PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C15719M6
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C15719M6
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 53 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Signaling events mediated by Stem cell factor receptor (c-Kit) 281
Class IB PI3K non-lipid kinase events 280
EGFR-dependent Endothelin signaling events 234
Reelin signaling pathway 228
HIF-1-alpha transcription factor network 207
Signaling mediated by p38-alpha and p38-beta 198
FOXA2 and FOXA3 transcription factor networks 165
p75(NTR)-mediated signaling 162
Glucocorticoid receptor regulatory network 155
Angiopoietin receptor Tie2-mediated signaling 148
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 1037 . 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 ( 1037 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2710 281 21957 78 -0.62 0.19 1000 -1000 -0.066 -1000
Class IB PI3K non-lipid kinase events 0.2700 280 840 3 -0.22 -1000 1000 -1000 -0.031 -1000
EGFR-dependent Endothelin signaling events 0.2257 234 4921 21 -0.34 0 1000 -1000 -0.055 -1000
Reelin signaling pathway 0.2199 228 12810 56 -0.48 0 1000 -1000 -0.095 -1000
HIF-1-alpha transcription factor network 0.1996 207 15775 76 -0.76 0.019 1000 -1000 -0.08 -1000
Signaling mediated by p38-alpha and p38-beta 0.1909 198 8715 44 -0.4 0 1000 -1000 -0.046 -1000
FOXA2 and FOXA3 transcription factor networks 0.1591 165 7599 46 -1.2 0.024 1000 -1000 -0.031 -1000
p75(NTR)-mediated signaling 0.1562 162 20344 125 -0.39 0 1000 -1000 -0.098 -1000
Glucocorticoid receptor regulatory network 0.1495 155 17682 114 -0.94 0.35 1000 -1000 -0.064 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1427 148 13069 88 -0.37 0.038 1000 -1000 -0.091 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1369 142 7703 54 -0.48 0.022 1000 -1000 -0.092 -1000
FOXM1 transcription factor network 0.1360 141 7240 51 -0.44 0.014 1000 -1000 -0.13 -1000
Arf6 signaling events 0.1321 137 8508 62 -0.34 0.017 1000 -1000 -0.061 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1321 137 9346 68 -0.52 0.17 1000 -1000 -0.12 -1000
Aurora B signaling 0.1311 136 9176 67 -0.32 0.008 1000 -1000 -0.058 -1000
Endothelins 0.1302 135 12966 96 -0.38 0.037 1000 -1000 -0.06 -1000
Wnt signaling 0.1273 132 927 7 -0.17 -0.007 1000 -1000 -0.047 -1000
IL4-mediated signaling events 0.1205 125 11424 91 -1 0.52 1000 -1000 -0.14 -1000
ErbB2/ErbB3 signaling events 0.1176 122 7970 65 -0.4 0.018 1000 -1000 -0.058 -1000
Ephrin B reverse signaling 0.1148 119 5736 48 -0.32 0.18 1000 -1000 -0.064 -1000
EPHB forward signaling 0.1148 119 10129 85 -0.32 0.17 1000 -1000 -0.084 -1000
Syndecan-1-mediated signaling events 0.1032 107 3655 34 -0.22 0 1000 -1000 -0.058 -1000
IGF1 pathway 0.1022 106 6058 57 -0.18 0.081 1000 -1000 -0.091 -1000
Signaling events regulated by Ret tyrosine kinase 0.1013 105 8625 82 -0.17 0 1000 -1000 -0.077 -1000
ErbB4 signaling events 0.1003 104 7212 69 -0.42 0.057 1000 -1000 -0.076 -1000
BMP receptor signaling 0.0964 100 8100 81 -0.55 0.026 1000 -1000 -0.076 -1000
Calcium signaling in the CD4+ TCR pathway 0.0945 98 3052 31 -0.32 0.012 1000 -1000 -0.1 -1000
Noncanonical Wnt signaling pathway 0.0935 97 2531 26 -0.17 0 1000 -1000 -0.069 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0935 97 8299 85 -0.24 0.011 1000 -1000 -0.069 -1000
Nongenotropic Androgen signaling 0.0916 95 4991 52 -0.23 0.1 1000 -1000 -0.053 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0916 95 11467 120 -0.6 0.24 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.0897 93 5626 60 -0.46 0.017 1000 -1000 -0.13 -1000
Glypican 1 network 0.0887 92 4451 48 -0.32 0.03 1000 -1000 -0.042 -1000
Plasma membrane estrogen receptor signaling 0.0887 92 7953 86 -0.19 0.094 1000 -1000 -0.076 -1000
Aurora C signaling 0.0839 87 614 7 -0.17 0 1000 -1000 -0.038 -1000
Integrins in angiogenesis 0.0810 84 7098 84 -0.33 0 1000 -1000 -0.088 -1000
Signaling events mediated by PTP1B 0.0791 82 6280 76 -0.65 0.07 1000 -1000 -0.073 -1000
amb2 Integrin signaling 0.0752 78 6421 82 -0.49 0 1000 -1000 -0.079 -1000
IL6-mediated signaling events 0.0752 78 5916 75 -0.28 0.051 1000 -1000 -0.081 -1000
Visual signal transduction: Rods 0.0752 78 4104 52 -0.48 0 1000 -1000 -0.08 -1000
Ephrin A reverse signaling 0.0723 75 526 7 -0.081 0 1000 -1000 -0.025 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0675 70 3666 52 -0.19 0.03 1000 -1000 -0.064 -1000
Syndecan-3-mediated signaling events 0.0665 69 2436 35 -0.36 0 1000 -1000 -0.069 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0656 68 2343 34 -0.095 0 1000 -1000 -0.052 -1000
LPA receptor mediated events 0.0617 64 6561 102 -0.29 0.029 1000 -1000 -0.082 -1000
Signaling events mediated by the Hedgehog family 0.0608 63 3322 52 -0.22 0.03 1000 -1000 -0.081 -1000
PDGFR-alpha signaling pathway 0.0598 62 2758 44 -0.36 0.019 1000 -1000 -0.059 -1000
PLK1 signaling events 0.0588 61 5189 85 -0.22 0.029 1000 -1000 -0.051 -1000
Visual signal transduction: Cones 0.0569 59 2253 38 -0.18 0.008 1000 -1000 -0.059 -1000
Fc-epsilon receptor I signaling in mast cells 0.0569 59 5762 97 -0.24 0.028 1000 -1000 -0.079 -1000
Nectin adhesion pathway 0.0511 53 3393 63 -0.086 0.002 1000 -1000 -0.065 -1000
E-cadherin signaling in keratinocytes 0.0511 53 2285 43 -0.29 0.04 1000 -1000 -0.071 -1000
Presenilin action in Notch and Wnt signaling 0.0501 52 3226 61 -0.42 0.014 1000 -1000 -0.069 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0492 51 1713 33 -0.55 0 1000 -1000 -0.062 -1000
Rapid glucocorticoid signaling 0.0492 51 1025 20 -0.19 0.027 1000 -1000 -0.037 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0482 50 3758 74 -0.29 0.07 1000 -1000 -0.084 -1000
Signaling events mediated by HDAC Class III 0.0473 49 1983 40 -0.57 0.019 1000 -1000 -0.047 -1000
FAS signaling pathway (CD95) 0.0473 49 2339 47 -0.47 0.013 1000 -1000 -0.044 -1000
LPA4-mediated signaling events 0.0444 46 552 12 -0.16 0.02 1000 -1000 -0.02 -1000
TCGA08_rtk_signaling 0.0444 46 1204 26 -0.29 0.027 1000 -1000 -0.03 -1000
Signaling events mediated by PRL 0.0444 46 1583 34 -0.18 0.02 1000 -1000 -0.063 -1000
S1P1 pathway 0.0434 45 1634 36 -0.33 0.008 1000 -1000 -0.072 -1000
IL27-mediated signaling events 0.0424 44 2259 51 -0.29 0.033 1000 -1000 -0.074 -1000
Syndecan-4-mediated signaling events 0.0424 44 2967 67 -0.32 0.005 1000 -1000 -0.076 -1000
Canonical Wnt signaling pathway 0.0415 43 2220 51 -0.42 0.14 1000 -1000 -0.057 -1000
TCR signaling in naïve CD8+ T cells 0.0386 40 3806 93 -0.16 0.079 1000 -1000 -0.07 -1000
Regulation of Androgen receptor activity 0.0366 38 2681 70 -0.26 0.022 1000 -1000 -0.069 -1000
Coregulation of Androgen receptor activity 0.0357 37 2882 76 -0.2 0.035 1000 -1000 -0.047 -1000
IL12-mediated signaling events 0.0357 37 3288 87 -0.35 0.048 1000 -1000 -0.098 -1000
Insulin Pathway 0.0357 37 2794 74 -0.2 0.033 1000 -1000 -0.084 -1000
Ras signaling in the CD4+ TCR pathway 0.0357 37 637 17 -0.12 -0.001 1000 -1000 -0.059 -1000
Osteopontin-mediated events 0.0347 36 1375 38 -0.24 0.022 1000 -1000 -0.086 -1000
Effects of Botulinum toxin 0.0347 36 947 26 -0.098 0.001 1000 -1000 -0.052 -1000
Regulation of nuclear SMAD2/3 signaling 0.0338 35 4787 136 -0.32 0.053 1000 -1000 -0.065 -1000
Regulation of Telomerase 0.0328 34 3501 102 -0.34 0.022 1000 -1000 -0.09 -1000
Thromboxane A2 receptor signaling 0.0309 32 3425 105 -0.29 0.066 1000 -1000 -0.059 -1000
Regulation of p38-alpha and p38-beta 0.0309 32 1737 54 -0.36 0.029 1000 -1000 -0.069 -1000
TCGA08_retinoblastoma 0.0309 32 262 8 -0.052 0.01 1000 -1000 -0.024 -1000
Syndecan-2-mediated signaling events 0.0299 31 2173 69 -0.2 0.034 1000 -1000 -0.054 -1000
IL2 signaling events mediated by STAT5 0.0299 31 703 22 -0.12 0.063 1000 -1000 -0.042 -1000
BCR signaling pathway 0.0280 29 2898 99 -0.13 0.043 1000 -1000 -0.082 -1000
Aurora A signaling 0.0260 27 1651 60 -0.21 0.006 1000 -1000 -0.06 -1000
Arf6 trafficking events 0.0251 26 1907 71 -0.44 0.032 1000 -1000 -0.068 -1000
Hedgehog signaling events mediated by Gli proteins 0.0183 19 1290 65 -0.068 0.04 1000 -1000 -0.07 -1000
TRAIL signaling pathway 0.0183 19 923 48 -0.079 0.044 1000 -1000 -0.057 -1000
Glypican 2 network 0.0183 19 78 4 -0.035 -0.03 1000 -1000 -0.038 -1000
E-cadherin signaling events 0.0183 19 99 5 -0.025 0 1000 -1000 -0.046 -1000
Class I PI3K signaling events mediated by Akt 0.0174 18 1249 68 -0.25 0.054 1000 -1000 -0.062 -1000
Ceramide signaling pathway 0.0174 18 1405 76 -0.18 0.048 1000 -1000 -0.074 -1000
Retinoic acid receptors-mediated signaling 0.0174 18 1093 58 -0.1 0.037 1000 -1000 -0.059 -1000
BARD1 signaling events 0.0164 17 981 57 -0.11 0.024 1000 -1000 -0.064 -1000
Caspase cascade in apoptosis 0.0154 16 1211 74 -0.049 0.045 1000 -1000 -0.062 -1000
Cellular roles of Anthrax toxin 0.0154 16 628 39 -0.14 0.02 1000 -1000 -0.031 -1000
Signaling mediated by p38-gamma and p38-delta 0.0145 15 233 15 -0.018 0.022 1000 -1000 -0.052 -1000
IL2 signaling events mediated by PI3K 0.0145 15 877 58 -0.042 0.06 1000 -1000 -0.074 -1000
PLK2 and PLK4 events 0.0135 14 44 3 -0.012 0.013 1000 -1000 -0.029 -1000
JNK signaling in the CD4+ TCR pathway 0.0135 14 245 17 -0.019 0.043 1000 -1000 -0.061 -1000
E-cadherin signaling in the nascent adherens junction 0.0135 14 1065 76 -0.025 0.048 1000 -1000 -0.071 -1000
IL1-mediated signaling events 0.0125 13 810 62 -0.037 0.032 1000 -1000 -0.084 -1000
S1P5 pathway 0.0116 12 213 17 -0.039 0.022 1000 -1000 -0.055 -1000
S1P3 pathway 0.0116 12 510 42 -0.028 0.022 1000 -1000 -0.057 -1000
p38 MAPK signaling pathway 0.0106 11 491 44 -0.07 0.026 1000 -1000 -0.056 -1000
mTOR signaling pathway 0.0096 10 547 53 -0.02 0.026 1000 -1000 -0.054 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0087 9 262 28 -0.039 0.017 1000 -1000 -0.048 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0087 9 347 37 -0.048 0.033 1000 -1000 -0.071 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0087 9 788 83 -0.039 0.051 1000 -1000 -0.071 -1000
S1P4 pathway 0.0087 9 241 25 -0.039 0 1000 -1000 -0.051 -1000
Signaling events mediated by HDAC Class II 0.0077 8 660 75 -0.16 0 1000 -1000 -0.055 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0077 8 1023 125 -0.17 0.083 1000 -1000 -0.096 -1000
HIF-2-alpha transcription factor network 0.0068 7 313 43 -0.18 0.18 1000 -1000 -0.072 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0068 7 341 45 -0.026 0.073 1000 -1000 -0.089 -1000
VEGFR1 specific signals 0.0068 7 438 56 -0.17 0.065 1000 -1000 -0.07 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0058 6 143 23 -0.03 0.041 1000 -1000 -0.061 -1000
EPO signaling pathway 0.0058 6 380 55 -0.036 0.057 1000 -1000 -0.08 -1000
Class I PI3K signaling events 0.0058 6 454 73 -0.041 0.059 1000 -1000 -0.07 -1000
PDGFR-beta signaling pathway 0.0058 6 657 97 -0.024 0.052 1000 -1000 -0.08 -1000
FoxO family signaling 0.0048 5 343 64 -0.04 0.091 1000 -1000 -0.071 -1000
Atypical NF-kappaB pathway 0.0048 5 164 31 -0.02 0.03 1000 -1000 -0.071 -1000
Circadian rhythm pathway 0.0039 4 100 22 -0.015 0.041 1000 -1000 -0.064 -1000
Signaling events mediated by HDAC Class I 0.0039 4 481 104 -0.094 0.046 1000 -1000 -0.065 -1000
Canonical NF-kappaB pathway 0.0029 3 153 39 -0.021 0.077 1000 -1000 -0.072 -1000
a4b1 and a4b7 Integrin signaling 0.0029 3 18 5 -0.009 -0.002 1000 -1000 -0.035 -1000
Arf6 downstream pathway 0.0029 3 129 43 -0.01 0.021 1000 -1000 -0.049 -1000
IFN-gamma pathway 0.0029 3 237 68 -0.07 0.075 1000 -1000 -0.094 -1000
ceramide signaling pathway 0.0029 3 192 49 -0.028 0.053 1000 -1000 -0.051 -1000
Insulin-mediated glucose transport 0.0019 2 83 32 -0.13 0.032 1000 -1000 -0.057 -1000
Paxillin-dependent events mediated by a4b1 0.0019 2 91 36 -0.011 0.022 1000 -1000 -0.067 -1000
TCGA08_p53 0.0000 0 0 7 -0.024 0.017 1000 -1000 -0.022 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 7 27 -0.001 0.029 1000 -1000 -0.05 -1000
Arf1 pathway 0.0000 0 23 54 -0.001 0.025 1000 -1000 -0.038 -1000
Alternative NF-kappaB pathway 0.0000 0 1 13 -0.003 0 1000 -1000 -0.057 -1000
Total NA 7693 457762 7203 -31 -990 131000 -131000 -8.6 -131000
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.16 0.22 -10000 0 -0.39 472 472
CRKL -0.17 0.23 -10000 0 -0.41 472 472
HRAS -0.16 0.18 -10000 0 -0.46 60 60
mol:PIP3 -0.17 0.21 -10000 0 -0.4 474 474
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.18 0.24 -10000 0 -0.44 473 473
FOXO3 -0.15 0.21 -10000 0 -0.37 471 471
AKT1 -0.16 0.22 -10000 0 -0.41 472 472
BAD -0.15 0.21 -10000 0 -0.37 471 471
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 474 474
GSK3B -0.15 0.21 -10000 0 -0.37 471 471
RAF1 -0.092 0.17 -10000 0 -0.4 39 39
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 473 473
STAT1 -0.45 0.56 -10000 0 -1 483 483
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.36 60 60
cell proliferation -0.18 0.24 -10000 0 -0.44 474 474
PIK3CA 0 0.009 -10000 0 -0.29 1 1
TEC -0.002 0.043 -10000 0 -0.8 3 3
RPS6KB1 -0.18 0.24 -10000 0 -0.44 473 473
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.36 60 60
LYN/TEC/p62DOK -0.19 0.2 -10000 0 -0.4 473 473
MAPK3 -0.054 0.13 -10000 0 -0.32 21 21
STAP1 -0.2 0.24 -10000 0 -0.45 475 475
GRAP2 -0.015 0.11 -10000 0 -0.73 21 21
JAK2 -0.4 0.44 -10000 0 -0.87 483 483
STAT1 (dimer) -0.44 0.55 -10000 0 -1 483 483
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.19 0.2 -10000 0 -0.41 473 473
actin filament polymerization -0.18 0.24 -10000 0 -0.44 473 473
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.34 -10000 0 -0.62 475 475
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.36 470 470
PI3K -0.19 0.21 -10000 0 -0.41 477 477
PTEN -0.002 0.035 -10000 0 -0.8 2 2
SCF/KIT/EPO/EPOR -0.56 0.7 -10000 0 -1.3 471 471
MAPK8 -0.19 0.24 -10000 0 -0.45 474 474
STAT3 (dimer) -0.18 0.23 -10000 0 -0.43 473 473
positive regulation of transcription -0.041 0.11 -10000 0 -0.26 21 21
mol:GDP -0.17 0.18 -10000 0 -0.36 463 463
PIK3C2B -0.18 0.24 -10000 0 -0.44 473 473
CBL/CRKL -0.17 0.19 -10000 0 -0.38 471 471
FER -0.19 0.24 -10000 0 -0.44 478 478
SH2B3 -0.18 0.24 -10000 0 -0.44 473 473
PDPK1 -0.15 0.2 -10000 0 -0.36 473 473
SNAI2 -0.19 0.25 -10000 0 -0.45 475 475
positive regulation of cell proliferation -0.32 0.41 -10000 0 -0.75 483 483
KITLG 0.001 0.07 -10000 0 -0.7 8 8
cell motility -0.32 0.41 -10000 0 -0.75 483 483
PTPN6 0.015 0.021 -10000 0 -0.3 1 1
EPOR -0.096 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 485 485
SOCS1 -0.005 0.042 -10000 0 -0.8 1 1
cell migration 0.19 0.24 0.44 481 -10000 0 481
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.044 0.11 -10000 0 -0.3 171 171
VAV1 -0.003 0.045 -10000 0 -0.6 5 5
GRB10 -0.18 0.24 -10000 0 -0.44 473 473
PTPN11 0.013 0.013 -10000 0 -10000 0 0
SCF/KIT -0.22 0.23 -10000 0 -0.47 478 478
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.064 0.14 -10000 0 -0.35 22 22
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.73 -10000 0 -1.4 469 469
MAP2K2 -0.064 0.14 -10000 0 -0.35 22 22
SHC/Grb2/SOS1 -0.19 0.2 -10000 0 -0.4 471 471
STAT5A -0.27 0.35 -10000 0 -0.64 485 485
GRB2 0 0.009 -10000 0 -0.29 1 1
response to radiation -0.18 0.24 -10000 0 -0.44 475 475
SHC/GRAP2 -0.011 0.081 -10000 0 -0.61 18 18
PTPRO -0.18 0.24 -10000 0 -0.44 474 474
SH2B2 -0.19 0.24 -10000 0 -0.45 473 473
DOK1 -0.001 0.018 -10000 0 -0.29 4 4
MATK -0.19 0.25 -10000 0 -0.45 481 481
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.13 0.3 -10000 0 -1.5 36 36
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.22 0.36 0.8 280 -10000 0 280
PI3K Class IB/PDE3B -0.22 0.36 -10000 0 -0.8 280 280
PDE3B -0.22 0.36 -10000 0 -0.8 280 280
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS -0.003 0.027 -9999 0 -0.29 9 9
EGFR -0.29 0.39 -9999 0 -0.8 383 383
EGF/EGFR -0.28 0.31 -9999 0 -0.55 530 530
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.25 0.27 -9999 0 -0.5 519 519
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.025 -9999 0 -0.8 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.16 0.32 -9999 0 -0.8 202 202
EGF/EGFR dimer/SHC -0.29 0.31 -9999 0 -0.58 519 519
mol:GDP -0.25 0.26 -9999 0 -0.49 519 519
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.062 0.21 -9999 0 -0.8 81 81
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.23 0.25 -9999 0 -0.46 519 519
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.23 0.25 -9999 0 -0.46 519 519
FRAP1 -0.24 0.26 -9999 0 -0.48 519 519
EGF/EGFR dimer -0.34 0.35 -9999 0 -0.67 519 519
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
ETA receptor/Endothelin-1 -0.048 0.16 -9999 0 -0.61 81 81
Reelin signaling pathway

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
CDK5R1/CDK5 -0.006 0.034 -9999 0 -10000 0 0
VLDLR -0.024 0.14 -9999 0 -0.8 31 31
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.002 0.035 -9999 0 -0.8 2 2
ITGA3 -0.004 0.052 -9999 0 -0.58 7 7
RELN/VLDLR/Fyn -0.33 0.28 -9999 0 -0.55 631 631
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.047 -9999 0 -0.45 11 11
AKT1 -0.2 0.17 -9999 0 -0.33 636 636
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.068 -9999 0 -0.29 61 61
RELN/LRP8/DAB1 -0.32 0.25 -9999 0 -0.52 624 624
LRPAP1/LRP8 -0.02 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.3 0.24 -9999 0 -0.48 624 624
DAB1/alpha3/beta1 Integrin -0.28 0.23 -9999 0 -0.5 265 265
long-term memory -0.36 0.3 -9999 0 -0.54 677 677
DAB1/LIS1 -0.29 0.23 -9999 0 -0.46 631 631
DAB1/CRLK/C3G -0.28 0.22 -9999 0 -0.58 139 139
PIK3CA 0 0.009 -9999 0 -0.29 1 1
DAB1/NCK2 -0.29 0.24 -9999 0 -0.47 631 631
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.094 0.26 -9999 0 -0.76 129 129
CDK5R1 -0.008 0.048 -9999 0 -0.29 29 29
RELN -0.48 0.39 -9999 0 -0.8 626 626
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
RELN/LRP8/Fyn -0.33 0.27 -9999 0 -0.55 623 623
GRIN2A/RELN/LRP8/DAB1/Fyn -0.34 0.29 -9999 0 -0.55 644 644
MAPK8 -0.006 0.07 -9999 0 -0.8 8 8
RELN/VLDLR/DAB1 -0.32 0.26 -9999 0 -0.52 631 631
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.31 0.26 -9999 0 -0.5 635 635
RELN/LRP8 -0.33 0.27 -9999 0 -0.55 623 623
GRIN2B/RELN/LRP8/DAB1/Fyn -0.33 0.26 -9999 0 -0.5 660 660
PI3K -0.006 0.06 -9999 0 -0.61 10 10
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.039 -9999 0 -0.61 4 4
RAP1A -0.26 0.21 -9999 0 -0.54 139 139
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.048 -9999 0 -0.46 9 9
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.056 0.2 -9999 0 -0.79 73 73
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.13 0.11 -9999 0 -0.48 12 12
neuron adhesion -0.24 0.2 -9999 0 -0.51 141 141
LRP8 -0.031 0.089 -9999 0 -0.29 111 111
GSK3B -0.17 0.18 -9999 0 -0.45 66 66
RELN/VLDLR/DAB1/Fyn -0.3 0.24 -9999 0 -0.48 631 631
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.22 0.18 -9999 0 -0.35 636 636
CDK5 -0.002 0.024 -9999 0 -0.29 7 7
MAPT -0.047 0.24 -9999 0 -0.73 115 115
neuron migration -0.23 0.24 -9999 0 -0.42 624 624
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.11 -9999 0 -0.48 12 12
RELN/VLDLR -0.32 0.26 -9999 0 -0.52 631 631
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.41 0.46 -9999 0 -0.99 294 294
HDAC7 0 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.33 0.31 -9999 0 -0.77 238 238
SMAD4 -0.001 0.025 -9999 0 -0.8 1 1
ID2 -0.41 0.46 -9999 0 -0.99 291 291
AP1 -0.19 0.29 -9999 0 -0.63 308 308
ABCG2 -0.44 0.5 -9999 0 -1.1 301 301
HIF1A -0.052 0.063 -9999 0 -10000 0 0
TFF3 -0.49 0.52 -9999 0 -1.1 371 371
GATA2 -0.015 0.14 -9999 0 -0.63 42 42
AKT1 -0.053 0.08 -9999 0 -10000 0 0
response to hypoxia -0.075 0.086 -9999 0 -0.24 45 45
MCL1 -0.41 0.46 -9999 0 -0.99 290 290
NDRG1 -0.42 0.46 -9999 0 -1 292 292
SERPINE1 -0.42 0.46 -9999 0 -0.99 298 298
FECH -0.41 0.46 -9999 0 -0.99 291 291
FURIN -0.41 0.46 -9999 0 -0.99 294 294
NCOA2 -0.026 0.17 -9999 0 -0.8 45 45
EP300 -0.053 0.12 -9999 0 -0.35 55 55
HMOX1 -0.42 0.46 -9999 0 -0.99 293 293
BHLHE40 -0.42 0.46 -9999 0 -0.99 293 293
BHLHE41 -0.42 0.47 -9999 0 -1 292 292
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.05 0.055 -9999 0 -0.61 1 1
ENG -0.035 0.061 -9999 0 -0.55 1 1
JUN -0.004 0.066 -9999 0 -0.8 7 7
RORA -0.41 0.46 -9999 0 -0.99 293 293
ABCB1 -0.34 0.55 -9999 0 -1.4 205 205
TFRC -0.42 0.46 -9999 0 -0.99 295 295
CXCR4 -0.42 0.46 -9999 0 -1 292 292
TF -0.65 0.57 -9999 0 -1.1 563 563
CITED2 -0.41 0.46 -9999 0 -0.99 290 290
HIF1A/ARNT -0.5 0.52 -9999 0 -1.1 298 298
LDHA -0.049 0.047 -9999 0 -10000 0 0
ETS1 -0.42 0.46 -9999 0 -1 293 293
PGK1 -0.41 0.46 -9999 0 -0.99 294 294
NOS2 -0.42 0.46 -9999 0 -1 293 293
ITGB2 -0.42 0.46 -9999 0 -0.99 293 293
ALDOA -0.42 0.46 -9999 0 -0.99 294 294
Cbp/p300/CITED2 -0.43 0.44 -9999 0 -1 267 267
FOS -0.24 0.37 -9999 0 -0.8 307 307
HK2 -0.42 0.46 -9999 0 -1 289 289
SP1 0.012 0.024 -9999 0 -10000 0 0
GCK -0.14 0.37 -9999 0 -1.6 56 56
HK1 -0.41 0.46 -9999 0 -0.99 293 293
NPM1 -0.41 0.46 -9999 0 -0.99 293 293
EGLN1 -0.41 0.46 -9999 0 -0.99 293 293
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.41 0.46 -9999 0 -0.99 291 291
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.19 0.41 -9999 0 -1.1 139 139
IGFBP1 -0.51 0.53 -9999 0 -1.1 369 369
VEGFA -0.25 0.31 -9999 0 -0.75 120 120
HIF1A/JAB1 -0.029 0.026 -9999 0 -10000 0 0
CP -0.53 0.55 -9999 0 -1.1 397 397
CXCL12 -0.44 0.5 -9999 0 -1.1 306 306
COPS5 0.008 0.011 -9999 0 -0.29 1 1
SMAD3/SMAD4 -0.001 0.019 -9999 0 -0.61 1 1
BNIP3 -0.42 0.46 -9999 0 -0.99 293 293
EGLN3 -0.42 0.47 -9999 0 -1 297 297
CA9 -0.46 0.48 -9999 0 -1 321 321
TERT -0.43 0.47 -9999 0 -1 297 297
ENO1 -0.41 0.46 -9999 0 -0.99 291 291
PFKL -0.41 0.46 -9999 0 -0.99 293 293
NCOA1 -0.001 0.025 -9999 0 -0.8 1 1
ADM -0.44 0.49 -9999 0 -1 314 314
ARNT -0.052 0.063 -9999 0 -10000 0 0
HNF4A -0.002 0.043 -9999 0 -0.32 3 3
ADFP -0.42 0.46 -9999 0 -1 295 295
SLC2A1 -0.25 0.32 -9999 0 -0.75 128 128
LEP -0.76 0.52 -9999 0 -1.1 629 629
HIF1A/ARNT/Cbp/p300 -0.34 0.33 -9999 0 -0.8 239 239
EPO -0.24 0.27 -9999 0 -0.85 45 45
CREBBP -0.053 0.12 -9999 0 -0.35 55 55
HIF1A/ARNT/Cbp/p300/HDAC7 -0.32 0.31 -9999 0 -0.78 222 222
PFKFB3 -0.42 0.47 -9999 0 -1 291 291
NT5E -0.42 0.47 -9999 0 -1 293 293
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.4 0.62 -9999 0 -1.3 350 350
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.082 0.15 -9999 0 -0.4 13 13
ATF2/c-Jun -0.053 0.15 -9999 0 -0.79 14 14
MAPK11 -0.084 0.16 -9999 0 -0.47 19 19
MITF -0.093 0.2 -9999 0 -0.36 357 357
MAPKAPK5 -0.089 0.19 -9999 0 -0.35 353 353
KRT8 -0.095 0.19 -9999 0 -0.36 354 354
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.009 -9999 0 -0.29 1 1
p38alpha-beta/CK2 -0.12 0.24 -9999 0 -0.45 353 353
CEBPB -0.089 0.19 -9999 0 -0.35 353 353
SLC9A1 -0.089 0.19 -9999 0 -0.35 353 353
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.34 354 354
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.56 16 16
JUN -0.051 0.15 -9999 0 -0.78 14 14
PPARGC1A -0.21 0.37 -9999 0 -0.58 431 431
USF1 -0.089 0.19 -9999 0 -0.35 353 353
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.38 16 16
NOS2 -0.093 0.22 -9999 0 -0.82 18 18
DDIT3 -0.089 0.19 -9999 0 -0.35 353 353
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.074 0.17 -9999 0 -0.43 50 50
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.56 16 16
CREB1 -0.094 0.2 -9999 0 -0.37 353 353
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.07 0.17 -9999 0 -0.51 15 15
RPS6KA4 -0.089 0.19 -9999 0 -0.49 19 19
PLA2G4A -0.13 0.27 -9999 0 -0.73 126 126
GDI1 -0.089 0.19 -9999 0 -0.35 353 353
TP53 -0.12 0.24 -9999 0 -0.44 353 353
RPS6KA5 -0.095 0.2 -9999 0 -0.36 361 361
ESR1 -0.18 0.25 -9999 0 -0.42 483 483
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.19 -9999 0 -0.35 353 353
MEF2A -0.09 0.19 -9999 0 -0.35 353 353
EIF4EBP1 -0.094 0.2 -9999 0 -0.37 353 353
KRT19 -0.1 0.2 -9999 0 -0.37 357 357
ELK4 -0.089 0.19 -9999 0 -0.35 353 353
ATF6 -0.089 0.19 -9999 0 -0.35 353 353
ATF1 -0.094 0.2 -9999 0 -0.37 353 353
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.56 17 17
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.53 19 19
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.28 -9999 0 -0.75 135 135
PCK1 -1.1 0.7 -9999 0 -1.6 650 650
HNF4A -0.25 0.28 -9999 0 -0.86 78 78
KCNJ11 -0.28 0.31 -9999 0 -0.84 143 143
AKT1 -0.15 0.14 -9999 0 -0.38 65 65
response to starvation -0.001 0.007 -9999 0 -10000 0 0
DLK1 -0.5 0.56 -9999 0 -1.2 350 350
NKX2-1 -0.054 0.15 -9999 0 -0.55 2 2
ACADM -0.25 0.28 -9999 0 -0.78 130 130
TAT -1.2 0.68 -9999 0 -1.6 751 751
CEBPB 0.005 0.006 -9999 0 -10000 0 0
CEBPA -0.001 0.075 -9999 0 -0.8 9 9
TTR -0.46 0.29 -9999 0 -0.74 387 387
PKLR -0.25 0.28 -9999 0 -0.76 131 131
APOA1 -0.3 0.3 -9999 0 -0.89 98 98
CPT1C -0.25 0.28 -9999 0 -0.78 125 125
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.7 418 418
FOXF1 -0.004 0.056 -9999 0 -0.8 4 4
NF1 0.017 0.025 -9999 0 -0.8 1 1
HNF1A (dimer) 0.003 0.025 -9999 0 -0.29 5 5
CPT1A -0.24 0.28 -9999 0 -0.76 129 129
HMGCS1 -0.24 0.28 -9999 0 -0.78 116 116
NR3C1 -0.11 0.13 -9999 0 -0.53 37 37
CPT1B -0.24 0.28 -9999 0 -0.79 117 117
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.007 -9999 0 -10000 0 0
GCK -0.28 0.36 -9999 0 -0.92 163 163
CREB1 -0.059 0.066 -9999 0 -10000 0 0
IGFBP1 -0.45 0.6 -9999 0 -1.5 236 236
PDX1 -0.13 0.15 -9999 0 -0.5 14 14
UCP2 -0.24 0.28 -9999 0 -0.77 120 120
ALDOB -0.27 0.3 -9999 0 -0.81 140 140
AFP -0.7 0.61 -9999 0 -1.2 504 504
BDH1 -0.24 0.28 -9999 0 -0.76 135 135
HADH -0.26 0.3 -9999 0 -0.82 121 121
F2 -0.3 0.3 -9999 0 -0.84 126 126
HNF1A 0.003 0.025 -9999 0 -0.29 5 5
G6PC -0.2 0.12 -9999 0 -0.64 8 8
SLC2A2 -0.16 0.17 -9999 0 -0.52 11 11
INS 0.024 0.066 -9999 0 -10000 0 0
FOXA1 -0.25 0.28 -9999 0 -0.59 289 289
FOXA3 -0.43 0.23 -9999 0 -0.53 754 754
FOXA2 -0.32 0.34 -9999 0 -0.82 213 213
ABCC8 -0.35 0.44 -9999 0 -1.1 197 197
ALB -0.96 0.64 -9999 0 -1.4 682 682
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.019 -10000 0 -0.61 1 1
Necdin/E2F1 -0.082 0.15 -10000 0 -0.69 41 41
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.15 0.22 -10000 0 -0.46 334 334
NGF (dimer)/p75(NTR)/BEX1 -0.26 0.32 -10000 0 -0.63 410 410
NT-4/5 (dimer)/p75(NTR) -0.39 0.42 -10000 0 -0.77 525 525
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
AKT1 -0.15 0.22 -10000 0 -0.46 337 337
IKBKG 0 0 -10000 0 -10000 0 0
BDNF -0.07 0.22 -10000 0 -0.8 81 81
MGDIs/NGR/p75(NTR)/LINGO1 -0.2 0.25 -10000 0 -0.56 325 325
FURIN -0.001 0.013 -10000 0 -0.29 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.21 0.29 -10000 0 -0.58 370 370
LINGO1 -0.069 0.12 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.001 0.025 -10000 0 -0.8 1 1
proBDNF (dimer) -0.07 0.22 -10000 0 -0.8 81 81
NTRK1 -0.01 0.066 -10000 0 -0.36 29 29
RTN4R -0.011 0.056 -10000 0 -10000 0 0
neuron apoptosis -0.14 0.27 -10000 0 -0.5 325 325
IRAK1 -0.001 0.018 -10000 0 -0.29 4 4
SHC1 -0.16 0.27 -10000 0 -0.54 332 332
ARHGDIA 0 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.014 -10000 0 -0.45 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.16 0.23 -10000 0 -0.49 332 332
MAGEH1 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.18 0.26 -10000 0 -0.53 346 346
Mammalian IAPs/DIABLO -0.006 0.046 -10000 0 -0.48 9 9
proNGF (dimer) -0.014 0.098 -10000 0 -0.64 22 22
MAGED1 -0.001 0.018 -10000 0 -0.29 4 4
APP 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.28 0.38 -10000 0 -0.8 363 363
ZNF274 0 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.15 0.22 -10000 0 -0.46 332 332
NGF -0.014 0.099 -10000 0 -0.64 22 22
cell cycle arrest -0.12 0.23 -10000 0 -0.45 332 332
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.11 0.16 -10000 0 -0.33 332 332
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.34 0.37 -10000 0 -0.68 525 525
NCSTN 0 0 -10000 0 -10000 0 0
mol:GTP -0.18 0.26 -10000 0 -0.55 332 332
PSENEN 0 0.009 -10000 0 -0.29 1 1
mol:ceramide -0.14 0.24 -10000 0 -0.49 332 332
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.085 0.13 -10000 0 -0.48 13 13
p75(NTR)/beta APP -0.19 0.28 -10000 0 -0.61 325 325
BEX1 -0.15 0.28 -10000 0 -0.52 302 302
mol:GDP -0.16 0.27 -10000 0 -0.55 332 332
NGF (dimer) -0.082 0.18 -10000 0 -0.5 162 162
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.18 0.23 -10000 0 -0.52 325 325
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
RAC1/GTP -0.15 0.22 -10000 0 -0.47 332 332
MYD88 0 0 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.18 0.26 -10000 0 -0.56 332 332
RHOB 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.058 0.086 -10000 0 -10000 0 0
NT3 (dimer) -0.13 0.29 -10000 0 -0.76 176 176
TP53 -0.17 0.24 -10000 0 -0.46 370 370
PRDM4 -0.14 0.25 -10000 0 -0.49 332 332
BDNF (dimer) -0.17 0.23 -10000 0 -0.58 216 216
PIK3CA 0 0.009 -10000 0 -0.29 1 1
SORT1 -0.001 0.025 -10000 0 -0.8 1 1
activation of caspase activity -0.15 0.22 -10000 0 -0.46 334 334
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.16 0.23 -10000 0 -0.49 332 332
RHOC 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.16 0.27 -10000 0 -0.5 338 338
DIABLO 0 0 -10000 0 -10000 0 0
SMPD2 -0.14 0.25 -10000 0 -0.49 332 332
APH1B -0.001 0.025 -10000 0 -0.8 1 1
APH1A 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.18 0.26 -10000 0 -0.54 332 332
PSEN1 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.28 0.36 -10000 0 -0.7 421 421
MAPK8 -0.11 0.24 -10000 0 -0.44 325 325
MAPK9 -0.11 0.24 -10000 0 -0.44 325 325
APAF1 0 0 -10000 0 -10000 0 0
NTF3 -0.13 0.29 -10000 0 -0.76 176 176
NTF4 -0.28 0.38 -10000 0 -0.8 363 363
NDN -0.032 0.16 -10000 0 -0.8 41 41
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.14 0.21 -10000 0 -0.44 332 332
p75 CTF/Sortilin/TRAF6/NRIF 0 0.015 -10000 0 -0.48 1 1
RhoA-B-C/GTP -0.18 0.26 -10000 0 -0.55 332 332
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.18 0.25 -10000 0 -0.5 370 370
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.19 0.27 -10000 0 -0.53 370 370
PRKACB -0.016 0.074 -10000 0 -0.32 51 51
proBDNF (dimer)/p75 ECD -0.052 0.17 -10000 0 -0.61 81 81
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.08 -10000 0 -0.8 9 9
BIRC2 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.13 0.26 0.24 72 -0.47 333 405
BAD -0.12 0.24 -10000 0 -0.45 327 327
RIPK2 -0.001 0.02 -10000 0 -0.29 5 5
NGFR -0.25 0.37 -10000 0 -0.8 325 325
CYCS -0.15 0.22 -10000 0 -0.46 332 332
ADAM17 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.16 0.23 -10000 0 -0.49 332 332
BCL2L11 -0.12 0.24 -10000 0 -0.45 327 327
BDNF (dimer)/p75(NTR) -0.24 0.33 -10000 0 -0.66 370 370
PI3K -0.16 0.24 -10000 0 -0.5 337 337
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.16 0.23 -10000 0 -0.49 332 332
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
NGF (dimer)/p75(NTR) -0.2 0.3 -10000 0 -0.63 332 332
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.16 0.23 -10000 0 -0.5 332 332
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.025 -10000 0 -0.8 1 1
PLG -0.001 0.02 -10000 0 -0.29 5 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.19 0.27 -10000 0 -0.53 377 377
SQSTM1 0 0.009 -10000 0 -0.29 1 1
NGFRAP1 -0.002 0.035 -10000 0 -0.8 2 2
CASP3 -0.11 0.23 -10000 0 -0.42 327 327
E2F1 -0.092 0.14 -10000 0 -0.29 330 330
CASP9 0 0 -10000 0 -10000 0 0
IKK complex -0.067 0.12 -10000 0 -0.58 20 20
NGF (dimer)/TRKA -0.017 0.088 -10000 0 -0.62 19 19
MMP7 -0.12 0.28 -10000 0 -0.72 178 178
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.15 0.22 -10000 0 -0.46 332 332
MMP3 -0.12 0.16 -10000 0 -0.31 400 400
APAF-1/Caspase 9 -0.11 0.16 -10000 0 -0.66 15 15
Glucocorticoid receptor regulatory network

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
PCK2 0.023 0.078 0.34 8 -10000 0 8
SMARCC2 0.012 0.01 -10000 0 -10000 0 0
SMARCC1 0.012 0.01 -10000 0 -10000 0 0
TBX21 -0.14 0.26 -10000 0 -0.85 77 77
SUMO2 0 0.01 -10000 0 -0.29 1 1
STAT1 (dimer) 0.014 0.041 -10000 0 -0.28 19 19
FKBP4 -0.003 0.027 -10000 0 -0.29 9 9
FKBP5 -0.013 0.098 -10000 0 -0.68 20 20
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.34 63 -0.42 14 77
PRL -0.089 0.12 -10000 0 -0.5 4 4
cortisol/GR alpha (dimer)/TIF2 0.27 0.29 0.53 473 -0.55 28 501
RELA -0.039 0.083 -10000 0 -0.3 1 1
FGG 0.24 0.22 0.49 290 -0.5 1 291
GR beta/TIF2 0.11 0.19 0.33 144 -0.57 47 191
IFNG -0.43 0.35 -10000 0 -0.79 404 404
apoptosis -0.28 0.3 0.59 3 -0.67 266 269
CREB1 -0.009 0.03 -10000 0 -10000 0 0
histone acetylation 0.021 0.14 0.39 43 -0.37 38 81
BGLAP -0.1 0.15 -10000 0 -0.52 20 20
GR/PKAc 0.12 0.12 0.32 72 -0.46 3 75
NF kappa B1 p50/RelA -0.066 0.15 -10000 0 -0.42 34 34
SMARCD1 0.012 0.01 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.25 276 -10000 0 276
GATA3 -0.026 0.16 -10000 0 -0.64 54 54
AKT1 0 0.004 -10000 0 -10000 0 0
CSF2 -0.041 0.11 -10000 0 -0.6 7 7
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.21 0.27 0.56 3 -0.62 171 174
CSN2 0.2 0.18 0.41 242 -10000 0 242
BRG1/BAF155/BAF170/BAF60A -0.002 0.032 -10000 0 -0.46 5 5
NFATC1 0 0.044 -10000 0 -0.8 3 3
POU2F1 0.007 0.013 -10000 0 -0.29 1 1
CDKN1A 0.046 0.074 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN -0.015 0.097 -10000 0 -0.5 31 31
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.34 47 -0.45 6 53
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.37 0.43 0.54 3 -0.9 361 364
JUN -0.32 0.29 -10000 0 -0.58 493 493
IL4 -0.13 0.16 -10000 0 -0.56 23 23
CDK5R1 -0.008 0.049 -10000 0 -0.3 29 29
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.42 0.41 -10000 0 -0.74 569 569
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.35 41 -0.48 2 43
cortisol/GR alpha (monomer) 0.35 0.32 0.63 500 -0.44 2 502
NCOA2 -0.035 0.16 -10000 0 -0.8 45 45
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.28 0.38 -10000 0 -0.87 307 307
AP-1/NFAT1-c-4 -0.66 0.52 -10000 0 -1 654 654
AFP -0.62 0.7 -10000 0 -1.6 360 360
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.42 189 -10000 0 189
TP53 0.031 0.024 -10000 0 -0.5 2 2
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.84 0.8 -10000 0 -1.6 517 517
KRT14 -0.83 0.77 -10000 0 -1.6 548 548
TBP 0.019 0.005 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.28 413 -10000 0 413
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.001 0.004 -10000 0 -10000 0 0
AP-1 -0.67 0.52 -10000 0 -1 655 655
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.13 0.29 -10000 0 -0.81 162 162
MAPK11 -0.002 0.044 -10000 0 -0.81 3 3
KRT5 -0.94 0.81 -10000 0 -1.7 560 560
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.011 0.026 -10000 0 -0.8 1 1
STAT1 0.014 0.041 -10000 0 -0.28 19 19
CGA -0.16 0.18 -10000 0 -0.48 134 134
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.18 0.38 488 -10000 0 488
MAPK3 0 0.003 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.56 230 230
NFKB1 -0.039 0.083 -10000 0 -10000 0 0
MAPK8 -0.24 0.22 -10000 0 -0.44 447 447
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.3 0.32 0.59 3 -0.72 266 269
BAX 0.048 0.032 -10000 0 -10000 0 0
POMC -0.19 0.3 -10000 0 -0.9 90 90
EP300 0.14 0.14 0.28 426 -10000 0 426
cortisol/GR alpha (dimer)/p53 0.31 0.26 0.56 456 -10000 0 456
proteasomal ubiquitin-dependent protein catabolic process 0.087 0.079 0.24 62 -10000 0 62
SGK1 0.23 0.2 -10000 0 -1.2 6 6
IL13 -0.32 0.28 -10000 0 -0.68 246 246
IL6 -0.5 0.63 -10000 0 -1.3 388 388
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.27 0.22 -10000 0 -0.75 54 54
IL2 -0.42 0.35 -10000 0 -0.75 468 468
CDK5 -0.002 0.024 -10000 0 -0.3 7 7
PRKACB -0.016 0.074 -10000 0 -0.32 51 51
HSP90AA1 0 0.009 -10000 0 -10000 0 0
IL8 -0.2 0.3 -10000 0 -0.67 203 203
CDK5R1/CDK5 -0.007 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.058 0.097 -10000 0 -0.51 7 7
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.52 448 -0.48 1 449
SMARCA4 0.012 0.013 -10000 0 -0.29 1 1
chromatin remodeling 0.2 0.16 0.37 362 -0.34 1 363
NF kappa B1 p50/RelA/Cbp 0.061 0.17 0.34 90 -0.45 2 92
JUN (dimer) -0.32 0.29 -10000 0 -0.57 495 495
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.14 0.25 -10000 0 -0.77 90 90
NR3C1 0.2 0.2 0.44 294 -0.48 7 301
NR4A1 -0.053 0.23 -10000 0 -0.74 97 97
TIF2/SUV420H1 -0.027 0.12 -10000 0 -0.61 45 45
MAPKKK cascade -0.28 0.3 0.59 3 -0.67 266 269
cortisol/GR alpha (dimer)/Src-1 0.3 0.26 0.53 496 -10000 0 496
PBX1 0.005 0.039 -10000 0 -0.8 2 2
POU1F1 0.003 0.015 -10000 0 -0.28 2 2
SELE -0.23 0.36 -10000 0 -0.75 229 229
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.37 361 -0.34 1 362
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.29 0.24 0.52 448 -0.48 1 449
mol:cortisol 0.2 0.2 0.36 520 -10000 0 520
MMP1 -0.22 0.11 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.12 0.41 -10000 0 -0.91 221 221
NCK1/PAK1/Dok-R -0.09 0.17 -10000 0 -0.42 221 221
NCK1/Dok-R -0.24 0.47 -10000 0 -1.1 221 221
PIK3CA 0.003 0.011 -10000 0 -0.29 1 1
mol:beta2-estradiol 0.037 0.099 0.24 196 -10000 0 196
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.003 0.005 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.038 0.11 0.25 185 -0.31 8 193
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.22 0.44 -10000 0 -1.1 221 221
FN1 -0.12 0.14 -10000 0 -0.29 414 414
PLD2 -0.19 0.52 -10000 0 -1.2 221 221
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.22 -10000 0 -0.47 221 221
ELK1 -0.16 0.46 -10000 0 -1 221 221
GRB7 -0.021 0.077 -10000 0 -0.3 72 72
PAK1 -0.007 0.044 -10000 0 -0.29 24 24
Tie2/Ang1/alpha5/beta1 Integrin -0.2 0.49 -10000 0 -1.1 221 221
CDKN1A -0.063 0.28 -10000 0 -0.61 156 156
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.24 0.47 -10000 0 -1.1 221 221
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.067 0.31 -10000 0 -0.66 221 221
PLG -0.2 0.52 -10000 0 -1.2 221 221
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.18 0.37 -10000 0 -0.88 221 221
GRB2 0 0.009 -10000 0 -0.29 1 1
PIK3R1 -0.002 0.08 -10000 0 -0.81 10 10
ANGPT2 -0.11 0.27 -10000 0 -0.75 108 108
BMX -0.37 0.59 -10000 0 -1.4 224 224
ANGPT1 -0.24 0.57 -10000 0 -1.4 196 196
tube development -0.08 0.31 -10000 0 -0.64 220 220
ANGPT4 -0.24 0.37 -10000 0 -0.8 313 313
response to hypoxia -0.01 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.28 0.54 -10000 0 -1.3 221 221
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.32 0.39 -10000 0 -0.8 416 416
STAT5A (dimer) -0.096 0.35 -10000 0 -0.78 180 180
mol:L-citrulline -0.067 0.31 -10000 0 -0.66 221 221
AGTR1 -0.2 0.34 -10000 0 -0.7 308 308
MAPK14 -0.18 0.5 -10000 0 -1.1 221 221
Tie2/SHP2 -0.098 0.28 -10000 0 -1.3 48 48
TEK -0.1 0.32 -10000 0 -1.5 48 48
RPS6KB1 -0.12 0.4 -10000 0 -0.87 221 221
Angiotensin II/AT1 -0.16 0.26 -10000 0 -0.55 293 293
Tie2/Ang1/GRB2 -0.26 0.52 -10000 0 -1.2 221 221
MAPK3 -0.17 0.48 -10000 0 -1.1 221 221
MAPK1 -0.17 0.48 -10000 0 -1.1 221 221
Tie2/Ang1/GRB7 -0.26 0.52 -10000 0 -1.2 222 222
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.2 0.53 -10000 0 -1.2 221 221
PI3K -0.16 0.48 -10000 0 -1.1 221 221
FES -0.18 0.5 -10000 0 -1.1 221 221
Crk/Dok-R -0.24 0.47 -10000 0 -1.1 221 221
Tie2/Ang1/ABIN2 -0.26 0.52 -10000 0 -1.2 221 221
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.1 0.37 -10000 0 -0.8 221 221
STAT5A -0.006 0.07 -10000 0 -0.8 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.12 0.4 -10000 0 -0.87 221 221
Tie2/Ang2 -0.13 0.41 -10000 0 -0.93 186 186
Tie2/Ang1 -0.22 0.58 -10000 0 -1.3 221 221
FOXO1 -0.098 0.38 -10000 0 -0.81 222 222
ELF1 0.014 0.022 -10000 0 -10000 0 0
ELF2 -0.19 0.52 -10000 0 -1.2 221 221
mol:Choline -0.18 0.5 -10000 0 -1.1 221 221
cell migration -0.04 0.1 -10000 0 -0.24 221 221
FYN -0.098 0.35 -10000 0 -0.77 186 186
DOK2 -0.003 0.047 -10000 0 -0.8 3 3
negative regulation of cell cycle -0.053 0.25 -10000 0 -0.54 177 177
ETS1 -0.028 0.11 -10000 0 -0.98 5 5
PXN -0.079 0.33 -10000 0 -0.71 221 221
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.086 0.35 -10000 0 -0.75 221 221
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.041 0.14 -10000 0 -0.78 19 19
MAPKKK cascade -0.18 0.5 -10000 0 -1.1 221 221
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.24 0.53 -10000 0 -1.2 221 221
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.054 0.28 -10000 0 -0.59 221 221
mol:Phosphatidic acid -0.18 0.5 -10000 0 -1.1 221 221
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.067 0.31 -10000 0 -0.66 221 221
Rac1/GTP -0.17 0.33 -10000 0 -0.81 221 221
MMP2 -0.2 0.53 -10000 0 -1.2 222 222
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.024 0.14 -9999 0 -0.8 31 31
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.33 0.27 -9999 0 -0.55 623 623
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.009 -9999 0 -0.29 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.29 0.26 -9999 0 -0.5 623 623
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.068 -9999 0 -0.29 61 61
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.016 0.094 -9999 0 -0.43 39 39
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.009 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.02 0.057 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.008 0.048 -9999 0 -0.29 29 29
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.043 0.1 -9999 0 -0.29 155 155
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.34 0.28 -9999 0 -0.56 631 631
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.24 0.19 -9999 0 -0.46 178 178
MAP1B -0.007 0.051 -9999 0 -0.38 19 19
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.26 0.21 -9999 0 -0.44 623 623
RELN -0.48 0.39 -9999 0 -0.8 626 626
PAFAH/LIS1 -0.009 0.059 -9999 0 -0.53 11 11
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -9999 0 -0.44 5 5
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.21 0.17 -9999 0 -0.34 634 634
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.26 0.2 -9999 0 -0.44 393 393
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 -0.034 0.093 -9999 0 -0.29 122 122
PAFAH1B2 -0.004 0.056 -9999 0 -0.8 5 5
MAP1B/LIS1/Dynein heavy chain -0.004 0.032 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.22 0.18 -9999 0 -0.46 96 96
LRP8 -0.031 0.089 -9999 0 -0.29 111 111
NDEL1/Katanin 60 -0.24 0.19 -9999 0 -0.46 179 179
P39/CDK5 -0.28 0.22 -9999 0 -0.46 623 623
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.26 0.24 -9999 0 -0.46 623 623
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.29 0.24 -9999 0 -0.48 631 631
RELN/VLDLR -0.32 0.26 -9999 0 -0.52 631 631
CDC42 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.23 0.43 -9999 0 -0.93 154 154
PLK1 -0.085 0.1 -9999 0 -10000 0 0
BIRC5 -0.097 0.1 -9999 0 -10000 0 0
HSPA1B -0.23 0.43 -9999 0 -0.91 168 168
MAP2K1 0.008 0.029 -9999 0 -10000 0 0
BRCA2 -0.23 0.43 -9999 0 -0.92 170 170
FOXM1 -0.28 0.51 -9999 0 -1 215 215
XRCC1 -0.23 0.43 -9999 0 -0.91 172 172
FOXM1B/p19 -0.28 0.41 -9999 0 -0.9 235 235
Cyclin D1/CDK4 -0.22 0.4 -9999 0 -0.89 143 143
CDC2 -0.25 0.45 -9999 0 -0.91 215 215
TGFA -0.22 0.42 -9999 0 -0.91 152 152
SKP2 -0.23 0.43 -9999 0 -0.9 182 182
CCNE1 -0.055 0.12 -9999 0 -0.3 210 210
CKS1B -0.23 0.43 -9999 0 -0.93 155 155
RB1 -0.12 0.12 -9999 0 -0.89 1 1
FOXM1C/SP1 -0.29 0.44 -9999 0 -0.96 215 215
AURKB -0.077 0.11 -9999 0 -10000 0 0
CENPF -0.26 0.45 -9999 0 -0.93 206 206
CDK4 0.007 0.02 -9999 0 -0.3 3 3
MYC -0.21 0.41 -9999 0 -0.84 181 181
CHEK2 0.008 0.033 -9999 0 -0.31 2 2
ONECUT1 -0.23 0.42 -9999 0 -0.89 180 180
CDKN2A -0.037 0.11 -9999 0 -0.28 169 169
LAMA4 -0.23 0.44 -9999 0 -0.91 183 183
FOXM1B/HNF6 -0.26 0.48 -9999 0 -1 179 179
FOS -0.44 0.67 -9999 0 -1.3 351 351
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.23 0.43 -9999 0 -0.91 172 172
response to radiation -0.007 0.03 -9999 0 -10000 0 0
CENPB -0.23 0.43 -9999 0 -0.91 167 167
CENPA -0.26 0.45 -9999 0 -0.93 201 201
NEK2 -0.28 0.44 -9999 0 -0.95 191 191
HIST1H2BA -0.24 0.43 -9999 0 -0.9 182 182
CCNA2 -0.11 0.15 -9999 0 -0.3 413 413
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.27 0.48 -9999 0 -1 194 194
CCNB2 -0.26 0.45 -9999 0 -0.93 204 204
CCNB1 -0.25 0.46 -9999 0 -0.95 195 195
ETV5 -0.23 0.43 -9999 0 -0.97 132 132
ESR1 -0.33 0.58 -9999 0 -1.2 241 241
CCND1 -0.22 0.42 -9999 0 -0.91 145 145
GSK3A 0.014 0.021 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.081 0.14 -9999 0 -0.33 182 182
CDK2 0.006 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.009 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.32 0.37 -9999 0 -0.88 243 243
GAS1 -0.27 0.49 -9999 0 -1 204 204
MMP2 -0.24 0.44 -9999 0 -0.96 155 155
RB1/FOXM1C -0.23 0.44 -9999 0 -0.91 178 178
CREBBP 0 0 -9999 0 -10000 0 0
Arf6 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
CENTA1/KIF3B -0.004 0.045 -9999 0 -0.66 4 4
ARNO/beta Arrestin1-2 -0.13 0.19 -9999 0 -0.44 240 240
EGFR -0.29 0.39 -9999 0 -0.8 383 383
EPHA2 -0.005 0.061 -9999 0 -0.8 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.34 0.35 -9999 0 -0.67 519 519
ARRB2 -0.054 0.16 -9999 0 -0.44 143 143
mol:GTP 0.017 0.018 -9999 0 -0.16 4 4
ARRB1 -0.002 0.036 -9999 0 -0.63 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.036 0.16 -9999 0 -0.75 50 50
EGF -0.16 0.32 -9999 0 -0.8 202 202
somatostatin receptor activity 0 0 -9999 0 -0.001 366 366
ARAP2 -0.004 0.056 -9999 0 -0.8 5 5
mol:GDP -0.14 0.18 -9999 0 -0.35 332 332
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 317 317
ITGA2B -0.018 0.078 -9999 0 -0.8 3 3
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.037 -9999 0 -0.48 6 6
ADAP1 -0.005 0.05 -9999 0 -0.43 11 11
KIF13B -0.002 0.035 -9999 0 -0.8 2 2
HGF/MET -0.14 0.28 -9999 0 -0.66 220 220
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.31 365 365
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.29 0.31 -9999 0 -0.58 519 519
ADRB2 -0.18 0.34 -9999 0 -0.8 239 239
receptor agonist activity 0 0 -9999 0 0 375 375
actin filament binding 0 0 -9999 0 -0.001 370 370
SRC 0 0.009 -9999 0 -0.29 1 1
ITGB3 -0.028 0.15 -9999 0 -0.75 39 39
GNAQ -0.002 0.035 -9999 0 -0.8 2 2
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 362 362
ARF6/GDP -0.014 0.084 -9999 0 -0.42 17 17
ARF6/GDP/GULP/ACAP1 -0.15 0.2 -9999 0 -0.47 217 217
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.025 0.096 -9999 0 -0.5 38 38
ACAP1 -0.019 0.095 -9999 0 -0.39 49 49
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.091 0.23 -9999 0 -0.66 143 143
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.053 0.2 -9999 0 -0.8 68 68
CYTH3 0.01 0.02 -9999 0 -0.62 1 1
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 382 382
endosomal lumen acidification 0 0 -9999 0 -0.001 311 311
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.051 0.2 -9999 0 -0.8 66 66
GNAQ/ARNO 0.004 0.022 -9999 0 -0.46 2 2
mol:Phosphatidic acid 0 0 -9999 0 0 2 2
PIP3-E 0 0 -9999 0 0 402 402
MET -0.13 0.3 -9999 0 -0.8 172 172
GNA14 -0.014 0.088 -9999 0 -0.46 31 31
GNA15 -0.003 0.034 -9999 0 -0.8 1 1
GIT1 -0.001 0.02 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 365 365
GNA11 -0.002 0.035 -9999 0 -0.8 2 2
LHCGR -0.11 0.28 -9999 0 -0.8 143 143
AGTR1 -0.21 0.34 -9999 0 -0.7 308 308
desensitization of G-protein coupled receptor protein signaling pathway -0.091 0.23 -9999 0 -0.66 143 143
IPCEF1/ARNO -0.24 0.25 -9999 0 -0.47 519 519
alphaIIb/beta3 Integrin -0.033 0.12 -9999 0 -0.63 38 38
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.075 0.16 -10000 0 -0.39 134 134
NFATC2 -0.057 0.27 -10000 0 -0.77 115 115
NFATC3 -0.056 0.12 -10000 0 -0.31 51 51
CD40LG -0.38 0.58 -10000 0 -1.1 313 313
ITCH 0.013 0.098 -10000 0 -10000 0 0
CBLB 0.013 0.098 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.36 -10000 0 -1.2 92 92
JUNB -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.1 -10000 0 -0.34 109 109
T cell anergy -0.028 0.16 -10000 0 -0.48 109 109
TLE4 -0.031 0.26 -10000 0 -0.69 108 108
Jun/NFAT1-c-4/p21SNFT -0.31 0.44 -10000 0 -1.1 201 201
AP-1/NFAT1-c-4 -0.52 0.66 -10000 0 -1.4 312 312
IKZF1 -0.02 0.21 -10000 0 -0.63 82 82
T-helper 2 cell differentiation -0.12 0.3 -10000 0 -0.86 100 100
AP-1/NFAT1 -0.23 0.32 -10000 0 -0.64 353 353
CALM1 -0.019 0.054 -10000 0 -10000 0 0
EGR2 -0.31 0.66 -10000 0 -1.6 171 171
EGR3 -0.4 0.74 -10000 0 -1.6 278 278
NFAT1/FOXP3 -0.12 0.22 -10000 0 -0.65 89 89
EGR1 -0.25 0.37 -10000 0 -0.8 328 328
JUN -0.004 0.068 -10000 0 -0.81 7 7
EGR4 -0.021 0.075 -10000 0 -0.29 75 75
mol:Ca2+ -0.022 0.063 -10000 0 -10000 0 0
GBP3 -0.024 0.22 -10000 0 -0.62 109 109
FOSL1 -0.011 0.073 -10000 0 -0.8 6 6
NFAT1-c-4/MAF/IRF4 -0.32 0.48 -10000 0 -1.1 202 202
DGKA -0.018 0.21 -10000 0 -0.59 98 98
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.41 0.53 -10000 0 -1.1 305 305
CTLA4 -0.087 0.24 -10000 0 -0.67 79 79
NFAT1-c-4 (dimer)/EGR1 -0.44 0.58 -10000 0 -1.3 309 309
NFAT1-c-4 (dimer)/EGR4 -0.3 0.46 -10000 0 -0.96 279 279
FOS -0.24 0.37 -10000 0 -0.82 307 307
IFNG -0.16 0.27 -10000 0 -0.91 83 83
T cell activation -0.18 0.35 -10000 0 -0.8 190 190
MAF -0.001 0.025 -10000 0 -0.8 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.17 0.37 0.92 95 -10000 0 95
TNF -0.33 0.53 -10000 0 -1.1 286 286
FASLG -0.38 0.69 -10000 0 -1.3 334 334
TBX21 -0.024 0.16 -10000 0 -0.67 55 55
BATF3 -0.002 0.029 -10000 0 -0.42 4 4
PRKCQ -0.027 0.17 -10000 0 -0.7 57 57
PTPN1 -0.02 0.21 -10000 0 -0.64 75 75
NFAT1-c-4/ICER1 -0.3 0.45 -10000 0 -0.96 280 280
GATA3 -0.035 0.16 -10000 0 -0.58 66 66
T-helper 1 cell differentiation -0.15 0.26 -10000 0 -0.88 83 83
IL2RA -0.24 0.34 -10000 0 -0.99 110 110
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.21 -10000 0 -0.66 65 65
E2F1 -0.078 0.14 -10000 0 -0.28 330 330
PPARG -0.19 0.34 -10000 0 -0.8 243 243
SLC3A2 -0.018 0.21 -10000 0 -0.63 78 78
IRF4 -0.072 0.23 -10000 0 -0.8 89 89
PTGS2 -0.48 0.66 -10000 0 -1.3 367 367
CSF2 -0.37 0.56 -10000 0 -1.1 308 308
JunB/Fra1/NFAT1-c-4 -0.29 0.44 -10000 0 -1 200 200
IL4 -0.12 0.32 -10000 0 -0.93 95 95
IL5 -0.37 0.56 -10000 0 -1.1 307 307
IL2 -0.18 0.36 -10000 0 -0.82 186 186
IL3 -0.064 0.065 -10000 0 -10000 0 0
RNF128 -0.052 0.28 -10000 0 -0.86 109 109
NFATC1 -0.17 0.37 -10000 0 -0.93 93 93
CDK4 0.09 0.23 0.62 28 -10000 0 28
PTPRK -0.023 0.23 -10000 0 -0.66 89 89
IL8 -0.37 0.56 -10000 0 -1.1 316 316
POU2F1 0.001 0.01 -10000 0 -0.29 1 1
Aurora B signaling

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
Condensin I complex -0.051 0.065 -9999 0 -10000 0 0
STMN1 -0.11 0.12 -9999 0 -0.36 78 78
Aurora B/RasGAP/Survivin -0.18 0.13 -9999 0 -0.29 473 473
Chromosomal passenger complex/Cul3 protein complex -0.16 0.15 -9999 0 -0.33 420 420
BIRC5 -0.21 0.14 -9999 0 -0.29 743 743
DES -0.29 0.34 -9999 0 -0.65 476 476
Aurora C/Aurora B/INCENP -0.068 0.075 -9999 0 -0.63 1 1
Aurora B/TACC1 -0.099 0.13 -9999 0 -0.62 37 37
Aurora B/PP2A -0.098 0.095 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.008 0.016 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.17 -9999 0 -0.36 526 526
Cul3 protein complex -0.22 0.26 -9999 0 -0.53 420 420
KIF2C -0.042 0.032 -9999 0 -10000 0 0
PEBP1 0.002 0.005 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.29 777 777
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.098 0.095 -9999 0 -10000 0 0
SEPT1 -0.009 0.049 -9999 0 -0.29 31 31
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.004 0.035 -9999 0 -0.29 15 15
NSUN2/NPM1/Nucleolin 0.007 0.018 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.035 0.043 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -0.29 598 598
AURKC -0.005 0.042 -9999 0 -0.32 15 15
CDCA8 -0.098 0.14 -9999 0 -0.3 354 354
cytokinesis -0.11 0.077 -9999 0 -10000 0 0
Aurora B/Septin1 -0.095 0.086 -9999 0 -10000 0 0
AURKA -0.14 0.15 -9999 0 -10000 0 0
INCENP 0.003 0.005 -9999 0 -10000 0 0
KLHL13 -0.32 0.39 -9999 0 -0.8 419 419
BUB1 -0.2 0.14 -9999 0 -0.29 711 711
hSgo1/Aurora B/Survivin -0.25 0.18 -9999 0 -0.38 635 635
EVI5 0.008 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.1 0.099 -9999 0 -0.34 16 16
SGOL1 -0.18 0.14 -9999 0 -0.29 650 650
CENPA -0.056 0.061 -9999 0 -10000 0 0
NCAPG -0.14 0.14 -9999 0 -0.29 507 507
Aurora B/HC8 Proteasome -0.098 0.095 -9999 0 -10000 0 0
NCAPD2 -0.002 0.025 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.098 0.095 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.11 0.14 -9999 0 -0.29 410 410
NPM1 -0.017 0.023 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.002 0.035 -9999 0 -0.8 2 2
mitotic prometaphase -0.006 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.098 0.095 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.11 0.11 -9999 0 -0.36 41 41
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.017 0.023 -9999 0 -10000 0 0
MYLK -0.088 0.15 -9999 0 -0.47 130 130
KIF23 -0.091 0.14 -9999 0 -0.29 318 318
VIM -0.094 0.1 -9999 0 -0.69 2 2
RACGAP1 -0.011 0.06 -9999 0 -0.3 45 45
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.017 0.023 -9999 0 -10000 0 0
Chromosomal passenger complex -0.081 0.076 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.16 0.18 -9999 0 -0.36 289 289
TACC1 -0.029 0.15 -9999 0 -0.8 37 37
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.011 0.2 -9999 0 -0.6 85 85
PTK2B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.2 -9999 0 -0.93 33 33
EDN1 -0.038 0.24 -9999 0 -0.82 84 84
EDN3 -0.38 0.4 -9999 0 -0.8 486 486
EDN2 -0.075 0.14 -9999 0 -0.31 253 253
HRAS/GDP -0.029 0.21 -9999 0 -0.52 104 104
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.003 0.14 -9999 0 -0.36 93 93
ADCY4 -0.15 0.29 -9999 0 -0.57 294 294
ADCY5 -0.28 0.36 -9999 0 -0.61 491 491
ADCY6 -0.13 0.27 -9999 0 -0.54 278 278
ADCY7 -0.13 0.27 -9999 0 -0.54 278 278
ADCY1 -0.15 0.29 -9999 0 -0.57 293 293
ADCY2 -0.17 0.32 -9999 0 -0.61 306 306
ADCY3 -0.13 0.27 -9999 0 -0.54 278 278
ADCY8 -0.14 0.27 -9999 0 -0.55 278 278
ADCY9 -0.13 0.27 -9999 0 -0.54 278 278
arachidonic acid secretion -0.1 0.29 -9999 0 -0.47 339 339
ETB receptor/Endothelin-1/Gq/GTP -0.034 0.18 -9999 0 -0.38 179 179
GNAO1 -0.031 0.13 -9999 0 -0.48 66 66
HRAS -0.003 0.027 -9999 0 -0.29 9 9
ETA receptor/Endothelin-1/G12/GTP 0.037 0.21 -9999 0 -0.56 85 85
ETA receptor/Endothelin-1/Gs/GTP -0.091 0.32 -9999 0 -0.57 278 278
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.02 0.21 -9999 0 -0.6 85 85
EDNRB -0.073 0.24 -9999 0 -0.8 105 105
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.026 0.24 -9999 0 -0.69 102 102
CYSLTR1 -0.022 0.24 -9999 0 -0.68 97 97
SLC9A1 0.001 0.1 -9999 0 -0.3 84 84
mol:GDP -0.037 0.22 -9999 0 -0.53 120 120
SLC9A3 -0.053 0.28 -9999 0 -0.63 174 174
RAF1 -0.083 0.25 -9999 0 -0.54 156 156
JUN 0.027 0.18 -9999 0 -0.78 34 34
JAK2 -0.011 0.2 -9999 0 -0.6 85 85
mol:IP3 -0.028 0.18 -9999 0 -0.44 107 107
ETA receptor/Endothelin-1 0.034 0.25 -9999 0 -0.66 95 95
PLCB1 -0.051 0.21 -9999 0 -0.81 74 74
PLCB2 0.007 0.027 -9999 0 -0.55 2 2
ETA receptor/Endothelin-3 -0.28 0.32 -9999 0 -0.62 485 485
FOS -0.25 0.49 -9999 0 -0.98 317 317
Gai/GDP -0.015 0.16 -9999 0 -0.81 26 26
CRK 0 0 -9999 0 -10000 0 0
mol:Ca ++ -0.05 0.25 -9999 0 -0.64 122 122
BCAR1 0.002 0.005 -9999 0 -10000 0 0
PRKCB1 -0.031 0.17 -9999 0 -0.42 110 110
GNAQ 0.008 0.037 -9999 0 -0.81 2 2
GNAZ -0.007 0.075 -9999 0 -0.8 9 9
GNAL -0.19 0.34 -9999 0 -0.8 244 244
Gs family/GDP -0.17 0.26 -9999 0 -0.54 290 290
ETA receptor/Endothelin-1/Gq/GTP 0.017 0.13 -9999 0 -0.38 68 68
MAPK14 -0.031 0.17 -9999 0 -0.47 93 93
TRPC6 0.018 0.22 -9999 0 -1.1 31 31
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.039 0.17 -9999 0 -0.8 50 50
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.04 0.18 -9999 0 -0.39 174 174
ETB receptor/Endothelin-2 -0.11 0.21 -9999 0 -0.66 112 112
ETB receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.66 540 540
ETB receptor/Endothelin-1 -0.084 0.28 -9999 0 -0.67 174 174
MAPK3 -0.19 0.41 -9999 0 -0.78 324 324
MAPK1 -0.19 0.41 -9999 0 -0.78 324 324
Rac1/GDP -0.028 0.2 -9999 0 -0.51 104 104
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.6 293 293
MAPK8 0.019 0.19 -9999 0 -0.74 41 41
SRC 0 0.009 -9999 0 -0.29 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.048 0.18 -9999 0 -0.53 86 86
p130Cas/CRK/Src/PYK2 -0.014 0.22 -9999 0 -0.6 78 78
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.028 0.2 -9999 0 -0.52 102 102
COL1A2 -0.056 0.26 -9999 0 -0.69 100 100
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.12 -9999 0 -0.43 22 22
mol:DAG -0.029 0.18 -9999 0 -0.44 107 107
MAP2K2 -0.13 0.32 -9999 0 -0.57 324 324
MAP2K1 -0.13 0.32 -9999 0 -0.57 324 324
EDNRA 0.027 0.069 -9999 0 -0.46 4 4
positive regulation of muscle contraction -0.012 0.17 -9999 0 -0.52 85 85
Gq family/GDP -0.074 0.16 -9999 0 -0.57 64 64
HRAS/GTP -0.051 0.21 -9999 0 -0.47 143 143
PRKCH -0.023 0.17 -9999 0 -0.47 85 85
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.035 0.2 -9999 0 -0.52 104 104
PRKCB -0.034 0.19 -9999 0 -0.55 80 80
PRKCE -0.023 0.17 -9999 0 -0.5 69 69
PRKCD -0.024 0.17 -9999 0 -0.47 85 85
PRKCG -0.032 0.18 -9999 0 -0.49 81 81
regulation of vascular smooth muscle contraction -0.29 0.57 -9999 0 -1.1 317 317
PRKCQ -0.046 0.22 -9999 0 -0.54 119 119
PLA2G4A -0.12 0.33 -9999 0 -0.52 339 339
GNA14 -0.004 0.09 -9999 0 -0.46 31 31
GNA15 0.006 0.036 -9999 0 -0.35 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.036 -9999 0 -0.8 2 2
Rac1/GTP 0.037 0.21 -9999 0 -0.56 85 85
MMP1 -0.12 0.13 -9999 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.16 0.24 -9999 0 -0.44 366 366
FZD6 -0.007 0.075 -9999 0 -0.8 9 9
WNT6 -0.17 0.32 -9999 0 -0.71 247 247
WNT4 -0.022 0.12 -9999 0 -0.53 42 42
FZD3 -0.009 0.082 -9999 0 -0.8 11 11
WNT5A -0.014 0.1 -9999 0 -0.6 25 25
WNT11 -0.17 0.32 -9999 0 -0.77 227 227
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.46 0.46 -10000 0 -1.1 221 221
STAT6 (cleaved dimer) -0.5 0.45 -10000 0 -1 364 364
IGHG1 -0.16 0.16 -10000 0 -0.36 83 83
IGHG3 -0.46 0.44 -10000 0 -0.99 327 327
AKT1 -0.21 0.24 -10000 0 -0.67 79 79
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.2 -10000 0 -0.62 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.25 -10000 0 -0.69 81 81
THY1 -0.46 0.46 -10000 0 -1.1 245 245
MYB -0.016 0.11 -10000 0 -0.73 22 22
HMGA1 -0.014 0.061 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.69 213 213
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.23 -10000 0 -0.64 61 61
SP1 0.018 0.004 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.024 0.029 -10000 0 -0.78 1 1
STAT6 (dimer)/ETS1 -0.49 0.44 -10000 0 -1 321 321
SOCS1 -0.3 0.31 -10000 0 -0.74 192 192
SOCS3 -0.23 0.26 -10000 0 -0.81 68 68
FCER2 -0.6 0.65 -10000 0 -1.5 327 327
PARP14 0.003 0.018 -10000 0 -0.3 3 3
CCL17 -0.47 0.46 -10000 0 -1.1 230 230
GRB2 0 0.009 -10000 0 -0.29 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.62 24 24
T cell proliferation -0.46 0.48 -10000 0 -1.1 247 247
IL4R/JAK1 -0.46 0.46 -10000 0 -1.1 232 232
EGR2 -0.61 0.64 -10000 0 -1.5 292 292
JAK2 -0.008 0.036 -10000 0 -0.83 1 1
JAK3 0.01 0.036 -10000 0 -0.29 14 14
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
JAK1 0.004 0.027 -10000 0 -0.8 1 1
COL1A2 -0.14 0.16 -10000 0 -1.7 2 2
CCL26 -0.46 0.46 -10000 0 -1.1 258 258
IL4R -0.5 0.49 -10000 0 -1.2 240 240
PTPN6 0.022 0.018 -10000 0 -0.27 1 1
IL13RA2 -0.46 0.46 -10000 0 -1.1 226 226
IL13RA1 -0.007 0.026 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.6 108 108
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.28 -10000 0 -0.69 162 162
GTF3A 0.013 0.016 -10000 0 -0.28 2 2
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL13RA1/JAK2 -0.014 0.042 -10000 0 -0.63 1 1
IRF4/BCL6 -0.2 0.43 -10000 0 -1.4 107 107
CD40LG -0.032 0.18 -10000 0 -0.78 55 55
MAPK14 -0.26 0.28 -10000 0 -0.71 145 145
mitosis -0.2 0.23 -10000 0 -0.63 79 79
STAT6 -0.53 0.54 -10000 0 -1.2 311 311
SPI1 0.007 0.024 -10000 0 -0.28 6 6
RPS6KB1 -0.19 0.22 -10000 0 -0.64 59 59
STAT6 (dimer) -0.53 0.54 -10000 0 -1.2 311 311
STAT6 (dimer)/PARP14 -0.52 0.51 -10000 0 -1.1 346 346
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.23 -10000 0 -0.66 69 69
FRAP1 -0.21 0.24 -10000 0 -0.67 79 79
LTA -0.47 0.46 -10000 0 -1.1 249 249
FES -0.002 0.043 -10000 0 -0.8 3 3
T-helper 1 cell differentiation 0.52 0.52 1.2 311 -10000 0 311
CCL11 -0.49 0.44 -10000 0 -1.1 265 265
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.24 -10000 0 -0.66 70 70
IL2RG -0.005 0.09 -10000 0 -0.36 52 52
IL10 -0.46 0.47 -10000 0 -1.1 232 232
IRS1 -0.033 0.16 -10000 0 -0.8 43 43
IRS2 -0.032 0.16 -10000 0 -0.8 41 41
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.47 0.46 -10000 0 -1.2 210 210
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.83 278 278
COL1A1 -0.18 0.17 -10000 0 -1.8 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.48 -10000 0 -1.2 194 194
IL2R gamma/JAK3 -0.013 0.072 -10000 0 -0.46 20 20
TFF3 -0.57 0.59 -10000 0 -1.3 310 310
ALOX15 -0.54 0.57 -10000 0 -1.3 273 273
MYBL1 -0.043 0.1 -10000 0 -0.29 154 154
T-helper 2 cell differentiation -0.4 0.38 -10000 0 -0.87 292 292
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.008 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.24 -10000 0 -0.67 67 67
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.67 79 79
PI3K -0.22 0.26 -10000 0 -0.72 79 79
DOK2 -0.003 0.047 -10000 0 -0.8 3 3
ETS1 0.019 0.056 -10000 0 -0.76 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.18 -10000 0 -0.68 15 15
ITGB3 -0.48 0.5 -10000 0 -1.2 233 233
PIGR -1 0.75 -10000 0 -1.5 661 661
IGHE 0.046 0.04 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.67 15 15
BCL6 0.002 0.057 -10000 0 -0.8 5 5
OPRM1 -0.47 0.46 -10000 0 -1.1 249 249
RETNLB -0.47 0.46 -10000 0 -1.2 219 219
SELP -0.63 0.68 -10000 0 -1.6 312 312
AICDA -0.45 0.44 -10000 0 -1.1 205 205
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.39 20 20
NFATC4 -0.088 0.16 -9999 0 -0.36 27 27
ERBB2IP 0.007 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.009 -9999 0 -10000 0 0
mammary gland morphogenesis -0.15 0.19 -9999 0 -0.39 380 380
JUN -0.018 0.08 -9999 0 -0.37 6 6
HRAS -0.003 0.027 -9999 0 -0.29 9 9
DOCK7 -0.12 0.19 -9999 0 -0.37 380 380
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.22 -9999 0 -0.47 380 380
AKT1 0.007 0.006 -9999 0 -10000 0 0
BAD 0.018 0.008 -9999 0 -10000 0 0
MAPK10 -0.11 0.14 -9999 0 -0.35 171 171
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.2 -9999 0 -0.43 380 380
RAF1 -0.08 0.16 -9999 0 -0.4 15 15
ErbB2/ErbB3/neuregulin 2 -0.26 0.25 -9999 0 -0.51 513 513
STAT3 0.001 0.004 -9999 0 -10000 0 0
cell migration -0.062 0.13 -9999 0 -0.3 96 96
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.13 0.22 -9999 0 -0.51 162 162
FOS -0.16 0.26 -9999 0 -0.54 309 309
NRAS -0.001 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.15 0.19 -9999 0 -0.39 380 380
MAPK3 -0.1 0.18 -9999 0 -0.42 159 159
MAPK1 -0.1 0.18 -9999 0 -0.42 159 159
JAK2 -0.12 0.19 -9999 0 -0.37 381 381
NF2 -0.006 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.17 -9999 0 -0.36 380 380
NRG1 -0.29 0.39 -9999 0 -0.8 378 378
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.33 384 384
MAPK9 -0.069 0.088 -9999 0 -0.22 18 18
ERBB2 -0.016 0.055 -9999 0 -10000 0 0
ERBB3 0.001 0.044 -9999 0 -0.81 3 3
SHC1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.015 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0.001 0.004 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.007 0.005 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.099 0.12 -9999 0 -0.32 23 23
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.042 -9999 0 -10000 0 0
CHRNA1 -0.09 0.16 -9999 0 -0.41 55 55
myelination -0.082 0.16 -9999 0 -0.36 27 27
PPP3CB -0.13 0.16 -9999 0 -0.36 167 167
KRAS -0.001 0.013 -9999 0 -0.29 2 2
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.3 380 380
NRG2 -0.4 0.4 -9999 0 -0.8 510 510
mol:GDP -0.12 0.18 -9999 0 -0.36 380 380
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.072 0.15 -9999 0 -0.4 13 13
SRC 0 0.009 -9999 0 -0.29 1 1
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.37 380 380
MAP2K1 -0.13 0.21 -9999 0 -0.48 158 158
heart morphogenesis -0.15 0.19 -9999 0 -0.39 380 380
RAS family/GDP -0.11 0.14 -9999 0 -0.39 17 17
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA -0.01 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.023 -9999 0 -0.18 6 6
HSP90AA1 0 0.009 -9999 0 -10000 0 0
activation of caspase activity -0.007 0.006 -9999 0 -10000 0 0
nervous system development -0.15 0.19 -9999 0 -0.39 380 380
CDC42 0 0 -9999 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 -0.004 0.039 -10000 0 -0.29 19 19
EFNB1 0.017 0.053 -10000 0 -0.62 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.17 0.21 -10000 0 -0.42 415 415
Ephrin B2/EPHB1-2 -0.2 0.24 -10000 0 -0.49 414 414
neuron projection morphogenesis -0.16 0.2 -10000 0 -0.4 415 415
Ephrin B1/EPHB1-2/Tiam1 -0.18 0.22 -10000 0 -0.45 415 415
DNM1 -0.006 0.067 -10000 0 -0.74 8 8
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.005 0.14 -10000 0 -0.74 33 33
YES1 -0.027 0.17 -10000 0 -0.99 32 32
Ephrin B1/EPHB1-2/NCK2 -0.18 0.22 -10000 0 -0.45 415 415
PI3K -0.028 0.14 -10000 0 -0.71 41 41
mol:GDP -0.18 0.22 -10000 0 -0.45 415 415
ITGA2B -0.018 0.078 -10000 0 -0.8 3 3
endothelial cell proliferation 0 0.005 -10000 0 -10000 0 0
FYN -0.027 0.17 -10000 0 -0.98 32 32
MAP3K7 -0.023 0.14 -10000 0 -0.8 32 32
FGR -0.029 0.17 -10000 0 -0.99 32 32
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.047 0.17 -10000 0 -0.64 68 68
LYN -0.027 0.17 -10000 0 -0.98 32 32
Ephrin B1/EPHB1-2/Src Family Kinases -0.028 0.16 -10000 0 -0.93 32 32
Ephrin B1/EPHB1-2 -0.03 0.15 -10000 0 -0.87 32 32
SRC -0.029 0.17 -10000 0 -0.99 32 32
ITGB3 -0.028 0.15 -10000 0 -0.75 39 39
EPHB1 -0.32 0.39 -10000 0 -0.8 415 415
EPHB4 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.033 0.12 -10000 0 -0.63 38 38
BLK -0.029 0.17 -10000 0 -0.99 32 32
HCK -0.029 0.17 -10000 0 -0.99 32 32
regulation of stress fiber formation 0.18 0.22 0.45 415 -10000 0 415
MAPK8 0 0.14 -10000 0 -0.72 37 37
Ephrin B1/EPHB1-2/RGS3 -0.18 0.22 -10000 0 -0.45 415 415
endothelial cell migration -0.017 0.12 -10000 0 -0.7 32 32
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.019 0.16 -10000 0 -0.92 32 32
regulation of focal adhesion formation 0.18 0.22 0.45 415 -10000 0 415
chemotaxis 0.18 0.22 0.45 415 -10000 0 415
PIK3CA 0 0.009 -10000 0 -0.29 1 1
Rac1/GTP -0.17 0.2 -10000 0 -0.41 415 415
angiogenesis -0.03 0.15 -10000 0 -0.86 32 32
LCK -0.031 0.17 -10000 0 -0.99 32 32
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.057 0.16 -10000 0 -0.54 104 104
cell-cell adhesion 0.17 0.22 0.68 73 -10000 0 73
Ephrin B/EPHB2/RasGAP -0.04 0.12 -10000 0 -0.45 87 87
ITSN1 -0.001 0.025 -10000 0 -0.8 1 1
PIK3CA 0 0.009 -10000 0 -0.29 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.017 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.22 0.26 -10000 0 -0.54 414 414
HRAS/GDP -0.18 0.23 -10000 0 -0.66 94 94
Ephrin B/EPHB1/GRB7 -0.22 0.28 -10000 0 -0.53 434 434
Endophilin/SYNJ1 -0.037 0.12 -10000 0 -0.42 87 87
KRAS -0.001 0.013 -10000 0 -0.29 2 2
Ephrin B/EPHB1/Src -0.22 0.28 -10000 0 -0.52 433 433
endothelial cell migration -0.005 0.044 -10000 0 -0.45 10 10
GRB2 0 0.009 -10000 0 -0.29 1 1
GRB7 -0.021 0.077 -10000 0 -0.3 72 72
PAK1 -0.046 0.14 -10000 0 -0.46 96 96
HRAS -0.003 0.027 -10000 0 -0.29 9 9
RRAS -0.038 0.12 -10000 0 -0.43 87 87
DNM1 -0.006 0.066 -10000 0 -0.74 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.21 0.26 -10000 0 -0.49 433 433
lamellipodium assembly -0.17 0.22 -10000 0 -0.68 73 73
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.15 0.19 -10000 0 -0.37 414 414
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
EPHB2 -0.005 0.039 -10000 0 -0.29 19 19
EPHB3 -0.004 0.033 -10000 0 -0.29 14 14
EPHB1 -0.32 0.39 -10000 0 -0.8 415 415
EPHB4 0 0.009 -10000 0 -0.29 1 1
mol:GDP -0.16 0.21 -10000 0 -0.64 92 92
Ephrin B/EPHB2 -0.04 0.13 -10000 0 -0.46 87 87
Ephrin B/EPHB3 -0.04 0.13 -10000 0 -0.46 87 87
JNK cascade -0.18 0.22 -10000 0 -0.44 414 414
Ephrin B/EPHB1 -0.22 0.28 -10000 0 -0.53 433 433
RAP1/GDP -0.13 0.18 -10000 0 -0.56 86 86
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.067 0.22 -10000 0 -0.8 87 87
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.2 0.24 -10000 0 -0.49 414 414
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.18 0.23 -10000 0 -0.69 91 91
Rap1/GTP -0.17 0.22 -10000 0 -0.71 72 72
axon guidance -0.057 0.16 -10000 0 -0.54 104 104
MAPK3 -0.1 0.19 -10000 0 -0.53 68 68
MAPK1 -0.1 0.19 -10000 0 -0.53 68 68
Rac1/GDP -0.14 0.19 -10000 0 -0.59 87 87
actin cytoskeleton reorganization -0.13 0.17 -10000 0 -0.52 77 77
CDC42/GDP -0.14 0.19 -10000 0 -0.59 87 87
PI3K -0.005 0.045 -10000 0 -0.46 10 10
EFNA5 -0.081 0.24 -10000 0 -0.8 105 105
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.028 0.094 -10000 0 -0.33 87 87
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.17 0.22 -10000 0 -0.67 76 76
PTK2 0.042 0.051 -10000 0 -10000 0 0
MAP4K4 -0.18 0.22 -10000 0 -0.45 414 414
SRC 0 0.009 -10000 0 -0.29 1 1
KALRN -0.014 0.1 -10000 0 -0.8 18 18
Intersectin/N-WASP -0.001 0.019 -10000 0 -0.61 1 1
neuron projection morphogenesis -0.14 0.18 -10000 0 -0.55 76 76
MAP2K1 -0.14 0.18 -10000 0 -0.56 69 69
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.19 0.24 -10000 0 -0.48 414 414
cell migration -0.12 0.22 -10000 0 -0.64 69 69
NRAS -0.001 0.013 -10000 0 -10000 0 0
SYNJ1 -0.038 0.12 -10000 0 -0.43 87 87
PXN 0 0 -10000 0 -10000 0 0
TF -0.25 0.27 -10000 0 -0.46 596 596
HRAS/GTP -0.19 0.24 -10000 0 -0.45 433 433
Ephrin B1/EPHB1-2 -0.2 0.24 -10000 0 -0.49 414 414
cell adhesion mediated by integrin 0.007 0.13 0.42 87 -10000 0 87
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.2 0.26 -10000 0 -0.48 433 433
RAC1-CDC42/GTP -0.17 0.22 -10000 0 -0.69 73 73
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.13 0.18 -10000 0 -0.56 86 86
ruffle organization -0.18 0.22 -10000 0 -0.71 73 73
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.003 0.14 -10000 0 -0.43 89 89
Ephrin B/EPHB2/KALRN -0.047 0.15 -10000 0 -0.49 96 96
ROCK1 0.022 0.024 -10000 0 -0.49 1 1
RAS family/GDP -0.12 0.16 -10000 0 -0.53 69 69
Rac1/GTP -0.18 0.24 -10000 0 -0.75 73 73
Ephrin B/EPHB1/Src/Paxillin -0.16 0.2 -10000 0 -0.38 433 433
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0.009 -9999 0 -0.29 1 1
CCL5 -0.015 0.081 -9999 0 -0.36 44 44
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.078 0.11 -9999 0 -0.32 150 150
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 -0.072 0.097 -9999 0 -0.35 44 44
Syndecan-1/Syntenin -0.072 0.097 -9999 0 -0.32 103 103
MAPK3 -0.046 0.096 -9999 0 -0.48 5 5
HGF/MET -0.14 0.28 -9999 0 -0.66 220 220
TGFB1/TGF beta receptor Type II 0 0.009 -9999 0 -0.29 1 1
BSG 0 0.009 -9999 0 -0.29 1 1
keratinocyte migration -0.071 0.096 -9999 0 -0.32 102 102
Syndecan-1/RANTES -0.08 0.11 -9999 0 -0.34 106 106
Syndecan-1/CD147 -0.063 0.094 -9999 0 -0.46 7 7
Syndecan-1/Syntenin/PIP2 -0.069 0.094 -9999 0 -0.31 103 103
LAMA5 0 0.009 -9999 0 -0.29 1 1
positive regulation of cell-cell adhesion -0.068 0.092 -9999 0 -0.3 103 103
MMP7 -0.12 0.28 -9999 0 -0.72 178 178
HGF -0.053 0.2 -9999 0 -0.8 68 68
Syndecan-1/CASK -0.074 0.1 -9999 0 -0.3 150 150
Syndecan-1/HGF/MET -0.17 0.25 -9999 0 -0.6 223 223
regulation of cell adhesion -0.039 0.093 -9999 0 -0.46 5 5
HPSE -0.007 0.052 -9999 0 -0.34 20 20
positive regulation of cell migration -0.078 0.11 -9999 0 -0.32 150 150
SDC1 -0.078 0.11 -9999 0 -0.32 150 150
Syndecan-1/Collagen -0.078 0.11 -9999 0 -0.32 150 150
PPIB -0.001 0.016 -9999 0 -0.29 3 3
MET -0.13 0.3 -9999 0 -0.8 172 172
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.29 453 453
MAPK1 -0.046 0.096 -9999 0 -0.48 5 5
homophilic cell adhesion -0.077 0.11 -9999 0 -0.32 150 150
MMP1 -0.22 0.12 -9999 0 -0.29 787 787
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.1 0.24 -10000 0 -0.5 240 240
GRB2/SOS1/SHC 0 0.004 -10000 0 -10000 0 0
HRAS -0.003 0.027 -10000 0 -0.29 9 9
IRS1/Crk -0.12 0.23 -10000 0 -0.5 254 254
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.24 -10000 0 -0.54 240 240
AKT1 -0.069 0.22 -10000 0 -0.74 47 47
BAD -0.056 0.2 -10000 0 -0.68 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.24 -10000 0 -0.49 254 254
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.23 -10000 0 -0.5 254 254
RAF1 -0.048 0.19 -10000 0 -0.64 45 45
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.22 -10000 0 -0.48 240 240
YWHAZ -0.001 0.016 -10000 0 -0.29 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.25 -10000 0 -0.54 254 254
PIK3CA 0 0.009 -10000 0 -0.29 1 1
RPS6KB1 -0.069 0.22 -10000 0 -0.74 47 47
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.041 0.16 -10000 0 -0.52 45 45
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.2 -10000 0 -0.73 44 44
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.19 -10000 0 -0.43 240 240
IGF-1R heterotetramer -0.034 0.14 -10000 0 -0.85 24 24
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.23 -10000 0 -0.5 254 254
Crk/p130 Cas/Paxillin -0.11 0.21 -10000 0 -0.45 240 240
IGF1R -0.034 0.14 -10000 0 -0.85 24 24
IGF1 -0.18 0.35 -10000 0 -0.83 231 231
IRS2/Crk -0.13 0.25 -10000 0 -0.52 256 256
PI3K -0.12 0.23 -10000 0 -0.49 241 241
apoptosis 0.081 0.15 0.56 46 -10000 0 46
HRAS/GDP -0.002 0.018 -10000 0 -10000 0 0
PRKCD -0.095 0.25 -10000 0 -0.54 240 240
RAF1/14-3-3 E -0.076 0.14 -10000 0 -0.53 45 45
BAD/14-3-3 -0.086 0.16 -10000 0 -0.61 46 46
PRKCZ -0.069 0.22 -10000 0 -0.74 48 48
Crk/p130 Cas/Paxillin/FAK1 -0.085 0.16 -10000 0 -0.63 45 45
PTPN1 -0.003 0.03 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.14 0.25 -10000 0 -0.57 240 240
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.21 -10000 0 -0.47 240 240
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.23 -10000 0 -0.49 254 254
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.1 0.24 -10000 0 -0.49 254 254
IRS1 -0.13 0.25 -10000 0 -0.54 254 254
IRS2 -0.12 0.28 -10000 0 -0.54 267 267
IGF-1R heterotetramer/IGF1 -0.16 0.29 -10000 0 -0.67 240 240
GRB2 0 0.009 -10000 0 -0.29 1 1
PDPK1 -0.11 0.21 -10000 0 -0.8 48 48
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.58 246 246
SHC1 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.036 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.082 0.16 -9999 0 -0.39 196 196
JUN -0.051 0.14 -9999 0 -0.42 61 61
HRAS -0.003 0.027 -9999 0 -0.29 9 9
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.2 -9999 0 -0.53 198 198
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.028 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.2 -9999 0 -0.53 198 198
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.19 -9999 0 -0.5 189 189
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.48 198 198
GRB7 -0.021 0.077 -9999 0 -0.3 72 72
RET51/GFRalpha1/GDNF -0.15 0.2 -9999 0 -0.53 198 198
MAPKKK cascade -0.1 0.17 -9999 0 -0.43 195 195
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.24 -9999 0 -0.57 201 201
lamellipodium assembly -0.083 0.15 -9999 0 -0.37 196 196
RET51/GFRalpha1/GDNF/SHC -0.15 0.2 -9999 0 -0.53 198 198
PIK3CA 0 0.009 -9999 0 -0.29 1 1
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.5 189 189
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.5 189 189
MAPK3 -0.12 0.17 -9999 0 -0.45 195 195
DOK1 -0.001 0.018 -9999 0 -0.29 4 4
DOK6 -0.013 0.095 -9999 0 -0.8 14 14
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.54 54 54
DOK5 -0.02 0.12 -9999 0 -0.72 29 29
GFRA1 -0.16 0.31 -9999 0 -0.69 245 245
MAPK8 -0.077 0.14 -9999 0 -0.34 200 200
HRAS/GTP -0.12 0.19 -9999 0 -0.49 195 195
tube development -0.096 0.18 -9999 0 -0.47 189 189
MAPK1 -0.12 0.17 -9999 0 -0.45 195 195
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.066 0.13 -9999 0 -0.34 189 189
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.15 0.2 -9999 0 -0.52 204 204
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.2 -9999 0 -0.53 198 198
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.56 213 213
PRKCA -0.021 0.13 -9999 0 -0.77 29 29
HRAS/GDP -0.002 0.018 -9999 0 -10000 0 0
CREB1 -0.073 0.15 -9999 0 -0.38 189 189
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.065 0.13 -9999 0 -0.34 189 189
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.55 200 200
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.16 -9999 0 -0.31 386 386
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.05 0.14 -9999 0 -0.41 61 61
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.5 189 189
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.066 0.13 -9999 0 -0.34 189 189
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.14 -9999 0 -0.36 195 195
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.083 0.14 -9999 0 -0.36 195 195
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.084 0.15 -9999 0 -0.37 195 195
PI3K -0.13 0.24 -9999 0 -0.59 202 202
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.096 0.18 -9999 0 -0.47 189 189
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.078 0.13 -9999 0 -0.41 46 46
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.2 -9999 0 -0.53 198 198
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.8 43 43
IRS2 -0.032 0.16 -9999 0 -0.8 41 41
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.084 0.15 -9999 0 -0.37 195 195
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.22 -9999 0 -0.55 223 223
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.016 0.065 -9999 0 -0.29 56 56
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.24 -9999 0 -0.6 209 209
Rac1/GTP -0.1 0.18 -9999 0 -0.45 196 196
RET9/GFRalpha1/GDNF -0.12 0.21 -9999 0 -0.54 193 193
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.62 193 193
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.027 0.063 -10000 0 -0.5 2 2
epithelial cell differentiation -0.021 0.062 -10000 0 -0.48 7 7
ITCH 0.009 0.021 -10000 0 -10000 0 0
WWP1 0.007 0.068 -10000 0 -10000 0 0
FYN -0.002 0.035 -10000 0 -0.8 2 2
EGFR -0.29 0.39 -10000 0 -0.8 383 383
PRL -0.004 0.032 -10000 0 -0.29 13 13
neuron projection morphogenesis -0.11 0.21 -10000 0 -0.47 70 70
PTPRZ1 -0.42 0.4 -10000 0 -0.8 551 551
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.16 0.2 -10000 0 -0.42 378 378
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.2 0.24 -10000 0 -0.5 378 378
ADAM17 0.009 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.057 0.13 -10000 0 -0.54 57 57
NCOR1 -0.001 0.025 -10000 0 -0.8 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.18 0.22 -10000 0 -0.47 378 378
GRIN2B -0.18 0.26 -10000 0 -0.47 427 427
ErbB4/ErbB2/betacellulin -0.05 0.11 -10000 0 -0.47 58 58
STAT1 -0.005 0.039 -10000 0 -0.29 19 19
HBEGF -0.002 0.035 -10000 0 -0.8 2 2
PRLR -0.007 0.065 -10000 0 -0.53 13 13
E4ICDs/ETO2 -0.036 0.093 -10000 0 -0.56 19 19
axon guidance 0.044 0.12 -10000 0 -0.42 2 2
NEDD4 0.009 0.021 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.007 0.053 -10000 0 -0.62 6 6
CBFA2T3 -0.016 0.11 -10000 0 -0.7 24 24
ErbB4/ErbB2/HBEGF -0.025 0.051 -10000 0 -0.45 2 2
MAPK3 -0.15 0.19 -10000 0 -0.49 70 70
STAT1 (dimer) -0.028 0.063 -10000 0 -10000 0 0
MAPK1 -0.15 0.19 -10000 0 -0.49 70 70
JAK2 -0.001 0.025 -10000 0 -0.8 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.22 -10000 0 -0.48 378 378
NRG1 -0.21 0.31 -10000 0 -0.62 378 378
NRG3 -0.051 0.19 -10000 0 -0.65 82 82
NRG2 -0.4 0.4 -10000 0 -0.8 510 510
NRG4 -0.005 0.039 -10000 0 -0.29 19 19
heart development 0.044 0.12 -10000 0 -0.42 2 2
neural crest cell migration -0.19 0.22 -10000 0 -0.47 378 378
ERBB2 0.01 0.058 -10000 0 -10000 0 0
WWOX/E4ICDs -0.026 0.059 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.19 0.22 -10000 0 -0.47 378 378
apoptosis 0.057 0.14 0.53 57 -10000 0 57
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.27 0.24 -10000 0 -0.51 510 510
ErbB4/ErbB2/epiregulin -0.085 0.15 -10000 0 -0.46 124 124
ErbB4/ErbB4/betacellulin/betacellulin -0.054 0.13 -10000 0 -0.51 58 58
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.022 0.065 -10000 0 -0.52 9 9
MDM2 0.008 0.075 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.18 0.23 -10000 0 -0.48 378 378
STAT5A 0.044 0.12 -10000 0 -0.47 7 7
ErbB4/EGFR/neuregulin 1 beta -0.35 0.36 -10000 0 -0.66 526 526
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.056 -10000 0 -0.47 1 1
STAT5A (dimer) -0.022 0.067 -10000 0 -0.52 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.026 0.12 -10000 0 -0.44 4 4
LRIG1 -0.002 0.035 -10000 0 -0.8 2 2
EREG -0.12 0.26 -10000 0 -0.61 200 200
BTC -0.045 0.18 -10000 0 -0.79 60 60
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.044 0.12 -10000 0 -0.42 2 2
ERBB4 -0.032 0.073 -10000 0 -10000 0 0
STAT5B -0.002 0.043 -10000 0 -0.8 3 3
YAP1 -0.01 0.044 -10000 0 -0.64 4 4
GRB2 0 0.009 -10000 0 -0.29 1 1
ErbB4/ErbB2/neuregulin 4 -0.026 0.052 -10000 0 -10000 0 0
glial cell differentiation 0.024 0.055 0.46 1 -10000 0 1
WWOX -0.001 0.013 -10000 0 -10000 0 0
cell proliferation -0.12 0.24 -10000 0 -0.47 200 200
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.12 0.2 -9999 0 -0.6 132 132
SMAD6-7/SMURF1 -0.001 0.016 -9999 0 -0.53 1 1
NOG -0.026 0.13 -9999 0 -0.6 45 45
SMAD9 -0.11 0.26 -9999 0 -0.78 116 116
SMAD4 -0.001 0.025 -9999 0 -0.8 1 1
SMAD5 -0.076 0.18 -9999 0 -0.5 118 118
BMP7/USAG1 -0.35 0.35 -9999 0 -0.67 535 535
SMAD5/SKI -0.088 0.16 -9999 0 -0.52 87 87
SMAD1 0.026 0.03 -9999 0 -10000 0 0
BMP2 -0.14 0.31 -9999 0 -0.8 185 185
SMAD1/SMAD1/SMAD4 -0.002 0.015 -9999 0 -10000 0 0
BMPR1A -0.002 0.035 -9999 0 -0.8 2 2
BMPR1B -0.14 0.18 -9999 0 -0.32 445 445
BMPR1A-1B/BAMBI -0.092 0.14 -9999 0 -0.6 57 57
AHSG -0.004 0.033 -9999 0 -0.29 14 14
CER1 -0.001 0.016 -9999 0 -0.29 3 3
BMP2-4/CER1 -0.13 0.25 -9999 0 -0.58 232 232
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.2 -9999 0 -0.61 100 100
BMP2-4 (homodimer) -0.15 0.28 -9999 0 -0.66 232 232
RGMB -0.001 0.025 -9999 0 -0.8 1 1
BMP6/BMPR2/BMPR1A-1B -0.097 0.16 -9999 0 -0.55 103 103
RGMA -0.11 0.27 -9999 0 -0.8 138 138
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.62 103 103
BMP2-4/USAG1 -0.38 0.37 -9999 0 -0.66 592 592
SMAD6/SMURF1/SMAD5 -0.088 0.16 -9999 0 -0.52 87 87
SOSTDC1 -0.39 0.4 -9999 0 -0.8 507 507
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.57 107 107
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.061 0.21 -9999 0 -0.8 78 78
HFE2 -0.003 0.027 -9999 0 -0.29 9 9
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.009 -9999 0 -0.29 1 1
BMP2-4/CHRD -0.14 0.27 -9999 0 -0.62 236 236
SMAD5/SMAD5/SMAD4 -0.088 0.16 -9999 0 -0.52 88 88
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.087 0.17 -9999 0 -0.53 101 101
BMP7 (homodimer) -0.077 0.23 -9999 0 -0.65 123 123
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.05 0.16 -9999 0 -0.62 78 78
SMAD1/SKI 0.004 0.019 -9999 0 -10000 0 0
SMAD6 -0.001 0.025 -9999 0 -0.8 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.13 0.25 -9999 0 -0.58 232 232
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.038 0.12 -9999 0 -0.36 109 109
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.09 0.12 -9999 0 -0.62 27 27
CHRDL1 -0.55 0.37 -9999 0 -0.8 712 712
ENDOFIN/SMAD1 0.004 0.019 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.014 -9999 0 -0.37 1 1
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.034 0.14 -9999 0 -0.51 70 70
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.48 0.37 -9999 0 -0.68 729 729
BMP2-4/GREM1 -0.15 0.26 -9999 0 -0.59 237 237
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.1 0.24 -9999 0 -0.73 116 116
SMAD1/SMAD6 0.004 0.019 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.077 0.23 -9999 0 -0.65 123 123
BMP6 -0.061 0.21 -9999 0 -0.8 78 78
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.19 -9999 0 -0.6 100 100
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.004 0.019 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA -0.001 0.02 -9999 0 -0.29 5 5
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.13 0.24 -9999 0 -0.59 163 163
CHRD -0.032 0.13 -9999 0 -0.43 78 78
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.24 -9999 0 -0.54 190 190
BMP4 -0.053 0.2 -9999 0 -0.8 69 69
FST -0.036 0.16 -9999 0 -0.76 49 49
BMP2-4/NOG -0.14 0.26 -9999 0 -0.6 247 247
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.095 0.16 -9999 0 -0.54 107 107
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.039 -9999 0 -0.55 3 3
NFATC2 -0.04 0.16 -9999 0 -0.56 93 93
NFATC3 0.012 0.025 -9999 0 -10000 0 0
CD40LG -0.21 0.37 -9999 0 -0.72 287 287
PTGS2 -0.32 0.47 -9999 0 -0.86 403 403
JUNB -0.001 0.013 -9999 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.009 -9999 0 -10000 0 0
CALM1 0 0.003 -9999 0 -10000 0 0
JUN -0.005 0.067 -9999 0 -0.81 7 7
mol:Ca2+ -0.007 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -10000 0 0
FOSL1 -0.011 0.073 -9999 0 -0.8 6 6
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.075 0.15 -9999 0 -0.54 71 71
FOS -0.24 0.37 -9999 0 -0.82 307 307
IFNG -0.22 0.35 -9999 0 -0.69 286 286
AP-1/NFAT1-c-4 -0.31 0.38 -9999 0 -0.85 283 283
FASLG -0.2 0.35 -9999 0 -0.69 284 284
NFAT1-c-4/ICER1 -0.058 0.14 -9999 0 -0.48 93 93
IL2RA -0.21 0.35 -9999 0 -0.69 286 286
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.2 0.34 -9999 0 -0.68 283 283
JunB/Fra1/NFAT1-c-4 -0.057 0.14 -9999 0 -0.5 72 72
IL4 -0.2 0.34 -9999 0 -0.68 280 280
IL2 -0.01 0.025 -9999 0 -10000 0 0
IL3 -0.024 0.026 -9999 0 -10000 0 0
FKBP1A 0 0.009 -9999 0 -0.29 1 1
BATF3 -0.002 0.029 -9999 0 -0.42 4 4
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -0.29 1 1
Noncanonical Wnt signaling pathway

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
NFATC2 -0.072 0.23 -9999 0 -0.8 93 93
GNB1/GNG2 -0.14 0.23 -9999 0 -0.64 120 120
mol:DAG -0.13 0.2 -9999 0 -0.6 105 105
PLCG1 -0.13 0.21 -9999 0 -0.63 105 105
YES1 -0.15 0.23 -9999 0 -0.62 127 127
FZD3 -0.009 0.082 -9999 0 -0.8 11 11
FZD6 -0.007 0.075 -9999 0 -0.8 9 9
G protein -0.13 0.21 -9999 0 -0.63 107 107
MAP3K7 -0.068 0.18 -9999 0 -0.49 103 103
mol:Ca2+ -0.092 0.21 -9999 0 -0.58 105 105
mol:IP3 -0.13 0.2 -9999 0 -0.6 105 105
NLK -0.005 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.082 0.2 -9999 0 -0.53 110 110
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.16 0.24 -9999 0 -0.44 366 366
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.15 0.23 -9999 0 -0.66 112 112
GO:0007205 -0.093 0.22 -9999 0 -0.59 105 105
WNT6 -0.17 0.32 -9999 0 -0.71 247 247
WNT4 -0.022 0.12 -9999 0 -0.53 42 42
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.56 184 184
GNG2 -0.009 0.086 -9999 0 -0.8 12 12
WNT5A -0.014 0.1 -9999 0 -0.6 25 25
WNT11 -0.17 0.32 -9999 0 -0.77 227 227
CDC42 -0.11 0.23 -9999 0 -0.62 111 111
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.1 0.23 -10000 0 -0.61 172 172
CRKL -0.039 0.16 -10000 0 -0.35 172 172
mol:PIP3 -0.018 0.036 0.79 2 -10000 0 2
AKT1 0.003 0.022 0.49 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.029 0.15 -10000 0 -0.33 172 172
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
HGF/MET/SHIP2 -0.12 0.24 -10000 0 -0.57 220 220
MAP3K5 -0.02 0.15 -10000 0 -0.54 24 24
HGF/MET/CIN85/CBL/ENDOPHILINS -0.11 0.22 -10000 0 -0.52 220 220
AP1 -0.19 0.27 -10000 0 -0.59 308 308
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.23 0.36 -10000 0 -0.78 308 308
STAT3 (dimer) -0.038 0.16 -10000 0 -0.34 220 220
GAB1/CRKL/SHP2/PI3K -0.063 0.13 -10000 0 -0.54 26 26
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.065 0.13 -10000 0 -0.33 172 172
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.035 -10000 0 -0.8 2 2
ELK1 -0.043 0.1 -10000 0 -0.27 172 172
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.045 0.092 -10000 0 -0.42 20 20
PAK1 0.008 0.029 0.45 2 -10000 0 2
HGF/MET/RANBP10 -0.12 0.24 -10000 0 -0.57 220 220
HRAS -0.15 0.3 -10000 0 -0.78 172 172
DOCK1 -0.029 0.15 -10000 0 -0.55 20 20
GAB1 -0.049 0.16 -10000 0 -0.35 220 220
CRK -0.039 0.16 -10000 0 -0.33 220 220
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.3 -10000 0 -0.71 220 220
JUN -0.005 0.066 -10000 0 -0.8 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.076 0.15 -10000 0 -0.36 220 220
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
cell morphogenesis -0.017 0.17 -10000 0 -0.6 26 26
GRB2/SHC -0.065 0.13 -10000 0 -0.33 172 172
FOS -0.24 0.37 -10000 0 -0.8 307 307
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.043 0.1 -10000 0 -0.27 172 172
HGF/MET/MUC20 -0.12 0.25 -10000 0 -0.58 220 220
cell migration -0.064 0.13 -10000 0 -0.33 172 172
GRB2 0 0.009 -10000 0 -0.29 1 1
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.1 0.23 -10000 0 -0.61 172 172
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.075 0.15 -10000 0 -0.36 220 220
MET/MUC20 -0.1 0.23 -10000 0 -0.62 172 172
RAP1B -0.019 0.14 -10000 0 -0.5 20 20
RAP1A -0.019 0.14 -10000 0 -0.5 20 20
HGF/MET/RANBP9 -0.12 0.24 -10000 0 -0.57 220 220
RAF1 -0.1 0.29 -10000 0 -0.72 172 172
STAT3 -0.072 0.14 -10000 0 -0.34 220 220
cell proliferation -0.059 0.23 -10000 0 -0.48 220 220
RPS6KB1 -0.026 0.052 -10000 0 -10000 0 0
MAPK3 -0.043 0.092 -10000 0 -0.25 172 172
MAPK1 -0.043 0.092 -10000 0 -0.25 172 172
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.002 0.14 -10000 0 -0.48 31 31
SRC -0.07 0.14 -10000 0 -0.62 20 20
PI3K -0.07 0.14 -10000 0 -0.35 180 180
MET/Glomulin -0.093 0.21 -10000 0 -0.56 172 172
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.083 0.27 -10000 0 -0.65 172 172
MET -0.13 0.3 -10000 0 -0.8 172 172
MAP4K1 -0.028 0.15 -10000 0 -0.33 173 173
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.083 0.27 -10000 0 -0.65 172 172
BAD 0.011 0.021 0.45 2 -10000 0 2
MAP2K4 -0.01 0.14 -10000 0 -0.48 25 25
SHP2/GRB2/SOS1/GAB1 -0.094 0.19 -10000 0 -0.51 172 172
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.07 0.14 -10000 0 -0.36 172 172
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.053 0.2 -10000 0 -0.8 68 68
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.066 0.13 -10000 0 -0.33 172 172
PDPK1 -0.006 0.026 0.57 2 -10000 0 2
HGF/MET/SHIP -0.12 0.24 -10000 0 -0.57 220 220
Nongenotropic Androgen signaling

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
PTK2 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.068 0.17 -10000 0 -0.49 142 142
regulation of S phase of mitotic cell cycle -0.041 0.12 -10000 0 -0.35 134 134
GNAO1 -0.031 0.13 -10000 0 -0.48 66 66
HRAS -0.003 0.027 -10000 0 -0.29 9 9
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.001 -10000 0 -10000 0 0
MAP2K1 -0.042 0.16 -10000 0 -0.43 131 131
T-DHT/AR -0.079 0.21 -10000 0 -0.63 131 131
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 307 307
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.039 0.17 -10000 0 -0.8 50 50
mol:GDP -0.08 0.21 -10000 0 -0.62 133 133
cell proliferation -0.1 0.24 -10000 0 -0.54 112 112
PIK3CA 0 0.009 -10000 0 -0.29 1 1
FOS -0.23 0.42 -10000 0 -0.87 307 307
mol:Ca2+ -0.016 0.027 -10000 0 -0.077 132 132
MAPK3 -0.073 0.2 -10000 0 -0.61 61 61
MAPK1 -0.045 0.12 -10000 0 -0.3 59 59
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
mol:IP3 -0.001 0.002 -10000 0 -0.005 307 307
cAMP biosynthetic process 0.012 0.024 -10000 0 -10000 0 0
GNG2 -0.009 0.086 -10000 0 -0.8 12 12
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 307 307
HRAS/GTP -0.066 0.15 -10000 0 -0.46 131 131
actin cytoskeleton reorganization -0.004 0.042 -10000 0 -0.43 10 10
SRC 0 0.009 -10000 0 -0.29 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 307 307
PI3K -0.005 0.053 -10000 0 -0.54 10 10
apoptosis 0.1 0.23 0.43 307 -10000 0 307
T-DHT/AR/PELP1 -0.069 0.18 -10000 0 -0.54 131 131
HRAS/GDP -0.077 0.2 -10000 0 -0.6 132 132
CREB1 -0.11 0.24 -10000 0 -0.46 307 307
RAC1-CDC42/GTP -0.004 0.043 -10000 0 -0.44 10 10
AR -0.1 0.27 -10000 0 -0.8 132 132
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.043 0.16 -10000 0 -0.45 131 131
RAC1-CDC42/GDP -0.072 0.19 -10000 0 -0.56 131 131
T-DHT/AR/PELP1/Src -0.063 0.17 -10000 0 -0.5 131 131
MAP2K2 -0.042 0.16 -10000 0 -0.43 131 131
T-DHT/AR/PELP1/Src/PI3K -0.042 0.12 -10000 0 -0.35 134 134
GNAZ -0.007 0.075 -10000 0 -0.8 9 9
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.037 0.11 -10000 0 -0.49 36 36
mol:T-DHT -0.001 0.001 0.001 57 -0.003 249 306
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.005 0.059 -10000 0 -0.62 9 9
Gi family/GTP -0.048 0.1 -10000 0 -0.3 84 84
CDC42 0 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.1 0.12 -10000 0 -0.34 77 77
NT3 (dimer)/TRKC -0.3 0.37 -10000 0 -0.7 441 441
NT3 (dimer)/TRKB -0.51 0.45 -10000 0 -0.8 666 666
SHC/Grb2/SOS1/GAB1/PI3K -0.003 0.032 -10000 0 -0.32 10 10
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.07 0.22 -10000 0 -0.8 81 81
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DYNLT1 0 0.009 -10000 0 -10000 0 0
NTRK1 -0.01 0.066 -10000 0 -0.36 29 29
NTRK2 -0.42 0.4 -10000 0 -0.8 549 549
NTRK3 -0.28 0.38 -10000 0 -0.8 361 361
NT-4/5 (dimer)/TRKB -0.6 0.49 -10000 0 -0.87 716 716
neuron apoptosis 0.24 0.24 0.59 291 -10000 0 291
SHC 2-3/Grb2 -0.27 0.28 -10000 0 -0.66 291 291
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.25 0.29 -10000 0 -0.68 275 275
SHC3 -0.25 0.28 -10000 0 -0.66 280 280
STAT3 (dimer) -0.005 0.03 -10000 0 -0.38 4 4
NT3 (dimer)/TRKA -0.25 0.32 -10000 0 -0.62 421 421
RIN/GDP -0.067 0.12 -10000 0 -0.28 63 63
GIPC1 -0.001 0.016 -10000 0 -0.29 3 3
KRAS -0.001 0.013 -10000 0 -0.29 2 2
DNAJA3 -0.14 0.21 -10000 0 -0.43 332 332
RIN/GTP 0 0.009 -10000 0 -10000 0 0
CCND1 0.018 0.076 -10000 0 -1 4 4
MAGED1 -0.001 0.018 -10000 0 -0.29 4 4
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.28 0.38 -10000 0 -0.8 363 363
SHC/GRB2/SOS1 0 0.004 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
NGF (dimer)/TRKA/MATK -0.027 0.11 -10000 0 -0.56 35 35
TRKA/NEDD4-2 -0.007 0.051 -10000 0 -0.61 5 5
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.014 0.099 -10000 0 -0.64 22 22
HRAS -0.003 0.027 -10000 0 -0.29 9 9
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.004 0.044 -10000 0 -0.38 11 11
RIT2 -0.001 0.013 -10000 0 -0.29 2 2
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.028 -10000 0 -10000 0 0
DNM1 -0.006 0.066 -10000 0 -0.74 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.14 0.2 -10000 0 -0.42 332 332
mol:GDP -0.1 0.18 -10000 0 -0.37 226 226
NGF (dimer) -0.014 0.098 -10000 0 -0.64 22 22
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.063 0.12 -10000 0 -0.28 64 64
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
BDNF (dimer)/TRKB -0.32 0.3 -10000 0 -0.58 575 575
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0.004 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.13 0.29 -10000 0 -0.76 176 176
RAP1/GDP -0.074 0.085 -10000 0 -0.25 38 38
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.07 0.22 -10000 0 -0.8 81 81
ubiquitin-dependent protein catabolic process -0.015 0.076 -10000 0 -0.53 20 20
Schwann cell development -0.06 0.044 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.001 0.011 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.44 0.39 -10000 0 -0.67 679 679
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.11 0.099 -10000 0 -10000 0 0
STAT3 -0.005 0.03 -10000 0 -0.38 4 4
axon guidance -0.41 0.35 -10000 0 -0.62 679 679
MAPK3 0.006 0.1 -10000 0 -0.51 35 35
MAPK1 0.006 0.1 -10000 0 -0.51 35 35
CDC42/GDP -0.063 0.12 -10000 0 -0.28 65 65
NTF3 -0.13 0.29 -10000 0 -0.76 176 176
NTF4 -0.28 0.38 -10000 0 -0.8 363 363
NGF (dimer)/TRKA/FAIM -0.014 0.075 -10000 0 -0.53 19 19
PI3K -0.006 0.06 -10000 0 -0.61 10 10
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.16 0.22 -10000 0 -0.45 335 335
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.25 0.34 -10000 0 -0.61 443 443
RGS19 -0.001 0.013 -10000 0 -0.29 2 2
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.083 -10000 0 -10000 0 0
Rac1/GDP -0.063 0.12 -10000 0 -0.28 64 64
NGF (dimer)/TRKA/GRIT -0.015 0.076 -10000 0 -0.54 19 19
neuron projection morphogenesis -0.11 0.21 -10000 0 -0.63 23 23
NGF (dimer)/TRKA/NEDD4-2 -0.015 0.076 -10000 0 -0.53 20 20
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.25 0.37 -10000 0 -0.8 325 325
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.053 -10000 0 -0.34 25 25
RAS family/GTP/PI3K -0.004 0.033 -10000 0 -0.34 10 10
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.01 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.025 -10000 0 -0.8 1 1
MAPKKK cascade -0.065 0.12 -10000 0 -0.82 19 19
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.007 0.047 -10000 0 -0.61 4 4
SQSTM1 0 0.009 -10000 0 -0.29 1 1
BDNF (dimer)/TRKB/GIPC -0.3 0.28 -10000 0 -0.53 575 575
NGF (dimer)/TRKA/p62/Atypical PKCs -0.012 0.064 -10000 0 -0.45 20 20
MATK -0.021 0.11 -10000 0 -0.8 18 18
NEDD4L -0.001 0.025 -10000 0 -0.8 1 1
RAS family/GDP -0.067 0.08 -10000 0 -0.24 3 3
NGF (dimer)/TRKA -0.15 0.22 -10000 0 -0.46 337 337
Rac1/GTP -0.13 0.14 -10000 0 -0.34 251 251
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
IL23-mediated signaling events

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.17 0.39 -9999 0 -1.1 73 73
IL23A -0.18 0.4 -9999 0 -1.1 77 77
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.32 -9999 0 -0.89 132 132
positive regulation of T cell mediated cytotoxicity -0.19 0.42 -9999 0 -0.86 226 226
ITGA3 -0.17 0.39 -9999 0 -0.95 108 108
IL17F -0.11 0.28 -9999 0 -0.65 90 90
IL12B -0.049 0.12 -9999 0 -0.29 155 155
STAT1 (dimer) -0.22 0.38 -9999 0 -0.85 199 199
CD4 -0.16 0.38 -9999 0 -0.94 96 96
IL23 -0.18 0.38 -9999 0 -1 77 77
IL23R -0.013 0.087 -9999 0 -10000 0 0
IL1B -0.18 0.41 -9999 0 -1 120 120
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.17 0.38 -9999 0 -0.93 108 108
TYK2 0.011 0.017 -9999 0 -10000 0 0
STAT4 -0.032 0.16 -9999 0 -0.79 42 42
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.026 0.15 -9999 0 -0.74 42 42
IL12RB1 -0.002 0.071 -9999 0 -0.32 42 42
PIK3CA 0 0.009 -9999 0 -0.29 1 1
IL12Rbeta1/TYK2 -0.003 0.052 -9999 0 -0.62 2 2
IL23R/JAK2 -0.011 0.11 -9999 0 -0.65 1 1
positive regulation of chronic inflammatory response -0.19 0.42 -9999 0 -0.86 226 226
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.017 0.035 -9999 0 -0.84 1 1
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
NFKB1 0.003 0.006 -9999 0 -10000 0 0
RELA 0.003 0.006 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.37 -9999 0 -0.99 78 78
ALOX12B -0.17 0.38 -9999 0 -0.96 94 94
CXCL1 -0.35 0.64 -9999 0 -1.4 277 277
T cell proliferation -0.19 0.42 -9999 0 -0.86 226 226
NFKBIA 0.003 0.006 -9999 0 -10000 0 0
IL17A -0.072 0.24 -9999 0 -0.54 60 60
PI3K -0.25 0.33 -9999 0 -0.83 186 186
IFNG -0.005 0.026 -9999 0 -0.095 10 10
STAT3 (dimer) -0.24 0.31 -9999 0 -0.86 142 142
IL18R1 -0.009 0.1 -9999 0 -0.8 17 17
IL23/IL23R/JAK2/TYK2/SOCS3 -0.086 0.24 -9999 0 -0.55 65 65
IL18/IL18R -0.031 0.12 -9999 0 -0.54 53 53
macrophage activation -0.014 0.017 -9999 0 -0.042 96 96
TNF -0.18 0.41 -9999 0 -1.1 96 96
STAT3/STAT4 -0.26 0.35 -9999 0 -0.85 212 212
STAT4 (dimer) -0.23 0.4 -9999 0 -0.88 215 215
IL18 -0.003 0.046 -9999 0 -0.29 25 25
IL19 -0.18 0.38 -9999 0 -0.92 119 119
STAT5A (dimer) -0.22 0.38 -9999 0 -0.85 203 203
STAT1 -0.005 0.039 -9999 0 -0.29 19 19
SOCS3 -0.005 0.061 -9999 0 -0.8 6 6
CXCL9 -0.19 0.39 -9999 0 -0.93 124 124
MPO -0.21 0.47 -9999 0 -1.2 140 140
positive regulation of humoral immune response -0.19 0.42 -9999 0 -0.86 226 226
IL23/IL23R/JAK2/TYK2 -0.2 0.44 -9999 0 -0.89 225 225
IL6 -0.46 0.7 -9999 0 -1.3 388 388
STAT5A -0.006 0.07 -9999 0 -0.8 8 8
IL2 0.004 0.028 -9999 0 -0.3 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.18 0.41 -9999 0 -0.99 125 125
keratinocyte proliferation -0.19 0.42 -9999 0 -0.86 226 226
NOS2 -0.17 0.39 -9999 0 -0.9 129 129
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.27 -10000 0 -0.54 422 422
fibroblast growth factor receptor signaling pathway -0.22 0.26 -10000 0 -0.54 422 422
LAMA1 -0.094 0.26 -10000 0 -0.79 123 123
PRNP -0.012 0.099 -10000 0 -0.8 16 16
GPC1/SLIT2 -0.068 0.19 -10000 0 -0.62 113 113
SMAD2 0.01 0.11 -10000 0 -0.48 46 46
GPC1/PrPc/Cu2+ -0.01 0.069 -10000 0 -0.54 17 17
GPC1/Laminin alpha1 -0.073 0.2 -10000 0 -0.61 121 121
TDGF1 -0.008 0.079 -10000 0 -0.76 11 11
CRIPTO/GPC1 -0.008 0.064 -10000 0 -0.61 11 11
APP/GPC1 -0.001 0.023 -10000 0 -0.61 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.018 0.061 -10000 0 -0.53 12 12
FLT1 -0.001 0.025 -10000 0 -0.8 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.024 0.11 -10000 0 -0.53 46 46
SERPINC1 -0.016 0.066 -10000 0 -0.29 57 57
FYN 0.018 0.063 -10000 0 -0.53 13 13
FGR 0.018 0.061 -10000 0 -0.53 12 12
positive regulation of MAPKKK cascade 0.03 0.074 -10000 0 -0.53 13 13
SLIT2 -0.087 0.25 -10000 0 -0.8 112 112
GPC1/NRG -0.23 0.3 -10000 0 -0.62 379 379
NRG1 -0.29 0.39 -10000 0 -0.8 378 378
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.029 -10000 0 -0.53 2 2
LYN 0.019 0.058 -10000 0 -0.53 11 11
mol:Spermine 0.01 0.024 -10000 0 -0.62 1 1
cell growth -0.22 0.26 -10000 0 -0.54 422 422
BMP signaling pathway 0.002 0.032 0.37 6 -10000 0 6
SRC 0.019 0.058 -10000 0 -0.53 11 11
TGFBR1 0 0.009 -10000 0 -0.29 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.27 0.37 -10000 0 -0.77 362 362
GPC1 -0.002 0.032 -10000 0 -0.38 6 6
TGFBR1 (dimer) 0 0.009 -10000 0 -0.29 1 1
VEGFA -0.003 0.03 -10000 0 -10000 0 0
BLK -0.006 0.087 -10000 0 -0.57 13 13
HCK 0.017 0.061 -10000 0 -0.53 11 11
FGF2 -0.32 0.39 -10000 0 -0.8 416 416
FGFR1 -0.009 0.084 -10000 0 -0.69 14 14
VEGFR1 homodimer -0.001 0.025 -10000 0 -0.8 1 1
TGFBR2 -0.035 0.16 -10000 0 -0.8 45 45
cell death -0.001 0.023 -10000 0 -0.61 1 1
ATIII/GPC1 -0.012 0.048 -10000 0 -0.62 1 1
PLA2G2A/GPC1 -0.2 0.29 -10000 0 -0.62 336 336
LCK 0.006 0.09 -10000 0 -0.54 24 24
neuron differentiation -0.23 0.29 -10000 0 -0.61 379 379
PrPc/Cu2+ -0.01 0.077 -10000 0 -0.62 16 16
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.035 0.16 -10000 0 -0.8 45 45
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.096 0.18 -10000 0 -0.48 185 185
ER alpha/Gai/GDP/Gbeta gamma -0.092 0.19 -10000 0 -0.48 169 169
AKT1 -0.1 0.32 -10000 0 -0.84 161 161
PIK3CA 0 0.009 -10000 0 -0.29 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.1 0.32 -10000 0 -0.86 158 158
mol:Ca2+ -0.028 0.15 -10000 0 -0.46 85 85
IGF1R -0.021 0.12 -10000 0 -0.8 22 22
E2/ER alpha (dimer)/Striatin -0.11 0.2 -10000 0 -0.55 174 174
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.094 0.3 0.8 161 -10000 0 161
RhoA/GTP -0.071 0.14 -10000 0 -0.4 158 158
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.093 0.21 -10000 0 -0.54 167 167
regulation of stress fiber formation 0.024 0.14 0.46 11 -10000 0 11
E2/ERA-ERB (dimer) -0.11 0.2 -10000 0 -0.55 177 177
KRAS -0.001 0.013 -10000 0 -0.29 2 2
G13/GTP -0.091 0.18 -10000 0 -0.5 158 158
pseudopodium formation -0.024 0.14 -10000 0 -0.46 11 11
E2/ER alpha (dimer)/PELP1 -0.099 0.19 -10000 0 -0.54 158 158
GRB2 0 0.009 -10000 0 -0.29 1 1
GNG2 -0.009 0.086 -10000 0 -0.8 12 12
GNAO1 -0.031 0.13 -10000 0 -0.48 66 66
HRAS -0.003 0.027 -10000 0 -0.29 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.06 0.22 -10000 0 -0.55 168 168
E2/ER beta (dimer) -0.012 0.086 -10000 0 -0.62 20 20
mol:GDP -0.087 0.21 -10000 0 -0.54 177 177
mol:NADP -0.06 0.22 -10000 0 -0.55 168 168
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
mol:IP3 -0.03 0.15 -10000 0 -0.48 85 85
IGF-1R heterotetramer -0.021 0.12 -10000 0 -0.8 22 22
PLCB1 -0.064 0.14 -10000 0 -0.5 84 84
PLCB2 -0.034 0.093 -10000 0 -0.67 14 14
IGF1 -0.18 0.33 -10000 0 -0.8 231 231
mol:L-citrulline -0.06 0.22 -10000 0 -0.55 168 168
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.038 0.15 -10000 0 -0.85 25 25
JNK cascade -0.012 0.085 -10000 0 -0.62 20 20
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.015 0.11 -10000 0 -0.8 20 20
GNAQ -0.002 0.035 -10000 0 -0.8 2 2
ESR1 -0.16 0.29 -10000 0 -0.58 276 276
Gq family/GDP/Gbeta gamma -0.007 0.071 -10000 0 -0.48 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.024 0.13 -10000 0 -0.32 158 158
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.093 0.21 -10000 0 -0.54 167 167
GNAZ -0.007 0.075 -10000 0 -0.8 9 9
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.62 158 158
STRN -0.015 0.11 -10000 0 -0.8 19 19
GNAL -0.19 0.34 -10000 0 -0.8 244 244
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.006 0.082 -10000 0 -0.54 23 23
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.039 0.17 -10000 0 -0.8 50 50
HBEGF -0.069 0.19 -10000 0 -0.45 178 178
cAMP biosynthetic process -0.19 0.26 -10000 0 -0.51 369 369
SRC -0.051 0.2 -10000 0 -0.45 169 169
PI3K -0.006 0.06 -10000 0 -0.61 10 10
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.079 0.19 -10000 0 -0.47 185 185
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.54 205 205
Gs family/GTP -0.19 0.26 -10000 0 -0.53 369 369
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.014 -10000 0 -10000 0 0
vasodilation -0.056 0.21 -10000 0 -0.52 168 168
mol:DAG -0.03 0.15 -10000 0 -0.48 85 85
Gs family/GDP/Gbeta gamma -0.16 0.23 -10000 0 -0.45 370 370
MSN -0.028 0.15 -10000 0 -0.5 11 11
Gq family/GTP -0.038 0.098 -10000 0 -0.64 16 16
mol:PI-3-4-5-P3 -0.099 0.31 -10000 0 -0.82 158 158
NRAS -0.001 0.013 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.056 0.21 0.52 168 -10000 0 168
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.08 0.19 -10000 0 -0.5 177 177
NOS3 -0.065 0.24 -10000 0 -0.57 168 168
GNA11 -0.002 0.035 -10000 0 -0.8 2 2
MAPKKK cascade -0.068 0.26 -10000 0 -0.64 174 174
E2/ER alpha (dimer)/PELP1/Src -0.098 0.22 -10000 0 -0.57 167 167
ruffle organization -0.024 0.14 -10000 0 -0.46 11 11
ROCK2 -0.075 0.14 -10000 0 -0.45 31 31
GNA14 -0.014 0.088 -10000 0 -0.46 31 31
GNA15 -0.003 0.034 -10000 0 -0.8 1 1
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.095 0.2 -10000 0 -0.48 176 176
MMP2 -0.043 0.19 -10000 0 -0.43 174 174
Aurora C 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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.075 0.066 -9999 0 -0.62 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.019 0.017 -9999 0 -10000 0 0
AURKB -0.17 0.14 -9999 0 -0.29 598 598
AURKC -0.005 0.042 -9999 0 -0.32 15 15
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.046 -9999 0 -0.61 5 5
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.55 429 429
PTK2 -0.091 0.2 -9999 0 -0.67 43 43
IGF1R -0.021 0.12 -9999 0 -0.8 22 22
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.092 -9999 0 -0.62 20 20
SRC 0 0.009 -9999 0 -0.29 1 1
CDKN1B -0.089 0.13 -9999 0 -0.9 11 11
VEGFA -0.003 0.03 -9999 0 -10000 0 0
ILK -0.086 0.12 -9999 0 -0.84 8 8
ROCK1 -0.001 0.025 -9999 0 -0.8 1 1
AKT1 -0.076 0.11 -9999 0 -0.78 8 8
PTK2B -0.019 0.095 -9999 0 -0.5 36 36
alphaV/beta3 Integrin/JAM-A -0.21 0.25 -9999 0 -0.49 433 433
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.019 0.097 -9999 0 -0.53 35 35
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.26 -9999 0 -0.56 254 254
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.013 0.063 -9999 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 -0.029 0.1 -9999 0 -0.54 36 36
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.33 0.36 -9999 0 -0.77 332 332
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
alphaV/beta3 Integrin/Osteopontin -0.056 0.11 -9999 0 -0.55 35 35
RPS6KB1 -0.3 0.32 -9999 0 -0.7 333 333
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.33 0.39 -9999 0 -0.77 429 429
GPR124 -0.009 0.086 -9999 0 -0.8 12 12
MAPK1 -0.33 0.39 -9999 0 -0.77 429 429
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
alphaV/beta3 Integrin/Tumstatin -0.11 0.22 -9999 0 -0.55 214 214
cell adhesion -0.023 0.11 -9999 0 -0.51 45 45
ANGPTL3 -0.001 0.018 -9999 0 -0.29 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.04 -9999 0 -0.53 5 5
IGF-1R heterotetramer -0.021 0.12 -9999 0 -0.8 22 22
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.035 0.16 -9999 0 -0.8 45 45
ITGB3 -0.028 0.15 -9999 0 -0.75 39 39
IGF1 -0.18 0.33 -9999 0 -0.8 231 231
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.024 0.12 -9999 0 -0.6 41 41
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.025 -9999 0 -0.8 1 1
alphaV/beta3 Integrin/CD47 -0.019 0.097 -9999 0 -0.53 36 36
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.05 0.18 -9999 0 -0.67 74 74
CSF1 -0.005 0.066 -9999 0 -0.8 7 7
PIK3C2A -0.087 0.12 -9999 0 -0.86 9 9
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.62 67 67
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.02 0.1 -9999 0 -0.54 36 36
FAK1/Vinculin -0.066 0.16 -9999 0 -0.51 40 40
alphaV beta3/Integrin/ppsTEM5 -0.024 0.12 -9999 0 -0.6 41 41
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.026 0.1 -9999 0 -0.34 80 80
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.32 0.39 -9999 0 -0.8 416 416
F11R -0.23 0.31 -9999 0 -0.61 416 416
alphaV/beta3 Integrin/Lactadherin -0.026 0.12 -9999 0 -0.57 44 44
alphaV/beta3 Integrin/TGFBR2 -0.04 0.17 -9999 0 -0.68 61 61
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.039 -9999 0 -0.48 7 7
HSP90AA1 0 0.009 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.017 0.089 -9999 0 -0.49 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -0.29 414 414
alphaV/beta3 Integrin/Pyk2 -0.019 0.096 -9999 0 -0.5 36 36
SDC1 -0.021 0.078 -9999 0 -0.3 74 74
VAV3 -0.008 0.053 -9999 0 -0.45 14 14
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.8 43 43
FAK1/Paxillin -0.066 0.16 -9999 0 -0.51 40 40
cell migration -0.052 0.15 -9999 0 -0.45 40 40
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.23 -9999 0 -0.44 435 435
SPP1 -0.077 0.13 -9999 0 -0.29 277 277
KDR -0.004 0.056 -9999 0 -0.8 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.14 0.31 -9999 0 -0.79 190 190
angiogenesis -0.3 0.39 -9999 0 -0.75 431 431
Rac1/GTP -0.007 0.048 -9999 0 -0.41 14 14
EDIL3 -0.051 0.19 -9999 0 -0.7 75 75
cell proliferation -0.04 0.17 -9999 0 -0.67 61 61
Signaling events mediated by PTP1B

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
PDGFRB -0.003 0.05 -10000 0 -0.8 4 4
Jak2/Leptin Receptor -0.16 0.24 -10000 0 -0.53 280 280
PTP1B/AKT1 -0.069 0.11 -10000 0 -0.34 106 106
FYN -0.002 0.035 -10000 0 -0.8 2 2
p210 bcr-abl/PTP1B -0.07 0.13 -10000 0 -0.39 108 108
EGFR -0.3 0.39 -10000 0 -0.81 383 383
EGF/EGFR -0.29 0.31 -10000 0 -0.57 521 521
CSF1 -0.005 0.066 -10000 0 -0.8 7 7
AKT1 0 0.002 -10000 0 -10000 0 0
INSR 0 0.009 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.097 0.12 -10000 0 -0.37 112 112
Insulin Receptor/Insulin -0.049 0.08 -10000 0 -0.41 19 19
HCK -0.004 0.032 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.059 0.12 -10000 0 -0.37 106 106
EGF -0.16 0.32 -10000 0 -0.81 202 202
YES1 -0.001 0.025 -10000 0 -0.8 1 1
CAV1 -0.17 0.24 -10000 0 -0.51 277 277
TXN 0 0.016 -10000 0 -0.29 3 3
PTP1B/IRS1/GRB2 -0.086 0.14 -10000 0 -0.5 79 79
cell migration 0.07 0.13 0.39 108 -10000 0 108
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.005 0.066 -10000 0 -0.53 13 13
ITGA2B -0.018 0.078 -10000 0 -0.81 3 3
CSF1R -0.001 0.026 -10000 0 -0.55 2 2
Prolactin Receptor/Prolactin -0.006 0.054 -10000 0 -0.62 6 6
FGR -0.001 0.026 -10000 0 -0.8 1 1
PTP1B/p130 Cas -0.074 0.11 -10000 0 -0.37 106 106
Crk/p130 Cas -0.068 0.11 -10000 0 -0.36 94 94
DOK1 -0.045 0.12 -10000 0 -0.33 91 91
JAK2 -0.041 0.079 -10000 0 -0.33 24 24
Jak2/Leptin Receptor/Leptin -0.37 0.18 -10000 0 -0.48 594 594
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
PTPN1 -0.071 0.13 -10000 0 -0.39 108 108
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.055 0.12 -10000 0 -0.3 193 193
SRC -0.013 0.047 -10000 0 -10000 0 0
ITGB3 -0.028 0.15 -10000 0 -0.77 38 38
CAT1/PTP1B -0.084 0.17 -10000 0 -0.48 77 77
CAPN1 0 0.009 -10000 0 -0.29 1 1
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.043 0.09 -10000 0 -0.54 16 16
mol:H2O2 -0.005 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.33 0.16 -10000 0 -0.44 521 521
negative regulation of transcription -0.04 0.078 -10000 0 -0.32 24 24
FCGR2A 0 0.009 -10000 0 -0.29 1 1
FER -0.008 0.084 -10000 0 -0.82 11 11
alphaIIb/beta3 Integrin -0.033 0.12 -10000 0 -0.63 38 38
BLK -0.041 0.11 -10000 0 -0.3 142 142
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0.001 0.003 -10000 0 -10000 0 0
LEPR -0.21 0.36 -10000 0 -0.81 276 276
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.009 -10000 0 -0.29 1 1
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.031 0.13 -10000 0 -0.51 15 15
PRL -0.004 0.033 -10000 0 -0.29 13 13
SOCS3 0.017 0.12 -10000 0 -1.5 6 6
SPRY2 -0.091 0.26 -10000 0 -0.82 116 116
Insulin Receptor/Insulin/IRS1 -0.023 0.11 -10000 0 -0.55 43 43
CSF1/CSF1R -0.071 0.12 -10000 0 -0.36 110 110
Ras protein signal transduction 0.037 0.036 -10000 0 -10000 0 0
IRS1 -0.033 0.16 -10000 0 -0.8 43 43
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.65 0.32 -10000 0 -0.8 839 839
STAT5B -0.057 0.11 -10000 0 -0.32 110 110
STAT5A -0.058 0.11 -10000 0 -0.32 113 113
GRB2 0 0.009 -10000 0 -0.29 1 1
PDGFB-D/PDGFRB -0.076 0.12 -10000 0 -0.38 108 108
CSN2 0.018 0.034 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
LAT -0.014 0.053 -10000 0 -0.58 2 2
YBX1 -0.001 0.014 -10000 0 -10000 0 0
LCK -0.02 0.1 -10000 0 -0.43 49 49
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.004 0.046 -10000 0 -0.81 2 2
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.023 0.062 -9999 0 -0.58 10 10
alphaM/beta2 Integrin/GPIbA -0.025 0.059 -9999 0 -0.53 9 9
alphaM/beta2 Integrin/proMMP-9 -0.082 0.081 -9999 0 -0.34 17 17
PLAUR -0.021 0.074 -9999 0 -10000 0 0
HMGB1 -0.013 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.018 0.028 -9999 0 -10000 0 0
AGER -0.015 0.041 -9999 0 -0.86 2 2
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG 0 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.075 0.097 -9999 0 -0.7 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.29 453 453
CYR61 -0.044 0.18 -9999 0 -0.8 57 57
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.058 0.11 -9999 0 -0.53 21 21
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.34 -9999 0 -0.8 243 243
MYH2 -0.07 0.16 -9999 0 -0.4 113 113
MST1R -0.011 0.086 -9999 0 -0.57 20 20
leukocyte activation during inflammatory response -0.3 0.23 -9999 0 -0.48 636 636
APOB -0.49 0.39 -9999 0 -0.8 636 636
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.008 0.079 -9999 0 -0.8 10 10
JAM3 -0.005 0.066 -9999 0 -0.8 7 7
GP1BA -0.012 0.079 -9999 0 -0.4 32 32
alphaM/beta2 Integrin/CTGF -0.025 0.07 -9999 0 -0.59 13 13
alphaM/beta2 Integrin -0.073 0.13 -9999 0 -0.37 85 85
JAM3 homodimer -0.005 0.066 -9999 0 -0.8 7 7
ICAM2 -0.004 0.056 -9999 0 -0.8 5 5
ICAM1 -0.004 0.035 -9999 0 -0.29 15 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.062 0.14 -9999 0 -0.37 85 85
cell adhesion -0.025 0.059 -9999 0 -0.53 9 9
NFKB1 -0.14 0.18 -9999 0 -0.66 14 14
THY1 -0.002 0.024 -9999 0 -0.29 7 7
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.34 0.27 -9999 0 -0.55 636 636
alphaM/beta2 Integrin/LRP/tPA -0.035 0.11 -9999 0 -0.56 43 43
IL6 -0.3 0.48 -9999 0 -0.94 380 380
ITGB2 -0.017 0.037 -9999 0 -0.3 14 14
elevation of cytosolic calcium ion concentration -0.024 0.048 -9999 0 -0.39 1 1
alphaM/beta2 Integrin/JAM2/JAM3 -0.043 0.13 -9999 0 -0.55 61 61
JAM2 -0.046 0.19 -9999 0 -0.8 59 59
alphaM/beta2 Integrin/ICAM1 -0.022 0.083 -9999 0 -0.54 21 21
alphaM/beta2 Integrin/uPA/Plg -0.019 0.032 -9999 0 -10000 0 0
RhoA/GTP -0.089 0.16 -9999 0 -0.39 186 186
positive regulation of phagocytosis -0.049 0.09 -9999 0 -0.46 18 18
Ron/MSP -0.017 0.1 -9999 0 -0.67 22 22
alphaM/beta2 Integrin/uPAR/uPA -0.024 0.048 -9999 0 -0.4 1 1
alphaM/beta2 Integrin/uPAR -0.028 0.046 -9999 0 -0.44 1 1
PLAU -0.008 0.047 -9999 0 -0.29 28 28
PLAT -0.029 0.15 -9999 0 -0.76 39 39
actin filament polymerization -0.067 0.16 -9999 0 -0.39 113 113
MST1 -0.012 0.092 -9999 0 -0.64 19 19
alphaM/beta2 Integrin/lipoprotein(a) -0.3 0.23 -9999 0 -0.48 636 636
TNF -0.089 0.22 -9999 0 -0.96 18 18
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.021 0.036 -9999 0 -0.29 1 1
fibrinolysis -0.019 0.032 -9999 0 -10000 0 0
HCK -0.004 0.032 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.062 0.14 -9999 0 -0.37 85 85
VTN -0.026 0.1 -9999 0 -0.34 80 80
alphaM/beta2 Integrin/CYR61 -0.047 0.13 -9999 0 -0.58 57 57
LPA -0.001 0.02 -9999 0 -0.29 5 5
LRP1 -0.009 0.082 -9999 0 -0.8 11 11
cell migration -0.071 0.083 -9999 0 -0.48 15 15
FN1 -0.12 0.14 -9999 0 -0.29 414 414
alphaM/beta2 Integrin/Thy1 -0.019 0.031 -9999 0 -10000 0 0
MPO -0.055 0.2 -9999 0 -0.78 73 73
KNG1 -0.005 0.039 -9999 0 -0.29 19 19
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.066 0.16 -9999 0 -0.4 109 109
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.02 -9999 0 -0.29 5 5
CTGF -0.011 0.091 -9999 0 -0.71 16 16
alphaM/beta2 Integrin/Hck -0.019 0.035 -9999 0 -10000 0 0
ITGAM -0.015 0.028 -9999 0 -0.3 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.21 -9999 0 -0.51 243 243
HP -0.16 0.31 -9999 0 -0.8 194 194
leukocyte adhesion -0.076 0.13 -9999 0 -0.6 41 41
SELP -0.19 0.34 -9999 0 -0.8 243 243
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.065 0.22 -9999 0 -0.68 40 40
CRP -0.069 0.22 -9999 0 -0.68 40 40
cell cycle arrest -0.083 0.25 -9999 0 -0.72 67 67
TIMP1 -0.062 0.21 -9999 0 -0.56 64 64
IL6ST -0.083 0.26 -9999 0 -0.8 124 124
Rac1/GDP -0.13 0.23 -9999 0 -0.68 88 88
AP1 -0.13 0.24 -9999 0 -0.47 307 307
GAB2 0.004 0.045 -9999 0 -0.38 11 11
TNFSF11 -0.075 0.22 -9999 0 -0.66 48 48
HSP90B1 0.015 0.047 -9999 0 -10000 0 0
GAB1 0 0.002 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.76 82 82
AKT1 0.038 0.04 -9999 0 -10000 0 0
FOXO1 0.047 0.057 -9999 0 -0.42 10 10
MAP2K6 -0.15 0.26 -9999 0 -0.72 103 103
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.087 0.23 -9999 0 -0.64 84 84
MITF -0.14 0.26 -9999 0 -0.72 95 95
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.014 0.12 -9999 0 -1.5 7 7
CEBPB 0.016 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.056 0.084 -9999 0 -0.44 10 10
STAT3 -0.092 0.26 -9999 0 -0.79 67 67
STAT1 -0.013 0.022 -9999 0 -10000 0 0
CEBPD -0.067 0.22 -9999 0 -0.67 54 54
PIK3CA 0.012 0.009 -9999 0 -0.29 1 1
PI3K -0.006 0.06 -9999 0 -0.61 10 10
JUN -0.005 0.066 -9999 0 -0.8 7 7
PIAS3/MITF -0.16 0.22 -9999 0 -0.72 84 84
MAPK11 -0.13 0.25 -9999 0 -0.77 83 83
STAT3 (dimer)/FOXO1 -0.035 0.22 -9999 0 -0.59 63 63
GRB2/SOS1/GAB family -0.14 0.2 -9999 0 -0.72 68 68
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.26 -9999 0 -0.51 209 209
GRB2 0 0.009 -9999 0 -0.29 1 1
JAK2 -0.001 0.025 -9999 0 -0.8 1 1
LBP -0.24 0.45 -9999 0 -0.97 259 259
PIK3R1 0.003 0.08 -9999 0 -0.8 10 10
JAK1 0.003 0.026 -9999 0 -0.8 1 1
MYC -0.078 0.26 -9999 0 -0.82 63 63
FGG -0.075 0.22 -9999 0 -0.69 40 40
macrophage differentiation -0.083 0.25 -9999 0 -0.72 67 67
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.23 0.28 -9999 0 -0.51 472 472
JUNB -0.064 0.21 -9999 0 -0.61 58 58
FOS -0.24 0.37 -9999 0 -0.8 307 307
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.16 0.26 -9999 0 -0.52 220 220
STAT1/PIAS1 -0.14 0.22 -9999 0 -0.59 119 119
GRB2/SOS1/GAB family/SHP2/PI3K -0.002 0.031 -9999 0 -0.29 5 5
STAT3 (dimer) -0.087 0.26 -9999 0 -0.76 67 67
PRKCD -0.061 0.22 -9999 0 -0.61 76 76
IL6R -0.028 0.16 -9999 0 -0.8 40 40
SOCS3 -0.12 0.24 -9999 0 -0.75 80 80
gp130 (dimer)/JAK1/JAK1/LMO4 -0.056 0.18 -9999 0 -0.53 126 126
Rac1/GTP -0.15 0.21 -9999 0 -0.68 88 88
HCK -0.004 0.032 -9999 0 -10000 0 0
MAPKKK cascade -0.006 0.085 -9999 0 -1 2 2
bone resorption -0.071 0.21 -9999 0 -0.61 55 55
IRF1 -0.065 0.22 -9999 0 -0.63 60 60
mol:GDP -0.13 0.25 -9999 0 -0.65 109 109
SOS1 0 0.003 -9999 0 -10000 0 0
VAV1 -0.14 0.26 -9999 0 -0.67 106 106
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.17 0.25 -9999 0 -0.82 85 85
PTPN11 -0.014 0.02 -9999 0 -10000 0 0
IL6/IL6RA -0.24 0.32 -9999 0 -0.64 398 398
gp130 (dimer)/TYK2/TYK2/LMO4 -0.058 0.18 -9999 0 -0.53 126 126
gp130 (dimer)/JAK2/JAK2/LMO4 -0.058 0.18 -9999 0 -0.53 126 126
IL6 -0.28 0.39 -9999 0 -0.8 381 381
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.003 0.026 -9999 0 -0.81 1 1
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.18 0.24 -9999 0 -0.41 471 471
LMO4 0.009 0.051 -9999 0 -0.8 3 3
STAT3 (dimer)/PIAS3 -0.15 0.21 -9999 0 -0.79 67 67
MCL1 0.051 0.032 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.023 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.039 -9999 0 -0.31 2 2
PDE6G/GNAT1/GTP -0.009 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.035 -9999 0 -10000 0 0
GRK1 -0.003 0.028 -9999 0 -0.29 10 10
CNG Channel -0.14 0.2 -9999 0 -0.44 302 302
mol:Na + -0.13 0.19 -9999 0 -0.43 297 297
mol:ADP -0.003 0.028 -9999 0 -0.29 10 10
RGS9-1/Gbeta5/R9AP -0.064 0.16 -9999 0 -0.54 104 104
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.14 0.2 -9999 0 -0.44 297 297
CNGB1 -0.015 0.064 -9999 0 -10000 0 0
RDH5 -0.48 0.4 -9999 0 -0.8 614 614
SAG -0.014 0.063 -9999 0 -0.29 51 51
mol:Ca2+ -0.12 0.18 -9999 0 -0.54 24 24
Na + (4 Units) -0.12 0.18 -9999 0 -0.52 24 24
RGS9 -0.084 0.24 -9999 0 -0.74 118 118
GNB1/GNGT1 -0.029 0.067 -9999 0 -10000 0 0
GNAT1/GDP -0.057 0.14 -9999 0 -0.47 104 104
GUCY2D -0.007 0.06 -9999 0 -0.8 4 4
GNGT1 -0.046 0.11 -9999 0 -0.29 165 165
GUCY2F -0.001 0.013 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.019 0.071 -9999 0 -0.46 21 21
mol:11-cis-retinal -0.48 0.39 -9999 0 -0.8 614 614
mol:cGMP -0.011 0.051 -9999 0 -0.46 9 9
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.37 0.3 -9999 0 -0.62 614 614
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.23 0.36 -9999 0 -0.8 297 297
Metarhodopsin II -0.003 0.021 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.012 0.054 -9999 0 -0.49 9 9
RGS9BP -0.019 0.072 -9999 0 -0.29 68 68
Metarhodopsin II/Transducin -0.009 0.02 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.008 0.044 -9999 0 -0.5 5 5
PDE6A/B -0.017 0.091 -9999 0 -0.62 21 21
mol:Pi -0.064 0.16 -9999 0 -0.54 104 104
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.023 0.05 -9999 0 -10000 0 0
PDE6B -0.017 0.11 -9999 0 -0.74 24 24
PDE6A -0.006 0.043 -9999 0 -10000 0 0
PDE6G -0.013 0.059 -9999 0 -10000 0 0
RHO -0.004 0.035 -9999 0 -0.29 15 15
PDE6 -0.065 0.15 -9999 0 -0.46 121 121
GUCA1A -0.013 0.059 -9999 0 -0.29 45 45
GC2/GCAP Family -0.009 0.044 -9999 0 -0.5 5 5
GUCA1C 0 0.009 -9999 0 -0.29 1 1
GUCA1B -0.004 0.056 -9999 0 -0.8 5 5
Ephrin A reverse 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
MAPKKK cascade -0.055 0.16 -9999 0 -0.54 104 104
EFNA5 -0.081 0.24 -9999 0 -0.8 105 105
FYN -0.034 0.16 -9999 0 -0.5 105 105
neuron projection morphogenesis -0.055 0.16 -9999 0 -0.54 104 104
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.055 0.16 -9999 0 -0.54 104 104
EPHA5 -0.001 0.018 -9999 0 -0.29 4 4
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.031 -9999 0 -10000 0 0
VDR 0 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.036 0.16 -9999 0 -0.43 20 20
RXRs/LXRs/DNA/Oxysterols -0.016 0.15 -9999 0 -0.5 19 19
MED1 -0.007 0.044 -9999 0 -0.29 24 24
mol:9cRA 0.005 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.023 0.092 -9999 0 -0.36 65 65
RXRs/NUR77 -0.15 0.24 -9999 0 -0.51 312 312
RXRs/PPAR -0.13 0.23 -9999 0 -0.38 427 427
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.007 0.052 -9999 0 -0.46 13 13
RARA -0.004 0.033 -9999 0 -0.29 14 14
NCOA1 -0.001 0.025 -9999 0 -0.8 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.007 0.053 -9999 0 -0.46 13 13
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.022 0.088 -9999 0 -0.35 65 65
THRA -0.001 0.025 -9999 0 -0.8 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.2 -9999 0 -0.48 256 256
NR1H4 -0.003 0.03 -9999 0 -0.29 11 11
RXRs/LXRs/DNA -0.11 0.19 -9999 0 -0.43 256 256
NR1H2 0.016 0.006 -9999 0 -10000 0 0
NR1H3 0.016 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.19 -9999 0 -0.45 256 256
NR4A1 -0.063 0.22 -9999 0 -0.8 81 81
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.045 0.13 -9999 0 -0.27 256 256
RXRG -0.19 0.35 -9999 0 -0.79 259 259
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.006 -9999 0 -10000 0 0
RXRB 0.016 0.007 -9999 0 -10000 0 0
THRB -0.043 0.18 -9999 0 -0.8 56 56
PPARG -0.19 0.34 -9999 0 -0.8 243 243
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.018 0.19 -9999 0 -1.2 15 15
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.016 0.15 -9999 0 -0.5 19 19
PPARA -0.005 0.061 -9999 0 -0.8 6 6
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.089 -9999 0 -0.8 13 13
RXRs/NUR77/BCL2 -0.12 0.19 -9999 0 -0.38 334 334
SREBF1 -0.006 0.14 -9999 0 -0.63 8 8
RXRs/RXRs/DNA/9cRA -0.12 0.2 -9999 0 -0.48 256 256
ABCA1 -0.01 0.16 -9999 0 -1 10 10
RARs/THRs -0.032 0.12 -9999 0 -0.48 65 65
RXRs/FXR -0.12 0.21 -9999 0 -0.48 256 256
BCL2 -0.028 0.15 -9999 0 -0.8 36 36
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.003 0.027 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.18 0.2 -9999 0 -0.41 458 458
Syndecan-3/Neurocan -0.007 0.027 -9999 0 -10000 0 0
POMC -0.024 0.12 -9999 0 -0.48 51 51
EGFR -0.29 0.39 -9999 0 -0.8 383 383
Syndecan-3/EGFR -0.16 0.22 -9999 0 -0.45 378 378
AGRP -0.003 0.028 -9999 0 -0.29 10 10
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0.009 -9999 0 -0.29 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.025 -9999 0 -0.8 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.019 0.072 -9999 0 -0.29 68 68
long-term memory -0.002 0.021 -9999 0 -0.42 2 2
Syndecan-3/IL8 -0.016 0.067 -9999 0 -0.45 20 20
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.002 0.035 -9999 0 -0.8 2 2
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.004 0.032 -9999 0 -0.29 13 13
SRC 0 0.009 -9999 0 -0.29 1 1
PTN -0.36 0.4 -9999 0 -0.8 460 460
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.18 0.2 -9999 0 -0.4 458 458
Syndecan-3/AgRP -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.015 -9999 0 -10000 0 0
Fyn/Cortactin -0.003 0.032 -9999 0 -0.61 2 2
SDC3 0 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.015 0.066 -9999 0 -0.44 20 20
IL8 -0.033 0.13 -9999 0 -0.41 84 84
Syndecan-3/Fyn/Cortactin -0.002 0.021 -9999 0 -0.43 2 2
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.019 0.092 -9999 0 -0.6 21 21
Gamma Secretase -0.001 0.014 -9999 0 -0.45 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.095 0.2 0.64 110 -10000 0 110
KIRREL -0.084 0.25 -10000 0 -0.81 110 110
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.095 0.2 -10000 0 -0.64 110 110
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.069 0.15 -10000 0 -0.49 110 110
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.042 0.11 -10000 0 -0.36 110 110
FYN -0.064 0.15 -10000 0 -0.47 110 110
mol:Ca2+ -0.068 0.15 -10000 0 -0.49 110 110
mol:DAG -0.069 0.15 -10000 0 -0.49 110 110
NPHS2 -0.008 0.031 -10000 0 -0.29 5 5
mol:IP3 -0.069 0.15 -10000 0 -0.49 110 110
regulation of endocytosis -0.054 0.14 -10000 0 -0.44 110 110
Nephrin/NEPH1/podocin/Cholesterol -0.071 0.16 -10000 0 -0.5 110 110
establishment of cell polarity -0.095 0.2 -10000 0 -0.64 110 110
Nephrin/NEPH1/podocin/NCK1-2 -0.056 0.14 -10000 0 -0.45 110 110
Nephrin/NEPH1/beta Arrestin2 -0.055 0.14 -10000 0 -0.45 110 110
NPHS1 -0.051 0.11 -10000 0 -0.36 17 17
Nephrin/NEPH1/podocin -0.064 0.15 -10000 0 -0.48 110 110
TJP1 -0.001 0.025 -10000 0 -0.8 1 1
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.069 0.15 -10000 0 -0.49 110 110
CD2AP 0 0.009 -10000 0 -0.29 1 1
Nephrin/NEPH1/podocin/GRB2 -0.069 0.15 -10000 0 -0.49 110 110
GRB2 0 0.009 -10000 0 -0.29 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.073 0.17 -10000 0 -0.51 118 118
cytoskeleton organization -0.054 0.14 -10000 0 -0.46 110 110
Nephrin/NEPH1 -0.069 0.15 -10000 0 -0.48 110 110
Nephrin/NEPH1/ZO-1 -0.075 0.16 -10000 0 -0.53 110 110
LPA receptor mediated events

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
GNB1/GNG2 -0.018 0.094 -9999 0 -0.52 32 32
NF kappa B1 p50/RelA/I kappa B alpha -0.044 0.11 -9999 0 -0.48 5 5
AP1 -0.19 0.25 -9999 0 -0.48 400 400
mol:PIP3 -0.2 0.25 -9999 0 -0.47 387 387
AKT1 -0.015 0.073 -9999 0 -0.59 7 7
PTK2B 0.014 0.061 -9999 0 -0.3 21 21
RHOA 0.029 0.027 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.007 0.13 -9999 0 -0.36 122 122
MAGI3 -0.001 0.025 -9999 0 -0.8 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.062 0.15 -9999 0 -0.43 139 139
HRAS/GDP -0.002 0.018 -9999 0 -0.2 9 9
positive regulation of microtubule depolymerization -0.02 0.15 -9999 0 -0.41 117 117
NF kappa B1 p50/RelA -0.054 0.14 -9999 0 -0.64 9 9
endothelial cell migration 0.008 0.12 -9999 0 -0.65 30 30
ADCY4 -0.001 0.15 -9999 0 -0.65 35 35
ADCY5 -0.071 0.19 -9999 0 -0.61 72 72
ADCY6 0.008 0.13 -9999 0 -0.61 28 28
ADCY7 0.008 0.13 -9999 0 -0.61 28 28
ADCY1 0 0.14 -9999 0 -0.64 34 34
ADCY2 -0.011 0.16 -9999 0 -0.63 41 41
ADCY3 0.008 0.13 -9999 0 -0.61 28 28
ADCY8 0.005 0.13 -9999 0 -0.62 28 28
ADCY9 0.008 0.13 -9999 0 -0.61 28 28
GSK3B 0.021 0.058 -9999 0 -0.36 9 9
arachidonic acid secretion 0.011 0.12 -9999 0 -0.56 31 31
GNG2 -0.009 0.086 -9999 0 -0.8 12 12
TRIP6 -0.001 0.017 -9999 0 -0.52 1 1
GNAO1 -0.006 0.13 -9999 0 -0.53 52 52
HRAS -0.003 0.027 -9999 0 -0.29 9 9
NFKBIA -0.004 0.15 -9999 0 -0.4 122 122
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.004 -9999 0 -10000 0 0
JUN -0.005 0.066 -9999 0 -0.8 7 7
LPA/LPA2/NHERF2 -0.002 0.016 -9999 0 -10000 0 0
TIAM1 0.001 0.004 -9999 0 -10000 0 0
PIK3R1 -0.008 0.078 -9999 0 -0.8 10 10
mol:IP3 -0.008 0.13 -9999 0 -0.36 122 122
PLCB3 0.024 0.018 -9999 0 -10000 0 0
FOS -0.24 0.37 -9999 0 -0.8 307 307
positive regulation of mitosis 0.011 0.12 -9999 0 -0.56 31 31
LPA/LPA1-2-3 -0.074 0.17 -9999 0 -0.5 139 139
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.1 -9999 0 -0.39 22 22
GNAZ 0.009 0.1 -9999 0 -0.49 38 38
EGFR/PI3K-beta/Gab1 -0.21 0.26 -9999 0 -0.64 161 161
positive regulation of dendritic cell cytokine production -0.073 0.17 -9999 0 -0.49 139 139
LPA/LPA2/MAGI-3 -0.002 0.02 -9999 0 -0.53 1 1
ARHGEF1 -0.01 0.068 -9999 0 -0.45 21 21
GNAI2 0.013 0.086 -9999 0 -0.47 30 30
GNAI3 0.013 0.086 -9999 0 -0.47 30 30
GNAI1 -0.013 0.15 -9999 0 -0.55 73 73
LPA/LPA3 -0.081 0.2 -9999 0 -0.62 122 122
LPA/LPA2 -0.002 0.016 -9999 0 -10000 0 0
LPA/LPA1 -0.016 0.095 -9999 0 -0.55 30 30
HB-EGF/EGFR -0.26 0.26 -9999 0 -0.58 383 383
HBEGF -0.069 0.11 -9999 0 -0.62 3 3
mol:DAG -0.008 0.13 -9999 0 -0.36 122 122
cAMP biosynthetic process -0.01 0.15 -9999 0 -0.57 50 50
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.004 0.15 -9999 0 -0.4 122 122
GNAQ -0.054 0.13 -9999 0 -0.42 124 124
LPAR2 -0.001 0.016 -9999 0 -0.29 3 3
LPAR3 -0.11 0.26 -9999 0 -0.8 122 122
LPAR1 -0.018 0.11 -9999 0 -0.8 21 21
IL8 -0.19 0.23 -9999 0 -0.44 403 403
PTK2 -0.068 0.16 -9999 0 -0.46 139 139
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.062 0.15 -9999 0 -0.43 139 139
EGFR -0.29 0.39 -9999 0 -0.8 383 383
PLCG1 -0.031 0.15 -9999 0 -0.43 122 122
PLD2 -0.068 0.16 -9999 0 -0.46 139 139
G12/G13 -0.012 0.074 -9999 0 -0.49 21 21
PI3K-beta -0.017 0.086 -9999 0 -0.72 7 7
cell migration -0.021 0.054 -9999 0 -0.24 7 7
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
PXN 0.002 0.1 -9999 0 -0.4 22 22
HRAS/GTP -0.033 0.12 -9999 0 -0.58 31 31
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.14 -9999 0 -0.29 453 453
PRKCE 0 0.001 -9999 0 -10000 0 0
PRKCD 0 0.13 -9999 0 -0.39 10 10
Gi(beta/gamma) -0.034 0.12 -9999 0 -0.58 35 35
mol:LPA -0.002 0.02 -9999 0 -0.22 9 9
TRIP6/p130 Cas/FAK1/Paxillin -0.056 0.14 -9999 0 -0.64 10 10
MAPKKK cascade 0.011 0.12 -9999 0 -0.56 31 31
contractile ring contraction involved in cytokinesis 0.029 0.026 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.059 0.14 -9999 0 -0.43 130 130
GNA15 -0.054 0.13 -9999 0 -0.42 123 123
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.022 0.15 -9999 0 -0.43 117 117
GNA11 -0.054 0.13 -9999 0 -0.42 124 124
Rac1/GTP 0.001 0.005 -9999 0 -10000 0 0
MMP2 0.008 0.12 -9999 0 -0.65 30 30
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.054 0.3 -10000 0 -0.82 124 124
IHH -0.014 0.082 -10000 0 -0.46 6 6
SHH Np/Cholesterol/GAS1 -0.03 0.12 -10000 0 -0.5 57 57
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.03 0.11 0.5 57 -10000 0 57
SMO/beta Arrestin2 -0.076 0.23 -10000 0 -0.85 78 78
SMO -0.037 0.26 -10000 0 -0.91 78 78
AKT1 0.008 0.11 -10000 0 -0.33 77 77
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.06 0.21 -10000 0 -0.8 78 78
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.035 0.26 -10000 0 -0.88 78 78
STIL -0.04 0.21 -10000 0 -0.71 80 80
DHH N/PTCH2 -0.066 0.2 -10000 0 -0.64 105 105
DHH N/PTCH1 -0.09 0.24 -10000 0 -0.78 101 101
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DHH -0.023 0.13 -10000 0 -0.8 29 29
PTHLH -0.082 0.38 -10000 0 -1.1 124 124
determination of left/right symmetry -0.035 0.26 -10000 0 -0.88 78 78
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
skeletal system development -0.079 0.37 -10000 0 -1 124 124
IHH N/Hhip -0.014 0.046 -10000 0 -0.66 1 1
DHH N/Hhip -0.02 0.11 -10000 0 -0.62 30 30
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.035 0.26 -10000 0 -0.88 78 78
pancreas development -0.004 0.038 -10000 0 -0.34 11 11
HHAT -0.001 0.025 -10000 0 -0.8 1 1
PI3K -0.006 0.06 -10000 0 -0.61 10 10
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.043 0.18 -10000 0 -0.8 56 56
somite specification -0.035 0.26 -10000 0 -0.88 78 78
SHH Np/Cholesterol/PTCH1 -0.072 0.21 -10000 0 -0.76 77 77
SHH Np/Cholesterol/PTCH2 -0.042 0.14 -10000 0 -0.5 83 83
SHH Np/Cholesterol/Megalin -0.14 0.22 -10000 0 -0.5 272 272
SHH 0.01 0.036 -10000 0 -0.62 1 1
catabolic process -0.048 0.26 -10000 0 -0.86 86 86
SMO/Vitamin D3 -0.075 0.23 -10000 0 -0.82 78 78
SHH Np/Cholesterol/Hhip -0.005 0.034 -10000 0 -0.5 2 2
LRP2 -0.22 0.35 -10000 0 -0.8 271 271
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.83 94 94
SHH Np/Cholesterol/BOC -0.041 0.13 -10000 0 -0.5 79 79
SHH Np/Cholesterol/CDO -0.01 0.06 -10000 0 -0.49 14 14
mesenchymal cell differentiation 0.005 0.034 0.5 2 -10000 0 2
mol:Vitamin D3 -0.031 0.22 -10000 0 -0.77 77 77
IHH N/PTCH2 -0.065 0.19 -10000 0 -0.67 86 86
CDON -0.01 0.089 -10000 0 -0.8 13 13
IHH N/PTCH1 -0.046 0.26 -10000 0 -0.87 86 86
Megalin/LRPAP1 -0.16 0.27 -10000 0 -0.61 271 271
PTCH2 -0.064 0.22 -10000 0 -0.8 82 82
SHH Np/Cholesterol -0.004 0.026 -10000 0 -0.5 1 1
PTCH1 -0.048 0.26 -10000 0 -0.87 86 86
HHIP -0.004 0.038 -10000 0 -0.34 11 11
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.049 0.2 -9999 0 -0.82 65 65
PDGF/PDGFRA/CRKL -0.038 0.15 -9999 0 -0.62 64 64
positive regulation of JUN kinase activity -0.029 0.11 -9999 0 -0.47 64 64
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.042 0.15 -9999 0 -0.62 64 64
AP1 -0.36 0.54 -9999 0 -1.2 307 307
mol:IP3 -0.033 0.16 -9999 0 -0.64 64 64
PLCG1 -0.033 0.16 -9999 0 -0.64 64 64
PDGF/PDGFRA/alphaV Integrin -0.038 0.15 -9999 0 -0.62 64 64
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.033 0.16 -9999 0 -0.64 64 64
CAV3 -0.001 0.016 -9999 0 -0.29 3 3
CAV1 -0.17 0.33 -9999 0 -0.8 224 224
SHC/Grb2/SOS1 -0.03 0.12 -9999 0 -0.48 64 64
PDGF/PDGFRA/Shf -0.039 0.15 -9999 0 -0.62 64 64
FOS -0.32 0.55 -9999 0 -1.1 341 341
JUN -0.024 0.061 -9999 0 -0.68 7 7
oligodendrocyte development -0.038 0.15 -9999 0 -0.62 64 64
GRB2 0 0.009 -9999 0 -0.29 1 1
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
mol:DAG -0.033 0.16 -9999 0 -0.64 64 64
PDGF/PDGFRA -0.049 0.2 -9999 0 -0.82 65 65
actin cytoskeleton reorganization -0.039 0.15 -9999 0 -0.62 65 65
SRF 0.015 0.021 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.038 0.14 -9999 0 -0.54 73 73
PDGF/PDGFRA/Crk/C3G -0.033 0.13 -9999 0 -0.53 64 64
JAK1 -0.023 0.15 -9999 0 -0.62 65 65
ELK1/SRF -0.026 0.12 -9999 0 -0.48 64 64
SHB -0.001 0.026 -9999 0 -0.8 1 1
SHF -0.001 0.026 -9999 0 -0.55 2 2
CSNK2A1 0.019 0.027 -9999 0 -10000 0 0
GO:0007205 -0.034 0.16 -9999 0 -0.66 64 64
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.029 0.11 -9999 0 -0.47 64 64
PDGF/PDGFRA/SHB -0.039 0.15 -9999 0 -0.62 65 65
PDGF/PDGFRA/Caveolin-1 -0.17 0.32 -9999 0 -0.72 246 246
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.033 0.15 -9999 0 -0.59 64 64
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PDGF/PDGFRA/Crk -0.038 0.15 -9999 0 -0.62 64 64
JAK-STAT cascade -0.022 0.15 -9999 0 -0.62 65 65
cell proliferation -0.039 0.15 -9999 0 -0.62 64 64
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.028 0.03 -9999 0 -10000 0 0
BUB1B -0.038 0.051 -9999 0 -10000 0 0
PLK1 -0.007 0.023 -9999 0 -10000 0 0
PLK1S1 0.001 0.013 -9999 0 -10000 0 0
KIF2A 0.002 0.021 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.008 0.023 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.17 0.12 -9999 0 -0.28 506 506
WEE1 -0.002 0.023 -9999 0 -10000 0 0
cytokinesis -0.053 0.056 -9999 0 -0.24 28 28
PP2A-alpha B56 0.029 0.02 -9999 0 -10000 0 0
AURKA 0 0.014 -9999 0 -10000 0 0
PICH/PLK1 -0.075 0.095 -9999 0 -0.34 11 11
CENPE -0.05 0.085 -9999 0 -0.17 173 173
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.002 0.021 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.005 0.016 -9999 0 -10000 0 0
PAK1 -0.007 0.043 -9999 0 -0.28 24 24
SPC24 -0.18 0.14 -9999 0 -0.29 645 645
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.005 0.018 -9999 0 -10000 0 0
GORASP1 0 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.004 0.013 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
STAG2 -0.001 0.025 -9999 0 -0.8 1 1
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.008 0.023 -9999 0 -10000 0 0
ODF2 0 0 -9999 0 -10000 0 0
BUB1 0.023 0.016 -9999 0 -10000 0 0
TPT1 0.001 0.013 -9999 0 -10000 0 0
CDC25C -0.007 0.015 -9999 0 -10000 0 0
CDC25B -0.001 0.041 -9999 0 -0.29 20 20
SGOL1 -0.028 0.03 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.022 0.042 -9999 0 -10000 0 0
CDC14B -0.009 0.11 -9999 0 -0.63 32 32
CDC20 -0.16 0.14 -9999 0 -0.29 563 563
PLK1/PBIP1 -0.029 0.054 -9999 0 -0.18 4 4
mitosis -0.006 0.007 -9999 0 -0.022 2 2
FBXO5 0 0.022 -9999 0 -0.15 1 1
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.18 0.14 -9999 0 -0.29 634 634
metaphase plate congression -0.002 0.015 -9999 0 -10000 0 0
ERCC6L -0.064 0.089 -9999 0 -10000 0 0
NLP/gamma Tubulin 0 0.013 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.001 0.013 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.1 -9999 0 -0.28 267 267
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.003 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.002 0.023 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.05 -9999 0 -0.3 26 26
microtubule-based process -0.11 0.068 -9999 0 -0.17 213 213
Golgi organization -0.008 0.023 -9999 0 -10000 0 0
Cohesin/SA2 -0.01 0.018 -9999 0 -0.46 1 1
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.12 -9999 0 -0.29 777 777
APC/C/CDC20 -0.087 0.079 -9999 0 -0.17 418 418
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.029 0.053 -9999 0 -0.18 4 4
PRC1 -0.075 0.13 -9999 0 -0.29 268 268
ECT2 -0.004 0.039 -9999 0 -0.19 5 5
C13orf34 0 0.021 -9999 0 -10000 0 0
NUDC -0.002 0.015 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.038 0.051 -9999 0 -10000 0 0
spindle assembly -0.003 0.019 -9999 0 -10000 0 0
spindle stabilization 0.001 0.013 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.094 -9999 0 -0.54 32 32
MKLP2/PLK1 -0.12 0.068 -9999 0 -0.17 213 213
CCNB1 -0.057 0.12 -9999 0 -0.29 215 215
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 -0.008 0.086 -9999 0 -0.52 28 28
TUBG1 0.001 0.013 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.04 -9999 0 -10000 0 0
MLF1IP -0.027 0.075 -9999 0 -0.2 78 78
INCENP 0 0.002 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.008 0.056 -9999 0 -0.46 15 15
RGS9BP -0.019 0.072 -9999 0 -0.29 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.028 -9999 0 -0.29 10 10
mol:Na + -0.02 0.052 -9999 0 -10000 0 0
mol:ADP 0.008 0.026 -9999 0 -10000 0 0
GNAT2 -0.001 0.018 -9999 0 -0.29 4 4
RGS9-1/Gbeta5/R9AP -0.064 0.16 -9999 0 -0.54 104 104
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
GRK7 -0.002 0.024 -9999 0 -0.29 7 7
CNGB3 -0.011 0.054 -9999 0 -0.29 38 38
Cone Metarhodopsin II/X-Arrestin -0.002 0.017 -9999 0 -10000 0 0
mol:Ca2+ -0.095 0.084 -9999 0 -0.28 82 82
Cone PDE6 -0.056 0.14 -9999 0 -0.47 104 104
Cone Metarhodopsin II -0.002 0.018 -9999 0 -10000 0 0
Na + (4 Units) -0.098 0.08 -9999 0 -0.27 82 82
GNAT2/GDP -0.055 0.14 -9999 0 -0.47 104 104
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.007 0.016 -9999 0 -10000 0 0
Cone Transducin -0.008 0.059 -9999 0 -0.49 15 15
SLC24A2 -0.18 0.14 -9999 0 -0.29 631 631
GNB3/GNGT2 -0.009 0.074 -9999 0 -0.61 15 15
GNB3 -0.011 0.091 -9999 0 -0.71 16 16
GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
CNGA3 -0.027 0.084 -9999 0 -0.29 96 96
ARR3 -0.002 0.025 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.02 0.052 -9999 0 -10000 0 0
mol:Pi -0.064 0.16 -9999 0 -0.54 104 104
Cone CNG Channel -0.016 0.039 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.18 0.14 -9999 0 -0.29 631 631
RGS9 -0.084 0.24 -9999 0 -0.74 118 118
PDE6C 0 0.009 -9999 0 -0.29 1 1
GNGT2 -0.002 0.035 -9999 0 -0.8 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.002 0.022 -9999 0 -0.29 6 6
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.002 0.035 -9999 0 -0.8 2 2
LAT2 -0.062 0.14 -9999 0 -0.43 86 86
AP1 -0.15 0.22 -9999 0 -0.44 328 328
mol:PIP3 -0.027 0.2 -9999 0 -0.51 89 89
IKBKB 0.002 0.12 -9999 0 -0.32 49 49
AKT1 -0.082 0.17 -9999 0 -0.67 43 43
IKBKG 0.002 0.12 -9999 0 -0.32 49 49
MS4A2 -0.067 0.22 -9999 0 -0.78 89 89
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
MAP3K1 0.006 0.13 -9999 0 -0.44 41 41
mol:Ca2+ -0.012 0.15 -9999 0 -0.37 89 89
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.061 0.14 -9999 0 -0.43 86 86
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.063 0.16 -9999 0 -0.49 133 133
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.097 0.21 -9999 0 -0.49 203 203
PTPN13 -0.031 0.17 -9999 0 -0.54 64 64
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.007 0.15 -9999 0 -0.42 40 40
SYK 0.011 0.01 -9999 0 -0.29 1 1
GRB2 0 0.009 -9999 0 -0.29 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.086 0.18 -9999 0 -0.52 89 89
LAT -0.063 0.14 -9999 0 -0.43 87 87
PAK2 -0.003 0.14 -9999 0 -0.49 41 41
NFATC2 -0.1 0.24 -9999 0 -0.82 93 93
HRAS -0.012 0.15 -9999 0 -0.53 43 43
GAB2 -0.004 0.044 -9999 0 -0.38 11 11
PLA2G1B 0.028 0.018 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.25 -9999 0 -0.61 203 203
Antigen/IgE/Fc epsilon R1 -0.11 0.24 -9999 0 -0.56 203 203
mol:GDP -0.019 0.15 -9999 0 -0.55 43 43
JUN -0.005 0.066 -9999 0 -0.8 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.079 -9999 0 -0.81 10 10
FOS -0.24 0.37 -9999 0 -0.8 307 307
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.066 0.15 -9999 0 -0.45 88 88
CHUK 0.002 0.12 -9999 0 -0.32 49 49
KLRG1 -0.061 0.13 -9999 0 -0.5 48 48
VAV1 -0.063 0.14 -9999 0 -0.44 89 89
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.061 0.14 -9999 0 -0.43 86 86
negative regulation of mast cell degranulation -0.056 0.12 -9999 0 -0.51 39 39
BTK -0.06 0.14 -9999 0 -0.43 87 87
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.085 0.2 -9999 0 -0.43 205 205
GAB2/PI3K/SHP2 -0.091 0.19 -9999 0 -0.74 45 45
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.069 0.16 -9999 0 -0.68 40 40
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.22 -9999 0 -0.52 205 205
FCER1G 0.003 0.012 -9999 0 -0.29 1 1
FCER1A -0.11 0.29 -9999 0 -0.81 153 153
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.22 -9999 0 -0.53 203 203
MAPK3 0.026 0.019 -9999 0 -10000 0 0
MAPK1 0.026 0.019 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.079 -9999 0 -0.67 9 9
DUSP1 -0.1 0.27 -9999 0 -0.8 133 133
NF-kappa-B/RelA -0.027 0.054 -9999 0 -0.24 1 1
actin cytoskeleton reorganization -0.026 0.15 -9999 0 -0.56 37 37
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.057 0.13 -9999 0 -0.52 48 48
FER -0.066 0.15 -9999 0 -0.45 93 93
RELA 0 0 -9999 0 -10000 0 0
ITK -0.036 0.12 -9999 0 -0.6 39 39
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.016 0.16 -9999 0 -0.57 42 42
cytokine secretion -0.019 0.04 -9999 0 -10000 0 0
SPHK1 -0.064 0.14 -9999 0 -0.44 89 89
PTK2 -0.028 0.16 -9999 0 -0.58 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.089 0.19 -9999 0 -0.55 89 89
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.022 0.2 -9999 0 -0.49 90 90
MAP2K2 0.022 0.019 -9999 0 -10000 0 0
MAP2K1 0.022 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.057 0.12 -9999 0 -0.51 39 39
MAP2K4 0.016 0.034 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.11 0.24 -9999 0 -0.56 205 205
mol:Choline -0.095 0.2 -9999 0 -0.48 203 203
SHC/Grb2/SOS1 -0.055 0.13 -9999 0 -0.53 37 37
FYN -0.002 0.035 -9999 0 -0.8 2 2
DOK1 -0.001 0.018 -9999 0 -0.29 4 4
PXN -0.018 0.15 -9999 0 -0.53 37 37
HCLS1 -0.061 0.14 -9999 0 -0.43 86 86
PRKCB -0.014 0.16 -9999 0 -0.39 94 94
FCGR2B -0.003 0.051 -9999 0 -0.8 4 4
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.057 0.12 -9999 0 -0.52 39 39
LCP2 0 0.009 -9999 0 -0.29 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.51 186 186
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.095 0.2 -9999 0 -0.48 203 203
IKK complex 0.02 0.093 -9999 0 -0.23 45 45
WIPF1 0 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.003 0.05 -9999 0 -0.8 4 4
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.61 35 35
PTK2 -0.065 0.19 -9999 0 -0.58 112 112
positive regulation of JNK cascade -0.037 0.11 -9999 0 -0.34 112 112
CDC42/GDP -0.001 0.16 -9999 0 -0.46 112 112
Rac1/GDP 0.002 0.16 -9999 0 -0.46 112 112
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.046 0.13 -9999 0 -0.42 112 112
nectin-3/I-afadin -0.069 0.2 -9999 0 -0.64 112 112
RAPGEF1 -0.009 0.18 -9999 0 -0.53 112 112
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.023 0.21 -9999 0 -0.62 112 112
PDGFB-D/PDGFRB -0.003 0.05 -9999 0 -0.8 4 4
TLN1 0.001 0.1 -9999 0 -0.53 14 14
Rap1/GTP -0.04 0.11 -9999 0 -0.36 112 112
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.037 -9999 0 -0.49 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.069 0.2 -9999 0 -0.64 112 112
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.012 0.2 -9999 0 -0.58 112 112
MLLT4 -0.005 0.062 -9999 0 -0.73 7 7
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.057 0.17 -9999 0 -0.5 117 117
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.004 0.047 -9999 0 -0.61 6 6
positive regulation of lamellipodium assembly -0.039 0.11 -9999 0 -0.36 112 112
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.086 0.25 -9999 0 -0.8 111 111
PVRL2 -0.001 0.016 -9999 0 -10000 0 0
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
CDH1 -0.025 0.14 -9999 0 -0.8 32 32
CLDN1 -0.036 0.15 -9999 0 -0.58 64 64
JAM-A/CLDN1 -0.074 0.19 -9999 0 -0.52 140 140
SRC -0.077 0.22 -9999 0 -0.7 112 112
ITGB3 -0.028 0.15 -9999 0 -0.75 39 39
nectin-1(dimer)/I-afadin/I-afadin -0.004 0.047 -9999 0 -0.61 6 6
FARP2 -0.017 0.2 -9999 0 -0.57 112 112
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.06 0.17 -9999 0 -0.55 112 112
nectin-1/I-afadin -0.004 0.047 -9999 0 -0.61 6 6
nectin-2/I-afadin -0.004 0.048 -9999 0 -0.61 6 6
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.06 0.17 -9999 0 -0.55 112 112
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.037 0.11 -9999 0 -0.34 112 112
alphaV/beta3 Integrin/Talin -0.04 0.13 -9999 0 -0.6 40 40
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.048 -9999 0 -0.61 6 6
nectin-2(dimer)/I-afadin/I-afadin -0.004 0.048 -9999 0 -0.61 6 6
PIP5K1C -0.032 0.1 -9999 0 -0.29 116 116
VAV2 -0.018 0.2 -9999 0 -0.58 112 112
RAP1/GDP -0.047 0.13 -9999 0 -0.43 112 112
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.06 0.17 -9999 0 -0.55 112 112
nectin-3(dimer)/I-afadin/I-afadin -0.069 0.2 -9999 0 -0.64 112 112
Rac1/GTP -0.048 0.14 -9999 0 -0.44 112 112
PTPRM -0.037 0.11 -9999 0 -0.33 116 116
E-cadherin/beta catenin/alpha catenin -0.016 0.082 -9999 0 -0.44 37 37
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.009 0.049 -10000 0 -0.43 10 10
adherens junction organization 0.03 0.067 -10000 0 -0.31 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 -10000 0 -0.38 385 385
FMN1 0.022 0.094 -10000 0 -0.46 23 23
mol:IP3 -0.009 0.048 -10000 0 -0.4 10 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.057 -10000 0 -0.32 33 33
CTNNB1 0.001 0.004 -10000 0 -10000 0 0
AKT1 -0.01 0.05 -10000 0 -0.39 10 10
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.016 0.088 -10000 0 -0.51 32 32
CTNND1 0.011 0.01 -10000 0 -0.28 1 1
mol:PI-4-5-P2 0.032 0.06 -10000 0 -10000 0 0
VASP 0.032 0.061 -10000 0 -10000 0 0
ZYX 0.032 0.061 -10000 0 -10000 0 0
JUB 0.03 0.067 -10000 0 -0.42 4 4
EGFR(dimer) -0.16 0.21 -10000 0 -0.43 393 393
E-cadherin/beta catenin-gamma catenin -0.016 0.09 -10000 0 -0.51 33 33
mol:PI-3-4-5-P3 -0.01 0.054 -10000 0 -0.42 10 10
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PI3K -0.011 0.055 -10000 0 -0.42 10 10
FYN 0.04 0.054 -10000 0 -0.38 2 2
mol:Ca2+ -0.009 0.047 -10000 0 -0.39 10 10
JUP 0 0.027 -10000 0 -0.55 2 2
PIK3R1 -0.008 0.078 -10000 0 -0.8 10 10
mol:DAG -0.009 0.048 -10000 0 -0.4 10 10
CDH1 -0.025 0.14 -10000 0 -0.8 32 32
RhoA/GDP -0.14 0.18 -10000 0 -0.57 21 21
establishment of polarity of embryonic epithelium 0.032 0.06 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.29 0.39 -10000 0 -0.8 383 383
CASR 0.008 0.054 -10000 0 -0.37 10 10
RhoA/GTP -0.008 0.042 -10000 0 -10000 0 0
AKT2 -0.01 0.05 -10000 0 -0.39 10 10
actin cable formation 0.029 0.091 -10000 0 -0.44 22 22
apoptosis 0.01 0.05 0.4 10 -10000 0 10
CTNNA1 0.011 0.002 -10000 0 -10000 0 0
mol:GDP -0.16 0.2 -10000 0 -0.41 385 385
PIP5K1A 0.032 0.061 -10000 0 -10000 0 0
PLCG1 -0.009 0.049 -10000 0 -0.41 10 10
Rac1/GTP -0.15 0.19 -10000 0 -0.4 379 379
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.005 0.052 -10000 0 -0.54 9 9
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.001 0.004 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.068 0.22 -10000 0 -0.8 88 88
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
TLE1 -0.005 0.07 -10000 0 -0.8 8 8
AP1 -0.11 0.18 -10000 0 -0.37 311 311
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.002 0.043 -10000 0 -0.8 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.045 -10000 0 -0.34 1 1
NICD/RBPSUH -0.002 0.038 -10000 0 -0.71 3 3
WIF1 -0.42 0.4 -10000 0 -0.79 554 554
NOTCH1 -0.002 0.041 -10000 0 -0.76 3 3
PSENEN 0 0.009 -10000 0 -0.29 1 1
KREMEN2 -0.14 0.14 -10000 0 -0.29 500 500
DKK1 -0.079 0.19 -10000 0 -0.42 194 194
beta catenin/beta TrCP1 -0.009 0.025 -10000 0 -10000 0 0
APH1B -0.001 0.025 -10000 0 -0.8 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.014 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.04 -10000 0 -0.34 8 8
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.24 0.37 -10000 0 -0.8 307 307
JUN -0.005 0.066 -10000 0 -0.8 7 7
MAP3K7 0.001 0.01 -10000 0 -0.29 1 1
CTNNB1 -0.003 0.035 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.083 0.11 -10000 0 -0.61 28 28
HNF1A -0.001 0.024 -10000 0 -0.29 7 7
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC -0.033 0.22 -10000 0 -1.5 23 23
NKD1 -0.009 0.07 -10000 0 -0.43 22 22
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.04 0.13 -10000 0 -0.45 91 91
apoptosis -0.11 0.17 -10000 0 -0.37 311 311
Delta 1/NOTCHprecursor -0.005 0.051 -10000 0 -0.53 9 9
DLL1 -0.005 0.061 -10000 0 -0.8 6 6
PPARD -0.001 0.012 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.014 -10000 0 -0.45 1 1
APC 0.003 0.014 -10000 0 -10000 0 0
DVL1 -0.038 0.036 -10000 0 -10000 0 0
CSNK2A1 0 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.58 53 53
LRP6 -0.001 0.013 -10000 0 -0.29 2 2
CSNK1A1 0 0.001 -10000 0 -10000 0 0
NLK 0.002 0.01 -10000 0 -10000 0 0
CCND1 -0.012 0.096 -10000 0 -1.5 4 4
WNT1 -0.001 0.013 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.01 0.037 -10000 0 -10000 0 0
DKK2 -0.022 0.13 -10000 0 -0.77 30 30
NOTCH1 precursor/DVL1 -0.019 0.039 -10000 0 -0.66 3 3
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 0.001 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.04 0.13 -10000 0 -0.45 91 91
PPP2R5D -0.015 0.038 0.36 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.25 0.24 -10000 0 -0.48 540 540
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.014 0.004 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.55 0.37 -9999 0 -0.8 709 709
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.007 0.044 -9999 0 -0.29 25 25
TCEB1 -0.001 0.013 -9999 0 -0.29 2 2
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.007 -9999 0 -10000 0 0
COPS5 0 0.009 -9999 0 -0.29 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.016 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.05 0.11 -9999 0 -0.29 179 179
ARNT/IPAS -0.42 0.29 -9999 0 -0.61 709 709
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.001 0.005 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0.009 -9999 0 -0.29 1 1
RACK1/Elongin B/Elongin C -0.004 0.022 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.006 -9999 0 -10000 0 0
PHD1-3/OS9 -0.01 0.038 -9999 0 -0.48 2 2
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.014 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -10000 0 0
HIF1A/JAB1 -0.001 0.007 -9999 0 -10000 0 0
EGLN3 -0.022 0.08 -9999 0 -0.3 78 78
EGLN2 -0.002 0.022 -9999 0 -0.29 6 6
EGLN1 -0.001 0.025 -9999 0 -0.8 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.001 0.005 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.019 0.039 -9999 0 -10000 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.48 247 247
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.021 -10000 0 -10000 0 0
GNB1/GNG2 -0.006 0.058 -10000 0 -0.54 12 12
GNB1 0 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 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.12 0.21 -10000 0 -0.5 244 244
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 0.027 0.048 0.11 244 -10000 0 244
GNAL -0.19 0.34 -10000 0 -0.8 244 244
GNG2 -0.009 0.086 -10000 0 -0.8 12 12
CRH -0.003 0.03 -10000 0 -0.29 11 11
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.04 -10000 0 -0.45 8 8
MAPK11 0.007 0.025 -10000 0 -0.45 3 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.058 -10000 0 -0.33 33 33
epithelial cell differentiation -0.014 0.078 -10000 0 -0.45 32 32
CYFIP2 -0.01 0.067 -10000 0 -0.36 30 30
ENAH 0.056 0.063 -10000 0 -10000 0 0
EGFR -0.29 0.39 -10000 0 -0.8 383 383
EPHA2 -0.005 0.061 -10000 0 -0.8 6 6
MYO6 -0.014 0.075 -10000 0 -0.43 33 33
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.039 -10000 0 -0.53 4 4
AQP5 -0.24 0.3 -10000 0 -0.6 412 412
CTNND1 0 0.009 -10000 0 -0.29 1 1
mol:PI-4-5-P2 -0.013 0.073 -10000 0 -0.42 32 32
regulation of calcium-dependent cell-cell adhesion -0.036 0.12 -10000 0 -0.43 86 86
EGF -0.16 0.32 -10000 0 -0.8 202 202
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.039 0.14 -10000 0 -0.57 56 56
cortical microtubule organization -0.014 0.078 -10000 0 -0.45 32 32
GO:0000145 0.024 0.076 -10000 0 -0.4 32 32
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.079 -10000 0 -0.46 32 32
MLLT4 -0.005 0.062 -10000 0 -0.73 7 7
ARF6/GDP -0.013 0.066 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.037 -10000 0 -0.48 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.035 0.08 -10000 0 -0.39 32 32
PVRL2 -0.001 0.016 -10000 0 -10000 0 0
ZYX -0.013 0.074 -10000 0 -0.43 32 32
ARF6/GTP -0.003 0.034 -10000 0 -0.44 6 6
CDH1 -0.025 0.14 -10000 0 -0.8 32 32
EGFR/EGFR/EGF/EGF -0.24 0.26 -10000 0 -0.47 533 533
RhoA/GDP -0.013 0.073 -10000 0 -0.42 32 32
actin cytoskeleton organization 0.031 0.079 -10000 0 -0.4 33 33
IGF-1R heterotetramer -0.021 0.12 -10000 0 -0.8 22 22
GIT1 -0.001 0.02 -10000 0 -10000 0 0
IGF1R -0.021 0.12 -10000 0 -0.8 22 22
IGF1 -0.18 0.33 -10000 0 -0.8 231 231
DIAPH1 -0.002 0.045 -10000 0 -0.7 4 4
Wnt receptor signaling pathway 0.014 0.078 0.45 32 -10000 0 32
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.066 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL 0.031 0.08 -10000 0 -0.41 33 33
EFNA1 0 0 -10000 0 -10000 0 0
LPP 0.028 0.087 -10000 0 -0.4 40 40
Ephrin A1/EPHA2 -0.015 0.077 -10000 0 -0.41 38 38
SEC6/SEC8 -0.014 0.072 -10000 0 -0.76 1 1
MGAT3 -0.037 0.12 -10000 0 -0.44 86 86
HGF/MET -0.11 0.21 -10000 0 -0.46 244 244
HGF -0.053 0.2 -10000 0 -0.8 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.011 0.058 -10000 0 -0.33 33 33
actin cable formation 0.07 0.061 -10000 0 -0.33 1 1
KIAA1543 0.03 0.089 -10000 0 -0.44 33 33
KIFC3 -0.014 0.076 -10000 0 -0.43 34 34
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.014 0.075 -10000 0 -0.43 33 33
NCK1/GIT1 -0.001 0.013 -10000 0 -10000 0 0
mol:GDP -0.014 0.078 -10000 0 -0.45 32 32
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.013 0.074 -10000 0 -0.43 32 32
PIP5K1C -0.013 0.074 -10000 0 -0.43 32 32
LIMA1 -0.001 0.025 -10000 0 -0.8 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.012 0.059 -10000 0 -10000 0 0
adherens junction assembly 0.046 0.086 -10000 0 -0.64 4 4
IGF-1R heterotetramer/IGF1 -0.12 0.2 -10000 0 -0.44 267 267
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.048 -10000 0 -0.61 6 6
MET -0.13 0.3 -10000 0 -0.8 172 172
PLEKHA7 -0.014 0.081 -10000 0 -0.46 32 32
mol:GTP -0.003 0.037 -10000 0 -0.48 6 6
establishment of epithelial cell apical/basal polarity -0.013 0.068 -10000 0 -0.72 1 1
cortical actin cytoskeleton stabilization -0.01 0.058 -10000 0 -0.33 33 33
regulation of cell-cell adhesion 0.031 0.079 -10000 0 -0.4 33 33
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.058 -10000 0 -0.33 33 33
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.025 -10000 0 -0.8 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.012 0.077 0.62 1 -10000 0 1
CDKN1A -0.002 0.042 -10000 0 -0.95 2 2
KAT2B -0.001 0.025 -10000 0 -0.8 1 1
BAX -0.001 0.02 -10000 0 -0.29 5 5
FOXO3 -0.001 0.018 -10000 0 -0.33 3 3
FOXO1 -0.008 0.079 -10000 0 -0.8 10 10
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.57 0.36 -10000 0 -0.79 753 753
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.03 -10000 0 -0.61 1 1
PPARGC1A -0.17 0.33 -10000 0 -0.78 229 229
FHL2 -0.005 0.061 -10000 0 -0.8 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.007 -10000 0 -10000 0 0
HIST2H4A -0.012 0.077 -10000 0 -0.62 1 1
SIRT1/FOXO3a 0 0.015 -10000 0 -0.25 3 3
SIRT1 0 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.018 -10000 0 -0.53 1 1
SIRT1/Histone H1b -0.003 0.012 -10000 0 -10000 0 0
apoptosis 0 0.012 -10000 0 -10000 0 0
SIRT1/PGC1A -0.12 0.22 -10000 0 -0.54 218 218
p53/SIRT1 0.001 0.019 0.43 2 -10000 0 2
SIRT1/FOXO4 0 0.007 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.007 0.061 -10000 0 -0.49 16 16
HIST1H1E -0.005 0.015 -10000 0 -10000 0 0
SIRT1/p300 0 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.024 0.53 1 -10000 0 1
TP53 0 0.009 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.012 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.44 0.28 -10000 0 -0.62 727 727
ACSS2 0.019 0.02 -10000 0 -0.62 1 1
SIRT1/PCAF/MYOD -0.002 0.024 -10000 0 -0.53 1 1
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.053 0.29 36 -10000 0 36
RFC1 0.011 0.053 0.29 36 -10000 0 36
PRKDC 0.01 0.054 0.29 36 -10000 0 36
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.023 0.037 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.016 0.067 0.25 17 -0.38 15 32
MAP2K4 -0.058 0.16 -10000 0 -0.42 30 30
mol:ceramide -0.031 0.11 -10000 0 -0.54 19 19
GSN 0.004 0.077 0.29 35 -0.5 13 48
FASLG/FAS/FADD/FAF1/Caspase 8 -0.03 0.071 0.23 14 -0.46 15 29
FAS 0.004 0.051 -10000 0 -0.81 4 4
BID 0.001 0.011 0.32 1 -10000 0 1
MAP3K1 -0.021 0.093 -10000 0 -0.29 14 14
MAP3K7 0 0.009 -10000 0 -0.29 1 1
RB1 0.01 0.053 0.29 35 -0.3 1 36
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.14 0.27 -10000 0 -0.6 236 236
ARHGDIB 0.01 0.054 0.29 36 -10000 0 36
FADD 0.003 0.038 -10000 0 -0.3 15 15
actin filament polymerization -0.004 0.077 0.5 13 -0.29 35 48
NFKB1 -0.076 0.1 -10000 0 -0.32 2 2
MAPK8 -0.12 0.24 -10000 0 -0.43 385 385
DFFA 0.011 0.053 0.29 36 -10000 0 36
DNA fragmentation during apoptosis 0.011 0.053 0.29 36 -10000 0 36
FAS/FADD/MET -0.094 0.21 -10000 0 -0.56 173 173
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.002 0.052 -10000 0 -0.31 26 26
FAF1 0.008 0.006 -10000 0 -10000 0 0
PARP1 0.011 0.053 0.29 36 -10000 0 36
DFFB 0.011 0.053 0.29 36 -10000 0 36
CHUK -0.066 0.088 -10000 0 -10000 0 0
FASLG -0.015 0.11 -10000 0 -0.42 54 54
FAS/FADD -0.005 0.048 -10000 0 -0.67 4 4
HGF -0.053 0.2 -10000 0 -0.8 68 68
LMNA 0.01 0.048 0.26 36 -10000 0 36
CASP6 0.011 0.053 0.29 36 -10000 0 36
CASP10 0.004 0.051 -10000 0 -0.81 4 4
CASP3 0.013 0.064 0.34 37 -10000 0 37
PTPN13 -0.025 0.14 -10000 0 -0.8 32 32
CASP8 0.003 0.02 0.45 1 -10000 0 1
IL6 -0.47 0.67 -10000 0 -1.4 380 380
MET -0.13 0.3 -10000 0 -0.8 172 172
ICAD/CAD 0.01 0.049 0.26 36 -10000 0 36
FASLG/FAS/FADD/FAF1/Caspase 10 -0.032 0.12 -10000 0 -0.55 19 19
activation of caspase activity by cytochrome c 0.001 0.011 0.32 1 -10000 0 1
PAK2 0.011 0.052 0.28 36 -10000 0 36
BCL2 -0.023 0.15 -10000 0 -0.8 36 36
LPA4-mediated signaling events

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
ADCY4 0 0.1 -9999 0 -0.54 38 38
ADCY5 -0.16 0.26 -9999 0 -0.54 339 339
ADCY6 0.02 0 -9999 0 -10000 0 0
ADCY7 0.02 0 -9999 0 -10000 0 0
ADCY1 -0.007 0.097 -9999 0 -0.54 26 26
ADCY2 -0.029 0.15 -9999 0 -0.54 80 80
ADCY3 0.02 0.005 -9999 0 -10000 0 0
ADCY8 0.009 0.028 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.031 0.1 -9999 0 -0.31 69 69
TCGA08_rtk_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
PDGFRA -0.05 0.19 -10000 0 -0.8 65 65
HRAS -0.003 0.027 -10000 0 -0.29 9 9
EGFR -0.29 0.39 -10000 0 -0.8 383 383
AKT 0.014 0.079 -10000 0 -0.56 17 17
FOXO3 -0.002 0.043 -10000 0 -0.8 3 3
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.008 0.079 -10000 0 -0.8 10 10
AKT3 -0.013 0.1 -10000 0 -0.8 17 17
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.13 0.3 -10000 0 -0.8 172 172
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
PIK3CG -0.014 0.1 -10000 0 -0.7 20 20
PIK3R3 0 0.009 -10000 0 -0.29 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.025 -10000 0 -0.8 1 1
RAS -0.093 0.16 0.26 1 -0.37 194 195
ERBB2 -0.023 0.078 -10000 0 -0.29 82 82
proliferation/survival/translation -0.005 0.057 0.27 12 -10000 0 12
PI3K -0.084 0.16 -10000 0 -0.36 201 201
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
KRAS -0.001 0.013 -10000 0 -0.29 2 2
FOXO 0.027 0.029 -10000 0 -0.5 1 1
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.035 -10000 0 -0.8 2 2
Signaling events mediated by PRL

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
CCNE1 -0.059 0.12 -9999 0 -0.29 210 210
mol:Halofuginone 0 0.003 -9999 0 -10000 0 0
ITGA1 -0.008 0.079 -9999 0 -0.8 10 10
CDKN1A -0.058 0.09 -9999 0 -0.85 2 2
PRL-3/alpha Tubulin -0.002 0.018 -9999 0 -10000 0 0
mol:Ca2+ -0.035 0.098 -9999 0 -0.56 17 17
AGT -0.049 0.13 -9999 0 -0.34 152 152
CCNA2 -0.16 0.24 -9999 0 -0.56 176 176
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.18 0.29 -9999 0 -0.61 328 328
CDK2/Cyclin E1 -0.068 0.091 -9999 0 -0.82 2 2
MAPK3 0.02 0.02 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.008 -9999 0 -10000 0 0
MAPK1 0.02 0.02 -9999 0 -10000 0 0
PTP4A1 -0.12 0.24 -9999 0 -0.47 328 328
PTP4A3 -0.003 0.028 -9999 0 -0.29 10 10
PTP4A2 -0.001 0.013 -9999 0 -0.29 2 2
ITGB1 0.02 0.02 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1 -0.056 0.083 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.14 0.2 -9999 0 -0.6 2 2
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0.001 0.009 -9999 0 -10000 0 0
RHOC -0.056 0.083 -9999 0 -10000 0 0
RHOA -0.056 0.083 -9999 0 -10000 0 0
cell motility -0.035 0.1 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.14 0.2 -9999 0 -0.63 1 1
PRL-3/alpha1 Integrin -0.008 0.062 -9999 0 -0.61 10 10
ROCK1 -0.035 0.11 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.12 0.24 -9999 0 -0.47 328 328
ATF5 -0.001 0.018 -9999 0 -0.29 4 4
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.047 -9999 0 -0.63 5 5
PDGFRB 0.004 0.051 -9999 0 -0.81 4 4
SPHK1 -0.025 0.056 -9999 0 -1.1 2 2
mol:S1P -0.031 0.058 -9999 0 -0.97 2 2
S1P1/S1P/Gi -0.099 0.23 -9999 0 -0.6 85 85
GNAO1 -0.024 0.14 -9999 0 -0.49 66 66
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.6 65 65
PLCG1 -0.088 0.22 -9999 0 -0.63 64 64
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.051 -9999 0 -0.81 4 4
GNAI2 0.008 0.006 -9999 0 -10000 0 0
GNAI3 0.008 0.006 -9999 0 -10000 0 0
GNAI1 -0.032 0.18 -9999 0 -0.82 50 50
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.006 0.045 -9999 0 -0.55 5 5
S1P1/S1P -0.045 0.075 -9999 0 -0.62 7 7
negative regulation of cAMP metabolic process -0.096 0.22 -9999 0 -0.58 85 85
MAPK3 -0.16 0.31 -9999 0 -0.57 351 351
calcium-dependent phospholipase C activity -0.003 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 0.056 -9999 0 -0.81 5 5
PLCB2 -0.008 0.086 -9999 0 -0.53 8 8
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.061 -9999 0 -0.5 7 7
receptor internalization -0.042 0.07 -9999 0 -0.57 7 7
PTGS2 -0.33 0.55 -9999 0 -1.1 350 350
Rac1/GTP -0.037 0.061 -9999 0 -0.5 7 7
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.03 -9999 0 -0.3 1 1
negative regulation of T cell proliferation -0.096 0.22 -9999 0 -0.58 85 85
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.076 -9999 0 -0.81 9 9
MAPK1 -0.16 0.31 -9999 0 -0.57 351 351
S1P1/S1P/PDGFB-D/PDGFRB -0.02 0.11 -9999 0 -0.68 9 9
ABCC1 0 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.002 0.011 -10000 0 -0.29 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.033 0.13 0.42 42 -10000 0 42
IL27/IL27R/JAK1 -0.071 0.18 -10000 0 -0.65 48 48
TBX21 -0.043 0.22 -10000 0 -0.64 67 67
IL12B -0.054 0.12 -10000 0 -0.29 214 214
IL12A -0.03 0.15 -10000 0 -0.57 68 68
IL6ST -0.088 0.27 -10000 0 -0.81 124 124
IL27RA/JAK1 -0.007 0.063 -10000 0 -1.1 3 3
IL27 -0.023 0.092 -10000 0 -10000 0 0
TYK2 0.01 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.13 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.033 0.13 0.42 42 -10000 0 42
T cell proliferation during immune response 0.033 0.13 0.42 42 -10000 0 42
MAPKKK cascade -0.033 0.13 -10000 0 -0.42 42 42
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.04 -10000 0 -0.29 19 19
IL12RB1 -0.013 0.066 -10000 0 -0.32 42 42
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.058 0.23 -10000 0 -0.62 98 98
IL27/IL27R/JAK2/TYK2 -0.033 0.13 -10000 0 -0.42 42 42
positive regulation of T cell mediated cytotoxicity -0.033 0.13 -10000 0 -0.42 42 42
STAT1 (dimer) -0.092 0.23 0.47 19 -0.74 55 74
JAK2 0.004 0.026 -10000 0 -0.81 1 1
JAK1 0 0.025 -10000 0 -0.8 1 1
STAT2 (dimer) -0.044 0.11 -10000 0 -0.43 26 26
T cell proliferation -0.19 0.25 -10000 0 -0.47 398 398
IL12/IL12R/TYK2/JAK2 0.011 0.072 -10000 0 -10000 0 0
IL17A -0.13 0.18 -10000 0 -10000 0 0
mast cell activation 0.033 0.13 0.42 42 -10000 0 42
IFNG 0 0.025 -10000 0 -0.084 3 3
T cell differentiation -0.004 0.006 -10000 0 -0.019 21 21
STAT3 (dimer) -0.044 0.11 -10000 0 -0.45 22 22
STAT5A (dimer) -0.047 0.12 -10000 0 -0.46 32 32
STAT4 (dimer) -0.062 0.14 -10000 0 -0.5 63 63
STAT4 -0.032 0.16 -10000 0 -0.79 42 42
T cell activation -0.009 0.008 0.13 2 -10000 0 2
IL27R/JAK2/TYK2 -0.06 0.16 -10000 0 -0.52 73 73
GATA3 -0.039 0.27 -10000 0 -1.5 37 37
IL18 0.006 0.032 -10000 0 -0.2 8 8
positive regulation of mast cell cytokine production -0.043 0.11 -10000 0 -0.44 22 22
IL27/EBI3 -0.025 0.083 -10000 0 -0.54 13 13
IL27RA 0 0.067 -10000 0 -1.4 2 2
IL6 -0.29 0.39 -10000 0 -0.8 380 380
STAT5A -0.006 0.07 -10000 0 -0.8 8 8
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.004 0.026 0.48 2 -10000 0 2
IL1B 0.001 0.077 -10000 0 -0.53 19 19
EBI3 -0.004 0.077 -10000 0 -0.52 18 18
TNF -0.002 0.079 -10000 0 -0.62 14 14
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.001 0.035 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.023 0.035 -9999 0 -0.64 1 1
positive regulation of JNK cascade -0.049 0.11 -9999 0 -0.42 35 35
Syndecan-4/ADAM12 -0.031 0.053 -9999 0 -0.55 2 2
CCL5 -0.015 0.081 -9999 0 -0.36 44 44
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.021 -9999 0 -0.29 5 5
ADAM12 -0.019 0.077 -9999 0 -0.3 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.002 0.022 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.054 0.044 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.073 0.14 -9999 0 -0.47 62 62
Syndecan-4/CXCL12/CXCR4 -0.051 0.11 -9999 0 -0.46 19 19
Syndecan-4/Laminin alpha3 -0.13 0.2 -9999 0 -0.49 190 190
MDK -0.011 0.056 -9999 0 -0.29 41 41
Syndecan-4/FZD7 -0.031 0.067 -9999 0 -0.47 13 13
Syndecan-4/Midkine -0.027 0.04 -9999 0 -0.64 1 1
FZD7 -0.015 0.11 -9999 0 -0.8 20 20
Syndecan-4/FGFR1/FGF -0.19 0.21 -9999 0 -0.49 155 155
THBS1 -0.003 0.05 -9999 0 -0.8 4 4
integrin-mediated signaling pathway -0.033 0.073 -9999 0 -0.47 16 16
positive regulation of MAPKKK cascade -0.049 0.11 -9999 0 -0.42 35 35
Syndecan-4/TACI -0.034 0.066 -9999 0 -0.5 7 7
CXCR4 -0.007 0.045 -9999 0 -10000 0 0
cell adhesion -0.02 0.062 -9999 0 -0.34 27 27
Syndecan-4/Dynamin -0.022 0.034 -9999 0 -0.64 1 1
Syndecan-4/TSP1 -0.024 0.043 -9999 0 -0.5 4 4
Syndecan-4/GIPC -0.023 0.035 -9999 0 -0.64 1 1
Syndecan-4/RANTES -0.03 0.052 -9999 0 -0.49 6 6
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.094 0.26 -9999 0 -0.79 123 123
LAMA3 -0.2 0.35 -9999 0 -0.8 259 259
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.003 0.13 -9999 0 -0.73 29 29
Syndecan-4/alpha-Actinin -0.023 0.037 -9999 0 -0.55 2 2
TFPI -0.037 0.17 -9999 0 -0.8 48 48
F2 0.001 0.029 -9999 0 -0.29 10 10
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.24 -9999 0 -0.53 200 200
ACTN1 -0.001 0.025 -9999 0 -0.8 1 1
TNC -0.021 0.12 -9999 0 -0.8 24 24
Syndecan-4/CXCL12 -0.056 0.11 -9999 0 -0.46 37 37
FGF6 -0.002 0.035 -9999 0 -0.8 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.062 0.21 -9999 0 -0.8 80 80
TNFRSF13B -0.026 0.11 -9999 0 -0.8 15 15
FGF2 -0.32 0.39 -9999 0 -0.8 416 416
FGFR1 -0.009 0.084 -9999 0 -0.69 14 14
Syndecan-4/PI-4-5-P2 -0.016 0.047 -9999 0 -0.65 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.15 -9999 0 -0.3 413 413
cell migration -0.024 0.019 -9999 0 -10000 0 0
PRKCD 0.005 0.014 -9999 0 -0.28 1 1
vasculogenesis -0.024 0.042 -9999 0 -0.46 5 5
SDC4 -0.016 0.05 -9999 0 -0.69 1 1
Syndecan-4/Tenascin C -0.033 0.075 -9999 0 -0.49 16 16
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.022 0.034 -9999 0 -0.64 1 1
MMP9 -0.12 0.15 -9999 0 -0.29 453 453
Rac1/GTP -0.028 0.058 -9999 0 -0.35 27 27
cytoskeleton organization -0.023 0.034 -9999 0 -0.61 1 1
GIPC1 -0.001 0.016 -9999 0 -0.29 3 3
Syndecan-4/TFPI -0.043 0.096 -9999 0 -0.47 31 31
Canonical Wnt signaling 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
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.004 0.015 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
SMAD4 -0.001 0.025 -10000 0 -0.8 1 1
DKK2 -0.022 0.13 -10000 0 -0.77 30 30
TLE1 -0.002 0.072 -10000 0 -0.8 8 8
MACF1 0 0.002 -10000 0 -10000 0 0
CTNNB1 0.1 0.087 -10000 0 -10000 0 0
WIF1 -0.42 0.4 -10000 0 -0.79 554 554
beta catenin/RanBP3 0.014 0.079 0.38 39 -10000 0 39
KREMEN2 -0.14 0.14 -10000 0 -0.29 500 500
DKK1 -0.079 0.19 -10000 0 -0.42 194 194
beta catenin/beta TrCP1 0.1 0.084 -10000 0 -10000 0 0
FZD1 0 0.001 -10000 0 -10000 0 0
AXIN2 -0.016 0.22 -10000 0 -1.6 20 20
AXIN1 0.007 0.006 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.007 0.024 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.093 0.078 0.3 1 -0.5 6 7
Axin1/APC/GSK3 0.001 0.014 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.077 0.033 -10000 0 -10000 0 0
HNF1A 0.002 0.028 -10000 0 -0.3 3 3
CTBP1 0.004 0.016 -10000 0 -10000 0 0
MYC -0.019 0.23 -10000 0 -1.5 24 24
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.083 0.11 -10000 0 -0.61 28 28
NKD1 -0.009 0.07 -10000 0 -0.43 22 22
TCF4 -0.003 0.076 -10000 0 -0.8 9 9
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.007 -10000 0 -10000 0 0
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.015 0.1 0.45 44 -0.43 1 45
LEF1 -0.033 0.1 -10000 0 -0.3 119 119
DVL1 0.072 0.065 0.22 1 -10000 0 1
CSNK2A1 0 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.099 0.09 -10000 0 -0.58 5 5
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.58 53 53
LRP6 0 0.013 -10000 0 -0.29 2 2
CSNK1A1 0.005 0.018 -10000 0 -10000 0 0
NLK 0.01 0.014 -10000 0 -0.3 2 2
CCND1 0.001 0.11 -10000 0 -1.6 4 4
WNT1 0 0.013 -10000 0 -10000 0 0
GSK3A 0.006 0.006 -10000 0 -10000 0 0
GSK3B 0 0.001 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.044 0.045 0.31 9 -10000 0 9
APC 0 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.14 0.13 0.27 540 -10000 0 540
CREBBP 0.004 0.016 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.036 0.12 -10000 0 -0.59 40 40
FYN 0.015 0.18 -10000 0 -0.72 46 46
LAT/GRAP2/SLP76 -0.029 0.15 -10000 0 -0.66 42 42
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
AKT1 0.03 0.12 -10000 0 -0.47 43 43
B2M 0.011 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.027 -10000 0 -0.16 2 2
MAP3K8 -0.006 0.066 -10000 0 -0.74 8 8
mol:Ca2+ -0.025 0.048 -10000 0 -0.12 203 203
integrin-mediated signaling pathway -0.002 0.029 -10000 0 -0.54 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.021 0.18 -10000 0 -0.7 45 45
TRPV6 -0.16 0.32 -10000 0 -0.78 216 216
CD28 -0.008 0.071 -10000 0 -0.52 16 16
SHC1 0.01 0.18 -10000 0 -0.78 42 42
receptor internalization -0.002 0.2 -10000 0 -0.8 49 49
PRF1 -0.002 0.23 -10000 0 -1.1 35 35
KRAS -0.001 0.013 -10000 0 -0.29 2 2
GRB2 0 0.009 -10000 0 -0.29 1 1
COT/AKT1 0.032 0.1 -10000 0 -0.38 44 44
LAT 0.008 0.19 -10000 0 -0.78 44 44
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.49 73 73
CD3E -0.018 0.14 -10000 0 -0.51 60 60
CD3G -0.033 0.16 -10000 0 -0.56 77 77
RASGRP2 -0.006 0.039 -10000 0 -0.18 44 44
RASGRP1 0.035 0.12 -10000 0 -0.46 45 45
HLA-A 0.009 0.027 -10000 0 -0.29 8 8
RASSF5 -0.003 0.044 -10000 0 -0.8 3 3
RAP1A/GTP/RAPL -0.002 0.029 -10000 0 -0.54 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.033 0.043 -10000 0 -0.12 39 39
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.048 -10000 0 -0.24 29 29
PRKCA -0.013 0.086 -10000 0 -0.31 57 57
GRAP2 -0.015 0.11 -10000 0 -0.73 21 21
mol:IP3 0.019 0.15 0.27 174 -0.45 41 215
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.007 0.21 -10000 0 -0.92 40 40
ORAI1 0.079 0.15 0.38 202 -10000 0 202
CSK 0.008 0.19 -10000 0 -0.8 41 41
B7 family/CD28 -0.026 0.18 -10000 0 -0.66 59 59
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.003 0.22 -10000 0 -0.77 60 60
PTPN6 0.007 0.19 -10000 0 -0.76 45 45
VAV1 0.009 0.19 -10000 0 -0.77 44 44
Monovalent TCR/CD3 -0.031 0.21 -10000 0 -0.68 68 68
CBL 0 0 -10000 0 -10000 0 0
LCK 0.009 0.2 -10000 0 -0.76 48 48
PAG1 0.008 0.19 -10000 0 -0.79 43 43
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.003 0.22 -10000 0 -0.78 57 57
CD80 -0.077 0.13 -10000 0 -0.29 278 278
CD86 -0.002 0.022 -10000 0 -0.29 6 6
PDK1/CARD11/BCL10/MALT1 -0.018 0.058 -10000 0 -0.28 35 35
HRAS -0.003 0.027 -10000 0 -0.29 9 9
GO:0035030 -0.037 0.14 -10000 0 -0.54 57 57
CD8A -0.001 0.079 -10000 0 -0.38 34 34
CD8B -0.023 0.15 -10000 0 -0.6 55 55
PTPRC -0.002 0.078 -10000 0 -0.5 20 20
PDK1/PKC theta 0.033 0.16 -10000 0 -0.6 45 45
CSK/PAG1 0.013 0.18 -10000 0 -0.78 40 40
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.001 0.016 -10000 0 -10000 0 0
GRAP2/SLP76 -0.036 0.17 -10000 0 -0.75 45 45
STIM1 0.041 0.079 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.054 -10000 0 -0.18 31 31
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.006 0.23 -10000 0 -0.89 49 49
mol:DAG -0.008 0.1 -10000 0 -0.41 42 42
RAP1A/GDP 0.015 0.019 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.012 0.12 -10000 0 -0.59 37 37
cytotoxic T cell degranulation 0.001 0.21 -10000 0 -0.97 38 38
RAP1A/GTP -0.003 0.014 -10000 0 -0.068 27 27
mol:PI-3-4-5-P3 0.026 0.14 -10000 0 -0.55 46 46
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.18 0.29 165 -0.61 42 207
NRAS -0.001 0.013 -10000 0 -10000 0 0
ZAP70 -0.03 0.12 -10000 0 -0.8 20 20
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.026 0.14 -10000 0 -0.63 42 42
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.033 0.14 -10000 0 -0.57 53 53
CARD11 -0.007 0.052 -10000 0 -0.8 2 2
PRKCB -0.012 0.085 -10000 0 -0.33 45 45
PRKCE -0.006 0.069 -10000 0 -0.29 34 34
PRKCQ 0.023 0.18 -10000 0 -0.68 48 48
LCP2 0 0.009 -10000 0 -0.29 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.031 0.1 -10000 0 -0.39 43 43
IKK complex 0.041 0.045 -10000 0 -0.12 27 27
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.036 0.081 -10000 0 -0.29 37 37
PDPK1 0.033 0.12 -10000 0 -0.45 40 40
TCR/CD3/MHC I/CD8/Fyn -0.007 0.24 -10000 0 -0.94 49 49
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.005 0.02 -9999 0 -0.56 1 1
REL -0.006 0.091 -9999 0 -0.8 13 13
HDAC7 0.009 0.13 -9999 0 -0.59 14 14
JUN -0.005 0.066 -9999 0 -0.8 7 7
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.025 -9999 0 -0.8 1 1
KAT5 0.002 0.005 -9999 0 -10000 0 0
MAPK14 0.008 0.09 -9999 0 -0.62 20 20
FOXO1 -0.008 0.079 -9999 0 -0.8 10 10
T-DHT/AR -0.004 0.13 -9999 0 -0.59 17 17
MAP2K6 -0.008 0.11 -9999 0 -0.79 21 21
BRM/BAF57 -0.001 0.011 -9999 0 -10000 0 0
MAP2K4 0.007 0.026 -9999 0 -0.81 1 1
SMARCA2 0 0 -9999 0 -10000 0 0
PDE9A -0.09 0.29 -9999 0 -1.2 62 62
NCOA2 -0.035 0.16 -9999 0 -0.8 45 45
CEBPA -0.005 0.075 -9999 0 -0.8 9 9
EHMT2 0.002 0.004 -9999 0 -10000 0 0
cell proliferation 0.014 0.14 -9999 0 -0.51 22 22
NR0B1 -0.01 0.053 -9999 0 -0.29 36 36
EGR1 -0.26 0.37 -9999 0 -0.8 328 328
RXRs/9cRA -0.12 0.21 -9999 0 -0.49 256 256
AR/RACK1/Src -0.003 0.11 -9999 0 -0.49 28 28
AR/GR -0.052 0.13 -9999 0 -0.45 49 49
GNB2L1 0.001 0.004 -9999 0 -10000 0 0
PKN1 0 0.009 -9999 0 -0.29 1 1
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.014 0.061 -9999 0 -0.62 9 9
T-DHT/AR/TIF2/CARM1 -0.014 0.15 -9999 0 -0.52 65 65
SRC 0.022 0.09 -9999 0 -0.47 28 28
NR3C1 -0.011 0.093 -9999 0 -0.8 14 14
KLK3 -0.22 0.43 -9999 0 -1.2 158 158
APPBP2 0 0.016 -9999 0 -10000 0 0
TRIM24 0.004 0.011 -9999 0 -0.29 1 1
T-DHT/AR/TIP60 -0.026 0.095 -9999 0 -0.52 28 28
TMPRSS2 -0.17 0.42 -9999 0 -1.2 135 135
RXRG -0.2 0.35 -9999 0 -0.8 259 259
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.001 0.004 -9999 0 -10000 0 0
NR2C2 -0.008 0.079 -9999 0 -0.8 10 10
KLK2 -0.041 0.24 -9999 0 -0.76 92 92
AR -0.026 0.14 -9999 0 -0.35 139 139
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -10000 0 0
MDM2 0.005 0.023 -9999 0 -0.29 4 4
SRY 0.004 0.01 -9999 0 -10000 0 0
GATA2 -0.026 0.13 -9999 0 -0.63 42 42
MYST2 0.002 0.01 -9999 0 -0.29 1 1
HOXB13 -0.13 0.15 -9999 0 -0.29 475 475
T-DHT/AR/RACK1/Src -0.013 0.1 -9999 0 -0.5 28 28
positive regulation of transcription -0.026 0.13 -9999 0 -0.63 42 42
DNAJA1 0.001 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.014 -9999 0 -10000 0 0
NCOA1 0.012 0.027 -9999 0 -0.83 1 1
SPDEF -0.06 0.21 -9999 0 -0.65 103 103
T-DHT/AR/TIF2 0.013 0.099 -9999 0 -0.5 18 18
T-DHT/AR/Hsp90 -0.033 0.091 -9999 0 -0.52 28 28
GSK3B 0.005 0.006 -9999 0 -10000 0 0
NR2C1 0.003 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.015 0.095 -9999 0 -0.51 28 28
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.006 0.014 -9999 0 -10000 0 0
POU2F1 0.021 0.026 -9999 0 -0.42 1 1
T-DHT/AR/DAX-1 -0.035 0.096 -9999 0 -0.53 28 28
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.016 -9999 0 -0.3 3 3
Coregulation of Androgen receptor activity

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
NRIP1 -0.003 0.033 -10000 0 -0.8 1 1
SVIL -0.005 0.054 -10000 0 -0.8 4 4
ZNF318 0.024 0.059 0.22 1 -10000 0 1
JMJD2C -0.003 0.041 -10000 0 -0.12 98 98
T-DHT/AR/Ubc9 -0.079 0.18 -10000 0 -0.55 132 132
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.002 0.012 -10000 0 -0.29 1 1
PELP1 0.005 0.013 -10000 0 -10000 0 0
CTNNB1 0 0.015 -10000 0 -10000 0 0
AKT1 0.008 0.019 -10000 0 -10000 0 0
PTK2B 0 0.013 -10000 0 -10000 0 0
MED1 0.002 0.048 -10000 0 -0.29 20 20
MAK 0.013 0.11 0.22 9 -0.59 20 29
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.064 -10000 0 -0.8 6 6
GSN -0.013 0.092 -10000 0 -0.8 13 13
NCOA2 -0.035 0.16 -10000 0 -0.8 45 45
NCOA6 -0.002 0.021 -10000 0 -0.29 1 1
DNA-PK 0.024 0.06 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 0 0.015 -10000 0 -10000 0 0
cell proliferation -0.007 0.12 -10000 0 -0.91 12 12
XRCC5 0.007 0.016 -10000 0 -10000 0 0
UBE3A -0.006 0.032 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.092 0.21 -10000 0 -0.59 145 145
FHL2 -0.017 0.13 -10000 0 -1.3 6 6
RANBP9 -0.001 0.019 -10000 0 -10000 0 0
JMJD1A -0.011 0.056 -10000 0 -0.14 147 147
CDK6 -0.008 0.087 -10000 0 -0.73 14 14
TGFB1I1 -0.004 0.048 -10000 0 -0.8 3 3
T-DHT/AR/CyclinD1 -0.092 0.19 -10000 0 -0.56 137 137
XRCC6 0.007 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.065 0.21 -10000 0 -0.54 148 148
CTDSP1 0 0 -10000 0 -10000 0 0
CTDSP2 0.016 0.04 -10000 0 -10000 0 0
BRCA1 -0.003 0.035 -10000 0 -0.49 3 3
TCF4 0.006 0.081 -10000 0 -0.8 9 9
CDKN2A -0.041 0.11 -10000 0 -0.29 154 154
SRF 0.024 0.02 -10000 0 -10000 0 0
NKX3-1 -0.081 0.19 -10000 0 -1.3 19 19
KLK3 -0.2 0.53 -10000 0 -1.6 135 135
TMF1 0 0 -10000 0 -10000 0 0
HNRNPA1 0.009 0.022 -10000 0 -10000 0 0
AOF2 -0.009 0.024 -10000 0 -0.072 135 135
APPL1 0.035 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.071 0.19 -10000 0 -0.55 131 131
AR -0.099 0.27 -10000 0 -0.81 132 132
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.009 0.022 -10000 0 -10000 0 0
PAWR -0.001 0.025 -10000 0 -0.8 1 1
PRKDC 0.006 0.024 -10000 0 -0.29 3 3
PA2G4 0.012 0.029 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.067 0.18 -10000 0 -0.51 131 131
RPS6KA3 -0.009 0.073 -10000 0 -0.8 8 8
T-DHT/AR/ARA70 -0.084 0.18 -10000 0 -0.55 132 132
LATS2 0.01 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.061 0.18 0.19 1 -0.51 131 132
Cyclin D3/CDK11 p58 0 0.006 -10000 0 -10000 0 0
VAV3 -0.011 0.078 -10000 0 -0.44 25 25
KLK2 -0.12 0.32 -10000 0 -1.2 76 76
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.096 0.2 -10000 0 -0.54 162 162
TMPRSS2 -0.18 0.4 -10000 0 -1.2 133 133
CCND1 -0.016 0.074 -10000 0 -0.34 42 42
PIAS1 -0.006 0.032 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.034 -10000 0 -0.079 177 177
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.013 0.051 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.082 0.2 -10000 0 -0.56 142 142
CMTM2 0.004 0.013 -10000 0 -0.29 1 1
SNURF -0.02 0.13 -10000 0 -0.8 26 26
ZMIZ1 0.004 0.031 -10000 0 -0.36 1 1
CCND3 0.002 0.011 -10000 0 -10000 0 0
TGIF1 0.009 0.022 -10000 0 -10000 0 0
FKBP4 -0.004 0.034 -10000 0 -0.3 9 9
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.005 0.13 -10000 0 -0.39 60 60
TBX21 -0.013 0.35 -10000 0 -1.3 52 52
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.004 0.073 -10000 0 -0.32 42 42
GADD45B 0.033 0.22 -10000 0 -0.8 34 34
IL12RB2 -0.058 0.2 -10000 0 -0.44 175 175
GADD45G 0.023 0.22 -10000 0 -0.81 35 35
natural killer cell activation 0.007 0.017 -10000 0 -10000 0 0
RELB -0.003 0.028 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL18 0.007 0.047 -10000 0 -0.29 25 25
IL2RA -0.028 0.11 -10000 0 -0.8 14 14
IFNG -0.041 0.1 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.22 -10000 0 -0.65 55 55
HLA-DRB5 -0.018 0.096 -10000 0 -0.33 80 80
FASLG 0.004 0.29 -10000 0 -1.1 42 42
NF kappa B2 p52/RelB -0.078 0.2 -10000 0 -0.8 51 51
CD4 0.008 0.006 -10000 0 -10000 0 0
SOCS1 -0.005 0.042 -10000 0 -0.8 1 1
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.027 0.14 -10000 0 -0.5 73 73
CD3E -0.021 0.14 -10000 0 -0.51 60 60
CD3G -0.034 0.17 -10000 0 -0.57 77 77
IL12Rbeta2/JAK2 -0.027 0.16 -10000 0 -0.6 55 55
CCL3 0.013 0.26 -10000 0 -1 37 37
CCL4 0.015 0.25 -10000 0 -0.98 34 34
HLA-A 0.009 0.028 -10000 0 -0.3 8 8
IL18/IL18R 0.022 0.14 -10000 0 -0.55 53 53
NOS2 0.019 0.25 -10000 0 -0.88 44 44
IL12/IL12R/TYK2/JAK2/SPHK2 -0.004 0.13 -10000 0 -0.41 53 53
IL1R1 0.002 0.3 -10000 0 -1.2 42 42
IL4 -0.005 0.018 -10000 0 -10000 0 0
JAK2 0.016 0.03 -10000 0 -0.81 1 1
EntrezGene:6957 -0.005 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.031 0.25 -10000 0 -1 47 47
RAB7A 0.047 0.19 -10000 0 -0.7 29 29
lysosomal transport 0.048 0.19 -10000 0 -0.65 30 30
FOS -0.35 0.66 -10000 0 -1.3 322 322
STAT4 (dimer) 0.022 0.26 -10000 0 -0.87 53 53
STAT5A (dimer) -0.086 0.22 -10000 0 -0.79 56 56
GZMA 0.003 0.28 -10000 0 -1.1 37 37
GZMB -0.007 0.3 -10000 0 -1.2 44 44
HLX -0.001 0.013 -10000 0 -0.29 2 2
LCK 0.004 0.29 -10000 0 -0.88 61 61
TCR/CD3/MHC II/CD4 -0.064 0.2 -10000 0 -0.55 86 86
IL2/IL2R -0.03 0.1 -10000 0 -0.48 38 38
MAPK14 0.037 0.22 -10000 0 -0.78 40 40
CCR5 0.026 0.22 -10000 0 -0.82 36 36
IL1B 0.004 0.1 -10000 0 -0.7 19 19
STAT6 0.026 0.087 -10000 0 -0.24 23 23
STAT4 -0.032 0.16 -10000 0 -0.79 42 42
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.039 -10000 0 -0.29 19 19
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0.009 -10000 0 -0.29 1 1
IL12B -0.046 0.12 -10000 0 -0.28 202 202
CD8A -0.002 0.079 -10000 0 -0.39 34 34
CD8B -0.023 0.15 -10000 0 -0.58 58 58
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.005 0.13 0.39 60 -10000 0 60
IL2RB -0.012 0.065 -10000 0 -0.31 41 41
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.24 -10000 0 -0.78 53 53
IL2RG -0.018 0.088 -10000 0 -0.36 52 52
IL12 -0.054 0.17 -10000 0 -0.6 65 65
STAT5A -0.006 0.07 -10000 0 -0.8 8 8
CD247 -0.013 0.12 -10000 0 -0.59 37 37
IL2 -0.002 0.025 -10000 0 -0.29 8 8
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.035 0.2 -10000 0 -0.69 76 76
IL12/IL12R/TYK2/JAK2 0.008 0.29 -10000 0 -0.84 67 67
MAP2K3 0.032 0.22 -10000 0 -0.78 40 40
RIPK2 -0.001 0.02 -10000 0 -0.29 5 5
MAP2K6 0.028 0.23 -10000 0 -0.77 44 44
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.027 -10000 0 -0.55 2 2
IL18RAP -0.016 0.15 -10000 0 -0.74 42 42
IL12Rbeta1/TYK2 0.014 0.056 -10000 0 -0.65 2 2
EOMES -0.022 0.18 -10000 0 -1.5 15 15
STAT1 (dimer) 0.029 0.22 -10000 0 -0.74 35 35
T cell proliferation 0.033 0.2 -10000 0 -0.62 52 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.1 -10000 0 -0.81 17 17
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.062 0.17 -10000 0 -0.73 47 47
ATF2 0.044 0.21 -10000 0 -0.73 38 38
Insulin Pathway

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
CBL/APS/CAP -0.13 0.22 -9999 0 -0.48 275 275
TC10/GTP -0.11 0.18 -9999 0 -0.42 260 260
Insulin Receptor/Insulin/IRS1/Shp2 -0.021 0.1 -9999 0 -0.5 43 43
HRAS -0.003 0.027 -9999 0 -0.29 9 9
APS homodimer -0.013 0.061 -9999 0 -0.29 48 48
GRB14 -0.1 0.22 -9999 0 -0.47 221 221
FOXO3 -0.014 0.067 -9999 0 -0.68 9 9
AKT1 -0.057 0.13 -9999 0 -0.52 11 11
INSR 0 0.009 -9999 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.026 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.2 0.35 -9999 0 -0.8 260 260
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.033 0.03 -9999 0 -10000 0 0
CAV1 -0.12 0.23 -9999 0 -0.52 242 242
CBL/APS/CAP/Crk-II/C3G -0.12 0.2 -9999 0 -0.46 260 260
Insulin Receptor/Insulin/IRS1/NCK2 -0.021 0.1 -9999 0 -0.5 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.022 0.096 -9999 0 -0.44 53 53
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.056 -9999 0 -10000 0 0
RPS6KB1 -0.008 0.14 -9999 0 -0.47 11 11
PARD6A -0.002 0.024 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.003 -9999 0 -10000 0 0
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.05 0.12 -9999 0 -0.49 11 11
HRAS/GTP -0.016 0.075 -9999 0 -0.38 43 43
Insulin Receptor 0 0.009 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.019 0.093 -9999 0 -0.46 43 43
PRKCI -0.013 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.063 0.14 -9999 0 -0.42 88 88
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.003 -9999 0 -10000 0 0
PI3K -0.023 0.098 -9999 0 -0.44 53 53
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.018 -9999 0 -10000 0 0
AKT2 -0.057 0.13 -9999 0 -0.52 11 11
PRKCZ -0.014 0.037 -9999 0 -0.61 1 1
SH2B2 -0.013 0.061 -9999 0 -0.29 48 48
SHC/SHIP -0.018 0.087 -9999 0 -0.44 43 43
F2RL2 -0.058 0.15 -9999 0 -0.36 170 170
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0.004 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.13 0.21 -9999 0 -0.49 260 260
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.003 -9999 0 -10000 0 0
INPP5D -0.019 0.093 -9999 0 -0.47 43 43
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.01 0.075 -9999 0 -0.99 6 6
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.8 43 43
p62DOK/RasGAP 0 0.003 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.092 -9999 0 -0.46 43 43
GRB2 0 0.009 -9999 0 -0.29 1 1
EIF4EBP1 -0.014 0.14 -9999 0 -0.47 23 23
PTPRA 0 0.001 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.013 0.065 -9999 0 -0.33 43 43
Insulin Receptor/Insulin/IRS1 -0.021 0.1 -9999 0 -0.51 43 43
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.026 0.075 -9999 0 -0.46 22 22
Ras signaling in the CD4+ TCR pathway

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.12 0.18 -9999 0 -0.52 60 60
MAP3K8 -0.006 0.067 -9999 0 -0.74 8 8
FOS -0.034 0.14 -9999 0 -0.46 35 35
PRKCA -0.013 0.13 -9999 0 -0.78 29 29
PTPN7 -0.008 0.071 -9999 0 -0.33 18 18
HRAS -0.003 0.027 -9999 0 -0.29 9 9
PRKCB -0.011 0.11 -9999 0 -0.55 36 36
NRAS -0.001 0.013 -9999 0 -10000 0 0
RAS family/GTP -0.002 0.015 -9999 0 -10000 0 0
MAPK3 -0.007 0.073 -9999 0 -10000 0 0
MAP2K1 -0.012 0.14 -9999 0 -0.6 44 44
ELK1 -0.003 0.005 -9999 0 -10000 0 0
BRAF -0.032 0.12 -9999 0 -0.57 44 44
mol:GTP -0.002 0.003 -9999 0 -0.006 307 307
MAPK1 -0.007 0.073 -9999 0 -0.29 1 1
RAF1 -0.032 0.12 -9999 0 -0.57 44 44
KRAS -0.001 0.013 -9999 0 -0.29 2 2
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.037 0.085 -9999 0 -0.44 35 35
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.07 -9999 0 -0.47 5 5
alphaV/beta3 Integrin/Osteopontin/Src -0.046 0.075 -9999 0 -10000 0 0
AP1 -0.14 0.21 -9999 0 -0.58 115 115
ILK -0.007 0.11 -9999 0 -0.47 35 35
bone resorption -0.038 0.11 -9999 0 -0.67 18 18
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.004 0.091 -9999 0 -0.42 35 35
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.017 0.1 -9999 0 -0.61 28 28
alphaV/beta3 Integrin/Osteopontin -0.05 0.11 -9999 0 -0.53 35 35
MAP3K1 -0.007 0.11 -9999 0 -0.49 35 35
JUN -0.005 0.066 -9999 0 -0.8 7 7
MAPK3 0.009 0.11 -9999 0 -0.44 35 35
MAPK1 0.009 0.11 -9999 0 -0.44 35 35
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.002 0.13 -9999 0 -0.54 37 37
ITGB3 -0.028 0.14 -9999 0 -0.78 36 36
NFKBIA 0.022 0.1 -9999 0 -0.42 35 35
FOS -0.24 0.37 -9999 0 -0.8 307 307
CD44 -0.001 0.016 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.021 0.1 -9999 0 -0.49 5 5
NF kappa B1 p50/RelA -0.022 0.066 -9999 0 -0.45 5 5
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.6 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.008 0.11 -9999 0 -0.48 35 35
VAV3 -0.003 0.11 -9999 0 -0.45 42 42
MAP3K14 -0.005 0.11 -9999 0 -0.48 35 35
ROCK2 -0.022 0.13 -9999 0 -0.8 28 28
SPP1 -0.075 0.12 -9999 0 -0.28 277 277
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.036 0.084 -9999 0 -0.41 42 42
MMP2 -0.074 0.21 -9999 0 -0.67 38 38
Effects of Botulinum toxin

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
STX1A 0.003 0.04 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.047 0.14 -9999 0 -0.61 46 46
STXBP1 -0.005 0.061 -9999 0 -0.8 6 6
ACh/CHRNA1 -0.062 0.081 -9999 0 -0.22 34 34
RAB3GAP2/RIMS1/UNC13B -0.039 0.11 -9999 0 -0.53 46 46
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 -0.067 0.18 -9999 0 -0.44 159 159
mol:ACh 0.001 0.032 -9999 0 -0.15 36 36
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.038 0.095 -9999 0 -0.4 52 52
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.062 0.081 -9999 0 -0.22 34 34
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.098 0.14 -9999 0 -0.29 353 353
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.06 0.12 -9999 0 -0.53 47 47
SNAP25 -0.017 0.07 -9999 0 -0.38 36 36
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.089 0.18 -9999 0 -0.8 40 40
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.009 0.05 -9999 0 -0.54 6 6
STX1A/SNAP25 fragment 1/VAMP2 -0.038 0.095 -9999 0 -0.4 52 52
Regulation of nuclear SMAD2/3 signaling

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.1 0.21 0.25 1 -0.57 158 159
AKT1 0.014 0.006 -10000 0 -10000 0 0
GSC -0.038 0.3 -10000 0 -1.5 41 41
NKX2-5 -0.044 0.1 -10000 0 -0.28 161 161
muscle cell differentiation 0.007 0.05 0.77 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.04 -10000 0 -0.46 2 2
SMAD4 0.014 0.042 -10000 0 -0.84 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.21 0.26 -10000 0 -0.53 407 407
SMAD3/SMAD4/VDR 0.005 0.031 -10000 0 -0.44 2 2
MYC -0.017 0.12 -10000 0 -0.81 23 23
CDKN2B 0.029 0.13 -10000 0 -1.5 7 7
AP1 -0.12 0.2 -10000 0 -0.42 308 308
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.016 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.041 -10000 0 -0.33 2 2
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.041 0.12 -10000 0 -0.28 185 185
SMAD3/SMAD4/GR -0.01 0.072 -10000 0 -0.57 15 15
GATA3 -0.037 0.15 -10000 0 -0.8 37 37
SKI/SIN3/HDAC complex/NCoR1 0.002 0.014 -10000 0 -10000 0 0
MEF2C/TIF2 -0.051 0.12 -10000 0 -0.55 44 44
endothelial cell migration -0.009 0.039 -10000 0 -10000 0 0
MAX 0.001 0.004 -10000 0 -10000 0 0
RBBP7 -0.002 0.025 -10000 0 -10000 0 0
RBBP4 0 0.025 -10000 0 -0.8 1 1
RUNX2 -0.004 0.035 -10000 0 -0.29 15 15
RUNX3 -0.005 0.063 -10000 0 -0.63 9 9
RUNX1 -0.001 0.025 -10000 0 -0.8 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.01 0.093 -10000 0 -0.81 14 14
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.051 0.079 -10000 0 -1.5 2 2
KAT2B 0 0.025 -10000 0 -0.8 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.028 0.07 -10000 0 -0.47 5 5
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0.002 -10000 0 -10000 0 0
SERPINE1 0.009 0.039 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.002 0.038 -10000 0 -0.56 3 3
SMAD3/SMAD4/ATF3 -0.082 0.2 -10000 0 -0.57 149 149
SAP30 -0.001 0.018 -10000 0 -0.29 4 4
Cbp/p300/PIAS3 0.005 0.023 -10000 0 -10000 0 0
JUN -0.075 0.23 -10000 0 -0.41 308 308
SMAD3/SMAD4/IRF7 -0.018 0.065 -10000 0 -0.55 1 1
TFE3 0.017 0.006 -10000 0 -10000 0 0
COL1A2 0.029 0.1 -10000 0 -1.3 2 2
mesenchymal cell differentiation 0.004 0.034 0.55 1 -10000 0 1
DLX1 -0.059 0.14 -10000 0 -0.34 181 181
TCF3 0 0.009 -10000 0 -0.29 1 1
FOS -0.22 0.37 -10000 0 -0.8 307 307
SMAD3/SMAD4/Max -0.002 0.029 -10000 0 -0.56 1 1
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 0.001 0.006 -10000 0 -10000 0 0
LAMC1 0.043 0.048 -10000 0 -0.63 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.028 -10000 0 -0.55 1 1
IRF7 -0.028 0.087 -10000 0 -0.3 91 91
ESR1 -0.16 0.29 -10000 0 -0.59 275 275
HNF4A -0.005 0.038 -10000 0 -10000 0 0
MEF2C 0.002 0.092 -10000 0 -0.66 3 3
SMAD2-3/SMAD4 -0.003 0.033 -10000 0 -0.55 1 1
Cbp/p300/Src-1 0.003 0.022 -10000 0 -0.53 1 1
IGHV3OR16-13 -0.001 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.002 0.007 -10000 0 -10000 0 0
SKIL -0.003 0.03 -10000 0 -0.29 11 11
HDAC1 0 0.002 -10000 0 -10000 0 0
HDAC2 0 0.002 -10000 0 -10000 0 0
SNIP1 0 0.002 -10000 0 -10000 0 0
GCN5L2 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.001 0.03 -10000 0 -0.55 1 1
MSG1/HSC70 -0.24 0.3 -10000 0 -0.61 407 407
SMAD2 0.015 0.021 -10000 0 -10000 0 0
SMAD3 0.015 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.035 0.037 -10000 0 -0.33 3 3
SMAD2/SMAD2/SMAD4 0.027 0.04 -10000 0 -1.1 1 1
NCOR1 0 0.025 -10000 0 -0.81 1 1
NCOA2 -0.035 0.16 -10000 0 -0.8 45 45
NCOA1 -0.001 0.025 -10000 0 -0.8 1 1
MYOD/E2A -0.003 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.013 0.044 -10000 0 -0.42 2 2
IFNB1 0.013 0.089 -10000 0 -0.43 7 7
SMAD3/SMAD4/MEF2C -0.026 0.072 -10000 0 -0.77 2 2
CITED1 -0.32 0.39 -10000 0 -0.78 422 422
SMAD2-3/SMAD4/ARC105 -0.001 0.029 -10000 0 -0.49 1 1
RBL1 -0.002 0.037 -10000 0 -0.55 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.045 0.064 -10000 0 -0.49 7 7
RUNX1-3/PEBPB2 -0.004 0.049 -10000 0 -0.61 6 6
SMAD7 -0.071 0.14 -10000 0 -0.53 12 12
MYC/MIZ-1 -0.013 0.092 -10000 0 -0.62 23 23
SMAD3/SMAD4 0.019 0.059 0.28 38 -0.45 1 39
IL10 0.019 0.12 -10000 0 -0.52 39 39
PIASy/HDAC complex 0.001 0.004 -10000 0 -10000 0 0
PIAS3 0.001 0.005 -10000 0 -10000 0 0
CDK2 0.002 0.008 -10000 0 -10000 0 0
IL5 0.014 0.11 -10000 0 -0.53 32 32
CDK4 0.001 0.018 -10000 0 -0.29 3 3
PIAS4 0.001 0.004 -10000 0 -10000 0 0
ATF3 -0.12 0.28 -10000 0 -0.8 148 148
SMAD3/SMAD4/SP1 0 0.033 -10000 0 -0.52 2 2
FOXG1 -0.022 0.075 -10000 0 -0.29 73 73
FOXO3 0.025 0.035 -10000 0 -0.61 3 3
FOXO1 0.02 0.063 -10000 0 -0.61 10 10
FOXO4 0.026 0.008 -10000 0 -10000 0 0
heart looping 0.003 0.092 -10000 0 -0.65 3 3
CEBPB 0.012 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.034 0.093 -10000 0 -0.56 19 19
MYOD1 -0.004 0.033 -10000 0 -0.29 14 14
SMAD3/SMAD4/HNF4 -0.006 0.036 -10000 0 -0.7 1 1
SMAD3/SMAD4/GATA3 -0.024 0.11 -10000 0 -0.58 37 37
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.03 -10000 0 -0.29 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0 0.051 -10000 0 -0.54 7 7
SMAD3/SMAD4/SP1-3 0.003 0.03 -10000 0 -0.46 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 0.019 0.013 -10000 0 -10000 0 0
SIN3B 0 0.002 -10000 0 -10000 0 0
SIN3A 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.009 0.089 -10000 0 -0.5 5 5
ITGB5 0.053 0.046 -10000 0 -0.43 1 1
TGIF/SIN3/HDAC complex/CtBP 0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.072 0.19 -10000 0 -0.57 132 132
AR -0.1 0.27 -10000 0 -0.8 132 132
negative regulation of cell growth -0.026 0.074 -10000 0 -0.49 2 2
SMAD3/SMAD4/MYOD -0.007 0.035 -10000 0 -0.55 1 1
E2F5 -0.006 0.04 -10000 0 -0.29 20 20
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.002 0.056 -10000 0 -0.55 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0 0.045 -10000 0 -0.34 4 4
TFDP1 -0.001 0.018 -10000 0 -0.29 4 4
SMAD3/SMAD4/AP1 -0.12 0.21 -10000 0 -0.42 308 308
SMAD3/SMAD4/RUNX2 -0.004 0.034 -10000 0 -0.55 1 1
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.002 0.035 -10000 0 -0.8 2 2
Regulation of Telomerase

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
Telomerase catalytic core complex -0.053 0.12 -9999 0 -0.62 4 4
RAD9A 0 0 -9999 0 -10000 0 0
AP1 -0.18 0.29 -9999 0 -0.62 308 308
IFNAR2 0.01 0.005 -9999 0 -10000 0 0
AKT1 -0.038 0.11 -9999 0 -0.29 158 158
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.46 258 258
NFX1/SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
EGF -0.16 0.32 -9999 0 -0.8 202 202
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.065 0.088 -9999 0 -0.58 4 4
SAP18 0 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.15 -9999 0 -0.29 528 528
WRN 0 0 -9999 0 -10000 0 0
SP1 0.011 0.005 -9999 0 -10000 0 0
SP3 0.007 0.006 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.05 0.077 -9999 0 -0.59 2 2
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.053 0.12 -9999 0 -0.64 4 4
CCND1 -0.046 0.13 -9999 0 -1.3 4 4
MAX 0.008 0.006 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -10000 0 0
RBBP4 -0.001 0.025 -9999 0 -0.8 1 1
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
Telomerase/911 0.008 0.021 -9999 0 -10000 0 0
CDKN1B 0.008 0.075 -9999 0 -0.88 3 3
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -0.29 4 4
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.004 0.006 -9999 0 -10000 0 0
JUN 0 0.067 -9999 0 -0.8 7 7
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.23 0.37 -9999 0 -0.8 307 307
IFN-gamma/IRF1 -0.025 0.063 -9999 0 -0.36 5 5
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.031 0.09 -9999 0 -0.29 112 112
Telomerase -0.005 0.027 -9999 0 -10000 0 0
IRF1 0.007 0.021 -9999 0 -0.28 3 3
ESR1 -0.16 0.29 -9999 0 -0.58 276 276
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.007 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC2 0.011 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.022 0.007 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.007 0.011 -9999 0 -0.29 1 1
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.016 -9999 0 -0.29 3 3
TERT/NF kappa B1/14-3-3 -0.064 0.1 -9999 0 -0.67 3 3
NR2F2 0.001 0.044 -9999 0 -0.8 3 3
MAPK3 0.014 0.019 -9999 0 -10000 0 0
MAPK1 0.014 0.019 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0 0.009 -9999 0 -0.29 1 1
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.39 -9999 0 -0.8 383 383
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.34 0.35 -9999 0 -0.67 519 519
MYC -0.009 0.12 -9999 0 -0.8 23 23
IL2 0.004 0.027 -9999 0 -0.29 8 8
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -10000 0 0
TGFB1 0 0.009 -9999 0 -0.29 1 1
TRF2/BLM -0.018 0.051 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.061 0.086 -9999 0 -0.6 3 3
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.05 0.077 -9999 0 -0.59 2 2
Smad3/Myc -0.012 0.078 -9999 0 -0.53 23 23
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.033 0.1 -9999 0 -10000 0 0
Telomerase/PinX1 -0.05 0.077 -9999 0 -0.59 2 2
Telomerase/AKT1/mTOR/p70S6K 0.003 0.055 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.05 0.077 -9999 0 -0.59 2 2
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.05 0.077 -9999 0 -0.59 2 2
E2F1 -0.084 0.14 -9999 0 -0.29 330 330
ZNFX1 0 0 -9999 0 -10000 0 0
PIF1 -0.058 0.12 -9999 0 -10000 0 0
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.013 -9999 0 -0.29 2 2
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 0.036 -10000 0 -0.29 15 15
GNB1/GNG2 -0.015 0.048 -10000 0 -0.19 65 65
AKT1 0.051 0.072 -10000 0 -0.2 60 60
EGF -0.16 0.32 -10000 0 -0.8 202 202
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.01 0.052 -10000 0 -0.44 4 4
mol:Ca2+ 0.047 0.099 -10000 0 -0.3 60 60
LYN -0.01 0.049 -10000 0 -0.39 3 3
RhoA/GTP -0.008 0.03 -10000 0 -0.14 5 5
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.053 0.11 -10000 0 -0.35 60 60
GNG2 -0.009 0.086 -10000 0 -0.8 12 12
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.029 0.055 -10000 0 -0.54 6 6
G beta5/gamma2 -0.019 0.064 -10000 0 -0.25 65 65
PRKCH 0.048 0.11 -10000 0 -0.35 60 60
DNM1 -0.006 0.066 -10000 0 -0.74 8 8
TXA2/TP beta/beta Arrestin3 -0.004 0.027 -10000 0 -0.31 7 7
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.031 0.15 -10000 0 -0.72 44 44
G12 family/GTP -0.021 0.073 -10000 0 -0.31 60 60
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.003 0.05 -10000 0 -0.8 4 4
RhoA/GTP/ROCK1 -0.001 0.017 -10000 0 -0.54 1 1
mol:GDP -0.036 0.08 0.34 23 -10000 0 23
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
PRKG1 -0.053 0.2 -10000 0 -0.8 69 69
mol:IP3 0.048 0.12 -10000 0 -0.38 60 60
cell morphogenesis -0.001 0.017 -10000 0 -0.54 1 1
PLCB2 0.045 0.15 -10000 0 -0.52 60 60
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.004 0.062 -10000 0 -0.39 8 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.01 0.049 -10000 0 -0.39 3 3
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.003 0.031 -10000 0 -0.29 12 12
PRKCB1 0.045 0.12 -10000 0 -0.38 60 60
GNAQ -0.002 0.035 -10000 0 -0.8 2 2
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.047 0.16 -10000 0 -0.55 60 60
LCK -0.014 0.072 -10000 0 -0.45 17 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.057 -10000 0 -0.3 31 31
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.035 -10000 0 -0.29 7 7
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.055 -10000 0 -0.3 36 36
MAPK14 0.051 0.079 -10000 0 -0.23 60 60
TGM2/GTP 0.047 0.13 -10000 0 -0.43 60 60
MAPK11 0.051 0.082 -10000 0 -0.24 60 60
ARHGEF1 0.039 0.061 -10000 0 -0.18 60 60
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.05 0.12 -10000 0 -0.4 60 60
RAB11/GDP -0.001 0.013 -10000 0 -0.29 2 2
ICAM1 0.046 0.092 -10000 0 -0.28 60 60
cAMP biosynthetic process 0.043 0.11 -10000 0 -0.36 60 60
Gq family/GTP/EBP50 0.006 0.036 -10000 0 -0.25 15 15
actin cytoskeleton reorganization -0.001 0.017 -10000 0 -0.54 1 1
SRC -0.01 0.049 -10000 0 -0.39 3 3
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.028 0.1 -10000 0 -0.31 40 40
VCAM1 0.044 0.1 -10000 0 -0.32 60 60
TP beta/Gq family/GDP/G beta5/gamma2 0.029 0.055 -10000 0 -0.54 6 6
platelet activation 0.066 0.1 -10000 0 -0.31 60 60
PGI2/IP -0.002 0.021 -10000 0 -0.2 12 12
PRKACA -0.015 0.07 -10000 0 -0.38 37 37
Gq family/GDP/G beta5/gamma2 0.027 0.057 -10000 0 -0.46 8 8
TXA2/TP beta/beta Arrestin2 -0.006 0.055 -10000 0 -0.66 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.065 -10000 0 -0.35 37 37
mol:DAG 0.047 0.13 -10000 0 -0.42 60 60
EGFR -0.29 0.39 -10000 0 -0.8 383 383
TXA2/TP alpha 0.048 0.15 -10000 0 -0.5 60 60
Gq family/GTP -0.003 0.034 -10000 0 -0.28 15 15
YES1 -0.01 0.05 -10000 0 -0.37 5 5
GNAI2/GTP -0.011 0.056 -10000 0 -0.41 5 5
PGD2/DP -0.024 0.12 -10000 0 -0.62 37 37
SLC9A3R1 -0.024 0.08 -10000 0 -0.29 87 87
FYN -0.011 0.053 -10000 0 -0.41 6 6
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.003 0.034 -10000 0 -0.8 1 1
PGK/cGMP -0.036 0.13 -10000 0 -0.54 69 69
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.017 0.08 -10000 0 -0.56 13 13
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.042 0.13 -10000 0 -0.36 77 77
PRKCB 0.043 0.12 -10000 0 -0.37 71 71
PRKCE 0.05 0.11 -10000 0 -0.35 60 60
PRKCD 0.048 0.12 -10000 0 -0.38 60 60
PRKCG 0.045 0.12 -10000 0 -0.39 60 60
muscle contraction 0.051 0.15 -10000 0 -0.5 60 60
PRKCZ 0.053 0.11 -10000 0 -0.35 60 60
ARR3 -0.002 0.025 -10000 0 -10000 0 0
TXA2/TP beta -0.013 0.063 -10000 0 -0.35 19 19
PRKCQ 0.036 0.14 -10000 0 -0.38 90 90
MAPKKK cascade 0.045 0.14 -10000 0 -0.48 60 60
SELE 0.039 0.12 -10000 0 -0.42 60 60
TP beta/GNAI2/GDP/G beta/gamma -0.016 0.079 -10000 0 -0.56 13 13
ROCK1 -0.001 0.025 -10000 0 -0.8 1 1
GNA14 -0.014 0.088 -10000 0 -0.46 31 31
chemotaxis 0.046 0.18 -10000 0 -0.63 60 60
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.002 0.035 -10000 0 -0.8 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.016 0.11 -9999 0 -0.78 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.025 -9999 0 -0.8 1 1
RAC1-CDC42/GTP/PAK family -0.12 0.14 -9999 0 -0.28 466 466
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.025 -9999 0 -0.8 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.002 0.035 -9999 0 -0.8 2 2
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.001 0.026 -9999 0 -0.8 1 1
p38 alpha/TAB1 -0.006 0.033 -9999 0 -0.32 4 4
PRKG1 -0.053 0.2 -9999 0 -0.8 69 69
DUSP8 -0.003 0.044 -9999 0 -0.68 4 4
PGK/cGMP/p38 alpha -0.032 0.1 -9999 0 -0.4 72 72
apoptosis -0.006 0.032 -9999 0 -0.31 4 4
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.1 0.27 -9999 0 -0.8 133 133
PAK1 -0.007 0.044 -9999 0 -0.29 24 24
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1/OSM/MEKK3/MKK3 0 0.006 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 -0.001 0.013 -9999 0 -0.29 2 2
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.018 0.067 -9999 0 -0.35 18 18
BLK -0.041 0.11 -9999 0 -0.3 142 142
HCK -0.004 0.032 -9999 0 -10000 0 0
MAP2K3 0 0.009 -9999 0 -0.29 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.016 -9999 0 -0.29 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.029 0.047 -9999 0 -0.34 4 4
positive regulation of innate immune response 0.025 0.073 -9999 0 -0.37 18 18
LCK -0.02 0.1 -9999 0 -0.43 49 49
p38alpha-beta/MKP7 -0.011 0.053 -9999 0 -0.39 7 7
p38alpha-beta/MKP5 -0.011 0.053 -9999 0 -0.35 17 17
PGK/cGMP -0.041 0.16 -9999 0 -0.62 69 69
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.058 0.14 -9999 0 -0.38 138 138
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.36 0.4 -9999 0 -0.8 466 466
TCGA08_retinoblastoma

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
CDKN2B -0.004 0.066 -10000 0 -0.68 9 9
CDKN2C 0.006 0.039 -10000 0 -0.79 2 2
CDKN2A -0.052 0.12 -10000 0 -0.3 179 179
CCND2 0.006 0.033 0.25 8 -0.16 12 20
RB1 -0.007 0.032 0.19 4 -0.25 8 12
CDK4 0.01 0.031 0.25 9 -10000 0 9
CDK6 0.006 0.038 0.27 8 -0.22 11 19
G1/S progression -0.006 0.036 0.25 8 -0.19 4 12
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.059 0.076 -9999 0 -0.41 6 6
EPHB2 -0.005 0.039 -9999 0 -0.29 19 19
Syndecan-2/TACI -0.017 0.076 -9999 0 -0.53 18 18
LAMA1 -0.094 0.26 -9999 0 -0.79 123 123
Syndecan-2/alpha2 ITGB1 -0.13 0.22 -9999 0 -0.47 275 275
HRAS -0.003 0.027 -9999 0 -0.29 9 9
Syndecan-2/CASK -0.002 0.03 -9999 0 -0.54 3 3
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.034 0.059 -9999 0 -0.51 11 11
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.027 -9999 0 -0.48 3 3
LAMA3 -0.2 0.35 -9999 0 -0.8 259 259
EZR -0.001 0.016 -9999 0 -0.29 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.098 0.26 -9999 0 -0.8 127 127
Syndecan-2/MMP2 -0.007 0.07 -9999 0 -0.67 10 10
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.015 0.096 -9999 0 -0.61 26 26
dendrite morphogenesis -0.005 0.035 -9999 0 -0.52 3 3
Syndecan-2/GM-CSF -0.005 0.037 -9999 0 -0.53 3 3
determination of left/right symmetry 0.017 0.036 -9999 0 -0.37 7 7
Syndecan-2/PKC delta -0.002 0.03 -9999 0 -0.53 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.036 -9999 0 -0.48 3 3
MAPK1 0.022 0.036 -9999 0 -0.48 3 3
Syndecan-2/RACK1 -0.003 0.028 -9999 0 -0.46 3 3
NF1 -0.001 0.025 -9999 0 -0.8 1 1
FGFR/FGF/Syndecan-2 0.017 0.036 -9999 0 -0.37 7 7
ITGA2 -0.02 0.13 -9999 0 -0.8 26 26
MAPK8 0.028 0.062 -9999 0 -0.56 11 11
Syndecan-2/alpha2/beta1 Integrin -0.065 0.18 -9999 0 -0.51 131 131
Syndecan-2/Kininogen -0.005 0.036 -9999 0 -0.53 3 3
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.003 0.026 -9999 0 -0.42 3 3
Syndecan-2/CASK/Protein 4.1 -0.002 0.027 -9999 0 -0.49 3 3
extracellular matrix organization -0.002 0.03 -9999 0 -0.52 3 3
actin cytoskeleton reorganization -0.059 0.075 -9999 0 -0.41 6 6
Syndecan-2/Caveolin-2/Ras -0.062 0.16 -9999 0 -0.49 127 127
Syndecan-2/Laminin alpha3 -0.14 0.23 -9999 0 -0.53 262 262
Syndecan-2/RasGAP -0.003 0.026 -9999 0 -0.43 3 3
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0.009 -9999 0 -0.29 1 1
Syndecan-2 dimer -0.005 0.035 -9999 0 -0.53 3 3
GO:0007205 0 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.024 -9999 0 -0.41 3 3
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.026 0.11 -9999 0 -0.8 15 15
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.015 0.096 -9999 0 -0.61 26 26
Syndecan-2/Synbindin -0.002 0.03 -9999 0 -0.53 3 3
TGFB1 0 0.009 -9999 0 -0.29 1 1
CASP3 0.03 0.029 -9999 0 -0.48 3 3
FN1 -0.12 0.14 -9999 0 -0.29 414 414
Syndecan-2/IL8 -0.021 0.085 -9999 0 -0.53 23 23
SDC2 0.017 0.036 -9999 0 -0.37 7 7
KNG1 -0.005 0.039 -9999 0 -0.29 19 19
Syndecan-2/Neurofibromin -0.003 0.034 -9999 0 -0.53 4 4
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.006 0.043 -9999 0 -10000 0 0
Syndecan-2/TGFB1 -0.002 0.03 -9999 0 -0.53 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.027 -9999 0 -0.49 3 3
Syndecan-2/Ezrin -0.002 0.027 -9999 0 -0.48 3 3
PRKACA 0.03 0.033 -9999 0 -0.48 4 4
angiogenesis -0.021 0.084 -9999 0 -0.53 23 23
MMP2 -0.008 0.079 -9999 0 -0.8 10 10
IL8 -0.033 0.13 -9999 0 -0.41 84 84
calcineurin-NFAT signaling pathway -0.017 0.076 -9999 0 -0.53 18 18
IL2 signaling events mediated by STAT5

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
GAB2 0.007 0.045 -9999 0 -0.38 11 11
ELF1 -0.011 0.049 -9999 0 -0.38 14 14
CCNA2 -0.12 0.14 -9999 0 -0.29 413 413
PIK3CA 0.01 0.01 -9999 0 -0.29 1 1
JAK3 -0.004 0.033 -9999 0 -0.29 14 14
PIK3R1 -0.008 0.078 -9999 0 -0.8 10 10
JAK1 0.01 0.025 -9999 0 -0.8 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.058 0.08 -9999 0 -0.61 8 8
SHC1 0.011 0.003 -9999 0 -10000 0 0
SP1 -0.005 0.043 -9999 0 -0.38 13 13
IL2RA 0.003 0.13 -9999 0 -1 14 14
IL2RB -0.012 0.065 -9999 0 -0.31 41 41
SOS1 0 0 -9999 0 -10000 0 0
IL2RG -0.018 0.087 -9999 0 -0.36 52 52
G1/S transition of mitotic cell cycle 0.004 0.14 -9999 0 -0.84 21 21
PTPN11 0 0 -9999 0 -10000 0 0
CCND2 0.016 0.12 -9999 0 -1 13 13
LCK -0.02 0.1 -9999 0 -0.42 49 49
GRB2 0 0.009 -9999 0 -0.29 1 1
IL2 -0.002 0.025 -9999 0 -0.29 8 8
CDK6 -0.01 0.087 -9999 0 -0.73 14 14
CCND3 0.063 0.07 -9999 0 -0.58 5 5
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.004 0.11 -10000 0 -0.44 35 35
IKBKB 0.016 0.053 -10000 0 -0.27 2 2
AKT1 0.003 0.082 0.25 2 -0.27 23 25
IKBKG 0.018 0.055 -10000 0 -0.28 3 3
CALM1 -0.011 0.093 -10000 0 -0.45 29 29
PIK3CA 0 0.009 -10000 0 -0.29 1 1
MAP3K1 -0.009 0.15 -10000 0 -0.66 31 31
MAP3K7 0 0.009 -10000 0 -0.29 1 1
mol:Ca2+ -0.02 0.098 -10000 0 -0.48 29 29
DOK1 -0.001 0.018 -10000 0 -0.29 4 4
AP-1 -0.041 0.11 -10000 0 -0.26 75 75
LYN 0 0 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.079 0.21 -10000 0 -0.64 112 112
CD22 -0.062 0.18 -10000 0 -0.55 96 96
CAMK2G -0.002 0.087 -10000 0 -0.5 16 16
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.047 0.14 -10000 0 -0.78 15 15
GO:0007205 -0.02 0.099 -10000 0 -0.49 29 29
SYK 0 0.009 -10000 0 -0.29 1 1
ELK1 -0.011 0.094 -10000 0 -0.46 29 29
NFATC1 -0.017 0.13 -10000 0 -0.58 32 32
B-cell antigen/BCR complex -0.079 0.21 -10000 0 -0.64 112 112
PAG1/CSK -0.001 0.013 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 -10000 0 -10000 0 0
HRAS -0.009 0.1 -10000 0 -0.47 30 30
NFKBIA 0.016 0.02 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.019 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.058 0.16 -10000 0 -0.53 95 95
mol:GDP -0.02 0.092 -10000 0 -0.46 29 29
PTEN -0.002 0.035 -10000 0 -0.8 2 2
CD79B -0.028 0.14 -10000 0 -0.6 48 48
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
PI3K/BCAP/CD19 -0.027 0.16 -10000 0 -0.48 95 95
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
mol:IP3 -0.03 0.098 -10000 0 -0.5 29 29
CSK 0 0 -10000 0 -10000 0 0
FOS -0.13 0.22 -10000 0 -0.45 327 327
CHUK 0.018 0.055 -10000 0 -0.28 3 3
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.023 0.078 -10000 0 -0.48 17 17
PTPN6 -0.057 0.17 -10000 0 -0.75 39 39
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.12 1 1
VAV2 -0.07 0.17 -10000 0 -0.81 32 32
ubiquitin-dependent protein catabolic process 0.019 0.019 -10000 0 -10000 0 0
BTK -0.004 0.006 -10000 0 -10000 0 0
CD19 -0.081 0.18 -10000 0 -0.54 93 93
MAP4K1 -0.013 0.067 -10000 0 -0.31 44 44
CD72 -0.009 0.054 -10000 0 -0.31 30 30
PAG1 -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0.002 0.13 -10000 0 -0.55 30 30
SH3BP5 0 0 -10000 0 -10000 0 0
PIK3AP1 -0.011 0.11 -10000 0 -0.54 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.042 0.13 -10000 0 -0.48 81 81
RAF1 -0.001 0.097 -10000 0 -0.44 29 29
RasGAP/p62DOK/SHIP -0.055 0.16 -10000 0 -0.5 95 95
CD79A -0.082 0.22 -10000 0 -0.8 79 79
re-entry into mitotic cell cycle -0.04 0.11 -10000 0 -0.25 82 82
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.016 0.083 -10000 0 -0.43 16 16
MAPK1 0.016 0.083 -10000 0 -0.43 16 16
CD72/SHP1 -0.055 0.16 -10000 0 -0.7 38 38
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.13 -10000 0 -0.52 38 38
actin cytoskeleton organization -0.026 0.15 -10000 0 -0.65 32 32
NF-kappa-B/RelA 0.043 0.032 -10000 0 -10000 0 0
Calcineurin -0.02 0.072 -10000 0 -0.44 16 16
PI3K -0.058 0.13 -10000 0 -0.54 41 41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.032 0.11 -10000 0 -0.57 29 29
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.048 0.17 -10000 0 -0.84 34 34
DAPP1 -0.051 0.2 -10000 0 -0.98 33 33
cytokine secretion -0.015 0.12 -10000 0 -0.52 33 33
mol:DAG -0.03 0.098 -10000 0 -0.5 29 29
PLCG2 -0.002 0.036 -10000 0 -0.63 3 3
MAP2K1 0.008 0.091 -10000 0 -0.48 16 16
B-cell antigen/BCR complex/FcgammaRIIB -0.069 0.19 -10000 0 -0.62 95 95
mol:PI-3-4-5-P3 -0.043 0.093 0.34 2 -0.36 41 43
ETS1 0.004 0.09 -10000 0 -0.49 19 19
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.057 0.16 -10000 0 -0.52 93 93
B-cell antigen/BCR complex/LYN -0.058 0.19 -10000 0 -0.58 93 93
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0.001 -10000 0 -10000 0 0
RAC1 -0.029 0.16 -10000 0 -0.71 32 32
B-cell antigen/BCR complex/LYN/SYK -0.058 0.18 -10000 0 -0.78 36 36
CARD11 -0.015 0.1 -10000 0 -0.49 29 29
FCGR2B -0.003 0.051 -10000 0 -0.8 4 4
PPP3CA -0.001 0.013 -10000 0 -0.29 2 2
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -10000 0 0
PTPRC -0.01 0.077 -10000 0 -0.5 20 20
PDPK1 -0.028 0.063 0.22 2 -0.27 23 25
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.014 -10000 0 -0.14 1 1
Aurora A 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
Aurora A/GADD45A -0.026 0.031 -9999 0 -10000 0 0
BIRC5 -0.21 0.13 -9999 0 -0.29 743 743
NFKBIA -0.024 0.034 -9999 0 -10000 0 0
CPEB1 -0.15 0.31 -9999 0 -0.8 194 194
AKT1 -0.024 0.034 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.024 0.033 -9999 0 -0.56 1 1
NDEL1/TACC3 -0.039 0.059 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.003 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.03 0.039 -9999 0 -10000 0 0
MDM2 -0.001 0.018 -9999 0 -0.29 4 4
JUB -0.003 0.05 -9999 0 -0.8 4 4
TPX2 -0.11 0.1 -9999 0 -10000 0 0
TP53 -0.011 0.016 -9999 0 -10000 0 0
DLG7 -0.03 0.036 -9999 0 -10000 0 0
AURKAIP1 -0.003 0.031 -9999 0 -0.29 12 12
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.042 0.063 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.023 0.033 -9999 0 -0.55 1 1
AURKA -0.037 0.045 -9999 0 -10000 0 0
AURKB -0.008 0.01 -9999 0 -10000 0 0
CDC25B -0.018 0.025 -9999 0 -10000 0 0
G2/M transition checkpoint -0.025 0.04 -9999 0 -0.5 4 4
mRNA polyadenylation -0.12 0.2 -9999 0 -0.53 193 193
Aurora A/CPEB -0.12 0.2 -9999 0 -0.53 193 193
Aurora A/TACC1/TRAP/chTOG -0.031 0.088 -9999 0 -0.48 37 37
BRCA1 -0.001 0.028 -9999 0 -0.46 3 3
centrosome duplication -0.029 0.039 -9999 0 -10000 0 0
regulation of centrosome cycle -0.039 0.059 -9999 0 -10000 0 0
spindle assembly -0.031 0.087 -9999 0 -0.48 37 37
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.071 -9999 0 -0.62 1 1
CENPA -0.004 0.011 -9999 0 -10000 0 0
Aurora A/PP2A -0.026 0.031 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.029 -9999 0 -10000 0 0
negative regulation of DNA binding -0.009 0.019 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.013 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.025 0.041 -9999 0 -0.51 4 4
mitotic prometaphase -0.013 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.045 -9999 0 -10000 0 0
TACC1 -0.029 0.15 -9999 0 -0.8 37 37
TACC3 -0.044 0.1 -9999 0 -0.29 159 159
Aurora A/Antizyme1 -0.021 0.025 -9999 0 -10000 0 0
Aurora A/RasGAP -0.026 0.031 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.003 0.003 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.004 0.023 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.11 0.1 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.11 0.088 -9999 0 -10000 0 0
PAK1 -0.007 0.044 -9999 0 -0.29 24 24
CKAP5 0 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.44 0.4 -10000 0 -0.8 572 572
CLTC 0.027 0.017 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.02 -10000 0 -10000 0 0
Dynamin 2/GTP -0.006 0.027 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.017 -10000 0 -10000 0 0
CPE 0.005 0.084 -10000 0 -0.54 24 24
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.002 0.019 -10000 0 -10000 0 0
CTNND1 0.025 0.031 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.014 -10000 0 -10000 0 0
TSHR -0.007 0.11 -10000 0 -0.54 45 45
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.007 0.075 -10000 0 -0.8 9 9
mol:Choline -0.002 0.019 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.036 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.027 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.005 0.048 -10000 0 -0.49 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.016 0.053 -10000 0 -0.38 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0.009 -10000 0 -0.29 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.004 0.036 -10000 0 -0.29 16 16
substrate adhesion-dependent cell spreading 0 0.001 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.034 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.005 -10000 0 -10000 0 0
ACAP1 -0.001 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.021 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0.001 -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 0.025 0.03 -10000 0 -10000 0 0
NME1 0.01 0.037 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.017 -10000 0 -10000 0 0
IL2RA 0.017 0.044 -10000 0 -0.37 7 7
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.22 0.2 -10000 0 -0.4 572 572
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.003 0.032 -10000 0 -0.34 9 9
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.014 -10000 0 -10000 0 0
SDC1 0.021 0.024 -10000 0 -0.35 1 1
ARF6/GDP -0.007 0.033 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.009 0.035 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.019 -10000 0 -10000 0 0
endocytosis 0.005 0.048 0.48 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.073 0.2 -10000 0 -0.43 239 239
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.025 -10000 0 -0.8 1 1
Dynamin 2/GDP -0.006 0.027 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.14 0.23 -10000 0 -0.43 390 390
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.008 0.03 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.004 -9999 0 -10000 0 0
HDAC2 0.001 0.004 -9999 0 -10000 0 0
GNB1/GNG2 -0.01 0.076 -9999 0 -0.56 19 19
forebrain development -0.025 0.2 -9999 0 -0.51 130 130
GNAO1 -0.029 0.14 -9999 0 -0.48 66 66
SMO/beta Arrestin2 -0.005 0.054 -9999 0 -0.62 8 8
SMO 0.004 0.072 -9999 0 -0.75 9 9
ARRB2 0.01 0.004 -9999 0 -10000 0 0
GLI3/SPOP -0.002 0.035 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.002 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.037 0.17 -9999 0 -0.8 50 50
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.055 0.16 -9999 0 -0.49 91 91
SAP30 0 0.018 -9999 0 -0.29 4 4
mol:GDP 0.004 0.072 -9999 0 -0.75 9 9
MIM/GLI2A 0.002 0.029 -9999 0 -0.29 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.002 0.005 -9999 0 -10000 0 0
GLI2 0.04 0.036 -9999 0 -10000 0 0
GLI3 0.039 0.04 -9999 0 -0.3 12 12
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.004 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.009 0.086 -9999 0 -0.8 12 12
Gi family/GTP -0.022 0.095 -9999 0 -0.36 47 47
SIN3B 0.001 0.004 -9999 0 -10000 0 0
SIN3A 0.001 0.004 -9999 0 -10000 0 0
GLI3/Su(fu) -0.002 0.026 -9999 0 -0.45 1 1
GLI2/Su(fu) 0.007 0.046 -9999 0 -0.39 6 6
FOXA2 -0.012 0.032 -9999 0 -10000 0 0
neural tube patterning -0.025 0.2 -9999 0 -0.51 130 130
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.026 -9999 0 -0.46 1 1
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 0.002 0.029 -9999 0 -0.29 9 9
embryonic limb morphogenesis -0.025 0.2 -9999 0 -0.51 130 130
SUFU -0.003 0.029 -9999 0 -0.31 9 9
LGALS3 -0.01 0.089 -9999 0 -0.8 13 13
catabolic process -0.004 0.027 -9999 0 -10000 0 0
GLI3A/CBP -0.021 0.096 -9999 0 -0.38 68 68
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.027 0.21 -9999 0 -0.53 130 130
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.025 -9999 0 -0.8 1 1
RBBP7 -0.001 0.026 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.008 0.065 -9999 0 -0.54 14 14
GNAZ -0.005 0.075 -9999 0 -0.8 9 9
RBBP4 0 0.025 -9999 0 -0.8 1 1
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.004 0.026 -9999 0 -10000 0 0
STK36 0.011 0.026 -9999 0 -0.8 1 1
Gi family/GNB1/GNG2/GDP -0.028 0.099 -9999 0 -0.47 25 25
PTCH1 -0.068 0.35 -9999 0 -1.2 78 78
MIM/GLI1 -0.052 0.18 -9999 0 -0.49 130 130
CREBBP -0.021 0.096 -9999 0 -0.38 68 68
Su(fu)/SIN3/HDAC complex 0.006 0.021 -9999 0 -10000 0 0
TRAIL signaling 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
TNFSF10 -0.007 0.075 -10000 0 -0.75 10 10
positive regulation of NF-kappaB transcription factor activity -0.065 0.19 -10000 0 -0.61 110 110
MAP2K4 0.041 0.039 -10000 0 -0.38 2 2
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.005 0.061 -10000 0 -0.8 6 6
SMPD1 -0.003 0.027 -10000 0 -0.29 9 9
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.079 0.24 -10000 0 -0.8 102 102
TRAIL/TRAILR2 -0.006 0.057 -10000 0 -0.61 9 9
TRAIL/TRAILR3 -0.009 0.071 -10000 0 -0.66 11 11
TRAIL/TRAILR1 -0.009 0.074 -10000 0 -0.61 15 15
TRAIL/TRAILR4 -0.065 0.19 -10000 0 -0.61 110 110
TRAIL/TRAILR1/DAP3/GTP -0.007 0.059 -10000 0 -0.49 15 15
IKK complex -0.003 0.02 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0.006 -10000 0 -0.2 1 1
MAPK3 0.017 0.059 -10000 0 -0.61 9 9
MAP3K1 -0.004 0.033 -10000 0 -0.32 10 10
TRAILR4 (trimer) -0.078 0.24 -10000 0 -0.8 102 102
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.005 0.061 -10000 0 -0.8 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.039 -10000 0 -0.33 15 15
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.059 -10000 0 -0.61 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.056 -10000 0 -0.46 15 15
mol:ceramide -0.003 0.027 -10000 0 -0.28 9 9
FADD -0.004 0.035 -10000 0 -0.29 15 15
MAPK8 0.044 0.057 -10000 0 -0.45 9 9
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
TRAILR3 (trimer) -0.005 0.05 -10000 0 -0.43 11 11
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.066 -10000 0 -0.54 15 15
DAP3 0 0.009 -10000 0 -0.29 1 1
CASP10 0.021 0.11 0.31 96 -0.5 13 109
JNK cascade -0.065 0.19 -10000 0 -0.61 110 110
TRAIL (trimer) -0.007 0.075 -10000 0 -0.75 10 10
TNFRSF10C -0.005 0.05 -10000 0 -0.43 11 11
TRAIL/TRAILR1/DAP3/GTP/FADD -0.008 0.057 -10000 0 -0.46 15 15
TRAIL/TRAILR2/FADD -0.007 0.052 -10000 0 -0.53 9 9
cell death -0.003 0.026 -10000 0 -0.28 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.03 -10000 0 -0.32 9 9
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.015 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.005 0.043 -10000 0 -0.45 9 9
Glypican 2 network

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
MDK -0.011 0.056 -9999 0 -0.29 41 41
GPC2 -0.035 0.1 -9999 0 -0.8 3 3
GPC2/Midkine -0.03 0.079 -9999 0 -0.41 17 17
neuron projection morphogenesis -0.03 0.079 -9999 0 -0.41 17 17
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.017 0.093 -9999 0 -0.53 33 33
E-cadherin/beta catenin -0.019 0.11 -9999 0 -0.61 32 32
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.026 -9999 0 -0.55 2 2
CDH1 -0.025 0.14 -9999 0 -0.8 32 32
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.001 0.008 -10000 0 -10000 0 0
CDKN1B 0.036 0.025 -10000 0 -0.43 3 3
CDKN1A 0.036 0.021 -10000 0 -0.43 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
FOXO3 0.036 0.025 -10000 0 -0.43 3 3
AKT1 0 0.001 -10000 0 -10000 0 0
BAD -0.001 0.013 -10000 0 -0.29 2 2
AKT3 0.009 0.058 -10000 0 -0.44 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.003 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.026 -10000 0 -0.42 4 4
BAD/YWHAZ -0.001 0.01 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.025 0.41 4 -10000 0 4
TSC1 0.037 0.003 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -0.29 3 3
AKT1/RAF1 0 0.001 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.037 0.003 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.021 0.042 -10000 0 -0.52 6 6
MAP3K5 -0.003 0.05 -10000 0 -0.8 4 4
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.021 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.003 -10000 0 -10000 0 0
CASP9 0.037 0.003 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.022 -10000 0 -0.4 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
AKT2/p21CIP1 -0.001 0.018 -10000 0 -0.41 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.004 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.054 0.029 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.037 0.009 -10000 0 -10000 0 0
MAPKKK cascade 0 0.001 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.005 -10000 0 -10000 0 0
TSC1/TSC2 0.044 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.005 -10000 0 -10000 0 0
glucose import -0.25 0.26 -10000 0 -0.48 575 575
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.031 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.25 0.26 -10000 0 -0.48 575 575
GSK3A 0.037 0.003 -10000 0 -10000 0 0
FOXO1 0.033 0.046 -10000 0 -0.43 10 10
GSK3B 0.037 0.003 -10000 0 -10000 0 0
SFN -0.015 0.097 -10000 0 -0.5 31 31
G1/S transition of mitotic cell cycle 0.044 0.002 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.043 0.031 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0.009 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.022 0.02 -10000 0 -0.61 1 1
MAP4K4 0.041 0.047 -10000 0 -0.69 1 1
BAG4 -0.006 0.057 -10000 0 -0.8 4 4
PKC zeta/ceramide -0.023 0.048 0.18 1 -0.58 1 2
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.08 -10000 0 -0.8 9 9
BAX -0.008 0.021 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.009 -10000 0 -10000 0 0
BAD -0.022 0.046 0.2 1 -0.25 1 2
SMPD1 0.025 0.034 -10000 0 -0.25 14 14
RB1 -0.022 0.047 0.2 1 -0.48 1 2
FADD/Caspase 8 0.048 0.048 -10000 0 -0.65 1 1
MAP2K4 -0.014 0.047 -10000 0 -0.46 2 2
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.046 -10000 0 -0.46 1 1
EGF -0.16 0.32 -10000 0 -0.8 202 202
mol:ceramide -0.033 0.048 0.21 1 -10000 0 1
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.023 -10000 0 -0.61 1 1
ASAH1 -0.001 0.016 -10000 0 -0.29 3 3
negative regulation of cell cycle -0.022 0.047 0.2 1 -0.48 1 2
cell proliferation -0.095 0.16 -10000 0 -0.39 231 231
BID 0.023 0.035 -10000 0 -0.4 1 1
MAP3K1 -0.022 0.047 0.2 1 -0.48 1 2
EIF2A -0.005 0.041 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.043 -10000 0 -0.42 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.043 -10000 0 -0.42 1 1
Cathepsin D/ceramide -0.028 0.05 0.18 1 -0.25 2 3
FADD 0.039 0.05 -10000 0 -0.47 3 3
KSR1 -0.022 0.048 0.2 1 -0.33 3 4
MAPK8 -0.012 0.055 0.2 1 -0.35 10 11
PRKRA -0.022 0.045 0.2 1 -10000 0 1
PDGFA -0.001 0.025 -10000 0 -0.8 1 1
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
IGF1 -0.18 0.33 -10000 0 -0.8 231 231
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.033 0.047 0.21 1 -10000 0 1
CTSD -0.011 0.055 -10000 0 -0.29 39 39
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 -0.1 0.17 -10000 0 -0.42 231 231
PRKCD 0 0.009 -10000 0 -0.29 1 1
PRKCZ -0.001 0.025 -10000 0 -0.8 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.023 -10000 0 -0.61 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.001 0.025 -10000 0 -0.8 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.043 -10000 0 -0.73 1 1
TNFR1A/BAG4/TNF-alpha -0.014 0.074 -10000 0 -0.54 18 18
mol:Sphingosine-1-phosphate 0.022 0.02 -10000 0 -0.61 1 1
MAP2K1 -0.005 0.044 -10000 0 -0.43 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.007 0.044 0.18 25 -10000 0 25
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.042 -10000 0 -0.61 4 4
EIF2AK2 -0.013 0.043 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.01 0.064 -10000 0 -0.53 14 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.021 -10000 0 -0.33 1 1
MAP2K2 -0.005 0.044 -10000 0 -0.43 1 1
SMPD3 0.025 0.043 -10000 0 -0.28 18 18
TNF -0.018 0.1 -10000 0 -0.48 38 38
PKC zeta/PAR4 -0.001 0.027 -10000 0 -0.61 2 2
mol:PHOSPHOCHOLINE 0.044 0.11 0.27 201 -10000 0 201
NF kappa B1/RelA/I kappa B alpha -0.001 0.02 -10000 0 -0.45 2 2
AIFM1 -0.007 0.044 0.18 25 -10000 0 25
BCL2 -0.028 0.15 -10000 0 -0.8 36 36
Retinoic acid receptors-mediated 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
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR 0 0 -10000 0 -10000 0 0
Cbp/p300/PCAF -0.001 0.016 -10000 0 -0.53 1 1
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.037 0.04 -10000 0 -0.32 4 4
KAT2B -0.001 0.025 -10000 0 -0.8 1 1
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.02 0.05 0.24 4 -0.34 12 16
RAR alpha/9cRA/Cyclin H -0.012 0.065 -10000 0 -0.38 27 27
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.034 0.05 -10000 0 -0.32 14 14
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.012 0.071 -10000 0 -0.64 9 9
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.006 0.12 -10000 0 -0.57 31 31
NCOA2 -0.035 0.16 -10000 0 -0.8 45 45
NCOA3 0 0.009 -10000 0 -10000 0 0
NCOA1 -0.001 0.025 -10000 0 -0.8 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0.009 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.071 -10000 0 -0.8 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.043 0.11 -10000 0 -0.63 27 27
RARA 0.014 0.064 -10000 0 -0.32 34 34
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.021 0.084 -10000 0 -0.3 56 56
PRKCA -0.008 0.13 -10000 0 -0.77 29 29
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.006 0.13 -10000 0 -0.58 33 33
RXRG -0.1 0.21 -10000 0 -0.45 277 277
RXRA 0.022 0.066 -10000 0 -0.33 34 34
RXRB 0.01 0.076 -10000 0 -0.44 27 27
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.024 0.096 -10000 0 -0.34 75 75
CRBP1/9-cic-RA -0.017 0.069 -10000 0 -0.24 75 75
RARB 0.003 0.091 -10000 0 -0.8 13 13
PRKCG -0.002 0.059 -10000 0 -0.29 43 43
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.12 -10000 0 -0.61 31 31
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.012 0.1 -10000 0 -0.49 32 32
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.057 -10000 0 -0.45 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.006 0.13 -10000 0 -0.58 34 34
positive regulation of DNA binding -0.011 0.062 -10000 0 -0.36 27 27
NRIP1 -0.004 0.12 -10000 0 -0.62 22 22
RXRs/RARs -0.013 0.13 -10000 0 -0.57 34 34
RXRs/RXRs/DNA/9cRA -0.046 0.12 -10000 0 -0.66 27 27
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.006 0.036 -10000 0 -0.52 1 1
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.01 0.076 -10000 0 -0.61 16 16
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 0.024 0.01 -10000 0 -10000 0 0
protein ubiquitination -0.028 0.072 -10000 0 -0.49 17 17
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0 0 -10000 0 -10000 0 0
DNA-PK -0.001 0.009 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.001 0.011 -10000 0 -10000 0 0
FANCF 0 0.009 -10000 0 -0.29 1 1
BRCA1 -0.001 0.028 -10000 0 -0.46 3 3
CCNE1 -0.059 0.12 -10000 0 -0.29 210 210
CDK2/Cyclin E1 -0.037 0.074 -10000 0 -10000 0 0
FANCG 0 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.011 0.079 -10000 0 -0.61 17 17
FANCE 0 0 -10000 0 -10000 0 0
FANCC 0 0 -10000 0 -10000 0 0
NBN 0 0 -10000 0 -10000 0 0
FANCA -0.05 0.11 -10000 0 -10000 0 0
DNA repair 0.008 0.093 -10000 0 -0.47 6 6
BRCA1/BARD1/ubiquitin -0.011 0.079 -10000 0 -0.61 17 17
BARD1/DNA-PK -0.008 0.06 -10000 0 -0.48 16 16
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.01 0.076 0.61 16 -10000 0 16
BRCA1/BARD1/CTIP/M/R/N Complex -0.005 0.039 -10000 0 -0.32 16 16
BRCA1/BACH1/BARD1/TopBP1 -0.009 0.068 -10000 0 -0.53 17 17
BRCA1/BARD1/P53 -0.008 0.061 -10000 0 -0.48 17 17
BARD1/CSTF1/BRCA1 -0.009 0.068 -10000 0 -0.53 17 17
BRCA1/BACH1 -0.001 0.028 -10000 0 -0.46 3 3
BARD1 -0.013 0.099 -10000 0 -0.77 17 17
PCNA -0.001 0.016 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.009 0.068 -10000 0 -0.53 17 17
BRCA1/BARD1/UbcH7 -0.009 0.068 -10000 0 -0.53 17 17
BRCA1/BARD1/RAD51/PCNA -0.052 0.085 -10000 0 -0.53 17 17
BARD1/DNA-PK/P53 -0.007 0.056 -10000 0 -0.45 16 16
BRCA1/BARD1/Ubiquitin -0.011 0.079 -10000 0 -0.61 17 17
BRCA1/BARD1/CTIP -0.008 0.061 -10000 0 -0.48 17 17
FA complex -0.005 0.011 -10000 0 -10000 0 0
BARD1/EWS -0.01 0.076 -10000 0 -0.61 16 16
RBBP8 0.022 0.006 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
TOPBP1 0 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.008 0.061 0.48 17 -10000 0 17
BRCA1/BARD1 -0.028 0.073 -10000 0 -0.49 17 17
CSTF1 0 0.009 -10000 0 -0.29 1 1
BARD1/EWS-Fli1 -0.01 0.077 -10000 0 -0.62 16 16
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.11 0.14 -10000 0 -0.29 386 386
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.011 0.079 -10000 0 -0.61 17 17
EWSR1 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.006 0.094 -10000 0 -0.46 33 33
ACTA1 -0.017 0.13 0.27 1 -0.66 32 33
NUMA1 0.006 0.094 -10000 0 -0.46 33 33
SPTAN1 -0.003 0.13 -10000 0 -0.64 31 31
LIMK1 -0.004 0.13 -10000 0 -0.64 31 31
BIRC3 -0.01 0.08 -10000 0 -0.8 9 9
BIRC2 0 0 -10000 0 -10000 0 0
BAX -0.001 0.02 -10000 0 -0.29 5 5
CASP10 -0.014 0.14 -10000 0 -0.68 34 34
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.006 0.094 -10000 0 -0.46 33 33
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.003 0.12 -10000 0 -0.62 31 31
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.009 0.14 -10000 0 -0.64 40 40
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.013 0.088 -10000 0 -0.69 15 15
BID 0.005 0.061 -10000 0 -0.3 33 33
MAP3K1 0.005 0.042 -10000 0 -0.28 8 8
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.004 0.13 -10000 0 -0.64 31 31
CASP9 0.001 0.003 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.18 7 -0.22 5 12
neuron apoptosis 0.022 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.004 0.12 -10000 0 -0.61 31 31
APAF1 0 0.002 -10000 0 -10000 0 0
CASP6 0.023 0.057 -10000 0 -0.42 4 4
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
ICAD/CAD 0.004 0.12 -10000 0 -0.61 31 31
CASP7 -0.007 0.037 0.35 9 -10000 0 9
KRT18 0.016 0.016 -10000 0 -10000 0 0
apoptosis 0.01 0.11 0.3 1 -0.54 31 32
DFFA -0.003 0.13 -10000 0 -0.64 31 31
DFFB -0.003 0.13 -10000 0 -0.64 31 31
PARP1 0.002 0.031 0.22 5 -0.18 7 12
actin filament polymerization -0.003 0.12 0.57 34 -10000 0 34
TNF -0.018 0.1 -10000 0 -0.48 38 38
CYCS 0.008 0.049 -10000 0 -0.22 32 32
SATB1 0.017 0.1 -10000 0 -0.49 28 28
SLK -0.003 0.13 -10000 0 -0.64 31 31
p15 BID/BAX -0.014 0.049 -10000 0 -0.34 9 9
CASP2 0.043 0.041 -10000 0 -0.46 1 1
JNK cascade -0.005 0.042 0.28 8 -10000 0 8
CASP3 -0.012 0.13 0.29 1 -0.65 34 35
LMNB2 0.04 0.038 -10000 0 -0.35 3 3
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.025 -10000 0 -0.8 1 1
Mammalian IAPs/DIABLO -0.006 0.046 -10000 0 -0.48 9 9
negative regulation of DNA binding 0.013 0.087 -10000 0 -0.68 15 15
stress fiber formation -0.003 0.12 -10000 0 -0.62 31 31
GZMB -0.028 0.15 -10000 0 -0.66 42 42
CASP1 0.014 0.035 -10000 0 -0.44 6 6
LMNB1 0.044 0.038 -10000 0 -0.35 3 3
APP 0.022 0.013 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.004 0.1 0.3 1 -0.52 31 32
LMNA 0.04 0.038 -10000 0 -0.35 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.037 -10000 0 -0.49 1 1
LRDD -0.001 0.018 -10000 0 -10000 0 0
SREBF1 -0.006 0.13 -10000 0 -0.64 31 31
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.006 0.093 -10000 0 -0.46 33 33
CFL2 0.003 0.12 -10000 0 -0.59 34 34
GAS2 -0.049 0.19 -10000 0 -0.52 123 123
positive regulation of apoptosis 0.045 0.038 -10000 0 -0.38 2 2
PRF1 -0.018 0.11 -10000 0 -0.64 29 29
Cellular roles of Anthrax toxin

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
ANTXR1 -0.002 0.036 -10000 0 -0.8 2 2
ANTXR2 -0.009 0.082 -10000 0 -0.8 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.011 -10000 0 -0.1 12 12
monocyte activation 0.003 0.075 -10000 0 -0.46 26 26
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.01 0.067 -10000 0 -0.48 20 20
CYAA 0.01 0.057 -10000 0 -0.5 12 12
MAP2K4 -0.001 0.018 -10000 0 -0.48 1 1
IL1B 0.007 0.066 -10000 0 -0.35 30 30
Channel -0.006 0.059 -10000 0 -0.54 12 12
NLRP1 -0.008 0.06 -10000 0 -0.5 15 15
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.011 0.1 12 -10000 0 12
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.14 0.21 -10000 0 -0.48 294 294
PA/Cellular Receptors -0.007 0.064 -10000 0 -0.58 12 12
apoptosis -0.001 0.011 -10000 0 -0.1 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.006 0.055 -10000 0 -0.5 12 12
macrophage activation 0.02 0.01 -10000 0 -10000 0 0
TNF -0.018 0.1 -10000 0 -0.48 38 38
VCAM1 -0.012 0.073 -10000 0 -0.46 26 26
platelet activation -0.001 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.014 0.021 0.2 3 -10000 0 3
IL18 0.011 0.037 -10000 0 -0.22 15 15
negative regulation of macrophage activation -0.001 0.011 -10000 0 -0.1 12 12
LEF -0.001 0.011 -10000 0 -0.1 12 12
CASP1 -0.005 0.03 -10000 0 -0.24 15 15
mol:cAMP -0.001 0.013 -10000 0 -10000 0 0
necrosis -0.001 0.011 -10000 0 -0.1 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.006 0.056 -10000 0 -0.51 12 12
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.03 0.008 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.046 -9999 0 -10000 0 0
MAPK12 0.019 0.079 -9999 0 -0.47 24 24
CCND1 0.015 0.042 -9999 0 -0.23 23 23
p38 gamma/SNTA1 -0.011 0.068 -9999 0 -0.47 20 20
MAP2K3 0 0.009 -9999 0 -0.29 1 1
PKN1 0 0.009 -9999 0 -0.29 1 1
G2/M transition checkpoint 0.019 0.078 -9999 0 -0.47 24 24
MAP2K6 0.012 0.08 -9999 0 -0.5 24 24
MAPT -0.018 0.14 -9999 0 -0.4 112 112
MAPK13 0.022 0.009 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0.029 -9999 0 -0.44 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 0.046 0.064 -10000 0 -0.67 1 1
UGCG -0.011 0.094 -10000 0 -0.82 13 13
AKT1/mTOR/p70S6K/Hsp90/TERT 0.054 0.091 -10000 0 -0.39 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.014 0.096 -10000 0 -0.81 13 13
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.091 -10000 0 -0.39 42 42
FRAP1 0.052 0.13 -10000 0 -0.41 64 64
FOXO3 0.06 0.11 -10000 0 -0.42 33 33
AKT1 0.055 0.11 -10000 0 -0.45 32 32
GAB2 0.007 0.045 -10000 0 -0.38 11 11
SMPD1 -0.002 0.014 -10000 0 -10000 0 0
SGMS1 -0.002 0.014 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.055 -10000 0 -0.54 10 10
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.033 0.09 -10000 0 -0.36 36 36
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.006 0.06 -10000 0 -0.62 10 10
RPS6KB1 0.022 0.032 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 21 21
JAK3 0.009 0.035 -10000 0 -0.29 14 14
PIK3R1 0.005 0.08 -10000 0 -0.8 10 10
JAK1 0.012 0.026 -10000 0 -0.8 1 1
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.046 0.18 -10000 0 -0.94 28 28
MYB 0.01 0.18 -10000 0 -1.3 19 19
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.053 0.094 -10000 0 -0.59 10 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.021 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.053 0.092 -10000 0 -0.57 10 10
Rac1/GDP -0.005 0.048 -10000 0 -0.49 10 10
T cell proliferation 0.058 0.088 -10000 0 -0.53 10 10
SHC1 0.011 0.004 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.01 -10000 0 -0.066 19 19
PRKCZ 0.058 0.091 -10000 0 -0.55 10 10
NF kappa B1 p50/RelA -0.025 0.089 -10000 0 -0.49 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.039 0.069 -10000 0 -0.57 5 5
HSP90AA1 0 0.009 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.018 0.12 -10000 0 -0.74 16 16
IL2RB 0 0.067 -10000 0 -0.31 41 41
TERT -0.042 0.1 -10000 0 -0.29 150 150
E2F1 0.022 0.064 -10000 0 -0.44 19 19
SOS1 0.011 0.004 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.03 19 -10000 0 19
PTPN11 0.011 0.004 -10000 0 -10000 0 0
IL2RG -0.005 0.09 -10000 0 -0.36 52 52
actin cytoskeleton organization 0.058 0.088 -10000 0 -0.53 10 10
GRB2 0.011 0.01 -10000 0 -0.29 1 1
IL2 0.006 0.026 -10000 0 -0.29 8 8
PIK3CA 0.013 0.01 -10000 0 -0.28 1 1
Rac1/GTP 0.026 0.049 -10000 0 -0.46 10 10
LCK -0.007 0.1 -10000 0 -0.42 49 49
BCL2 0.038 0.2 -10000 0 -0.86 42 42
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0 0.009 -9999 0 -10000 0 0
PLK4 -0.012 0.058 -9999 0 -0.29 44 44
regulation of centriole replication 0.013 0.042 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.017 0.085 -9999 0 -0.52 23 23
MAP4K1 -0.013 0.067 -9999 0 -0.31 44 44
MAP3K8 -0.006 0.066 -9999 0 -0.74 8 8
PRKCB -0.019 0.11 -9999 0 -0.55 36 36
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 -0.007 0.048 -9999 0 -0.47 4 4
JUN 0.017 0.11 -9999 0 -0.6 32 32
MAP3K7 -0.007 0.046 -9999 0 -0.49 3 3
GRAP2 -0.015 0.11 -9999 0 -0.73 21 21
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.043 0.057 -9999 0 -0.46 5 5
LAT -0.005 0.048 -9999 0 -0.8 2 2
LCP2 0 0.009 -9999 0 -0.29 1 1
MAPK8 0.013 0.11 -9999 0 -0.69 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.05 -9999 0 -0.35 18 18
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.016 0.079 -9999 0 -0.49 23 23
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.019 0.1 -9999 0 -0.58 32 32
KLHL20 -0.009 0.033 -9999 0 -0.24 3 3
CYFIP2 -0.01 0.067 -9999 0 -0.36 30 30
Rac1/GDP 0.048 0.072 -9999 0 -0.35 32 32
ENAH -0.018 0.1 -9999 0 -0.58 32 32
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.051 -9999 0 -0.5 1 1
ABI1/Sra1/Nap1 -0.006 0.025 -9999 0 -0.19 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.087 -9999 0 -0.48 34 34
RAPGEF1 0.037 0.094 -9999 0 -0.48 32 32
CTNND1 0 0.009 -9999 0 -0.29 1 1
regulation of calcium-dependent cell-cell adhesion -0.019 0.1 -9999 0 -0.6 32 32
CRK 0.028 0.1 -9999 0 -0.54 32 32
E-cadherin/gamma catenin/alpha catenin -0.017 0.093 -9999 0 -0.53 33 33
alphaE/beta7 Integrin -0.006 0.04 -9999 0 -0.61 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.037 -9999 0 -0.49 6 6
DLG1 -0.018 0.1 -9999 0 -0.58 32 32
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.041 -9999 0 -0.32 2 2
MLLT4 -0.005 0.062 -9999 0 -0.73 7 7
ARF6/GTP/NME1/Tiam1 -0.007 0.028 -9999 0 -10000 0 0
PI3K -0.011 0.053 -9999 0 -0.43 2 2
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.02 0.11 -9999 0 -0.61 33 33
TIAM1 -0.001 0.018 -9999 0 -0.29 4 4
E-cadherin(dimer)/Ca2+ -0.014 0.079 -9999 0 -0.46 32 32
AKT1 -0.006 0.03 -9999 0 -0.22 2 2
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
CDH1 -0.025 0.14 -9999 0 -0.8 32 32
RhoA/GDP 0.047 0.072 -9999 0 -0.35 32 32
actin cytoskeleton organization -0.007 0.025 -9999 0 -0.18 3 3
CDC42/GDP 0.047 0.072 -9999 0 -0.35 32 32
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.011 0.059 -9999 0 -0.34 33 33
ITGB7 -0.009 0.058 -9999 0 -0.8 2 2
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.015 0.083 -9999 0 -0.48 32 32
E-cadherin/Ca2+/beta catenin/alpha catenin -0.014 0.08 -9999 0 -0.46 32 32
mol:GDP 0.045 0.083 -9999 0 -0.41 32 32
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.026 -9999 0 -0.55 2 2
p120 catenin/RhoA/GDP -0.011 0.062 -9999 0 -0.35 32 32
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.029 -9999 0 -0.22 7 7
NME1 -0.014 0.063 -9999 0 -0.29 51 51
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.019 0.1 -9999 0 -0.57 33 33
regulation of cell-cell adhesion -0.008 0.044 -9999 0 -0.42 1 1
WASF2 -0.003 0.013 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.058 -9999 0 -0.59 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.082 -9999 0 -0.45 35 35
CCND1 -0.009 0.036 -9999 0 -0.27 7 7
VAV2 0.033 0.098 -9999 0 -0.51 32 32
RAP1/GDP -0.011 0.059 -9999 0 -0.57 1 1
adherens junction assembly -0.018 0.098 -9999 0 -0.55 33 33
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.017 0.078 -9999 0 -0.42 35 35
E-cadherin/beta catenin -0.015 0.086 -9999 0 -0.5 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.018 0.1 -9999 0 -0.58 32 32
PIK3CA 0 0.009 -9999 0 -0.29 1 1
Rac1/GTP -0.012 0.054 -9999 0 -0.36 6 6
E-cadherin/beta catenin/alpha catenin -0.016 0.092 -9999 0 -0.53 32 32
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.11 -9999 0 -0.62 32 32
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.025 -10000 0 -0.8 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.043 -10000 0 -0.48 4 4
IRAK/TOLLIP -0.001 0.01 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.031 0.12 -10000 0 -0.6 40 40
IL1A -0.006 0.041 -10000 0 -0.29 21 21
IL1B 0.01 0.096 -10000 0 -0.7 17 17
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.014 -10000 0 -10000 0 0
IL1R2 -0.037 0.16 -10000 0 -0.57 68 68
IL1R1 -0.015 0.11 -10000 0 -0.8 20 20
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.063 0.24 31 -0.33 17 48
TOLLIP 0 0.009 -10000 0 -0.29 1 1
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.032 0.078 -10000 0 -0.38 34 34
MAP3K7 0 0.009 -10000 0 -0.29 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.021 0.11 -10000 0 -0.48 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.012 0.072 -10000 0 -0.5 20 20
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.011 0.068 -10000 0 -0.47 20 20
IL1 beta fragment/IL1R1/IL1RAP -0.019 0.11 -10000 0 -0.56 35 35
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.028 0.072 -10000 0 -0.4 28 28
IRAK1 0.021 0.013 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.02 0.094 -10000 0 -0.61 22 22
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -0.29 1 1
TRAF6 0 0 -10000 0 -10000 0 0
PI3K -0.006 0.06 -10000 0 -0.61 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.011 0.062 -10000 0 -0.37 21 21
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.019 0.11 -10000 0 -0.56 35 35
IL1 beta/IL1R2 -0.034 0.13 -10000 0 -0.57 53 53
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.019 0.094 -10000 0 -0.93 4 4
IRAK3 -0.03 0.15 -10000 0 -0.79 39 39
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.017 0.098 -10000 0 -0.5 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.048 -10000 0 -0.34 20 20
IL1 alpha/IL1R1/IL1RAP -0.014 0.08 -10000 0 -0.55 20 20
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0.009 -10000 0 -0.29 1 1
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.008 -10000 0 -10000 0 0
IL1RAP -0.001 0.025 -10000 0 -0.8 1 1
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.014 0.078 -10000 0 -0.82 4 4
CASP1 -0.004 0.056 -10000 0 -0.8 5 5
IL1RN/IL1R2 -0.035 0.12 -10000 0 -0.59 44 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.018 0.1 -10000 0 -0.52 35 35
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -0.29 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.008 0.054 -10000 0 -0.39 20 20
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL1RN -0.012 0.065 -10000 0 -0.8 2 2
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.009 0.059 -10000 0 -0.42 20 20
S1P5 pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.022 0.076 0.51 6 -10000 0 6
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.036 -10000 0 -0.54 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.031 0.13 -10000 0 -0.48 66 66
RhoA/GTP -0.023 0.077 -10000 0 -0.52 6 6
negative regulation of cAMP metabolic process -0.026 0.086 -10000 0 -0.37 35 35
GNAZ -0.007 0.075 -10000 0 -0.8 9 9
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.059 -10000 0 -0.8 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.026 0.087 -10000 0 -0.37 35 35
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.039 0.17 -10000 0 -0.8 50 50
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.05 -9999 0 -0.8 4 4
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.028 0.093 -9999 0 -0.34 81 81
GNAO1 -0.019 0.14 -9999 0 -0.48 66 66
S1P/S1P3/G12/G13 -0.001 0.012 -9999 0 -10000 0 0
AKT1 -0.011 0.052 -9999 0 -0.68 4 4
AKT3 0.015 0.19 -9999 0 -1.4 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.05 -9999 0 -0.8 4 4
GNAI2 0.012 0.002 -9999 0 -10000 0 0
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GNAI1 -0.027 0.18 -9999 0 -0.81 50 50
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.028 -9999 0 -0.29 9 9
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.1 -9999 0 -0.39 38 38
MAPK3 0.02 0.099 -9999 0 -0.52 13 13
MAPK1 0.02 0.099 -9999 0 -0.52 13 13
JAK2 0.022 0.1 -9999 0 -0.48 16 16
CXCR4 0.016 0.1 -9999 0 -0.48 18 18
FLT1 0.013 0.026 -9999 0 -0.82 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.019 0.099 -9999 0 -0.52 13 13
S1P/S1P3/Gi 0.012 0.1 -9999 0 -0.4 38 38
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.083 -9999 0 -0.5 13 13
VEGFA 0.01 0.031 -9999 0 -0.35 1 1
S1P/S1P2/Gi 0.01 0.098 -9999 0 -0.37 37 37
VEGFR1 homodimer/VEGFA homodimer 0.021 0.03 -9999 0 -0.64 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.006 0.041 -9999 0 -0.34 15 15
GNAQ -0.002 0.035 -9999 0 -0.8 2 2
GNAZ 0.005 0.076 -9999 0 -0.8 9 9
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.014 0.088 -9999 0 -0.46 31 31
GNA15 -0.003 0.034 -9999 0 -0.8 1 1
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.035 -9999 0 -0.8 2 2
Rac1/GTP -0.024 0.083 -9999 0 -0.5 13 13
p38 MAPK 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
TRAF6/ASK1 -0.002 0.029 -10000 0 -0.47 4 4
TRAF2/ASK1 -0.003 0.035 -10000 0 -0.54 4 4
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.025 0.046 -10000 0 -0.39 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.062 -10000 0 -0.39 8 8
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.035 0.094 -10000 0 -0.29 125 125
TXN 0.008 0.005 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A 0 0 -10000 0 -10000 0 0
GADD45B 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.025 -10000 0 -0.8 1 1
MAP3K6 -0.001 0.025 -10000 0 -0.8 1 1
MAP3K7 0 0.009 -10000 0 -0.29 1 1
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.003 0.043 -10000 0 -0.61 5 5
TAK1/TAB family 0.001 0.012 0.22 3 -10000 0 3
RAC1/OSM/MEKK3 0 0.006 -10000 0 -10000 0 0
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
RAC1/OSM/MEKK3/MKK3 -0.006 0.024 -10000 0 -0.4 1 1
TRAF6 0.008 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.07 0.21 -10000 0 -0.6 121 121
CCM2 -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/CAMKIIB -0.045 0.14 -10000 0 -0.54 74 74
MAPK11 -0.002 0.043 -10000 0 -0.8 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.042 0.13 -10000 0 -0.5 77 77
OSM/MEKK3 0 0.008 -10000 0 -10000 0 0
TAOK1 -0.003 0.094 -10000 0 -0.44 45 45
TAOK2 0.017 0 -10000 0 -10000 0 0
TAOK3 0.017 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.003 0.05 -10000 0 -0.8 4 4
MAP3K10 0 0.009 -10000 0 -0.29 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.002 0.033 -10000 0 -0.53 4 4
GADD45/MTK1/MTK1 -0.013 0.035 -10000 0 -10000 0 0
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.018 0.08 0.33 1 -0.36 52 53
FRAP1 0.011 0.021 -10000 0 -10000 0 0
AKT1 -0.016 0.069 0.24 1 -0.42 11 12
INSR 0 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.012 0.053 -10000 0 -0.34 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.017 -10000 0 -10000 0 0
TSC2 0 0.001 -10000 0 -10000 0 0
RHEB/GDP -0.011 0.046 -10000 0 -0.31 11 11
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.017 0.084 -10000 0 -0.42 43 43
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.005 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.018 0.044 0.19 1 -0.26 11 12
MAP3K5 0.009 0.028 -10000 0 -0.44 4 4
PIK3R1 -0.008 0.079 -10000 0 -0.8 10 10
apoptosis 0.009 0.028 -10000 0 -0.44 4 4
mol:LY294002 0 0 -10000 0 -0.002 43 43
EIF4B 0.025 0.04 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.007 0.029 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.02 0.086 -10000 0 -0.39 53 53
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.031 0.18 1 -0.19 10 11
FKBP1A 0 0.009 -10000 0 -0.29 1 1
RHEB/GTP -0.01 0.046 -10000 0 -0.3 11 11
mol:Amino Acids 0 0 -10000 0 -0.002 43 43
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.016 0.072 0.26 1 -0.33 52 53
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.004 0.04 -10000 0 -0.63 4 4
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.013 0.057 -10000 0 -0.36 11 11
tumor necrosis factor receptor activity 0 0 0.002 43 -10000 0 43
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 -0.011 0.092 -10000 0 -0.45 43 43
INS 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.035 -10000 0 -0.8 2 2
PDK2 -0.018 0.078 0.26 1 -0.34 55 56
EIF4EBP1 0.013 0.012 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PPP2R5D 0.018 0.02 -10000 0 -10000 0 0
peptide biosynthetic process 0 0.004 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -0.003 10 12
EEF2 0 0.004 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.007 0.052 -9999 0 -0.34 21 21
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P -0.002 0.017 -9999 0 -0.36 2 2
GNAO1 -0.031 0.13 -9999 0 -0.48 66 66
mol:Sphinganine-1-P 0.017 0.039 -9999 0 -0.61 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.011 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.027 -9999 0 -0.29 9 9
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.015 -9999 0 -0.31 2 2
S1PR5 -0.008 0.059 -9999 0 -0.8 3 3
S1PR4 -0.015 0.081 -9999 0 -0.8 6 6
GNAI1 -0.039 0.17 -9999 0 -0.8 50 50
S1P/S1P5/G12 -0.005 0.033 -9999 0 -0.47 3 3
S1P/S1P3/Gq -0.004 0.036 -9999 0 -0.29 15 15
S1P/S1P4/Gi -0.026 0.083 -9999 0 -0.34 38 38
GNAQ -0.002 0.035 -9999 0 -0.8 2 2
GNAZ -0.007 0.075 -9999 0 -0.8 9 9
GNA14 -0.014 0.088 -9999 0 -0.46 31 31
GNA15 -0.003 0.034 -9999 0 -0.8 1 1
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.035 -9999 0 -0.8 2 2
ABCC1 0 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.004 0.025 -9999 0 -0.41 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.01 0.043 -9999 0 -0.46 3 3
EPO -0.048 0.11 -9999 0 -0.29 171 171
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.03 0.068 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.04 -9999 0 -0.4 10 10
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.006 0.06 -9999 0 -0.61 10 10
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.01 0.025 -9999 0 -0.51 1 1
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
MADCAM1 -0.011 0.056 -9999 0 -0.29 41 41
cell adhesion -0.01 0.043 -9999 0 -0.45 3 3
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.025 0.058 -9999 0 -0.48 12 12
ITGB7 -0.009 0.058 -9999 0 -0.8 2 2
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.059 -9999 0 -0.53 12 12
p130Cas/Crk/Dock1 -0.006 0.043 -9999 0 -0.4 12 12
VCAM1 -0.011 0.089 -9999 0 -0.63 18 18
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.033 0.055 -9999 0 -0.44 12 12
EPOR 0 0.009 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -10000 0 0
Rac1/GTP -0.003 0.041 -9999 0 -0.42 10 10
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.049 0.029 -10000 0 -0.36 4 4
NFATC2 0.017 0.064 -10000 0 -0.32 10 10
NFATC3 0 0.016 -10000 0 -0.52 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.096 -10000 0 -0.4 35 35
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 -0.019 0.078 -10000 0 -0.49 17 17
BCL2/BAX -0.022 0.11 -10000 0 -0.62 36 36
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0 0 -10000 0 -10000 0 0
BAD -0.001 0.013 -10000 0 -0.29 2 2
CABIN1/MEF2D -0.02 0.082 -10000 0 -0.52 17 17
Calcineurin A alpha-beta B1/BCL2 -0.028 0.15 -10000 0 -0.8 36 36
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.02 0.081 0.52 17 -10000 0 17
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.03 0.088 -10000 0 -0.29 107 107
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.015 0.097 -10000 0 -0.5 31 31
MAP3K8 -0.006 0.066 -10000 0 -0.74 8 8
NFAT4/CK1 alpha -0.001 0.017 -10000 0 -0.39 2 2
MEF2D/NFAT1/Cbp/p300 -0.034 0.089 -10000 0 -0.47 2 2
CABIN1 0.011 0.097 -10000 0 -0.41 35 35
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.025 -10000 0 -0.8 1 1
CAMK4 -0.011 0.06 -10000 0 -0.8 1 1
mol:Ca2+ 0 0.006 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.044 -10000 0 -0.61 1 1
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 -0.006 0.07 -10000 0 -0.8 8 8
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.009 -10000 0 -0.29 1 1
NFAT1-c-4/YWHAQ -0.002 0.022 -10000 0 -0.41 1 1
PRKCH -0.001 0.025 -10000 0 -0.8 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0 0 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -10000 0 -10000 0 0
apoptosis -0.007 0.036 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.023 -10000 0 -10000 0 0
PRKCB -0.019 0.11 -10000 0 -0.55 36 36
PRKCE 0 0 -10000 0 -10000 0 0
JNK2/NFAT4 0 0.014 -10000 0 -0.47 1 1
BAD/BCL-XL 0 0.008 -10000 0 -10000 0 0
PRKCD 0 0.009 -10000 0 -0.29 1 1
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.025 -10000 0 -0.8 1 1
PRKCA -0.021 0.13 -10000 0 -0.77 29 29
PRKCG -0.012 0.058 -10000 0 -0.29 43 43
PRKCQ -0.039 0.17 -10000 0 -0.7 57 57
FKBP38/BCL2 -0.021 0.11 -10000 0 -0.61 36 36
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.048 0.049 -10000 0 -0.38 9 9
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.006 0.033 -10000 0 -0.54 1 1
NFATc/ERK1 0.049 0.033 -10000 0 -0.37 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.019 0.077 -10000 0 -0.49 17 17
NR4A1 -0.004 0.21 -10000 0 -0.71 81 81
GSK3B 0 0 -10000 0 -10000 0 0
positive T cell selection 0 0.016 -10000 0 -0.51 1 1
NFAT1/CK1 alpha -0.015 0.039 -10000 0 -0.3 3 3
RCH1/ KPNB1 -0.019 0.056 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 -0.015 0.067 -10000 0 -0.3 52 52
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.016 -10000 0 -0.29 3 3
NFATc/p38 alpha 0.051 0.031 -10000 0 -0.37 1 1
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.028 0.15 -10000 0 -0.8 36 36
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.031 0.13 -9999 0 -0.48 66 66
CDC42/GTP -0.024 0.076 -9999 0 -0.5 4 4
PLCG1 -0.025 0.079 -9999 0 -0.51 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.024 0.075 -9999 0 -0.48 4 4
S1PR5 -0.008 0.059 -9999 0 -0.8 3 3
S1PR4 -0.015 0.081 -9999 0 -0.8 6 6
MAPK3 -0.025 0.079 -9999 0 -0.51 4 4
MAPK1 -0.025 0.079 -9999 0 -0.51 4 4
S1P/S1P5/Gi -0.026 0.087 -9999 0 -0.37 35 35
GNAI1 -0.039 0.17 -9999 0 -0.8 50 50
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.036 -9999 0 -0.54 3 3
RHOA -0.007 0.04 -9999 0 -0.45 6 6
S1P/S1P4/Gi -0.028 0.086 -9999 0 -0.35 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.075 -9999 0 -0.8 9 9
S1P/S1P4/G12/G13 -0.007 0.044 -9999 0 -0.49 6 6
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.006 0.051 -10000 0 -0.48 12 12
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.013 -10000 0 -0.4 1 1
GATA1/HDAC4 -0.004 0.03 -10000 0 -0.61 1 1
GATA1/HDAC5 -0.003 0.023 -10000 0 -10000 0 0
GATA2/HDAC5 -0.019 0.1 -10000 0 -0.61 28 28
HDAC5/BCL6/BCoR -0.004 0.043 -10000 0 -0.53 7 7
HDAC9 -0.01 0.077 -10000 0 -0.5 20 20
Glucocorticoid receptor/Hsp90/HDAC6 -0.007 0.061 -10000 0 -0.53 14 14
HDAC4/ANKRA2 -0.001 0.019 -10000 0 -0.61 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.026 0.13 -10000 0 -0.63 42 42
HDAC4/RFXANK -0.001 0.023 -10000 0 -0.61 1 1
BCOR -0.002 0.035 -10000 0 -0.8 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0.009 -10000 0 -0.29 1 1
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.066 -10000 0 -0.61 12 12
Histones -0.003 0.024 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.025 -10000 0 -0.8 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.019 -10000 0 -0.61 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.001 0.013 -10000 0 -10000 0 0
CAMK4 -0.011 0.06 -10000 0 -0.8 1 1
Tubulin/HDAC6 -0.001 0.018 -10000 0 -0.53 1 1
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 -0.005 0.037 -10000 0 -0.29 17 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.011 0.093 -10000 0 -0.8 14 14
SUMO1/HDAC4 0 0.014 -10000 0 -0.44 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.019 -10000 0 -0.61 1 1
Tubulin -0.001 0.021 -10000 0 -0.61 1 1
HDAC4/14-3-3 E -0.001 0.019 -10000 0 -0.61 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR -0.004 0.05 -10000 0 -0.61 7 7
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.016 -10000 0 -0.53 1 1
HDAC4/SRF -0.006 0.035 -10000 0 -0.53 2 2
HDAC4/ER alpha -0.12 0.22 -10000 0 -0.61 159 159
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.024 -10000 0 -10000 0 0
cell motility -0.001 0.017 -10000 0 -0.53 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.004 0.056 -10000 0 -0.8 5 5
HDAC4/CaMK II delta B -0.001 0.025 -10000 0 -0.8 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.16 0.29 -10000 0 -0.58 276 276
HDAC6/HDAC11 -0.001 0.013 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.001 0.025 -10000 0 -0.8 1 1
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.02 -10000 0 -0.45 2 2
GNG2 -0.009 0.086 -10000 0 -0.8 12 12
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.028 -10000 0 -0.8 1 1
HDAC11 -0.001 0.02 -10000 0 -0.29 5 5
HSP90AA1 0 0.009 -10000 0 -10000 0 0
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK -0.001 0.02 -10000 0 -0.29 5 5
nuclear import 0 0.014 0.44 1 -10000 0 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.61 35 35
AKT1 0.081 0.068 -9999 0 -0.68 6 6
PTK2B -0.02 0.11 -9999 0 -1 7 7
VEGFR2 homodimer/Frs2 -0.008 0.08 -9999 0 -0.85 8 8
CAV1 -0.17 0.33 -9999 0 -0.8 224 224
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.008 0.075 -9999 0 -0.79 8 8
endothelial cell proliferation 0.083 0.084 -9999 0 -0.69 6 6
mol:Ca2+ 0.05 0.072 -9999 0 -0.88 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.007 0.071 -9999 0 -0.95 5 5
RP11-342D11.1 0.042 0.072 -9999 0 -0.71 8 8
CDH5 -0.007 0.075 -9999 0 -0.8 9 9
VEGFA homodimer -0.001 0.012 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.02 0.13 -9999 0 -0.8 26 26
HRAS/GDP -0.005 0.057 -9999 0 -0.76 5 5
SH2D2A -0.034 0.098 -9999 0 -0.3 120 120
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.003 0.053 -9999 0 -0.69 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.02 0.085 -9999 0 -0.75 10 10
VEGFR1 homodimer -0.001 0.025 -9999 0 -0.8 1 1
SHC/GRB2/SOS1 -0.004 0.064 -9999 0 -0.85 5 5
GRB10 0.05 0.072 -9999 0 -0.88 5 5
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
PAK1 -0.007 0.044 -9999 0 -0.29 24 24
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.008 0.092 -9999 0 -1 7 7
HRAS -0.003 0.027 -9999 0 -0.29 9 9
VEGF/Rho/ROCK1/Integrin Complex -0.011 0.064 -9999 0 -0.59 7 7
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.028 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.007 0.069 -9999 0 -0.92 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.043 -9999 0 -0.8 3 3
Nck/Pak -0.004 0.028 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.008 0.082 -9999 0 -0.82 9 9
mol:GDP -0.004 0.061 -9999 0 -0.81 5 5
mol:NADP 0.073 0.05 -9999 0 -0.56 5 5
eNOS/Hsp90 0.075 0.047 -9999 0 -0.52 5 5
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
mol:IP3 0.051 0.073 -9999 0 -0.9 5 5
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.026 -9999 0 -0.8 1 1
VEGFA -0.003 0.029 -9999 0 -10000 0 0
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin 0.056 0.1 -9999 0 -0.97 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.022 0.12 -9999 0 -1.1 7 7
PTPN6 -0.001 0.013 -9999 0 -0.29 2 2
EPAS1 -0.006 0.069 -9999 0 -0.73 8 8
mol:L-citrulline 0.073 0.05 -9999 0 -0.56 5 5
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.008 0.071 -9999 0 -0.95 5 5
VEGFR2 homodimer/VEGFA homodimer -0.007 0.074 -9999 0 -0.78 8 8
VEGFR2/3 heterodimer -0.008 0.091 -9999 0 -0.92 9 9
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.055 0.078 -9999 0 -0.95 5 5
VEGFR2 homodimer 0.028 0.091 -9999 0 -0.95 8 8
FLT1 -0.001 0.025 -9999 0 -0.8 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.051 0.081 -9999 0 -0.85 6 6
MAPK1 0.051 0.081 -9999 0 -0.85 6 6
VEGFA145/NRP2 -0.004 0.04 -9999 0 -0.66 3 3
VEGFR1/2 heterodimer -0.007 0.085 -9999 0 -0.91 8 8
KDR 0.028 0.091 -9999 0 -0.96 8 8
VEGFA165/NRP1/VEGFR2 homodimer -0.006 0.081 -9999 0 -0.98 6 6
SRC 0 0.009 -9999 0 -0.29 1 1
platelet activating factor biosynthetic process 0.053 0.083 -9999 0 -0.88 6 6
PI3K -0.008 0.075 -9999 0 -0.9 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.007 0.075 -9999 0 -0.79 8 8
FES 0.049 0.079 -9999 0 -0.92 5 5
GAB1 -0.005 0.069 -9999 0 -0.94 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.075 -9999 0 -0.79 8 8
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.01 0.17 -9999 0 -0.57 13 13
VEGFR2 homodimer/VEGFA homodimer/Yes -0.008 0.076 -9999 0 -0.75 9 9
PI3K/GAB1 0.079 0.076 -9999 0 -0.72 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.002 0.07 -9999 0 -0.91 5 5
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.007 0.085 -9999 0 -0.86 9 9
HSP90AA1 0 0.009 -9999 0 -10000 0 0
CDC42 0.051 0.075 -9999 0 -0.92 5 5
actin cytoskeleton reorganization -0.02 0.084 -9999 0 -0.74 10 10
PTK2 0.052 0.11 -9999 0 -1.1 6 6
EDG1 0.042 0.072 -9999 0 -0.71 8 8
mol:DAG 0.051 0.073 -9999 0 -0.9 5 5
CaM/Ca2+ -0.006 0.061 -9999 0 -0.82 5 5
MAP2K3 0.056 0.077 -9999 0 -0.87 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.005 0.071 -9999 0 -0.94 5 5
PLCG1 0.051 0.075 -9999 0 -0.92 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.007 0.072 -9999 0 -0.95 5 5
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.025 -9999 0 -0.8 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.007 0.075 -9999 0 -0.79 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.007 0.075 -9999 0 -0.79 8 8
cell migration 0.078 0.089 -9999 0 -0.79 6 6
mol:PI-3-4-5-P3 -0.007 0.066 -9999 0 -0.79 6 6
FYN -0.002 0.035 -9999 0 -0.8 2 2
VEGFB/NRP1 -0.006 0.062 -9999 0 -0.83 5 5
mol:NO 0.073 0.05 -9999 0 -0.56 5 5
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.057 -9999 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.071 -9999 0 -0.94 5 5
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.028 0.15 -9999 0 -0.75 39 39
NOS3 0.075 0.056 -9999 0 -0.65 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.019 0.1 -9999 0 -0.55 34 34
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.045 0.11 -9999 0 -0.99 5 5
PRKCB 0.047 0.1 -9999 0 -0.9 7 7
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.006 0.067 -9999 0 -0.71 8 8
VEGFR1/2 heterodimer/VEGFA homodimer -0.008 0.08 -9999 0 -0.84 8 8
VEGFA165/NRP2 -0.004 0.04 -9999 0 -0.66 3 3
MAPKKK cascade -0.004 0.058 -9999 0 -0.77 5 5
NRP2 -0.003 0.044 -9999 0 -0.68 4 4
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 -0.001 0.025 -9999 0 -0.8 1 1
FAK1/Paxillin 0.056 0.1 -9999 0 -0.97 6 6
MAP3K13 0.049 0.081 -9999 0 -0.92 5 5
PDPK1 0.074 0.066 -9999 0 -0.67 6 6
HIF-2-alpha transcription factor network

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
MMP14 0 0.017 -10000 0 -10000 0 0
oxygen homeostasis 0.012 0.012 -10000 0 -10000 0 0
TCEB2 -0.007 0.044 -10000 0 -0.29 25 25
TCEB1 -0.001 0.013 -10000 0 -0.29 2 2
VHL/Elongin B/Elongin C/HIF2A -0.005 0.037 -10000 0 -0.43 2 2
EPO 0.15 0.15 -10000 0 -0.72 2 2
FIH (dimer) 0.023 0.012 -10000 0 -10000 0 0
APEX1 0.022 0.014 -10000 0 -0.3 1 1
SERPINE1 0.16 0.15 -10000 0 -0.69 4 4
FLT1 -0.003 0.079 -10000 0 -1 5 5
ADORA2A 0.14 0.16 -10000 0 -0.67 4 4
germ cell development 0.16 0.15 -10000 0 -0.64 7 7
SLC11A2 0.16 0.15 -10000 0 -0.69 4 4
BHLHE40 0.16 0.15 -10000 0 -0.81 5 5
HIF1AN 0.023 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.015 0.069 -10000 0 -0.44 4 4
ETS1 0.022 0.058 -10000 0 -0.81 5 5
CITED2 0.001 0.01 -10000 0 -10000 0 0
KDR -0.007 0.11 -10000 0 -1.2 8 8
PGK1 0.16 0.15 -10000 0 -0.69 4 4
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.18 0.16 -10000 0 -0.77 5 5
EPAS1 0.094 0.081 -10000 0 -0.42 4 4
SP1 0.018 0.002 -10000 0 -10000 0 0
ABCG2 0.13 0.25 -10000 0 -0.7 73 73
EFNA1 0.16 0.15 -10000 0 -0.69 4 4
FXN 0.16 0.15 -10000 0 -0.67 4 4
POU5F1 0.16 0.16 -10000 0 -0.67 7 7
neuron apoptosis -0.18 0.15 0.74 5 -10000 0 5
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.083 -10000 0 -0.28 78 78
EGLN2 0.021 0.026 -10000 0 -0.3 2 2
EGLN1 0.022 0.028 -10000 0 -0.81 1 1
VHL/Elongin B/Elongin C -0.004 0.022 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.023 0.01 -10000 0 -10000 0 0
SLC2A1 0.15 0.15 -10000 0 -0.67 5 5
TWIST1 0.14 0.21 -10000 0 -0.7 38 38
ELK1 0.019 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.008 0.062 -10000 0 -0.61 1 1
VEGFA 0.16 0.15 -10000 0 -0.71 4 4
CREBBP 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.006 0.057 -9999 0 -0.8 4 4
Caspase 8 (4 units) -0.009 0.047 -9999 0 -1 1 1
NEF -0.006 0.027 -9999 0 -0.22 9 9
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 0.034 0.084 -9999 0 -0.81 9 9
CYCS 0.04 0.059 -9999 0 -0.95 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.026 0.13 -9999 0 -0.62 37 37
MAP2K7 0.042 0.049 -9999 0 -0.81 1 1
protein ubiquitination 0.066 0.035 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.003 0.05 -9999 0 -0.8 4 4
BID -0.01 0.053 -9999 0 -1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.034 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.003 0.05 -9999 0 -0.8 4 4
CFLAR 0 0 -9999 0 -10000 0 0
FADD -0.004 0.035 -9999 0 -0.29 15 15
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.034 -9999 0 -10000 0 0
MAPK8 0.045 0.063 -9999 0 -0.48 9 9
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.018 -9999 0 -0.29 4 4
TRAF2 -0.001 0.018 -9999 0 -0.29 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.012 0.057 -9999 0 -0.34 20 20
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.032 -9999 0 -0.37 2 2
CHUK 0.067 0.037 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.005 0.048 -9999 0 -0.53 7 7
TCRz/NEF -0.025 0.11 -9999 0 -0.53 39 39
TNF -0.018 0.1 -9999 0 -0.48 38 38
FASLG -0.007 0.15 -9999 0 -0.65 39 39
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.014 0.074 -9999 0 -0.54 18 18
CASP6 -0.004 0.032 -9999 0 -0.71 1 1
CASP7 0.073 0.077 -9999 0 -0.62 9 9
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.073 0.077 -9999 0 -0.62 9 9
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.042 -9999 0 -0.61 4 4
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.062 0.04 -9999 0 -0.36 1 1
APAF-1/Caspase 9 -0.01 0.054 -9999 0 -0.51 9 9
BCL2 0.036 0.1 -9999 0 -0.44 42 42
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.001 0.028 -9999 0 -0.91 1 1
VEGFR1 homodimer/NRP1 -0.001 0.028 -9999 0 -0.92 1 1
mol:DAG 0.038 0.032 -9999 0 -0.65 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.029 -9999 0 -0.86 1 1
CaM/Ca2+ -0.001 0.028 -9999 0 -0.61 2 2
HIF1A 0 0.012 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.048 -9999 0 -0.72 1 1
PLCG1 0.038 0.032 -9999 0 -0.66 2 2
NOS3 0.062 0.032 -9999 0 -0.56 2 2
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.061 0.031 -9999 0 -0.54 2 2
FLT1 0.029 0.032 -9999 0 -1 1 1
PGF -0.001 0.028 -9999 0 -0.46 3 3
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.048 -9999 0 -0.79 3 3
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
eNOS/Hsp90 0.065 0.03 -9999 0 -0.65 1 1
endothelial cell proliferation 0.036 0.089 -9999 0 -0.65 5 5
mol:Ca2+ 0.038 0.032 -9999 0 -0.64 2 2
MAPK3 0.039 0.083 -9999 0 -0.44 28 28
MAPK1 0.039 0.083 -9999 0 -0.44 28 28
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
PLGF homodimer -0.001 0.028 -9999 0 -0.46 3 3
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.17 0.33 -9999 0 -0.8 224 224
VEGFA homodimer -0.003 0.03 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.002 0.031 -9999 0 -0.91 1 1
platelet activating factor biosynthetic process 0.046 0.081 -9999 0 -1.1 1 1
PI3K -0.006 0.052 -9999 0 -0.47 12 12
PRKCA 0.032 0.088 -9999 0 -0.47 28 28
PRKCB 0.034 0.077 -9999 0 -0.48 19 19
VEGFR1 homodimer/PLGF homodimer -0.002 0.033 -9999 0 -0.72 2 2
VEGFA -0.003 0.03 -9999 0 -10000 0 0
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.032 -9999 0 -0.65 2 2
RASA1 0.039 0.027 -9999 0 -0.84 1 1
NRP2 -0.003 0.044 -9999 0 -0.68 4 4
VEGFR1 homodimer 0.029 0.032 -9999 0 -1 1 1
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.03 0.19 -9999 0 -0.64 6 6
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.051 -9999 0 -0.47 12 12
mol:L-citrulline 0.061 0.031 -9999 0 -0.54 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.028 -9999 0 -0.8 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.029 -9999 0 -0.85 1 1
CD2AP 0 0.009 -9999 0 -0.29 1 1
PI3K/GAB1 -0.005 0.049 -9999 0 -0.45 12 12
PDPK1 -0.005 0.048 -9999 0 -0.74 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.029 -9999 0 -0.85 1 1
mol:NADP 0.061 0.031 -9999 0 -0.54 2 2
HSP90AA1 0 0.009 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.027 -9999 0 -0.79 1 1
VEGFR1 homodimer/NRP2 -0.002 0.048 -9999 0 -0.8 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.001 0.025 -9999 0 -0.8 1 1
SMAD2 0.014 0.005 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.004 0.016 -9999 0 -0.29 1 1
SMAD4/Ubc9/PIASy -0.001 0.016 -9999 0 -0.53 1 1
SMAD2/SMAD2/SMAD4 -0.01 0.031 -9999 0 -0.53 1 1
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0.015 -9999 0 -0.48 1 1
MAP3K1 -0.001 0.025 -9999 0 -0.8 1 1
TRAP-1/SMAD4 -0.009 0.073 -9999 0 -0.61 15 15
MAPK3 0 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
NUP214 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 -0.011 0.093 -9999 0 -0.8 14 14
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.009 -9999 0 -0.29 1 1
KPNA2 -0.03 0.088 -9999 0 -0.29 107 107
PIAS4 0 0 -9999 0 -10000 0 0
EPO signaling pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.058 0.077 -9999 0 -0.52 1 1
CRKL 0.028 0.05 -9999 0 -0.49 1 1
mol:DAG -0.007 0.026 -9999 0 -0.39 1 1
HRAS -0.006 0.022 -9999 0 -0.4 1 1
MAPK8 0.01 0.069 -9999 0 -0.52 8 8
RAP1A 0.028 0.05 -9999 0 -0.49 1 1
GAB1 0.028 0.05 -9999 0 -0.49 1 1
MAPK14 0.015 0.051 -9999 0 -10000 0 0
EPO -0.036 0.11 -9999 0 -0.28 171 171
PLCG1 -0.007 0.027 -9999 0 -0.4 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.01 -9999 0 -0.28 1 1
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.024 0.066 -9999 0 -0.64 6 6
GAB1/SHC/GRB2/SOS1 -0.007 0.022 -9999 0 -0.42 1 1
EPO/EPOR (dimer) -0.029 0.065 -9999 0 -10000 0 0
IRS2 0.009 0.11 -9999 0 -0.48 42 42
STAT1 0.048 0.057 -9999 0 -0.51 1 1
STAT5B -0.004 0.044 -9999 0 -0.44 4 4
cell proliferation 0.02 0.065 -9999 0 -0.48 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.01 0.042 -9999 0 -0.42 5 5
TEC 0.027 0.057 -9999 0 -0.49 4 4
SOCS3 -0.005 0.061 -9999 0 -0.8 6 6
STAT1 (dimer) 0.048 0.056 -9999 0 -0.5 1 1
JAK2 0.011 0.026 -9999 0 -0.82 1 1
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
EPO/EPOR (dimer)/JAK2 0.054 0.041 -9999 0 -0.52 1 1
EPO/EPOR -0.029 0.065 -9999 0 -10000 0 0
LYN 0.012 0.002 -9999 0 -10000 0 0
TEC/VAV2 -0.007 0.042 -9999 0 -0.47 4 4
elevation of cytosolic calcium ion concentration 0.012 0.01 -9999 0 -0.28 1 1
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.018 0.049 -9999 0 -10000 0 0
mol:IP3 -0.007 0.026 -9999 0 -0.39 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.029 0.094 -9999 0 -0.49 22 22
SH2B3 0.012 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.051 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.031 -9999 0 -0.32 7 7
PTPN6 0.02 0.052 -9999 0 -0.52 1 1
TEC/VAV2/GRB2 -0.011 0.035 -9999 0 -0.45 4 4
EPOR 0.012 0.01 -9999 0 -0.28 1 1
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.008 0.023 -9999 0 -0.43 1 1
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.002 0.036 -9999 0 -0.63 3 3
CRKL/CBL/C3G -0.009 0.025 -9999 0 -0.45 1 1
VAV2 0.028 0.05 -9999 0 -0.49 1 1
CBL 0.028 0.05 -9999 0 -0.49 1 1
SHC/Grb2/SOS1 0.005 0.028 -9999 0 -0.45 1 1
STAT5A -0.006 0.057 -9999 0 -0.48 9 9
GRB2 0 0.009 -9999 0 -0.29 1 1
STAT5 (dimer) 0.057 0.087 -9999 0 -0.57 5 5
LYN/PLCgamma2 -0.001 0.027 -9999 0 -0.61 2 2
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.028 0.051 -9999 0 -0.49 1 1
BCL2 0.035 0.2 -9999 0 -0.98 36 36
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.025 0.3 2 -0.4 1 3
DAPP1 0.036 0.054 -10000 0 -0.59 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.046 0.08 -10000 0 -0.57 10 10
mol:DAG 0.052 0.051 0.21 1 -0.27 7 8
HRAS -0.002 0.026 -10000 0 -0.28 9 9
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.003 0.026 -10000 0 -0.26 4 4
PLCG2 -0.002 0.036 -10000 0 -0.63 3 3
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.009 -10000 0 -0.29 1 1
mol:GTP -0.001 0.023 0.27 2 -0.4 2 4
ARF1/GTP -0.001 0.023 0.28 2 -0.38 2 4
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.025 -10000 0 -0.8 1 1
RAP1A/GTP -0.001 0.022 0.25 2 -0.39 2 4
ADAP1 -0.003 0.033 -10000 0 -0.42 3 3
ARAP3 -0.001 0.023 0.26 2 -0.4 2 4
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.057 -10000 0 -0.3 35 35
ARHGEF6 -0.012 0.096 -10000 0 -0.8 15 15
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
FYN -0.002 0.035 -10000 0 -0.8 2 2
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.001 0.026 -10000 0 -0.8 1 1
mol:Ca2+ 0.039 0.029 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
ZAP70 -0.03 0.12 -10000 0 -0.8 20 20
mol:IP3 0.047 0.039 -10000 0 -0.21 2 2
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.026 -10000 0 -0.3 2 2
RhoA/GDP -0.002 0.023 0.28 2 -10000 0 2
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.061 0.035 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
PLEKHA2 0.03 0.008 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.78 2 2
HSP90AA1 0 0.009 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.022 0.3 2 -10000 0 2
RhoA/GTP -0.001 0.021 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.011 0.058 -10000 0 -0.54 6 6
BLK -0.041 0.11 -10000 0 -0.3 142 142
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.001 0.021 -10000 0 -10000 0 0
HCK -0.004 0.032 -10000 0 -10000 0 0
CYTH3 -0.002 0.025 -10000 0 -0.42 1 1
CYTH2 -0.001 0.021 -10000 0 -0.37 2 2
KRAS -0.001 0.013 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.054 -10000 0 -0.56 9 9
SGK1 -0.004 0.056 0.23 2 -0.71 6 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.034 -10000 0 -0.28 4 4
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.009 -10000 0 -0.29 1 1
ARF6/GDP -0.002 0.023 0.29 2 -10000 0 2
mol:PI-3-4-5-P3 -0.001 0.025 0.36 2 -0.39 2 4
ARAP3/RAP1A/GTP -0.001 0.023 -10000 0 -0.4 2 2
VAV1 -0.003 0.045 -10000 0 -0.6 5 5
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.002 0.02 -10000 0 -0.4 2 2
PLEKHA1 0.03 0.018 -10000 0 -0.53 1 1
Rac1/GDP -0.003 0.026 -10000 0 -0.3 2 2
LAT -0.005 0.048 -10000 0 -0.8 2 2
Rac1/GTP -0.006 0.047 -10000 0 -0.37 15 15
ITK -0.02 0.087 0.26 1 -0.44 38 39
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.059 0.066 0.24 1 -0.39 7 8
LCK -0.02 0.1 -10000 0 -0.43 49 49
BTK -0.001 0.022 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.047 -9999 0 -0.56 6 6
PDGFB-D/PDGFRB/SLAP -0.004 0.042 -9999 0 -0.61 4 4
PDGFB-D/PDGFRB/APS/CBL -0.009 0.044 -9999 0 -0.53 4 4
AKT1 -0.011 0.05 -9999 0 -0.52 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.036 0.054 -9999 0 -0.6 6 6
PIK3CA 0 0.009 -9999 0 -0.29 1 1
FGR -0.003 0.04 -9999 0 -0.54 5 5
mol:Ca2+ 0.033 0.049 -9999 0 -0.69 4 4
MYC 0.039 0.14 -9999 0 -0.8 27 27
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.03 -9999 0 -0.43 4 4
LRP1/PDGFRB/PDGFB -0.008 0.07 -9999 0 -0.6 13 13
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.05 -9999 0 -0.7 4 4
PTEN -0.002 0.035 -9999 0 -0.8 2 2
GRB2 0 0.009 -9999 0 -0.29 1 1
GRB7 -0.021 0.077 -9999 0 -0.3 72 72
PDGFB-D/PDGFRB/SHP2 -0.002 0.038 -9999 0 -0.61 4 4
PDGFB-D/PDGFRB/GRB10 -0.002 0.038 -9999 0 -0.61 4 4
cell cycle arrest -0.004 0.041 -9999 0 -0.61 4 4
HRAS -0.003 0.027 -9999 0 -0.29 9 9
HIF1A 0.052 0.059 -9999 0 -0.45 3 3
GAB1 0.035 0.057 -9999 0 -0.68 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.04 0.054 -9999 0 -0.62 4 4
PDGFB-D/PDGFRB -0.003 0.036 -9999 0 -0.54 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.038 -9999 0 -0.61 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.051 -9999 0 -0.58 6 6
positive regulation of MAPKKK cascade -0.002 0.038 -9999 0 -0.61 4 4
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
mol:IP3 0.033 0.051 -9999 0 -0.71 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.016 0.063 -9999 0 -0.61 5 5
SHB -0.001 0.026 -9999 0 -0.8 1 1
BLK -0.002 0.051 -9999 0 -0.59 7 7
PTPN2 0.001 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.038 -9999 0 -0.61 4 4
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.064 -9999 0 -0.62 5 5
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.038 -9999 0 -0.61 4 4
LCK -0.01 0.083 -9999 0 -0.64 16 16
PDGFRB 0.008 0.051 -9999 0 -0.81 4 4
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.002 0.035 -9999 0 -0.52 4 4
ABL1 0.034 0.051 -9999 0 -0.64 4 4
PDGFB-D/PDGFRB/CBL 0.034 0.062 -9999 0 -0.8 4 4
PTPN1 -0.002 0.03 -9999 0 -0.3 1 1
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.005 0.039 -9999 0 -0.29 19 19
cell proliferation 0.04 0.12 -9999 0 -0.69 27 27
SLA -0.003 0.027 -9999 0 -0.29 9 9
actin cytoskeleton reorganization -0.003 0.029 -9999 0 -0.41 2 2
SRC -0.002 0.034 -9999 0 -0.51 4 4
PI3K -0.013 0.056 -9999 0 -0.59 3 3
PDGFB-D/PDGFRB/GRB7/SHC -0.012 0.051 -9999 0 -0.53 5 5
SH2B2 -0.013 0.061 -9999 0 -0.29 48 48
PLCgamma1/SPHK1 0.004 0.054 -9999 0 -0.62 6 6
LYN -0.002 0.035 -9999 0 -0.52 4 4
LRP1 -0.009 0.082 -9999 0 -0.8 11 11
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.002 0.043 -9999 0 -0.8 3 3
STAT5A -0.006 0.07 -9999 0 -0.8 8 8
NCK1-2/p130 Cas -0.002 0.028 -9999 0 -0.42 4 4
SPHK1 -0.007 0.052 -9999 0 -0.34 21 21
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.033 0.051 -9999 0 -0.71 4 4
PLCG1 0.033 0.052 -9999 0 -0.73 4 4
NHERF/PDGFRB -0.015 0.052 -9999 0 -0.53 4 4
YES1 -0.003 0.039 -9999 0 -0.53 5 5
cell migration -0.015 0.052 -9999 0 -0.52 4 4
SHC/Grb2/SOS1 -0.003 0.028 -9999 0 -0.42 4 4
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
SLC9A3R1 -0.024 0.08 -9999 0 -0.29 87 87
NHERF1-2/PDGFRB/PTEN -0.013 0.049 -9999 0 -0.48 6 6
FYN -0.004 0.063 -9999 0 -0.9 4 4
DOK1 0.005 0.037 -9999 0 -0.48 4 4
HRAS/GTP -0.002 0.018 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.046 0.084 -9999 0 -0.44 27 27
PRKCD 0.03 0.036 -9999 0 -0.48 4 4
FER 0.024 0.064 -9999 0 -0.49 15 15
MAPKKK cascade -0.002 0.028 -9999 0 -0.42 4 4
RASA1 0.03 0.036 -9999 0 -0.48 4 4
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.031 -9999 0 -0.44 4 4
PDGFB-D/PDGFRB/SHB -0.003 0.043 -9999 0 -0.61 5 5
chemotaxis 0.034 0.049 -9999 0 -0.62 4 4
STAT1-3-5/STAT1-3-5 -0.008 0.057 -9999 0 -0.84 2 2
Bovine Papilomavirus E5/PDGFRB -0.002 0.039 -9999 0 -0.62 4 4
PTPRJ 0 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.029 0.037 -9999 0 -10000 0 0
PLK1 0.007 0.12 -9999 0 -0.63 7 7
CDKN1B 0.08 0.071 -9999 0 -0.54 3 3
FOXO3 0.04 0.11 -9999 0 -0.57 11 11
KAT2B 0.008 0.029 -9999 0 -0.84 1 1
FOXO1/SIRT1 0.007 0.038 -9999 0 -0.32 10 10
CAT 0.043 0.12 -9999 0 -1.1 5 5
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.015 0.011 -9999 0 -10000 0 0
FOXO1 0.032 0.04 -9999 0 -0.36 10 10
MAPK10 -0.04 0.18 -9999 0 -0.46 162 162
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.063 0.089 -9999 0 -0.42 1 1
response to oxidative stress 0.005 0.012 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.016 0.068 -9999 0 -0.52 8 8
XPO1 0 0 -9999 0 -10000 0 0
EP300 0.009 0.005 -9999 0 -10000 0 0
BCL2L11 0.028 0.019 -9999 0 -10000 0 0
FOXO1/SKP2 -0.003 0.032 -9999 0 -0.32 10 10
mol:GDP 0.005 0.012 -9999 0 -10000 0 0
RAN 0.012 0.001 -9999 0 -10000 0 0
GADD45A 0.068 0.064 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.069 0.026 -9999 0 -10000 0 0
MST1 -0.003 0.094 -9999 0 -0.64 19 19
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.002 0.039 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.033 0.044 -9999 0 -0.46 8 8
MAPK9 0.036 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ -0.001 0.016 -9999 0 -0.29 3 3
SIRT1 0.002 0.008 -9999 0 -10000 0 0
SOD2 0.091 0.076 -9999 0 -10000 0 0
RBL2 0.06 0.082 -9999 0 -0.55 2 2
RAL/GDP 0.011 0.016 -9999 0 -10000 0 0
CHUK 0.009 0.012 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.03 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.004 0.18 -9999 0 -1.5 13 13
SKP2 0 0 -9999 0 -10000 0 0
USP7 0.012 0.001 -9999 0 -10000 0 0
IKBKB 0.008 0.018 -9999 0 -0.27 2 2
CCNB1 0.033 0.12 -9999 0 -0.74 3 3
FOXO1-3a-4/beta catenin -0.009 0.042 -9999 0 -0.41 6 6
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.032 -9999 0 -0.32 10 10
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.004 0.063 -9999 0 -0.81 6 6
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.068 0.079 -9999 0 -10000 0 0
SFN -0.015 0.097 -9999 0 -0.5 31 31
CDK2 0.002 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.027 0.05 -9999 0 -10000 0 0
CREBBP 0.002 0.005 -9999 0 -10000 0 0
FBXO32 0.042 0.13 -9999 0 -1.2 6 6
BCL6 0.055 0.12 -9999 0 -1.2 6 6
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0 0.008 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.007 0.059 -9999 0 -0.53 13 13
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.025 -9999 0 -10000 0 0
NFKBIA 0.024 0.035 -9999 0 -0.27 13 13
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0.006 -9999 0 -10000 0 0
ARRB2 0.017 0 -9999 0 -10000 0 0
REL -0.01 0.089 -9999 0 -0.8 13 13
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.009 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
NF kappa B1 p50 dimer 0 0.008 -9999 0 -10000 0 0
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
NFKB1 0.022 0.009 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.03 0.035 -9999 0 -0.27 13 13
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.024 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PI3K -0.006 0.06 -9999 0 -0.61 10 10
NF kappa B1 p50/RelA -0.004 0.03 -9999 0 -0.27 13 13
IKBKB -0.001 0.013 -9999 0 -0.29 2 2
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.009 -9999 0 -0.29 1 1
I kappa B alpha/PIK3R1 -0.008 0.051 -9999 0 -0.45 10 10
cell death -0.003 0.023 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.007 0.059 -9999 0 -0.53 13 13
LCK -0.02 0.1 -9999 0 -0.43 49 49
BCL3 -0.001 0.013 -9999 0 -0.29 2 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.004 0.019 -9999 0 -10000 0 0
CLOCK 0.005 0.087 -9999 0 -0.8 12 12
TIMELESS/CRY2 -0.002 0.011 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.011 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.041 0.017 -9999 0 -10000 0 0
ARNTL 0.014 0.002 -9999 0 -10000 0 0
TIMELESS 0.04 0.02 -9999 0 -10000 0 0
NPAS2 0.008 0.064 -9999 0 -0.63 9 9
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.014 0.003 -9999 0 -10000 0 0
CHEK1 -0.007 0.045 -9999 0 -0.29 26 26
mol:HEME 0.014 0.003 -9999 0 -10000 0 0
PER1 -0.015 0.11 -9999 0 -0.8 20 20
BMAL/CLOCK/NPAS2 -0.009 0.068 -9999 0 -0.52 18 18
BMAL1/CLOCK 0.041 0.055 -9999 0 -0.4 11 11
S phase of mitotic cell cycle -0.004 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.004 0.019 -9999 0 -10000 0 0
mol:NADPH 0.014 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.01 0.064 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.001 0.018 -9999 0 -0.29 4 4
Signaling events mediated by HDAC Class I

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.005 0.058 -9999 0 -0.49 14 14
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.047 -9999 0 -0.41 14 14
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.024 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.024 -9999 0 -10000 0 0
YY1/LSF -0.001 0.018 -9999 0 -0.4 2 2
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.006 0.042 -9999 0 -0.36 14 14
I kappa B alpha/HDAC1 -0.004 0.028 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.005 0.037 -9999 0 -0.32 14 14
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.028 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.033 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.026 0.13 -9999 0 -0.63 42 42
GATA1 -0.005 0.037 -9999 0 -0.29 17 17
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.008 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 -0.001 0.025 -9999 0 -0.8 1 1
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.005 0.033 -9999 0 -10000 0 0
KAT2B -0.001 0.025 -9999 0 -0.8 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.008 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -0.29 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.025 -9999 0 -0.8 1 1
YY1/HDAC3 -0.004 0.026 -9999 0 -10000 0 0
YY1/HDAC2 0 0.009 -9999 0 -0.3 1 1
YY1/HDAC1 0 0.009 -9999 0 -0.3 1 1
NuRD/MBD2 Complex (MeCP1) 0 0.006 -9999 0 -10000 0 0
PPARG -0.094 0.17 -9999 0 -0.38 252 252
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.028 -9999 0 -10000 0 0
MBD3L2 -0.001 0.013 -9999 0 -0.29 2 2
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.005 0.033 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0 0.011 -9999 0 -0.35 1 1
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 0 0 -9999 0 -10000 0 0
MXD1 0 0.009 -9999 0 -0.29 1 1
STAT3 0.025 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.017 -9999 0 -0.47 1 1
YY1/SAP30/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.025 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.033 -9999 0 -10000 0 0
histone deacetylation 0.046 0.008 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.025 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.019 0.083 -9999 0 -0.48 28 28
GATA1/HDAC1 -0.003 0.023 -9999 0 -10000 0 0
GATA1/HDAC3 -0.006 0.032 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.013 0.076 -9999 0 -0.61 14 14
SIN3/HDAC complex/Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD Complex 0 0.007 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.023 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.018 -9999 0 -0.48 1 1
GATA1/Fog1 -0.004 0.028 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.018 0.1 -9999 0 -0.48 38 38
negative regulation of cell growth 0.046 0.009 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.05 -9999 0 -0.43 14 14
SIN3/HDAC complex/NCoR1 0 0.01 -9999 0 -0.26 1 1
TFCP2 -0.001 0.025 -9999 0 -0.8 1 1
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0.009 -9999 0 -0.29 1 1
MBD2 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.077 0.036 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.007 0.039 -9999 0 -0.49 2 2
NFKBIA 0.047 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.013 -9999 0 -0.29 2 2
RIPK2 -0.001 0.02 -9999 0 -0.29 5 5
IKBKG 0 0.008 -9999 0 -10000 0 0
IKK complex/A20 -0.003 0.047 -9999 0 -10000 0 0
NEMO/A20/RIP2 -0.001 0.02 -9999 0 -0.29 5 5
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.008 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.007 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.009 0.054 -9999 0 -0.31 31 31
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.013 0.076 -9999 0 -0.61 14 14
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.021 0.13 -9999 0 -0.77 29 29
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.018 0.1 -9999 0 -0.48 38 38
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex 0 0.008 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.061 -9999 0 -0.38 27 27
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.058 -9999 0 -0.8 2 2
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.029 0.044 -10000 0 -10000 0 0
regulation of axonogenesis 0.004 0.03 0.32 9 -10000 0 9
myoblast fusion 0.007 0.025 -10000 0 -10000 0 0
mol:GTP -0.005 0.015 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.029 -10000 0 -10000 0 0
ARF1/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GM1 0.006 0.014 -10000 0 -10000 0 0
mol:Choline 0.021 0.052 -10000 0 -0.52 9 9
lamellipodium assembly -0.004 0.031 -10000 0 -10000 0 0
MAPK3 0.021 0.024 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.029 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.007 0.025 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.024 -10000 0 -10000 0 0
ARF6 0.007 0.007 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
TIAM1 0.011 0.019 -10000 0 -0.29 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.024 -10000 0 -10000 0 0
actin filament bundle formation 0.006 0.021 -10000 0 -10000 0 0
KALRN -0.01 0.065 -10000 0 -0.48 18 18
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.021 -10000 0 -10000 0 0
NME1 -0.003 0.065 -10000 0 -0.29 51 51
Rac1/GDP -0.006 0.021 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.015 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.004 0.031 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.005 0.015 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GDP -0.005 0.029 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.011 0.058 -10000 0 -0.59 9 9
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.031 -10000 0 -10000 0 0
ruffle organization -0.004 0.03 -10000 0 -0.32 9 9
regulation of epithelial cell migration -0.005 0.015 -10000 0 -10000 0 0
PLD2 0.017 0.013 -10000 0 -10000 0 0
PIP5K1A -0.004 0.03 -10000 0 -0.32 9 9
mol:Phosphatidic acid 0.021 0.052 -10000 0 -0.52 9 9
Rac1/GTP -0.004 0.031 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.011 0.036 -9999 0 -0.42 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.007 0.028 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.023 -9999 0 -0.53 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.04 -9999 0 -0.34 2 2
CaM/Ca2+ 0.009 0.032 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.012 0.036 -9999 0 -0.41 1 1
AKT1 -0.01 0.043 -9999 0 -0.46 2 2
MAP2K1 0.04 0.044 -9999 0 -10000 0 0
MAP3K11 0.03 0.043 -9999 0 -10000 0 0
IFNGR1 0.001 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.024 0.097 -9999 0 -0.41 24 24
Rap1/GTP -0.004 0.016 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.012 0.037 -9999 0 -0.44 2 2
CEBPB 0.075 0.04 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.008 0.056 -9999 0 -1.2 1 1
STAT1 -0.011 0.036 -9999 0 -0.4 1 1
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.039 0.098 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
STAT1 (dimer)/PIAS1 -0.01 0.032 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.001 0.013 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.035 -9999 0 -0.42 2 2
MAPK3 0.054 0.041 -9999 0 -10000 0 0
STAT1 (dimer) -0.007 0.054 -9999 0 -0.49 2 2
MAPK1 0.054 0.041 -9999 0 -10000 0 0
JAK2 0 0.025 -9999 0 -0.8 1 1
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
JAK1 0 0.025 -9999 0 -0.8 1 1
CAMK2D -0.002 0.043 -9999 0 -0.8 3 3
DAPK1 0.069 0.033 -9999 0 -10000 0 0
SMAD7 0.05 0.038 -9999 0 -0.18 1 1
CBL/CRKL/C3G -0.007 0.022 -9999 0 -10000 0 0
PI3K 0.004 0.052 -9999 0 -0.5 2 2
IFNG -0.039 0.098 -9999 0 -10000 0 0
apoptosis 0.053 0.029 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.009 0.049 -9999 0 -0.29 31 31
CAMK2B -0.07 0.21 -9999 0 -0.6 121 121
FRAP1 0.038 0.055 -9999 0 -0.43 2 2
PRKCD -0.01 0.044 -9999 0 -0.46 2 2
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.006 0.04 -9999 0 -0.34 2 2
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.064 0.047 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.033 -9999 0 -10000 0 0
SOCS1 0 0.05 -9999 0 -1.5 1 1
mol:GDP -0.007 0.021 -9999 0 -10000 0 0
CASP1 0.049 0.046 -9999 0 -0.36 5 5
PTGES2 0 0.009 -9999 0 -0.29 1 1
IRF9 0.057 0.019 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.047 -9999 0 -0.43 6 6
RAP1/GDP -0.004 0.016 -9999 0 -10000 0 0
CBL -0.01 0.028 -9999 0 -10000 0 0
MAP3K1 0.03 0.045 -9999 0 -0.42 2 2
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.04 -9999 0 -0.34 2 2
PTPN11 -0.011 0.032 -9999 0 -0.42 2 2
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
ceramide signaling pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.045 0.047 -10000 0 -0.55 1 1
BAG4 -0.006 0.057 -10000 0 -0.8 4 4
BAD 0.032 0.018 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.08 -10000 0 -0.8 9 9
BAX 0.031 0.02 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.013 -10000 0 -0.1 2 2
IKBKB 0.051 0.046 -10000 0 -0.52 1 1
MAP2K2 0.044 0.025 -10000 0 -0.47 1 1
MAP2K1 0.044 0.025 -10000 0 -0.47 1 1
SMPD1 0.021 0.013 -10000 0 -0.11 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.05 0.05 -10000 0 -0.45 3 3
MAP2K4 0.038 0.026 -10000 0 -0.39 2 2
protein ubiquitination 0.053 0.046 -10000 0 -0.52 1 1
EnzymeConsortium:2.7.1.37 0.049 0.027 -10000 0 -0.5 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.039 0.025 -10000 0 -0.5 1 1
CRADD 0 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.018 -10000 0 -0.15 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.023 -10000 0 -0.41 1 1
TRADD 0 0 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.046 0.024 -10000 0 -0.46 1 1
MAPK1 0.046 0.024 -10000 0 -0.46 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.043 0.051 -10000 0 -0.47 3 3
KSR1 0.032 0.025 -10000 0 -0.53 1 1
MAPK8 0.041 0.048 -10000 0 -0.43 9 9
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.051 0.045 -10000 0 -0.52 1 1
TNF R/SODD -0.004 0.042 -10000 0 -0.61 4 4
TNF -0.018 0.1 -10000 0 -0.8 14 14
CYCS 0.037 0.027 0.15 31 -10000 0 31
IKBKG 0.051 0.045 -10000 0 -0.52 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.038 0.05 -10000 0 -0.59 1 1
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.027 0.15 31 -10000 0 31
TNF/TNF R/SODD -0.014 0.074 -10000 0 -0.54 18 18
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.027 0.013 -10000 0 -10000 0 0
NSMAF 0.045 0.047 -10000 0 -0.55 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.028 0.15 -10000 0 -0.8 36 36
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.51 9 9
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 -0.001 0.013 -9999 0 -0.29 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.12 0.15 -9999 0 -0.35 11 11
YWHAZ -0.001 0.016 -9999 0 -0.29 3 3
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.019 0.048 -9999 0 -0.62 6 6
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.003 0.028 -9999 0 -10000 0 0
PRKCI 0 0.009 -9999 0 -0.29 1 1
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0.032 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.025 -9999 0 -0.8 1 1
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.004 0.031 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 -0.13 0.16 -9999 0 -0.39 11 11
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.015 0.097 -9999 0 -0.5 31 31
LNPEP -0.006 0.07 -9999 0 -0.8 8 8
YWHAE 0 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.014 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.033 -9999 0 -0.48 2 2
lamellipodium assembly -0.004 0.046 -9999 0 -0.46 10 10
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.006 0.06 -9999 0 -0.61 10 10
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.022 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.079 -9999 0 -0.8 10 10
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.011 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.058 -9999 0 -0.8 2 2
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.007 0.049 -9999 0 -0.45 12 12
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.011 0.089 -9999 0 -0.63 18 18
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.012 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.001 0.012 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.004 0.051 -9999 0 -0.52 10 10
TCGA08_p53

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
CDKN2A -0.024 0.078 -9999 0 -9999 0 0
TP53 -0.008 0.02 -9999 0 -9999 0 0
Senescence -0.008 0.02 -9999 0 -9999 0 0
Apoptosis -0.008 0.02 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.017 0.04 -9999 0 -9999 0 0
MDM4 0 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.012 -9999 0 -0.37 1 1
MDM2/SUMO1 0 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.025 -9999 0 -0.8 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.029 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0.014 -9999 0 -0.44 1 1
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0 0.007 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.018 -9999 0 -0.29 4 4
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.009 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB -0.001 0.02 -9999 0 -0.29 5 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.003 -9999 0 -10000 0 0
CD4 0 0 -9999 0 -10000 0 0
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0.016 -9999 0 -0.2 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.007 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.009 -9999 0 -10000 0 0
AP2M1 0 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.009 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.002 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.004 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0 0.001 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0.016 -9999 0 -0.2 6 6
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.016 -9999 0 -0.2 6 6
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.01 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.002 0.018 -9999 0 -10000 0 0
RELB -0.003 0.028 -9999 0 -10000 0 0
NFKB2 0 0.009 -9999 0 -0.29 1 1
NF kappa B2 p52/RelB -0.002 0.015 -9999 0 -10000 0 0
regulation of B cell activation -0.002 0.015 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1037 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.V7.A7HQ TCGA.S3.A6ZH TCGA.S3.A6ZG TCGA.S3.A6ZF
109_MAP3K5 -0.27 -0.27 0.054 0.054
47_PPARGC1A 0 -0.8 0 -0.8
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 -0.8 -0.8 -0.8 0
131_RELN/VLDLR -0.48 -0.48 -0.48 -0.48
30_TGFB1/TGF beta receptor Type II 0 0 0 0
84_STAT5B -0.43 -0.074 -0.074 -0.072
84_STAT5A -0.43 -0.074 -0.074 -0.072
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/8100368/BRCA-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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