PARADIGM pathway analysis of mRNASeq expression data
Brain Lower Grade Glioma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1DR2TC0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1DR2TC0
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 68 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 130
IL23-mediated signaling events 124
FOXM1 transcription factor network 98
TCGA08_retinoblastoma 97
IL12-mediated signaling events 88
Aurora B signaling 85
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 82
E-cadherin signaling events 79
Effects of Botulinum toxin 77
TCR signaling in naïve CD8+ T cells 71
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 513 . 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 ( 513 ).

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 0.2534 130 914 7 -0.15 0 1000 -1000 -0.026 -1000
IL23-mediated signaling events 0.2417 124 7455 60 -0.67 0.014 1000 -1000 -0.14 -1000
FOXM1 transcription factor network 0.1910 98 5038 51 -0.41 0.025 1000 -1000 -0.16 -1000
TCGA08_retinoblastoma 0.1891 97 779 8 -0.098 0.075 1000 -1000 -0.012 -1000
IL12-mediated signaling events 0.1715 88 7724 87 -0.56 0.12 1000 -1000 -0.12 -1000
Aurora B signaling 0.1657 85 5716 67 -0.34 0.014 1000 -1000 -0.065 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1598 82 5607 68 -0.48 0.23 1000 -1000 -0.1 -1000
E-cadherin signaling events 0.1540 79 398 5 -0.12 0.014 1000 -1000 -0.038 -1000
Effects of Botulinum toxin 0.1501 77 2022 26 -0.2 0.014 1000 -1000 -0.057 -1000
TCR signaling in naïve CD8+ T cells 0.1384 71 6693 93 -0.21 0.068 1000 -1000 -0.068 -1000
Signaling events mediated by the Hedgehog family 0.1306 67 3519 52 -0.19 0.15 1000 -1000 -0.065 -1000
Syndecan-1-mediated signaling events 0.1267 65 2231 34 -0.23 0.014 1000 -1000 -0.056 -1000
IL4-mediated signaling events 0.1267 65 5965 91 -0.61 0.44 1000 -1000 -0.13 -1000
Thromboxane A2 receptor signaling 0.1092 56 5971 105 -0.21 0.057 1000 -1000 -0.061 -1000
Signaling mediated by p38-alpha and p38-beta 0.1092 56 2505 44 -0.15 0.014 1000 -1000 -0.045 -1000
Glypican 2 network 0.1092 56 224 4 -0.059 -0.016 1000 -1000 -0.034 -1000
Syndecan-4-mediated signaling events 0.1092 56 3813 67 -0.18 0.037 1000 -1000 -0.088 -1000
amb2 Integrin signaling 0.1053 54 4435 82 -0.23 0.014 1000 -1000 -0.069 -1000
a4b1 and a4b7 Integrin signaling 0.1014 52 260 5 -0.076 -0.033 1000 -1000 -0.037 -1000
Signaling events regulated by Ret tyrosine kinase 0.1014 52 4327 82 -0.18 0.014 1000 -1000 -0.078 -1000
Endothelins 0.0994 51 4915 96 -0.19 0.014 1000 -1000 -0.074 -1000
Reelin signaling pathway 0.0975 50 2803 56 -0.28 0.014 1000 -1000 -0.074 -1000
Visual signal transduction: Cones 0.0955 49 1876 38 -0.15 0.017 1000 -1000 -0.054 -1000
Glypican 1 network 0.0936 48 2333 48 -0.17 0.03 1000 -1000 -0.042 -1000
Caspase cascade in apoptosis 0.0916 47 3528 74 -0.19 0.043 1000 -1000 -0.052 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0877 45 3885 85 -0.15 0.014 1000 -1000 -0.063 -1000
FOXA2 and FOXA3 transcription factor networks 0.0877 45 2113 46 -0.27 0.02 1000 -1000 -0.064 -1000
HIF-1-alpha transcription factor network 0.0858 44 3371 76 -0.19 0.086 1000 -1000 -0.085 -1000
Visual signal transduction: Rods 0.0858 44 2321 52 -0.2 0.014 1000 -1000 -0.074 -1000
Ras signaling in the CD4+ TCR pathway 0.0858 44 762 17 -0.13 0.023 1000 -1000 -0.043 -1000
Aurora C signaling 0.0838 43 301 7 -0.16 0 1000 -1000 -0.042 -1000
PDGFR-alpha signaling pathway 0.0838 43 1892 44 -0.17 0.027 1000 -1000 -0.049 -1000
Calcium signaling in the CD4+ TCR pathway 0.0838 43 1362 31 -0.18 0.014 1000 -1000 -0.074 -1000
Arf6 signaling events 0.0819 42 2637 62 -0.2 0.014 1000 -1000 -0.053 -1000
p75(NTR)-mediated signaling 0.0819 42 5362 125 -0.16 0.014 1000 -1000 -0.097 -1000
IL1-mediated signaling events 0.0799 41 2602 62 -0.19 0.064 1000 -1000 -0.081 -1000
Glucocorticoid receptor regulatory network 0.0760 39 4471 114 -0.43 0.23 1000 -1000 -0.062 -1000
PLK2 and PLK4 events 0.0741 38 115 3 -0.018 -0.013 1000 -1000 -0.012 -1000
PLK1 signaling events 0.0741 38 3295 85 -0.17 0.041 1000 -1000 -0.047 -1000
Osteopontin-mediated events 0.0721 37 1422 38 -0.13 0.016 1000 -1000 -0.096 -1000
Nongenotropic Androgen signaling 0.0721 37 1949 52 -0.11 0.037 1000 -1000 -0.052 -1000
BCR signaling pathway 0.0721 37 3668 99 -0.17 0.03 1000 -1000 -0.079 -1000
LPA receptor mediated events 0.0682 35 3609 102 -0.18 0.019 1000 -1000 -0.081 -1000
EGFR-dependent Endothelin signaling events 0.0682 35 740 21 -0.11 0.014 1000 -1000 -0.069 -1000
BMP receptor signaling 0.0663 34 2781 81 -0.17 0.05 1000 -1000 -0.083 -1000
IL6-mediated signaling events 0.0663 34 2561 75 -0.15 0.064 1000 -1000 -0.072 -1000
TCGA08_p53 0.0643 33 233 7 -0.074 0.049 1000 -1000 -0.015 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0643 33 2934 88 -0.18 0.019 1000 -1000 -0.11 -1000
Fc-epsilon receptor I signaling in mast cells 0.0624 32 3115 97 -0.19 0.04 1000 -1000 -0.068 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0624 32 1186 37 -0.13 0.014 1000 -1000 -0.055 -1000
Retinoic acid receptors-mediated signaling 0.0604 31 1817 58 -0.19 0.016 1000 -1000 -0.066 -1000
ErbB2/ErbB3 signaling events 0.0585 30 1963 65 -0.17 0.023 1000 -1000 -0.062 -1000
Coregulation of Androgen receptor activity 0.0585 30 2320 76 -0.14 0.027 1000 -1000 -0.043 -1000
Rapid glucocorticoid signaling 0.0585 30 614 20 -0.17 0.014 1000 -1000 -0.034 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0585 30 3681 120 -0.21 0.13 1000 -1000 -0.07 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0565 29 992 34 -0.062 0.014 1000 -1000 -0.06 -1000
Syndecan-2-mediated signaling events 0.0565 29 2034 69 -0.16 0.034 1000 -1000 -0.053 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0565 29 1508 52 -0.19 0.027 1000 -1000 -0.057 -1000
JNK signaling in the CD4+ TCR pathway 0.0546 28 482 17 -0.071 0.014 1000 -1000 -0.052 -1000
Wnt signaling 0.0546 28 197 7 -0.034 -0.013 1000 -1000 -0.03 -1000
IL2 signaling events mediated by STAT5 0.0546 28 631 22 -0.093 0.019 1000 -1000 -0.033 -1000
LPA4-mediated signaling events 0.0526 27 324 12 -0.052 0.014 1000 -1000 -0.021 -1000
Regulation of nuclear SMAD2/3 signaling 0.0526 27 3771 136 -0.22 0.22 1000 -1000 -0.065 -1000
Presenilin action in Notch and Wnt signaling 0.0526 27 1658 61 -0.28 0.03 1000 -1000 -0.069 -1000
S1P5 pathway 0.0526 27 460 17 -0.13 0.052 1000 -1000 -0.034 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0526 27 2056 74 -0.16 0.064 1000 -1000 -0.078 -1000
Signaling events mediated by HDAC Class III 0.0507 26 1064 40 -0.12 0.1 1000 -1000 -0.04 -1000
FAS signaling pathway (CD95) 0.0507 26 1237 47 -0.15 0.016 1000 -1000 -0.044 -1000
Ephrin B reverse signaling 0.0487 25 1200 48 -0.1 0.076 1000 -1000 -0.055 -1000
E-cadherin signaling in the nascent adherens junction 0.0487 25 1915 76 -0.12 0.014 1000 -1000 -0.07 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0468 24 1340 54 -0.16 0.029 1000 -1000 -0.095 -1000
Integrins in angiogenesis 0.0468 24 2065 84 -0.094 0.014 1000 -1000 -0.083 -1000
Canonical Wnt signaling pathway 0.0468 24 1236 51 -0.28 0.096 1000 -1000 -0.06 -1000
Cellular roles of Anthrax toxin 0.0448 23 932 39 -0.16 0.019 1000 -1000 -0.033 -1000
Signaling events mediated by PTP1B 0.0448 23 1786 76 -0.14 0.02 1000 -1000 -0.069 -1000
IL2 signaling events mediated by PI3K 0.0448 23 1391 58 -0.093 0.032 1000 -1000 -0.076 -1000
IL27-mediated signaling events 0.0448 23 1212 51 -0.16 0.019 1000 -1000 -0.092 -1000
Syndecan-3-mediated signaling events 0.0429 22 782 35 -0.16 0.014 1000 -1000 -0.06 -1000
Noncanonical Wnt signaling pathway 0.0409 21 547 26 -0.11 0.014 1000 -1000 -0.056 -1000
Ceramide signaling pathway 0.0409 21 1642 76 -0.15 0.022 1000 -1000 -0.063 -1000
ErbB4 signaling events 0.0390 20 1435 69 -0.15 0.041 1000 -1000 -0.082 -1000
TCGA08_rtk_signaling 0.0390 20 531 26 -0.15 0.028 1000 -1000 -0.02 -1000
S1P1 pathway 0.0370 19 714 36 -0.1 0.014 1000 -1000 -0.052 -1000
EPHB forward signaling 0.0370 19 1623 85 -0.1 0.035 1000 -1000 -0.076 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0351 18 507 28 -0.13 0.024 1000 -1000 -0.035 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0351 18 1519 83 -0.19 0.053 1000 -1000 -0.068 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0351 18 814 45 -0.15 0.031 1000 -1000 -0.088 -1000
E-cadherin signaling in keratinocytes 0.0351 18 781 43 -0.12 0.026 1000 -1000 -0.058 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0351 18 1432 78 -0.062 0.04 1000 -1000 -0.067 -1000
Aurora A signaling 0.0331 17 1069 60 -0.14 0.032 1000 -1000 -0.055 -1000
TRAIL signaling pathway 0.0331 17 861 48 -0.047 0.029 1000 -1000 -0.058 -1000
Signaling mediated by p38-gamma and p38-delta 0.0312 16 246 15 -0.027 0.026 1000 -1000 -0.025 -1000
Regulation of Telomerase 0.0312 16 1682 102 -0.14 0.045 1000 -1000 -0.096 -1000
S1P4 pathway 0.0312 16 412 25 -0.13 0.03 1000 -1000 -0.049 -1000
BARD1 signaling events 0.0273 14 802 57 -0.052 0.029 1000 -1000 -0.063 -1000
Insulin-mediated glucose transport 0.0273 14 479 32 -0.11 0.034 1000 -1000 -0.058 -1000
Paxillin-dependent events mediated by a4b1 0.0273 14 518 36 -0.13 0.03 1000 -1000 -0.064 -1000
Regulation of p38-alpha and p38-beta 0.0273 14 788 54 -0.12 0.014 1000 -1000 -0.06 -1000
Plasma membrane estrogen receptor signaling 0.0273 14 1276 86 -0.056 0.033 1000 -1000 -0.078 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0273 14 464 33 -0.1 0.041 1000 -1000 -0.058 -1000
Regulation of Androgen receptor activity 0.0273 14 988 70 -0.13 0.032 1000 -1000 -0.065 -1000
ceramide signaling pathway 0.0253 13 670 49 -0.15 0.02 1000 -1000 -0.041 -1000
p38 MAPK signaling pathway 0.0234 12 553 44 -0.071 0.02 1000 -1000 -0.064 -1000
EPO signaling pathway 0.0214 11 639 55 -0.11 0.057 1000 -1000 -0.081 -1000
Nectin adhesion pathway 0.0214 11 726 63 -0.12 0.048 1000 -1000 -0.072 -1000
Class I PI3K signaling events 0.0214 11 821 73 -0.11 0.03 1000 -1000 -0.065 -1000
Canonical NF-kappaB pathway 0.0195 10 404 39 -0.15 0.086 1000 -1000 -0.078 -1000
IFN-gamma pathway 0.0195 10 690 68 -0.23 0.058 1000 -1000 -0.078 -1000
Signaling events mediated by PRL 0.0195 10 347 34 -0.064 0.021 1000 -1000 -0.037 -1000
Circadian rhythm pathway 0.0175 9 201 22 -0.018 0.033 1000 -1000 -0.036 -1000
Atypical NF-kappaB pathway 0.0175 9 309 31 -0.081 0.029 1000 -1000 -0.039 -1000
Class IB PI3K non-lipid kinase events 0.0175 9 27 3 -0.004 0.004 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class I 0.0156 8 848 104 -0.15 0.058 1000 -1000 -0.059 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0156 8 1052 125 -0.073 0.075 1000 -1000 -0.092 -1000
S1P3 pathway 0.0156 8 350 42 -0.033 0.031 1000 -1000 -0.037 -1000
Hedgehog signaling events mediated by Gli proteins 0.0136 7 467 65 -0.043 0.064 1000 -1000 -0.056 -1000
HIF-2-alpha transcription factor network 0.0136 7 336 43 -0.097 0.098 1000 -1000 -0.079 -1000
Insulin Pathway 0.0136 7 531 74 -0.18 0.038 1000 -1000 -0.083 -1000
VEGFR1 specific signals 0.0136 7 426 56 -0.092 0.04 1000 -1000 -0.067 -1000
PDGFR-beta signaling pathway 0.0136 7 684 97 -0.055 0.063 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class II 0.0117 6 500 75 -0.17 0.038 1000 -1000 -0.054 -1000
Arf6 downstream pathway 0.0117 6 299 43 -0.027 0.028 1000 -1000 -0.032 -1000
FoxO family signaling 0.0097 5 363 64 -0.11 0.12 1000 -1000 -0.064 -1000
Arf6 trafficking events 0.0097 5 387 71 -0.11 0.047 1000 -1000 -0.061 -1000
Class I PI3K signaling events mediated by Akt 0.0078 4 334 68 -0.11 0.054 1000 -1000 -0.053 -1000
IGF1 pathway 0.0078 4 253 57 -0.048 0.053 1000 -1000 -0.089 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0039 2 51 23 -0.014 0.05 1000 -1000 -0.063 -1000
Alternative NF-kappaB pathway 0.0039 2 28 13 -0.005 0.014 1000 -1000 -0.066 -1000
mTOR signaling pathway 0.0019 1 87 53 -0.005 0.036 1000 -1000 -0.055 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 24 27 -0.004 0.036 1000 -1000 -0.053 -1000
Arf1 pathway 0.0000 0 19 54 -0.003 0.037 1000 -1000 -0.046 -1000
Total NA 4069 223962 7203 -20 5.5 131000 -131000 -8.2 -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 -0.14 0.22 -9999 0 -0.44 171 171
EFNA5 -0.084 0.21 -9999 0 -0.54 90 90
FYN -0.11 0.21 -9999 0 -0.39 171 171
neuron projection morphogenesis -0.14 0.22 -9999 0 -0.44 171 171
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.15 0.22 -9999 0 -0.44 171 171
EPHA5 -0.14 0.25 -9999 0 -0.55 140 140
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 -0.58 0.56 -10000 0 -1.2 209 209
IL23A -0.6 0.56 -10000 0 -1.2 195 195
NF kappa B1 p50/RelA/I kappa B alpha -0.57 0.51 -10000 0 -1.1 199 199
positive regulation of T cell mediated cytotoxicity -0.62 0.61 -10000 0 -1.3 203 203
ITGA3 -0.55 0.52 -10000 0 -1.1 188 188
IL17F -0.35 0.33 -10000 0 -0.71 181 181
IL12B -0.024 0.064 -10000 0 -0.54 6 6
STAT1 (dimer) -0.6 0.58 -10000 0 -1.2 202 202
CD4 -0.53 0.5 -10000 0 -1.1 181 181
IL23 -0.58 0.53 -10000 0 -1.2 196 196
IL23R -0.082 0.084 -10000 0 -0.51 1 1
IL1B -0.64 0.61 -10000 0 -1.3 208 208
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.53 0.5 -10000 0 -1.1 184 184
TYK2 -0.001 0.018 -10000 0 -10000 0 0
STAT4 -0.16 0.26 -10000 0 -0.53 161 161
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.077 0.21 -10000 0 -0.54 85 85
IL12RB1 -0.049 0.16 -10000 0 -0.59 42 42
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
IL12Rbeta1/TYK2 -0.039 0.12 -10000 0 -0.44 42 42
IL23R/JAK2 -0.093 0.1 -10000 0 -0.5 1 1
positive regulation of chronic inflammatory response -0.62 0.61 -10000 0 -1.3 203 203
natural killer cell activation 0.008 0.007 0.047 1 -10000 0 1
JAK2 0.008 0.018 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
NFKB1 0.011 0.003 -10000 0 -10000 0 0
RELA 0.011 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.55 0.49 -10000 0 -1.1 196 196
ALOX12B -0.6 0.56 -10000 0 -1.2 207 207
CXCL1 -0.59 0.55 -10000 0 -1.2 190 190
T cell proliferation -0.62 0.61 -10000 0 -1.3 203 203
NFKBIA 0.011 0.003 -10000 0 -10000 0 0
IL17A -0.26 0.26 -10000 0 -0.56 144 144
PI3K -0.58 0.52 -10000 0 -1.1 209 209
IFNG -0.023 0.031 -10000 0 -0.1 14 14
STAT3 (dimer) -0.55 0.48 -10000 0 -1.1 203 203
IL18R1 -0.049 0.18 -10000 0 -0.54 60 60
IL23/IL23R/JAK2/TYK2/SOCS3 -0.32 0.3 -10000 0 -0.65 154 154
IL18/IL18R -0.093 0.21 -10000 0 -0.4 138 138
macrophage activation -0.027 0.018 -10000 0 -0.044 181 181
TNF -0.63 0.6 -10000 0 -1.3 207 207
STAT3/STAT4 -0.64 0.53 -10000 0 -1.1 234 234
STAT4 (dimer) -0.66 0.59 -10000 0 -1.2 228 228
IL18 -0.029 0.15 -10000 0 -0.54 41 41
IL19 -0.53 0.5 -10000 0 -1.1 178 178
STAT5A (dimer) -0.6 0.58 -10000 0 -1.2 199 199
STAT1 -0.002 0.088 -10000 0 -0.49 16 16
SOCS3 -0.11 0.23 -10000 0 -0.52 124 124
CXCL9 -0.62 0.56 -10000 0 -1.2 221 221
MPO -0.62 0.56 -10000 0 -1.2 202 202
positive regulation of humoral immune response -0.62 0.61 -10000 0 -1.3 203 203
IL23/IL23R/JAK2/TYK2 -0.67 0.71 -10000 0 -1.4 203 203
IL6 -0.6 0.56 -10000 0 -1.2 202 202
STAT5A 0.001 0.088 -10000 0 -0.59 11 11
IL2 0.006 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.007 0.047 1 -10000 0 1
CD3E -0.61 0.56 -10000 0 -1.2 208 208
keratinocyte proliferation -0.62 0.61 -10000 0 -1.3 203 203
NOS2 -0.55 0.53 -10000 0 -1.1 186 186
FOXM1 transcription factor network

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
NFATC3 -0.21 0.64 -10000 0 -1.2 127 127
PLK1 -0.003 0.19 -10000 0 -0.55 38 38
BIRC5 -0.22 0.54 -10000 0 -1 136 136
HSPA1B -0.23 0.66 -10000 0 -1.2 132 132
MAP2K1 0.023 0.051 -10000 0 -0.54 1 1
BRCA2 -0.23 0.68 -10000 0 -1.3 134 134
FOXM1 -0.37 0.93 -10000 0 -1.7 136 136
XRCC1 -0.21 0.64 -10000 0 -1.2 127 127
FOXM1B/p19 -0.38 0.56 0.43 6 -1.3 134 140
Cyclin D1/CDK4 -0.2 0.6 -10000 0 -1.1 129 129
CDC2 -0.23 0.68 -10000 0 -1.3 135 135
TGFA -0.18 0.58 -10000 0 -1 132 132
SKP2 -0.22 0.65 -10000 0 -1.2 130 130
CCNE1 0.012 0.041 -10000 0 -0.5 3 3
CKS1B -0.21 0.64 -10000 0 -1.2 126 126
RB1 -0.17 0.27 -10000 0 -0.74 64 64
FOXM1C/SP1 -0.29 0.76 -10000 0 -1.4 136 136
AURKB -0.27 0.58 -10000 0 -1.5 92 92
CENPF -0.24 0.7 -10000 0 -1.3 131 131
CDK4 0.002 0.092 -10000 0 -0.5 16 16
MYC -0.18 0.57 -10000 0 -1 129 129
CHEK2 0.007 0.11 -10000 0 -0.56 16 16
ONECUT1 -0.22 0.64 -10000 0 -1.2 133 133
CDKN2A -0.1 0.23 -10000 0 -0.56 104 104
LAMA4 -0.21 0.65 -10000 0 -1.2 133 133
FOXM1B/HNF6 -0.31 0.78 -10000 0 -1.5 134 134
FOS -0.3 0.7 -10000 0 -1.2 171 171
SP1 0.014 0.006 -10000 0 -10000 0 0
CDC25B -0.21 0.64 -10000 0 -1.2 126 126
response to radiation 0.008 0.041 -10000 0 -10000 0 0
CENPB -0.21 0.64 -10000 0 -1.2 125 125
CENPA -0.26 0.71 -10000 0 -1.3 139 139
NEK2 -0.28 0.72 -10000 0 -1.3 144 144
HIST1H2BA -0.22 0.64 -10000 0 -1.2 127 127
CCNA2 -0.055 0.19 -10000 0 -0.54 66 66
EP300 0.009 0.053 -10000 0 -0.59 4 4
CCNB1/CDK1 -0.29 0.78 -10000 0 -1.5 130 130
CCNB2 -0.28 0.73 -10000 0 -1.4 144 144
CCNB1 -0.24 0.69 -10000 0 -1.3 131 131
ETV5 -0.23 0.65 -10000 0 -1.2 136 136
ESR1 -0.23 0.66 -10000 0 -1.2 140 140
CCND1 -0.2 0.62 -10000 0 -1.1 132 132
GSK3A 0.025 0.036 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.015 0.16 -10000 0 -0.39 69 69
CDK2 0.001 0.089 -10000 0 -0.54 13 13
G2/M transition of mitotic cell cycle 0.008 0.049 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.41 0.58 -10000 0 -1.3 142 142
GAS1 -0.22 0.65 -10000 0 -1.2 126 126
MMP2 -0.22 0.66 -10000 0 -1.2 128 128
RB1/FOXM1C -0.22 0.64 -10000 0 -1.2 131 131
CREBBP 0.014 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.059 0.19 -10000 0 -0.54 68 68
CDKN2C -0.022 0.13 -10000 0 -0.44 46 46
CDKN2A -0.098 0.22 -10000 0 -0.53 104 104
CCND2 0.064 0.14 0.29 111 -0.14 2 113
RB1 -0.068 0.15 -10000 0 -0.31 108 108
CDK4 0.075 0.15 0.33 108 -10000 0 108
CDK6 0.068 0.15 0.32 109 -0.16 15 124
G1/S progression 0.055 0.15 0.31 108 -10000 0 108
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.17 -10000 0 -0.4 89 89
TBX21 -0.47 0.5 -10000 0 -1 191 191
B2M 0.009 0.05 -10000 0 -0.5 5 5
TYK2 0.001 0.019 -10000 0 -10000 0 0
IL12RB1 -0.046 0.16 -10000 0 -0.58 42 42
GADD45B -0.35 0.39 -10000 0 -0.83 149 149
IL12RB2 -0.13 0.23 -10000 0 -0.54 123 123
GADD45G -0.37 0.41 -10000 0 -0.95 117 117
natural killer cell activation -0.016 0.023 -10000 0 -10000 0 0
RELB 0.009 0.052 -10000 0 -0.51 5 5
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.034 0.16 -10000 0 -0.56 41 41
IL2RA -0.062 0.18 -10000 0 -0.5 71 71
IFNG -0.002 0.049 -10000 0 -0.49 5 5
STAT3 (dimer) -0.36 0.36 -10000 0 -0.74 202 202
HLA-DRB5 -0.13 0.24 -10000 0 -0.54 129 129
FASLG -0.44 0.47 -10000 0 -0.96 191 191
NF kappa B2 p52/RelB -0.46 0.43 -10000 0 -0.91 205 205
CD4 0.006 0.056 -10000 0 -0.51 6 6
SOCS1 -0.032 0.15 -10000 0 -0.51 45 45
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D -0.11 0.23 -10000 0 -0.53 117 117
CD3E -0.13 0.24 -10000 0 -0.54 136 136
CD3G -0.035 0.14 -10000 0 -0.5 43 43
IL12Rbeta2/JAK2 -0.095 0.18 -10000 0 -0.4 123 123
CCL3 -0.56 0.58 -10000 0 -1.2 213 213
CCL4 -0.56 0.59 -10000 0 -1.2 199 199
HLA-A 0.005 0.07 -10000 0 -0.49 10 10
IL18/IL18R -0.091 0.22 -10000 0 -0.42 143 143
NOS2 -0.41 0.45 -10000 0 -0.94 166 166
IL12/IL12R/TYK2/JAK2/SPHK2 -0.1 0.15 -10000 0 -0.39 72 72
IL1R1 -0.45 0.48 -10000 0 -0.99 188 188
IL4 0.019 0.023 -10000 0 -10000 0 0
JAK2 0.001 0.019 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.23 -10000 0 -0.56 86 86
RAB7A -0.28 0.32 -10000 0 -0.74 101 101
lysosomal transport -0.27 0.3 -10000 0 -0.69 105 105
FOS -0.36 0.46 -10000 0 -0.96 146 146
STAT4 (dimer) -0.42 0.41 -10000 0 -0.86 193 193
STAT5A (dimer) -0.47 0.44 -10000 0 -0.92 209 209
GZMA -0.52 0.54 -10000 0 -1.1 205 205
GZMB -0.5 0.53 -10000 0 -1.1 190 190
HLX -0.002 0.092 -10000 0 -0.52 16 16
LCK -0.51 0.53 -10000 0 -1 226 226
TCR/CD3/MHC II/CD4 -0.16 0.24 -10000 0 -0.5 143 143
IL2/IL2R -0.12 0.21 -10000 0 -0.48 102 102
MAPK14 -0.35 0.39 -10000 0 -0.83 154 154
CCR5 -0.41 0.46 -10000 0 -0.93 167 167
IL1B -0.19 0.27 -10000 0 -0.56 173 173
STAT6 -0.11 0.12 -10000 0 -0.24 88 88
STAT4 -0.16 0.26 -10000 0 -0.53 161 161
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 -0.002 0.088 -10000 0 -0.49 16 16
NFKB1 0.014 0 -10000 0 -10000 0 0
NFKB2 0.011 0.044 -10000 0 -0.56 3 3
IL12B -0.016 0.06 -10000 0 -0.53 6 6
CD8A -0.076 0.21 -10000 0 -0.55 83 83
CD8B -0.031 0.16 -10000 0 -0.56 41 41
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.12 0.17 0.4 89 -10000 0 89
IL2RB -0.094 0.22 -10000 0 -0.53 102 102
proteasomal ubiquitin-dependent protein catabolic process -0.38 0.37 -10000 0 -0.78 193 193
IL2RG -0.042 0.16 -10000 0 -0.52 54 54
IL12 -0.035 0.11 -10000 0 -0.44 35 35
STAT5A 0.001 0.088 -10000 0 -0.59 11 11
CD247 -0.02 0.13 -10000 0 -0.52 31 31
IL2 0.001 0.003 -10000 0 -10000 0 0
SPHK2 0.014 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.033 0.14 -10000 0 -0.6 29 29
IL12/IL12R/TYK2/JAK2 -0.52 0.58 -10000 0 -1.1 216 216
MAP2K3 -0.36 0.4 -10000 0 -0.82 167 167
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.36 0.4 -10000 0 -0.81 170 170
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.091 0.22 -10000 0 -0.54 97 97
IL18RAP -0.082 0.21 -10000 0 -0.55 85 85
IL12Rbeta1/TYK2 -0.035 0.12 -10000 0 -0.43 42 42
EOMES -0.002 0.13 -10000 0 -1.3 1 1
STAT1 (dimer) -0.36 0.35 -10000 0 -0.75 182 182
T cell proliferation -0.31 0.29 -10000 0 -0.62 184 184
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.054 0.18 -10000 0 -0.55 60 60
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.36 0.29 -10000 0 -0.68 191 191
ATF2 -0.33 0.36 -10000 0 -0.78 145 145
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 -0.13 0.26 -9999 0 -0.58 113 113
STMN1 -0.1 0.2 -9999 0 -0.4 157 157
Aurora B/RasGAP/Survivin -0.17 0.28 -9999 0 -0.54 175 175
Chromosomal passenger complex/Cul3 protein complex -0.092 0.2 -9999 0 -0.4 130 130
BIRC5 -0.14 0.26 -9999 0 -0.57 137 137
DES -0.34 0.45 -9999 0 -0.92 167 167
Aurora C/Aurora B/INCENP -0.1 0.17 -9999 0 -0.33 169 169
Aurora B/TACC1 -0.094 0.16 -9999 0 -0.33 156 156
Aurora B/PP2A -0.11 0.19 -9999 0 -0.4 156 156
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.029 0.074 -9999 0 -0.17 93 93
mitotic metaphase/anaphase transition 0 0.006 -9999 0 -10000 0 0
NDC80 -0.19 0.32 -9999 0 -0.6 180 180
Cul3 protein complex -0.008 0.052 -9999 0 -0.36 11 11
KIF2C -0.13 0.28 -9999 0 -0.44 168 168
PEBP1 0.005 0.055 -9999 0 -0.61 4 4
KIF20A -0.17 0.27 -9999 0 -0.55 168 168
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.11 0.19 -9999 0 -0.4 156 156
SEPT1 0.009 0.052 -9999 0 -0.51 5 5
SMC2 0.014 0 -9999 0 -10000 0 0
SMC4 -0.016 0.12 -9999 0 -0.49 31 31
NSUN2/NPM1/Nucleolin -0.16 0.33 -9999 0 -0.83 92 92
PSMA3 0.014 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.076 0.15 -9999 0 -0.36 93 93
AURKB -0.16 0.27 -9999 0 -0.56 156 156
AURKC -0.022 0.14 -9999 0 -0.52 35 35
CDCA8 -0.062 0.18 -9999 0 -0.53 69 69
cytokinesis -0.27 0.4 -9999 0 -0.79 168 168
Aurora B/Septin1 -0.24 0.38 -9999 0 -0.75 166 166
AURKA -0.015 0.12 -9999 0 -0.5 29 29
INCENP 0.008 0.029 -9999 0 -0.62 1 1
KLHL13 0.012 0.038 -9999 0 -0.59 2 2
BUB1 -0.11 0.24 -9999 0 -0.55 117 117
hSgo1/Aurora B/Survivin -0.23 0.35 -9999 0 -0.66 188 188
EVI5 0.013 0.003 -9999 0 -10000 0 0
RhoA/GTP -0.24 0.35 -9999 0 -0.71 164 164
SGOL1 -0.12 0.24 -9999 0 -0.54 126 126
CENPA -0.17 0.32 -9999 0 -0.57 165 165
NCAPG -0.14 0.25 -9999 0 -0.55 141 141
Aurora B/HC8 Proteasome -0.11 0.19 -9999 0 -0.4 156 156
NCAPD2 0.009 0.05 -9999 0 -0.49 5 5
Aurora B/PP1-gamma -0.11 0.19 -9999 0 -0.4 156 156
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH -0.065 0.19 -9999 0 -0.54 74 74
NPM1 -0.13 0.24 -9999 0 -0.61 92 92
RASA1 0.014 0 -9999 0 -10000 0 0
KLHL9 0.004 0.08 -9999 0 -0.59 9 9
mitotic prometaphase -0.006 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.11 0.19 -9999 0 -0.39 156 156
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.26 0.39 -9999 0 -0.77 169 169
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.13 0.24 -9999 0 -0.61 92 92
MYLK -0.086 0.16 -9999 0 -0.3 169 169
KIF23 -0.11 0.23 -9999 0 -0.54 113 113
VIM -0.16 0.24 -9999 0 -0.43 213 213
RACGAP1 0.004 0.057 -9999 0 -0.52 6 6
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.13 0.24 -9999 0 -0.61 92 92
Chromosomal passenger complex -0.21 0.38 -9999 0 -0.68 169 169
Chromosomal passenger complex/EVI5 -0.18 0.31 -9999 0 -0.61 157 157
TACC1 0.014 0 -9999 0 -10000 0 0
PPP2R5D 0.014 0 -9999 0 -10000 0 0
CUL3 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.013 0.1 -10000 0 -0.57 12 12
NFATC2 -0.13 0.3 -10000 0 -0.69 92 92
NFATC3 -0.049 0.11 -10000 0 -0.31 13 13
CD40LG -0.38 0.49 -10000 0 -1 160 160
ITCH -0.031 0.12 -10000 0 -0.52 3 3
CBLB -0.032 0.13 -10000 0 -0.6 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.41 -10000 0 -0.94 117 117
JUNB -0.033 0.15 -10000 0 -0.51 46 46
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.084 0.12 -10000 0 -0.3 89 89
T cell anergy -0.095 0.19 -10000 0 -0.42 97 97
TLE4 -0.081 0.25 -10000 0 -0.68 52 52
Jun/NFAT1-c-4/p21SNFT -0.36 0.46 -10000 0 -1 140 140
AP-1/NFAT1-c-4 -0.46 0.6 -10000 0 -1.2 156 156
IKZF1 -0.093 0.28 -10000 0 -0.68 68 68
T-helper 2 cell differentiation -0.18 0.3 -10000 0 -0.83 55 55
AP-1/NFAT1 -0.17 0.26 -10000 0 -0.55 128 128
CALM1 -0.026 0.088 -10000 0 -0.69 2 2
EGR2 -0.31 0.56 -10000 0 -1.2 113 113
EGR3 -0.34 0.6 -10000 0 -1.3 122 122
NFAT1/FOXP3 -0.12 0.25 -10000 0 -0.62 76 76
EGR1 -0.11 0.23 -10000 0 -0.54 115 115
JUN -0.003 0.078 -10000 0 -0.51 11 11
EGR4 -0.19 0.27 -10000 0 -0.55 184 184
mol:Ca2+ -0.041 0.083 -10000 0 -0.3 1 1
GBP3 -0.16 0.35 -10000 0 -0.74 112 112
FOSL1 -0.093 0.22 -10000 0 -0.53 101 101
NFAT1-c-4/MAF/IRF4 -0.33 0.45 -10000 0 -0.98 133 133
DGKA -0.074 0.23 -10000 0 -0.58 61 61
CREM 0.012 0.035 -10000 0 -0.54 2 2
NFAT1-c-4/PPARG -0.34 0.46 -10000 0 -0.98 141 141
CTLA4 -0.12 0.29 -10000 0 -0.68 90 90
NFAT1-c-4 (dimer)/EGR1 -0.39 0.53 -10000 0 -1.1 157 157
NFAT1-c-4 (dimer)/EGR4 -0.43 0.49 -10000 0 -1 165 165
FOS -0.1 0.22 -10000 0 -0.56 99 99
IFNG -0.17 0.24 -10000 0 -0.75 47 47
T cell activation -0.17 0.29 -10000 0 -0.71 69 69
MAF 0.011 0.046 -10000 0 -0.59 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.23 0.42 0.84 124 -10000 0 124
TNF -0.48 0.51 -10000 0 -1 204 204
FASLG -0.35 0.57 -10000 0 -1.3 115 115
TBX21 -0.045 0.17 -10000 0 -0.53 56 56
BATF3 -0.035 0.16 -10000 0 -0.53 46 46
PRKCQ -0.005 0.11 -10000 0 -0.58 17 17
PTPN1 -0.074 0.23 -10000 0 -0.58 61 61
NFAT1-c-4/ICER1 -0.32 0.46 -10000 0 -0.97 140 140
GATA3 -0.11 0.23 -10000 0 -0.54 115 115
T-helper 1 cell differentiation -0.16 0.25 -10000 0 -0.73 48 48
IL2RA -0.3 0.34 -10000 0 -0.81 117 117
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.075 0.23 -10000 0 -0.62 51 51
E2F1 -0.01 0.12 -10000 0 -0.52 28 28
PPARG -0.014 0.12 -10000 0 -0.56 25 25
SLC3A2 -0.074 0.23 -10000 0 -0.59 60 60
IRF4 -0.042 0.17 -10000 0 -0.54 52 52
PTGS2 -0.41 0.53 -10000 0 -1.1 160 160
CSF2 -0.37 0.48 -10000 0 -1 148 148
JunB/Fra1/NFAT1-c-4 -0.37 0.47 -10000 0 -0.99 153 153
IL4 -0.19 0.31 -10000 0 -0.89 53 53
IL5 -0.36 0.48 -10000 0 -1 150 150
IL2 -0.17 0.29 -10000 0 -0.73 68 68
IL3 -0.063 0.06 -10000 0 -10000 0 0
RNF128 -0.15 0.29 -10000 0 -0.55 170 170
NFATC1 -0.23 0.43 -10000 0 -0.85 124 124
CDK4 0.13 0.25 0.6 50 -0.57 2 52
PTPRK -0.076 0.23 -10000 0 -0.6 62 62
IL8 -0.43 0.53 -10000 0 -1.1 172 172
POU2F1 0.014 0.001 -10000 0 -10000 0 0
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.085 0.15 -9999 0 -0.32 134 134
E-cadherin/beta catenin -0.095 0.17 -9999 0 -0.38 127 127
CTNNB1 0.014 0 -9999 0 -10000 0 0
JUP 0.003 0.081 -9999 0 -0.57 10 10
CDH1 -0.12 0.24 -9999 0 -0.54 127 127
Effects of Botulinum toxin

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
STX1A -0.048 0.14 -9999 0 -0.36 83 83
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.093 0.17 -9999 0 -0.4 120 120
STXBP1 -0.014 0.12 -9999 0 -0.5 28 28
ACh/CHRNA1 -0.13 0.17 -9999 0 -0.37 161 161
RAB3GAP2/RIMS1/UNC13B -0.077 0.14 -9999 0 -0.33 120 120
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.12 0.24 -9999 0 -0.55 120 120
mol:ACh -0.037 0.068 -9999 0 -0.13 163 163
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.14 0.2 -9999 0 -0.45 128 128
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.13 0.17 -9999 0 -0.37 161 161
UNC13B 0.013 0.027 -9999 0 -0.59 1 1
CHRNA1 -0.16 0.26 -9999 0 -0.53 161 161
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.15 0.21 -9999 0 -0.41 198 198
SNAP25 -0.074 0.13 -9999 0 -0.25 166 166
VAMP2 0.007 0.007 -9999 0 -0.14 1 1
SYT1 -0.2 0.27 -9999 0 -0.54 198 198
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.046 0.16 -9999 0 -0.38 85 85
STX1A/SNAP25 fragment 1/VAMP2 -0.14 0.2 -9999 0 -0.45 128 128
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.14 0.18 -10000 0 -0.44 107 107
FYN -0.14 0.27 -10000 0 -0.53 132 132
LAT/GRAP2/SLP76 -0.16 0.22 -10000 0 -0.49 126 126
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.1 0.19 -10000 0 -0.38 126 126
B2M 0.007 0.051 -10000 0 -0.5 5 5
IKBKG -0.034 0.046 -10000 0 -0.15 25 25
MAP3K8 -0.006 0.1 -10000 0 -0.51 20 20
mol:Ca2+ -0.025 0.042 -10000 0 -0.11 94 94
integrin-mediated signaling pathway -0.009 0.055 -10000 0 -0.32 15 15
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.16 0.26 -10000 0 -0.52 137 137
TRPV6 -0.11 0.23 -10000 0 -0.56 106 106
CD28 -0.075 0.2 -10000 0 -0.54 81 81
SHC1 -0.14 0.26 -10000 0 -0.52 129 129
receptor internalization -0.13 0.23 -10000 0 -0.48 119 119
PRF1 -0.17 0.36 -10000 0 -0.84 88 88
KRAS 0.013 0.022 -10000 0 -0.49 1 1
GRB2 0.013 0.022 -10000 0 -0.49 1 1
COT/AKT1 -0.082 0.16 -10000 0 -0.33 115 115
LAT -0.16 0.26 -10000 0 -0.52 138 138
EntrezGene:6955 -0.002 0.006 -10000 0 -10000 0 0
CD3D -0.11 0.23 -10000 0 -0.53 117 117
CD3E -0.13 0.25 -10000 0 -0.54 136 136
CD3G -0.035 0.14 -10000 0 -0.5 43 43
RASGRP2 -0.006 0.025 -10000 0 -0.18 3 3
RASGRP1 -0.11 0.2 -10000 0 -0.39 128 128
HLA-A 0.002 0.071 -10000 0 -0.5 10 10
RASSF5 -0.002 0.093 -10000 0 -0.54 15 15
RAP1A/GTP/RAPL -0.009 0.055 -10000 0 -0.32 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.015 0.062 -10000 0 -0.11 56 56
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.063 0.08 -10000 0 -0.22 61 61
PRKCA -0.079 0.1 -10000 0 -0.25 91 91
GRAP2 -0.047 0.17 -10000 0 -0.53 57 57
mol:IP3 -0.1 0.19 0.21 49 -0.38 112 161
EntrezGene:6957 -0.002 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.11 0.21 -10000 0 -0.44 116 116
ORAI1 0.068 0.12 0.31 105 -0.36 1 106
CSK -0.15 0.26 -10000 0 -0.53 130 130
B7 family/CD28 -0.21 0.27 -10000 0 -0.58 145 145
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.17 0.29 -10000 0 -0.56 144 144
PTPN6 -0.15 0.27 -10000 0 -0.54 136 136
VAV1 -0.16 0.27 -10000 0 -0.54 137 137
Monovalent TCR/CD3 -0.11 0.19 -10000 0 -0.36 171 171
CBL 0.014 0 -10000 0 -10000 0 0
LCK -0.17 0.29 -10000 0 -0.55 152 152
PAG1 -0.15 0.26 -10000 0 -0.53 130 130
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.17 0.29 -10000 0 -0.57 137 137
CD80 -0.046 0.16 -10000 0 -0.51 56 56
CD86 -0.026 0.14 -10000 0 -0.56 35 35
PDK1/CARD11/BCL10/MALT1 -0.077 0.097 -10000 0 -0.26 72 72
HRAS 0.014 0 -10000 0 -10000 0 0
GO:0035030 -0.15 0.24 -10000 0 -0.48 143 143
CD8A -0.078 0.21 -10000 0 -0.55 83 83
CD8B -0.034 0.16 -10000 0 -0.56 41 41
PTPRC -0.042 0.17 -10000 0 -0.54 51 51
PDK1/PKC theta -0.12 0.23 -10000 0 -0.46 122 122
CSK/PAG1 -0.14 0.25 -10000 0 -0.53 120 120
SOS1 0.014 0 -10000 0 -10000 0 0
peptide-MHC class I 0.004 0.071 -10000 0 -0.43 12 12
GRAP2/SLP76 -0.18 0.25 -10000 0 -0.54 138 138
STIM1 0.037 0.061 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.083 -10000 0 -0.17 33 33
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.13 0.24 -10000 0 -0.51 118 118
mol:DAG -0.11 0.15 -10000 0 -0.34 121 121
RAP1A/GDP -0.005 0.027 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 -0.02 0.13 -10000 0 -0.52 31 31
cytotoxic T cell degranulation -0.16 0.34 -10000 0 -0.79 88 88
RAP1A/GTP -0.004 0.007 -10000 0 -0.067 2 2
mol:PI-3-4-5-P3 -0.13 0.22 -10000 0 -0.44 134 134
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.14 0.23 0.24 40 -0.49 114 154
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.047 0.17 -10000 0 -0.53 57 57
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
LAT/GRAP2/SLP76/VAV1 -0.16 0.21 -10000 0 -0.48 129 129
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.027 -10000 0 -0.59 1 1
CD8 heterodimer -0.081 0.2 -10000 0 -0.46 105 105
CARD11 -0.009 0.11 -10000 0 -0.57 20 20
PRKCB -0.1 0.11 -10000 0 -0.27 127 127
PRKCE -0.082 0.1 -10000 0 -0.26 96 96
PRKCQ -0.15 0.25 -10000 0 -0.51 132 132
LCP2 -0.001 0.086 -10000 0 -0.5 15 15
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.087 0.16 -10000 0 -0.32 124 124
IKK complex -0.01 0.061 -10000 0 -0.11 25 25
RAS family/GDP -0.007 0.009 -10000 0 -10000 0 0
MAP3K14 -0.055 0.13 -10000 0 -0.27 78 78
PDPK1 -0.096 0.18 -10000 0 -0.37 117 117
TCR/CD3/MHC I/CD8/Fyn -0.17 0.3 -10000 0 -0.57 150 150
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.1 0.29 -10000 0 -0.72 65 65
IHH -0.014 0.086 -10000 0 -0.51 9 9
SHH Np/Cholesterol/GAS1 -0.069 0.16 -10000 0 -0.36 83 83
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.086 0.15 0.36 83 -10000 0 83
SMO/beta Arrestin2 -0.036 0.18 -10000 0 -0.69 16 16
SMO -0.046 0.18 -10000 0 -0.67 20 20
AKT1 0.002 0.083 -10000 0 -0.31 7 7
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC 0.007 0.062 -10000 0 -0.56 6 6
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.045 0.18 -10000 0 -0.61 24 24
STIL -0.093 0.22 -10000 0 -0.52 74 74
DHH N/PTCH2 -0.058 0.14 -10000 0 -0.4 73 73
DHH N/PTCH1 -0.069 0.19 -10000 0 -0.54 39 39
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
DHH -0.046 0.17 -10000 0 -0.54 55 55
PTHLH -0.12 0.34 -10000 0 -0.92 63 63
determination of left/right symmetry -0.045 0.18 -10000 0 -0.61 24 24
PIK3R1 0.014 0 -10000 0 -10000 0 0
skeletal system development -0.11 0.34 -10000 0 -0.91 63 63
IHH N/Hhip -0.12 0.21 -10000 0 -0.44 145 145
DHH N/Hhip -0.15 0.21 -10000 0 -0.42 178 178
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.045 0.18 -10000 0 -0.61 24 24
pancreas development -0.14 0.25 -10000 0 -0.55 140 140
HHAT -0.006 0.11 -10000 0 -0.57 18 18
PI3K -0.001 0.019 -10000 0 -0.43 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.014 0.12 -10000 0 -0.5 28 28
somite specification -0.045 0.18 -10000 0 -0.61 24 24
SHH Np/Cholesterol/PTCH1 -0.093 0.21 -10000 0 -0.54 64 64
SHH Np/Cholesterol/PTCH2 -0.067 0.16 -10000 0 -0.35 86 86
SHH Np/Cholesterol/Megalin -0.17 0.22 -10000 0 -0.36 257 257
SHH -0.079 0.19 -10000 0 -0.41 123 123
catabolic process -0.047 0.18 -10000 0 -0.6 26 26
SMO/Vitamin D3 -0.084 0.22 -10000 0 -0.56 54 54
SHH Np/Cholesterol/Hhip -0.14 0.21 -10000 0 -0.35 223 223
LRP2 -0.19 0.27 -10000 0 -0.55 185 185
receptor-mediated endocytosis -0.18 0.22 -10000 0 -0.55 97 97
SHH Np/Cholesterol/BOC -0.057 0.15 -10000 0 -0.31 126 126
SHH Np/Cholesterol/CDO -0.075 0.17 -10000 0 -0.33 148 148
mesenchymal cell differentiation 0.15 0.2 0.35 223 -10000 0 223
mol:Vitamin D3 -0.091 0.22 -10000 0 -0.54 63 63
IHH N/PTCH2 -0.011 0.11 -10000 0 -0.45 25 25
CDON -0.025 0.14 -10000 0 -0.56 35 35
IHH N/PTCH1 -0.047 0.19 -10000 0 -0.6 26 26
Megalin/LRPAP1 -0.14 0.19 -10000 0 -0.39 185 185
PTCH2 -0.009 0.11 -10000 0 -0.56 21 21
SHH Np/Cholesterol -0.075 0.14 -10000 0 -0.32 123 123
PTCH1 -0.047 0.18 -10000 0 -0.6 26 26
HHIP -0.14 0.25 -10000 0 -0.55 140 140
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.004 0.08 -9999 0 -0.59 9 9
CCL5 -0.086 0.21 -9999 0 -0.53 94 94
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.13 0.19 -9999 0 -0.48 74 74
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.12 0.18 -9999 0 -0.45 75 75
Syndecan-1/Syntenin -0.12 0.18 -9999 0 -0.45 74 74
MAPK3 -0.094 0.16 -9999 0 -0.48 42 42
HGF/MET -0.17 0.22 -9999 0 -0.43 203 203
TGFB1/TGF beta receptor Type II 0.004 0.079 -9999 0 -0.59 9 9
BSG 0.014 0 -9999 0 -10000 0 0
keratinocyte migration -0.12 0.18 -9999 0 -0.44 75 75
Syndecan-1/RANTES -0.17 0.22 -9999 0 -0.49 117 117
Syndecan-1/CD147 -0.11 0.17 -9999 0 -0.51 42 42
Syndecan-1/Syntenin/PIP2 -0.12 0.17 -9999 0 -0.44 74 74
LAMA5 0.012 0.035 -9999 0 -0.54 2 2
positive regulation of cell-cell adhesion -0.13 0.15 -9999 0 -0.43 74 74
MMP7 -0.15 0.25 -9999 0 -0.54 152 152
HGF -0.079 0.2 -9999 0 -0.51 91 91
Syndecan-1/CASK -0.13 0.18 -9999 0 -0.46 74 74
Syndecan-1/HGF/MET -0.23 0.25 -9999 0 -0.53 164 164
regulation of cell adhesion -0.084 0.16 -9999 0 -0.46 39 39
HPSE -0.053 0.19 -9999 0 -0.56 60 60
positive regulation of cell migration -0.13 0.19 -9999 0 -0.48 74 74
SDC1 -0.14 0.19 -9999 0 -0.48 74 74
Syndecan-1/Collagen -0.13 0.19 -9999 0 -0.48 74 74
PPIB 0.014 0 -9999 0 -10000 0 0
MET -0.15 0.25 -9999 0 -0.53 150 150
PRKACA 0.014 0 -9999 0 -10000 0 0
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
MAPK1 -0.094 0.16 -9999 0 -0.48 42 42
homophilic cell adhesion -0.13 0.18 -9999 0 -0.47 74 74
MMP1 -0.046 0.16 -9999 0 -0.49 55 55
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.39 0.43 -10000 0 -1.1 81 81
STAT6 (cleaved dimer) -0.47 0.43 -10000 0 -0.99 170 170
IGHG1 -0.16 0.21 -10000 0 -0.71 24 24
IGHG3 -0.38 0.41 -10000 0 -0.96 128 128
AKT1 -0.24 0.29 -10000 0 -0.74 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.75 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.26 -10000 0 -0.7 57 57
THY1 -0.4 0.46 -10000 0 -1.1 96 96
MYB -0.064 0.19 -10000 0 -0.54 72 72
HMGA1 0.01 0.047 -10000 0 -0.52 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.34 -10000 0 -0.77 136 136
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.27 -10000 0 -0.71 57 57
SP1 0.02 0.011 -10000 0 -10000 0 0
INPP5D 0.008 0.06 -10000 0 -0.54 6 6
SOCS5 0.027 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.45 -10000 0 -1 151 151
SOCS1 -0.3 0.33 -10000 0 -0.78 98 98
SOCS3 -0.35 0.4 -10000 0 -0.94 124 124
FCER2 -0.42 0.44 -10000 0 -1 121 121
PARP14 -0.002 0.085 -10000 0 -0.52 13 13
CCL17 -0.4 0.44 -10000 0 -1.1 92 92
GRB2 0.013 0.022 -10000 0 -0.49 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.23 -10000 0 -0.65 49 49
T cell proliferation -0.41 0.45 -10000 0 -1.1 111 111
IL4R/JAK1 -0.4 0.43 -10000 0 -1.1 96 96
EGR2 -0.51 0.54 -10000 0 -1.3 133 133
JAK2 -0.004 0.027 -10000 0 -10000 0 0
JAK3 -0.057 0.18 -10000 0 -0.53 67 67
PIK3R1 0.014 0 -10000 0 -10000 0 0
JAK1 0.005 0.012 -10000 0 -10000 0 0
COL1A2 -0.16 0.25 -10000 0 -0.75 45 45
CCL26 -0.4 0.44 -10000 0 -1.1 91 91
IL4R -0.42 0.46 -10000 0 -1.1 91 91
PTPN6 0.006 0.099 -10000 0 -0.54 16 16
IL13RA2 -0.61 0.58 -10000 0 -1.2 194 194
IL13RA1 -0.015 0.084 -10000 0 -0.61 9 9
IRF4 -0.17 0.33 -10000 0 -1.1 43 43
ARG1 -0.13 0.23 -10000 0 -0.84 29 29
CBL -0.3 0.32 -10000 0 -0.74 126 126
GTF3A 0.009 0.034 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
IL13RA1/JAK2 -0.015 0.07 -10000 0 -0.45 9 9
IRF4/BCL6 -0.15 0.31 -10000 0 -1 42 42
CD40LG -0.035 0.15 -10000 0 -0.5 46 46
MAPK14 -0.32 0.35 -10000 0 -0.8 128 128
mitosis -0.23 0.27 -10000 0 -0.7 75 75
STAT6 -0.45 0.5 -10000 0 -1.2 115 115
SPI1 -0.004 0.11 -10000 0 -0.54 19 19
RPS6KB1 -0.21 0.26 -10000 0 -0.68 67 67
STAT6 (dimer) -0.45 0.5 -10000 0 -1.2 114 114
STAT6 (dimer)/PARP14 -0.43 0.46 -10000 0 -1.1 126 126
mast cell activation 0.011 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.31 -10000 0 -0.79 90 90
FRAP1 -0.24 0.29 -10000 0 -0.74 75 75
LTA -0.42 0.48 -10000 0 -1.2 100 100
FES 0.01 0.047 -10000 0 -0.52 4 4
T-helper 1 cell differentiation 0.44 0.48 1.1 119 -10000 0 119
CCL11 -0.38 0.41 -10000 0 -1.1 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.25 0.3 -10000 0 -0.79 74 74
IL2RG -0.042 0.16 -10000 0 -0.52 54 54
IL10 -0.49 0.56 -10000 0 -1.3 129 129
IRS1 0.014 0 -10000 0 -10000 0 0
IRS2 0.012 0.035 -10000 0 -0.54 2 2
IL4 -0.097 0.11 -10000 0 -10000 0 0
IL5 -0.4 0.43 -10000 0 -1.1 85 85
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.32 0.35 -10000 0 -0.84 92 92
COL1A1 -0.35 0.5 -10000 0 -1.1 127 127
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.44 -10000 0 -1.1 78 78
IL2R gamma/JAK3 -0.073 0.19 -10000 0 -0.44 101 101
TFF3 -0.41 0.45 -10000 0 -1.1 99 99
ALOX15 -0.4 0.44 -10000 0 -1.1 86 86
MYBL1 0.01 0.044 -10000 0 -0.49 4 4
T-helper 2 cell differentiation -0.36 0.37 -10000 0 -0.88 115 115
SHC1 0.009 0.05 -10000 0 -0.49 5 5
CEBPB -0.003 0.11 -10000 0 -0.56 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.26 -10000 0 -0.68 59 59
mol:PI-3-4-5-P3 -0.24 0.29 -10000 0 -0.74 75 75
PI3K -0.25 0.31 -10000 0 -0.8 75 75
DOK2 -0.071 0.2 -10000 0 -0.53 80 80
ETS1 0.015 0.076 -10000 0 -0.51 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.22 -10000 0 -0.62 47 47
ITGB3 -0.43 0.48 -10000 0 -1.1 111 111
PIGR -0.49 0.55 -10000 0 -1.3 119 119
IGHE 0.021 0.061 -10000 0 -0.25 12 12
MAPKKK cascade -0.17 0.22 -10000 0 -0.61 47 47
BCL6 0.016 0.006 -10000 0 -10000 0 0
OPRM1 -0.41 0.44 -10000 0 -1.1 87 87
RETNLB -0.4 0.43 -10000 0 -1.1 86 86
SELP -0.4 0.44 -10000 0 -1.1 90 90
AICDA -0.38 0.42 -10000 0 -1 97 97
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.008 0.05 -10000 0 -0.49 5 5
GNB1/GNG2 -0.078 0.08 -10000 0 -0.19 149 149
AKT1 -0.059 0.12 -10000 0 -0.21 106 106
EGF -0.05 0.18 -10000 0 -0.56 58 58
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.017 0.07 -10000 0 -0.35 2 2
mol:Ca2+ -0.099 0.16 -10000 0 -0.3 152 152
LYN 0.014 0.079 -10000 0 -0.33 10 10
RhoA/GTP -0.051 0.052 -10000 0 -0.14 27 27
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.18 -10000 0 -0.35 153 153
GNG2 0.009 0.053 -10000 0 -0.59 4 4
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.01 0.098 -10000 0 -0.39 24 24
G beta5/gamma2 -0.097 0.1 -10000 0 -0.24 120 120
PRKCH -0.11 0.17 -10000 0 -0.34 144 144
DNM1 -0.1 0.22 -10000 0 -0.52 109 109
TXA2/TP beta/beta Arrestin3 -0.041 0.071 -10000 0 -0.24 30 30
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.039 0.16 -10000 0 -0.5 52 52
G12 family/GTP -0.13 0.13 -10000 0 -0.3 151 151
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 0.01 0.051 -10000 0 -0.57 4 4
RhoA/GTP/ROCK1 0.004 0.008 -10000 0 -10000 0 0
mol:GDP 0.057 0.11 0.31 25 -10000 0 25
mol:NADP 0.005 0.071 -10000 0 -0.52 9 9
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.039 0.17 -10000 0 -0.58 46 46
mol:IP3 -0.13 0.19 -10000 0 -0.37 153 153
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.17 0.25 -10000 0 -0.5 152 152
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.039 0.11 -10000 0 -0.34 16 16
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.009 0.088 -10000 0 -0.34 13 13
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.015 0.12 -10000 0 -0.52 28 28
PRKCB1 -0.12 0.19 -10000 0 -0.36 152 152
GNAQ 0.014 0 -10000 0 -10000 0 0
mol:L-citrulline 0.005 0.071 -10000 0 -0.52 9 9
TXA2/TXA2-R family -0.18 0.26 -10000 0 -0.52 156 156
LCK -0.024 0.12 -10000 0 -0.33 25 25
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.025 0.066 -10000 0 -0.37 5 5
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.045 -10000 0 -0.75 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.024 0.063 -10000 0 -0.38 4 4
MAPK14 -0.07 0.13 -10000 0 -0.23 143 143
TGM2/GTP -0.14 0.21 -10000 0 -0.42 155 155
MAPK11 -0.073 0.13 -10000 0 -0.24 144 144
ARHGEF1 -0.052 0.097 -10000 0 -0.18 51 51
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.13 0.2 -10000 0 -0.38 156 156
RAB11/GDP 0.015 0.001 -10000 0 -10000 0 0
ICAM1 -0.098 0.16 -10000 0 -0.29 159 159
cAMP biosynthetic process -0.12 0.18 -10000 0 -0.35 156 156
Gq family/GTP/EBP50 0.007 0.083 -10000 0 -0.29 27 27
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.019 0.068 -10000 0 -0.35 2 2
GNB5 0.014 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.024 0.11 -10000 0 -0.33 19 19
VCAM1 -0.12 0.19 -10000 0 -0.37 156 156
TP beta/Gq family/GDP/G beta5/gamma2 0.01 0.098 -10000 0 -0.39 24 24
platelet activation -0.093 0.17 -10000 0 -0.3 152 152
PGI2/IP -0.016 0.087 -10000 0 -0.38 28 28
PRKACA -0.01 0.08 -10000 0 -0.29 18 18
Gq family/GDP/G beta5/gamma2 0.009 0.093 -10000 0 -0.36 24 24
TXA2/TP beta/beta Arrestin2 -0.061 0.14 -10000 0 -0.53 34 34
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.005 0.086 -10000 0 -0.3 22 22
mol:DAG -0.14 0.21 -10000 0 -0.41 152 152
EGFR -0.083 0.21 -10000 0 -0.55 89 89
TXA2/TP alpha -0.17 0.24 -10000 0 -0.48 156 156
Gq family/GTP -0.016 0.068 -10000 0 -0.24 38 38
YES1 0.017 0.072 -10000 0 -0.31 4 4
GNAI2/GTP -0.024 0.061 -10000 0 -0.35 5 5
PGD2/DP -0.033 0.11 -10000 0 -0.36 52 52
SLC9A3R1 0.009 0.053 -10000 0 -0.59 4 4
FYN 0.019 0.068 -10000 0 -0.31 4 4
mol:NO 0.005 0.071 -10000 0 -0.52 9 9
GNA15 -0.007 0.11 -10000 0 -0.56 19 19
PGK/cGMP -0.037 0.11 -10000 0 -0.35 54 54
RhoA/GDP 0.015 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.023 0.074 -10000 0 -0.42 6 6
NOS3 0.005 0.071 -10000 0 -0.52 9 9
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.11 0.18 -10000 0 -0.34 144 144
PRKCB -0.13 0.2 -10000 0 -0.38 164 164
PRKCE -0.11 0.18 -10000 0 -0.35 144 144
PRKCD -0.13 0.2 -10000 0 -0.39 154 154
PRKCG -0.17 0.22 -10000 0 -0.42 188 188
muscle contraction -0.17 0.24 -10000 0 -0.49 159 159
PRKCZ -0.12 0.18 -10000 0 -0.35 160 160
ARR3 0.002 0.023 -10000 0 -0.49 1 1
TXA2/TP beta -0.025 0.07 -10000 0 -0.39 5 5
PRKCQ -0.12 0.18 -10000 0 -0.35 159 159
MAPKKK cascade -0.16 0.22 -10000 0 -0.45 157 157
SELE -0.12 0.18 -10000 0 -0.33 175 175
TP beta/GNAI2/GDP/G beta/gamma -0.021 0.067 -10000 0 -0.37 5 5
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.014 0.12 -10000 0 -0.56 25 25
chemotaxis -0.21 0.3 -10000 0 -0.6 156 156
GNA12 0.013 0.027 -10000 0 -0.59 1 1
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 0.004 0.08 -10000 0 -0.59 9 9
Rac1/GTP 0.004 0.005 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.38 -9999 0 -1 67 67
MKNK1 0.009 0.053 -9999 0 -0.59 4 4
MAPK14 -0.038 0.12 -9999 0 -0.36 8 8
ATF2/c-Jun -0.028 0.14 -9999 0 -0.55 19 19
MAPK11 -0.049 0.15 -9999 0 -0.55 16 16
MITF -0.042 0.16 -9999 0 -0.35 85 85
MAPKAPK5 -0.039 0.16 -9999 0 -0.34 88 88
KRT8 -0.11 0.22 -9999 0 -0.42 131 131
MAPKAPK3 0.012 0.038 -9999 0 -0.59 2 2
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.062 0.19 -9999 0 -0.43 88 88
CEBPB -0.053 0.18 -9999 0 -0.39 96 96
SLC9A1 -0.041 0.16 -9999 0 -0.35 85 85
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.045 0.17 -9999 0 -0.35 94 94
p38alpha-beta/MNK1 -0.039 0.16 -9999 0 -0.35 89 89
JUN -0.028 0.14 -9999 0 -0.54 19 19
PPARGC1A -0.056 0.18 -9999 0 -0.39 94 94
USF1 -0.039 0.16 -9999 0 -0.34 85 85
RAB5/GDP/GDI1 -0.052 0.095 -9999 0 -0.38 10 10
NOS2 -0.083 0.28 -9999 0 -1 27 27
DDIT3 -0.044 0.16 -9999 0 -0.35 86 86
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.042 0.15 -9999 0 -0.46 22 22
p38alpha-beta/HBP1 -0.036 0.16 -9999 0 -0.53 10 10
CREB1 -0.041 0.17 -9999 0 -0.37 87 87
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.028 0.14 -9999 0 -0.49 14 14
RPS6KA4 -0.039 0.16 -9999 0 -0.34 85 85
PLA2G4A -0.046 0.17 -9999 0 -0.53 30 30
GDI1 -0.039 0.16 -9999 0 -0.34 88 88
TP53 -0.061 0.2 -9999 0 -0.43 95 95
RPS6KA5 -0.047 0.17 -9999 0 -0.36 95 95
ESR1 -0.055 0.18 -9999 0 -0.37 100 100
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.05 0.17 -9999 0 -0.36 97 97
MEF2A -0.04 0.16 -9999 0 -0.35 85 85
EIF4EBP1 -0.044 0.17 -9999 0 -0.37 88 88
KRT19 -0.1 0.22 -9999 0 -0.41 134 134
ELK4 -0.039 0.16 -9999 0 -0.34 85 85
ATF6 -0.039 0.16 -9999 0 -0.34 88 88
ATF1 -0.041 0.17 -9999 0 -0.37 87 87
p38alpha-beta/MAPKAPK2 -0.036 0.16 -9999 0 -0.53 10 10
p38alpha-beta/MAPKAPK3 -0.037 0.16 -9999 0 -0.53 12 12
Glypican 2 network

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
MDK -0.042 0.17 -9999 0 -0.54 52 52
GPC2 -0.016 0.13 -9999 0 -0.57 26 26
GPC2/Midkine -0.059 0.15 -9999 0 -0.42 73 73
neuron projection morphogenesis -0.059 0.15 -9999 0 -0.41 73 73
Syndecan-4-mediated signaling events

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
PTK2 0 0.055 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.24 -9999 0 -0.56 99 99
positive regulation of JNK cascade -0.14 0.22 -9999 0 -0.52 107 107
Syndecan-4/ADAM12 -0.17 0.26 -9999 0 -0.57 118 118
CCL5 -0.086 0.21 -9999 0 -0.53 94 94
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.01 0.11 -9999 0 -0.5 24 24
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG 0.002 0.038 -9999 0 -0.48 3 3
ADAM12 -0.072 0.19 -9999 0 -0.5 85 85
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.03 0.042 -9999 0 -0.18 1 1
Syndecan-4/Laminin alpha1 -0.17 0.27 -9999 0 -0.59 115 115
Syndecan-4/CXCL12/CXCR4 -0.13 0.25 -9999 0 -0.55 107 107
Syndecan-4/Laminin alpha3 -0.16 0.26 -9999 0 -0.58 111 111
MDK -0.042 0.17 -9999 0 -0.54 52 52
Syndecan-4/FZD7 -0.16 0.28 -9999 0 -0.61 111 111
Syndecan-4/Midkine -0.16 0.26 -9999 0 -0.58 106 106
FZD7 -0.047 0.18 -9999 0 -0.58 53 53
Syndecan-4/FGFR1/FGF -0.14 0.2 -9999 0 -0.51 101 101
THBS1 -0.088 0.21 -9999 0 -0.51 100 100
integrin-mediated signaling pathway -0.15 0.26 -9999 0 -0.57 110 110
positive regulation of MAPKKK cascade -0.14 0.22 -9999 0 -0.52 107 107
Syndecan-4/TACI -0.14 0.24 -9999 0 -0.56 100 100
CXCR4 -0.013 0.12 -9999 0 -0.54 25 25
cell adhesion 0.021 0.052 -9999 0 -0.26 11 11
Syndecan-4/Dynamin -0.13 0.24 -9999 0 -0.56 99 99
Syndecan-4/TSP1 -0.18 0.26 -9999 0 -0.58 118 118
Syndecan-4/GIPC -0.13 0.24 -9999 0 -0.56 99 99
Syndecan-4/RANTES -0.18 0.26 -9999 0 -0.59 112 112
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
LAMA1 -0.065 0.2 -9999 0 -0.57 70 70
LAMA3 -0.041 0.17 -9999 0 -0.54 51 51
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.037 0.052 -9999 0 -0.53 1 1
Syndecan-4/alpha-Actinin -0.14 0.25 -9999 0 -0.57 110 110
TFPI -0.091 0.21 -9999 0 -0.52 100 100
F2 -0.007 0.066 -9999 0 -0.49 9 9
alpha5/beta1 Integrin -0.018 0.079 -9999 0 -0.36 25 25
positive regulation of cell adhesion -0.18 0.28 -9999 0 -0.6 124 124
ACTN1 -0.021 0.13 -9999 0 -0.5 35 35
TNC -0.049 0.18 -9999 0 -0.54 59 59
Syndecan-4/CXCL12 -0.13 0.24 -9999 0 -0.56 102 102
FGF6 0.001 0.003 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 0.003 0.077 -9999 0 -0.54 10 10
TNFRSF13B -0.005 0.072 -9999 0 -0.49 11 11
FGF2 0.011 0.044 -9999 0 -0.56 3 3
FGFR1 0.013 0.027 -9999 0 -0.59 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.24 -9999 0 -0.56 99 99
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0 0.093 -9999 0 -0.48 18 18
cell migration -0.007 0.018 -9999 0 -10000 0 0
PRKCD -0.014 0.13 -9999 0 -0.57 27 27
vasculogenesis -0.17 0.25 -9999 0 -0.56 118 118
SDC4 -0.14 0.25 -9999 0 -0.6 99 99
Syndecan-4/Tenascin C -0.16 0.27 -9999 0 -0.6 110 110
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.033 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.24 -9999 0 -0.56 99 99
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
Rac1/GTP 0.021 0.053 -9999 0 -0.26 11 11
cytoskeleton organization -0.12 0.23 -9999 0 -0.53 99 99
GIPC1 0.013 0.022 -9999 0 -0.49 1 1
Syndecan-4/TFPI -0.18 0.26 -9999 0 -0.6 107 107
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.079 0.17 -9999 0 -0.45 79 79
alphaM/beta2 Integrin/GPIbA -0.074 0.17 -9999 0 -0.45 73 73
alphaM/beta2 Integrin/proMMP-9 -0.15 0.21 -9999 0 -0.4 182 182
PLAUR -0.02 0.13 -9999 0 -0.5 34 34
HMGB1 -0.001 0.022 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.063 0.16 -9999 0 -0.48 57 57
AGER -0.029 0.13 -9999 0 -0.6 24 24
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG -0.023 0.14 -9999 0 -0.58 32 32
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.18 -9999 0 -0.53 63 63
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
CYR61 -0.1 0.23 -9999 0 -0.55 104 104
TLN1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP -0.089 0.13 -9999 0 -0.4 48 48
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.026 0.13 -9999 0 -0.49 37 37
MYH2 -0.086 0.15 -9999 0 -0.4 58 58
MST1R 0.006 0.069 -9999 0 -0.58 7 7
leukocyte activation during inflammatory response -0.11 0.18 -9999 0 -0.39 117 117
APOB -0.072 0.2 -9999 0 -0.55 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.013 0.12 -9999 0 -0.54 25 25
JAM3 0.014 0 -9999 0 -10000 0 0
GP1BA -0.004 0.1 -9999 0 -0.57 16 16
alphaM/beta2 Integrin/CTGF -0.088 0.18 -9999 0 -0.44 91 91
alphaM/beta2 Integrin -0.097 0.16 -9999 0 -0.42 70 70
JAM3 homodimer 0.014 0 -9999 0 -10000 0 0
ICAM2 0.013 0.022 -9999 0 -0.49 1 1
ICAM1 -0.028 0.14 -9999 0 -0.51 41 41
phagocytosis triggered by activation of immune response cell surface activating receptor -0.096 0.16 -9999 0 -0.41 70 70
cell adhesion -0.074 0.16 -9999 0 -0.45 73 73
NFKB1 -0.16 0.26 -9999 0 -0.62 81 81
THY1 -0.004 0.1 -9999 0 -0.56 16 16
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.068 0.14 -9999 0 -0.33 107 107
alphaM/beta2 Integrin/LRP/tPA -0.084 0.17 -9999 0 -0.43 80 80
IL6 -0.2 0.33 -9999 0 -0.77 97 97
ITGB2 -0.045 0.15 -9999 0 -0.57 39 39
elevation of cytosolic calcium ion concentration -0.11 0.2 -9999 0 -0.45 107 107
alphaM/beta2 Integrin/JAM2/JAM3 -0.052 0.15 -9999 0 -0.44 55 55
JAM2 0.013 0.027 -9999 0 -0.59 1 1
alphaM/beta2 Integrin/ICAM1 -0.089 0.18 -9999 0 -0.49 55 55
alphaM/beta2 Integrin/uPA/Plg -0.097 0.18 -9999 0 -0.43 95 95
RhoA/GTP -0.089 0.16 -9999 0 -0.41 58 58
positive regulation of phagocytosis -0.1 0.18 -9999 0 -0.51 61 61
Ron/MSP -0.034 0.11 -9999 0 -0.41 42 42
alphaM/beta2 Integrin/uPAR/uPA -0.11 0.2 -9999 0 -0.45 107 107
alphaM/beta2 Integrin/uPAR -0.083 0.18 -9999 0 -0.46 83 83
PLAU -0.059 0.18 -9999 0 -0.51 72 72
PLAT -0.05 0.17 -9999 0 -0.49 65 65
actin filament polymerization -0.083 0.15 -9999 0 -0.38 58 58
MST1 -0.026 0.15 -9999 0 -0.57 35 35
alphaM/beta2 Integrin/lipoprotein(a) -0.11 0.18 -9999 0 -0.4 117 117
TNF -0.23 0.35 -9999 0 -0.77 120 120
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
alphaM/beta2 Integrin/uPA -0.1 0.19 -9999 0 -0.43 115 115
fibrinolysis -0.096 0.18 -9999 0 -0.43 95 95
HCK -0.007 0.11 -9999 0 -0.54 20 20
dendritic cell antigen processing and presentation -0.096 0.16 -9999 0 -0.41 70 70
VTN -0.007 0.11 -9999 0 -0.56 19 19
alphaM/beta2 Integrin/CYR61 -0.13 0.22 -9999 0 -0.44 142 142
LPA -0.02 0.12 -9999 0 -0.49 31 31
LRP1 0.014 0 -9999 0 -10000 0 0
cell migration -0.13 0.22 -9999 0 -0.42 146 146
FN1 -0.004 0.093 -9999 0 -0.49 18 18
alphaM/beta2 Integrin/Thy1 -0.074 0.17 -9999 0 -0.46 72 72
MPO -0.12 0.24 -9999 0 -0.54 127 127
KNG1 -0.019 0.1 -9999 0 -0.49 24 24
RAP1/GDP -0.001 0.013 -9999 0 -0.29 1 1
ROCK1 -0.076 0.15 -9999 0 -0.39 53 53
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.038 -9999 0 -0.49 3 3
CTGF -0.029 0.15 -9999 0 -0.54 40 40
alphaM/beta2 Integrin/Hck -0.075 0.2 -9999 0 -0.55 60 60
ITGAM -0.045 0.16 -9999 0 -0.6 37 37
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.091 0.21 -9999 0 -0.5 82 82
HP -0.11 0.23 -9999 0 -0.53 115 115
leukocyte adhesion -0.11 0.17 -9999 0 -0.54 52 52
SELP -0.026 0.13 -9999 0 -0.49 37 37
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
ITGB7 -0.033 0.16 -9999 0 -0.54 44 44
ITGA4 -0.051 0.18 -9999 0 -0.53 61 61
alpha4/beta7 Integrin -0.076 0.17 -9999 0 -0.43 92 92
alpha4/beta1 Integrin -0.046 0.13 -9999 0 -0.39 61 61
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.038 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.091 0.14 -9999 0 -0.42 48 48
JUN -0.079 0.2 -9999 0 -0.52 58 58
HRAS 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.16 0.22 -9999 0 -0.44 144 144
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.012 0.035 -9999 0 -0.54 2 2
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.16 0.22 -9999 0 -0.44 143 143
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.094 0.17 -9999 0 -0.4 94 94
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.14 0.2 -9999 0 -0.54 70 70
GRB7 -0.031 0.14 -9999 0 -0.49 42 42
RET51/GFRalpha1/GDNF -0.15 0.21 -9999 0 -0.43 143 143
MAPKKK cascade -0.12 0.18 -9999 0 -0.56 50 50
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.089 0.16 -9999 0 -0.39 94 94
lamellipodium assembly -0.085 0.13 -9999 0 -0.39 49 49
RET51/GFRalpha1/GDNF/SHC -0.16 0.22 -9999 0 -0.44 143 143
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
RET9/GFRalpha1/GDNF/SHC -0.092 0.17 -9999 0 -0.36 131 131
RET9/GFRalpha1/GDNF/Shank3 -0.094 0.17 -9999 0 -0.35 137 137
MAPK3 -0.11 0.21 -9999 0 -0.57 54 54
DOK1 0.012 0.035 -9999 0 -0.54 2 2
DOK6 -0.048 0.18 -9999 0 -0.58 54 54
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.099 0.22 -9999 0 -0.54 68 68
DOK5 0.001 0.088 -9999 0 -0.59 11 11
GFRA1 -0.071 0.2 -9999 0 -0.56 76 76
MAPK8 -0.086 0.2 -9999 0 -0.54 55 55
HRAS/GTP -0.14 0.2 -9999 0 -0.59 56 56
tube development -0.088 0.16 -9999 0 -0.37 96 96
MAPK1 -0.11 0.21 -9999 0 -0.57 54 54
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.042 0.14 -9999 0 -0.31 94 94
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PDLIM7 0.005 0.066 -9999 0 -0.49 9 9
RET51/GFRalpha1/GDNF/Dok6 -0.17 0.25 -9999 0 -0.72 66 66
SHC1 0.009 0.05 -9999 0 -0.49 5 5
RET51/GFRalpha1/GDNF/Dok4 -0.16 0.22 -9999 0 -0.45 150 150
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.44 151 151
PRKCA 0.013 0.027 -9999 0 -0.59 1 1
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.068 0.18 -9999 0 -0.48 56 56
PIK3R1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.044 0.15 -9999 0 -0.32 94 94
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.23 -9999 0 -0.47 146 146
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.24 -9999 0 -0.55 118 118
DOK4 -0.005 0.1 -9999 0 -0.59 16 16
JNK cascade -0.077 0.19 -9999 0 -0.5 58 58
RET9/GFRalpha1/GDNF/FRS2 -0.09 0.17 -9999 0 -0.35 131 131
SHANK3 0.004 0.073 -9999 0 -0.51 10 10
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.013 0.027 -9999 0 -0.59 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.042 0.15 -9999 0 -0.32 94 94
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.092 0.2 -9999 0 -0.58 46 46
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.092 0.2 -9999 0 -0.49 65 65
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.096 0.21 -9999 0 -0.61 47 47
PI3K -0.089 0.23 -9999 0 -0.63 49 49
SOS1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.088 0.16 -9999 0 -0.37 96 96
GRB10 0.011 0.044 -9999 0 -0.56 3 3
activation of MAPKK activity -0.086 0.2 -9999 0 -0.46 82 82
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.43 143 143
GAB1 0.012 0.035 -9999 0 -0.54 2 2
IRS1 0.014 0 -9999 0 -10000 0 0
IRS2 0.012 0.035 -9999 0 -0.54 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.097 0.21 -9999 0 -0.62 47 47
RET51/GFRalpha1/GDNF/PKC alpha -0.15 0.22 -9999 0 -0.43 143 143
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PRKACA 0.014 0 -9999 0 -10000 0 0
GDNF -0.071 0.2 -9999 0 -0.57 73 73
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.15 0.21 -9999 0 -0.43 143 143
Rac1/GTP -0.1 0.15 -9999 0 -0.47 49 49
RET9/GFRalpha1/GDNF -0.1 0.18 -9999 0 -0.39 130 130
GFRalpha1/GDNF -0.12 0.21 -9999 0 -0.46 130 130
Endothelins

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
AKT1 -0.094 0.21 -10000 0 -0.56 50 50
PTK2B -0.009 0.11 -10000 0 -0.49 24 24
mol:Ca2+ -0.062 0.24 -10000 0 -0.72 41 41
EDN1 -0.082 0.18 -10000 0 -0.51 58 58
EDN3 -0.017 0.13 -10000 0 -0.58 27 27
EDN2 -0.017 0.1 -10000 0 -0.49 23 23
HRAS/GDP -0.093 0.21 -10000 0 -0.54 55 55
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.051 0.16 -10000 0 -0.42 48 48
ADCY4 -0.11 0.23 -10000 0 -0.52 89 89
ADCY5 -0.12 0.24 -10000 0 -0.56 88 88
ADCY6 -0.1 0.22 -10000 0 -0.51 85 85
ADCY7 -0.1 0.22 -10000 0 -0.51 85 85
ADCY1 -0.16 0.25 -10000 0 -0.53 118 118
ADCY2 -0.11 0.23 -10000 0 -0.52 91 91
ADCY3 -0.1 0.22 -10000 0 -0.51 85 85
ADCY8 -0.14 0.25 -10000 0 -0.53 113 113
ADCY9 -0.11 0.22 -10000 0 -0.51 87 87
arachidonic acid secretion -0.095 0.22 -10000 0 -0.52 72 72
ETB receptor/Endothelin-1/Gq/GTP -0.046 0.16 -10000 0 -0.4 56 56
GNAO1 0.008 0.06 -10000 0 -0.59 5 5
HRAS 0.013 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.095 0.2 0.26 18 -0.53 49 67
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.23 0.25 17 -0.54 85 102
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.19 0.32 -10000 0 -0.62 155 155
EDNRB -0.047 0.18 -10000 0 -0.59 50 50
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.11 0.26 -10000 0 -0.68 60 60
CYSLTR1 -0.11 0.24 -10000 0 -0.65 55 55
SLC9A1 -0.067 0.099 -10000 0 -0.31 32 32
mol:GDP -0.11 0.22 -10000 0 -0.53 71 71
SLC9A3 -0.096 0.27 -10000 0 -0.7 65 65
RAF1 -0.11 0.23 -10000 0 -0.51 81 81
JUN -0.044 0.2 -10000 0 -0.61 30 30
JAK2 -0.094 0.21 -10000 0 -0.56 51 51
mol:IP3 -0.059 0.18 -10000 0 -0.49 44 44
ETA receptor/Endothelin-1 -0.13 0.24 0.3 18 -0.64 52 70
PLCB1 -0.01 0.11 -10000 0 -0.59 19 19
PLCB2 -0.009 0.11 -10000 0 -0.57 19 19
ETA receptor/Endothelin-3 -0.072 0.15 -10000 0 -0.47 56 56
FOS -0.14 0.33 -10000 0 -0.84 78 78
Gai/GDP 0.006 0.11 -10000 0 -0.96 5 5
CRK 0.014 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.12 0.25 -10000 0 -0.55 88 88
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
PRKCB1 -0.058 0.17 -10000 0 -0.47 44 44
GNAQ 0.013 0.007 -10000 0 -10000 0 0
GNAZ 0.014 0 -10000 0 -10000 0 0
GNAL -0.055 0.19 -10000 0 -0.59 59 59
Gs family/GDP -0.15 0.21 -10000 0 -0.5 103 103
ETA receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.4 49 49
MAPK14 -0.038 0.16 -10000 0 -0.5 31 31
TRPC6 -0.066 0.25 -10000 0 -0.77 40 40
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.048 0.17 -10000 0 -0.43 51 51
ETB receptor/Endothelin-2 -0.048 0.15 -10000 0 -0.41 72 72
ETB receptor/Endothelin-3 -0.048 0.17 -10000 0 -0.46 70 70
ETB receptor/Endothelin-1 -0.099 0.19 -10000 0 -0.47 84 84
MAPK3 -0.14 0.3 -10000 0 -0.74 81 81
MAPK1 -0.14 0.3 -10000 0 -0.75 80 80
Rac1/GDP -0.092 0.21 -10000 0 -0.52 61 61
cAMP biosynthetic process -0.12 0.24 -10000 0 -0.52 100 100
MAPK8 -0.06 0.22 -10000 0 -0.6 47 47
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.021 0.12 -10000 0 -0.36 31 31
p130Cas/CRK/Src/PYK2 -0.098 0.23 -10000 0 -0.55 66 66
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.093 0.21 -10000 0 -0.53 57 57
COL1A2 -0.14 0.28 -10000 0 -0.69 79 79
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.069 0.14 -10000 0 -0.43 53 53
mol:DAG -0.059 0.18 -10000 0 -0.49 44 44
MAP2K2 -0.12 0.25 -10000 0 -0.59 82 82
MAP2K1 -0.12 0.25 -10000 0 -0.59 84 84
EDNRA -0.066 0.17 -10000 0 -0.48 49 49
positive regulation of muscle contraction -0.072 0.19 -10000 0 -0.5 49 49
Gq family/GDP -0.12 0.2 -10000 0 -0.54 62 62
HRAS/GTP -0.1 0.21 -10000 0 -0.5 71 71
PRKCH -0.05 0.17 -10000 0 -0.49 38 38
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.05 0.18 -10000 0 -0.51 37 37
PRKCB -0.087 0.2 -10000 0 -0.49 65 65
PRKCE -0.054 0.18 -10000 0 -0.5 41 41
PRKCD -0.066 0.2 -10000 0 -0.55 49 49
PRKCG -0.15 0.23 -10000 0 -0.47 124 124
regulation of vascular smooth muscle contraction -0.17 0.38 -10000 0 -1 74 74
PRKCQ -0.059 0.19 -10000 0 -0.5 49 49
PLA2G4A -0.1 0.24 -10000 0 -0.57 72 72
GNA14 -0.014 0.12 -10000 0 -0.56 25 25
GNA15 -0.008 0.11 -10000 0 -0.57 19 19
GNA12 0.013 0.027 -10000 0 -0.59 1 1
GNA11 0.003 0.08 -10000 0 -0.59 9 9
Rac1/GTP -0.095 0.2 0.27 18 -0.53 49 67
MMP1 0.014 0.16 -10000 0 -0.44 31 31
Reelin signaling pathway

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
CDK5R1/CDK5 -0.025 0.1 -9999 0 -0.42 30 30
VLDLR -0.007 0.11 -9999 0 -0.56 19 19
CRKL 0.013 0.022 -9999 0 -0.49 1 1
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
ITGA3 -0.009 0.11 -9999 0 -0.5 23 23
RELN/VLDLR/Fyn -0.1 0.16 -9999 0 -0.37 92 92
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.01 0.053 -9999 0 -10000 0 0
AKT1 -0.072 0.16 -9999 0 -0.44 39 39
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.089 0.22 -9999 0 -0.56 92 92
RELN/LRP8/DAB1 -0.14 0.18 -9999 0 -0.39 139 139
LRPAP1/LRP8 -0.002 0.027 -9999 0 -0.43 2 2
RELN/LRP8/DAB1/Fyn -0.12 0.17 -9999 0 -0.36 139 139
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.53 52 52
long-term memory -0.28 0.28 -9999 0 -0.64 161 161
DAB1/LIS1 -0.12 0.17 -9999 0 -0.54 40 40
DAB1/CRLK/C3G -0.12 0.16 -9999 0 -0.52 40 40
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
DAB1/NCK2 -0.12 0.17 -9999 0 -0.54 40 40
ARHGEF2 0.013 0.027 -9999 0 -0.59 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.15 0.26 -9999 0 -0.55 154 154
CDK5R1 -0.021 0.14 -9999 0 -0.59 30 30
RELN -0.14 0.25 -9999 0 -0.55 139 139
PIK3R1 0.014 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.089 0.15 -9999 0 -0.36 79 79
GRIN2A/RELN/LRP8/DAB1/Fyn -0.2 0.23 -9999 0 -0.59 103 103
MAPK8 -0.001 0.095 -9999 0 -0.59 13 13
RELN/VLDLR/DAB1 -0.14 0.19 -9999 0 -0.36 210 210
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
MAP1B -0.11 0.2 -9999 0 -0.37 141 141
RELN/LRP8 -0.089 0.15 -9999 0 -0.36 79 79
GRIN2B/RELN/LRP8/DAB1/Fyn -0.21 0.23 -9999 0 -0.59 104 104
PI3K -0.001 0.019 -9999 0 -0.43 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.017 0.078 -9999 0 -0.36 24 24
RAP1A -0.072 0.18 -9999 0 -0.49 40 40
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.053 -9999 0 -0.59 4 4
CRLK/C3G -0.001 0.015 -9999 0 -0.34 1 1
GRIN2B -0.18 0.26 -9999 0 -0.54 177 177
NCK2 0.014 0 -9999 0 -10000 0 0
neuron differentiation -0.042 0.14 -9999 0 -0.42 33 33
neuron adhesion -0.065 0.18 -9999 0 -0.47 52 52
LRP8 0.012 0.038 -9999 0 -0.59 2 2
GSK3B -0.061 0.15 -9999 0 -0.47 30 30
RELN/VLDLR/DAB1/Fyn -0.13 0.18 -9999 0 -0.37 148 148
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.085 0.17 -9999 0 -0.31 148 148
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT 0.011 0.082 -9999 0 -0.54 10 10
neuron migration -0.07 0.19 -9999 0 -0.51 42 42
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.043 0.14 -9999 0 -0.42 33 33
RELN/VLDLR -0.09 0.14 -9999 0 -0.34 93 93
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.042 0.11 -9999 0 -0.3 71 71
RGS9BP 0.003 0.081 -9999 0 -0.57 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.012 0.023 -9999 0 -0.49 1 1
mol:Na + -0.1 0.15 -9999 0 -0.32 161 161
mol:ADP 0.017 0.043 -9999 0 -0.34 7 7
GNAT2 0.01 0.032 -9999 0 -0.49 2 2
RGS9-1/Gbeta5/R9AP -0.038 0.12 -9999 0 -0.37 53 53
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.014 0.064 -9999 0 -0.3 24 24
GRK7 0.006 0.054 -9999 0 -0.49 6 6
CNGB3 -0.01 0.094 -9999 0 -0.49 19 19
Cone Metarhodopsin II/X-Arrestin -0.001 0.016 -9999 0 -0.35 1 1
mol:Ca2+ -0.14 0.2 -9999 0 -0.34 231 231
Cone PDE6 -0.044 0.11 -9999 0 -0.33 47 47
Cone Metarhodopsin II -0.004 0.03 -9999 0 -0.26 7 7
Na + (4 Units) -0.15 0.19 -9999 0 -0.34 231 231
GNAT2/GDP -0.033 0.1 -9999 0 -0.33 47 47
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.067 -9999 0 -0.27 29 29
Cone Transducin -0.044 0.11 -9999 0 -0.32 71 71
SLC24A2 -0.11 0.23 -9999 0 -0.55 112 112
GNB3/GNGT2 -0.057 0.14 -9999 0 -0.42 70 70
GNB3 -0.035 0.16 -9999 0 -0.57 43 43
GNAT2/GTP -0.001 0.022 -9999 0 -0.35 2 2
CNGA3 -0.14 0.24 -9999 0 -0.53 143 143
ARR3 0.002 0.023 -9999 0 -0.49 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.1 0.15 -9999 0 -0.32 161 161
mol:Pi -0.038 0.12 -9999 0 -0.37 53 53
Cone CNG Channel -0.091 0.14 -9999 0 -0.35 57 57
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.23 -9999 0 -0.55 112 112
RGS9 -0.04 0.17 -9999 0 -0.58 47 47
PDE6C 0.002 0.049 -9999 0 -0.49 5 5
GNGT2 -0.018 0.13 -9999 0 -0.55 29 29
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.013 0.1 -9999 0 -0.49 23 23
Glypican 1 network

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.005 0.043 -10000 0 -0.35 7 7
fibroblast growth factor receptor signaling pathway -0.005 0.043 -10000 0 -0.35 7 7
LAMA1 -0.065 0.2 -10000 0 -0.57 70 70
PRNP 0.014 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.095 0.17 -10000 0 -0.38 128 128
SMAD2 0.03 0.045 -10000 0 -0.41 2 2
GPC1/PrPc/Cu2+ -0.002 0.025 -10000 0 -0.29 4 4
GPC1/Laminin alpha1 -0.058 0.15 -10000 0 -0.41 72 72
TDGF1 -0.079 0.21 -10000 0 -0.57 82 82
CRIPTO/GPC1 -0.067 0.16 -10000 0 -0.42 83 83
APP/GPC1 -0.003 0.03 -10000 0 -0.34 4 4
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.033 0.15 -10000 0 -0.35 85 85
FLT1 0.013 0.027 -10000 0 -0.59 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.045 -10000 0 -0.32 10 10
SERPINC1 -0.004 0.087 -10000 0 -0.49 16 16
FYN -0.03 0.14 -10000 0 -0.34 83 83
FGR -0.032 0.14 -10000 0 -0.34 86 86
positive regulation of MAPKKK cascade -0.073 0.19 -10000 0 -0.46 72 72
SLIT2 -0.12 0.24 -10000 0 -0.54 125 125
GPC1/NRG -0.13 0.19 -10000 0 -0.4 165 165
NRG1 -0.17 0.27 -10000 0 -0.55 163 163
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.015 0.065 -10000 0 -0.29 26 26
LYN -0.037 0.15 -10000 0 -0.35 91 91
mol:Spermine 0.01 0.032 -10000 0 -0.35 4 4
cell growth -0.005 0.043 -10000 0 -0.35 7 7
BMP signaling pathway -0.01 0.044 0.49 4 -10000 0 4
SRC -0.03 0.14 -10000 0 -0.34 83 83
TGFBR1 0.012 0.035 -10000 0 -0.54 2 2
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.089 0.2 -10000 0 -0.51 93 93
GPC1 0.01 0.044 -10000 0 -0.49 4 4
TGFBR1 (dimer) 0.012 0.035 -10000 0 -0.54 2 2
VEGFA -0.007 0.1 -10000 0 -0.49 22 22
BLK -0.1 0.19 -10000 0 -0.35 182 182
HCK -0.043 0.16 -10000 0 -0.36 97 97
FGF2 0.011 0.044 -10000 0 -0.56 3 3
FGFR1 0.013 0.027 -10000 0 -0.59 1 1
VEGFR1 homodimer 0.013 0.027 -10000 0 -0.59 1 1
TGFBR2 0.009 0.05 -10000 0 -0.49 5 5
cell death -0.003 0.03 -10000 0 -0.34 4 4
ATIII/GPC1 -0.013 0.066 -10000 0 -0.34 20 20
PLA2G2A/GPC1 -0.068 0.14 -10000 0 -0.37 94 94
LCK -0.089 0.19 -10000 0 -0.37 153 153
neuron differentiation -0.13 0.19 -10000 0 -0.4 165 165
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.009 0.049 -10000 0 -0.49 5 5
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 -0.044 0.15 -10000 0 -0.32 90 90
ACTA1 -0.066 0.18 0.25 1 -0.39 99 100
NUMA1 -0.044 0.15 0.21 1 -0.32 90 91
SPTAN1 -0.055 0.18 0.25 3 -0.39 91 94
LIMK1 -0.055 0.18 0.25 3 -0.39 91 94
BIRC3 -0.033 0.16 -10000 0 -0.55 43 43
BIRC2 0.014 0 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.083 0.2 -10000 0 -0.39 140 140
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 -0.044 0.15 0.21 1 -0.32 91 92
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.054 0.18 0.25 3 -0.38 91 94
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
GSN -0.063 0.18 0.25 1 -0.39 97 98
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A -0.19 0.3 -10000 0 -0.65 138 138
BID -0.039 0.11 -10000 0 -0.24 103 103
MAP3K1 -0.014 0.069 -10000 0 -0.21 7 7
TRADD 0.013 0.027 -10000 0 -0.59 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.007 0.019 -10000 0 -0.34 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.058 0.18 0.25 3 -0.39 94 97
CASP9 0.013 0.022 -10000 0 -0.49 1 1
DNA repair 0.003 0.061 0.16 4 -0.19 19 23
neuron apoptosis 0.006 0.045 -10000 0 -0.42 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.048 0.17 -10000 0 -0.37 89 89
APAF1 0.014 0 -10000 0 -10000 0 0
CASP6 -0.029 0.12 -10000 0 -0.73 4 4
TRAF2 0.014 0 -10000 0 -10000 0 0
ICAD/CAD -0.046 0.17 0.24 3 -0.37 89 92
CASP7 0.019 0.077 0.28 34 -10000 0 34
KRT18 -0.089 0.21 -10000 0 -0.61 65 65
apoptosis -0.07 0.18 0.26 1 -0.37 96 97
DFFA -0.055 0.18 0.25 3 -0.39 92 95
DFFB -0.055 0.18 0.25 3 -0.39 91 94
PARP1 -0.003 0.061 0.19 19 -0.16 4 23
actin filament polymerization 0.043 0.17 0.36 85 -0.24 2 87
TNF -0.15 0.26 -10000 0 -0.54 156 156
CYCS -0.024 0.08 -10000 0 -0.21 35 35
SATB1 -0.025 0.12 -10000 0 -0.56 8 8
SLK -0.057 0.18 0.25 3 -0.39 92 95
p15 BID/BAX -0.028 0.099 -10000 0 -0.32 17 17
CASP2 -0.018 0.11 -10000 0 -0.42 12 12
JNK cascade 0.014 0.068 0.21 7 -10000 0 7
CASP3 -0.067 0.19 0.25 4 -0.41 95 99
LMNB2 -0.013 0.093 -10000 0 -0.4 9 9
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 -0.013 0.11 -10000 0 -0.5 27 27
Mammalian IAPs/DIABLO -0.024 0.08 -10000 0 -0.32 25 25
negative regulation of DNA binding -0.18 0.3 -10000 0 -0.64 138 138
stress fiber formation -0.055 0.18 0.25 3 -0.38 92 95
GZMB -0.11 0.22 -10000 0 -0.46 140 140
CASP1 -0.007 0.09 -10000 0 -0.3 41 41
LMNB1 -0.022 0.1 -10000 0 -0.38 17 17
APP 0.006 0.045 -10000 0 -0.42 1 1
TNFRSF1A 0.001 0.086 -10000 0 -0.55 12 12
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.065 -10000 0 -0.36 16 16
VIM -0.076 0.18 0.26 1 -0.38 96 97
LMNA -0.013 0.092 -10000 0 -0.39 9 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.028 0.12 -10000 0 -0.4 18 18
LRDD 0.006 0.069 -10000 0 -0.58 7 7
SREBF1 -0.065 0.18 0.24 2 -0.38 102 104
APAF-1/Caspase 9 -0.006 0.043 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.044 0.14 0.21 1 -0.32 90 91
CFL2 -0.045 0.17 0.25 1 -0.37 85 86
GAS2 -0.064 0.18 0.24 2 -0.4 96 98
positive regulation of apoptosis -0.014 0.097 -10000 0 -0.41 9 9
PRF1 -0.062 0.19 -10000 0 -0.54 71 71
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.11 0.17 -10000 0 -0.38 150 150
CRKL -0.046 0.13 -10000 0 -0.49 9 9
mol:PIP3 -0.018 0.024 0.52 1 -10000 0 1
AKT1 0.003 0.027 0.36 1 -0.34 2 3
PTK2B -0.009 0.11 -10000 0 -0.49 24 24
RAPGEF1 -0.036 0.12 -10000 0 -0.46 9 9
RANBP10 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
HGF/MET/SHIP2 -0.14 0.19 -10000 0 -0.36 203 203
MAP3K5 -0.04 0.13 -10000 0 -0.41 22 22
HGF/MET/CIN85/CBL/ENDOPHILINS -0.13 0.17 -10000 0 -0.39 109 109
AP1 -0.089 0.17 -10000 0 -0.4 100 100
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.009 0.05 -10000 0 -0.49 5 5
apoptosis -0.1 0.24 -10000 0 -0.76 57 57
STAT3 (dimer) -0.05 0.13 -10000 0 -0.42 14 14
GAB1/CRKL/SHP2/PI3K -0.058 0.093 -10000 0 -0.43 9 9
INPP5D 0.008 0.06 -10000 0 -0.54 6 6
CBL/CRK -0.035 0.12 -10000 0 -0.46 9 9
PTPN11 0.014 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
PTEN 0.013 0.027 -10000 0 -0.59 1 1
ELK1 -0.059 0.091 -10000 0 -0.2 150 150
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.048 0.071 -10000 0 -0.31 9 9
PAK1 -0.015 0.08 0.34 1 -0.31 8 9
HGF/MET/RANBP10 -0.14 0.19 -10000 0 -0.36 203 203
HRAS -0.1 0.23 -10000 0 -0.64 66 66
DOCK1 -0.038 0.12 -10000 0 -0.46 9 9
GAB1 -0.056 0.13 -10000 0 -0.3 71 71
CRK -0.046 0.13 -10000 0 -0.28 71 71
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.13 0.21 -10000 0 -0.58 79 79
JUN 0.003 0.075 -10000 0 -0.5 11 11
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.074 0.12 -10000 0 -0.28 109 109
PIK3R1 0.014 0 -10000 0 -10000 0 0
cell morphogenesis -0.02 0.14 -10000 0 -0.46 9 9
GRB2/SHC -0.052 0.12 -10000 0 -0.42 13 13
FOS -0.094 0.22 -10000 0 -0.55 99 99
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.059 0.091 -10000 0 -0.2 150 150
HGF/MET/MUC20 -0.15 0.2 -10000 0 -0.37 203 203
cell migration -0.052 0.12 -10000 0 -0.41 13 13
GRB2 0.013 0.022 -10000 0 -0.49 1 1
CBL 0.014 0 -10000 0 -10000 0 0
MET/RANBP10 -0.11 0.17 -10000 0 -0.38 150 150
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.062 0.14 -10000 0 -0.34 39 39
MET/MUC20 -0.11 0.18 -10000 0 -0.39 150 150
RAP1B -0.027 0.12 -10000 0 -0.41 10 10
RAP1A -0.026 0.12 -10000 0 -0.44 8 8
HGF/MET/RANBP9 -0.14 0.19 -10000 0 -0.36 203 203
RAF1 -0.089 0.22 -10000 0 -0.59 65 65
STAT3 -0.05 0.13 -10000 0 -0.43 14 14
cell proliferation -0.063 0.18 -10000 0 -0.4 75 75
RPS6KB1 -0.02 0.048 -10000 0 -10000 0 0
MAPK3 -0.059 0.083 -10000 0 -10000 0 0
MAPK1 -0.059 0.083 -10000 0 -10000 0 0
RANBP9 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.024 0.14 -10000 0 -0.43 26 26
SRC -0.05 0.13 -10000 0 -0.42 14 14
PI3K -0.05 0.11 -10000 0 -0.25 96 96
MET/Glomulin -0.09 0.16 -10000 0 -0.34 150 150
SOS1 0.014 0 -10000 0 -10000 0 0
MAP2K1 -0.075 0.2 -10000 0 -0.54 65 65
MET -0.15 0.25 -10000 0 -0.53 150 150
MAP4K1 -0.046 0.14 -10000 0 -0.44 18 18
PTK2 0.014 0 -10000 0 -10000 0 0
MAP2K2 -0.075 0.2 -10000 0 -0.54 65 65
BAD 0.01 0.025 0.34 1 -0.31 2 3
MAP2K4 -0.029 0.13 -10000 0 -0.4 20 20
SHP2/GRB2/SOS1/GAB1 -0.088 0.14 -10000 0 -0.38 66 66
INPPL1 0.014 0 -10000 0 -10000 0 0
PXN 0.014 0 -10000 0 -10000 0 0
SH3KBP1 0.014 0 -10000 0 -10000 0 0
HGS -0.06 0.12 -10000 0 -0.26 95 95
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.079 0.2 -10000 0 -0.51 91 91
RASA1 0.014 0 -10000 0 -10000 0 0
NCK1 0.013 0.027 -10000 0 -0.59 1 1
PTPRJ 0.013 0.022 -10000 0 -0.49 1 1
NCK/PLCgamma1 -0.049 0.12 -10000 0 -0.25 95 95
PDPK1 -0.007 0.03 0.41 1 -0.37 2 3
HGF/MET/SHIP -0.15 0.2 -10000 0 -0.37 205 205
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.18 0.39 -10000 0 -0.98 63 63
PCK1 -0.24 0.43 -10000 0 -1.1 77 77
HNF4A -0.21 0.42 -10000 0 -1.1 64 64
KCNJ11 -0.25 0.51 -10000 0 -1.2 83 83
AKT1 -0.076 0.17 -10000 0 -0.42 30 30
response to starvation -0.002 0.022 -10000 0 -10000 0 0
DLK1 -0.25 0.45 -10000 0 -1 92 92
NKX2-1 -0.076 0.22 -10000 0 -0.77 16 16
ACADM -0.18 0.39 -10000 0 -0.96 66 66
TAT -0.23 0.42 -10000 0 -1.1 71 71
CEBPB -0.005 0.1 -10000 0 -0.56 17 17
CEBPA -0.016 0.13 -10000 0 -0.56 27 27
TTR -0.15 0.28 -10000 0 -0.77 52 52
PKLR -0.19 0.4 -10000 0 -1 64 64
APOA1 -0.23 0.48 -10000 0 -1.2 66 66
CPT1C -0.18 0.39 -10000 0 -0.99 61 61
ALAS1 -0.062 0.2 -10000 0 -0.83 2 2
TFRC -0.17 0.31 -10000 0 -0.79 49 49
FOXF1 -0.006 0.094 -10000 0 -0.51 16 16
NF1 0.02 0.038 -10000 0 -0.59 2 2
HNF1A (dimer) 0.011 0.04 -10000 0 -0.65 1 1
CPT1A -0.18 0.39 -10000 0 -1 62 62
HMGCS1 -0.18 0.39 -10000 0 -0.99 63 63
NR3C1 -0.024 0.077 -10000 0 -0.23 7 7
CPT1B -0.2 0.41 -10000 0 -0.99 75 75
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.01 0.024 -10000 0 -10000 0 0
GCK -0.25 0.48 -10000 0 -1.1 101 101
CREB1 -0.003 0.054 -10000 0 -10000 0 0
IGFBP1 -0.26 0.5 -10000 0 -1.3 86 86
PDX1 -0.08 0.21 -10000 0 -0.66 14 14
UCP2 -0.2 0.42 -10000 0 -1 72 72
ALDOB -0.2 0.44 -10000 0 -1 73 73
AFP -0.09 0.17 -10000 0 -0.55 33 33
BDH1 -0.21 0.45 -10000 0 -1.1 77 77
HADH -0.18 0.41 -10000 0 -1 66 66
F2 -0.21 0.43 -10000 0 -1.1 54 54
HNF1A 0.011 0.04 -10000 0 -0.65 1 1
G6PC -0.07 0.21 -10000 0 -0.96 15 15
SLC2A2 -0.094 0.23 -10000 0 -0.73 7 7
INS 0.013 0.091 0.24 17 -0.56 5 22
FOXA1 -0.054 0.17 -10000 0 -0.48 58 58
FOXA3 -0.12 0.23 -10000 0 -0.55 99 99
FOXA2 -0.22 0.47 -10000 0 -1.1 80 80
ABCC8 -0.27 0.53 -10000 0 -1.2 91 91
ALB -0.13 0.3 -10000 0 -1.1 38 38
HIF-1-alpha transcription factor network

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
PKM2 -0.021 0.49 -9999 0 -1.1 56 56
HDAC7 0.017 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.14 0.34 -9999 0 -0.87 58 58
SMAD4 0.016 0.004 -9999 0 -10000 0 0
ID2 -0.021 0.49 -9999 0 -1.1 57 57
AP1 -0.065 0.18 -9999 0 -0.42 100 100
ABCG2 -0.022 0.49 -9999 0 -1.1 56 56
HIF1A 0.023 0.093 -9999 0 -0.62 2 2
TFF3 -0.061 0.5 -9999 0 -1.1 65 65
GATA2 -0.003 0.1 -9999 0 -0.56 16 16
AKT1 0.017 0.1 -9999 0 -10000 0 0
response to hypoxia 0 0.11 -9999 0 -0.24 14 14
MCL1 -0.021 0.49 -9999 0 -1.1 56 56
NDRG1 -0.026 0.5 -9999 0 -1.1 58 58
SERPINE1 -0.096 0.54 -9999 0 -1.1 79 79
FECH -0.021 0.49 -9999 0 -1.1 56 56
FURIN -0.021 0.49 -9999 0 -1.1 56 56
NCOA2 -0.025 0.15 -9999 0 -0.59 35 35
EP300 0.032 0.18 -9999 0 -0.34 37 37
HMOX1 -0.03 0.5 -9999 0 -1.1 59 59
BHLHE40 -0.029 0.5 -9999 0 -1.1 59 59
BHLHE41 -0.029 0.5 -9999 0 -1.1 59 59
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.013 0.059 -9999 0 -0.4 6 6
ENG 0.086 0.13 -9999 0 -0.54 6 6
JUN 0.003 0.075 -9999 0 -0.5 11 11
RORA -0.021 0.49 -9999 0 -1.1 56 56
ABCB1 -0.04 0.093 -9999 0 -1.1 2 2
TFRC -0.026 0.49 -9999 0 -1.1 60 60
CXCR4 -0.033 0.5 -9999 0 -1.1 60 60
TF -0.054 0.53 -9999 0 -1.1 65 65
CITED2 -0.022 0.49 -9999 0 -1.1 57 57
HIF1A/ARNT -0.19 0.49 -9999 0 -1.2 63 63
LDHA -0.03 0.09 -9999 0 -0.63 7 7
ETS1 -0.026 0.49 -9999 0 -1.1 58 58
PGK1 -0.021 0.49 -9999 0 -1.1 57 57
NOS2 -0.045 0.51 -9999 0 -1.1 65 65
ITGB2 -0.04 0.51 -9999 0 -1.1 62 62
ALDOA -0.021 0.49 -9999 0 -1.1 57 57
Cbp/p300/CITED2 -0.09 0.5 -9999 0 -1.1 59 59
FOS -0.094 0.22 -9999 0 -0.55 99 99
HK2 -0.033 0.5 -9999 0 -1.1 59 59
SP1 0.024 0.005 -9999 0 -10000 0 0
GCK -0.067 0.47 -9999 0 -1.2 62 62
HK1 -0.021 0.49 -9999 0 -1.1 57 57
NPM1 -0.021 0.49 -9999 0 -1.1 55 55
EGLN1 -0.021 0.49 -9999 0 -1.1 57 57
CREB1 0.023 0.003 -9999 0 -10000 0 0
PGM1 -0.021 0.49 -9999 0 -1.1 55 55
SMAD3 0.016 0.004 -9999 0 -10000 0 0
EDN1 -0.047 0.32 -9999 0 -0.99 30 30
IGFBP1 -0.079 0.52 -9999 0 -1.1 67 67
VEGFA 0.014 0.41 -9999 0 -0.85 47 47
HIF1A/JAB1 -0.008 0.037 -9999 0 -0.46 2 2
CP -0.11 0.55 -9999 0 -1.1 76 76
CXCL12 -0.026 0.49 -9999 0 -1.1 59 59
COPS5 0.015 0.003 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.004 -9999 0 -10000 0 0
BNIP3 -0.022 0.49 -9999 0 -1.1 57 57
EGLN3 -0.027 0.5 -9999 0 -1.1 58 58
CA9 -0.058 0.52 -9999 0 -1.1 65 65
TERT -0.088 0.51 -9999 0 -1.1 75 75
ENO1 -0.021 0.49 -9999 0 -1.1 57 57
PFKL -0.021 0.49 -9999 0 -1.1 57 57
NCOA1 0.015 0.001 -9999 0 -10000 0 0
ADM -0.056 0.52 -9999 0 -1.1 66 66
ARNT 0.014 0.087 -9999 0 -0.65 1 1
HNF4A -0.043 0.14 -9999 0 -0.49 41 41
ADFP -0.072 0.47 -9999 0 -1.1 59 59
SLC2A1 0.021 0.39 -9999 0 -0.8 43 43
LEP -0.056 0.48 -9999 0 -1.1 57 57
HIF1A/ARNT/Cbp/p300 -0.15 0.35 -9999 0 -0.91 59 59
EPO 0.022 0.36 -9999 0 -0.95 21 21
CREBBP 0.035 0.17 -9999 0 -0.33 31 31
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.34 -9999 0 -0.91 55 55
PFKFB3 -0.023 0.49 -9999 0 -1.1 56 56
NT5E -0.028 0.5 -9999 0 -1.1 59 59
Visual signal transduction: Rods

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
mol:K + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP -0.022 0.085 -9999 0 -0.36 31 31
Metarhodopsin II/Arrestin -0.029 0.092 -9999 0 -0.31 48 48
PDE6G/GNAT1/GTP -0.045 0.12 -9999 0 -0.33 69 69
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.019 0.12 -9999 0 -0.5 31 31
GRK1 0.012 0.023 -9999 0 -0.49 1 1
CNG Channel -0.19 0.19 -9999 0 -0.55 80 80
mol:Na + -0.2 0.2 -9999 0 -0.52 101 101
mol:ADP 0.012 0.023 -9999 0 -0.49 1 1
RGS9-1/Gbeta5/R9AP -0.038 0.12 -9999 0 -0.37 53 53
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.2 0.2 -9999 0 -0.53 101 101
CNGB1 -0.18 0.26 -9999 0 -0.53 179 179
RDH5 -0.019 0.12 -9999 0 -0.5 33 33
SAG 0.003 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.17 0.21 -9999 0 -0.49 101 101
Na + (4 Units) -0.18 0.18 -9999 0 -0.48 101 101
RGS9 -0.04 0.17 -9999 0 -0.58 47 47
GNB1/GNGT1 -0.001 0.021 -9999 0 -0.34 2 2
GNAT1/GDP -0.046 0.11 -9999 0 -0.33 49 49
GUCY2D -0.006 0.087 -9999 0 -0.49 16 16
GNGT1 -0.001 0.031 -9999 0 -0.49 2 2
GUCY2F 0.005 0.05 -9999 0 -0.49 5 5
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.06 0.16 -9999 0 -0.36 72 72
mol:11-cis-retinal -0.019 0.12 -9999 0 -0.5 33 33
mol:cGMP -0.082 0.17 -9999 0 -0.47 40 40
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.056 0.13 -9999 0 -0.36 80 80
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.056 0.19 -9999 0 -0.56 63 63
Metarhodopsin II -0.027 0.082 -9999 0 -0.28 49 49
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.11 0.17 -9999 0 -0.39 103 103
RGS9BP 0.003 0.081 -9999 0 -0.57 10 10
Metarhodopsin II/Transducin -0.011 0.072 -9999 0 -0.3 13 13
GCAP Family/Ca ++ -0.1 0.16 -9999 0 -0.34 152 152
PDE6A/B -0.068 0.16 -9999 0 -0.4 88 88
mol:Pi -0.038 0.12 -9999 0 -0.37 53 53
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.017 0.067 -9999 0 -0.27 32 32
PDE6B -0.034 0.16 -9999 0 -0.54 44 44
PDE6A -0.038 0.16 -9999 0 -0.53 49 49
PDE6G -0.032 0.16 -9999 0 -0.56 41 41
RHO -0.038 0.15 -9999 0 -0.51 48 48
PDE6 -0.093 0.16 -9999 0 -0.56 30 30
GUCA1A -0.14 0.25 -9999 0 -0.54 140 140
GC2/GCAP Family -0.1 0.16 -9999 0 -0.38 95 95
GUCA1C -0.012 0.089 -9999 0 -0.49 17 17
GUCA1B -0.007 0.11 -9999 0 -0.59 18 18
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.1 0.23 -9999 0 -0.45 122 122
MAP3K8 -0.008 0.1 -9999 0 -0.51 20 20
FOS -0.089 0.2 -9999 0 -0.49 83 83
PRKCA 0.011 0.028 -9999 0 -0.6 1 1
PTPN7 -0.13 0.24 -9999 0 -0.55 128 128
HRAS 0.014 0.001 -9999 0 -10000 0 0
PRKCB -0.063 0.19 -9999 0 -0.52 72 72
NRAS 0.014 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.023 0.017 -9999 0 -10000 0 0
MAPK3 -0.073 0.18 -9999 0 -0.46 75 75
MAP2K1 -0.016 0.12 -9999 0 -0.46 26 26
ELK1 0.012 0.007 -9999 0 -10000 0 0
BRAF -0.052 0.13 -9999 0 -0.43 42 42
mol:GTP -0.001 0.002 -9999 0 -0.005 97 97
MAPK1 -0.073 0.18 -9999 0 -0.48 70 70
RAF1 -0.037 0.1 -9999 0 -0.42 25 25
KRAS 0.013 0.022 -9999 0 -0.49 1 1
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.013 0.027 -9999 0 -0.59 1 1
Aurora C/Aurora B/INCENP -0.11 0.16 -9999 0 -0.35 108 108
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.032 0.045 -9999 0 -0.25 1 1
AURKB -0.16 0.26 -9999 0 -0.55 156 156
AURKC -0.022 0.14 -9999 0 -0.52 35 35
PDGFR-alpha signaling pathway

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
PDGFRA -0.061 0.19 -9999 0 -0.58 62 62
PDGF/PDGFRA/CRKL -0.049 0.13 -9999 0 -0.41 63 63
positive regulation of JUN kinase activity -0.038 0.1 -9999 0 -0.32 52 52
CRKL 0.013 0.022 -9999 0 -0.49 1 1
PDGF/PDGFRA/Caveolin-3 -0.056 0.15 -9999 0 -0.42 73 73
AP1 -0.17 0.32 -9999 0 -0.9 73 73
mol:IP3 -0.035 0.15 -9999 0 -0.42 62 62
PLCG1 -0.035 0.15 -9999 0 -0.42 62 62
PDGF/PDGFRA/alphaV Integrin -0.049 0.14 -9999 0 -0.41 62 62
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ -0.035 0.15 -9999 0 -0.42 62 62
CAV3 -0.007 0.084 -9999 0 -0.49 15 15
CAV1 -0.05 0.17 -9999 0 -0.49 65 65
SHC/Grb2/SOS1 -0.037 0.11 -9999 0 -0.32 52 52
PDGF/PDGFRA/Shf -0.052 0.14 -9999 0 -0.42 63 63
FOS -0.13 0.34 -9999 0 -0.89 73 73
JUN -0.02 0.061 -9999 0 -0.4 11 11
oligodendrocyte development -0.049 0.14 -9999 0 -0.41 62 62
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:DAG -0.035 0.15 -9999 0 -0.42 62 62
PDGF/PDGFRA -0.061 0.19 -9999 0 -0.58 62 62
actin cytoskeleton reorganization -0.048 0.13 -9999 0 -0.41 62 62
SRF 0.027 0.01 -9999 0 -10000 0 0
SHC1 0.009 0.05 -9999 0 -0.49 5 5
PI3K -0.041 0.11 -9999 0 -0.33 63 63
PDGF/PDGFRA/Crk/C3G -0.04 0.11 -9999 0 -0.33 62 62
JAK1 -0.029 0.14 -9999 0 -0.41 62 62
ELK1/SRF -0.001 0.11 -9999 0 -0.31 52 52
SHB 0.014 0 -9999 0 -10000 0 0
SHF 0.009 0.053 -9999 0 -0.59 4 4
CSNK2A1 0.014 0.022 -9999 0 -10000 0 0
GO:0007205 -0.037 0.15 -9999 0 -0.44 62 62
SOS1 0.014 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.038 0.1 -9999 0 -0.32 52 52
PDGF/PDGFRA/SHB -0.049 0.13 -9999 0 -0.41 62 62
PDGF/PDGFRA/Caveolin-1 -0.092 0.18 -9999 0 -0.41 117 117
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
ELK1 -0.028 0.14 -9999 0 -0.38 62 62
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
PDGF/PDGFRA/Crk -0.049 0.13 -9999 0 -0.41 62 62
JAK-STAT cascade -0.029 0.14 -9999 0 -0.4 62 62
cell proliferation -0.051 0.14 -9999 0 -0.42 63 63
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.011 0.096 -9999 0 -0.37 32 32
NFATC2 -0.041 0.13 -9999 0 -0.35 76 76
NFATC3 0.012 0.032 -9999 0 -0.34 2 2
CD40LG -0.15 0.29 -9999 0 -0.65 95 95
PTGS2 -0.18 0.32 -9999 0 -0.68 118 118
JUNB -0.033 0.15 -9999 0 -0.51 46 46
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.027 -9999 0 -0.41 2 2
CaM/Ca2+ -0.005 0.027 -9999 0 -0.41 2 2
CALM1 0.01 0.036 -9999 0 -0.55 2 2
JUN 0.001 0.075 -9999 0 -0.5 11 11
mol:Ca2+ -0.005 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.003 -9999 0 -10000 0 0
FOSL1 -0.093 0.22 -9999 0 -0.53 101 101
CREM 0.012 0.035 -9999 0 -0.54 2 2
Jun/NFAT1-c-4/p21SNFT -0.12 0.18 -9999 0 -0.5 66 66
FOS -0.097 0.22 -9999 0 -0.56 99 99
IFNG -0.13 0.27 -9999 0 -0.62 75 75
AP-1/NFAT1-c-4 -0.16 0.32 -9999 0 -0.7 96 96
FASLG -0.14 0.29 -9999 0 -0.65 86 86
NFAT1-c-4/ICER1 -0.056 0.15 -9999 0 -0.38 64 64
IL2RA -0.16 0.3 -9999 0 -0.66 96 96
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.13 0.26 -9999 0 -0.61 76 76
JunB/Fra1/NFAT1-c-4 -0.14 0.2 -9999 0 -0.48 96 96
IL4 -0.13 0.26 -9999 0 -0.62 73 73
IL2 -0.008 0.015 -9999 0 -10000 0 0
IL3 -0.016 0.021 -9999 0 -10000 0 0
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 -0.035 0.16 -9999 0 -0.53 46 46
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.014 0.001 -9999 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.023 0.084 -9999 0 -0.33 35 35
ARNO/beta Arrestin1-2 -0.023 0.084 -9999 0 -0.53 7 7
EGFR -0.083 0.21 -9999 0 -0.55 89 89
EPHA2 -0.016 0.12 -9999 0 -0.5 30 30
USP6 0.004 0.07 -9999 0 -0.49 10 10
IQSEC1 0.006 0.064 -9999 0 -0.5 8 8
EGFR/EGFR/EGF/EGF -0.11 0.2 -9999 0 -0.43 132 132
ARRB2 0.009 0.036 -9999 0 -0.2 15 15
mol:GTP 0.004 0.045 -9999 0 -0.16 23 23
ARRB1 -0.004 0.1 -9999 0 -0.59 15 15
FBXO8 0.013 0.027 -9999 0 -0.59 1 1
TSHR -0.2 0.27 -9999 0 -0.54 195 195
EGF -0.05 0.18 -9999 0 -0.56 58 58
somatostatin receptor activity 0 0 -9999 0 -0.001 78 78
ARAP2 -0.008 0.11 -9999 0 -0.59 19 19
mol:GDP -0.07 0.12 -9999 0 -0.28 85 85
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 38 38
ITGA2B -0.043 0.17 -9999 0 -0.57 50 50
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.017 0.066 -9999 0 -0.4 3 3
ADAP1 -0.024 0.14 -9999 0 -0.55 35 35
KIF13B 0.014 0 -9999 0 -10000 0 0
HGF/MET -0.17 0.23 -9999 0 -0.43 203 203
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.062 0.12 -9999 0 -0.28 73 73
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.097 0.17 -9999 0 -0.41 93 93
ADRB2 -0.015 0.13 -9999 0 -0.59 25 25
receptor agonist activity 0 0 -9999 0 0 84 84
actin filament binding 0 0 -9999 0 -0.001 80 80
SRC 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
GNAQ 0.014 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 57 57
ARF6/GDP -0.007 0.1 -9999 0 -0.39 17 17
ARF6/GDP/GULP/ACAP1 -0.11 0.16 -9999 0 -0.4 89 89
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.062 0.13 -9999 0 -0.35 54 54
ACAP1 -0.03 0.14 -9999 0 -0.5 44 44
ACAP2 0.013 0.027 -9999 0 -0.59 1 1
LHCGR/beta Arrestin2 0.002 0.05 -9999 0 -0.28 15 15
EFNA1 0.01 0.044 -9999 0 -0.49 4 4
HGF -0.079 0.2 -9999 0 -0.51 91 91
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.013 0.027 -9999 0 -0.59 1 1
fibronectin binding 0 0 -9999 0 0 82 82
endosomal lumen acidification 0 0 -9999 0 0 78 78
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.051 0.18 -9999 0 -0.57 57 57
GNAQ/ARNO 0.014 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 39 39
MET -0.15 0.25 -9999 0 -0.53 150 150
GNA14 -0.014 0.12 -9999 0 -0.56 25 25
GNA15 -0.007 0.11 -9999 0 -0.56 19 19
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 63 63
GNA11 0.003 0.08 -9999 0 -0.59 9 9
LHCGR -0.006 0.084 -9999 0 -0.49 15 15
AGTR1 -0.031 0.15 -9999 0 -0.54 41 41
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.05 -9999 0 -0.28 15 15
IPCEF1/ARNO -0.058 0.14 -9999 0 -0.48 15 15
alphaIIb/beta3 Integrin -0.084 0.17 -9999 0 -0.41 107 107
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 -0.002 0.027 -10000 0 -0.43 2 2
Necdin/E2F1 -0.049 0.14 -10000 0 -0.41 62 62
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.078 0.14 -10000 0 -0.55 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.18 -10000 0 -0.37 148 148
NT-4/5 (dimer)/p75(NTR) -0.065 0.15 -10000 0 -0.4 84 84
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.046 0.16 -10000 0 -0.34 81 81
IKBKG 0.014 0 -10000 0 -10000 0 0
BDNF -0.079 0.2 -10000 0 -0.51 92 92
MGDIs/NGR/p75(NTR)/LINGO1 -0.092 0.18 -10000 0 -0.39 122 122
FURIN 0.014 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.097 0.16 -10000 0 -0.33 149 149
LINGO1 -0.019 0.14 -10000 0 -0.59 28 28
Sortilin/TRAF6/NRIF -0.001 0.015 -10000 0 -10000 0 0
proBDNF (dimer) -0.079 0.2 -10000 0 -0.51 92 92
NTRK1 -0.01 0.11 -10000 0 -0.52 23 23
RTN4R -0.036 0.16 -10000 0 -0.56 45 45
neuron apoptosis -0.063 0.17 -10000 0 -0.52 26 26
IRAK1 0.014 0 -10000 0 -10000 0 0
SHC1 -0.075 0.18 -10000 0 -0.36 139 139
ARHGDIA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.09 0.16 -10000 0 -0.37 90 90
MAGEH1 0.004 0.08 -10000 0 -0.59 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.11 0.18 -10000 0 -0.4 108 108
Mammalian IAPs/DIABLO -0.024 0.08 -10000 0 -0.32 25 25
proNGF (dimer) -0.074 0.21 -10000 0 -0.55 79 79
MAGED1 0.014 0 -10000 0 -10000 0 0
APP 0.014 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.01 0.088 -10000 0 -0.5 16 16
ZNF274 0.014 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.053 0.15 -10000 0 -0.34 81 81
NGF -0.074 0.21 -10000 0 -0.55 79 79
cell cycle arrest -0.075 0.14 -10000 0 -0.32 79 79
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.033 0.13 -10000 0 -0.29 87 87
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.055 0.12 -10000 0 -0.33 85 85
NCSTN 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.094 0.17 -10000 0 -0.36 136 136
PSENEN 0.014 0 -10000 0 -10000 0 0
mol:ceramide -0.057 0.16 -10000 0 -0.36 82 82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.02 0.12 -10000 0 -0.4 20 20
p75(NTR)/beta APP -0.054 0.13 -10000 0 -0.38 72 72
BEX1 -0.007 0.11 -10000 0 -0.59 18 18
mol:GDP -0.082 0.18 -10000 0 -0.36 136 136
NGF (dimer) -0.13 0.18 -10000 0 -0.38 126 126
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.082 0.16 -10000 0 -0.4 80 80
PIK3R1 0.014 0 -10000 0 -10000 0 0
RAC1/GTP -0.081 0.14 -10000 0 -0.31 136 136
MYD88 0.004 0.077 -10000 0 -0.57 9 9
CHUK 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.095 0.17 -10000 0 -0.36 136 136
RHOB 0.011 0.038 -10000 0 -0.49 3 3
RHOA 0.014 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.02 0.082 -10000 0 -0.36 28 28
NT3 (dimer) -0.008 0.092 -10000 0 -0.49 18 18
TP53 -0.047 0.16 -10000 0 -0.51 24 24
PRDM4 -0.058 0.16 -10000 0 -0.36 82 82
BDNF (dimer) -0.16 0.19 -10000 0 -0.44 120 120
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
SORT1 0.013 0.027 -10000 0 -0.59 1 1
activation of caspase activity -0.077 0.14 -10000 0 -0.54 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.085 0.15 -10000 0 -0.37 83 83
RHOC 0.011 0.041 -10000 0 -0.52 3 3
XIAP 0.014 0 -10000 0 -10000 0 0
MAPK10 -0.042 0.16 -10000 0 -0.47 29 29
DIABLO 0.014 0 -10000 0 -10000 0 0
SMPD2 -0.058 0.16 -10000 0 -0.36 82 82
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.095 0.17 -10000 0 -0.36 137 137
PSEN1 0.014 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.015 -10000 0 -0.34 1 1
NT3 (dimer)/p75(NTR) -0.066 0.15 -10000 0 -0.39 86 86
MAPK8 -0.046 0.16 -10000 0 -0.46 32 32
MAPK9 -0.041 0.16 -10000 0 -0.48 25 25
APAF1 0.014 0 -10000 0 -10000 0 0
NTF3 -0.008 0.092 -10000 0 -0.49 18 18
NTF4 -0.01 0.088 -10000 0 -0.5 16 16
NDN -0.028 0.16 -10000 0 -0.59 36 36
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.072 0.13 -10000 0 -0.52 16 16
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.044 -10000 0 -0.36 7 7
RhoA-B-C/GTP -0.094 0.16 -10000 0 -0.35 136 136
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.079 0.13 -10000 0 -0.52 17 17
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.087 0.14 -10000 0 -0.39 56 56
PRKACB 0.014 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.068 0.15 -10000 0 -0.37 95 95
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.033 0.16 -10000 0 -0.55 43 43
BIRC2 0.014 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.089 0.16 0.2 5 -0.38 89 94
BAD -0.035 0.16 -10000 0 -0.45 28 28
RIPK2 0.014 0 -10000 0 -10000 0 0
NGFR -0.063 0.19 -10000 0 -0.54 72 72
CYCS -0.046 0.16 -10000 0 -0.55 15 15
ADAM17 0.007 0.065 -10000 0 -0.59 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.085 0.15 -10000 0 -0.37 82 82
BCL2L11 -0.036 0.16 -10000 0 -0.45 28 28
BDNF (dimer)/p75(NTR) -0.12 0.19 -10000 0 -0.4 148 148
PI3K -0.084 0.15 -10000 0 -0.37 81 81
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.085 0.15 -10000 0 -0.37 82 82
NDNL2 0.014 0 -10000 0 -10000 0 0
YWHAE 0.014 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.2 -10000 0 -0.43 136 136
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.085 0.15 -10000 0 -0.37 82 82
TRAF6 0.013 0.027 -10000 0 -0.59 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.015 0.12 -10000 0 -0.55 26 26
PLG -0.001 0.038 -10000 0 -0.49 3 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.092 0.18 -10000 0 -0.46 62 62
SQSTM1 0.014 0 -10000 0 -10000 0 0
NGFRAP1 0.014 0 -10000 0 -10000 0 0
CASP3 -0.03 0.15 -10000 0 -0.41 28 28
E2F1 -0.015 0.12 -10000 0 -0.51 28 28
CASP9 0.013 0.022 -10000 0 -0.49 1 1
IKK complex -0.067 0.12 -10000 0 -0.5 19 19
NGF (dimer)/TRKA -0.077 0.16 -10000 0 -0.4 98 98
MMP7 -0.15 0.25 -10000 0 -0.54 152 152
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.078 0.14 -10000 0 -0.55 16 16
MMP3 -0.037 0.14 -10000 0 -0.49 46 46
APAF-1/Caspase 9 -0.068 0.11 -10000 0 -0.44 21 21
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.003 0.03 -9999 0 -0.34 4 4
PRKCZ -0.015 0.12 -9999 0 -0.55 26 26
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0.022 -9999 0 -0.49 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.078 0.12 -9999 0 -0.39 31 31
IRAK/TOLLIP 0.03 0.025 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
IKBKG 0.014 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.17 0.21 -9999 0 -0.41 208 208
IL1A -0.093 0.22 -9999 0 -0.54 99 99
IL1B -0.13 0.21 -9999 0 -0.4 189 189
IRAK/TRAF6/p62/Atypical PKCs -0.014 0.057 -9999 0 -0.42 1 1
IL1R2 -0.12 0.24 -9999 0 -0.53 130 130
IL1R1 -0.031 0.15 -9999 0 -0.52 44 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.045 0.12 -9999 0 -0.42 20 20
TOLLIP 0.014 0 -9999 0 -10000 0 0
TICAM2 0 0.089 -9999 0 -0.57 12 12
MAP3K3 0.014 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.064 0.033 -9999 0 -10000 0 0
JUN 0.034 0.069 -9999 0 -0.45 4 4
MAP3K7 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.14 0.17 -9999 0 -0.54 48 48
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.11 0.17 -9999 0 -0.4 87 87
PIK3R1 0.014 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.099 0.16 -9999 0 -0.37 87 87
IL1 beta fragment/IL1R1/IL1RAP -0.14 0.21 -9999 0 -0.43 118 118
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0.033 0.058 -9999 0 -0.54 1 1
IRAK1 0.023 0.027 -9999 0 -0.28 4 4
IL1RN/IL1R1 -0.12 0.2 -9999 0 -0.42 143 143
IRAK4 0.013 0.022 -9999 0 -0.49 1 1
PRKCI 0.014 0 -9999 0 -10000 0 0
TRAF6 0.013 0.027 -9999 0 -0.59 1 1
PI3K -0.001 0.019 -9999 0 -0.43 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.063 0.14 -9999 0 -0.42 35 35
CHUK 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.14 0.21 -9999 0 -0.43 118 118
IL1 beta/IL1R2 -0.19 0.23 -9999 0 -0.38 267 267
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.022 -9999 0 -0.28 1 1
NF kappa B1 p50/RelA -0.12 0.15 -9999 0 -0.48 48 48
IRAK3 0.007 0.062 -9999 0 -0.56 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.14 0.18 -9999 0 -0.54 55 55
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.043 0.14 -9999 0 -0.38 31 31
IL1 alpha/IL1R1/IL1RAP -0.12 0.18 -9999 0 -0.36 165 165
RELA 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.014 0 -9999 0 -10000 0 0
MYD88 0.004 0.077 -9999 0 -0.57 9 9
IRAK/TRAF6/MEKK3 0.037 0.027 -9999 0 -10000 0 0
IL1RAP -0.037 0.16 -9999 0 -0.51 50 50
UBE2N 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.11 0.15 -9999 0 -0.45 56 56
CASP1 -0.016 0.12 -9999 0 -0.53 28 28
IL1RN/IL1R2 -0.18 0.24 -9999 0 -0.45 202 202
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.13 0.21 -9999 0 -0.41 124 124
TMEM189-UBE2V1 0.004 0.044 -9999 0 -0.49 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.024 0.12 -9999 0 -0.4 23 23
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
IL1RN -0.11 0.23 -9999 0 -0.53 118 118
TRAF6/TAK1/TAB1/TAB2 -0.002 0.023 -9999 0 -0.29 1 1
MAP2K6 0.033 0.029 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.019 0.11 0.32 1 -0.88 4 5
SMARCC2 0.015 0.01 -10000 0 -10000 0 0
SMARCC1 0.015 0.01 -10000 0 -10000 0 0
TBX21 -0.11 0.25 -10000 0 -0.7 61 61
SUMO2 0.013 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0 0.11 -10000 0 -0.59 16 16
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 -0.089 0.22 -10000 0 -0.56 92 92
GR alpha/HSP90/FKBP51/HSP90 0.02 0.16 0.28 31 -0.32 48 79
PRL -0.044 0.09 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.24 0.51 113 -0.42 10 123
RELA -0.063 0.097 -10000 0 -0.3 2 2
FGG 0.16 0.17 0.46 51 -0.48 2 53
GR beta/TIF2 0.063 0.16 0.29 47 -0.4 34 81
IFNG -0.23 0.21 -10000 0 -0.63 53 53
apoptosis -0.009 0.2 0.64 18 -0.7 2 20
CREB1 0.013 0.023 -10000 0 -10000 0 0
histone acetylation -0.044 0.12 -10000 0 -0.37 33 33
BGLAP -0.046 0.12 -10000 0 -0.48 16 16
GR/PKAc 0.087 0.093 0.29 28 -10000 0 28
NF kappa B1 p50/RelA -0.11 0.18 -10000 0 -0.43 67 67
SMARCD1 0.015 0.01 -10000 0 -10000 0 0
MDM2 0.079 0.077 0.25 38 -10000 0 38
GATA3 -0.1 0.23 -10000 0 -0.53 115 115
AKT1 0.002 0.018 -10000 0 -10000 0 0
CSF2 -0.061 0.099 -10000 0 -0.5 3 3
GSK3B 0.012 0.03 -10000 0 -0.6 1 1
NR1I3 0.028 0.19 0.63 16 -0.68 3 19
CSN2 0.14 0.13 0.41 24 -10000 0 24
BRG1/BAF155/BAF170/BAF60A 0.039 0.036 -10000 0 -0.29 1 1
NFATC1 -0.02 0.14 -10000 0 -0.57 31 31
POU2F1 0.015 0.007 -10000 0 -10000 0 0
CDKN1A -0.063 0.32 -10000 0 -1.4 22 22
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.012 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.53 117 117
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.041 0.19 0.27 16 -0.4 48 64
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.052 0.32 0.6 16 -0.81 54 70
JUN -0.16 0.19 -10000 0 -0.49 73 73
IL4 -0.081 0.15 -10000 0 -0.6 18 18
CDK5R1 -0.022 0.14 -10000 0 -0.59 30 30
PRKACA 0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.2 -10000 0 -0.48 116 116
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.029 0.15 0.29 23 -0.32 16 39
cortisol/GR alpha (monomer) 0.23 0.26 0.59 123 -10000 0 123
NCOA2 -0.027 0.15 -10000 0 -0.59 35 35
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.14 0.23 -10000 0 -0.59 99 99
AP-1/NFAT1-c-4 -0.31 0.3 -10000 0 -0.7 137 137
AFP -0.12 0.17 -10000 0 -0.64 19 19
SUV420H1 0.014 0 -10000 0 -10000 0 0
IRF1 0.11 0.15 0.47 13 -0.47 5 18
TP53 -0.014 0.15 -10000 0 -0.53 34 34
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.43 0.48 -10000 0 -1 172 172
KRT14 -0.12 0.18 -10000 0 -0.55 36 36
TBP 0.023 0.016 -10000 0 -10000 0 0
CREBBP 0.031 0.059 -10000 0 -10000 0 0
HDAC1 0.004 0.054 -10000 0 -0.59 4 4
HDAC2 0.014 0.001 -10000 0 -10000 0 0
AP-1 -0.31 0.31 -10000 0 -0.7 138 138
MAPK14 0.013 0.011 -10000 0 -10000 0 0
MAPK10 0.008 0.055 -10000 0 -0.59 4 4
MAPK11 0.002 0.08 -10000 0 -0.59 9 9
KRT5 -0.4 0.44 -10000 0 -0.92 171 171
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.017 0.01 -10000 0 -10000 0 0
STAT1 0 0.11 -10000 0 -0.59 16 16
CGA -0.064 0.12 -10000 0 -0.46 16 16
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.081 0.11 0.36 15 -10000 0 15
MAPK3 0.013 0.012 -10000 0 -10000 0 0
MAPK1 0.013 0.011 -10000 0 -10000 0 0
ICAM1 -0.2 0.28 -10000 0 -0.71 79 79
NFKB1 -0.063 0.097 -10000 0 -0.28 6 6
MAPK8 -0.13 0.17 -10000 0 -0.47 60 60
MAPK9 0.013 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.012 0.2 0.64 18 -0.74 2 20
BAX 0.001 0.11 -10000 0 -10000 0 0
POMC -0.13 0.24 -10000 0 -1.3 13 13
EP300 0.026 0.079 -10000 0 -0.57 4 4
cortisol/GR alpha (dimer)/p53 0.18 0.23 0.5 107 -0.54 2 109
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.068 0.24 21 -10000 0 21
SGK1 0.052 0.24 -10000 0 -1.4 13 13
IL13 -0.23 0.24 -10000 0 -0.7 62 62
IL6 -0.28 0.38 -10000 0 -0.8 142 142
PRKACG 0.005 0.044 -10000 0 -0.49 4 4
IL5 -0.2 0.19 -10000 0 -0.68 24 24
IL2 -0.23 0.21 -10000 0 -0.61 61 61
CDK5 0.014 0.006 -10000 0 -10000 0 0
PRKACB 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.32 0.41 -10000 0 -0.93 133 133
CDK5R1/CDK5 -0.02 0.1 -10000 0 -0.43 30 30
NF kappa B1 p50/RelA/PKAc -0.055 0.13 -10000 0 -0.39 8 8
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.2 0.2 0.49 114 -10000 0 114
SMARCA4 0.015 0.01 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.13 0.36 61 -0.34 4 65
NF kappa B1 p50/RelA/Cbp -0.052 0.16 -10000 0 -0.46 14 14
JUN (dimer) -0.16 0.19 -10000 0 -0.49 73 73
YWHAH -0.009 0.11 -10000 0 -0.49 24 24
VIPR1 -0.12 0.26 -10000 0 -0.71 73 73
NR3C1 0.14 0.14 0.41 70 -10000 0 70
NR4A1 -0.021 0.14 -10000 0 -0.5 40 40
TIF2/SUV420H1 -0.029 0.11 -10000 0 -0.43 35 35
MAPKKK cascade -0.009 0.2 0.64 18 -0.7 2 20
cortisol/GR alpha (dimer)/Src-1 0.21 0.21 0.51 123 -10000 0 123
PBX1 0.014 0.028 -10000 0 -0.59 1 1
POU1F1 0.004 0.024 -10000 0 -0.49 1 1
SELE -0.27 0.36 -10000 0 -0.76 140 140
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.13 0.36 61 -0.35 4 65
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.2 0.2 0.49 114 -10000 0 114
mol:cortisol 0.12 0.15 0.33 124 -10000 0 124
MMP1 -0.11 0.15 -10000 0 -0.57 30 30
PLK2 and PLK4 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
PLK2 -0.017 0.12 -9999 0 -0.5 31 31
PLK4 -0.013 0.12 -9999 0 -0.51 27 27
regulation of centriole replication -0.018 0.12 -9999 0 -0.36 57 57
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.041 0.095 0.2 126 -10000 0 126
BUB1B -0.059 0.14 -10000 0 -0.3 124 124
PLK1 -0.001 0.043 -10000 0 -0.14 27 27
PLK1S1 0.006 0.022 -10000 0 -0.13 1 1
KIF2A 0.006 0.048 -10000 0 -0.3 5 5
regulation of mitotic centrosome separation -0.001 0.043 -10000 0 -0.13 27 27
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.13 0.24 -10000 0 -0.43 180 180
WEE1 -0.007 0.088 -10000 0 -0.37 19 19
cytokinesis -0.11 0.21 -10000 0 -0.42 136 136
PP2A-alpha B56 -0.061 0.22 -10000 0 -0.67 59 59
AURKA 0.001 0.041 -10000 0 -0.15 23 23
PICH/PLK1 -0.031 0.16 -10000 0 -0.44 59 59
CENPE -0.045 0.14 -10000 0 -0.32 94 94
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.006 0.047 -10000 0 -0.3 5 5
PPP2CA 0.014 0 -10000 0 -10000 0 0
FZR1 0.014 0 -10000 0 -10000 0 0
TPX2 -0.02 0.081 -10000 0 -0.2 70 70
PAK1 -0.035 0.15 -10000 0 -0.5 49 49
SPC24 -0.12 0.24 -10000 0 -0.53 128 128
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN -0.037 0.1 -10000 0 -0.26 78 78
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase 0 0.004 -10000 0 -0.014 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0 0.022 -10000 0 -0.067 26 26
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.012 2 2
STAG2 0.014 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.01 -10000 0 -10000 0 0
spindle elongation -0.001 0.043 -10000 0 -0.13 27 27
ODF2 0.013 0.003 -10000 0 -10000 0 0
BUB1 -0.1 0.24 -10000 0 -0.74 59 59
TPT1 0.006 0.022 -10000 0 -0.11 2 2
CDC25C -0.05 0.13 -10000 0 -0.29 102 102
CDC25B 0.014 0.003 -10000 0 -10000 0 0
SGOL1 -0.041 0.095 -10000 0 -0.2 126 126
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.029 0.089 -10000 0 -0.33 31 31
CDC14B 0.012 0.001 -10000 0 -10000 0 0
CDC20 -0.11 0.23 -10000 0 -0.54 112 112
PLK1/PBIP1 -0.048 0.11 -10000 0 -0.32 70 70
mitosis 0.001 0.005 0.022 8 -0.022 1 9
FBXO5 0.004 0.05 -10000 0 -0.28 8 8
CDC2 0 0.004 -10000 0 -0.014 37 37
NDC80 -0.13 0.25 -10000 0 -0.55 134 134
metaphase plate congression 0.005 0.026 -10000 0 -10000 0 0
ERCC6L -0.056 0.14 -10000 0 -0.44 54 54
NLP/gamma Tubulin 0.003 0.025 -10000 0 -0.13 2 2
microtubule cytoskeleton organization 0.006 0.022 -10000 0 -0.11 2 2
G2/M transition DNA damage checkpoint 0 0.002 0.01 5 -10000 0 5
PPP1R12A 0.013 0.027 -10000 0 -0.59 1 1
interphase 0 0.002 0.01 5 -10000 0 5
PLK1/PRC1-2 -0.09 0.18 -10000 0 -0.34 168 168
GRASP65/GM130/RAB1/GTP/PLK1 -0.005 0.023 -10000 0 -10000 0 0
RAB1A 0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.036 -10000 0 -0.2 2 2
mitotic prometaphase -0.001 0.002 -10000 0 -0.013 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.061 -10000 0 -10000 0 0
microtubule-based process -0.093 0.17 -10000 0 -0.33 168 168
Golgi organization -0.001 0.043 -10000 0 -0.13 27 27
Cohesin/SA2 -0.012 0.029 -10000 0 -0.22 2 2
PPP1CB/MYPT1 0.003 0.021 -10000 0 -0.43 1 1
KIF20A -0.17 0.26 -10000 0 -0.55 168 168
APC/C/CDC20 -0.058 0.15 -10000 0 -0.33 112 112
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation -0.047 0.11 -10000 0 -0.32 70 70
PRC1 -0.005 0.098 -10000 0 -0.49 20 20
ECT2 -0.003 0.081 -10000 0 -0.35 22 22
C13orf34 0.006 0.036 -10000 0 -0.21 2 2
NUDC 0.005 0.026 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.058 0.14 -10000 0 -0.3 124 124
spindle assembly 0.002 0.035 -10000 0 -0.1 25 25
spindle stabilization 0.006 0.022 -10000 0 -0.13 1 1
APC/C/HCDH1 0.02 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 -0.094 0.17 -10000 0 -0.33 168 168
CCNB1 -0.019 0.13 -10000 0 -0.49 34 34
PPP1CB 0.014 0.001 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 -0.006 0.095 -10000 0 -0.44 21 21
TUBG1 0.006 0.022 -10000 0 -0.13 1 1
G2/M transition of mitotic cell cycle -0.031 0.087 -10000 0 -0.32 31 31
MLF1IP -0.043 0.14 -10000 0 -0.4 70 70
INCENP 0.011 0.027 -10000 0 -0.6 1 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.036 0.16 -9999 0 -0.49 25 25
NF kappa B1 p50/RelA/I kappa B alpha -0.013 0.16 -9999 0 -0.49 18 18
alphaV/beta3 Integrin/Osteopontin/Src -0.068 0.15 -9999 0 -0.38 92 92
AP1 -0.08 0.22 -9999 0 -0.59 47 47
ILK -0.045 0.17 -9999 0 -0.52 23 23
bone resorption -0.078 0.23 -9999 0 -0.53 79 79
PTK2B -0.009 0.11 -9999 0 -0.49 24 24
PYK2/p130Cas -0.094 0.16 -9999 0 -0.51 42 42
ITGAV 0.016 0.027 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.067 0.16 -9999 0 -0.42 83 83
alphaV/beta3 Integrin/Osteopontin -0.094 0.16 -9999 0 -0.39 102 102
MAP3K1 -0.05 0.17 -9999 0 -0.5 31 31
JUN 0.003 0.075 -9999 0 -0.5 11 11
MAPK3 -0.039 0.17 -9999 0 -0.5 28 28
MAPK1 -0.039 0.17 -9999 0 -0.51 26 26
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.045 0.18 -9999 0 -0.48 38 38
ITGB3 -0.05 0.18 -9999 0 -0.51 65 65
NFKBIA -0.029 0.17 -9999 0 -0.5 25 25
FOS -0.094 0.22 -9999 0 -0.55 99 99
CD44 -0.058 0.19 -9999 0 -0.55 65 65
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.067 0.27 -9999 0 -0.82 36 36
NF kappa B1 p50/RelA -0.074 0.13 -9999 0 -0.52 18 18
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.047 0.12 -9999 0 -0.36 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.061 0.19 -9999 0 -0.53 47 47
VAV3 -0.12 0.23 -9999 0 -0.56 72 72
MAP3K14 -0.048 0.17 -9999 0 -0.5 29 29
ROCK2 -0.011 0.12 -9999 0 -0.59 21 21
SPP1 -0.081 0.21 -9999 0 -0.53 91 91
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.19 -9999 0 -0.52 70 70
MMP2 -0.067 0.21 -9999 0 -0.55 47 47
Nongenotropic Androgen signaling

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.063 0.13 -10000 0 -0.3 113 113
regulation of S phase of mitotic cell cycle -0.02 0.11 -10000 0 -0.26 71 71
GNAO1 0.008 0.06 -10000 0 -0.59 5 5
HRAS 0.014 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.007 0.055 -10000 0 -0.36 12 12
PELP1 0.014 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.025 0.12 -10000 0 -0.36 23 23
T-DHT/AR -0.086 0.17 -10000 0 -0.41 109 109
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.006 95 95
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
mol:GDP -0.078 0.16 -10000 0 -0.43 78 78
cell proliferation -0.038 0.18 -10000 0 -0.41 62 62
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
FOS -0.085 0.28 -10000 0 -0.78 62 62
mol:Ca2+ -0.011 0.019 -10000 0 -0.061 35 35
MAPK3 -0.03 0.15 -10000 0 -0.44 26 26
MAPK1 -0.014 0.089 -10000 0 -0.27 19 19
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 99 99
cAMP biosynthetic process 0.002 0.055 -10000 0 -0.33 12 12
GNG2 0.009 0.053 -10000 0 -0.59 4 4
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 99 99
HRAS/GTP -0.059 0.11 -10000 0 -0.3 75 75
actin cytoskeleton reorganization -0.001 0.012 -10000 0 -0.28 1 1
SRC 0.014 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 99 99
PI3K 0.001 0.017 -10000 0 -0.36 1 1
apoptosis 0.037 0.16 0.42 62 -10000 0 62
T-DHT/AR/PELP1 -0.071 0.14 -10000 0 -0.34 109 109
HRAS/GDP -0.071 0.15 -10000 0 -0.43 71 71
CREB1 -0.041 0.18 -10000 0 -0.45 62 62
RAC1-CDC42/GTP -0.001 0.013 -10000 0 -0.28 1 1
AR -0.11 0.24 -10000 0 -0.56 109 109
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.029 0.12 -10000 0 -0.34 23 23
RAC1-CDC42/GDP -0.066 0.14 -10000 0 -0.4 71 71
T-DHT/AR/PELP1/Src -0.063 0.13 -10000 0 -0.3 109 109
MAP2K2 -0.024 0.12 -10000 0 -0.34 23 23
T-DHT/AR/PELP1/Src/PI3K -0.02 0.11 -10000 0 -0.26 71 71
GNAZ 0.014 0 -10000 0 -10000 0 0
SHBG 0 0.089 -10000 0 -0.57 12 12
Gi family/GNB1/GNG2/GDP 0.021 0.075 -10000 0 -0.45 6 6
mol:T-DHT 0 0.001 -10000 0 -0.003 72 72
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 0.001 0.067 -10000 0 -0.4 14 14
Gi family/GTP -0.014 0.081 -10000 0 -0.27 17 17
CDC42 0.014 0 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.037 0.14 -10000 0 -0.36 50 50
IKBKB -0.012 0.078 -10000 0 -0.26 15 15
AKT1 -0.049 0.1 -10000 0 -0.25 51 51
IKBKG -0.01 0.083 -10000 0 -0.27 22 22
CALM1 -0.055 0.15 -10000 0 -0.41 56 56
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
MAP3K1 -0.061 0.18 -10000 0 -0.49 54 54
MAP3K7 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.066 0.16 0.21 2 -0.44 57 59
DOK1 0.012 0.035 -10000 0 -0.54 2 2
AP-1 -0.034 0.099 0.18 2 -0.25 41 43
LYN 0.004 0.073 -10000 0 -0.51 10 10
BLNK -0.056 0.19 -10000 0 -0.57 61 61
SHC1 0.009 0.05 -10000 0 -0.49 5 5
BCR complex -0.076 0.18 -10000 0 -0.44 91 91
CD22 -0.17 0.21 -10000 0 -0.52 91 91
CAMK2G -0.044 0.14 -10000 0 -0.45 35 35
CSNK2A1 0.014 0 -10000 0 -10000 0 0
INPP5D 0.008 0.06 -10000 0 -0.54 6 6
SHC/GRB2/SOS1 -0.091 0.17 -10000 0 -0.55 43 43
GO:0007205 -0.067 0.16 0.21 2 -0.44 57 59
SYK -0.013 0.12 -10000 0 -0.57 24 24
ELK1 -0.055 0.15 -10000 0 -0.41 57 57
NFATC1 -0.062 0.17 -10000 0 -0.45 62 62
B-cell antigen/BCR complex -0.076 0.18 -10000 0 -0.44 91 91
PAG1/CSK -0.001 0.019 -10000 0 -0.43 1 1
NFKBIB 0.006 0.029 0.081 2 -10000 0 2
HRAS -0.049 0.16 -10000 0 -0.42 51 51
NFKBIA 0.007 0.028 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.013 0.023 -10000 0 -10000 0 0
RasGAP/Csk -0.12 0.18 -10000 0 -0.54 52 52
mol:GDP -0.062 0.16 -10000 0 -0.42 57 57
PTEN 0.013 0.027 -10000 0 -0.59 1 1
CD79B -0.048 0.17 -10000 0 -0.53 58 58
NF-kappa-B/RelA/I kappa B alpha 0.013 0.023 -10000 0 -10000 0 0
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PI3K/BCAP/CD19 -0.086 0.19 -10000 0 -0.48 73 73
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.068 0.16 0.21 2 -0.45 57 59
CSK 0.014 0 -10000 0 -10000 0 0
FOS -0.095 0.18 -10000 0 -0.47 63 63
CHUK -0.01 0.083 -10000 0 -0.28 18 18
IBTK 0.014 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.064 0.14 -10000 0 -0.51 35 35
PTPN6 -0.16 0.21 -10000 0 -0.53 89 89
RELA 0.014 0 -10000 0 -10000 0 0
BCL2A1 -0.005 0.045 -10000 0 -0.1 27 27
VAV2 -0.11 0.18 -10000 0 -0.55 52 52
ubiquitin-dependent protein catabolic process 0.011 0.028 0.085 2 -10000 0 2
BTK -0.041 0.2 0.36 1 -1.1 17 18
CD19 -0.11 0.18 -10000 0 -0.5 68 68
MAP4K1 -0.018 0.14 -10000 0 -0.58 28 28
CD72 -0.008 0.11 -10000 0 -0.51 22 22
PAG1 0.013 0.027 -10000 0 -0.59 1 1
MAPK14 -0.044 0.16 -10000 0 -0.42 49 49
SH3BP5 0.01 0.051 -10000 0 -0.57 4 4
PIK3AP1 -0.065 0.18 0.24 2 -0.48 64 66
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.066 0.22 -10000 0 -0.54 64 64
RAF1 -0.039 0.15 -10000 0 -0.45 36 36
RasGAP/p62DOK/SHIP -0.12 0.18 -10000 0 -0.54 53 53
CD79A -0.04 0.16 -10000 0 -0.54 50 50
re-entry into mitotic cell cycle -0.034 0.099 0.18 2 -0.25 42 44
RASA1 0.014 0 -10000 0 -10000 0 0
MAPK3 -0.017 0.12 -10000 0 -0.4 27 27
MAPK1 -0.017 0.12 -10000 0 -0.41 25 25
CD72/SHP1 -0.14 0.22 -10000 0 -0.54 83 83
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.051 0.16 -10000 0 -0.42 55 55
actin cytoskeleton organization -0.063 0.17 -10000 0 -0.48 47 47
NF-kappa-B/RelA 0.03 0.045 -10000 0 -10000 0 0
Calcineurin -0.057 0.12 -10000 0 -0.44 31 31
PI3K -0.13 0.17 -10000 0 -0.47 79 79
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.081 0.17 0.24 2 -0.49 57 59
SOS1 0.014 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.27 -10000 0 -0.79 58 58
DAPP1 -0.14 0.29 -10000 0 -0.89 54 54
cytokine secretion -0.057 0.16 -10000 0 -0.42 62 62
mol:DAG -0.068 0.16 0.21 2 -0.45 57 59
PLCG2 0 0.088 -10000 0 -0.55 13 13
MAP2K1 -0.028 0.14 -10000 0 -0.43 31 31
B-cell antigen/BCR complex/FcgammaRIIB -0.15 0.22 -10000 0 -0.41 185 185
mol:PI-3-4-5-P3 -0.099 0.12 -10000 0 -0.35 64 64
ETS1 -0.038 0.14 -10000 0 -0.43 33 33
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.1 0.2 -10000 0 -0.63 41 41
B-cell antigen/BCR complex/LYN -0.1 0.18 -10000 0 -0.47 76 76
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.013 0.027 -10000 0 -0.59 1 1
RAC1 -0.068 0.18 -10000 0 -0.52 47 47
B-cell antigen/BCR complex/LYN/SYK -0.17 0.23 -10000 0 -0.57 91 91
CARD11 -0.066 0.18 -10000 0 -0.48 61 61
FCGR2B -0.13 0.24 -10000 0 -0.53 138 138
PPP3CA 0.012 0.031 -10000 0 -0.49 2 2
BCL10 0.014 0 -10000 0 -10000 0 0
IKK complex 0.002 0.036 -10000 0 -0.12 1 1
PTPRC -0.041 0.17 -10000 0 -0.54 51 51
PDPK1 -0.049 0.098 -10000 0 -0.24 53 53
PPP3CB 0.011 0.038 -10000 0 -0.49 3 3
PPP3CC 0.014 0 -10000 0 -10000 0 0
POU2F2 0.013 0.024 -10000 0 -0.1 6 6
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.051 0.12 -9999 0 -0.34 54 54
NF kappa B1 p50/RelA/I kappa B alpha -0.041 0.089 -9999 0 -0.43 9 9
AP1 -0.12 0.17 -9999 0 -0.48 60 60
mol:PIP3 -0.097 0.15 -9999 0 -0.46 45 45
AKT1 0.019 0.098 -9999 0 -0.34 11 11
PTK2B -0.018 0.1 -9999 0 -0.31 34 34
RHOA 0.008 0.063 -9999 0 -0.32 7 7
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.086 -9999 0 -0.38 8 8
MAGI3 0.002 0.084 -9999 0 -0.59 10 10
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.042 0.13 -9999 0 -0.34 60 60
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.006 0.1 -9999 0 -0.33 24 24
NF kappa B1 p50/RelA -0.068 0.13 -9999 0 -0.49 26 26
endothelial cell migration -0.045 0.18 -9999 0 -0.44 72 72
ADCY4 -0.022 0.15 -9999 0 -0.41 56 56
ADCY5 -0.027 0.16 -9999 0 -0.42 63 63
ADCY6 -0.019 0.15 -9999 0 -0.41 55 55
ADCY7 -0.019 0.15 -9999 0 -0.41 55 55
ADCY1 -0.047 0.17 -9999 0 -0.43 64 64
ADCY2 -0.025 0.16 -9999 0 -0.42 59 59
ADCY3 -0.019 0.15 -9999 0 -0.41 55 55
ADCY8 -0.043 0.18 -9999 0 -0.48 61 61
ADCY9 -0.021 0.15 -9999 0 -0.41 55 55
GSK3B -0.009 0.1 -9999 0 -0.32 24 24
arachidonic acid secretion -0.012 0.14 -9999 0 -0.38 55 55
GNG2 0.009 0.053 -9999 0 -0.59 4 4
TRIP6 0.009 0.065 -9999 0 -0.4 5 5
GNAO1 -0.033 0.14 -9999 0 -0.35 80 80
HRAS 0.014 0 -9999 0 -10000 0 0
NFKBIA -0.011 0.12 -9999 0 -0.41 25 25
GAB1 0.012 0.035 -9999 0 -0.54 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.082 -9999 0 -1 3 3
JUN 0.003 0.075 -9999 0 -0.5 11 11
LPA/LPA2/NHERF2 -0.011 0.054 -9999 0 -0.33 13 13
TIAM1 -0.006 0.11 -9999 0 -1.3 3 3
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.006 0.088 -9999 0 -0.39 8 8
PLCB3 0.019 0.053 -9999 0 -0.3 11 11
FOS -0.094 0.22 -9999 0 -0.55 99 99
positive regulation of mitosis -0.012 0.14 -9999 0 -0.38 55 55
LPA/LPA1-2-3 -0.079 0.14 -9999 0 -0.38 67 67
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
stress fiber formation -0.021 0.12 -9999 0 -0.37 24 24
GNAZ -0.03 0.14 -9999 0 -0.34 76 76
EGFR/PI3K-beta/Gab1 -0.1 0.15 -9999 0 -0.48 45 45
positive regulation of dendritic cell cytokine production -0.079 0.14 -9999 0 -0.37 67 67
LPA/LPA2/MAGI-3 -0.017 0.07 -9999 0 -0.35 21 21
ARHGEF1 -0.009 0.12 -9999 0 -0.54 5 5
GNAI2 -0.03 0.14 -9999 0 -0.34 76 76
GNAI3 -0.03 0.14 -9999 0 -0.34 76 76
GNAI1 -0.042 0.15 -9999 0 -0.35 92 92
LPA/LPA3 -0.037 0.11 -9999 0 -0.36 49 49
LPA/LPA2 -0.013 0.062 -9999 0 -0.41 11 11
LPA/LPA1 -0.066 0.15 -9999 0 -0.38 89 89
HB-EGF/EGFR -0.13 0.21 -9999 0 -0.44 115 115
HBEGF -0.093 0.19 -9999 0 -0.38 148 148
mol:DAG 0.006 0.088 -9999 0 -0.39 8 8
cAMP biosynthetic process -0.023 0.16 -9999 0 -0.42 55 55
NFKB1 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN -0.015 0.13 -9999 0 -0.43 26 26
GNAQ -0.008 0.084 -9999 0 -0.32 17 17
LPAR2 0.002 0.084 -9999 0 -0.56 11 11
LPAR3 -0.041 0.15 -9999 0 -0.49 49 49
LPAR1 -0.065 0.2 -9999 0 -0.56 68 68
IL8 -0.18 0.23 -9999 0 -0.48 155 155
PTK2 -0.044 0.15 -9999 0 -0.5 18 18
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.042 0.13 -9999 0 -0.34 60 60
EGFR -0.084 0.21 -9999 0 -0.55 89 89
PLCG1 -0.009 0.09 -9999 0 -0.3 21 21
PLD2 -0.045 0.15 -9999 0 -0.35 66 66
G12/G13 -0.049 0.11 -9999 0 -0.34 51 51
PI3K-beta -0.038 0.086 -9999 0 -0.38 12 12
cell migration -0.026 0.055 -9999 0 -0.26 5 5
SLC9A3R2 0.012 0.031 -9999 0 -0.49 2 2
PXN -0.021 0.12 -9999 0 -0.37 24 24
HRAS/GTP -0.013 0.15 -9999 0 -0.39 55 55
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.14 0.24 -9999 0 -0.52 144 144
PRKCE 0.003 0.077 -9999 0 -0.52 11 11
PRKCD -0.003 0.11 -9999 0 -0.39 21 21
Gi(beta/gamma) -0.014 0.14 -9999 0 -0.38 56 56
mol:LPA -0.003 0.035 -9999 0 -0.19 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.065 0.12 -9999 0 -0.47 18 18
MAPKKK cascade -0.012 0.14 -9999 0 -0.38 55 55
contractile ring contraction involved in cytokinesis 0.008 0.062 -9999 0 -0.31 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.022 0.1 -9999 0 -0.32 35 35
GNA15 -0.019 0.099 -9999 0 -0.31 33 33
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
MAPT -0.007 0.11 -9999 0 -0.34 24 24
GNA11 -0.014 0.094 -9999 0 -0.32 26 26
Rac1/GTP -0.003 0.09 -9999 0 -1.1 3 3
MMP2 -0.045 0.18 -9999 0 -0.44 72 72
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.014 0 -9999 0 -10000 0 0
EGFR -0.083 0.21 -9999 0 -0.55 89 89
EGF/EGFR -0.11 0.17 -9999 0 -0.36 118 118
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.078 0.14 -9999 0 -0.53 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.02 0.14 -9999 0 -0.54 32 32
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.05 0.18 -9999 0 -0.56 58 58
EGF/EGFR dimer/SHC -0.095 0.17 -9999 0 -0.4 92 92
mol:GDP -0.078 0.14 -9999 0 -0.52 17 17
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.037 0.16 -9999 0 -0.52 49 49
GRB2/SOS1 -0.001 0.015 -9999 0 -0.34 1 1
HRAS/GTP -0.07 0.13 -9999 0 -0.48 17 17
SHC1 0.009 0.05 -9999 0 -0.49 5 5
HRAS/GDP -0.072 0.13 -9999 0 -0.49 17 17
FRAP1 -0.045 0.15 -9999 0 -0.5 17 17
EGF/EGFR dimer -0.11 0.2 -9999 0 -0.43 132 132
SOS1 0.014 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -0.49 1 1
ETA receptor/Endothelin-1 -0.059 0.14 -9999 0 -0.39 78 78
BMP receptor signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.059 0.12 -9999 0 -0.32 73 73
SMAD6-7/SMURF1 -0.004 0.036 -9999 0 -0.33 6 6
NOG -0.063 0.2 -9999 0 -0.58 67 67
SMAD9 -0.028 0.16 -9999 0 -0.56 36 36
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD5 -0.001 0.12 -9999 0 -0.48 17 17
BMP7/USAG1 -0.092 0.16 -9999 0 -0.38 126 126
SMAD5/SKI 0.007 0.12 -9999 0 -0.46 16 16
SMAD1 0.044 0.029 -9999 0 -10000 0 0
BMP2 -0.078 0.22 -9999 0 -0.59 78 78
SMAD1/SMAD1/SMAD4 -0.003 0.025 -9999 0 -10000 0 0
BMPR1A 0.014 0 -9999 0 -10000 0 0
BMPR1B -0.022 0.14 -9999 0 -0.59 31 31
BMPR1A-1B/BAMBI -0.027 0.1 -9999 0 -0.39 35 35
AHSG -0.076 0.21 -9999 0 -0.55 81 81
CER1 -0.014 0.099 -9999 0 -0.49 21 21
BMP2-4/CER1 -0.081 0.19 -9999 0 -0.45 93 93
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.014 0.16 -9999 0 -0.48 36 36
BMP2-4 (homodimer) -0.082 0.2 -9999 0 -0.51 83 83
RGMB 0.004 0.074 -9999 0 -0.55 9 9
BMP6/BMPR2/BMPR1A-1B -0.028 0.092 -9999 0 -0.33 36 36
RGMA -0.002 0.097 -9999 0 -0.58 14 14
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.021 0.15 -9999 0 -0.46 36 36
BMP2-4/USAG1 -0.14 0.22 -9999 0 -0.42 171 171
SMAD6/SMURF1/SMAD5 0.007 0.12 -9999 0 -0.46 16 16
SOSTDC1 -0.11 0.23 -9999 0 -0.52 120 120
BMP7/BMPR2/BMPR1A-1B -0.023 0.083 -9999 0 -0.32 38 38
SKI 0.014 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.004 0.097 -9999 0 -0.52 17 17
HFE2 0.003 0.062 -9999 0 -0.49 8 8
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.075 0.17 -9999 0 -0.43 89 89
SMAD5/SMAD5/SMAD4 0.007 0.12 -9999 0 -0.46 16 16
MAPK1 0.014 0 -9999 0 -10000 0 0
TAK1/TAB family -0.047 0.11 -9999 0 -0.4 34 34
BMP7 (homodimer) 0.006 0.07 -9999 0 -0.59 7 7
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.074 0.16 -9999 0 -0.41 93 93
SMAD1/SKI 0.05 0.028 -9999 0 -10000 0 0
SMAD6 0.007 0.062 -9999 0 -0.56 6 6
CTDSP2 0.01 0.044 -9999 0 -0.49 4 4
BMP2-4/FETUA -0.12 0.21 -9999 0 -0.42 148 148
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.17 0.26 -9999 0 -0.55 166 166
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.005 0.039 -9999 0 -0.28 10 10
BMPR1A-1B (homodimer) -0.026 0.1 -9999 0 -0.43 31 31
CHRDL1 -0.078 0.21 -9999 0 -0.57 81 81
ENDOFIN/SMAD1 0.05 0.028 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.029 -9999 0 -10000 0 0
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI 0.005 0.069 -9999 0 -0.51 9 9
SMURF2 0.011 0.046 -9999 0 -0.59 3 3
BMP2-4/CHRDL1 -0.12 0.2 -9999 0 -0.41 153 153
BMP2-4/GREM1 -0.17 0.22 -9999 0 -0.41 219 219
SMAD7 0.014 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.019 0.15 -9999 0 -0.52 36 36
SMAD1/SMAD6 0.05 0.028 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.006 0.07 -9999 0 -0.59 7 7
BMP6 -0.004 0.097 -9999 0 -0.53 17 17
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.014 0.14 -9999 0 -0.42 36 36
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.048 0.037 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0.027 -9999 0 -0.59 1 1
PPP1CA 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
PPP1R15A 0.004 0.07 -9999 0 -0.49 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.052 0.18 -9999 0 -0.48 53 53
CHRD 0.006 0.07 -9999 0 -0.59 7 7
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.029 0.16 -9999 0 -0.51 36 36
BMP4 -0.014 0.13 -9999 0 -0.58 24 24
FST -0.067 0.2 -9999 0 -0.54 75 75
BMP2-4/NOG -0.11 0.24 -9999 0 -0.54 108 108
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.021 0.076 -9999 0 -0.29 38 38
IL6-mediated signaling events

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
BCL2L1 -0.036 0.23 -10000 0 -0.7 15 15
CRP -0.043 0.23 -10000 0 -0.68 18 18
cell cycle arrest -0.056 0.25 -10000 0 -0.67 38 38
TIMP1 -0.08 0.27 -10000 0 -0.64 53 53
IL6ST -0.03 0.16 -10000 0 -0.59 37 37
Rac1/GDP -0.067 0.2 -10000 0 -0.44 74 74
AP1 -0.017 0.14 -10000 0 -0.48 13 13
GAB2 0.014 0.027 -10000 0 -0.59 1 1
TNFSF11 -0.044 0.23 -10000 0 -0.7 17 17
HSP90B1 0.005 0.16 -10000 0 -0.92 13 13
GAB1 0.013 0.035 -10000 0 -0.54 2 2
MAPK14 -0.097 0.23 -10000 0 -0.48 103 103
AKT1 0.058 0.03 -10000 0 -0.45 1 1
FOXO1 0.063 0.036 -10000 0 -0.42 1 1
MAP2K6 -0.085 0.2 0.26 1 -0.46 77 78
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.054 0.21 -10000 0 -0.5 53 53
MITF -0.066 0.18 0.27 1 -0.42 74 75
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.014 0 -10000 0 -10000 0 0
A2M 0.018 0.072 -10000 0 -1.4 1 1
CEBPB 0.003 0.11 -10000 0 -0.57 17 17
GRB2/SOS1/GAB family/SHP2 0.004 0.078 -10000 0 -0.82 1 1
STAT3 -0.06 0.26 -10000 0 -0.71 38 38
STAT1 -0.008 0.035 -10000 0 -10000 0 0
CEBPD -0.078 0.33 -10000 0 -0.93 47 47
PIK3CA 0.015 0.027 -10000 0 -0.59 1 1
PI3K 0.023 0.02 -10000 0 -0.43 1 1
JUN 0.003 0.075 -10000 0 -0.5 11 11
PIAS3/MITF -0.055 0.18 -10000 0 -0.42 57 57
MAPK11 -0.1 0.23 -10000 0 -0.5 99 99
STAT3 (dimer)/FOXO1 0.015 0.21 -10000 0 -0.58 15 15
GRB2/SOS1/GAB family -0.072 0.12 -10000 0 -0.46 30 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.064 0.17 -10000 0 -0.42 61 61
GRB2 0.014 0.022 -10000 0 -0.49 1 1
JAK2 0.014 0 -10000 0 -10000 0 0
LBP -0.034 0.23 -10000 0 -0.65 25 25
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.012 0.009 -10000 0 -10000 0 0
MYC -0.063 0.3 -10000 0 -0.94 34 34
FGG -0.044 0.23 -10000 0 -0.66 22 22
macrophage differentiation -0.056 0.25 -10000 0 -0.67 38 38
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.17 -10000 0 -0.43 71 71
JUNB -0.057 0.27 -10000 0 -0.8 31 31
FOS -0.094 0.22 -10000 0 -0.55 99 99
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.077 0.19 0.29 1 -0.42 83 84
STAT1/PIAS1 -0.054 0.18 0.29 1 -0.42 61 62
GRB2/SOS1/GAB family/SHP2/PI3K 0.045 0.032 -10000 0 -0.38 2 2
STAT3 (dimer) -0.058 0.26 -10000 0 -0.7 38 38
PRKCD -0.058 0.25 -10000 0 -0.59 55 55
IL6R -0.015 0.12 -10000 0 -0.57 24 24
SOCS3 -0.15 0.34 -10000 0 -0.73 96 96
gp130 (dimer)/JAK1/JAK1/LMO4 -0.001 0.1 -10000 0 -0.35 37 37
Rac1/GTP -0.069 0.2 -10000 0 -0.45 73 73
HCK -0.008 0.11 -10000 0 -0.54 20 20
MAPKKK cascade 0.025 0.068 -10000 0 -0.91 1 1
bone resorption -0.04 0.22 -10000 0 -0.66 18 18
IRF1 -0.044 0.24 -10000 0 -0.69 22 22
mol:GDP -0.079 0.2 0.28 1 -0.44 87 88
SOS1 0.015 0.002 -10000 0 -10000 0 0
VAV1 -0.081 0.2 0.28 1 -0.44 87 88
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.22 -10000 0 -0.46 111 111
PTPN11 -0.002 0.017 -10000 0 -10000 0 0
IL6/IL6RA -0.1 0.2 -10000 0 -0.41 147 147
gp130 (dimer)/TYK2/TYK2/LMO4 -0.003 0.1 -10000 0 -0.35 37 37
gp130 (dimer)/JAK2/JAK2/LMO4 -0.003 0.1 -10000 0 -0.35 37 37
IL6 -0.13 0.24 -10000 0 -0.53 134 134
PIAS3 0.014 0 -10000 0 -10000 0 0
PTPRE 0.012 0.032 -10000 0 -0.6 1 1
PIAS1 0.009 0.053 -10000 0 -0.59 4 4
RAC1 0.015 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.067 0.16 0.26 1 -0.41 52 53
LMO4 0.014 0.012 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.2 -10000 0 -0.66 37 37
MCL1 0.064 0.027 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.074 0.17 -10000 0 -0.42 104 104
TP53 -0.034 0.089 -10000 0 -0.43 14 14
Senescence -0.034 0.089 -10000 0 -0.43 14 14
Apoptosis -0.034 0.089 -10000 0 -0.43 14 14
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.049 0.1 0.27 76 -0.26 2 78
MDM4 0.005 0.066 -10000 0 -0.49 9 9
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 -0.087 0.28 -10000 0 -0.89 38 38
NCK1/PAK1/Dok-R -0.096 0.13 -10000 0 -0.41 52 52
NCK1/Dok-R -0.11 0.32 -10000 0 -1.1 38 38
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
mol:beta2-estradiol 0.015 0.064 0.22 30 -10000 0 30
RELA 0.014 0 -10000 0 -10000 0 0
SHC1 0.009 0.05 -10000 0 -0.49 5 5
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.014 0.088 0.25 17 -0.48 7 24
TNIP2 0.014 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.11 0.26 -10000 0 -1 37 37
FN1 -0.004 0.093 -10000 0 -0.49 18 18
PLD2 -0.084 0.31 -10000 0 -1.1 37 37
PTPN11 0.014 0 -10000 0 -10000 0 0
GRB14 -0.18 0.26 -10000 0 -0.53 184 184
ELK1 -0.061 0.28 -10000 0 -0.99 37 37
GRB7 -0.031 0.14 -10000 0 -0.49 42 42
PAK1 -0.035 0.15 -10000 0 -0.5 49 49
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.29 -10000 0 -1 42 42
CDKN1A -0.1 0.29 -10000 0 -0.68 75 75
ITGA5 -0.01 0.11 -10000 0 -0.5 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.11 0.32 -10000 0 -1.1 38 38
CRK 0.014 0 -10000 0 -10000 0 0
mol:NO -0.059 0.22 -10000 0 -0.64 40 40
PLG -0.092 0.31 -10000 0 -1.1 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.078 0.26 -10000 0 -0.85 38 38
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PIK3R1 0.014 0.002 -10000 0 -10000 0 0
ANGPT2 -0.11 0.29 -10000 0 -0.68 77 77
BMX -0.11 0.32 -10000 0 -1.1 38 38
ANGPT1 -0.13 0.34 -10000 0 -1.2 42 42
tube development -0.085 0.26 -10000 0 -0.66 63 63
ANGPT4 -0.05 0.18 -10000 0 -0.54 58 58
response to hypoxia -0.008 0.021 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.18 0.36 -10000 0 -1.3 39 39
alpha5/beta1 Integrin -0.018 0.079 -10000 0 -0.36 25 25
FGF2 0.011 0.044 -10000 0 -0.56 3 3
STAT5A (dimer) -0.11 0.32 -10000 0 -0.76 71 71
mol:L-citrulline -0.059 0.22 -10000 0 -0.64 40 40
AGTR1 -0.031 0.15 -10000 0 -0.55 41 41
MAPK14 -0.09 0.31 -10000 0 -1.1 36 36
Tie2/SHP2 -0.042 0.16 -10000 0 -1.2 8 8
TEK -0.023 0.19 -10000 0 -1.3 8 8
RPS6KB1 -0.073 0.27 -10000 0 -0.85 37 37
Angiotensin II/AT1 -0.023 0.11 -10000 0 -0.4 41 41
Tie2/Ang1/GRB2 -0.087 0.32 -10000 0 -1.2 37 37
MAPK3 -0.068 0.29 -10000 0 -1 37 37
MAPK1 -0.068 0.29 -10000 0 -1 37 37
Tie2/Ang1/GRB7 -0.11 0.33 -10000 0 -1.2 37 37
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.091 0.32 -10000 0 -1.1 37 37
PI3K -0.096 0.31 -10000 0 -1 37 37
FES -0.09 0.31 -10000 0 -1.1 36 36
Crk/Dok-R -0.11 0.32 -10000 0 -1.1 38 38
Tie2/Ang1/ABIN2 -0.087 0.32 -10000 0 -1.2 37 37
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.076 0.26 -10000 0 -0.79 38 38
STAT5A 0.001 0.088 -10000 0 -0.59 11 11
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.073 0.27 -10000 0 -0.85 37 37
Tie2/Ang2 -0.13 0.34 -10000 0 -0.92 59 59
Tie2/Ang1 -0.099 0.34 -10000 0 -1.2 37 37
FOXO1 -0.084 0.28 -10000 0 -0.73 57 57
ELF1 0.019 0.032 -10000 0 -0.64 1 1
ELF2 -0.088 0.31 -10000 0 -1.1 37 37
mol:Choline -0.078 0.3 -10000 0 -1.1 37 37
cell migration -0.054 0.073 -10000 0 -0.23 43 43
FYN -0.1 0.29 -10000 0 -0.76 61 61
DOK2 -0.071 0.2 -10000 0 -0.53 80 80
negative regulation of cell cycle -0.091 0.26 -10000 0 -0.61 77 77
ETS1 -0.01 0.1 -10000 0 -0.58 10 10
PXN -0.052 0.23 -10000 0 -0.7 37 37
ITGB1 0.012 0.031 -10000 0 -0.49 2 2
NOS3 -0.069 0.25 -10000 0 -0.74 39 39
RAC1 0.014 0 -10000 0 -10000 0 0
TNF -0.17 0.27 -10000 0 -0.55 157 157
MAPKKK cascade -0.078 0.3 -10000 0 -1.1 37 37
RASA1 0.014 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.092 0.33 -10000 0 -1.2 37 37
NCK1 0.013 0.027 -10000 0 -0.59 1 1
vasculogenesis -0.05 0.2 -10000 0 -0.57 40 40
mol:Phosphatidic acid -0.078 0.3 -10000 0 -1.1 37 37
mol:Angiotensin II -0.001 0.008 -10000 0 -10000 0 0
mol:NADP -0.059 0.22 -10000 0 -0.64 40 40
Rac1/GTP -0.12 0.22 -10000 0 -0.79 37 37
MMP2 -0.097 0.32 -10000 0 -1.1 38 38
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.013 0.022 -9999 0 -0.49 1 1
LAT2 -0.052 0.18 -9999 0 -0.56 36 36
AP1 -0.11 0.18 -9999 0 -0.52 59 59
mol:PIP3 -0.064 0.2 -9999 0 -0.58 40 40
IKBKB -0.03 0.11 -9999 0 -0.29 32 32
AKT1 -0.035 0.14 -9999 0 -0.42 23 23
IKBKG -0.03 0.11 -9999 0 -0.28 41 41
MS4A2 -0.024 0.11 -9999 0 -0.49 26 26
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
MAP3K1 -0.019 0.16 -9999 0 -0.52 31 31
mol:Ca2+ -0.044 0.15 -9999 0 -0.41 40 40
LYN 0.003 0.074 -9999 0 -0.52 10 10
CBLB -0.039 0.14 -9999 0 -0.5 24 24
SHC1 0.009 0.05 -9999 0 -0.49 5 5
RasGAP/p62DOK -0.019 0.071 -9999 0 -0.28 34 34
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.008 0.06 -9999 0 -0.54 6 6
PLD2 -0.071 0.16 -9999 0 -0.36 73 73
PTPN13 -0.03 0.14 -9999 0 -0.56 20 20
PTPN11 0.01 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.004 0.12 -9999 0 -0.34 19 19
SYK -0.014 0.13 -9999 0 -0.58 24 24
GRB2 0.013 0.022 -9999 0 -0.49 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.17 -9999 0 -0.59 39 39
LAT -0.055 0.15 -9999 0 -0.42 48 48
PAK2 -0.028 0.17 -9999 0 -0.61 30 30
NFATC2 -0.099 0.19 -9999 0 -0.5 74 74
HRAS -0.041 0.19 -9999 0 -0.67 32 32
GAB2 0.013 0.027 -9999 0 -0.59 1 1
PLA2G1B 0.04 0.022 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.19 -9999 0 -0.36 179 179
Antigen/IgE/Fc epsilon R1 -0.11 0.17 -9999 0 -0.34 149 149
mol:GDP -0.05 0.2 -9999 0 -0.69 35 35
JUN 0.003 0.075 -9999 0 -0.5 11 11
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
FOS -0.094 0.22 -9999 0 -0.55 99 99
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.065 0.14 -9999 0 -0.49 29 29
CHUK -0.03 0.11 -9999 0 -0.29 32 32
KLRG1 -0.043 0.14 -9999 0 -0.51 23 23
VAV1 -0.054 0.18 -9999 0 -0.62 34 34
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.038 0.14 -9999 0 -0.52 22 22
negative regulation of mast cell degranulation -0.035 0.14 -9999 0 -0.52 24 24
BTK -0.073 0.2 -9999 0 -0.75 30 30
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.19 -9999 0 -0.39 107 107
GAB2/PI3K/SHP2 -0.082 0.13 -9999 0 -0.46 23 23
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.056 0.16 -9999 0 -0.42 46 46
RAF1 0.029 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.18 0.22 -9999 0 -0.45 142 142
FCER1G -0.021 0.14 -9999 0 -0.57 30 30
FCER1A -0.15 0.25 -9999 0 -0.54 148 148
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.16 -9999 0 -0.37 92 92
MAPK3 0.039 0.022 -9999 0 -10000 0 0
MAPK1 0.039 0.022 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.003 0.11 -9999 0 -0.6 13 13
DUSP1 -0.02 0.13 -9999 0 -0.53 32 32
NF-kappa-B/RelA -0.033 0.049 -9999 0 -0.23 1 1
actin cytoskeleton reorganization -0.035 0.13 -9999 0 -0.53 20 20
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.069 0.16 -9999 0 -0.63 30 30
FER -0.051 0.15 -9999 0 -0.45 43 43
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.067 0.12 -9999 0 -0.3 79 79
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG1 -0.048 0.21 -9999 0 -0.68 35 35
cytokine secretion -0.024 0.036 -9999 0 -10000 0 0
SPHK1 -0.06 0.16 -9999 0 -0.48 41 41
PTK2 -0.037 0.14 -9999 0 -0.56 20 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.19 -9999 0 -0.66 35 35
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.052 0.19 -9999 0 -0.55 38 38
MAP2K2 0.035 0.022 -9999 0 -10000 0 0
MAP2K1 0.034 0.025 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.048 0.13 -9999 0 -0.48 23 23
MAP2K4 0.02 0.014 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.19 0.22 -9999 0 -0.46 161 161
mol:Choline -0.07 0.16 -9999 0 -0.35 73 73
SHC/Grb2/SOS1 -0.059 0.11 -9999 0 -0.51 21 21
FYN 0.014 0 -9999 0 -10000 0 0
DOK1 0.012 0.035 -9999 0 -0.54 2 2
PXN -0.027 0.13 -9999 0 -0.51 20 20
HCLS1 -0.055 0.17 -9999 0 -0.56 37 37
PRKCB -0.053 0.14 -9999 0 -0.38 50 50
FCGR2B -0.13 0.24 -9999 0 -0.53 138 138
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.036 0.14 -9999 0 -0.53 24 24
LCP2 -0.001 0.086 -9999 0 -0.5 15 15
PLA2G4A -0.055 0.16 -9999 0 -0.46 45 45
RASA1 0.014 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.07 0.16 -9999 0 -0.35 73 73
IKK complex -0.008 0.086 -9999 0 -0.22 21 21
WIPF1 0.014 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.029 0.14 -9999 0 -0.42 38 38
CRKL 0.013 0.022 -9999 0 -0.49 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.009 0.053 -9999 0 -0.59 4 4
ITGA4 -0.051 0.18 -9999 0 -0.53 61 61
alpha4/beta7 Integrin/MAdCAM1 -0.12 0.17 -9999 0 -0.4 97 97
EPO -0.007 0.098 -9999 0 -0.5 20 20
alpha4/beta7 Integrin -0.076 0.17 -9999 0 -0.43 92 92
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.046 0.13 -9999 0 -0.39 61 61
EPO/EPOR (dimer) -0.014 0.071 -9999 0 -0.36 20 20
lamellipodium assembly 0.009 0.022 -9999 0 -0.29 1 1
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
PI3K -0.001 0.019 -9999 0 -0.43 1 1
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 0 0.089 -9999 0 -0.27 32 32
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
MADCAM1 -0.11 0.23 -9999 0 -0.53 119 119
cell adhesion -0.12 0.17 -9999 0 -0.4 97 97
CRKL/CBL -0.001 0.015 -9999 0 -0.34 1 1
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
SRC -0.086 0.17 -9999 0 -0.35 122 122
ITGB7 -0.033 0.16 -9999 0 -0.54 44 44
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.12 0.18 -9999 0 -0.35 179 179
p130Cas/Crk/Dock1 -0.053 0.16 -9999 0 -0.5 17 17
VCAM1 -0.13 0.25 -9999 0 -0.56 132 132
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.034 0.093 -9999 0 -0.33 27 27
BCAR1 -0.072 0.17 -9999 0 -0.55 15 15
EPOR 0.013 0.022 -9999 0 -0.49 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP 0.009 0.022 -9999 0 -0.3 1 1
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.009 0.053 -10000 0 -0.59 4 4
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR -0.064 0.19 -10000 0 -0.53 73 73
Cbp/p300/PCAF -0.003 0.034 -10000 0 -0.36 4 4
EP300 0.009 0.053 -10000 0 -0.59 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.063 -10000 0 -0.4 5 5
KAT2B 0.013 0.022 -10000 0 -0.49 1 1
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.008 0.07 0.22 7 -0.34 3 10
RAR alpha/9cRA/Cyclin H -0.052 0.084 -10000 0 -0.9 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.058 -10000 0 -0.33 5 5
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.064 0.11 -10000 0 -0.52 13 13
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.055 0.14 -10000 0 -0.39 73 73
RXRs/RARs/NRIP1/9cRA -0.06 0.2 -10000 0 -0.46 76 76
NCOA2 -0.027 0.15 -10000 0 -0.59 35 35
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.064 0.19 -10000 0 -0.53 73 73
RARG 0.014 0.022 -10000 0 -0.49 1 1
RAR gamma1/9cRA -0.001 0.013 -10000 0 -0.29 1 1
MAPK3 0.015 0 -10000 0 -10000 0 0
MAPK1 0.014 0 -10000 0 -10000 0 0
MAPK8 0 0.095 -10000 0 -0.59 13 13
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.15 0.22 -10000 0 -0.55 94 94
RARA -0.052 0.12 -10000 0 -0.25 101 101
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.004 0.097 -10000 0 -0.37 18 18
PRKCA 0.016 0.027 -10000 0 -0.59 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.073 0.2 -10000 0 -0.46 89 89
RXRG -0.13 0.22 -10000 0 -0.44 123 123
RXRA -0.036 0.11 -10000 0 -0.83 1 1
RXRB -0.075 0.15 -10000 0 -0.34 89 89
VDR/Vit D3/DNA -0.055 0.14 -10000 0 -0.39 73 73
RBP1 -0.074 0.2 -10000 0 -0.5 88 88
CRBP1/9-cic-RA -0.062 0.14 -10000 0 -0.36 88 88
RARB 0.013 0.046 -10000 0 -0.59 3 3
PRKCG -0.19 0.27 -10000 0 -0.54 190 190
MNAT1 0.013 0.022 -10000 0 -0.49 1 1
RAR alpha/RXRs -0.063 0.21 -10000 0 -0.47 89 89
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.047 0.17 -10000 0 -0.39 76 76
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.095 -10000 0 -0.44 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.072 0.2 -10000 0 -0.46 89 89
positive regulation of DNA binding -0.05 0.079 -10000 0 -0.81 1 1
NRIP1 -0.064 0.18 -10000 0 -0.58 26 26
RXRs/RARs -0.08 0.2 -10000 0 -0.46 89 89
RXRs/RXRs/DNA/9cRA -0.12 0.2 -10000 0 -0.52 89 89
PRKACA 0.014 0 -10000 0 -10000 0 0
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH -0.001 0.012 -10000 0 -0.28 1 1
RAR alpha/9cRA -0.037 0.063 -10000 0 -0.79 1 1
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.012 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.018 0.006 -9999 0 -10000 0 0
RAS family/GTP -0.07 0.15 -9999 0 -0.51 25 25
NFATC4 -0.061 0.13 -9999 0 -0.37 35 35
ERBB2IP 0.015 0.027 -9999 0 -0.59 1 1
HSP90 (dimer) 0.014 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.089 0.15 -9999 0 -0.47 27 27
JUN -0.02 0.1 -9999 0 -0.35 21 21
HRAS 0.014 0.001 -9999 0 -10000 0 0
DOCK7 -0.082 0.15 -9999 0 -0.46 30 30
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.12 0.18 -9999 0 -0.37 141 141
AKT1 0.01 0.004 -9999 0 -10000 0 0
BAD 0.02 0.003 -9999 0 -10000 0 0
MAPK10 -0.043 0.078 -9999 0 -0.25 21 21
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.094 0.17 -9999 0 -0.51 27 27
RAF1 -0.063 0.15 -9999 0 -0.49 25 25
ErbB2/ErbB3/neuregulin 2 -0.044 0.12 -9999 0 -0.33 66 66
STAT3 0.004 0.005 -9999 0 -10000 0 0
cell migration -0.02 0.094 -9999 0 -0.24 23 23
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.15 0.27 -9999 0 -0.6 99 99
FOS -0.12 0.22 -9999 0 -0.42 144 144
NRAS 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.089 0.15 -9999 0 -0.47 27 27
MAPK3 -0.12 0.22 -9999 0 -0.51 86 86
MAPK1 -0.12 0.22 -9999 0 -0.51 86 86
JAK2 -0.079 0.15 -9999 0 -0.44 27 27
NF2 -0.003 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.09 0.18 -9999 0 -0.33 141 141
NRG1 -0.17 0.27 -9999 0 -0.56 163 163
GRB2/SOS1 0.008 0.019 -9999 0 -0.34 1 1
MAPK8 -0.075 0.15 -9999 0 -0.39 34 34
MAPK9 -0.041 0.076 -9999 0 -0.23 25 25
ERBB2 -0.006 0.047 -9999 0 -0.38 8 8
ERBB3 -0.058 0.19 -9999 0 -0.57 62 62
SHC1 0.009 0.05 -9999 0 -0.49 5 5
RAC1 0.014 0 -9999 0 -10000 0 0
apoptosis -0.001 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0.01 0.009 -9999 0 -10000 0 0
RNF41 0.023 0.009 -9999 0 -10000 0 0
FRAP1 0.009 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.071 0.097 -9999 0 -0.33 26 26
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.038 -9999 0 -0.31 8 8
CHRNA1 -0.14 0.26 -9999 0 -0.59 98 98
myelination -0.053 0.13 -9999 0 -0.36 35 35
PPP3CB -0.075 0.14 -9999 0 -0.4 29 29
KRAS 0.013 0.022 -9999 0 -0.49 1 1
RAC1-CDC42/GDP -0.063 0.16 -9999 0 -0.51 26 26
NRG2 0.012 0.038 -9999 0 -0.59 2 2
mol:GDP -0.09 0.17 -9999 0 -0.33 141 141
SOS1 0.014 0.001 -9999 0 -10000 0 0
MAP2K2 -0.06 0.15 -9999 0 -0.42 40 40
SRC 0.014 0 -9999 0 -10000 0 0
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.079 0.15 -9999 0 -0.44 27 27
MAP2K1 -0.13 0.22 -9999 0 -0.5 79 79
heart morphogenesis -0.089 0.15 -9999 0 -0.47 27 27
RAS family/GDP -0.067 0.15 -9999 0 -0.51 25 25
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PRKACA -0.007 0.009 -9999 0 -10000 0 0
CHRNE 0.002 0.044 -9999 0 -0.19 21 21
HSP90AA1 0.014 0 -9999 0 -10000 0 0
activation of caspase activity -0.01 0.004 -9999 0 -10000 0 0
nervous system development -0.089 0.15 -9999 0 -0.47 27 27
CDC42 0.014 0 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.004 -9999 0 -10000 0 0
SVIL -0.011 0.11 -9999 0 -0.5 24 24
ZNF318 0.019 0.018 -9999 0 -10000 0 0
JMJD2C -0.003 0.021 -9999 0 -0.076 35 35
T-DHT/AR/Ubc9 -0.069 0.16 -9999 0 -0.36 109 109
CARM1 0.014 0.001 -9999 0 -10000 0 0
PRDX1 -0.014 0.13 -9999 0 -0.59 24 24
PELP1 0.015 0.003 -9999 0 -10000 0 0
CTNNB1 0.013 0.004 -9999 0 -10000 0 0
AKT1 0.015 0.005 -9999 0 -10000 0 0
PTK2B -0.01 0.11 -9999 0 -0.49 24 24
MED1 0.015 0.005 -9999 0 -10000 0 0
MAK -0.033 0.16 -9999 0 -0.5 51 51
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 -0.002 0.096 -9999 0 -0.59 13 13
GSN 0 0.089 -9999 0 -0.58 12 12
NCOA2 -0.027 0.15 -9999 0 -0.59 35 35
NCOA6 0.013 0.004 -9999 0 -10000 0 0
DNA-PK 0.008 0.025 -9999 0 -10000 0 0
NCOA4 0.014 0.001 -9999 0 -10000 0 0
PIAS3 0.013 0.004 -9999 0 -10000 0 0
cell proliferation -0.041 0.11 -9999 0 -0.38 27 27
XRCC5 0.015 0.004 -9999 0 -10000 0 0
UBE3A 0.012 0.009 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.082 0.18 -9999 0 -0.38 122 122
FHL2 -0.047 0.21 -9999 0 -0.78 27 27
RANBP9 0.013 0.004 -9999 0 -10000 0 0
JMJD1A -0.009 0.053 -9999 0 -0.11 97 97
CDK6 -0.032 0.15 -9999 0 -0.54 43 43
TGFB1I1 0.003 0.076 -9999 0 -0.53 10 10
T-DHT/AR/CyclinD1 -0.088 0.18 -9999 0 -0.38 127 127
XRCC6 0.015 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.077 0.18 -9999 0 -0.37 118 118
CTDSP1 0.013 0.004 -9999 0 -10000 0 0
CTDSP2 0.013 0.046 -9999 0 -0.49 4 4
BRCA1 0.009 0.044 -9999 0 -0.49 4 4
TCF4 0.015 0.028 -9999 0 -0.59 1 1
CDKN2A -0.1 0.23 -9999 0 -0.56 104 104
SRF 0.017 0.027 -9999 0 -10000 0 0
NKX3-1 -0.06 0.18 -9999 0 -1 12 12
KLK3 -0.018 0.11 -9999 0 -0.4 8 8
TMF1 0.012 0.027 -9999 0 -0.59 1 1
HNRNPA1 0.016 0.006 -9999 0 -10000 0 0
AOF2 -0.002 0.008 -9999 0 -10000 0 0
APPL1 0.027 0.01 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.077 0.17 -9999 0 -0.36 121 121
AR -0.12 0.24 -9999 0 -0.57 109 109
UBA3 0.013 0.004 -9999 0 -10000 0 0
PATZ1 0.016 0.006 -9999 0 -10000 0 0
PAWR -0.034 0.16 -9999 0 -0.53 45 45
PRKDC 0.015 0.004 -9999 0 -10000 0 0
PA2G4 0.016 0.007 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.062 0.15 -9999 0 -0.33 110 110
RPS6KA3 0.012 0.027 -9999 0 -0.59 1 1
T-DHT/AR/ARA70 -0.07 0.16 -9999 0 -0.36 109 109
LATS2 -0.001 0.094 -9999 0 -0.52 16 16
T-DHT/AR/PRX1 -0.076 0.17 -9999 0 -0.36 121 121
Cyclin D3/CDK11 p58 0 0.016 -9999 0 -0.35 1 1
VAV3 -0.12 0.23 -9999 0 -0.52 126 126
KLK2 -0.066 0.12 -9999 0 -0.44 36 36
CASP8 -0.001 0.089 -9999 0 -0.5 16 16
T-DHT/AR/TIF2/CARM1 -0.077 0.18 -9999 0 -0.36 131 131
TMPRSS2 -0.14 0.31 -9999 0 -0.88 62 62
CCND1 -0.017 0.13 -9999 0 -0.53 29 29
PIAS1 0.007 0.054 -9999 0 -0.59 4 4
mol:T-DHT -0.011 0.031 -9999 0 -0.081 52 52
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.01 0.015 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.096 0.19 -9999 0 -0.38 139 139
CMTM2 -0.007 0.11 -9999 0 -0.56 19 19
SNURF -0.008 0.11 -9999 0 -0.58 19 19
ZMIZ1 0.006 0.027 -9999 0 -10000 0 0
CCND3 0.013 0.022 -9999 0 -0.49 1 1
TGIF1 -0.007 0.11 -9999 0 -0.53 21 21
FKBP4 0.013 0.004 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.037 0.1 -10000 0 -0.32 61 61
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.12 0.19 -10000 0 -0.39 173 173
GNB1/GNG2 -0.003 0.032 -10000 0 -0.36 4 4
GNB1 0.014 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.039 0.11 -10000 0 -0.34 59 59
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.01 0.028 0.087 59 -10000 0 59
GNAL -0.055 0.19 -10000 0 -0.59 59 59
GNG2 0.009 0.053 -10000 0 -0.59 4 4
CRH -0.17 0.26 -10000 0 -0.54 173 173
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.059 -10000 0 -0.36 13 13
MAPK11 0.003 0.049 -10000 0 -0.36 9 9
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0.022 -10000 0 -0.49 1 1
RAS family/GTP/Tiam1 0.029 0.038 -10000 0 -0.51 1 1
NT3 (dimer)/TRKC -0.015 0.078 -10000 0 -0.39 20 20
NT3 (dimer)/TRKB -0.073 0.15 -10000 0 -0.36 103 103
SHC/Grb2/SOS1/GAB1/PI3K 0.037 0.03 -10000 0 -0.45 1 1
RAPGEF1 0.014 0 -10000 0 -10000 0 0
BDNF -0.079 0.2 -10000 0 -0.51 92 92
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
DYNLT1 0.012 0.038 -10000 0 -0.59 2 2
NTRK1 -0.01 0.11 -10000 0 -0.52 23 23
NTRK2 -0.018 0.14 -10000 0 -0.59 27 27
NTRK3 0.009 0.053 -10000 0 -0.59 4 4
NT-4/5 (dimer)/TRKB -0.072 0.16 -10000 0 -0.37 101 101
neuron apoptosis 0.13 0.16 0.41 97 -10000 0 97
SHC 2-3/Grb2 -0.12 0.2 -10000 0 -0.44 97 97
SHC1 0.009 0.05 -10000 0 -0.49 5 5
SHC2 -0.07 0.11 -10000 0 -0.4 28 28
SHC3 -0.16 0.23 -10000 0 -0.54 113 113
STAT3 (dimer) 0.007 0.069 -10000 0 -0.34 12 12
NT3 (dimer)/TRKA -0.068 0.14 -10000 0 -0.34 102 102
RIN/GDP -0.038 0.11 -10000 0 -0.26 20 20
GIPC1 0.013 0.022 -10000 0 -0.49 1 1
KRAS 0.013 0.022 -10000 0 -0.49 1 1
DNAJA3 -0.069 0.12 -10000 0 -0.38 45 45
RIN/GTP -0.16 0.2 -10000 0 -0.4 204 204
CCND1 -0.001 0.15 -10000 0 -0.58 29 29
MAGED1 0.014 0 -10000 0 -10000 0 0
PTPN11 0.014 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.01 0.088 -10000 0 -0.5 16 16
SHC/GRB2/SOS1 -0.003 0.03 -10000 0 -0.28 6 6
GRB2 0.013 0.022 -10000 0 -0.49 1 1
NGF (dimer)/TRKA/MATK -0.12 0.2 -10000 0 -0.38 168 168
TRKA/NEDD4-2 -0.026 0.097 -10000 0 -0.38 35 35
ELMO1 0.001 0.088 -10000 0 -0.59 11 11
RhoG/GTP/ELMO1/DOCK1 -0.011 0.062 -10000 0 -0.36 15 15
NGF -0.074 0.21 -10000 0 -0.55 79 79
HRAS 0.014 0 -10000 0 -10000 0 0
DOCK1 0.009 0.053 -10000 0 -0.59 4 4
GAB2 0.013 0.027 -10000 0 -0.59 1 1
RIT2 -0.21 0.28 -10000 0 -0.55 204 204
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.012 0.035 -10000 0 -0.54 2 2
DNM1 -0.1 0.22 -10000 0 -0.52 109 109
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.073 0.13 -10000 0 -0.37 56 56
mol:GDP 0.045 0.066 -10000 0 -0.46 2 2
NGF (dimer) -0.074 0.21 -10000 0 -0.55 79 79
RhoG/GDP -0.009 0.063 -10000 0 -0.44 11 11
RIT1/GDP 0.04 0.048 -10000 0 -0.29 2 2
TIAM1 0.013 0.027 -10000 0 -0.59 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.075 0.14 -10000 0 -0.32 120 120
KIDINS220/CRKL/C3G -0.001 0.015 -10000 0 -0.34 1 1
SHC/RasGAP -0.003 0.034 -10000 0 -0.34 5 5
FRS2 family/SHP2 -0.001 0.02 -10000 0 -0.32 2 2
SHC/GRB2/SOS1/GAB1 -0.004 0.036 -10000 0 -0.57 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.008 0.092 -10000 0 -0.49 18 18
RAP1/GDP -0.005 0.023 -10000 0 -0.24 2 2
KIDINS220/CRKL 0.013 0.022 -10000 0 -0.49 1 1
BDNF (dimer) -0.079 0.2 -10000 0 -0.51 92 92
ubiquitin-dependent protein catabolic process -0.071 0.15 -10000 0 -0.35 106 106
Schwann cell development -0.02 0.027 -10000 0 -10000 0 0
EHD4 0.007 0.059 -10000 0 -0.49 7 7
FRS2 family/GRB2/SOS1 -0.002 0.021 -10000 0 -0.32 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.043 0.018 -10000 0 -10000 0 0
RAP1B 0.013 0.022 -10000 0 -0.49 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.061 0.12 -10000 0 -0.48 18 18
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
Rap1/GTP -0.022 0.044 -10000 0 -10000 0 0
STAT3 0.007 0.068 -10000 0 -0.34 12 12
axon guidance -0.059 0.11 -10000 0 -0.46 18 18
MAPK3 -0.087 0.19 -10000 0 -0.39 109 109
MAPK1 -0.087 0.19 -10000 0 -0.39 109 109
CDC42/GDP 0.04 0.048 -10000 0 -0.29 2 2
NTF3 -0.008 0.092 -10000 0 -0.49 18 18
NTF4 -0.01 0.088 -10000 0 -0.5 16 16
NGF (dimer)/TRKA/FAIM -0.067 0.14 -10000 0 -0.34 101 101
PI3K -0.001 0.019 -10000 0 -0.43 1 1
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.009 0.053 -10000 0 -0.59 4 4
GAB1 0.012 0.035 -10000 0 -0.54 2 2
RASGRF1 -0.12 0.17 -10000 0 -0.39 107 107
SOS1 0.014 0 -10000 0 -10000 0 0
MCF2L 0.013 0.072 -10000 0 -0.32 21 21
RGS19 0.014 0 -10000 0 -10000 0 0
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.074 -10000 0 -10000 0 0
Rac1/GDP 0.04 0.048 -10000 0 -0.29 2 2
NGF (dimer)/TRKA/GRIT -0.066 0.14 -10000 0 -0.34 98 98
neuron projection morphogenesis -0.037 0.13 -10000 0 -0.48 14 14
NGF (dimer)/TRKA/NEDD4-2 -0.072 0.15 -10000 0 -0.35 106 106
MAP2K1 0.038 0.04 -10000 0 -0.53 1 1
NGFR -0.063 0.19 -10000 0 -0.54 72 72
NGF (dimer)/TRKA/GIPC/GAIP -0.05 0.14 -10000 0 -0.3 90 90
RAS family/GTP/PI3K 0.033 0.015 -10000 0 -0.26 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.019 -10000 0 -0.29 1 1
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
PRKCI 0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.015 0.12 -10000 0 -0.55 26 26
MAPKKK cascade -0.086 0.2 -10000 0 -0.61 61 61
RASA1 0.014 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.016 0.077 -10000 0 -0.37 23 23
SQSTM1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.064 0.12 -10000 0 -0.35 43 43
NGF (dimer)/TRKA/p62/Atypical PKCs -0.066 0.13 -10000 0 -0.33 71 71
MATK -0.093 0.22 -10000 0 -0.55 97 97
NEDD4L 0 0.086 -10000 0 -0.53 13 13
RAS family/GDP -0.004 0.021 -10000 0 -0.26 1 1
NGF (dimer)/TRKA -0.075 0.13 -10000 0 -0.33 91 91
Rac1/GTP -0.065 0.096 -10000 0 -0.31 40 40
FRS2 family/SHP2/CRK family -0.001 0.019 -10000 0 -0.29 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.062 0.15 0.4 79 -10000 0 79
KIRREL -0.036 0.16 -10000 0 -0.59 40 40
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.062 0.15 -10000 0 -0.4 79 79
PLCG1 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
WASL 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.045 0.11 -10000 0 -0.34 41 41
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.004 0.095 -10000 0 -0.42 6 6
FYN -0.023 0.11 -10000 0 -0.32 41 41
mol:Ca2+ -0.044 0.11 -10000 0 -0.33 41 41
mol:DAG -0.045 0.11 -10000 0 -0.34 41 41
NPHS2 -0.006 0.039 -10000 0 -0.54 2 2
mol:IP3 -0.045 0.11 -10000 0 -0.34 41 41
regulation of endocytosis -0.014 0.1 -10000 0 -0.3 37 37
Nephrin/NEPH1/podocin/Cholesterol -0.046 0.11 -10000 0 -0.3 75 75
establishment of cell polarity -0.062 0.15 -10000 0 -0.4 79 79
Nephrin/NEPH1/podocin/NCK1-2 -0.04 0.098 -10000 0 -0.53 5 5
Nephrin/NEPH1/beta Arrestin2 -0.013 0.1 -10000 0 -0.3 37 37
NPHS1 -0.034 0.14 -10000 0 -0.5 43 43
Nephrin/NEPH1/podocin -0.026 0.11 -10000 0 -0.32 41 41
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.013 0.027 -10000 0 -0.59 1 1
NCK2 0.014 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.045 0.11 -10000 0 -0.34 41 41
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.045 0.11 -10000 0 -0.34 41 41
GRB2 0.013 0.022 -10000 0 -0.49 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.042 0.13 -10000 0 -0.34 54 54
cytoskeleton organization -0.003 0.11 -10000 0 -0.46 7 7
Nephrin/NEPH1 -0.044 0.11 -10000 0 -0.28 79 79
Nephrin/NEPH1/ZO-1 -0.048 0.12 -10000 0 -0.36 40 40
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0 0.093 -9999 0 -0.32 40 40
EPHB2 0 0.087 -9999 0 -0.52 14 14
Syndecan-2/TACI -0.011 0.086 -9999 0 -0.33 33 33
LAMA1 -0.065 0.2 -9999 0 -0.57 70 70
Syndecan-2/alpha2 ITGB1 -0.028 0.15 -9999 0 -0.38 55 55
HRAS 0.014 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.015 0.071 -9999 0 -0.34 23 23
ITGA5 -0.01 0.11 -9999 0 -0.5 24 24
BAX 0.02 0.085 -9999 0 -10000 0 0
EPB41 0.011 0.044 -9999 0 -0.56 3 3
positive regulation of cell-cell adhesion -0.013 0.062 -9999 0 -0.3 23 23
LAMA3 -0.041 0.17 -9999 0 -0.54 51 51
EZR 0.004 0.08 -9999 0 -0.59 9 9
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.016 0.12 -9999 0 -0.5 30 30
Syndecan-2/MMP2 -0.006 0.1 -9999 0 -0.33 47 47
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.034 0.11 -9999 0 -0.38 46 46
dendrite morphogenesis 0.002 0.096 -9999 0 -0.35 34 34
Syndecan-2/GM-CSF -0.014 0.071 -9999 0 -0.34 23 23
determination of left/right symmetry 0.003 0.088 -9999 0 -0.4 23 23
Syndecan-2/PKC delta -0.009 0.12 -9999 0 -0.4 43 43
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.012 0.068 -9999 0 -0.32 16 16
MAPK1 0.012 0.068 -9999 0 -0.32 16 16
Syndecan-2/RACK1 -0.012 0.058 -9999 0 -0.3 16 16
NF1 0.012 0.038 -9999 0 -0.59 2 2
FGFR/FGF/Syndecan-2 0.003 0.088 -9999 0 -0.4 23 23
ITGA2 -0.033 0.16 -9999 0 -0.54 44 44
MAPK8 0.011 0.095 -9999 0 -0.35 29 29
Syndecan-2/alpha2/beta1 Integrin -0.041 0.17 -9999 0 -0.38 79 79
Syndecan-2/Kininogen -0.021 0.093 -9999 0 -0.31 47 47
ITGB1 0.012 0.031 -9999 0 -0.49 2 2
SRC 0.027 0.061 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 -0.015 0.072 -9999 0 -0.33 24 24
extracellular matrix organization 0.004 0.093 -9999 0 -0.36 30 30
actin cytoskeleton reorganization 0 0.093 -9999 0 -0.32 40 40
Syndecan-2/Caveolin-2/Ras 0.003 0.096 -9999 0 -0.33 20 20
Syndecan-2/Laminin alpha3 -0.023 0.13 -9999 0 -0.35 69 69
Syndecan-2/RasGAP -0.011 0.053 -9999 0 -0.28 16 16
alpha5/beta1 Integrin -0.018 0.079 -9999 0 -0.36 25 25
PRKCD -0.018 0.14 -9999 0 -0.59 27 27
Syndecan-2 dimer 0.002 0.096 -9999 0 -0.35 34 34
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.034 0.06 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.005 0.072 -9999 0 -0.49 11 11
RASA1 0.014 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.034 0.11 -9999 0 -0.38 46 46
Syndecan-2/Synbindin 0.011 0.075 -9999 0 -0.33 23 23
TGFB1 0.004 0.08 -9999 0 -0.59 9 9
CASP3 0.002 0.12 -9999 0 -0.38 36 36
FN1 -0.004 0.093 -9999 0 -0.49 18 18
Syndecan-2/IL8 -0.096 0.18 -9999 0 -0.33 176 176
SDC2 0.003 0.088 -9999 0 -0.4 23 23
KNG1 -0.019 0.1 -9999 0 -0.49 24 24
Syndecan-2/Neurofibromin 0.009 0.08 -9999 0 -0.35 24 24
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 0.001 0.003 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.004 0.094 -9999 0 -0.36 30 30
Syndecan-2/Syntenin/PI-4-5-P2 -0.013 0.063 -9999 0 -0.3 23 23
Syndecan-2/Ezrin 0.014 0.093 -9999 0 -0.36 27 27
PRKACA 0.019 0.073 -9999 0 -0.33 18 18
angiogenesis -0.096 0.18 -9999 0 -0.33 176 176
MMP2 -0.013 0.12 -9999 0 -0.54 25 25
IL8 -0.16 0.26 -9999 0 -0.53 162 162
calcineurin-NFAT signaling pathway -0.011 0.085 -9999 0 -0.33 33 33
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.002 0.17 -9999 0 -1.3 9 9
VDR -0.064 0.19 -9999 0 -0.53 73 73
FAM120B 0.014 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.048 0.16 -9999 0 -0.45 31 31
RXRs/LXRs/DNA/Oxysterols -0.075 0.22 -9999 0 -0.45 96 96
MED1 0.014 0 -9999 0 -10000 0 0
mol:9cRA -0.009 0.024 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.027 0.056 -9999 0 -10000 0 0
RXRs/NUR77 -0.035 0.14 -9999 0 -0.42 30 30
RXRs/PPAR -0.017 0.12 -9999 0 -0.39 24 24
NCOR2 0.014 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.055 0.14 -9999 0 -0.39 73 73
RARs/VDR/DNA/Vit D3 -0.039 0.097 -9999 0 -0.31 34 34
RARA 0.014 0 -9999 0 -10000 0 0
NCOA1 0.014 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.064 0.19 -9999 0 -0.53 73 73
RARs/RARs/DNA/9cRA 0.017 0.032 -9999 0 -0.3 4 4
RARG 0.013 0.022 -9999 0 -0.49 1 1
RPS6KB1 0.02 0.067 -9999 0 -0.4 9 9
RARs/THRs/DNA/SMRT 0.027 0.056 -9999 0 -10000 0 0
THRA 0.011 0.046 -9999 0 -0.59 3 3
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.055 0.14 -9999 0 -0.39 73 73
RXRs/PPAR/9cRA/PGJ2/DNA -0.037 0.13 -9999 0 -0.35 60 60
NR1H4 -0.12 0.24 -9999 0 -0.53 131 131
RXRs/LXRs/DNA -0.024 0.14 -9999 0 -0.43 23 23
NR1H2 0.011 0.017 -9999 0 -10000 0 0
NR1H3 0.009 0.02 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.058 0.16 -9999 0 -0.39 65 65
NR4A1 -0.019 0.13 -9999 0 -0.51 32 32
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.067 0.14 -9999 0 -0.32 85 85
RXRG -0.066 0.2 -9999 0 -0.59 65 65
RXR alpha/CCPG 0.017 0.013 -9999 0 -10000 0 0
RXRA 0.011 0.017 -9999 0 -10000 0 0
RXRB 0.009 0.02 -9999 0 -10000 0 0
THRB -0.012 0.12 -9999 0 -0.53 25 25
PPARG -0.014 0.12 -9999 0 -0.56 25 25
PPARD 0.014 0 -9999 0 -10000 0 0
TNF -0.19 0.41 -9999 0 -1 88 88
mol:Oxysterols -0.007 0.022 -9999 0 -10000 0 0
cholesterol transport -0.074 0.21 -9999 0 -0.44 96 96
PPARA 0.014 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.011 0.046 -9999 0 -0.59 3 3
RXRs/NUR77/BCL2 -0.024 0.12 -9999 0 -0.37 33 33
SREBF1 -0.079 0.26 -9999 0 -0.88 31 31
RXRs/RXRs/DNA/9cRA -0.036 0.13 -9999 0 -0.35 60 60
ABCA1 -0.079 0.26 -9999 0 -0.87 32 32
RARs/THRs -0.016 0.062 -9999 0 -10000 0 0
RXRs/FXR -0.095 0.19 -9999 0 -0.39 113 113
BCL2 0.005 0.075 -9999 0 -0.59 8 8
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.071 0.14 -9999 0 -0.37 79 79
MAP4K1 -0.018 0.14 -9999 0 -0.58 28 28
MAP3K8 -0.006 0.1 -9999 0 -0.51 20 20
PRKCB -0.061 0.19 -9999 0 -0.52 72 72
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.013 0.022 -9999 0 -0.49 1 1
MAP3K1 -0.004 0.11 -9999 0 -0.43 8 8
JUN -0.028 0.16 -9999 0 -0.56 36 36
MAP3K7 0 0.1 -9999 0 -0.44 7 7
GRAP2 -0.047 0.17 -9999 0 -0.53 57 57
CRK 0.014 0 -9999 0 -10000 0 0
MAP2K4 0.003 0.11 -9999 0 -0.41 11 11
LAT -0.017 0.13 -9999 0 -0.59 27 27
LCP2 -0.001 0.086 -9999 0 -0.5 15 15
MAPK8 -0.033 0.16 -9999 0 -0.59 35 35
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.01 0.11 -9999 0 -0.47 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.066 0.13 -9999 0 -0.34 79 79
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.031 0.13 -9999 0 -0.44 20 20
FZD6 -0.016 0.12 -9999 0 -0.49 31 31
WNT6 -0.034 0.16 -9999 0 -0.53 45 45
WNT4 -0.032 0.15 -9999 0 -0.52 45 45
FZD3 0.011 0.046 -9999 0 -0.59 3 3
WNT5A -0.013 0.12 -9999 0 -0.56 24 24
WNT11 -0.017 0.13 -9999 0 -0.54 29 29
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0.027 -9999 0 -0.59 1 1
ELF1 -0.015 0.089 -9999 0 -0.37 8 8
CCNA2 -0.055 0.18 -9999 0 -0.52 66 66
PIK3CA 0.014 0.027 -9999 0 -0.59 1 1
JAK3 -0.056 0.18 -9999 0 -0.53 67 67
PIK3R1 0.015 0.001 -9999 0 -10000 0 0
JAK1 0.015 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.025 0.16 -9999 0 -0.39 50 50
SHC1 0.01 0.05 -9999 0 -0.49 5 5
SP1 0.016 0.044 -9999 0 -0.34 4 4
IL2RA -0.041 0.17 -9999 0 -0.45 72 72
IL2RB -0.093 0.22 -9999 0 -0.53 102 102
SOS1 0.015 0.001 -9999 0 -10000 0 0
IL2RG -0.041 0.16 -9999 0 -0.52 54 54
G1/S transition of mitotic cell cycle -0.034 0.18 -9999 0 -0.49 50 50
PTPN11 0.015 0.001 -9999 0 -10000 0 0
CCND2 0.019 0.095 -9999 0 -0.54 13 13
LCK -0.08 0.21 -9999 0 -0.53 89 89
GRB2 0.014 0.022 -9999 0 -0.49 1 1
IL2 0.001 0.003 -9999 0 -10000 0 0
CDK6 -0.032 0.15 -9999 0 -0.54 43 43
CCND3 -0.011 0.14 -9999 0 -0.5 5 5
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.008 0.066 -9999 0 -0.31 21 21
ADCY5 0 0.091 -9999 0 -0.37 28 28
ADCY6 0.014 0.048 -9999 0 -0.31 11 11
ADCY7 0.014 0.048 -9999 0 -0.31 11 11
ADCY1 -0.052 0.15 -9999 0 -0.35 101 101
ADCY2 0.004 0.081 -9999 0 -0.35 24 24
ADCY3 0.014 0.048 -9999 0 -0.31 11 11
ADCY8 -0.03 0.13 -9999 0 -0.35 70 70
PRKCE 0.004 0.057 -9999 0 -0.38 11 11
ADCY9 0.012 0.06 -9999 0 -0.34 14 14
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.008 0.098 -9999 0 -0.35 22 22
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.009 0.056 -10000 0 -0.59 4 4
HSPA8 0.013 0.027 -10000 0 -0.59 1 1
SMAD3/SMAD4/ER alpha -0.025 0.11 0.22 3 -0.39 25 28
AKT1 0.008 0.023 -10000 0 -10000 0 0
GSC -0.16 0.48 -10000 0 -1.4 66 66
NKX2-5 -0.093 0.2 -10000 0 -0.5 102 102
muscle cell differentiation 0.15 0.19 0.49 89 -10000 0 89
SMAD2-3/SMAD4/SP1 -0.007 0.11 -10000 0 -0.4 10 10
SMAD4 -0.016 0.065 -10000 0 -0.34 2 2
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.014 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.022 0.11 -10000 0 -0.33 47 47
SMAD3/SMAD4/VDR -0.034 0.12 -10000 0 -0.38 18 18
MYC -0.008 0.12 -10000 0 -0.55 25 25
CDKN2B -0.12 0.45 -10000 0 -1.4 55 55
AP1 -0.029 0.16 -10000 0 -0.52 25 25
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.043 0.063 -10000 0 -0.54 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.011 0.13 -10000 0 -0.34 54 54
SP3 0.016 0.008 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 -0.016 0.1 -10000 0 -0.56 16 16
SMAD3/SMAD4/GR -0.01 0.062 -10000 0 -0.36 2 2
GATA3 -0.13 0.24 -10000 0 -0.56 115 115
SKI/SIN3/HDAC complex/NCoR1 0.045 0.036 -10000 0 -0.36 1 1
MEF2C/TIF2 -0.077 0.18 -10000 0 -0.51 44 44
endothelial cell migration 0.22 0.48 1.4 71 -10000 0 71
MAX 0.023 0.019 -10000 0 -10000 0 0
RBBP7 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.013 0.027 -10000 0 -0.59 1 1
RUNX2 -0.006 0.1 -10000 0 -0.53 19 19
RUNX3 -0.03 0.15 -10000 0 -0.55 40 40
RUNX1 -0.053 0.18 -10000 0 -0.53 64 64
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.023 0.019 -10000 0 -10000 0 0
VDR -0.064 0.19 -10000 0 -0.53 73 73
CDKN1A -0.048 0.29 -10000 0 -1.2 23 23
KAT2B 0.013 0.023 -10000 0 -0.49 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.027 0.12 -10000 0 -0.36 27 27
DCP1A 0.014 0 -10000 0 -10000 0 0
SKI 0.014 0.002 -10000 0 -10000 0 0
SERPINE1 -0.22 0.49 -10000 0 -1.4 71 71
SMAD3/SMAD4/ATF2 -0.027 0.08 -10000 0 -0.38 15 15
SMAD3/SMAD4/ATF3 -0.05 0.12 -10000 0 -0.39 45 45
SAP30 0.013 0.027 -10000 0 -0.59 1 1
Cbp/p300/PIAS3 0.014 0.056 -10000 0 -0.35 4 4
JUN -0.023 0.16 -10000 0 -0.53 24 24
SMAD3/SMAD4/IRF7 -0.033 0.097 -10000 0 -0.41 20 20
TFE3 0.008 0.029 -10000 0 -10000 0 0
COL1A2 -0.046 0.16 -10000 0 -0.46 58 58
mesenchymal cell differentiation 0.03 0.091 0.4 19 -10000 0 19
DLX1 -0.16 0.26 -10000 0 -0.54 160 160
TCF3 0.012 0.038 -10000 0 -0.59 2 2
FOS -0.091 0.22 -10000 0 -0.55 99 99
SMAD3/SMAD4/Max -0.01 0.062 -10000 0 -0.36 2 2
Cbp/p300/SNIP1 0.007 0.039 -10000 0 -0.35 4 4
ZBTB17 0.019 0.018 -10000 0 -10000 0 0
LAMC1 0.001 0.11 -10000 0 -0.5 17 17
TGIF2/HDAC complex/SMAD3/SMAD4 -0.022 0.073 -10000 0 -0.43 8 8
IRF7 -0.01 0.11 -10000 0 -0.52 23 23
ESR1 -0.013 0.12 -10000 0 -0.54 26 26
HNF4A -0.033 0.14 -10000 0 -0.49 41 41
MEF2C -0.064 0.18 -10000 0 -0.52 33 33
SMAD2-3/SMAD4 -0.035 0.073 -10000 0 -0.35 8 8
Cbp/p300/Src-1 0.01 0.045 -10000 0 -0.35 4 4
IGHV3OR16-13 -0.015 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.007 0.063 -10000 0 -0.57 6 6
CREBBP 0.014 0.012 -10000 0 -10000 0 0
SKIL 0.006 0.07 -10000 0 -0.59 7 7
HDAC1 0.009 0.053 -10000 0 -0.59 4 4
HDAC2 0.014 0.002 -10000 0 -10000 0 0
SNIP1 0.014 0.005 -10000 0 -10000 0 0
GCN5L2 -0.001 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.008 0.083 -10000 0 -0.4 5 5
MSG1/HSC70 -0.021 0.12 -10000 0 -0.37 53 53
SMAD2 -0.004 0.047 -10000 0 -10000 0 0
SMAD3 -0.005 0.056 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.009 0.074 -10000 0 -0.4 3 3
SMAD2/SMAD2/SMAD4 -0.003 0.032 -10000 0 -10000 0 0
NCOR1 0.012 0.038 -10000 0 -0.59 2 2
NCOA2 -0.027 0.15 -10000 0 -0.59 35 35
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A -0.14 0.19 -10000 0 -0.39 179 179
SMAD2-3/SMAD4/SP1/MIZ-1 0.004 0.11 -10000 0 -0.44 7 7
IFNB1 -0.007 0.1 -10000 0 -0.48 10 10
SMAD3/SMAD4/MEF2C -0.068 0.18 -10000 0 -0.53 31 31
CITED1 -0.041 0.16 -10000 0 -0.53 52 52
SMAD2-3/SMAD4/ARC105 -0.011 0.073 -10000 0 -0.35 4 4
RBL1 -0.009 0.11 -10000 0 -0.57 20 20
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.027 0.19 -10000 0 -0.52 58 58
RUNX1-3/PEBPB2 -0.064 0.14 -10000 0 -0.35 94 94
SMAD7 -0.011 0.14 -10000 0 -0.56 8 8
MYC/MIZ-1 -0.001 0.099 -10000 0 -0.38 24 24
SMAD3/SMAD4 -0.042 0.19 0.29 45 -0.42 62 107
IL10 -0.14 0.28 -10000 0 -0.61 112 112
PIASy/HDAC complex 0.016 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.007 -10000 0 -10000 0 0
CDK2 0 0.086 -10000 0 -0.53 13 13
IL5 -0.085 0.19 -10000 0 -0.52 40 40
CDK4 -0.001 0.089 -10000 0 -0.49 16 16
PIAS4 0.016 0.013 -10000 0 -10000 0 0
ATF3 -0.037 0.16 -10000 0 -0.51 50 50
SMAD3/SMAD4/SP1 -0.009 0.1 -10000 0 -0.42 7 7
FOXG1 -0.024 0.15 -10000 0 -0.58 33 33
FOXO3 0.017 0.032 -10000 0 -10000 0 0
FOXO1 0.014 0.045 -10000 0 -0.42 3 3
FOXO4 0.016 0.039 -10000 0 -0.51 1 1
heart looping -0.063 0.18 -10000 0 -0.52 33 33
CEBPB -0.008 0.11 -10000 0 -0.57 17 17
SMAD3/SMAD4/DLX1 -0.12 0.17 -10000 0 -0.38 135 135
MYOD1 -0.18 0.27 -10000 0 -0.55 177 177
SMAD3/SMAD4/HNF4 -0.045 0.1 -10000 0 -0.38 21 21
SMAD3/SMAD4/GATA3 -0.13 0.19 -10000 0 -0.47 78 78
SnoN/SIN3/HDAC complex/NCoR1 0.006 0.07 -10000 0 -0.59 7 7
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.061 0.14 -10000 0 -0.41 46 46
SMAD3/SMAD4/SP1-3 0.008 0.098 -10000 0 -0.44 5 5
MED15 0.014 0 -10000 0 -10000 0 0
SP1 0.004 0.041 -10000 0 -10000 0 0
SIN3B 0.014 0.002 -10000 0 -10000 0 0
SIN3A 0.014 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.073 0.16 -10000 0 -0.42 42 42
ITGB5 0.019 0.11 -10000 0 -0.66 6 6
TGIF/SIN3/HDAC complex/CtBP 0.043 0.044 -10000 0 -0.44 1 1
SMAD3/SMAD4/AR -0.093 0.16 -10000 0 -0.38 98 98
AR -0.11 0.23 -10000 0 -0.56 109 109
negative regulation of cell growth -0.007 0.12 -10000 0 -0.43 20 20
SMAD3/SMAD4/MYOD -0.14 0.18 -10000 0 -0.4 131 131
E2F5 0.011 0.046 -10000 0 -0.59 3 3
E2F4 0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.007 0.097 -10000 0 -0.34 13 13
SMAD2-3/SMAD4/FOXO1-3a-4 -0.01 0.13 -10000 0 -0.35 52 52
TFDP1 0.013 0.027 -10000 0 -0.59 1 1
SMAD3/SMAD4/AP1 -0.029 0.16 -10000 0 -0.54 24 24
SMAD3/SMAD4/RUNX2 -0.03 0.092 -10000 0 -0.41 19 19
TGIF2 0.007 0.063 -10000 0 -0.57 6 6
TGIF1 -0.008 0.11 -10000 0 -0.53 21 21
ATF2 -0.001 0.095 -10000 0 -0.59 13 13
Presenilin action in Notch and Wnt signaling

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.044 0.15 -10000 0 -0.72 19 19
HDAC1 0.008 0.054 -10000 0 -0.59 4 4
AES 0.014 0.004 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 0.004 0.078 -10000 0 -0.58 9 9
LRP6/FZD1 -0.005 0.04 -10000 0 -0.34 7 7
TLE1 0.012 0.038 -10000 0 -0.59 2 2
AP1 -0.028 0.12 -10000 0 -0.3 69 69
NCSTN 0.014 0 -10000 0 -10000 0 0
ADAM10 0 0.092 -10000 0 -0.59 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.072 -10000 0 -10000 0 0
NICD/RBPSUH -0.02 0.11 -10000 0 -0.59 19 19
WIF1 -0.28 0.28 -10000 0 -0.54 269 269
NOTCH1 -0.023 0.12 -10000 0 -0.63 19 19
PSENEN 0.014 0 -10000 0 -10000 0 0
KREMEN2 -0.052 0.18 -10000 0 -0.53 63 63
DKK1 -0.12 0.24 -10000 0 -0.53 124 124
beta catenin/beta TrCP1 0.017 0.046 0.33 3 -10000 0 3
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 -0.001 0.045 0.24 3 -0.26 2 5
CtBP/CBP/TCF1/TLE1/AES 0.03 0.051 0.28 4 -0.26 6 10
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.094 0.22 -10000 0 -0.55 99 99
JUN 0.003 0.075 -10000 0 -0.5 11 11
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
CTNNB1 0.009 0.049 0.32 4 -10000 0 4
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 163 163
HNF1A 0.013 0.027 -10000 0 -0.59 1 1
CTBP1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.038 0.29 -10000 0 -1.4 21 21
NKD1 -0.004 0.099 -10000 0 -0.54 17 17
FZD1 0.008 0.054 -10000 0 -0.49 6 6
NOTCH1 precursor/Deltex homolog 1 -0.025 0.12 -10000 0 -0.6 19 19
apoptosis -0.028 0.12 -10000 0 -0.29 69 69
Delta 1/NOTCHprecursor -0.043 0.15 -10000 0 -0.71 19 19
DLL1 -0.033 0.16 -10000 0 -0.59 40 40
PPARD 0.02 0.027 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.002 0.061 0.23 4 -0.49 3 7
DVL1 -0.021 0.025 -10000 0 -10000 0 0
CSNK2A1 0.014 0.003 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.35 168 168
LRP6 0.013 0.022 -10000 0 -0.49 1 1
CSNK1A1 0.014 0.003 -10000 0 -10000 0 0
NLK 0.016 0.015 -10000 0 -10000 0 0
CCND1 -0.023 0.23 -10000 0 -1.4 12 12
WNT1 -0.028 0.13 -10000 0 -0.49 40 40
Axin1/APC/beta catenin 0.017 0.062 0.31 4 -0.52 1 5
DKK2 -0.11 0.23 -10000 0 -0.54 117 117
NOTCH1 precursor/DVL1 -0.022 0.11 -10000 0 -0.56 19 19
GSK3B 0.013 0.027 -10000 0 -0.59 1 1
FRAT1 0.01 0.049 -10000 0 -0.54 4 4
NOTCH/Deltex homolog 1 -0.027 0.12 -10000 0 -0.61 19 19
PPP2R5D -0.003 0.05 0.25 17 -10000 0 17
MAPK1 0.014 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.16 0.18 -10000 0 -0.37 144 144
RBPJ 0.013 0.022 -10000 0 -0.49 1 1
CREBBP 0.017 0.005 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.052 0.099 0.51 8 -10000 0 8
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.086 0.15 -10000 0 -0.34 132 132
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.008 0.06 -10000 0 -0.59 5 5
RhoA/GTP -0.053 0.1 -10000 0 -0.53 8 8
negative regulation of cAMP metabolic process -0.033 0.13 -10000 0 -0.28 79 79
GNAZ 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.013 0.027 -10000 0 -0.59 1 1
S1PR5 -0.13 0.25 -10000 0 -0.55 132 132
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.033 0.13 -10000 0 -0.28 79 79
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.026 0.11 -10000 0 -0.26 68 68
epithelial cell differentiation -0.064 0.11 -10000 0 -0.3 60 60
CYFIP2 0.008 0.06 -10000 0 -0.54 6 6
ENAH 0.008 0.1 -10000 0 -0.32 7 7
EGFR -0.083 0.21 -10000 0 -0.55 89 89
EPHA2 -0.016 0.12 -10000 0 -0.5 30 30
MYO6 -0.029 0.12 -10000 0 -0.28 60 60
CTNNB1 0.014 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.004 0.034 -10000 0 -0.32 6 6
AQP5 -0.14 0.18 -10000 0 -0.48 88 88
CTNND1 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.028 0.12 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.034 0.13 -10000 0 -0.28 69 69
EGF -0.05 0.18 -10000 0 -0.56 58 58
NCKAP1 0.014 0 -10000 0 -10000 0 0
AQP3 -0.076 0.12 -10000 0 -0.51 19 19
cortical microtubule organization -0.064 0.11 -10000 0 -0.3 60 60
GO:0000145 -0.027 0.12 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.065 0.11 -10000 0 -0.3 60 60
MLLT4 0.013 0.027 -10000 0 -0.59 1 1
ARF6/GDP -0.058 0.096 -10000 0 -0.4 11 11
ARF6 0.014 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.017 0.066 -10000 0 -0.4 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.029 0.12 -10000 0 -0.35 10 10
PVRL2 0.012 0.035 -10000 0 -0.54 2 2
ZYX -0.033 0.13 -10000 0 -0.28 60 60
ARF6/GTP -0.015 0.059 -10000 0 -0.53 1 1
CDH1 -0.12 0.24 -10000 0 -0.54 127 127
EGFR/EGFR/EGF/EGF -0.13 0.17 -10000 0 -0.52 47 47
RhoA/GDP -0.059 0.1 -10000 0 -0.27 60 60
actin cytoskeleton organization -0.022 0.12 -10000 0 -0.54 1 1
IGF-1R heterotetramer 0.013 0.022 -10000 0 -0.49 1 1
GIT1 0.014 0 -10000 0 -10000 0 0
IGF1R 0.013 0.022 -10000 0 -0.49 1 1
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
DIAPH1 -0.001 0.052 -10000 0 -0.65 3 3
Wnt receptor signaling pathway 0.064 0.11 0.3 60 -10000 0 60
RHOA 0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.058 0.097 -10000 0 -0.4 11 11
CTNNA1 0.014 0 -10000 0 -10000 0 0
VCL -0.023 0.12 -10000 0 -0.56 1 1
EFNA1 0.01 0.044 -10000 0 -0.49 4 4
LPP -0.043 0.14 -10000 0 -0.45 10 10
Ephrin A1/EPHA2 -0.07 0.11 -10000 0 -0.46 10 10
SEC6/SEC8 -0.051 0.092 -10000 0 -0.47 3 3
MGAT3 -0.035 0.13 -10000 0 -0.29 69 69
HGF/MET -0.16 0.18 -10000 0 -0.51 74 74
HGF -0.079 0.2 -10000 0 -0.51 91 91
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.026 0.11 -10000 0 -0.26 68 68
actin cable formation 0.019 0.1 -10000 0 -0.32 3 3
KIAA1543 -0.064 0.17 -10000 0 -0.55 25 25
KIFC3 -0.03 0.12 -10000 0 -0.58 1 1
NCK1 0.013 0.027 -10000 0 -0.59 1 1
EXOC3 0.014 0 -10000 0 -10000 0 0
ACTN1 -0.046 0.14 -10000 0 -0.3 67 67
NCK1/GIT1 -0.001 0.019 -10000 0 -0.43 1 1
mol:GDP -0.064 0.11 -10000 0 -0.3 60 60
EXOC4 0.014 0 -10000 0 -10000 0 0
STX4 -0.029 0.12 -10000 0 -0.28 60 60
PIP5K1C -0.029 0.12 -10000 0 -10000 0 0
LIMA1 0.004 0.08 -10000 0 -0.59 9 9
ABI1 0.014 0 -10000 0 -10000 0 0
ROCK1 -0.003 0.11 -10000 0 -0.37 6 6
adherens junction assembly -0.044 0.17 -10000 0 -0.52 25 25
IGF-1R heterotetramer/IGF1 -0.066 0.12 -10000 0 -0.54 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.031 -10000 0 -0.4 3 3
MET -0.15 0.25 -10000 0 -0.53 150 150
PLEKHA7 -0.038 0.14 -10000 0 -0.3 65 65
mol:GTP -0.017 0.065 -10000 0 -0.4 3 3
establishment of epithelial cell apical/basal polarity 0.003 0.12 -10000 0 -0.45 3 3
cortical actin cytoskeleton stabilization -0.026 0.11 -10000 0 -0.26 68 68
regulation of cell-cell adhesion -0.022 0.12 -10000 0 -0.54 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.026 0.11 -10000 0 -0.26 68 68
Signaling events mediated by HDAC Class III

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
EP300 0.009 0.053 -10000 0 -0.59 4 4
HDAC4 0.014 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.027 0.038 0.34 3 -10000 0 3
CDKN1A -0.054 0.18 -10000 0 -0.48 61 61
KAT2B 0.013 0.022 -10000 0 -0.49 1 1
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.004 0.04 0.45 4 -10000 0 4
FOXO1 0.011 0.044 -10000 0 -0.56 3 3
FOXO4 0.022 0.031 -10000 0 -0.29 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.082 0.21 -10000 0 -0.53 90 90
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.12 0.2 -10000 0 -0.39 177 177
PPARGC1A -0.011 0.12 -10000 0 -0.57 22 22
FHL2 -0.03 0.15 -10000 0 -0.52 43 43
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.013 0.036 -10000 0 -10000 0 0
HIST2H4A 0.028 0.038 -10000 0 -0.34 3 3
SIRT1/FOXO3a 0.013 0.04 0.29 4 -10000 0 4
SIRT1 0.016 0.046 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.011 0.04 -10000 0 -0.28 2 2
SIRT1/Histone H1b -0.002 0.07 -10000 0 -0.26 19 19
apoptosis -0.012 0.035 -10000 0 -10000 0 0
SIRT1/PGC1A -0.004 0.08 -10000 0 -0.35 22 22
p53/SIRT1 0.024 0.12 0.3 60 -0.43 13 73
SIRT1/FOXO4 0.012 0.046 -10000 0 -0.24 5 5
FOXO1/FHL2/SIRT1 -0.014 0.088 -10000 0 -0.28 40 40
HIST1H1E 0.003 0.073 -10000 0 -0.3 20 20
SIRT1/p300 0.009 0.053 -10000 0 -0.43 4 4
muscle cell differentiation 0.1 0.16 0.32 176 -10000 0 176
TP53 -0.001 0.11 -10000 0 -0.56 15 15
KU70/SIRT1/BAX 0.012 0.035 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.012 0.031 -10000 0 -0.49 2 2
HIV-1 Tat/SIRT1 -0.056 0.15 -10000 0 -0.38 90 90
ACSS2 0.03 0.025 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.1 0.16 -10000 0 -0.32 176 176
FAS signaling pathway (CD95)

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
SPTAN1 0.009 0.057 0.27 8 -10000 0 8
RFC1 0.009 0.057 0.27 8 -10000 0 8
PRKDC 0.009 0.057 0.27 8 -10000 0 8
RIPK1 0.016 0.003 -10000 0 -10000 0 0
CASP7 -0.004 0.072 0.25 15 -0.38 3 18
FASLG/FAS/FADD/FAF1 -0.009 0.086 0.22 20 -0.31 15 35
MAP2K4 -0.003 0.12 -10000 0 -0.36 15 15
mol:ceramide -0.003 0.096 -10000 0 -0.39 11 11
GSN 0 0.072 0.25 6 -0.34 10 16
FASLG/FAS/FADD/FAF1/Caspase 8 -0.001 0.091 -10000 0 -0.32 18 18
FAS -0.008 0.1 -10000 0 -0.55 18 18
BID 0.006 0.079 0.3 17 -0.3 12 29
MAP3K1 0.01 0.091 0.22 15 -0.29 8 23
MAP3K7 0.013 0.004 -10000 0 -10000 0 0
RB1 0.008 0.06 0.22 23 -0.36 1 24
CFLAR 0.015 0.022 -10000 0 -0.47 1 1
HGF/MET -0.15 0.2 -10000 0 -0.44 113 113
ARHGDIB 0.006 0.064 0.22 23 -0.36 3 26
FADD 0.011 0.007 -10000 0 -10000 0 0
actin filament polymerization 0 0.072 0.34 10 -0.25 6 16
NFKB1 -0.039 0.066 -10000 0 -0.26 4 4
MAPK8 -0.026 0.17 -10000 0 -0.42 51 51
DFFA 0.009 0.057 0.22 24 -10000 0 24
DNA fragmentation during apoptosis 0.009 0.057 0.22 22 -10000 0 22
FAS/FADD/MET -0.1 0.16 -10000 0 -0.34 157 157
CFLAR/RIP1 0.014 0.017 -10000 0 -0.32 1 1
FAIM3 -0.027 0.15 -10000 0 -0.54 39 39
FAF1 0.011 0.027 -10000 0 -0.59 1 1
PARP1 0.008 0.059 0.27 8 -0.28 1 9
DFFB 0.009 0.057 0.22 22 -10000 0 22
CHUK -0.032 0.057 -10000 0 -10000 0 0
FASLG -0.028 0.13 -10000 0 -0.5 34 34
FAS/FADD 0.002 0.077 -10000 0 -0.4 18 18
HGF -0.079 0.2 -10000 0 -0.51 91 91
LMNA 0.006 0.061 0.25 8 -0.35 3 11
CASP6 0.007 0.064 0.27 8 -0.38 3 11
CASP10 0.01 0.024 -10000 0 -0.5 1 1
CASP3 0.01 0.068 0.26 24 -10000 0 24
PTPN13 0.006 0.069 -10000 0 -0.58 7 7
CASP8 0.01 0.1 0.31 34 -0.34 15 49
IL6 -0.14 0.37 -10000 0 -1 60 60
MET -0.15 0.25 -10000 0 -0.53 150 150
ICAD/CAD 0.009 0.053 0.25 8 -10000 0 8
FASLG/FAS/FADD/FAF1/Caspase 10 -0.003 0.097 -10000 0 -0.39 11 11
activation of caspase activity by cytochrome c 0.006 0.079 0.3 17 -0.3 12 29
PAK2 0.008 0.057 0.27 8 -10000 0 8
BCL2 0.005 0.075 -10000 0 -0.59 8 8
Ephrin B reverse signaling

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
EFNB2 0.002 0.08 -10000 0 -0.52 12 12
EPHB2 -0.001 0.088 -10000 0 -0.52 14 14
EFNB1 -0.061 0.17 -10000 0 -0.37 110 110
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.076 0.14 -10000 0 -0.56 20 20
Ephrin B2/EPHB1-2 -0.034 0.12 -10000 0 -0.34 60 60
neuron projection morphogenesis -0.073 0.13 -10000 0 -0.54 20 20
Ephrin B1/EPHB1-2/Tiam1 -0.053 0.17 -10000 0 -0.38 68 68
DNM1 -0.1 0.22 -10000 0 -0.52 109 109
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.011 0.082 -10000 0 -0.72 6 6
YES1 -0.009 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/NCK2 -0.052 0.17 -10000 0 -0.38 68 68
PI3K 0.012 0.083 -10000 0 -0.67 7 7
mol:GDP -0.075 0.16 -10000 0 -0.38 68 68
ITGA2B -0.043 0.17 -10000 0 -0.57 50 50
endothelial cell proliferation -0.005 0.048 -10000 0 -0.31 12 12
FYN -0.008 0.1 -10000 0 -0.94 6 6
MAP3K7 -0.007 0.083 -10000 0 -0.76 6 6
FGR -0.008 0.1 -10000 0 -0.94 6 6
TIAM1 0.013 0.027 -10000 0 -0.59 1 1
PIK3R1 0.014 0 -10000 0 -10000 0 0
RGS3 0.011 0.038 -10000 0 -0.49 3 3
cell adhesion -0.034 0.14 -10000 0 -0.59 14 14
LYN -0.009 0.1 -10000 0 -0.94 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.098 -10000 0 -0.91 6 6
Ephrin B1/EPHB1-2 -0.013 0.09 -10000 0 -0.82 6 6
SRC -0.008 0.1 -10000 0 -0.94 6 6
ITGB3 -0.052 0.18 -10000 0 -0.51 65 65
EPHB1 -0.035 0.16 -10000 0 -0.59 41 41
EPHB4 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.004 0.048 -10000 0 -0.31 12 12
alphaIIb/beta3 Integrin -0.085 0.17 -10000 0 -0.41 107 107
BLK -0.028 0.11 -10000 0 -0.98 6 6
HCK -0.012 0.11 -10000 0 -1 6 6
regulation of stress fiber formation 0.075 0.15 0.43 41 -10000 0 41
MAPK8 0.01 0.095 -10000 0 -0.72 6 6
Ephrin B1/EPHB1-2/RGS3 -0.054 0.17 -10000 0 -0.38 68 68
endothelial cell migration -0.008 0.082 -10000 0 -0.54 9 9
NCK2 0.014 0 -10000 0 -10000 0 0
PTPN13 0.003 0.082 -10000 0 -0.68 7 7
regulation of focal adhesion formation 0.075 0.15 0.43 41 -10000 0 41
chemotaxis 0.076 0.16 0.38 68 -10000 0 68
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
Rac1/GTP -0.075 0.14 -10000 0 -0.55 20 20
angiogenesis -0.013 0.089 -10000 0 -0.82 6 6
LCK -0.026 0.11 -10000 0 -0.96 6 6
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.036 0.16 -9999 0 -0.46 60 60
KLHL20 -0.027 0.056 -9999 0 -0.27 9 9
CYFIP2 0.008 0.06 -9999 0 -0.54 6 6
Rac1/GDP 0.007 0.11 -9999 0 -10000 0 0
ENAH -0.036 0.16 -9999 0 -0.46 60 60
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.036 0.067 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.017 0.039 -9999 0 -0.18 9 9
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.093 0.15 -9999 0 -0.38 74 74
RAPGEF1 -0.015 0.15 -9999 0 -0.39 60 60
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.074 0.16 -9999 0 -0.48 60 60
CRK -0.025 0.16 -9999 0 -0.42 60 60
E-cadherin/gamma catenin/alpha catenin -0.085 0.15 -9999 0 -0.32 134 134
alphaE/beta7 Integrin -0.033 0.11 -9999 0 -0.38 44 44
IQGAP1 0.004 0.076 -9999 0 -0.53 10 10
NCKAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.018 -9999 0 -0.29 2 2
DLG1 -0.036 0.16 -9999 0 -0.46 61 61
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.026 0.048 -9999 0 -10000 0 0
MLLT4 0.013 0.027 -9999 0 -0.59 1 1
ARF6/GTP/NME1/Tiam1 0 0.015 -9999 0 -0.32 1 1
PI3K -0.033 0.061 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.1 0.18 -9999 0 -0.39 134 134
TIAM1 0.013 0.027 -9999 0 -0.59 1 1
E-cadherin(dimer)/Ca2+ -0.065 0.11 -9999 0 -0.3 60 60
AKT1 -0.019 0.035 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
CDH1 -0.12 0.24 -9999 0 -0.54 127 127
RhoA/GDP 0.007 0.11 -9999 0 -10000 0 0
actin cytoskeleton organization -0.02 0.041 -9999 0 -0.19 9 9
CDC42/GDP 0.007 0.11 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.033 0.11 -9999 0 -0.27 66 66
ITGB7 -0.033 0.16 -9999 0 -0.54 44 44
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.042 0.14 -9999 0 -0.32 60 60
E-cadherin/Ca2+/beta catenin/alpha catenin -0.067 0.12 -9999 0 -0.27 127 127
mol:GDP -0.003 0.12 -9999 0 -0.32 8 8
CDC42/GTP/IQGAP1 -0.006 0.044 -9999 0 -0.32 10 10
JUP 0.003 0.081 -9999 0 -0.57 10 10
p120 catenin/RhoA/GDP -0.043 0.086 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 -0.006 0.044 -9999 0 -0.32 10 10
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.01 0.063 -9999 0 -0.21 29 29
NME1 0.014 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.036 0.16 -9999 0 -0.46 60 60
regulation of cell-cell adhesion -0.032 0.059 -9999 0 -10000 0 0
WASF2 -0.008 0.02 -9999 0 -10000 0 0
Rap1/GTP -0.042 0.077 -9999 0 -0.32 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.091 0.15 -9999 0 -0.57 20 20
CCND1 0.01 0.077 -9999 0 -0.26 29 29
VAV2 -0.019 0.15 -9999 0 -0.42 60 60
RAP1/GDP -0.04 0.081 -9999 0 -0.31 1 1
adherens junction assembly -0.034 0.16 -9999 0 -0.44 60 60
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.052 0.16 -9999 0 -0.55 20 20
E-cadherin/beta catenin -0.068 0.13 -9999 0 -0.38 60 60
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.037 0.16 -9999 0 -0.46 60 60
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
Rac1/GTP -0.042 0.09 -9999 0 -0.45 9 9
E-cadherin/beta catenin/alpha catenin -0.078 0.14 -9999 0 -0.32 127 127
ITGAE 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.076 0.16 -9999 0 -0.49 60 60
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR -0.007 0.11 -9999 0 -0.56 19 19
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.089 0.15 -9999 0 -0.36 79 79
CaM/Ca2+ -0.002 0.025 -9999 0 -0.4 2 2
KATNA1 0.014 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.052 0.15 -9999 0 -0.32 79 79
IQGAP1/CaM -0.009 0.057 -9999 0 -0.38 12 12
DAB1 -0.089 0.22 -9999 0 -0.56 92 92
IQGAP1 0.004 0.076 -9999 0 -0.53 10 10
PLA2G7 -0.04 0.17 -9999 0 -0.55 49 49
CALM1 0.012 0.035 -9999 0 -0.54 2 2
DYNLT1 0.012 0.038 -9999 0 -0.59 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.002 0.027 -9999 0 -0.43 2 2
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.014 0 -9999 0 -10000 0 0
CDK5R1 -0.021 0.14 -9999 0 -0.59 30 30
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.23 -9999 0 -0.57 103 103
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.21 -9999 0 -0.39 210 210
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.069 0.19 -9999 0 -0.54 43 43
MAP1B -0.001 0.016 -9999 0 -0.31 1 1
RAC1 -0.003 0.019 -9999 0 -10000 0 0
p35/CDK5 -0.047 0.16 -9999 0 -0.57 16 16
RELN -0.14 0.25 -9999 0 -0.55 139 139
PAFAH/LIS1 -0.005 0.11 -9999 0 -0.33 49 49
LIS1/CLIP170 0.029 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.08 0.13 -9999 0 -0.43 39 39
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.085 0.2 -9999 0 -0.64 34 34
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.082 0.2 -9999 0 -0.59 43 43
LIS1/IQGAP1 0.022 0.047 -9999 0 -0.31 10 10
RHOA -0.003 0.019 -9999 0 -10000 0 0
PAFAH1B1 0.025 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0 -9999 0 -10000 0 0
PAFAH1B2 -0.005 0.1 -9999 0 -0.59 16 16
MAP1B/LIS1/Dynein heavy chain 0.027 0.011 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.1 0.16 -9999 0 -0.52 42 42
LRP8 0.012 0.038 -9999 0 -0.59 2 2
NDEL1/Katanin 60 -0.069 0.19 -9999 0 -0.54 43 43
P39/CDK5 -0.089 0.19 -9999 0 -0.53 40 40
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.029 0 -9999 0 -10000 0 0
CDK5 -0.039 0.14 -9999 0 -0.59 1 1
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.1 0.2 -9999 0 -0.57 38 38
RELN/VLDLR -0.09 0.14 -9999 0 -0.34 93 93
CDC42 -0.003 0.019 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.021 0.088 -9999 0 -0.37 29 29
alphaV beta3 Integrin -0.04 0.11 -9999 0 -0.31 67 67
PTK2 -0.012 0.14 -9999 0 -0.46 22 22
IGF1R 0.013 0.022 -9999 0 -0.49 1 1
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.01 0.051 -9999 0 -0.57 4 4
SRC 0.014 0 -9999 0 -10000 0 0
CDKN1B -0.028 0.089 -9999 0 -0.49 15 15
VEGFA -0.007 0.1 -9999 0 -0.49 22 22
ILK -0.028 0.089 -9999 0 -0.49 15 15
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 0.009 0.092 -9999 0 -0.45 15 15
PTK2B -0.021 0.14 -9999 0 -0.5 20 20
alphaV/beta3 Integrin/JAM-A -0.012 0.13 -9999 0 -0.35 36 36
CBL 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.039 0.1 -9999 0 -0.3 66 66
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.012 0.058 -9999 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.011 0.085 -9999 0 -0.37 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.064 0.14 -9999 0 -0.36 92 92
PI4KA 0.005 0.066 -9999 0 -0.49 9 9
IGF-1R heterotetramer/IGF1/IRS1 -0.045 0.11 -9999 0 -0.47 19 19
PI4 Kinase -0.006 0.045 -9999 0 -0.34 9 9
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
alphaV/beta3 Integrin/Osteopontin -0.094 0.16 -9999 0 -0.36 134 134
RPS6KB1 0.009 0.12 -9999 0 -0.44 19 19
TLN1 0.014 0 -9999 0 -10000 0 0
MAPK3 0.006 0.12 -9999 0 -0.44 23 23
GPR124 0.01 0.044 -9999 0 -0.49 4 4
MAPK1 0.006 0.12 -9999 0 -0.44 23 23
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.085 0.16 -9999 0 -0.34 127 127
cell adhesion -0.033 0.085 -9999 0 -0.34 14 14
ANGPTL3 0.006 0.007 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.017 0.073 -9999 0 -0.44 5 5
IGF-1R heterotetramer 0.013 0.022 -9999 0 -0.49 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.009 0.05 -9999 0 -0.49 5 5
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
IGF1 -0.008 0.11 -9999 0 -0.56 20 20
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.04 0.1 -9999 0 -0.3 68 68
apoptosis 0.013 0.027 -9999 0 -0.59 1 1
CD47 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.038 0.1 -9999 0 -0.3 66 66
VCL 0.008 0.058 -9999 0 -0.52 6 6
alphaV/beta3 Integrin/Del1 -0.085 0.16 -9999 0 -0.35 124 124
CSF1 -0.006 0.11 -9999 0 -0.59 17 17
PIK3C2A -0.031 0.097 -9999 0 -0.5 17 17
PI4 Kinase/Pyk2 -0.057 0.12 -9999 0 -0.43 32 32
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.049 0.12 -9999 0 -0.43 35 35
FAK1/Vinculin -0.003 0.13 -9999 0 -0.41 16 16
alphaV beta3/Integrin/ppsTEM5 -0.04 0.1 -9999 0 -0.3 68 68
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.007 0.11 -9999 0 -0.56 19 19
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
FGF2 0.011 0.044 -9999 0 -0.56 3 3
F11R 0.014 0.065 -9999 0 -0.36 15 15
alphaV/beta3 Integrin/Lactadherin -0.041 0.1 -9999 0 -0.3 70 70
alphaV/beta3 Integrin/TGFBR2 -0.041 0.11 -9999 0 -0.31 68 68
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.012 0.06 -9999 0 -0.32 19 19
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.034 0.09 -9999 0 -0.27 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.004 0.093 -9999 0 -0.49 18 18
alphaV/beta3 Integrin/Pyk2 -0.02 0.14 -9999 0 -0.5 20 20
SDC1 -0.032 0.15 -9999 0 -0.51 45 45
VAV3 -0.039 0.14 -9999 0 -0.55 6 6
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.001 0.12 -9999 0 -0.38 14 14
cell migration 0.007 0.12 -9999 0 -0.41 9 9
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
PI3K -0.042 0.097 -9999 0 -0.47 9 9
SPP1 -0.084 0.21 -9999 0 -0.54 91 91
KDR 0.005 0.071 -9999 0 -0.52 9 9
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.027 -9999 0 -0.59 1 1
COL4A3 -0.069 0.2 -9999 0 -0.52 80 80
angiogenesis 0.008 0.13 -9999 0 -0.46 20 20
Rac1/GTP -0.062 0.11 -9999 0 -0.5 6 6
EDIL3 -0.067 0.2 -9999 0 -0.57 71 71
cell proliferation -0.041 0.11 -9999 0 -0.31 68 68
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.003 0.058 -10000 0 -0.58 4 4
AES 0.01 0.022 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.001 0.041 -10000 0 -0.34 7 7
SMAD4 0.014 0 -10000 0 -10000 0 0
DKK2 -0.11 0.23 -10000 0 -0.54 117 117
TLE1 0.008 0.044 -10000 0 -0.6 2 2
MACF1 0.015 0 -10000 0 -10000 0 0
CTNNB1 0.06 0.083 -10000 0 -10000 0 0
WIF1 -0.28 0.28 -10000 0 -0.54 269 269
beta catenin/RanBP3 0.02 0.11 0.39 33 -10000 0 33
KREMEN2 -0.052 0.18 -10000 0 -0.53 63 63
DKK1 -0.12 0.24 -10000 0 -0.53 124 124
beta catenin/beta TrCP1 0.066 0.078 -10000 0 -10000 0 0
FZD1 0.009 0.054 -10000 0 -0.49 6 6
AXIN2 -0.002 0.11 -10000 0 -0.9 5 5
AXIN1 0.015 0.001 -10000 0 -10000 0 0
RAN 0.014 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.023 0.044 -10000 0 -0.56 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.09 0.052 0.3 2 -10000 0 2
Axin1/APC/GSK3 0.008 0.037 0.25 3 -10000 0 3
Axin1/APC/GSK3/beta catenin/Macf1 0.051 0.068 -10000 0 -10000 0 0
HNF1A 0.006 0.036 -10000 0 -0.6 1 1
CTBP1 0.007 0.024 -10000 0 -10000 0 0
MYC -0.05 0.3 -10000 0 -1.5 21 21
RANBP3 0.014 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 163 163
NKD1 -0.004 0.099 -10000 0 -0.54 17 17
TCF4 0.006 0.034 -10000 0 -0.55 1 1
TCF3 0.005 0.04 -10000 0 -0.53 2 2
WNT1/LRP6/FZD1/Axin1 -0.02 0.073 -10000 0 -0.5 1 1
Ran/GTP 0.002 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.034 0.13 0.49 31 -10000 0 31
LEF1 0.002 0.054 -10000 0 -0.49 5 5
DVL1 0.06 0.046 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.086 0.079 -10000 0 -0.44 2 2
DKK1/LRP6/Kremen 2 -0.11 0.17 -10000 0 -0.34 168 168
LRP6 0.014 0.022 -10000 0 -0.49 1 1
CSNK1A1 0.009 0.026 -10000 0 -10000 0 0
NLK 0.012 0.033 -10000 0 -0.51 2 2
CCND1 -0.036 0.24 -10000 0 -1.4 13 13
WNT1 -0.028 0.13 -10000 0 -0.49 40 40
GSK3A 0.015 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.027 -10000 0 -0.59 1 1
FRAT1 0.01 0.049 -10000 0 -0.54 4 4
PPP2R5D 0.043 0.049 0.27 17 -10000 0 17
APC 0.019 0.078 -10000 0 -0.46 1 1
WNT1/LRP6/FZD1 0.096 0.1 0.24 109 -10000 0 109
CREBBP 0.007 0.024 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.008 0.06 -10000 0 -0.59 5 5
ANTXR2 0.002 0.079 -10000 0 -0.51 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.012 -10000 0 -0.066 17 17
monocyte activation -0.16 0.25 -10000 0 -0.51 145 145
MAP2K2 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 -0.002 0.017 -10000 0 -0.32 1 1
MAP2K7 -0.002 0.01 -10000 0 -10000 0 0
MAP2K6 -0.002 0.017 -10000 0 -0.32 1 1
CYAA 0.007 0.052 -10000 0 -0.27 17 17
MAP2K4 -0.003 0.022 -10000 0 -0.32 2 2
IL1B -0.082 0.14 -10000 0 -0.28 173 173
Channel -0.01 0.052 -10000 0 -0.29 17 17
NLRP1 -0.003 0.022 -10000 0 -0.32 2 2
CALM1 0.012 0.035 -10000 0 -0.54 2 2
negative regulation of phagocytosis -0.004 0.028 -10000 0 -0.54 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.012 0.066 17 -10000 0 17
MAPK3 -0.002 0.01 -10000 0 -10000 0 0
MAPK1 -0.002 0.01 -10000 0 -10000 0 0
PGR -0.035 0.099 -10000 0 -0.32 53 53
PA/Cellular Receptors -0.011 0.058 -10000 0 -0.32 17 17
apoptosis -0.002 0.012 -10000 0 -0.066 17 17
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.009 0.051 -10000 0 -0.26 17 17
macrophage activation 0.019 0.011 -10000 0 -10000 0 0
TNF -0.15 0.26 -10000 0 -0.54 156 156
VCAM1 -0.16 0.26 -10000 0 -0.51 145 145
platelet activation -0.004 0.028 -10000 0 -0.54 1 1
MAPKKK cascade -0.015 0.017 0.18 2 -10000 0 2
IL18 -0.009 0.088 -10000 0 -0.29 41 41
negative regulation of macrophage activation -0.002 0.012 -10000 0 -0.066 17 17
LEF -0.002 0.012 -10000 0 -0.066 17 17
CASP1 -0.004 0.022 -10000 0 -0.27 2 2
mol:cAMP -0.004 0.028 -10000 0 -0.55 1 1
necrosis -0.002 0.012 -10000 0 -0.066 17 17
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.008 0.053 -10000 0 -0.27 17 17
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.038 -10000 0 -0.49 3 3
Jak2/Leptin Receptor -0.009 0.1 0.2 17 -0.43 12 29
PTP1B/AKT1 -0.006 0.085 -10000 0 -0.3 14 14
FYN 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.015 0.093 -10000 0 -0.28 28 28
EGFR -0.084 0.22 -10000 0 -0.55 89 89
EGF/EGFR -0.096 0.16 -10000 0 -0.38 97 97
CSF1 -0.006 0.11 -10000 0 -0.59 17 17
AKT1 0.014 0.002 -10000 0 -10000 0 0
INSR 0.014 0.002 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.007 0.09 -10000 0 -0.31 17 17
Insulin Receptor/Insulin -0.025 0.059 -10000 0 -0.3 9 9
HCK -0.007 0.11 -10000 0 -0.54 20 20
CRK 0.014 0 -10000 0 -10000 0 0
TYK2 -0.006 0.089 -10000 0 -0.31 14 14
EGF -0.052 0.18 -10000 0 -0.56 58 58
YES1 0.009 0.053 -10000 0 -0.59 4 4
CAV1 -0.031 0.12 -10000 0 -0.34 35 35
TXN 0.011 0.023 -10000 0 -0.5 1 1
PTP1B/IRS1/GRB2 -0.002 0.085 -10000 0 -0.33 9 9
cell migration 0.015 0.093 0.28 28 -10000 0 28
STAT3 0.014 0.001 -10000 0 -10000 0 0
PRLR -0.019 0.14 -10000 0 -0.55 31 31
ITGA2B -0.043 0.17 -10000 0 -0.57 50 50
CSF1R -0.022 0.14 -10000 0 -0.57 32 32
Prolactin Receptor/Prolactin -0.017 0.1 -10000 0 -0.4 33 33
FGR 0.011 0.038 -10000 0 -0.49 3 3
PTP1B/p130 Cas -0.008 0.09 -10000 0 -0.32 14 14
Crk/p130 Cas -0.002 0.085 -10000 0 -0.34 9 9
DOK1 0.002 0.085 -10000 0 -0.33 9 9
JAK2 0.001 0.084 -10000 0 -0.34 13 13
Jak2/Leptin Receptor/Leptin -0.11 0.18 -10000 0 -0.43 106 106
PIK3R1 0.014 0 -10000 0 -10000 0 0
PTPN1 -0.015 0.094 -10000 0 -0.28 28 28
LYN 0.004 0.073 -10000 0 -0.51 10 10
CDH2 0.013 0.027 -10000 0 -0.59 1 1
SRC 0.012 0.038 -10000 0 -10000 0 0
ITGB3 -0.053 0.18 -10000 0 -0.51 65 65
CAT1/PTP1B -0.06 0.15 -10000 0 -0.4 45 45
CAPN1 0.014 0.027 -10000 0 -0.6 1 1
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.018 0.053 -10000 0 -0.35 2 2
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.11 0.18 -10000 0 -0.43 108 108
negative regulation of transcription 0.001 0.083 -10000 0 -0.34 13 13
FCGR2A -0.031 0.15 -10000 0 -0.54 42 42
FER -0.013 0.12 -10000 0 -0.6 22 22
alphaIIb/beta3 Integrin -0.082 0.17 -10000 0 -0.41 107 107
BLK -0.11 0.22 -10000 0 -0.52 114 114
Insulin Receptor/Insulin/Shc -0.003 0.045 -10000 0 -0.32 10 10
RHOA 0.015 0.002 -10000 0 -10000 0 0
LEPR 0.001 0.09 -10000 0 -0.53 14 14
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
p210 bcr-abl/Grb2 0.013 0.022 -10000 0 -0.49 1 1
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.069 0.16 -10000 0 -0.43 49 49
PRL 0.002 0.031 -10000 0 -0.48 2 2
SOCS3 -0.14 0.34 -10000 0 -1.4 31 31
SPRY2 0.006 0.064 -10000 0 -0.5 8 8
Insulin Receptor/Insulin/IRS1 0 0.035 -10000 0 -0.36 4 4
CSF1/CSF1R -0.03 0.14 -10000 0 -0.4 45 45
Ras protein signal transduction 0.02 0.034 -10000 0 -0.4 1 1
IRS1 0.014 0 -10000 0 -10000 0 0
INS -0.005 0.056 -10000 0 -0.57 5 5
LEP -0.002 0.058 -10000 0 -0.49 7 7
STAT5B -0.003 0.084 -10000 0 -0.27 18 18
STAT5A -0.007 0.088 -10000 0 -0.28 20 20
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PDGFB-D/PDGFRB -0.008 0.092 -10000 0 -0.31 19 19
CSN2 -0.001 0.042 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
LAT -0.038 0.15 -10000 0 -0.48 46 46
YBX1 0.02 0.038 -10000 0 -0.58 2 2
LCK -0.081 0.21 -10000 0 -0.54 89 89
SHC1 0.009 0.05 -10000 0 -0.49 5 5
NOX4 -0.067 0.19 -10000 0 -0.52 77 77
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.037 0.16 -10000 0 -0.59 5 5
UGCG -0.022 0.14 -10000 0 -0.67 20 20
AKT1/mTOR/p70S6K/Hsp90/TERT -0.038 0.16 -10000 0 -0.41 42 42
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.021 0.14 -10000 0 -0.66 20 20
mol:DAG -0.004 0.043 -10000 0 -0.97 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.069 0.12 -10000 0 -0.46 24 24
FRAP1 -0.026 0.18 -10000 0 -0.53 26 26
FOXO3 -0.018 0.17 -10000 0 -0.43 39 39
AKT1 -0.029 0.18 -10000 0 -0.46 42 42
GAB2 0.013 0.027 -10000 0 -0.6 1 1
SMPD1 0.004 0.036 -10000 0 -10000 0 0
SGMS1 0.003 0.046 -10000 0 -0.67 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.018 -10000 0 -0.36 1 1
CALM1 0.012 0.035 -10000 0 -0.54 2 2
cell proliferation -0.014 0.11 -10000 0 -0.3 40 40
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.024 0.021 -10000 0 -0.42 1 1
RPS6KB1 -0.004 0.064 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.043 -10000 0 -0.97 1 1
natural killer cell activation 0 0.002 -10000 0 -0.012 11 11
JAK3 -0.054 0.18 -10000 0 -0.53 67 67
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
MYC -0.038 0.24 -10000 0 -0.93 25 25
MYB -0.093 0.34 -10000 0 -0.92 62 62
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.036 0.17 -10000 0 -0.4 58 58
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.013 0.06 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.035 0.16 -10000 0 -0.39 58 58
Rac1/GDP 0.028 0.017 -10000 0 -0.32 1 1
T cell proliferation -0.036 0.18 -10000 0 -0.46 46 46
SHC1 0.009 0.05 -10000 0 -0.49 5 5
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.02 -10000 0 -0.05 72 72
PRKCZ -0.038 0.18 -10000 0 -0.48 46 46
NF kappa B1 p50/RelA -0.062 0.12 -10000 0 -0.48 20 20
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.051 0.17 -10000 0 -0.43 58 58
HSP90AA1 0.014 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
IL2RA -0.062 0.18 -10000 0 -0.5 71 71
IL2RB -0.092 0.22 -10000 0 -0.53 102 102
TERT -0.082 0.21 -10000 0 -0.56 81 81
E2F1 -0.031 0.15 -10000 0 -0.4 62 62
SOS1 0.014 0.003 -10000 0 -10000 0 0
RPS6 0.013 0.022 -10000 0 -0.49 1 1
mol:cAMP 0.001 0.01 0.024 72 -10000 0 72
PTPN11 0.014 0.004 -10000 0 -10000 0 0
IL2RG -0.04 0.16 -10000 0 -0.52 54 54
actin cytoskeleton organization -0.036 0.18 -10000 0 -0.46 46 46
GRB2 0.013 0.022 -10000 0 -0.49 1 1
IL2 0.003 0.004 -10000 0 -10000 0 0
PIK3CA 0.015 0.027 -10000 0 -0.59 1 1
Rac1/GTP 0.032 0.022 -10000 0 -0.3 1 1
LCK -0.079 0.21 -10000 0 -0.53 89 89
BCL2 -0.014 0.18 -10000 0 -0.7 15 15
IL27-mediated signaling events

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
TGFB1 0.004 0.08 -10000 0 -0.59 9 9
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.004 0.1 0.44 6 -10000 0 6
IL27/IL27R/JAK1 -0.034 0.15 -10000 0 -0.63 3 3
TBX21 -0.057 0.21 -10000 0 -0.55 40 40
IL12B -0.002 0.054 -10000 0 -0.5 6 6
IL12A -0.012 0.1 -10000 0 -0.42 29 29
IL6ST -0.03 0.16 -10000 0 -0.6 37 37
IL27RA/JAK1 0.019 0.036 -10000 0 -10000 0 0
IL27 -0.016 0.11 -10000 0 -0.49 27 27
TYK2 0.015 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.054 0.12 -10000 0 -0.72 2 2
T-helper 2 cell differentiation 0.004 0.1 0.44 6 -10000 0 6
T cell proliferation during immune response 0.004 0.1 0.44 6 -10000 0 6
MAPKKK cascade -0.004 0.1 -10000 0 -0.44 6 6
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.01 0.044 -10000 0 -0.49 4 4
STAT1 -0.002 0.088 -10000 0 -0.49 16 16
IL12RB1 -0.032 0.16 -10000 0 -0.56 42 42
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.085 0.24 -10000 0 -0.62 29 29
IL27/IL27R/JAK2/TYK2 -0.005 0.1 -10000 0 -0.44 6 6
positive regulation of T cell mediated cytotoxicity -0.004 0.1 -10000 0 -0.44 6 6
STAT1 (dimer) -0.059 0.24 0.52 27 -0.72 11 38
JAK2 0.015 0.004 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
STAT2 (dimer) 0.002 0.1 -10000 0 -0.41 6 6
T cell proliferation -0.067 0.16 -10000 0 -0.48 20 20
IL12/IL12R/TYK2/JAK2 -0.006 0.094 -10000 0 -0.56 5 5
IL17A -0.054 0.12 -10000 0 -0.72 2 2
mast cell activation 0.004 0.1 0.44 6 -10000 0 6
IFNG 0.001 0.021 -10000 0 -0.091 4 4
T cell differentiation -0.004 0.005 -10000 0 -0.021 5 5
STAT3 (dimer) 0.004 0.097 -10000 0 -0.41 6 6
STAT5A (dimer) -0.003 0.11 -10000 0 -0.46 11 11
STAT4 (dimer) -0.084 0.17 -10000 0 -0.48 25 25
STAT4 -0.16 0.26 -10000 0 -0.53 161 161
T cell activation -0.009 0.007 0.061 3 -10000 0 3
IL27R/JAK2/TYK2 -0.012 0.089 -10000 0 -10000 0 0
GATA3 -0.16 0.41 -10000 0 -1.4 51 51
IL18 -0.02 0.11 -10000 0 -0.4 41 41
positive regulation of mast cell cytokine production 0.004 0.096 -10000 0 -0.41 6 6
IL27/EBI3 -0.02 0.12 -10000 0 -0.4 46 46
IL27RA 0.014 0.034 -10000 0 -10000 0 0
IL6 -0.13 0.24 -10000 0 -0.52 134 134
STAT5A 0.001 0.088 -10000 0 -0.59 11 11
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.001 0.02 -10000 0 -10000 0 0
IL1B -0.12 0.19 -10000 0 -0.39 173 173
EBI3 -0.012 0.12 -10000 0 -0.57 22 22
TNF -0.11 0.19 -10000 0 -0.39 156 156
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.014 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.005 0.043 -9999 0 -0.82 1 1
Syndecan-3/Neurocan -0.021 0.082 -9999 0 -0.32 31 31
POMC -0.005 0.1 -9999 0 -0.54 18 18
EGFR -0.083 0.21 -9999 0 -0.55 89 89
Syndecan-3/EGFR -0.047 0.1 -9999 0 -0.3 50 50
AGRP 0.005 0.05 -9999 0 -0.49 5 5
NCSTN 0.014 0 -9999 0 -10000 0 0
PSENEN 0.014 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
NCAN -0.026 0.15 -9999 0 -0.58 35 35
long-term memory -0.002 0.026 -9999 0 -0.56 1 1
Syndecan-3/IL8 -0.082 0.12 -9999 0 -0.3 68 68
PSEN1 0.014 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
limb bud formation -0.002 0.029 -9999 0 -0.62 1 1
MC4R -0.11 0.24 -9999 0 -0.56 112 112
SRC 0.014 0 -9999 0 -10000 0 0
PTN 0.007 0.062 -9999 0 -0.52 7 7
FGFR/FGF/Syndecan-3 -0.002 0.03 -9999 0 -0.63 1 1
neuron projection morphogenesis -0.021 0.08 -9999 0 -0.65 3 3
Syndecan-3/AgRP -0.004 0.036 -9999 0 -0.6 1 1
Syndecan-3/AgRP/MC4R -0.06 0.12 -9999 0 -0.56 3 3
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.002 0.03 -9999 0 -0.64 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.081 0.12 -9999 0 -0.3 68 68
IL8 -0.16 0.26 -9999 0 -0.53 162 162
Syndecan-3/Fyn/Cortactin -0.002 0.027 -9999 0 -0.57 1 1
Syndecan-3/CASK -0.002 0.028 -9999 0 -0.6 1 1
alpha-MSH/MC4R -0.1 0.18 -9999 0 -0.42 123 123
Gamma Secretase 0 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.068 0.2 -9999 0 -0.55 74 74
GNB1/GNG2 -0.014 0.12 -9999 0 -0.42 20 20
mol:DAG -0.004 0.12 -9999 0 -0.44 10 10
PLCG1 -0.005 0.12 -9999 0 -0.46 10 10
YES1 -0.022 0.13 -9999 0 -0.43 22 22
FZD3 0.011 0.046 -9999 0 -0.59 3 3
FZD6 -0.016 0.12 -9999 0 -0.49 31 31
G protein -0.005 0.12 -9999 0 -0.46 10 10
MAP3K7 -0.098 0.16 -9999 0 -0.41 45 45
mol:Ca2+ -0.004 0.11 -9999 0 -0.43 10 10
mol:IP3 -0.004 0.12 -9999 0 -0.44 10 10
NLK -0.005 0.011 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.17 -9999 0 -0.44 47 47
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.031 0.13 -9999 0 -0.44 20 20
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.02 0.12 -9999 0 -0.41 20 20
GO:0007205 -0.004 0.11 -9999 0 -0.45 9 9
WNT6 -0.034 0.16 -9999 0 -0.53 45 45
WNT4 -0.032 0.15 -9999 0 -0.52 45 45
NFAT1/CK1 alpha -0.038 0.16 -9999 0 -0.44 37 37
GNG2 0.009 0.053 -9999 0 -0.59 4 4
WNT5A -0.013 0.12 -9999 0 -0.56 24 24
WNT11 -0.017 0.13 -9999 0 -0.54 29 29
CDC42 -0.013 0.12 -9999 0 -0.41 22 22
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.007 0.1 -10000 0 -0.35 44 44
MAP4K4 -0.022 0.12 -10000 0 -0.46 17 17
BAG4 -0.001 0.095 -10000 0 -0.59 13 13
PKC zeta/ceramide -0.013 0.073 0.15 5 -0.27 25 30
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.033 0.16 -10000 0 -0.55 43 43
BAX 0.006 0.025 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AKT1 0.022 0.014 -10000 0 -10000 0 0
BAD 0.003 0.048 0.16 9 -10000 0 9
SMPD1 -0.027 0.089 -10000 0 -0.2 76 76
RB1 0.003 0.051 0.16 9 -0.4 1 10
FADD/Caspase 8 -0.013 0.12 -10000 0 -0.49 13 13
MAP2K4 0.006 0.057 -10000 0 -0.26 8 8
NSMAF 0.014 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.011 0.045 -10000 0 -10000 0 0
EGF -0.05 0.18 -10000 0 -0.56 58 58
mol:ceramide -0.006 0.052 0.15 37 -10000 0 37
MADD 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.007 0.1 -10000 0 -0.35 44 44
ASAH1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.002 0.051 0.16 9 -0.4 1 10
cell proliferation -0.002 0.092 -10000 0 -0.33 31 31
BID -0.01 0.091 -10000 0 -0.38 12 12
MAP3K1 0 0.057 0.16 9 -0.27 7 16
EIF2A 0.015 0.052 -10000 0 -0.28 5 5
TRADD 0.013 0.027 -10000 0 -0.59 1 1
CRADD 0.014 0 -10000 0 -10000 0 0
MAPK3 0.022 0.043 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.043 -10000 0 -10000 0 0
Cathepsin D/ceramide 0.001 0.046 0.15 8 -10000 0 8
FADD -0.022 0.12 -10000 0 -0.46 17 17
KSR1 0.003 0.048 0.16 9 -10000 0 9
MAPK8 -0.003 0.073 0.17 1 -0.25 25 26
PRKRA 0.003 0.048 0.16 9 -10000 0 9
PDGFA -0.029 0.14 -10000 0 -0.5 44 44
TRAF2 0.014 0 -10000 0 -10000 0 0
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.006 0.051 0.15 19 -10000 0 19
CTSD 0.013 0.022 -10000 0 -0.49 1 1
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0 0.1 -10000 0 -0.36 31 31
PRKCD -0.018 0.14 -10000 0 -0.59 27 27
PRKCZ -0.015 0.12 -10000 0 -0.55 26 26
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.007 0.1 -10000 0 -0.35 44 44
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.034 0.16 -10000 0 -0.53 45 45
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.032 0.13 -10000 0 -0.49 17 17
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -10000 0 -0.34 171 171
mol:Sphingosine-1-phosphate -0.007 0.1 -10000 0 -0.34 44 44
MAP2K1 0.018 0.045 -10000 0 -0.23 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
CYCS 0.008 0.038 0.19 4 -10000 0 4
TNFRSF1A 0.001 0.086 -10000 0 -0.55 12 12
NFKB1 0.014 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.02 0.093 -10000 0 -0.44 23 23
EIF2AK2 0.007 0.055 -10000 0 -0.3 5 5
TNF-alpha/TNFR1A/FAN -0.1 0.15 -10000 0 -0.32 165 165
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.081 -10000 0 -0.44 3 3
MAP2K2 0.018 0.043 -10000 0 -10000 0 0
SMPD3 -0.046 0.13 -10000 0 -0.26 107 107
TNF -0.15 0.26 -10000 0 -0.54 156 156
PKC zeta/PAR4 -0.053 0.14 -10000 0 -0.4 67 67
mol:PHOSPHOCHOLINE 0.007 0.077 0.21 48 -10000 0 48
NF kappa B1/RelA/I kappa B alpha -0.035 0.095 -10000 0 -0.53 4 4
AIFM1 0.008 0.038 0.19 4 -10000 0 4
BCL2 0.005 0.075 -10000 0 -0.59 8 8
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.017 0.068 -10000 0 -0.36 3 3
epithelial cell differentiation -0.042 0.085 -10000 0 -0.47 7 7
ITCH 0.019 0.013 -10000 0 -10000 0 0
WWP1 0.024 0.05 -10000 0 -10000 0 0
FYN 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.21 -10000 0 -0.55 89 89
PRL 0 0.031 -10000 0 -0.49 2 2
neuron projection morphogenesis -0.031 0.15 -10000 0 -0.46 12 12
PTPRZ1 0.004 0.077 -10000 0 -0.57 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.089 0.13 -10000 0 -0.47 17 17
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.078 0.17 -10000 0 -0.34 117 117
ADAM17 0.011 0.066 -10000 0 -0.58 6 6
ErbB4/ErbB4 0.02 0.064 -10000 0 -0.41 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.004 0.12 -10000 0 -0.38 39 39
NCOR1 0.012 0.038 -10000 0 -0.59 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.065 0.16 -10000 0 -0.39 27 27
GRIN2B -0.15 0.21 -10000 0 -0.5 84 84
ErbB4/ErbB2/betacellulin -0.031 0.14 -10000 0 -0.42 21 21
STAT1 -0.002 0.088 -10000 0 -0.49 16 16
HBEGF 0.004 0.07 -10000 0 -0.49 10 10
PRLR -0.02 0.14 -10000 0 -0.56 31 31
E4ICDs/ETO2 0.017 0.07 -10000 0 -0.37 8 8
axon guidance -0.016 0.078 -10000 0 -0.36 2 2
NEDD4 0.007 0.08 -10000 0 -0.52 11 11
Prolactin receptor/Prolactin receptor/Prolactin -0.026 0.099 -10000 0 -0.4 33 33
CBFA2T3 0.006 0.07 -10000 0 -0.59 7 7
ErbB4/ErbB2/HBEGF 0.022 0.075 -10000 0 -0.36 8 8
MAPK3 -0.041 0.15 -10000 0 -0.48 12 12
STAT1 (dimer) 0.013 0.075 -10000 0 -0.39 4 4
MAPK1 -0.041 0.15 -10000 0 -0.48 12 12
JAK2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.07 0.16 -10000 0 -0.4 32 32
NRG1 -0.11 0.21 -10000 0 -0.41 166 166
NRG3 -0.031 0.16 -10000 0 -0.59 38 38
NRG2 0.012 0.038 -10000 0 -0.59 2 2
NRG4 -0.042 0.16 -10000 0 -0.51 54 54
heart development -0.016 0.078 -10000 0 -0.36 2 2
neural crest cell migration -0.069 0.16 -10000 0 -0.4 32 32
ERBB2 0.016 0.069 -10000 0 -0.38 15 15
WWOX/E4ICDs 0.022 0.054 -10000 0 -0.36 1 1
SHC1 0.009 0.05 -10000 0 -0.49 5 5
ErbB4/EGFR/neuregulin 4 -0.055 0.16 -10000 0 -0.47 35 35
apoptosis 0.041 0.11 0.41 39 -10000 0 39
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.021 0.061 -10000 0 -0.44 3 3
ErbB4/ErbB2/epiregulin 0.005 0.086 -10000 0 -0.39 10 10
ErbB4/ErbB4/betacellulin/betacellulin -0.041 0.14 -10000 0 -0.36 63 63
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.029 0.076 -10000 0 -0.47 4 4
MDM2 0.026 0.058 -10000 0 -0.36 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.096 0.14 -10000 0 -0.37 27 27
STAT5A -0.013 0.091 -10000 0 -0.41 9 9
ErbB4/EGFR/neuregulin 1 beta -0.12 0.2 -10000 0 -0.5 61 61
DLG4 0.004 0.07 -10000 0 -0.49 10 10
GRB2/SHC -0.004 0.037 -10000 0 -0.34 6 6
E4ICDs/TAB2/NCoR1 -0.014 0.049 -10000 0 -0.55 2 2
STAT5A (dimer) -0.044 0.091 -10000 0 -0.51 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.073 -10000 0 -0.35 1 1
LRIG1 -0.002 0.099 -10000 0 -0.59 14 14
EREG -0.013 0.11 -10000 0 -0.49 24 24
BTC -0.086 0.22 -10000 0 -0.56 88 88
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.016 0.079 -10000 0 -0.36 2 2
ERBB4 0.02 0.064 -10000 0 -0.41 1 1
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 -0.036 0.13 -10000 0 -0.59 27 27
GRB2 0.013 0.022 -10000 0 -0.49 1 1
ErbB4/ErbB2/neuregulin 4 -0.004 0.11 -10000 0 -0.4 16 16
glial cell differentiation 0.014 0.048 0.54 2 -10000 0 2
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.1 0.19 -10000 0 -0.52 45 45
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.057 0.19 -10000 0 -0.57 62 62
HRAS 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.21 -10000 0 -0.55 89 89
AKT 0.02 0.045 -10000 0 -0.38 4 4
FOXO3 0.014 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
FOXO1 0.011 0.044 -10000 0 -0.56 3 3
AKT3 0.008 0.06 -10000 0 -0.59 5 5
FOXO4 0.013 0.027 -10000 0 -0.59 1 1
MET -0.15 0.25 -10000 0 -0.53 150 150
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
PIK3CB 0.014 0 -10000 0 -10000 0 0
NRAS 0.014 0 -10000 0 -10000 0 0
PIK3CG -0.059 0.19 -10000 0 -0.53 69 69
PIK3R3 0.011 0.041 -10000 0 -0.52 3 3
PIK3R2 0.014 0 -10000 0 -10000 0 0
NF1 0.012 0.038 -10000 0 -0.59 2 2
RAS -0.054 0.11 0.22 1 -0.3 49 50
ERBB2 0.005 0.068 -10000 0 -0.5 9 9
proliferation/survival/translation -0.008 0.051 0.2 12 -10000 0 12
PI3K -0.046 0.11 -10000 0 -0.26 69 69
PIK3R1 0.014 0 -10000 0 -10000 0 0
KRAS 0.013 0.022 -10000 0 -0.49 1 1
FOXO 0.028 0.03 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
PTEN 0.013 0.027 -10000 0 -0.59 1 1
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.005 0.092 -9999 0 -0.37 29 29
PDGFRB 0.01 0.039 -9999 0 -0.5 3 3
SPHK1 -0.042 0.14 -9999 0 -0.75 18 18
mol:S1P -0.041 0.12 -9999 0 -0.61 21 21
S1P1/S1P/Gi -0.021 0.15 -9999 0 -0.35 65 65
GNAO1 0.006 0.06 -9999 0 -0.6 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.01 0.14 -9999 0 -0.53 11 11
PLCG1 -0.014 0.15 -9999 0 -0.54 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.039 -9999 0 -0.5 3 3
GNAI2 0.012 0.006 -9999 0 -10000 0 0
GNAI3 0.012 0.006 -9999 0 -10000 0 0
GNAI1 -0.007 0.11 -9999 0 -0.59 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.003 0.079 -9999 0 -0.31 29 29
S1P1/S1P -0.051 0.11 -9999 0 -0.45 28 28
negative regulation of cAMP metabolic process -0.02 0.15 -9999 0 -0.34 65 65
MAPK3 -0.039 0.21 -9999 0 -0.53 61 61
calcium-dependent phospholipase C activity -0.001 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.004 0.071 -9999 0 -0.53 9 9
PLCB2 -0.017 0.13 -9999 0 -0.46 25 25
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.042 0.094 -9999 0 -0.41 22 22
receptor internalization -0.048 0.1 -9999 0 -0.41 29 29
PTGS2 -0.1 0.36 -9999 0 -1 62 62
Rac1/GTP -0.042 0.094 -9999 0 -0.41 22 22
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA -0.009 0.1 -9999 0 -0.49 22 22
negative regulation of T cell proliferation -0.02 0.15 -9999 0 -0.34 65 65
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.012 0.006 -9999 0 -10000 0 0
MAPK1 -0.039 0.21 -9999 0 -0.53 61 61
S1P1/S1P/PDGFB-D/PDGFRB -0.011 0.13 -9999 0 -0.42 28 28
ABCC1 0.01 0.045 -9999 0 -0.49 4 4
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.066 0.14 -10000 0 -0.35 98 98
cell-cell adhesion 0.035 0.099 0.47 14 -10000 0 14
Ephrin B/EPHB2/RasGAP -0.022 0.081 -10000 0 -0.36 18 18
ITSN1 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
SHC1 0.009 0.05 -10000 0 -0.49 5 5
Ephrin B1/EPHB3 -0.003 0.028 -10000 0 -0.29 5 5
Ephrin B1/EPHB1 -0.031 0.1 -10000 0 -0.37 43 43
HRAS/GDP -0.031 0.094 -10000 0 -0.47 12 12
Ephrin B/EPHB1/GRB7 -0.058 0.14 -10000 0 -0.4 50 50
Endophilin/SYNJ1 0.016 0.089 -10000 0 -0.34 19 19
KRAS 0.013 0.022 -10000 0 -0.49 1 1
Ephrin B/EPHB1/Src -0.039 0.11 -10000 0 -0.35 50 50
endothelial cell migration -0.006 0.039 -10000 0 -0.29 4 4
GRB2 0.013 0.022 -10000 0 -0.49 1 1
GRB7 -0.031 0.14 -10000 0 -0.49 42 42
PAK1 -0.008 0.13 -10000 0 -0.47 20 20
HRAS 0.014 0 -10000 0 -10000 0 0
RRAS 0.016 0.09 -10000 0 -0.35 19 19
DNM1 -0.1 0.22 -10000 0 -0.52 109 109
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.001 0.12 -10000 0 -0.33 50 50
lamellipodium assembly -0.035 0.099 -10000 0 -0.47 14 14
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.11 -10000 0 -0.48 13 13
PIK3R1 0.014 0 -10000 0 -10000 0 0
EPHB2 0 0.087 -10000 0 -0.52 14 14
EPHB3 0.012 0.031 -10000 0 -0.49 2 2
EPHB1 -0.034 0.16 -10000 0 -0.59 41 41
EPHB4 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.091 -10000 0 -0.39 20 20
Ephrin B/EPHB2 -0.023 0.083 -10000 0 -0.37 18 18
Ephrin B/EPHB3 -0.017 0.068 -10000 0 -0.33 14 14
JNK cascade 0.006 0.11 -10000 0 -0.32 44 44
Ephrin B/EPHB1 -0.04 0.12 -10000 0 -0.36 50 50
RAP1/GDP -0.026 0.078 -10000 0 -0.4 11 11
EFNB2 0.002 0.08 -10000 0 -0.52 12 12
EFNB3 -0.004 0.1 -10000 0 -0.56 16 16
EFNB1 0.011 0.038 -10000 0 -0.49 3 3
Ephrin B2/EPHB1-2 -0.04 0.12 -10000 0 -0.34 60 60
RAP1B 0.013 0.022 -10000 0 -0.49 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.037 0.11 -10000 0 -0.51 14 14
Rap1/GTP -0.035 0.099 -10000 0 -0.48 14 14
axon guidance -0.066 0.14 -10000 0 -0.34 98 98
MAPK3 0.023 0.1 -10000 0 -0.43 13 13
MAPK1 0.023 0.1 -10000 0 -0.43 13 13
Rac1/GDP 0.02 0.099 -10000 0 -0.39 15 15
actin cytoskeleton reorganization -0.027 0.076 -10000 0 -0.37 13 13
CDC42/GDP 0.02 0.099 -10000 0 -0.39 15 15
PI3K -0.006 0.039 -10000 0 -0.3 4 4
EFNA5 -0.084 0.21 -10000 0 -0.54 90 90
Ephrin B2/EPHB4 -0.007 0.047 -10000 0 -0.31 12 12
Ephrin B/EPHB2/Intersectin/N-WASP 0.022 0.07 -10000 0 -0.29 18 18
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.034 0.096 -10000 0 -0.46 14 14
PTK2 0.009 0.026 -10000 0 -10000 0 0
MAP4K4 0.006 0.11 -10000 0 -0.32 44 44
SRC 0.014 0 -10000 0 -10000 0 0
KALRN -0.003 0.093 -10000 0 -0.5 17 17
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.018 0.12 -10000 0 -0.38 15 15
MAP2K1 0.015 0.11 -10000 0 -0.46 13 13
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.035 0.1 -10000 0 -0.35 44 44
cell migration 0.018 0.12 -10000 0 -0.48 13 13
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 0.016 0.09 -10000 0 -0.35 19 19
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.012 0.14 -10000 0 -0.54 15 15
HRAS/GTP -0.038 0.11 -10000 0 -0.51 14 14
Ephrin B1/EPHB1-2 -0.035 0.11 -10000 0 -0.34 53 53
cell adhesion mediated by integrin 0.011 0.068 0.28 25 -10000 0 25
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.041 0.12 -10000 0 -0.55 14 14
RAC1-CDC42/GTP -0.035 0.1 -10000 0 -0.48 15 15
RASA1 0.014 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.077 -10000 0 -0.4 11 11
ruffle organization 0.023 0.12 -10000 0 -0.48 14 14
NCK1 0.013 0.027 -10000 0 -0.59 1 1
receptor internalization -0.032 0.14 -10000 0 -0.58 11 11
Ephrin B/EPHB2/KALRN -0.03 0.09 -10000 0 -0.36 21 21
ROCK1 0.025 0.027 -10000 0 -0.25 5 5
RAS family/GDP -0.025 0.072 -10000 0 -0.42 7 7
Rac1/GTP -0.037 0.1 -10000 0 -0.51 14 14
Ephrin B/EPHB1/Src/Paxillin 0.005 0.11 -10000 0 -0.47 11 11
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.014 0 -9999 0 -10000 0 0
SPHK1 -0.029 0.15 -9999 0 -0.54 40 40
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P 0.005 0.07 -9999 0 -0.3 20 20
GNAO1 0.008 0.06 -9999 0 -0.59 5 5
mol:Sphinganine-1-P -0.007 0.11 -9999 0 -0.38 40 40
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.024 0.071 -9999 0 -0.5 4 4
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.019 -9999 0 -0.43 1 1
S1PR3 -0.034 0.15 -9999 0 -0.52 47 47
S1PR2 0.007 0.062 -9999 0 -0.56 6 6
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.015 0.055 -9999 0 -0.26 20 20
S1PR5 -0.13 0.25 -9999 0 -0.55 132 132
S1PR4 0 0.086 -9999 0 -0.51 14 14
GNAI1 -0.005 0.1 -9999 0 -0.59 16 16
S1P/S1P5/G12 -0.062 0.15 -9999 0 -0.34 83 83
S1P/S1P3/Gq -0.009 0.12 -9999 0 -0.48 15 15
S1P/S1P4/Gi 0.024 0.07 -9999 0 -0.37 6 6
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.014 0 -9999 0 -10000 0 0
GNA14 -0.014 0.12 -9999 0 -0.56 25 25
GNA15 -0.007 0.11 -9999 0 -0.56 19 19
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.004 0.08 -9999 0 -0.59 9 9
ABCC1 0.01 0.044 -9999 0 -0.49 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0.022 -10000 0 -0.49 1 1
NFATC1 0.029 0.095 -10000 0 -0.44 2 2
NFATC2 0.008 0.078 -10000 0 -0.27 17 17
NFATC3 0.007 0.082 -10000 0 -0.4 17 17
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.063 0.18 -10000 0 -0.52 42 42
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.15 0.19 -10000 0 -0.48 90 90
BCL2/BAX -0.007 0.053 -10000 0 -0.43 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.026 -10000 0 -0.4 2 2
CaM/Ca2+ 0.01 0.026 -10000 0 -0.4 2 2
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.003 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.054 0.17 -10000 0 -0.49 43 43
Calcineurin A alpha-beta B1/BCL2 0.005 0.075 -10000 0 -0.59 8 8
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.053 0.17 0.48 43 -10000 0 43
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.012 0.031 -10000 0 -0.49 2 2
XPO1 0.014 0 -10000 0 -10000 0 0
SFN -0.11 0.23 -10000 0 -0.53 117 117
MAP3K8 -0.007 0.1 -10000 0 -0.51 20 20
NFAT4/CK1 alpha -0.014 0.057 -10000 0 -0.4 3 3
MEF2D/NFAT1/Cbp/p300 0.025 0.11 -10000 0 -0.43 13 13
CABIN1 -0.064 0.18 -10000 0 -0.52 42 42
CALM1 0.012 0.035 -10000 0 -0.54 2 2
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.007 0.059 -10000 0 -0.49 7 7
CAMK4 -0.17 0.27 -10000 0 -0.56 167 167
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.014 0 -10000 0 -10000 0 0
YWHAH -0.009 0.11 -10000 0 -0.49 24 24
Calcineurin A alpha-beta B1/AKAP79/PKA -0.012 0.1 -10000 0 -0.35 45 45
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.095 -10000 0 -0.59 13 13
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.001 0.079 -10000 0 -0.49 13 13
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.037 0.1 -10000 0 -0.43 5 5
PRKCH 0.014 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.003 0.038 -10000 0 -0.43 4 4
CASP3 0.013 0.022 -10000 0 -0.49 1 1
PIM1 0.008 0.054 -10000 0 -0.49 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.003 -10000 0 -10000 0 0
apoptosis -0.002 0.021 -10000 0 -0.34 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.076 -10000 0 -0.31 4 4
PRKCB -0.061 0.19 -10000 0 -0.52 72 72
PRKCE 0.003 0.077 -10000 0 -0.52 11 11
JNK2/NFAT4 0.014 0.074 -10000 0 -0.36 17 17
BAD/BCL-XL -0.001 0.015 -10000 0 -0.34 1 1
PRKCD -0.018 0.14 -10000 0 -0.59 27 27
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ -0.015 0.12 -10000 0 -0.55 26 26
PRKCA 0.013 0.027 -10000 0 -0.59 1 1
PRKCG -0.19 0.27 -10000 0 -0.54 190 190
PRKCQ -0.005 0.11 -10000 0 -0.58 17 17
FKBP38/BCL2 -0.007 0.053 -10000 0 -0.43 8 8
EP300 0.01 0.053 -10000 0 -0.59 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.026 0.1 -10000 0 -0.45 3 3
CaM/Ca2+/FKBP38 0.018 0.023 -10000 0 -0.33 2 2
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.02 0.023 -10000 0 -0.33 2 2
CaM/Ca2+/CAMK IV -0.1 0.17 -10000 0 -0.35 168 168
NFATc/ERK1 0.036 0.091 -10000 0 -0.49 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.15 0.19 -10000 0 -0.48 90 90
NR4A1 0.017 0.14 -10000 0 -0.47 35 35
GSK3B 0.013 0.027 -10000 0 -0.59 1 1
positive T cell selection 0.007 0.081 -10000 0 -0.4 17 17
NFAT1/CK1 alpha -0.02 0.05 -10000 0 -0.36 4 4
RCH1/ KPNB1 -0.001 0.021 -10000 0 -0.34 2 2
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0.003 -10000 0 -10000 0 0
AKAP5 -0.031 0.14 -10000 0 -0.5 45 45
MEF2D 0.012 0.032 -10000 0 -0.5 2 2
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.034 0.091 -10000 0 -0.49 1 1
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0.005 0.075 -10000 0 -0.59 8 8
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.001 0.095 -9999 0 -0.59 13 13
Caspase 8 (4 units) -0.011 0.082 -9999 0 -0.36 15 15
NEF -0.004 0.031 -9999 0 -10000 0 0
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 0 0.16 -9999 0 -0.54 43 43
CYCS 0.023 0.084 -9999 0 -0.32 12 12
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.024 0.15 -9999 0 -0.6 31 31
MAP2K7 0.017 0.075 -9999 0 -0.31 4 4
protein ubiquitination 0.017 0.093 -9999 0 -0.4 7 7
CRADD 0.014 0 -9999 0 -10000 0 0
DAXX 0.014 0 -9999 0 -10000 0 0
FAS -0.005 0.1 -9999 0 -0.54 18 18
BID 0.016 0.088 -9999 0 -0.33 15 15
NF-kappa-B/RelA/I kappa B alpha -0.021 0.071 -9999 0 -10000 0 0
TRADD 0.013 0.027 -9999 0 -0.59 1 1
MAP3K5 0.006 0.07 -9999 0 -0.59 7 7
CFLAR 0.013 0.022 -9999 0 -0.49 1 1
FADD 0.014 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.072 -9999 0 -10000 0 0
MAPK8 0.017 0.085 -9999 0 -0.41 2 2
APAF1 0.014 0 -9999 0 -10000 0 0
TRAF1 0.004 0.078 -9999 0 -0.58 9 9
TRAF2 0.014 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.091 -9999 0 -0.32 20 20
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.11 -9999 0 -0.53 8 8
CHUK 0.016 0.099 -9999 0 -0.44 7 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.02 0.072 -9999 0 -0.31 19 19
TCRz/NEF -0.038 0.13 -9999 0 -0.42 47 47
TNF -0.15 0.26 -9999 0 -0.54 156 156
FASLG -0.027 0.17 -9999 0 -0.56 42 42
NFKB1 0.009 0.029 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.11 0.17 -9999 0 -0.34 171 171
CASP6 -0.019 0.067 -9999 0 -0.58 3 3
CASP7 0.031 0.16 -9999 0 -0.51 33 33
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 0.031 0.16 -9999 0 -0.51 33 33
TNFRSF1A 0.001 0.086 -9999 0 -0.55 12 12
TNFR1A/BAG4 -0.02 0.093 -9999 0 -0.44 23 23
CASP8 -0.002 0.089 -9999 0 -0.5 16 16
CASP9 0.013 0.022 -9999 0 -0.49 1 1
MAP3K14 0.008 0.11 -9999 0 -0.48 8 8
APAF-1/Caspase 9 -0.038 0.11 -9999 0 -0.4 35 35
BCL2 0.02 0.088 -9999 0 -0.48 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.019 0.066 -10000 0 -0.35 3 3
adherens junction organization -0.03 0.12 -10000 0 -0.35 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.12 -10000 0 -0.36 17 17
FMN1 -0.061 0.15 -10000 0 -0.36 59 59
mol:IP3 0.01 0.067 -10000 0 -0.4 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.016 0.11 -10000 0 -0.27 66 66
CTNNB1 0.016 0.004 -10000 0 -10000 0 0
AKT1 0.012 0.076 -10000 0 -0.38 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.031 0.15 -10000 0 -0.41 61 61
CTNND1 0.014 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.007 0.1 -10000 0 -0.5 3 3
VASP -0.008 0.1 -10000 0 -0.52 3 3
ZYX -0.011 0.11 -10000 0 -0.5 4 4
JUB -0.021 0.12 -10000 0 -0.36 23 23
EGFR(dimer) -0.056 0.15 -10000 0 -0.43 26 26
E-cadherin/beta catenin-gamma catenin -0.083 0.14 -10000 0 -0.32 134 134
mol:PI-3-4-5-P3 -0.03 0.061 -10000 0 -0.37 4 4
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
PI3K -0.031 0.062 -10000 0 -0.38 4 4
FYN 0.02 0.066 -10000 0 -0.32 2 2
mol:Ca2+ 0.01 0.066 -10000 0 -0.32 4 4
JUP 0.005 0.081 -10000 0 -0.57 10 10
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG 0.01 0.067 -10000 0 -0.4 2 2
CDH1 -0.12 0.24 -10000 0 -0.54 127 127
RhoA/GDP -0.02 0.12 -10000 0 -0.36 17 17
establishment of polarity of embryonic epithelium -0.007 0.1 -10000 0 -0.5 3 3
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
EGFR -0.083 0.21 -10000 0 -0.55 89 89
CASR 0.008 0.074 -10000 0 -0.31 5 5
RhoA/GTP -0.02 0.042 -10000 0 -0.35 2 2
AKT2 0.012 0.076 -10000 0 -0.38 3 3
actin cable formation -0.052 0.15 -10000 0 -0.48 25 25
apoptosis 0.026 0.054 0.34 4 -10000 0 4
CTNNA1 0.014 0.002 -10000 0 -10000 0 0
mol:GDP -0.03 0.12 -10000 0 -0.4 17 17
PIP5K1A -0.007 0.1 -10000 0 -0.52 3 3
PLCG1 0.01 0.068 -10000 0 -0.4 2 2
Rac1/GTP -0.077 0.12 -10000 0 -0.39 26 26
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.011 0.12 -10000 0 -0.42 19 19
CRKL 0.02 0.11 -10000 0 -0.42 20 20
HRAS 0.002 0.14 -10000 0 -0.48 14 14
mol:PIP3 0.003 0.1 -10000 0 -0.39 21 21
SPRED1 0.014 0 -10000 0 -10000 0 0
SPRED2 0.011 0.038 -10000 0 -0.49 3 3
GAB1 0.012 0.12 -10000 0 -0.45 20 20
FOXO3 0.025 0.1 -10000 0 -0.38 18 18
AKT1 0.017 0.11 -10000 0 -0.4 20 20
BAD 0.025 0.1 -10000 0 -0.37 19 19
megakaryocyte differentiation 0.006 0.12 -10000 0 -0.39 32 32
GSK3B 0.024 0.1 -10000 0 -0.39 18 18
RAF1 0.014 0.12 -10000 0 -0.38 13 13
SHC1 0.009 0.05 -10000 0 -0.49 5 5
STAT3 0.014 0.11 -10000 0 -0.44 20 20
STAT1 0.004 0.24 -10000 0 -1 22 22
HRAS/SPRED1 0.011 0.12 -10000 0 -0.38 13 13
cell proliferation 0.006 0.13 -10000 0 -0.46 24 24
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
TEC -0.004 0.1 -10000 0 -0.54 17 17
RPS6KB1 0.013 0.11 -10000 0 -0.43 20 20
HRAS/SPRED2 0.01 0.12 -10000 0 -0.38 15 15
LYN/TEC/p62DOK -0.038 0.12 -10000 0 -0.45 28 28
MAPK3 0.025 0.089 -10000 0 -0.27 10 10
STAP1 -0.004 0.13 -10000 0 -0.47 25 25
GRAP2 -0.047 0.17 -10000 0 -0.53 57 57
JAK2 -0.05 0.18 -10000 0 -0.8 22 22
STAT1 (dimer) 0.005 0.23 -10000 0 -0.89 27 27
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.057 0.13 -10000 0 -0.46 31 31
actin filament polymerization 0.007 0.12 -10000 0 -0.44 20 20
LYN 0.004 0.073 -10000 0 -0.51 10 10
STAP1/STAT5A (dimer) -0.004 0.18 -10000 0 -0.6 30 30
PIK3R1 0.014 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.029 0.1 -10000 0 -0.38 18 18
PI3K 0.022 0.11 -10000 0 -0.42 19 19
PTEN 0.013 0.027 -10000 0 -0.59 1 1
SCF/KIT/EPO/EPOR -0.004 0.28 -10000 0 -1.3 20 20
MAPK8 0.006 0.13 -10000 0 -0.47 24 24
STAT3 (dimer) 0.014 0.11 -10000 0 -0.43 20 20
positive regulation of transcription 0.026 0.077 0.18 2 -0.24 5 7
mol:GDP -0.062 0.12 0.22 2 -0.47 22 24
PIK3C2B 0.009 0.12 -10000 0 -0.42 23 23
CBL/CRKL 0.027 0.11 -10000 0 -0.4 18 18
FER 0 0.14 -10000 0 -0.51 24 24
SH2B3 0.013 0.12 -10000 0 -0.44 20 20
PDPK1 0.01 0.1 -10000 0 -0.38 20 20
SNAI2 -0.007 0.14 -10000 0 -0.46 27 27
positive regulation of cell proliferation 0.01 0.18 -10000 0 -0.72 24 24
KITLG 0.004 0.093 -10000 0 -0.59 12 12
cell motility 0.01 0.18 -10000 0 -0.72 24 24
PTPN6 -0.012 0.097 -10000 0 -0.55 16 16
EPOR 0.038 0.078 -10000 0 -10000 0 0
STAT5A (dimer) 0.007 0.16 -10000 0 -0.62 25 25
SOCS1 -0.032 0.15 -10000 0 -0.51 45 45
cell migration 0.04 0.16 0.46 34 -10000 0 34
SOS1 0.014 0 -10000 0 -10000 0 0
EPO -0.006 0.099 -10000 0 -0.5 20 20
VAV1 -0.019 0.14 -10000 0 -0.56 30 30
GRB10 0.012 0.12 -10000 0 -0.44 20 20
PTPN11 0.013 0.005 -10000 0 -10000 0 0
SCF/KIT 0.006 0.12 -10000 0 -0.4 29 29
GO:0007205 -0.002 0.006 -10000 0 -10000 0 0
MAP2K1 0.022 0.097 -10000 0 -0.29 13 13
CBL 0.014 0 -10000 0 -10000 0 0
KIT -0.01 0.27 -10000 0 -1.3 20 20
MAP2K2 0.022 0.097 -10000 0 -0.29 13 13
SHC/Grb2/SOS1 -0.028 0.092 -10000 0 -0.41 19 19
STAT5A 0.007 0.17 -10000 0 -0.64 25 25
GRB2 0.013 0.022 -10000 0 -0.49 1 1
response to radiation -0.006 0.13 -10000 0 -0.45 27 27
SHC/GRAP2 -0.045 0.13 -10000 0 -0.39 60 60
PTPRO 0.005 0.13 -10000 0 -0.4 32 32
SH2B2 0.007 0.12 -10000 0 -0.45 20 20
DOK1 0.012 0.035 -10000 0 -0.54 2 2
MATK -0.041 0.16 -10000 0 -0.47 34 34
CREBBP 0.039 0.012 -10000 0 -10000 0 0
BCL2 0.022 0.18 -10000 0 -1.3 8 8
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.006 0.095 -9999 0 -0.33 29 29
BIRC5 -0.14 0.25 -9999 0 -0.55 137 137
NFKBIA 0.029 0.049 -9999 0 -0.28 2 2
CPEB1 -0.002 0.099 -9999 0 -0.59 14 14
AKT1 0.029 0.049 -9999 0 -0.28 2 2
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.002 0.052 -9999 0 -0.32 6 6
NDEL1/TACC3 -0.012 0.092 -9999 0 -0.37 20 20
GADD45A -0.017 0.12 -9999 0 -0.49 32 32
GSK3B 0.017 0.03 -9999 0 -0.6 1 1
PAK1/Aurora A -0.006 0.1 -9999 0 -0.3 37 37
MDM2 0.012 0.031 -9999 0 -0.49 2 2
JUB -0.013 0.12 -9999 0 -0.57 24 24
TPX2 -0.038 0.15 -9999 0 -0.38 81 81
TP53 0.021 0.063 -9999 0 -0.3 11 11
DLG7 0.018 0.049 -9999 0 -0.29 2 2
AURKAIP1 0.013 0.022 -9999 0 -0.49 1 1
ARHGEF7 0.014 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.01 0.1 -9999 0 -0.39 20 20
G2/M transition of mitotic cell cycle 0.002 0.052 -9999 0 -0.32 6 6
AURKA 0.023 0.061 -9999 0 -0.34 2 2
AURKB -0.083 0.13 -9999 0 -0.3 120 120
CDC25B 0.024 0.048 -9999 0 -0.27 2 2
G2/M transition checkpoint -0.011 0.074 -9999 0 -0.29 23 23
mRNA polyadenylation -0.005 0.073 -9999 0 -0.36 15 15
Aurora A/CPEB -0.005 0.074 -9999 0 -0.36 15 15
Aurora A/TACC1/TRAP/chTOG 0.011 0.047 -9999 0 -10000 0 0
BRCA1 0.01 0.044 -9999 0 -0.49 4 4
centrosome duplication -0.005 0.1 -9999 0 -0.3 37 37
regulation of centrosome cycle -0.023 0.084 -9999 0 -0.36 20 20
spindle assembly 0.005 0.043 -9999 0 -10000 0 0
TDRD7 0.012 0.038 -9999 0 -0.59 2 2
Aurora A/RasGAP/Survivin -0.071 0.12 -9999 0 -0.32 64 64
CENPA -0.057 0.13 -9999 0 -0.32 77 77
Aurora A/PP2A 0.025 0.047 -9999 0 -0.28 2 2
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.032 0.046 -9999 0 -0.26 2 2
negative regulation of DNA binding 0.021 0.062 -9999 0 -0.3 11 11
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.011 0.074 -9999 0 -0.29 23 23
mitotic prometaphase 0.022 0.037 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.061 -9999 0 -0.34 2 2
TACC1 0.014 0 -9999 0 -10000 0 0
TACC3 -0.026 0.14 -9999 0 -0.5 40 40
Aurora A/Antizyme1 0.032 0.044 -9999 0 -10000 0 0
Aurora A/RasGAP 0.025 0.047 -9999 0 -0.28 2 2
OAZ1 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.018 0.014 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.028 0.085 -9999 0 -0.36 6 6
Importin alpha/Importin beta/TPX2 -0.038 0.15 -9999 0 -0.38 81 81
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.015 0.13 -9999 0 -0.36 43 43
PAK1 -0.035 0.15 -9999 0 -0.5 49 49
CKAP5 0.014 0 -9999 0 -10000 0 0
TRAIL signaling pathway

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.014 0.12 -10000 0 -0.54 26 26
positive regulation of NF-kappaB transcription factor activity -0.03 0.1 -10000 0 -0.37 41 41
MAP2K4 0.029 0.064 -10000 0 -0.35 3 3
IKBKB 0.014 0 -10000 0 -10000 0 0
TNFRSF10B 0.01 0.051 -10000 0 -0.57 4 4
TNFRSF10A -0.026 0.15 -10000 0 -0.56 36 36
SMPD1 0.01 0.048 -10000 0 -0.23 14 14
IKBKG 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.001 0.087 -10000 0 -0.5 15 15
TRAIL/TRAILR2 -0.022 0.094 -10000 0 -0.4 29 29
TRAIL/TRAILR3 -0.042 0.13 -10000 0 -0.41 53 53
TRAIL/TRAILR1 -0.047 0.13 -10000 0 -0.41 59 59
TRAIL/TRAILR4 -0.03 0.1 -10000 0 -0.37 41 41
TRAIL/TRAILR1/DAP3/GTP -0.036 0.1 -10000 0 -0.31 59 59
IKK complex -0.01 0.03 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.004 0.089 -10000 0 -0.38 26 26
MAP3K1 0.023 0.064 -10000 0 -0.34 2 2
TRAILR4 (trimer) -0.001 0.087 -10000 0 -0.5 15 15
TRADD 0.013 0.027 -10000 0 -0.59 1 1
TRAILR1 (trimer) -0.026 0.15 -10000 0 -0.56 36 36
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.082 -10000 0 -0.28 3 3
CFLAR 0.013 0.022 -10000 0 -0.49 1 1
MAPK1 0.004 0.089 -10000 0 -0.38 26 26
TRAIL/TRAILR1/FADD/TRADD/RIP -0.032 0.091 -10000 0 -0.3 40 40
mol:ceramide 0.01 0.048 -10000 0 -0.23 14 14
FADD 0.014 0 -10000 0 -10000 0 0
MAPK8 0.029 0.082 -10000 0 -0.36 8 8
TRAF2 0.014 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.02 0.13 -10000 0 -0.53 32 32
CHUK 0.014 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.039 0.11 -10000 0 -0.34 59 59
DAP3 0.014 0 -10000 0 -10000 0 0
CASP10 -0.022 0.087 0.27 1 -0.38 15 16
JNK cascade -0.03 0.1 -10000 0 -0.37 41 41
TRAIL (trimer) -0.014 0.12 -10000 0 -0.54 26 26
TNFRSF10C -0.02 0.13 -10000 0 -0.53 32 32
TRAIL/TRAILR1/DAP3/GTP/FADD -0.033 0.092 -10000 0 -0.31 39 39
TRAIL/TRAILR2/FADD -0.019 0.078 -10000 0 -0.33 29 29
cell death 0.01 0.048 -10000 0 -0.22 14 14
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.027 0.059 -10000 0 -0.52 1 1
TRAILR2 (trimer) 0.01 0.051 -10000 0 -0.56 4 4
CASP8 -0.003 0.05 -10000 0 -0.8 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.016 0.065 -10000 0 -0.31 15 15
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.007 0.091 -9999 0 -0.32 37 37
SNTA1 -0.027 0.15 -9999 0 -0.57 36 36
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.006 0.094 -9999 0 -0.32 39 39
MAPK12 0.026 0.044 -9999 0 -0.33 6 6
CCND1 0.007 0.072 -9999 0 -0.41 12 12
p38 gamma/SNTA1 0.01 0.09 -9999 0 -0.3 34 34
MAP2K3 0.011 0.038 -9999 0 -0.49 3 3
PKN1 0.014 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.026 0.044 -9999 0 -0.33 6 6
MAP2K6 0.022 0.032 -9999 0 -0.32 2 2
MAPT 0.011 0.085 -9999 0 -0.31 25 25
MAPK13 -0.005 0.11 -9999 0 -0.38 37 37
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0.031 -9999 0 -0.22 9 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.13 0.38 -9999 0 -1.1 59 59
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.067 0.18 -9999 0 -0.42 100 100
IFNAR2 0.013 0.006 -9999 0 -10000 0 0
AKT1 0.001 0.049 -9999 0 -0.22 15 15
ER alpha/Oestrogen -0.011 0.089 -9999 0 -0.39 26 26
NFX1/SIN3/HDAC complex 0.04 0.032 -9999 0 -10000 0 0
EGF -0.051 0.18 -9999 0 -0.56 58 58
SMG5 0.013 0.022 -9999 0 -0.49 1 1
SMG6 0.014 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.012 -9999 0 -10000 0 0
TERT/c-Abl -0.13 0.34 -9999 0 -1 58 58
SAP18 0.013 0.004 -9999 0 -10000 0 0
MRN complex -0.001 0.016 -9999 0 -0.36 1 1
WT1 -0.037 0.14 -9999 0 -0.49 44 44
WRN 0.009 0.053 -9999 0 -0.59 4 4
SP1 0.013 0.009 -9999 0 -10000 0 0
SP3 0.012 0.006 -9999 0 -10000 0 0
TERF2IP 0.014 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.13 0.29 -9999 0 -0.9 58 58
Mad/Max 0.019 0.009 -9999 0 -10000 0 0
TERT -0.14 0.4 -9999 0 -1.2 59 59
CCND1 -0.12 0.36 -9999 0 -1 67 67
MAX 0.012 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.004 -9999 0 -10000 0 0
RBBP4 0.012 0.027 -9999 0 -0.6 1 1
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.014 0 -9999 0 -10000 0 0
SIN3A 0.013 0.004 -9999 0 -10000 0 0
Telomerase/911 0.032 0.039 -9999 0 -10000 0 0
CDKN1B 0.011 0.077 -9999 0 -0.54 2 2
RAD1 0.014 0 -9999 0 -10000 0 0
XRCC5 0.014 0 -9999 0 -10000 0 0
XRCC6 0.014 0 -9999 0 -10000 0 0
SAP30 0.012 0.027 -9999 0 -0.59 1 1
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.012 0.005 -9999 0 -10000 0 0
JUN 0.002 0.075 -9999 0 -0.5 11 11
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.007 -9999 0 -10000 0 0
FOS -0.096 0.22 -9999 0 -0.55 99 99
IFN-gamma/IRF1 -0.011 0.088 -9999 0 -0.35 30 30
PARP2 0.014 0 -9999 0 -10000 0 0
BLM -0.053 0.18 -9999 0 -0.53 63 63
Telomerase -0.037 0.1 -9999 0 -0.4 29 29
IRF1 -0.009 0.11 -9999 0 -0.48 27 27
ESR1 -0.015 0.12 -9999 0 -0.54 26 26
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0.022 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.033 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.045 0.034 -9999 0 -10000 0 0
HDAC1 0.008 0.053 -9999 0 -0.59 4 4
HDAC2 0.012 0.009 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.019 0.059 -9999 0 -0.42 9 9
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.012 0.006 -9999 0 -10000 0 0
MRE11A 0.014 0 -9999 0 -10000 0 0
HUS1 0.013 0.022 -9999 0 -0.49 1 1
RPS6KB1 0.014 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.33 -9999 0 -1 58 58
NR2F2 -0.009 0.12 -9999 0 -0.51 25 25
MAPK3 0.011 0.008 -9999 0 -10000 0 0
MAPK1 0.011 0.008 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.004 0.079 -9999 0 -0.59 9 9
NFKB1 0.014 0 -9999 0 -10000 0 0
HNRNPC 0.014 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.014 0 -9999 0 -10000 0 0
EGFR -0.084 0.21 -9999 0 -0.55 89 89
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.097 0.2 -9999 0 -0.43 132 132
MYC -0.016 0.13 -9999 0 -0.58 25 25
IL2 -0.003 0.014 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0.027 -9999 0 -0.59 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 0.004 0.079 -9999 0 -0.59 9 9
TRF2/BLM -0.043 0.12 -9999 0 -0.35 63 63
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.35 -9999 0 -1 58 58
SP1/HDAC2 0.019 0.017 -9999 0 -10000 0 0
PINX1 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.13 0.29 -9999 0 -0.9 58 58
Smad3/Myc 0.006 0.096 -9999 0 -0.37 29 29
911 complex -0.001 0.012 -9999 0 -0.28 1 1
IFNG 0.003 0.049 -9999 0 -0.49 5 5
Telomerase/PinX1 -0.13 0.29 -9999 0 -0.9 58 58
Telomerase/AKT1/mTOR/p70S6K 0.009 0.074 -9999 0 -10000 0 0
SIN3B 0.013 0.004 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.13 0.29 -9999 0 -0.91 58 58
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.001 0.012 -9999 0 -0.28 1 1
TRF2/WRN -0.003 0.035 -9999 0 -0.4 4 4
Telomerase/hnRNP C1/C2 -0.13 0.29 -9999 0 -0.9 58 58
E2F1 -0.016 0.12 -9999 0 -0.52 28 28
ZNFX1 0.013 0.004 -9999 0 -10000 0 0
PIF1 -0.051 0.18 -9999 0 -0.54 60 60
NCL 0.014 0 -9999 0 -10000 0 0
DKC1 0.014 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.06 -9999 0 -0.59 5 5
CDC42/GTP -0.012 0.049 -9999 0 -0.38 3 3
PLCG1 0.03 0.061 -9999 0 -0.4 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.001 0.019 -9999 0 -0.43 1 1
cell migration -0.011 0.048 -9999 0 -0.38 3 3
S1PR5 -0.13 0.25 -9999 0 -0.55 132 132
S1PR4 0 0.086 -9999 0 -0.51 14 14
MAPK3 0.03 0.061 -9999 0 -0.4 3 3
MAPK1 0.03 0.061 -9999 0 -0.4 3 3
S1P/S1P5/Gi -0.033 0.13 -9999 0 -0.28 79 79
GNAI1 -0.005 0.1 -9999 0 -0.59 16 16
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.086 0.15 -9999 0 -0.34 132 132
RHOA 0.026 0.048 -9999 0 -0.3 4 4
S1P/S1P4/Gi 0.023 0.064 -9999 0 -0.31 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.014 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.008 0.046 -9999 0 -0.32 4 4
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.025 0.099 -10000 0 -0.42 30 30
ATM 0.014 0 -10000 0 -10000 0 0
UBE2D3 0.014 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
ATR 0.014 0 -10000 0 -10000 0 0
UBE2L3 0.014 0 -10000 0 -10000 0 0
FANCD2 0.015 0.057 -10000 0 -0.34 6 6
protein ubiquitination -0.026 0.092 -10000 0 -0.58 5 5
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex -0.001 0.016 -10000 0 -0.36 1 1
MRE11A 0.014 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.014 0.055 -10000 0 -0.4 5 5
FANCF 0.014 0 -10000 0 -10000 0 0
BRCA1 0.01 0.044 -10000 0 -0.49 4 4
CCNE1 0.011 0.038 -10000 0 -0.49 3 3
CDK2/Cyclin E1 -0.011 0.067 -10000 0 -0.39 15 15
FANCG 0.013 0.022 -10000 0 -0.49 1 1
BRCA1/BACH1/BARD1 -0.027 0.1 -10000 0 -0.42 33 33
FANCE 0.014 0 -10000 0 -10000 0 0
FANCC 0.011 0.041 -10000 0 -0.52 3 3
NBN 0.014 0 -10000 0 -10000 0 0
FANCA -0.027 0.14 -10000 0 -0.51 40 40
DNA repair 0.017 0.15 -10000 0 -0.56 12 12
BRCA1/BARD1/ubiquitin -0.027 0.1 -10000 0 -0.42 33 33
BARD1/DNA-PK -0.018 0.073 -10000 0 -0.32 28 28
FANCL 0.014 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.025 0.099 0.42 30 -10000 0 30
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.075 -10000 0 -0.47 3 3
BRCA1/BACH1/BARD1/TopBP1 -0.023 0.091 -10000 0 -0.36 33 33
BRCA1/BARD1/P53 -0.029 0.096 -10000 0 -0.34 41 41
BARD1/CSTF1/BRCA1 -0.023 0.087 -10000 0 -0.35 33 33
BRCA1/BACH1 0.01 0.044 -10000 0 -0.49 4 4
BARD1 -0.021 0.14 -10000 0 -0.58 30 30
PCNA 0.012 0.031 -10000 0 -0.49 2 2
BRCA1/BARD1/UbcH5C -0.023 0.087 -10000 0 -0.35 33 33
BRCA1/BARD1/UbcH7 -0.023 0.087 -10000 0 -0.35 33 33
BRCA1/BARD1/RAD51/PCNA -0.052 0.12 -10000 0 -0.38 44 44
BARD1/DNA-PK/P53 -0.025 0.085 -10000 0 -0.6 2 2
BRCA1/BARD1/Ubiquitin -0.027 0.1 -10000 0 -0.42 33 33
BRCA1/BARD1/CTIP 0.012 0.093 -10000 0 -0.34 29 29
FA complex 0.028 0.057 -10000 0 -10000 0 0
BARD1/EWS -0.025 0.099 -10000 0 -0.42 30 30
RBBP8 0.023 0.028 -10000 0 -0.34 3 3
TP53 -0.003 0.1 -10000 0 -0.58 15 15
TOPBP1 0.013 0.027 -10000 0 -0.59 1 1
G1/S transition of mitotic cell cycle 0.029 0.095 0.33 41 -10000 0 41
BRCA1/BARD1 -0.026 0.094 -10000 0 -0.59 5 5
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.025 0.1 -10000 0 -0.43 30 30
CDK2 0 0.086 -10000 0 -0.53 13 13
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.049 0.17 -10000 0 -0.51 61 61
RAD50 0.013 0.027 -10000 0 -0.59 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.027 0.1 -10000 0 -0.42 33 33
EWSR1 0.014 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.034 0.093 0.18 3 -0.4 18 21
CaM/Ca2+ -0.002 0.025 -10000 0 -0.4 2 2
AKT1 0.014 0 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
STXBP4 0.013 0.027 -10000 0 -0.59 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.027 0.14 0.25 61 -0.46 16 77
YWHAZ 0.014 0 -10000 0 -10000 0 0
CALM1 0.012 0.035 -10000 0 -0.54 2 2
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.025 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH -0.009 0.11 -10000 0 -0.49 24 24
YWHAB 0.014 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.02 -10000 0 -0.32 2 2
YWHAG 0.001 0.079 -10000 0 -0.49 13 13
ASIP -0.097 0.22 -10000 0 -0.55 100 100
PRKCI 0.014 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ -0.002 0.025 -10000 0 -0.4 2 2
RHOQ 0.014 0 -10000 0 -10000 0 0
GYS1 0.034 0.014 -10000 0 -0.29 1 1
PRKCZ -0.015 0.12 -10000 0 -0.55 26 26
TRIP10 0.007 0.065 -10000 0 -0.55 7 7
TC10/GTP/CIP4/Exocyst -0.005 0.039 -10000 0 -0.33 7 7
AS160/14-3-3 0.003 0.087 -10000 0 -0.37 3 3
VAMP2 0.013 0.022 -10000 0 -0.49 1 1
SLC2A4 0.026 0.15 0.28 34 -0.51 16 50
STX4 0.014 0 -10000 0 -10000 0 0
GSK3B 0.028 0.016 -10000 0 -0.34 1 1
SFN -0.11 0.23 -10000 0 -0.53 117 117
LNPEP -0.012 0.12 -10000 0 -0.59 22 22
YWHAE 0.014 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0.022 -10000 0 -0.49 1 1
Rac1/GDP 0.006 0.017 -10000 0 -10000 0 0
DOCK1 0.009 0.053 -10000 0 -0.59 4 4
ITGA4 -0.051 0.18 -10000 0 -0.53 61 61
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.076 0.17 -10000 0 -0.43 92 92
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.038 0.1 -10000 0 -0.32 61 61
alpha4/beta7 Integrin/Paxillin -0.027 0.14 -10000 0 -0.36 56 56
lamellipodium assembly 0.004 0.038 -10000 0 -0.37 1 1
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
PI3K -0.001 0.019 -10000 0 -0.43 1 1
ARF6 0.014 0 -10000 0 -10000 0 0
TLN1 0.014 0 -10000 0 -10000 0 0
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
ARF6/GTP -0.027 0.076 -10000 0 -0.43 2 2
cell adhesion -0.03 0.084 -10000 0 -0.46 2 2
CRKL/CBL -0.001 0.015 -10000 0 -0.34 1 1
alpha4/beta1 Integrin/Paxillin -0.002 0.1 -10000 0 -0.33 27 27
ITGB1 0.012 0.031 -10000 0 -0.49 2 2
ITGB7 -0.033 0.16 -10000 0 -0.54 44 44
ARF6/GDP 0.006 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.072 0.17 -10000 0 -0.54 15 15
p130Cas/Crk/Dock1 -0.003 0.035 -10000 0 -0.36 5 5
VCAM1 -0.13 0.25 -10000 0 -0.56 132 132
alpha4/beta1 Integrin/Paxillin/Talin 0.008 0.099 -10000 0 -0.47 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.008 0.099 -10000 0 -0.47 2 2
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
mol:GDP 0.03 0.084 0.46 2 -10000 0 2
CBL 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0 -10000 0 -10000 0 0
GIT1 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.008 0.099 -10000 0 -0.47 2 2
Rac1/GTP 0.004 0.041 -10000 0 -0.41 1 1
Regulation of p38-alpha and p38-beta

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.013 0.027 -9999 0 -0.59 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.012 0.031 -9999 0 -0.49 2 2
RAC1-CDC42/GTP/PAK family -0.032 0.1 -9999 0 -0.22 107 107
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.009 0.053 -9999 0 -0.59 4 4
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
MAP3K12 0.014 0 -9999 0 -10000 0 0
FGR 0.011 0.038 -9999 0 -0.49 3 3
p38 alpha/TAB1 -0.026 0.057 -9999 0 -0.33 7 7
PRKG1 -0.039 0.17 -9999 0 -0.58 46 46
DUSP8 0 0.086 -9999 0 -0.53 13 13
PGK/cGMP/p38 alpha -0.044 0.09 -9999 0 -0.31 34 34
apoptosis -0.025 0.055 -9999 0 -0.32 7 7
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.004 0.073 -9999 0 -0.51 10 10
DUSP1 -0.02 0.13 -9999 0 -0.53 32 32
PAK1 -0.035 0.15 -9999 0 -0.5 49 49
SRC 0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.021 -9999 0 -10000 0 0
TRAF6 0.013 0.027 -9999 0 -0.59 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0.022 -9999 0 -0.49 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.005 0.1 -9999 0 -0.38 13 13
BLK -0.11 0.22 -9999 0 -0.52 114 114
HCK -0.007 0.11 -9999 0 -0.54 20 20
MAP2K3 0.011 0.038 -9999 0 -0.49 3 3
DUSP16 0.014 0 -9999 0 -10000 0 0
DUSP10 -0.004 0.1 -9999 0 -0.55 17 17
TRAF6/MEKK3 -0.001 0.015 -9999 0 -0.33 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.007 0.081 -9999 0 -0.34 8 8
positive regulation of innate immune response 0 0.11 -9999 0 -0.42 11 11
LCK -0.081 0.21 -9999 0 -0.54 89 89
p38alpha-beta/MKP7 0.007 0.1 -9999 0 -0.43 8 8
p38alpha-beta/MKP5 -0.001 0.12 -9999 0 -0.43 12 12
PGK/cGMP -0.038 0.12 -9999 0 -0.42 46 46
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.008 0.12 -9999 0 -0.42 13 13
CDC42 0.014 0 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
PAK3 -0.12 0.24 -9999 0 -0.56 116 116
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.025 0.081 -10000 0 -0.31 30 30
ER alpha/Gai/GDP/Gbeta gamma 0.026 0.088 -10000 0 -0.38 16 16
AKT1 0.017 0.12 -10000 0 -0.72 13 13
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.015 0.12 -10000 0 -0.73 13 13
mol:Ca2+ -0.008 0.14 -10000 0 -0.49 25 25
IGF1R 0.013 0.022 -10000 0 -0.49 1 1
E2/ER alpha (dimer)/Striatin -0.035 0.11 -10000 0 -0.35 52 52
SHC1 0.009 0.05 -10000 0 -0.49 5 5
apoptosis -0.017 0.12 0.69 13 -10000 0 13
RhoA/GTP -0.011 0.049 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.02 0.074 -10000 0 -0.39 16 16
regulation of stress fiber formation -0.015 0.099 0.4 9 -10000 0 9
E2/ERA-ERB (dimer) -0.028 0.096 -10000 0 -0.35 41 41
KRAS 0.013 0.022 -10000 0 -0.49 1 1
G13/GTP -0.015 0.065 -10000 0 -0.29 26 26
pseudopodium formation 0.015 0.099 -10000 0 -0.4 9 9
E2/ER alpha (dimer)/PELP1 -0.016 0.072 -10000 0 -0.32 26 26
GRB2 0.013 0.022 -10000 0 -0.49 1 1
GNG2 0.009 0.053 -10000 0 -0.59 4 4
GNAO1 0.008 0.06 -10000 0 -0.59 5 5
HRAS 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.027 0.096 -10000 0 -0.43 13 13
E2/ER beta (dimer) -0.014 0.074 -10000 0 -0.41 17 17
mol:GDP -0.023 0.082 -10000 0 -0.36 26 26
mol:NADP 0.027 0.096 -10000 0 -0.43 13 13
PIK3R1 0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.01 0.14 -10000 0 -0.51 25 25
IGF-1R heterotetramer 0.013 0.022 -10000 0 -0.49 1 1
PLCB1 -0.007 0.13 -10000 0 -0.48 21 21
PLCB2 -0.007 0.14 -10000 0 -0.53 23 23
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
mol:L-citrulline 0.027 0.096 -10000 0 -0.43 13 13
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.013 0.078 -10000 0 -0.7 5 5
JNK cascade -0.014 0.074 -10000 0 -0.41 17 17
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
ESR2 -0.005 0.1 -10000 0 -0.56 17 17
GNAQ 0.014 0 -10000 0 -10000 0 0
ESR1 -0.014 0.12 -10000 0 -0.54 26 26
Gq family/GDP/Gbeta gamma 0.01 0.12 -10000 0 -0.45 24 24
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.032 0.054 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.021 0.078 -10000 0 -0.4 17 17
GNAZ 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.02 0.086 -10000 0 -0.39 26 26
STRN -0.017 0.13 -10000 0 -0.59 27 27
GNAL -0.055 0.19 -10000 0 -0.59 59 59
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.002 0.082 -10000 0 -0.35 26 26
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.1 -10000 0 -0.59 16 16
HBEGF -0.004 0.12 -10000 0 -0.48 8 8
cAMP biosynthetic process -0.055 0.12 -10000 0 -0.3 94 94
SRC 0.033 0.084 -10000 0 -0.35 16 16
PI3K -0.001 0.019 -10000 0 -0.43 1 1
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.021 0.073 -10000 0 -0.34 14 14
SOS1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.024 0.074 -10000 0 -0.34 16 16
Gs family/GTP -0.056 0.12 -10000 0 -0.3 94 94
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0.011 -10000 0 -10000 0 0
vasodilation 0.027 0.092 -10000 0 -0.41 13 13
mol:DAG -0.01 0.14 -10000 0 -0.51 25 25
Gs family/GDP/Gbeta gamma -0.045 0.1 -10000 0 -0.36 22 22
MSN 0.014 0.11 -10000 0 -0.43 9 9
Gq family/GTP -0.005 0.12 -10000 0 -0.5 19 19
mol:PI-3-4-5-P3 0.016 0.12 -10000 0 -0.7 13 13
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.027 0.092 0.41 13 -10000 0 13
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
RhoA/GDP -0.021 0.076 -10000 0 -0.33 26 26
NOS3 0.027 0.099 -10000 0 -0.45 13 13
GNA11 0.004 0.08 -10000 0 -0.59 9 9
MAPKKK cascade 0.022 0.13 -10000 0 -0.4 37 37
E2/ER alpha (dimer)/PELP1/Src -0.021 0.076 -10000 0 -0.4 16 16
ruffle organization 0.015 0.099 -10000 0 -0.4 9 9
ROCK2 0.027 0.083 -10000 0 -0.51 2 2
GNA14 -0.014 0.12 -10000 0 -0.56 25 25
GNA15 -0.007 0.11 -10000 0 -0.56 19 19
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.033 0.14 -10000 0 -0.44 16 16
MMP2 0.027 0.1 -10000 0 -0.48 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.1 0.23 -9999 0 -0.55 103 103
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.014 0 -9999 0 -10000 0 0
TCEB1 0.014 0 -9999 0 -10000 0 0
HIF1A/p53 0.021 0.056 -9999 0 -0.27 14 14
HIF1A 0.023 0.025 -9999 0 -0.24 1 1
COPS5 0.014 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.1 0.23 -9999 0 -0.56 104 104
ARNT/IPAS -0.08 0.16 -9999 0 -0.39 104 104
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.03 0.028 -9999 0 -0.3 1 1
CUL2 0.014 0 -9999 0 -10000 0 0
OS9 0.003 0.073 -9999 0 -0.49 11 11
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.03 0.024 -9999 0 -10000 0 0
PHD1-3/OS9 -0.013 0.06 -9999 0 -0.32 13 13
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.014 -9999 0 -10000 0 0
VHL 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.03 0.024 -9999 0 -10000 0 0
EGLN3 -0.001 0.095 -9999 0 -0.59 13 13
EGLN2 0.014 0 -9999 0 -10000 0 0
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 -0.003 0.1 -9999 0 -0.58 15 15
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.041 0.006 -9999 0 -10000 0 0
ARNT 0.013 0.022 -9999 0 -0.49 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.028 0.12 -9999 0 -0.28 84 84
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.04 -9999 0 -0.43 4 4
SMARCC1 0.01 0.013 -9999 0 -10000 0 0
REL -0.017 0.13 -9999 0 -0.56 29 29
HDAC7 0.021 0.1 -9999 0 -0.52 2 2
JUN 0.002 0.074 -9999 0 -0.5 11 11
EP300 0.009 0.053 -9999 0 -0.59 4 4
KAT2B 0.013 0.022 -9999 0 -0.49 1 1
KAT5 0.014 0 -9999 0 -10000 0 0
MAPK14 0.023 0.023 -9999 0 -0.42 1 1
FOXO1 0.011 0.044 -9999 0 -0.56 3 3
T-DHT/AR 0.017 0.11 -9999 0 -0.43 7 7
MAP2K6 0.012 0.027 -9999 0 -0.59 1 1
BRM/BAF57 0.004 0.021 -9999 0 -0.43 1 1
MAP2K4 0.012 0.032 -9999 0 -0.5 2 2
SMARCA2 0.012 0.027 -9999 0 -0.59 1 1
PDE9A -0.021 0.097 -9999 0 -1.2 2 2
NCOA2 -0.028 0.15 -9999 0 -0.59 35 35
CEBPA -0.016 0.13 -9999 0 -0.56 27 27
EHMT2 0.013 0.004 -9999 0 -10000 0 0
cell proliferation 0.032 0.12 -9999 0 -0.47 8 8
NR0B1 -0.1 0.23 -9999 0 -0.55 103 103
EGR1 -0.11 0.23 -9999 0 -0.54 115 115
RXRs/9cRA -0.035 0.11 -9999 0 -0.33 58 58
AR/RACK1/Src -0.01 0.078 -9999 0 -0.41 7 7
AR/GR -0.015 0.12 -9999 0 -0.37 20 20
GNB2L1 0.014 0.001 -9999 0 -10000 0 0
PKN1 0.014 0 -9999 0 -10000 0 0
RCHY1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.011 0.075 -9999 0 -0.42 15 15
T-DHT/AR/TIF2/CARM1 -0.002 0.14 -9999 0 -0.54 21 21
SRC 0.029 0.062 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.046 0.14 -9999 0 -0.46 27 27
APPBP2 0.014 0.005 -9999 0 -10000 0 0
TRIM24 0.012 0.023 -9999 0 -0.49 1 1
T-DHT/AR/TIP60 0.012 0.085 -9999 0 -0.44 7 7
TMPRSS2 -0.13 0.31 -9999 0 -1.1 44 44
RXRG -0.061 0.2 -9999 0 -0.58 65 65
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.014 0.001 -9999 0 -10000 0 0
RXRB 0.014 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.001 -9999 0 -10000 0 0
NR2C2 0.002 0.084 -9999 0 -0.59 10 10
KLK2 -0.008 0.15 -9999 0 -0.47 24 24
AR -0.023 0.13 -9999 0 -0.3 71 71
SENP1 0.014 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.013 0.032 -9999 0 -0.49 2 2
SRY -0.02 0.11 -9999 0 -0.49 26 26
GATA2 -0.004 0.1 -9999 0 -0.56 16 16
MYST2 0.014 0.001 -9999 0 -10000 0 0
HOXB13 -0.053 0.16 -9999 0 -0.5 60 60
T-DHT/AR/RACK1/Src 0.019 0.085 -9999 0 -0.42 7 7
positive regulation of transcription -0.004 0.1 -9999 0 -0.56 16 16
DNAJA1 0.014 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.026 -9999 0 -0.24 4 4
NCOA1 0.017 0.005 -9999 0 -10000 0 0
SPDEF -0.043 0.17 -9999 0 -0.54 52 52
T-DHT/AR/TIF2 0.015 0.12 -9999 0 -0.58 13 13
T-DHT/AR/Hsp90 0.012 0.085 -9999 0 -0.44 7 7
GSK3B 0.013 0.027 -9999 0 -0.59 1 1
NR2C1 0.014 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.023 0.066 -9999 0 -0.31 15 15
SIRT1 0.014 0 -9999 0 -10000 0 0
ZMIZ2 0.015 0.005 -9999 0 -10000 0 0
POU2F1 0.025 0.014 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.049 0.15 -9999 0 -0.4 42 42
CREBBP 0.014 0 -9999 0 -10000 0 0
SMARCE1 0.013 0.003 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.017 0.13 -10000 0 -0.5 17 17
BAG4 -0.001 0.095 -10000 0 -0.59 13 13
BAD 0.008 0.045 -10000 0 -0.19 2 2
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.033 0.16 -10000 0 -0.55 43 43
BAX 0.008 0.045 -10000 0 -0.19 2 2
EnzymeConsortium:3.1.4.12 -0.003 0.033 -10000 0 -0.1 17 17
IKBKB -0.008 0.12 -10000 0 -0.46 17 17
MAP2K2 0.018 0.049 -10000 0 -10000 0 0
MAP2K1 0.017 0.05 -10000 0 -0.3 1 1
SMPD1 0.003 0.033 -10000 0 -0.14 2 2
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.47 17 17
MAP2K4 0.011 0.055 -10000 0 -0.28 3 3
protein ubiquitination -0.006 0.12 -10000 0 -0.46 17 17
EnzymeConsortium:2.7.1.37 0.019 0.056 -10000 0 -0.29 1 1
response to UV 0 0.001 -10000 0 -0.002 3 3
RAF1 0.013 0.049 -10000 0 -0.2 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0 0.047 -10000 0 -0.16 12 12
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.005 0.053 -10000 0 -0.22 9 9
TRADD 0.013 0.027 -10000 0 -0.59 1 1
RELA/p50 0.014 0 -10000 0 -10000 0 0
MAPK3 0.02 0.049 -10000 0 -0.21 1 1
MAPK1 0.02 0.049 -10000 0 -0.21 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD -0.016 0.13 -10000 0 -0.5 17 17
KSR1 0.007 0.047 -10000 0 -0.2 2 2
MAPK8 0.011 0.068 -10000 0 -0.26 16 16
TRAF2 0.014 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.008 0.12 -10000 0 -0.46 17 17
TNF R/SODD -0.018 0.094 -10000 0 -0.44 23 23
TNF -0.15 0.26 -10000 0 -0.54 156 156
CYCS 0.011 0.044 0.14 4 -0.19 2 6
IKBKG -0.008 0.12 -10000 0 -0.46 17 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.026 0.13 -10000 0 -0.53 17 17
RELA 0.014 0 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AIFM1 0.011 0.044 0.14 4 -0.19 2 6
TNF/TNF R/SODD -0.11 0.17 -10000 0 -0.34 171 171
TNFRSF1A 0.001 0.085 -10000 0 -0.55 12 12
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.051 -10000 0 -0.72 1 1
NSMAF -0.016 0.12 -10000 0 -0.48 17 17
response to hydrogen peroxide 0 0.001 -10000 0 -0.002 3 3
BCL2 0.005 0.075 -10000 0 -0.59 8 8
p38 MAPK signaling 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
TRAF6/ASK1 0.01 0.04 -10000 0 -0.31 8 8
TRAF2/ASK1 -0.005 0.042 -10000 0 -0.36 7 7
ATM 0.014 0 -10000 0 -10000 0 0
MAP2K3 0.02 0.054 -10000 0 -0.3 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.019 0.071 -10000 0 -0.41 7 7
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.031 0.15 -10000 0 -0.54 42 42
TXN 0.009 0.01 -10000 0 -0.21 1 1
CALM1 0.012 0.035 -10000 0 -0.54 2 2
GADD45A -0.017 0.12 -10000 0 -0.49 32 32
GADD45B -0.027 0.14 -10000 0 -0.52 39 39
MAP3K1 0.007 0.059 -10000 0 -0.49 7 7
MAP3K6 0.006 0.062 -10000 0 -0.49 8 8
MAP3K7 0.014 0 -10000 0 -10000 0 0
MAP3K4 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.011 0.065 -10000 0 -0.38 15 15
TAK1/TAB family 0.003 0.026 0.18 9 -0.17 1 10
RAC1/OSM/MEKK3 0 0.011 -10000 0 -0.25 1 1
TRAF2 0.014 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.027 -10000 0 -10000 0 0
TRAF6 0.009 0.016 -10000 0 -0.36 1 1
RAC1 0.014 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.071 0.2 -10000 0 -0.54 79 79
CCM2 0.013 0.022 -10000 0 -0.49 1 1
CaM/Ca2+/CAMKIIB -0.052 0.12 -10000 0 -0.34 79 79
MAPK11 0.004 0.08 -10000 0 -0.59 9 9
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.05 0.12 -10000 0 -0.31 82 82
OSM/MEKK3 -0.001 0.015 -10000 0 -0.34 1 1
TAOK1 -0.015 0.11 -10000 0 -0.35 46 46
TAOK2 0.019 0 -10000 0 -10000 0 0
TAOK3 0.019 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.014 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.006 0.07 -10000 0 -0.59 7 7
MAP3K10 0.005 0.066 -10000 0 -0.49 9 9
MAP3K3 0.014 0 -10000 0 -10000 0 0
TRX/ASK1 0.012 0.047 -10000 0 -0.38 7 7
GADD45/MTK1/MTK1 -0.056 0.13 -10000 0 -0.37 50 50
EPO 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
BCL2L1 0.06 0.098 -9999 0 -0.65 4 4
CRKL 0.035 0.074 -9999 0 -0.46 4 4
mol:DAG 0.04 0.078 -9999 0 -0.47 5 5
HRAS 0.057 0.075 -9999 0 -0.6 2 2
MAPK8 0.015 0.097 -9999 0 -0.4 18 18
RAP1A 0.035 0.073 -9999 0 -0.46 4 4
GAB1 0.034 0.079 -9999 0 -0.53 4 4
MAPK14 0.024 0.073 -9999 0 -0.35 9 9
EPO -0.005 0.099 -9999 0 -0.5 20 20
PLCG1 0.04 0.08 -9999 0 -0.48 5 5
EPOR/TRPC2/IP3 Receptors 0.015 0.024 -9999 0 -0.52 1 1
RAPGEF1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.062 0.16 -9999 0 -0.33 127 127
GAB1/SHC/GRB2/SOS1 -0.015 0.062 -9999 0 -0.47 5 5
EPO/EPOR (dimer) 0.01 0.077 -9999 0 -0.36 20 20
IRS2 0.034 0.079 -9999 0 -0.53 4 4
STAT1 0.043 0.097 -9999 0 -0.52 7 7
STAT5B 0.045 0.083 -9999 0 -0.56 4 4
cell proliferation 0.023 0.091 -9999 0 -0.46 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.016 0.067 -9999 0 -0.47 6 6
TEC 0.026 0.094 -9999 0 -0.44 10 10
SOCS3 -0.11 0.23 -9999 0 -0.52 124 124
STAT1 (dimer) 0.043 0.095 -9999 0 -0.5 7 7
JAK2 0.015 0.007 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.042 0.08 -9999 0 -0.49 4 4
EPO/EPOR 0.01 0.077 -9999 0 -0.36 20 20
LYN 0.006 0.073 -9999 0 -0.51 10 10
TEC/VAV2 0.035 0.092 -9999 0 -0.42 10 10
elevation of cytosolic calcium ion concentration 0.015 0.024 -9999 0 -0.51 1 1
SHC1 0.009 0.05 -9999 0 -0.49 5 5
EPO/EPOR (dimer)/LYN 0.022 0.083 -9999 0 -0.36 14 14
mol:IP3 0.04 0.078 -9999 0 -0.47 5 5
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.084 -9999 0 -0.44 9 9
SH2B3 0.013 0.032 -9999 0 -0.48 2 2
NFKB1 0.024 0.073 -9999 0 -0.4 5 5
EPO/EPOR (dimer)/JAK2/SOCS3 -0.039 0.074 -9999 0 -0.24 38 38
PTPN6 0.028 0.076 -9999 0 -0.49 4 4
TEC/VAV2/GRB2 0.04 0.09 -9999 0 -0.41 9 9
EPOR 0.015 0.024 -9999 0 -0.52 1 1
INPP5D 0.008 0.06 -9999 0 -0.54 6 6
mol:GDP -0.015 0.063 -9999 0 -0.48 5 5
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG2 0 0.088 -9999 0 -0.55 13 13
CRKL/CBL/C3G 0.049 0.07 -9999 0 -0.42 4 4
VAV2 0.035 0.073 -9999 0 -0.46 4 4
CBL 0.035 0.073 -9999 0 -0.46 4 4
SHC/Grb2/SOS1 -0.015 0.061 -9999 0 -0.45 5 5
STAT5A 0.037 0.11 -9999 0 -0.58 10 10
GRB2 0.013 0.022 -9999 0 -0.49 1 1
STAT5 (dimer) 0.056 0.12 -9999 0 -0.57 10 10
LYN/PLCgamma2 0.005 0.093 -9999 0 -0.47 18 18
PTPN11 0.014 0 -9999 0 -10000 0 0
BTK 0.023 0.11 -9999 0 -0.49 15 15
BCL2 0.052 0.15 -9999 0 -0.92 9 9
Nectin adhesion 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
PDGFRB 0.011 0.038 -9999 0 -0.49 3 3
alphaV beta3 Integrin -0.046 0.12 -9999 0 -0.36 66 66
PTK2 -0.03 0.099 -9999 0 -0.48 19 19
positive regulation of JNK cascade -0.009 0.045 -9999 0 -0.31 10 10
CDC42/GDP 0.046 0.073 -9999 0 -0.41 10 10
Rac1/GDP 0.048 0.073 -9999 0 -0.41 10 10
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.014 0 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.055 -9999 0 -0.38 10 10
nectin-3/I-afadin -0.008 0.059 -9999 0 -0.43 10 10
RAPGEF1 0.04 0.081 -9999 0 -0.46 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.033 0.09 -9999 0 -0.53 10 10
PDGFB-D/PDGFRB 0.011 0.038 -9999 0 -0.49 3 3
TLN1 0.032 0.029 -9999 0 -10000 0 0
Rap1/GTP -0.009 0.048 -9999 0 -0.32 10 10
IQGAP1 0.004 0.076 -9999 0 -0.53 10 10
Rap1/GTP/I-afadin -0.001 0.018 -9999 0 -0.29 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.008 0.059 -9999 0 -0.43 10 10
PVR 0.014 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.014 0 -9999 0 -10000 0 0
mol:GDP 0.044 0.087 -9999 0 -0.51 10 10
MLLT4 0.013 0.027 -9999 0 -0.59 1 1
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
PI3K -0.008 0.049 -9999 0 -0.6 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.014 0.076 -9999 0 -0.43 17 17
positive regulation of lamellipodium assembly -0.009 0.047 -9999 0 -0.32 10 10
PVRL1 -0.005 0.1 -9999 0 -0.59 16 16
PVRL3 0.004 0.08 -9999 0 -0.59 9 9
PVRL2 0.012 0.035 -9999 0 -0.54 2 2
PIK3R1 0.014 0 -9999 0 -10000 0 0
CDH1 -0.12 0.24 -9999 0 -0.54 127 127
CLDN1 -0.019 0.13 -9999 0 -0.53 31 31
JAM-A/CLDN1 -0.029 0.091 -9999 0 -0.35 27 27
SRC -0.019 0.088 -9999 0 -0.6 10 10
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
nectin-1(dimer)/I-afadin/I-afadin -0.014 0.076 -9999 0 -0.43 17 17
FARP2 0.037 0.085 -9999 0 -0.5 10 10
RAC1 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.007 0.049 -9999 0 -0.36 10 10
nectin-1/I-afadin -0.014 0.076 -9999 0 -0.43 17 17
nectin-2/I-afadin -0.002 0.031 -9999 0 -0.4 3 3
RAC1/GTP/IQGAP1/filamentous actin -0.006 0.044 -9999 0 -0.32 10 10
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.018 0.081 -9999 0 -0.37 25 25
CDC42/GTP/IQGAP1/filamentous actin -0.006 0.044 -9999 0 -0.32 10 10
F11R 0.002 0.078 -9999 0 -0.5 12 12
positive regulation of filopodium formation -0.009 0.045 -9999 0 -0.31 10 10
alphaV/beta3 Integrin/Talin 0.012 0.094 -9999 0 -0.4 4 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.4 3 3
nectin-2(dimer)/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.4 3 3
PIP5K1C 0.025 0.031 -9999 0 -10000 0 0
VAV2 0.037 0.086 -9999 0 -0.51 10 10
RAP1/GDP -0.011 0.055 -9999 0 -0.38 10 10
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.008 0.053 -9999 0 -0.36 11 11
nectin-3(dimer)/I-afadin/I-afadin -0.008 0.059 -9999 0 -0.43 10 10
Rac1/GTP -0.01 0.057 -9999 0 -0.39 10 10
PTPRM 0.017 0.034 -9999 0 -0.22 10 10
E-cadherin/beta catenin/alpha catenin -0.069 0.12 -9999 0 -0.58 9 9
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.012 0.044 -9999 0 -10000 0 0
DAPP1 -0.034 0.14 -9999 0 -0.42 36 36
Src family/SYK family/BLNK-LAT/BTK-ITK -0.083 0.22 -9999 0 -0.52 68 68
mol:DAG -0.025 0.11 -9999 0 -0.29 26 26
HRAS 0.014 0.003 -9999 0 -10000 0 0
RAP1A 0.014 0.003 -9999 0 -10000 0 0
ARF5/GDP 0.03 0.057 -9999 0 -0.29 6 6
PLCG2 0 0.088 -9999 0 -0.55 13 13
PLCG1 0.014 0 -9999 0 -10000 0 0
ARF5 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.014 0.051 -9999 0 -10000 0 0
ARF1/GTP -0.011 0.041 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
YES1 0.009 0.053 -9999 0 -0.59 4 4
RAP1A/GTP -0.013 0.05 -9999 0 -10000 0 0
ADAP1 -0.029 0.085 -9999 0 -0.47 8 8
ARAP3 -0.014 0.051 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PREX1 0.002 0.084 -9999 0 -0.59 10 10
ARHGEF6 0.008 0.06 -9999 0 -0.59 5 5
ARHGEF7 0.014 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0.003 -9999 0 -10000 0 0
FYN 0.014 0 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
FGR 0.011 0.038 -9999 0 -0.49 3 3
mol:Ca2+ -0.003 0.057 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.013 0.027 -9999 0 -0.59 1 1
ZAP70 -0.046 0.17 -9999 0 -0.53 57 57
mol:IP3 -0.009 0.076 -9999 0 -0.22 8 8
LYN 0.004 0.073 -9999 0 -0.51 10 10
ARF1/GDP 0.03 0.057 -9999 0 -0.29 6 6
RhoA/GDP -0.013 0.043 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.022 -9999 0 -0.36 2 2
BLNK -0.056 0.19 -9999 0 -0.57 61 61
actin cytoskeleton reorganization 0.044 0.074 -9999 0 -0.38 5 5
SRC 0.014 0 -9999 0 -10000 0 0
PLEKHA2 0.028 0.038 -9999 0 -0.36 3 3
RAC1 0.014 0 -9999 0 -10000 0 0
PTEN 0.001 0.027 -9999 0 -0.57 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.012 0.044 -9999 0 -10000 0 0
RhoA/GTP -0.012 0.046 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.077 0.2 -9999 0 -0.51 58 58
BLK -0.11 0.22 -9999 0 -0.52 114 114
PDPK1 0.012 0.038 -9999 0 -0.59 2 2
CYTH1 -0.012 0.046 -9999 0 -10000 0 0
HCK -0.007 0.11 -9999 0 -0.54 20 20
CYTH3 -0.012 0.046 -9999 0 -10000 0 0
CYTH2 -0.012 0.046 -9999 0 -10000 0 0
KRAS 0.013 0.022 -9999 0 -0.49 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.026 0.085 -9999 0 -0.45 13 13
SGK1 -0.02 0.081 -9999 0 -0.49 13 13
INPP5D 0.008 0.06 -9999 0 -0.54 6 6
mol:GDP 0.023 0.059 -9999 0 -0.31 6 6
SOS1 0.014 0 -9999 0 -10000 0 0
SYK -0.013 0.12 -9999 0 -0.57 24 24
ARF6/GDP -0.013 0.043 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.013 0.05 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.014 0.051 -9999 0 -10000 0 0
VAV1 -0.019 0.14 -9999 0 -0.56 30 30
mol:PI-3-4-P2 0.02 0.044 -9999 0 -0.38 6 6
RAS family/GTP/PI3K Class I 0.018 0.059 -9999 0 -10000 0 0
PLEKHA1 0.024 0.05 -9999 0 -0.3 12 12
Rac1/GDP 0.03 0.057 -9999 0 -0.29 6 6
LAT -0.017 0.13 -9999 0 -0.59 27 27
Rac1/GTP 0.024 0.085 -9999 0 -0.57 6 6
ITK -0.063 0.12 -9999 0 -0.42 20 20
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.041 0.14 -9999 0 -0.39 34 34
LCK -0.081 0.21 -9999 0 -0.54 89 89
BTK -0.023 0.069 -9999 0 -0.42 1 1
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.018 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.086 0.03 -9999 0 -10000 0 0
ERC1 0.013 0.022 -9999 0 -0.49 1 1
RIP2/NOD2 -0.022 0.088 -9999 0 -0.37 30 30
NFKBIA 0.05 0 -9999 0 -10000 0 0
BIRC2 0.014 0 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
RIPK2 0.014 0 -9999 0 -10000 0 0
IKBKG -0.007 0.032 -9999 0 -10000 0 0
IKK complex/A20 -0.071 0.1 -9999 0 -0.45 7 7
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.046 0.041 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.024 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.016 -9999 0 -0.36 1 1
NOD2 -0.017 0.13 -9999 0 -0.53 30 30
NFKB1 0.018 0 -9999 0 -10000 0 0
RELA 0.018 0 -9999 0 -10000 0 0
MALT1 0.014 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.12 0.18 -9999 0 -0.39 165 165
TRAF6 0.013 0.027 -9999 0 -0.59 1 1
PRKCA 0.013 0.027 -9999 0 -0.59 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.15 0.26 -9999 0 -0.54 156 156
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.05 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.018 0 -9999 0 -10000 0 0
TNFRSF1A 0.001 0.086 -9999 0 -0.55 12 12
IKK complex 0.053 0.04 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.026 -9999 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.034 0.03 -9999 0 -0.29 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.013 0.022 -9999 0 -0.49 1 1
STAT1 (dimer)/Cbp/p300 0.044 0.095 -9999 0 -0.42 13 13
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.003 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.055 0.077 -9999 0 -0.32 21 21
CaM/Ca2+ -0.003 0.025 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.034 0.062 -9999 0 -0.33 6 6
AKT1 0.052 0.028 -9999 0 -10000 0 0
MAP2K1 0.046 0.044 -9999 0 -10000 0 0
MAP3K11 0.041 0.028 -9999 0 -0.28 1 1
IFNGR1 0.015 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.19 -9999 0 -0.46 106 106
Rap1/GTP -0.002 0.016 -9999 0 -10000 0 0
CRKL/C3G -0.001 0.015 -9999 0 -0.34 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0 0.024 -9999 0 -10000 0 0
CEBPB 0.058 0.11 -9999 0 -0.46 17 17
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.001 0.17 -9999 0 -1 10 10
STAT1 0.034 0.063 -9999 0 -0.33 6 6
CALM1 0.012 0.035 -9999 0 -0.54 2 2
IFN-gamma (dimer) 0.001 0.049 -9999 0 -0.49 5 5
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
STAT1 (dimer)/PIAS1 0.038 0.065 -9999 0 -0.38 1 1
CEBPB/PTGES2/Cbp/p300 -0.015 0.061 -9999 0 -0.36 9 9
mol:Ca2+ 0.022 0.03 -9999 0 -0.29 1 1
MAPK3 0.054 0.05 -9999 0 -10000 0 0
STAT1 (dimer) -0.072 0.11 -9999 0 -0.46 21 21
MAPK1 0.054 0.05 -9999 0 -10000 0 0
JAK2 0.015 0.003 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.015 0.003 -9999 0 -10000 0 0
CAMK2D 0.013 0.027 -9999 0 -0.59 1 1
DAPK1 0.049 0.13 -9999 0 -0.63 18 18
SMAD7 0.005 0.065 -9999 0 -0.19 5 5
CBL/CRKL/C3G 0.037 0.033 -9999 0 -10000 0 0
PI3K -0.002 0.021 -9999 0 -10000 0 0
IFNG 0.001 0.049 -9999 0 -0.49 5 5
apoptosis 0.03 0.097 -9999 0 -0.45 18 18
CAMK2G 0.013 0.027 -9999 0 -0.59 1 1
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.23 0.28 -9999 0 -0.54 228 228
CAMK2B -0.071 0.2 -9999 0 -0.54 79 79
FRAP1 0.05 0.027 -9999 0 -10000 0 0
PRKCD 0.038 0.073 -9999 0 -10000 0 0
RAP1B 0.013 0.022 -9999 0 -0.49 1 1
negative regulation of cell growth -0.055 0.077 -9999 0 -0.32 21 21
PTPN2 0.014 0 -9999 0 -10000 0 0
EP300 0.01 0.053 -9999 0 -0.59 4 4
IRF1 0.032 0.15 -9999 0 -0.58 18 18
STAT1 (dimer)/PIASy 0.04 0.062 -9999 0 -0.39 1 1
SOCS1 -0.048 0.2 -9999 0 -1.4 8 8
mol:GDP -0.001 0.019 -9999 0 -10000 0 0
CASP1 -0.003 0.089 -9999 0 -0.28 28 28
PTGES2 0.014 0 -9999 0 -10000 0 0
IRF9 0.05 0.047 -9999 0 -0.24 4 4
mol:PI-3-4-5-P3 -0.002 0.021 -9999 0 -10000 0 0
RAP1/GDP -0.002 0.017 -9999 0 -10000 0 0
CBL 0.041 0.027 -9999 0 -10000 0 0
MAP3K1 0.038 0.042 -9999 0 -0.29 1 1
PIAS1 0.009 0.053 -9999 0 -0.59 4 4
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.055 0.077 -9999 0 -0.32 21 21
PTPN11 0.034 0.028 -9999 0 -0.29 1 1
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.011 0.038 -10000 0 -0.49 3 3
mol:Halofuginone 0.005 0.01 -10000 0 -0.23 1 1
ITGA1 -0.012 0.12 -10000 0 -0.52 25 25
CDKN1A -0.024 0.11 -10000 0 -0.44 22 22
PRL-3/alpha Tubulin -0.003 0.034 -10000 0 -0.34 5 5
mol:Ca2+ -0.02 0.095 0.23 3 -0.43 25 28
AGT -0.015 0.13 -10000 0 -0.58 25 25
CCNA2 -0.057 0.16 -10000 0 -0.52 15 15
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 -0.064 0.17 -10000 0 -0.38 116 116
CDK2/Cyclin E1 -0.014 0.12 -10000 0 -0.42 22 22
MAPK3 0.021 0.036 -10000 0 -0.34 5 5
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.036 -10000 0 -0.34 5 5
PTP4A1 -0.031 0.14 -10000 0 -0.95 1 1
PTP4A3 0.009 0.05 -10000 0 -0.49 5 5
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0.02 0.043 -10000 0 -0.34 7 7
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.003 0.062 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.025 0.13 -10000 0 -0.89 1 1
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.001 0.03 0.23 5 -0.44 1 6
RHOC 0.002 0.065 -10000 0 -0.39 1 1
RHOA 0.003 0.062 -10000 0 -0.27 1 1
cell motility 0.006 0.066 -10000 0 -0.3 1 1
PRL-1/alpha Tubulin -0.022 0.13 -10000 0 -0.89 1 1
PRL-3/alpha1 Integrin -0.021 0.088 -10000 0 -0.38 29 29
ROCK1 0.006 0.066 -10000 0 -0.3 1 1
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 0 0.086 -10000 0 -0.53 13 13
mitosis -0.031 0.14 -10000 0 -0.94 1 1
ATF5 0.007 0.059 -10000 0 -0.49 7 7
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.032 0.085 -10000 0 -0.54 6 6
CLOCK -0.018 0.14 -10000 0 -0.59 30 30
TIMELESS/CRY2 0.025 0.082 -10000 0 -0.63 1 1
DEC1/BMAL1 0.008 0.059 -10000 0 -0.34 14 14
ATR 0.014 0 -10000 0 -10000 0 0
NR1D1 0.025 0.12 -10000 0 -1.3 3 3
ARNTL 0.014 0.04 -10000 0 -0.5 3 3
TIMELESS 0.025 0.081 -10000 0 -10000 0 0
NPAS2 0.006 0.079 -10000 0 -0.55 10 10
CRY2 0.008 0.06 -10000 0 -0.59 5 5
mol:CO -0.012 0.019 0.084 16 -10000 0 16
CHEK1 0.008 0.054 -10000 0 -0.49 6 6
mol:HEME 0.012 0.019 -10000 0 -0.084 16 16
PER1 0.004 0.08 -10000 0 -0.59 9 9
BMAL/CLOCK/NPAS2 0.013 0.11 -10000 0 -0.36 37 37
BMAL1/CLOCK 0.015 0.13 -10000 0 -0.73 6 6
S phase of mitotic cell cycle 0.032 0.085 -10000 0 -0.54 6 6
TIMELESS/CHEK1/ATR 0.033 0.086 -10000 0 -0.55 6 6
mol:NADPH 0.012 0.019 -10000 0 -0.084 16 16
PER1/TIMELESS 0.022 0.085 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.002 0.073 -10000 0 -0.49 11 11
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.008 0.052 -9999 0 -0.34 12 12
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.009 0.083 -9999 0 -0.33 29 29
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.08 -9999 0 -0.5 2 2
NFKBIA -0.01 0.091 -9999 0 -0.23 59 59
MAPK14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.029 0 -9999 0 -10000 0 0
ARRB2 0.019 0 -9999 0 -10000 0 0
REL -0.018 0.13 -9999 0 -0.56 29 29
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.047 -9999 0 -0.28 12 12
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.029 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
NF kappa B1 p50 dimer 0.022 0 -9999 0 -10000 0 0
PIK3R1 0.014 0 -9999 0 -10000 0 0
NFKB1 0.025 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.002 0.087 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.019 0.079 -9999 0 -0.48 2 2
SRC 0.014 0 -9999 0 -10000 0 0
PI3K -0.001 0.019 -9999 0 -0.43 1 1
NF kappa B1 p50/RelA -0.002 0.087 -9999 0 -0.44 2 2
IKBKB 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
SYK -0.013 0.12 -9999 0 -0.57 24 24
I kappa B alpha/PIK3R1 -0.002 0.085 -9999 0 -0.54 2 2
cell death 0.018 0.076 -9999 0 -0.46 2 2
NF kappa B1 p105/c-Rel 0.009 0.083 -9999 0 -0.33 29 29
LCK -0.081 0.21 -9999 0 -0.54 89 89
BCL3 0.002 0.076 -9999 0 -0.49 12 12
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.004 0.077 0.57 9 -10000 0 9
PI3K Class IB/PDE3B 0.004 0.077 -10000 0 -0.57 9 9
PDE3B 0.004 0.077 -10000 0 -0.57 9 9
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.085 0.13 -10000 0 -0.35 79 79
Ran/GTP/Exportin 1/HDAC1 -0.002 0.023 -10000 0 -0.26 4 4
NF kappa B1 p50/RelA/I kappa B alpha -0.034 0.14 -10000 0 -0.31 76 76
SUMO1 0.014 0 -10000 0 -10000 0 0
ZFPM1 0.013 0.027 -10000 0 -0.59 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -10000 0 -10000 0 0
FKBP3 0.014 0 -10000 0 -10000 0 0
Histones -0.005 0.087 -10000 0 -0.44 4 4
YY1/LSF 0.031 0.03 -10000 0 -0.34 1 1
SMG5 0.013 0.022 -10000 0 -0.49 1 1
RAN 0.014 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.041 0.12 -10000 0 -0.44 3 3
I kappa B alpha/HDAC1 -0.024 0.094 -10000 0 -0.39 7 7
SAP18 0.014 0 -10000 0 -10000 0 0
RELA -0.031 0.11 -10000 0 -0.38 6 6
HDAC1/Smad7 -0.003 0.031 -10000 0 -0.36 4 4
RANGAP1 0.014 0 -10000 0 -10000 0 0
HDAC3/TR2 -0.021 0.086 -10000 0 -0.29 3 3
NuRD/MBD3 Complex 0.05 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.022 0.1 -10000 0 -0.35 6 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.004 0.1 -10000 0 -0.56 16 16
GATA1 0.004 0.058 -10000 0 -0.49 7 7
Mad/Max 0 0 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.058 0.029 -10000 0 -10000 0 0
RBBP7 0.014 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
RBBP4 0.013 0.027 -10000 0 -0.59 1 1
MAX 0.014 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
NFKBIA -0.033 0.096 -10000 0 -0.33 3 3
KAT2B 0.013 0.022 -10000 0 -0.49 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.045 0.026 -10000 0 -10000 0 0
SIN3 complex -0.001 0.014 -10000 0 -0.32 1 1
SMURF1 0.014 0 -10000 0 -10000 0 0
CHD3 0.013 0.027 -10000 0 -0.59 1 1
SAP30 0.013 0.027 -10000 0 -0.59 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.012 0.038 -10000 0 -0.59 2 2
YY1/HDAC3 -0.007 0.084 -10000 0 -0.31 3 3
YY1/HDAC2 0.032 0.025 -10000 0 -10000 0 0
YY1/HDAC1 0.029 0.041 -10000 0 -0.34 4 4
NuRD/MBD2 Complex (MeCP1) 0.05 0.023 -10000 0 -10000 0 0
PPARG -0.091 0.14 -10000 0 -0.35 93 93
HDAC8/hEST1B -0.001 0.02 -10000 0 -0.32 2 2
UBE2I 0.014 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -10000 0 -10000 0 0
TNFRSF1A 0.001 0.086 -10000 0 -0.55 12 12
HDAC3/SMRT (N-CoR2) -0.021 0.086 -10000 0 -0.29 3 3
MBD3L2 0 0.001 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.003 0.031 -10000 0 -0.36 4 4
CREBBP 0.014 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.024 -10000 0 -10000 0 0
HDAC1 0.009 0.053 -10000 0 -0.59 4 4
HDAC3 -0.033 0.096 -10000 0 -0.33 3 3
HDAC2 0.014 0 -10000 0 -10000 0 0
YY1 0.03 0.029 -10000 0 -0.28 4 4
HDAC8 0.013 0.027 -10000 0 -0.59 1 1
SMAD7 0.014 0 -10000 0 -10000 0 0
NCOR2 0.014 0 -10000 0 -10000 0 0
MXD1 0.014 0 -10000 0 -10000 0 0
STAT3 0.025 0.033 -10000 0 -0.34 4 4
NFKB1 0.014 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.014 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.035 0.04 -10000 0 -0.3 5 5
YY1/SAP30/HDAC1 0.035 0.04 -10000 0 -0.3 5 5
EP300 0.009 0.053 -10000 0 -0.59 4 4
STAT3 (dimer non-phopshorylated) 0.025 0.033 -10000 0 -0.34 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.033 0.096 -10000 0 -0.33 3 3
histone deacetylation 0.05 0.023 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.01 0.085 -10000 0 -0.36 3 3
nuclear export 0.001 0.02 0.32 2 -10000 0 2
PRKACA 0.014 0 -10000 0 -10000 0 0
GATAD2B 0.014 0 -10000 0 -10000 0 0
GATAD2A 0.014 0 -10000 0 -10000 0 0
GATA2/HDAC3 -0.031 0.1 -10000 0 -0.36 14 14
GATA1/HDAC1 -0.008 0.055 -10000 0 -0.37 11 11
GATA1/HDAC3 -0.033 0.089 -10000 0 -0.34 5 5
CHD4 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.12 0.18 -10000 0 -0.39 165 165
SIN3/HDAC complex/Mad/Max 0.05 0.023 -10000 0 -10000 0 0
NuRD Complex 0.058 0.024 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.038 0.065 -10000 0 -0.43 4 4
SIN3B 0.014 0 -10000 0 -10000 0 0
MTA2 0.014 0 -10000 0 -10000 0 0
SIN3A 0.014 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.031 0.028 -10000 0 -0.29 4 4
HDAC complex -0.003 0.031 -10000 0 -0.32 5 5
GATA1/Fog1 -0.006 0.044 -10000 0 -0.35 8 8
FKBP25/HDAC1/HDAC2 -0.003 0.031 -10000 0 -0.36 4 4
TNF -0.15 0.26 -10000 0 -0.54 156 156
negative regulation of cell growth 0.05 0.023 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.05 0.023 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.044 0.14 -10000 0 -0.33 79 79
SIN3/HDAC complex/NCoR1 0.047 0.03 -10000 0 -0.39 1 1
TFCP2 0.013 0.027 -10000 0 -0.59 1 1
NR2C1 0.014 0 -10000 0 -10000 0 0
MBD3 0.014 0 -10000 0 -10000 0 0
MBD2 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.046 0.12 -9999 0 -0.36 66 66
AKT1 0.074 0.085 -9999 0 -0.64 3 3
PTK2B -0.002 0.14 -9999 0 -0.48 23 23
VEGFR2 homodimer/Frs2 0.029 0.074 -9999 0 -0.72 3 3
CAV1 -0.05 0.17 -9999 0 -0.49 65 65
CALM1 0.012 0.035 -9999 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.018 0.08 -9999 0 -0.61 5 5
endothelial cell proliferation 0.061 0.1 -9999 0 -0.49 4 4
mol:Ca2+ 0.036 0.093 -9999 0 -0.55 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.021 0.083 -9999 0 -0.6 6 6
RP11-342D11.1 0.027 0.092 -9999 0 -0.56 5 5
CDH5 0.011 0.038 -9999 0 -0.49 3 3
VEGFA homodimer -0.012 0.053 -9999 0 -0.32 1 1
SHC1 0.009 0.05 -9999 0 -0.49 5 5
SHC2 0.013 0.027 -9999 0 -0.59 1 1
HRAS/GDP -0.019 0.072 -9999 0 -0.49 6 6
SH2D2A -0.073 0.2 -9999 0 -0.54 81 81
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.022 0.07 -9999 0 -0.48 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.06 0.14 -9999 0 -0.59 15 15
VEGFR1 homodimer 0.013 0.027 -9999 0 -0.59 1 1
SHC/GRB2/SOS1 -0.021 0.08 -9999 0 -0.55 6 6
GRB10 0.034 0.1 -9999 0 -0.57 7 7
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.013 0.022 -9999 0 -0.49 1 1
PAK1 -0.035 0.15 -9999 0 -0.5 49 49
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.021 0.088 -9999 0 -0.62 7 7
HRAS 0.014 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.079 -9999 0 -0.37 5 5
HIF1A 0.012 0.035 -9999 0 -0.54 2 2
FRS2 0.012 0.035 -9999 0 -0.54 2 2
oxygen and reactive oxygen species metabolic process -0.021 0.082 -9999 0 -0.59 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.005 0.071 -9999 0 -0.52 9 9
Nck/Pak -0.034 0.1 -9999 0 -0.35 50 50
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.017 0.079 -9999 0 -0.61 5 5
mol:GDP -0.021 0.078 -9999 0 -0.53 6 6
mol:NADP 0.061 0.081 -9999 0 -0.43 5 5
eNOS/Hsp90 0.065 0.077 -9999 0 -0.4 5 5
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.036 0.094 -9999 0 -0.56 5 5
HIF1A/ARNT -0.002 0.028 -9999 0 -0.37 3 3
SHB 0.014 0 -9999 0 -10000 0 0
VEGFA -0.005 0.1 -9999 0 -0.48 22 22
VEGFC -0.004 0.096 -9999 0 -0.52 17 17
FAK1/Vinculin 0.035 0.12 -9999 0 -0.62 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.046 0.12 -9999 0 -0.5 22 22
PTPN6 -0.004 0.099 -9999 0 -0.55 16 16
EPAS1 0.02 0.038 -9999 0 -0.34 3 3
mol:L-citrulline 0.061 0.081 -9999 0 -0.43 5 5
ITGAV 0.013 0.027 -9999 0 -0.59 1 1
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.018 0.075 -9999 0 -0.58 5 5
VEGFR2 homodimer/VEGFA homodimer -0.024 0.086 -9999 0 -0.61 5 5
VEGFR2/3 heterodimer 0.025 0.091 -9999 0 -0.73 5 5
VEGFB 0.013 0.022 -9999 0 -0.49 1 1
MAPK11 0.035 0.099 -9999 0 -0.53 7 7
VEGFR2 homodimer 0.029 0.081 -9999 0 -0.54 9 9
FLT1 0.013 0.027 -9999 0 -0.59 1 1
NEDD4 0.005 0.078 -9999 0 -0.52 11 11
MAPK3 0.029 0.098 -9999 0 -0.5 5 5
MAPK1 0.029 0.098 -9999 0 -0.5 5 5
VEGFA145/NRP2 -0.022 0.089 -9999 0 -0.37 31 31
VEGFR1/2 heterodimer 0.03 0.072 -9999 0 -0.72 3 3
KDR 0.029 0.081 -9999 0 -0.54 9 9
VEGFA165/NRP1/VEGFR2 homodimer 0.029 0.1 -9999 0 -0.53 6 6
SRC 0.014 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.031 0.099 -9999 0 -0.49 6 6
PI3K 0.061 0.092 -9999 0 -0.67 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.018 0.08 -9999 0 -0.61 5 5
FES 0.034 0.098 -9999 0 -0.55 6 6
GAB1 -0.017 0.074 -9999 0 -0.62 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.017 0.079 -9999 0 -0.61 5 5
CTNNB1 0.014 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
ARNT 0.013 0.022 -9999 0 -0.49 1 1
eNOS/Caveolin-1 0.038 0.11 -9999 0 -0.48 6 6
VEGFR2 homodimer/VEGFA homodimer/Yes -0.02 0.085 -9999 0 -0.6 6 6
PI3K/GAB1 0.075 0.085 -9999 0 -0.54 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.036 0.09 -9999 0 -0.55 6 6
PRKACA 0.014 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.018 0.094 -9999 0 -0.64 7 7
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.036 0.095 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.06 0.14 -9999 0 -0.58 15 15
PTK2 0.031 0.11 -9999 0 -0.62 5 5
EDG1 0.027 0.092 -9999 0 -0.56 5 5
mol:DAG 0.036 0.094 -9999 0 -0.56 5 5
CaM/Ca2+ -0.02 0.071 -9999 0 -0.51 5 5
MAP2K3 0.034 0.11 -9999 0 -0.55 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.034 0.1 -9999 0 -0.58 7 7
PLCG1 0.036 0.095 -9999 0 -0.57 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.016 0.073 -9999 0 -0.58 5 5
IQGAP1 0.004 0.076 -9999 0 -0.53 10 10
YES1 0.009 0.053 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.017 0.079 -9999 0 -0.61 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.026 0.094 -9999 0 -0.59 7 7
cell migration 0.057 0.11 -9999 0 -0.56 7 7
mol:PI-3-4-5-P3 0.06 0.087 -9999 0 -0.61 3 3
FYN 0.014 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.033 0.088 -9999 0 -0.52 5 5
mol:NO 0.061 0.081 -9999 0 -0.43 5 5
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.019 0.072 -9999 0 -0.49 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.034 0.1 -9999 0 -0.58 7 7
VHL 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.052 0.18 -9999 0 -0.51 65 65
NOS3 0.062 0.088 -9999 0 -0.49 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.018 0.082 -9999 0 -0.61 6 6
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.043 0.089 -9999 0 -0.52 5 5
PRKCB 0.005 0.14 -9999 0 -0.5 18 18
VCL 0.008 0.058 -9999 0 -0.52 6 6
VEGFA165/NRP1 0.027 0.093 -9999 0 -0.56 5 5
VEGFR1/2 heterodimer/VEGFA homodimer -0.018 0.08 -9999 0 -0.61 5 5
VEGFA165/NRP2 -0.022 0.089 -9999 0 -0.37 31 31
MAPKKK cascade 0.057 0.098 -9999 0 -0.52 7 7
NRP2 0.003 0.08 -9999 0 -0.56 10 10
VEGFC homodimer -0.004 0.096 -9999 0 -0.52 17 17
NCK1 0.013 0.027 -9999 0 -0.59 1 1
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.038 0.11 -9999 0 -0.57 5 5
MAP3K13 0.028 0.11 -9999 0 -0.56 6 6
PDPK1 0.065 0.085 -9999 0 -0.6 3 3
S1P3 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
PDGFRB 0.011 0.038 -9999 0 -0.49 3 3
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.06 -9999 0 -0.27 17 17
GNAO1 0.01 0.06 -9999 0 -0.6 5 5
S1P/S1P3/G12/G13 0.002 0.09 -9999 0 -0.35 12 12
AKT1 0.027 0.04 -9999 0 -0.3 2 2
AKT3 0.027 0.14 -9999 0 -1.3 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.038 -9999 0 -0.49 3 3
GNAI2 0.016 0.002 -9999 0 -10000 0 0
GNAI3 0.016 0.002 -9999 0 -10000 0 0
GNAI1 -0.003 0.11 -9999 0 -0.59 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.033 0.15 -9999 0 -0.51 47 47
S1PR2 0.007 0.062 -9999 0 -0.56 6 6
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.019 0.092 -9999 0 -0.49 7 7
MAPK3 0.027 0.088 -9999 0 -0.46 7 7
MAPK1 0.027 0.088 -9999 0 -0.46 7 7
JAK2 0.023 0.096 -9999 0 -0.42 11 11
CXCR4 0.012 0.11 -9999 0 -0.44 14 14
FLT1 0.016 0.028 -9999 0 -0.61 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.027 0.088 -9999 0 -0.46 7 7
S1P/S1P3/Gi 0.019 0.093 -9999 0 -0.49 7 7
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.02 0.07 -9999 0 -0.44 7 7
VEGFA -0.004 0.1 -9999 0 -0.49 22 22
S1P/S1P2/Gi 0.031 0.069 -9999 0 -0.34 10 10
VEGFR1 homodimer/VEGFA homodimer 0.013 0.078 -9999 0 -0.34 23 23
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.009 0.11 -9999 0 -0.3 49 49
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ 0.016 0.002 -9999 0 -10000 0 0
G12/G13 -0.001 0.019 -9999 0 -0.43 1 1
GNA14 -0.014 0.12 -9999 0 -0.56 25 25
GNA15 -0.007 0.11 -9999 0 -0.56 19 19
GNA12 0.013 0.027 -9999 0 -0.59 1 1
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.004 0.08 -9999 0 -0.59 9 9
Rac1/GTP -0.02 0.07 -9999 0 -0.44 7 7
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.009 0.053 -9999 0 -0.59 4 4
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.008 0.052 -9999 0 -0.36 11 11
forebrain development -0.006 0.15 -9999 0 -0.43 43 43
GNAO1 0.008 0.06 -9999 0 -0.6 5 5
SMO/beta Arrestin2 0.016 0.053 -9999 0 -0.43 7 7
SMO 0.006 0.07 -9999 0 -0.59 7 7
ARRB2 0.014 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.04 0.066 -9999 0 -0.45 2 2
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.013 0.027 -9999 0 -0.59 1 1
GNAI2 0.014 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.004 0.019 -9999 0 -0.32 1 1
GNAI1 -0.005 0.1 -9999 0 -0.59 16 16
XPO1 0.015 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.043 0.11 -9999 0 -0.51 14 14
SAP30 0.013 0.027 -9999 0 -0.59 1 1
mol:GDP 0.006 0.07 -9999 0 -0.59 7 7
MIM/GLI2A 0.01 0.059 -9999 0 -0.58 5 5
IFT88 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0.003 -9999 0 -10000 0 0
GLI2 0.043 0.036 -9999 0 -10000 0 0
GLI3 0.034 0.07 -9999 0 -0.48 2 2
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0 -9999 0 -10000 0 0
GNG2 0.009 0.053 -9999 0 -0.59 4 4
Gi family/GTP 0.024 0.067 -9999 0 -0.28 16 16
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.052 0.058 -9999 0 -0.46 2 2
GLI2/Su(fu) 0.053 0.057 -9999 0 -0.77 1 1
FOXA2 -0.04 0.13 -9999 0 -0.66 10 10
neural tube patterning -0.006 0.15 -9999 0 -0.43 43 43
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.027 0.051 -9999 0 -0.39 5 5
GNB1 0.014 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
CSNK1G3 0.014 0 -9999 0 -10000 0 0
MTSS1 0.01 0.059 -9999 0 -0.58 5 5
embryonic limb morphogenesis -0.006 0.15 -9999 0 -0.43 43 43
SUFU 0.026 0.045 -9999 0 -0.78 1 1
LGALS3 -0.027 0.14 -9999 0 -0.5 41 41
catabolic process 0.064 0.064 -9999 0 -0.49 1 1
GLI3A/CBP -0.018 0.1 -9999 0 -0.34 32 32
KIF3A 0.013 0.027 -9999 0 -0.59 1 1
GLI1 -0.007 0.16 -9999 0 -0.44 43 43
RAB23 0.013 0.027 -9999 0 -0.59 1 1
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.011 0.046 -9999 0 -0.59 3 3
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.008 0.089 -9999 0 -0.46 5 5
GNAZ 0.014 0.003 -9999 0 -10000 0 0
RBBP4 0.013 0.027 -9999 0 -0.59 1 1
CSNK1G1 0.013 0.022 -9999 0 -0.49 1 1
PIAS1 0.009 0.053 -9999 0 -0.59 4 4
PRKACA 0.014 0 -9999 0 -10000 0 0
GLI2/SPOP 0.047 0.034 -9999 0 -10000 0 0
STK36 0.014 0.027 -9999 0 -0.59 1 1
Gi family/GNB1/GNG2/GDP 0.03 0.069 -9999 0 -0.48 3 3
PTCH1 -0.007 0.19 -9999 0 -0.83 15 15
MIM/GLI1 -0.009 0.17 -9999 0 -0.52 26 26
CREBBP -0.018 0.1 -9999 0 -0.34 32 32
Su(fu)/SIN3/HDAC complex 0.051 0.03 -9999 0 -0.28 1 1
HIF-2-alpha transcription factor network

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.05 0.21 -10000 0 -0.9 24 24
oxygen homeostasis 0.007 0.017 -10000 0 -10000 0 0
TCEB2 0.014 0 -10000 0 -10000 0 0
TCEB1 0.014 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.005 0.049 -10000 0 -0.32 2 2
EPO 0.092 0.23 -10000 0 -0.72 14 14
FIH (dimer) 0.021 0.017 -10000 0 -10000 0 0
APEX1 0.02 0.017 -10000 0 -10000 0 0
SERPINE1 0.01 0.33 -10000 0 -0.74 28 28
FLT1 -0.003 0.1 -10000 0 -0.9 5 5
ADORA2A 0.09 0.23 -10000 0 -0.71 14 14
germ cell development 0.074 0.25 -10000 0 -0.71 18 18
SLC11A2 0.093 0.23 -10000 0 -0.75 12 12
BHLHE40 0.083 0.26 -10000 0 -0.78 18 18
HIF1AN 0.021 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.024 0.086 -10000 0 -0.44 8 8
ETS1 0.02 0.08 -10000 0 -0.54 10 10
CITED2 0.003 0.037 -10000 0 -0.44 2 2
KDR -0.012 0.13 -10000 0 -0.9 8 8
PGK1 0.093 0.23 -10000 0 -0.73 13 13
SIRT1 0.015 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.098 0.27 -10000 0 -0.91 13 13
EPAS1 0.066 0.11 -10000 0 -0.35 7 7
SP1 0.019 0.017 -10000 0 -10000 0 0
ABCG2 0.092 0.24 -10000 0 -0.88 9 9
EFNA1 0.091 0.24 -10000 0 -0.76 13 13
FXN 0.091 0.23 -10000 0 -0.77 10 10
POU5F1 0.073 0.26 -10000 0 -0.75 18 18
neuron apoptosis -0.097 0.26 0.86 13 -10000 0 13
EP300 0.009 0.053 -10000 0 -0.59 4 4
EGLN3 0.006 0.098 -10000 0 -0.59 13 13
EGLN2 0.021 0.017 -10000 0 -10000 0 0
EGLN1 0.021 0.017 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.014 0 -10000 0 -10000 0 0
ARNT 0.019 0.029 -10000 0 -0.52 1 1
SLC2A1 0.09 0.23 -10000 0 -0.73 13 13
TWIST1 0.064 0.28 -10000 0 -0.78 23 23
ELK1 0.023 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.024 0.086 -10000 0 -0.44 8 8
VEGFA 0.084 0.26 -10000 0 -0.81 15 15
CREBBP 0.014 0 -10000 0 -10000 0 0
Insulin Pathway

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.01 0.052 -9999 0 -0.57 1 1
TC10/GTP -0.007 0.046 -9999 0 -0.55 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.027 -9999 0 -0.29 4 4
HRAS 0.014 0 -9999 0 -10000 0 0
APS homodimer 0 0.089 -9999 0 -0.57 12 12
GRB14 -0.18 0.26 -9999 0 -0.53 184 184
FOXO3 -0.026 0.091 -9999 0 -0.58 13 13
AKT1 -0.039 0.13 -9999 0 -0.45 4 4
INSR 0.016 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.036 0.028 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.011 0.044 -9999 0 -0.56 3 3
SORBS1 0.011 0.046 -9999 0 -0.59 3 3
CRK 0.014 0 -9999 0 -10000 0 0
PTPN1 0.035 0.028 -9999 0 -10000 0 0
CAV1 -0.007 0.097 -9999 0 -0.37 6 6
CBL/APS/CAP/Crk-II/C3G -0.008 0.051 -9999 0 -0.6 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.027 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.026 -9999 0 -0.28 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.032 -9999 0 -10000 0 0
RPS6KB1 -0.028 0.12 -9999 0 -0.4 4 4
PARD6A 0.014 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.001 0.038 -9999 0 -0.82 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.064 0.088 -9999 0 -0.4 4 4
HRAS/GTP -0.006 0.037 -9999 0 -0.42 1 1
Insulin Receptor 0.016 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.005 0.035 -9999 0 -10000 0 0
PRKCI -0.022 0.053 -9999 0 -0.55 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.081 0.11 -9999 0 -0.48 4 4
SHC1 0.009 0.05 -9999 0 -0.49 5 5
negative regulation of MAPKKK cascade -0.001 0.035 -9999 0 -0.5 2 2
PI3K -0.003 0.027 -9999 0 -0.29 1 1
NCK2 0.014 0 -9999 0 -10000 0 0
RHOQ 0.014 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 -0.039 0.13 -9999 0 -0.45 4 4
PRKCZ -0.043 0.12 -9999 0 -0.59 20 20
SH2B2 0 0.089 -9999 0 -0.57 12 12
SHC/SHIP 0.029 0.05 -9999 0 -0.49 1 1
F2RL2 -0.094 0.21 -9999 0 -0.51 105 105
TRIP10 0.007 0.065 -9999 0 -0.55 7 7
Insulin Receptor/Insulin/Shc -0.005 0.038 -9999 0 -0.28 9 9
TC10/GTP/CIP4/Exocyst -0.005 0.039 -9999 0 -0.33 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.005 0.035 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
RASA1 0.014 0 -9999 0 -10000 0 0
NCK1 0.013 0.027 -9999 0 -0.59 1 1
CBL/APS/CAP/Crk-II -0.009 0.056 -9999 0 -0.34 12 12
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.007 0.044 -9999 0 -0.3 6 6
INPP5D 0.023 0.046 -9999 0 -0.36 4 4
SOS1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.027 0.14 -9999 0 -0.87 13 13
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.014 0 -9999 0 -10000 0 0
p62DOK/RasGAP -0.001 0.036 -9999 0 -0.51 2 2
INS -0.002 0.056 -9999 0 -0.57 5 5
mol:PI-3-4-P2 0.023 0.046 -9999 0 -0.36 4 4
GRB2 0.013 0.022 -9999 0 -0.49 1 1
EIF4EBP1 -0.034 0.13 -9999 0 -0.42 12 12
PTPRA 0.016 0.003 -9999 0 -10000 0 0
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
TC10/GTP/CIP4 -0.005 0.039 -9999 0 -0.33 7 7
PDPK1 0.012 0.038 -9999 0 -0.59 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.031 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.028 -9999 0 -0.3 4 4
Insulin Receptor/Insulin/IRS3 -0.004 0.04 -9999 0 -0.4 5 5
Par3/Par6 -0.054 0.1 -9999 0 -0.31 28 28
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.042 -9999 0 -0.72 1 1
VEGFR1 homodimer/NRP1 0.022 0.039 -9999 0 -0.54 2 2
mol:DAG -0.02 0.13 -9999 0 -0.66 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.013 0.06 -9999 0 -0.67 1 1
CaM/Ca2+ -0.012 0.12 -9999 0 -0.57 2 2
HIF1A 0.02 0.038 -9999 0 -0.46 3 3
GAB1 0.012 0.035 -9999 0 -0.54 2 2
AKT1 0.005 0.13 -9999 0 -0.71 2 2
PLCG1 -0.02 0.13 -9999 0 -0.66 1 1
NOS3 0.007 0.13 -9999 0 -0.47 4 4
CBL 0.014 0 -9999 0 -10000 0 0
mol:NO 0.008 0.12 -9999 0 -0.45 4 4
FLT1 0.03 0.045 -9999 0 -0.62 2 2
PGF -0.092 0.22 -9999 0 -0.55 96 96
VEGFR1 homodimer/NRP2/VEGFR121 0.021 0.082 -9999 0 -0.58 2 2
CALM1 0.012 0.035 -9999 0 -0.54 2 2
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
eNOS/Hsp90 0.015 0.12 -9999 0 -0.45 3 3
endothelial cell proliferation -0.033 0.16 -9999 0 -0.52 17 17
mol:Ca2+ -0.02 0.13 -9999 0 -0.65 1 1
MAPK3 -0.001 0.12 -9999 0 -0.57 1 1
MAPK1 -0.001 0.12 -9999 0 -0.57 1 1
PIK3R1 0.014 0 -9999 0 -10000 0 0
PLGF homodimer -0.092 0.22 -9999 0 -0.55 96 96
PRKACA 0.014 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.05 0.17 -9999 0 -0.49 65 65
VEGFA homodimer -0.007 0.1 -9999 0 -0.49 22 22
VEGFR1 homodimer/VEGFA homodimer 0.019 0.073 -9999 0 -0.72 1 1
platelet activating factor biosynthetic process 0.007 0.11 -9999 0 -0.55 1 1
PI3K -0.011 0.13 -9999 0 -0.61 2 2
PRKCA -0.01 0.12 -9999 0 -0.61 1 1
PRKCB -0.049 0.16 -9999 0 -0.55 17 17
VEGFR1 homodimer/PLGF homodimer -0.034 0.14 -9999 0 -0.72 1 1
VEGFA -0.007 0.1 -9999 0 -0.49 22 22
VEGFB 0.013 0.022 -9999 0 -0.49 1 1
mol:IP3 -0.02 0.13 -9999 0 -0.66 1 1
RASA1 0.04 0.039 -9999 0 -0.66 1 1
NRP2 0.003 0.08 -9999 0 -0.56 10 10
VEGFR1 homodimer 0.03 0.045 -9999 0 -0.61 2 2
VEGFB homodimer 0.013 0.022 -9999 0 -0.49 1 1
NCK1 0.013 0.027 -9999 0 -0.59 1 1
eNOS/Caveolin-1 -0.015 0.14 -9999 0 -0.47 13 13
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.05 0.11 -9999 0 -0.6 2 2
mol:L-citrulline 0.008 0.12 -9999 0 -0.45 4 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.035 0.064 -9999 0 -0.63 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.069 -9999 0 -0.67 1 1
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.048 0.1 -9999 0 -0.57 2 2
PDPK1 -0.003 0.12 -9999 0 -0.71 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.027 0.067 -9999 0 -0.67 1 1
mol:NADP 0.008 0.12 -9999 0 -0.45 4 4
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.011 0.053 -9999 0 -0.62 1 1
VEGFR1 homodimer/NRP2 0.026 0.064 -9999 0 -0.72 1 1
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.015 0.077 -9999 0 -0.36 11 11
PDGFB-D/PDGFRB/SLAP -0.006 0.1 -9999 0 -0.4 32 32
PDGFB-D/PDGFRB/APS/CBL -0.005 0.061 -9999 0 -0.36 14 14
AKT1 0.058 0.037 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.009 0.086 -9999 0 -0.36 11 11
PIK3CA 0.013 0.027 -9999 0 -0.59 1 1
FGR 0.001 0.028 -9999 0 -10000 0 0
mol:Ca2+ 0.019 0.041 -9999 0 -10000 0 0
MYC 0.003 0.18 -9999 0 -0.82 21 21
SHC1 0.009 0.05 -9999 0 -0.49 5 5
HRAS/GDP 0.037 0.021 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.003 0.024 -9999 0 -0.28 3 3
GRB10 0.011 0.044 -9999 0 -0.56 3 3
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0.019 0.041 -9999 0 -10000 0 0
PTEN 0.013 0.027 -9999 0 -0.59 1 1
GRB2 0.013 0.022 -9999 0 -0.49 1 1
GRB7 -0.031 0.14 -9999 0 -0.49 42 42
PDGFB-D/PDGFRB/SHP2 0.017 0.028 -9999 0 -0.34 3 3
PDGFB-D/PDGFRB/GRB10 0.015 0.043 -9999 0 -0.37 6 6
cell cycle arrest -0.006 0.1 -9999 0 -0.39 32 32
HRAS 0.014 0 -9999 0 -10000 0 0
HIF1A 0.063 0.041 -9999 0 -0.44 1 1
GAB1 0.006 0.072 -9999 0 -0.36 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.01 0.074 -9999 0 -0.36 5 5
PDGFB-D/PDGFRB 0.011 0.029 -9999 0 -0.29 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.028 -9999 0 -0.34 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.025 0.085 -9999 0 -0.41 12 12
positive regulation of MAPKKK cascade 0.017 0.028 -9999 0 -0.34 3 3
PIK3R1 0.014 0 -9999 0 -10000 0 0
mol:IP3 0.019 0.042 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.014 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.015 0.1 -9999 0 -0.35 44 44
SHB 0.014 0 -9999 0 -10000 0 0
BLK -0.055 0.14 -9999 0 -0.55 32 32
PTPN2 0.014 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.017 0.028 -9999 0 -0.34 3 3
BCAR1 0.013 0.027 -9999 0 -0.59 1 1
VAV2 0.008 0.086 -9999 0 -0.4 7 7
CBL 0.014 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.017 0.033 -9999 0 -0.34 4 4
LCK -0.053 0.15 -9999 0 -0.52 41 41
PDGFRB 0.011 0.039 -9999 0 -0.49 3 3
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.009 0.091 -9999 0 -0.61 10 10
ABL1 0.008 0.062 -9999 0 -0.32 4 4
PDGFB-D/PDGFRB/CBL 0.007 0.07 -9999 0 -0.37 3 3
PTPN1 0.014 0.003 -9999 0 -10000 0 0
SNX15 0.014 0 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
STAT1 -0.002 0.088 -9999 0 -0.49 16 16
cell proliferation 0.007 0.16 -9999 0 -0.7 22 22
SLA -0.018 0.13 -9999 0 -0.54 30 30
actin cytoskeleton reorganization 0.048 0.032 -9999 0 -10000 0 0
SRC 0.003 0.026 -9999 0 -10000 0 0
PI3K -0.005 0.031 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.023 0.092 -9999 0 -0.3 47 47
SH2B2 0 0.089 -9999 0 -0.57 12 12
PLCgamma1/SPHK1 0.008 0.088 -9999 0 -0.37 11 11
LYN -0.001 0.051 -9999 0 -0.63 2 2
LRP1 0.014 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
STAT5B 0.014 0 -9999 0 -10000 0 0
STAT5A 0.001 0.088 -9999 0 -0.59 11 11
NCK1-2/p130 Cas 0.008 0.031 -9999 0 -10000 0 0
SPHK1 -0.028 0.15 -9999 0 -0.54 40 40
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.019 0.042 -9999 0 -10000 0 0
PLCG1 0.019 0.042 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.044 -9999 0 -0.32 9 9
YES1 -0.002 0.056 -9999 0 -0.55 4 4
cell migration -0.004 0.042 -9999 0 -0.31 9 9
SHC/Grb2/SOS1 0.006 0.041 -9999 0 -0.46 2 2
SLC9A3R2 0.012 0.031 -9999 0 -0.49 2 2
SLC9A3R1 0.009 0.053 -9999 0 -0.59 4 4
NHERF1-2/PDGFRB/PTEN 0.007 0.044 -9999 0 -0.32 5 5
FYN 0.003 0.026 -9999 0 -10000 0 0
DOK1 0.032 0.03 -9999 0 -0.33 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.014 0 -9999 0 -10000 0 0
RAC1 0.013 0.11 -9999 0 -0.44 23 23
PRKCD 0.015 0.083 -9999 0 -0.32 27 27
FER 0.018 0.075 -9999 0 -0.32 21 21
MAPKKK cascade -0.004 0.034 -9999 0 -0.45 2 2
RASA1 0.033 0.023 -9999 0 -0.26 1 1
NCK1 0.013 0.027 -9999 0 -0.59 1 1
NCK2 0.014 0 -9999 0 -10000 0 0
p62DOK/Csk 0.04 0.027 -9999 0 -0.3 1 1
PDGFB-D/PDGFRB/SHB 0.017 0.028 -9999 0 -0.34 3 3
chemotaxis 0.008 0.061 -9999 0 -0.31 4 4
STAT1-3-5/STAT1-3-5 -0.013 0.052 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.008 0.028 -9999 0 -0.35 3 3
PTPRJ 0.013 0.022 -9999 0 -0.49 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.002 0.028 -9999 0 -0.32 4 4
HDAC3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.005 0.04 -9999 0 -0.34 7 7
GATA1/HDAC5 -0.005 0.04 -9999 0 -0.34 7 7
GATA2/HDAC5 -0.012 0.07 -9999 0 -0.4 16 16
HDAC5/BCL6/BCoR -0.001 0.012 -9999 0 -0.28 1 1
HDAC9 -0.002 0.094 -9999 0 -0.54 15 15
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -9999 0 -10000 0 0
GATA2 -0.004 0.1 -9999 0 -0.56 16 16
HDAC4/RFXANK -0.001 0.015 -9999 0 -0.34 1 1
BCOR 0.013 0.022 -9999 0 -0.49 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0 -9999 0 -10000 0 0
HDAC5 0.014 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.003 0.038 -9999 0 -0.43 4 4
Histones 0.038 0.036 -9999 0 -10000 0 0
ADRBK1 0.014 0 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.014 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.014 0 -9999 0 -10000 0 0
HDAC6 0.014 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.015 -9999 0 -0.34 1 1
CAMK4 -0.17 0.27 -9999 0 -0.56 167 167
Tubulin/HDAC6 -0.001 0.016 -9999 0 -0.36 1 1
SUMO1 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
GATA1 0.004 0.058 -9999 0 -0.49 7 7
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.033 0 -9999 0 -10000 0 0
SRF 0.014 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.001 0.019 -9999 0 -0.43 1 1
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.015 -9999 0 -0.34 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.11 0.16 -9999 0 -0.34 167 167
HDAC4/ER alpha -0.019 0.084 -9999 0 -0.38 26 26
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.038 0.036 -9999 0 -10000 0 0
cell motility -0.001 0.016 -9999 0 -0.36 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.014 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.014 0.12 -9999 0 -0.54 26 26
HDAC6/HDAC11 -0.001 0.019 -9999 0 -0.43 1 1
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.008 0.1 -9999 0 -0.5 22 22
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.01 0.046 -9999 0 -10000 0 0
GNG2 0.009 0.053 -9999 0 -0.59 4 4
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.013 0.027 -9999 0 -0.59 1 1
HDAC11 0.013 0.027 -9999 0 -0.59 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
ANKRA2 0.014 0 -9999 0 -10000 0 0
RFXANK 0.013 0.022 -9999 0 -0.49 1 1
nuclear import -0.032 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.017 0.12 -10000 0 -1.1 2 2
regulation of axonogenesis -0.005 0.069 0.21 34 -10000 0 34
myoblast fusion -0.004 0.059 0.41 2 -10000 0 2
mol:GTP -0.01 0.034 -10000 0 -0.23 2 2
regulation of calcium-dependent cell-cell adhesion -0.027 0.04 0.34 1 -10000 0 1
ARF1/GTP -0.006 0.022 -10000 0 -10000 0 0
mol:GM1 0.004 0.028 -10000 0 -0.17 2 2
mol:Choline -0.006 0.1 -10000 0 -0.32 45 45
lamellipodium assembly -0.016 0.055 -10000 0 -0.45 2 2
MAPK3 0.018 0.054 -10000 0 -0.33 2 2
ARF6/GTP/NME1/Tiam1 0.028 0.04 -10000 0 -0.34 1 1
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP 0.004 0.059 -10000 0 -0.41 2 2
ARF1/GDP 0.014 0.055 -10000 0 -0.37 2 2
ARF6 0.008 0.02 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 0.014 0.027 -10000 0 -0.59 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.054 -10000 0 -0.33 2 2
actin filament bundle formation -0.013 0.054 0.37 2 -10000 0 2
KALRN -0.018 0.058 -10000 0 -0.24 19 19
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.055 -10000 0 -0.38 2 2
NME1 0.015 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.055 -10000 0 -0.38 2 2
substrate adhesion-dependent cell spreading -0.01 0.034 -10000 0 -0.23 2 2
cortical actin cytoskeleton organization -0.016 0.055 -10000 0 -0.45 2 2
RAC1 0.014 0 -10000 0 -10000 0 0
liver development -0.01 0.034 -10000 0 -0.23 2 2
ARF6/GTP -0.01 0.034 -10000 0 -0.23 2 2
RhoA/GTP -0.006 0.022 -10000 0 -10000 0 0
mol:GDP -0.016 0.054 -10000 0 -0.42 2 2
ARF6/GTP/RAB11FIP3/RAB11A -0.004 0.017 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
PLD1 -0.019 0.11 -10000 0 -0.38 44 44
RAB11FIP3 0.014 0 -10000 0 -10000 0 0
tube morphogenesis -0.016 0.055 -10000 0 -0.45 2 2
ruffle organization 0.005 0.069 -10000 0 -0.21 34 34
regulation of epithelial cell migration -0.01 0.034 -10000 0 -0.23 2 2
PLD2 0.015 0.033 -10000 0 -0.4 1 1
PIP5K1A 0.005 0.069 -10000 0 -0.21 34 34
mol:Phosphatidic acid -0.006 0.1 -10000 0 -0.32 45 45
Rac1/GTP -0.016 0.055 -10000 0 -0.45 2 2
FoxO family signaling

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.012 0.17 -9999 0 -1.3 6 6
PLK1 0.05 0.21 -9999 0 -0.98 9 9
CDKN1B 0.098 0.11 -9999 0 -10000 0 0
FOXO3 0.064 0.16 -9999 0 -0.58 9 9
KAT2B 0.022 0.026 -9999 0 -0.47 1 1
FOXO1/SIRT1 -0.004 0.069 -9999 0 -0.4 6 6
CAT 0.066 0.16 -9999 0 -0.81 3 3
CTNNB1 0.014 0 -9999 0 -10000 0 0
AKT1 0.024 0.017 -9999 0 -10000 0 0
FOXO1 0.027 0.083 -9999 0 -0.39 9 9
MAPK10 0.038 0.034 -9999 0 -0.31 4 4
mol:GTP 0.002 0.002 -9999 0 -10000 0 0
FOXO4 0.094 0.067 -9999 0 -0.49 1 1
response to oxidative stress 0.01 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.011 0.14 -9999 0 -0.56 8 8
XPO1 0.015 0.001 -9999 0 -10000 0 0
EP300 0.011 0.054 -9999 0 -0.59 4 4
BCL2L11 0.028 0.11 -9999 0 -1.4 3 3
FOXO1/SKP2 0.025 0.088 -9999 0 -0.41 11 11
mol:GDP 0.01 0.02 -9999 0 -10000 0 0
RAN 0.016 0.001 -9999 0 -10000 0 0
GADD45A 0.079 0.14 -9999 0 -0.5 10 10
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.043 0.071 -9999 0 -10000 0 0
MST1 -0.017 0.15 -9999 0 -0.57 35 35
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.01 0.1 -9999 0 -0.38 3 3
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.032 0.056 -9999 0 -0.3 13 13
MAPK9 0.04 0.014 -9999 0 -10000 0 0
YWHAG 0.001 0.079 -9999 0 -0.49 13 13
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.009 0.011 -9999 0 -10000 0 0
SOD2 0.094 0.16 -9999 0 -0.63 4 4
RBL2 0.083 0.13 -9999 0 -1.2 1 1
RAL/GDP 0.029 0.017 -9999 0 -10000 0 0
CHUK 0.023 0.014 -9999 0 -10000 0 0
Ran/GTP 0.014 0.005 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
RAL/GTP 0.037 0.019 -9999 0 -10000 0 0
CSNK1G1 0.013 0.022 -9999 0 -0.49 1 1
FASLG 0.005 0.1 -9999 0 -0.4 8 8
SKP2 0.005 0.071 -9999 0 -0.55 8 8
USP7 0.016 0.001 -9999 0 -10000 0 0
IKBKB 0.023 0.014 -9999 0 -10000 0 0
CCNB1 0.056 0.18 -9999 0 -0.73 5 5
FOXO1-3a-4/beta catenin 0.12 0.13 -9999 0 -0.42 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.088 -9999 0 -0.41 11 11
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 0.006 0.099 -9999 0 -0.58 14 14
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.009 -9999 0 -10000 0 0
ZFAND5 0.097 0.06 -9999 0 -0.39 1 1
SFN -0.11 0.23 -9999 0 -0.53 117 117
CDK2 0 0.086 -9999 0 -0.53 13 13
FOXO3A/14-3-3 0.023 0.093 -9999 0 -0.37 2 2
CREBBP 0.014 0.013 -9999 0 -10000 0 0
FBXO32 0.055 0.19 -9999 0 -0.99 5 5
BCL6 0.085 0.12 -9999 0 -10000 0 0
RALB 0.015 0.001 -9999 0 -10000 0 0
RALA 0.015 0.001 -9999 0 -10000 0 0
YWHAH -0.009 0.11 -9999 0 -0.49 24 24
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.062 0.19 -10000 0 -0.55 69 69
CLTC 0.031 0.015 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.016 0.046 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0 -10000 0 -10000 0 0
EXOC4 0.014 0 -10000 0 -10000 0 0
CD59 0.025 0.022 -10000 0 -10000 0 0
CPE 0.007 0.07 -10000 0 -0.36 18 18
CTNNB1 0.014 0 -10000 0 -10000 0 0
membrane fusion 0.014 0.048 -10000 0 -10000 0 0
CTNND1 0.035 0 -10000 0 -10000 0 0
DNM2 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.025 -10000 0 -10000 0 0
TSHR -0.11 0.17 -10000 0 -0.33 195 195
INS 0.006 0.048 -10000 0 -0.52 4 4
BIN1 0.013 0.027 -10000 0 -0.59 1 1
mol:Choline 0.014 0.048 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.021 0.04 -10000 0 -0.29 4 4
ASAP2/amphiphysin II -0.001 0.014 -10000 0 -0.32 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 -0.021 0.089 -10000 0 -0.29 13 13
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.014 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.014 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.047 0.006 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.027 0.051 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.012 0.044 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.021 0.086 -10000 0 -0.29 6 6
clathrin heavy chain/ACAP1 0.031 0.03 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.014 0 -10000 0 -10000 0 0
exocyst 0.047 0.006 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.035 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.031 0.015 -10000 0 -10000 0 0
IL2RA 0.002 0.057 -10000 0 -0.29 1 1
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.036 0.083 -10000 0 -0.31 13 13
EXOC6 0.014 0 -10000 0 -10000 0 0
PLD1 -0.021 0.071 -10000 0 -0.28 33 33
PLD2 -0.001 0.012 -10000 0 -0.28 1 1
EXOC5 0.014 0 -10000 0 -10000 0 0
PIP5K1C 0.028 0.025 -10000 0 -10000 0 0
SDC1 0.011 0.05 -10000 0 -10000 0 0
ARF6/GDP 0.02 0 -10000 0 -10000 0 0
EXOC7 0.013 0.022 -10000 0 -0.49 1 1
E-cadherin/beta catenin -0.026 0.053 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.014 0.048 -10000 0 -10000 0 0
endocytosis 0.001 0.014 0.32 1 -10000 0 1
SCAMP2 0.014 0 -10000 0 -10000 0 0
ADRB2 0.022 0.071 -10000 0 -0.29 24 24
EXOC3 0.014 0 -10000 0 -10000 0 0
ASAP2 0.014 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0 -10000 0 -10000 0 0
KLC1 0.014 0 -10000 0 -10000 0 0
AVPR2 0.025 0.055 -10000 0 -10000 0 0
RALA 0.014 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.045 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0.016 -10000 0 -0.34 1 1
BAD/BCL-XL/YWHAZ 0.036 0.012 -10000 0 -10000 0 0
CDKN1B 0.04 0.009 -10000 0 -10000 0 0
CDKN1A 0.008 0.089 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
FOXO3 0.04 0.009 -10000 0 -10000 0 0
AKT1 0 0.007 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
AKT3 0.013 0.061 -10000 0 -0.55 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.04 0.016 -10000 0 -10000 0 0
AKT1/ASK1 0.034 0.038 -10000 0 -0.39 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.014 0 -10000 0 -10000 0 0
RAF1 0.014 0 -10000 0 -10000 0 0
JNK cascade 0.004 0.033 0.38 1 -10000 0 1
TSC1 0.04 0.009 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
AKT1/RAF1 0.04 0.009 -10000 0 -10000 0 0
EP300 0.009 0.053 -10000 0 -0.59 4 4
mol:GDP 0.033 0.009 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.04 0.009 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.025 0.02 -10000 0 -0.3 2 2
MAP3K5 0.006 0.07 -10000 0 -0.59 7 7
MAPKAP1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.059 0.27 1 -10000 0 1
YWHAH -0.009 0.11 -10000 0 -0.49 24 24
AKT1S1 0.04 0.009 -10000 0 -10000 0 0
CASP9 0.04 0.014 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.047 0.008 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.022 -10000 0 -0.36 2 2
YWHAE 0.014 0 -10000 0 -10000 0 0
SRC 0.014 0 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.027 0.073 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.003 -10000 0 -10000 0 0
CHUK 0.04 0.009 -10000 0 -10000 0 0
BAD/BCL-XL 0.054 0.013 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0.023 -10000 0 -0.35 2 2
FOXO1-3a-4/14-3-3 family 0.03 0.063 -10000 0 -0.29 1 1
PDPK1 0.012 0.038 -10000 0 -0.59 2 2
MDM2 0.039 0.018 -10000 0 -10000 0 0
MAPKKK cascade -0.039 0.008 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.05 0.035 -10000 0 -0.37 2 2
TSC1/TSC2 0.047 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.034 -10000 0 -0.35 2 2
glucose import -0.011 0.11 -10000 0 -0.29 71 71
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.034 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.11 -10000 0 -0.29 71 71
GSK3A 0.04 0.009 -10000 0 -10000 0 0
FOXO1 0.038 0.024 -10000 0 -10000 0 0
GSK3B 0.04 0.021 -10000 0 -0.41 1 1
SFN -0.11 0.23 -10000 0 -0.53 117 117
G1/S transition of mitotic cell cycle 0.046 0.02 -10000 0 -0.39 1 1
p27Kip1/14-3-3 family 0.007 0.085 -10000 0 -0.39 3 3
PRKACA 0.014 0 -10000 0 -10000 0 0
KPNA1 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
YWHAG 0.001 0.079 -10000 0 -0.49 13 13
RHEB 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.014 0 -10000 0 -10000 0 0
PTK2 0.014 0 -10000 0 -10000 0 0
CRKL 0.018 0.057 -10000 0 -0.29 14 14
GRB2/SOS1/SHC -0.003 0.03 -10000 0 -0.28 6 6
HRAS 0.014 0 -10000 0 -10000 0 0
IRS1/Crk 0.018 0.056 -10000 0 -0.29 14 14
IGF-1R heterotetramer/IGF1/PTP1B -0.012 0.061 -10000 0 -0.33 14 14
AKT1 0.038 0.057 -10000 0 -0.53 1 1
BAD 0.044 0.054 -10000 0 -0.49 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.018 0.056 -10000 0 -0.29 14 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.056 -10000 0 -0.29 14 14
RAF1 0.048 0.054 -10000 0 -0.52 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.025 0.055 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.009 0.061 -10000 0 -0.32 14 14
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
RPS6KB1 0.038 0.057 -10000 0 -0.53 1 1
GNB2L1 0.014 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.041 0.048 -10000 0 -0.44 1 1
PXN 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.014 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.001 0.015 -10000 0 -0.34 1 1
HRAS/GTP -0.01 0.047 -10000 0 -0.36 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.012 0.055 -10000 0 -0.43 2 2
IGF-1R heterotetramer 0.011 0.026 -10000 0 -0.48 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.018 0.057 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.009 0.045 -10000 0 -10000 0 0
IGF1R 0.011 0.026 -10000 0 -0.48 1 1
IGF1 -0.008 0.11 -10000 0 -0.56 20 20
IRS2/Crk 0.025 0.058 -10000 0 -0.47 1 1
PI3K 0.025 0.055 -10000 0 -0.29 1 1
apoptosis -0.048 0.048 0.42 1 -10000 0 1
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD 0.015 0.12 -10000 0 -0.54 14 14
RAF1/14-3-3 E 0.053 0.049 -10000 0 -0.44 1 1
BAD/14-3-3 0.051 0.051 -10000 0 -0.45 1 1
PRKCZ 0.024 0.085 -10000 0 -0.46 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.008 0.038 -10000 0 -0.44 1 1
PTPN1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.024 0.075 -10000 0 -0.4 14 14
BCAR1 0.013 0.027 -10000 0 -0.59 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.015 0.065 -10000 0 -0.4 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.014 0 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.056 -10000 0 -10000 0 0
GRB10 0.011 0.044 -10000 0 -0.56 3 3
PTPN11 0.018 0.056 -10000 0 -0.29 14 14
IRS1 0.009 0.061 -10000 0 -0.32 14 14
IRS2 0.017 0.061 -10000 0 -0.3 15 15
IGF-1R heterotetramer/IGF1 0.002 0.085 -10000 0 -0.41 21 21
GRB2 0.013 0.022 -10000 0 -0.49 1 1
PDPK1 0.031 0.059 -10000 0 -0.57 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
PRKD1 0.031 0.071 -10000 0 -0.37 14 14
SHC1 0.009 0.05 -10000 0 -0.49 5 5
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.014 0 -9999 0 -10000 0 0
SMAD2 0.016 0.018 -9999 0 -0.25 1 1
SMAD3 0.044 0.018 -9999 0 -10000 0 0
SMAD3/SMAD4 0.05 0.01 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.014 -9999 0 -10000 0 0
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.012 0.035 -9999 0 -0.54 2 2
SMAD2/SMAD4 0.023 0.015 -9999 0 -10000 0 0
MAP3K1 0.007 0.059 -9999 0 -0.49 7 7
TRAP-1/SMAD4 -0.014 0.076 -9999 0 -0.43 17 17
MAPK3 0.014 0 -9999 0 -10000 0 0
MAPK1 0.014 0 -9999 0 -10000 0 0
NUP214 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.01 0.044 -9999 0 -0.49 4 4
CTDSPL 0.013 0.027 -9999 0 -0.59 1 1
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.006 0.11 -9999 0 -0.59 17 17
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.014 0 -9999 0 -10000 0 0
KPNA2 0.012 0.031 -9999 0 -0.49 2 2
PIAS4 0.014 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.004 0.035 -9999 0 -0.47 1 1
NFKB1 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.003 0.035 -9999 0 -0.36 5 5
RELB 0.009 0.052 -9999 0 -0.51 5 5
NFKB2 0.011 0.044 -9999 0 -0.56 3 3
NF kappa B2 p52/RelB -0.005 0.043 -9999 0 -0.36 7 7
regulation of B cell activation -0.005 0.043 -9999 0 -0.36 7 7
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.009 0.053 -10000 0 -0.59 4 4
mol:PIP3 0 0.018 0.29 1 -0.3 1 2
FRAP1 0.016 0.01 -10000 0 -10000 0 0
AKT1 0.03 0.026 0.23 1 -0.45 1 2
INSR 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.035 -10000 0 -0.35 5 5
mol:GTP -0.001 0.018 -10000 0 -0.37 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.007 -10000 0 -10000 0 0
TSC2 0.014 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.016 -10000 0 -0.34 1 1
TSC1 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.001 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.03 0.017 0.18 1 -0.28 1 2
MAP3K5 0.006 0.046 -10000 0 -0.39 7 7
PIK3R1 0.014 0 -10000 0 -10000 0 0
apoptosis 0.006 0.046 -10000 0 -0.38 7 7
mol:LY294002 0 0 0.001 1 -10000 0 1
EIF4B 0.036 0.016 -10000 0 -0.24 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.013 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.002 0.016 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.026 0.015 -10000 0 -0.31 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.034 0.014 0.17 1 -0.2 1 2
FKBP1A 0.014 0 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.016 -10000 0 -0.33 1 1
mol:Amino Acids 0 0 0.001 1 -10000 0 1
FKBP12/Rapamycin 0.011 0.001 -10000 0 -10000 0 0
PDPK1 -0.001 0.03 0.24 1 -0.42 2 3
EIF4E 0.014 0 -10000 0 -10000 0 0
ASK1/PP5C 0.015 0.073 -10000 0 -0.6 7 7
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.001 0.019 -10000 0 -0.4 1 1
tumor necrosis factor receptor activity 0 0 -10000 0 -0.001 1 1
RPS6 0.013 0.022 -10000 0 -0.49 1 1
PPP5C 0.014 0 -10000 0 -10000 0 0
EIF4G1 0.014 0 -10000 0 -10000 0 0
IRS1 0.009 0.001 -10000 0 -10000 0 0
INS -0.005 0.056 -10000 0 -0.57 5 5
PTEN 0.012 0.027 -10000 0 -0.59 1 1
PDK2 -0.001 0.021 0.24 1 -0.28 2 3
EIF4EBP1 -0.003 0.13 -10000 0 -1.1 7 7
PIK3CA 0.013 0.027 -10000 0 -0.59 1 1
PPP2R5D 0.023 0.009 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.032 -10000 0 -0.31 5 5
RHEB 0.014 0 -10000 0 -10000 0 0
EIF4A1 0.014 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.003 1 2
EEF2 0.016 0.032 -10000 0 -0.31 5 5
eIF4E/4E-BP1 0.005 0.12 -10000 0 -1 7 7
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.009 0.053 -9999 0 -0.59 4 4
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.032 0.016 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.002 0.021 -9999 0 -0.24 4 4
SUMO1 0.014 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.031 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.033 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.031 0.028 -9999 0 -0.29 4 4
RANGAP1 0.014 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.004 0.035 -9999 0 -0.32 5 5
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.024 0 -9999 0 -10000 0 0
Ran/GTP 0.029 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.012 0.031 -9999 0 -0.49 2 2
UBE2I 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.013 0.027 -9999 0 -0.59 1 1
PIAS1 0.009 0.053 -9999 0 -0.59 4 4
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.009 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.005 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.001 -9999 0 -10000 0 0
CLTB 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.028 0 -9999 0 -10000 0 0
CD4 0.008 0.056 -9999 0 -0.51 6 6
CLTA 0.014 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0.016 -9999 0 -0.35 1 1
mol:PI-4-5-P2 0 0.008 -9999 0 -0.19 1 1
ARF1/GTP 0 0.004 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0.011 -9999 0 -0.22 1 1
mol:Choline 0 0.009 -9999 0 -0.2 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 0 0.009 -9999 0 -0.2 1 1
ARF1/GDP -0.001 0.011 -9999 0 -0.24 1 1
AP2M1 0.014 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.012 -9999 0 -0.24 1 1
ARFIP2 0.012 0 -9999 0 -10000 0 0
COPA 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.028 0.003 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.002 -9999 0 -10000 0 0
AP2A1 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.03 0.007 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.02 0.004 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.001 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.001 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.037 0.017 -9999 0 -10000 0 0
PLD2 0 0.009 -9999 0 -0.2 1 1
ARF-GAP1/v-SNARE 0.012 0.016 -9999 0 -0.35 1 1
PIP5K1A 0 0.009 -9999 0 -0.19 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.004 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.009 -9999 0 -0.2 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.012 0.016 -9999 0 -0.35 1 1
GOSR2 0 0.004 -9999 0 -10000 0 0
USO1 0 0.004 -9999 0 -10000 0 0
GBF1 0 0.004 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.003 0.032 -9999 0 -0.36 1 1
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 0.059 -0.21 0.059 -0.21
47_PPARGC1A 0.014 0.014 0.014 0.014
105_BMP4 0.014 0.014 0.014 0.014
105_BMP6 0.014 0.014 0.014 0.014
105_BMP7 0.014 0.014 0.014 0.014
105_BMP2 0.014 0.014 0.014 0.014
131_RELN/VLDLR 0 0 -0.32 0
30_TGFB1/TGF beta receptor Type II 0.014 0.014 0.014 0.014
84_STAT5B 0.011 0.049 0.049 0.049
84_STAT5A 0.011 0.049 0.049 0.049
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LGG-TP/11493537/LGG-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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