
PRKCA 0.026 0.021 -10000 0 -0.43 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.08 0.2 -10000 0 -0.56 40 40
RXRG -0.061 0.16 -10000 0 -0.38 93 93
RXRA -0.022 0.088 -10000 0 -0.36 10 10
RXRB -0.027 0.099 -10000 0 -0.28 65 65
VDR/Vit D3/DNA -0.009 0.08 -10000 0 -0.29 33 33
RBP1 -0.006 0.082 -10000 0 -0.43 10 10
CRBP1/9-cic-RA -0.002 0.056 -10000 0 -0.27 12 12
RARB 0.024 0.035 -10000 0 -0.43 3 3
PRKCG -0.065 0.15 -10000 0 -0.26 159 159
MNAT1 0.025 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.08 0.19 -10000 0 -0.45 79 79
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.059 0.16 -10000 0 -0.47 32 32
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.096 0.21 2 -0.35 17 19
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.076 0.19 -10000 0 -0.59 32 32
positive regulation of DNA binding -0.014 0.1 -10000 0 -0.36 11 11
NRIP1 -0.066 0.18 -10000 0 -0.66 13 13
RXRs/RARs -0.076 0.2 -10000 0 -0.57 38 38
RXRs/RXRs/DNA/9cRA -0.088 0.18 -10000 0 -0.44 86 86
PRKACA 0.025 0.005 -10000 0 -10000 0 0
CDK7 0.026 0.003 -10000 0 -10000 0 0
TFIIH 0.051 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.007 0.092 -10000 0 -0.31 9 9
CCNH 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.017 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.022 0.14 -10000 0 -0.41 55 55
HRAS 0.025 0.006 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.4 46 46
AKT 0.038 0.11 0.27 44 -0.28 4 48
FOXO3 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.005 -10000 0 -10000 0 0
FOXO1 0.024 0.022 -10000 0 -0.28 2 2
AKT3 0.022 0.04 -10000 0 -0.43 4 4
FOXO4 0.025 0.02 -10000 0 -0.43 1 1
MET -0.047 0.14 -10000 0 -0.43 52 52
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PIK3CB 0.026 0.003 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
PIK3CG -0.01 0.1 -10000 0 -0.27 53 53
PIK3R3 0.02 0.024 -10000 0 -0.23 3 3
PIK3R2 0.025 0.005 -10000 0 -10000 0 0
NF1 0.025 0.02 -10000 0 -0.43 1 1
RAS -0.008 0.07 0.16 3 -0.15 73 76
ERBB2 0.023 0.027 -10000 0 -0.17 8 8
proliferation/survival/translation -0.025 0.081 0.31 16 -0.22 13 29
PI3K 0.021 0.11 0.25 61 -0.15 53 114
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.005 -10000 0 -10000 0 0
FOXO 0.061 0.087 0.22 78 -10000 0 78
AKT2 0.022 0.01 -10000 0 -10000 0 0
PTEN 0.025 0.006 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.008 0.086 -10000 0 -0.22 58 58
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.058 0.11 -10000 0 -0.3 79 79
GNB1/GNG2 0.027 0.028 -10000 0 -0.26 4 4
GNB1 0.022 0.01 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.012 0.079 -10000 0 -0.23 61 61
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 0.008 0.02 0.062 61 -10000 0 61
GNAL -0.028 0.15 -10000 0 -0.42 61 61
GNG2 0.022 0.04 -10000 0 -0.43 4 4
CRH -0.075 0.16 -10000 0 -0.43 79 79
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.047 -10000 0 -0.3 13 13
MAPK11 0.002 0.037 -10000 0 -0.3 8 8
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.002 0.053 0.19 1 -0.29 3 4
adherens junction organization -0.019 0.09 -10000 0 -0.25 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.082 -10000 0 -0.29 8 8
FMN1 -0.032 0.11 -10000 0 -0.27 60 60
mol:IP3 0.004 0.053 -10000 0 -0.23 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.09 -10000 0 -0.24 56 56
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.008 0.064 0.18 2 -0.27 4 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.36 55 55
CTNND1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.009 0.083 -10000 0 -0.23 55 55
VASP -0.011 0.081 -10000 0 -0.24 40 40
ZYX -0.012 0.078 -10000 0 -0.24 48 48
JUB -0.009 0.085 -10000 0 -0.23 56 56
EGFR(dimer) -0.017 0.1 -10000 0 -0.25 56 56
E-cadherin/beta catenin-gamma catenin -0.001 0.1 -10000 0 -0.25 63 63
mol:PI-3-4-5-P3 0.024 0.074 0.21 2 -0.28 4 6
PIK3CA 0.026 0.02 -10000 0 -0.41 1 1
PI3K 0.024 0.075 0.21 2 -0.29 4 6
FYN 0.002 0.05 -10000 0 -0.26 5 5
mol:Ca2+ 0.004 0.052 -10000 0 -0.23 4 4
JUP 0.021 0.05 -10000 0 -0.39 7 7
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:DAG 0.004 0.053 -10000 0 -0.23 4 4
CDH1 -0.046 0.15 -10000 0 -0.43 59 59
RhoA/GDP 0.011 0.094 0.22 4 -0.29 8 12
establishment of polarity of embryonic epithelium -0.011 0.08 -10000 0 -0.23 40 40
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.4 46 46
CASR -0.005 0.049 -10000 0 -0.24 2 2
RhoA/GTP 0.016 0.053 -10000 0 -0.3 1 1
AKT2 0.01 0.056 0.18 2 -0.26 4 6
actin cable formation -0.03 0.098 0.18 1 -0.28 45 46
apoptosis -0.003 0.064 0.28 5 -0.2 4 9
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.017 0.076 0.15 5 -0.27 12 17
PIP5K1A -0.01 0.084 -10000 0 -0.23 55 55
PLCG1 0.004 0.053 -10000 0 -0.24 4 4
Rac1/GTP -0.007 0.1 -10000 0 -0.33 12 12
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.04 -10000 0 -0.43 4 4
HDAC4 0.025 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.012 0.025 -10000 0 -0.13 18 18
CDKN1A -0.034 0.13 -10000 0 -0.65 20 20
KAT2B 0.025 0.008 -10000 0 -10000 0 0
BAX 0.021 0.01 -10000 0 -10000 0 0
FOXO3 -0.003 0.033 0.36 4 -10000 0 4
FOXO1 0.024 0.022 -10000 0 -0.28 2 2
FOXO4 0.013 0.026 -10000 0 -0.25 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
TAT -0.025 0.12 -10000 0 -0.26 88 88
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.064 0.12 -10000 0 -0.3 93 93
PPARGC1A 0.009 0.082 -10000 0 -0.37 21 21
FHL2 0.006 0.077 -10000 0 -0.22 43 43
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.04 0.025 -10000 0 -10000 0 0
HIST2H4A 0.012 0.025 0.13 18 -10000 0 18
SIRT1/FOXO3a 0.02 0.038 0.17 20 -0.19 4 24
SIRT1 0.03 0.033 0.2 18 -10000 0 18
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.028 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.022 0.057 0.23 1 -0.22 19 20
apoptosis -0.045 0.031 -10000 0 -10000 0 0
SIRT1/PGC1A 0.025 0.057 0.14 17 -0.25 17 34
p53/SIRT1 0.037 0.085 0.39 18 -0.31 12 30
SIRT1/FOXO4 0.031 0.037 0.16 18 -0.22 5 23
FOXO1/FHL2/SIRT1 0.042 0.05 -10000 0 -0.23 13 13
HIST1H1E 0.004 0.05 -10000 0 -0.24 20 20
SIRT1/p300 0.037 0.039 0.16 18 -0.31 4 22
muscle cell differentiation 0.03 0.12 0.25 93 -0.22 10 103
TP53 0.02 0.077 0.2 19 -0.43 12 31
KU70/SIRT1/BAX 0.045 0.031 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
MEF2D 0.025 0.011 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.003 0.097 0.18 1 -0.3 38 39
ACSS2 0.013 0.024 0.13 18 -10000 0 18
SIRT1/PCAF/MYOD -0.03 0.12 0.22 10 -0.25 93 103
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.026 0.008 -10000 0 -0.13 1 1
RAS family/GTP/Tiam1 0.016 0.023 -10000 0 -0.26 2 2
NT3 (dimer)/TRKC 0.028 0.033 -10000 0 -0.34 2 2
NT3 (dimer)/TRKB 0.01 0.098 -10000 0 -0.26 55 55
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.026 -10000 0 -0.48 1 1
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
BDNF -0.01 0.089 -10000 0 -0.43 14 14
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
DYNLT1 0.024 0.029 -10000 0 -0.43 2 2
NTRK1 0.016 0.055 -10000 0 -0.22 20 20
NTRK2 0.006 0.092 -10000 0 -0.43 22 22
NTRK3 0.022 0.04 -10000 0 -0.43 4 4
NT-4/5 (dimer)/TRKB 0.004 0.093 -10000 0 -0.25 52 52
neuron apoptosis 0.057 0.15 0.36 75 -10000 0 75
SHC 2-3/Grb2 -0.062 0.16 -10000 0 -0.39 75 75
SHC1 0.024 0.014 -10000 0 -10000 0 0
SHC2 -0.029 0.1 -10000 0 -0.41 13 13
SHC3 -0.099 0.21 -10000 0 -0.52 84 84
STAT3 (dimer) 0.021 0.055 -10000 0 -0.33 11 11
NT3 (dimer)/TRKA 0.018 0.087 -10000 0 -0.25 46 46
RIN/GDP -0.004 0.081 0.23 6 -0.3 2 8
GIPC1 0.025 0.009 -10000 0 -0.13 1 1
KRAS 0.025 0.005 -10000 0 -10000 0 0
DNAJA3 -0.047 0.099 -10000 0 -0.26 76 76
RIN/GTP -0.072 0.13 -10000 0 -0.3 119 119
CCND1 0.002 0.11 -10000 0 -0.7 11 11
MAGED1 0.026 0.002 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.033 -10000 0 -0.16 12 12
SHC/GRB2/SOS1 0.05 0.014 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.014 0.12 -10000 0 -0.28 83 83
TRKA/NEDD4-2 0.025 0.054 -10000 0 -0.31 10 10
ELMO1 0.017 0.049 -10000 0 -0.43 6 6
RhoG/GTP/ELMO1/DOCK1 0.024 0.038 -10000 0 -0.25 8 8
NGF -0.025 0.13 -10000 0 -0.43 46 46
HRAS 0.025 0.006 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
GAB2 0.025 0.005 -10000 0 -10000 0 0
RIT2 -0.11 0.19 -10000 0 -0.43 119 119
RIT1 0.026 0.004 -10000 0 -10000 0 0
FRS2 0.026 0.004 -10000 0 -10000 0 0
DNM1 -0.027 0.12 -10000 0 -0.22 108 108
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.032 0.1 -10000 0 -0.25 71 71
mol:GDP 0.03 0.073 0.27 8 -0.62 1 9
NGF (dimer) -0.025 0.13 -10000 0 -0.43 46 46
RhoG/GDP 0.013 0.035 -10000 0 -0.3 6 6
RIT1/GDP 0.027 0.053 0.2 4 -0.37 1 5
TIAM1 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.03 0.083 -10000 0 -0.26 36 36
KIDINS220/CRKL/C3G 0.037 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.052 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.061 0.024 -10000 0 -0.24 1 1
RIT1/GTP 0.019 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.006 0.032 -10000 0 -10000 0 0
RAP1/GDP 0.023 0.04 -10000 0 -0.31 1 1
KIDINS220/CRKL 0.025 0.008 -10000 0 -0.13 1 1
BDNF (dimer) -0.01 0.089 -10000 0 -0.43 14 14
ubiquitin-dependent protein catabolic process -0.001 0.098 -10000 0 -0.26 55 55
Schwann cell development -0.014 0.019 -10000 0 -10000 0 0
EHD4 0.024 0.019 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.063 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.033 0.03 -10000 0 -0.42 1 1
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.016 0.069 -10000 0 -0.22 27 27
ABL1 0.025 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.089 -10000 0 -0.32 9 9
STAT3 0.021 0.055 -10000 0 -0.33 11 11
axon guidance -0.002 0.064 -10000 0 -0.22 27 27
MAPK3 -0.037 0.11 0.18 11 -0.26 78 89
MAPK1 -0.036 0.11 0.18 11 -0.26 77 88
CDC42/GDP 0.032 0.052 0.22 6 -0.37 1 7
NTF3 0.006 0.032 -10000 0 -10000 0 0
NTF4 -0.003 0.033 -10000 0 -0.16 12 12
NGF (dimer)/TRKA/FAIM 0.008 0.096 -10000 0 -0.26 55 55
PI3K 0.038 0.007 -10000 0 -10000 0 0
FRS3 0.026 0.002 -10000 0 -10000 0 0
FAIM 0.022 0.04 -10000 0 -0.43 4 4
GAB1 0.025 0.02 -10000 0 -0.43 1 1
RASGRF1 -0.07 0.12 -10000 0 -0.26 121 121
SOS1 0.026 0.002 -10000 0 -10000 0 0
MCF2L 0.002 0.028 -10000 0 -0.28 3 3
RGS19 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.069 -10000 0 -0.61 2 2
Rac1/GDP 0.025 0.053 0.22 5 -0.36 1 6
NGF (dimer)/TRKA/GRIT -0.008 0.088 -10000 0 -0.25 53 53
neuron projection morphogenesis -0.029 0.12 0.35 1 -0.53 7 8
NGF (dimer)/TRKA/NEDD4-2 0.006 0.098 -10000 0 -0.25 59 59
MAP2K1 0.024 0.05 0.2 35 -0.23 1 36
NGFR -0.017 0.12 -10000 0 -0.28 72 72
NGF (dimer)/TRKA/GIPC/GAIP -0.023 0.096 -10000 0 -0.24 73 73
RAS family/GTP/PI3K 0.019 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.072 0.022 -10000 0 -10000 0 0
NRAS 0.021 0.01 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
MAPKKK cascade -0.11 0.23 -10000 0 -0.47 135 135
RASA1 0.026 0.003 -10000 0 -10000 0 0
TRKA/c-Abl 0.029 0.042 -10000 0 -0.3 6 6
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.043 0.075 -10000 0 -0.25 27 27
NGF (dimer)/TRKA/p62/Atypical PKCs 0.022 0.1 -10000 0 -0.24 58 58
MATK -0.027 0.13 -10000 0 -0.43 46 46
NEDD4L 0.02 0.044 -10000 0 -0.43 4 4
RAS family/GDP -0.006 0.02 -10000 0 -0.28 1 1
NGF (dimer)/TRKA -0.035 0.11 -10000 0 -0.27 76 76
Rac1/GTP -0.04 0.077 -10000 0 -0.25 27 27
FRS2 family/SHP2/CRK family 0.074 0.018 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.022 -10000 0 -0.43 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.001 0.088 0.38 4 -0.48 2 6
IL27/IL27R/JAK1 0.022 0.12 0.88 2 -10000 0 2
TBX21 -0.019 0.16 0.46 14 -0.4 19 33
IL12B -0.001 0.024 -10000 0 -0.13 6 6
IL12A -0.008 0.065 -10000 0 -0.3 23 23
IL6ST -0.002 0.11 -10000 0 -0.43 32 32
IL27RA/JAK1 0.024 0.051 -10000 0 -10000 0 0
IL27 0.014 0.038 -10000 0 -0.13 24 24
TYK2 0.025 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.01 0.12 0.43 1 -0.5 3 4
T-helper 2 cell differentiation 0.001 0.088 0.38 4 -0.48 2 6
T cell proliferation during immune response 0.001 0.088 0.38 4 -0.48 2 6
MAPKKK cascade -0.001 0.088 0.48 2 -0.38 4 6
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT2 0.025 0.014 -10000 0 -0.13 4 4
STAT1 0.021 0.029 -10000 0 -0.13 16 16
IL12RB1 -0.001 0.098 -10000 0 -0.31 39 39
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.034 0.16 0.45 13 -0.4 29 42
IL27/IL27R/JAK2/TYK2 -0.001 0.089 0.48 2 -0.38 4 6
positive regulation of T cell mediated cytotoxicity -0.001 0.088 0.48 2 -0.38 4 6
STAT1 (dimer) 0.009 0.19 0.56 26 -0.48 4 30
JAK2 0.025 0.007 -10000 0 -10000 0 0
JAK1 0.021 0.012 -10000 0 -10000 0 0
STAT2 (dimer) 0.018 0.097 0.39 3 -0.37 3 6
T cell proliferation -0.021 0.1 0.44 2 -0.39 7 9
IL12/IL12R/TYK2/JAK2 0.001 0.13 -10000 0 -0.78 10 10
IL17A -0.009 0.11 0.43 1 -0.47 2 3
mast cell activation 0.001 0.088 0.38 4 -0.48 2 6
IFNG 0.005 0.026 0.12 4 -0.11 5 9
T cell differentiation -0.002 0.004 -10000 0 -0.015 6 6
STAT3 (dimer) 0.018 0.098 0.39 3 -0.36 4 7
STAT5A (dimer) 0.013 0.11 0.39 3 -0.42 7 10
STAT4 (dimer) -0.011 0.13 0.39 3 -0.4 12 15
STAT4 -0.064 0.16 -10000 0 -0.26 162 162
T cell activation -0.006 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.025 0.074 -10000 0 -10000 0 0
GATA3 -0.085 0.44 0.62 39 -1.3 49 88
IL18 -0.009 0.063 -10000 0 -0.2 39 39
positive regulation of mast cell cytokine production 0.018 0.096 0.39 3 -0.36 4 7
IL27/EBI3 0.019 0.067 0.24 2 -0.28 18 20
IL27RA 0.009 0.033 -10000 0 -10000 0 0
IL6 -0.035 0.12 -10000 0 -0.43 37 37
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.015 0.023 -10000 0 -10000 0 0
IL1B -0.056 0.11 -10000 0 -0.18 173 173
EBI3 0.011 0.078 -10000 0 -0.38 18 18
TNF -0.049 0.1 -10000 0 -0.3 68 68
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.023 0.042 -10000 0 -0.25 5 5
PDGFRB 0.025 0.013 -10000 0 -0.14 2 2
SPHK1 -0.02 0.14 -10000 0 -0.72 19 19
mol:S1P -0.019 0.13 -10000 0 -0.63 19 19
S1P1/S1P/Gi -0.028 0.13 -10000 0 -0.35 59 59
GNAO1 0.017 0.047 -10000 0 -0.43 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.014 0.13 0.28 10 -0.34 52 62
PLCG1 -0.027 0.12 -10000 0 -0.34 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -0.14 2 2
GNAI2 0.021 0.016 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.015 0.038 -10000 0 -0.43 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.005 0.028 -10000 0 -0.2 5 5
S1P1/S1P -0.016 0.1 -10000 0 -0.47 18 18
negative regulation of cAMP metabolic process -0.027 0.13 -10000 0 -0.34 59 59
MAPK3 -0.05 0.18 -10000 0 -0.53 59 59
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
KDR 0.017 0.04 -10000 0 -0.23 9 9
PLCB2 -0.012 0.11 0.31 3 -0.44 19 22
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.087 -10000 0 -0.4 18 18
receptor internalization -0.016 0.096 -10000 0 -0.42 19 19
PTGS2 -0.095 0.33 -10000 0 -1 58 58
Rac1/GTP -0.015 0.083 -10000 0 -0.38 17 17
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.016 0.034 -10000 0 -0.13 21 21
negative regulation of T cell proliferation -0.027 0.13 -10000 0 -0.34 59 59
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.021 0.016 -10000 0 -10000 0 0
MAPK1 -0.051 0.18 -10000 0 -0.53 60 60
S1P1/S1P/PDGFB-D/PDGFRB -0.006 0.1 0.22 1 -0.4 18 19
ABCC1 0.025 0.015 -10000 0 -0.14 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.032 0.13 -10000 0 -0.49 18 18
UGCG -0.018 0.15 -10000 0 -0.69 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.037 0.15 0.23 2 -0.4 37 39
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.018 0.14 -10000 0 -0.68 22 22
mol:DAG -0.016 0.16 -10000 0 -0.82 18 18
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.018 0.15 0.25 1 -0.42 36 37
FRAP1 -0.028 0.17 0.27 2 -0.48 37 39
FOXO3 -0.027 0.15 0.27 2 -0.42 41 43
AKT1 -0.029 0.16 0.28 1 -0.45 42 43
GAB2 0.025 0.006 -10000 0 -10000 0 0
SMPD1 -0.013 0.12 -10000 0 -0.58 21 21
SGMS1 -0.008 0.11 -10000 0 -0.56 18 18
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 0.005 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -0.13 1 1
cell proliferation -0.011 0.14 0.25 3 -0.46 19 22
EIF3A 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.039 0.012 -10000 0 -10000 0 0
RPS6KB1 0.002 0.076 -10000 0 -1.1 1 1
mol:sphingomyelin -0.016 0.16 -10000 0 -0.82 18 18
natural killer cell activation 0 0.002 -10000 0 -0.011 14 14
JAK3 -0.008 0.1 -10000 0 -0.24 65 65
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.023 0.011 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MYC -0.025 0.24 0.35 4 -0.84 28 32
MYB -0.075 0.33 -10000 0 -1.1 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.027 0.14 -10000 0 -0.39 36 36
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.078 -10000 0 -1 1 1
mol:PI-3-4-5-P3 -0.026 0.13 -10000 0 -0.38 36 36
Rac1/GDP 0.019 0.013 -10000 0 -10000 0 0
T cell proliferation -0.018 0.12 0.22 1 -0.38 27 28
SHC1 0.024 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.018 -10000 0 -0.064 38 38
PRKCZ -0.015 0.12 0.22 1 -0.4 26 27
NF kappa B1 p50/RelA -0.009 0.15 0.27 2 -0.43 33 35
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.033 0.14 -10000 0 -0.42 44 44
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
IL2RA -0.007 0.072 -10000 0 -0.43 8 8
IL2RB -0.027 0.13 -10000 0 -0.43 39 39
TERT -0.042 0.13 -10000 0 -0.32 74 74
E2F1 -0.014 0.13 -10000 0 -0.45 42 42
SOS1 0.026 0.004 -10000 0 -10000 0 0
RPS6 0.024 0.01 -10000 0 -0.13 1 1
mol:cAMP 0.001 0.009 0.031 38 -10000 0 38
PTPN11 0.025 0.008 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.22 52 52
actin cytoskeleton organization -0.018 0.12 0.22 1 -0.38 27 28
GRB2 0.025 0.007 -10000 0 -10000 0 0
IL2 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0.026 0.021 -10000 0 -0.43 1 1
Rac1/GTP 0.041 0.025 -10000 0 -10000 0 0
LCK -0.019 0.11 -10000 0 -0.43 30 30
BCL2 -0.023 0.16 -10000 0 -0.63 17 17
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.002 0.099 0.22 12 -0.41 18 30
CRKL 0 0.098 -10000 0 -0.43 20 20
HRAS 0.007 0.11 -10000 0 -0.38 20 20
mol:PIP3 0.012 0.1 0.31 7 -0.38 18 25
SPRED1 0.026 0.003 -10000 0 -10000 0 0
SPRED2 0.025 0.012 -10000 0 -0.13 3 3
GAB1 0.002 0.1 0.2 2 -0.44 21 23
FOXO3 0.017 0.13 0.29 8 -0.41 25 33
AKT1 0.018 0.14 0.3 10 -0.43 29 39
BAD 0.021 0.14 0.32 10 -0.41 27 37
megakaryocyte differentiation 0 0.1 0.2 3 -0.42 22 25
GSK3B 0.017 0.13 0.31 9 -0.41 26 35
RAF1 0.006 0.094 0.25 1 -0.32 16 17
SHC1 0.024 0.014 -10000 0 -10000 0 0
STAT3 0.004 0.1 0.2 3 -0.43 21 24
STAT1 -0.013 0.22 -10000 0 -0.89 28 28
HRAS/SPRED1 0.018 0.099 0.25 1 -0.33 16 17
cell proliferation -0.003 0.11 0.2 3 -0.45 22 25
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
TEC 0.015 0.063 -10000 0 -0.29 17 17
RPS6KB1 0.014 0.12 0.26 4 -0.44 23 27
HRAS/SPRED2 0.018 0.099 0.25 1 -0.33 16 17
LYN/TEC/p62DOK 0.029 0.12 -10000 0 -0.43 23 23
MAPK3 0.014 0.082 0.22 18 -0.29 6 24
STAP1 -0.001 0.1 -10000 0 -0.42 23 23
GRAP2 -0.007 0.1 -10000 0 -0.43 25 25
JAK2 -0.014 0.2 -10000 0 -0.77 28 28
STAT1 (dimer) -0.011 0.22 -10000 0 -0.87 28 28
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.023 0.12 -10000 0 -0.42 25 25
actin filament polymerization -0.005 0.099 0.32 5 -0.4 21 26
LYN 0.021 0.035 -10000 0 -0.43 2 2
STAP1/STAT5A (dimer) -0.011 0.16 -10000 0 -0.61 27 27
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.021 0.099 -10000 0 -0.4 19 19
PI3K 0.036 0.12 0.27 3 -0.42 20 23
PTEN 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.007 0.25 -10000 0 -1.2 20 20
MAPK8 -0.003 0.11 0.2 3 -0.46 22 25
STAT3 (dimer) 0.004 0.1 0.2 3 -0.42 21 24
positive regulation of transcription 0.015 0.071 0.2 20 -0.23 6 26
mol:GDP 0.003 0.11 -10000 0 -0.39 22 22
PIK3C2B 0.002 0.1 0.2 3 -0.42 21 24
CBL/CRKL 0.011 0.099 -10000 0 -0.41 19 19
FER -0.005 0.12 0.2 3 -0.45 24 27
SH2B3 0.003 0.1 0.2 3 -0.43 21 24
PDPK1 0.011 0.1 0.32 8 -0.38 17 25
SNAI2 -0.003 0.11 0.29 2 -0.42 25 27
positive regulation of cell proliferation -0.007 0.18 -10000 0 -0.71 27 27
KITLG 0.017 0.066 -10000 0 -0.44 10 10
cell motility -0.007 0.18 -10000 0 -0.71 27 27
PTPN6 0.013 0.063 -10000 0 -0.42 10 10
EPOR 0.031 0.084 -10000 0 -1.2 1 1
STAT5A (dimer) -0.004 0.16 -10000 0 -0.59 29 29
SOCS1 0.008 0.068 -10000 0 -0.43 8 8
cell migration 0.017 0.11 0.42 25 -0.2 2 27
SOS1 0.026 0.002 -10000 0 -10000 0 0
EPO 0.016 0.03 -10000 0 -0.24 3 3
VAV1 0.005 0.09 -10000 0 -0.34 29 29
GRB10 -0.001 0.094 0.24 1 -0.41 20 21
PTPN11 0.025 0.006 -10000 0 -10000 0 0
SCF/KIT 0.006 0.11 0.21 3 -0.45 21 24
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.008 0.081 0.22 5 -0.26 15 20
CBL 0.025 0.007 -10000 0 -10000 0 0
KIT -0.012 0.26 -10000 0 -1.2 20 20
MAP2K2 0.013 0.086 0.26 16 -0.26 14 30
SHC/Grb2/SOS1 0.037 0.11 -10000 0 -0.42 19 19
STAT5A -0.004 0.16 -10000 0 -0.61 29 29
GRB2 0.025 0.006 -10000 0 -10000 0 0
response to radiation -0.002 0.1 0.28 2 -0.41 25 27
SHC/GRAP2 0.012 0.079 -10000 0 -0.3 26 26
PTPRO 0 0.1 0.2 3 -0.42 22 25
SH2B2 -0.007 0.096 0.23 2 -0.4 21 23
DOK1 0.025 0.021 -10000 0 -0.28 2 2
MATK -0.017 0.11 0.2 2 -0.43 25 27
CREBBP 0.034 0.033 -10000 0 -10000 0 0
BCL2 0.012 0.19 -10000 0 -1.4 8 8
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.013 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.006 0.12 0.24 3 -0.38 31 34
PTP1B/AKT1 0.013 0.092 0.2 4 -0.33 11 15
FYN 0.025 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.003 0.094 0.21 5 -0.32 15 20
EGFR -0.019 0.13 -10000 0 -0.42 45 45
EGF/EGFR -0.018 0.12 -10000 0 -0.29 65 65
CSF1 0.017 0.045 -10000 0 -0.43 5 5
AKT1 0.026 0.006 -10000 0 -10000 0 0
INSR 0.025 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.013 0.096 0.21 4 -0.32 15 19
Insulin Receptor/Insulin 0.018 0.087 -10000 0 -0.41 6 6
HCK 0.014 0.063 -10000 0 -0.27 19 19
CRK 0.026 0.002 -10000 0 -10000 0 0
TYK2 0.008 0.1 0.3 20 -0.32 13 33
EGF -0.012 0.12 -10000 0 -0.43 34 34
YES1 0.022 0.04 -10000 0 -0.43 4 4
CAV1 0.017 0.12 0.25 38 -0.32 19 57
TXN 0.026 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.021 0.094 0.22 1 -0.34 10 11
cell migration -0.003 0.094 0.32 15 -0.21 5 20
STAT3 0.026 0.003 -10000 0 -10000 0 0
PRLR 0.007 0.088 -10000 0 -0.43 19 19
ITGA2B -0.012 0.12 -10000 0 -0.43 40 40
CSF1R 0.002 0.099 -10000 0 -0.43 25 25
Prolactin Receptor/Prolactin 0.02 0.066 -10000 0 -0.31 18 18
FGR 0.021 0.015 -10000 0 -0.13 3 3
PTP1B/p130 Cas 0.012 0.095 0.21 4 -0.31 15 19
Crk/p130 Cas 0.023 0.097 0.22 2 -0.33 11 13
DOK1 0.008 0.093 0.21 11 -0.38 9 20
JAK2 0.001 0.13 0.21 1 -0.39 33 34
Jak2/Leptin Receptor/Leptin -0.019 0.1 -10000 0 -0.32 23 23
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PTPN1 0.003 0.095 0.21 5 -0.32 15 20
LYN 0.021 0.035 -10000 0 -0.43 2 2
CDH2 0.025 0.02 -10000 0 -0.43 1 1
SRC 0.024 0.052 -10000 0 -0.37 4 4
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
CAT1/PTP1B -0.015 0.16 0.28 37 -0.37 42 79
CAPN1 0.025 0.021 -10000 0 -0.43 1 1
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.027 0.085 -10000 0 -0.42 5 5
mol:H2O2 0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.02 0.099 -10000 0 -0.34 22 22
negative regulation of transcription 0.001 0.12 0.21 1 -0.38 33 34
FCGR2A 0.001 0.092 -10000 0 -0.43 20 20
FER 0.008 0.09 -10000 0 -0.42 21 21
alphaIIb/beta3 Integrin -0.01 0.11 -10000 0 -0.31 53 53
BLK -0.03 0.11 -10000 0 -0.43 29 29
Insulin Receptor/Insulin/Shc 0.039 0.031 -10000 0 -0.26 4 4
RHOA 0.027 0.005 -10000 0 -10000 0 0
LEPR 0.017 0.04 -10000 0 -0.42 3 3
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
p210 bcr-abl/Grb2 0.025 0.006 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.032 0.17 0.26 19 -0.42 45 64
PRL 0.003 0.02 -10000 0 -10000 0 0
SOCS3 -0.072 0.31 -10000 0 -1.3 33 33
SPRY2 0.024 0.028 -10000 0 -0.18 6 6
Insulin Receptor/Insulin/IRS1 0.04 0.03 -10000 0 -0.26 4 4
CSF1/CSF1R 0.005 0.11 0.22 2 -0.31 26 28
Ras protein signal transduction 0.018 0.12 0.51 24 -10000 0 24
IRS1 0.026 0.003 -10000 0 -10000 0 0
INS 0.005 0.042 -10000 0 -0.43 4 4
LEP 0.007 0.02 -10000 0 -0.13 4 4
STAT5B 0.009 0.1 0.2 5 -0.33 17 22
STAT5A 0.005 0.11 0.21 4 -0.34 18 22
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.095 0.2 3 -0.3 15 18
CSN2 -0.01 0.06 -10000 0 -0.56 2 2
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
LAT -0.015 0.14 -10000 0 -0.45 46 46
YBX1 0.026 0.031 -10000 0 -0.42 2 2
LCK -0.019 0.11 -10000 0 -0.43 30 30
SHC1 0.024 0.014 -10000 0 -10000 0 0
NOX4 -0.009 0.1 -10000 0 -0.42 23 23
EPO signaling 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
BCL2L1 0.06 0.08 0.36 1 -0.48 4 5
CRKL 0.052 0.081 0.23 38 -0.38 1 39
mol:DAG 0.028 0.049 -10000 0 -0.35 3 3
HRAS 0.049 0.086 0.27 36 -0.3 1 37
MAPK8 0.032 0.071 0.16 79 -0.24 12 91
RAP1A 0.047 0.08 0.24 39 -0.36 1 40
GAB1 0.051 0.083 0.28 23 -0.35 2 25
MAPK14 0.04 0.063 0.16 88 -0.26 2 90
EPO 0.019 0.03 -10000 0 -0.46 1 1
PLCG1 0.028 0.05 -10000 0 -0.36 3 3
EPOR/TRPC2/IP3 Receptors 0.029 0.013 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.024 0.075 -10000 0 -0.27 23 23
GAB1/SHC/GRB2/SOS1 0.07 0.073 0.26 21 -0.33 2 23
EPO/EPOR (dimer) 0.031 0.03 -10000 0 -0.34 1 1
IRS2 0.049 0.081 0.28 19 -0.35 2 21
STAT1 0.035 0.059 -10000 0 -0.35 5 5
STAT5B 0.03 0.053 -10000 0 -0.34 4 4
cell proliferation 0.028 0.095 0.2 100 -0.23 11 111
GAB1/SHIP/PIK3R1/SHP2/SHC 0.047 0.056 0.22 1 -0.33 3 4
TEC 0.047 0.085 0.24 36 -0.24 6 42
SOCS3 -0.029 0.12 -10000 0 -0.43 30 30
STAT1 (dimer) 0.035 0.058 -10000 0 -0.34 5 5
JAK2 0.03 0.014 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.057 0.06 -10000 0 -0.21 7 7
EPO/EPOR 0.031 0.03 -10000 0 -0.34 1 1
LYN 0.022 0.036 -10000 0 -0.44 2 2
TEC/VAV2 0.047 0.071 0.26 7 -0.23 6 13
elevation of cytosolic calcium ion concentration 0.029 0.013 -10000 0 -10000 0 0
SHC1 0.024 0.014 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.045 0.037 -10000 0 -0.29 2 2
mol:IP3 0.028 0.049 -10000 0 -0.35 3 3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.069 0.08 0.28 18 -0.33 3 21
SH2B3 0.03 0.016 -10000 0 -0.13 2 2
NFKB1 0.039 0.062 0.16 85 -0.26 2 87
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.05 -10000 0 -0.21 24 24
PTPN6 0.048 0.082 0.29 20 -0.39 1 21
TEC/VAV2/GRB2 0.055 0.072 0.27 7 -0.26 3 10
EPOR 0.029 0.013 -10000 0 -10000 0 0
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
mol:GDP 0.07 0.073 0.26 21 -0.33 2 23
SOS1 0.026 0.002 -10000 0 -10000 0 0
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
CRKL/CBL/C3G 0.059 0.065 0.27 7 -10000 0 7
VAV2 0.05 0.081 0.28 23 -0.38 1 24
CBL 0.05 0.079 0.28 21 -0.21 1 22
SHC/Grb2/SOS1 0.028 0.04 -10000 0 -0.36 1 1
STAT5A 0.025 0.074 -10000 0 -0.36 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.079 -10000 0 -0.39 9 9
LYN/PLCgamma2 0.029 0.051 -10000 0 -0.28 11 11
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK 0.046 0.096 0.27 24 -0.28 14 38
BCL2 0.056 0.12 0.36 1 -0.74 9 10
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.008 0.11 0.23 1 -0.47 17 18
BAG4 0.014 0.071 -10000 0 -0.43 13 13
BAD 0.005 0.058 0.24 14 -0.17 5 19
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 -0.002 0.099 -10000 0 -0.3 42 42
BAX 0.007 0.05 0.18 17 -0.15 7 24
EnzymeConsortium:3.1.4.12 0 0.03 0.065 5 -0.096 20 25
IKBKB -0.003 0.12 0.24 5 -0.44 17 22
MAP2K2 0.003 0.057 0.18 23 -0.2 1 24
MAP2K1 -0.001 0.051 0.18 9 -0.2 1 10
SMPD1 0.001 0.038 0.13 8 -0.13 10 18
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.001 0.12 0.3 7 -0.48 14 21
MAP2K4 -0.001 0.048 0.17 9 -0.17 5 14
protein ubiquitination -0.005 0.11 0.22 1 -0.47 16 17
EnzymeConsortium:2.7.1.37 -0.001 0.058 0.19 10 -0.2 2 12
response to UV 0 0.001 0.002 9 -0.002 3 12
RAF1 0 0.051 0.18 10 -0.19 2 12
CRADD 0.026 0.003 -10000 0 -10000 0 0
mol:ceramide 0.002 0.046 0.12 7 -0.14 19 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.008 -10000 0 -10000 0 0
MADD 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 0.001 0.048 0.16 8 -0.15 14 22
TRADD 0.025 0.02 -10000 0 -0.43 1 1
RELA/p50 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.005 0.055 0.18 10 -0.2 2 12
MAPK1 0.004 0.056 0.18 10 -0.23 2 12
p50/RELA/I-kappa-B-alpha 0.037 0.009 -10000 0 -10000 0 0
FADD -0.006 0.11 0.26 7 -0.48 15 22
KSR1 0 0.047 0.15 5 -0.18 4 9
MAPK8 -0.006 0.05 0.19 4 -0.19 10 14
TRAF2 0.025 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.007 0.11 0.23 2 -0.46 16 18
TNF R/SODD 0.023 0.063 -10000 0 -0.31 17 17
TNF -0.06 0.16 -10000 0 -0.27 151 151
CYCS 0.016 0.061 0.19 27 -0.14 3 30
IKBKG -0.007 0.11 0.22 1 -0.46 16 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.006 0.12 -10000 0 -0.44 22 22
RELA 0.025 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
AIFM1 0.008 0.052 0.16 26 -0.15 4 30
TNF/TNF R/SODD 0 0.12 -10000 0 -0.27 77 77
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.022 0.08 -10000 0 -0.85 3 3
NSMAF -0.002 0.12 0.24 6 -0.45 17 23
response to hydrogen peroxide 0 0.001 0.002 9 -0.002 3 12
BCL2 0.021 0.045 -10000 0 -0.43 5 5
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.009 -10000 0 -0.13 1 1
NFATC1 0.002 0.11 0.25 4 -0.36 24 28
NFATC2 -0.011 0.082 0.14 2 -0.23 40 42
NFATC3 0.007 0.059 -10000 0 -0.34 14 14
YWHAE 0.026 0.002 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.044 0.15 0.17 3 -0.41 48 51
Exportin 1/Ran/NUP214 0.051 0.012 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.064 0.17 -10000 0 -0.37 73 73
BCL2/BAX 0.029 0.034 -10000 0 -0.28 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.008 -10000 0 -0.089 1 1
CaM/Ca2+ 0.018 0.008 -10000 0 -0.089 1 1
BAX 0.021 0.01 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
BAD 0.025 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D -0.03 0.15 -10000 0 -0.4 46 46
Calcineurin A alpha-beta B1/BCL2 0.021 0.045 -10000 0 -0.43 5 5
FKBP8 0.025 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.03 0.14 0.39 46 -10000 0 46
KPNB1 0.026 0.003 -10000 0 -10000 0 0
KPNA2 0.025 0.009 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
SFN -0.023 0.11 -10000 0 -0.22 90 90
MAP3K8 0.016 0.047 -10000 0 -0.2 17 17
NFAT4/CK1 alpha 0.016 0.042 -10000 0 -0.19 13 13
MEF2D/NFAT1/Cbp/p300 0.019 0.1 -10000 0 -0.28 25 25
CABIN1 -0.044 0.15 0.17 3 -0.42 48 51
CALM1 0.025 0.009 -10000 0 -0.14 1 1
RAN 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 0.024 0.019 -10000 0 -10000 0 0
CAMK4 -0.094 0.19 -10000 0 -0.43 121 121
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.002 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.024 0.043 -10000 0 -0.3 3 3
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.014 0.071 -10000 0 -0.43 13 13
MAPK9 0.026 0.004 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.13 0.26 1 -0.35 37 38
PRKCH 0.025 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.035 0.032 -10000 0 -0.3 4 4
CASP3 0.025 0.009 -10000 0 -0.13 1 1
PIM1 0.024 0.017 -10000 0 -0.13 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.004 -10000 0 -10000 0 0
apoptosis 0.015 0.019 -10000 0 -0.31 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.046 -10000 0 -0.22 2 2
PRKCB -0.007 0.098 -10000 0 -0.22 68 68
PRKCE 0.022 0.034 -10000 0 -0.2 9 9
JNK2/NFAT4 -0.001 0.078 -10000 0 -0.31 14 14
BAD/BCL-XL 0.036 0.01 -10000 0 -10000 0 0
PRKCD 0.003 0.1 -10000 0 -0.43 26 26
NUP214 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
PRKCG -0.066 0.15 -10000 0 -0.26 159 159
PRKCQ 0.015 0.061 -10000 0 -0.43 9 9
FKBP38/BCL2 0.033 0.034 -10000 0 -0.3 5 5
EP300 0.022 0.04 -10000 0 -0.43 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.008 0.11 0.26 1 -0.35 25 26
CaM/Ca2+/FKBP38 0.032 0.012 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
CSNK1A1 0.012 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.044 0.12 -10000 0 -0.25 122 122
NFATc/ERK1 0.015 0.11 0.26 3 -0.35 23 26
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.067 0.17 -10000 0 -0.37 78 78
NR4A1 -0.001 0.099 0.22 3 -0.38 15 18
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
positive T cell selection 0.007 0.059 -10000 0 -0.34 14 14
NFAT1/CK1 alpha -0.003 0.06 -10000 0 -0.19 22 22
RCH1/ KPNB1 0.037 0.009 -10000 0 -10000 0 0
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
AKAP5 0.009 0.058 -10000 0 -0.16 45 45
MEF2D 0.024 0.012 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
NFATc/p38 alpha 0.014 0.11 0.26 3 -0.35 24 27
CREBBP 0.026 0.006 -10000 0 -10000 0 0
BCL2 0.021 0.045 -10000 0 -0.43 5 5
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.013 0.052 -10000 0 -0.33 8 8
CCNA2 -0.007 0.099 -10000 0 -0.24 63 63
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
JAK3 -0.009 0.1 -10000 0 -0.25 65 65
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.022 0.01 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.017 0.13 -10000 0 -0.42 21 21
SHC1 0.025 0.015 -10000 0 -10000 0 0
SP1 0.027 0.034 -10000 0 -0.33 4 4
IL2RA -0.015 0.093 -10000 0 -0.7 8 8
IL2RB -0.028 0.13 -10000 0 -0.43 39 39
SOS1 0.027 0.002 -10000 0 -10000 0 0
IL2RG 0.001 0.087 -10000 0 -0.22 52 52
G1/S transition of mitotic cell cycle 0.004 0.17 0.28 5 -0.48 40 45
PTPN11 0.026 0.004 -10000 0 -10000 0 0
CCND2 0.013 0.066 -10000 0 -0.7 4 4
LCK -0.019 0.11 -10000 0 -0.43 30 30
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL2 0.016 0.004 -10000 0 -10000 0 0
CDK6 0.004 0.083 -10000 0 -0.43 17 17
CCND3 -0.012 0.12 -10000 0 -0.47 6 6
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.009 0.027 -10000 0 -0.26 5 5
ADCY5 -0.014 0.046 -10000 0 -0.27 15 15
ADCY6 -0.007 0.017 -10000 0 -0.26 2 2
ADCY7 -0.007 0.017 -10000 0 -0.26 2 2
ADCY1 -0.03 0.069 -10000 0 -0.24 46 46
ADCY2 -0.012 0.04 -10000 0 -0.26 13 13
ADCY3 -0.007 0.017 -10000 0 -0.26 2 2
ADCY8 -0.031 0.075 -10000 0 -0.26 51 51
PRKCE 0.005 0.022 -10000 0 -0.3 2 2
ADCY9 -0.008 0.023 -10000 0 -0.26 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.001 0.076 0.18 22 -0.22 17 39
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.008 -10000 0 -0.13 1 1
Rac1/GDP 0.022 0.014 -10000 0 -10000 0 0
DOCK1 0.022 0.035 -10000 0 -0.43 3 3
ITGA4 -0.008 0.1 -10000 0 -0.26 61 61
RAC1 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.005 0.1 -10000 0 -0.28 56 56
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.033 0.067 -10000 0 -0.25 25 25
alpha4/beta7 Integrin/Paxillin 0.009 0.083 0.18 3 -0.24 42 45
lamellipodium assembly 0.023 0.049 0.27 1 -0.43 3 4
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.038 0.007 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
TLN1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.013 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.037 0.057 -10000 0 -0.21 22 22
cell adhesion 0.037 0.06 -10000 0 -0.22 22 22
CRKL/CBL 0.036 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.02 0.062 0.17 1 -0.24 22 23
ITGB1 0.023 0.012 -10000 0 -10000 0 0
ITGB7 0.001 0.091 -10000 0 -0.26 44 44
ARF6/GDP 0.024 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0 0.097 -10000 0 -0.23 67 67
p130Cas/Crk/Dock1 0.047 0.031 -10000 0 -0.26 4 4
VCAM1 -0.033 0.13 -10000 0 -0.3 85 85
alpha4/beta1 Integrin/Paxillin/Talin 0.038 0.061 -10000 0 -0.22 22 22
alpha4/beta1 Integrin/Paxillin/GIT1 0.039 0.061 -10000 0 -0.22 22 22
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
mol:GDP -0.038 0.06 0.22 22 -10000 0 22
CBL 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.038 0.061 -10000 0 -0.22 22 22
Rac1/GTP 0.023 0.054 0.28 1 -0.48 3 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.039 -10000 0 -0.25 5 5
alphaV beta3 Integrin 0.044 0.053 -10000 0 -0.26 14 14
PTK2 0.01 0.11 0.34 7 -0.37 16 23
IGF1R 0.026 0.004 -10000 0 -10000 0 0
PI4KB 0.026 0.004 -10000 0 -10000 0 0
MFGE8 0.023 0.035 -10000 0 -0.35 4 4
SRC 0.025 0.005 -10000 0 -10000 0 0
CDKN1B 0.005 0.08 -10000 0 -0.41 17 17
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
ILK 0.005 0.078 -10000 0 -0.38 18 18
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.002 0.072 0.18 1 -0.37 17 18
PTK2B 0 0.061 0.18 21 -0.22 14 35
alphaV/beta3 Integrin/JAM-A 0.04 0.069 0.2 1 -0.23 27 28
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.029 0.054 -10000 0 -0.26 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.057 0.048 -10000 0 -0.23 12 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.011 0.056 -10000 0 -0.28 6 6
alphaV/beta3 Integrin/Syndecan-1 0.035 0.071 -10000 0 -0.21 38 38
PI4KA 0.023 0.021 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.038 0.068 -10000 0 -0.21 26 26
PI4 Kinase 0.035 0.018 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
alphaV/beta3 Integrin/Osteopontin 0.014 0.099 -10000 0 -0.22 74 74
RPS6KB1 -0.021 0.062 0.38 3 -0.25 2 5
TLN1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.002 0.085 -10000 0 -0.39 16 16
GPR124 0.024 0.015 -10000 0 -0.13 4 4
MAPK1 -0.001 0.084 -10000 0 -0.39 16 16
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.031 0.086 -10000 0 -0.25 41 41
cell adhesion 0.028 0.056 -10000 0 -0.25 15 15
ANGPTL3 0.002 0.02 -10000 0 -0.13 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.028 -10000 0 -0.2 4 4
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
TGFBR2 0.024 0.016 -10000 0 -0.13 5 5
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
IGF1 0.012 0.076 -10000 0 -0.34 20 20
RAC1 0.023 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.03 0.059 -10000 0 -0.24 14 14
apoptosis 0.026 0.002 -10000 0 -10000 0 0
CD47 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.047 0.048 -10000 0 -0.26 12 12
VCL 0.022 0.032 -10000 0 -0.23 6 6
alphaV/beta3 Integrin/Del1 0.015 0.11 -10000 0 -0.28 59 59
CSF1 0.017 0.045 -10000 0 -0.43 5 5
PIK3C2A 0.003 0.084 -10000 0 -0.41 19 19
PI4 Kinase/Pyk2 0.006 0.069 -10000 0 -0.21 29 29
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.061 -10000 0 -0.23 15 15
FAK1/Vinculin 0.019 0.095 0.26 14 -0.32 14 28
alphaV beta3/Integrin/ppsTEM5 0.044 0.05 -10000 0 -0.24 14 14
RHOA 0.026 0.004 -10000 0 -10000 0 0
VTN 0.012 0.075 -10000 0 -0.35 19 19
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
FGF2 0.024 0.029 -10000 0 -0.43 2 2
F11R 0.01 0.024 -10000 0 -0.3 2 2
alphaV/beta3 Integrin/Lactadherin 0.045 0.054 -10000 0 -0.26 15 15
alphaV/beta3 Integrin/TGFBR2 0.045 0.051 -10000 0 -0.23 15 15
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.042 -10000 0 -0.24 5 5
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.044 0.045 -10000 0 -0.23 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.029 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.032 0.064 0.18 16 -0.22 15 31
SDC1 0.007 0.07 -10000 0 -0.19 43 43
VAV3 -0.008 0.074 0.18 26 -0.23 31 57
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.02 0.095 0.27 16 -0.31 14 30
cell migration 0.014 0.088 0.24 17 -0.31 11 28
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PI3K 0.05 0.067 -10000 0 -0.21 25 25
SPP1 -0.024 0.12 -10000 0 -0.26 87 87
KDR 0.021 0.039 -10000 0 -0.23 9 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.002 -10000 0 -10000 0 0
COL4A3 -0.011 0.1 -10000 0 -0.22 78 78
angiogenesis 0 0.097 -10000 0 -0.42 16 16
Rac1/GTP 0.003 0.068 -10000 0 -0.21 29 29
EDIL3 -0.024 0.14 -10000 0 -0.43 53 53
cell proliferation 0.03 0.06 -10000 0 -0.23 15 15
Wnt signaling

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
Noncanonical Wnts/FZD -0.007 0.087 -9999 0 -0.27 44 44
FZD6 0.015 0.04 -9999 0 -0.43 1 1
WNT6 0.003 0.087 -9999 0 -0.43 17 17
WNT4 0.008 0.057 -9999 0 -0.43 5 5
FZD3 0.023 0.035 -9999 0 -0.43 3 3
WNT5A 0.01 0.078 -9999 0 -0.33 22 22
WNT11 0.009 0.075 -9999 0 -0.43 13 13
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.036 0.064 -10000 0 -0.22 25 25
ER alpha/Gai/GDP/Gbeta gamma -0.023 0.12 -10000 0 -0.42 14 14
AKT1 -0.009 0.17 -10000 0 -0.67 30 30
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.005 0.18 -10000 0 -0.69 30 30
mol:Ca2+ -0.018 0.093 -10000 0 -0.38 23 23
IGF1R 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.011 0.076 -10000 0 -0.26 34 34
SHC1 0.024 0.014 -10000 0 -10000 0 0
apoptosis 0.008 0.16 0.64 30 -10000 0 30
RhoA/GTP 0.012 0.033 -10000 0 -0.2 9 9
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0 0.12 -10000 0 -0.4 14 14
regulation of stress fiber formation 0.003 0.066 0.39 2 -0.17 16 18
E2/ERA-ERB (dimer) 0.018 0.06 -10000 0 -0.24 23 23
KRAS 0.025 0.005 -10000 0 -10000 0 0
G13/GTP 0.024 0.041 -10000 0 -0.23 11 11
pseudopodium formation -0.003 0.066 0.17 16 -0.39 2 18
E2/ER alpha (dimer)/PELP1 0.025 0.045 -10000 0 -0.26 11 11
GRB2 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.022 0.04 -10000 0 -0.43 4 4
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
HRAS 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.004 0.13 0.28 2 -0.41 23 25
E2/ER beta (dimer) 0.012 0.045 -10000 0 -0.3 10 10
mol:GDP 0 0.068 -10000 0 -0.28 22 22
mol:NADP 0.004 0.13 0.28 2 -0.41 23 25
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 -0.019 0.097 -10000 0 -0.4 23 23
IGF-1R heterotetramer 0.026 0.004 -10000 0 -10000 0 0
PLCB1 -0.01 0.09 -10000 0 -0.38 20 20
PLCB2 -0.01 0.096 -10000 0 -0.4 22 22
IGF1 0.012 0.076 -10000 0 -0.34 20 20
mol:L-citrulline 0.004 0.13 0.28 2 -0.41 23 25
RHOA 0.026 0.004 -10000 0 -10000 0 0
Gai/GDP 0.008 0.11 -10000 0 -0.6 15 15
JNK cascade 0.011 0.045 -10000 0 -0.3 10 10
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
ESR2 0.015 0.065 -10000 0 -0.33 15 15
GNAQ 0.026 0.004 -10000 0 -10000 0 0
ESR1 0.011 0.07 -10000 0 -0.26 25 25
Gq family/GDP/Gbeta gamma -0.024 0.17 -10000 0 -0.6 27 27
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.029 0.071 -10000 0 -1.2 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.001 0.11 -10000 0 -0.4 13 13
GNAZ 0.026 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.009 0.049 -10000 0 -0.3 11 11
STRN 0.005 0.096 -10000 0 -0.42 25 25
GNAL -0.028 0.15 -10000 0 -0.42 61 61
PELP1 0.026 0.002 -10000 0 -10000 0 0
MAPK11 0.003 0.05 -10000 0 -0.26 18 18
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
HBEGF -0.019 0.14 0.35 21 -0.38 16 37
cAMP biosynthetic process -0.011 0.089 -10000 0 -0.21 78 78
SRC -0.025 0.12 -10000 0 -0.37 19 19
PI3K 0.038 0.007 -10000 0 -10000 0 0
GNB1 0.022 0.01 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.022 0.072 -10000 0 -0.27 19 19
SOS1 0.026 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.023 0.09 -10000 0 -0.31 21 21
Gs family/GTP -0.005 0.093 -10000 0 -0.22 78 78
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.022 -10000 0 -10000 0 0
vasodilation 0.005 0.12 0.28 2 -0.38 24 26
mol:DAG -0.019 0.097 -10000 0 -0.4 23 23
Gs family/GDP/Gbeta gamma -0.014 0.088 -10000 0 -0.29 24 24
MSN -0.003 0.069 0.18 16 -0.42 2 18
Gq family/GTP 0.001 0.089 -10000 0 -0.39 19 19
mol:PI-3-4-5-P3 -0.004 0.17 -10000 0 -0.66 30 30
NRAS 0.021 0.01 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.005 0.12 0.38 24 -0.28 2 26
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.073 -10000 0 -0.28 20 20
NOS3 0.003 0.14 0.34 1 -0.43 23 24
GNA11 0.017 0.06 -10000 0 -0.43 9 9
MAPKKK cascade -0.006 0.15 0.37 3 -0.46 32 35
E2/ER alpha (dimer)/PELP1/Src 0.003 0.12 0.26 9 -0.41 14 23
ruffle organization -0.003 0.066 0.17 16 -0.39 2 18
ROCK2 0.002 0.07 0.32 1 -0.28 2 3
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.43 12 12
GNA13 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.039 0.13 0.33 4 -0.37 24 28
MMP2 -0.014 0.13 0.28 12 -0.44 9 21
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
CDC42/GTP 0.026 0.051 -10000 0 -0.23 8 8
PLCG1 0.005 0.054 -10000 0 -0.24 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.01 -10000 0 -10000 0 0
G12/G13 0.032 0.015 -10000 0 -10000 0 0
cell migration 0.025 0.05 -10000 0 -0.23 8 8
S1PR5 -0.053 0.16 -10000 0 -0.3 124 124
S1PR4 0.019 0.042 -10000 0 -0.43 3 3
MAPK3 0.006 0.055 -10000 0 -0.24 8 8
MAPK1 0.007 0.05 -10000 0 -0.21 7 7
S1P/S1P5/Gi -0.019 0.1 -10000 0 -0.24 67 67
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
CDC42/GDP 0.016 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.016 0.094 -10000 0 -0.26 61 61
RHOA 0.045 0.087 0.22 81 -0.22 3 84
S1P/S1P4/Gi 0.011 0.058 -10000 0 -0.26 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.04 0.029 -10000 0 -0.23 3 3
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.014 0.071 -10000 0 -0.43 13 13
Caspase 8 (4 units) 0.031 0.06 -10000 0 -0.3 4 4
NEF -0.001 0.011 -10000 0 -10000 0 0
NFKBIA 0.02 0.029 -10000 0 -0.14 1 1
BIRC3 -0.005 0.1 -10000 0 -0.45 24 24
CYCS 0.007 0.048 0.18 9 -0.33 2 11
RIPK1 0.026 0.003 -10000 0 -10000 0 0
CD247 0.01 0.068 -10000 0 -0.25 25 25
MAP2K7 0.025 0.086 -10000 0 -0.61 4 4
protein ubiquitination 0.018 0.089 0.25 7 -0.36 7 14
CRADD 0.026 0.003 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.014 0.063 -10000 0 -0.28 18 18
BID 0.01 0.048 0.18 6 -0.22 11 17
NF-kappa-B/RelA/I kappa B alpha 0.038 0.069 -10000 0 -0.24 24 24
TRADD 0.025 0.02 -10000 0 -0.43 1 1
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
CFLAR 0.026 0.007 -10000 0 -10000 0 0
FADD 0.025 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.038 0.069 -10000 0 -0.25 24 24
MAPK8 0.019 0.083 -10000 0 -0.55 4 4
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.019 0.053 -10000 0 -0.43 7 7
TRAF2 0.026 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.013 0.047 -10000 0 -0.23 12 12
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.003 0.088 -10000 0 -0.42 10 10
CHUK 0.017 0.094 0.25 7 -0.37 8 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.061 0.054 -10000 0 -0.22 13 13
TCRz/NEF 0.009 0.052 -10000 0 -0.19 25 25
TNF -0.06 0.16 -10000 0 -0.26 151 151
FASLG -0.006 0.051 -10000 0 -0.26 8 8
NFKB1 0.021 0.027 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0.12 -10000 0 -0.27 77 77
CASP6 0.027 0.099 -10000 0 -0.59 7 7
CASP7 0.007 0.13 0.29 14 -0.47 26 40
RELA 0.019 0.03 -10000 0 -10000 0 0
CASP2 0.02 0.011 -10000 0 -10000 0 0
CASP3 0.007 0.13 0.29 14 -0.47 27 41
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
TNFR1A/BAG4 0.023 0.063 -10000 0 -0.31 17 17
CASP8 0.021 0.033 -10000 0 -0.43 1 1
CASP9 0.022 0.012 -10000 0 -0.13 1 1
MAP3K14 0.014 0.094 -10000 0 -0.4 9 9
APAF-1/Caspase 9 0.004 0.083 -10000 0 -0.32 22 22
BCL2 0.015 0.083 0.27 1 -0.51 4 5
Signaling events mediated by PRL

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
CCNE1 0.021 0.014 -10000 0 -0.13 2 2
mol:Halofuginone 0.003 0.009 -10000 0 -0.2 1 1
ITGA1 0.015 0.059 -10000 0 -0.22 23 23
CDKN1A -0.059 0.16 -10000 0 -0.37 95 95
PRL-3/alpha Tubulin 0.033 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.06 -10000 0 -0.32 21 21
AGT 0.006 0.092 -10000 0 -0.4 24 24
CCNA2 -0.038 0.079 -10000 0 -0.31 7 7
TUBA1B 0.026 0.004 -10000 0 -10000 0 0
EGR1 -0.027 0.095 -10000 0 -0.3 53 53
CDK2/Cyclin E1 -0.029 0.15 -10000 0 -0.37 56 56
MAPK3 0.012 0.008 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.032 0.015 -10000 0 -10000 0 0
MAPK1 0.012 0.008 -10000 0 -10000 0 0
PTP4A1 -0.025 0.074 -10000 0 -0.62 1 1
PTP4A3 0.023 0.013 -10000 0 -0.13 2 2
PTP4A2 0.022 0.01 -10000 0 -10000 0 0
ITGB1 0.01 0.01 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.006 0.036 -10000 0 -0.31 2 2
Rab GGTase beta/Rab GGTase alpha 0.032 0.016 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.008 0.079 -10000 0 -0.57 1 1
RABGGTA 0.026 0.004 -10000 0 -10000 0 0
BCAR1 -0.017 0.019 0.24 1 -0.32 1 2
RHOC -0.057 0.15 -10000 0 -0.36 95 95
RHOA 0.002 0.055 -10000 0 -0.32 10 10
cell motility -0.014 0.095 0.28 1 -0.28 33 34
PRL-1/alpha Tubulin -0.004 0.084 -10000 0 -0.58 1 1
PRL-3/alpha1 Integrin 0.027 0.042 -10000 0 -0.28 6 6
ROCK1 -0.017 0.093 0.28 1 -0.28 34 35
RABGGTB 0.022 0.01 -10000 0 -10000 0 0
CDK2 0.02 0.044 -10000 0 -0.43 4 4
mitosis -0.025 0.073 -10000 0 -0.61 1 1
ATF5 0.02 0.018 -10000 0 -0.13 5 5
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.005 -10000 0 -10000 0 0
SMARCC1 0.014 0.032 -10000 0 -0.69 1 1
REL 0.007 0.086 -10000 0 -0.32 28 28
HDAC7 -0.017 0.079 -10000 0 -0.29 16 16
JUN 0.019 0.023 -10000 0 -0.13 9 9
EP300 0.022 0.04 -10000 0 -0.43 4 4
KAT2B 0.025 0.008 -10000 0 -10000 0 0
KAT5 0.025 0.005 -10000 0 -10000 0 0
MAPK14 0.007 0.02 -10000 0 -0.3 1 1
FOXO1 0.024 0.022 -10000 0 -0.28 2 2
T-DHT/AR 0.002 0.092 -10000 0 -0.3 17 17
MAP2K6 0.021 0.024 -10000 0 -0.43 1 1
BRM/BAF57 0.036 0.01 -10000 0 -10000 0 0
MAP2K4 0.022 0.018 -10000 0 -0.15 1 1
SMARCA2 0.025 0.006 -10000 0 -10000 0 0
PDE9A 0.008 0.092 -10000 0 -0.92 3 3
NCOA2 -0.005 0.11 -10000 0 -0.43 34 34
CEBPA 0.015 0.049 -10000 0 -0.43 5 5
EHMT2 0.026 0.003 -10000 0 -10000 0 0
cell proliferation 0.001 0.11 0.36 9 -0.42 8 17
NR0B1 -0.041 0.15 -10000 0 -0.31 102 102
EGR1 -0.038 0.14 -10000 0 -0.27 111 111
RXRs/9cRA 0.019 0.085 -10000 0 -0.23 52 52
AR/RACK1/Src 0.001 0.074 0.22 1 -0.26 10 11
AR/GR -0.012 0.1 0.23 2 -0.24 69 71
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
PKN1 0.025 0.005 -10000 0 -10000 0 0
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0 0.052 -10000 0 -0.31 13 13
T-DHT/AR/TIF2/CARM1 -0.002 0.1 0.35 1 -0.37 20 21
SRC -0.013 0.044 0.2 8 -0.22 12 20
NR3C1 0.026 0.004 -10000 0 -10000 0 0
KLK3 -0.042 0.1 -10000 0 -0.45 3 3
APPBP2 0.022 0.014 -10000 0 -10000 0 0
TRIM24 0.02 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.003 0.073 0.21 8 -0.3 10 18
TMPRSS2 -0.066 0.29 -10000 0 -0.99 45 45
RXRG -0.027 0.14 -10000 0 -0.4 63 63
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.025 0.005 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.025 0.006 -10000 0 -10000 0 0
NR2C2 0.018 0.06 -10000 0 -0.43 9 9
KLK2 -0.02 0.1 0.44 1 -0.39 14 15
AR -0.029 0.099 0.13 3 -0.26 73 76
SENP1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
MDM2 0.026 0.004 -10000 0 -10000 0 0
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 0.015 0.065 -10000 0 -0.43 10 10
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.009 0.048 -10000 0 -0.13 57 57
T-DHT/AR/RACK1/Src 0.003 0.079 0.27 5 -0.27 10 15
positive regulation of transcription 0.015 0.064 -10000 0 -0.43 10 10
DNAJA1 0.022 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.008 -10000 0 -10000 0 0
NCOA1 0.03 0.011 -10000 0 -10000 0 0
SPDEF -0.005 0.1 -10000 0 -0.28 51 51
T-DHT/AR/TIF2 -0.003 0.1 0.23 3 -0.37 21 24
T-DHT/AR/Hsp90 -0.004 0.072 0.22 6 -0.3 11 17
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
NR2C1 0.026 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.04 -10000 0 -0.24 13 13
SIRT1 0.025 0.005 -10000 0 -10000 0 0
ZMIZ2 0.023 0.009 -10000 0 -10000 0 0
POU2F1 0.021 0.042 -10000 0 -0.43 1 1
T-DHT/AR/DAX-1 -0.032 0.1 0.22 7 -0.25 55 62
CREBBP 0.026 0.003 -10000 0 -10000 0 0
SMARCE1 0.026 0.003 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.02 0.076 -10000 0 -0.3 26 26
ATM 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
PRKDC 0.025 0.005 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
UBE2L3 0.026 0.004 -10000 0 -10000 0 0
FANCD2 0.016 0.029 -10000 0 -0.29 4 4
protein ubiquitination 0.04 0.07 -10000 0 -0.22 27 27
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.046 0.018 -10000 0 -10000 0 0
MRE11A 0.025 0.006 -10000 0 -10000 0 0
DNA-PK 0.05 0.014 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.024 0.062 -10000 0 -0.48 4 4
FANCF 0.025 0.005 -10000 0 -10000 0 0
BRCA1 0.025 0.012 -10000 0 -0.13 3 3
CCNE1 0.021 0.014 -10000 0 -0.13 2 2
CDK2/Cyclin E1 0.027 0.037 -10000 0 -0.28 5 5
FANCG 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.02 0.076 -10000 0 -0.3 27 27
FANCE 0.026 0.003 -10000 0 -10000 0 0
FANCC 0.024 0.022 -10000 0 -0.43 1 1
NBN 0.024 0.007 -10000 0 -10000 0 0
FANCA 0.009 0.069 -10000 0 -0.2 38 38
DNA repair 0.01 0.09 0.27 9 -0.4 7 16
BRCA1/BARD1/ubiquitin 0.02 0.076 -10000 0 -0.3 27 27
BARD1/DNA-PK 0.049 0.065 -10000 0 -0.24 24 24
FANCL 0.026 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.019 0.075 0.3 26 -10000 0 26
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.058 -10000 0 -0.38 2 2
BRCA1/BACH1/BARD1/TopBP1 0.035 0.072 -10000 0 -0.26 27 27
BRCA1/BARD1/P53 0.043 0.083 -10000 0 -0.25 37 37
BARD1/CSTF1/BRCA1 0.035 0.069 -10000 0 -0.26 26 26
BRCA1/BACH1 0.025 0.012 -10000 0 -0.13 3 3
BARD1 0.002 0.1 -10000 0 -0.41 28 28
PCNA 0.025 0.011 -10000 0 -0.13 2 2
BRCA1/BARD1/UbcH5C 0.035 0.069 -10000 0 -0.25 27 27
BRCA1/BARD1/UbcH7 0.036 0.068 -10000 0 -0.25 26 26
BRCA1/BARD1/RAD51/PCNA 0.04 0.085 -10000 0 -0.24 39 39
BARD1/DNA-PK/P53 0.051 0.08 -10000 0 -0.23 34 34
BRCA1/BARD1/Ubiquitin 0.02 0.076 -10000 0 -0.3 27 27
BRCA1/BARD1/CTIP 0.028 0.06 0.21 1 -0.24 24 25
FA complex 0.024 0.037 -10000 0 -10000 0 0
BARD1/EWS 0.021 0.074 -10000 0 -0.3 25 25
RBBP8 0.013 0.005 -10000 0 -10000 0 0
TP53 0.014 0.072 -10000 0 -0.41 14 14
TOPBP1 0.025 0.02 -10000 0 -0.43 1 1
G1/S transition of mitotic cell cycle -0.041 0.082 0.24 37 -10000 0 37
BRCA1/BARD1 0.045 0.073 -10000 0 -0.22 27 27
CSTF1 0.025 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.003 0.071 -10000 0 -0.3 26 26
CDK2 0.02 0.044 -10000 0 -0.43 4 4
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.001 0.085 -10000 0 -0.2 61 61
RAD50 0.026 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.02 0.076 -10000 0 -0.3 27 27
EWSR1 0.026 0.004 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.021 0.01 -9999 0 -10000 0 0
SPHK1 0.004 0.086 -9999 0 -0.43 17 17
GNAI2 0.025 0.005 -9999 0 -10000 0 0
mol:S1P 0 0.064 -9999 0 -0.34 16 16
GNAO1 0.022 0.045 -9999 0 -0.43 5 5
mol:Sphinganine-1-P 0.003 0.041 -9999 0 -0.3 7 7
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.022 0.074 -9999 0 -0.28 16 16
GNAI3 0.021 0.01 -9999 0 -10000 0 0
G12/G13 0.032 0.015 -9999 0 -10000 0 0
S1PR3 0.005 0.075 -9999 0 -0.43 11 11
S1PR2 0.022 0.036 -9999 0 -0.43 3 3
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.014 0.062 -9999 0 -0.29 17 17
S1PR5 -0.053 0.16 -9999 0 -0.3 124 124
S1PR4 0.019 0.042 -9999 0 -0.43 3 3
GNAI1 0.019 0.036 -9999 0 -0.43 3 3
S1P/S1P5/G12 -0.016 0.11 -9999 0 -0.26 71 71
S1P/S1P3/Gq -0.006 0.11 -9999 0 -0.38 29 29
S1P/S1P4/Gi 0.003 0.084 -9999 0 -0.28 17 17
GNAQ 0.026 0.004 -9999 0 -10000 0 0
GNAZ 0.026 0.004 -9999 0 -10000 0 0
GNA14 0.009 0.081 -9999 0 -0.34 23 23
GNA15 0.013 0.07 -9999 0 -0.43 12 12
GNA12 0.022 0.009 -9999 0 -10000 0 0
GNA13 0.025 0.005 -9999 0 -10000 0 0
GNA11 0.017 0.06 -9999 0 -0.43 9 9
ABCC1 0.025 0.014 -9999 0 -0.13 4 4
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.029 0.023 -10000 0 -0.3 2 2
VEGFR1 homodimer/NRP1 0.012 0.02 -10000 0 -0.3 2 2
mol:DAG -0.014 0.074 -10000 0 -0.23 49 49
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.027 -10000 0 -0.27 2 2
CaM/Ca2+ 0 0.076 -10000 0 -0.22 49 49
HIF1A 0.03 0.021 -10000 0 -0.42 1 1
GAB1 0.025 0.02 -10000 0 -0.43 1 1
AKT1 -0.015 0.082 -10000 0 -0.49 1 1
PLCG1 -0.014 0.075 -10000 0 -0.23 49 49
NOS3 -0.009 0.07 -10000 0 -0.3 3 3
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.005 0.081 0.28 1 -0.29 3 4
FLT1 0.017 0.024 -10000 0 -0.35 2 2
PGF -0.034 0.14 -10000 0 -0.31 90 90
VEGFR1 homodimer/NRP2/VEGFR121 0.042 0.035 -10000 0 -0.23 6 6
CALM1 0.025 0.009 -10000 0 -0.13 1 1
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
eNOS/Hsp90 0.021 0.089 0.28 3 -0.29 2 5
endothelial cell proliferation -0.026 0.097 0.27 1 -0.32 15 16
mol:Ca2+ -0.014 0.074 -10000 0 -0.23 49 49
MAPK3 -0.027 0.061 0.18 2 -0.26 1 3
MAPK1 -0.027 0.061 0.17 3 -0.26 1 4
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
PLGF homodimer -0.034 0.14 -10000 0 -0.31 90 90
PRKACA 0.025 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.006 0.051 -10000 0 -0.43 2 2
VEGFA homodimer 0.019 0.032 -10000 0 -0.13 22 22
VEGFR1 homodimer/VEGFA homodimer 0.027 0.03 -10000 0 -0.3 2 2
platelet activating factor biosynthetic process -0.027 0.059 -10000 0 -0.26 1 1
PI3K 0.028 0.088 -10000 0 -0.22 55 55
PRKCA -0.027 0.064 0.18 3 -0.27 1 4
PRKCB -0.038 0.074 0.18 3 -0.28 11 14
VEGFR1 homodimer/PLGF homodimer -0.007 0.091 -10000 0 -0.26 57 57
VEGFA 0.019 0.032 -10000 0 -0.13 22 22
VEGFB 0.025 0.005 -10000 0 -10000 0 0
mol:IP3 -0.014 0.074 -10000 0 -0.23 49 49
RASA1 0.014 0.021 -10000 0 -0.32 1 1
NRP2 0.021 0.046 -10000 0 -0.32 8 8
VEGFR1 homodimer 0.017 0.024 -10000 0 -0.35 2 2
VEGFB homodimer 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
eNOS/Caveolin-1 0.002 0.076 -10000 0 -0.3 1 1
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.026 0.087 -10000 0 -0.22 55 55
mol:L-citrulline 0.005 0.081 0.28 1 -0.29 3 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.055 0.031 -10000 0 -0.26 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.044 0.021 -10000 0 -0.23 1 1
CD2AP 0.026 0.002 -10000 0 -10000 0 0
PI3K/GAB1 0.036 0.089 -10000 0 -0.23 1 1
PDPK1 -0.012 0.075 -10000 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.025 -10000 0 -0.27 2 2
mol:NADP 0.005 0.081 0.28 1 -0.29 3 4
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.053 0.03 -10000 0 -0.26 2 2
VEGFR1 homodimer/NRP2 0.027 0.034 -10000 0 -0.25 6 6
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.012 0.07 -10000 0 -0.26 25 25
positive regulation of NF-kappaB transcription factor activity 0.022 0.06 -10000 0 -0.3 13 13
MAP2K4 0.016 0.048 0.21 1 -0.24 1 2
IKBKB 0.025 0.005 -10000 0 -10000 0 0
TNFRSF10B 0.022 0.036 -10000 0 -0.35 4 4
TNFRSF10A 0 0.098 -10000 0 -0.43 24 24
SMPD1 0.007 0.031 -10000 0 -0.18 13 13
IKBKG 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.019 0.038 -10000 0 -0.17 15 15
TRAIL/TRAILR2 0.024 0.061 -10000 0 -0.32 13 13
TRAIL/TRAILR3 0.015 0.08 -10000 0 -0.32 22 22
TRAIL/TRAILR1 0.008 0.089 -10000 0 -0.29 38 38
TRAIL/TRAILR4 0.022 0.06 -10000 0 -0.3 13 13
TRAIL/TRAILR1/DAP3/GTP 0.027 0.073 -10000 0 -0.23 35 35
IKK complex 0.014 0.044 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.003 -10000 0 -10000 0 0
MAPK3 0.004 0.048 -10000 0 -0.3 11 11
MAP3K1 0.02 0.049 -10000 0 -0.25 2 2
TRAILR4 (trimer) 0.019 0.038 -10000 0 -0.17 15 15
TRADD 0.025 0.02 -10000 0 -0.43 1 1
TRAILR1 (trimer) 0 0.098 -10000 0 -0.43 24 24
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.011 0.059 -10000 0 -0.21 31 31
CFLAR 0.026 0.007 -10000 0 -10000 0 0
MAPK1 0.004 0.048 -10000 0 -0.3 11 11
TRAIL/TRAILR1/FADD/TRADD/RIP 0.05 0.077 -10000 0 -0.22 33 33
mol:ceramide 0.007 0.031 -10000 0 -0.18 13 13
FADD 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.059 0.2 2 -0.28 4 6
TRAF2 0.026 0.005 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.009 0.074 -10000 0 -0.25 31 31
CHUK 0.025 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.028 0.078 -10000 0 -0.26 33 33
DAP3 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.001 0.062 0.16 17 -0.27 11 28
JNK cascade 0.022 0.06 -10000 0 -0.3 13 13
TRAIL (trimer) 0.012 0.07 -10000 0 -0.26 25 25
TNFRSF10C 0.009 0.074 -10000 0 -0.25 31 31
TRAIL/TRAILR1/DAP3/GTP/FADD 0.037 0.072 -10000 0 -0.22 33 33
TRAIL/TRAILR2/FADD 0.042 0.051 -10000 0 -0.26 13 13
cell death 0.007 0.031 -10000 0 -0.18 13 13
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.04 -10000 0 -0.22 13 13
TRAILR2 (trimer) 0.022 0.036 -10000 0 -0.35 4 4
CASP8 0.013 0.043 -10000 0 -0.77 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.063 0.053 -10000 0 -0.22 13 13
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 0.034 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.021 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.021 0.069 -10000 0 -0.19 62 62
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.04 -10000 0 -0.43 4 4
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
MAP3K12 0.026 0.004 -10000 0 -10000 0 0
FGR 0.021 0.015 -10000 0 -0.13 3 3
p38 alpha/TAB1 -0.034 0.071 -10000 0 -0.3 18 18
PRKG1 -0.009 0.12 -10000 0 -0.38 43 43
DUSP8 0.02 0.039 -10000 0 -0.43 3 3
PGK/cGMP/p38 alpha -0.011 0.11 -10000 0 -0.31 25 25
apoptosis -0.033 0.068 -10000 0 -0.28 18 18
RAL/GTP 0.031 0.012 -10000 0 -10000 0 0
LYN 0.021 0.035 -10000 0 -0.43 2 2
DUSP1 0.008 0.077 -10000 0 -0.25 32 32
PAK1 0.008 0.061 -10000 0 -0.43 5 5
SRC 0.025 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.056 0.026 -10000 0 -10000 0 0
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.026 0.016 -10000 0 -10000 0 0
MAPK11 0 0.13 0.28 26 -0.33 23 49
BLK -0.03 0.11 -10000 0 -0.43 29 29
HCK 0.014 0.063 -10000 0 -0.27 19 19
MAP2K3 0.026 0.01 -10000 0 -10000 0 0
DUSP16 0.025 0.005 -10000 0 -10000 0 0
DUSP10 0.015 0.065 -10000 0 -0.43 10 10
TRAF6/MEKK3 0.031 0.015 -10000 0 -0.23 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.11 0.24 26 -0.35 14 40
positive regulation of innate immune response 0.003 0.14 0.3 27 -0.38 21 48
LCK -0.019 0.11 -10000 0 -0.43 30 30
p38alpha-beta/MKP7 0.013 0.14 0.31 25 -0.37 18 43
p38alpha-beta/MKP5 0.006 0.14 0.29 23 -0.36 25 48
PGK/cGMP -0.005 0.082 -10000 0 -0.3 36 36
PAK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.007 0.15 0.31 24 -0.38 22 46
CDC42 0.022 0.01 -10000 0 -10000 0 0
RALB 0.026 0.002 -10000 0 -10000 0 0
RALA 0.023 0.009 -10000 0 -10000 0 0
PAK3 -0.055 0.16 -10000 0 -0.43 80 80
Class I PI3K signaling events

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
ARF5/GTP 0 0.04 0.29 2 -10000 0 2
DAPP1 -0.033 0.14 0.26 6 -0.4 38 44
Src family/SYK family/BLNK-LAT/BTK-ITK -0.074 0.22 0.32 7 -0.52 62 69
mol:DAG -0.02 0.099 0.29 13 -0.26 23 36
HRAS 0.025 0.008 -10000 0 -10000 0 0
RAP1A 0.022 0.011 -10000 0 -10000 0 0
ARF5/GDP 0.021 0.06 0.2 3 -0.31 6 9
PLCG2 0.018 0.055 -10000 0 -0.29 13 13
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.051 0.21 17 -10000 0 17
ARF1/GTP 0.003 0.035 0.24 4 -10000 0 4
RHOA 0.026 0.004 -10000 0 -10000 0 0
YES1 0.022 0.04 -10000 0 -0.43 4 4
RAP1A/GTP -0.004 0.041 0.17 18 -10000 0 18
ADAP1 -0.006 0.046 0.25 4 -0.21 5 9
ARAP3 0 0.05 0.21 17 -10000 0 17
INPPL1 0.025 0.005 -10000 0 -10000 0 0
PREX1 0.016 0.063 -10000 0 -0.43 10 10
ARHGEF6 0.023 0.04 -10000 0 -0.43 4 4
ARHGEF7 0.025 0.005 -10000 0 -10000 0 0
ARF1 0.026 0.004 -10000 0 -10000 0 0
NRAS 0.022 0.011 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
FGR 0.021 0.015 -10000 0 -0.13 3 3
mol:Ca2+ -0.01 0.059 0.23 11 -0.14 14 25
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.026 0.004 -10000 0 -10000 0 0
ZAP70 -0.004 0.098 -10000 0 -0.43 22 22
mol:IP3 -0.017 0.076 0.26 12 -0.2 18 30
LYN 0.021 0.035 -10000 0 -0.43 2 2
ARF1/GDP 0.033 0.07 0.21 4 -0.3 9 13
RhoA/GDP 0.037 0.06 0.24 14 -10000 0 14
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.26 2 2
BLNK -0.021 0.13 -10000 0 -0.43 49 49
actin cytoskeleton reorganization 0.022 0.1 0.28 25 -0.38 9 34
SRC 0.025 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.009 0.02 -10000 0 -0.26 3 3
RAC1 0.023 0.009 -10000 0 -10000 0 0
PTEN 0.022 0.013 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.043 0.23 6 -10000 0 6
RhoA/GTP 0.005 0.054 0.21 16 -10000 0 16
Src family/SYK family/BLNK-LAT -0.067 0.17 -10000 0 -0.43 62 62
BLK -0.03 0.11 -10000 0 -0.43 29 29
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
CYTH1 -0.004 0.043 0.24 4 -10000 0 4
HCK 0.014 0.063 -10000 0 -0.27 19 19
CYTH3 -0.003 0.041 0.28 3 -10000 0 3
CYTH2 -0.004 0.043 0.27 4 -10000 0 4
KRAS 0.026 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.008 0.08 0.21 1 -0.4 16 17
SGK1 -0.001 0.1 -10000 0 -0.38 30 30
INPP5D 0.022 0.037 -10000 0 -0.28 6 6
mol:GDP 0.022 0.072 0.2 11 -0.31 9 20
SOS1 0.026 0.002 -10000 0 -10000 0 0
SYK 0.009 0.083 -10000 0 -0.35 23 23
ARF6/GDP 0.033 0.064 0.26 17 -0.22 1 18
mol:PI-3-4-5-P3 -0.011 0.027 0.19 6 -10000 0 6
ARAP3/RAP1A/GTP -0.004 0.041 0.17 18 -10000 0 18
VAV1 0.005 0.09 -10000 0 -0.34 29 29
mol:PI-3-4-P2 0.01 0.026 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.032 0.04 0.19 8 -10000 0 8
PLEKHA1 -0.009 0.021 -10000 0 -0.26 3 3
Rac1/GDP 0.024 0.063 0.2 3 -0.3 7 10
LAT 0.003 0.1 -10000 0 -0.43 26 26
Rac1/GTP 0.019 0.075 -10000 0 -0.42 9 9
ITK -0.022 0.064 0.26 4 -0.21 19 23
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.035 0.12 0.35 8 -0.37 25 33
LCK -0.019 0.11 -10000 0 -0.43 30 30
BTK -0.01 0.055 0.27 4 -0.21 2 6
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.37 -9999 0 -1.1 58 58
RAD9A 0.025 0.005 -9999 0 -10000 0 0
AP1 -0.016 0.1 -9999 0 -0.28 56 56
IFNAR2 0.02 0.018 -9999 0 -10000 0 0
AKT1 0.004 0.035 -9999 0 -0.24 1 1
ER alpha/Oestrogen 0.005 0.05 -9999 0 -0.25 15 15
NFX1/SIN3/HDAC complex -0.004 0.072 -9999 0 -0.23 10 10
EGF -0.014 0.11 -9999 0 -0.41 35 35
SMG5 0.025 0.005 -9999 0 -10000 0 0
SMG6 0.026 0.002 -9999 0 -10000 0 0
SP3/HDAC2 0.03 0.027 -9999 0 -10000 0 0
TERT/c-Abl -0.099 0.34 -9999 0 -1 59 59
SAP18 0.025 0.006 -9999 0 -10000 0 0
MRN complex 0.046 0.018 -9999 0 -10000 0 0
WT1 0 0.046 -9999 0 -0.16 5 5
WRN 0.023 0.035 -9999 0 -0.43 3 3
SP1 0.019 0.022 -9999 0 -10000 0 0
SP3 0.022 0.015 -9999 0 -10000 0 0
TERF2IP 0.026 0.003 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.072 0.31 -9999 0 -0.9 58 58
Mad/Max 0.03 0.023 -9999 0 -10000 0 0
TERT -0.13 0.39 -9999 0 -1.2 58 58
CCND1 -0.11 0.34 -9999 0 -0.99 63 63
MAX 0.021 0.015 -9999 0 -10000 0 0
RBBP7 0.025 0.004 -9999 0 -10000 0 0
RBBP4 0.021 0.022 -9999 0 -0.43 1 1
TERF2 0.021 0.006 -9999 0 -10000 0 0
PTGES3 0.026 0.003 -9999 0 -10000 0 0
SIN3A 0.025 0.003 -9999 0 -10000 0 0
Telomerase/911 0.031 0.056 -9999 0 -0.32 3 3
CDKN1B 0.009 0.024 -9999 0 -10000 0 0
RAD1 0.026 0.003 -9999 0 -10000 0 0
XRCC5 0.026 0.003 -9999 0 -10000 0 0
XRCC6 0.026 0.004 -9999 0 -10000 0 0
SAP30 0.025 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0.036 0.007 -9999 0 -10000 0 0
UBE3A 0.022 0.014 -9999 0 -10000 0 0
JUN 0.015 0.025 -9999 0 -0.13 9 9
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.015 -9999 0 -10000 0 0
FOS -0.035 0.14 -9999 0 -0.37 60 60
IFN-gamma/IRF1 0.025 0.035 -9999 0 -10000 0 0
PARP2 0.026 0.004 -9999 0 -10000 0 0
BLM -0.008 0.1 -9999 0 -0.25 62 62
Telomerase -0.016 0.098 -9999 0 -0.33 32 32
IRF1 0.017 0.036 -9999 0 -10000 0 0
ESR1 0.01 0.07 -9999 0 -0.26 25 25
KU/TER 0.038 0.007 -9999 0 -10000 0 0
ATM/TRF2 0.037 0.009 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.072 -9999 0 -0.31 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.074 -9999 0 -0.31 4 4
HDAC1 0.022 0.01 -9999 0 -10000 0 0
HDAC2 0.019 0.022 -9999 0 -10000 0 0
ATM 0.01 0.002 -9999 0 -10000 0 0
SMAD3 0.012 0.016 -9999 0 -0.3 1 1
ABL1 0.025 0.005 -9999 0 -10000 0 0
MXD1 0.022 0.015 -9999 0 -10000 0 0
MRE11A 0.025 0.006 -9999 0 -10000 0 0
HUS1 0.023 0.009 -9999 0 -10000 0 0
RPS6KB1 0.025 0.005 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.086 0.34 -9999 0 -1 54 54
NR2F2 0.017 0.061 -9999 0 -0.22 24 24
MAPK3 -0.014 0.01 -9999 0 -10000 0 0
MAPK1 -0.013 0.009 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.022 -9999 0 -0.42 1 1
NFKB1 0.026 0.004 -9999 0 -10000 0 0
HNRNPC 0.026 0.004 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.002 -9999 0 -10000 0 0
NBN 0.024 0.007 -9999 0 -10000 0 0
EGFR -0.02 0.12 -9999 0 -0.4 46 46
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.025 0.12 -9999 0 -0.32 69 69
MYC 0.001 0.088 -9999 0 -0.4 22 22
IL2 0.007 0.024 -9999 0 -10000 0 0
KU 0.038 0.007 -9999 0 -10000 0 0
RAD50 0.026 0.003 -9999 0 -10000 0 0
HSP90AA1 0.025 0.005 -9999 0 -10000 0 0
TGFB1 0.021 0.022 -9999 0 -0.42 1 1
TRF2/BLM 0.012 0.072 -9999 0 -0.28 24 24
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.09 0.35 -9999 0 -1 58 58
SP1/HDAC2 0.029 0.032 -9999 0 -10000 0 0
PINX1 0.025 0.005 -9999 0 -10000 0 0
Telomerase/EST1A -0.071 0.31 -9999 0 -0.9 58 58
Smad3/Myc 0.01 0.058 -9999 0 -0.27 19 19
911 complex 0.044 0.021 -9999 0 -10000 0 0
IFNG 0.015 0.021 -9999 0 -0.14 2 2
Telomerase/PinX1 -0.073 0.31 -9999 0 -0.9 58 58
Telomerase/AKT1/mTOR/p70S6K -0.01 0.1 -9999 0 -0.48 8 8
SIN3B 0.025 0.006 -9999 0 -10000 0 0
YWHAE 0.026 0.002 -9999 0 -10000 0 0
Telomerase/EST1B -0.072 0.31 -9999 0 -0.9 58 58
response to DNA damage stimulus 0.006 0.009 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.065 0.026 -9999 0 -10000 0 0
TRF2/WRN 0.033 0.025 -9999 0 -0.28 3 3
Telomerase/hnRNP C1/C2 -0.07 0.31 -9999 0 -0.9 58 58
E2F1 0.009 0.058 -9999 0 -0.21 24 24
ZNFX1 0.025 0.005 -9999 0 -10000 0 0
PIF1 -0.01 0.11 -9999 0 -0.27 61 61
NCL 0.026 0.004 -9999 0 -10000 0 0
DKC1 0.026 0.003 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.026 0.056 -10000 0 -10000 0 0
epithelial cell differentiation -0.014 0.086 -10000 0 -0.38 5 5
ITCH 0.03 0.013 -10000 0 -10000 0 0
WWP1 0.017 0.063 -10000 0 -10000 0 0
FYN 0.025 0.005 -10000 0 -10000 0 0
EGFR -0.016 0.12 -10000 0 -0.4 46 46
PRL -0.011 0.016 -10000 0 -0.13 2 2
neuron projection morphogenesis -0.019 0.11 0.28 18 -0.4 2 20
PTPRZ1 0.016 0.046 -10000 0 -0.43 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.008 0.11 -10000 0 -0.34 5 5
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.1 -10000 0 -0.32 14 14
ADAM17 0.025 0.046 -10000 0 -0.42 5 5
ErbB4/ErbB4 0.006 0.051 -10000 0 -0.36 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.013 0.082 -10000 0 -0.34 10 10
NCOR1 0.024 0.028 -10000 0 -0.43 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.027 0.1 -10000 0 -0.34 8 8
GRIN2B -0.068 0.13 0.24 10 -0.36 40 50
ErbB4/ErbB2/betacellulin -0.001 0.096 -10000 0 -0.34 12 12
STAT1 0.021 0.028 -10000 0 -0.13 16 16
HBEGF 0.023 0.022 -10000 0 -0.13 10 10
PRLR 0.006 0.088 -10000 0 -0.32 30 30
E4ICDs/ETO2 0.022 0.065 -10000 0 -0.35 3 3
axon guidance -0.024 0.079 -10000 0 -0.38 8 8
NEDD4 0.025 0.041 -10000 0 -0.22 10 10
Prolactin receptor/Prolactin receptor/Prolactin 0.016 0.065 -10000 0 -0.31 18 18
CBFA2T3 0.02 0.053 -10000 0 -0.43 7 7
ErbB4/ErbB2/HBEGF 0.027 0.052 -10000 0 -0.28 3 3
MAPK3 -0.017 0.11 0.27 12 -0.41 2 14
STAT1 (dimer) 0.026 0.059 -10000 0 -0.32 1 1
MAPK1 -0.017 0.11 0.27 12 -0.41 2 14
JAK2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.037 0.1 -10000 0 -0.34 8 8
NRG1 -0.061 0.13 -10000 0 -0.31 101 101
NRG3 0.001 0.1 -10000 0 -0.43 27 27
NRG2 0.025 0.02 -10000 0 -0.43 1 1
NRG4 0.001 0.079 -10000 0 -0.43 12 12
heart development -0.024 0.079 -10000 0 -0.38 8 8
neural crest cell migration -0.036 0.099 -10000 0 -0.33 8 8
ERBB2 0.01 0.036 -10000 0 -0.3 6 6
WWOX/E4ICDs 0.025 0.057 -10000 0 -0.32 1 1
SHC1 0.024 0.014 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.004 0.1 -10000 0 -0.34 17 17
apoptosis -0.001 0.11 0.37 32 -10000 0 32
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.026 0.057 -10000 0 -0.37 1 1
ErbB4/ErbB2/epiregulin 0.025 0.056 -10000 0 -0.31 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.005 0.1 -10000 0 -0.38 10 10
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.045 0.076 -10000 0 -0.32 1 1
MDM2 0.01 0.055 0.25 4 -0.32 1 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.1 -10000 0 -0.29 12 12
STAT5A -0.028 0.084 -10000 0 -0.4 7 7
ErbB4/EGFR/neuregulin 1 beta -0.045 0.12 -10000 0 -0.35 28 28
DLG4 0.023 0.021 -10000 0 -0.13 9 9
GRB2/SHC 0.036 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.022 0.056 -10000 0 -0.5 1 1
STAT5A (dimer) -0.007 0.097 -10000 0 -0.4 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.012 0.083 -10000 0 -0.38 6 6
LRIG1 0.015 0.069 -10000 0 -0.43 12 12
EREG 0.008 0.036 -10000 0 -0.13 24 24
BTC -0.04 0.14 -10000 0 -0.33 87 87
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.075 -10000 0 -0.38 8 8
ERBB4 0.006 0.051 -10000 0 -0.36 1 1
STAT5B 0.026 0.003 -10000 0 -10000 0 0
YAP1 -0.015 0.13 -10000 0 -0.55 27 27
GRB2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.021 0.067 -10000 0 -0.31 5 5
glial cell differentiation -0.021 0.056 0.5 1 -10000 0 1
WWOX 0.026 0.003 -10000 0 -10000 0 0
cell proliferation -0.071 0.14 -10000 0 -0.47 19 19
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.004 0.15 0.24 5 -0.38 21 26
CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
AKT1 0.025 0.005 -10000 0 -10000 0 0
AKT2 0.022 0.01 -10000 0 -10000 0 0
STXBP4 0.025 0.02 -10000 0 -0.43 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.013 0.15 0.23 21 -0.34 42 63
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -0.13 1 1
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
TBC1D4 0.013 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -10000 0 0
YWHAB 0.025 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.051 0.017 -10000 0 -0.26 1 1
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
ASIP -0.04 0.14 -10000 0 -0.32 94 94
PRKCI 0.026 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.006 -10000 0 -10000 0 0
RHOQ 0.026 0.002 -10000 0 -10000 0 0
GYS1 0.01 0.016 0.24 1 -0.25 1 2
PRKCZ 0.007 0.076 -10000 0 -0.43 14 14
TRIP10 0.021 0.041 -10000 0 -0.37 5 5
TC10/GTP/CIP4/Exocyst 0.032 0.024 -10000 0 -0.26 3 3
AS160/14-3-3 0.01 0.054 -10000 0 -0.51 1 1
VAMP2 0.026 0.002 -10000 0 -10000 0 0
SLC2A4 -0.018 0.16 0.26 6 -0.39 39 45
STX4 0.026 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.016 -10000 0 -0.29 1 1
SFN -0.023 0.11 -10000 0 -0.22 90 90
LNPEP 0.008 0.088 -10000 0 -0.43 20 20
YWHAE 0.026 0.002 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.033 0.2 1 -10000 0 1
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.008 -10000 0 -0.13 1 1
STAT1 (dimer)/Cbp/p300 0.038 0.05 0.29 2 -0.23 2 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.025 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.074 -10000 0 -0.21 40 40
CaM/Ca2+ 0.046 0.034 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.019 0.033 -10000 0 -10000 0 0
AKT1 0.002 0.039 0.24 3 -10000 0 3
MAP2K1 -0.002 0.036 0.23 4 -10000 0 4
MAP3K11 0.011 0.032 0.24 3 -10000 0 3
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.059 0.19 -10000 0 -0.41 101 101
Rap1/GTP 0.012 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.056 0.035 -10000 0 -10000 0 0
CEBPB 0.016 0.11 0.29 2 -0.46 18 20
STAT3 0.026 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.031 0.15 -10000 0 -1.1 8 8
STAT1 0.01 0.036 0.24 4 -10000 0 4
CALM1 0.025 0.009 -10000 0 -0.13 1 1
IFN-gamma (dimer) 0.011 0.021 -10000 0 -0.13 5 5
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
STAT1 (dimer)/PIAS1 0.022 0.043 0.26 3 -0.2 4 7
CEBPB/PTGES2/Cbp/p300 0.028 0.075 -10000 0 -0.32 15 15
mol:Ca2+ 0.042 0.031 -10000 0 -10000 0 0
MAPK3 0.016 0.065 -10000 0 -0.74 2 2
STAT1 (dimer) -0.021 0.1 -10000 0 -0.28 38 38
MAPK1 0.011 0.089 -10000 0 -0.69 6 6
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
JAK1 0.022 0.011 -10000 0 -10000 0 0
CAMK2D 0.025 0.02 -10000 0 -0.43 1 1
DAPK1 0.011 0.12 0.32 3 -0.59 18 21
SMAD7 -0.009 0.046 0.17 3 -0.14 9 12
CBL/CRKL/C3G 0.035 0.032 0.29 1 -10000 0 1
PI3K 0.044 0.035 -10000 0 -10000 0 0
IFNG 0.011 0.021 -10000 0 -0.13 5 5
apoptosis 0.007 0.11 0.26 4 -0.44 23 27
CAMK2G 0.024 0.021 -10000 0 -0.43 1 1
STAT3 (dimer) 0.026 0.003 -10000 0 -10000 0 0
CAMK2A -0.099 0.17 -10000 0 -0.26 222 222
CAMK2B -0.018 0.12 -10000 0 -0.43 33 33
FRAP1 -0.002 0.036 0.2 5 -10000 0 5
PRKCD -0.008 0.055 0.22 5 -0.2 18 23
RAP1B 0.026 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.023 0.074 -10000 0 -0.21 40 40
PTPN2 0.026 0.004 -10000 0 -10000 0 0
EP300 0.022 0.04 -10000 0 -0.43 4 4
IRF1 -0.001 0.062 0.26 4 -0.31 7 11
STAT1 (dimer)/PIASy 0.022 0.041 0.28 3 -10000 0 3
SOCS1 0.001 0.17 -10000 0 -1.4 8 8
mol:GDP 0.032 0.03 0.27 1 -10000 0 1
CASP1 -0.012 0.058 0.2 3 -0.24 14 17
PTGES2 0.025 0.005 -10000 0 -10000 0 0
IRF9 0.022 0.041 0.15 8 -0.16 4 12
mol:PI-3-4-5-P3 0.031 0.028 -10000 0 -10000 0 0
RAP1/GDP 0.028 0.025 -10000 0 -10000 0 0
CBL 0.01 0.031 0.24 3 -10000 0 3
MAP3K1 0.01 0.033 0.24 3 -10000 0 3
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
PIAS4 0.025 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.023 0.074 -10000 0 -0.21 40 40
PTPN11 0.013 0.029 0.18 7 -10000 0 7
CREBBP 0.026 0.003 -10000 0 -10000 0 0
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.015 0.075 0.31 7 -0.3 10 17
PDGFB-D/PDGFRB/SLAP 0.021 0.061 -10000 0 -0.3 15 15
PDGFB-D/PDGFRB/APS/CBL 0.034 0.044 -10000 0 -0.26 8 8
AKT1 0.007 0.071 0.33 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.02 0.082 0.32 10 -0.31 8 18
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
FGR -0.041 0.14 0.34 2 -0.37 74 76
mol:Ca2+ 0.019 0.073 0.29 15 -0.3 3 18
MYC 0.032 0.21 0.4 32 -0.75 22 54
SHC1 0.024 0.014 -10000 0 -10000 0 0
HRAS/GDP 0.03 0.029 0.18 9 -10000 0 9
LRP1/PDGFRB/PDGFB 0.051 0.014 -10000 0 -10000 0 0
GRB10 0.021 0.03 -10000 0 -0.43 2 2
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0.018 0.074 0.29 15 -0.3 3 18
PTEN 0.025 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.001 0.044 -10000 0 -0.13 41 41
PDGFB-D/PDGFRB/SHP2 0.038 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.031 0.027 -10000 0 -0.31 2 2
cell cycle arrest 0.021 0.06 -10000 0 -0.3 15 15
HRAS 0.025 0.006 -10000 0 -10000 0 0
HIF1A 0.005 0.066 0.31 11 -10000 0 11
GAB1 0.012 0.091 0.31 14 -0.36 5 19
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.015 0.096 0.34 18 -0.32 6 24
PDGFB-D/PDGFRB 0.049 0.022 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.011 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.015 0.079 0.22 2 -0.33 11 13
positive regulation of MAPKKK cascade 0.037 0.012 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.019 0.074 0.3 15 -0.31 3 18
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.026 0.036 -10000 0 -0.18 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
BLK -0.018 0.12 0.31 1 -0.47 31 32
PTPN2 0.026 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.037 0.012 -10000 0 -10000 0 0
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
VAV2 0.015 0.1 0.34 13 -0.36 10 23
CBL 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.037 0.012 -10000 0 -10000 0 0
LCK -0.072 0.18 0.34 2 -0.41 104 106
PDGFRB 0.025 0.014 -10000 0 -0.15 1 1
ACP1 0.026 0.004 -10000 0 -10000 0 0
HCK 0.003 0.083 0.31 1 -0.58 9 10
ABL1 0.006 0.094 0.29 17 -0.35 9 26
PDGFB-D/PDGFRB/CBL 0.015 0.093 0.3 13 -0.41 4 17
PTPN1 0.025 0.007 -10000 0 -10000 0 0
SNX15 0.025 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.028 -10000 0 -0.13 16 16
cell proliferation 0.035 0.19 0.35 46 -0.66 22 68
SLA 0.006 0.077 -10000 0 -0.28 28 28
actin cytoskeleton reorganization 0.033 0.047 0.33 4 -10000 0 4
SRC 0.011 0.025 -10000 0 -10000 0 0
PI3K 0.006 0.024 -10000 0 -0.21 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.044 0.031 -10000 0 -0.21 1 1
SH2B2 0.014 0.057 -10000 0 -0.43 8 8
PLCgamma1/SPHK1 0.02 0.084 0.33 10 -0.32 8 18
LYN 0.01 0.054 0.3 1 -0.5 4 5
LRP1 0.026 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
STAT5B 0.026 0.003 -10000 0 -10000 0 0
STAT5A 0.016 0.066 -10000 0 -0.43 11 11
NCK1-2/p130 Cas 0.072 0.032 -10000 0 -0.22 2 2
SPHK1 0.005 0.086 -10000 0 -0.43 17 17
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.019 0.074 0.3 15 -0.31 3 18
PLCG1 0.018 0.075 0.3 15 -0.32 2 17
NHERF/PDGFRB 0.048 0.031 -10000 0 -0.26 4 4
YES1 0.001 0.085 -10000 0 -0.49 13 13
cell migration 0.047 0.031 -10000 0 -0.26 4 4
SHC/Grb2/SOS1 0.07 0.03 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.01 -10000 0 -0.13 2 2
SLC9A3R1 0.022 0.04 -10000 0 -0.43 4 4
NHERF1-2/PDGFRB/PTEN 0.059 0.034 -10000 0 -0.24 4 4
FYN 0.002 0.078 0.3 1 -0.41 14 15
DOK1 0.015 0.024 0.18 7 -0.24 1 8
HRAS/GTP 0.018 0.005 -10000 0 -10000 0 0
PDGFB 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.031 0.15 0.4 26 -0.44 21 47
PRKCD 0.006 0.066 0.18 17 -0.24 26 43
FER 0.009 0.06 0.19 16 -0.24 20 36
MAPKKK cascade 0.006 0.066 0.38 7 -10000 0 7
RASA1 0.019 0.033 0.19 16 -10000 0 16
NCK1 0.025 0.02 -10000 0 -0.43 1 1
NCK2 0.026 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.033 0.026 0.18 4 -0.22 1 5
PDGFB-D/PDGFRB/SHB 0.037 0.011 -10000 0 -10000 0 0
chemotaxis 0.006 0.093 0.29 17 -0.34 9 26
STAT1-3-5/STAT1-3-5 0.055 0.045 -10000 0 -0.22 10 10
Bovine Papilomavirus E5/PDGFRB 0.017 0.012 -10000 0 -10000 0 0
PTPRJ 0.025 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.028 0.023 -10000 0 -10000 0 0
FBXW11 0.026 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.016 0.054 -10000 0 -0.26 18 18
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.082 0.2 2 -0.29 14 16
NFKBIA -0.014 0.073 -10000 0 -0.23 46 46
MAPK14 0.026 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.008 -10000 0 -10000 0 0
ARRB2 0.014 0.002 -10000 0 -10000 0 0
REL 0.007 0.086 -10000 0 -0.32 28 28
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.019 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
NF kappa B1 p50 dimer 0.02 0.011 0.25 1 -10000 0 1
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.009 0.077 -10000 0 -0.22 39 39
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.009 0.082 0.2 1 -0.28 14 15
SRC 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.038 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.009 0.077 -10000 0 -0.23 39 39
IKBKB 0.025 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
SYK 0.009 0.083 -10000 0 -0.35 23 23
I kappa B alpha/PIK3R1 -0.001 0.087 0.19 3 -0.3 16 19
cell death 0.008 0.079 0.19 1 -0.27 14 15
NF kappa B1 p105/c-Rel 0.016 0.054 -10000 0 -0.26 18 18
LCK -0.019 0.11 -10000 0 -0.43 30 30
BCL3 0.018 0.024 -10000 0 -0.13 11 11
Insulin 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
CBL/APS/CAP 0.03 0.046 -10000 0 -0.2 13 13
TC10/GTP 0.031 0.04 -10000 0 -0.21 9 9
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.033 -10000 0 -0.22 4 4
HRAS 0.025 0.006 -10000 0 -10000 0 0
APS homodimer 0.014 0.057 -10000 0 -0.43 8 8
GRB14 -0.071 0.16 -10000 0 -0.25 180 180
FOXO3 -0.019 0.15 -10000 0 -0.61 31 31
AKT1 -0.034 0.089 0.34 7 -0.36 1 8
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.03 -10000 0 -0.43 2 2
SORBS1 0.023 0.035 -10000 0 -0.43 3 3
CRK 0.026 0.002 -10000 0 -10000 0 0
PTPN1 0.01 0.035 -10000 0 -10000 0 0
CAV1 0.005 0.039 0.18 11 -0.23 4 15
CBL/APS/CAP/Crk-II/C3G 0.049 0.052 -10000 0 -0.22 10 10
Insulin Receptor/Insulin/IRS1/NCK2 0.055 0.032 -10000 0 -0.22 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.028 -10000 0 -0.19 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.036 -10000 0 -0.42 1 1
RPS6KB1 -0.033 0.082 0.33 7 -0.33 1 8
PARD6A 0.026 0.002 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.04 -10000 0 -0.6 2 2
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.011 0.078 -10000 0 -0.27 2 2
HRAS/GTP 0.014 0.025 -10000 0 -0.21 3 3
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.061 0.037 -10000 0 -0.21 4 4
PRKCI 0.019 0.048 -10000 0 -0.44 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.019 0.084 -10000 0 -0.21 70 70
SHC1 0.024 0.014 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.038 0.045 -10000 0 -0.5 2 2
PI3K 0.055 0.031 -10000 0 -0.2 4 4
NCK2 0.026 0.002 -10000 0 -10000 0 0
RHOQ 0.026 0.002 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
AKT2 -0.037 0.082 0.47 3 -0.29 2 5
PRKCZ -0.042 0.15 -10000 0 -0.44 34 34
SH2B2 0.014 0.057 -10000 0 -0.43 8 8
SHC/SHIP 0.032 0.049 0.21 13 -0.21 7 20
F2RL2 -0.019 0.1 -10000 0 -0.19 104 104
TRIP10 0.021 0.041 -10000 0 -0.37 5 5
Insulin Receptor/Insulin/Shc 0.039 0.029 -10000 0 -0.22 4 4
TC10/GTP/CIP4/Exocyst 0.032 0.024 -10000 0 -0.26 3 3
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.062 0.037 -10000 0 -0.21 4 4
RAPGEF1 0.025 0.005 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.025 0.02 -10000 0 -0.43 1 1
CBL/APS/CAP/Crk-II 0.043 0.049 -10000 0 -0.23 10 10
TC10/GDP 0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.047 0.038 -10000 0 -0.23 5 5
INPP5D 0.018 0.051 0.18 30 -0.22 7 37
SOS1 0.026 0.002 -10000 0 -10000 0 0
SGK1 -0.034 0.18 -10000 0 -0.75 31 31
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.003 -10000 0 -10000 0 0
p62DOK/RasGAP 0.039 0.045 -10000 0 -0.51 2 2
INS 0.015 0.041 -10000 0 -0.43 4 4
mol:PI-3-4-P2 0.018 0.05 0.18 30 -0.22 7 37
GRB2 0.025 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.035 0.086 0.33 7 -0.25 8 15
PTPRA 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
TC10/GTP/CIP4 0.032 0.024 -10000 0 -0.26 3 3
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.022 0.024 -10000 0 -0.21 4 4
Insulin Receptor/Insulin/IRS1 0.04 0.028 -10000 0 -0.22 4 4
Insulin Receptor/Insulin/IRS3 0.029 0.033 -10000 0 -0.31 4 4
Par3/Par6 0.047 0.061 -10000 0 -0.22 23 23
Aurora A signaling

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
Aurora A/GADD45A 0.025 0.045 0.21 3 -0.27 3 6
BIRC5 -0.058 0.16 -10000 0 -0.43 74 74
NFKBIA 0.013 0.035 0.25 3 -0.24 2 5
CPEB1 0.013 0.074 -10000 0 -0.43 14 14
AKT1 0.013 0.033 0.23 2 -0.24 2 4
NDEL1 0.026 0.002 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.031 -10000 0 -0.22 2 2
NDEL1/TACC3 0.043 0.043 0.2 2 -0.23 4 6
GADD45A 0.012 0.042 -10000 0 -0.43 1 1
GSK3B 0.028 0.025 -10000 0 -0.44 1 1
PAK1/Aurora A 0.024 0.05 -10000 0 -0.25 7 7
MDM2 0.026 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.013 0.077 -10000 0 -0.3 30 30
TP53 0.017 0.052 -10000 0 -0.24 17 17
DLG7 0.013 0.03 -10000 0 -0.24 2 2
AURKAIP1 0.022 0.01 -10000 0 -10000 0 0
ARHGEF7 0.025 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.043 0.048 0.21 2 -0.25 4 6
G2/M transition of mitotic cell cycle 0.028 0.031 -10000 0 -0.22 2 2
AURKA 0.022 0.039 0.14 10 -0.29 2 12
AURKB -0.043 0.13 -10000 0 -0.29 97 97
CDC25B 0.021 0.029 -10000 0 -0.23 2 2
G2/M transition checkpoint 0.012 0.026 -10000 0 -0.22 2 2
mRNA polyadenylation 0.022 0.051 -10000 0 -0.24 14 14
Aurora A/CPEB 0.023 0.051 -10000 0 -0.24 14 14
Aurora A/TACC1/TRAP/chTOG 0.058 0.039 -10000 0 -0.24 3 3
BRCA1 0.025 0.012 -10000 0 -0.13 3 3
centrosome duplication 0.024 0.05 -10000 0 -0.25 7 7
regulation of centrosome cycle 0.039 0.045 0.19 2 -0.23 4 6
spindle assembly 0.056 0.039 -10000 0 -0.24 3 3
TDRD7 0.025 0.021 -10000 0 -0.43 1 1
Aurora A/RasGAP/Survivin 0.018 0.09 0.2 3 -0.21 38 41
CENPA -0.03 0.12 -10000 0 -0.38 49 49
Aurora A/PP2A 0.033 0.034 -10000 0 -0.24 2 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.016 0.036 0.18 1 -0.23 2 3
negative regulation of DNA binding 0.017 0.053 -10000 0 -0.24 17 17
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.003 -10000 0 -10000 0 0
Ajuba/Aurora A 0.012 0.027 -10000 0 -0.22 2 2
mitotic prometaphase 0.011 0.035 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.039 0.14 10 -0.29 2 12
TACC1 0.025 0.005 -10000 0 -10000 0 0
TACC3 0.011 0.053 -10000 0 -0.43 3 3
Aurora A/Antizyme1 0.04 0.035 -10000 0 -0.22 2 2
Aurora A/RasGAP 0.033 0.032 -10000 0 -0.24 1 1
OAZ1 0.025 0.006 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.028 0.015 -10000 0 -10000 0 0
GIT1 0.026 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.032 -10000 0 -0.26 4 4
Importin alpha/Importin beta/TPX2 -0.013 0.077 -10000 0 -0.3 30 30
PPP2R5D 0.026 0.002 -10000 0 -10000 0 0
Aurora A/TPX2 0.004 0.064 -10000 0 -0.21 31 31
PAK1 0.008 0.061 -10000 0 -0.43 5 5
CKAP5 0.025 0.005 -10000 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.025 0.013 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.018 0.063 -10000 0 -0.3 12 12
PTK2 0.009 0.088 -10000 0 -0.35 14 14
positive regulation of JNK cascade -0.007 0.092 -10000 0 -0.33 10 10
CDC42/GDP 0.02 0.12 -10000 0 -0.43 10 10
Rac1/GDP 0.004 0.12 -10000 0 -0.43 9 9
RAP1B 0.026 0.004 -10000 0 -10000 0 0
RAP1A 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.002 0.11 -10000 0 -0.41 10 10
nectin-3/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
RAPGEF1 0 0.12 0.29 1 -0.44 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.013 0.12 -10000 0 -0.48 8 8
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -10000 0 0
TLN1 0.002 0.017 -10000 0 -10000 0 0
Rap1/GTP -0.006 0.083 -10000 0 -0.32 8 8
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
Rap1/GTP/I-afadin 0.037 0.025 -10000 0 -0.23 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
PVR 0.022 0.01 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.01 -10000 0 -10000 0 0
mol:GDP -0.002 0.14 -10000 0 -0.53 10 10
MLLT4 0.024 0.021 -10000 0 -0.43 1 1
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PI3K 0.066 0.043 -10000 0 -0.22 8 8
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
positive regulation of lamellipodium assembly -0.003 0.088 -10000 0 -0.33 7 7
PVRL1 0.011 0.077 -10000 0 -0.43 15 15
PVRL3 0.019 0.056 -10000 0 -0.43 8 8
PVRL2 0.02 0.023 -10000 0 -0.43 1 1
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.046 0.15 -10000 0 -0.43 59 59
CLDN1 0.01 0.073 -10000 0 -0.26 28 28
JAM-A/CLDN1 0.049 0.063 -10000 0 -0.24 20 20
SRC -0.014 0.12 -10000 0 -0.53 9 9
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
nectin-1(dimer)/I-afadin/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
FARP2 -0.01 0.15 -10000 0 -0.6 9 9
RAC1 0.023 0.009 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.042 -10000 0 -0.26 7 7
nectin-1/I-afadin 0.024 0.06 -10000 0 -0.3 16 16
nectin-2/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.027 0.029 -10000 0 -0.26 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.033 0.067 -10000 0 -0.27 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.028 -10000 0 -0.23 4 4
F11R 0.022 0.03 -10000 0 -0.43 1 1
positive regulation of filopodium formation -0.007 0.092 -10000 0 -0.33 10 10
alphaV/beta3 Integrin/Talin 0.035 0.062 0.2 23 -0.22 12 35
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
nectin-2(dimer)/I-afadin/I-afadin 0.03 0.027 -10000 0 -0.3 2 2
PIP5K1C 0.005 0.02 -10000 0 -0.16 7 7
VAV2 0.002 0.14 -10000 0 -0.53 9 9
RAP1/GDP 0.011 0.11 -10000 0 -0.38 10 10
ITGAV 0.026 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.044 -10000 0 -0.26 8 8
nectin-3(dimer)/I-afadin/I-afadin 0.031 0.046 -10000 0 -0.3 9 9
Rac1/GTP -0.001 0.11 -10000 0 -0.4 7 7
PTPRM 0.01 0.025 -10000 0 -0.17 9 9
E-cadherin/beta catenin/alpha catenin 0.022 0.1 -10000 0 -0.23 60 60
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.01 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.041 -10000 0 -0.26 13 13
SNTA1 -0.001 0.1 -10000 0 -0.43 27 27
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.012 0.032 -10000 0 -0.26 7 7
MAPK12 -0.003 0.017 -10000 0 -0.22 3 3
CCND1 0 0.061 -10000 0 -0.41 11 11
p38 gamma/SNTA1 0.013 0.062 0.19 18 -0.21 25 43
MAP2K3 0.026 0.01 -10000 0 -10000 0 0
PKN1 0.025 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.003 0.017 -10000 0 -0.22 3 3
MAP2K6 0.003 0.011 -10000 0 -0.24 1 1
MAPT 0.004 0.06 0.24 5 -0.23 19 24
MAPK13 0.001 0.053 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.036 0.018 -10000 0 -10000 0 0
CDKN1B 0.014 0.063 -10000 0 -0.28 16 16
CDKN1A 0.002 0.066 -10000 0 -0.29 15 15
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.005 -10000 0 -10000 0 0
FOXO3 0.015 0.044 -10000 0 -0.28 9 9
AKT1 0.007 0.058 -10000 0 -0.3 18 18
BAD 0.025 0.005 -10000 0 -10000 0 0
AKT3 0.01 0.046 -10000 0 -0.48 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.062 -10000 0 -0.28 17 17
AKT1/ASK1 0.027 0.064 -10000 0 -0.27 18 18
BAD/YWHAZ 0.044 0.02 -10000 0 -10000 0 0
RICTOR 0.026 0.003 -10000 0 -10000 0 0
RAF1 0.026 0.004 -10000 0 -10000 0 0
JNK cascade -0.026 0.062 0.26 18 -10000 0 18
TSC1 0.009 0.057 -10000 0 -0.28 17 17
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
AKT1/RAF1 0.032 0.06 -10000 0 -0.28 15 15
EP300 0.022 0.04 -10000 0 -0.43 4 4
mol:GDP 0.011 0.06 -10000 0 -0.29 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.01 0.059 -10000 0 -0.28 17 17
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
TBC1D4 0.005 0.016 -10000 0 -0.25 2 2
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
MAPKAP1 0.025 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.024 0.068 0.46 2 -0.19 7 9
YWHAH 0.019 0.033 -10000 0 -10000 0 0
AKT1S1 0.016 0.037 -10000 0 -0.28 4 4
CASP9 0.011 0.05 -10000 0 -0.28 11 11
YWHAB 0.025 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.033 0.065 0.24 2 -0.27 15 17
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.048 0.024 -10000 0 -0.26 2 2
YWHAE 0.026 0.002 -10000 0 -10000 0 0
SRC 0.025 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.001 0.061 -10000 0 -0.26 8 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.018 -10000 0 -10000 0 0
CHUK 0.01 0.056 -10000 0 -0.28 15 15
BAD/BCL-XL 0.032 0.061 -10000 0 -0.27 17 17
mTORC2 0.032 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.02 -10000 0 -0.29 2 2
FOXO1-3a-4/14-3-3 family 0.023 0.08 0.23 1 -0.48 2 3
PDPK1 0.024 0.028 -10000 0 -0.43 2 2
MDM2 0.013 0.061 0.26 1 -0.28 16 17
MAPKKK cascade -0.032 0.059 0.28 15 -10000 0 15
MDM2/Cbp/p300 0.043 0.064 0.26 1 -0.27 13 14
TSC1/TSC2 0.014 0.068 0.24 15 -0.28 17 32
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.062 0.25 1 -0.26 13 14
glucose import -0.016 0.064 0.21 2 -0.24 35 37
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.047 0.2 14 -10000 0 14
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.012 0.051 -10000 0 -0.22 27 27
GSK3A 0.017 0.041 -10000 0 -0.28 5 5
FOXO1 0.011 0.059 -10000 0 -0.28 16 16
GSK3B 0.011 0.057 -10000 0 -0.28 16 16
SFN -0.023 0.11 -10000 0 -0.22 90 90
G1/S transition of mitotic cell cycle 0.02 0.051 0.26 10 -0.28 4 14
p27Kip1/14-3-3 family 0.024 0.066 -10000 0 -0.93 1 1
PRKACA 0.025 0.005 -10000 0 -10000 0 0
KPNA1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
RHEB 0.02 0.011 -10000 0 -10000 0 0
CREBBP 0.026 0.003 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.016 0.12 -9999 0 -0.28 70 70
Ran/GTP/Exportin 1/HDAC1 0.006 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.12 -9999 0 -0.28 65 65
SUMO1 0.026 0.002 -9999 0 -10000 0 0
ZFPM1 0.025 0.02 -9999 0 -0.43 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
FKBP3 0.026 0.004 -9999 0 -10000 0 0
Histones 0.026 0.075 -9999 0 -0.33 1 1
YY1/LSF 0.027 0.04 -9999 0 -0.25 5 5
SMG5 0.025 0.005 -9999 0 -10000 0 0
RAN 0.026 0.003 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.016 0.087 -9999 0 -0.23 67 67
I kappa B alpha/HDAC1 0.009 0.073 -9999 0 -0.31 9 9
SAP18 0.025 0.005 -9999 0 -10000 0 0
RELA -0.006 0.083 -9999 0 -0.21 64 64
HDAC1/Smad7 0.034 0.026 -9999 0 -10000 0 0
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
HDAC3/TR2 0.01 0.071 -9999 0 -0.27 4 4
NuRD/MBD3 Complex 0.019 0.023 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.008 0.088 -9999 0 -0.29 9 9
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.015 0.065 -9999 0 -0.43 10 10
GATA1 0.013 0.025 -9999 0 -0.13 7 7
Mad/Max 0.037 0.008 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.015 0.066 -9999 0 -0.36 1 1
RBBP7 0.026 0.003 -9999 0 -10000 0 0
NPC 0.016 0.001 -9999 0 -10000 0 0
RBBP4 0.021 0.022 -9999 0 -0.43 1 1
MAX 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
NFKBIA -0.013 0.075 -9999 0 -0.19 68 68
KAT2B 0.025 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.021 0.017 -9999 0 -10000 0 0
SIN3 complex 0.059 0.023 -9999 0 -10000 0 0
SMURF1 0.021 0.011 -9999 0 -10000 0 0
CHD3 0.025 0.02 -9999 0 -0.43 1 1
SAP30 0.025 0.005 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.024 0.028 -9999 0 -0.43 2 2
YY1/HDAC3 0.002 0.062 -9999 0 -0.29 2 2
YY1/HDAC2 0.028 0.036 -9999 0 -0.21 5 5
YY1/HDAC1 0.022 0.038 -9999 0 -0.21 7 7
NuRD/MBD2 Complex (MeCP1) 0.019 0.029 -9999 0 -0.34 1 1
PPARG -0.026 0.12 -9999 0 -0.29 78 78
HDAC8/hEST1B 0.049 0.016 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
TNFRSF1A 0.017 0.054 -9999 0 -0.34 10 10
HDAC3/SMRT (N-CoR2) 0.01 0.071 -9999 0 -0.27 4 4
MBD3L2 -0.015 0.005 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.026 -9999 0 -10000 0 0
CREBBP 0.026 0.003 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.014 0.063 -9999 0 -10000 0 0
HDAC1 0.022 0.01 -9999 0 -10000 0 0
HDAC3 -0.01 0.064 -9999 0 -0.26 3 3
HDAC2 0.025 0.005 -9999 0 -10000 0 0
YY1 0.017 0.024 -9999 0 -0.24 4 4
HDAC8 0.026 0.003 -9999 0 -10000 0 0
SMAD7 0.026 0.004 -9999 0 -10000 0 0
NCOR2 0.026 0.003 -9999 0 -10000 0 0
MXD1 0.026 0.002 -9999 0 -10000 0 0
STAT3 0.019 0.027 -9999 0 -0.28 4 4
NFKB1 0.026 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.034 0.042 -9999 0 -0.24 4 4
YY1/SAP30/HDAC1 0.034 0.039 -9999 0 -0.19 7 7
EP300 0.022 0.04 -9999 0 -0.43 4 4
STAT3 (dimer non-phopshorylated) 0.018 0.027 -9999 0 -0.28 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.075 -9999 0 -0.19 68 68
histone deacetylation 0.031 0.037 -9999 0 -0.33 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.005 0.061 -9999 0 -0.23 7 7
nuclear export -0.048 0.015 -9999 0 -10000 0 0
PRKACA 0.025 0.005 -9999 0 -10000 0 0
GATAD2B 0.026 0.004 -9999 0 -10000 0 0
GATAD2A 0.025 0.005 -9999 0 -10000 0 0
GATA2/HDAC3 0.006 0.08 -9999 0 -0.26 14 14
GATA1/HDAC1 0.029 0.02 -9999 0 -10000 0 0
GATA1/HDAC3 0.007 0.072 -9999 0 -0.25 6 6
CHD4 0.025 0.007 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.031 0.12 -9999 0 -0.32 69 69
SIN3/HDAC complex/Mad/Max 0.017 0.034 -9999 0 -10000 0 0
NuRD Complex 0.016 0.066 -9999 0 -0.25 1 1
positive regulation of chromatin silencing 0.025 0.073 -9999 0 -0.33 1 1
SIN3B 0.025 0.006 -9999 0 -10000 0 0
MTA2 0.025 0.005 -9999 0 -10000 0 0
SIN3A 0.026 0.003 -9999 0 -10000 0 0
XPO1 0.026 0.002 -9999 0 -10000 0 0
SUMO1/HDAC1 0.034 0.024 -9999 0 -0.23 1 1
HDAC complex 0.053 0.031 -9999 0 -0.24 1 1
GATA1/Fog1 0.034 0.022 -9999 0 -0.31 1 1
FKBP25/HDAC1/HDAC2 0.042 0.023 -9999 0 -10000 0 0
TNF -0.06 0.16 -9999 0 -0.26 151 151
negative regulation of cell growth 0.02 0.047 -9999 0 -0.24 6 6
NuRD/MBD2/PRMT5 Complex 0.019 0.029 -9999 0 -0.34 1 1
Ran/GTP/Exportin 1 0.043 0.019 -9999 0 -0.21 1 1
NF kappa B/RelA/I kappa B alpha -0.019 0.11 -9999 0 -0.29 69 69
SIN3/HDAC complex/NCoR1 0.021 0.047 -9999 0 -0.25 9 9
TFCP2 0.025 0.02 -9999 0 -0.43 1 1
NR2C1 0.026 0.003 -9999 0 -10000 0 0
MBD3 0.025 0.006 -9999 0 -10000 0 0
MBD2 0.026 0.004 -9999 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.06 0.21 9 -0.28 1 10
ERC1 0.024 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.051 -10000 0 -0.3 9 9
NFKBIA 0.019 0.034 0.21 15 -10000 0 15
BIRC2 0.025 0.005 -10000 0 -10000 0 0
IKBKB 0.025 0.005 -10000 0 -10000 0 0
RIPK2 0.024 0.007 -10000 0 -10000 0 0
IKBKG 0.02 0.033 -10000 0 -10000 0 0
IKK complex/A20 0.03 0.099 -10000 0 -0.36 5 5
NEMO/A20/RIP2 0.024 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.038 0.044 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.045 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.041 0.025 -10000 0 -0.23 1 1
NOD2 0.011 0.069 -10000 0 -0.43 10 10
NFKB1 0.028 0.004 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
MALT1 0.026 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.037 0.01 -10000 0 -10000 0 0
ATM 0.025 0.005 -10000 0 -10000 0 0
TNF/TNFR1A -0.031 0.12 -10000 0 -0.32 69 69
TRAF6 0.024 0.021 -10000 0 -0.43 1 1
PRKCA 0.024 0.021 -10000 0 -0.43 1 1
CHUK 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.026 0.004 -10000 0 -10000 0 0
TNF -0.06 0.16 -10000 0 -0.26 151 151
NF kappa B1 p50/RelA 0.056 0.016 -10000 0 -10000 0 0
BCL10 0.021 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.034 0.21 15 -10000 0 15
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.017 0.054 -10000 0 -0.34 10 10
IKK complex 0.053 0.05 0.25 1 -10000 0 1
CYLD 0.026 0.003 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.059 0.054 -10000 0 -0.36 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.005 0.21 -10000 0 -0.94 22 22
oxygen homeostasis 0.002 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.003 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.035 0.09 -10000 0 -0.32 5 5
EPO 0.027 0.13 -10000 0 -0.52 5 5
FIH (dimer) 0.022 0.021 -10000 0 -10000 0 0
APEX1 0.022 0.024 -10000 0 -10000 0 0
SERPINE1 -0.011 0.19 -10000 0 -0.45 64 64
FLT1 0.013 0.14 -10000 0 -0.65 16 16
ADORA2A 0.017 0.15 0.34 3 -0.47 9 12
germ cell development 0.016 0.16 -10000 0 -0.48 19 19
SLC11A2 0.023 0.15 -10000 0 -0.52 6 6
BHLHE40 0.018 0.16 -10000 0 -0.55 13 13
HIF1AN 0.022 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.036 0.12 -10000 0 -0.37 7 7
ETS1 0.026 0.054 -10000 0 -0.31 10 10
CITED2 0.017 0.12 -10000 0 -0.66 9 9
KDR 0.016 0.14 -10000 0 -0.73 16 16
PGK1 0.023 0.15 -10000 0 -0.52 6 6
SIRT1 0.025 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.059 0.18 -10000 0 -0.53 10 10
EPAS1 0.012 0.073 -10000 0 -0.31 7 7
SP1 0.025 0.024 -10000 0 -0.12 1 1
ABCG2 0.022 0.16 -10000 0 -0.6 6 6
EFNA1 0.023 0.15 -10000 0 -0.5 8 8
FXN 0.018 0.14 0.34 3 -0.52 5 8
POU5F1 0.015 0.17 -10000 0 -0.49 19 19
neuron apoptosis -0.058 0.18 0.52 10 -10000 0 10
EP300 0.022 0.04 -10000 0 -0.43 4 4
EGLN3 0.012 0.069 -10000 0 -0.43 11 11
EGLN2 0.018 0.022 -10000 0 -10000 0 0
EGLN1 0.022 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.049 0.015 -10000 0 -10000 0 0
VHL 0.026 0.004 -10000 0 -10000 0 0
ARNT 0.021 0.025 -10000 0 -10000 0 0
SLC2A1 0.015 0.14 0.35 2 -0.5 7 9
TWIST1 0.011 0.15 0.34 2 -0.5 14 16
ELK1 0.031 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.042 0.12 -10000 0 -0.39 5 5
VEGFA 0.022 0.15 -10000 0 -0.5 7 7
CREBBP 0.026 0.003 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.002 0.14 -10000 0 -1.3 5 5
PLK1 0.024 0.16 -10000 0 -1.3 5 5
CDKN1B 0.052 0.11 -10000 0 -0.34 7 7
FOXO3 0.042 0.098 -10000 0 -0.52 5 5
KAT2B 0.03 0.014 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.076 -10000 0 -0.57 5 5
CAT 0.036 0.12 -10000 0 -1.2 1 1
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.016 -10000 0 -10000 0 0
FOXO1 0.008 0.08 -10000 0 -0.62 5 5
MAPK10 0.044 0.061 0.19 68 -0.21 2 70
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.06 0.065 0.29 2 -0.36 1 3
response to oxidative stress 0.008 0.01 -10000 0 -0.087 1 1
FOXO3A/SIRT1 0.044 0.1 -10000 0 -0.49 5 5
XPO1 0.027 0.002 -10000 0 -10000 0 0
EP300 0.023 0.041 -10000 0 -0.43 4 4
BCL2L11 0.024 0.12 -10000 0 -1.3 4 4
FOXO1/SKP2 0.018 0.082 -10000 0 -0.48 8 8
mol:GDP 0.008 0.01 -10000 0 -0.087 1 1
RAN 0.027 0.003 -10000 0 -10000 0 0
GADD45A -0.033 0.22 -10000 0 -0.55 28 28
YWHAQ 0.026 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.035 0.071 -10000 0 -0.57 2 2
MST1 0.006 0.1 -10000 0 -0.36 32 32
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.001 0.094 -10000 0 -0.66 2 2
YWHAB 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.035 0.064 0.19 54 -0.22 11 65
MAPK9 0.046 0.059 0.19 71 -10000 0 71
YWHAG 0.019 0.024 -10000 0 -0.13 11 11
YWHAE 0.026 0.002 -10000 0 -10000 0 0
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
SIRT1 0.024 0.007 -10000 0 -10000 0 0
SOD2 0.054 0.1 -10000 0 -0.68 2 2
RBL2 0.057 0.095 -10000 0 -1.1 1 1
RAL/GDP 0.037 0.018 -10000 0 -10000 0 0
CHUK 0.03 0.013 -10000 0 -10000 0 0
Ran/GTP 0.022 0.004 -10000 0 -10000 0 0
CSNK1G2 0.025 0.006 -10000 0 -10000 0 0
RAL/GTP 0.04 0.019 -10000 0 -10000 0 0
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
FASLG 0.025 0.023 -10000 0 -10000 0 0
SKP2 0.021 0.046 -10000 0 -0.43 5 5
USP7 0.027 0.002 -10000 0 -10000 0 0
IKBKB 0.03 0.013 -10000 0 -10000 0 0
CCNB1 0.032 0.1 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.079 0.091 -10000 0 -0.39 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.081 -10000 0 -0.47 8 8
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
SGK1 0.019 0.07 -10000 0 -0.42 12 12
CSNK1G3 0.026 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.006 -10000 0 -10000 0 0
ZFAND5 0.059 0.064 0.35 3 -10000 0 3
SFN -0.023 0.11 -10000 0 -0.22 90 90
CDK2 0.02 0.046 -10000 0 -0.43 4 4
FOXO3A/14-3-3 0.008 0.086 -10000 0 -0.68 2 2
CREBBP 0.026 0.014 -10000 0 -0.13 1 1
FBXO32 0.051 0.15 -10000 0 -1.2 3 3
BCL6 0.052 0.11 -10000 0 -0.72 4 4
RALB 0.027 0.002 -10000 0 -10000 0 0
RALA 0.023 0.009 -10000 0 -10000 0 0
YWHAH 0.019 0.033 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.026 0.002 -10000 0 -10000 0 0
PTK2 0.023 0.008 -10000 0 -10000 0 0
CRKL 0.01 0.037 0.16 2 -0.22 11 13
GRB2/SOS1/SHC 0.05 0.014 -10000 0 -10000 0 0
HRAS 0.025 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.02 0.039 -10000 0 -0.22 12 12
IGF-1R heterotetramer/IGF1/PTP1B 0.042 0.046 -10000 0 -0.24 12 12
AKT1 -0.009 0.041 0.17 7 -0.2 10 17
BAD -0.009 0.038 0.16 7 -0.22 1 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0.038 0.16 2 -0.22 12 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.027 0.041 0.2 1 -0.22 12 13
RAF1 0.008 0.059 -10000 0 -0.42 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.052 0.045 -10000 0 -0.21 11 11
YWHAZ 0.023 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.028 0.043 -10000 0 -0.24 12 12
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
RPS6KB1 -0.008 0.043 0.19 7 -0.2 12 19
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.002 0.049 -10000 0 -0.34 4 4
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.034 -10000 0 -0.2 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.064 0.047 -10000 0 -0.19 12 12
IGF-1R heterotetramer 0.025 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.042 0.044 -10000 0 -0.22 12 12
Crk/p130 Cas/Paxillin 0.051 0.046 0.21 2 -0.2 13 15
IGF1R 0.025 0.016 -10000 0 -10000 0 0
IGF1 0.014 0.077 -10000 0 -0.36 19 19
IRS2/Crk 0.019 0.039 0.16 2 -0.21 13 15
PI3K 0.054 0.045 -10000 0 -0.21 12 12
apoptosis -0.014 0.04 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
PRKCD -0.001 0.086 -10000 0 -0.42 16 16
RAF1/14-3-3 E 0.025 0.058 -10000 0 -0.37 5 5
BAD/14-3-3 0.015 0.041 -10000 0 -10000 0 0
PRKCZ -0.013 0.05 0.17 6 -0.21 17 23
Crk/p130 Cas/Paxillin/FAK1 0.028 0.041 -10000 0 -0.21 1 1
PTPN1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.012 0.062 -10000 0 -0.34 15 15
BCAR1 0.025 0.02 -10000 0 -0.43 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.046 0.051 -10000 0 -0.21 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
IRS1/NCK2 0.027 0.042 -10000 0 -0.22 12 12
GRB10 0.021 0.03 -10000 0 -0.43 2 2
PTPN11 0.01 0.038 0.16 2 -0.22 12 14
IRS1 0.012 0.043 0.12 11 -0.24 12 23
IRS2 0.009 0.039 0.16 2 -0.22 13 15
IGF-1R heterotetramer/IGF1 0.027 0.058 -10000 0 -0.32 13 13
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDPK1 0.012 0.045 0.19 8 -0.2 13 21
YWHAE 0.026 0.002 -10000 0 -10000 0 0
PRKD1 0.008 0.06 -10000 0 -0.32 15 15
SHC1 0.024 0.014 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.013 -10000 0 -10000 0 0
mol:S1P 0.001 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.039 -10000 0 -0.25 8 8
GNAO1 0.022 0.046 -10000 0 -0.44 5 5
S1P/S1P3/G12/G13 0.038 0.043 -10000 0 -0.23 9 9
AKT1 0.015 0.074 -10000 0 -0.38 14 14
AKT3 0.013 0.13 -10000 0 -1 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.013 -10000 0 -10000 0 0
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.022 0.012 -10000 0 -10000 0 0
GNAI1 0.02 0.036 -10000 0 -0.43 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.006 0.075 -10000 0 -0.43 11 11
S1PR2 0.022 0.036 -10000 0 -0.43 3 3
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.074 -10000 0 -0.27 19 19
MAPK3 0.006 0.07 -10000 0 -0.28 15 15
MAPK1 0.008 0.065 -10000 0 -0.26 14 14
JAK2 0.008 0.076 0.2 3 -0.3 13 16
CXCR4 0.001 0.078 -10000 0 -0.28 20 20
FLT1 0.026 0.024 -10000 0 -0.49 1 1
RhoA/GDP 0.019 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.007 -10000 0 -10000 0 0
SRC 0.005 0.066 -10000 0 -0.29 13 13
S1P/S1P3/Gi 0.011 0.075 -10000 0 -0.27 19 19
RAC1 0.023 0.009 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.073 -10000 0 -0.27 15 15
VEGFA 0.021 0.033 -10000 0 -0.13 22 22
S1P/S1P2/Gi 0.014 0.062 -10000 0 -0.27 9 9
VEGFR1 homodimer/VEGFA homodimer 0.036 0.034 -10000 0 -0.4 1 1
RHOA 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.002 0.08 -10000 0 -0.25 41 41
GNAQ 0.026 0.004 -10000 0 -10000 0 0
GNAZ 0.026 0.008 -10000 0 -10000 0 0
G12/G13 0.032 0.015 -10000 0 -10000 0 0
GNA14 0.009 0.081 -10000 0 -0.34 23 23
GNA15 0.013 0.07 -10000 0 -0.43 12 12
GNA12 0.022 0.009 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.017 0.06 -10000 0 -0.43 9 9
Rac1/GTP 0.012 0.068 -10000 0 -0.28 13 13
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.029 0.13 -10000 0 -0.43 46 46
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.003 -10000 0 -10000 0 0
TCEB1 0.025 0.006 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.058 -10000 0 -0.26 8 8
HIF1A 0.009 0.034 -10000 0 -0.25 6 6
COPS5 0.025 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.065 0.03 -10000 0 -10000 0 0
FIH (dimer) 0.025 0.005 -10000 0 -10000 0 0
CDKN2A -0.013 0.11 -10000 0 -0.3 55 55
ARNT/IPAS -0.006 0.096 -10000 0 -0.3 43 43
HIF1AN 0.025 0.005 -10000 0 -10000 0 0
GNB2L1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.018 0.047 -10000 0 -0.27 7 7
CUL2 0.024 0.007 -10000 0 -10000 0 0
OS9 0.025 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.049 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.021 0.047 -10000 0 -0.26 8 8
PHD1-3/OS9 0.047 0.046 -10000 0 -0.22 9 9
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.051 0.29 1 -0.26 6 7
VHL 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.019 0.047 -10000 0 -0.27 6 6
EGLN3 0.016 0.066 -10000 0 -0.43 11 11
EGLN2 0.022 0.01 -10000 0 -10000 0 0
EGLN1 0.026 0.004 -10000 0 -10000 0 0
TP53 0.014 0.072 -10000 0 -0.41 14 14
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.065 -10000 0 -0.53 6 6
ARNT 0.025 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.006 0.069 0.31 1 -0.28 8 9
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.018 0.063 -10000 0 -0.3 12 12
AKT1 0.034 0.078 0.32 5 -0.52 4 9
PTK2B 0.005 0.073 0.35 2 -0.45 4 6
VEGFR2 homodimer/Frs2 0.028 0.052 -10000 0 -0.61 3 3
CAV1 0.006 0.051 -10000 0 -0.43 2 2
CALM1 0.025 0.009 -10000 0 -0.13 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.044 0.053 -10000 0 -0.57 3 3
endothelial cell proliferation 0.043 0.084 0.28 17 -0.45 4 21
mol:Ca2+ 0.019 0.06 0.36 1 -0.38 5 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.047 0.061 -10000 0 -0.36 7 7
RP11-342D11.1 0.008 0.058 0.18 2 -0.41 5 7
CDH5 0.025 0.012 -10000 0 -10000 0 0
VEGFA homodimer 0.063 0.024 -10000 0 -0.23 1 1
SHC1 0.024 0.014 -10000 0 -10000 0 0
SHC2 0.025 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.038 0.049 -10000 0 -0.42 3 3
SH2D2A -0.02 0.12 -10000 0 -0.27 77 77
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.059 0.081 0.28 5 -0.41 6 11
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.089 -10000 0 -0.26 37 37
VEGFR1 homodimer 0.024 0.021 -10000 0 -0.43 1 1
SHC/GRB2/SOS1 0.065 0.058 -10000 0 -0.37 5 5
GRB10 0.015 0.066 0.36 1 -0.52 5 6
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
PAK1 0.008 0.061 -10000 0 -0.43 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.063 0.062 -10000 0 -0.53 3 3
HRAS 0.025 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.019 0.052 -10000 0 -0.36 5 5
HIF1A 0.025 0.021 -10000 0 -0.43 1 1
FRS2 0.026 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.046 0.06 -10000 0 -0.35 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.021 0.039 -10000 0 -0.43 3 3
Nck/Pak 0.023 0.05 -10000 0 -0.3 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.044 0.053 -10000 0 -0.57 3 3
mol:GDP 0.051 0.054 -10000 0 -0.36 5 5
mol:NADP 0.042 0.071 0.27 6 -0.37 6 12
eNOS/Hsp90 0.053 0.068 0.28 5 -0.36 5 10
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.019 0.06 0.36 1 -0.38 5 6
HIF1A/ARNT 0.036 0.018 -10000 0 -0.3 1 1
SHB 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.02 0.033 -10000 0 -10000 0 0
VEGFC 0.017 0.051 -10000 0 -0.21 18 18
FAK1/Vinculin 0.038 0.082 0.3 2 -0.53 5 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.072 -10000 0 -0.28 14 14
PTPN6 0.014 0.064 -10000 0 -0.43 10 10
EPAS1 0.03 0.029 -10000 0 -0.33 3 3
mol:L-citrulline 0.042 0.071 0.27 6 -0.37 6 12
ITGAV 0.026 0.002 -10000 0 -10000 0 0
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.055 0.051 -10000 0 -0.49 3 3
VEGFR2 homodimer/VEGFA homodimer 0.047 0.06 -10000 0 -0.36 8 8
VEGFR2/3 heterodimer 0.026 0.058 -10000 0 -0.47 5 5
VEGFB 0.025 0.005 -10000 0 -10000 0 0
MAPK11 0.004 0.072 0.32 5 -0.52 4 9
VEGFR2 homodimer 0.015 0.056 -10000 0 -0.69 3 3
FLT1 0.024 0.021 -10000 0 -0.43 1 1
NEDD4 0.022 0.04 -10000 0 -0.22 10 10
MAPK3 0.004 0.064 0.28 4 -0.38 4 8
MAPK1 0.005 0.064 0.27 5 -0.38 4 9
VEGFA145/NRP2 0.03 0.043 -10000 0 -0.28 6 6
VEGFR1/2 heterodimer 0.028 0.052 -10000 0 -0.61 3 3
KDR 0.015 0.056 -10000 0 -0.7 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.043 0.062 -10000 0 -0.41 5 5
SRC 0.025 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.006 0.068 0.28 5 -0.4 4 9
PI3K 0.041 0.063 -10000 0 -0.54 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.045 0.053 -10000 0 -0.57 3 3
FES 0.017 0.062 -10000 0 -0.42 5 5
GAB1 0.028 0.059 -10000 0 -0.5 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.05 -10000 0 -0.51 3 3
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
SOS1 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.025 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.066 0.31 2 -0.39 5 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.042 0.055 -10000 0 -0.36 7 7
PI3K/GAB1 0.046 0.066 -10000 0 -0.47 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.063 0.063 -10000 0 -0.53 3 3
PRKACA 0.025 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.063 -10000 0 -0.34 10 10
HSP90AA1 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.015 0.062 0.36 1 -0.42 5 6
actin cytoskeleton reorganization 0.023 0.089 -10000 0 -0.25 37 37
PTK2 0.016 0.065 -10000 0 -0.57 3 3
EDG1 0.008 0.058 0.18 2 -0.41 5 7
mol:DAG 0.019 0.06 0.36 1 -0.38 5 6
CaM/Ca2+ 0.028 0.055 -10000 0 -0.36 5 5
MAP2K3 0.005 0.069 0.36 1 -0.51 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.065 0.088 -10000 0 -0.53 5 5
PLCG1 0.019 0.061 0.36 1 -0.39 5 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.055 0.052 -10000 0 -0.49 3 3
IQGAP1 0.02 0.043 -10000 0 -0.25 10 10
YES1 0.022 0.04 -10000 0 -0.43 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.045 0.053 -10000 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.037 0.065 -10000 0 -0.32 11 11
cell migration 0.046 0.09 0.32 3 -0.51 6 9
mol:PI-3-4-5-P3 0.04 0.06 -10000 0 -0.5 3 3
FYN 0.025 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0.022 0.058 -10000 0 -0.39 5 5
mol:NO 0.042 0.071 0.27 6 -0.37 6 12
PXN 0.026 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.046 -10000 0 -0.42 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.066 -10000 0 -0.53 5 5
VHL 0.026 0.004 -10000 0 -10000 0 0
ITGB3 -0.001 0.082 -10000 0 -0.19 64 64
NOS3 0.043 0.075 0.3 3 -0.41 6 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.042 0.054 -10000 0 -0.57 3 3
RAC1 0.023 0.009 -10000 0 -10000 0 0
PRKCA 0.011 0.055 0.36 1 -0.39 3 4
PRKCB -0.001 0.071 0.36 2 -0.3 12 14
VCL 0.022 0.032 -10000 0 -0.23 6 6
VEGFA165/NRP1 0.029 0.059 -10000 0 -0.41 5 5
VEGFR1/2 heterodimer/VEGFA homodimer 0.044 0.053 -10000 0 -0.57 3 3
VEGFA165/NRP2 0.03 0.043 -10000 0 -0.28 6 6
MAPKKK cascade 0.034 0.069 0.3 4 -0.42 5 9
NRP2 0.021 0.046 -10000 0 -0.32 8 8
VEGFC homodimer 0.017 0.051 -10000 0 -0.21 18 18
NCK1 0.025 0.02 -10000 0 -0.43 1 1
ROCK1 0.026 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.08 0.29 3 -0.56 4 7
MAP3K13 0.014 0.072 0.36 1 -0.4 6 7
PDPK1 0.026 0.061 0.27 2 -0.5 3 5
Arf6 trafficking events

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
SLC2A4 -0.019 0.13 -10000 0 -0.43 41 41
CLTC 0.024 0.054 -10000 0 -0.36 6 6
calcium ion-dependent exocytosis 0.012 0.05 -10000 0 -0.27 3 3
Dynamin 2/GTP 0.025 0.008 -10000 0 -10000 0 0
EXOC4 0.02 0.011 -10000 0 -10000 0 0
CD59 0.015 0.047 -10000 0 -0.31 8 8
CPE 0.007 0.041 -10000 0 -0.26 12 12
CTNNB1 0.026 0.004 -10000 0 -10000 0 0
membrane fusion 0.015 0.053 -10000 0 -0.15 32 32
CTNND1 0.014 0.024 0.18 10 -10000 0 10
DNM2 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.039 -10000 0 -0.25 2 2
TSHR -0.05 0.1 -10000 0 -0.26 90 90
INS -0.008 0.11 -10000 0 -0.45 27 27
BIN1 0.025 0.02 -10000 0 -0.43 1 1
mol:Choline 0.015 0.053 -10000 0 -0.15 32 32
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.007 -10000 0 -10000 0 0
JUP 0.012 0.055 -10000 0 -0.31 10 10
ASAP2/amphiphysin II 0.048 0.016 -10000 0 -0.23 1 1
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 -0.008 0.079 -10000 0 -0.28 18 18
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.002 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.026 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0.022 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.016 0.071 0.3 7 -10000 0 7
positive regulation of phagocytosis 0.012 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.006 -10000 0 -10000 0 0
ACAP1 0.02 0.05 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.01 0.07 -10000 0 -0.31 11 11
clathrin heavy chain/ACAP1 0.026 0.058 0.2 18 -0.28 6 24
JIP4/KLC1 0.048 0.012 -10000 0 -10000 0 0
EXOC1 0.025 0.006 -10000 0 -10000 0 0
exocyst 0.02 0.02 -10000 0 -10000 0 0
RALA/GTP 0.017 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.007 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 0.014 0.023 0.18 9 -10000 0 9
NME1 0.014 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.026 0.057 0.25 2 -0.36 6 8
IL2RA 0.006 0.054 -10000 0 -0.31 9 9
VAMP3 0.012 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.07 -10000 0 -0.27 11 11
EXOC6 0.025 0.005 -10000 0 -10000 0 0
PLD1 -0.004 0.066 -10000 0 -0.26 31 31
PLD2 0.012 0.013 -10000 0 -0.25 1 1
EXOC5 0.026 0.004 -10000 0 -10000 0 0
PIP5K1C 0.016 0.037 -10000 0 -0.26 2 2
SDC1 0.011 0.053 -10000 0 -0.31 8 8
ARF6/GDP 0.024 0.005 -10000 0 -10000 0 0
EXOC7 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.018 0.073 -10000 0 -0.31 7 7
mol:Phosphatidic acid 0.015 0.053 -10000 0 -0.15 32 32
endocytosis -0.047 0.015 0.23 1 -10000 0 1
SCAMP2 0.026 0.003 -10000 0 -10000 0 0
ADRB2 0.015 0.074 0.27 3 -0.35 8 11
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ASAP2 0.026 0.003 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.009 -10000 0 -10000 0 0
KLC1 0.025 0.005 -10000 0 -10000 0 0
AVPR2 0.022 0.061 0.24 3 -0.34 7 10
RALA 0.023 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.073 -10000 0 -0.31 6 6
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.02 0.045 0.38 6 -10000 0 6
PI3K Class IB/PDE3B 0.02 0.045 -10000 0 -0.38 6 6
PDE3B 0.02 0.045 -10000 0 -0.38 6 6
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.015 0.032 -10000 0 -0.21 8 8
TRAF2/ASK1 0.03 0.032 -10000 0 -0.26 6 6
ATM 0.025 0.005 -10000 0 -10000 0 0
MAP2K3 0.011 0.072 -10000 0 -0.39 4 4
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.004 0.092 0.2 4 -0.32 15 19
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.002 0.09 -10000 0 -0.43 19 19
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.009 -10000 0 -0.13 1 1
GADD45A 0.012 0.042 -10000 0 -0.43 1 1
GADD45B 0.01 0.067 -10000 0 -0.21 33 33
MAP3K1 0.024 0.019 -10000 0 -10000 0 0
MAP3K6 0.02 0.019 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
MAP3K4 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.026 0.041 -10000 0 -0.3 6 6
TAK1/TAB family -0.002 0.025 0.16 7 -0.13 5 12
RAC1/OSM/MEKK3 0.042 0.02 -10000 0 -10000 0 0
TRAF2 0.026 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.014 0.059 -10000 0 -0.32 3 3
TRAF6 0.006 0.013 -10000 0 -0.3 1 1
RAC1 0.023 0.009 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.018 0.12 -10000 0 -0.43 33 33
CCM2 0.022 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.073 -10000 0 -0.25 34 34
MAPK11 0.019 0.056 -10000 0 -0.43 8 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.021 0.08 -10000 0 -0.25 36 36
OSM/MEKK3 0.032 0.015 -10000 0 -10000 0 0
TAOK1 -0.012 0.085 -10000 0 -0.29 44 44
TAOK2 0.014 0.003 -10000 0 -10000 0 0
TAOK3 0.014 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.026 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.049 -10000 0 -0.43 6 6
MAP3K10 0.019 0.023 -10000 0 -10000 0 0
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.021 0.028 -10000 0 -0.2 7 7
GADD45/MTK1/MTK1 0.027 0.068 -10000 0 -0.22 24 24
Circadian rhythm 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
chromatin modification 0.037 0.05 -10000 0 -0.41 1 1
CLOCK 0.002 0.1 -10000 0 -0.43 28 28
TIMELESS/CRY2 0.026 0.047 -10000 0 -10000 0 0
DEC1/BMAL1 0.031 0.022 -10000 0 -10000 0 0
ATR 0.026 0.003 -10000 0 -10000 0 0
NR1D1 0.009 0.1 -10000 0 -1.3 3 3
ARNTL 0.025 0.015 -10000 0 -0.13 3 3
TIMELESS 0.013 0.041 -10000 0 -10000 0 0
NPAS2 0.021 0.052 -10000 0 -0.31 10 10
CRY2 0.023 0.035 -10000 0 -0.43 3 3
mol:CO -0.007 0.011 0.13 3 -10000 0 3
CHEK1 0.023 0.018 -10000 0 -0.13 6 6
mol:HEME 0.007 0.011 -10000 0 -0.13 3 3
PER1 0.018 0.06 -10000 0 -0.43 9 9
BMAL/CLOCK/NPAS2 0.037 0.078 -10000 0 -0.25 33 33
BMAL1/CLOCK 0.005 0.11 -10000 0 -0.86 3 3
S phase of mitotic cell cycle 0.037 0.05 -10000 0 -0.41 1 1
TIMELESS/CHEK1/ATR 0.038 0.05 -10000 0 -0.42 1 1
mol:NADPH 0.007 0.011 -10000 0 -0.13 3 3
PER1/TIMELESS 0.025 0.054 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.008 0.029 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.025 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.038 -10000 0 -0.25 5 5
forebrain development 0.018 0.14 0.46 2 -0.46 23 25
GNAO1 0.022 0.045 -10000 0 -0.43 5 5
SMO/beta Arrestin2 0.029 0.031 -10000 0 -0.3 3 3
SMO 0.018 0.036 -10000 0 -0.43 3 3
ARRB2 0.026 0.004 -10000 0 -10000 0 0
GLI3/SPOP 0.016 0.087 0.22 1 -0.35 13 14
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.025 0.02 -10000 0 -0.43 1 1
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.023 -10000 0 -10000 0 0
GNAI1 0.019 0.036 -10000 0 -0.43 3 3
XPO1 0.027 0.007 -10000 0 -10000 0 0
GLI1/Su(fu) 0.012 0.11 -10000 0 -0.76 5 5
SAP30 0.025 0.005 -10000 0 -10000 0 0
mol:GDP 0.018 0.036 -10000 0 -0.43 3 3
MIM/GLI2A 0.017 0.043 -10000 0 -0.37 5 5
IFT88 0.025 0.005 -10000 0 -10000 0 0
GNAI3 0.021 0.011 -10000 0 -10000 0 0
GLI2 0.031 0.048 0.27 2 -10000 0 2
GLI3 0.006 0.088 0.22 2 -0.36 14 16
CSNK1D 0.025 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.004 -10000 0 -10000 0 0
SAP18 0.025 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.022 0.04 -10000 0 -0.43 4 4
Gi family/GTP 0.002 0.055 -10000 0 -0.28 10 10
SIN3B 0.025 0.006 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.072 -10000 0 -0.44 5 5
GLI2/Su(fu) 0.027 0.049 -10000 0 -0.34 4 4
FOXA2 0.012 0.093 -10000 0 -0.75 5 5
neural tube patterning 0.018 0.14 0.46 2 -0.46 23 25
SPOP 0.026 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.046 -10000 0 -0.22 4 4
GNB1 0.022 0.01 -10000 0 -10000 0 0
CSNK1G2 0.025 0.006 -10000 0 -10000 0 0
CSNK1G3 0.026 0.003 -10000 0 -10000 0 0
MTSS1 0.017 0.043 -10000 0 -0.37 5 5
embryonic limb morphogenesis 0.018 0.14 0.46 2 -0.46 23 25
SUFU 0.018 0.018 -10000 0 -10000 0 0
LGALS3 0.012 0.053 -10000 0 -0.16 39 39
catabolic process 0.042 0.09 0.29 1 -0.58 3 4
GLI3A/CBP 0.004 0.087 -10000 0 -0.32 31 31
KIF3A 0.025 0.02 -10000 0 -0.43 1 1
GLI1 0.018 0.14 0.46 2 -0.47 23 25
RAB23 0.025 0.02 -10000 0 -0.43 1 1
CSNK1A1 0.026 0.003 -10000 0 -10000 0 0
IFT172 0.023 0.035 -10000 0 -0.43 3 3
RBBP7 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.045 0.047 -10000 0 -0.24 4 4
GNAZ 0.026 0.006 -10000 0 -10000 0 0
RBBP4 0.021 0.022 -10000 0 -0.43 1 1
CSNK1G1 0.026 0.008 -10000 0 -0.13 1 1
PIAS1 0.022 0.04 -10000 0 -0.43 4 4
PRKACA 0.025 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.04 0.051 -10000 0 -0.52 1 1
STK36 0.026 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.011 0.053 -10000 0 -0.37 6 6
PTCH1 0.015 0.16 0.57 1 -1.1 7 8
MIM/GLI1 0.022 0.14 0.55 1 -0.63 8 9
CREBBP 0.004 0.087 -10000 0 -0.32 31 31
Su(fu)/SIN3/HDAC complex -0.006 0.11 0.24 2 -0.35 19 21
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.013 0.066 -10000 0 -0.97 2 2
regulation of axonogenesis 0.002 0.055 0.28 9 -10000 0 9
myoblast fusion -0.008 0.041 0.35 4 -10000 0 4
mol:GTP 0.019 0.026 -10000 0 -0.16 7 7
regulation of calcium-dependent cell-cell adhesion -0.043 0.027 0.2 2 -10000 0 2
ARF1/GTP 0.034 0.024 -10000 0 -0.15 2 2
mol:GM1 0.008 0.018 -10000 0 -0.15 2 2
mol:Choline -0.009 0.065 -10000 0 -0.24 35 35
lamellipodium assembly 0.003 0.047 -10000 0 -0.37 6 6
MAPK3 0.02 0.026 -10000 0 -0.3 2 2
ARF6/GTP/NME1/Tiam1 0.044 0.027 -10000 0 -0.2 2 2
ARF1 0.026 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.008 0.041 -10000 0 -0.35 4 4
ARF1/GDP 0.012 0.048 -10000 0 -0.28 7 7
ARF6 0.032 0.012 -10000 0 -0.14 1 1
RAB11A 0.026 0.003 -10000 0 -10000 0 0
TIAM1 0.025 0.007 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.026 -10000 0 -0.3 2 2
actin filament bundle formation -0.016 0.047 0.27 7 -10000 0 7
KALRN 0.005 0.028 -10000 0 -0.25 4 4
RAB11FIP3/RAB11A 0.038 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.047 -10000 0 -0.28 7 7
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.045 -10000 0 -0.25 6 6
substrate adhesion-dependent cell spreading 0.019 0.026 -10000 0 -0.16 7 7
cortical actin cytoskeleton organization 0.003 0.048 -10000 0 -0.37 6 6
RAC1 0.023 0.009 -10000 0 -10000 0 0
liver development 0.019 0.026 -10000 0 -0.16 7 7
ARF6/GTP 0.019 0.026 -10000 0 -0.16 7 7
RhoA/GTP 0.035 0.023 -10000 0 -0.15 2 2
mol:GDP 0.008 0.032 -10000 0 -0.32 4 4
ARF6/GTP/RAB11FIP3/RAB11A 0.049 0.025 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
PLD1 -0.004 0.075 -10000 0 -0.27 35 35
RAB11FIP3 0.026 0.002 -10000 0 -10000 0 0
tube morphogenesis 0.003 0.047 -10000 0 -0.37 6 6
ruffle organization -0.002 0.055 -10000 0 -0.28 9 9
regulation of epithelial cell migration 0.019 0.026 -10000 0 -0.16 7 7
PLD2 0.016 0.026 -10000 0 -0.19 3 3
PIP5K1A -0.002 0.055 -10000 0 -0.28 9 9
mol:Phosphatidic acid -0.009 0.065 -10000 0 -0.24 35 35
Rac1/GTP 0.003 0.048 -10000 0 -0.37 6 6
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.052 0.037 -9999 0 -0.22 4 4
HDAC3 0.026 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.034 0.016 -9999 0 -10000 0 0
GATA1/HDAC5 0.035 0.016 -9999 0 -10000 0 0
GATA2/HDAC5 0.03 0.049 -9999 0 -0.3 10 10
HDAC5/BCL6/BCoR 0.052 0.01 -9999 0 -10000 0 0
HDAC9 0.015 0.055 -9999 0 -0.3 12 12
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.013 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.037 0.009 -9999 0 -10000 0 0
HDAC5/YWHAB 0.037 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.003 -9999 0 -10000 0 0
GATA2 0.015 0.065 -9999 0 -0.43 10 10
HDAC4/RFXANK 0.036 0.011 -9999 0 -10000 0 0
BCOR 0.026 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.026 0.004 -9999 0 -10000 0 0
HDAC5 0.026 0.003 -9999 0 -10000 0 0
GNB1/GNG2 0.03 0.033 -9999 0 -0.3 4 4
Histones 0.03 0.044 -9999 0 -0.23 2 2
ADRBK1 0.025 0.005 -9999 0 -10000 0 0
HDAC4 0.025 0.005 -9999 0 -10000 0 0
XPO1 0.026 0.002 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.006 -9999 0 -10000 0 0
HDAC4/Ubc9 0.037 0.008 -9999 0 -10000 0 0
HDAC7 0.026 0.004 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.005 -9999 0 -10000 0 0
TUBA1B 0.026 0.004 -9999 0 -10000 0 0
HDAC6 0.026 0.002 -9999 0 -10000 0 0
HDAC5/RFXANK 0.037 0.011 -9999 0 -10000 0 0
CAMK4 -0.094 0.19 -9999 0 -0.43 121 121
Tubulin/HDAC6 0.051 0.012 -9999 0 -10000 0 0
SUMO1 0.026 0.002 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.025 0.005 -9999 0 -10000 0 0
GATA1 0.013 0.025 -9999 0 -0.13 7 7
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.002 -9999 0 -10000 0 0
NR3C1 0.026 0.004 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0.021 -9999 0 -0.21 1 1
SRF 0.026 0.002 -9999 0 -10000 0 0
HDAC4/YWHAB 0.036 0.011 -9999 0 -10000 0 0
Tubulin 0.038 0.007 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.037 0.008 -9999 0 -10000 0 0
GNB1 0.022 0.01 -9999 0 -10000 0 0
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
BCL6/BCoR 0.038 0.007 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.05 0.014 -9999 0 -10000 0 0
HDAC4/SRF -0.019 0.13 -9999 0 -0.26 119 119
HDAC4/ER alpha 0.026 0.054 -9999 0 -0.3 11 11
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.03 0.044 -9999 0 -0.23 2 2
cell motility 0.05 0.012 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
HDAC7/HDAC3 0.038 0.007 -9999 0 -10000 0 0
BCL6 0.026 0.004 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.025 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.008 -9999 0 -10000 0 0
ESR1 0.011 0.07 -9999 0 -0.26 25 25
HDAC6/HDAC11 0.037 0.017 -9999 0 -0.3 1 1
Ran/GTP/Exportin 1 0.043 0.019 -9999 0 -0.21 1 1
NPC 0.016 0.001 -9999 0 -10000 0 0
MEF2C 0.019 0.04 -9999 0 -0.16 20 20
RAN 0.026 0.003 -9999 0 -10000 0 0
HDAC4/MEF2C 0.071 0.029 -9999 0 -0.22 2 2
GNG2 0.022 0.04 -9999 0 -0.43 4 4
NCOR2 0.026 0.003 -9999 0 -10000 0 0
TUBB2A 0.026 0.004 -9999 0 -10000 0 0
HDAC11 0.025 0.02 -9999 0 -0.43 1 1
HSP90AA1 0.025 0.005 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
ANKRA2 0.026 0.003 -9999 0 -10000 0 0
RFXANK 0.025 0.009 -9999 0 -10000 0 0
nuclear import -0.032 0.01 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.017 0.044 -9999 0 -0.43 2 2
PLK4 0.016 0.05 -9999 0 -0.43 4 4
regulation of centriole replication 0.001 0.042 -9999 0 -0.28 6 6
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.022 0.01 -10000 0 -10000 0 0
mol:PIP3 0.009 0.016 -10000 0 -0.16 3 3
FRAP1 0.021 0.044 0.27 2 -0.31 2 4
AKT1 0.009 0.034 0.17 15 -0.18 1 16
INSR 0.025 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0.027 -10000 0 -0.26 4 4
mol:GTP 0.032 0.038 0.2 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.017 -10000 0 -0.16 1 1
TSC2 0.026 0.002 -10000 0 -10000 0 0
RHEB/GDP 0.015 0.025 -10000 0 -10000 0 0
TSC1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.017 -10000 0 -0.18 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.028 0.023 -10000 0 -0.18 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.025 0.007 -10000 0 -10000 0 0
RPS6KB1 0.026 0.05 0.26 9 -0.32 1 10
MAP3K5 -0.005 0.051 -10000 0 -0.22 25 25
PIK3R1 0.026 0.003 -10000 0 -10000 0 0
apoptosis -0.005 0.051 -10000 0 -0.22 25 25
mol:LY294002 0 0 -10000 0 -0.001 3 3
EIF4B 0.024 0.048 0.25 10 -0.28 1 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.033 0.19 3 -0.25 1 4
eIF4E/eIF4G1/eIF4A1 0.016 0.023 -10000 0 -0.2 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.041 0.019 -10000 0 -0.17 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.022 0.13 4 -10000 0 4
FKBP1A 0.025 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.032 0.18 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 3 3
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.003 0.022 0.18 2 -0.23 1 3
EIF4E 0.026 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.005 0.14 -10000 0 -0.57 25 25
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.045 -10000 0 -0.23 11 11
TSC1/TSC2 0.039 0.048 0.27 6 -10000 0 6
tumor necrosis factor receptor activity 0 0 0.001 3 -10000 0 3
RPS6 0.024 0.01 -10000 0 -0.13 1 1
PPP5C 0.022 0.01 -10000 0 -10000 0 0
EIF4G1 0.026 0.004 -10000 0 -10000 0 0
IRS1 0.008 0.018 -10000 0 -0.2 3 3
INS -0.018 0.037 -10000 0 -0.43 4 4
PTEN 0.025 0.006 -10000 0 -10000 0 0
PDK2 -0.003 0.021 0.18 2 -0.19 1 3
EIF4EBP1 0.003 0.15 -10000 0 -1.1 9 9
PIK3CA 0.025 0.02 -10000 0 -0.43 1 1
PPP2R5D 0.02 0.043 0.26 2 -0.28 2 4
peptide biosynthetic process -0.008 0.033 0.18 10 -0.23 4 14
RHEB 0.02 0.011 -10000 0 -10000 0 0
EIF4A1 0.026 0.003 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 26 -10000 0 26
EEF2 -0.008 0.033 0.18 10 -0.23 4 14
eIF4E/4E-BP1 0.016 0.14 -10000 0 -1 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.026 0.004 -9999 0 -10000 0 0
SMAD2 -0.001 0.035 -9999 0 -0.25 2 2
SMAD3 0.025 0.025 -9999 0 -10000 0 0
SMAD3/SMAD4 0.038 0.044 -9999 0 -0.71 1 1
SMAD4/Ubc9/PIASy 0.05 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.047 0.044 -9999 0 -10000 0 0
PPM1A 0.025 0.005 -9999 0 -10000 0 0
CALM1 0.025 0.009 -9999 0 -0.13 1 1
SMAD2/SMAD4 0.014 0.036 -9999 0 -0.23 2 2
MAP3K1 0.024 0.019 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.06 -9999 0 -0.3 16 16
MAPK3 0.026 0.002 -9999 0 -10000 0 0
MAPK1 0.026 0.003 -9999 0 -10000 0 0
NUP214 0.025 0.005 -9999 0 -10000 0 0
CTDSP1 0.026 0.003 -9999 0 -10000 0 0
CTDSP2 0.025 0.006 -9999 0 -10000 0 0
CTDSPL 0.025 0.02 -9999 0 -0.43 1 1
KPNB1 0.026 0.003 -9999 0 -10000 0 0
TGFBRAP1 0.012 0.079 -9999 0 -0.43 16 16
UBE2I 0.026 0.002 -9999 0 -10000 0 0
NUP153 0.026 0.003 -9999 0 -10000 0 0
KPNA2 0.025 0.009 -9999 0 -10000 0 0
PIAS4 0.025 0.005 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.013 0.028 0.15 21 -10000 0 21
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.012 0.027 -10000 0 -10000 0 0
AP2 0.031 0.016 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.028 0.015 -10000 0 -10000 0 0
CLTB 0.026 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.007 -10000 0 -10000 0 0
CD4 0.022 0.032 -10000 0 -0.23 6 6
CLTA 0.026 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.007 0.004 -10000 0 -0.084 1 1
mol:PI-4-5-P2 0.004 0.017 -10000 0 -0.16 1 1
ARF1/GTP 0.025 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.01 0.005 -10000 0 -10000 0 0
mol:Choline 0.004 0.017 -10000 0 -0.17 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.015 -10000 0 -10000 0 0
DDEF1 0.003 0.017 -10000 0 -0.17 1 1
ARF1/GDP 0.002 0.018 -10000 0 -10000 0 0
AP2M1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.008 0.009 -10000 0 -10000 0 0
Rac/GTP 0.014 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.028 0.021 -10000 0 -10000 0 0
ARFIP2 0.023 0.008 -10000 0 -10000 0 0
COPA 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.023 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.014 0.011 -10000 0 -10000 0 0
GGA3 0.025 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.019 0.019 -10000 0 -10000 0 0
AP2A1 0.021 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.014 0.015 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.022 0.019 -10000 0 -0.21 1 1
Arfaptin 2/Rac/GDP 0.029 0.014 -10000 0 -10000 0 0
CYTH2 0.022 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.019 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.007 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.008 0.042 -10000 0 -0.26 2 2
PLD2 0.004 0.017 -10000 0 -0.17 1 1
ARF-GAP1/v-SNARE 0.007 0.004 -10000 0 -0.084 1 1
PIP5K1A 0.004 0.017 -10000 0 -0.16 1 1
ARF1/GTP/Membrin/GBF1/p115 0.014 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.017 -10000 0 -0.17 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.004 -10000 0 -0.084 1 1
GOSR2 0.012 0.009 -10000 0 -10000 0 0
USO1 0.006 0.045 -10000 0 -0.33 9 9
GBF1 0.005 0.046 -10000 0 -0.32 10 10
ARF1/GTP/Arfaptin 2 0.027 0.021 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.039 0.029 -10000 0 -0.23 2 2
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.037 0.009 -9999 0 -10000 0 0
FBXW11 0.026 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -9999 0 -10000 0 0
CHUK 0.025 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.059 0.04 -9999 0 -0.22 3 3
NFKB1 0.026 0.004 -9999 0 -10000 0 0
MAP3K14 0.026 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.031 0.018 -9999 0 -10000 0 0
RELB 0.02 0.025 -9999 0 -0.43 1 1
NFKB2 0.023 0.03 -9999 0 -0.33 3 3
NF kappa B2 p52/RelB 0.026 0.027 -9999 0 -0.22 4 4
regulation of B cell activation 0.026 0.027 -9999 0 -0.22 4 4
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.005 -9999 0 -10000 0 0
MDM2/SUMO1 0.041 0.02 -9999 0 -0.23 1 1
HDAC4 0.025 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.006 -9999 0 -10000 0 0
SUMO1 0.026 0.002 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.012 0.012 -9999 0 -0.26 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.011 0.002 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.003 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.026 0.002 -9999 0 -10000 0 0
SUMO1/HDAC4 0.04 0.021 -9999 0 -0.21 1 1
SUMO1/HDAC1 0.034 0.024 -9999 0 -0.23 1 1
RANGAP1 0.026 0.004 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.061 0.033 -9999 0 -0.24 5 5
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.003 -9999 0 -10000 0 0
Ran/GTP 0.029 0.019 -9999 0 -0.24 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.026 0.004 -9999 0 -10000 0 0
UBE2I 0.026 0.002 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0.017 -9999 0 -0.21 1 1
NPC 0.016 0.001 -9999 0 -10000 0 0
PIAS2 0.025 0.02 -9999 0 -0.43 1 1
PIAS1 0.022 0.04 -9999 0 -0.43 4 4
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 513 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.16 -0.16 0.064 -0.19
47_PPARGC1A 0.026 0.026 0.026 0.026
105_BMP4 0.026 0.026 0.026 0.026
105_BMP6 0.026 0.026 0.026 0.026
105_BMP7 0.026 0.026 0.026 0.026
105_BMP2 0.026 0.026 0.026 0.026
131_RELN/VLDLR 0 0.068 -0.23 0
30_TGFB1/TGF beta receptor Type II 0.026 0.026 0.027 0.026
84_STAT5B 0.097 0.033 0.066 0.033
84_STAT5A 0.097 0.033 0.066 0.033
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/22309339/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LGG-TP/22506738/GDAC_Gistic2Report_22532790/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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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