PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1SB4541
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1SB4541
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 54 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
Class IB PI3K non-lipid kinase events 309
Signaling events mediated by Stem cell factor receptor (c-Kit) 289
Reelin signaling pathway 250
EGFR-dependent Endothelin signaling events 249
HIF-1-alpha transcription factor network 210
FOXA2 and FOXA3 transcription factor networks 172
p75(NTR)-mediated signaling 171
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 162
Glucocorticoid receptor regulatory network 160
Angiopoietin receptor Tie2-mediated signaling 157
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 1093 . 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 ( 1093 ).

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
Class IB PI3K non-lipid kinase events 0.2827 309 927 3 -0.22 -1000 1000 -1000 -0.02 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2644 289 22613 78 -0.61 0.19 1000 -1000 -0.074 -1000
Reelin signaling pathway 0.2287 250 14022 56 -0.47 0 1000 -1000 -0.086 -1000
EGFR-dependent Endothelin signaling events 0.2278 249 5231 21 -0.33 0 1000 -1000 -0.064 -1000
HIF-1-alpha transcription factor network 0.1921 210 16001 76 -0.75 0.019 1000 -1000 -0.072 -1000
FOXA2 and FOXA3 transcription factor networks 0.1574 172 7957 46 -1.2 0.023 1000 -1000 -0.031 -1000
p75(NTR)-mediated signaling 0.1565 171 21391 125 -0.37 0 1000 -1000 -0.087 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1482 162 11035 68 -0.5 0.15 1000 -1000 -0.096 -1000
Glucocorticoid receptor regulatory network 0.1464 160 18269 114 -0.92 0.34 1000 -1000 -0.07 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1436 157 13858 88 -0.38 0.04 1000 -1000 -0.11 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1418 155 8406 54 -0.47 0.022 1000 -1000 -0.08 -1000
IL4-mediated signaling events 0.1400 153 13975 91 -0.98 0.51 1000 -1000 -0.12 -1000
Arf6 signaling events 0.1299 142 8826 62 -0.33 0.017 1000 -1000 -0.063 -1000
Aurora B signaling 0.1299 142 9523 67 -0.31 0.009 1000 -1000 -0.06 -1000
Signaling mediated by p38-alpha and p38-beta 0.1272 139 6120 44 -0.4 0 1000 -1000 -0.056 -1000
Wnt signaling 0.1272 139 978 7 -0.17 -0.007 1000 -1000 -0.046 -1000
FOXM1 transcription factor network 0.1263 138 7063 51 -0.44 0.014 1000 -1000 -0.14 -1000
Endothelins 0.1253 137 13174 96 -0.37 0.038 1000 -1000 -0.065 -1000
IGF1 pathway 0.1153 126 7191 57 -0.18 0.08 1000 -1000 -0.083 -1000
ErbB2/ErbB3 signaling events 0.1125 123 8048 65 -0.38 0.018 1000 -1000 -0.061 -1000
Ephrin B reverse signaling 0.1107 121 5852 48 -0.3 0.17 1000 -1000 -0.067 -1000
EPHB forward signaling 0.1080 118 10032 85 -0.3 0.16 1000 -1000 -0.09 -1000
BMP receptor signaling 0.1025 112 9129 81 -0.54 0.026 1000 -1000 -0.076 -1000
ErbB4 signaling events 0.0997 109 7586 69 -0.41 0.056 1000 -1000 -0.074 -1000
Calcium signaling in the CD4+ TCR pathway 0.0988 108 3375 31 -0.32 0.012 1000 -1000 -0.082 -1000
Signaling events regulated by Ret tyrosine kinase 0.0979 107 8811 82 -0.17 0 1000 -1000 -0.079 -1000
Nongenotropic Androgen signaling 0.0952 104 5417 52 -0.23 0.11 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0933 102 8740 85 -0.24 0.011 1000 -1000 -0.067 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0933 102 12321 120 -0.58 0.24 1000 -1000 -0.071 -1000
Noncanonical Wnt signaling pathway 0.0924 101 2635 26 -0.17 0 1000 -1000 -0.075 -1000
Plasma membrane estrogen receptor signaling 0.0915 100 8667 86 -0.19 0.094 1000 -1000 -0.068 -1000
Glypican 1 network 0.0897 98 4710 48 -0.32 0.032 1000 -1000 -0.045 -1000
IL23-mediated signaling events 0.0860 94 5640 60 -0.46 0.018 1000 -1000 -0.13 -1000
Aurora C signaling 0.0842 92 644 7 -0.17 0 1000 -1000 -0.038 -1000
IL6-mediated signaling events 0.0842 92 6929 75 -0.28 0.05 1000 -1000 -0.083 -1000
Signaling events mediated by PTP1B 0.0833 91 6939 76 -0.64 0.071 1000 -1000 -0.072 -1000
Visual signal transduction: Rods 0.0796 87 4569 52 -0.48 0 1000 -1000 -0.075 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0732 80 2735 34 -0.096 0 1000 -1000 -0.059 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0732 80 4161 52 -0.19 0.029 1000 -1000 -0.057 -1000
Integrins in angiogenesis 0.0732 80 6739 84 -0.33 0 1000 -1000 -0.095 -1000
amb2 Integrin signaling 0.0723 79 6529 82 -0.48 0 1000 -1000 -0.068 -1000
Ephrin A reverse signaling 0.0677 74 521 7 -0.074 0 1000 -1000 -0.035 -1000
S1P1 pathway 0.0668 73 2649 36 -0.33 0.008 1000 -1000 -0.058 -1000
Syndecan-3-mediated signaling events 0.0668 73 2564 35 -0.34 0 1000 -1000 -0.061 -1000
Signaling events mediated by the Hedgehog family 0.0631 69 3591 52 -0.22 0.032 1000 -1000 -0.07 -1000
PDGFR-alpha signaling pathway 0.0631 69 3037 44 -0.36 0.019 1000 -1000 -0.06 -1000
LPA receptor mediated events 0.0622 68 6973 102 -0.29 0.028 1000 -1000 -0.088 -1000
Syndecan-1-mediated signaling events 0.0613 67 2311 34 -0.22 0 1000 -1000 -0.068 -1000
Fc-epsilon receptor I signaling in mast cells 0.0604 66 6431 97 -0.24 0.028 1000 -1000 -0.078 -1000
E-cadherin signaling in keratinocytes 0.0604 66 2865 43 -0.29 0.04 1000 -1000 -0.066 -1000
TCGA08_rtk_signaling 0.0540 59 1538 26 -0.29 0.027 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 0.0531 58 1002 17 -0.12 -0.001 1000 -1000 -0.062 -1000
Nectin adhesion pathway 0.0512 56 3540 63 -0.087 0.001 1000 -1000 -0.067 -1000
Rapid glucocorticoid signaling 0.0503 55 1104 20 -0.19 0.027 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 0.0494 54 2057 38 -0.17 0.011 1000 -1000 -0.061 -1000
Glypican 2 network 0.0494 54 217 4 -0.038 -0.032 1000 -1000 -0.027 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0494 54 1812 33 -0.54 0 1000 -1000 -0.063 -1000
FAS signaling pathway (CD95) 0.0476 52 2474 47 -0.47 0.013 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class III 0.0467 51 2067 40 -0.56 0.022 1000 -1000 -0.042 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0467 51 3835 74 -0.29 0.072 1000 -1000 -0.093 -1000
LPA4-mediated signaling events 0.0448 49 589 12 -0.16 0.02 1000 -1000 -0.018 -1000
PLK1 signaling events 0.0448 49 4206 85 -0.22 0.029 1000 -1000 -0.05 -1000
IL27-mediated signaling events 0.0448 49 2505 51 -0.29 0.035 1000 -1000 -0.075 -1000
Presenilin action in Notch and Wnt signaling 0.0412 45 2760 61 -0.41 0.014 1000 -1000 -0.067 -1000
IL12-mediated signaling events 0.0393 43 3745 87 -0.35 0.047 1000 -1000 -0.099 -1000
TCR signaling in naïve CD8+ T cells 0.0384 42 3931 93 -0.16 0.077 1000 -1000 -0.071 -1000
Insulin Pathway 0.0384 42 3114 74 -0.2 0.033 1000 -1000 -0.081 -1000
Regulation of Androgen receptor activity 0.0384 42 3003 70 -0.25 0.021 1000 -1000 -0.064 -1000
Syndecan-4-mediated signaling events 0.0375 41 2798 67 -0.32 0.005 1000 -1000 -0.083 -1000
Coregulation of Androgen receptor activity 0.0366 40 3070 76 -0.17 0.034 1000 -1000 -0.053 -1000
Signaling events mediated by PRL 0.0348 38 1315 34 -0.17 0.021 1000 -1000 -0.064 -1000
Regulation of Telomerase 0.0329 36 3747 102 -0.33 0.026 1000 -1000 -0.08 -1000
BCR signaling pathway 0.0320 35 3536 99 -0.13 0.042 1000 -1000 -0.079 -1000
Regulation of p38-alpha and p38-beta 0.0311 34 1889 54 -0.35 0.029 1000 -1000 -0.065 -1000
TCGA08_retinoblastoma 0.0311 34 275 8 -0.052 0.01 1000 -1000 -0.02 -1000
IL2 signaling events mediated by STAT5 0.0302 33 735 22 -0.11 0.063 1000 -1000 -0.038 -1000
Thromboxane A2 receptor signaling 0.0293 32 3427 105 -0.29 0.066 1000 -1000 -0.063 -1000
Canonical Wnt signaling pathway 0.0293 32 1677 51 -0.41 0.14 1000 -1000 -0.058 -1000
Regulation of nuclear SMAD2/3 signaling 0.0284 31 4251 136 -0.3 0.052 1000 -1000 -0.071 -1000
Aurora A signaling 0.0256 28 1737 60 -0.21 0.006 1000 -1000 -0.054 -1000
Arf6 trafficking events 0.0256 28 2052 71 -0.44 0.032 1000 -1000 -0.064 -1000
Osteopontin-mediated events 0.0247 27 1039 38 -0.24 0.022 1000 -1000 -0.098 -1000
Syndecan-2-mediated signaling events 0.0247 27 1919 69 -0.2 0.033 1000 -1000 -0.054 -1000
Insulin-mediated glucose transport 0.0247 27 878 32 -0.13 0.032 1000 -1000 -0.053 -1000
TCGA08_p53 0.0247 27 191 7 -0.025 0.017 1000 -1000 -0.023 -1000
Effects of Botulinum toxin 0.0247 27 721 26 -0.099 0.001 1000 -1000 -0.059 -1000
S1P5 pathway 0.0229 25 431 17 -0.045 0.024 1000 -1000 -0.045 -1000
S1P4 pathway 0.0220 24 620 25 -0.045 0.008 1000 -1000 -0.047 -1000
BARD1 signaling events 0.0201 22 1264 57 -0.11 0.024 1000 -1000 -0.062 -1000
Hedgehog signaling events mediated by Gli proteins 0.0192 21 1384 65 -0.067 0.044 1000 -1000 -0.074 -1000
Caspase cascade in apoptosis 0.0174 19 1408 74 -0.046 0.045 1000 -1000 -0.047 -1000
Class I PI3K signaling events mediated by Akt 0.0174 19 1333 68 -0.25 0.053 1000 -1000 -0.063 -1000
Ceramide signaling pathway 0.0174 19 1500 76 -0.18 0.049 1000 -1000 -0.063 -1000
TRAIL signaling pathway 0.0174 19 947 48 -0.075 0.044 1000 -1000 -0.061 -1000
Retinoic acid receptors-mediated signaling 0.0174 19 1127 58 -0.1 0.037 1000 -1000 -0.065 -1000
Signaling mediated by p38-gamma and p38-delta 0.0165 18 273 15 -0.018 0.022 1000 -1000 -0.042 -1000
Cellular roles of Anthrax toxin 0.0156 17 694 39 -0.14 0.019 1000 -1000 -0.038 -1000
IL2 signaling events mediated by PI3K 0.0156 17 1018 58 -0.044 0.06 1000 -1000 -0.075 -1000
E-cadherin signaling events 0.0156 17 87 5 -0.02 0 1000 -1000 -0.048 -1000
JNK signaling in the CD4+ TCR pathway 0.0146 16 280 17 -0.019 0.043 1000 -1000 -0.057 -1000
S1P3 pathway 0.0146 16 708 42 -0.033 0.021 1000 -1000 -0.049 -1000
PLK2 and PLK4 events 0.0137 15 47 3 -0.012 0.013 1000 -1000 -0.025 -1000
IL1-mediated signaling events 0.0137 15 940 62 -0.037 0.031 1000 -1000 -0.089 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0110 12 355 28 -0.045 0.02 1000 -1000 -0.053 -1000
E-cadherin signaling in the nascent adherens junction 0.0110 12 966 76 -0.02 0.05 1000 -1000 -0.075 -1000
mTOR signaling pathway 0.0101 11 618 53 -0.021 0.025 1000 -1000 -0.06 -1000
p38 MAPK signaling pathway 0.0101 11 519 44 -0.066 0.025 1000 -1000 -0.06 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0091 10 393 37 -0.047 0.034 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class II 0.0082 9 713 75 -0.15 0 1000 -1000 -0.057 -1000
a4b1 and a4b7 Integrin signaling 0.0082 9 48 5 -0.009 -0.002 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0082 9 827 83 -0.038 0.053 1000 -1000 -0.071 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 9 1169 125 -0.17 0.082 1000 -1000 -0.095 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0073 8 371 45 -0.025 0.072 1000 -1000 -0.077 -1000
Class I PI3K signaling events 0.0073 8 598 73 -0.044 0.059 1000 -1000 -0.061 -1000
VEGFR1 specific signals 0.0073 8 492 56 -0.17 0.065 1000 -1000 -0.071 -1000
EPO signaling pathway 0.0064 7 396 55 -0.036 0.058 1000 -1000 -0.082 -1000
HIF-2-alpha transcription factor network 0.0064 7 342 43 -0.17 0.18 1000 -1000 -0.069 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0055 6 150 23 -0.029 0.041 1000 -1000 -0.055 -1000
FoxO family signaling 0.0055 6 385 64 -0.038 0.09 1000 -1000 -0.07 -1000
PDGFR-beta signaling pathway 0.0055 6 620 97 -0.026 0.05 1000 -1000 -0.084 -1000
ceramide signaling pathway 0.0046 5 248 49 -0.027 0.054 1000 -1000 -0.043 -1000
Atypical NF-kappaB pathway 0.0046 5 182 31 -0.02 0.03 1000 -1000 -0.075 -1000
IFN-gamma pathway 0.0037 4 327 68 -0.066 0.075 1000 -1000 -0.081 -1000
Signaling events mediated by HDAC Class I 0.0037 4 501 104 -0.095 0.046 1000 -1000 -0.065 -1000
Canonical NF-kappaB pathway 0.0027 3 127 39 -0.021 0.077 1000 -1000 -0.073 -1000
Circadian rhythm pathway 0.0027 3 87 22 -0.015 0.042 1000 -1000 -0.066 -1000
Arf6 downstream pathway 0.0027 3 142 43 -0.023 0.023 1000 -1000 -0.038 -1000
Paxillin-dependent events mediated by a4b1 0.0027 3 139 36 -0.011 0.022 1000 -1000 -0.072 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 -0.001 0.029 1000 -1000 -0.05 -1000
Arf1 pathway 0.0000 0 25 54 -0.001 0.025 1000 -1000 -0.041 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 -0.003 0 1000 -1000 -0.062 -1000
Total NA 8183 481286 7203 -30 -990 131000 -131000 -8.5 -131000
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.22 0.35 0.78 309 -10000 0 309
PI3K Class IB/PDE3B -0.22 0.35 -10000 0 -0.79 309 309
PDE3B -0.22 0.36 -10000 0 -0.79 309 309
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.16 0.22 -10000 0 -0.39 499 499
CRKL -0.17 0.23 -10000 0 -0.41 498 498
HRAS -0.16 0.17 -10000 0 -0.5 44 44
mol:PIP3 -0.17 0.21 -10000 0 -0.4 501 501
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.18 0.24 -10000 0 -0.44 500 500
FOXO3 -0.15 0.21 -10000 0 -0.37 498 498
AKT1 -0.16 0.22 -10000 0 -0.41 499 499
BAD -0.15 0.21 -10000 0 -0.37 498 498
megakaryocyte differentiation -0.18 0.23 -10000 0 -0.43 500 500
GSK3B -0.15 0.21 -10000 0 -0.37 498 498
RAF1 -0.092 0.17 -10000 0 -0.46 23 23
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 500 500
STAT1 -0.45 0.56 -10000 0 -1 510 510
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.42 31 31
cell proliferation -0.18 0.24 -10000 0 -0.44 501 501
PIK3CA 0 0.009 -10000 0 -0.29 1 1
TEC -0.002 0.041 -10000 0 -0.79 3 3
RPS6KB1 -0.18 0.24 -10000 0 -0.44 500 500
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.42 31 31
LYN/TEC/p62DOK -0.19 0.2 -10000 0 -0.4 500 500
MAPK3 -0.054 0.13 -10000 0 -0.32 21 21
STAP1 -0.2 0.24 -10000 0 -0.45 502 502
GRAP2 -0.014 0.1 -10000 0 -0.72 21 21
JAK2 -0.4 0.44 -10000 0 -0.87 504 504
STAT1 (dimer) -0.44 0.54 -10000 0 -1 510 510
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.19 0.2 -10000 0 -0.41 500 500
actin filament polymerization -0.18 0.24 -10000 0 -0.44 500 500
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.33 -10000 0 -0.62 500 500
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.36 496 496
PI3K -0.19 0.21 -10000 0 -0.41 504 504
PTEN -0.001 0.034 -10000 0 -0.79 2 2
SCF/KIT/EPO/EPOR -0.56 0.69 -10000 0 -1.3 498 498
MAPK8 -0.19 0.24 -10000 0 -0.45 501 501
STAT3 (dimer) -0.18 0.23 -10000 0 -0.43 500 500
positive regulation of transcription -0.041 0.11 -10000 0 -0.25 21 21
mol:GDP -0.17 0.18 -10000 0 -0.55 38 38
PIK3C2B -0.18 0.24 -10000 0 -0.44 500 500
CBL/CRKL -0.15 0.22 -10000 0 -0.38 498 498
FER -0.19 0.24 -10000 0 -0.44 505 505
SH2B3 -0.18 0.24 -10000 0 -0.44 500 500
PDPK1 -0.15 0.2 -10000 0 -0.36 500 500
SNAI2 -0.19 0.25 -10000 0 -0.45 502 502
positive regulation of cell proliferation -0.32 0.4 -10000 0 -0.75 510 510
KITLG 0.002 0.067 -10000 0 -0.69 8 8
cell motility -0.32 0.4 -10000 0 -0.75 510 510
PTPN6 0.015 0.021 -10000 0 -0.29 2 2
EPOR -0.096 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 503 503
SOCS1 -0.005 0.043 -10000 0 -0.32 18 18
cell migration 0.19 0.24 0.44 508 -10000 0 508
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.044 0.11 -10000 0 -0.3 177 177
VAV1 -0.003 0.043 -10000 0 -0.79 3 3
GRB10 -0.18 0.24 -10000 0 -0.44 500 500
PTPN11 0.013 0.013 -10000 0 -10000 0 0
SCF/KIT -0.22 0.23 -10000 0 -0.47 500 500
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.064 0.14 -10000 0 -0.35 21 21
CBL 0 0 -10000 0 -10000 0 0
KIT -0.61 0.73 -10000 0 -1.4 496 496
MAP2K2 -0.064 0.14 -10000 0 -0.35 21 21
SHC/Grb2/SOS1 -0.19 0.2 -10000 0 -0.4 498 498
STAT5A -0.27 0.35 -10000 0 -0.64 500 500
GRB2 0 0.009 -10000 0 -0.29 1 1
response to radiation -0.18 0.24 -10000 0 -0.44 502 502
SHC/GRAP2 -0.01 0.077 -10000 0 -0.6 18 18
PTPRO -0.18 0.24 -10000 0 -0.44 500 500
SH2B2 -0.19 0.24 -10000 0 -0.44 500 500
DOK1 -0.001 0.018 -10000 0 -10000 0 0
MATK -0.19 0.25 -10000 0 -0.45 508 508
CREBBP 0.02 0.018 -10000 0 -10000 0 0
BCL2 -0.13 0.3 -10000 0 -1.5 37 37
Reelin signaling pathway

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
CDK5R1/CDK5 -0.006 0.034 -9999 0 -10000 0 0
VLDLR -0.025 0.14 -9999 0 -0.79 35 35
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
ITGA3 -0.004 0.05 -9999 0 -0.57 7 7
RELN/VLDLR/Fyn -0.32 0.27 -9999 0 -0.54 660 660
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.046 -9999 0 -0.44 12 12
AKT1 -0.18 0.18 -9999 0 -0.32 667 667
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -0.29 65 65
RELN/LRP8/DAB1 -0.31 0.24 -9999 0 -0.5 656 656
LRPAP1/LRP8 -0.019 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.29 0.23 -9999 0 -0.47 652 652
DAB1/alpha3/beta1 Integrin -0.27 0.22 -9999 0 -0.58 145 145
long-term memory -0.35 0.29 -9999 0 -0.53 706 706
DAB1/LIS1 -0.28 0.23 -9999 0 -0.45 660 660
DAB1/CRLK/C3G -0.27 0.22 -9999 0 -0.43 660 660
PIK3CA 0 0.009 -9999 0 -0.29 1 1
DAB1/NCK2 -0.28 0.23 -9999 0 -0.46 660 660
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.091 0.25 -9999 0 -0.74 135 135
CDK5R1 -0.008 0.049 -9999 0 -0.29 31 31
RELN -0.47 0.39 -9999 0 -0.78 654 654
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
RELN/LRP8/Fyn -0.32 0.26 -9999 0 -0.54 651 651
GRIN2A/RELN/LRP8/DAB1/Fyn -0.33 0.29 -9999 0 -0.53 672 672
MAPK8 -0.006 0.071 -9999 0 -0.79 9 9
RELN/VLDLR/DAB1 -0.31 0.25 -9999 0 -0.5 660 660
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.3 0.25 -9999 0 -0.49 667 667
RELN/LRP8 -0.32 0.26 -9999 0 -0.53 651 651
GRIN2B/RELN/LRP8/DAB1/Fyn -0.31 0.25 -9999 0 -0.49 689 689
PI3K -0.008 0.068 -9999 0 -0.6 14 14
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.037 -9999 0 -0.6 4 4
RAP1A -0.25 0.2 -9999 0 -0.54 142 142
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.046 -9999 0 -0.48 8 8
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.053 0.2 -9999 0 -0.79 73 73
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.12 0.13 -9999 0 -0.27 129 129
neuron adhesion -0.23 0.19 -9999 0 -0.5 145 145
LRP8 -0.03 0.089 -9999 0 -0.29 113 113
GSK3B -0.17 0.18 -9999 0 -0.46 71 71
RELN/VLDLR/DAB1/Fyn -0.29 0.24 -9999 0 -0.47 660 660
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.18 -9999 0 -0.35 667 667
CDK5 -0.002 0.023 -9999 0 -0.29 7 7
MAPT -0.045 0.24 -9999 0 -0.69 127 127
neuron migration -0.22 0.23 -9999 0 -0.41 652 652
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.11 -9999 0 -0.28 129 129
RELN/VLDLR -0.31 0.25 -9999 0 -0.5 660 660
EGFR-dependent Endothelin signaling events

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
HRAS -0.003 0.028 -9999 0 -0.29 10 10
EGFR -0.29 0.38 -9999 0 -0.78 410 410
EGF/EGFR -0.28 0.3 -9999 0 -0.53 563 563
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.25 0.26 -9999 0 -0.49 552 552
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.002 0.035 -9999 0 -0.62 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.15 0.31 -9999 0 -0.78 214 214
EGF/EGFR dimer/SHC -0.29 0.3 -9999 0 -0.57 552 552
mol:GDP -0.24 0.26 -9999 0 -0.48 552 552
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.059 0.21 -9999 0 -0.79 82 82
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.23 0.24 -9999 0 -0.45 552 552
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.23 0.24 -9999 0 -0.45 552 552
FRAP1 -0.24 0.25 -9999 0 -0.46 552 552
EGF/EGFR dimer -0.33 0.35 -9999 0 -0.66 552 552
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
ETA receptor/Endothelin-1 -0.046 0.16 -9999 0 -0.6 84 84
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 -0.99 299 299
HDAC7 0 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.32 0.31 -9999 0 -0.77 240 240
SMAD4 -0.001 0.024 -9999 0 -0.78 1 1
ID2 -0.41 0.46 -9999 0 -1 265 265
AP1 -0.18 0.28 -9999 0 -0.61 330 330
ABCG2 -0.43 0.5 -9999 0 -1.1 311 311
HIF1A -0.051 0.064 -9999 0 -10000 0 0
TFF3 -0.48 0.52 -9999 0 -1.1 350 350
GATA2 -0.013 0.13 -9999 0 -0.76 30 30
AKT1 -0.052 0.08 -9999 0 -10000 0 0
response to hypoxia -0.074 0.086 -9999 0 -0.25 33 33
MCL1 -0.41 0.46 -9999 0 -0.99 297 297
NDRG1 -0.41 0.46 -9999 0 -1 298 298
SERPINE1 -0.41 0.46 -9999 0 -1 298 298
FECH -0.41 0.46 -9999 0 -0.99 298 298
FURIN -0.41 0.46 -9999 0 -1 297 297
NCOA2 -0.03 0.17 -9999 0 -0.79 54 54
EP300 -0.051 0.12 -9999 0 -0.35 56 56
HMOX1 -0.41 0.46 -9999 0 -1 299 299
BHLHE40 -0.41 0.46 -9999 0 -1 296 296
BHLHE41 -0.41 0.47 -9999 0 -1 298 298
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.049 0.055 -9999 0 -0.6 1 1
ENG -0.025 0.078 -9999 0 -0.54 1 1
JUN 0.003 0.064 -9999 0 -0.79 7 7
RORA -0.41 0.46 -9999 0 -1 279 279
ABCB1 -0.34 0.55 -9999 0 -1.4 215 215
TFRC -0.41 0.46 -9999 0 -0.99 301 301
CXCR4 -0.41 0.46 -9999 0 -1 299 299
TF -0.64 0.57 -9999 0 -1.1 585 585
CITED2 -0.41 0.46 -9999 0 -0.99 297 297
HIF1A/ARNT -0.48 0.53 -9999 0 -1.2 304 304
LDHA -0.048 0.047 -9999 0 -10000 0 0
ETS1 -0.41 0.46 -9999 0 -1 297 297
PGK1 -0.41 0.46 -9999 0 -0.99 301 301
NOS2 -0.41 0.46 -9999 0 -1 298 298
ITGB2 -0.41 0.46 -9999 0 -1 282 282
ALDOA -0.41 0.46 -9999 0 -1 299 299
Cbp/p300/CITED2 -0.42 0.44 -9999 0 -1.1 261 261
FOS -0.23 0.37 -9999 0 -0.79 329 329
HK2 -0.41 0.46 -9999 0 -1 271 271
SP1 0.012 0.023 -9999 0 -10000 0 0
GCK -0.13 0.36 -9999 0 -1.6 56 56
HK1 -0.41 0.46 -9999 0 -0.99 299 299
NPM1 -0.41 0.46 -9999 0 -0.99 297 297
EGLN1 -0.41 0.46 -9999 0 -0.99 298 298
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.41 0.46 -9999 0 -0.99 298 298
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.19 0.4 -9999 0 -1.2 120 120
IGFBP1 -0.5 0.52 -9999 0 -1.1 369 369
VEGFA -0.24 0.31 -9999 0 -0.74 128 128
HIF1A/JAB1 -0.028 0.026 -9999 0 -10000 0 0
CP -0.52 0.55 -9999 0 -1.1 404 404
CXCL12 -0.43 0.5 -9999 0 -1.1 310 310
COPS5 0.009 0.006 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.018 -9999 0 -0.6 1 1
BNIP3 -0.41 0.46 -9999 0 -1 297 297
EGLN3 -0.41 0.46 -9999 0 -1 300 300
CA9 -0.45 0.48 -9999 0 -1 321 321
TERT -0.42 0.47 -9999 0 -1 304 304
ENO1 -0.41 0.46 -9999 0 -0.99 298 298
PFKL -0.41 0.46 -9999 0 -0.99 298 298
NCOA1 0 0.024 -9999 0 -0.79 1 1
ADM -0.44 0.49 -9999 0 -1 320 320
ARNT -0.051 0.064 -9999 0 -10000 0 0
HNF4A -0.002 0.046 -9999 0 -0.29 22 22
ADFP -0.41 0.46 -9999 0 -1 302 302
SLC2A1 -0.24 0.32 -9999 0 -0.72 165 165
LEP -0.75 0.52 -9999 0 -1.1 602 602
HIF1A/ARNT/Cbp/p300 -0.33 0.33 -9999 0 -0.8 245 245
EPO -0.23 0.28 -9999 0 -0.77 77 77
CREBBP -0.051 0.12 -9999 0 -0.35 56 56
HIF1A/ARNT/Cbp/p300/HDAC7 -0.31 0.31 -9999 0 -0.76 240 240
PFKFB3 -0.41 0.46 -9999 0 -1 299 299
NT5E -0.41 0.47 -9999 0 -1 297 297
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.28 -9999 0 -0.77 120 120
PCK1 -1 0.7 -9999 0 -1.6 660 660
HNF4A -0.25 0.28 -9999 0 -0.85 80 80
KCNJ11 -0.27 0.31 -9999 0 -0.83 154 154
AKT1 -0.14 0.14 -9999 0 -0.37 80 80
response to starvation -0.001 0.008 -9999 0 -10000 0 0
DLK1 -0.49 0.55 -9999 0 -1.2 363 363
NKX2-1 -0.054 0.15 -9999 0 -0.55 2 2
ACADM -0.24 0.28 -9999 0 -0.76 143 143
TAT -1.2 0.68 -9999 0 -1.6 777 777
CEBPB 0.006 0.007 -9999 0 -10000 0 0
CEBPA -0.002 0.076 -9999 0 -0.79 10 10
TTR -0.45 0.28 -9999 0 -0.72 442 442
PKLR -0.24 0.28 -9999 0 -0.79 112 112
APOA1 -0.3 0.3 -9999 0 -0.92 84 84
CPT1C -0.24 0.28 -9999 0 -0.77 128 128
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.7 405 405
FOXF1 -0.003 0.053 -9999 0 -0.52 9 9
NF1 0.017 0.024 -9999 0 -0.78 1 1
HNF1A (dimer) 0.003 0.027 -9999 0 -0.3 8 8
CPT1A -0.24 0.28 -9999 0 -0.76 127 127
HMGCS1 -0.24 0.28 -9999 0 -0.77 124 124
NR3C1 -0.11 0.13 -9999 0 -0.45 61 61
CPT1B -0.24 0.28 -9999 0 -0.76 134 134
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.007 -9999 0 -10000 0 0
GCK -0.28 0.35 -9999 0 -0.91 169 169
CREB1 -0.059 0.067 -9999 0 -10000 0 0
IGFBP1 -0.44 0.59 -9999 0 -1.5 244 244
PDX1 -0.13 0.15 -9999 0 -10000 0 0
UCP2 -0.24 0.28 -9999 0 -0.74 145 145
ALDOB -0.26 0.3 -9999 0 -0.79 158 158
AFP -0.68 0.6 -9999 0 -1.1 599 599
BDH1 -0.24 0.28 -9999 0 -0.78 118 118
HADH -0.26 0.3 -9999 0 -0.78 154 154
F2 -0.29 0.3 -9999 0 -0.9 93 93
HNF1A 0.003 0.027 -9999 0 -0.3 8 8
G6PC -0.2 0.12 -9999 0 -0.64 8 8
SLC2A2 -0.16 0.17 -9999 0 -10000 0 0
INS 0.023 0.066 -9999 0 -10000 0 0
FOXA1 -0.24 0.28 -9999 0 -0.55 335 335
FOXA3 -0.42 0.23 -9999 0 -0.54 768 768
FOXA2 -0.31 0.34 -9999 0 -0.82 212 212
ABCC8 -0.34 0.43 -9999 0 -1.1 216 216
ALB -0.93 0.64 -9999 0 -1.4 706 706
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.018 -9999 0 -0.6 1 1
Necdin/E2F1 -0.082 0.15 -9999 0 -0.68 43 43
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.14 0.21 -9999 0 -0.45 344 344
NGF (dimer)/p75(NTR)/BEX1 -0.25 0.31 -9999 0 -0.62 422 422
NT-4/5 (dimer)/p75(NTR) -0.37 0.41 -9999 0 -0.75 541 541
IKBKB -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.14 0.22 -9999 0 -0.45 348 348
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.064 0.21 -9999 0 -0.66 105 105
MGDIs/NGR/p75(NTR)/LINGO1 -0.2 0.24 -9999 0 -0.55 334 334
FURIN 0 0.009 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.2 0.28 -9999 0 -0.56 378 378
LINGO1 -0.07 0.12 -9999 0 -0.29 261 261
Sortilin/TRAF6/NRIF -0.001 0.024 -9999 0 -0.78 1 1
proBDNF (dimer) -0.064 0.21 -9999 0 -0.66 105 105
NTRK1 -0.011 0.07 -9999 0 -0.79 5 5
RTN4R -0.011 0.056 -9999 0 -0.29 41 41
neuron apoptosis -0.13 0.26 -9999 0 -0.48 334 334
IRAK1 -0.001 0.018 -9999 0 -0.29 4 4
SHC1 -0.15 0.26 -9999 0 -0.52 342 342
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.014 -9999 0 -0.44 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.15 0.23 -9999 0 -0.48 342 342
MAGEH1 -0.001 0.024 -9999 0 -0.79 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.17 0.26 -9999 0 -0.52 356 356
Mammalian IAPs/DIABLO -0.005 0.044 -9999 0 -0.47 9 9
proNGF (dimer) -0.014 0.097 -9999 0 -0.62 24 24
MAGED1 -0.001 0.018 -9999 0 -0.29 4 4
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.27 0.37 -9999 0 -0.79 371 371
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.14 0.21 -9999 0 -0.45 342 342
NGF -0.014 0.098 -9999 0 -0.62 24 24
cell cycle arrest -0.11 0.23 -9999 0 -0.43 342 342
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.1 0.16 -9999 0 -0.33 342 342
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.33 0.36 -9999 0 -0.66 541 541
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.17 0.25 -9999 0 -0.54 342 342
PSENEN -0.001 0.013 -9999 0 -0.29 2 2
mol:ceramide -0.13 0.24 -9999 0 -0.47 342 342
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.082 0.12 -9999 0 -0.26 342 342
p75(NTR)/beta APP -0.18 0.28 -9999 0 -0.6 334 334
BEX1 -0.15 0.27 -9999 0 -0.79 142 142
mol:GDP -0.16 0.26 -9999 0 -0.53 342 342
NGF (dimer) -0.081 0.18 -9999 0 -0.48 172 172
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.18 0.22 -9999 0 -0.5 334 334
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
RAC1/GTP -0.14 0.22 -9999 0 -0.46 342 342
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.17 0.26 -9999 0 -0.54 342 342
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.059 0.087 -9999 0 -10000 0 0
NT3 (dimer) -0.13 0.29 -9999 0 -0.75 185 185
TP53 -0.16 0.22 -9999 0 -0.45 378 378
PRDM4 -0.13 0.24 -9999 0 -0.48 342 342
BDNF (dimer) -0.17 0.23 -9999 0 -0.56 226 226
PIK3CA 0 0.009 -9999 0 -0.29 1 1
SORT1 -0.001 0.024 -9999 0 -0.79 1 1
activation of caspase activity -0.14 0.21 -9999 0 -0.44 344 344
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.15 0.23 -9999 0 -0.48 342 342
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.15 0.27 -9999 0 -0.49 349 349
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.13 0.24 -9999 0 -0.48 342 342
APH1B -0.001 0.024 -9999 0 -0.79 1 1
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.17 0.25 -9999 0 -0.53 342 342
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.27 0.35 -9999 0 -0.68 434 434
MAPK8 -0.1 0.24 -9999 0 -0.43 334 334
MAPK9 -0.1 0.23 -9999 0 -0.43 334 334
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.13 0.29 -9999 0 -0.75 185 185
NTF4 -0.27 0.37 -9999 0 -0.79 371 371
NDN -0.031 0.15 -9999 0 -0.79 43 43
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.14 0.2 -9999 0 -0.42 342 342
p75 CTF/Sortilin/TRAF6/NRIF 0 0.014 -9999 0 -0.47 1 1
RhoA-B-C/GTP -0.17 0.25 -9999 0 -0.54 342 342
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.17 0.24 -9999 0 -0.48 378 378
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.18 0.26 -9999 0 -0.51 378 378
PRKACB -0.016 0.077 -9999 0 -0.33 53 53
proBDNF (dimer)/p75 ECD -0.048 0.16 -9999 0 -0.6 79 79
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.077 -9999 0 -0.5 21 21
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.12 0.25 -9999 0 -0.46 342 342
BAD -0.11 0.24 -9999 0 -0.44 337 337
RIPK2 -0.001 0.02 -9999 0 -0.29 5 5
NGFR -0.24 0.36 -9999 0 -0.79 334 334
CYCS -0.14 0.21 -9999 0 -0.44 342 342
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.15 0.22 -9999 0 -0.48 342 342
BCL2L11 -0.11 0.24 -9999 0 -0.44 337 337
BDNF (dimer)/p75(NTR) -0.23 0.32 -9999 0 -0.65 378 378
PI3K -0.16 0.23 -9999 0 -0.49 348 348
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.15 0.23 -9999 0 -0.48 342 342
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0.009 -9999 0 -0.29 1 1
NGF (dimer)/p75(NTR) -0.19 0.29 -9999 0 -0.61 342 342
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.15 0.23 -9999 0 -0.48 342 342
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.024 -9999 0 -0.79 1 1
PLG -0.002 0.025 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.18 0.26 -9999 0 -0.51 386 386
SQSTM1 0 0.009 -9999 0 -0.29 1 1
NGFRAP1 -0.002 0.041 -9999 0 -0.79 3 3
CASP3 -0.1 0.22 -9999 0 -0.41 337 337
E2F1 -0.092 0.14 -9999 0 -0.29 345 345
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.064 0.11 -9999 0 -0.56 22 22
NGF (dimer)/TRKA -0.018 0.088 -9999 0 -0.6 21 21
MMP7 -0.12 0.28 -9999 0 -0.7 191 191
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.14 0.21 -9999 0 -0.45 342 342
MMP3 -0.12 0.16 -9999 0 -0.31 421 421
APAF-1/Caspase 9 -0.1 0.16 -9999 0 -0.56 23 23
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.078 0.16 -10000 0 -0.34 284 284
NFATC2 -0.055 0.27 -10000 0 -0.76 127 127
NFATC3 -0.048 0.12 -10000 0 -0.31 43 43
CD40LG -0.36 0.57 -10000 0 -1.1 337 337
ITCH 0.016 0.095 -10000 0 -10000 0 0
CBLB 0.016 0.095 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.36 -10000 0 -1.1 124 124
JUNB -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.034 0.1 -10000 0 -10000 0 0
T cell anergy -0.024 0.16 -10000 0 -0.5 79 79
TLE4 -0.031 0.26 -10000 0 -0.68 121 121
Jun/NFAT1-c-4/p21SNFT -0.28 0.43 -10000 0 -0.92 296 296
AP-1/NFAT1-c-4 -0.5 0.65 -10000 0 -1.4 340 340
IKZF1 -0.019 0.21 -10000 0 -0.64 82 82
T-helper 2 cell differentiation -0.11 0.3 -10000 0 -0.8 130 130
AP-1/NFAT1 -0.23 0.32 -10000 0 -0.64 375 375
CALM1 -0.018 0.053 -10000 0 -10000 0 0
EGR2 -0.27 0.63 -10000 0 -1.6 166 166
EGR3 -0.36 0.71 -10000 0 -1.5 285 285
NFAT1/FOXP3 -0.12 0.22 -10000 0 -0.56 150 150
EGR1 -0.24 0.37 -10000 0 -0.79 347 347
JUN -0.001 0.066 -10000 0 -0.8 7 7
EGR4 -0.015 0.078 -10000 0 -0.29 80 80
mol:Ca2+ -0.021 0.061 -10000 0 -10000 0 0
GBP3 -0.023 0.22 -10000 0 -0.67 91 91
FOSL1 -0.009 0.061 -10000 0 -0.34 30 30
NFAT1-c-4/MAF/IRF4 -0.3 0.46 -10000 0 -0.94 325 325
DGKA -0.018 0.21 -10000 0 -0.63 81 81
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.38 0.52 -10000 0 -1.1 343 343
CTLA4 -0.089 0.24 -10000 0 -0.6 115 115
NFAT1-c-4 (dimer)/EGR1 -0.42 0.56 -10000 0 -1.2 340 340
NFAT1-c-4 (dimer)/EGR4 -0.28 0.45 -10000 0 -0.9 330 330
FOS -0.24 0.37 -10000 0 -0.8 329 329
IFNG -0.15 0.27 -10000 0 -0.86 101 101
T cell activation -0.17 0.35 -10000 0 -0.78 203 203
MAF -0.001 0.024 -10000 0 -0.79 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.36 0.66 325 -10000 0 325
TNF -0.3 0.51 -10000 0 -1 328 328
FASLG -0.34 0.67 -10000 0 -1.3 329 329
TBX21 -0.022 0.15 -10000 0 -0.66 55 55
BATF3 -0.002 0.03 -10000 0 -0.79 1 1
PRKCQ -0.023 0.16 -10000 0 -0.73 51 51
PTPN1 -0.019 0.21 -10000 0 -0.61 91 91
NFAT1-c-4/ICER1 -0.28 0.44 -10000 0 -0.9 328 328
GATA3 -0.035 0.15 -10000 0 -0.57 70 70
T-helper 1 cell differentiation -0.15 0.26 -10000 0 -0.84 103 103
IL2RA -0.24 0.34 -10000 0 -0.89 156 156
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.21 -10000 0 -0.61 91 91
E2F1 -0.078 0.14 -10000 0 -0.28 345 345
PPARG -0.19 0.34 -10000 0 -0.79 268 268
SLC3A2 -0.018 0.21 -10000 0 -0.61 92 92
IRF4 -0.07 0.22 -10000 0 -0.73 106 106
PTGS2 -0.46 0.65 -10000 0 -1.2 403 403
CSF2 -0.35 0.55 -10000 0 -1.1 329 329
JunB/Fra1/NFAT1-c-4 -0.27 0.42 -10000 0 -0.88 311 311
IL4 -0.12 0.32 -10000 0 -0.86 126 126
IL5 -0.35 0.55 -10000 0 -1.1 329 329
IL2 -0.17 0.36 -10000 0 -0.8 201 201
IL3 -0.062 0.065 -10000 0 -10000 0 0
RNF128 -0.045 0.27 -10000 0 -0.85 109 109
NFATC1 -0.15 0.36 -10000 0 -0.67 325 325
CDK4 0.079 0.23 0.56 74 -10000 0 74
PTPRK -0.023 0.23 -10000 0 -0.66 92 92
IL8 -0.35 0.56 -10000 0 -1.1 332 332
POU2F1 0.001 0.01 -10000 0 -0.29 1 1
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 0.024 0.079 0.35 5 -10000 0 5
SMARCC2 0.012 0.01 -10000 0 -10000 0 0
SMARCC1 0.012 0.01 -10000 0 -10000 0 0
TBX21 -0.13 0.25 -10000 0 -0.83 80 80
SUMO2 0 0.01 -10000 0 -0.29 1 1
STAT1 (dimer) 0.014 0.04 -10000 0 -0.29 19 19
FKBP4 -0.002 0.026 -10000 0 -0.29 9 9
FKBP5 -0.015 0.1 -10000 0 -0.68 24 24
GR alpha/HSP90/FKBP51/HSP90 0.11 0.14 0.32 99 -0.41 22 121
PRL -0.086 0.12 -10000 0 -0.44 10 10
cortisol/GR alpha (dimer)/TIF2 0.26 0.3 0.53 487 -0.54 32 519
RELA -0.039 0.083 -10000 0 -10000 0 0
FGG 0.23 0.22 0.49 302 -0.52 2 304
GR beta/TIF2 0.1 0.2 0.32 163 -0.57 56 219
IFNG -0.42 0.35 -10000 0 -0.77 467 467
apoptosis -0.27 0.3 0.59 3 -0.68 263 266
CREB1 -0.009 0.031 -10000 0 -10000 0 0
histone acetylation 0.022 0.14 0.39 44 -0.36 42 86
BGLAP -0.1 0.15 -10000 0 -0.51 25 25
GR/PKAc 0.11 0.12 0.32 75 -0.46 4 79
NF kappa B1 p50/RelA -0.066 0.15 -10000 0 -0.43 32 32
SMARCD1 0.012 0.01 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.26 237 -10000 0 237
GATA3 -0.026 0.16 -10000 0 -0.57 70 70
AKT1 0 0.004 -10000 0 -10000 0 0
CSF2 -0.039 0.11 -10000 0 -0.59 8 8
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.56 3 -0.63 158 161
CSN2 0.19 0.18 0.41 236 -0.53 1 237
BRG1/BAF155/BAF170/BAF60A -0.003 0.032 -10000 0 -0.46 5 5
NFATC1 0.001 0.042 -10000 0 -0.79 3 3
POU2F1 0.007 0.013 -10000 0 -0.29 1 1
CDKN1A 0.046 0.072 -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 -0.016 0.099 -10000 0 -0.5 36 36
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.32 76 -0.41 20 96
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.43 0.54 3 -0.9 382 385
JUN -0.31 0.29 -10000 0 -0.59 475 475
IL4 -0.12 0.16 -10000 0 -0.49 52 52
CDK5R1 -0.008 0.05 -10000 0 -0.3 31 31
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.41 0.4 -10000 0 -0.74 585 585
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.32 82 -0.42 11 93
cortisol/GR alpha (monomer) 0.34 0.32 0.63 513 -0.51 3 516
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.28 0.38 -10000 0 -0.86 329 329
AP-1/NFAT1-c-4 -0.65 0.52 -10000 0 -1 662 662
AFP -0.6 0.7 -10000 0 -1.5 371 371
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.44 152 -10000 0 152
TP53 0.032 0.023 -10000 0 -0.5 2 2
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.82 0.8 -10000 0 -1.6 508 508
KRT14 -0.81 0.77 -10000 0 -1.5 567 567
TBP 0.019 0.007 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.29 353 -10000 0 353
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.001 0.004 -10000 0 -10000 0 0
AP-1 -0.66 0.52 -10000 0 -1 665 665
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.12 0.29 -10000 0 -0.79 171 171
MAPK11 -0.002 0.042 -10000 0 -0.8 3 3
KRT5 -0.92 0.81 -10000 0 -1.6 582 582
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.014 0.024 -10000 0 -0.78 1 1
STAT1 0.014 0.04 -10000 0 -0.29 19 19
CGA -0.16 0.18 -10000 0 -0.49 128 128
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.18 0.37 519 -10000 0 519
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 -0.56 240 240
NFKB1 -0.039 0.083 -10000 0 -10000 0 0
MAPK8 -0.23 0.22 -10000 0 -0.44 465 465
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.31 0.59 3 -0.72 263 266
BAX 0.048 0.032 -10000 0 -10000 0 0
POMC -0.19 0.32 -10000 0 -0.95 94 94
EP300 0.14 0.14 0.28 466 -10000 0 466
cortisol/GR alpha (dimer)/p53 0.31 0.26 0.55 508 -0.56 1 509
proteasomal ubiquitin-dependent protein catabolic process 0.085 0.079 0.24 60 -10000 0 60
SGK1 0.22 0.21 0.41 82 -1.2 7 89
IL13 -0.31 0.28 -10000 0 -0.76 151 151
IL6 -0.49 0.62 -10000 0 -1.3 417 417
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.27 0.23 -10000 0 -0.69 90 90
IL2 -0.41 0.35 -10000 0 -0.74 509 509
CDK5 -0.002 0.024 -10000 0 -0.3 7 7
PRKACB -0.016 0.077 -10000 0 -0.33 53 53
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
IL8 -0.2 0.3 -10000 0 -0.66 219 219
CDK5R1/CDK5 -0.007 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.055 0.1 -10000 0 -0.54 7 7
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.28 0.24 0.51 478 -0.49 2 480
SMARCA4 0.012 0.013 -10000 0 -0.29 1 1
chromatin remodeling 0.2 0.16 0.38 340 -0.66 1 341
NF kappa B1 p50/RelA/Cbp 0.06 0.17 0.34 69 -0.45 2 71
JUN (dimer) -0.31 0.29 -10000 0 -0.58 477 477
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.13 0.25 -10000 0 -0.77 93 93
NR3C1 0.2 0.2 0.43 333 -0.49 9 342
NR4A1 -0.063 0.24 -10000 0 -0.73 117 117
TIF2/SUV420H1 -0.03 0.13 -10000 0 -0.6 54 54
MAPKKK cascade -0.27 0.3 0.59 3 -0.68 263 266
cortisol/GR alpha (dimer)/Src-1 0.3 0.26 0.54 504 -0.57 1 505
PBX1 0.005 0.037 -10000 0 -0.78 2 2
POU1F1 0.003 0.015 -10000 0 -0.29 2 2
SELE -0.22 0.36 -10000 0 -0.84 186 186
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.38 335 -0.66 1 336
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.28 0.24 0.51 478 -0.49 2 480
mol:cortisol 0.19 0.2 0.36 528 -10000 0 528
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 -0.14 0.42 -10000 0 -0.91 248 248
NCK1/PAK1/Dok-R -0.096 0.18 -10000 0 -0.42 248 248
NCK1/Dok-R -0.26 0.48 -10000 0 -1.1 248 248
PIK3CA 0.003 0.011 -10000 0 -0.29 1 1
mol:beta2-estradiol 0.039 0.1 0.24 216 -10000 0 216
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.008 0.006 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.04 0.11 0.26 146 -0.32 11 157
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.24 0.44 -10000 0 -1 248 248
FN1 -0.12 0.14 -10000 0 -10000 0 0
PLD2 -0.21 0.54 -10000 0 -1.2 248 248
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.22 -10000 0 -0.48 231 231
ELK1 -0.17 0.48 -10000 0 -1 248 248
GRB7 -0.023 0.085 -10000 0 -0.31 79 79
PAK1 -0.007 0.044 -10000 0 -0.29 25 25
Tie2/Ang1/alpha5/beta1 Integrin -0.22 0.5 -10000 0 -1.1 248 248
CDKN1A -0.072 0.28 -10000 0 -0.64 147 147
ITGA5 0 0.009 -10000 0 -0.29 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.26 0.48 -10000 0 -1.1 248 248
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.077 0.32 -10000 0 -0.66 248 248
PLG -0.22 0.54 -10000 0 -1.2 248 248
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.19 0.38 -10000 0 -0.88 248 248
GRB2 0 0.009 -10000 0 -0.29 1 1
PIK3R1 -0.002 0.09 -10000 0 -0.79 14 14
ANGPT2 -0.12 0.28 -10000 0 -0.74 121 121
BMX -0.38 0.6 -10000 0 -1.4 248 248
ANGPT1 -0.25 0.58 -10000 0 -1.4 218 218
tube development -0.09 0.31 -10000 0 -0.67 206 206
ANGPT4 -0.24 0.36 -10000 0 -0.79 331 331
response to hypoxia -0.011 0.031 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.3 0.55 -10000 0 -1.3 248 248
alpha5/beta1 Integrin 0 0.006 -10000 0 -10000 0 0
FGF2 -0.32 0.39 -10000 0 -0.79 446 446
STAT5A (dimer) -0.11 0.36 -10000 0 -0.8 182 182
mol:L-citrulline -0.077 0.32 -10000 0 -0.66 248 248
AGTR1 -0.2 0.34 -10000 0 -0.7 328 328
MAPK14 -0.2 0.52 -10000 0 -1.1 248 248
Tie2/SHP2 -0.11 0.3 -10000 0 -1.3 58 58
TEK -0.11 0.34 -10000 0 -1.5 58 58
RPS6KB1 -0.13 0.41 -10000 0 -0.87 248 248
Angiotensin II/AT1 -0.15 0.26 -10000 0 -0.61 268 268
Tie2/Ang1/GRB2 -0.28 0.53 -10000 0 -1.2 248 248
MAPK3 -0.18 0.49 -10000 0 -1.1 248 248
MAPK1 -0.18 0.49 -10000 0 -1.1 248 248
Tie2/Ang1/GRB7 -0.27 0.53 -10000 0 -1.2 248 248
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.21 0.54 -10000 0 -1.2 248 248
PI3K -0.17 0.48 -10000 0 -1.1 248 248
FES -0.2 0.51 -10000 0 -1.1 248 248
Crk/Dok-R -0.26 0.48 -10000 0 -1.1 248 248
Tie2/Ang1/ABIN2 -0.28 0.53 -10000 0 -1.2 248 248
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.11 0.38 -10000 0 -0.8 248 248
STAT5A -0.004 0.067 -10000 0 -0.79 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.41 -10000 0 -0.87 248 248
Tie2/Ang2 -0.15 0.42 -10000 0 -0.95 197 197
Tie2/Ang1 -0.24 0.59 -10000 0 -1.3 248 248
FOXO1 -0.11 0.38 -10000 0 -0.81 248 248
ELF1 0.013 0.024 -10000 0 -10000 0 0
ELF2 -0.21 0.53 -10000 0 -1.2 248 248
mol:Choline -0.2 0.51 -10000 0 -1.1 248 248
cell migration -0.045 0.11 -10000 0 -0.24 248 248
FYN -0.11 0.35 -10000 0 -0.78 198 198
DOK2 -0.003 0.045 -10000 0 -0.5 7 7
negative regulation of cell cycle -0.061 0.26 -10000 0 -0.57 148 148
ETS1 -0.031 0.12 -10000 0 -0.96 6 6
PXN -0.09 0.34 -10000 0 -0.71 248 248
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.097 0.36 -10000 0 -0.75 248 248
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.042 0.14 -10000 0 -0.5 38 38
MAPKKK cascade -0.2 0.51 -10000 0 -1.1 248 248
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.23 0.55 -10000 0 -1.2 248 248
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.063 0.29 -10000 0 -0.58 248 248
mol:Phosphatidic acid -0.2 0.51 -10000 0 -1.1 248 248
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.077 0.32 -10000 0 -0.66 248 248
Rac1/GTP -0.18 0.34 -10000 0 -0.81 248 248
MMP2 -0.21 0.54 -10000 0 -1.2 248 248
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 -0.025 0.14 -9999 0 -0.79 35 35
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.32 0.26 -9999 0 -0.53 651 651
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 -0.28 0.25 -9999 0 -0.48 651 651
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -0.29 65 65
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.015 0.091 -9999 0 -0.43 39 39
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.019 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 0.049 -9999 0 -0.29 31 31
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.044 0.1 -9999 0 -0.29 164 164
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.33 0.27 -9999 0 -0.54 663 663
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.23 0.19 -9999 0 -0.45 184 184
MAP1B -0.008 0.054 -9999 0 -0.37 23 23
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.26 0.21 -9999 0 -0.42 651 651
RELN -0.47 0.39 -9999 0 -0.78 654 654
PAFAH/LIS1 -0.009 0.056 -9999 0 -0.52 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 -0.4 25 25
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.18 -9999 0 -0.33 663 663
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.25 0.2 -9999 0 -0.41 651 651
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 -0.035 0.095 -9999 0 -0.29 131 131
PAFAH1B2 -0.005 0.063 -9999 0 -0.79 7 7
MAP1B/LIS1/Dynein heavy chain -0.005 0.034 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.22 0.18 -9999 0 -0.43 185 185
LRP8 -0.03 0.089 -9999 0 -0.29 113 113
NDEL1/Katanin 60 -0.23 0.19 -9999 0 -0.45 185 185
P39/CDK5 -0.27 0.22 -9999 0 -0.44 652 652
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.26 0.24 -9999 0 -0.45 651 651
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 -0.28 0.24 -9999 0 -0.46 660 660
RELN/VLDLR -0.31 0.25 -9999 0 -0.5 660 660
CDC42 0 0 -9999 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.45 0.46 -10000 0 -1.1 247 247
STAT6 (cleaved dimer) -0.5 0.45 -10000 0 -0.96 429 429
IGHG1 -0.16 0.16 -10000 0 -0.35 166 166
IGHG3 -0.45 0.44 -10000 0 -0.93 400 400
AKT1 -0.2 0.24 -10000 0 -0.61 124 124
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.2 -10000 0 -0.58 63 63
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.59 154 154
THY1 -0.45 0.46 -10000 0 -1.1 264 264
MYB -0.017 0.11 -10000 0 -0.73 26 26
HMGA1 -0.014 0.063 -10000 0 -0.29 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.66 244 244
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.23 -10000 0 -0.56 131 131
SP1 0.018 0.006 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.024 0.028 -10000 0 -0.76 1 1
STAT6 (dimer)/ETS1 -0.48 0.44 -10000 0 -0.97 396 396
SOCS1 -0.29 0.31 -10000 0 -0.72 236 236
SOCS3 -0.22 0.26 -10000 0 -0.81 67 67
FCER2 -0.58 0.64 -10000 0 -1.4 355 355
PARP14 0.004 0.018 -10000 0 -0.3 3 3
CCL17 -0.46 0.46 -10000 0 -1.1 303 303
GRB2 0 0.009 -10000 0 -0.29 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.19 -10000 0 -0.56 36 36
T cell proliferation -0.45 0.48 -10000 0 -1.1 318 318
IL4R/JAK1 -0.45 0.46 -10000 0 -1.1 304 304
EGR2 -0.58 0.62 -10000 0 -1.4 339 339
JAK2 -0.008 0.035 -10000 0 -0.81 1 1
JAK3 0.01 0.035 -10000 0 -0.29 11 11
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
JAK1 0.004 0.026 -10000 0 -0.78 1 1
COL1A2 -0.14 0.16 -10000 0 -0.93 7 7
CCL26 -0.46 0.46 -10000 0 -1.1 270 270
IL4R -0.48 0.49 -10000 0 -1.1 310 310
PTPN6 0.022 0.018 -10000 0 -0.28 2 2
IL13RA2 -0.46 0.46 -10000 0 -1.1 244 244
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.5 114 114
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.28 -10000 0 -0.63 230 230
GTF3A 0.013 0.015 -10000 0 -0.29 2 2
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL13RA1/JAK2 -0.013 0.041 -10000 0 -0.61 1 1
IRF4/BCL6 -0.2 0.42 -10000 0 -1.4 118 118
CD40LG -0.031 0.18 -10000 0 -0.71 67 67
MAPK14 -0.25 0.28 -10000 0 -0.68 168 168
mitosis -0.2 0.23 -10000 0 -0.58 126 126
STAT6 -0.52 0.54 -10000 0 -1.1 396 396
SPI1 0.007 0.024 -10000 0 -0.29 6 6
RPS6KB1 -0.18 0.22 -10000 0 -0.58 95 95
STAT6 (dimer) -0.52 0.54 -10000 0 -1.1 396 396
STAT6 (dimer)/PARP14 -0.5 0.51 -10000 0 -1.1 407 407
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.23 -10000 0 -0.57 128 128
FRAP1 -0.2 0.24 -10000 0 -0.61 124 124
LTA -0.46 0.46 -10000 0 -1.1 248 248
FES -0.002 0.041 -10000 0 -0.79 3 3
T-helper 1 cell differentiation 0.51 0.52 1.1 396 -10000 0 396
CCL11 -0.48 0.44 -10000 0 -1.1 303 303
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.23 -10000 0 -0.6 101 101
IL2RG -0.004 0.088 -10000 0 -0.36 53 53
IL10 -0.46 0.46 -10000 0 -1.1 255 255
IRS1 -0.032 0.16 -10000 0 -0.79 45 45
IRS2 -0.033 0.16 -10000 0 -0.79 46 46
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.46 0.46 -10000 0 -1.1 252 252
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.36 -10000 0 -0.81 313 313
COL1A1 -0.18 0.17 -10000 0 -1.7 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.47 -10000 0 -1.1 250 250
IL2R gamma/JAK3 -0.011 0.071 -10000 0 -0.45 20 20
TFF3 -0.56 0.58 -10000 0 -1.3 335 335
ALOX15 -0.53 0.57 -10000 0 -1.3 318 318
MYBL1 -0.042 0.1 -10000 0 -0.29 155 155
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.83 353 353
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.009 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.23 -10000 0 -0.57 142 142
mol:PI-3-4-5-P3 -0.2 0.24 -10000 0 -0.61 124 124
PI3K -0.21 0.25 -10000 0 -0.65 120 120
DOK2 -0.003 0.045 -10000 0 -0.5 7 7
ETS1 0.018 0.058 -10000 0 -0.75 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.18 -10000 0 -0.56 26 26
ITGB3 -0.48 0.5 -10000 0 -1.1 300 300
PIGR -0.98 0.75 -10000 0 -1.5 688 688
IGHE 0.045 0.04 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.55 26 26
BCL6 0.001 0.059 -10000 0 -0.78 6 6
OPRM1 -0.46 0.46 -10000 0 -1.1 301 301
RETNLB -0.46 0.46 -10000 0 -1.1 250 250
SELP -0.62 0.68 -10000 0 -1.5 329 329
AICDA -0.44 0.44 -10000 0 -1 304 304
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 0.043 -9999 0 -0.64 4 4
ARNO/beta Arrestin1-2 -0.12 0.18 -9999 0 -0.42 254 254
EGFR -0.29 0.38 -9999 0 -0.78 410 410
EPHA2 -0.004 0.058 -9999 0 -0.79 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.33 0.35 -9999 0 -0.66 552 552
ARRB2 -0.051 0.15 -9999 0 -0.44 148 148
mol:GTP 0.017 0.018 -9999 0 -0.17 2 2
ARRB1 -0.002 0.035 -9999 0 -0.62 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.037 0.16 -9999 0 -0.74 54 54
EGF -0.15 0.31 -9999 0 -0.78 214 214
somatostatin receptor activity 0 0 -9999 0 -0.001 386 386
ARAP2 -0.004 0.058 -9999 0 -0.79 6 6
mol:GDP -0.14 0.18 -9999 0 -0.35 354 354
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 341 341
ITGA2B -0.018 0.078 -9999 0 -0.79 3 3
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -9999 0 -0.47 6 6
ADAP1 -0.005 0.05 -9999 0 -0.41 13 13
KIF13B -0.001 0.034 -9999 0 -0.79 2 2
HGF/MET -0.14 0.27 -9999 0 -0.64 240 240
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.31 383 383
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.29 0.3 -9999 0 -0.57 552 552
ADRB2 -0.18 0.33 -9999 0 -0.79 253 253
receptor agonist activity 0 0 -9999 0 0 393 393
actin filament binding 0 0 -9999 0 -0.001 373 373
SRC 0 0.009 -9999 0 -0.29 1 1
ITGB3 -0.028 0.14 -9999 0 -0.74 41 41
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 355 355
ARF6/GDP -0.014 0.083 -9999 0 -0.41 18 18
ARF6/GDP/GULP/ACAP1 -0.15 0.2 -9999 0 -0.51 191 191
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.025 0.094 -9999 0 -0.48 40 40
ACAP1 -0.02 0.095 -9999 0 -0.38 57 57
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.088 0.22 -9999 0 -0.65 148 148
EFNA1 0 0.009 -9999 0 -0.29 1 1
HGF -0.053 0.2 -9999 0 -0.79 73 73
CYTH3 0.01 0.027 -9999 0 -0.61 2 2
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 319 319
endosomal lumen acidification 0 0 -9999 0 -0.001 313 313
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.053 0.2 -9999 0 -0.79 73 73
GNAQ/ARNO 0.004 0.025 -9999 0 -0.45 3 3
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 407 407
MET -0.14 0.3 -9999 0 -0.78 189 189
GNA14 -0.013 0.084 -9999 0 -0.46 30 30
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GIT1 -0.001 0.02 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 382 382
GNA11 -0.003 0.048 -9999 0 -0.79 4 4
LHCGR -0.11 0.27 -9999 0 -0.79 148 148
AGTR1 -0.21 0.34 -9999 0 -0.7 328 328
desensitization of G-protein coupled receptor protein signaling pathway -0.088 0.22 -9999 0 -0.65 148 148
IPCEF1/ARNO -0.23 0.24 -9999 0 -0.46 552 552
alphaIIb/beta3 Integrin -0.033 0.12 -9999 0 -0.62 40 40
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.053 0.067 -9999 0 -10000 0 0
STMN1 -0.11 0.12 -9999 0 -0.37 80 80
Aurora B/RasGAP/Survivin -0.18 0.13 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.16 0.15 -9999 0 -0.33 435 435
BIRC5 -0.21 0.14 -9999 0 -0.3 780 780
DES -0.29 0.34 -9999 0 -0.65 499 499
Aurora C/Aurora B/INCENP -0.069 0.076 -9999 0 -0.62 1 1
Aurora B/TACC1 -0.1 0.13 -9999 0 -0.61 42 42
Aurora B/PP2A -0.098 0.097 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.008 0.017 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.18 -9999 0 -0.37 550 550
Cul3 protein complex -0.21 0.25 -9999 0 -0.52 435 435
KIF2C -0.045 0.034 -9999 0 -10000 0 0
PEBP1 0.002 0.005 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.3 820 820
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.098 0.097 -9999 0 -10000 0 0
SEPT1 -0.009 0.052 -9999 0 -0.29 35 35
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.004 0.034 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.005 0.019 -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 -0.034 0.046 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -0.29 625 625
AURKC -0.005 0.043 -9999 0 -0.32 18 18
CDCA8 -0.099 0.14 -9999 0 -0.3 373 373
cytokinesis -0.11 0.08 -9999 0 -10000 0 0
Aurora B/Septin1 -0.098 0.088 -9999 0 -10000 0 0
AURKA -0.14 0.15 -9999 0 -0.3 506 506
INCENP 0.003 0.005 -9999 0 -10000 0 0
KLHL13 -0.31 0.38 -9999 0 -0.79 434 434
BUB1 -0.2 0.14 -9999 0 -0.3 731 731
hSgo1/Aurora B/Survivin -0.26 0.18 -9999 0 -0.38 666 666
EVI5 0.009 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.1 0.1 -9999 0 -0.34 35 35
SGOL1 -0.18 0.14 -9999 0 -0.29 682 682
CENPA -0.059 0.064 -9999 0 -10000 0 0
NCAPG -0.14 0.15 -9999 0 -0.29 537 537
Aurora B/HC8 Proteasome -0.098 0.097 -9999 0 -10000 0 0
NCAPD2 -0.002 0.025 -9999 0 -0.29 8 8
Aurora B/PP1-gamma -0.098 0.097 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.11 0.14 -9999 0 -0.29 422 422
NPM1 -0.019 0.025 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.001 0.034 -9999 0 -0.79 2 2
mitotic prometaphase -0.006 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.098 0.096 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.12 0.11 -9999 0 -0.37 37 37
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.019 0.025 -9999 0 -10000 0 0
MYLK -0.088 0.15 -9999 0 -0.47 140 140
KIF23 -0.088 0.14 -9999 0 -0.3 334 334
VIM -0.094 0.1 -9999 0 -0.68 2 2
RACGAP1 -0.007 0.058 -9999 0 -0.3 41 41
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.019 0.025 -9999 0 -10000 0 0
Chromosomal passenger complex -0.084 0.079 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.16 0.18 -9999 0 -0.37 211 211
TACC1 -0.03 0.15 -9999 0 -0.79 42 42
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
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.4 0.62 -9999 0 -1.3 369 369
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.081 0.15 -9999 0 -0.42 9 9
ATF2/c-Jun -0.052 0.15 -9999 0 -0.78 14 14
MAPK11 -0.083 0.16 -9999 0 -0.5 16 16
MITF -0.092 0.2 -9999 0 -0.54 26 26
MAPKAPK5 -0.088 0.19 -9999 0 -0.49 19 19
KRT8 -0.095 0.2 -9999 0 -0.36 373 373
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.009 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.12 0.23 -9999 0 -0.44 372 372
CEBPB -0.088 0.19 -9999 0 -0.35 372 372
SLC9A1 -0.088 0.19 -9999 0 -0.49 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.56 18 18
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.56 16 16
JUN -0.051 0.15 -9999 0 -0.77 14 14
PPARGC1A -0.21 0.36 -9999 0 -0.78 241 241
USF1 -0.088 0.19 -9999 0 -0.49 19 19
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.39 15 15
NOS2 -0.092 0.21 -9999 0 -1.1 11 11
DDIT3 -0.088 0.19 -9999 0 -0.35 372 372
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.074 0.17 -9999 0 -0.43 54 54
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.57 15 15
CREB1 -0.093 0.2 -9999 0 -0.37 372 372
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.069 0.17 -9999 0 -0.53 12 12
RPS6KA4 -0.088 0.19 -9999 0 -0.49 19 19
PLA2G4A -0.13 0.27 -9999 0 -0.72 139 139
GDI1 -0.088 0.19 -9999 0 -0.35 372 372
TP53 -0.11 0.23 -9999 0 -0.44 372 372
RPS6KA5 -0.095 0.2 -9999 0 -0.36 381 381
ESR1 -0.17 0.25 -9999 0 -0.42 506 506
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.2 -9999 0 -0.55 20 20
MEF2A -0.089 0.19 -9999 0 -0.35 372 372
EIF4EBP1 -0.093 0.2 -9999 0 -0.37 372 372
KRT19 -0.1 0.21 -9999 0 -0.37 377 377
ELK4 -0.088 0.19 -9999 0 -0.49 19 19
ATF6 -0.088 0.19 -9999 0 -0.49 19 19
ATF1 -0.093 0.2 -9999 0 -0.37 372 372
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.56 16 16
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.56 16 16
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.16 0.25 -9999 0 -0.44 385 385
FZD6 -0.007 0.075 -9999 0 -0.79 10 10
WNT6 -0.16 0.31 -9999 0 -0.69 255 255
WNT4 -0.021 0.12 -9999 0 -0.55 43 43
FZD3 -0.011 0.092 -9999 0 -0.79 15 15
WNT5A -0.016 0.1 -9999 0 -0.61 28 28
WNT11 -0.17 0.32 -9999 0 -0.76 242 242
FOXM1 transcription factor network

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
NFATC3 -0.24 0.44 -9999 0 -0.93 175 175
PLK1 -0.087 0.11 -9999 0 -10000 0 0
BIRC5 -0.1 0.1 -9999 0 -10000 0 0
HSPA1B -0.24 0.44 -9999 0 -0.95 159 159
MAP2K1 0.008 0.03 -9999 0 -10000 0 0
BRCA2 -0.24 0.44 -9999 0 -0.94 181 181
FOXM1 -0.29 0.52 -9999 0 -1.1 217 217
XRCC1 -0.24 0.44 -9999 0 -0.98 142 142
FOXM1B/p19 -0.29 0.42 -9999 0 -0.92 242 242
Cyclin D1/CDK4 -0.22 0.41 -9999 0 -0.9 154 154
CDC2 -0.26 0.46 -9999 0 -0.94 217 217
TGFA -0.22 0.42 -9999 0 -0.92 158 158
SKP2 -0.24 0.44 -9999 0 -0.99 135 135
CCNE1 -0.056 0.13 -9999 0 -0.3 223 223
CKS1B -0.24 0.44 -9999 0 -0.98 142 142
RB1 -0.12 0.13 -9999 0 -0.9 1 1
FOXM1C/SP1 -0.3 0.45 -9999 0 -0.99 218 218
AURKB -0.079 0.11 -9999 0 -10000 0 0
CENPF -0.27 0.46 -9999 0 -0.96 199 199
CDK4 0.007 0.022 -9999 0 -0.3 4 4
MYC -0.21 0.41 -9999 0 -0.9 155 155
CHEK2 0.008 0.033 -9999 0 -0.32 2 2
ONECUT1 -0.24 0.43 -9999 0 -0.9 198 198
CDKN2A -0.038 0.11 -9999 0 -0.29 188 188
LAMA4 -0.24 0.44 -9999 0 -0.99 142 142
FOXM1B/HNF6 -0.27 0.49 -9999 0 -1.1 188 188
FOS -0.44 0.67 -9999 0 -1.3 348 348
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.24 0.44 -9999 0 -0.99 138 138
response to radiation -0.007 0.03 -9999 0 -10000 0 0
CENPB -0.24 0.44 -9999 0 -0.98 141 141
CENPA -0.27 0.46 -9999 0 -0.96 200 200
NEK2 -0.29 0.45 -9999 0 -0.97 200 200
HIST1H2BA -0.24 0.44 -9999 0 -0.99 139 139
CCNA2 -0.11 0.15 -9999 0 -0.3 427 427
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.28 0.49 -9999 0 -1.1 185 185
CCNB2 -0.27 0.46 -9999 0 -0.98 189 189
CCNB1 -0.26 0.46 -9999 0 -0.99 189 189
ETV5 -0.24 0.44 -9999 0 -0.98 141 141
ESR1 -0.34 0.58 -9999 0 -1.2 251 251
CCND1 -0.23 0.42 -9999 0 -0.92 154 154
GSK3A 0.014 0.021 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.081 0.14 -9999 0 -0.33 189 189
CDK2 0.006 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.01 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.33 0.38 -9999 0 -0.91 242 242
GAS1 -0.28 0.5 -9999 0 -1.1 167 167
MMP2 -0.24 0.44 -9999 0 -1 136 136
RB1/FOXM1C -0.24 0.44 -9999 0 -0.93 187 187
CREBBP 0 0 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.01 0.2 -9999 0 -0.6 89 89
PTK2B 0.006 0.006 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.2 -9999 0 -0.97 33 33
EDN1 -0.035 0.24 -9999 0 -0.81 85 85
EDN3 -0.37 0.39 -9999 0 -0.78 511 511
EDN2 -0.076 0.14 -9999 0 -0.31 269 269
HRAS/GDP -0.03 0.21 -9999 0 -0.54 103 103
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.003 0.14 -9999 0 -0.39 84 84
ADCY4 -0.14 0.29 -9999 0 -0.55 313 313
ADCY5 -0.27 0.36 -9999 0 -0.6 515 515
ADCY6 -0.13 0.27 -9999 0 -0.52 294 294
ADCY7 -0.13 0.27 -9999 0 -0.52 294 294
ADCY1 -0.15 0.29 -9999 0 -0.56 309 309
ADCY2 -0.17 0.32 -9999 0 -0.59 327 327
ADCY3 -0.13 0.27 -9999 0 -0.52 294 294
ADCY8 -0.14 0.27 -9999 0 -0.53 294 294
ADCY9 -0.13 0.27 -9999 0 -0.52 294 294
arachidonic acid secretion -0.11 0.3 -9999 0 -0.58 214 214
ETB receptor/Endothelin-1/Gq/GTP -0.034 0.18 -9999 0 -0.39 167 167
GNAO1 -0.03 0.13 -9999 0 -0.48 67 67
HRAS 0.003 0.029 -9999 0 -0.29 10 10
ETA receptor/Endothelin-1/G12/GTP 0.038 0.21 -9999 0 -0.56 89 89
ETA receptor/Endothelin-1/Gs/GTP -0.087 0.32 -9999 0 -0.56 294 294
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.019 0.21 -9999 0 -0.6 89 89
EDNRB -0.074 0.24 -9999 0 -0.79 114 114
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.025 0.25 -9999 0 -0.69 107 107
CYSLTR1 -0.021 0.24 -9999 0 -0.67 102 102
SLC9A1 0.002 0.1 -9999 0 -0.3 88 88
mol:GDP -0.038 0.22 -9999 0 -0.57 109 109
SLC9A3 -0.053 0.28 -9999 0 -0.63 184 184
RAF1 -0.085 0.25 -9999 0 -0.54 168 168
JUN 0.027 0.18 -9999 0 -0.85 30 30
JAK2 -0.01 0.2 -9999 0 -0.6 89 89
mol:IP3 -0.03 0.18 -9999 0 -0.47 96 96
ETA receptor/Endothelin-1 0.035 0.25 -9999 0 -0.69 89 89
PLCB1 -0.052 0.21 -9999 0 -0.79 82 82
PLCB2 0.007 0.026 -9999 0 -0.54 2 2
ETA receptor/Endothelin-3 -0.27 0.31 -9999 0 -0.6 510 510
FOS -0.25 0.5 -9999 0 -0.99 335 335
Gai/GDP -0.016 0.16 -9999 0 -0.66 40 40
CRK 0.006 0.006 -9999 0 -10000 0 0
mol:Ca ++ -0.051 0.25 -9999 0 -0.67 117 117
BCAR1 0.005 0.006 -9999 0 -10000 0 0
PRKCB1 -0.032 0.17 -9999 0 -0.44 106 106
GNAQ 0.008 0.043 -9999 0 -0.79 3 3
GNAZ -0.007 0.075 -9999 0 -0.79 10 10
GNAL -0.19 0.33 -9999 0 -0.79 258 258
Gs family/GDP -0.17 0.26 -9999 0 -0.54 307 307
ETA receptor/Endothelin-1/Gq/GTP 0.017 0.13 -9999 0 -0.39 68 68
MAPK14 -0.032 0.17 -9999 0 -0.57 63 63
TRPC6 0.018 0.22 -9999 0 -1.1 33 33
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.041 0.18 -9999 0 -0.42 146 146
ETB receptor/Endothelin-2 -0.11 0.21 -9999 0 -0.65 121 121
ETB receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.65 568 568
ETB receptor/Endothelin-1 -0.082 0.27 -9999 0 -0.66 183 183
MAPK3 -0.2 0.41 -9999 0 -0.79 339 339
MAPK1 -0.2 0.41 -9999 0 -0.79 339 339
Rac1/GDP -0.028 0.2 -9999 0 -0.53 104 104
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.59 310 310
MAPK8 0.019 0.2 -9999 0 -0.78 41 41
SRC 0 0.009 -9999 0 -0.29 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.05 0.18 -9999 0 -0.44 134 134
p130Cas/CRK/Src/PYK2 -0.015 0.22 -9999 0 -0.62 80 80
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.028 0.2 -9999 0 -0.53 104 104
COL1A2 -0.056 0.26 -9999 0 -0.7 105 105
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.03 0.12 -9999 0 -0.45 24 24
mol:DAG -0.03 0.18 -9999 0 -0.47 96 96
MAP2K2 -0.13 0.32 -9999 0 -0.57 344 344
MAP2K1 -0.13 0.32 -9999 0 -0.57 342 342
EDNRA 0.025 0.08 -9999 0 -0.56 6 6
positive regulation of muscle contraction -0.011 0.17 -9999 0 -0.52 89 89
Gq family/GDP -0.074 0.16 -9999 0 -0.59 66 66
HRAS/GTP -0.053 0.21 -9999 0 -0.47 151 151
PRKCH -0.024 0.17 -9999 0 -0.51 73 73
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.036 0.2 -9999 0 -0.58 87 87
PRKCB -0.035 0.2 -9999 0 -0.55 85 85
PRKCE -0.024 0.17 -9999 0 -0.52 68 68
PRKCD -0.025 0.17 -9999 0 -0.51 74 74
PRKCG -0.034 0.18 -9999 0 -0.48 93 93
regulation of vascular smooth muscle contraction -0.3 0.57 -9999 0 -1.1 335 335
PRKCQ -0.045 0.21 -9999 0 -0.58 103 103
PLA2G4A -0.12 0.33 -9999 0 -0.64 222 222
GNA14 -0.003 0.086 -9999 0 -0.46 30 30
GNA15 0.007 0.035 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.006 0.049 -9999 0 -0.79 4 4
Rac1/GTP 0.038 0.21 -9999 0 -0.56 89 89
MMP1 -0.12 0.13 -9999 0 -10000 0 0
IGF1 pathway

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
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.1 0.23 -10000 0 -0.48 271 271
GRB2/SOS1/SHC 0 0.004 -10000 0 -10000 0 0
HRAS -0.003 0.028 -10000 0 -0.29 10 10
IRS1/Crk -0.12 0.22 -10000 0 -0.48 271 271
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.23 -10000 0 -0.53 256 256
AKT1 -0.068 0.21 -10000 0 -0.42 258 258
BAD -0.055 0.2 -10000 0 -0.66 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.23 -10000 0 -0.48 271 271
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.23 -10000 0 -0.48 271 271
RAF1 -0.048 0.19 -10000 0 -0.62 49 49
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.21 -10000 0 -0.45 271 271
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.24 -10000 0 -0.52 271 271
PIK3CA 0 0.009 -10000 0 -0.29 1 1
RPS6KB1 -0.068 0.21 -10000 0 -0.71 54 54
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.041 0.16 -10000 0 -0.5 52 52
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.19 -10000 0 -0.7 47 47
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.098 0.19 -10000 0 -0.42 256 256
IGF-1R heterotetramer -0.033 0.13 -10000 0 -0.65 36 36
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.23 -10000 0 -0.48 271 271
Crk/p130 Cas/Paxillin -0.1 0.2 -10000 0 -0.44 256 256
IGF1R -0.033 0.13 -10000 0 -0.66 36 36
IGF1 -0.18 0.34 -10000 0 -0.81 247 247
IRS2/Crk -0.13 0.25 -10000 0 -0.5 285 285
PI3K -0.12 0.22 -10000 0 -0.48 258 258
apoptosis 0.08 0.15 0.54 53 -10000 0 53
HRAS/GDP -0.002 0.019 -10000 0 -10000 0 0
PRKCD -0.094 0.25 -10000 0 -0.53 256 256
RAF1/14-3-3 E -0.033 0.16 -10000 0 -0.52 49 49
BAD/14-3-3 -0.044 0.18 -10000 0 -0.59 53 53
PRKCZ -0.068 0.21 -10000 0 -0.42 259 259
Crk/p130 Cas/Paxillin/FAK1 -0.085 0.16 -10000 0 -0.61 49 49
PTPN1 -0.003 0.029 -10000 0 -0.29 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.13 0.24 -10000 0 -0.56 256 256
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.2 -10000 0 -0.46 256 256
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.22 -10000 0 -0.48 271 271
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.1 0.23 -10000 0 -0.48 271 271
IRS1 -0.12 0.25 -10000 0 -0.52 271 271
IRS2 -0.12 0.27 -10000 0 -0.53 285 285
IGF-1R heterotetramer/IGF1 -0.16 0.28 -10000 0 -0.66 256 256
GRB2 0 0.009 -10000 0 -0.29 1 1
PDPK1 -0.11 0.21 -10000 0 -0.45 258 258
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.56 269 269
SHC1 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.43 23 23
NFATC4 -0.087 0.16 -9999 0 -0.38 31 31
ERBB2IP 0.008 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.009 -9999 0 -0.29 1 1
mammary gland morphogenesis -0.15 0.18 -9999 0 -0.39 403 403
JUN -0.018 0.08 -9999 0 -0.37 6 6
HRAS -0.003 0.028 -9999 0 -0.29 10 10
DOCK7 -0.12 0.19 -9999 0 -0.36 403 403
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.22 -9999 0 -0.46 403 403
AKT1 0.008 0.005 -9999 0 -10000 0 0
BAD 0.018 0.006 -9999 0 -10000 0 0
MAPK10 -0.11 0.13 -9999 0 -0.35 174 174
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.2 -9999 0 -0.42 403 403
RAF1 -0.08 0.16 -9999 0 -0.44 17 17
ErbB2/ErbB3/neuregulin 2 -0.25 0.25 -9999 0 -0.5 528 528
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration -0.062 0.13 -9999 0 -0.31 94 94
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.22 -9999 0 -0.51 174 174
FOS -0.16 0.26 -9999 0 -0.53 331 331
NRAS -0.001 0.013 -9999 0 -0.3 2 2
mol:Ca2+ -0.15 0.18 -9999 0 -0.39 403 403
MAPK3 -0.11 0.19 -9999 0 -0.48 59 59
MAPK1 -0.11 0.19 -9999 0 -0.48 64 64
JAK2 -0.12 0.19 -9999 0 -0.36 404 404
NF2 -0.006 0.009 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.18 -9999 0 -0.36 403 403
NRG1 -0.29 0.38 -9999 0 -0.78 406 406
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.32 408 408
MAPK9 -0.069 0.087 -9999 0 -0.3 3 3
ERBB2 -0.017 0.059 -9999 0 -0.63 1 1
ERBB3 0 0.054 -9999 0 -0.79 5 5
SHC1 0.002 0.004 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.014 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0.001 0.003 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.008 0.004 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.098 0.12 -9999 0 -0.33 26 26
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.046 -9999 0 -0.54 1 1
CHRNA1 -0.092 0.16 -9999 0 -0.41 58 58
myelination -0.081 0.16 -9999 0 -0.36 31 31
PPP3CB -0.12 0.18 -9999 0 -0.34 403 403
KRAS -0.001 0.012 -9999 0 -0.29 2 2
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.39 28 28
NRG2 -0.38 0.39 -9999 0 -0.79 523 523
mol:GDP -0.12 0.18 -9999 0 -0.35 403 403
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.072 0.15 -9999 0 -0.5 9 9
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 -0.36 403 403
MAP2K1 -0.13 0.21 -9999 0 -0.48 172 172
heart morphogenesis -0.15 0.18 -9999 0 -0.39 403 403
RAS family/GDP -0.11 0.14 -9999 0 -0.47 15 15
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 -0.29 1 1
activation of caspase activity -0.008 0.005 -9999 0 -10000 0 0
nervous system development -0.15 0.18 -9999 0 -0.39 403 403
CDC42 0 0 -9999 0 -10000 0 0
Ephrin B reverse 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
EFNB2 -0.001 0.024 -10000 0 -0.79 1 1
EPHB2 -0.003 0.039 -10000 0 -0.3 5 5
EFNB1 0.017 0.05 -10000 0 -0.6 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.16 0.2 -10000 0 -0.41 424 424
Ephrin B2/EPHB1-2 -0.18 0.23 -10000 0 -0.47 424 424
neuron projection morphogenesis -0.15 0.19 -10000 0 -0.39 424 424
Ephrin B1/EPHB1-2/Tiam1 -0.17 0.22 -10000 0 -0.44 424 424
DNM1 -0.005 0.064 -10000 0 -0.73 8 8
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.003 0.13 -10000 0 -0.74 33 33
YES1 -0.025 0.17 -10000 0 -0.98 32 32
Ephrin B1/EPHB1-2/NCK2 -0.17 0.22 -10000 0 -0.44 424 424
PI3K -0.028 0.14 -10000 0 -0.68 45 45
mol:GDP -0.17 0.21 -10000 0 -0.44 424 424
ITGA2B -0.018 0.077 -10000 0 -0.79 3 3
endothelial cell proliferation -0.001 0.016 -10000 0 -0.52 1 1
FYN -0.025 0.16 -10000 0 -0.97 32 32
MAP3K7 -0.022 0.14 -10000 0 -0.79 32 32
FGR -0.027 0.16 -10000 0 -0.98 32 32
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.046 0.16 -10000 0 -0.62 72 72
LYN -0.025 0.16 -10000 0 -0.97 32 32
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.16 -10000 0 -0.92 32 32
Ephrin B1/EPHB1-2 -0.028 0.14 -10000 0 -0.86 32 32
SRC -0.027 0.16 -10000 0 -0.98 32 32
ITGB3 -0.028 0.14 -10000 0 -0.74 41 41
EPHB1 -0.3 0.38 -10000 0 -0.78 424 424
EPHB4 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.017 -10000 0 -0.52 1 1
alphaIIb/beta3 Integrin -0.033 0.12 -10000 0 -0.62 40 40
BLK -0.027 0.17 -10000 0 -0.98 32 32
HCK -0.027 0.16 -10000 0 -0.98 32 32
regulation of stress fiber formation 0.17 0.21 0.44 424 -10000 0 424
MAPK8 0.001 0.14 -10000 0 -0.7 38 38
Ephrin B1/EPHB1-2/RGS3 -0.17 0.22 -10000 0 -0.44 424 424
endothelial cell migration -0.016 0.12 -10000 0 -0.68 33 33
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.017 0.15 -10000 0 -0.9 32 32
regulation of focal adhesion formation 0.17 0.21 0.44 424 -10000 0 424
chemotaxis 0.17 0.21 0.44 424 -10000 0 424
PIK3CA 0 0.009 -10000 0 -0.29 1 1
Rac1/GTP -0.16 0.2 -10000 0 -0.4 424 424
angiogenesis -0.028 0.14 -10000 0 -0.85 32 32
LCK -0.029 0.17 -10000 0 -0.98 32 32
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.052 0.15 -10000 0 -0.52 103 103
cell-cell adhesion 0.16 0.21 0.67 79 -10000 0 79
Ephrin B/EPHB2/RasGAP -0.041 0.13 -10000 0 -0.44 96 96
ITSN1 -0.001 0.034 -10000 0 -0.79 2 2
PIK3CA 0 0.009 -10000 0 -0.29 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.2 0.26 -10000 0 -0.52 423 423
HRAS/GDP -0.17 0.22 -10000 0 -0.72 80 80
Ephrin B/EPHB1/GRB7 -0.22 0.28 -10000 0 -0.52 448 448
Endophilin/SYNJ1 -0.038 0.12 -10000 0 -0.41 96 96
KRAS -0.001 0.013 -10000 0 -0.29 2 2
Ephrin B/EPHB1/Src -0.21 0.27 -10000 0 -0.51 446 446
endothelial cell migration -0.006 0.054 -10000 0 -0.47 14 14
GRB2 0 0.009 -10000 0 -0.29 1 1
GRB7 -0.023 0.085 -10000 0 -0.31 79 79
PAK1 -0.047 0.14 -10000 0 -0.46 105 105
HRAS -0.003 0.028 -10000 0 -0.29 10 10
RRAS -0.039 0.12 -10000 0 -0.42 96 96
DNM1 -0.005 0.063 -10000 0 -0.73 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.2 0.26 -10000 0 -0.48 446 446
lamellipodium assembly -0.16 0.21 -10000 0 -0.67 79 79
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.15 0.19 -10000 0 -0.36 424 424
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
EPHB2 -0.005 0.038 -10000 0 -10000 0 0
EPHB3 -0.004 0.035 -10000 0 -0.29 16 16
EPHB1 -0.3 0.38 -10000 0 -0.79 424 424
EPHB4 0 0.009 -10000 0 -0.29 1 1
mol:GDP -0.15 0.21 -10000 0 -0.64 96 96
Ephrin B/EPHB2 -0.041 0.13 -10000 0 -0.45 96 96
Ephrin B/EPHB3 -0.041 0.13 -10000 0 -0.45 96 96
JNK cascade -0.17 0.21 -10000 0 -0.43 423 423
Ephrin B/EPHB1 -0.21 0.28 -10000 0 -0.52 446 446
RAP1/GDP -0.13 0.18 -10000 0 -0.6 75 75
EFNB2 -0.001 0.024 -10000 0 -0.79 1 1
EFNB3 -0.069 0.22 -10000 0 -0.79 96 96
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.19 0.23 -10000 0 -0.48 424 424
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.17 0.23 -10000 0 -0.75 79 79
Rap1/GTP -0.17 0.22 -10000 0 -0.69 78 78
axon guidance -0.052 0.15 -10000 0 -0.52 103 103
MAPK3 -0.095 0.19 -10000 0 -0.52 74 74
MAPK1 -0.095 0.19 -10000 0 -0.52 74 74
Rac1/GDP -0.14 0.19 -10000 0 -0.58 95 95
actin cytoskeleton reorganization -0.13 0.16 -10000 0 -0.53 75 75
CDC42/GDP -0.14 0.19 -10000 0 -0.58 95 95
PI3K -0.006 0.055 -10000 0 -0.48 14 14
EFNA5 -0.074 0.23 -10000 0 -0.79 103 103
Ephrin B2/EPHB4 -0.001 0.017 -10000 0 -0.52 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.03 0.099 -10000 0 -0.72 4 4
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.16 0.21 -10000 0 -0.66 83 83
PTK2 0.04 0.05 -10000 0 -10000 0 0
MAP4K4 -0.17 0.21 -10000 0 -0.43 423 423
SRC 0 0.009 -10000 0 -0.29 1 1
KALRN -0.014 0.11 -10000 0 -0.79 20 20
Intersectin/N-WASP -0.001 0.026 -10000 0 -0.6 2 2
neuron projection morphogenesis -0.13 0.17 -10000 0 -0.54 84 84
MAP2K1 -0.11 0.2 -10000 0 -0.55 74 74
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.18 0.23 -10000 0 -0.47 423 423
cell migration -0.12 0.22 -10000 0 -0.63 74 74
NRAS -0.001 0.013 -10000 0 -0.29 2 2
SYNJ1 -0.039 0.12 -10000 0 -0.42 96 96
PXN 0 0 -10000 0 -10000 0 0
TF -0.24 0.26 -10000 0 -0.45 624 624
HRAS/GTP -0.18 0.23 -10000 0 -0.73 82 82
Ephrin B1/EPHB1-2 -0.19 0.23 -10000 0 -0.48 423 423
cell adhesion mediated by integrin 0.01 0.13 0.42 96 -10000 0 96
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.19 0.25 -10000 0 -0.47 446 446
RAC1-CDC42/GTP -0.16 0.21 -10000 0 -0.68 80 80
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.13 0.18 -10000 0 -0.6 75 75
ruffle organization -0.17 0.22 -10000 0 -0.69 79 79
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.002 0.14 -10000 0 -0.42 98 98
Ephrin B/EPHB2/KALRN -0.049 0.15 -10000 0 -0.49 105 105
ROCK1 0.022 0.024 -10000 0 -0.48 1 1
RAS family/GDP -0.11 0.15 -10000 0 -0.52 75 75
Rac1/GTP -0.18 0.23 -10000 0 -0.73 79 79
Ephrin B/EPHB1/Src/Paxillin -0.15 0.2 -10000 0 -0.37 446 446
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.12 0.21 -9999 0 -0.6 141 141
SMAD6-7/SMURF1 0 0.016 -9999 0 -0.52 1 1
NOG -0.025 0.13 -9999 0 -0.58 47 47
SMAD9 -0.11 0.26 -9999 0 -0.77 123 123
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
SMAD5 -0.075 0.18 -9999 0 -0.47 141 141
BMP7/USAG1 -0.34 0.34 -9999 0 -0.66 559 559
SMAD5/SKI -0.087 0.16 -9999 0 -0.47 117 117
SMAD1 0.026 0.03 -9999 0 -10000 0 0
BMP2 -0.14 0.3 -9999 0 -0.78 194 194
SMAD1/SMAD1/SMAD4 -0.002 0.014 -9999 0 -10000 0 0
BMPR1A -0.002 0.041 -9999 0 -0.79 3 3
BMPR1B -0.14 0.18 -9999 0 -0.32 468 468
BMPR1A-1B/BAMBI -0.091 0.14 -9999 0 -0.59 59 59
AHSG -0.005 0.038 -9999 0 -0.29 19 19
CER1 -0.001 0.015 -9999 0 -0.29 3 3
BMP2-4/CER1 -0.13 0.24 -9999 0 -0.56 242 242
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.2 -9999 0 -0.51 152 152
BMP2-4 (homodimer) -0.14 0.27 -9999 0 -0.64 242 242
RGMB -0.001 0.024 -9999 0 -0.79 1 1
BMP6/BMPR2/BMPR1A-1B -0.097 0.16 -9999 0 -0.54 109 109
RGMA -0.11 0.27 -9999 0 -0.79 147 147
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.41 250 250
BMP2-4/USAG1 -0.37 0.36 -9999 0 -0.64 621 621
SMAD6/SMURF1/SMAD5 -0.087 0.16 -9999 0 -0.45 138 138
SOSTDC1 -0.38 0.39 -9999 0 -0.78 531 531
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.57 111 111
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.059 0.21 -9999 0 -0.77 84 84
HFE2 -0.003 0.029 -9999 0 -0.29 11 11
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.009 -9999 0 -0.29 1 1
BMP2-4/CHRD -0.14 0.26 -9999 0 -0.6 246 246
SMAD5/SMAD5/SMAD4 -0.087 0.16 -9999 0 -0.46 128 128
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.086 0.17 -9999 0 -0.52 107 107
BMP7 (homodimer) -0.075 0.22 -9999 0 -0.64 129 129
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.049 0.16 -9999 0 -0.61 82 82
SMAD1/SKI 0.004 0.018 -9999 0 -10000 0 0
SMAD6 -0.001 0.024 -9999 0 -0.79 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.13 0.24 -9999 0 -0.56 242 242
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.037 0.12 -9999 0 -0.36 113 113
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.009 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.091 0.12 -9999 0 -0.62 29 29
CHRDL1 -0.54 0.36 -9999 0 -0.79 750 750
ENDOFIN/SMAD1 0.004 0.018 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.013 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.033 0.14 -9999 0 -0.5 72 72
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.47 0.36 -9999 0 -0.66 768 768
BMP2-4/GREM1 -0.14 0.25 -9999 0 -0.57 248 248
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.1 0.24 -9999 0 -0.72 123 123
SMAD1/SMAD6 0.004 0.018 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.075 0.22 -9999 0 -0.64 129 129
BMP6 -0.06 0.21 -9999 0 -0.78 84 84
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.099 0.19 -9999 0 -0.45 176 176
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.004 0.018 -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 0.018 -9999 0 -0.29 4 4
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 -0.46 281 281
CHRD -0.032 0.13 -9999 0 -0.42 83 83
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.23 -9999 0 -0.43 320 320
BMP4 -0.051 0.19 -9999 0 -0.78 72 72
FST -0.04 0.17 -9999 0 -0.76 57 57
BMP2-4/NOG -0.14 0.26 -9999 0 -0.58 258 258
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.094 0.16 -9999 0 -0.53 111 111
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.027 0.062 -10000 0 -0.48 2 2
epithelial cell differentiation -0.021 0.065 -10000 0 -0.48 10 10
ITCH 0.01 0.021 -10000 0 -10000 0 0
WWP1 0.007 0.068 -10000 0 -10000 0 0
FYN -0.001 0.034 -10000 0 -0.79 2 2
EGFR -0.29 0.38 -10000 0 -0.78 410 410
PRL -0.003 0.032 -10000 0 -0.29 13 13
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.46 76 76
PTPRZ1 -0.41 0.39 -10000 0 -0.78 570 570
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.16 0.2 -10000 0 -0.41 401 401
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.19 0.23 -10000 0 -0.49 401 401
ADAM17 0.01 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.055 0.13 -10000 0 -0.53 56 56
NCOR1 -0.001 0.024 -10000 0 -0.79 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.18 0.22 -10000 0 -0.46 401 401
GRIN2B -0.17 0.25 -10000 0 -0.45 451 451
ErbB4/ErbB2/betacellulin -0.05 0.11 -10000 0 -0.47 62 62
STAT1 -0.005 0.038 -10000 0 -0.29 19 19
HBEGF -0.001 0.034 -10000 0 -0.79 2 2
PRLR -0.008 0.071 -10000 0 -0.54 16 16
E4ICDs/ETO2 -0.035 0.09 -10000 0 -0.55 19 19
axon guidance 0.042 0.12 -10000 0 -0.43 3 3
NEDD4 0.01 0.021 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.008 0.058 -10000 0 -0.6 8 8
CBFA2T3 -0.015 0.1 -10000 0 -0.68 24 24
ErbB4/ErbB2/HBEGF -0.026 0.054 -10000 0 -0.48 3 3
MAPK3 -0.15 0.18 -10000 0 -0.48 76 76
STAT1 (dimer) -0.028 0.063 -10000 0 -0.31 7 7
MAPK1 -0.15 0.18 -10000 0 -0.48 76 76
JAK2 -0.001 0.024 -10000 0 -0.79 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.22 -10000 0 -0.47 401 401
NRG1 -0.21 0.3 -10000 0 -0.61 401 401
NRG3 -0.048 0.18 -10000 0 -0.79 56 56
NRG2 -0.38 0.39 -10000 0 -0.79 523 523
NRG4 -0.005 0.038 -10000 0 -0.29 19 19
heart development 0.042 0.12 -10000 0 -0.43 3 3
neural crest cell migration -0.18 0.22 -10000 0 -0.46 401 401
ERBB2 0.009 0.062 -10000 0 -0.59 1 1
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 0.21 -10000 0 -0.45 405 405
apoptosis 0.056 0.14 0.54 57 -10000 0 57
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.26 0.24 -10000 0 -0.5 523 523
ErbB4/ErbB2/epiregulin -0.082 0.14 -10000 0 -0.45 126 126
ErbB4/ErbB4/betacellulin/betacellulin -0.053 0.12 -10000 0 -0.5 62 62
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.023 0.067 -10000 0 -0.52 11 11
MDM2 0.008 0.075 -10000 0 -0.31 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.18 0.22 -10000 0 -0.47 401 401
STAT5A 0.043 0.12 -10000 0 -0.44 9 9
ErbB4/EGFR/neuregulin 1 beta -0.34 0.35 -10000 0 -0.65 558 558
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.055 -10000 0 -0.45 1 1
STAT5A (dimer) -0.022 0.07 -10000 0 -0.53 9 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.024 0.11 -10000 0 -0.42 6 6
LRIG1 -0.002 0.041 -10000 0 -0.79 3 3
EREG -0.11 0.25 -10000 0 -0.6 203 203
BTC -0.045 0.18 -10000 0 -0.76 64 64
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.042 0.12 -10000 0 -0.43 3 3
ERBB4 -0.032 0.072 -10000 0 -10000 0 0
STAT5B -0.002 0.041 -10000 0 -0.79 3 3
YAP1 -0.01 0.043 -10000 0 -0.64 4 4
GRB2 0 0.009 -10000 0 -0.29 1 1
ErbB4/ErbB2/neuregulin 4 -0.027 0.055 -10000 0 -0.56 1 1
glial cell differentiation 0.024 0.055 0.45 1 -10000 0 1
WWOX -0.001 0.013 -10000 0 -0.29 2 2
cell proliferation -0.12 0.23 -10000 0 -0.46 217 217
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.038 -9999 0 -0.53 3 3
NFATC2 -0.041 0.16 -9999 0 -0.55 104 104
NFATC3 0.012 0.025 -9999 0 -10000 0 0
CD40LG -0.22 0.36 -9999 0 -0.71 311 311
PTGS2 -0.32 0.46 -9999 0 -0.85 427 427
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 0.064 -9999 0 -0.8 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 -0.009 0.061 -9999 0 -0.34 30 30
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.077 0.15 -9999 0 -0.53 78 78
FOS -0.24 0.37 -9999 0 -0.8 329 329
IFNG -0.22 0.35 -9999 0 -0.68 323 323
AP-1/NFAT1-c-4 -0.31 0.38 -9999 0 -0.81 326 326
FASLG -0.21 0.35 -9999 0 -0.68 313 313
NFAT1-c-4/ICER1 -0.06 0.14 -9999 0 -0.46 107 107
IL2RA -0.21 0.35 -9999 0 -0.68 308 308
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.2 0.34 -9999 0 -0.67 304 304
JunB/Fra1/NFAT1-c-4 -0.057 0.14 -9999 0 -0.46 98 98
IL4 -0.2 0.34 -9999 0 -0.67 302 302
IL2 -0.009 0.024 -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 0.03 -9999 0 -0.79 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -0.29 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.035 0.049 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.082 0.16 -9999 0 -0.46 98 98
JUN -0.051 0.14 -9999 0 -0.53 27 27
HRAS -0.003 0.028 -9999 0 -0.29 10 10
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.2 -9999 0 -0.52 210 210
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.29 11 11
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.2 -9999 0 -0.52 210 210
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 -0.48 201 201
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.46 210 210
GRB7 -0.023 0.085 -9999 0 -0.31 79 79
RET51/GFRalpha1/GDNF -0.15 0.2 -9999 0 -0.52 210 210
MAPKKK cascade -0.1 0.16 -9999 0 -0.53 50 50
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.23 -9999 0 -0.56 213 213
lamellipodium assembly -0.083 0.15 -9999 0 -0.36 210 210
RET51/GFRalpha1/GDNF/SHC -0.15 0.2 -9999 0 -0.52 210 210
PIK3CA 0 0.009 -9999 0 -0.29 1 1
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.48 201 201
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.48 201 201
MAPK3 -0.12 0.17 -9999 0 -0.44 207 207
DOK1 -0.001 0.018 -9999 0 -10000 0 0
DOK6 -0.013 0.094 -9999 0 -0.79 15 15
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.53 57 57
DOK5 -0.019 0.12 -9999 0 -0.7 30 30
GFRA1 -0.16 0.3 -9999 0 -0.68 257 257
MAPK8 -0.068 0.14 -9999 0 -0.43 57 57
HRAS/GTP -0.12 0.18 -9999 0 -0.48 207 207
tube development -0.094 0.17 -9999 0 -0.45 201 201
MAPK1 -0.12 0.17 -9999 0 -0.44 207 207
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.065 0.13 -9999 0 -0.33 201 201
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 -0.14 0.2 -9999 0 -0.5 216 216
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.2 -9999 0 -0.52 210 210
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.54 226 226
PRKCA -0.021 0.13 -9999 0 -0.79 29 29
HRAS/GDP -0.002 0.019 -9999 0 -10000 0 0
CREB1 -0.073 0.15 -9999 0 -0.38 201 201
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.065 0.13 -9999 0 -0.33 201 201
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.54 212 212
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.11 0.16 -9999 0 -0.31 401 401
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.049 0.14 -9999 0 -0.52 27 27
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.48 201 201
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 -0.065 0.13 -9999 0 -0.33 201 201
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.14 -9999 0 -0.35 207 207
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.082 0.14 -9999 0 -0.35 207 207
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.084 0.14 -9999 0 -0.36 207 207
PI3K -0.13 0.24 -9999 0 -0.59 212 212
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.094 0.17 -9999 0 -0.45 201 201
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.078 0.13 -9999 0 -0.33 201 201
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.2 -9999 0 -0.52 210 210
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.79 45 45
IRS2 -0.033 0.16 -9999 0 -0.79 46 46
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.084 0.14 -9999 0 -0.36 207 207
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.21 -9999 0 -0.53 237 237
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.015 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 -0.59 221 221
Rac1/GTP -0.1 0.18 -9999 0 -0.44 210 210
RET9/GFRalpha1/GDNF -0.11 0.21 -9999 0 -0.53 206 206
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.6 206 206
Nongenotropic Androgen signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.071 0.17 -10000 0 -0.48 159 159
regulation of S phase of mitotic cell cycle -0.044 0.12 -10000 0 -0.34 152 152
GNAO1 -0.03 0.13 -10000 0 -0.48 67 67
HRAS -0.003 0.028 -10000 0 -0.3 10 10
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 -0.045 0.16 -10000 0 -0.42 146 146
T-DHT/AR -0.082 0.21 -10000 0 -0.61 147 147
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 327 327
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
mol:GDP -0.084 0.21 -10000 0 -0.6 152 152
cell proliferation -0.11 0.24 -10000 0 -0.55 113 113
PIK3CA 0 0.009 -10000 0 -0.29 1 1
FOS -0.23 0.42 -10000 0 -0.86 329 329
mol:Ca2+ -0.017 0.028 -10000 0 -0.076 151 151
MAPK3 -0.076 0.2 -10000 0 -0.6 66 66
MAPK1 -0.047 0.12 -10000 0 -0.3 66 66
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
mol:IP3 -0.001 0.002 -10000 0 -0.005 329 329
cAMP biosynthetic process 0.013 0.025 -10000 0 -10000 0 0
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 329 329
HRAS/GTP -0.068 0.15 -10000 0 -0.45 146 146
actin cytoskeleton reorganization -0.005 0.047 -10000 0 -0.42 14 14
SRC 0 0.009 -10000 0 -0.29 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 329 329
PI3K -0.007 0.059 -10000 0 -0.52 14 14
apoptosis 0.11 0.23 0.43 329 -10000 0 329
T-DHT/AR/PELP1 -0.071 0.18 -10000 0 -0.53 146 146
HRAS/GDP -0.08 0.2 -10000 0 -0.58 148 148
CREB1 -0.12 0.24 -10000 0 -0.46 329 329
RAC1-CDC42/GTP -0.006 0.048 -10000 0 -0.43 14 14
AR -0.11 0.27 -10000 0 -0.79 147 147
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.045 0.16 -10000 0 -0.44 146 146
RAC1-CDC42/GDP -0.075 0.19 -10000 0 -0.55 146 146
T-DHT/AR/PELP1/Src -0.065 0.16 -10000 0 -0.48 146 146
MAP2K2 -0.045 0.16 -10000 0 -0.42 146 146
T-DHT/AR/PELP1/Src/PI3K -0.044 0.12 -10000 0 -0.35 152 152
GNAZ -0.007 0.075 -10000 0 -0.79 10 10
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.04 0.11 -10000 0 -0.48 40 40
mol:T-DHT -0.001 0.001 0.002 9 -0.003 263 272
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.006 0.056 -10000 0 -0.61 9 9
Gi family/GTP -0.051 0.1 -10000 0 -0.3 98 98
CDC42 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.1 0.23 -10000 0 -0.6 188 188
CRKL -0.04 0.16 -10000 0 -0.34 188 188
mol:PIP3 -0.018 0.035 0.77 2 -10000 0 2
AKT1 0.003 0.021 0.48 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.03 0.15 -10000 0 -0.53 22 22
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 -0.56 240 240
MAP3K5 -0.021 0.15 -10000 0 -0.53 25 25
HGF/MET/CIN85/CBL/ENDOPHILINS -0.11 0.22 -10000 0 -0.51 240 240
AP1 -0.19 0.26 -10000 0 -0.58 330 330
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.24 0.37 -10000 0 -0.78 330 330
STAT3 (dimer) -0.039 0.16 -10000 0 -0.33 240 240
GAB1/CRKL/SHP2/PI3K -0.066 0.13 -10000 0 -0.52 35 35
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.032 0.15 -10000 0 -0.54 21 21
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 -0.001 0.034 -10000 0 -0.79 2 2
ELK1 -0.044 0.1 -10000 0 -0.27 188 188
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.046 0.092 -10000 0 -0.22 188 188
PAK1 0.008 0.028 0.45 2 -10000 0 2
HGF/MET/RANBP10 -0.12 0.24 -10000 0 -0.56 240 240
HRAS -0.15 0.3 -10000 0 -0.76 191 191
DOCK1 -0.03 0.15 -10000 0 -0.54 21 21
GAB1 -0.05 0.16 -10000 0 -0.35 240 240
CRK -0.04 0.16 -10000 0 -0.34 188 188
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.3 -10000 0 -0.7 240 240
JUN -0.005 0.063 -10000 0 -0.79 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.078 0.15 -10000 0 -0.35 240 240
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
cell morphogenesis -0.019 0.18 -10000 0 -0.59 31 31
GRB2/SHC -0.066 0.13 -10000 0 -0.33 188 188
FOS -0.24 0.36 -10000 0 -0.79 329 329
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.044 0.1 -10000 0 -0.27 188 188
HGF/MET/MUC20 -0.12 0.24 -10000 0 -0.56 240 240
cell migration -0.065 0.13 -10000 0 -0.32 188 188
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 -0.6 188 188
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.077 0.15 -10000 0 -0.35 240 240
MET/MUC20 -0.1 0.23 -10000 0 -0.61 188 188
RAP1B -0.021 0.14 -10000 0 -0.5 21 21
RAP1A -0.021 0.14 -10000 0 -0.5 21 21
HGF/MET/RANBP9 -0.12 0.24 -10000 0 -0.56 240 240
RAF1 -0.1 0.29 -10000 0 -0.71 188 188
STAT3 -0.073 0.14 -10000 0 -0.33 240 240
cell proliferation -0.061 0.23 -10000 0 -0.48 240 240
RPS6KB1 -0.027 0.052 -10000 0 -0.18 21 21
MAPK3 -0.044 0.092 -10000 0 -0.24 185 185
MAPK1 -0.044 0.092 -10000 0 -0.24 188 188
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.14 -10000 0 -0.48 33 33
SRC -0.071 0.14 -10000 0 -0.61 21 21
PI3K -0.072 0.14 -10000 0 -0.35 197 197
MET/Glomulin -0.094 0.21 -10000 0 -0.55 188 188
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.086 0.27 -10000 0 -0.64 188 188
MET -0.14 0.3 -10000 0 -0.78 189 189
MAP4K1 -0.03 0.15 -10000 0 -0.5 27 27
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.086 0.27 -10000 0 -0.64 188 188
BAD 0.011 0.02 0.45 2 -10000 0 2
MAP2K4 -0.011 0.14 -10000 0 -0.47 26 26
SHP2/GRB2/SOS1/GAB1 -0.096 0.19 -10000 0 -0.5 188 188
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 -0.071 0.14 -10000 0 -0.32 240 240
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.053 0.2 -10000 0 -0.79 73 73
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 -0.067 0.13 -10000 0 -0.32 188 188
PDPK1 -0.006 0.025 0.56 2 -10000 0 2
HGF/MET/SHIP -0.12 0.24 -10000 0 -0.56 240 240
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.1 0.12 -10000 0 -0.33 85 85
NT3 (dimer)/TRKC -0.29 0.36 -10000 0 -0.68 465 465
NT3 (dimer)/TRKB -0.49 0.44 -10000 0 -0.77 696 696
SHC/Grb2/SOS1/GAB1/PI3K -0.004 0.036 -10000 0 -0.32 14 14
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.064 0.21 -10000 0 -0.66 105 105
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 -0.011 0.07 -10000 0 -0.79 5 5
NTRK2 -0.41 0.39 -10000 0 -0.79 573 573
NTRK3 -0.27 0.37 -10000 0 -0.78 377 377
NT-4/5 (dimer)/TRKB -0.58 0.48 -10000 0 -0.84 746 746
neuron apoptosis 0.24 0.24 0.58 298 -10000 0 298
SHC 2-3/Grb2 -0.26 0.27 -10000 0 -0.66 298 298
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.24 0.29 -10000 0 -0.66 292 292
SHC3 -0.24 0.28 -10000 0 -0.65 291 291
STAT3 (dimer) -0.005 0.03 -10000 0 -0.38 4 4
NT3 (dimer)/TRKA -0.24 0.31 -10000 0 -0.6 434 434
RIN/GDP -0.065 0.12 -10000 0 -0.26 103 103
GIPC1 0 0.009 -10000 0 -10000 0 0
KRAS -0.001 0.013 -10000 0 -0.29 2 2
DNAJA3 -0.14 0.2 -10000 0 -0.43 342 342
RIN/GTP -0.001 0.01 -10000 0 -10000 0 0
CCND1 0.018 0.075 -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) -0.27 0.37 -10000 0 -0.79 371 371
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 -0.028 0.11 -10000 0 -0.55 38 38
TRKA/NEDD4-2 -0.008 0.053 -10000 0 -0.6 6 6
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.014 0.098 -10000 0 -0.62 24 24
HRAS -0.003 0.028 -10000 0 -0.29 10 10
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.004 0.042 -10000 0 -0.39 10 10
RIT2 -0.001 0.015 -10000 0 -0.29 3 3
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.029 -10000 0 -0.29 11 11
DNM1 -0.005 0.063 -10000 0 -0.73 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 -0.13 0.2 -10000 0 -0.42 334 334
mol:GDP -0.1 0.18 -10000 0 -0.36 238 238
NGF (dimer) -0.014 0.097 -10000 0 -0.62 24 24
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.061 0.12 -10000 0 -0.26 81 81
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
BDNF (dimer)/TRKB -0.31 0.3 -10000 0 -0.56 598 598
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 -0.75 185 185
RAP1/GDP -0.072 0.084 -10000 0 -0.24 39 39
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.064 0.21 -10000 0 -0.66 105 105
ubiquitin-dependent protein catabolic process -0.015 0.076 -10000 0 -0.51 22 22
Schwann cell development -0.058 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 -0.42 0.38 -10000 0 -0.65 711 711
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.1 0.097 -10000 0 -10000 0 0
STAT3 -0.005 0.03 -10000 0 -0.38 4 4
axon guidance -0.4 0.34 -10000 0 -0.61 711 711
MAPK3 0.006 0.1 -10000 0 -0.5 38 38
MAPK1 0.006 0.1 -10000 0 -0.5 38 38
CDC42/GDP -0.061 0.12 -10000 0 -0.27 78 78
NTF3 -0.13 0.29 -10000 0 -0.75 185 185
NTF4 -0.27 0.37 -10000 0 -0.79 371 371
NGF (dimer)/TRKA/FAIM -0.015 0.075 -10000 0 -0.52 21 21
PI3K -0.008 0.068 -10000 0 -0.6 14 14
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 -0.15 0.21 -10000 0 -0.45 345 345
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.24 0.33 -10000 0 -0.59 467 467
RGS19 -0.001 0.013 -10000 0 -0.29 2 2
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.082 -10000 0 -10000 0 0
Rac1/GDP -0.061 0.12 -10000 0 -0.27 79 79
NGF (dimer)/TRKA/GRIT -0.015 0.076 -10000 0 -0.52 21 21
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.41 270 270
NGF (dimer)/TRKA/NEDD4-2 -0.015 0.076 -10000 0 -0.52 22 22
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.24 0.36 -10000 0 -0.79 334 334
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.053 -10000 0 -0.33 27 27
RAS family/GTP/PI3K -0.005 0.038 -10000 0 -0.34 14 14
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.29 2 2
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 0.024 -10000 0 -0.79 1 1
MAPKKK cascade -0.064 0.12 -10000 0 -0.82 21 21
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.05 -10000 0 -0.6 5 5
SQSTM1 0 0.009 -10000 0 -0.29 1 1
BDNF (dimer)/TRKB/GIPC -0.28 0.27 -10000 0 -0.51 598 598
NGF (dimer)/TRKA/p62/Atypical PKCs -0.012 0.064 -10000 0 -0.44 22 22
MATK -0.022 0.11 -10000 0 -0.48 49 49
NEDD4L -0.001 0.024 -10000 0 -0.79 1 1
RAS family/GDP -0.065 0.078 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.15 0.22 -10000 0 -0.46 342 342
Rac1/GTP -0.12 0.14 -10000 0 -0.34 261 261
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.075 0.23 -9999 0 -0.79 104 104
GNB1/GNG2 -0.14 0.23 -9999 0 -0.68 116 116
mol:DAG -0.097 0.22 -9999 0 -0.6 116 116
PLCG1 -0.13 0.21 -9999 0 -0.63 116 116
YES1 -0.14 0.23 -9999 0 -0.66 120 120
FZD3 -0.011 0.092 -9999 0 -0.79 15 15
FZD6 -0.007 0.075 -9999 0 -0.79 10 10
G protein -0.13 0.22 -9999 0 -0.64 118 118
MAP3K7 -0.069 0.19 -9999 0 -0.49 113 113
mol:Ca2+ -0.093 0.22 -9999 0 -0.58 116 116
mol:IP3 -0.097 0.22 -9999 0 -0.6 116 116
NLK -0.005 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.083 0.2 -9999 0 -0.53 120 120
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.16 0.25 -9999 0 -0.44 385 385
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.14 0.23 -9999 0 -0.66 121 121
GO:0007205 -0.094 0.22 -9999 0 -0.59 116 116
WNT6 -0.16 0.31 -9999 0 -0.69 255 255
WNT4 -0.021 0.12 -9999 0 -0.55 43 43
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.63 145 145
GNG2 -0.011 0.092 -9999 0 -0.79 15 15
WNT5A -0.016 0.1 -9999 0 -0.61 28 28
WNT11 -0.17 0.32 -9999 0 -0.76 242 242
CDC42 -0.11 0.24 -9999 0 -0.66 105 105
Plasma membrane estrogen 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
GNB1/GNG2 -0.095 0.18 -10000 0 -0.46 197 197
ER alpha/Gai/GDP/Gbeta gamma -0.093 0.19 -10000 0 -0.47 189 189
AKT1 -0.1 0.32 -10000 0 -0.83 171 171
PIK3CA 0 0.009 -10000 0 -0.29 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.1 0.32 -10000 0 -0.85 168 168
mol:Ca2+ -0.028 0.15 -10000 0 -0.45 93 93
IGF1R -0.02 0.12 -10000 0 -0.6 36 36
E2/ER alpha (dimer)/Striatin -0.11 0.2 -10000 0 -0.53 183 183
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.094 0.3 0.78 171 -10000 0 171
RhoA/GTP -0.069 0.14 -10000 0 -0.39 165 165
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.093 0.2 -10000 0 -0.54 175 175
regulation of stress fiber formation 0.023 0.14 0.45 12 -10000 0 12
E2/ERA-ERB (dimer) -0.11 0.2 -10000 0 -0.54 187 187
KRAS -0.001 0.013 -10000 0 -0.29 2 2
G13/GTP -0.088 0.17 -10000 0 -0.48 165 165
pseudopodium formation -0.023 0.14 -10000 0 -0.45 12 12
E2/ER alpha (dimer)/PELP1 -0.096 0.19 -10000 0 -0.52 165 165
GRB2 0 0.009 -10000 0 -0.29 1 1
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
GNAO1 -0.03 0.13 -10000 0 -0.48 67 67
HRAS -0.003 0.028 -10000 0 -0.29 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.061 0.22 -10000 0 -0.54 179 179
E2/ER beta (dimer) -0.013 0.089 -10000 0 -0.61 24 24
mol:GDP -0.086 0.2 -10000 0 -0.53 187 187
mol:NADP -0.061 0.22 -10000 0 -0.54 179 179
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
mol:IP3 -0.03 0.15 -10000 0 -0.47 93 93
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.59 36 36
PLCB1 -0.065 0.14 -10000 0 -0.49 92 92
PLCB2 -0.034 0.089 -10000 0 -0.62 15 15
IGF1 -0.18 0.33 -10000 0 -0.79 247 247
mol:L-citrulline -0.061 0.22 -10000 0 -0.54 179 179
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.04 0.15 -10000 0 -0.85 26 26
JNK cascade -0.013 0.089 -10000 0 -0.61 24 24
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.017 0.12 -10000 0 -0.79 24 24
GNAQ -0.002 0.041 -10000 0 -0.79 3 3
ESR1 -0.15 0.28 -10000 0 -0.58 288 288
Gq family/GDP/Gbeta gamma -0.009 0.078 -10000 0 -0.71 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.023 0.13 -10000 0 -0.32 165 165
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.093 0.2 -10000 0 -0.54 175 175
GNAZ -0.007 0.075 -10000 0 -0.79 10 10
E2/ER alpha (dimer) -0.11 0.22 -10000 0 -0.61 165 165
STRN -0.015 0.11 -10000 0 -0.79 21 21
GNAL -0.19 0.33 -10000 0 -0.79 258 258
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.005 0.084 -10000 0 -0.52 27 27
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
HBEGF -0.071 0.19 -10000 0 -0.45 187 187
cAMP biosynthetic process -0.19 0.25 -10000 0 -0.5 389 389
SRC -0.052 0.2 -10000 0 -0.45 177 177
PI3K -0.008 0.068 -10000 0 -0.6 14 14
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.079 0.18 -10000 0 -0.46 197 197
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.51 252 252
Gs family/GTP -0.19 0.26 -10000 0 -0.52 389 389
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.014 -10000 0 -10000 0 0
vasodilation -0.057 0.21 -10000 0 -0.51 179 179
mol:DAG -0.03 0.15 -10000 0 -0.47 93 93
Gs family/GDP/Gbeta gamma -0.16 0.23 -10000 0 -0.44 385 385
MSN -0.027 0.15 -10000 0 -0.49 12 12
Gq family/GTP -0.038 0.094 -10000 0 -0.66 14 14
mol:PI-3-4-5-P3 -0.099 0.31 -10000 0 -0.81 168 168
NRAS -0.001 0.013 -10000 0 -0.29 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.057 0.21 0.51 179 -10000 0 179
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.079 0.19 -10000 0 -0.49 187 187
NOS3 -0.066 0.24 -10000 0 -0.57 179 179
GNA11 -0.003 0.048 -10000 0 -0.79 4 4
MAPKKK cascade -0.069 0.26 -10000 0 -0.63 183 183
E2/ER alpha (dimer)/PELP1/Src -0.098 0.22 -10000 0 -0.56 175 175
ruffle organization -0.023 0.14 -10000 0 -0.45 12 12
ROCK2 -0.074 0.14 -10000 0 -0.37 194 194
GNA14 -0.013 0.084 -10000 0 -0.46 30 30
GNA15 -0.003 0.033 -10000 0 -0.36 8 8
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.097 0.2 -10000 0 -0.48 187 187
MMP2 -0.045 0.19 -10000 0 -0.43 184 184
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.26 -10000 0 -0.52 452 452
fibroblast growth factor receptor signaling pathway -0.22 0.26 -10000 0 -0.52 452 452
LAMA1 -0.088 0.25 -10000 0 -0.77 124 124
PRNP -0.013 0.1 -10000 0 -0.79 18 18
GPC1/SLIT2 -0.07 0.19 -10000 0 -0.6 125 125
SMAD2 0.01 0.1 -10000 0 -0.47 50 50
GPC1/PrPc/Cu2+ -0.01 0.069 -10000 0 -0.52 19 19
GPC1/Laminin alpha1 -0.068 0.19 -10000 0 -0.6 121 121
TDGF1 -0.005 0.063 -10000 0 -0.79 7 7
CRIPTO/GPC1 -0.006 0.053 -10000 0 -0.6 8 8
APP/GPC1 -0.002 0.023 -10000 0 -0.6 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.02 0.051 -10000 0 -0.52 9 9
FLT1 -0.001 0.024 -10000 0 -0.79 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.025 0.11 -10000 0 -0.52 50 50
SERPINC1 -0.018 0.07 -10000 0 -0.29 67 67
FYN 0.02 0.053 -10000 0 -0.52 10 10
FGR 0.02 0.051 -10000 0 -0.52 9 9
positive regulation of MAPKKK cascade 0.032 0.066 -10000 0 -0.52 10 10
SLIT2 -0.089 0.25 -10000 0 -0.79 124 124
GPC1/NRG -0.22 0.29 -10000 0 -0.6 402 402
NRG1 -0.29 0.38 -10000 0 -0.78 406 406
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.029 -10000 0 -0.52 2 2
LYN 0.021 0.048 -10000 0 -0.51 8 8
mol:Spermine 0.009 0.024 -10000 0 -0.61 1 1
cell growth -0.22 0.26 -10000 0 -0.52 452 452
BMP signaling pathway 0.002 0.032 0.36 7 -10000 0 7
SRC 0.021 0.048 -10000 0 -0.51 8 8
TGFBR1 0 0.009 -10000 0 -0.29 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.26 0.37 -10000 0 -0.75 382 382
GPC1 -0.002 0.032 -10000 0 -0.36 7 7
TGFBR1 (dimer) 0 0.009 -10000 0 -0.29 1 1
VEGFA -0.003 0.031 -10000 0 -10000 0 0
BLK -0.006 0.082 -10000 0 -0.56 10 10
HCK 0.018 0.052 -10000 0 -0.51 8 8
FGF2 -0.32 0.39 -10000 0 -0.79 446 446
FGFR1 -0.009 0.08 -10000 0 -0.68 14 14
VEGFR1 homodimer -0.001 0.024 -10000 0 -0.79 1 1
TGFBR2 -0.035 0.16 -10000 0 -0.79 49 49
cell death -0.002 0.023 -10000 0 -0.6 1 1
ATIII/GPC1 -0.013 0.05 -10000 0 -0.61 1 1
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.6 356 356
LCK 0.008 0.082 -10000 0 -0.53 21 21
neuron differentiation -0.22 0.29 -10000 0 -0.6 402 402
PrPc/Cu2+ -0.01 0.077 -10000 0 -0.61 18 18
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.035 0.16 -10000 0 -0.79 49 49
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.16 0.39 -9999 0 -0.99 96 96
IL23A -0.17 0.39 -9999 0 -1 88 88
NF kappa B1 p50/RelA/I kappa B alpha -0.23 0.32 -9999 0 -0.88 140 140
positive regulation of T cell mediated cytotoxicity -0.18 0.42 -9999 0 -0.85 231 231
ITGA3 -0.16 0.38 -9999 0 -1 88 88
IL17F -0.1 0.28 -9999 0 -0.65 92 92
IL12B -0.05 0.12 -9999 0 -0.31 117 117
STAT1 (dimer) -0.21 0.37 -9999 0 -0.84 212 212
CD4 -0.16 0.38 -9999 0 -0.94 95 95
IL23 -0.17 0.38 -9999 0 -1 77 77
IL23R -0.012 0.087 -9999 0 -10000 0 0
IL1B -0.17 0.41 -9999 0 -1.1 90 90
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.16 0.38 -9999 0 -0.9 121 121
TYK2 0.012 0.017 -9999 0 -10000 0 0
STAT4 -0.032 0.16 -9999 0 -0.78 45 45
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.021 0.14 -9999 0 -0.73 42 42
IL12RB1 -0.001 0.07 -9999 0 -0.32 42 42
PIK3CA 0 0.009 -9999 0 -0.29 1 1
IL12Rbeta1/TYK2 -0.002 0.052 -9999 0 -0.6 2 2
IL23R/JAK2 -0.009 0.11 -9999 0 -0.63 1 1
positive regulation of chronic inflammatory response -0.18 0.42 -9999 0 -0.85 231 231
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.018 0.034 -9999 0 -0.83 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
NFKB1 0.005 0.007 -9999 0 -10000 0 0
RELA 0.005 0.007 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.37 -9999 0 -0.96 85 85
ALOX12B -0.16 0.38 -9999 0 -0.96 93 93
CXCL1 -0.34 0.63 -9999 0 -1.3 279 279
T cell proliferation -0.18 0.42 -9999 0 -0.85 231 231
NFKBIA 0.005 0.007 -9999 0 -10000 0 0
IL17A -0.068 0.24 -9999 0 -0.53 61 61
PI3K -0.24 0.32 -9999 0 -0.85 174 174
IFNG -0.005 0.027 -9999 0 -0.09 20 20
STAT3 (dimer) -0.23 0.31 -9999 0 -0.86 140 140
IL18R1 -0.007 0.11 -9999 0 -0.78 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.081 0.24 -9999 0 -0.56 58 58
IL18/IL18R -0.03 0.12 -9999 0 -0.53 56 56
macrophage activation -0.013 0.016 -9999 0 -0.042 91 91
TNF -0.17 0.4 -9999 0 -1 111 111
STAT3/STAT4 -0.25 0.34 -9999 0 -0.83 231 231
STAT4 (dimer) -0.23 0.39 -9999 0 -0.88 217 217
IL18 0.001 0.047 -9999 0 -0.3 27 27
IL19 -0.17 0.38 -9999 0 -0.92 114 114
STAT5A (dimer) -0.21 0.37 -9999 0 -0.84 210 210
STAT1 -0.005 0.038 -9999 0 -0.29 19 19
SOCS3 -0.004 0.058 -9999 0 -0.79 6 6
CXCL9 -0.18 0.38 -9999 0 -0.96 109 109
MPO -0.2 0.46 -9999 0 -1.2 135 135
positive regulation of humoral immune response -0.18 0.42 -9999 0 -0.85 231 231
IL23/IL23R/JAK2/TYK2 -0.19 0.44 -9999 0 -0.88 230 230
IL6 -0.46 0.7 -9999 0 -1.3 410 410
STAT5A -0.006 0.067 -9999 0 -0.79 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 -0.17 0.41 -9999 0 -1 106 106
keratinocyte proliferation -0.18 0.42 -9999 0 -0.85 231 231
NOS2 -0.16 0.38 -9999 0 -0.96 103 103
Aurora C 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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.076 0.068 -9999 0 -0.61 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.02 0.018 -9999 0 -10000 0 0
AURKB -0.17 0.14 -9999 0 -0.29 625 625
AURKC -0.005 0.043 -9999 0 -0.32 18 18
IL6-mediated signaling events

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
BCL2L1 -0.065 0.22 -9999 0 -0.68 41 41
CRP -0.07 0.22 -9999 0 -0.65 54 54
cell cycle arrest -0.084 0.24 -9999 0 -0.71 70 70
TIMP1 -0.063 0.2 -9999 0 -0.56 63 63
IL6ST -0.086 0.26 -9999 0 -0.78 138 138
Rac1/GDP -0.12 0.23 -9999 0 -0.67 91 91
AP1 -0.13 0.23 -9999 0 -0.48 270 270
GAB2 0.005 0.043 -9999 0 -0.39 10 10
TNFSF11 -0.076 0.22 -9999 0 -0.66 49 49
HSP90B1 0.015 0.047 -9999 0 -10000 0 0
GAB1 0.008 0.006 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.72 96 96
AKT1 0.038 0.042 -9999 0 -10000 0 0
FOXO1 0.046 0.061 -9999 0 -0.42 12 12
MAP2K6 -0.15 0.26 -9999 0 -0.5 229 229
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.086 0.23 -9999 0 -0.64 88 88
MITF -0.14 0.26 -9999 0 -0.57 157 157
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.013 0.13 -9999 0 -1.5 8 8
CEBPB 0.016 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.044 0.093 -9999 0 -0.42 11 11
STAT3 -0.091 0.26 -9999 0 -0.78 70 70
STAT1 -0.013 0.021 -9999 0 -10000 0 0
CEBPD -0.067 0.22 -9999 0 -0.71 41 41
PIK3CA 0.012 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.067 -9999 0 -0.6 14 14
JUN -0.005 0.063 -9999 0 -0.79 7 7
PIAS3/MITF -0.16 0.22 -9999 0 -0.7 91 91
MAPK11 -0.13 0.25 -9999 0 -0.73 97 97
STAT3 (dimer)/FOXO1 -0.036 0.22 -9999 0 -0.6 63 63
GRB2/SOS1/GAB family -0.14 0.2 -9999 0 -0.71 72 72
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.26 -9999 0 -0.38 501 501
GRB2 0.008 0.011 -9999 0 -0.29 1 1
JAK2 -0.001 0.024 -9999 0 -0.79 1 1
LBP -0.24 0.45 -9999 0 -0.96 277 277
PIK3R1 0.002 0.09 -9999 0 -0.79 14 14
JAK1 0.009 0.025 -9999 0 -0.79 1 1
MYC -0.078 0.26 -9999 0 -0.88 53 53
FGG -0.075 0.22 -9999 0 -0.68 45 45
macrophage differentiation -0.084 0.24 -9999 0 -0.71 70 70
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.23 0.28 -9999 0 -0.5 504 504
JUNB -0.064 0.21 -9999 0 -0.65 42 42
FOS -0.24 0.36 -9999 0 -0.79 329 329
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.15 0.26 -9999 0 -0.47 292 292
STAT1/PIAS1 -0.13 0.23 -9999 0 -0.47 209 209
GRB2/SOS1/GAB family/SHP2/PI3K 0.002 0.037 -9999 0 -0.32 2 2
STAT3 (dimer) -0.087 0.25 -9999 0 -0.75 70 70
PRKCD -0.061 0.22 -9999 0 -0.61 78 78
IL6R -0.022 0.16 -9999 0 -0.79 44 44
SOCS3 -0.12 0.24 -9999 0 -0.74 87 87
gp130 (dimer)/JAK1/JAK1/LMO4 -0.057 0.18 -9999 0 -0.52 140 140
Rac1/GTP -0.15 0.21 -9999 0 -0.67 93 93
HCK -0.004 0.033 -9999 0 -0.29 14 14
MAPKKK cascade -0.006 0.084 -9999 0 -1 2 2
bone resorption -0.072 0.21 -9999 0 -0.6 59 59
IRF1 -0.066 0.22 -9999 0 -0.63 59 59
mol:GDP -0.13 0.25 -9999 0 -0.51 186 186
SOS1 0 0.003 -9999 0 -10000 0 0
VAV1 -0.13 0.25 -9999 0 -0.6 136 136
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.25 -9999 0 -0.8 92 92
PTPN11 -0.013 0.019 -9999 0 -10000 0 0
IL6/IL6RA -0.24 0.31 -9999 0 -0.62 419 419
gp130 (dimer)/TYK2/TYK2/LMO4 -0.06 0.18 -9999 0 -0.51 140 140
gp130 (dimer)/JAK2/JAK2/LMO4 -0.06 0.18 -9999 0 -0.52 140 140
IL6 -0.28 0.38 -9999 0 -0.78 401 401
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.003 0.035 -9999 0 -0.79 2 2
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 -0.4 503 503
LMO4 0.009 0.049 -9999 0 -0.44 10 10
STAT3 (dimer)/PIAS3 -0.15 0.21 -9999 0 -0.78 70 70
MCL1 0.05 0.035 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.003 0.048 -10000 0 -0.79 4 4
Jak2/Leptin Receptor -0.16 0.23 0.18 1 -0.52 301 302
PTP1B/AKT1 -0.07 0.11 -10000 0 -0.34 117 117
FYN -0.001 0.034 -10000 0 -0.79 2 2
p210 bcr-abl/PTP1B -0.071 0.13 -10000 0 -0.38 122 122
EGFR -0.29 0.39 -10000 0 -0.79 410 410
EGF/EGFR -0.29 0.3 -10000 0 -0.56 556 556
CSF1 -0.006 0.071 -10000 0 -0.79 9 9
AKT1 0.001 0.003 -10000 0 -10000 0 0
INSR 0.001 0.01 -10000 0 -0.3 1 1
PTP1B/N-cadherin -0.097 0.12 -10000 0 -0.36 129 129
Insulin Receptor/Insulin -0.049 0.08 -10000 0 -0.4 22 22
HCK -0.004 0.033 -10000 0 -0.29 14 14
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.06 0.12 -10000 0 -0.36 117 117
EGF -0.15 0.32 -10000 0 -0.79 214 214
YES1 -0.001 0.024 -10000 0 -0.79 1 1
CAV1 -0.18 0.24 -10000 0 -0.51 299 299
TXN 0 0.018 -10000 0 -0.3 4 4
PTP1B/IRS1/GRB2 -0.087 0.14 -10000 0 -0.41 138 138
cell migration 0.071 0.13 0.38 122 -10000 0 122
STAT3 0 0.001 -10000 0 -10000 0 0
PRLR -0.006 0.072 -10000 0 -0.54 16 16
ITGA2B -0.018 0.078 -10000 0 -0.34 35 35
CSF1R -0.001 0.025 -10000 0 -0.79 1 1
Prolactin Receptor/Prolactin -0.007 0.058 -10000 0 -0.6 8 8
FGR -0.001 0.025 -10000 0 -0.54 2 2
PTP1B/p130 Cas -0.074 0.12 -10000 0 -0.36 115 115
Crk/p130 Cas -0.069 0.11 -10000 0 -0.36 99 99
DOK1 -0.046 0.12 -10000 0 -0.33 100 100
JAK2 -0.042 0.08 -10000 0 -0.31 34 34
Jak2/Leptin Receptor/Leptin -0.36 0.18 -10000 0 -0.47 629 629
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
PTPN1 -0.072 0.13 -10000 0 -0.38 122 122
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.054 0.12 -10000 0 -0.3 200 200
SRC -0.013 0.047 -10000 0 -10000 0 0
ITGB3 -0.028 0.14 -10000 0 -0.74 41 41
CAT1/PTP1B -0.084 0.17 -10000 0 -0.42 131 131
CAPN1 0.001 0.01 -10000 0 -0.29 1 1
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.044 0.094 -10000 0 -0.54 21 21
mol:H2O2 -0.005 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.32 0.16 -10000 0 -0.43 551 551
negative regulation of transcription -0.041 0.079 -10000 0 -0.31 34 34
FCGR2A -0.001 0.013 -10000 0 -0.29 2 2
FER -0.007 0.08 -10000 0 -0.8 11 11
alphaIIb/beta3 Integrin -0.033 0.12 -10000 0 -0.62 40 40
BLK -0.044 0.11 -10000 0 -0.3 159 159
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0.002 0.004 -10000 0 -10000 0 0
LEPR -0.2 0.35 -10000 0 -0.79 292 292
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 -0.03 0.13 -10000 0 -0.43 24 24
PRL -0.004 0.032 -10000 0 -0.3 13 13
SOCS3 0.018 0.11 -10000 0 -1.5 6 6
SPRY2 -0.095 0.26 -10000 0 -0.8 130 130
Insulin Receptor/Insulin/IRS1 -0.022 0.11 -10000 0 -0.53 45 45
CSF1/CSF1R -0.073 0.12 -10000 0 -0.37 114 114
Ras protein signal transduction 0.037 0.036 -10000 0 -10000 0 0
IRS1 -0.032 0.16 -10000 0 -0.79 45 45
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.64 0.31 -10000 0 -0.79 881 881
STAT5B -0.058 0.11 -10000 0 -0.31 123 123
STAT5A -0.059 0.11 -10000 0 -0.31 127 127
GRB2 0 0.009 -10000 0 -0.29 1 1
PDGFB-D/PDGFRB -0.076 0.12 -10000 0 -0.37 119 119
CSN2 0.018 0.035 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
LAT -0.014 0.053 -10000 0 -0.57 2 2
YBX1 -0.001 0.014 -10000 0 -10000 0 0
LCK -0.02 0.1 -10000 0 -0.41 53 53
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.004 0.05 -10000 0 -0.41 13 13
Visual signal transduction: Rods

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
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 0.04 -9999 0 -0.31 2 2
PDE6G/GNAT1/GTP -0.008 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 0.034 -9999 0 -0.29 15 15
GRK1 -0.003 0.029 -9999 0 -0.29 11 11
CNG Channel -0.14 0.2 -9999 0 -0.43 316 316
mol:Na + -0.13 0.18 -9999 0 -0.41 309 309
mol:ADP -0.003 0.029 -9999 0 -0.29 11 11
RGS9-1/Gbeta5/R9AP -0.061 0.16 -9999 0 -0.52 109 109
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.13 0.19 -9999 0 -0.42 309 309
CNGB1 -0.015 0.064 -9999 0 -0.29 55 55
RDH5 -0.48 0.38 -9999 0 -0.79 660 660
SAG -0.015 0.064 -9999 0 -0.29 55 55
mol:Ca2+ -0.12 0.18 -9999 0 -0.44 62 62
Na + (4 Units) -0.12 0.17 -9999 0 -0.43 62 62
RGS9 -0.08 0.23 -9999 0 -0.73 121 121
GNB1/GNGT1 -0.03 0.068 -9999 0 -10000 0 0
GNAT1/GDP -0.054 0.14 -9999 0 -0.46 106 106
GUCY2D -0.008 0.057 -9999 0 -0.36 24 24
GNGT1 -0.047 0.11 -9999 0 -0.29 175 175
GUCY2F -0.001 0.013 -9999 0 -0.29 2 2
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.018 0.069 -9999 0 -0.45 22 22
mol:11-cis-retinal -0.48 0.38 -9999 0 -0.79 660 660
mol:cGMP -0.011 0.048 -9999 0 -0.45 8 8
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.37 0.29 -9999 0 -0.6 660 660
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.22 0.35 -9999 0 -0.78 310 310
Metarhodopsin II -0.003 0.022 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.012 0.051 -9999 0 -0.48 8 8
RGS9BP -0.019 0.072 -9999 0 -0.29 70 70
Metarhodopsin II/Transducin -0.009 0.021 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.008 0.042 -9999 0 -0.48 5 5
PDE6A/B -0.017 0.089 -9999 0 -0.6 22 22
mol:Pi -0.061 0.16 -9999 0 -0.52 109 109
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.023 0.051 -9999 0 -0.28 2 2
PDE6B -0.017 0.11 -9999 0 -0.73 25 25
PDE6A -0.006 0.042 -9999 0 -0.29 23 23
PDE6G -0.012 0.058 -9999 0 -0.29 44 44
RHO -0.004 0.035 -9999 0 -0.29 16 16
PDE6 -0.062 0.14 -9999 0 -0.44 124 124
GUCA1A -0.012 0.059 -9999 0 -0.29 46 46
GC2/GCAP Family -0.008 0.043 -9999 0 -0.48 5 5
GUCA1C 0 0.009 -9999 0 -0.29 1 1
GUCA1B -0.004 0.053 -9999 0 -0.79 5 5
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.096 0.2 0.63 121 -10000 0 121
KIRREL -0.079 0.25 -10000 0 -0.79 121 121
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.096 0.2 -10000 0 -0.63 121 121
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 -0.07 0.15 -10000 0 -0.48 121 121
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.043 0.11 -10000 0 -0.36 121 121
FYN -0.065 0.14 -10000 0 -0.46 121 121
mol:Ca2+ -0.069 0.15 -10000 0 -0.47 121 121
mol:DAG -0.069 0.15 -10000 0 -0.48 121 121
NPHS2 -0.008 0.031 -10000 0 -0.29 5 5
mol:IP3 -0.069 0.15 -10000 0 -0.48 121 121
regulation of endocytosis -0.055 0.14 -10000 0 -0.43 121 121
Nephrin/NEPH1/podocin/Cholesterol -0.072 0.15 -10000 0 -0.49 121 121
establishment of cell polarity -0.096 0.2 -10000 0 -0.63 121 121
Nephrin/NEPH1/podocin/NCK1-2 -0.062 0.14 -10000 0 -0.44 121 121
Nephrin/NEPH1/beta Arrestin2 -0.056 0.14 -10000 0 -0.43 121 121
NPHS1 -0.047 0.11 -10000 0 -0.29 177 177
Nephrin/NEPH1/podocin -0.065 0.14 -10000 0 -0.46 121 121
TJP1 -0.001 0.024 -10000 0 -0.79 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 -0.07 0.15 -10000 0 -0.48 121 121
CD2AP 0 0.009 -10000 0 -0.29 1 1
Nephrin/NEPH1/podocin/GRB2 -0.07 0.15 -10000 0 -0.48 121 121
GRB2 0 0.009 -10000 0 -0.29 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.057 0.18 -10000 0 -0.5 130 130
cytoskeleton organization -0.055 0.14 -10000 0 -0.44 121 121
Nephrin/NEPH1 -0.069 0.15 -10000 0 -0.47 121 121
Nephrin/NEPH1/ZO-1 -0.076 0.16 -10000 0 -0.52 121 121
RXR and RAR heterodimerization with other nuclear receptor

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
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 -0.034 0.16 -9999 0 -0.3 271 271
RXRs/LXRs/DNA/Oxysterols -0.014 0.14 -9999 0 -0.42 33 33
MED1 -0.006 0.043 -9999 0 -10000 0 0
mol:9cRA 0.005 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.024 0.092 -9999 0 -0.35 72 72
RXRs/NUR77 -0.16 0.24 -9999 0 -0.5 337 337
RXRs/PPAR -0.13 0.23 -9999 0 -0.38 453 453
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.008 0.054 -9999 0 -0.45 15 15
RARA -0.004 0.035 -9999 0 -0.29 16 16
NCOA1 -0.001 0.024 -9999 0 -0.79 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.008 0.055 -9999 0 -0.46 15 15
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.029 0.052 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.023 0.088 -9999 0 -0.34 72 72
THRA -0.001 0.024 -9999 0 -0.79 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 -0.46 268 268
NR1H4 -0.003 0.032 -9999 0 -0.29 13 13
RXRs/LXRs/DNA -0.1 0.18 -9999 0 -0.42 268 268
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 -0.44 268 268
NR4A1 -0.071 0.23 -9999 0 -0.79 99 99
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.043 0.13 -9999 0 -0.27 268 268
RXRG -0.18 0.34 -9999 0 -0.78 271 271
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 -0.044 0.18 -9999 0 -0.79 61 61
PPARG -0.19 0.34 -9999 0 -0.79 268 268
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.014 0.18 -9999 0 -1.2 14 14
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.014 0.14 -9999 0 -0.42 33 33
PPARA -0.006 0.067 -9999 0 -0.79 8 8
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.011 0.092 -9999 0 -0.79 15 15
RXRs/NUR77/BCL2 -0.12 0.19 -9999 0 -0.37 359 359
SREBF1 -0.005 0.14 -9999 0 -0.63 7 7
RXRs/RXRs/DNA/9cRA -0.12 0.2 -9999 0 -0.46 268 268
ABCA1 -0.008 0.16 -9999 0 -1.1 10 10
RARs/THRs -0.032 0.12 -9999 0 -0.47 72 72
RXRs/FXR -0.11 0.2 -9999 0 -0.47 268 268
BCL2 -0.027 0.14 -9999 0 -0.79 37 37
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.048 -9999 0 -0.6 6 6
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.54 459 459
PTK2 -0.089 0.19 -9999 0 -0.67 45 45
IGF1R -0.02 0.12 -9999 0 -0.6 36 36
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.091 -9999 0 -0.62 21 21
SRC 0 0.009 -9999 0 -0.29 1 1
CDKN1B -0.088 0.12 -9999 0 -0.88 11 11
VEGFA -0.003 0.031 -9999 0 -10000 0 0
ILK -0.086 0.12 -9999 0 -0.83 8 8
ROCK1 -0.001 0.024 -9999 0 -0.79 1 1
AKT1 -0.076 0.1 -9999 0 -0.77 8 8
PTK2B -0.019 0.095 -9999 0 -0.49 38 38
alphaV/beta3 Integrin/JAM-A -0.2 0.24 -9999 0 -0.47 463 463
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.019 0.095 -9999 0 -0.52 37 37
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.25 -9999 0 -0.54 271 271
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.013 0.062 -9999 0 -0.53 7 7
alphaV/beta3 Integrin/Syndecan-1 -0.028 0.1 -9999 0 -0.53 38 38
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.33 0.35 -9999 0 -0.76 354 354
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 -0.54 37 37
RPS6KB1 -0.3 0.32 -9999 0 -0.69 355 355
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.33 0.39 -9999 0 -0.76 459 459
GPR124 -0.009 0.085 -9999 0 -0.79 13 13
MAPK1 -0.33 0.39 -9999 0 -0.76 459 459
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
alphaV/beta3 Integrin/Tumstatin -0.1 0.21 -9999 0 -0.53 214 214
cell adhesion -0.023 0.11 -9999 0 -0.51 47 47
ANGPTL3 -0.001 0.018 -9999 0 -0.29 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.005 0.041 -9999 0 -0.52 6 6
IGF-1R heterotetramer -0.02 0.12 -9999 0 -0.59 36 36
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.035 0.16 -9999 0 -0.79 49 49
ITGB3 -0.028 0.14 -9999 0 -0.74 41 41
IGF1 -0.18 0.33 -9999 0 -0.79 247 247
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.024 0.12 -9999 0 -0.59 43 43
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.024 -9999 0 -0.79 1 1
alphaV/beta3 Integrin/CD47 -0.018 0.095 -9999 0 -0.52 38 38
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.05 0.18 -9999 0 -0.65 80 80
CSF1 -0.006 0.071 -9999 0 -0.79 9 9
PIK3C2A -0.087 0.12 -9999 0 -0.85 9 9
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.6 76 76
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.02 0.1 -9999 0 -0.53 38 38
FAK1/Vinculin -0.064 0.16 -9999 0 -0.51 42 42
alphaV beta3/Integrin/ppsTEM5 -0.024 0.12 -9999 0 -0.59 43 43
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.027 0.1 -9999 0 -0.34 88 88
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.32 0.39 -9999 0 -0.79 446 446
F11R -0.23 0.31 -9999 0 -0.6 446 446
alphaV/beta3 Integrin/Lactadherin -0.025 0.12 -9999 0 -0.57 46 46
alphaV/beta3 Integrin/TGFBR2 -0.04 0.16 -9999 0 -0.66 66 66
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.004 0.042 -9999 0 -0.47 9 9
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
alphaV/beta3 Integrin/Talin -0.017 0.086 -9999 0 -0.48 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.019 0.096 -9999 0 -0.5 38 38
SDC1 -0.02 0.076 -9999 0 -0.3 73 73
VAV3 -0.008 0.054 -9999 0 -0.44 16 16
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.79 45 45
FAK1/Paxillin -0.064 0.16 -9999 0 -0.51 42 42
cell migration -0.05 0.14 -9999 0 -0.45 42 42
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.23 -9999 0 -0.67 74 74
SPP1 -0.077 0.13 -9999 0 -0.29 288 288
KDR -0.004 0.058 -9999 0 -0.79 6 6
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 -0.13 0.29 -9999 0 -0.78 187 187
angiogenesis -0.3 0.39 -9999 0 -0.74 461 461
Rac1/GTP -0.007 0.049 -9999 0 -0.4 16 16
EDIL3 -0.052 0.19 -9999 0 -0.7 81 81
cell proliferation -0.04 0.16 -9999 0 -0.65 66 66
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.023 0.062 -9999 0 -0.56 11 11
alphaM/beta2 Integrin/GPIbA -0.024 0.057 -9999 0 -0.52 9 9
alphaM/beta2 Integrin/proMMP-9 -0.083 0.082 -9999 0 -0.39 8 8
PLAUR -0.023 0.079 -9999 0 -0.29 86 86
HMGB1 -0.013 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.017 0.029 -9999 0 -10000 0 0
AGER -0.015 0.04 -9999 0 -0.66 3 3
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 -0.074 0.096 -9999 0 -0.46 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 483 483
CYR61 -0.043 0.18 -9999 0 -0.79 59 59
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.057 0.11 -9999 0 -0.52 22 22
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.18 0.33 -9999 0 -0.79 257 257
MYH2 -0.07 0.16 -9999 0 -0.4 121 121
MST1R -0.011 0.083 -9999 0 -0.55 21 21
leukocyte activation during inflammatory response -0.29 0.22 -9999 0 -0.46 668 668
APOB -0.48 0.38 -9999 0 -0.79 668 668
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 -0.79 11 11
JAM3 -0.005 0.063 -9999 0 -0.79 7 7
GP1BA -0.012 0.077 -9999 0 -0.4 33 33
alphaM/beta2 Integrin/CTGF -0.025 0.071 -9999 0 -0.57 15 15
alphaM/beta2 Integrin -0.071 0.13 -9999 0 -0.35 101 101
JAM3 homodimer -0.005 0.063 -9999 0 -0.79 7 7
ICAM2 -0.004 0.053 -9999 0 -0.79 5 5
ICAM1 -0.004 0.035 -9999 0 -0.29 16 16
phagocytosis triggered by activation of immune response cell surface activating receptor -0.061 0.14 -9999 0 -0.35 101 101
cell adhesion -0.024 0.057 -9999 0 -0.52 9 9
NFKB1 -0.096 0.21 -9999 0 -0.66 15 15
THY1 -0.002 0.025 -9999 0 -0.29 8 8
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.33 0.26 -9999 0 -0.53 668 668
alphaM/beta2 Integrin/LRP/tPA -0.034 0.11 -9999 0 -0.54 46 46
IL6 -0.3 0.48 -9999 0 -0.93 400 400
ITGB2 -0.017 0.039 -9999 0 -0.33 5 5
elevation of cytosolic calcium ion concentration -0.025 0.049 -9999 0 -0.36 2 2
alphaM/beta2 Integrin/JAM2/JAM3 -0.044 0.13 -9999 0 -0.53 68 68
JAM2 -0.048 0.19 -9999 0 -0.79 66 66
alphaM/beta2 Integrin/ICAM1 -0.022 0.08 -9999 0 -0.53 21 21
alphaM/beta2 Integrin/uPA/Plg -0.019 0.033 -9999 0 -10000 0 0
RhoA/GTP -0.088 0.16 -9999 0 -0.37 220 220
positive regulation of phagocytosis -0.049 0.089 -9999 0 -0.45 19 19
Ron/MSP -0.016 0.098 -9999 0 -0.66 22 22
alphaM/beta2 Integrin/uPAR/uPA -0.025 0.05 -9999 0 -0.36 2 2
alphaM/beta2 Integrin/uPAR -0.029 0.048 -9999 0 -0.34 4 4
PLAU -0.007 0.045 -9999 0 -0.29 27 27
PLAT -0.028 0.14 -9999 0 -0.74 41 41
actin filament polymerization -0.066 0.15 -9999 0 -0.38 123 123
MST1 -0.012 0.089 -9999 0 -0.58 22 22
alphaM/beta2 Integrin/lipoprotein(a) -0.29 0.22 -9999 0 -0.47 668 668
TNF -0.087 0.22 -9999 0 -0.86 21 21
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.021 0.036 -9999 0 -10000 0 0
fibrinolysis -0.019 0.032 -9999 0 -10000 0 0
HCK -0.004 0.033 -9999 0 -0.29 14 14
dendritic cell antigen processing and presentation -0.061 0.14 -9999 0 -0.35 101 101
VTN -0.027 0.1 -9999 0 -0.34 88 88
alphaM/beta2 Integrin/CYR61 -0.046 0.13 -9999 0 -0.57 59 59
LPA -0.001 0.02 -9999 0 -0.29 5 5
LRP1 -0.009 0.085 -9999 0 -0.79 13 13
cell migration -0.073 0.084 -9999 0 -0.5 13 13
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.018 0.031 -9999 0 -10000 0 0
MPO -0.051 0.19 -9999 0 -0.77 72 72
KNG1 -0.006 0.041 -9999 0 -0.29 22 22
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.065 0.16 -9999 0 -0.4 120 120
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.002 0.025 -9999 0 -10000 0 0
CTGF -0.012 0.093 -9999 0 -0.79 15 15
alphaM/beta2 Integrin/Hck -0.019 0.035 -9999 0 -0.33 2 2
ITGAM -0.015 0.028 -9999 0 -0.31 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.21 -9999 0 -0.5 257 257
HP -0.16 0.31 -9999 0 -0.71 244 244
leukocyte adhesion -0.076 0.13 -9999 0 -0.58 46 46
SELP -0.18 0.33 -9999 0 -0.79 257 257
Ephrin A reverse signaling

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
MAPKKK cascade -0.05 0.15 -9999 0 -0.53 103 103
EFNA5 -0.074 0.23 -9999 0 -0.79 103 103
FYN -0.026 0.15 -9999 0 -0.48 104 104
neuron projection morphogenesis -0.05 0.15 -9999 0 -0.53 103 103
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.051 0.16 -9999 0 -0.53 103 103
EPHA5 -0.001 0.02 -9999 0 -0.29 5 5
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.049 -9999 0 -0.61 6 6
PDGFRB 0.005 0.049 -9999 0 -0.79 4 4
SPHK1 -0.025 0.055 -9999 0 -1.1 2 2
mol:S1P -0.031 0.057 -9999 0 -0.97 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.39 381 381
GNAO1 -0.023 0.14 -9999 0 -0.5 67 67
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.59 77 77
PLCG1 -0.091 0.22 -9999 0 -0.56 99 99
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.049 -9999 0 -0.79 4 4
GNAI2 0.008 0.006 -9999 0 -10000 0 0
GNAI3 0.008 0.006 -9999 0 -10000 0 0
GNAI1 -0.038 0.19 -9999 0 -0.8 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.005 0.046 -9999 0 -0.54 6 6
S1P1/S1P -0.044 0.075 -9999 0 -0.58 8 8
negative regulation of cAMP metabolic process -0.098 0.22 -9999 0 -0.38 381 381
MAPK3 -0.16 0.31 -9999 0 -0.57 370 370
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 0.059 -9999 0 -0.8 6 6
PLCB2 -0.008 0.086 -9999 0 -0.5 9 9
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.038 0.061 -9999 0 -0.48 8 8
receptor internalization -0.043 0.07 -9999 0 -0.53 8 8
PTGS2 -0.33 0.55 -9999 0 -1.1 370 370
Rac1/GTP -0.038 0.061 -9999 0 -0.48 8 8
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.031 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.098 0.22 -9999 0 -0.38 381 381
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.077 -9999 0 -0.79 10 10
MAPK1 -0.16 0.31 -9999 0 -0.57 370 370
S1P1/S1P/PDGFB-D/PDGFRB -0.021 0.11 -9999 0 -0.64 10 10
ABCC1 0 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.002 0.026 -9999 0 -0.29 9 9
Syndecan-3/Src/Cortactin -0.18 0.2 -9999 0 -0.4 478 478
Syndecan-3/Neurocan -0.007 0.028 -9999 0 -10000 0 0
POMC -0.024 0.12 -9999 0 -0.49 54 54
EGFR -0.29 0.38 -9999 0 -0.78 410 410
Syndecan-3/EGFR -0.16 0.21 -9999 0 -0.44 405 405
AGRP -0.003 0.028 -9999 0 -0.29 10 10
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN -0.001 0.013 -9999 0 -0.29 2 2
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.024 -9999 0 -0.79 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.019 0.073 -9999 0 -0.29 72 72
long-term memory -0.002 0.02 -9999 0 -0.41 2 2
Syndecan-3/IL8 -0.016 0.066 -9999 0 -0.44 22 22
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.003 0.032 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PTN -0.34 0.39 -9999 0 -0.78 480 480
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.17 0.19 -9999 0 -0.39 478 478
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 0.031 -9999 0 -0.6 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 0.065 -9999 0 -0.43 22 22
IL8 -0.033 0.13 -9999 0 -0.42 87 87
Syndecan-3/Fyn/Cortactin -0.002 0.02 -9999 0 -0.42 2 2
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.02 0.094 -9999 0 -0.6 24 24
Gamma Secretase -0.001 0.014 -9999 0 -0.44 1 1
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.054 0.3 -10000 0 -0.81 131 131
IHH -0.014 0.082 -10000 0 -0.42 9 9
SHH Np/Cholesterol/GAS1 -0.032 0.12 -10000 0 -0.49 66 66
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.032 0.12 0.48 66 -10000 0 66
SMO/beta Arrestin2 -0.076 0.23 -10000 0 -0.84 82 82
SMO -0.036 0.26 -10000 0 -0.86 91 91
AKT1 0.006 0.12 -10000 0 -0.45 28 28
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.058 0.21 -10000 0 -0.79 81 81
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.035 0.26 -10000 0 -0.83 91 91
STIL -0.039 0.21 -10000 0 -0.7 86 86
DHH N/PTCH2 -0.061 0.19 -10000 0 -0.63 104 104
DHH N/PTCH1 -0.09 0.24 -10000 0 -0.74 116 116
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DHH -0.022 0.13 -10000 0 -0.76 32 32
PTHLH -0.081 0.38 -10000 0 -1.1 131 131
determination of left/right symmetry -0.035 0.26 -10000 0 -0.83 91 91
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
skeletal system development -0.079 0.37 -10000 0 -1 131 131
IHH N/Hhip -0.009 0.051 -10000 0 -0.53 3 3
DHH N/Hhip -0.019 0.1 -10000 0 -0.61 32 32
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.035 0.26 -10000 0 -0.83 91 91
pancreas development -0.003 0.041 -10000 0 -0.4 9 9
HHAT -0.001 0.024 -10000 0 -0.79 1 1
PI3K -0.008 0.068 -10000 0 -0.6 14 14
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.047 0.19 -10000 0 -0.79 65 65
somite specification -0.035 0.26 -10000 0 -0.83 91 91
SHH Np/Cholesterol/PTCH1 -0.071 0.2 -10000 0 -0.71 91 91
SHH Np/Cholesterol/PTCH2 -0.039 0.13 -10000 0 -0.48 82 82
SHH Np/Cholesterol/Megalin -0.14 0.21 -10000 0 -0.48 292 292
SHH 0.01 0.035 -10000 0 -0.61 1 1
catabolic process -0.047 0.26 -10000 0 -0.82 97 97
SMO/Vitamin D3 -0.075 0.22 -10000 0 -0.81 83 83
SHH Np/Cholesterol/Hhip -0.005 0.035 -10000 0 -0.38 6 6
LRP2 -0.22 0.35 -10000 0 -0.74 318 318
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.82 99 99
SHH Np/Cholesterol/BOC -0.039 0.13 -10000 0 -0.49 82 82
SHH Np/Cholesterol/CDO -0.009 0.059 -10000 0 -0.48 15 15
mesenchymal cell differentiation 0.005 0.035 0.38 6 -10000 0 6
mol:Vitamin D3 -0.03 0.22 -10000 0 -0.72 91 91
IHH N/PTCH2 -0.055 0.18 -10000 0 -0.67 81 81
CDON -0.01 0.089 -10000 0 -0.79 14 14
IHH N/PTCH1 -0.045 0.26 -10000 0 -0.83 97 97
Megalin/LRPAP1 -0.16 0.26 -10000 0 -0.6 291 291
PTCH2 -0.058 0.21 -10000 0 -0.79 81 81
SHH Np/Cholesterol -0.003 0.025 -10000 0 -0.49 1 1
PTCH1 -0.047 0.26 -10000 0 -0.82 97 97
HHIP -0.003 0.041 -10000 0 -0.4 9 9
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.052 0.2 -9999 0 -0.8 74 74
PDGF/PDGFRA/CRKL -0.041 0.15 -9999 0 -0.6 73 73
positive regulation of JUN kinase activity -0.031 0.12 -9999 0 -0.46 73 73
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.044 0.15 -9999 0 -0.61 73 73
AP1 -0.36 0.54 -9999 0 -1.2 329 329
mol:IP3 -0.035 0.16 -9999 0 -0.63 73 73
PLCG1 -0.035 0.16 -9999 0 -0.63 73 73
PDGF/PDGFRA/alphaV Integrin -0.041 0.15 -9999 0 -0.6 73 73
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.035 0.16 -9999 0 -0.63 73 73
CAV3 -0.001 0.015 -9999 0 -0.29 3 3
CAV1 -0.17 0.33 -9999 0 -0.79 241 241
SHC/Grb2/SOS1 -0.031 0.12 -9999 0 -0.46 73 73
PDGF/PDGFRA/Shf -0.041 0.15 -9999 0 -0.61 73 73
FOS -0.32 0.55 -9999 0 -1.1 329 329
JUN -0.024 0.059 -9999 0 -0.67 7 7
oligodendrocyte development -0.04 0.15 -9999 0 -0.6 73 73
GRB2 0 0.009 -9999 0 -0.29 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
mol:DAG -0.035 0.16 -9999 0 -0.63 73 73
PDGF/PDGFRA -0.052 0.2 -9999 0 -0.8 74 74
actin cytoskeleton reorganization -0.041 0.15 -9999 0 -0.6 74 74
SRF 0.015 0.022 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.041 0.15 -9999 0 -0.54 83 83
PDGF/PDGFRA/Crk/C3G -0.035 0.13 -9999 0 -0.52 73 73
JAK1 -0.025 0.16 -9999 0 -0.6 74 74
ELK1/SRF -0.027 0.12 -9999 0 -0.47 73 73
SHB -0.001 0.025 -9999 0 -0.54 2 2
SHF -0.001 0.027 -9999 0 -0.46 3 3
CSNK2A1 0.019 0.027 -9999 0 -10000 0 0
GO:0007205 -0.037 0.17 -9999 0 -0.65 73 73
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.031 0.12 -9999 0 -0.46 73 73
PDGF/PDGFRA/SHB -0.041 0.15 -9999 0 -0.6 74 74
PDGF/PDGFRA/Caveolin-1 -0.17 0.32 -9999 0 -0.7 266 266
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.035 0.16 -9999 0 -0.59 73 73
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PDGF/PDGFRA/Crk -0.041 0.15 -9999 0 -0.6 73 73
JAK-STAT cascade -0.025 0.16 -9999 0 -0.6 74 74
cell proliferation -0.041 0.15 -9999 0 -0.61 73 73
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.019 0.097 -9999 0 -0.51 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.043 0.11 -9999 0 -0.46 6 6
AP1 -0.19 0.25 -9999 0 -0.47 423 423
mol:PIP3 -0.2 0.24 -9999 0 -0.58 191 191
AKT1 -0.016 0.078 -9999 0 -0.59 10 10
PTK2B 0.014 0.062 -9999 0 -0.3 25 25
RHOA 0.028 0.028 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.007 0.13 -9999 0 -0.35 128 128
MAGI3 -0.001 0.034 -9999 0 -0.79 2 2
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.062 0.15 -9999 0 -0.42 147 147
HRAS/GDP -0.002 0.019 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.019 0.14 -9999 0 -0.4 124 124
NF kappa B1 p50/RelA -0.053 0.14 -9999 0 -0.63 10 10
endothelial cell migration 0.007 0.12 -9999 0 -0.63 34 34
ADCY4 -0.004 0.15 -9999 0 -0.63 41 41
ADCY5 -0.071 0.19 -9999 0 -0.59 82 82
ADCY6 0.006 0.13 -9999 0 -0.6 31 31
ADCY7 0.006 0.13 -9999 0 -0.6 31 31
ADCY1 -0.003 0.14 -9999 0 -0.64 37 37
ADCY2 -0.015 0.16 -9999 0 -0.62 49 49
ADCY3 0.006 0.13 -9999 0 -0.6 31 31
ADCY8 0.003 0.13 -9999 0 -0.59 33 33
ADCY9 0.006 0.13 -9999 0 -0.6 31 31
GSK3B 0.021 0.059 -9999 0 -0.35 10 10
arachidonic acid secretion 0.009 0.13 -9999 0 -0.45 58 58
GNG2 -0.011 0.092 -9999 0 -0.79 15 15
TRIP6 -0.001 0.016 -9999 0 -0.51 1 1
GNAO1 -0.006 0.13 -9999 0 -0.52 56 56
HRAS -0.003 0.028 -9999 0 -0.29 10 10
NFKBIA -0.003 0.15 -9999 0 -0.39 128 128
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 0.063 -9999 0 -0.79 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 -0.01 0.088 -9999 0 -0.79 14 14
mol:IP3 -0.007 0.13 -9999 0 -0.35 128 128
PLCB3 0.026 0.016 -9999 0 -10000 0 0
FOS -0.24 0.36 -9999 0 -0.79 329 329
positive regulation of mitosis 0.009 0.13 -9999 0 -0.45 58 58
LPA/LPA1-2-3 -0.073 0.17 -9999 0 -0.49 147 147
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 -0.38 25 25
GNAZ 0.008 0.1 -9999 0 -0.48 43 43
EGFR/PI3K-beta/Gab1 -0.2 0.26 -9999 0 -0.63 176 176
positive regulation of dendritic cell cytokine production -0.072 0.17 -9999 0 -0.48 147 147
LPA/LPA2/MAGI-3 -0.002 0.025 -9999 0 -0.52 2 2
ARHGEF1 -0.011 0.069 -9999 0 -0.44 24 24
GNAI2 0.013 0.087 -9999 0 -0.46 34 34
GNAI3 0.013 0.087 -9999 0 -0.46 34 34
GNAI1 -0.018 0.16 -9999 0 -0.53 89 89
LPA/LPA3 -0.08 0.2 -9999 0 -0.6 128 128
LPA/LPA2 -0.002 0.016 -9999 0 -10000 0 0
LPA/LPA1 -0.017 0.096 -9999 0 -0.54 34 34
HB-EGF/EGFR -0.26 0.25 -9999 0 -0.57 410 410
HBEGF -0.071 0.11 -9999 0 -0.6 3 3
mol:DAG -0.007 0.13 -9999 0 -0.35 128 128
cAMP biosynthetic process -0.012 0.15 -9999 0 -0.56 56 56
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 -0.003 0.15 -9999 0 -0.39 128 128
GNAQ -0.053 0.13 -9999 0 -0.41 131 131
LPAR2 -0.001 0.015 -9999 0 -0.29 3 3
LPAR3 -0.1 0.26 -9999 0 -0.66 171 171
LPAR1 -0.019 0.12 -9999 0 -0.79 24 24
IL8 -0.19 0.23 -9999 0 -0.44 432 432
PTK2 -0.066 0.16 -9999 0 -0.45 147 147
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.062 0.15 -9999 0 -0.42 147 147
EGFR -0.29 0.38 -9999 0 -0.78 410 410
PLCG1 -0.029 0.15 -9999 0 -0.42 128 128
PLD2 -0.066 0.16 -9999 0 -0.45 147 147
G12/G13 -0.013 0.074 -9999 0 -0.48 24 24
PI3K-beta -0.019 0.093 -9999 0 -0.72 10 10
cell migration -0.021 0.053 -9999 0 -0.24 6 6
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
PXN 0.002 0.1 -9999 0 -0.39 25 25
HRAS/GTP -0.035 0.12 -9999 0 -0.46 57 57
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 483 483
PRKCE 0.01 0.002 -9999 0 -10000 0 0
PRKCD 0.001 0.12 -9999 0 -0.39 8 8
Gi(beta/gamma) -0.037 0.12 -9999 0 -0.58 39 39
mol:LPA -0.002 0.021 -9999 0 -0.22 10 10
TRIP6/p130 Cas/FAK1/Paxillin -0.055 0.14 -9999 0 -0.49 26 26
MAPKKK cascade 0.009 0.13 -9999 0 -0.45 58 58
contractile ring contraction involved in cytokinesis 0.028 0.028 -9999 0 -0.23 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.057 0.14 -9999 0 -0.42 136 136
GNA15 -0.053 0.13 -9999 0 -0.41 129 129
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.021 0.15 -9999 0 -0.41 124 124
GNA11 -0.053 0.13 -9999 0 -0.41 132 132
Rac1/GTP 0.001 0.005 -9999 0 -10000 0 0
MMP2 0.007 0.12 -9999 0 -0.63 34 34
Syndecan-1-mediated 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
TGFB1 -0.001 0.015 -9999 0 -0.29 3 3
CCL5 -0.014 0.079 -9999 0 -0.36 44 44
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.08 0.11 -9999 0 -0.34 106 106
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 -0.074 0.096 -9999 0 -0.35 46 46
Syndecan-1/Syntenin -0.074 0.096 -9999 0 -0.48 6 6
MAPK3 -0.047 0.095 -9999 0 -0.48 5 5
HGF/MET -0.14 0.27 -9999 0 -0.64 240 240
TGFB1/TGF beta receptor Type II -0.001 0.015 -9999 0 -0.29 3 3
BSG 0 0.009 -9999 0 -0.29 1 1
keratinocyte migration -0.073 0.095 -9999 0 -0.35 46 46
Syndecan-1/RANTES -0.081 0.11 -9999 0 -0.39 50 50
Syndecan-1/CD147 -0.065 0.093 -9999 0 -0.49 6 6
Syndecan-1/Syntenin/PIP2 -0.071 0.093 -9999 0 -0.46 6 6
LAMA5 0 0.009 -9999 0 -0.29 1 1
positive regulation of cell-cell adhesion -0.07 0.091 -9999 0 -0.45 6 6
MMP7 -0.12 0.28 -9999 0 -0.7 191 191
HGF -0.053 0.2 -9999 0 -0.79 73 73
Syndecan-1/CASK -0.076 0.1 -9999 0 -0.33 106 106
Syndecan-1/HGF/MET -0.17 0.24 -9999 0 -0.58 243 243
regulation of cell adhesion -0.038 0.093 -9999 0 -0.48 4 4
HPSE -0.007 0.051 -9999 0 -0.34 21 21
positive regulation of cell migration -0.08 0.11 -9999 0 -0.34 106 106
SDC1 -0.08 0.11 -9999 0 -0.35 106 106
Syndecan-1/Collagen -0.08 0.11 -9999 0 -0.34 106 106
PPIB -0.001 0.015 -9999 0 -0.29 3 3
MET -0.14 0.3 -9999 0 -0.78 189 189
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 483 483
MAPK1 -0.047 0.095 -9999 0 -0.48 5 5
homophilic cell adhesion -0.079 0.11 -9999 0 -0.34 106 106
MMP1 -0.22 0.13 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.001 0.034 -9999 0 -0.79 2 2
LAT2 -0.063 0.14 -9999 0 -0.43 95 95
AP1 -0.15 0.21 -9999 0 -0.57 154 154
mol:PIP3 -0.027 0.2 -9999 0 -0.5 99 99
IKBKB 0.002 0.12 -9999 0 -0.32 54 54
AKT1 -0.082 0.17 -9999 0 -0.66 46 46
IKBKG 0.002 0.12 -9999 0 -0.32 55 55
MS4A2 -0.069 0.22 -9999 0 -0.76 99 99
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.3 1 1
MAP3K1 0.005 0.13 -9999 0 -0.45 43 43
mol:Ca2+ -0.013 0.15 -9999 0 -0.36 109 109
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.062 0.14 -9999 0 -0.43 95 95
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.062 0.16 -9999 0 -0.48 142 142
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.096 0.2 -9999 0 -0.48 217 217
PTPN13 -0.031 0.17 -9999 0 -0.54 68 68
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.006 0.15 -9999 0 -0.41 45 45
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 -0.5 109 109
LAT -0.064 0.14 -9999 0 -0.43 96 96
PAK2 -0.004 0.14 -9999 0 -0.5 44 44
NFATC2 -0.1 0.24 -9999 0 -0.8 104 104
HRAS -0.014 0.15 -9999 0 -0.54 47 47
GAB2 -0.004 0.042 -9999 0 -0.39 10 10
PLA2G1B 0.028 0.018 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.25 -9999 0 -0.6 217 217
Antigen/IgE/Fc epsilon R1 -0.11 0.23 -9999 0 -0.55 217 217
mol:GDP -0.02 0.16 -9999 0 -0.55 47 47
JUN -0.005 0.063 -9999 0 -0.79 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
FOS -0.24 0.36 -9999 0 -0.79 329 329
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.067 0.15 -9999 0 -0.45 99 99
CHUK 0.002 0.12 -9999 0 -0.32 55 55
KLRG1 -0.062 0.14 -9999 0 -0.4 99 99
VAV1 -0.064 0.14 -9999 0 -0.44 98 98
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.062 0.14 -9999 0 -0.43 95 95
negative regulation of mast cell degranulation -0.056 0.12 -9999 0 -0.51 43 43
BTK -0.061 0.14 -9999 0 -0.52 52 52
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.086 0.2 -9999 0 -0.43 219 219
GAB2/PI3K/SHP2 -0.091 0.19 -9999 0 -0.73 48 48
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.069 0.16 -9999 0 -0.37 171 171
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.22 -9999 0 -0.51 219 219
FCER1G 0.003 0.012 -9999 0 -0.29 1 1
FCER1A -0.11 0.29 -9999 0 -0.8 161 161
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.22 -9999 0 -0.51 217 217
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 0.009 0.081 -9999 0 -0.68 10 10
DUSP1 -0.1 0.26 -9999 0 -0.79 142 142
NF-kappa-B/RelA -0.027 0.054 -9999 0 -0.24 1 1
actin cytoskeleton reorganization -0.027 0.15 -9999 0 -0.42 95 95
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.059 0.14 -9999 0 -0.53 53 53
FER -0.066 0.15 -9999 0 -0.44 102 102
RELA 0 0 -9999 0 -10000 0 0
ITK -0.035 0.11 -9999 0 -0.6 39 39
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.017 0.16 -9999 0 -0.57 46 46
cytokine secretion -0.019 0.04 -9999 0 -10000 0 0
SPHK1 -0.065 0.14 -9999 0 -0.44 98 98
PTK2 -0.029 0.16 -9999 0 -0.44 95 95
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.089 0.19 -9999 0 -0.44 217 217
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.022 0.2 -9999 0 -0.48 100 100
MAP2K2 0.023 0.019 -9999 0 -10000 0 0
MAP2K1 0.023 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.057 0.13 -9999 0 -0.51 43 43
MAP2K4 0.017 0.033 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.11 0.23 -9999 0 -0.55 219 219
mol:Choline -0.094 0.2 -9999 0 -0.47 217 217
SHC/Grb2/SOS1 -0.056 0.13 -9999 0 -0.54 41 41
FYN -0.001 0.034 -9999 0 -0.79 2 2
DOK1 -0.001 0.018 -9999 0 -10000 0 0
PXN -0.019 0.15 -9999 0 -0.54 41 41
HCLS1 -0.062 0.14 -9999 0 -0.43 95 95
PRKCB -0.015 0.16 -9999 0 -0.38 105 105
FCGR2B -0.004 0.054 -9999 0 -0.7 6 6
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.057 0.13 -9999 0 -0.52 43 43
LCP2 0 0.009 -9999 0 -0.29 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.5 207 207
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.094 0.2 -9999 0 -0.47 217 217
IKK complex 0.019 0.093 -9999 0 -0.23 51 51
WIPF1 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.009 0.053 -10000 0 -0.42 14 14
adherens junction organization 0.032 0.061 -10000 0 -0.3 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 -10000 0 -0.37 412 412
FMN1 0.025 0.086 -10000 0 -0.44 22 22
mol:IP3 -0.009 0.05 -10000 0 -0.39 14 14
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.052 -10000 0 -0.31 29 29
CTNNB1 0.001 0.004 -10000 0 -10000 0 0
AKT1 -0.01 0.051 -10000 0 -0.38 14 14
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.079 -10000 0 -0.5 28 28
CTNND1 0.011 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.055 -10000 0 -10000 0 0
VASP 0.033 0.056 -10000 0 -10000 0 0
ZYX 0.033 0.056 -10000 0 -10000 0 0
JUB 0.032 0.062 -10000 0 -0.3 33 33
EGFR(dimer) -0.16 0.21 -10000 0 -0.42 406 406
E-cadherin/beta catenin-gamma catenin -0.013 0.081 -10000 0 -0.5 29 29
mol:PI-3-4-5-P3 -0.01 0.055 -10000 0 -0.4 14 14
PIK3CA 0.011 0.009 -10000 0 -0.29 1 1
PI3K -0.011 0.056 -10000 0 -0.41 14 14
FYN 0.04 0.055 -10000 0 -0.38 2 2
mol:Ca2+ -0.009 0.049 -10000 0 -0.38 14 14
JUP 0 0.026 -10000 0 -0.54 2 2
PIK3R1 0.001 0.09 -10000 0 -0.79 14 14
mol:DAG -0.009 0.05 -10000 0 -0.39 14 14
CDH1 -0.02 0.12 -10000 0 -0.79 28 28
RhoA/GDP -0.14 0.18 -10000 0 -0.37 412 412
establishment of polarity of embryonic epithelium 0.033 0.055 -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 0.38 -10000 0 -0.78 410 410
CASR 0.033 0.056 -10000 0 -0.36 14 14
RhoA/GTP -0.008 0.044 -10000 0 -0.34 14 14
AKT2 -0.01 0.051 -10000 0 -0.38 14 14
actin cable formation 0.032 0.084 -10000 0 -0.42 21 21
apoptosis 0.01 0.052 0.39 14 -10000 0 14
CTNNA1 0.012 0.002 -10000 0 -10000 0 0
mol:GDP -0.15 0.2 -10000 0 -0.4 412 412
PIP5K1A 0.033 0.056 -10000 0 -10000 0 0
PLCG1 -0.009 0.051 -10000 0 -0.4 14 14
Rac1/GTP -0.15 0.19 -10000 0 -0.39 406 406
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.053 0.2 -10000 0 -0.78 74 74
HRAS -0.003 0.028 -10000 0 -0.29 10 10
EGFR -0.29 0.38 -10000 0 -0.78 410 410
AKT 0.013 0.084 -10000 0 -0.57 20 20
FOXO3 -0.002 0.041 -10000 0 -0.79 3 3
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.009 0.082 -10000 0 -0.79 12 12
AKT3 -0.014 0.11 -10000 0 -0.79 20 20
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.3 -10000 0 -0.78 189 189
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 -0.29 2 2
PIK3CG -0.013 0.099 -10000 0 -0.79 17 17
PIK3R3 0 0.009 -10000 0 -0.29 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.024 -10000 0 -0.79 1 1
RAS -0.095 0.16 0.25 1 -0.27 437 438
ERBB2 -0.024 0.083 -10000 0 -0.3 89 89
proliferation/survival/translation -0.004 0.059 0.28 14 -10000 0 14
PI3K -0.087 0.16 -10000 0 -0.36 218 218
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
KRAS -0.001 0.013 -10000 0 -0.29 2 2
FOXO 0.027 0.029 -10000 0 -0.49 1 1
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.12 0.18 -9999 0 -0.39 330 330
MAP3K8 0.001 0.073 -9999 0 -0.74 10 10
FOS -0.035 0.14 -9999 0 -0.46 40 40
PRKCA -0.013 0.13 -9999 0 -0.76 31 31
PTPN7 -0.009 0.073 -9999 0 -0.3 63 63
HRAS -0.003 0.028 -9999 0 -0.3 10 10
PRKCB -0.011 0.12 -9999 0 -0.55 39 39
NRAS -0.001 0.013 -9999 0 -0.3 2 2
RAS family/GTP -0.002 0.015 -9999 0 -10000 0 0
MAPK3 -0.008 0.073 -9999 0 -10000 0 0
MAP2K1 -0.013 0.14 -9999 0 -0.6 48 48
ELK1 -0.003 0.01 -9999 0 -0.29 1 1
BRAF -0.033 0.12 -9999 0 -0.57 48 48
mol:GTP -0.002 0.003 -9999 0 -0.006 329 329
MAPK1 -0.008 0.073 -9999 0 -0.29 1 1
RAF1 -0.033 0.12 -9999 0 -0.57 48 48
KRAS -0.001 0.012 -9999 0 -0.29 2 2
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.048 -9999 0 -0.79 4 4
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.6 37 37
PTK2 -0.066 0.19 -9999 0 -0.57 122 122
positive regulation of JNK cascade -0.038 0.11 -9999 0 -0.34 122 122
CDC42/GDP -0.001 0.16 -9999 0 -0.46 122 122
Rac1/GDP 0.001 0.16 -9999 0 -0.45 122 122
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 -0.047 0.13 -9999 0 -0.42 122 122
nectin-3/I-afadin -0.069 0.2 -9999 0 -0.62 122 122
RAPGEF1 -0.01 0.18 -9999 0 -0.52 122 122
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.024 0.21 -9999 0 -0.61 122 122
PDGFB-D/PDGFRB -0.003 0.047 -9999 0 -0.79 4 4
TLN1 0 0.1 -9999 0 -0.56 14 14
Rap1/GTP -0.041 0.11 -9999 0 -0.36 122 122
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.035 -9999 0 -0.48 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.069 0.2 -9999 0 -0.62 122 122
PVR 0 0.009 -9999 0 -0.29 1 1
Necl-5(dimer) 0 0.009 -9999 0 -0.29 1 1
mol:GDP -0.013 0.2 -9999 0 -0.58 122 122
MLLT4 -0.005 0.059 -9999 0 -0.72 7 7
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.058 0.17 -9999 0 -0.5 128 128
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
positive regulation of lamellipodium assembly -0.04 0.11 -9999 0 -0.35 122 122
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.087 0.25 -9999 0 -0.79 121 121
PVRL2 -0.001 0.015 -9999 0 -0.29 3 3
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
CDH1 -0.02 0.12 -9999 0 -0.79 28 28
CLDN1 -0.036 0.15 -9999 0 -0.79 40 40
JAM-A/CLDN1 -0.074 0.18 -9999 0 -0.51 154 154
SRC -0.078 0.22 -9999 0 -0.69 122 122
ITGB3 -0.028 0.14 -9999 0 -0.74 41 41
nectin-1(dimer)/I-afadin/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
FARP2 -0.018 0.2 -9999 0 -0.57 122 122
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 -0.54 122 122
nectin-1/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
nectin-2/I-afadin -0.004 0.046 -9999 0 -0.6 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 -0.54 122 122
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 -0.038 0.11 -9999 0 -0.34 122 122
alphaV/beta3 Integrin/Talin -0.04 0.13 -9999 0 -0.61 42 42
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
nectin-2(dimer)/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
PIP5K1C -0.033 0.1 -9999 0 -0.58 15 15
VAV2 -0.02 0.2 -9999 0 -0.58 122 122
RAP1/GDP -0.048 0.13 -9999 0 -0.42 122 122
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 -0.54 122 122
nectin-3(dimer)/I-afadin/I-afadin -0.069 0.2 -9999 0 -0.62 122 122
Rac1/GTP -0.049 0.14 -9999 0 -0.44 122 122
PTPRM -0.037 0.12 -9999 0 -0.32 126 126
E-cadherin/beta catenin/alpha catenin -0.013 0.074 -9999 0 -0.43 33 33
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.11 0.2 -10000 0 -0.47 262 262
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.022 -10000 0 -0.2 13 13
GNB1/GNG2 -0.007 0.061 -10000 0 -0.52 15 15
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 -0.49 258 258
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 0.11 258 -10000 0 258
GNAL -0.19 0.33 -10000 0 -0.79 258 258
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
CRH -0.003 0.032 -10000 0 -0.29 13 13
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.041 -10000 0 -0.44 9 9
MAPK11 0.007 0.024 -10000 0 -0.44 3 3
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.007 0.054 -9999 0 -0.45 15 15
RGS9BP -0.019 0.072 -9999 0 -0.29 70 70
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -0.29 11 11
mol:Na + -0.02 0.053 -9999 0 -10000 0 0
mol:ADP 0.007 0.028 -9999 0 -10000 0 0
GNAT2 -0.001 0.018 -9999 0 -0.29 4 4
RGS9-1/Gbeta5/R9AP -0.061 0.16 -9999 0 -0.52 109 109
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
GRK7 -0.002 0.026 -9999 0 -0.29 9 9
CNGB3 -0.01 0.054 -9999 0 -0.29 39 39
Cone Metarhodopsin II/X-Arrestin -0.001 0.017 -9999 0 -10000 0 0
mol:Ca2+ -0.092 0.088 -9999 0 -10000 0 0
Cone PDE6 -0.053 0.14 -9999 0 -0.46 106 106
Cone Metarhodopsin II -0.003 0.019 -9999 0 -10000 0 0
Na + (4 Units) -0.097 0.082 -9999 0 -10000 0 0
GNAT2/GDP -0.052 0.14 -9999 0 -0.45 106 106
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.016 -9999 0 -10000 0 0
Cone Transducin -0.008 0.057 -9999 0 -0.48 15 15
SLC24A2 -0.17 0.14 -9999 0 -0.29 649 649
GNB3/GNGT2 -0.009 0.071 -9999 0 -0.6 15 15
GNB3 -0.011 0.088 -9999 0 -0.63 19 19
GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
CNGA3 -0.028 0.086 -9999 0 -10000 0 0
ARR3 -0.002 0.025 -9999 0 -0.29 8 8
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.02 0.053 -9999 0 -10000 0 0
mol:Pi -0.061 0.16 -9999 0 -0.52 109 109
Cone CNG Channel -0.016 0.04 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.17 0.14 -9999 0 -0.29 649 649
RGS9 -0.08 0.23 -9999 0 -0.73 121 121
PDE6C 0 0.009 -9999 0 -0.29 1 1
GNGT2 -0.001 0.034 -9999 0 -0.79 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.002 0.022 -9999 0 -10000 0 0
Glypican 2 network

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
MDK -0.012 0.057 -9999 0 -0.29 43 43
GPC2 -0.038 0.1 -9999 0 -0.3 136 136
GPC2/Midkine -0.032 0.081 -9999 0 -0.4 19 19
neuron projection morphogenesis -0.032 0.081 -9999 0 -0.4 19 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.54 0.36 -9999 0 -0.79 751 751
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.007 0.045 -9999 0 -0.29 27 27
TCEB1 -0.001 0.015 -9999 0 -10000 0 0
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.008 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.018 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.05 0.11 -9999 0 -0.29 188 188
ARNT/IPAS -0.41 0.28 -9999 0 -0.6 751 751
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 -0.001 0.013 -9999 0 -0.29 2 2
RACK1/Elongin B/Elongin C -0.004 0.024 -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 -0.011 0.039 -9999 0 -0.47 2 2
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.016 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
HIF1A/JAB1 -0.001 0.005 -9999 0 -10000 0 0
EGLN3 -0.023 0.081 -9999 0 -0.3 83 83
EGLN2 -0.002 0.022 -9999 0 -0.29 6 6
EGLN1 -0.001 0.024 -9999 0 -0.79 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 0.04 -9999 0 -10000 0 0
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 0.052 0.28 37 -10000 0 37
RFC1 0.011 0.052 0.28 37 -10000 0 37
PRKDC 0.01 0.053 0.28 37 -10000 0 37
RIPK1 0 0.001 -10000 0 -10000 0 0
CASP7 -0.023 0.037 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.017 0.067 0.25 16 -0.38 18 34
MAP2K4 -0.058 0.16 -10000 0 -0.4 40 40
mol:ceramide -0.032 0.12 -10000 0 -0.54 23 23
GSN 0.004 0.076 0.28 36 -0.49 14 50
FASLG/FAS/FADD/FAF1/Caspase 8 -0.031 0.074 0.23 14 -0.46 18 32
FAS 0.003 0.06 -10000 0 -0.8 6 6
BID 0.001 0.015 0.32 2 -10000 0 2
MAP3K1 -0.021 0.094 -10000 0 -0.28 17 17
MAP3K7 0.006 0.011 -10000 0 -0.29 1 1
RB1 0.01 0.052 0.28 36 -0.29 1 37
CFLAR -0.001 0.023 -10000 0 -0.76 1 1
HGF/MET -0.14 0.26 -10000 0 -0.58 256 256
ARHGDIB 0.01 0.053 0.28 37 -10000 0 37
FADD 0.003 0.037 -10000 0 -0.31 15 15
actin filament polymerization -0.004 0.076 0.49 14 -0.28 36 50
NFKB1 -0.076 0.1 -10000 0 -0.32 2 2
MAPK8 -0.12 0.24 -10000 0 -0.43 406 406
DFFA 0.011 0.052 0.28 37 -10000 0 37
DNA fragmentation during apoptosis 0.01 0.052 0.28 37 -10000 0 37
FAS/FADD/MET -0.096 0.21 -10000 0 -0.55 190 190
CFLAR/RIP1 -0.001 0.017 -10000 0 -0.56 1 1
FAIM3 -0.002 0.056 -10000 0 -0.78 2 2
FAF1 0.008 0.006 -10000 0 -10000 0 0
PARP1 0.01 0.052 0.28 37 -10000 0 37
DFFB 0.011 0.052 0.28 37 -10000 0 37
CHUK -0.066 0.088 -10000 0 -10000 0 0
FASLG -0.015 0.11 -10000 0 -0.42 58 58
FAS/FADD -0.006 0.053 -10000 0 -0.64 6 6
HGF -0.053 0.2 -10000 0 -0.79 73 73
LMNA 0.01 0.047 0.26 37 -10000 0 37
CASP6 0.01 0.052 0.28 37 -10000 0 37
CASP10 0.005 0.049 -10000 0 -0.8 4 4
CASP3 0.013 0.063 0.34 39 -10000 0 39
PTPN13 -0.023 0.13 -10000 0 -0.79 32 32
CASP8 0.003 0.023 0.45 2 -10000 0 2
IL6 -0.47 0.67 -10000 0 -1.4 400 400
MET -0.14 0.3 -10000 0 -0.78 189 189
ICAD/CAD 0.01 0.048 0.26 37 -10000 0 37
FASLG/FAS/FADD/FAF1/Caspase 10 -0.033 0.12 -10000 0 -0.55 23 23
activation of caspase activity by cytochrome c 0.001 0.015 0.32 2 -10000 0 2
PAK2 0.01 0.052 0.28 37 -10000 0 37
BCL2 -0.022 0.14 -10000 0 -0.79 37 37
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.79 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.011 0.076 0.6 1 -10000 0 1
CDKN1A -0.002 0.04 -10000 0 -0.94 2 2
KAT2B -0.001 0.024 -10000 0 -0.79 1 1
BAX -0.001 0.018 -10000 0 -0.29 4 4
FOXO3 -0.001 0.017 -10000 0 -0.33 3 3
FOXO1 -0.009 0.082 -10000 0 -0.79 12 12
FOXO4 0.022 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 -0.56 0.35 -10000 0 -0.77 788 788
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.029 -10000 0 -0.6 1 1
PPARGC1A -0.17 0.32 -10000 0 -0.79 230 230
FHL2 -0.004 0.054 -10000 0 -0.79 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.007 -10000 0 -10000 0 0
HIST2H4A -0.011 0.076 -10000 0 -0.6 1 1
SIRT1/FOXO3a 0 0.014 -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 0.017 -10000 0 -0.52 1 1
SIRT1/Histone H1b -0.003 0.012 -10000 0 -10000 0 0
apoptosis 0 0.011 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.21 -10000 0 -0.52 230 230
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 0.059 -10000 0 -0.48 17 17
HIST1H1E 0.015 0.022 -10000 0 -10000 0 0
SIRT1/p300 0 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.023 0.51 1 -10000 0 1
TP53 0 0.009 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0 0.011 -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 -0.42 0.27 -10000 0 -0.6 760 760
ACSS2 0.02 0.019 -10000 0 -0.6 1 1
SIRT1/PCAF/MYOD -0.002 0.023 -10000 0 -0.52 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.009 0.052 -10000 0 -0.32 29 29
epithelial cell differentiation -0.011 0.069 -10000 0 -0.44 28 28
CYFIP2 -0.01 0.065 -10000 0 -0.36 31 31
ENAH 0.058 0.057 -10000 0 -10000 0 0
EGFR -0.29 0.38 -10000 0 -0.78 410 410
EPHA2 -0.004 0.058 -10000 0 -0.79 6 6
MYO6 -0.011 0.067 -10000 0 -0.42 29 29
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.038 -10000 0 -0.52 4 4
AQP5 -0.23 0.29 -10000 0 -0.58 428 428
CTNND1 0 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.065 -10000 0 -0.41 28 28
regulation of calcium-dependent cell-cell adhesion -0.032 0.11 -10000 0 -0.41 85 85
EGF -0.15 0.31 -10000 0 -0.78 214 214
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.037 0.14 -10000 0 -0.59 56 56
cortical microtubule organization -0.011 0.069 -10000 0 -0.44 28 28
GO:0000145 0.027 0.068 -10000 0 -0.39 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.07 -10000 0 -0.44 28 28
MLLT4 -0.005 0.059 -10000 0 -0.72 7 7
ARF6/GDP -0.011 0.059 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -10000 0 -0.47 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.037 0.071 -10000 0 -0.38 28 28
PVRL2 -0.001 0.015 -10000 0 -0.29 3 3
ZYX -0.011 0.066 -10000 0 -0.42 28 28
ARF6/GTP -0.003 0.033 -10000 0 -0.43 6 6
CDH1 -0.02 0.12 -10000 0 -0.79 28 28
EGFR/EGFR/EGF/EGF -0.24 0.26 -10000 0 -0.46 562 562
RhoA/GDP -0.011 0.065 -10000 0 -0.41 28 28
actin cytoskeleton organization 0.033 0.07 -10000 0 -0.39 29 29
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.59 36 36
GIT1 -0.001 0.02 -10000 0 -10000 0 0
IGF1R -0.02 0.12 -10000 0 -0.6 36 36
IGF1 -0.18 0.33 -10000 0 -0.79 247 247
DIAPH1 -0.002 0.043 -10000 0 -0.69 4 4
Wnt receptor signaling pathway 0.011 0.069 0.44 28 -10000 0 28
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.011 0.06 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL 0.033 0.072 -10000 0 -0.4 29 29
EFNA1 0 0.009 -10000 0 -0.29 1 1
LPP 0.031 0.078 -10000 0 -0.39 36 36
Ephrin A1/EPHA2 -0.012 0.069 -10000 0 -0.4 34 34
SEC6/SEC8 -0.012 0.065 -10000 0 -0.74 1 1
MGAT3 -0.033 0.11 -10000 0 -0.42 85 85
HGF/MET -0.11 0.2 -10000 0 -0.44 262 262
HGF -0.053 0.2 -10000 0 -0.79 73 73
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.009 0.052 -10000 0 -0.32 29 29
actin cable formation 0.072 0.055 -10000 0 -0.32 1 1
KIAA1543 0.032 0.087 -10000 0 -0.46 29 29
KIFC3 -0.011 0.068 -10000 0 -0.42 30 30
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.011 0.067 -10000 0 -0.42 29 29
NCK1/GIT1 -0.001 0.013 -10000 0 -10000 0 0
mol:GDP -0.011 0.069 -10000 0 -0.44 28 28
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.011 0.066 -10000 0 -0.42 28 28
PIP5K1C -0.011 0.066 -10000 0 -0.42 28 28
LIMA1 -0.001 0.024 -10000 0 -0.79 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.01 0.053 -10000 0 -10000 0 0
adherens junction assembly 0.048 0.083 -10000 0 -0.62 7 7
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.43 279 279
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.046 -10000 0 -0.6 6 6
MET -0.14 0.3 -10000 0 -0.78 189 189
PLEKHA7 -0.012 0.076 -10000 0 -0.46 28 28
mol:GTP -0.003 0.035 -10000 0 -0.46 6 6
establishment of epithelial cell apical/basal polarity -0.011 0.061 -10000 0 -0.7 1 1
cortical actin cytoskeleton stabilization -0.009 0.052 -10000 0 -0.32 29 29
regulation of cell-cell adhesion 0.033 0.07 -10000 0 -0.39 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.009 0.052 -10000 0 -0.32 29 29
LPA4-mediated signaling events

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
ADCY4 0 0.1 -9999 0 -0.53 41 41
ADCY5 -0.16 0.26 -9999 0 -0.53 354 354
ADCY6 0.02 0 -9999 0 -10000 0 0
ADCY7 0.02 0 -9999 0 -10000 0 0
ADCY1 -0.008 0.097 -9999 0 -0.53 29 29
ADCY2 -0.032 0.15 -9999 0 -0.53 90 90
ADCY3 0.02 0.005 -9999 0 -10000 0 0
ADCY8 0.01 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 -0.032 0.1 -9999 0 -0.31 75 75
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.029 0.031 0.078 2 -10000 0 2
BUB1B -0.041 0.053 -10000 0 -0.13 18 18
PLK1 -0.008 0.024 -10000 0 -10000 0 0
PLK1S1 0 0.014 -10000 0 -10000 0 0
KIF2A 0.002 0.021 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.008 0.024 -10000 0 -10000 0 0
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.17 0.12 -10000 0 -0.28 534 534
WEE1 -0.002 0.024 -10000 0 -10000 0 0
cytokinesis -0.056 0.058 -10000 0 -0.26 21 21
PP2A-alpha B56 0.027 0.019 -10000 0 -10000 0 0
AURKA 0 0.015 -10000 0 -10000 0 0
PICH/PLK1 -0.072 0.098 -10000 0 -0.34 11 11
CENPE -0.053 0.087 -10000 0 -0.17 386 386
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.002 0.021 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 -0.006 0.017 -10000 0 -10000 0 0
PAK1 -0.006 0.043 -10000 0 -0.29 25 25
SPC24 -0.18 0.14 -10000 0 -0.29 689 689
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN -0.006 0.019 -10000 0 -10000 0 0
GORASP1 0 0 -10000 0 -10000 0 0
metaphase 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.005 0.013 -10000 0 -0.052 2 2
G2 phase of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
STAG2 -0.001 0.024 -10000 0 -0.79 1 1
GRASP65/GM130/RAB1/GTP 0.008 0.009 -10000 0 -10000 0 0
spindle elongation -0.008 0.024 -10000 0 -10000 0 0
ODF2 0.002 0.004 -10000 0 -10000 0 0
BUB1 0.021 0.015 -10000 0 -10000 0 0
TPT1 0 0.014 -10000 0 -10000 0 0
CDC25C -0.009 0.017 -10000 0 -10000 0 0
CDC25B 0.005 0.041 -10000 0 -0.29 11 11
SGOL1 -0.029 0.031 -10000 0 -0.078 2 2
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.021 0.044 -10000 0 -10000 0 0
CDC14B -0.01 0.11 -10000 0 -0.62 36 36
CDC20 -0.16 0.15 -10000 0 -10000 0 0
PLK1/PBIP1 -0.028 0.053 -10000 0 -0.19 2 2
mitosis -0.006 0.007 -10000 0 -0.022 2 2
FBXO5 0 0.023 -10000 0 -10000 0 0
CDC2 -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.18 0.14 -10000 0 -0.29 662 662
metaphase plate congression -0.002 0.016 -10000 0 -10000 0 0
ERCC6L -0.064 0.089 -10000 0 -10000 0 0
NLP/gamma Tubulin -0.001 0.014 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0 0.014 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0 0 -10000 0 -10000 0 0
interphase -0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.1 -10000 0 -0.29 274 274
GRASP65/GM130/RAB1/GTP/PLK1 -0.002 0.004 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.003 0.024 -10000 0 -0.17 2 2
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.014 0.051 -10000 0 -0.29 30 30
microtubule-based process -0.12 0.069 -10000 0 -0.19 23 23
Golgi organization -0.008 0.024 -10000 0 -10000 0 0
Cohesin/SA2 -0.01 0.018 -10000 0 -0.45 1 1
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.22 0.13 -10000 0 -0.29 820 820
APC/C/CDC20 -0.088 0.081 -10000 0 -0.2 7 7
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation -0.028 0.052 -10000 0 -0.19 2 2
PRC1 -0.074 0.13 -10000 0 -0.29 275 275
ECT2 -0.004 0.039 -10000 0 -0.17 38 38
C13orf34 -0.001 0.022 -10000 0 -10000 0 0
NUDC -0.002 0.016 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.04 0.052 -10000 0 -0.12 18 18
spindle assembly -0.004 0.02 -10000 0 -10000 0 0
spindle stabilization 0 0.014 -10000 0 -10000 0 0
APC/C/HCDH1 -0.017 0.094 -10000 0 -0.53 36 36
MKLP2/PLK1 -0.12 0.069 -10000 0 -0.19 23 23
CCNB1 -0.05 0.12 -10000 0 -0.29 221 221
PPP1CB 0 0 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 -0.01 0.089 -10000 0 -0.51 32 32
TUBG1 0 0.014 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.041 -10000 0 -10000 0 0
MLF1IP -0.025 0.074 -10000 0 -10000 0 0
INCENP 0.002 0.004 -10000 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 0.001 0.017 -10000 0 -0.29 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.035 0.13 0.42 43 -10000 0 43
IL27/IL27R/JAK1 -0.074 0.19 -10000 0 -0.64 55 55
TBX21 -0.043 0.21 -10000 0 -0.63 70 70
IL12B -0.055 0.12 -10000 0 -0.29 229 229
IL12A -0.027 0.14 -10000 0 -0.51 76 76
IL6ST -0.091 0.27 -10000 0 -0.79 138 138
IL27RA/JAK1 -0.008 0.073 -10000 0 -1.1 4 4
IL27 -0.025 0.095 -10000 0 -0.29 121 121
TYK2 0.01 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.12 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.035 0.13 0.42 43 -10000 0 43
T cell proliferation during immune response 0.035 0.13 0.42 43 -10000 0 43
MAPKKK cascade -0.035 0.13 -10000 0 -0.42 43 43
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.004 0.039 -10000 0 -0.3 19 19
IL12RB1 -0.004 0.067 -10000 0 -0.32 43 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.059 0.23 -10000 0 -0.61 99 99
IL27/IL27R/JAK2/TYK2 -0.035 0.13 -10000 0 -0.43 43 43
positive regulation of T cell mediated cytotoxicity -0.035 0.13 -10000 0 -0.42 43 43
STAT1 (dimer) -0.092 0.22 0.46 21 -0.74 58 79
JAK2 0.005 0.025 -10000 0 -0.79 1 1
JAK1 0 0.024 -10000 0 -0.79 1 1
STAT2 (dimer) -0.044 0.11 -10000 0 -0.46 22 22
T cell proliferation -0.18 0.25 -10000 0 -0.46 421 421
IL12/IL12R/TYK2/JAK2 0.012 0.069 -10000 0 -10000 0 0
IL17A -0.12 0.18 -10000 0 -10000 0 0
mast cell activation 0.035 0.13 0.42 43 -10000 0 43
IFNG -0.001 0.025 -10000 0 -0.079 8 8
T cell differentiation -0.004 0.006 -10000 0 -0.019 23 23
STAT3 (dimer) -0.044 0.11 -10000 0 -0.45 23 23
STAT5A (dimer) -0.048 0.12 -10000 0 -0.47 31 31
STAT4 (dimer) -0.062 0.15 -10000 0 -0.49 67 67
STAT4 -0.032 0.16 -10000 0 -0.78 45 45
T cell activation -0.009 0.009 0.13 3 -10000 0 3
IL27R/JAK2/TYK2 -0.062 0.17 -10000 0 -0.61 30 30
GATA3 -0.039 0.28 -10000 0 -1.4 40 40
IL18 0.006 0.032 -10000 0 -0.2 27 27
positive regulation of mast cell cytokine production -0.044 0.11 -10000 0 -0.44 23 23
IL27/EBI3 -0.026 0.083 -10000 0 -0.52 14 14
IL27RA -0.001 0.078 -10000 0 -1.4 3 3
IL6 -0.29 0.38 -10000 0 -0.79 401 401
STAT5A -0.006 0.067 -10000 0 -0.79 8 8
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.004 0.03 0.48 3 -10000 0 3
IL1B 0.002 0.073 -10000 0 -0.61 15 15
EBI3 -0.004 0.076 -10000 0 -0.49 21 21
TNF -0.001 0.074 -10000 0 -0.34 38 38
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.005 0.056 -10000 0 -0.54 11 11
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 -0.07 0.22 -10000 0 -0.79 97 97
LRP6/FZD1 0 0.006 -10000 0 -10000 0 0
TLE1 -0.005 0.067 -10000 0 -0.79 8 8
AP1 -0.11 0.17 -10000 0 -0.36 332 332
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.003 0.048 -10000 0 -0.79 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.044 -10000 0 -0.34 1 1
NICD/RBPSUH -0.003 0.042 -10000 0 -0.7 4 4
WIF1 -0.41 0.39 -10000 0 -0.78 581 581
NOTCH1 -0.003 0.045 -10000 0 -0.74 4 4
PSENEN -0.001 0.013 -10000 0 -0.29 2 2
KREMEN2 -0.14 0.15 -10000 0 -10000 0 0
DKK1 -0.08 0.19 -10000 0 -0.79 54 54
beta catenin/beta TrCP1 -0.002 0.029 -10000 0 -10000 0 0
APH1B -0.001 0.024 -10000 0 -0.79 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.015 -10000 0 -0.22 1 1
CtBP/CBP/TCF1/TLE1/AES 0.003 0.039 -10000 0 -0.34 6 6
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.24 0.36 -10000 0 -0.79 329 329
JUN -0.005 0.063 -10000 0 -0.79 7 7
MAP3K7 0.001 0.01 -10000 0 -0.3 1 1
CTNNB1 -0.002 0.034 0.23 2 -10000 0 2
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.085 0.12 -10000 0 -0.61 33 33
HNF1A -0.001 0.025 -10000 0 -0.29 8 8
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC -0.032 0.22 -10000 0 -1.5 24 24
NKD1 -0.009 0.069 -10000 0 -0.42 24 24
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.041 0.13 -10000 0 -0.44 101 101
apoptosis -0.11 0.17 -10000 0 -0.36 332 332
Delta 1/NOTCHprecursor -0.005 0.055 -10000 0 -0.53 11 11
DLL1 -0.005 0.063 -10000 0 -0.79 7 7
PPARD -0.001 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.014 -10000 0 -0.44 1 1
APC 0.003 0.015 -10000 0 -10000 0 0
DVL1 -0.037 0.035 -10000 0 -10000 0 0
CSNK2A1 0.011 0.003 -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 -0.57 55 55
LRP6 0 0.009 -10000 0 -0.29 1 1
CSNK1A1 0.011 0.003 -10000 0 -10000 0 0
NLK 0.002 0.01 -10000 0 -10000 0 0
CCND1 -0.012 0.094 -10000 0 -1.5 4 4
WNT1 -0.001 0.013 -10000 0 -0.29 2 2
Axin1/APC/beta catenin 0.011 0.037 -10000 0 -10000 0 0
DKK2 -0.024 0.14 -10000 0 -0.76 35 35
NOTCH1 precursor/DVL1 -0.018 0.041 -10000 0 -0.64 4 4
GSK3B 0.001 0.003 -10000 0 -10000 0 0
FRAT1 0.001 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.041 0.13 -10000 0 -0.44 101 101
PPP2R5D -0.015 0.037 0.35 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.24 0.23 -10000 0 -0.47 566 566
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.014 0.004 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.004 0.13 -10000 0 -0.39 59 59
TBX21 -0.013 0.34 -10000 0 -1.3 56 56
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.004 0.072 -10000 0 -0.33 41 41
GADD45B 0.031 0.22 -10000 0 -0.8 36 36
IL12RB2 -0.056 0.19 -10000 0 -0.43 184 184
GADD45G 0.021 0.22 -10000 0 -0.75 45 45
natural killer cell activation 0.007 0.018 -10000 0 -10000 0 0
RELB -0.003 0.028 -10000 0 -0.29 10 10
RELA 0 0 -10000 0 -10000 0 0
IL18 0.007 0.048 -10000 0 -0.29 27 27
IL2RA -0.031 0.12 -10000 0 -0.38 87 87
IFNG -0.04 0.1 -10000 0 -0.29 150 150
STAT3 (dimer) 0.024 0.22 -10000 0 -0.64 62 62
HLA-DRB5 -0.017 0.096 -10000 0 -0.33 84 84
FASLG 0.002 0.29 -10000 0 -0.98 56 56
NF kappa B2 p52/RelB -0.079 0.2 -10000 0 -0.81 53 53
CD4 0.008 0.006 -10000 0 -10000 0 0
SOCS1 -0.005 0.043 -10000 0 -0.32 18 18
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.026 0.14 -10000 0 -0.49 78 78
CD3E -0.019 0.13 -10000 0 -0.5 61 61
CD3G -0.035 0.17 -10000 0 -0.57 82 82
IL12Rbeta2/JAK2 -0.026 0.15 -10000 0 -0.59 54 54
CCL3 0.012 0.26 -10000 0 -0.95 43 43
CCL4 0.014 0.25 -10000 0 -0.88 47 47
HLA-A 0.008 0.032 -10000 0 -0.3 11 11
IL18/IL18R 0.02 0.14 -10000 0 -0.54 56 56
NOS2 0.018 0.25 -10000 0 -0.92 42 42
IL12/IL12R/TYK2/JAK2/SPHK2 -0.003 0.13 -10000 0 -0.36 74 74
IL1R1 -0.001 0.31 -10000 0 -1.2 48 48
IL4 -0.004 0.018 -10000 0 -10000 0 0
JAK2 0.016 0.029 -10000 0 -0.82 1 1
EntrezGene:6957 -0.005 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.032 0.25 -10000 0 -0.96 53 53
RAB7A 0.045 0.19 -10000 0 -0.74 25 25
lysosomal transport 0.047 0.19 -10000 0 -0.68 28 28
FOS -0.35 0.66 -10000 0 -1.3 340 340
STAT4 (dimer) 0.02 0.26 -10000 0 -0.84 59 59
STAT5A (dimer) -0.086 0.22 -10000 0 -0.76 67 67
GZMA 0.002 0.28 -10000 0 -1 48 48
GZMB -0.012 0.31 -10000 0 -1.1 53 53
HLX -0.001 0.015 -10000 0 -0.29 3 3
LCK 0.003 0.29 -10000 0 -0.82 76 76
TCR/CD3/MHC II/CD4 -0.065 0.19 -10000 0 -0.52 94 94
IL2/IL2R -0.03 0.1 -10000 0 -0.48 41 41
MAPK14 0.035 0.22 -10000 0 -0.76 46 46
CCR5 0.025 0.22 -10000 0 -0.87 32 32
IL1B 0.005 0.098 -10000 0 -0.72 18 18
STAT6 0.025 0.087 0.22 1 -0.22 38 39
STAT4 -0.032 0.16 -10000 0 -0.78 45 45
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.038 -10000 0 -0.29 19 19
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0.009 -10000 0 -10000 0 0
IL12B -0.047 0.12 -10000 0 -0.3 138 138
CD8A 0 0.074 -10000 0 -0.37 34 34
CD8B -0.022 0.14 -10000 0 -0.61 52 52
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.003 0.13 0.39 59 -10000 0 59
IL2RB -0.012 0.064 -10000 0 -0.32 42 42
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.24 -10000 0 -0.76 59 59
IL2RG -0.017 0.085 -10000 0 -0.36 53 53
IL12 -0.052 0.16 -10000 0 -0.59 65 65
STAT5A -0.006 0.067 -10000 0 -0.79 8 8
CD247 -0.011 0.12 -10000 0 -0.58 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 -0.031 0.19 -10000 0 -0.68 76 76
IL12/IL12R/TYK2/JAK2 0.007 0.29 -10000 0 -0.83 73 73
MAP2K3 0.03 0.22 -10000 0 -0.76 45 45
RIPK2 -0.001 0.02 -10000 0 -0.29 5 5
MAP2K6 0.026 0.23 -10000 0 -0.76 49 49
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.026 -10000 0 -0.54 2 2
IL18RAP -0.014 0.15 -10000 0 -0.73 42 42
IL12Rbeta1/TYK2 0.014 0.056 -10000 0 -0.63 2 2
EOMES -0.024 0.18 -10000 0 -1.5 17 17
STAT1 (dimer) 0.027 0.22 -10000 0 -0.66 52 52
T cell proliferation 0.031 0.2 -10000 0 -0.6 60 60
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0 0.11 -10000 0 -0.79 20 20
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 -0.72 51 51
ATF2 0.041 0.21 -10000 0 -0.71 45 45
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 -0.035 0.12 -10000 0 -0.61 37 37
FYN 0.017 0.18 -10000 0 -0.73 43 43
LAT/GRAP2/SLP76 -0.028 0.14 -10000 0 -0.65 42 42
IKBKB -0.001 0.013 -10000 0 -10000 0 0
AKT1 0.031 0.12 -10000 0 -0.46 44 44
B2M 0.012 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.026 -10000 0 -0.14 19 19
MAP3K8 -0.007 0.072 -10000 0 -0.74 10 10
mol:Ca2+ -0.024 0.047 -10000 0 -0.12 211 211
integrin-mediated signaling pathway -0.002 0.028 -10000 0 -0.52 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.022 0.17 -10000 0 -0.71 44 44
TRPV6 -0.16 0.32 -10000 0 -0.77 225 225
CD28 0.002 0.074 -10000 0 -0.52 18 18
SHC1 0.012 0.18 -10000 0 -0.77 42 42
receptor internalization -0.001 0.2 -10000 0 -0.8 49 49
PRF1 0 0.22 -10000 0 -1 40 40
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 -0.37 48 48
LAT 0.01 0.18 -10000 0 -0.75 46 46
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.48 78 78
CD3E -0.016 0.13 -10000 0 -0.49 61 61
CD3G -0.031 0.16 -10000 0 -0.56 82 82
RASGRP2 0.004 0.041 -10000 0 -0.18 45 45
RASGRP1 0.036 0.12 -10000 0 -0.47 44 44
HLA-A 0.009 0.031 -10000 0 -0.29 11 11
RASSF5 -0.002 0.042 -10000 0 -0.66 4 4
RAP1A/GTP/RAPL -0.002 0.028 -10000 0 -0.52 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 -0.014 0.047 -10000 0 -0.23 33 33
PRKCA -0.013 0.084 -10000 0 -0.31 57 57
GRAP2 -0.013 0.1 -10000 0 -0.72 21 21
mol:IP3 0.019 0.15 0.27 181 -0.45 41 222
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.2 -10000 0 -0.9 40 40
ORAI1 0.077 0.15 0.38 211 -10000 0 211
CSK 0.009 0.18 -10000 0 -0.77 43 43
B7 family/CD28 -0.026 0.18 -10000 0 -0.67 56 56
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.001 0.21 -10000 0 -0.86 48 48
PTPN6 0.008 0.18 -10000 0 -0.76 45 45
VAV1 0.011 0.18 -10000 0 -0.78 42 42
Monovalent TCR/CD3 -0.023 0.2 -10000 0 -0.67 70 70
CBL 0 0 -10000 0 -10000 0 0
LCK 0.011 0.19 -10000 0 -0.78 45 45
PAG1 0.009 0.18 -10000 0 -0.79 42 42
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.21 -10000 0 -0.85 48 48
CD80 -0.068 0.13 -10000 0 -0.29 285 285
CD86 0.008 0.023 -10000 0 -0.3 6 6
PDK1/CARD11/BCL10/MALT1 -0.017 0.057 -10000 0 -0.28 35 35
HRAS -0.003 0.028 -10000 0 -0.29 10 10
GO:0035030 0 0.15 -10000 0 -0.55 55 55
CD8A 0 0.073 -10000 0 -0.37 34 34
CD8B -0.021 0.15 -10000 0 -0.66 45 45
PTPRC -0.001 0.071 -10000 0 -0.48 19 19
PDK1/PKC theta 0.034 0.15 -10000 0 -0.6 44 44
CSK/PAG1 0.014 0.18 -10000 0 -0.77 40 40
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.002 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.034 0.17 -10000 0 -0.75 45 45
STIM1 0.04 0.078 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.054 -10000 0 -0.18 30 30
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.005 0.22 -10000 0 -0.91 47 47
mol:DAG -0.007 0.1 -10000 0 -0.41 42 42
RAP1A/GDP 0.016 0.018 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.008 0.12 -10000 0 -0.58 37 37
cytotoxic T cell degranulation 0.003 0.21 -10000 0 -0.9 43 43
RAP1A/GTP -0.003 0.013 -10000 0 -0.071 5 5
mol:PI-3-4-5-P3 0.027 0.14 -10000 0 -0.56 44 44
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.17 0.29 170 -0.6 42 212
NRAS -0.001 0.013 -10000 0 -0.29 2 2
ZAP70 -0.031 0.12 -10000 0 -0.42 81 81
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.025 0.14 -10000 0 -0.62 42 42
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.031 0.13 -10000 0 -0.56 53 53
CARD11 -0.007 0.052 -10000 0 -0.34 23 23
PRKCB -0.012 0.084 -10000 0 -0.32 52 52
PRKCE -0.006 0.068 -10000 0 -0.29 36 36
PRKCQ 0.025 0.17 -10000 0 -0.69 47 47
LCP2 0 0.009 -10000 0 -0.29 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.032 0.1 -10000 0 -0.39 44 44
IKK complex 0.041 0.044 -10000 0 -0.12 28 28
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.036 0.08 -10000 0 -0.29 39 39
PDPK1 0.034 0.11 -10000 0 -0.44 41 41
TCR/CD3/MHC I/CD8/Fyn -0.004 0.23 -10000 0 -0.92 50 50
Insulin Pathway

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
CBL/APS/CAP -0.13 0.22 -9999 0 -0.46 301 301
TC10/GTP -0.11 0.18 -9999 0 -0.4 285 285
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.097 -9999 0 -0.49 45 45
HRAS -0.003 0.028 -9999 0 -0.29 10 10
APS homodimer -0.013 0.06 -9999 0 -0.29 49 49
GRB14 -0.1 0.22 -9999 0 -0.48 231 231
FOXO3 -0.015 0.07 -9999 0 -0.7 10 10
AKT1 -0.058 0.12 -9999 0 -0.51 11 11
INSR 0.012 0.009 -9999 0 -0.29 1 1
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 -0.79 285 285
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.033 0.03 -9999 0 -10000 0 0
CAV1 -0.099 0.24 -9999 0 -0.5 259 259
CBL/APS/CAP/Crk-II/C3G -0.12 0.2 -9999 0 -0.45 285 285
Insulin Receptor/Insulin/IRS1/NCK2 -0.02 0.097 -9999 0 -0.49 45 45
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.096 -9999 0 -0.42 59 59
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.009 0.13 -9999 0 -0.46 11 11
PARD6A -0.002 0.023 -9999 0 -0.29 7 7
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.05 0.11 -9999 0 -0.48 11 11
HRAS/GTP -0.016 0.073 -9999 0 -0.47 2 2
Insulin Receptor 0.012 0.009 -9999 0 -0.29 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.019 0.09 -9999 0 -0.45 45 45
PRKCI -0.013 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.063 0.14 -9999 0 -0.4 143 143
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.002 -9999 0 -10000 0 0
PI3K -0.023 0.097 -9999 0 -0.43 59 59
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.019 -9999 0 -10000 0 0
AKT2 -0.058 0.12 -9999 0 -0.38 96 96
PRKCZ -0.014 0.036 -9999 0 -0.6 1 1
SH2B2 -0.013 0.061 -9999 0 -0.29 49 49
SHC/SHIP -0.017 0.085 -9999 0 -0.42 45 45
F2RL2 -0.06 0.15 -9999 0 -0.36 185 185
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 -0.48 285 285
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.003 -9999 0 -10000 0 0
INPP5D 0.007 0.096 -9999 0 -0.46 45 45
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.01 0.08 -9999 0 -1 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.032 0.16 -9999 0 -0.79 45 45
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 0.007 0.095 -9999 0 -0.45 45 45
GRB2 0 0.009 -9999 0 -0.29 1 1
EIF4EBP1 -0.014 0.14 -9999 0 -0.46 26 26
PTPRA 0.012 0.002 -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 0.064 -9999 0 -0.32 45 45
Insulin Receptor/Insulin/IRS1 -0.021 0.098 -9999 0 -0.5 45 45
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.027 0.075 -9999 0 -0.45 24 24
Regulation 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
HDAC1 0.021 0.003 -9999 0 -10000 0 0
SMARCC1 0.005 0.019 -9999 0 -10000 0 0
REL -0.006 0.09 -9999 0 -0.79 14 14
HDAC7 0.008 0.13 -9999 0 -0.58 19 19
JUN 0 0.063 -9999 0 -0.79 7 7
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.024 -9999 0 -0.79 1 1
KAT5 0.002 0.005 -9999 0 -10000 0 0
MAPK14 0.006 0.095 -9999 0 -0.61 25 25
FOXO1 -0.009 0.082 -9999 0 -0.79 12 12
T-DHT/AR -0.004 0.14 -9999 0 -0.52 35 35
MAP2K6 -0.01 0.12 -9999 0 -0.78 26 26
BRM/BAF57 -0.001 0.01 -9999 0 -10000 0 0
MAP2K4 0.008 0.025 -9999 0 -0.79 1 1
SMARCA2 0.004 0.006 -9999 0 -10000 0 0
PDE9A -0.088 0.29 -9999 0 -1.2 66 66
NCOA2 -0.032 0.17 -9999 0 -0.79 54 54
CEBPA -0.005 0.075 -9999 0 -0.79 10 10
EHMT2 0.005 0.006 -9999 0 -10000 0 0
cell proliferation 0.014 0.15 -9999 0 -0.49 26 26
NR0B1 -0.01 0.053 -9999 0 -0.29 37 37
EGR1 -0.25 0.37 -9999 0 -0.79 347 347
RXRs/9cRA -0.12 0.21 -9999 0 -0.48 268 268
AR/RACK1/Src -0.005 0.11 -9999 0 -0.48 34 34
AR/GR -0.054 0.13 -9999 0 -0.33 159 159
GNB2L1 0.002 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 0.015 0.061 -9999 0 -0.61 10 10
T-DHT/AR/TIF2/CARM1 -0.018 0.16 -9999 0 -0.51 78 78
SRC 0.021 0.094 -9999 0 -0.46 34 34
NR3C1 -0.012 0.095 -9999 0 -0.79 16 16
KLK3 -0.2 0.41 -9999 0 -1.2 150 150
APPBP2 0.008 0.017 -9999 0 -0.29 3 3
TRIM24 0.005 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.028 0.099 -9999 0 -0.51 34 34
TMPRSS2 -0.16 0.41 -9999 0 -1.2 137 137
RXRG -0.19 0.34 -9999 0 -0.78 271 271
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 0.008 0.006 -9999 0 -10000 0 0
NR2C2 -0.008 0.079 -9999 0 -0.79 11 11
KLK2 -0.043 0.24 -9999 0 -0.73 103 103
AR -0.028 0.14 -9999 0 -0.34 172 172
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
MDM2 0.004 0.024 -9999 0 -0.29 5 5
SRY 0.003 0.01 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.79 28 28
MYST2 0.002 0.01 -9999 0 -0.29 1 1
HOXB13 -0.14 0.15 -9999 0 -0.3 501 501
T-DHT/AR/RACK1/Src -0.013 0.1 -9999 0 -0.49 34 34
positive regulation of transcription -0.024 0.13 -9999 0 -0.79 28 28
DNAJA1 0.009 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.013 -9999 0 -10000 0 0
NCOA1 0.012 0.026 -9999 0 -0.82 1 1
SPDEF -0.057 0.2 -9999 0 -0.61 110 110
T-DHT/AR/TIF2 0.011 0.1 -9999 0 -0.45 27 27
T-DHT/AR/Hsp90 -0.035 0.095 -9999 0 -0.51 34 34
GSK3B 0.008 0.006 -9999 0 -10000 0 0
NR2C1 0.003 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.014 0.099 -9999 0 -0.5 34 34
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.005 0.013 -9999 0 -10000 0 0
POU2F1 0.021 0.026 -9999 0 -0.42 1 1
T-DHT/AR/DAX-1 -0.036 0.099 -9999 0 -0.52 34 34
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0.004 0.017 -9999 0 -0.3 3 3
Syndecan-4-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
PTK2 -0.002 0.036 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.024 0.037 -9999 0 -0.63 1 1
positive regulation of JNK cascade -0.05 0.1 -9999 0 -0.46 7 7
Syndecan-4/ADAM12 -0.032 0.055 -9999 0 -0.63 1 1
CCL5 -0.014 0.079 -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 0.009 -9999 0 -0.29 1 1
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.026 -9999 0 -0.3 2 2
ADAM12 -0.019 0.077 -9999 0 -0.31 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.001 0.02 -9999 0 -0.29 5 5
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 -0.07 0.13 -9999 0 -0.47 31 31
Syndecan-4/CXCL12/CXCR4 -0.053 0.11 -9999 0 -0.5 4 4
Syndecan-4/Laminin alpha3 -0.13 0.19 -9999 0 -0.48 167 167
MDK -0.012 0.057 -9999 0 -0.29 43 43
Syndecan-4/FZD7 -0.033 0.068 -9999 0 -0.56 2 2
Syndecan-4/Midkine -0.028 0.042 -9999 0 -0.63 1 1
FZD7 -0.017 0.11 -9999 0 -0.79 23 23
Syndecan-4/FGFR1/FGF -0.19 0.2 -9999 0 -0.5 112 112
THBS1 -0.004 0.053 -9999 0 -0.79 5 5
integrin-mediated signaling pathway -0.034 0.072 -9999 0 -0.7 2 2
positive regulation of MAPKKK cascade -0.05 0.1 -9999 0 -0.46 7 7
Syndecan-4/TACI -0.036 0.066 -9999 0 -0.52 5 5
CXCR4 -0.007 0.045 -9999 0 -0.29 26 26
cell adhesion -0.02 0.061 -9999 0 -0.34 29 29
Syndecan-4/Dynamin -0.024 0.036 -9999 0 -0.63 1 1
Syndecan-4/TSP1 -0.026 0.046 -9999 0 -0.54 2 2
Syndecan-4/GIPC -0.024 0.036 -9999 0 -0.63 1 1
Syndecan-4/RANTES -0.03 0.052 -9999 0 -0.54 3 3
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.088 0.25 -9999 0 -0.77 124 124
LAMA3 -0.2 0.34 -9999 0 -0.79 276 276
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.004 0.13 -9999 0 -0.73 30 30
Syndecan-4/alpha-Actinin -0.024 0.038 -9999 0 -0.63 1 1
TFPI -0.041 0.18 -9999 0 -0.78 58 58
F2 0 0.034 -9999 0 -0.29 14 14
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.23 -9999 0 -0.56 137 137
ACTN1 -0.001 0.024 -9999 0 -0.79 1 1
TNC -0.022 0.12 -9999 0 -0.64 37 37
Syndecan-4/CXCL12 -0.056 0.11 -9999 0 -0.5 8 8
FGF6 -0.001 0.034 -9999 0 -0.79 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.061 0.21 -9999 0 -0.79 85 85
TNFRSF13B -0.028 0.11 -9999 0 -0.79 15 15
FGF2 -0.32 0.39 -9999 0 -0.79 446 446
FGFR1 -0.009 0.08 -9999 0 -0.68 14 14
Syndecan-4/PI-4-5-P2 -0.018 0.048 -9999 0 -0.64 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.15 -9999 0 -0.3 425 425
cell migration -0.024 0.019 -9999 0 -10000 0 0
PRKCD 0.005 0.014 -9999 0 -0.29 1 1
vasculogenesis -0.025 0.044 -9999 0 -0.49 3 3
SDC4 -0.018 0.051 -9999 0 -0.68 1 1
Syndecan-4/Tenascin C -0.035 0.075 -9999 0 -0.74 2 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.024 0.036 -9999 0 -0.63 1 1
MMP9 -0.12 0.15 -9999 0 -0.29 483 483
Rac1/GTP -0.028 0.057 -9999 0 -0.34 29 29
cytoskeleton organization -0.024 0.036 -9999 0 -0.6 1 1
GIPC1 0 0.009 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.046 0.098 -9999 0 -0.51 10 10
Coregulation of Androgen receptor activity

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
NRIP1 -0.002 0.032 -10000 0 -0.79 1 1
SVIL -0.004 0.056 -10000 0 -0.79 5 5
ZNF318 0.022 0.057 0.22 1 -10000 0 1
JMJD2C -0.003 0.041 -10000 0 -0.13 85 85
T-DHT/AR/Ubc9 -0.081 0.18 -10000 0 -0.54 147 147
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.003 0.012 -10000 0 -0.29 1 1
PELP1 0.005 0.012 -10000 0 -10000 0 0
CTNNB1 0.001 0.015 -10000 0 -10000 0 0
AKT1 0.007 0.018 -10000 0 -10000 0 0
PTK2B 0.001 0.013 -10000 0 -10000 0 0
MED1 0.002 0.047 -10000 0 -10000 0 0
MAK 0.011 0.1 0.26 1 -0.55 20 21
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.005 0.061 -10000 0 -0.79 6 6
GSN -0.012 0.091 -10000 0 -0.79 14 14
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
NCOA6 -0.001 0.02 -10000 0 -0.29 1 1
DNA-PK 0.022 0.058 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 0.001 0.015 -10000 0 -10000 0 0
cell proliferation -0.008 0.11 -10000 0 -0.87 11 11
XRCC5 0.006 0.015 -10000 0 -10000 0 0
UBE3A -0.005 0.03 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.094 0.21 -10000 0 -0.57 163 163
FHL2 -0.018 0.12 -10000 0 -1.2 5 5
RANBP9 0 0.018 -10000 0 -10000 0 0
JMJD1A -0.011 0.056 -10000 0 -0.14 152 152
CDK6 -0.009 0.093 -10000 0 -0.79 15 15
TGFB1I1 -0.003 0.046 -10000 0 -0.79 3 3
T-DHT/AR/CyclinD1 -0.094 0.19 -10000 0 -0.52 163 163
XRCC6 0.006 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.067 0.21 -10000 0 -0.53 164 164
CTDSP1 0.004 0.005 -10000 0 -10000 0 0
CTDSP2 0.015 0.038 -10000 0 -10000 0 0
BRCA1 -0.002 0.034 -10000 0 -0.49 3 3
TCF4 0.003 0.088 -10000 0 -0.78 12 12
CDKN2A -0.042 0.11 -10000 0 -0.29 167 167
SRF 0.024 0.019 -10000 0 -10000 0 0
NKX3-1 -0.082 0.19 -10000 0 -1.2 23 23
KLK3 -0.17 0.5 -10000 0 -1.5 127 127
TMF1 0.004 0.005 -10000 0 -10000 0 0
HNRNPA1 0.008 0.021 -10000 0 -10000 0 0
AOF2 -0.008 0.023 -10000 0 -0.072 127 127
APPL1 0.034 0.032 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.074 0.19 -10000 0 -0.53 147 147
AR -0.1 0.27 -10000 0 -0.79 147 147
UBA3 0.004 0.005 -10000 0 -10000 0 0
PATZ1 0.008 0.021 -10000 0 -10000 0 0
PAWR 0.003 0.025 -10000 0 -0.79 1 1
PRKDC 0.005 0.024 -10000 0 -0.29 4 4
PA2G4 0.011 0.027 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.069 0.17 -10000 0 -0.49 147 147
RPS6KA3 -0.008 0.074 -10000 0 -0.79 9 9
T-DHT/AR/ARA70 -0.085 0.18 -10000 0 -0.54 147 147
LATS2 0.009 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.064 0.18 0.19 1 -0.49 147 148
Cyclin D3/CDK11 p58 0 0.006 -10000 0 -10000 0 0
VAV3 -0.01 0.075 -10000 0 -0.43 26 26
KLK2 -0.12 0.32 -10000 0 -1.2 79 79
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.099 0.2 -10000 0 -0.54 181 181
TMPRSS2 -0.17 0.39 -10000 0 -1.2 135 135
CCND1 -0.016 0.074 -10000 0 -0.34 46 46
PIAS1 -0.005 0.03 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.033 -10000 0 -0.079 180 180
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.011 0.049 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.085 0.2 -10000 0 -0.54 161 161
CMTM2 0.003 0.013 -10000 0 -0.29 1 1
SNURF -0.021 0.13 -10000 0 -0.79 29 29
ZMIZ1 0.004 0.03 -10000 0 -0.36 1 1
CCND3 0.002 0.01 -10000 0 -0.29 1 1
TGIF1 0.008 0.021 -10000 0 -10000 0 0
FKBP4 -0.003 0.033 -10000 0 -0.3 9 9
Signaling events mediated by PRL

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
CCNE1 -0.06 0.12 -9999 0 -0.29 223 223
mol:Halofuginone 0 0.003 -9999 0 -10000 0 0
ITGA1 -0.008 0.079 -9999 0 -0.79 11 11
CDKN1A -0.057 0.087 -9999 0 -0.84 2 2
PRL-3/alpha Tubulin -0.002 0.018 -9999 0 -10000 0 0
mol:Ca2+ -0.033 0.096 -9999 0 -0.55 18 18
AGT -0.047 0.13 -9999 0 -0.34 151 151
CCNA2 -0.16 0.24 -9999 0 -0.56 183 183
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.17 0.29 -9999 0 -0.6 347 347
CDK2/Cyclin E1 -0.067 0.09 -9999 0 -0.81 2 2
MAPK3 0.021 0.02 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.006 -9999 0 -10000 0 0
MAPK1 0.021 0.02 -9999 0 -10000 0 0
PTP4A1 -0.12 0.23 -9999 0 -0.67 1 1
PTP4A3 -0.003 0.028 -9999 0 -0.29 10 10
PTP4A2 0 0.009 -9999 0 -0.29 1 1
ITGB1 0.021 0.02 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1 -0.055 0.081 -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 -0.59 2 2
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0.001 0.009 -9999 0 -10000 0 0
RHOC -0.055 0.081 -9999 0 -10000 0 0
RHOA -0.055 0.081 -9999 0 -10000 0 0
cell motility -0.034 0.1 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.13 0.2 -9999 0 -0.62 1 1
PRL-3/alpha1 Integrin -0.008 0.062 -9999 0 -0.6 11 11
ROCK1 -0.034 0.1 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.12 0.23 -9999 0 -0.45 347 347
ATF5 -0.001 0.018 -9999 0 -0.29 4 4
Regulation of Telomerase

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
Telomerase catalytic core complex -0.055 0.12 -9999 0 -0.57 6 6
RAD9A 0 0.009 -9999 0 -0.29 1 1
AP1 -0.18 0.28 -9999 0 -0.61 330 330
IFNAR2 0.01 0.025 -9999 0 -0.79 1 1
AKT1 -0.036 0.11 -9999 0 -0.28 165 165
ER alpha/Oestrogen -0.11 0.22 -9999 0 -0.43 288 288
NFX1/SIN3/HDAC complex 0.026 0.025 -9999 0 -10000 0 0
EGF -0.15 0.31 -9999 0 -0.78 214 214
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 -0.067 0.089 -9999 0 -0.55 5 5
SAP18 0.006 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.15 -9999 0 -0.29 561 561
WRN 0 0 -9999 0 -10000 0 0
SP1 0.011 0.006 -9999 0 -10000 0 0
SP3 0.009 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.052 0.078 -9999 0 -0.52 4 4
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.056 0.12 -9999 0 -0.61 5 5
CCND1 -0.048 0.13 -9999 0 -1.3 4 4
MAX 0.009 0.005 -9999 0 -10000 0 0
RBBP7 0.004 0.026 -9999 0 -0.29 8 8
RBBP4 0.005 0.025 -9999 0 -0.79 1 1
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
Telomerase/911 0.012 0.024 -9999 0 -10000 0 0
CDKN1B 0.009 0.074 -9999 0 -0.86 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 0.005 0.019 -9999 0 -0.29 4 4
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.009 0.005 -9999 0 -10000 0 0
JUN 0.002 0.064 -9999 0 -0.79 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 -0.79 329 329
IFN-gamma/IRF1 -0.025 0.063 -9999 0 -0.36 5 5
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.03 0.089 -9999 0 -0.29 113 113
Telomerase -0.006 0.028 -9999 0 -10000 0 0
IRF1 0.011 0.02 -9999 0 -0.28 3 3
ESR1 -0.15 0.29 -9999 0 -0.58 288 288
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 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.011 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.011 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.009 0.01 -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 0.015 -9999 0 -0.29 3 3
TERT/NF kappa B1/14-3-3 -0.065 0.1 -9999 0 -0.67 3 3
NR2F2 0.001 0.042 -9999 0 -0.79 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 0.001 0.016 -9999 0 -0.29 3 3
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 0.38 -9999 0 -0.78 410 410
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.33 0.35 -9999 0 -0.66 552 552
MYC -0.008 0.12 -9999 0 -0.79 24 24
IL2 0.004 0.026 -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 -0.29 1 1
TGFB1 0.001 0.016 -9999 0 -0.29 3 3
TRF2/BLM -0.017 0.051 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.063 0.087 -9999 0 -0.58 4 4
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.052 0.078 -9999 0 -0.52 4 4
Smad3/Myc -0.012 0.076 -9999 0 -0.52 24 24
911 complex 0 0.004 -9999 0 -10000 0 0
IFNG -0.03 0.1 -9999 0 -10000 0 0
Telomerase/PinX1 -0.052 0.078 -9999 0 -0.52 4 4
Telomerase/AKT1/mTOR/p70S6K 0.003 0.055 -9999 0 -10000 0 0
SIN3B 0.006 0.006 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.052 0.078 -9999 0 -0.52 4 4
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 -0.052 0.078 -9999 0 -0.52 4 4
E2F1 -0.085 0.14 -9999 0 -0.29 345 345
ZNFX1 0.006 0.006 -9999 0 -10000 0 0
PIF1 -0.061 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
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.004 0.11 -10000 0 -0.44 36 36
IKBKB 0.015 0.053 -10000 0 -0.26 3 3
AKT1 0.002 0.082 0.24 2 -0.25 39 41
IKBKG 0.018 0.055 -10000 0 -0.24 18 18
CALM1 -0.011 0.092 -10000 0 -0.45 30 30
PIK3CA 0 0.009 -10000 0 -0.29 1 1
MAP3K1 -0.01 0.15 -10000 0 -0.62 36 36
MAP3K7 0 0.009 -10000 0 -0.29 1 1
mol:Ca2+ -0.019 0.097 0.24 1 -0.48 30 31
DOK1 -0.001 0.018 -10000 0 -10000 0 0
AP-1 -0.041 0.11 -10000 0 -0.26 72 72
LYN 0 0.001 -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 -0.62 119 119
CD22 -0.061 0.18 -10000 0 -0.54 100 100
CAMK2G -0.002 0.086 -10000 0 -0.41 30 30
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.047 0.13 -10000 0 -0.76 16 16
GO:0007205 -0.02 0.098 0.24 1 -0.49 30 31
SYK 0 0.009 -10000 0 -0.29 1 1
ELK1 -0.011 0.093 -10000 0 -0.46 30 30
NFATC1 -0.018 0.13 -10000 0 -0.56 34 34
B-cell antigen/BCR complex -0.079 0.21 -10000 0 -0.62 119 119
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 31 31
NFKBIA 0.015 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 -0.51 100 100
mol:GDP -0.02 0.09 0.22 1 -0.46 30 31
PTEN -0.001 0.034 -10000 0 -0.79 2 2
CD79B -0.027 0.13 -10000 0 -0.58 52 52
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 -0.029 0.16 -10000 0 -0.47 101 101
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
mol:IP3 -0.029 0.096 0.24 1 -0.5 30 31
CSK 0 0 -10000 0 -10000 0 0
FOS -0.13 0.22 -10000 0 -0.44 349 349
CHUK 0.018 0.055 -10000 0 -0.24 17 17
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.023 0.077 -10000 0 -0.48 18 18
PTPN6 -0.057 0.16 -10000 0 -0.5 101 101
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.12 1 1
VAV2 -0.071 0.16 -10000 0 -0.52 97 97
ubiquitin-dependent protein catabolic process 0.019 0.019 -10000 0 -10000 0 0
BTK -0.004 0.005 -10000 0 -10000 0 0
CD19 -0.081 0.17 -10000 0 -0.53 97 97
MAP4K1 -0.015 0.07 -10000 0 -0.31 53 53
CD72 -0.009 0.054 -10000 0 -0.31 32 32
PAG1 -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0.002 0.13 -10000 0 -0.54 31 31
SH3BP5 -0.001 0.024 -10000 0 -0.79 1 1
PIK3AP1 -0.01 0.1 0.27 1 -0.53 30 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.041 0.13 -10000 0 -0.47 85 85
RAF1 0 0.096 -10000 0 -0.44 30 30
RasGAP/p62DOK/SHIP -0.055 0.15 -10000 0 -0.49 100 100
CD79A -0.083 0.22 -10000 0 -0.53 171 171
re-entry into mitotic cell cycle -0.04 0.11 -10000 0 -0.26 70 70
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.016 0.082 -10000 0 -0.42 17 17
MAPK1 0.016 0.082 -10000 0 -0.42 17 17
CD72/SHP1 -0.055 0.15 -10000 0 -0.65 45 45
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.13 -10000 0 -0.51 41 41
actin cytoskeleton organization -0.027 0.15 -10000 0 -0.43 97 97
NF-kappa-B/RelA 0.042 0.033 -10000 0 -10000 0 0
Calcineurin -0.02 0.07 -10000 0 -0.44 17 17
PI3K -0.06 0.13 -10000 0 -0.52 45 45
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.031 0.11 0.27 1 -0.57 30 31
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.048 0.17 -10000 0 -0.82 36 36
DAPP1 -0.05 0.19 -10000 0 -0.96 35 35
cytokine secretion -0.015 0.12 -10000 0 -0.52 34 34
mol:DAG -0.029 0.096 0.24 1 -0.5 30 31
PLCG2 -0.002 0.035 -10000 0 -0.62 3 3
MAP2K1 0.008 0.089 -10000 0 -0.48 17 17
B-cell antigen/BCR complex/FcgammaRIIB -0.07 0.19 -10000 0 -0.55 122 122
mol:PI-3-4-5-P3 -0.044 0.093 0.34 2 -0.36 44 46
ETS1 0.004 0.089 -10000 0 -0.48 21 21
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.056 0.16 -10000 0 -0.51 97 97
B-cell antigen/BCR complex/LYN -0.057 0.18 -10000 0 -0.56 101 101
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0.001 0.003 -10000 0 -10000 0 0
RAC1 -0.03 0.16 -10000 0 -0.46 97 97
B-cell antigen/BCR complex/LYN/SYK -0.057 0.17 -10000 0 -0.55 98 98
CARD11 -0.014 0.1 -10000 0 -0.48 30 30
FCGR2B -0.004 0.054 -10000 0 -0.7 6 6
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 -0.098 1 1
PTPRC -0.008 0.07 -10000 0 -0.48 19 19
PDPK1 -0.029 0.063 0.22 2 -0.26 26 28
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
Regulation of p38-alpha and p38-beta

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
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 -0.018 0.12 -9999 0 -0.77 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.024 -9999 0 -0.79 1 1
RAC1-CDC42/GTP/PAK family -0.12 0.14 -9999 0 -0.27 487 487
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.79 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 -0.001 0.034 -9999 0 -0.79 2 2
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.001 0.025 -9999 0 -0.54 2 2
p38 alpha/TAB1 -0.007 0.033 -9999 0 -0.32 4 4
PRKG1 -0.053 0.2 -9999 0 -0.79 74 74
DUSP8 -0.002 0.042 -9999 0 -0.66 4 4
PGK/cGMP/p38 alpha -0.032 0.1 -9999 0 -0.39 77 77
apoptosis -0.006 0.032 -9999 0 -0.3 4 4
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.1 0.26 -9999 0 -0.79 142 142
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
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 0.068 -9999 0 -0.34 21 21
BLK -0.044 0.11 -9999 0 -0.3 159 159
HCK -0.004 0.033 -9999 0 -0.29 14 14
MAP2K3 0 0.009 -9999 0 -0.29 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.015 -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 0.048 -9999 0 -0.34 4 4
positive regulation of innate immune response 0.024 0.074 -9999 0 -0.36 21 21
LCK -0.02 0.1 -9999 0 -0.41 53 53
p38alpha-beta/MKP7 -0.012 0.054 -9999 0 -0.34 21 21
p38alpha-beta/MKP5 -0.012 0.054 -9999 0 -0.34 21 21
PGK/cGMP -0.041 0.15 -9999 0 -0.61 74 74
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.058 0.13 -9999 0 -0.37 158 158
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 -0.35 0.39 -9999 0 -0.79 487 487
TCGA08_retinoblastoma

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
CDKN2B -0.003 0.063 -10000 0 -0.66 9 9
CDKN2C 0.006 0.037 -10000 0 -0.78 2 2
CDKN2A -0.052 0.12 -10000 0 -0.31 188 188
CCND2 0.006 0.033 0.23 9 -0.16 12 21
RB1 -0.007 0.032 0.19 4 -0.25 8 12
CDK4 0.01 0.03 0.25 9 -10000 0 9
CDK6 0.006 0.039 0.27 8 -0.21 14 22
G1/S progression -0.006 0.036 0.25 8 -0.18 4 12
IL2 signaling events mediated by STAT5

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
GAB2 0.008 0.043 -9999 0 -0.39 10 10
ELF1 -0.012 0.051 -9999 0 -0.38 16 16
CCNA2 -0.11 0.14 -9999 0 -0.29 427 427
PIK3CA 0.012 0.009 -9999 0 -0.29 1 1
JAK3 0.008 0.034 -9999 0 -0.29 14 14
PIK3R1 0.001 0.09 -9999 0 -0.79 14 14
JAK1 0.011 0.024 -9999 0 -0.79 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.057 0.08 -9999 0 -0.58 9 9
SHC1 0.012 0.001 -9999 0 -10000 0 0
SP1 -0.005 0.041 -9999 0 -0.38 13 13
IL2RA 0.001 0.13 -9999 0 -1 16 16
IL2RB -0.001 0.066 -9999 0 -0.32 42 42
SOS1 0.012 0.001 -9999 0 -10000 0 0
IL2RG -0.006 0.087 -9999 0 -0.36 53 53
G1/S transition of mitotic cell cycle 0.004 0.13 -9999 0 -0.8 24 24
PTPN11 0.012 0.001 -9999 0 -10000 0 0
CCND2 0.017 0.11 -9999 0 -1 13 13
LCK -0.009 0.1 -9999 0 -0.41 53 53
GRB2 0.011 0.009 -9999 0 -0.29 1 1
IL2 0.004 0.026 -9999 0 -0.29 8 8
CDK6 -0.011 0.092 -9999 0 -0.79 15 15
CCND3 0.063 0.071 -9999 0 -0.57 5 5
Thromboxane A2 receptor signaling

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
TGM2 0.005 0.035 -10000 0 -0.29 15 15
GNB1/GNG2 -0.015 0.048 -10000 0 -0.19 69 69
AKT1 0.05 0.072 -10000 0 -0.2 64 64
EGF -0.15 0.31 -10000 0 -0.78 214 214
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.01 0.053 -10000 0 -0.42 6 6
mol:Ca2+ 0.047 0.1 -10000 0 -0.3 64 64
LYN -0.01 0.05 -10000 0 -0.39 5 5
RhoA/GTP -0.008 0.03 -10000 0 -0.14 16 16
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.052 0.11 -10000 0 -0.35 64 64
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.063 -10000 0 -0.55 9 9
G beta5/gamma2 -0.019 0.065 -10000 0 -0.25 70 70
PRKCH 0.048 0.11 -10000 0 -0.35 64 64
DNM1 -0.005 0.063 -10000 0 -0.73 8 8
TXA2/TP beta/beta Arrestin3 -0.004 0.026 -10000 0 -0.3 7 7
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.031 0.15 -10000 0 -0.71 47 47
G12 family/GTP -0.021 0.073 -10000 0 -0.31 64 64
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.004 0.053 -10000 0 -0.79 5 5
RhoA/GTP/ROCK1 0 0.016 -10000 0 -0.52 1 1
mol:GDP -0.036 0.081 0.35 25 -10000 0 25
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 -0.79 74 74
mol:IP3 0.047 0.12 -10000 0 -0.38 64 64
cell morphogenesis 0 0.016 -10000 0 -0.52 1 1
PLCB2 0.044 0.15 -10000 0 -0.52 64 64
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.008 0.062 -10000 0 -0.4 9 9
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.011 0.051 -10000 0 -0.39 5 5
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.002 0.026 -10000 0 -0.29 9 9
PRKCB1 0.045 0.12 -10000 0 -0.38 64 64
GNAQ -0.002 0.041 -10000 0 -0.79 3 3
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.047 0.16 -10000 0 -0.54 64 64
LCK -0.015 0.071 -10000 0 -0.45 17 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.056 -10000 0 -0.35 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.037 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.055 -10000 0 -0.34 1 1
MAPK14 0.051 0.079 -10000 0 -0.24 37 37
TGM2/GTP 0.047 0.13 -10000 0 -0.43 64 64
MAPK11 0.051 0.082 -10000 0 -0.24 64 64
ARHGEF1 0.039 0.061 -10000 0 -0.18 32 32
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.049 0.12 -10000 0 -0.4 64 64
RAB11/GDP -0.001 0.012 -10000 0 -0.29 2 2
ICAM1 0.046 0.093 -10000 0 -0.28 64 64
cAMP biosynthetic process 0.043 0.12 -10000 0 -0.36 65 65
Gq family/GTP/EBP50 0.017 0.04 -10000 0 -0.25 18 18
actin cytoskeleton reorganization 0 0.016 -10000 0 -0.52 1 1
SRC -0.01 0.05 -10000 0 -0.39 5 5
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.028 0.1 -10000 0 -0.3 49 49
VCAM1 0.044 0.1 -10000 0 -0.32 64 64
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.063 -10000 0 -0.55 9 9
platelet activation 0.066 0.1 -10000 0 -0.31 64 64
PGI2/IP -0.002 0.018 -10000 0 -10000 0 0
PRKACA -0.014 0.07 -10000 0 -0.37 40 40
Gq family/GDP/G beta5/gamma2 0.026 0.065 -10000 0 -0.55 9 9
TXA2/TP beta/beta Arrestin2 -0.005 0.052 -10000 0 -0.65 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.01 0.07 -10000 0 -0.34 40 40
mol:DAG 0.046 0.13 -10000 0 -0.42 64 64
EGFR -0.29 0.38 -10000 0 -0.78 410 410
TXA2/TP alpha 0.048 0.15 -10000 0 -0.5 64 64
Gq family/GTP -0.004 0.036 -10000 0 -0.27 18 18
YES1 -0.01 0.051 -10000 0 -0.4 5 5
GNAI2/GTP -0.012 0.058 -10000 0 -0.44 6 6
PGD2/DP -0.024 0.12 -10000 0 -0.55 47 47
SLC9A3R1 -0.026 0.083 -10000 0 -10000 0 0
FYN -0.011 0.054 -10000 0 -0.43 6 6
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.003 0.033 -10000 0 -0.36 8 8
PGK/cGMP -0.036 0.13 -10000 0 -0.52 74 74
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.017 0.082 -10000 0 -0.56 15 15
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.041 0.13 -10000 0 -0.38 72 72
PRKCB 0.043 0.12 -10000 0 -0.37 76 76
PRKCE 0.05 0.11 -10000 0 -0.35 64 64
PRKCD 0.048 0.12 -10000 0 -0.38 64 64
PRKCG 0.044 0.12 -10000 0 -0.39 64 64
muscle contraction 0.05 0.15 -10000 0 -0.5 64 64
PRKCZ 0.052 0.11 -10000 0 -0.35 64 64
ARR3 -0.002 0.025 -10000 0 -0.29 8 8
TXA2/TP beta -0.013 0.065 -10000 0 -0.49 6 6
PRKCQ 0.037 0.14 -10000 0 -0.39 78 78
MAPKKK cascade 0.044 0.14 -10000 0 -0.48 64 64
SELE 0.038 0.12 -10000 0 -0.42 64 64
TP beta/GNAI2/GDP/G beta/gamma -0.016 0.082 -10000 0 -0.56 15 15
ROCK1 -0.001 0.024 -10000 0 -0.79 1 1
GNA14 -0.013 0.084 -10000 0 -0.46 30 30
chemotaxis 0.046 0.18 -10000 0 -0.62 64 64
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.003 0.048 -10000 0 -0.79 4 4
Rac1/GTP 0 0 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.006 -10000 0 -10000 0 0
SMAD4 -0.001 0.024 -10000 0 -0.79 1 1
DKK2 -0.024 0.14 -10000 0 -0.76 35 35
TLE1 -0.002 0.069 -10000 0 -0.79 8 8
MACF1 0.006 0.006 -10000 0 -10000 0 0
CTNNB1 0.1 0.087 -10000 0 -10000 0 0
WIF1 -0.41 0.39 -10000 0 -0.77 581 581
beta catenin/RanBP3 0.014 0.078 0.38 40 -10000 0 40
KREMEN2 -0.14 0.15 -10000 0 -10000 0 0
DKK1 -0.08 0.19 -10000 0 -0.79 54 54
beta catenin/beta TrCP1 0.1 0.083 -10000 0 -10000 0 0
FZD1 0 0.002 -10000 0 -10000 0 0
AXIN2 -0.014 0.21 -10000 0 -1.5 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 0.092 0.078 0.3 1 -0.49 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 0.029 -10000 0 -0.29 7 7
CTBP1 0.004 0.016 -10000 0 -10000 0 0
MYC -0.018 0.23 -10000 0 -1.5 25 25
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.085 0.12 -10000 0 -0.6 33 33
NKD1 -0.009 0.069 -10000 0 -0.42 24 24
TCF4 -0.005 0.083 -10000 0 -0.78 12 12
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.099 0.45 45 -0.42 1 46
LEF1 -0.036 0.1 -10000 0 -0.3 140 140
DVL1 0.071 0.065 0.22 1 -10000 0 1
CSNK2A1 0 0.002 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.098 0.089 -10000 0 -0.58 5 5
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.57 55 55
LRP6 0.002 0.01 -10000 0 -0.29 1 1
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.011 0.014 -10000 0 -0.3 2 2
CCND1 0.002 0.11 -10000 0 -1.6 4 4
WNT1 0.005 0.014 -10000 0 -0.29 2 2
GSK3A 0.009 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 0.34 7 -10000 0 7
APC 0.001 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.14 0.13 0.27 566 -10000 0 566
CREBBP 0.004 0.016 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0.001 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.099 0.2 0.24 2 -0.56 165 167
AKT1 0.014 0.006 -10000 0 -10000 0 0
GSC -0.036 0.3 -10000 0 -1.5 42 42
NKX2-5 -0.045 0.1 -10000 0 -0.29 171 171
muscle cell differentiation 0.007 0.051 0.76 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.04 -10000 0 -0.45 2 2
SMAD4 0.014 0.041 -10000 0 -0.82 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0.001 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.19 0.25 -10000 0 -0.51 406 406
SMAD3/SMAD4/VDR 0.005 0.03 -10000 0 -0.43 2 2
MYC -0.017 0.12 -10000 0 -0.79 24 24
CDKN2B 0.029 0.13 -10000 0 -1.5 7 7
AP1 -0.12 0.2 -10000 0 -0.52 56 56
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.002 0.02 -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 -0.044 0.12 -10000 0 -0.29 204 204
SMAD3/SMAD4/GR -0.01 0.073 -10000 0 -0.56 17 17
GATA3 -0.037 0.15 -10000 0 -0.58 67 67
SKI/SIN3/HDAC complex/NCoR1 0.002 0.014 -10000 0 -10000 0 0
MEF2C/TIF2 -0.055 0.13 -10000 0 -0.57 47 47
endothelial cell migration -0.008 0.06 1.5 1 -10000 0 1
MAX 0.001 0.005 -10000 0 -10000 0 0
RBBP7 -0.002 0.025 -10000 0 -0.29 8 8
RBBP4 0 0.024 -10000 0 -0.79 1 1
RUNX2 -0.005 0.036 -10000 0 -0.29 17 17
RUNX3 -0.006 0.066 -10000 0 -0.79 7 7
RUNX1 -0.001 0.024 -10000 0 -0.79 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.011 0.095 -10000 0 -0.79 16 16
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.05 0.078 -10000 0 -1.5 2 2
KAT2B 0 0.024 -10000 0 -0.79 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.03 0.072 -10000 0 -0.46 6 6
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0.001 0.002 -10000 0 -10000 0 0
SERPINE1 0.007 0.061 -10000 0 -1.5 1 1
SMAD3/SMAD4/ATF2 -0.003 0.04 -10000 0 -0.56 4 4
SMAD3/SMAD4/ATF3 -0.078 0.19 -10000 0 -0.55 154 154
SAP30 -0.001 0.018 -10000 0 -0.29 4 4
Cbp/p300/PIAS3 0.005 0.023 -10000 0 -10000 0 0
JUN -0.074 0.22 -10000 0 -0.53 47 47
SMAD3/SMAD4/IRF7 -0.02 0.068 -10000 0 -0.36 12 12
TFE3 0.017 0.006 -10000 0 -10000 0 0
COL1A2 0.027 0.1 -10000 0 -1.2 3 3
mesenchymal cell differentiation 0.004 0.034 0.54 1 -10000 0 1
DLX1 -0.053 0.13 -10000 0 -0.32 184 184
TCF3 0 0.009 -10000 0 -0.29 1 1
FOS -0.22 0.37 -10000 0 -0.78 329 329
SMAD3/SMAD4/Max -0.002 0.029 -10000 0 -0.54 1 1
Cbp/p300/SNIP1 0 0.002 -10000 0 -10000 0 0
ZBTB17 0 0.006 -10000 0 -10000 0 0
LAMC1 0.042 0.047 -10000 0 -0.62 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.028 -10000 0 -0.54 1 1
IRF7 -0.031 0.092 -10000 0 -0.31 104 104
ESR1 -0.15 0.28 -10000 0 -0.58 287 287
HNF4A -0.006 0.041 -10000 0 -0.29 22 22
MEF2C 0 0.097 -10000 0 -0.68 4 4
SMAD2-3/SMAD4 -0.003 0.033 -10000 0 -0.53 1 1
Cbp/p300/Src-1 0.003 0.022 -10000 0 -0.52 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 0.029 -10000 0 -0.29 11 11
HDAC1 0.001 0.002 -10000 0 -10000 0 0
HDAC2 0.001 0.002 -10000 0 -10000 0 0
SNIP1 0.001 0.003 -10000 0 -10000 0 0
GCN5L2 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.001 0.029 -10000 0 -0.53 1 1
MSG1/HSC70 -0.22 0.29 -10000 0 -0.6 406 406
SMAD2 0.015 0.02 -10000 0 -10000 0 0
SMAD3 0.015 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.034 0.038 -10000 0 -0.35 2 2
SMAD2/SMAD2/SMAD4 0.026 0.039 -10000 0 -1.1 1 1
NCOR1 0 0.024 -10000 0 -0.79 1 1
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
NCOA1 -0.001 0.024 -10000 0 -0.79 1 1
MYOD/E2A -0.003 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.028 0.051 -10000 0 -0.41 2 2
IFNB1 0.011 0.093 -10000 0 -0.42 18 18
SMAD3/SMAD4/MEF2C -0.027 0.078 -10000 0 -0.76 3 3
CITED1 -0.3 0.38 -10000 0 -0.77 421 421
SMAD2-3/SMAD4/ARC105 -0.001 0.028 -10000 0 -0.47 1 1
RBL1 -0.003 0.043 -10000 0 -0.59 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.047 0.062 -10000 0 -0.49 7 7
RUNX1-3/PEBPB2 -0.004 0.049 -10000 0 -0.58 7 7
SMAD7 -0.067 0.14 -10000 0 -0.58 8 8
MYC/MIZ-1 -0.012 0.09 -10000 0 -0.61 24 24
SMAD3/SMAD4 0.017 0.06 0.28 29 -0.43 2 31
IL10 0.018 0.12 -10000 0 -0.5 42 42
PIASy/HDAC complex 0.011 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 -0.5 40 40
CDK4 0.001 0.02 -10000 0 -0.29 4 4
PIAS4 0.011 0.004 -10000 0 -10000 0 0
ATF3 -0.11 0.27 -10000 0 -0.78 154 154
SMAD3/SMAD4/SP1 0 0.032 -10000 0 -0.52 2 2
FOXG1 -0.023 0.077 -10000 0 -0.29 80 80
FOXO3 0.025 0.034 -10000 0 -0.6 3 3
FOXO1 0.02 0.066 -10000 0 -0.6 12 12
FOXO4 0.026 0.008 -10000 0 -10000 0 0
heart looping 0 0.096 -10000 0 -0.68 4 4
CEBPB 0.012 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.029 0.078 -10000 0 -0.55 10 10
MYOD1 -0.004 0.033 -10000 0 -0.29 14 14
SMAD3/SMAD4/HNF4 -0.006 0.037 -10000 0 -0.68 1 1
SMAD3/SMAD4/GATA3 -0.024 0.11 -10000 0 -0.56 40 40
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.029 -10000 0 -0.29 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0 0.051 -10000 0 -0.52 8 8
SMAD3/SMAD4/SP1-3 0.003 0.029 -10000 0 -0.45 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 0.019 0.015 -10000 0 -10000 0 0
SIN3B 0.001 0.002 -10000 0 -10000 0 0
SIN3A 0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.091 -10000 0 -0.46 7 7
ITGB5 0.052 0.046 -10000 0 -0.41 1 1
TGIF/SIN3/HDAC complex/CtBP 0.002 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.074 0.19 -10000 0 -0.55 147 147
AR -0.1 0.27 -10000 0 -0.78 147 147
negative regulation of cell growth -0.025 0.072 -10000 0 -0.48 2 2
SMAD3/SMAD4/MYOD -0.006 0.034 -10000 0 -0.54 1 1
E2F5 -0.005 0.039 -10000 0 -0.29 20 20
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.002 0.057 -10000 0 -0.44 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.002 0.046 -10000 0 -0.34 5 5
TFDP1 -0.001 0.018 -10000 0 -0.29 4 4
SMAD3/SMAD4/AP1 -0.12 0.2 -10000 0 -0.56 41 41
SMAD3/SMAD4/RUNX2 -0.004 0.034 -10000 0 -0.54 1 1
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.002 0.041 -10000 0 -0.79 3 3
Aurora A signaling

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
Aurora A/GADD45A -0.026 0.031 -9999 0 -10000 0 0
BIRC5 -0.21 0.13 -9999 0 -0.29 780 780
NFKBIA -0.024 0.034 -9999 0 -10000 0 0
CPEB1 -0.15 0.31 -9999 0 -0.78 204 204
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 -0.55 1 1
NDEL1/TACC3 -0.041 0.061 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.003 0.004 -9999 0 -10000 0 0
PAK1/Aurora A -0.03 0.04 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
JUB -0.003 0.048 -9999 0 -0.79 4 4
TPX2 -0.11 0.1 -9999 0 -10000 0 0
TP53 -0.011 0.017 -9999 0 -10000 0 0
DLG7 -0.03 0.037 -9999 0 -10000 0 0
AURKAIP1 -0.003 0.031 -9999 0 -10000 0 0
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 -0.043 0.065 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.033 -9999 0 -0.54 1 1
AURKA -0.037 0.046 -9999 0 -10000 0 0
AURKB -0.009 0.011 -9999 0 -10000 0 0
CDC25B -0.018 0.026 -9999 0 -10000 0 0
G2/M transition checkpoint -0.025 0.04 -9999 0 -0.49 4 4
mRNA polyadenylation -0.11 0.19 -9999 0 -0.52 203 203
Aurora A/CPEB -0.11 0.2 -9999 0 -0.52 203 203
Aurora A/TACC1/TRAP/chTOG -0.032 0.089 -9999 0 -0.47 42 42
BRCA1 -0.001 0.027 -9999 0 -0.46 3 3
centrosome duplication -0.03 0.039 -9999 0 -10000 0 0
regulation of centrosome cycle -0.04 0.061 -9999 0 -10000 0 0
spindle assembly -0.032 0.088 -9999 0 -0.46 42 42
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.072 -9999 0 -0.61 1 1
CENPA -0.006 0.012 -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 0.02 -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 0.04 -9999 0 -0.49 4 4
mitotic prometaphase -0.013 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.046 -9999 0 -10000 0 0
TACC1 -0.03 0.15 -9999 0 -0.79 42 42
TACC3 -0.046 0.11 -9999 0 -0.29 173 173
Aurora A/Antizyme1 -0.022 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 0.004 -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 0.09 -9999 0 -10000 0 0
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
CKAP5 0 0 -9999 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.44 0.39 -10000 0 -0.79 610 610
CLTC 0.027 0.018 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.02 -10000 0 -10000 0 0
Dynamin 2/GTP -0.007 0.028 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.019 -10000 0 -0.26 2 2
CPE 0.006 0.081 -10000 0 -0.53 25 25
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.002 0.019 -10000 0 -10000 0 0
CTNND1 0.025 0.032 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.014 -10000 0 -10000 0 0
TSHR -0.007 0.11 -10000 0 -0.53 49 49
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.007 0.072 -10000 0 -0.74 10 10
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 0.009 0.038 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.028 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -0.26 1 1
ASAP2/amphiphysin II -0.004 0.045 -10000 0 -0.48 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.018 0.049 -10000 0 -0.27 28 28
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 -0.005 0.037 -10000 0 -0.29 18 18
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 0.008 0.032 -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 0.022 -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 0.031 -10000 0 -10000 0 0
NME1 0.009 0.038 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.018 -10000 0 -10000 0 0
IL2RA 0.017 0.045 -10000 0 -0.31 16 16
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.22 0.2 -10000 0 -0.39 610 610
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.003 0.032 -10000 0 -0.34 10 10
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 -0.008 0.034 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.008 0.033 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.019 -10000 0 -10000 0 0
endocytosis 0.004 0.045 0.47 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.071 0.19 -10000 0 -0.42 253 253
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.024 -10000 0 -0.79 1 1
Dynamin 2/GDP -0.007 0.028 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.13 0.22 -10000 0 -0.42 397 397
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.028 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.037 0.084 -9999 0 -0.43 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.069 -9999 0 -0.46 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.046 0.076 -9999 0 -10000 0 0
AP1 -0.14 0.21 -9999 0 -0.79 38 38
ILK -0.006 0.11 -9999 0 -0.46 37 37
bone resorption -0.038 0.11 -9999 0 -0.67 22 22
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.004 0.089 -9999 0 -0.49 9 9
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.018 0.1 -9999 0 -0.6 32 32
alphaV/beta3 Integrin/Osteopontin -0.05 0.1 -9999 0 -0.52 37 37
MAP3K1 -0.007 0.11 -9999 0 -0.48 37 37
JUN -0.005 0.063 -9999 0 -0.79 7 7
MAPK3 0.009 0.1 -9999 0 -0.43 37 37
MAPK1 0.009 0.1 -9999 0 -0.43 37 37
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.002 0.13 -9999 0 -0.53 39 39
ITGB3 -0.027 0.14 -9999 0 -0.73 41 41
NFKBIA 0.022 0.1 -9999 0 -0.42 27 27
FOS -0.24 0.36 -9999 0 -0.79 329 329
CD44 -0.001 0.015 -9999 0 -0.29 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.021 0.1 -9999 0 -0.51 1 1
NF kappa B1 p50/RelA -0.022 0.065 -9999 0 -10000 0 0
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 -0.59 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.008 0.11 -9999 0 -0.47 37 37
VAV3 -0.002 0.11 -9999 0 -0.44 44 44
MAP3K14 -0.004 0.11 -9999 0 -0.47 37 37
ROCK2 -0.023 0.13 -9999 0 -0.79 32 32
SPP1 -0.075 0.12 -9999 0 -0.29 25 25
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.036 0.083 -9999 0 -0.47 13 13
MMP2 -0.074 0.21 -9999 0 -0.68 38 38
Syndecan-2-mediated signaling 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
Syndecan-2/Fibronectin -0.06 0.077 -9999 0 -0.42 7 7
EPHB2 -0.005 0.038 -9999 0 -10000 0 0
Syndecan-2/TACI -0.018 0.075 -9999 0 -0.52 19 19
LAMA1 -0.088 0.25 -9999 0 -0.77 124 124
Syndecan-2/alpha2 ITGB1 -0.12 0.21 -9999 0 -0.46 293 293
HRAS -0.003 0.028 -9999 0 -0.29 10 10
Syndecan-2/CASK -0.003 0.033 -9999 0 -0.52 4 4
ITGA5 0 0.009 -9999 0 -0.29 1 1
BAX 0.033 0.061 -9999 0 -0.52 12 12
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.03 -9999 0 -0.47 4 4
LAMA3 -0.2 0.34 -9999 0 -0.79 276 276
EZR -0.001 0.015 -9999 0 -0.29 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.1 0.27 -9999 0 -0.79 146 146
Syndecan-2/MMP2 -0.008 0.07 -9999 0 -0.63 12 12
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.016 0.096 -9999 0 -0.6 29 29
dendrite morphogenesis -0.005 0.037 -9999 0 -0.51 4 4
Syndecan-2/GM-CSF -0.006 0.039 -9999 0 -0.52 4 4
determination of left/right symmetry 0.017 0.039 -9999 0 -0.39 8 8
Syndecan-2/PKC delta -0.003 0.033 -9999 0 -0.52 4 4
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.039 -9999 0 -0.47 4 4
MAPK1 0.022 0.039 -9999 0 -0.47 4 4
Syndecan-2/RACK1 -0.003 0.032 -9999 0 -0.48 4 4
NF1 -0.001 0.024 -9999 0 -0.79 1 1
FGFR/FGF/Syndecan-2 0.017 0.039 -9999 0 -0.39 8 8
ITGA2 -0.021 0.13 -9999 0 -0.79 29 29
MAPK8 0.027 0.065 -9999 0 -0.57 12 12
Syndecan-2/alpha2/beta1 Integrin -0.062 0.18 -9999 0 -0.5 133 133
Syndecan-2/Kininogen -0.005 0.039 -9999 0 -0.52 4 4
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.003 0.029 -9999 0 -0.45 4 4
Syndecan-2/CASK/Protein 4.1 -0.002 0.03 -9999 0 -0.48 4 4
extracellular matrix organization -0.003 0.033 -9999 0 -0.51 4 4
actin cytoskeleton reorganization -0.06 0.077 -9999 0 -0.42 7 7
Syndecan-2/Caveolin-2/Ras -0.066 0.17 -9999 0 -0.48 146 146
Syndecan-2/Laminin alpha3 -0.13 0.23 -9999 0 -0.52 280 280
Syndecan-2/RasGAP -0.003 0.03 -9999 0 -0.45 4 4
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
PRKCD 0 0.009 -9999 0 -0.29 1 1
Syndecan-2 dimer -0.005 0.037 -9999 0 -0.52 4 4
GO:0007205 0 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.003 0.028 -9999 0 -0.43 4 4
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.028 0.11 -9999 0 -0.79 15 15
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.016 0.096 -9999 0 -0.6 29 29
Syndecan-2/Synbindin -0.002 0.032 -9999 0 -0.52 4 4
TGFB1 -0.001 0.015 -9999 0 -0.29 3 3
CASP3 0.03 0.032 -9999 0 -0.46 4 4
FN1 -0.12 0.14 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.022 0.085 -9999 0 -0.52 26 26
SDC2 0.017 0.04 -9999 0 -0.39 8 8
KNG1 -0.006 0.041 -9999 0 -0.29 22 22
Syndecan-2/Neurofibromin -0.003 0.036 -9999 0 -0.52 5 5
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.007 0.045 -9999 0 -0.29 26 26
Syndecan-2/TGFB1 -0.003 0.033 -9999 0 -0.52 4 4
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.03 -9999 0 -0.48 4 4
Syndecan-2/Ezrin -0.002 0.03 -9999 0 -0.47 4 4
PRKACA 0.029 0.035 -9999 0 -0.47 5 5
angiogenesis -0.021 0.085 -9999 0 -0.52 26 26
MMP2 -0.008 0.079 -9999 0 -0.79 11 11
IL8 -0.033 0.13 -9999 0 -0.42 87 87
calcineurin-NFAT signaling pathway -0.018 0.075 -9999 0 -0.52 19 19
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.39 20 20
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 -0.25 395 395
YWHAZ -0.001 0.015 -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 0.046 -9999 0 -0.6 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 0.029 -9999 0 -0.29 11 11
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 0.024 -9999 0 -0.79 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 -0.28 395 395
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.016 0.099 -9999 0 -0.5 36 36
LNPEP -0.006 0.067 -9999 0 -0.79 8 8
YWHAE 0 0 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.025 0.079 -9999 0 -0.2 188 188
TP53 -0.008 0.02 -9999 0 -10000 0 0
Senescence -0.008 0.02 -9999 0 -10000 0 0
Apoptosis -0.008 0.02 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.017 0.041 -9999 0 -0.2 3 3
MDM4 0 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.003 0.041 -9999 0 -0.2 43 43
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.046 0.13 -9999 0 -0.6 46 46
STXBP1 -0.006 0.067 -9999 0 -0.79 8 8
ACh/CHRNA1 -0.062 0.082 -9999 0 -0.28 9 9
RAB3GAP2/RIMS1/UNC13B -0.038 0.11 -9999 0 -0.52 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 -0.066 0.18 -9999 0 -0.79 46 46
mol:ACh 0.001 0.031 -9999 0 -0.15 35 35
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.038 0.093 -9999 0 -0.39 54 54
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.062 0.082 -9999 0 -0.27 9 9
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.099 0.14 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.059 0.12 -9999 0 -0.42 75 75
SNAP25 -0.009 0.068 -9999 0 -0.37 35 35
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.087 0.18 -9999 0 -0.38 253 253
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.01 0.053 -9999 0 -0.52 8 8
STX1A/SNAP25 fragment 1/VAMP2 -0.038 0.093 -9999 0 -0.39 54 54
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.077 0.32 36 -10000 0 36
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.035 -10000 0 -0.52 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.03 0.13 -10000 0 -0.48 67 67
RhoA/GTP -0.025 0.078 -10000 0 -0.32 36 36
negative regulation of cAMP metabolic process -0.028 0.087 -10000 0 -0.3 96 96
GNAZ -0.007 0.075 -10000 0 -0.79 10 10
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.058 -10000 0 -0.35 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.028 0.088 -10000 0 -0.3 96 96
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.03 0.13 -9999 0 -0.48 67 67
CDC42/GTP -0.026 0.077 -9999 0 -0.31 40 40
PLCG1 0.008 0.092 -9999 0 -0.32 40 40
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 -0.025 0.076 -9999 0 -0.3 40 40
S1PR5 -0.008 0.058 -9999 0 -0.35 25 25
S1PR4 -0.014 0.079 -9999 0 -0.36 44 44
MAPK3 0.008 0.092 -9999 0 -0.32 40 40
MAPK1 0.008 0.092 -9999 0 -0.32 40 40
S1P/S1P5/Gi -0.028 0.088 -9999 0 -0.3 96 96
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.035 -9999 0 -0.52 3 3
RHOA -0.006 0.038 -9999 0 -0.44 6 6
S1P/S1P4/Gi -0.029 0.087 -9999 0 -0.3 101 101
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.075 -9999 0 -0.79 10 10
S1P/S1P4/G12/G13 -0.007 0.042 -9999 0 -0.48 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
BARD1 signaling events

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
BARD1/CSTF1 -0.011 0.079 -10000 0 -0.6 19 19
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 -0.029 0.073 -10000 0 -0.47 20 20
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 0.027 -10000 0 -0.46 3 3
CCNE1 -0.06 0.12 -10000 0 -0.29 223 223
CDK2/Cyclin E1 -0.038 0.075 -10000 0 -10000 0 0
FANCG 0 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.011 0.081 -10000 0 -0.6 20 20
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 -0.051 0.11 -10000 0 -0.29 192 192
DNA repair 0.008 0.094 -10000 0 -0.47 6 6
BRCA1/BARD1/ubiquitin -0.011 0.081 -10000 0 -0.6 20 20
BARD1/DNA-PK -0.009 0.062 -10000 0 -0.47 19 19
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.011 0.079 0.6 19 -10000 0 19
BRCA1/BARD1/CTIP/M/R/N Complex -0.006 0.041 -10000 0 -0.31 19 19
BRCA1/BACH1/BARD1/TopBP1 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/P53 -0.009 0.063 -10000 0 -0.47 20 20
BARD1/CSTF1/BRCA1 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BACH1 -0.001 0.027 -10000 0 -0.46 3 3
BARD1 -0.014 0.1 -10000 0 -0.79 19 19
PCNA -0.001 0.015 -10000 0 -0.29 3 3
BRCA1/BARD1/UbcH5C -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/UbcH7 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/RAD51/PCNA -0.053 0.086 -10000 0 -0.51 20 20
BARD1/DNA-PK/P53 -0.008 0.057 -10000 0 -0.44 19 19
BRCA1/BARD1/Ubiquitin -0.011 0.081 -10000 0 -0.6 20 20
BRCA1/BARD1/CTIP -0.009 0.063 -10000 0 -0.47 20 20
FA complex -0.005 0.011 -10000 0 -10000 0 0
BARD1/EWS -0.011 0.079 -10000 0 -0.6 19 19
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 0.009 0.063 0.46 20 -10000 0 20
BRCA1/BARD1 -0.029 0.074 -10000 0 -0.48 20 20
CSTF1 0 0.009 -10000 0 -0.29 1 1
BARD1/EWS-Fli1 -0.011 0.08 -10000 0 -0.61 19 19
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.11 0.14 -10000 0 -0.29 396 396
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.011 0.081 -10000 0 -0.6 20 20
EWSR1 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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 0.001 0.004 -9999 0 -10000 0 0
HDAC2 0.001 0.004 -9999 0 -10000 0 0
GNB1/GNG2 -0.011 0.081 -9999 0 -0.56 22 22
forebrain development -0.024 0.2 -9999 0 -0.51 136 136
GNAO1 -0.021 0.13 -9999 0 -0.48 67 67
SMO/beta Arrestin2 -0.005 0.055 -9999 0 -0.6 9 9
SMO 0.004 0.073 -9999 0 -0.79 9 9
ARRB2 0.011 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.037 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.01 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.035 0.18 -9999 0 -0.79 62 62
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.054 0.16 -9999 0 -0.51 83 83
SAP30 0 0.018 -9999 0 -0.29 4 4
mol:GDP 0.004 0.073 -9999 0 -0.79 9 9
MIM/GLI2A 0.002 0.028 -9999 0 -0.3 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GLI2 0.04 0.037 -9999 0 -10000 0 0
GLI3 0.04 0.039 -9999 0 -10000 0 0
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 -0.011 0.092 -9999 0 -0.79 15 15
Gi family/GTP -0.002 0.1 -9999 0 -0.31 91 91
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 0.025 -9999 0 -0.44 1 1
GLI2/Su(fu) 0.008 0.048 -9999 0 -0.39 7 7
FOXA2 -0.012 0.031 -9999 0 -10000 0 0
neural tube patterning -0.024 0.2 -9999 0 -0.51 136 136
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.026 -9999 0 -0.45 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 0.028 -9999 0 -0.3 9 9
embryonic limb morphogenesis -0.024 0.2 -9999 0 -0.51 136 136
SUFU 0.004 0.032 -9999 0 -0.36 3 3
LGALS3 -0.012 0.095 -9999 0 -0.79 16 16
catabolic process -0.004 0.027 -9999 0 -10000 0 0
GLI3A/CBP -0.008 0.097 -9999 0 -0.38 70 70
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.026 0.21 -9999 0 -0.52 136 136
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.024 -9999 0 -0.79 1 1
RBBP7 -0.001 0.025 -9999 0 -0.29 8 8
Su(fu)/Galectin3 -0.009 0.067 -9999 0 -0.51 17 17
GNAZ 0.003 0.076 -9999 0 -0.79 10 10
RBBP4 0.001 0.024 -9999 0 -0.79 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 0.027 -9999 0 -10000 0 0
STK36 0.011 0.024 -9999 0 -0.79 1 1
Gi family/GNB1/GNG2/GDP -0.031 0.1 -9999 0 -0.47 28 28
PTCH1 -0.067 0.34 -9999 0 -1.1 95 95
MIM/GLI1 -0.018 0.19 -9999 0 -0.5 122 122
CREBBP -0.008 0.097 -9999 0 -0.38 70 70
Su(fu)/SIN3/HDAC complex 0.008 0.023 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.005 0.094 0.23 1 -0.44 38 39
ACTA1 -0.018 0.13 0.27 1 -0.61 39 40
NUMA1 0.005 0.094 0.23 1 -0.44 38 39
SPTAN1 -0.005 0.12 0.27 1 -0.6 36 37
LIMK1 -0.005 0.12 0.27 1 -0.58 39 40
BIRC3 -0.01 0.077 -10000 0 -0.5 21 21
BIRC2 0 0 -10000 0 -10000 0 0
BAX -0.001 0.018 -10000 0 -0.29 4 4
CASP10 -0.015 0.14 -10000 0 -0.58 48 48
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.094 0.23 1 -0.44 38 39
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.12 0.27 1 -0.58 37 38
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.011 0.14 0.27 1 -0.61 45 46
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.014 0.083 -10000 0 -0.67 15 15
BID 0.005 0.062 -10000 0 -0.29 38 38
MAP3K1 0.004 0.042 -10000 0 -0.27 9 9
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 -0.005 0.12 0.27 1 -0.61 35 36
CASP9 0.002 0.004 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.18 7 -0.22 4 11
neuron apoptosis 0.022 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.12 -10000 0 -0.58 35 35
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.023 0.057 -10000 0 -0.35 10 10
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
ICAD/CAD 0.003 0.12 -10000 0 -0.58 35 35
CASP7 -0.007 0.037 0.36 9 -10000 0 9
KRT18 0.015 0.024 -10000 0 -0.59 1 1
apoptosis 0.009 0.11 0.26 4 -0.51 35 39
DFFA -0.005 0.12 0.27 1 -0.61 35 36
DFFB -0.005 0.12 0.27 1 -0.61 35 36
PARP1 0.002 0.031 0.22 4 -0.18 7 11
actin filament polymerization -0.002 0.12 0.55 39 -10000 0 39
TNF -0.016 0.095 -10000 0 -0.46 38 38
CYCS 0.007 0.05 -10000 0 -0.21 38 38
SATB1 0.016 0.099 -10000 0 -0.46 33 33
SLK -0.005 0.12 0.27 1 -0.58 39 40
p15 BID/BAX -0.014 0.049 -10000 0 -0.35 8 8
CASP2 0.044 0.039 -10000 0 -0.45 1 1
JNK cascade -0.004 0.042 0.27 9 -10000 0 9
CASP3 -0.014 0.13 0.28 1 -0.62 39 40
LMNB2 0.041 0.036 -10000 0 -0.38 2 2
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.024 -10000 0 -0.79 1 1
Mammalian IAPs/DIABLO -0.005 0.044 -10000 0 -0.47 9 9
negative regulation of DNA binding 0.014 0.082 -10000 0 -0.66 15 15
stress fiber formation -0.004 0.12 0.27 1 -0.56 39 40
GZMB -0.029 0.15 -10000 0 -0.64 47 47
CASP1 0.014 0.033 -10000 0 -0.44 6 6
LMNB1 0.044 0.037 -10000 0 -0.38 2 2
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 0.003 0.1 0.26 4 -0.49 36 40
LMNA 0.04 0.036 -10000 0 -0.38 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.034 -10000 0 -0.48 1 1
LRDD -0.002 0.022 -10000 0 -0.29 6 6
SREBF1 -0.007 0.13 0.27 1 -0.58 39 40
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.005 0.092 0.23 1 -0.43 38 39
CFL2 0.001 0.12 -10000 0 -0.56 39 39
GAS2 -0.046 0.18 -10000 0 -0.52 126 126
positive regulation of apoptosis 0.045 0.036 -10000 0 -0.37 2 2
PRF1 -0.017 0.11 -10000 0 -0.63 29 29
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.007 -10000 0 -10000 0 0
CDKN1B 0.036 0.024 -10000 0 -0.42 3 3
CDKN1A 0.036 0.02 -10000 0 -0.42 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
FOXO3 0.036 0.024 -10000 0 -0.42 3 3
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
AKT3 0.008 0.061 -10000 0 -0.44 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.003 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.025 -10000 0 -0.41 4 4
BAD/YWHAZ -0.001 0.009 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.024 0.39 4 -10000 0 4
TSC1 0.037 0.003 -10000 0 -10000 0 0
YWHAZ -0.001 0.015 -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 0.022 0.04 -10000 0 -0.51 6 6
MAP3K5 -0.003 0.048 -10000 0 -0.79 4 4
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.022 -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 0.021 -10000 0 -0.39 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 0.017 -10000 0 -0.4 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.003 -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 0.053 0.03 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.01 -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 0.25 -10000 0 -0.47 612 612
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 0.25 -10000 0 -0.47 612 612
GSK3A 0.037 0.003 -10000 0 -10000 0 0
FOXO1 0.032 0.048 -10000 0 -0.42 12 12
GSK3B 0.037 0.003 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.5 36 36
G1/S transition of mitotic cell cycle 0.044 0.003 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.042 0.032 -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 -0.29 1 1
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 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
SPHK2 0.022 0.02 -10000 0 -0.6 1 1
MAP4K4 0.041 0.044 -10000 0 -0.68 1 1
BAG4 -0.006 0.055 -10000 0 -0.43 14 14
PKC zeta/ceramide -0.023 0.047 0.18 1 -0.57 1 2
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.077 -10000 0 -0.5 21 21
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 -0.021 0.045 0.2 1 -0.25 1 2
SMPD1 0.026 0.032 -10000 0 -0.24 13 13
RB1 -0.022 0.047 0.2 1 -0.47 1 2
FADD/Caspase 8 0.049 0.046 -10000 0 -0.44 3 3
MAP2K4 -0.014 0.046 -10000 0 -0.44 2 2
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.045 -10000 0 -0.3 3 3
EGF -0.15 0.31 -10000 0 -0.78 214 214
mol:ceramide -0.033 0.047 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 -0.6 1 1
ASAH1 -0.001 0.015 -10000 0 -0.29 3 3
negative regulation of cell cycle -0.022 0.046 0.2 1 -0.46 1 2
cell proliferation -0.094 0.16 -10000 0 -0.38 247 247
BID 0.024 0.033 -10000 0 -0.39 1 1
MAP3K1 -0.022 0.047 0.2 1 -0.47 1 2
EIF2A -0.005 0.04 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.001 0.043 -10000 0 -0.41 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.043 -10000 0 -0.41 1 1
Cathepsin D/ceramide -0.027 0.049 0.18 1 -0.25 2 3
FADD 0.04 0.048 -10000 0 -0.47 3 3
KSR1 -0.022 0.048 0.2 1 -0.32 3 4
MAPK8 -0.012 0.054 0.2 1 -0.34 11 12
PRKRA -0.021 0.045 0.2 1 -10000 0 1
PDGFA -0.001 0.025 -10000 0 -0.54 2 2
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
IGF1 -0.18 0.33 -10000 0 -0.79 247 247
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.032 0.047 0.21 1 -10000 0 1
CTSD -0.01 0.053 -10000 0 -0.29 37 37
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 -0.41 247 247
PRKCD 0 0.009 -10000 0 -0.29 1 1
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.023 -10000 0 -0.6 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 0.024 -10000 0 -0.79 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.04 -10000 0 -0.72 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.069 -10000 0 -0.52 17 17
mol:Sphingosine-1-phosphate 0.022 0.02 -10000 0 -0.6 1 1
MAP2K1 -0.005 0.043 -10000 0 -0.42 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.007 0.043 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 0.04 -10000 0 -0.6 4 4
EIF2AK2 -0.013 0.042 0.2 1 -10000 0 1
TNF-alpha/TNFR1A/FAN -0.009 0.06 -10000 0 -0.52 13 13
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0.02 -10000 0 -0.32 1 1
MAP2K2 -0.005 0.043 -10000 0 -0.42 1 1
SMPD3 0.026 0.039 -10000 0 -0.27 16 16
TNF -0.016 0.095 -10000 0 -0.46 38 38
PKC zeta/PAR4 -0.001 0.026 -10000 0 -0.6 2 2
mol:PHOSPHOCHOLINE 0.044 0.11 0.27 213 -10000 0 213
NF kappa B1/RelA/I kappa B alpha -0.001 0.019 -10000 0 -0.43 2 2
AIFM1 -0.007 0.043 0.18 25 -10000 0 25
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.007 0.072 -10000 0 -0.74 10 10
positive regulation of NF-kappaB transcription factor activity -0.062 0.18 -10000 0 -0.6 113 113
MAP2K4 0.042 0.038 -10000 0 -0.37 2 2
IKBKB -0.001 0.013 -10000 0 -10000 0 0
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.005 0.063 -10000 0 -0.79 7 7
SMPD1 -0.002 0.026 -10000 0 -0.28 9 9
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.075 0.23 -10000 0 -0.78 105 105
TRAIL/TRAILR2 -0.005 0.054 -10000 0 -0.6 9 9
TRAIL/TRAILR3 -0.008 0.068 -10000 0 -0.64 11 11
TRAIL/TRAILR1 -0.009 0.072 -10000 0 -0.6 16 16
TRAIL/TRAILR4 -0.062 0.18 -10000 0 -0.6 113 113
TRAIL/TRAILR1/DAP3/GTP -0.007 0.057 -10000 0 -0.48 16 16
IKK complex -0.003 0.019 -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 -10000 0 0
MAPK3 0.017 0.056 -10000 0 -0.6 9 9
MAP3K1 -0.004 0.032 -10000 0 -0.32 10 10
TRAILR4 (trimer) -0.075 0.23 -10000 0 -0.78 105 105
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.005 0.063 -10000 0 -0.79 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.039 -10000 0 -0.32 16 16
CFLAR -0.001 0.024 -10000 0 -0.79 1 1
MAPK1 0.017 0.056 -10000 0 -0.6 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.055 -10000 0 -0.44 16 16
mol:ceramide -0.002 0.025 -10000 0 -0.28 9 9
FADD -0.004 0.034 -10000 0 -0.29 15 15
MAPK8 0.044 0.057 -10000 0 -0.43 10 10
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
TRAILR3 (trimer) -0.004 0.048 -10000 0 -0.43 11 11
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.065 -10000 0 -0.52 16 16
DAP3 0 0.009 -10000 0 -0.29 1 1
CASP10 0.021 0.11 0.31 98 -0.49 13 111
JNK cascade -0.062 0.18 -10000 0 -0.6 113 113
TRAIL (trimer) -0.007 0.072 -10000 0 -0.74 10 10
TNFRSF10C -0.004 0.048 -10000 0 -0.43 11 11
TRAIL/TRAILR1/DAP3/GTP/FADD -0.008 0.056 -10000 0 -0.45 16 16
TRAIL/TRAILR2/FADD -0.006 0.05 -10000 0 -0.52 9 9
cell death -0.002 0.025 -10000 0 -0.28 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.029 -10000 0 -0.32 9 9
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.016 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.005 0.041 -10000 0 -0.44 9 9
Retinoic acid receptors-mediated signaling

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
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 0.016 -10000 0 -0.52 1 1
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.037 0.043 -10000 0 -0.34 6 6
KAT2B -0.001 0.024 -10000 0 -0.79 1 1
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.019 0.054 0.24 4 -0.36 14 18
RAR alpha/9cRA/Cyclin H -0.012 0.067 -10000 0 -0.39 29 29
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.033 0.052 -10000 0 -0.33 16 16
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 -0.013 0.074 -10000 0 -0.66 10 10
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 0.13 -10000 0 -0.58 35 35
NCOA2 -0.039 0.17 -10000 0 -0.79 54 54
NCOA3 0 0.009 -10000 0 -0.29 1 1
NCOA1 -0.001 0.024 -10000 0 -0.79 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0.012 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.011 0.002 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.072 -10000 0 -0.79 9 9
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.11 -10000 0 -0.63 29 29
RARA 0.014 0.066 -10000 0 -0.32 36 36
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.019 0.09 -10000 0 -0.3 66 66
PRKCA -0.007 0.13 -10000 0 -0.79 29 29
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.006 0.14 -10000 0 -0.6 36 36
RXRG -0.1 0.21 -10000 0 -0.44 290 290
RXRA 0.021 0.067 -10000 0 -0.33 36 36
RXRB 0.01 0.076 -10000 0 -0.43 29 29
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.026 0.097 -10000 0 -0.33 86 86
CRBP1/9-cic-RA -0.018 0.07 -10000 0 -0.61 7 7
RARB 0.002 0.093 -10000 0 -0.79 15 15
PRKCG -0.003 0.062 -10000 0 -0.29 49 49
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.13 -10000 0 -0.62 33 33
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.012 0.11 -10000 0 -0.51 34 34
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.062 -10000 0 -0.48 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.006 0.14 -10000 0 -0.6 36 36
positive regulation of DNA binding -0.011 0.063 -10000 0 -0.37 29 29
NRIP1 -0.004 0.13 -10000 0 -0.59 32 32
RXRs/RARs -0.013 0.13 -10000 0 -0.6 36 36
RXRs/RXRs/DNA/9cRA -0.046 0.12 -10000 0 -0.66 29 29
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 -0.007 0.038 -10000 0 -0.53 2 2
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
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.03 0.007 -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 0.017 0.082 -9999 0 -0.46 30 30
CCND1 0.015 0.043 -9999 0 -0.22 29 29
p38 gamma/SNTA1 -0.012 0.071 -9999 0 -0.42 30 30
MAP2K3 0 0.009 -9999 0 -0.29 1 1
PKN1 0 0.009 -9999 0 -0.29 1 1
G2/M transition checkpoint 0.017 0.082 -9999 0 -0.45 30 30
MAP2K6 0.01 0.084 -9999 0 -0.49 30 30
MAPT -0.018 0.13 -9999 0 -0.4 117 117
MAPK13 0.022 0.009 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.031 -9999 0 -0.44 5 5
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.048 -10000 0 -0.79 4 4
ANTXR2 -0.009 0.082 -10000 0 -0.79 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.012 -10000 0 -0.1 14 14
monocyte activation 0.004 0.073 -10000 0 -0.46 26 26
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.01 -10000 0 -10000 0 0
MAP2K7 -0.001 0.01 -10000 0 -10000 0 0
MAP2K6 -0.012 0.071 -10000 0 -0.47 25 25
CYAA 0.009 0.062 -10000 0 -0.52 14 14
MAP2K4 -0.002 0.017 -10000 0 -0.46 1 1
IL1B 0.007 0.064 -10000 0 -0.42 19 19
Channel -0.007 0.064 -10000 0 -0.55 14 14
NLRP1 -0.008 0.059 -10000 0 -0.49 16 16
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.012 0.1 14 -10000 0 14
MAPK3 -0.001 0.01 -10000 0 -10000 0 0
MAPK1 -0.001 0.01 -10000 0 -10000 0 0
PGR -0.14 0.21 -10000 0 -0.47 313 313
PA/Cellular Receptors -0.008 0.069 -10000 0 -0.59 14 14
apoptosis -0.001 0.012 -10000 0 -0.1 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.007 0.06 -10000 0 -0.51 14 14
macrophage activation 0.019 0.011 -10000 0 -10000 0 0
TNF -0.016 0.095 -10000 0 -0.46 38 38
VCAM1 -0.011 0.071 -10000 0 -0.46 26 26
platelet activation -0.002 0.014 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.022 0.1 27 -10000 0 27
IL18 0.01 0.037 -10000 0 -0.22 16 16
negative regulation of macrophage activation -0.001 0.012 -10000 0 -0.1 14 14
LEF -0.001 0.012 -10000 0 -0.1 14 14
CASP1 -0.005 0.031 -10000 0 -0.23 17 17
mol:cAMP -0.002 0.014 -10000 0 -10000 0 0
necrosis -0.001 0.012 -10000 0 -0.1 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.007 0.061 -10000 0 -0.52 14 14
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.045 0.065 -10000 0 -0.66 1 1
UGCG -0.011 0.095 -10000 0 -0.79 15 15
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 0.013 0.097 -10000 0 -0.78 15 15
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.09 -10000 0 -0.38 43 43
FRAP1 0.052 0.13 -10000 0 -0.41 64 64
FOXO3 0.06 0.11 -10000 0 -0.42 32 32
AKT1 0.055 0.11 -10000 0 -0.45 34 34
GAB2 0.008 0.043 -10000 0 -0.39 10 10
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 0.015 0.062 -10000 0 -0.52 14 14
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.032 0.089 -10000 0 -0.35 39 39
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.008 0.068 -10000 0 -0.6 14 14
RPS6KB1 0.021 0.034 -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 22 22
JAK3 0.01 0.034 -10000 0 -0.29 14 14
PIK3R1 0.003 0.09 -10000 0 -0.79 14 14
JAK1 0.013 0.024 -10000 0 -0.78 1 1
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.046 0.18 -10000 0 -0.94 29 29
MYB 0.006 0.19 -10000 0 -1.3 23 23
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.052 0.094 -10000 0 -0.56 11 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.023 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.092 -10000 0 -0.54 11 11
Rac1/GDP -0.006 0.053 -10000 0 -0.47 14 14
T cell proliferation 0.058 0.087 -10000 0 -0.5 11 11
SHC1 0.011 0.003 -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 23 23
PRKCZ 0.058 0.09 -10000 0 -0.53 11 11
NF kappa B1 p50/RelA -0.025 0.088 -10000 0 -0.53 12 12
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.039 0.07 -10000 0 -0.52 6 6
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.02 0.12 -10000 0 -0.38 87 87
IL2RB 0.001 0.066 -10000 0 -0.31 42 42
TERT -0.044 0.1 -10000 0 -0.29 165 165
E2F1 0.02 0.068 -10000 0 -0.44 23 23
SOS1 0.011 0.003 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.03 23 -10000 0 23
PTPN11 0.011 0.003 -10000 0 -10000 0 0
IL2RG -0.004 0.087 -10000 0 -0.36 53 53
actin cytoskeleton organization 0.058 0.087 -10000 0 -0.5 11 11
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 -0.29 1 1
Rac1/GTP 0.025 0.055 -10000 0 -0.45 14 14
LCK -0.007 0.1 -10000 0 -0.41 53 53
BCL2 0.039 0.2 -10000 0 -0.88 41 41
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.014 0.083 -9999 0 -0.52 29 29
E-cadherin/beta catenin -0.015 0.095 -9999 0 -0.6 28 28
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.025 -9999 0 -0.54 2 2
CDH1 -0.02 0.12 -9999 0 -0.79 28 28
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.017 0.082 -9999 0 -0.51 23 23
MAP4K1 -0.015 0.07 -9999 0 -0.31 53 53
MAP3K8 -0.007 0.072 -9999 0 -0.74 10 10
PRKCB -0.019 0.11 -9999 0 -0.55 39 39
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.036 0.053 -9999 0 -0.47 4 4
JUN 0.016 0.12 -9999 0 -0.6 35 35
MAP3K7 0.036 0.052 -9999 0 -0.48 3 3
GRAP2 -0.014 0.1 -9999 0 -0.72 21 21
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.043 0.056 -9999 0 -0.46 5 5
LAT -0.005 0.048 -9999 0 -0.35 17 17
LCP2 0 0.009 -9999 0 -0.29 1 1
MAPK8 0.012 0.12 -9999 0 -0.68 28 28
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.048 -9999 0 -0.35 18 18
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.016 0.077 -9999 0 -0.48 23 23
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 0.048 -9999 0 -0.79 4 4
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.03 0.095 -9999 0 -0.33 95 95
GNAO1 -0.018 0.13 -9999 0 -0.48 67 67
S1P/S1P3/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.011 0.051 -9999 0 -0.68 4 4
AKT3 0.012 0.2 -9999 0 -1.4 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.047 -9999 0 -0.79 4 4
GNAI2 0.013 0.003 -9999 0 -10000 0 0
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GNAI1 -0.033 0.19 -9999 0 -0.79 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.029 -9999 0 -0.3 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.009 0.11 -9999 0 -0.39 40 40
MAPK3 0.017 0.1 -9999 0 -0.51 14 14
MAPK1 0.017 0.1 -9999 0 -0.47 17 17
JAK2 0.019 0.1 -9999 0 -0.36 43 43
CXCR4 0.014 0.1 -9999 0 -0.37 42 42
FLT1 0.013 0.025 -9999 0 -0.8 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.017 0.1 -9999 0 -0.36 40 40
S1P/S1P3/Gi 0.009 0.11 -9999 0 -0.39 40 40
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.026 0.084 -9999 0 -0.44 18 18
VEGFA 0.01 0.032 -9999 0 -0.35 1 1
S1P/S1P2/Gi 0.008 0.1 -9999 0 -0.3 95 95
VEGFR1 homodimer/VEGFA homodimer 0.021 0.03 -9999 0 -0.62 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.007 0.043 -9999 0 -0.34 18 18
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
GNAZ 0.005 0.076 -9999 0 -0.79 10 10
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.013 0.084 -9999 0 -0.46 30 30
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.003 0.048 -9999 0 -0.79 4 4
Rac1/GTP -0.026 0.084 -9999 0 -0.46 17 17
PLK2 and PLK4 events

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
PLK2 0 0.009 -9999 0 -0.29 1 1
PLK4 -0.012 0.059 -9999 0 -0.29 46 46
regulation of centriole replication 0.013 0.042 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.79 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 0.042 -10000 0 -0.44 5 5
IRAK/TOLLIP -0.001 0.01 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.031 0.12 -10000 0 -0.58 43 43
IL1A -0.005 0.039 -10000 0 -10000 0 0
IL1B 0.011 0.092 -10000 0 -0.69 17 17
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.014 -10000 0 -0.39 1 1
IL1R2 -0.037 0.15 -10000 0 -0.57 71 71
IL1R1 -0.017 0.12 -10000 0 -0.79 24 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.063 0.23 33 -0.32 19 52
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 0.031 0.08 -10000 0 -0.37 40 40
MAP3K7 0 0.009 -10000 0 -0.29 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.023 0.11 -10000 0 -0.49 51 51
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.013 0.075 -10000 0 -0.49 25 25
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.012 0.07 -10000 0 -0.45 25 25
IL1 beta fragment/IL1R1/IL1RAP -0.02 0.11 -10000 0 -0.53 40 40
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.027 0.075 -10000 0 -0.39 34 34
IRAK1 0.021 0.013 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.021 0.097 -10000 0 -0.6 26 26
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 -0.008 0.068 -10000 0 -0.6 14 14
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.063 -10000 0 -0.35 26 26
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.02 0.11 -10000 0 -0.53 40 40
IL1 beta/IL1R2 -0.033 0.13 -10000 0 -0.56 55 55
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.021 0.099 -10000 0 -0.84 7 7
IRAK3 -0.031 0.15 -10000 0 -0.78 44 44
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.018 0.097 -10000 0 -0.48 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.051 -10000 0 -0.33 25 25
IL1 alpha/IL1R1/IL1RAP -0.015 0.083 -10000 0 -0.54 25 25
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 0.034 -10000 0 -0.79 2 2
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.078 -10000 0 -0.81 4 4
CASP1 -0.004 0.053 -10000 0 -0.79 5 5
IL1RN/IL1R2 -0.035 0.12 -10000 0 -0.57 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.019 0.1 -10000 0 -0.5 40 40
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -0.29 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.009 0.057 -10000 0 -0.38 24 24
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL1RN -0.012 0.064 -10000 0 -0.32 41 41
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.01 0.062 -10000 0 -0.41 25 25
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 23 23
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0.02 0.019 -9999 0 -0.36 2 2
GNAO1 -0.03 0.13 -9999 0 -0.48 67 67
mol:Sphinganine-1-P 0.017 0.039 -9999 0 -0.6 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 0.028 -9999 0 -0.29 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.014 -9999 0 -0.31 2 2
S1PR5 -0.008 0.058 -9999 0 -0.35 25 25
S1PR4 -0.014 0.079 -9999 0 -0.36 44 44
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
S1P/S1P5/G12 -0.005 0.032 -9999 0 -0.46 3 3
S1P/S1P3/Gq -0.005 0.038 -9999 0 -0.29 18 18
S1P/S1P4/Gi -0.028 0.084 -9999 0 -0.33 42 42
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
GNAZ -0.007 0.075 -9999 0 -0.79 10 10
GNA14 -0.013 0.084 -9999 0 -0.46 30 30
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.003 0.048 -9999 0 -0.79 4 4
ABCC1 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.016 0.092 -9999 0 -0.58 28 28
KLHL20 -0.008 0.031 -9999 0 -0.24 3 3
CYFIP2 -0.01 0.065 -9999 0 -0.36 31 31
Rac1/GDP 0.05 0.065 -9999 0 -0.34 28 28
ENAH -0.015 0.091 -9999 0 -0.57 28 28
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 -0.008 0.045 -9999 0 -0.49 1 1
ABI1/Sra1/Nap1 -0.006 0.023 -9999 0 -0.19 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.078 -9999 0 -0.47 30 30
RAPGEF1 0.04 0.085 -9999 0 -0.48 28 28
CTNND1 0 0.009 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.016 0.095 -9999 0 -0.6 28 28
CRK 0.032 0.092 -9999 0 -0.53 28 28
E-cadherin/gamma catenin/alpha catenin -0.014 0.083 -9999 0 -0.52 29 29
alphaE/beta7 Integrin -0.006 0.04 -9999 0 -0.6 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.035 -9999 0 -0.48 6 6
DLG1 -0.015 0.091 -9999 0 -0.57 28 28
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.039 -9999 0 -0.31 2 2
MLLT4 -0.005 0.059 -9999 0 -0.72 7 7
ARF6/GTP/NME1/Tiam1 -0.007 0.029 -9999 0 -10000 0 0
PI3K -0.01 0.051 -9999 0 -0.42 2 2
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.016 0.097 -9999 0 -0.6 29 29
TIAM1 -0.001 0.018 -9999 0 -0.29 4 4
E-cadherin(dimer)/Ca2+ -0.011 0.07 -9999 0 -0.44 28 28
AKT1 -0.006 0.028 -9999 0 -0.22 2 2
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
CDH1 -0.02 0.12 -9999 0 -0.79 28 28
RhoA/GDP 0.05 0.065 -9999 0 -0.34 28 28
actin cytoskeleton organization -0.006 0.023 -9999 0 -0.17 3 3
CDC42/GDP 0.05 0.065 -9999 0 -0.34 28 28
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.009 0.054 -9999 0 -0.33 29 29
ITGB7 -0.009 0.058 -9999 0 -0.32 32 32
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.012 0.074 -9999 0 -0.47 28 28
E-cadherin/Ca2+/beta catenin/alpha catenin -0.012 0.071 -9999 0 -0.45 28 28
mol:GDP 0.047 0.075 -9999 0 -0.41 28 28
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.025 -9999 0 -0.54 2 2
p120 catenin/RhoA/GDP -0.009 0.056 -9999 0 -0.44 2 2
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 -0.015 0.065 -9999 0 -0.29 56 56
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.015 0.092 -9999 0 -0.57 29 29
regulation of cell-cell adhesion -0.007 0.04 -9999 0 -0.42 1 1
WASF2 -0.003 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.009 0.053 -9999 0 -0.58 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.015 0.074 -9999 0 -0.44 31 31
CCND1 -0.009 0.035 -9999 0 -0.27 7 7
VAV2 0.036 0.089 -9999 0 -0.51 28 28
RAP1/GDP -0.009 0.053 -9999 0 -0.56 1 1
adherens junction assembly -0.015 0.088 -9999 0 -0.55 29 29
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 -0.014 0.07 -9999 0 -0.41 31 31
E-cadherin/beta catenin -0.012 0.077 -9999 0 -0.49 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.015 0.091 -9999 0 -0.57 28 28
PIK3CA 0 0.009 -9999 0 -0.29 1 1
Rac1/GTP -0.01 0.051 -9999 0 -0.35 6 6
E-cadherin/beta catenin/alpha catenin -0.013 0.082 -9999 0 -0.52 28 28
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.097 -9999 0 -0.61 28 28
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.082 0.33 1 -0.36 58 59
FRAP1 0.01 0.023 -10000 0 -10000 0 0
AKT1 -0.017 0.071 0.24 1 -0.31 58 59
INSR 0 0.009 -10000 0 -0.29 1 1
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.013 0.055 -10000 0 -0.33 15 15
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.018 -10000 0 -10000 0 0
TSC2 0 0.002 -10000 0 -10000 0 0
RHEB/GDP -0.011 0.048 -10000 0 -0.34 1 1
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.017 0.082 -10000 0 -0.42 45 45
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.005 0.021 -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 0.045 -10000 0 -0.25 15 15
MAP3K5 0.009 0.027 -10000 0 -0.44 4 4
PIK3R1 -0.01 0.089 -10000 0 -0.79 14 14
apoptosis 0.009 0.027 -10000 0 -0.44 4 4
mol:LY294002 0 0 -10000 0 -0.002 45 45
EIF4B 0.024 0.041 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.007 0.03 -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 -0.021 0.087 -10000 0 -0.38 59 59
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.033 0.18 1 -10000 0 1
FKBP1A 0 0.009 -10000 0 -0.29 1 1
RHEB/GTP -0.011 0.047 -10000 0 -0.34 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 45 45
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.017 0.074 0.26 1 -0.33 58 59
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.004 0.039 -10000 0 -0.62 4 4
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.014 0.059 -10000 0 -0.35 15 15
tumor necrosis factor receptor activity 0 0 0.002 45 -10000 0 45
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 0.09 -10000 0 -0.45 45 45
INS 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
PDK2 -0.019 0.079 0.26 1 -0.34 61 62
EIF4EBP1 0.013 0.01 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PPP2R5D 0.017 0.021 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.005 -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 14 16
EEF2 0.016 0.005 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 -0.002 0.028 -10000 0 -0.46 4 4
TRAF2/ASK1 -0.002 0.033 -10000 0 -0.52 4 4
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.025 0.045 -10000 0 -0.39 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.064 -10000 0 -0.38 9 9
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.038 0.098 -10000 0 -0.29 141 141
TXN 0.008 0.006 -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 0.024 -10000 0 -0.79 1 1
MAP3K6 -0.001 0.024 -10000 0 -0.79 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 0.04 -10000 0 -0.6 5 5
TAK1/TAB family 0.001 0.011 0.21 3 -10000 0 3
RAC1/OSM/MEKK3 0 0.005 -10000 0 -10000 0 0
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
RAC1/OSM/MEKK3/MKK3 -0.006 0.023 -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 -0.066 0.2 -10000 0 -0.59 123 123
CCM2 -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/CAMKIIB -0.042 0.13 -10000 0 -0.52 74 74
MAPK11 -0.002 0.041 -10000 0 -0.79 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.04 0.12 -10000 0 -0.48 77 77
OSM/MEKK3 0 0.008 -10000 0 -10000 0 0
TAOK1 -0.006 0.099 -10000 0 -0.44 55 55
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 0.048 -10000 0 -0.79 4 4
MAP3K10 0 0.009 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.002 0.031 -10000 0 -0.52 4 4
GADD45/MTK1/MTK1 -0.014 0.037 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.004 0.024 -9999 0 -0.4 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 -0.45 3 3
EPO -0.047 0.11 -9999 0 -0.29 177 177
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.44 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 0.069 -9999 0 -10000 0 0
lamellipodium assembly -0.004 0.046 -9999 0 -0.4 14 14
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.068 -9999 0 -0.6 14 14
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.01 0.025 -9999 0 -0.5 1 1
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
MADCAM1 -0.012 0.057 -9999 0 -0.29 43 43
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 0.057 -9999 0 -0.47 13 13
ITGB7 -0.009 0.058 -9999 0 -0.32 32 32
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.058 -9999 0 -0.52 13 13
p130Cas/Crk/Dock1 -0.006 0.042 -9999 0 -10000 0 0
VCAM1 -0.011 0.088 -9999 0 -0.63 19 19
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.034 0.054 -9999 0 -0.43 13 13
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 -0.005 0.047 -9999 0 -0.41 14 14
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.006 0.054 -10000 0 -0.47 15 15
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.012 -10000 0 -0.39 1 1
GATA1/HDAC4 -0.004 0.03 -10000 0 -0.6 1 1
GATA1/HDAC5 -0.003 0.024 -10000 0 -10000 0 0
GATA2/HDAC5 -0.018 0.097 -10000 0 -0.6 28 28
HDAC5/BCL6/BCoR -0.004 0.044 -10000 0 -0.52 8 8
HDAC9 -0.01 0.081 -10000 0 -0.52 22 22
Glucocorticoid receptor/Hsp90/HDAC6 -0.008 0.062 -10000 0 -0.52 16 16
HDAC4/ANKRA2 -0.001 0.018 -10000 0 -0.6 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0.001 -10000 0 -10000 0 0
GATA2 -0.024 0.13 -10000 0 -0.79 28 28
HDAC4/RFXANK -0.002 0.023 -10000 0 -0.6 1 1
BCOR -0.001 0.034 -10000 0 -0.79 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 -0.001 0.013 -10000 0 -0.29 2 2
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.008 0.07 -10000 0 -0.6 15 15
Histones -0.003 0.026 -10000 0 -0.26 11 11
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.79 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.018 -10000 0 -0.6 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 0.014 -10000 0 -10000 0 0
CAMK4 -0.011 0.059 -10000 0 -0.79 1 1
Tubulin/HDAC6 -0.001 0.017 -10000 0 -0.52 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 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.012 0.095 -10000 0 -0.79 16 16
SUMO1/HDAC4 0 0.013 -10000 0 -0.43 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.018 -10000 0 -0.6 1 1
Tubulin -0.001 0.02 -10000 0 -0.6 1 1
HDAC4/14-3-3 E -0.001 0.018 -10000 0 -0.6 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0.009 -10000 0 -0.29 1 1
BCL6/BCoR -0.004 0.051 -10000 0 -0.6 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0 0.016 -10000 0 -0.52 1 1
HDAC4/SRF -0.006 0.034 -10000 0 -0.52 2 2
HDAC4/ER alpha -0.11 0.21 -10000 0 -0.6 166 166
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.025 -10000 0 -0.25 11 11
cell motility -0.001 0.017 -10000 0 -0.51 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 0.058 -10000 0 -0.79 6 6
HDAC4/CaMK II delta B -0.001 0.024 -10000 0 -0.79 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.15 0.28 -10000 0 -0.58 288 288
HDAC6/HDAC11 -0.001 0.011 -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 0.034 -10000 0 -0.79 2 2
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.023 -10000 0 -0.44 3 3
GNG2 -0.011 0.092 -10000 0 -0.79 15 15
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.027 -10000 0 -0.46 3 3
HDAC11 -0.001 0.018 -10000 0 -0.29 4 4
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK -0.002 0.022 -10000 0 -0.29 6 6
nuclear import 0 0.013 0.43 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.058 -9999 0 -0.32 32 32
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.44 6 6
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.049 0.029 -10000 0 -0.36 4 4
NFATC2 0.015 0.064 -10000 0 -0.31 11 11
NFATC3 0 0.015 -10000 0 -0.51 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.094 -10000 0 -0.39 38 38
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 0.075 -10000 0 -0.49 17 17
BCL2/BAX -0.021 0.11 -10000 0 -0.61 37 37
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 0.018 -10000 0 -0.29 4 4
MAPK14 0.01 0.003 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
CABIN1/MEF2D -0.02 0.08 -10000 0 -0.52 17 17
Calcineurin A alpha-beta B1/BCL2 -0.027 0.14 -10000 0 -0.79 37 37
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.019 0.079 0.51 17 -10000 0 17
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.029 0.087 -10000 0 -0.29 108 108
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.5 36 36
MAP3K8 0.004 0.073 -10000 0 -0.74 10 10
NFAT4/CK1 alpha -0.001 0.016 -10000 0 -0.38 2 2
MEF2D/NFAT1/Cbp/p300 -0.038 0.093 -10000 0 -0.46 3 3
CABIN1 0.012 0.095 -10000 0 -0.39 38 38
CALM1 0.001 0.003 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.024 -10000 0 -0.79 1 1
CAMK4 -0.011 0.059 -10000 0 -0.79 1 1
mol:Ca2+ -0.001 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 -0.6 1 1
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.072 -10000 0 -0.79 9 9
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 0.021 -10000 0 -0.4 1 1
PRKCH -0.001 0.024 -10000 0 -0.79 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0.01 0.003 -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 0.035 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.024 -10000 0 -10000 0 0
PRKCB -0.019 0.11 -10000 0 -0.55 39 39
PRKCE 0 0 -10000 0 -10000 0 0
JNK2/NFAT4 0 0.014 -10000 0 -0.46 1 1
BAD/BCL-XL 0 0.006 -10000 0 -10000 0 0
PRKCD 0 0.009 -10000 0 -0.29 1 1
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.024 -10000 0 -0.79 1 1
PRKCA -0.021 0.13 -10000 0 -0.79 29 29
PRKCG -0.013 0.061 -10000 0 -0.29 49 49
PRKCQ -0.036 0.16 -10000 0 -0.79 45 45
FKBP38/BCL2 -0.02 0.11 -10000 0 -0.6 37 37
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 0.047 0.049 -10000 0 -0.36 12 12
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.006 0.032 -10000 0 -0.52 1 1
NFATc/ERK1 0.053 0.027 -10000 0 -0.36 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.019 0.075 -10000 0 -0.48 17 17
NR4A1 -0.014 0.22 -10000 0 -0.7 99 99
GSK3B 0.011 0.003 -10000 0 -10000 0 0
positive T cell selection 0 0.015 -10000 0 -0.5 1 1
NFAT1/CK1 alpha -0.016 0.039 -10000 0 -0.29 3 3
RCH1/ KPNB1 -0.018 0.056 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0.01 0.003 -10000 0 -10000 0 0
AKAP5 -0.015 0.067 -10000 0 -0.3 54 54
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
NFATc/p38 alpha 0.051 0.031 -10000 0 -0.36 1 1
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.6 37 37
AKT1 0.079 0.073 -9999 0 -0.68 7 7
PTK2B 0.035 0.12 -9999 0 -1 8 8
VEGFR2 homodimer/Frs2 -0.009 0.083 -9999 0 -0.81 10 10
CAV1 -0.17 0.33 -9999 0 -0.79 241 241
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.009 0.077 -9999 0 -0.74 10 10
endothelial cell proliferation 0.082 0.087 -9999 0 -0.69 7 7
mol:Ca2+ 0.05 0.074 -9999 0 -0.84 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.007 0.073 -9999 0 -0.9 6 6
RP11-342D11.1 0.042 0.074 -9999 0 -0.67 10 10
CDH5 -0.007 0.075 -9999 0 -0.79 10 10
VEGFA homodimer -0.001 0.012 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.02 0.12 -9999 0 -0.77 28 28
HRAS/GDP -0.006 0.06 -9999 0 -0.75 6 6
SH2D2A -0.035 0.1 -9999 0 -0.3 125 125
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.003 0.055 -9999 0 -0.67 6 6
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.021 0.087 -9999 0 -0.7 13 13
VEGFR1 homodimer -0.001 0.024 -9999 0 -0.79 1 1
SHC/GRB2/SOS1 -0.005 0.066 -9999 0 -0.82 6 6
GRB10 0.05 0.074 -9999 0 -0.84 6 6
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 25 25
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.009 0.095 -9999 0 -1 8 8
HRAS -0.003 0.028 -9999 0 -0.29 10 10
VEGF/Rho/ROCK1/Integrin Complex -0.011 0.065 -9999 0 -0.59 8 8
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.29 11 11
oxygen and reactive oxygen species metabolic process -0.007 0.071 -9999 0 -0.88 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.041 -9999 0 -0.79 3 3
Nck/Pak -0.004 0.028 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.084 -9999 0 -0.77 11 11
mol:GDP -0.005 0.062 -9999 0 -0.78 6 6
mol:NADP 0.073 0.053 -9999 0 -0.55 6 6
eNOS/Hsp90 0.074 0.049 -9999 0 -0.51 6 6
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
mol:IP3 0.05 0.076 -9999 0 -0.86 6 6
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.025 -9999 0 -0.54 2 2
VEGFA -0.003 0.03 -9999 0 -10000 0 0
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin 0.056 0.1 -9999 0 -0.96 7 7
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 8 8
PTPN6 -0.001 0.013 -9999 0 -0.29 2 2
EPAS1 -0.006 0.071 -9999 0 -0.69 10 10
mol:L-citrulline 0.073 0.053 -9999 0 -0.55 6 6
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 0.073 -9999 0 -0.9 6 6
VEGFR2 homodimer/VEGFA homodimer -0.008 0.076 -9999 0 -0.74 10 10
VEGFR2/3 heterodimer -0.009 0.092 -9999 0 -0.86 11 11
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.054 0.08 -9999 0 -0.9 6 6
VEGFR2 homodimer 0.027 0.094 -9999 0 -0.9 10 10
FLT1 -0.001 0.024 -9999 0 -0.79 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.05 0.084 -9999 0 -0.83 7 7
MAPK1 0.05 0.084 -9999 0 -0.83 7 7
VEGFA145/NRP2 -0.004 0.039 -9999 0 -0.65 3 3
VEGFR1/2 heterodimer -0.008 0.087 -9999 0 -0.85 10 10
KDR 0.027 0.094 -9999 0 -0.91 10 10
VEGFA165/NRP1/VEGFR2 homodimer -0.006 0.082 -9999 0 -0.93 7 7
SRC 0 0.009 -9999 0 -0.29 1 1
platelet activating factor biosynthetic process 0.052 0.085 -9999 0 -0.86 7 7
PI3K -0.009 0.079 -9999 0 -0.9 7 7
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.008 0.077 -9999 0 -0.74 10 10
FES 0.049 0.081 -9999 0 -0.88 6 6
GAB1 -0.006 0.071 -9999 0 -0.9 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.077 -9999 0 -0.74 10 10
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 -0.6 13 13
VEGFR2 homodimer/VEGFA homodimer/Yes -0.008 0.078 -9999 0 -0.72 11 11
PI3K/GAB1 0.078 0.081 -9999 0 -0.72 7 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.003 0.071 -9999 0 -0.87 6 6
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.008 0.086 -9999 0 -0.8 11 11
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
CDC42 0.05 0.077 -9999 0 -0.88 6 6
actin cytoskeleton reorganization -0.021 0.086 -9999 0 -0.69 13 13
PTK2 0.051 0.11 -9999 0 -1.1 7 7
EDG1 0.042 0.074 -9999 0 -0.67 10 10
mol:DAG 0.05 0.076 -9999 0 -0.86 6 6
CaM/Ca2+ -0.006 0.063 -9999 0 -0.79 6 6
MAP2K3 0.055 0.079 -9999 0 -0.83 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.005 0.072 -9999 0 -0.9 6 6
PLCG1 0.05 0.077 -9999 0 -0.88 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.008 0.074 -9999 0 -0.9 6 6
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.79 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.008 0.077 -9999 0 -0.74 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.077 -9999 0 -0.74 10 10
cell migration 0.078 0.091 -9999 0 -0.79 7 7
mol:PI-3-4-5-P3 -0.008 0.07 -9999 0 -0.79 7 7
FYN -0.001 0.034 -9999 0 -0.79 2 2
VEGFB/NRP1 -0.007 0.064 -9999 0 -0.8 6 6
mol:NO 0.073 0.053 -9999 0 -0.55 6 6
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.06 -9999 0 -0.75 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.073 -9999 0 -0.9 6 6
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.028 0.14 -9999 0 -0.74 41 41
NOS3 0.075 0.059 -9999 0 -0.63 6 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.019 0.1 -9999 0 -0.54 37 37
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.045 0.11 -9999 0 -0.99 6 6
PRKCB 0.046 0.1 -9999 0 -0.86 8 8
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.007 0.069 -9999 0 -0.67 10 10
VEGFR1/2 heterodimer/VEGFA homodimer -0.008 0.082 -9999 0 -0.79 10 10
VEGFA165/NRP2 -0.004 0.039 -9999 0 -0.65 3 3
MAPKKK cascade -0.004 0.06 -9999 0 -0.75 6 6
NRP2 -0.002 0.042 -9999 0 -0.66 4 4
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 -0.001 0.024 -9999 0 -0.79 1 1
FAK1/Paxillin 0.056 0.1 -9999 0 -0.96 7 7
MAP3K13 0.048 0.083 -9999 0 -0.88 6 6
PDPK1 0.073 0.07 -9999 0 -0.67 7 7
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.006 0.055 -9999 0 -0.43 14 14
Caspase 8 (4 units) -0.01 0.052 -9999 0 -0.85 2 2
NEF -0.006 0.028 -9999 0 -0.22 11 11
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 0.035 0.081 -9999 0 -0.79 9 9
CYCS 0.04 0.06 -9999 0 -0.93 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.025 0.12 -9999 0 -0.61 37 37
MAP2K7 0.042 0.049 -9999 0 -0.8 1 1
protein ubiquitination 0.066 0.034 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.004 0.058 -9999 0 -0.79 6 6
BID 0.033 0.063 -9999 0 -1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.033 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.003 0.048 -9999 0 -0.79 4 4
CFLAR -0.001 0.024 -9999 0 -0.79 1 1
FADD -0.004 0.034 -9999 0 -0.29 15 15
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.033 -9999 0 -10000 0 0
MAPK8 0.045 0.064 -9999 0 -0.48 10 10
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.015 -9999 0 -0.29 3 3
TRAF2 -0.001 0.018 -9999 0 -0.29 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.012 0.058 -9999 0 -0.33 24 24
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.03 -9999 0 -0.37 2 2
CHUK 0.068 0.035 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.005 0.049 -9999 0 -0.5 9 9
TCRz/NEF -0.025 0.11 -9999 0 -0.51 41 41
TNF -0.016 0.095 -9999 0 -0.46 38 38
FASLG -0.007 0.15 -9999 0 -0.66 41 41
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.069 -9999 0 -0.52 17 17
CASP6 -0.005 0.037 -9999 0 -0.68 2 2
CASP7 0.072 0.077 -9999 0 -0.6 10 10
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.072 0.077 -9999 0 -0.6 10 10
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.04 -9999 0 -0.6 4 4
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.038 -9999 0 -0.36 1 1
APAF-1/Caspase 9 -0.01 0.053 -9999 0 -0.5 9 9
BCL2 0.036 0.1 -9999 0 -0.42 44 44
Class I PI3K signaling events

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
ARF5/GTP -0.002 0.028 0.3 2 -0.44 2 4
DAPP1 0.036 0.052 -10000 0 -0.58 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.046 0.078 -10000 0 -0.56 10 10
mol:DAG 0.052 0.05 0.21 1 -0.27 7 8
HRAS 0.009 0.029 -10000 0 -0.29 10 10
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP 0.038 0.032 -10000 0 -0.3 2 2
PLCG2 -0.002 0.035 -10000 0 -0.62 3 3
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.009 -10000 0 -0.29 1 1
mol:GTP -0.001 0.022 0.26 2 -0.38 2 4
ARF1/GTP -0.001 0.023 0.28 2 -0.37 2 4
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.024 -10000 0 -0.79 1 1
RAP1A/GTP -0.001 0.022 0.25 2 -0.38 2 4
ADAP1 -0.003 0.032 0.26 2 -0.39 5 7
ARAP3 -0.001 0.022 0.26 2 -0.39 2 4
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.057 -10000 0 -0.31 36 36
ARHGEF6 -0.011 0.092 -10000 0 -0.79 15 15
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS 0.011 0.013 -10000 0 -0.29 2 2
FYN -0.001 0.034 -10000 0 -0.79 2 2
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.001 0.025 -10000 0 -0.54 2 2
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 -0.031 0.12 -10000 0 -0.42 81 81
mol:IP3 0.047 0.038 -10000 0 -0.22 1 1
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.032 -10000 0 -0.3 2 2
RhoA/GDP -0.002 0.022 0.27 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 0.007 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.033 -10000 0 -0.76 2 2
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
ARF6/GTP -0.001 0.021 0.3 2 -0.35 2 4
RhoA/GTP -0.001 0.021 0.25 2 -0.36 2 4
Src family/SYK family/BLNK-LAT -0.011 0.056 -10000 0 -0.53 6 6
BLK -0.044 0.11 -10000 0 -0.3 159 159
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.001 0.021 0.26 2 -0.36 2 4
HCK -0.004 0.033 -10000 0 -0.29 14 14
CYTH3 -0.002 0.028 0.26 2 -0.41 4 6
CYTH2 -0.001 0.021 0.26 2 -0.36 2 4
KRAS 0.011 0.013 -10000 0 -0.29 2 2
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.055 -10000 0 -0.55 10 10
SGK1 -0.004 0.057 0.23 2 -0.7 7 9
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.033 -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 0.28 2 -10000 0 2
mol:PI-3-4-5-P3 -0.001 0.024 0.36 2 -0.38 2 4
ARAP3/RAP1A/GTP -0.001 0.022 0.25 2 -0.38 2 4
VAV1 -0.003 0.043 -10000 0 -0.79 3 3
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.002 0.019 -10000 0 -0.39 2 2
PLEKHA1 0.03 0.017 -10000 0 -0.52 1 1
Rac1/GDP 0.038 0.032 -10000 0 -0.3 2 2
LAT -0.005 0.048 -10000 0 -0.35 17 17
Rac1/GTP -0.006 0.045 -10000 0 -0.37 15 15
ITK -0.019 0.083 0.26 1 -0.43 38 39
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.059 0.065 0.24 1 -0.39 7 8
LCK -0.02 0.1 -10000 0 -0.41 53 53
BTK -0.001 0.021 0.26 2 -0.36 2 4
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.001 0.027 -9999 0 -0.89 1 1
VEGFR1 homodimer/NRP1 -0.001 0.027 -9999 0 -0.9 1 1
mol:DAG 0.038 0.032 -9999 0 -0.64 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.028 -9999 0 -0.84 1 1
CaM/Ca2+ -0.002 0.027 -9999 0 -0.6 2 2
HIF1A 0 0.011 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.006 0.052 -9999 0 -0.71 1 1
PLCG1 0.038 0.032 -9999 0 -0.64 2 2
NOS3 0.061 0.033 -9999 0 -0.55 2 2
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.06 0.032 -9999 0 -0.53 2 2
FLT1 0.029 0.031 -9999 0 -1 1 1
PGF -0.002 0.031 -9999 0 -0.38 6 6
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.046 -9999 0 -0.78 3 3
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
eNOS/Hsp90 0.065 0.031 -9999 0 -0.64 1 1
endothelial cell proliferation 0.036 0.089 -9999 0 -0.56 8 8
mol:Ca2+ 0.038 0.031 -9999 0 -0.63 2 2
MAPK3 0.039 0.082 -9999 0 -0.43 30 30
MAPK1 0.039 0.082 -9999 0 -0.43 30 30
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
PLGF homodimer -0.002 0.031 -9999 0 -0.38 6 6
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 -0.79 241 241
VEGFA homodimer -0.003 0.03 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.002 0.031 -9999 0 -0.89 1 1
platelet activating factor biosynthetic process 0.046 0.079 -9999 0 -1.1 1 1
PI3K -0.007 0.056 -9999 0 -0.45 16 16
PRKCA 0.032 0.086 -9999 0 -0.46 30 30
PRKCB 0.034 0.077 -9999 0 -0.47 21 21
VEGFR1 homodimer/PLGF homodimer -0.002 0.032 -9999 0 -0.7 2 2
VEGFA -0.003 0.031 -9999 0 -10000 0 0
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.032 -9999 0 -0.64 2 2
RASA1 0.039 0.026 -9999 0 -0.83 1 1
NRP2 -0.002 0.042 -9999 0 -0.66 4 4
VEGFR1 homodimer 0.029 0.031 -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 0.18 -9999 0 -0.58 9 9
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.055 -9999 0 -0.45 16 16
mol:L-citrulline 0.06 0.032 -9999 0 -0.53 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.027 -9999 0 -0.79 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.028 -9999 0 -0.83 1 1
CD2AP 0 0.009 -9999 0 -0.29 1 1
PI3K/GAB1 -0.007 0.053 -9999 0 -0.74 1 1
PDPK1 -0.007 0.052 -9999 0 -0.42 16 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.028 -9999 0 -0.83 1 1
mol:NADP 0.06 0.032 -9999 0 -0.53 2 2
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
ubiquitin-dependent protein catabolic process -0.002 0.026 -9999 0 -0.78 1 1
VEGFR1 homodimer/NRP2 -0.002 0.046 -9999 0 -0.78 3 3
EPO 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
BCL2L1 0.058 0.076 -9999 0 -0.51 1 1
CRKL 0.028 0.05 -9999 0 -0.48 1 1
mol:DAG -0.007 0.026 -9999 0 -0.39 1 1
HRAS -0.006 0.022 -9999 0 -10000 0 0
MAPK8 0.01 0.07 -9999 0 -0.5 9 9
RAP1A 0.028 0.05 -9999 0 -0.48 1 1
GAB1 0.028 0.05 -9999 0 -0.48 1 1
MAPK14 0.015 0.052 -9999 0 -10000 0 0
EPO -0.036 0.11 -9999 0 -0.28 177 177
PLCG1 -0.007 0.026 -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 0.065 -9999 0 -0.62 6 6
GAB1/SHC/GRB2/SOS1 -0.008 0.022 -9999 0 -0.41 1 1
EPO/EPOR (dimer) -0.027 0.067 -9999 0 -10000 0 0
IRS2 0.009 0.11 -9999 0 -0.46 47 47
STAT1 0.049 0.056 -9999 0 -0.5 1 1
STAT5B -0.004 0.043 -9999 0 -0.43 4 4
cell proliferation 0.02 0.065 -9999 0 -0.46 9 9
GAB1/SHIP/PIK3R1/SHP2/SHC -0.011 0.044 -9999 0 -0.42 4 4
TEC 0.027 0.056 -9999 0 -0.48 4 4
SOCS3 -0.004 0.058 -9999 0 -0.79 6 6
STAT1 (dimer) 0.048 0.056 -9999 0 -0.49 1 1
JAK2 0.011 0.025 -9999 0 -0.8 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
EPO/EPOR (dimer)/JAK2 0.054 0.04 -9999 0 -0.51 1 1
EPO/EPOR -0.027 0.067 -9999 0 -10000 0 0
LYN 0.013 0.002 -9999 0 -10000 0 0
TEC/VAV2 0.034 0.055 -9999 0 -0.46 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 -0.017 0.05 -9999 0 -10000 0 0
mol:IP3 -0.007 0.026 -9999 0 -0.39 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.03 0.096 -9999 0 -0.49 23 23
SH2B3 0.012 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.052 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.031 -9999 0 -0.32 7 7
PTPN6 0.021 0.052 -9999 0 -0.51 1 1
TEC/VAV2/GRB2 -0.01 0.034 -9999 0 -0.46 3 3
EPOR 0.012 0.01 -9999 0 -0.28 1 1
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.008 0.022 -9999 0 -0.42 1 1
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.002 0.035 -9999 0 -0.62 3 3
CRKL/CBL/C3G -0.009 0.025 -9999 0 -0.44 1 1
VAV2 0.028 0.05 -9999 0 -0.48 1 1
CBL 0.028 0.05 -9999 0 -0.48 1 1
SHC/Grb2/SOS1 0.005 0.028 -9999 0 -0.44 1 1
STAT5A -0.006 0.055 -9999 0 -0.47 9 9
GRB2 0 0.009 -9999 0 -0.29 1 1
STAT5 (dimer) 0.058 0.085 -9999 0 -0.56 5 5
LYN/PLCgamma2 -0.001 0.026 -9999 0 -0.6 2 2
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.028 0.051 -9999 0 -0.48 1 1
BCL2 0.036 0.19 -9999 0 -0.98 37 37
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0 0.017 -10000 0 -10000 0 0
oxygen homeostasis 0.012 0.012 -10000 0 -10000 0 0
TCEB2 -0.007 0.045 -10000 0 -0.29 27 27
TCEB1 -0.001 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.007 0.039 -10000 0 -0.43 2 2
EPO 0.14 0.15 -10000 0 -0.58 5 5
FIH (dimer) 0.023 0.012 -10000 0 -10000 0 0
APEX1 0.022 0.014 -10000 0 -0.31 1 1
SERPINE1 0.16 0.15 -10000 0 -0.66 5 5
FLT1 -0.004 0.085 -10000 0 -1.1 6 6
ADORA2A 0.14 0.16 -10000 0 -0.64 5 5
germ cell development 0.16 0.15 -10000 0 -0.65 5 5
SLC11A2 0.16 0.15 -10000 0 -0.68 4 4
BHLHE40 0.16 0.16 -10000 0 -0.8 5 5
HIF1AN 0.023 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.013 0.07 -10000 0 -0.42 5 5
ETS1 0.022 0.061 -10000 0 -0.8 6 6
CITED2 0.001 0.011 -10000 0 -10000 0 0
KDR -0.008 0.12 -10000 0 -1.3 9 9
PGK1 0.16 0.15 -10000 0 -0.68 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 0.091 0.083 -10000 0 -0.41 5 5
SP1 0.019 0.002 -10000 0 -10000 0 0
ABCG2 0.12 0.25 -10000 0 -0.69 80 80
EFNA1 0.16 0.15 -10000 0 -0.68 4 4
FXN 0.15 0.15 -10000 0 -0.66 4 4
POU5F1 0.16 0.15 -10000 0 -0.68 5 5
neuron apoptosis -0.17 0.16 0.74 5 -10000 0 5
EP300 0 0 -10000 0 -10000 0 0
EGLN3 -0.001 0.085 -10000 0 -0.29 83 83
EGLN2 0.021 0.026 -10000 0 -0.3 3 3
EGLN1 0.022 0.027 -10000 0 -0.8 1 1
VHL/Elongin B/Elongin C -0.004 0.024 -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 0.16 -10000 0 -0.64 6 6
TWIST1 0.13 0.21 -10000 0 -0.68 46 46
ELK1 0.019 0.009 -10000 0 -0.29 1 1
HIF2A/ARNT/Cbp/p300 0.008 0.063 -10000 0 -0.6 1 1
VEGFA 0.16 0.15 -10000 0 -0.71 4 4
CREBBP 0 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
SMAD2 0.014 0.004 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.004 0.015 -9999 0 -0.29 1 1
SMAD4/Ubc9/PIASy 0 0.016 -9999 0 -0.52 1 1
SMAD2/SMAD2/SMAD4 -0.009 0.031 -9999 0 -0.52 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 -0.47 1 1
MAP3K1 -0.001 0.024 -9999 0 -0.79 1 1
TRAP-1/SMAD4 -0.01 0.076 -9999 0 -0.6 18 18
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 -0.012 0.097 -9999 0 -0.79 17 17
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.009 -9999 0 -0.29 1 1
KPNA2 -0.029 0.087 -9999 0 -0.29 108 108
PIAS4 0 0 -9999 0 -10000 0 0
FoxO family signaling

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
G6PC 0.029 0.039 -9999 0 -10000 0 0
PLK1 0.004 0.12 -9999 0 -0.62 8 8
CDKN1B 0.079 0.072 -9999 0 -0.54 3 3
FOXO3 0.039 0.11 -9999 0 -0.56 12 12
KAT2B 0.008 0.028 -9999 0 -0.83 1 1
FOXO1/SIRT1 0.007 0.039 -9999 0 -0.32 12 12
CAT 0.041 0.13 -9999 0 -1.2 6 6
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.015 0.011 -9999 0 -10000 0 0
FOXO1 0.031 0.042 -9999 0 -0.36 12 12
MAPK10 -0.038 0.18 -9999 0 -0.44 171 171
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.063 0.089 -9999 0 -0.38 3 3
response to oxidative stress 0.005 0.012 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.016 0.069 -9999 0 -0.52 8 8
XPO1 0.012 0.001 -9999 0 -10000 0 0
EP300 0.01 0.005 -9999 0 -10000 0 0
BCL2L11 0.028 0.02 -9999 0 -10000 0 0
FOXO1/SKP2 -0.004 0.033 -9999 0 -0.32 12 12
mol:GDP 0.005 0.012 -9999 0 -10000 0 0
RAN 0.013 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 0.027 -9999 0 -10000 0 0
MST1 -0.003 0.092 -9999 0 -0.59 22 22
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.049 0.045 -9999 0 -0.35 4 4
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.033 0.044 -9999 0 -0.44 9 9
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 0.015 -9999 0 -0.29 3 3
SIRT1 0.004 0.009 -9999 0 -10000 0 0
SOD2 0.09 0.079 -9999 0 -0.45 1 1
RBL2 0.06 0.083 -9999 0 -0.56 2 2
RAL/GDP 0.012 0.016 -9999 0 -10000 0 0
CHUK 0.009 0.013 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.031 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.002 0.18 -9999 0 -1.5 15 15
SKP2 0 0 -9999 0 -10000 0 0
USP7 0.013 0.001 -9999 0 -10000 0 0
IKBKB 0.008 0.018 -9999 0 -10000 0 0
CCNB1 0.032 0.12 -9999 0 -0.64 6 6
FOXO1-3a-4/beta catenin -0.009 0.043 -9999 0 -0.41 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.033 -9999 0 -0.32 12 12
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.004 0.065 -9999 0 -0.79 7 7
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 -0.016 0.099 -9999 0 -0.5 36 36
CDK2 0.004 0.006 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.044 0.048 -9999 0 -10000 0 0
CREBBP 0.004 0.006 -9999 0 -10000 0 0
FBXO32 0.042 0.12 -9999 0 -1 6 6
BCL6 0.054 0.13 -9999 0 -1.2 7 7
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.045 -9999 0 -0.56 6 6
PDGFB-D/PDGFRB/SLAP -0.004 0.041 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/APS/CBL -0.008 0.043 -9999 0 -0.51 4 4
AKT1 -0.012 0.052 -9999 0 -0.49 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.052 -9999 0 -0.58 6 6
PIK3CA 0 0.009 -9999 0 -0.29 1 1
FGR -0.003 0.038 -9999 0 -0.53 5 5
mol:Ca2+ 0.033 0.048 -9999 0 -0.68 4 4
MYC 0.039 0.14 -9999 0 -0.83 26 26
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.028 -9999 0 -0.42 4 4
LRP1/PDGFRB/PDGFB -0.008 0.07 -9999 0 -0.58 15 15
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.048 -9999 0 -0.69 4 4
PTEN -0.001 0.034 -9999 0 -0.79 2 2
GRB2 0 0.009 -9999 0 -0.29 1 1
GRB7 -0.023 0.085 -9999 0 -0.31 79 79
PDGFB-D/PDGFRB/SHP2 -0.002 0.036 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/GRB10 -0.002 0.036 -9999 0 -0.6 4 4
cell cycle arrest -0.004 0.04 -9999 0 -0.6 4 4
HRAS -0.003 0.028 -9999 0 -0.29 10 10
HIF1A 0.05 0.061 -9999 0 -0.43 4 4
GAB1 0.035 0.055 -9999 0 -0.67 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.04 0.053 -9999 0 -0.61 4 4
PDGFB-D/PDGFRB -0.003 0.035 -9999 0 -0.52 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.036 -9999 0 -0.6 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.049 -9999 0 -0.57 6 6
positive regulation of MAPKKK cascade -0.002 0.036 -9999 0 -0.6 4 4
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
mol:IP3 0.033 0.049 -9999 0 -0.7 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.017 0.067 -9999 0 -0.6 7 7
SHB -0.001 0.025 -9999 0 -0.54 2 2
BLK -0.002 0.049 -9999 0 -0.58 7 7
PTPN2 0.002 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.036 -9999 0 -0.6 4 4
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.062 -9999 0 -0.61 5 5
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.036 -9999 0 -0.6 4 4
LCK -0.01 0.08 -9999 0 -0.63 16 16
PDGFRB 0.009 0.049 -9999 0 -0.79 4 4
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.002 0.033 -9999 0 -0.5 4 4
ABL1 0.034 0.049 -9999 0 -0.63 4 4
PDGFB-D/PDGFRB/CBL 0.034 0.06 -9999 0 -0.79 4 4
PTPN1 -0.001 0.03 -9999 0 -0.29 11 11
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.005 0.038 -9999 0 -0.29 19 19
cell proliferation 0.041 0.12 -9999 0 -0.7 27 27
SLA -0.003 0.029 -9999 0 -0.29 11 11
actin cytoskeleton reorganization -0.002 0.028 -9999 0 -0.4 2 2
SRC -0.002 0.033 -9999 0 -0.5 4 4
PI3K -0.014 0.059 -9999 0 -0.56 4 4
PDGFB-D/PDGFRB/GRB7/SHC -0.013 0.054 -9999 0 -0.52 7 7
SH2B2 -0.013 0.061 -9999 0 -0.29 49 49
PLCgamma1/SPHK1 0.036 0.054 -9999 0 -0.61 6 6
LYN -0.002 0.033 -9999 0 -0.5 4 4
LRP1 -0.009 0.085 -9999 0 -0.79 13 13
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.002 0.041 -9999 0 -0.79 3 3
STAT5A -0.006 0.067 -9999 0 -0.79 8 8
NCK1-2/p130 Cas -0.002 0.026 -9999 0 -0.41 4 4
SPHK1 0.004 0.054 -9999 0 -0.33 23 23
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.033 0.049 -9999 0 -0.7 4 4
PLCG1 0.033 0.05 -9999 0 -0.72 4 4
NHERF/PDGFRB -0.015 0.052 -9999 0 -0.51 4 4
YES1 -0.003 0.038 -9999 0 -0.52 5 5
cell migration -0.015 0.052 -9999 0 -0.51 4 4
SHC/Grb2/SOS1 -0.002 0.026 -9999 0 -0.41 4 4
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
SLC9A3R1 -0.026 0.083 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.014 0.049 -9999 0 -0.47 6 6
FYN -0.003 0.06 -9999 0 -0.89 4 4
DOK1 0.029 0.035 -9999 0 -0.47 4 4
HRAS/GTP -0.002 0.019 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.046 0.082 -9999 0 -0.44 28 28
PRKCD 0.03 0.035 -9999 0 -0.47 4 4
FER 0.025 0.061 -9999 0 -0.48 15 15
MAPKKK cascade -0.002 0.027 -9999 0 -0.4 4 4
RASA1 0.03 0.035 -9999 0 -0.47 4 4
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.029 -9999 0 -0.43 4 4
PDGFB-D/PDGFRB/SHB -0.003 0.041 -9999 0 -0.6 5 5
chemotaxis 0.034 0.048 -9999 0 -0.6 4 4
STAT1-3-5/STAT1-3-5 -0.008 0.054 -9999 0 -0.46 13 13
Bovine Papilomavirus E5/PDGFRB -0.002 0.037 -9999 0 -0.61 4 4
PTPRJ 0 0 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.046 0.045 -10000 0 -0.55 1 1
BAG4 -0.006 0.055 -10000 0 -0.43 14 14
BAD 0.032 0.017 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.077 -10000 0 -0.5 21 21
BAX 0.032 0.018 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.012 -10000 0 -0.1 2 2
IKBKB 0.052 0.043 -10000 0 -0.51 1 1
MAP2K2 0.044 0.024 -10000 0 -0.46 1 1
MAP2K1 0.044 0.024 -10000 0 -0.46 1 1
SMPD1 0.021 0.012 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.051 0.048 -10000 0 -0.45 3 3
MAP2K4 0.038 0.025 -10000 0 -0.38 2 2
protein ubiquitination 0.054 0.044 -10000 0 -0.52 1 1
EnzymeConsortium:2.7.1.37 0.049 0.026 -10000 0 -0.48 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.039 0.024 -10000 0 -0.49 1 1
CRADD 0.011 0.002 -10000 0 -10000 0 0
mol:ceramide 0.025 0.017 -10000 0 -0.14 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.011 0.002 -10000 0 -10000 0 0
MAP3K1 0.032 0.021 -10000 0 -0.4 1 1
TRADD 0.011 0.002 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.047 0.023 -10000 0 -0.45 1 1
MAPK1 0.047 0.023 -10000 0 -0.45 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.044 0.049 -10000 0 -0.47 3 3
KSR1 0.032 0.024 -10000 0 -0.52 1 1
MAPK8 0.041 0.047 -10000 0 -0.41 10 10
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.052 0.043 -10000 0 -0.51 1 1
TNF R/SODD -0.004 0.04 -10000 0 -0.6 4 4
TNF -0.005 0.097 -10000 0 -0.46 38 38
CYCS 0.037 0.025 0.15 32 -10000 0 32
IKBKG 0.052 0.043 -10000 0 -0.51 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.039 0.047 -10000 0 -0.35 9 9
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.025 0.15 32 -10000 0 32
TNF/TNF R/SODD -0.013 0.069 -10000 0 -0.52 17 17
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.028 0.012 -10000 0 -10000 0 0
NSMAF 0.046 0.045 -10000 0 -0.54 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.01 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.007 0.058 -9999 0 -0.52 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.024 -9999 0 -10000 0 0
NFKBIA 0.024 0.034 -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 -0.79 14 14
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.01 -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 -0.01 0.089 -9999 0 -0.79 14 14
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 0.033 -9999 0 -0.26 13 13
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.023 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.068 -9999 0 -0.6 14 14
NF kappa B1 p50/RelA -0.004 0.029 -9999 0 -0.26 13 13
IKBKB -0.001 0.013 -9999 0 -10000 0 0
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 -0.009 0.056 -9999 0 -0.44 14 14
cell death -0.003 0.022 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.007 0.058 -9999 0 -0.52 14 14
LCK -0.02 0.1 -9999 0 -0.41 53 53
BCL3 -0.001 0.015 -9999 0 -0.29 3 3
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.035 -9999 0 -0.41 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 0.022 -9999 0 -0.52 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.039 -9999 0 -0.33 2 2
CaM/Ca2+ 0.009 0.031 -9999 0 -0.38 2 2
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.036 -9999 0 -0.38 2 2
AKT1 -0.011 0.047 -9999 0 -0.38 14 14
MAP2K1 0.04 0.044 -9999 0 -0.38 2 2
MAP3K11 0.03 0.043 -9999 0 -0.38 2 2
IFNGR1 0.012 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.023 0.093 -9999 0 -0.41 24 24
Rap1/GTP -0.004 0.015 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.013 0.036 -9999 0 -0.43 2 2
CEBPB 0.075 0.039 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.007 0.055 -9999 0 -1.2 1 1
STAT1 -0.011 0.036 -9999 0 -0.38 2 2
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.03 0.1 -9999 0 -0.29 4 4
PIK3CA 0 0.009 -9999 0 -0.29 1 1
STAT1 (dimer)/PIAS1 -0.01 0.032 -9999 0 -0.36 2 2
CEBPB/PTGES2/Cbp/p300 -0.001 0.012 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.034 -9999 0 -0.41 2 2
MAPK3 0.054 0.04 -9999 0 -10000 0 0
STAT1 (dimer) -0.006 0.054 -9999 0 -0.48 2 2
MAPK1 0.054 0.04 -9999 0 -10000 0 0
JAK2 0.011 0.024 -9999 0 -0.79 1 1
PIK3R1 -0.01 0.089 -9999 0 -0.79 14 14
JAK1 0.011 0.024 -9999 0 -0.78 1 1
CAMK2D -0.002 0.041 -9999 0 -0.79 3 3
DAPK1 0.07 0.033 -9999 0 -10000 0 0
SMAD7 0.05 0.038 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.007 0.022 -9999 0 -0.35 1 1
PI3K 0.002 0.055 -9999 0 -0.4 16 16
IFNG -0.03 0.1 -9999 0 -0.29 4 4
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 -0.01 0.053 -9999 0 -0.29 37 37
CAMK2B -0.066 0.2 -9999 0 -0.59 123 123
FRAP1 0.037 0.058 -9999 0 -0.35 14 14
PRKCD -0.011 0.047 -9999 0 -0.39 8 8
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.006 0.039 -9999 0 -0.33 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 -0.36 2 2
SOCS1 0 0.049 -9999 0 -1.5 1 1
mol:GDP -0.007 0.021 -9999 0 -0.34 1 1
CASP1 0.049 0.045 -9999 0 -0.35 5 5
PTGES2 0 0.009 -9999 0 -0.29 1 1
IRF9 0.058 0.019 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.012 0.05 -9999 0 -0.39 16 16
RAP1/GDP -0.004 0.015 -9999 0 -10000 0 0
CBL 0.029 0.043 -9999 0 -0.38 2 2
MAP3K1 0.031 0.045 -9999 0 -0.39 3 3
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.039 -9999 0 -0.33 2 2
PTPN11 0.021 0.044 -9999 0 -0.41 2 2
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.004 0.053 -9999 0 -0.48 13 13
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.044 -9999 0 -0.4 13 13
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.026 -9999 0 -0.29 9 9
NPC/RanGAP1/SUMO1/Ubc9 0 0.001 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.022 -9999 0 -10000 0 0
YY1/LSF -0.001 0.017 -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 -0.005 0.039 -9999 0 -0.35 13 13
I kappa B alpha/HDAC1 -0.004 0.026 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.004 0.034 -9999 0 -0.31 13 13
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0.009 -9999 0 -0.29 1 1
HDAC3/TR2 -0.004 0.026 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.03 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.79 28 28
GATA1 -0.005 0.037 -9999 0 -0.29 18 18
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.007 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -0.29 8 8
NPC 0 0 -9999 0 -10000 0 0
RBBP4 -0.001 0.024 -9999 0 -0.79 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 -0.004 0.03 -9999 0 -10000 0 0
KAT2B -0.001 0.024 -9999 0 -0.79 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 0.024 -9999 0 -0.79 1 1
YY1/HDAC3 -0.003 0.024 -9999 0 -10000 0 0
YY1/HDAC2 0 0.009 -9999 0 -10000 0 0
YY1/HDAC1 0 0.009 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0.006 -9999 0 -10000 0 0
PPARG -0.095 0.17 -9999 0 -0.37 277 277
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 0.026 -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 -0.004 0.03 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0.029 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 -10000 0 0
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 0.016 -9999 0 -0.46 1 1
YY1/SAP30/HDAC1 -0.001 0.01 -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 -0.004 0.03 -9999 0 -10000 0 0
histone deacetylation 0.046 0.008 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.023 -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 -0.017 0.079 -9999 0 -0.47 28 28
GATA1/HDAC1 -0.003 0.024 -9999 0 -10000 0 0
GATA1/HDAC3 -0.006 0.031 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.011 0.07 -9999 0 -0.6 13 13
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 0.021 -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 0.001 -9999 0 -10000 0 0
HDAC complex -0.001 0.017 -9999 0 -0.47 1 1
GATA1/Fog1 -0.005 0.029 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.016 0.095 -9999 0 -0.46 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 0.046 -9999 0 -0.42 13 13
SIN3/HDAC complex/NCoR1 0 0.01 -9999 0 -10000 0 0
TFCP2 -0.001 0.024 -9999 0 -0.79 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 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
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 0.04 -9999 0 -0.48 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 -10000 0 0
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 0.043 -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 0.007 -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 -0.01 0.056 -9999 0 -0.31 35 35
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 -0.011 0.07 -9999 0 -0.6 13 13
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.021 0.13 -9999 0 -0.79 29 29
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.016 0.095 -9999 0 -0.46 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 0.06 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.003 0.019 -9999 0 -10000 0 0
CLOCK 0.006 0.083 -9999 0 -0.78 12 12
TIMELESS/CRY2 -0.001 0.01 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.014 -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 0.019 -9999 0 -10000 0 0
NPAS2 0.009 0.061 -9999 0 -0.62 9 9
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.014 0.003 -9999 0 -10000 0 0
CHEK1 -0.006 0.043 -9999 0 -10000 0 0
mol:HEME 0.014 0.003 -9999 0 -10000 0 0
PER1 -0.015 0.11 -9999 0 -0.79 21 21
BMAL/CLOCK/NPAS2 0.03 0.07 -9999 0 -0.51 18 18
BMAL1/CLOCK 0.042 0.053 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.003 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.003 0.019 -9999 0 -10000 0 0
mol:NADPH 0.014 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.01 0.062 -9999 0 -0.45 21 21
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.002 0.022 -9999 0 -0.29 6 6
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.027 0.047 -10000 0 -10000 0 0
regulation of axonogenesis -0.023 0.034 0.31 10 -10000 0 10
myoblast fusion 0.008 0.026 -10000 0 -10000 0 0
mol:GTP -0.005 0.016 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.031 -10000 0 -10000 0 0
ARF1/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GM1 0.006 0.015 -10000 0 -10000 0 0
mol:Choline 0.02 0.052 -10000 0 -0.51 10 10
lamellipodium assembly -0.004 0.031 -10000 0 -10000 0 0
MAPK3 0.02 0.026 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.031 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.026 -10000 0 -10000 0 0
ARF1/GDP -0.004 0.024 -10000 0 -10000 0 0
ARF6 0.007 0.008 -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 0.02 0.026 -10000 0 -10000 0 0
actin filament bundle formation 0.006 0.021 -10000 0 -10000 0 0
KALRN -0.011 0.065 -10000 0 -0.47 20 20
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.021 -10000 0 -10000 0 0
NME1 -0.004 0.067 -10000 0 -0.29 56 56
Rac1/GDP -0.006 0.021 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.016 -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 0.016 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.016 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GDP -0.006 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 -0.57 10 10
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.031 -10000 0 -10000 0 0
ruffle organization 0.023 0.034 -10000 0 -0.31 10 10
regulation of epithelial cell migration -0.005 0.016 -10000 0 -10000 0 0
PLD2 0.016 0.014 -10000 0 -10000 0 0
PIP5K1A -0.004 0.03 -10000 0 -0.31 10 10
mol:Phosphatidic acid 0.02 0.052 -10000 0 -0.51 10 10
Rac1/GTP -0.004 0.031 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
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 -0.44 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 0.032 -9999 0 -0.47 2 2
lamellipodium assembly -0.005 0.052 -9999 0 -0.46 14 14
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.008 0.068 -9999 0 -0.6 14 14
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 -0.01 0.089 -9999 0 -0.79 14 14
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 -0.32 32 32
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.007 0.049 -9999 0 -0.44 13 13
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.011 0.088 -9999 0 -0.63 19 19
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 -0.006 0.058 -9999 0 -0.51 14 14
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 0.011 -9999 0 -0.36 1 1
MDM2/SUMO1 -0.001 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.024 -9999 0 -0.79 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 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.029 0.001 -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 0.013 -9999 0 -0.43 1 1
SUMO1/HDAC1 0 0.001 -9999 0 -10000 0 0
RANGAP1 0 0.009 -9999 0 -0.29 1 1
MDM2/SUMO1/SUMO1 -0.001 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0.001 -9999 0 -10000 0 0
Ran/GTP 0 0.001 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
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 0.008 -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 0.018 -9999 0 -0.29 4 4
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 0.017 -9999 0 -0.2 7 7
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 0.008 -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 0.01 -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 0.017 -9999 0 -0.2 7 7
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 0.017 -9999 0 -0.2 7 7
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 -0.29 10 10
NFKB2 0 0.009 -9999 0 -10000 0 0
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 1093 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z7.A8R6 TCGA.Z7.A8R5 TCGA.XX.A89A TCGA.XX.A899
109_MAP3K5 -0.27 0.054 0.054 0.054
47_PPARGC1A -0.79 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 -0.79 0 0 0
131_RELN/VLDLR -0.47 -0.47 0 0
30_TGFB1/TGF beta receptor Type II 0.013 0 0.013 0.012
84_STAT5B -0.1 -0.073 0.032 0.046
84_STAT5A -0.1 -0.073 0.032 0.046
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/22315252/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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