PARADIGM pathway analysis of mRNASeq expression data
Lung Squamous Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1RB73VF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1RB73VF
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 37 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling events mediated by the Hedgehog family 157
Angiopoietin receptor Tie2-mediated signaling 157
Aurora B signaling 127
FOXM1 transcription factor network 114
Aurora C signaling 102
Endothelins 83
TCGA08_retinoblastoma 64
Glypican 2 network 61
amb2 Integrin signaling 59
Thromboxane A2 receptor signaling 57
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 501 . 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 ( 501 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by the Hedgehog family 0.3134 157 8188 52 -0.64 0.34 1000 -1000 -0.1 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3134 157 13835 88 -0.75 0.06 1000 -1000 -0.11 -1000
Aurora B signaling 0.2535 127 8553 67 -0.62 0.005 1000 -1000 -0.09 -1000
FOXM1 transcription factor network 0.2275 114 5846 51 -0.71 0.002 1000 -1000 -0.21 -1000
Aurora C signaling 0.2036 102 720 7 -0.41 0 1000 -1000 -0.044 -1000
Endothelins 0.1657 83 8008 96 -0.44 0.036 1000 -1000 -0.095 -1000
TCGA08_retinoblastoma 0.1277 64 516 8 -0.28 0.087 1000 -1000 -0.044 -1000
Glypican 2 network 0.1218 61 247 4 -0.085 -0.068 1000 -1000 -0.048 -1000
amb2 Integrin signaling 0.1178 59 4898 82 -0.68 0 1000 -1000 -0.1 -1000
Thromboxane A2 receptor signaling 0.1138 57 6012 105 -0.18 0.041 1000 -1000 -0.087 -1000
Fc-epsilon receptor I signaling in mast cells 0.1078 54 5324 97 -0.26 0.033 1000 -1000 -0.11 -1000
Visual signal transduction: Cones 0.1058 53 2030 38 -0.29 0.009 1000 -1000 -0.074 -1000
IL4-mediated signaling events 0.1038 52 4772 91 -0.81 0.45 1000 -1000 -0.18 -1000
Glucocorticoid receptor regulatory network 0.0958 48 5490 114 -0.56 0.36 1000 -1000 -0.081 -1000
Signaling events regulated by Ret tyrosine kinase 0.0898 45 3742 82 -0.2 0 1000 -1000 -0.1 -1000
PLK1 signaling events 0.0858 43 3702 85 -0.38 0.072 1000 -1000 -0.062 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0858 43 2237 52 -0.38 0.057 1000 -1000 -0.071 -1000
BMP receptor signaling 0.0778 39 3236 81 -0.39 0.037 1000 -1000 -0.11 -1000
Nectin adhesion pathway 0.0778 39 2465 63 -0.27 0 1000 -1000 -0.083 -1000
Arf6 signaling events 0.0739 37 2333 62 -0.3 0.015 1000 -1000 -0.075 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0739 37 2899 78 -0.13 0.036 1000 -1000 -0.11 -1000
HIF-1-alpha transcription factor network 0.0699 35 2668 76 -0.44 0.017 1000 -1000 -0.19 -1000
TCGA08_p53 0.0679 34 242 7 -0.19 0.097 1000 -1000 -0.026 -1000
Integrins in angiogenesis 0.0679 34 2900 84 -0.46 0.031 1000 -1000 -0.11 -1000
Signaling mediated by p38-alpha and p38-beta 0.0659 33 1494 44 -0.13 0 1000 -1000 -0.065 -1000
Calcium signaling in the CD4+ TCR pathway 0.0639 32 999 31 -0.21 0.012 1000 -1000 -0.13 -1000
Glypican 1 network 0.0619 31 1529 48 -0.22 0.032 1000 -1000 -0.059 -1000
Nongenotropic Androgen signaling 0.0619 31 1620 52 -0.15 0.048 1000 -1000 -0.074 -1000
FOXA2 and FOXA3 transcription factor networks 0.0599 30 1423 46 -0.77 0.072 1000 -1000 -0.12 -1000
IL23-mediated signaling events 0.0599 30 1837 60 -0.24 0.018 1000 -1000 -0.18 -1000
Canonical Wnt signaling pathway 0.0559 28 1428 51 -0.47 0.16 1000 -1000 -0.067 -1000
Coregulation of Androgen receptor activity 0.0539 27 2092 76 -0.4 0.031 1000 -1000 -0.066 -1000
IL6-mediated signaling events 0.0539 27 2056 75 -0.48 0.05 1000 -1000 -0.12 -1000
LPA4-mediated signaling events 0.0519 26 323 12 -0.14 0.017 1000 -1000 -0.044 -1000
Presenilin action in Notch and Wnt signaling 0.0519 26 1591 61 -0.47 0.016 1000 -1000 -0.076 -1000
Syndecan-3-mediated signaling events 0.0519 26 938 35 -0.34 0 1000 -1000 -0.086 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0519 26 1773 68 -0.23 0.015 1000 -1000 -0.15 -1000
ErbB4 signaling events 0.0459 23 1603 69 -0.38 0.2 1000 -1000 -0.11 -1000
Reelin signaling pathway 0.0459 23 1328 56 -0.13 0.003 1000 -1000 -0.11 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0459 23 2907 125 -0.2 0 1000 -1000 -0.13 -1000
Aurora A signaling 0.0439 22 1334 60 -0.49 0.028 1000 -1000 -0.078 -1000
Regulation of Androgen receptor activity 0.0439 22 1591 70 -0.42 0.018 1000 -1000 -0.087 -1000
Syndecan-1-mediated signaling events 0.0419 21 716 34 -0.36 0 1000 -1000 -0.088 -1000
HIF-2-alpha transcription factor network 0.0419 21 926 43 -0.38 0.21 1000 -1000 -0.11 -1000
Visual signal transduction: Rods 0.0419 21 1135 52 -0.18 0 1000 -1000 -0.1 -1000
IL12-mediated signaling events 0.0399 20 1786 87 -0.16 0.019 1000 -1000 -0.14 -1000
Osteopontin-mediated events 0.0399 20 762 38 -0.29 0 1000 -1000 -0.12 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0399 20 686 33 -0.27 0 1000 -1000 -0.073 -1000
Plasma membrane estrogen receptor signaling 0.0379 19 1644 86 -0.18 0.031 1000 -1000 -0.099 -1000
p75(NTR)-mediated signaling 0.0359 18 2337 125 -0.34 0 1000 -1000 -0.12 -1000
Wnt signaling 0.0359 18 132 7 -0.094 0 1000 -1000 -0.069 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0359 18 2274 120 -0.27 0.13 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 0.0339 17 121 7 -0.024 0.002 1000 -1000 -0.035 -1000
TCR signaling in naïve CD8+ T cells 0.0339 17 1652 93 -0.066 0.035 1000 -1000 -0.1 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0319 16 865 54 -0.15 0.02 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 0.0319 16 708 44 -0.2 0.021 1000 -1000 -0.076 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0279 14 1271 85 -0.16 0.011 1000 -1000 -0.092 -1000
Effects of Botulinum toxin 0.0279 14 377 26 -0.071 0.005 1000 -1000 -0.07 -1000
Regulation of nuclear SMAD2/3 signaling 0.0259 13 1853 136 -0.34 0.094 1000 -1000 -0.094 -1000
Caspase cascade in apoptosis 0.0220 11 844 74 -0.071 0.035 1000 -1000 -0.062 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0220 11 314 28 -0.18 0.02 1000 -1000 -0.069 -1000
Noncanonical Wnt signaling pathway 0.0220 11 290 26 -0.1 0 1000 -1000 -0.11 -1000
Syndecan-2-mediated signaling events 0.0220 11 770 69 -0.17 0.031 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class III 0.0220 11 447 40 -0.15 0.05 1000 -1000 -0.049 -1000
FAS signaling pathway (CD95) 0.0220 11 547 47 -0.19 0.009 1000 -1000 -0.055 -1000
BCR signaling pathway 0.0220 11 1131 99 -0.11 0.04 1000 -1000 -0.11 -1000
Ras signaling in the CD4+ TCR pathway 0.0220 11 194 17 -0.057 0.008 1000 -1000 -0.073 -1000
JNK signaling in the CD4+ TCR pathway 0.0200 10 175 17 -0.044 0.022 1000 -1000 -0.077 -1000
S1P1 pathway 0.0200 10 378 36 -0.061 0.01 1000 -1000 -0.079 -1000
EGFR-dependent Endothelin signaling events 0.0200 10 228 21 -0.065 0 1000 -1000 -0.093 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0180 9 313 34 -0.029 0 1000 -1000 -0.08 -1000
Syndecan-4-mediated signaling events 0.0180 9 623 67 -0.17 0.01 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 0.0160 8 571 65 -0.6 0.044 1000 -1000 -0.094 -1000
IL2 signaling events mediated by STAT5 0.0160 8 183 22 -0.15 0.06 1000 -1000 -0.06 -1000
S1P4 pathway 0.0160 8 220 25 -0.065 0.003 1000 -1000 -0.059 -1000
Signaling events mediated by PTP1B 0.0140 7 547 76 -0.1 0.033 1000 -1000 -0.096 -1000
TRAIL signaling pathway 0.0140 7 368 48 -0.096 0.046 1000 -1000 -0.075 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0140 7 590 74 -0.17 0.068 1000 -1000 -0.11 -1000
Cellular roles of Anthrax toxin 0.0120 6 265 39 -0.092 0.017 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0120 6 383 58 -0.22 0.034 1000 -1000 -0.086 -1000
Regulation of p38-alpha and p38-beta 0.0120 6 344 54 -0.087 0.036 1000 -1000 -0.09 -1000
IL27-mediated signaling events 0.0120 6 348 51 -0.12 0.011 1000 -1000 -0.096 -1000
S1P3 pathway 0.0120 6 275 42 -0.18 0.041 1000 -1000 -0.064 -1000
BARD1 signaling events 0.0100 5 304 57 -0.13 0.022 1000 -1000 -0.079 -1000
IL1-mediated signaling events 0.0100 5 367 62 -0.061 0.042 1000 -1000 -0.12 -1000
IL2 signaling events mediated by PI3K 0.0100 5 306 58 -0.23 0.074 1000 -1000 -0.092 -1000
LPA receptor mediated events 0.0100 5 573 102 -0.1 0.035 1000 -1000 -0.11 -1000
IGF1 pathway 0.0100 5 308 57 -0.021 0.04 1000 -1000 -0.12 -1000
Insulin Pathway 0.0100 5 440 74 -0.1 0.032 1000 -1000 -0.12 -1000
Signaling events mediated by PRL 0.0100 5 198 34 -0.13 0.028 1000 -1000 -0.08 -1000
ErbB2/ErbB3 signaling events 0.0080 4 265 65 -0.078 0.054 1000 -1000 -0.09 -1000
Signaling events mediated by HDAC Class II 0.0080 4 350 75 -0.081 0 1000 -1000 -0.072 -1000
a4b1 and a4b7 Integrin signaling 0.0080 4 20 5 -0.009 -0.001 1000 -1000 -0.042 -1000
Ephrin B reverse signaling 0.0080 4 207 48 -0.071 0.04 1000 -1000 -0.083 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0080 4 391 83 -0.069 0.05 1000 -1000 -0.086 -1000
Signaling events mediated by HDAC Class I 0.0080 4 452 104 -0.081 0.041 1000 -1000 -0.085 -1000
Class I PI3K signaling events 0.0080 4 352 73 -0.054 0.026 1000 -1000 -0.087 -1000
Arf6 trafficking events 0.0080 4 298 71 -0.085 0.032 1000 -1000 -0.093 -1000
Regulation of Telomerase 0.0080 4 415 102 -0.12 0.025 1000 -1000 -0.12 -1000
p38 MAPK signaling pathway 0.0080 4 219 44 -0.069 0.034 1000 -1000 -0.082 -1000
IFN-gamma pathway 0.0060 3 256 68 -0.069 0.065 1000 -1000 -0.12 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0060 3 145 45 -0.027 0.061 1000 -1000 -0.1 -1000
EPHB forward signaling 0.0060 3 330 85 -0.072 0.033 1000 -1000 -0.11 -1000
TCGA08_rtk_signaling 0.0060 3 91 26 -0.065 0.038 1000 -1000 -0.033 -1000
VEGFR1 specific signals 0.0060 3 212 56 -0.2 0.043 1000 -1000 -0.1 -1000
Circadian rhythm pathway 0.0040 2 59 22 -0.032 0.038 1000 -1000 -0.074 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0040 2 107 37 -0.012 0.025 1000 -1000 -0.09 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 79 36 -0.01 0.02 1000 -1000 -0.084 -1000
PDGFR-beta signaling pathway 0.0040 2 232 97 -0.044 0.054 1000 -1000 -0.1 -1000
Class IB PI3K non-lipid kinase events 0.0040 2 6 3 -0.003 -1000 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 0.0020 1 52 32 -0.057 0.034 1000 -1000 -0.072 -1000
Ceramide signaling pathway 0.0020 1 139 76 -0.028 0.041 1000 -1000 -0.077 -1000
S1P5 pathway 0.0020 1 30 17 -0.01 0.006 1000 -1000 -0.063 -1000
FoxO family signaling 0.0020 1 97 64 -0.089 0.081 1000 -1000 -0.096 -1000
Signaling mediated by p38-gamma and p38-delta 0.0020 1 15 15 -0.001 0.027 1000 -1000 -0.06 -1000
Rapid glucocorticoid signaling 0.0020 1 31 20 -0.007 0.007 1000 -1000 -0.046 -1000
E-cadherin signaling in keratinocytes 0.0020 1 56 43 -0.023 0.043 1000 -1000 -0.095 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 2 23 -0.001 0.036 1000 -1000 -0.078 -1000
Canonical NF-kappaB pathway 0.0000 0 33 39 -0.019 0.072 1000 -1000 -0.09 -1000
PLK2 and PLK4 events 0.0000 0 2 3 -0.001 0.019 1000 -1000 -0.026 -1000
Arf6 downstream pathway 0.0000 0 13 43 -0.024 0.025 1000 -1000 -0.052 -1000
EPO signaling pathway 0.0000 0 52 55 -0.007 0.066 1000 -1000 -0.12 -1000
mTOR signaling pathway 0.0000 0 14 53 -0.004 0.03 1000 -1000 -0.074 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 60 68 -0.057 0.043 1000 -1000 -0.085 -1000
ceramide signaling pathway 0.0000 0 47 49 -0.013 0.044 1000 -1000 -0.058 -1000
Atypical NF-kappaB pathway 0.0000 0 6 31 -0.001 0.03 1000 -1000 -0.082 -1000
E-cadherin signaling in the nascent adherens junction 0.0000 0 52 76 -0.026 0.053 1000 -1000 -0.11 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 -0.001 0.025 1000 -1000 -0.07 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0 1000 -1000 -0.059 -1000
Arf1 pathway 0.0000 0 32 54 -0.022 0.022 1000 -1000 -0.06 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 -0.001 0 1000 -1000 -0.068 -1000
Total NA 2681 166042 7203 -25 -990 131000 -131000 -12 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.43 0.29 -10000 0 -0.69 233 233
IHH -0.47 0.38 -10000 0 -0.81 278 278
SHH Np/Cholesterol/GAS1 -0.069 0.16 -10000 0 -0.44 78 78
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.068 0.16 0.44 78 -10000 0 78
SMO/beta Arrestin2 -0.36 0.25 -10000 0 -0.59 239 239
SMO -0.38 0.27 -10000 0 -0.63 240 240
AKT1 -0.15 0.11 -10000 0 -0.34 1 1
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.004 0.049 -10000 0 -0.63 3 3
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.37 0.26 -10000 0 -0.62 240 240
STIL -0.32 0.24 -10000 0 -0.7 84 84
DHH N/PTCH2 -0.046 0.16 -10000 0 -0.56 41 41
DHH N/PTCH1 -0.36 0.24 -10000 0 -0.57 246 246
PIK3CA 0 0 -10000 0 -10000 0 0
DHH -0.053 0.19 -10000 0 -0.74 36 36
PTHLH -0.58 0.36 -10000 0 -0.92 233 233
determination of left/right symmetry -0.37 0.26 -10000 0 -0.62 240 240
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.58 0.35 -10000 0 -0.91 233 233
IHH N/Hhip -0.64 0.38 -10000 0 -0.81 396 396
DHH N/Hhip -0.4 0.3 -10000 0 -0.59 339 339
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.37 0.26 -10000 0 -0.62 240 240
pancreas development -0.48 0.35 -10000 0 -0.74 330 330
HHAT 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.013 0.098 -10000 0 -0.74 9 9
somite specification -0.37 0.26 -10000 0 -0.62 240 240
SHH Np/Cholesterol/PTCH1 -0.35 0.25 -10000 0 -0.55 255 255
SHH Np/Cholesterol/PTCH2 -0.066 0.16 -10000 0 -0.43 77 77
SHH Np/Cholesterol/Megalin -0.28 0.26 -10000 0 -0.49 284 284
SHH -0.062 0.2 -10000 0 -0.54 72 72
catabolic process -0.37 0.25 -10000 0 -0.61 227 227
SMO/Vitamin D3 -0.37 0.26 -10000 0 -0.59 255 255
SHH Np/Cholesterol/Hhip -0.35 0.26 -10000 0 -0.5 351 351
LRP2 -0.37 0.37 -10000 0 -0.74 250 250
receptor-mediated endocytosis -0.49 0.31 -10000 0 -0.78 223 223
SHH Np/Cholesterol/BOC -0.063 0.15 -10000 0 -0.44 66 66
SHH Np/Cholesterol/CDO -0.066 0.16 -10000 0 -0.44 70 70
mesenchymal cell differentiation 0.34 0.26 0.49 351 -10000 0 351
mol:Vitamin D3 -0.35 0.26 -10000 0 -0.56 255 255
IHH N/PTCH2 -0.3 0.27 -10000 0 -0.54 278 278
CDON -0.007 0.073 -10000 0 -0.74 5 5
IHH N/PTCH1 -0.38 0.26 -10000 0 -0.62 227 227
Megalin/LRPAP1 -0.28 0.28 -10000 0 -0.56 250 250
PTCH2 -0.008 0.075 -10000 0 -0.68 6 6
SHH Np/Cholesterol -0.062 0.15 -10000 0 -0.43 72 72
PTCH1 -0.37 0.25 -10000 0 -0.61 227 227
HHIP -0.49 0.35 -10000 0 -0.74 330 330
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.51 0.54 -10000 0 -1 263 263
NCK1/PAK1/Dok-R -0.24 0.23 -10000 0 -0.46 263 263
NCK1/Dok-R -0.67 0.67 -10000 0 -1.3 263 263
PIK3CA 0.007 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.06 0.1 0.25 108 -10000 0 108
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.003 0.005 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.05 0.14 0.26 29 -0.57 10 39
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.59 0.58 -10000 0 -1.1 263 263
FN1 -0.019 0.12 -10000 0 -0.74 13 13
PLD2 -0.66 0.72 -10000 0 -1.3 263 263
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.044 0.17 -10000 0 -0.73 30 30
ELK1 -0.56 0.61 -10000 0 -1.1 263 263
GRB7 -0.005 0.051 -10000 0 -0.57 4 4
PAK1 -0.001 0.026 -10000 0 -0.57 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.64 0.63 -10000 0 -1.2 263 263
CDKN1A -0.34 0.36 -10000 0 -0.68 252 252
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.67 0.67 -10000 0 -1.3 263 263
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.35 0.38 -10000 0 -0.71 263 263
PLG -0.66 0.72 -10000 0 -1.3 263 263
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.49 0.49 -10000 0 -0.95 263 263
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 0.003 0.005 -10000 0 -10000 0 0
ANGPT2 -0.33 0.34 -10000 0 -0.74 176 176
BMX -0.73 0.76 -10000 0 -1.4 263 263
ANGPT1 -0.37 0.62 -10000 0 -1.5 118 118
tube development -0.4 0.41 -10000 0 -0.78 262 262
ANGPT4 -0.33 0.37 -10000 0 -0.74 222 222
response to hypoxia -0.034 0.037 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.73 0.72 -10000 0 -1.4 263 263
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.015 0.12 -10000 0 -0.74 14 14
STAT5A (dimer) -0.47 0.48 -10000 0 -0.91 262 262
mol:L-citrulline -0.35 0.38 -10000 0 -0.71 263 263
AGTR1 -0.3 0.37 -10000 0 -0.74 205 205
MAPK14 -0.68 0.71 -10000 0 -1.3 263 263
Tie2/SHP2 -0.59 0.62 -10000 0 -1.2 229 229
TEK -0.66 0.69 -10000 0 -1.4 229 229
RPS6KB1 -0.48 0.51 -10000 0 -0.96 263 263
Angiotensin II/AT1 -0.23 0.28 -10000 0 -0.56 205 205
Tie2/Ang1/GRB2 -0.71 0.72 -10000 0 -1.4 263 263
MAPK3 -0.58 0.63 -10000 0 -1.2 263 263
MAPK1 -0.58 0.63 -10000 0 -1.2 263 263
Tie2/Ang1/GRB7 -0.71 0.72 -10000 0 -1.4 263 263
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.66 0.72 -10000 0 -1.3 263 263
PI3K -0.61 0.64 -10000 0 -1.2 263 263
FES -0.67 0.71 -10000 0 -1.3 263 263
Crk/Dok-R -0.67 0.67 -10000 0 -1.3 263 263
Tie2/Ang1/ABIN2 -0.71 0.72 -10000 0 -1.4 263 263
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.44 0.47 -10000 0 -0.88 263 263
STAT5A 0.004 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.48 0.51 -10000 0 -0.96 263 263
Tie2/Ang2 -0.6 0.6 -10000 0 -1.2 262 262
Tie2/Ang1 -0.75 0.83 -10000 0 -1.5 263 263
FOXO1 -0.44 0.47 -10000 0 -0.89 263 263
ELF1 -0.032 0.052 -10000 0 -10000 0 0
ELF2 -0.67 0.73 -10000 0 -1.3 263 263
mol:Choline -0.61 0.66 -10000 0 -1.2 263 263
cell migration -0.13 0.12 -10000 0 -0.26 95 95
FYN -0.47 0.48 -10000 0 -0.92 262 262
DOK2 -0.068 0.21 -10000 0 -0.74 46 46
negative regulation of cell cycle -0.31 0.32 -10000 0 -0.61 256 256
ETS1 -0.061 0.15 -10000 0 -0.82 12 12
PXN -0.38 0.41 -10000 0 -0.77 263 263
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.41 0.44 -10000 0 -0.83 263 263
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.062 0.16 -10000 0 -0.81 13 13
MAPKKK cascade -0.61 0.66 -10000 0 -1.2 263 263
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.7 0.74 -10000 0 -1.4 263 263
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.31 0.34 -10000 0 -0.63 263 263
mol:Phosphatidic acid -0.61 0.66 -10000 0 -1.2 263 263
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.35 0.38 -10000 0 -0.71 263 263
Rac1/GTP -0.47 0.44 -10000 0 -0.88 263 263
MMP2 -0.66 0.72 -10000 0 -1.3 263 263
Aurora B signaling

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
Condensin I complex -0.18 0.15 -9999 0 -0.4 85 85
STMN1 -0.29 0.19 -9999 0 -0.41 359 359
Aurora B/RasGAP/Survivin -0.51 0.22 -9999 0 -0.64 338 338
Chromosomal passenger complex/Cul3 protein complex -0.2 0.1 -9999 0 -0.33 124 124
BIRC5 -0.49 0.21 -9999 0 -0.58 426 426
DES -0.56 0.38 -9999 0 -0.83 322 322
Aurora C/Aurora B/INCENP -0.22 0.15 -9999 0 -0.32 213 213
Aurora B/TACC1 -0.25 0.16 -9999 0 -0.35 359 359
Aurora B/PP2A -0.29 0.19 -9999 0 -0.41 359 359
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.059 0.044 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.003 -9999 0 -10000 0 0
NDC80 -0.41 0.29 -9999 0 -0.56 374 374
Cul3 protein complex -0.01 0.062 -9999 0 -0.37 14 14
KIF2C -0.17 0.087 -9999 0 -0.24 258 258
PEBP1 -0.002 0.048 -9999 0 -0.75 2 2
KIF20A -0.3 0.29 -9999 0 -0.58 259 259
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.29 0.19 -9999 0 -0.41 359 359
SEPT1 -0.001 0.026 -9999 0 -0.57 1 1
SMC2 0 0 -9999 0 -10000 0 0
SMC4 0 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.11 0.067 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B -0.15 0.1 -9999 0 -10000 0 0
AURKB -0.41 0.26 -9999 0 -0.58 359 359
AURKC -0.003 0.042 -9999 0 -0.66 2 2
CDCA8 -0.15 0.26 -9999 0 -0.59 130 130
cytokinesis -0.32 0.16 -9999 0 -0.5 158 158
Aurora B/Septin1 -0.3 0.16 -9999 0 -0.48 142 142
AURKA -0.018 0.13 -9999 0 -0.58 24 24
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.013 0.084 -9999 0 -0.57 11 11
BUB1 -0.05 0.17 -9999 0 -0.58 47 47
hSgo1/Aurora B/Survivin -0.62 0.31 -9999 0 -0.79 365 365
EVI5 0.005 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.27 0.18 -9999 0 -0.55 112 112
SGOL1 -0.3 0.29 -9999 0 -0.57 261 261
CENPA -0.24 0.12 -9999 0 -0.31 346 346
NCAPG -0.11 0.23 -9999 0 -0.57 98 98
Aurora B/HC8 Proteasome -0.29 0.19 -9999 0 -0.41 359 359
NCAPD2 -0.001 0.026 -9999 0 -0.57 1 1
Aurora B/PP1-gamma -0.29 0.19 -9999 0 -0.41 359 359
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.3 0.29 -9999 0 -0.57 257 257
NPM1 -0.14 0.084 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.004 0.057 -9999 0 -0.74 3 3
mitotic prometaphase -0.012 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.29 0.19 -9999 0 -0.4 359 359
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.3 0.2 -9999 0 -0.55 153 153
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.14 0.084 -9999 0 -10000 0 0
MYLK -0.15 0.11 -9999 0 -0.61 3 3
KIF23 -0.11 0.23 -9999 0 -0.58 99 99
VIM -0.3 0.21 -9999 0 -0.42 360 360
RACGAP1 0.001 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.14 0.084 -9999 0 -10000 0 0
Chromosomal passenger complex -0.27 0.15 -9999 0 -0.35 341 341
Chromosomal passenger complex/EVI5 -0.49 0.25 -9999 0 -0.63 350 350
TACC1 -0.003 0.046 -9999 0 -0.74 2 2
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
FOXM1 transcription factor network

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.58 0.44 -9999 0 -1 139 139
PLK1 -0.18 0.2 -9999 0 -10000 0 0
BIRC5 -0.33 0.16 -9999 0 -10000 0 0
HSPA1B -0.58 0.44 -9999 0 -1.1 128 128
MAP2K1 -0.012 0.024 -9999 0 -10000 0 0
BRCA2 -0.58 0.44 -9999 0 -1 139 139
FOXM1 -0.71 0.56 -9999 0 -1.3 185 185
XRCC1 -0.58 0.44 -9999 0 -1 141 141
FOXM1B/p19 -0.6 0.44 -9999 0 -1.1 172 172
Cyclin D1/CDK4 -0.54 0.41 -9999 0 -1 115 115
CDC2 -0.61 0.46 -9999 0 -1.1 185 185
TGFA -0.52 0.39 -9999 0 -0.95 117 117
SKP2 -0.58 0.44 -9999 0 -1 142 142
CCNE1 -0.13 0.24 -9999 0 -0.59 111 111
CKS1B -0.58 0.44 -9999 0 -1.1 139 139
RB1 -0.26 0.16 -9999 0 -0.66 5 5
FOXM1C/SP1 -0.64 0.49 -9999 0 -1.1 177 177
AURKB -0.28 0.19 -9999 0 -10000 0 0
CENPF -0.64 0.48 -9999 0 -1.1 210 210
CDK4 0.002 0.028 -9999 0 -0.6 1 1
MYC -0.51 0.39 -9999 0 -0.91 140 140
CHEK2 -0.012 0.024 -9999 0 -10000 0 0
ONECUT1 -0.57 0.44 -9999 0 -1 150 150
CDKN2A -0.26 0.29 -9999 0 -0.57 233 233
LAMA4 -0.58 0.44 -9999 0 -1.1 139 139
FOXM1B/HNF6 -0.66 0.51 -9999 0 -1.2 150 150
FOS -0.64 0.51 -9999 0 -1.2 163 163
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.58 0.44 -9999 0 -1.1 128 128
response to radiation -0.024 0.023 -9999 0 -10000 0 0
CENPB -0.58 0.44 -9999 0 -1.1 130 130
CENPA -0.7 0.47 -9999 0 -1.1 249 249
NEK2 -0.68 0.49 -9999 0 -1.1 233 233
HIST1H2BA -0.58 0.44 -9999 0 -1 146 146
CCNA2 -0.15 0.26 -9999 0 -0.59 129 129
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.66 0.51 -9999 0 -1.2 166 166
CCNB2 -0.66 0.49 -9999 0 -1.1 202 202
CCNB1 -0.62 0.47 -9999 0 -1.1 163 163
ETV5 -0.58 0.44 -9999 0 -1.1 140 140
ESR1 -0.6 0.46 -9999 0 -1.1 150 150
CCND1 -0.55 0.42 -9999 0 -1 120 120
GSK3A -0.004 0.019 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.17 0.24 -9999 0 -0.45 187 187
CDK2 0.002 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.03 0.028 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.64 0.42 -9999 0 -1.1 196 196
GAS1 -0.58 0.45 -9999 0 -1.1 144 144
MMP2 -0.58 0.44 -9999 0 -1.1 141 141
RB1/FOXM1C -0.58 0.45 -9999 0 -1.1 141 141
CREBBP 0 0 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.23 0.14 -9999 0 -0.32 359 359
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.064 0.041 -9999 0 -10000 0 0
AURKB -0.41 0.26 -9999 0 -0.57 359 359
AURKC -0.003 0.042 -9999 0 -0.66 2 2
Endothelins

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
AKT1 -0.032 0.24 -9999 0 -0.65 44 44
PTK2B 0.003 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.086 0.3 -9999 0 -0.98 35 35
EDN1 -0.043 0.26 -9999 0 -0.79 44 44
EDN3 -0.086 0.23 -9999 0 -0.7 62 62
EDN2 -0.088 0.21 -9999 0 -0.59 74 74
HRAS/GDP -0.19 0.31 -9999 0 -0.63 133 133
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.057 0.21 -9999 0 -0.49 65 65
ADCY4 -0.08 0.23 -9999 0 -0.67 45 45
ADCY5 -0.091 0.24 -9999 0 -0.67 50 50
ADCY6 -0.056 0.2 -9999 0 -0.62 35 35
ADCY7 -0.054 0.19 -9999 0 -0.61 35 35
ADCY1 -0.055 0.2 -9999 0 -0.61 35 35
ADCY2 -0.087 0.22 -9999 0 -0.65 41 41
ADCY3 -0.054 0.19 -9999 0 -0.61 35 35
ADCY8 -0.18 0.25 -9999 0 -0.66 60 60
ADCY9 -0.055 0.2 -9999 0 -0.61 36 36
arachidonic acid secretion -0.15 0.28 -9999 0 -0.52 148 148
ETB receptor/Endothelin-1/Gq/GTP -0.32 0.36 -9999 0 -0.62 233 233
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
HRAS 0.006 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.035 0.27 -9999 0 -0.63 40 40
ETA receptor/Endothelin-1/Gs/GTP 0.029 0.26 -9999 0 -0.59 46 46
mol:GTP 0 0.004 -9999 0 -10000 0 0
COL3A1 -0.047 0.26 -9999 0 -0.73 35 35
EDNRB -0.44 0.36 -9999 0 -0.73 302 302
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.048 0.29 -9999 0 -0.83 39 39
CYSLTR1 -0.094 0.37 -9999 0 -0.9 73 73
SLC9A1 -0.008 0.13 -9999 0 -0.36 23 23
mol:GDP -0.21 0.34 -9999 0 -0.69 137 137
SLC9A3 -0.37 0.4 -9999 0 -0.68 259 259
RAF1 -0.21 0.33 -9999 0 -0.66 148 148
JUN -0.061 0.24 -9999 0 -0.66 36 36
JAK2 -0.032 0.24 -9999 0 -0.63 48 48
mol:IP3 -0.22 0.31 -9999 0 -0.66 139 139
ETA receptor/Endothelin-1 0.015 0.33 -9999 0 -0.69 56 56
PLCB1 0.002 0.033 -9999 0 -0.74 1 1
PLCB2 -0.005 0.094 -9999 0 -0.74 8 8
ETA receptor/Endothelin-3 -0.054 0.21 -9999 0 -0.54 68 68
FOS -0.21 0.36 -9999 0 -0.8 109 109
Gai/GDP -0.005 0.067 -9999 0 -0.95 1 1
CRK 0.003 0.005 -9999 0 -10000 0 0
mol:Ca ++ -0.26 0.38 -9999 0 -0.76 146 146
BCAR1 0.007 0.005 -9999 0 -10000 0 0
PRKCB1 -0.2 0.3 -9999 0 -0.62 142 142
GNAQ 0.008 0.034 -9999 0 -0.74 1 1
GNAZ -0.009 0.08 -9999 0 -0.74 6 6
GNAL -0.004 0.057 -9999 0 -0.74 3 3
Gs family/GDP -0.21 0.27 -9999 0 -0.61 136 136
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.24 -9999 0 -0.53 75 75
MAPK14 -0.24 0.29 -9999 0 -0.65 139 139
TRPC6 -0.094 0.32 -9999 0 -1.1 33 33
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.001 0.033 -9999 0 -0.74 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.26 0.31 -9999 0 -0.62 171 171
ETB receptor/Endothelin-2 -0.39 0.3 -9999 0 -0.59 333 333
ETB receptor/Endothelin-3 -0.39 0.31 -9999 0 -0.6 328 328
ETB receptor/Endothelin-1 -0.37 0.34 -9999 0 -0.61 315 315
MAPK3 -0.22 0.37 -9999 0 -0.72 150 150
MAPK1 -0.22 0.37 -9999 0 -0.72 150 150
Rac1/GDP -0.18 0.31 -9999 0 -0.63 133 133
cAMP biosynthetic process -0.079 0.21 -9999 0 -0.6 48 48
MAPK8 -0.085 0.28 -9999 0 -0.64 71 71
SRC 0 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.17 -9999 0 -0.44 69 69
p130Cas/CRK/Src/PYK2 -0.19 0.33 -9999 0 -0.67 135 135
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.18 0.31 -9999 0 -0.63 133 133
COL1A2 -0.26 0.32 -9999 0 -0.79 92 92
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.051 0.2 -9999 0 -0.46 78 78
mol:DAG -0.22 0.31 -9999 0 -0.66 139 139
MAP2K2 -0.21 0.33 -9999 0 -0.65 152 152
MAP2K1 -0.21 0.33 -9999 0 -0.65 152 152
EDNRA 0.015 0.15 -9999 0 -0.93 6 6
positive regulation of muscle contraction -0.033 0.21 -9999 0 -0.63 33 33
Gq family/GDP -0.21 0.31 -9999 0 -0.68 129 129
HRAS/GTP -0.22 0.33 -9999 0 -0.68 142 142
PRKCH -0.2 0.3 -9999 0 -0.65 127 127
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.2 0.3 -9999 0 -0.66 128 128
PRKCB -0.22 0.33 -9999 0 -0.7 136 136
PRKCE -0.2 0.3 -9999 0 -0.65 127 127
PRKCD -0.2 0.3 -9999 0 -0.65 127 127
PRKCG -0.22 0.31 -9999 0 -0.66 140 140
regulation of vascular smooth muscle contraction -0.25 0.43 -9999 0 -0.93 112 112
PRKCQ -0.24 0.34 -9999 0 -0.71 145 145
PLA2G4A -0.17 0.3 -9999 0 -0.57 148 148
GNA14 -0.17 0.32 -9999 0 -0.74 123 123
GNA15 0.008 0.006 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.006 -9999 0 -10000 0 0
Rac1/GTP 0.036 0.27 -9999 0 -0.64 37 37
MMP1 -0.23 0.24 -9999 0 -0.44 236 236
TCGA08_retinoblastoma

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
CDKN2B -0.065 0.2 -10000 0 -0.71 46 46
CDKN2C 0.03 0.033 -10000 0 -10000 0 0
CDKN2A -0.28 0.3 -10000 0 -0.6 233 233
CCND2 0.075 0.084 0.27 47 -10000 0 47
RB1 -0.082 0.087 -10000 0 -0.27 48 48
CDK4 0.087 0.09 0.27 47 -10000 0 47
CDK6 0.084 0.092 0.29 47 -10000 0 47
G1/S progression 0.075 0.094 0.27 48 -10000 0 48
Glypican 2 network

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
MDK -0.01 0.076 -9999 0 -0.57 9 9
GPC2 -0.085 0.2 -9999 0 -0.57 74 74
GPC2/Midkine -0.069 0.16 -9999 0 -0.42 82 82
neuron projection morphogenesis -0.068 0.16 -9999 0 -0.42 82 82
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.063 0.22 -9999 0 -0.71 44 44
alphaM/beta2 Integrin/GPIbA -0.064 0.21 -9999 0 -0.7 45 45
alphaM/beta2 Integrin/proMMP-9 -0.079 0.21 -9999 0 -0.67 46 46
PLAUR 0 0 -9999 0 -10000 0 0
HMGB1 0 0.002 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.059 0.2 -9999 0 -0.69 43 43
AGER -0.68 0.21 -9999 0 -0.74 459 459
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG -0.05 0.18 -9999 0 -0.74 34 34
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.47 0.26 -9999 0 -0.52 459 459
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.032 0.13 -9999 0 -0.57 28 28
CYR61 -0.04 0.17 -9999 0 -0.74 27 27
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.2 0.29 -9999 0 -0.63 116 116
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.32 -9999 0 -0.74 131 131
MYH2 -0.31 0.35 -9999 0 -0.79 141 141
MST1R -0.047 0.18 -9999 0 -0.74 32 32
leukocyte activation during inflammatory response -0.088 0.22 -9999 0 -0.58 67 67
APOB -0.047 0.18 -9999 0 -0.72 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.006 0.066 -9999 0 -0.74 4 4
JAM3 -0.001 0.033 -9999 0 -0.74 1 1
GP1BA -0.007 0.07 -9999 0 -0.7 5 5
alphaM/beta2 Integrin/CTGF -0.077 0.25 -9999 0 -0.74 52 52
alphaM/beta2 Integrin -0.26 0.37 -9999 0 -0.76 120 120
JAM3 homodimer -0.001 0.033 -9999 0 -0.74 1 1
ICAM2 -0.051 0.19 -9999 0 -0.74 35 35
ICAM1 -0.06 0.2 -9999 0 -0.74 41 41
phagocytosis triggered by activation of immune response cell surface activating receptor -0.24 0.36 -9999 0 -0.74 120 120
cell adhesion -0.063 0.21 -9999 0 -0.7 45 45
NFKB1 -0.46 0.31 -9999 0 -0.94 111 111
THY1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.043 0.14 -9999 0 -0.45 48 48
alphaM/beta2 Integrin/LRP/tPA -0.059 0.19 -9999 0 -0.64 43 43
IL6 -0.48 0.38 -9999 0 -1.1 112 112
ITGB2 -0.031 0.15 -9999 0 -0.74 21 21
elevation of cytosolic calcium ion concentration -0.074 0.2 -9999 0 -0.64 43 43
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.28 -9999 0 -0.64 97 97
JAM2 -0.12 0.27 -9999 0 -0.74 80 80
alphaM/beta2 Integrin/ICAM1 -0.11 0.28 -9999 0 -0.64 86 86
alphaM/beta2 Integrin/uPA/Plg -0.078 0.2 -9999 0 -0.66 43 43
RhoA/GTP -0.29 0.36 -9999 0 -0.86 117 117
positive regulation of phagocytosis -0.18 0.27 -9999 0 -0.77 68 68
Ron/MSP -0.036 0.14 -9999 0 -0.55 33 33
alphaM/beta2 Integrin/uPAR/uPA -0.074 0.2 -9999 0 -0.65 43 43
alphaM/beta2 Integrin/uPAR -0.059 0.2 -9999 0 -0.69 43 43
PLAU -0.037 0.14 -9999 0 -0.57 32 32
PLAT -0.007 0.063 -9999 0 -0.57 6 6
actin filament polymerization -0.29 0.32 -9999 0 -0.73 141 141
MST1 -0.001 0.026 -9999 0 -0.57 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.089 0.22 -9999 0 -0.59 67 67
TNF -0.42 0.28 -9999 0 -0.85 111 111
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.081 0.22 -9999 0 -0.68 46 46
fibrinolysis -0.078 0.2 -9999 0 -0.66 43 43
HCK -0.009 0.08 -9999 0 -0.74 6 6
dendritic cell antigen processing and presentation -0.24 0.36 -9999 0 -0.74 120 120
VTN -0.28 0.36 -9999 0 -0.74 191 191
alphaM/beta2 Integrin/CYR61 -0.084 0.25 -9999 0 -0.74 57 57
LPA -0.021 0.11 -9999 0 -0.57 18 18
LRP1 0 0 -9999 0 -10000 0 0
cell migration -0.075 0.21 -9999 0 -0.66 44 44
FN1 -0.019 0.12 -9999 0 -0.74 13 13
alphaM/beta2 Integrin/Thy1 -0.059 0.2 -9999 0 -0.69 43 43
MPO -0.035 0.16 -9999 0 -0.74 24 24
KNG1 -0.015 0.091 -9999 0 -0.57 13 13
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.25 0.34 -9999 0 -0.77 116 116
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.006 0.057 -9999 0 -0.57 5 5
CTGF -0.029 0.14 -9999 0 -0.74 20 20
alphaM/beta2 Integrin/Hck -0.065 0.22 -9999 0 -0.72 45 45
ITGAM -0.063 0.21 -9999 0 -0.74 42 42
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.19 0.36 -9999 0 -0.66 146 146
HP -0.22 0.34 -9999 0 -0.74 151 151
leukocyte adhesion -0.44 0.31 -9999 0 -0.82 149 149
SELP -0.19 0.32 -9999 0 -0.74 131 131
Thromboxane A2 receptor 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
TGM2 -0.061 0.21 -10000 0 -0.74 45 45
GNB1/GNG2 -0.071 0.09 -10000 0 -0.2 97 97
AKT1 -0.038 0.13 -10000 0 -0.22 55 55
EGF -0.014 0.097 -10000 0 -0.69 10 10
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.039 0.13 -10000 0 -0.59 19 19
mol:Ca2+ -0.078 0.18 -10000 0 -0.31 182 182
LYN -0.016 0.076 -10000 0 -0.52 7 7
RhoA/GTP -0.048 0.059 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.086 0.2 -10000 0 -0.35 175 175
GNG2 -0.007 0.073 -10000 0 -0.74 5 5
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.019 0.099 -10000 0 -0.54 5 5
G beta5/gamma2 -0.094 0.12 -10000 0 -0.29 77 77
PRKCH -0.092 0.21 -10000 0 -0.36 173 173
DNM1 -0.002 0.036 -10000 0 -0.57 2 2
TXA2/TP beta/beta Arrestin3 -0.002 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.024 0.13 -10000 0 -0.74 16 16
G12 family/GTP -0.12 0.14 -10000 0 -0.31 175 175
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.001 0.033 -10000 0 -0.74 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.13 0.41 21 -10000 0 21
mol:NADP -0.007 0.073 -10000 0 -0.74 5 5
RAB11A 0 0 -10000 0 -10000 0 0
PRKG1 -0.068 0.21 -10000 0 -0.74 46 46
mol:IP3 -0.1 0.22 -10000 0 -0.39 182 182
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.16 0.3 -10000 0 -0.53 182 182
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.03 0.1 -10000 0 -0.64 7 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.019 0.088 -10000 0 -0.59 8 8
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.016 0.11 -10000 0 -0.74 11 11
PRKCB1 -0.1 0.22 -10000 0 -0.39 178 178
GNAQ -0.001 0.033 -10000 0 -0.74 1 1
mol:L-citrulline -0.007 0.073 -10000 0 -0.74 5 5
TXA2/TXA2-R family -0.15 0.3 -10000 0 -0.55 175 175
LCK -0.016 0.075 -10000 0 -0.52 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.018 0.089 -10000 0 -0.65 6 6
TXA2-R family/G12 family/GDP/G beta/gamma 0.019 0.042 -10000 0 -0.5 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.018 0.088 -10000 0 -0.61 7 7
MAPK14 -0.046 0.14 -10000 0 -0.24 72 72
TGM2/GTP -0.13 0.26 -10000 0 -0.46 186 186
MAPK11 -0.046 0.14 -10000 0 -0.24 86 86
ARHGEF1 -0.037 0.11 -10000 0 -0.2 10 10
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade -0.1 0.23 -10000 0 -0.4 175 175
RAB11/GDP 0 0 -10000 0 -10000 0 0
ICAM1 -0.078 0.19 -10000 0 -0.32 173 173
cAMP biosynthetic process -0.099 0.21 -10000 0 -0.36 186 186
Gq family/GTP/EBP50 -0.037 0.11 -10000 0 -0.23 123 123
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.015 0.071 -10000 0 -0.52 6 6
GNB5 0 0 -10000 0 -10000 0 0
GNB1 -0.001 0.033 -10000 0 -0.74 1 1
EGF/EGFR 0.023 0.097 -10000 0 -0.42 11 11
VCAM1 -0.072 0.17 -10000 0 -0.3 174 174
TP beta/Gq family/GDP/G beta5/gamma2 -0.019 0.099 -10000 0 -0.54 5 5
platelet activation -0.064 0.19 -10000 0 -0.31 175 175
PGI2/IP -0.012 0.083 -10000 0 -0.56 11 11
PRKACA -0.02 0.1 -10000 0 -0.44 23 23
Gq family/GDP/G beta5/gamma2 -0.021 0.1 -10000 0 -0.52 6 6
TXA2/TP beta/beta Arrestin2 -0.002 0.011 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.11 -10000 0 -0.43 25 25
mol:DAG -0.12 0.25 -10000 0 -0.44 176 176
EGFR -0.023 0.12 -10000 0 -0.63 18 18
TXA2/TP alpha -0.14 0.29 -10000 0 -0.5 186 186
Gq family/GTP -0.068 0.12 -10000 0 -0.28 123 123
YES1 -0.015 0.071 -10000 0 -0.52 6 6
GNAI2/GTP -0.017 0.084 -10000 0 -0.62 6 6
PGD2/DP -0.018 0.099 -10000 0 -0.56 16 16
SLC9A3R1 -0.005 0.051 -10000 0 -0.57 4 4
FYN -0.016 0.076 -10000 0 -0.56 6 6
mol:NO -0.007 0.073 -10000 0 -0.74 5 5
GNA15 0 0 -10000 0 -10000 0 0
PGK/cGMP -0.049 0.15 -10000 0 -0.51 48 48
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.054 0.16 -10000 0 -0.73 19 19
NOS3 -0.007 0.073 -10000 0 -0.74 5 5
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.093 0.21 -10000 0 -0.36 174 174
PRKCB -0.1 0.22 -10000 0 -0.39 177 177
PRKCE -0.092 0.21 -10000 0 -0.37 163 163
PRKCD -0.1 0.22 -10000 0 -0.39 173 173
PRKCG -0.11 0.23 -10000 0 -0.41 177 177
muscle contraction -0.14 0.28 -10000 0 -0.5 177 177
PRKCZ -0.085 0.2 -10000 0 -0.35 175 175
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.02 0.095 -10000 0 -0.63 8 8
PRKCQ -0.11 0.23 -10000 0 -0.4 181 181
MAPKKK cascade -0.13 0.27 -10000 0 -0.48 178 178
SELE -0.11 0.23 -10000 0 -0.42 173 173
TP beta/GNAI2/GDP/G beta/gamma -0.022 0.099 -10000 0 -0.69 7 7
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 123 123
chemotaxis -0.18 0.34 -10000 0 -0.62 174 174
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 0 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0 0 -9999 0 -10000 0 0
LAT2 -0.16 0.25 -9999 0 -0.66 76 76
AP1 -0.2 0.27 -9999 0 -0.64 113 113
mol:PIP3 -0.16 0.29 -9999 0 -0.65 91 91
IKBKB -0.072 0.16 -9999 0 -0.34 82 82
AKT1 -0.18 0.24 -9999 0 -0.67 72 72
IKBKG -0.072 0.16 -9999 0 -0.33 83 83
MS4A2 -0.17 0.32 -9999 0 -0.74 118 118
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.006 0.005 -9999 0 -10000 0 0
MAP3K1 -0.1 0.23 -9999 0 -0.53 85 85
mol:Ca2+ -0.11 0.21 -9999 0 -0.46 91 91
LYN 0.005 0.049 -9999 0 -0.76 2 2
CBLB -0.16 0.24 -9999 0 -0.64 76 76
SHC1 0.001 0.004 -9999 0 -10000 0 0
RasGAP/p62DOK -0.052 0.14 -9999 0 -0.44 59 59
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.001 0.033 -9999 0 -0.74 1 1
PLD2 -0.21 0.28 -9999 0 -0.75 76 76
PTPN13 -0.13 0.24 -9999 0 -0.6 76 76
PTPN11 0.005 0.011 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.083 0.19 -9999 0 -0.41 78 78
SYK 0.006 0.035 -9999 0 -0.77 1 1
GRB2 0 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.2 0.27 -9999 0 -0.69 91 91
LAT -0.16 0.24 -9999 0 -0.64 76 76
PAK2 -0.13 0.26 -9999 0 -0.6 90 90
NFATC2 -0.18 0.32 -9999 0 -0.92 71 71
HRAS -0.15 0.29 -9999 0 -0.68 91 91
GAB2 -0.021 0.12 -9999 0 -0.74 14 14
PLA2G1B -0.002 0.037 -9999 0 -10000 0 0
Fc epsilon R1 -0.26 0.34 -9999 0 -0.63 205 205
Antigen/IgE/Fc epsilon R1 -0.24 0.32 -9999 0 -0.58 205 205
mol:GDP -0.16 0.32 -9999 0 -0.74 92 92
JUN 0 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.006 0.005 -9999 0 -10000 0 0
FOS -0.09 0.24 -9999 0 -0.74 61 61
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.17 0.26 -9999 0 -0.54 125 125
CHUK -0.072 0.16 -9999 0 -0.34 82 82
KLRG1 -0.16 0.24 -9999 0 -0.63 77 77
VAV1 -0.16 0.25 -9999 0 -0.66 77 77
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.16 0.24 -9999 0 -0.64 76 76
negative regulation of mast cell degranulation -0.14 0.22 -9999 0 -0.58 76 76
BTK -0.21 0.33 -9999 0 -0.8 95 95
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.2 0.31 -9999 0 -0.56 157 157
GAB2/PI3K/SHP2 -0.2 0.27 -9999 0 -0.75 72 72
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.17 0.25 -9999 0 -0.67 78 78
RAF1 0.025 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.23 0.32 -9999 0 -0.61 158 158
FCER1G -0.015 0.13 -9999 0 -0.75 14 14
FCER1A -0.22 0.35 -9999 0 -0.75 148 148
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.3 -9999 0 -0.55 205 205
MAPK3 0.033 0.023 -9999 0 -10000 0 0
MAPK1 0.033 0.023 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.022 0.071 -9999 0 -10000 0 0
DUSP1 -0.087 0.24 -9999 0 -0.74 59 59
NF-kappa-B/RelA -0.06 0.076 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.14 0.25 -9999 0 -0.62 76 76
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.16 0.24 -9999 0 -0.62 85 85
FER -0.16 0.24 -9999 0 -0.64 76 76
RELA 0 0 -9999 0 -10000 0 0
ITK -0.078 0.18 -9999 0 -0.66 38 38
SOS1 0.001 0.004 -9999 0 -10000 0 0
PLCG1 -0.16 0.32 -9999 0 -0.73 92 92
cytokine secretion -0.044 0.055 -9999 0 -10000 0 0
SPHK1 -0.16 0.24 -9999 0 -0.64 76 76
PTK2 -0.14 0.26 -9999 0 -0.66 76 76
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.21 0.29 -9999 0 -0.72 91 91
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.15 0.28 -9999 0 -0.63 91 91
MAP2K2 0.03 0.024 -9999 0 -10000 0 0
MAP2K1 0.03 0.024 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.15 0.22 -9999 0 -0.58 77 77
MAP2K4 0.009 0.013 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.24 0.33 -9999 0 -0.59 206 206
mol:Choline -0.2 0.28 -9999 0 -0.74 76 76
SHC/Grb2/SOS1 -0.15 0.22 -9999 0 -0.6 75 75
FYN -0.001 0.033 -9999 0 -0.74 1 1
DOK1 0 0 -9999 0 -10000 0 0
PXN -0.13 0.24 -9999 0 -0.6 75 75
HCLS1 -0.16 0.24 -9999 0 -0.64 76 76
PRKCB -0.12 0.22 -9999 0 -0.48 92 92
FCGR2B -0.013 0.098 -9999 0 -0.74 9 9
IGHE -0.005 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.15 0.22 -9999 0 -0.6 76 76
LCP2 -0.009 0.081 -9999 0 -0.74 6 6
PLA2G4A -0.16 0.24 -9999 0 -0.64 78 78
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.2 0.28 -9999 0 -0.74 76 76
IKK complex -0.04 0.12 -9999 0 -0.28 25 25
WIPF1 0 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.019 0.082 -9999 0 -0.42 16 16
RGS9BP -0.013 0.098 -9999 0 -0.74 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.036 -9999 0 -0.57 2 2
mol:Na + -0.18 0.18 -9999 0 -0.36 253 253
mol:ADP -0.012 0.099 -9999 0 -0.42 28 28
GNAT2 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.059 0.16 -9999 0 -0.49 60 60
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.03 0.13 -9999 0 -0.57 26 26
CNGB3 -0.29 0.29 -9999 0 -0.57 251 251
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.21 0.21 -9999 0 -0.36 304 304
Cone PDE6 -0.051 0.14 -9999 0 -0.42 60 60
Cone Metarhodopsin II -0.018 0.075 -9999 0 -0.33 28 28
Na + (4 Units) -0.22 0.2 -9999 0 -0.36 304 304
GNAT2/GDP -0.05 0.14 -9999 0 -0.42 60 60
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.005 -9999 0 -10000 0 0
Cone Transducin -0.02 0.087 -9999 0 -0.43 17 17
SLC24A2 -0.11 0.23 -9999 0 -0.57 97 97
GNB3/GNGT2 -0.025 0.11 -9999 0 -0.5 25 25
GNB3 -0.01 0.076 -9999 0 -0.57 9 9
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 -0.002 0.036 -9999 0 -0.57 2 2
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.18 0.18 -9999 0 -0.36 253 253
mol:Pi -0.058 0.16 -9999 0 -0.49 60 60
Cone CNG Channel -0.14 0.14 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.23 -9999 0 -0.57 97 97
RGS9 -0.078 0.23 -9999 0 -0.74 53 53
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.024 0.13 -9999 0 -0.74 16 16
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.4 0.54 -10000 0 -1.2 108 108
STAT6 (cleaved dimer) -0.46 0.48 -10000 0 -1.1 145 145
IGHG1 -0.12 0.19 -10000 0 -0.41 3 3
IGHG3 -0.39 0.52 -10000 0 -1.1 132 132
AKT1 -0.14 0.26 -10000 0 -0.89 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.1 0.22 -10000 0 -1 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.27 -10000 0 -0.92 9 9
THY1 -0.4 0.54 -10000 0 -1.2 110 110
MYB -0.02 0.11 -10000 0 -0.59 17 17
HMGA1 -0.005 0.051 -10000 0 -0.57 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.2 0.31 -10000 0 -0.64 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.27 -10000 0 -0.95 9 9
SP1 0.017 0.002 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
SOCS5 0.019 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.45 0.48 -10000 0 -1.2 116 116
SOCS1 -0.23 0.36 -10000 0 -0.77 74 74
SOCS3 -0.16 0.27 -10000 0 -1.1 6 6
FCER2 -0.34 0.5 -10000 0 -1.2 86 86
PARP14 0.008 0.005 -10000 0 -10000 0 0
CCL17 -0.47 0.62 -10000 0 -1.3 131 131
GRB2 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.12 0.22 -10000 0 -0.89 6 6
T cell proliferation -0.39 0.55 -10000 0 -1.2 113 113
IL4R/JAK1 -0.4 0.54 -10000 0 -1.2 111 111
EGR2 -0.42 0.57 -10000 0 -1.2 116 116
JAK2 -0.004 0.034 -10000 0 -10000 0 0
JAK3 0.013 0.007 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
JAK1 0.009 0.014 -10000 0 -10000 0 0
COL1A2 -0.1 0.18 -10000 0 -0.66 2 2
CCL26 -0.43 0.56 -10000 0 -1.2 124 124
IL4R -0.42 0.58 -10000 0 -1.3 111 111
PTPN6 0.019 0.014 -10000 0 -10000 0 0
IL13RA2 -0.43 0.57 -10000 0 -1.3 121 121
IL13RA1 -0.004 0.034 -10000 0 -10000 0 0
IRF4 -0.17 0.36 -10000 0 -0.88 83 83
ARG1 -0.12 0.24 -10000 0 -0.82 31 31
CBL -0.18 0.29 -10000 0 -0.63 54 54
GTF3A 0.013 0.013 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.003 0.051 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.31 -10000 0 -0.82 81 81
CD40LG -0.11 0.28 -10000 0 -0.74 86 86
MAPK14 -0.18 0.29 -10000 0 -0.68 34 34
mitosis -0.14 0.25 -10000 0 -0.82 8 8
STAT6 -0.47 0.64 -10000 0 -1.4 122 122
SPI1 -0.045 0.2 -10000 0 -0.74 37 37
RPS6KB1 -0.13 0.24 -10000 0 -0.82 7 7
STAT6 (dimer) -0.47 0.64 -10000 0 -1.4 122 122
STAT6 (dimer)/PARP14 -0.43 0.58 -10000 0 -1.3 111 111
mast cell activation 0.008 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.29 -10000 0 -0.75 40 40
FRAP1 -0.14 0.26 -10000 0 -0.89 8 8
LTA -0.4 0.54 -10000 0 -1.2 109 109
FES -0.001 0.033 -10000 0 -0.74 1 1
T-helper 1 cell differentiation 0.45 0.62 1.3 122 -10000 0 122
CCL11 -0.4 0.53 -10000 0 -1.2 114 114
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.26 -10000 0 -1 8 8
IL2RG 0.002 0.087 -10000 0 -0.73 7 7
IL10 -0.4 0.55 -10000 0 -1.2 111 111
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.004 0.057 -10000 0 -0.74 3 3
IL4 -0.079 0.14 -10000 0 -10000 0 0
IL5 -0.4 0.54 -10000 0 -1.2 111 111
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.31 0.42 -10000 0 -0.9 111 111
COL1A1 -0.14 0.23 -10000 0 -0.69 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.41 0.55 -10000 0 -1.3 106 106
IL2R gamma/JAK3 -0.001 0.066 -10000 0 -0.55 7 7
TFF3 -0.45 0.62 -10000 0 -1.4 118 118
ALOX15 -0.63 0.77 -10000 0 -1.5 188 188
MYBL1 -0.001 0.026 -10000 0 -0.57 1 1
T-helper 2 cell differentiation -0.32 0.43 -10000 0 -0.92 113 113
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.009 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.26 -10000 0 -0.99 8 8
mol:PI-3-4-5-P3 -0.14 0.26 -10000 0 -0.89 8 8
PI3K -0.15 0.27 -10000 0 -0.99 8 8
DOK2 -0.068 0.21 -10000 0 -0.74 46 46
ETS1 0.001 0.11 -10000 0 -0.7 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.11 0.21 -10000 0 -0.86 6 6
ITGB3 -0.41 0.56 -10000 0 -1.3 111 111
PIGR -0.81 0.83 -10000 0 -1.6 264 264
IGHE 0.029 0.044 -10000 0 -10000 0 0
MAPKKK cascade -0.11 0.21 -10000 0 -0.84 6 6
BCL6 0.001 0.004 -10000 0 -10000 0 0
OPRM1 -0.4 0.54 -10000 0 -1.2 110 110
RETNLB -0.4 0.54 -10000 0 -1.2 110 110
SELP -0.58 0.75 -10000 0 -1.6 159 159
AICDA -0.39 0.52 -10000 0 -1.2 109 109
Glucocorticoid receptor regulatory network

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
PCK2 0.059 0.098 -10000 0 -10000 0 0
SMARCC2 0.012 0 -10000 0 -10000 0 0
SMARCC1 0.012 0 -10000 0 -10000 0 0
TBX21 -0.2 0.35 -10000 0 -1 65 65
SUMO2 0.002 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0 -10000 0 -10000 0 0
FKBP4 -0.001 0.026 -10000 0 -0.57 1 1
FKBP5 0 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.13 0.1 0.33 48 -10000 0 48
PRL -0.083 0.12 -10000 0 -0.63 1 1
cortisol/GR alpha (dimer)/TIF2 0.31 0.25 0.6 156 -10000 0 156
RELA -0.046 0.1 -10000 0 -0.29 10 10
FGG -0.13 0.47 0.54 53 -0.62 235 288
GR beta/TIF2 0.14 0.12 0.36 57 -0.38 1 58
IFNG -0.34 0.24 -10000 0 -0.68 100 100
apoptosis 0.026 0.12 0.46 2 -0.57 2 4
CREB1 0.001 0.028 -10000 0 -10000 0 0
histone acetylation -0.011 0.15 0.31 4 -0.39 22 26
BGLAP -0.094 0.14 -10000 0 -0.56 7 7
GR/PKAc 0.12 0.099 0.32 39 -10000 0 39
NF kappa B1 p50/RelA -0.084 0.18 -10000 0 -0.48 39 39
SMARCD1 0.012 0 -10000 0 -10000 0 0
MDM2 0.11 0.097 0.29 59 -0.31 1 60
GATA3 -0.013 0.13 -10000 0 -0.71 17 17
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.16 0.41 -10000 0 -1.3 51 51
GSK3B 0.002 0.006 -10000 0 -10000 0 0
NR1I3 0.045 0.11 0.47 1 -0.5 1 2
CSN2 0.16 0.16 0.45 35 -10000 0 35
BRG1/BAF155/BAF170/BAF60A 0 0 -10000 0 -10000 0 0
NFATC1 0.001 0.034 -10000 0 -0.74 1 1
POU2F1 0.005 0.014 -10000 0 -10000 0 0
CDKN1A 0.025 0.024 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.58 49 49
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.093 0.14 0.33 38 -10000 0 38
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.031 0.16 0.46 1 -0.9 11 12
JUN -0.29 0.16 -10000 0 -0.5 118 118
IL4 -0.11 0.15 -10000 0 -0.52 16 16
CDK5R1 -0.01 0.081 -10000 0 -0.58 10 10
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.45 0.24 -10000 0 -0.56 343 343
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.099 0.34 33 -10000 0 33
cortisol/GR alpha (monomer) 0.36 0.32 0.72 167 -10000 0 167
NCOA2 -0.001 0.033 -10000 0 -0.74 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.25 -10000 0 -0.82 61 61
AP-1/NFAT1-c-4 -0.53 0.25 -10000 0 -0.68 282 282
AFP -0.19 0.15 -10000 0 -0.7 11 11
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.18 0.15 0.52 23 -10000 0 23
TP53 0.028 0.034 -10000 0 -0.72 1 1
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.54 0.25 -10000 0 -0.7 288 288
KRT14 -0.37 0.23 -10000 0 -0.62 128 128
TBP 0.018 0 -10000 0 -10000 0 0
CREBBP 0.11 0.067 0.34 1 -10000 0 1
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.01 0.03 -10000 0 -10000 0 0
AP-1 -0.54 0.25 -10000 0 -0.69 283 283
MAPK14 0.002 0.005 -10000 0 -10000 0 0
MAPK10 -0.01 0.093 -10000 0 -0.74 8 8
MAPK11 0.002 0.006 -10000 0 -10000 0 0
KRT5 -0.56 0.26 -10000 0 -0.79 181 181
interleukin-1 receptor activity 0.007 0.028 -10000 0 -10000 0 0
NCOA1 0.013 0.001 -10000 0 -10000 0 0
STAT1 0.017 0 -10000 0 -10000 0 0
CGA -0.12 0.17 -10000 0 -0.6 18 18
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.19 0.49 101 -10000 0 101
MAPK3 0.002 0.006 -10000 0 -10000 0 0
MAPK1 0.002 0.005 -10000 0 -10000 0 0
ICAM1 -0.26 0.43 -10000 0 -1.1 74 74
NFKB1 -0.046 0.1 -10000 0 -10000 0 0
MAPK8 -0.24 0.17 -10000 0 -0.46 124 124
MAPK9 0.002 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.023 0.12 0.46 2 -0.6 2 4
BAX 0.025 0.024 -10000 0 -10000 0 0
POMC -0.21 0.26 -10000 0 -0.76 45 45
EP300 0.11 0.068 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0.32 0.25 0.62 152 -10000 0 152
proteasomal ubiquitin-dependent protein catabolic process 0.075 0.074 0.25 15 -0.27 1 16
SGK1 0.17 0.077 -10000 0 -10000 0 0
IL13 -0.27 0.2 -10000 0 -0.74 46 46
IL6 -0.34 0.52 -10000 0 -1.3 101 101
PRKACG -0.001 0.026 -10000 0 -0.57 1 1
IL5 -0.24 0.17 -10000 0 -0.68 35 35
IL2 -0.34 0.2 -10000 0 -0.67 85 85
CDK5 0.001 0.004 -10000 0 -10000 0 0
PRKACB 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.2 0.28 -10000 0 -0.79 51 51
CDK5R1/CDK5 -0.006 0.059 -10000 0 -0.42 10 10
NF kappa B1 p50/RelA/PKAc -0.058 0.13 -10000 0 -0.49 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 146 -10000 0 146
SMARCA4 0.012 0 -10000 0 -10000 0 0
chromatin remodeling 0.19 0.14 0.41 94 -10000 0 94
NF kappa B1 p50/RelA/Cbp 0.035 0.18 0.38 15 -0.52 4 19
JUN (dimer) -0.29 0.16 -10000 0 -0.5 118 118
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.41 0.51 -10000 0 -1 185 185
NR3C1 0.2 0.2 0.5 105 -10000 0 105
NR4A1 -0.096 0.26 -10000 0 -0.73 67 67
TIF2/SUV420H1 -0.001 0.025 -10000 0 -0.56 1 1
MAPKKK cascade 0.026 0.12 0.46 2 -0.57 2 4
cortisol/GR alpha (dimer)/Src-1 0.32 0.25 0.6 163 -10000 0 163
PBX1 0.002 0.049 -10000 0 -0.74 2 2
POU1F1 -0.002 0.046 -10000 0 -0.57 3 3
SELE -0.47 0.61 -10000 0 -1.3 163 163
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.19 0.14 0.41 92 -10000 0 92
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.57 146 -10000 0 146
mol:cortisol 0.19 0.2 0.41 170 -0.23 4 174
MMP1 -0.33 0.19 -10000 0 -0.52 77 77
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.044 0.055 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.099 0.14 -9999 0 -0.43 19 19
JUN -0.063 0.14 -9999 0 -0.42 16 16
HRAS 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.22 -9999 0 -0.48 129 129
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.22 -9999 0 -0.48 129 129
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 -0.16 0.22 -9999 0 -0.48 125 125
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.2 -9999 0 -0.49 53 53
GRB7 -0.005 0.051 -9999 0 -0.57 4 4
RET51/GFRalpha1/GDNF -0.17 0.22 -9999 0 -0.48 129 129
MAPKKK cascade -0.13 0.17 -9999 0 -0.59 18 18
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.16 0.22 -9999 0 -0.48 125 125
lamellipodium assembly -0.095 0.13 -9999 0 -0.4 19 19
RET51/GFRalpha1/GDNF/SHC -0.17 0.22 -9999 0 -0.48 129 129
PIK3CA 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.16 0.22 -9999 0 -0.48 125 125
RET9/GFRalpha1/GDNF/Shank3 -0.16 0.22 -9999 0 -0.48 125 125
MAPK3 -0.14 0.18 -9999 0 -0.62 20 20
DOK1 0 0 -9999 0 -10000 0 0
DOK6 -0.063 0.21 -9999 0 -0.74 43 43
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.14 0.18 -9999 0 -0.54 40 40
DOK5 -0.005 0.059 -9999 0 -0.66 4 4
GFRA1 -0.18 0.32 -9999 0 -0.74 125 125
MAPK8 -0.074 0.15 -9999 0 -0.44 16 16
HRAS/GTP -0.14 0.19 -9999 0 -0.62 20 20
tube development -0.15 0.2 -9999 0 -0.45 125 125
MAPK1 -0.14 0.18 -9999 0 -0.62 20 20
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.33 125 125
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.19 0.25 -9999 0 -0.78 41 41
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.22 -9999 0 -0.48 129 129
RET51/GFRalpha1/GDNF/Dok5 -0.17 0.22 -9999 0 -0.49 129 129
PRKCA -0.003 0.046 -9999 0 -0.74 2 2
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.11 0.15 -9999 0 -0.36 125 125
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.47 15 15
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.22 -9999 0 -0.48 130 130
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.02 0.1 -9999 0 -0.57 17 17
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.062 0.14 -9999 0 -0.41 16 16
RET9/GFRalpha1/GDNF/FRS2 -0.16 0.22 -9999 0 -0.48 125 125
SHANK3 -0.003 0.046 -9999 0 -0.74 2 2
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.33 125 125
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.14 -9999 0 -0.47 16 16
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.1 0.14 -9999 0 -0.47 16 16
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.48 16 16
PI3K -0.14 0.2 -9999 0 -0.47 125 125
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.2 -9999 0 -0.45 125 125
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.1 0.14 -9999 0 -0.48 16 16
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.22 -9999 0 -0.48 129 129
GAB1 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
IRS2 -0.004 0.057 -9999 0 -0.74 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -9999 0 -0.48 16 16
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.22 -9999 0 -0.48 130 130
GRB2 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.093 0.21 -9999 0 -0.57 81 81
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.22 -9999 0 -0.48 129 129
Rac1/GTP -0.11 0.16 -9999 0 -0.49 19 19
RET9/GFRalpha1/GDNF -0.18 0.24 -9999 0 -0.46 191 191
GFRalpha1/GDNF -0.2 0.27 -9999 0 -0.54 191 191
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.072 0.075 0.14 261 -10000 0 261
BUB1B -0.13 0.1 -10000 0 -0.22 200 200
PLK1 -0.014 0.037 -10000 0 -0.13 10 10
PLK1S1 -0.003 0.02 -10000 0 -10000 0 0
KIF2A -0.005 0.034 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.014 0.037 -10000 0 -0.13 10 10
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.2 0.23 -10000 0 -0.41 240 240
WEE1 -0.007 0.039 -10000 0 -10000 0 0
cytokinesis -0.11 0.13 -10000 0 -0.28 72 72
PP2A-alpha B56 -0.008 0.023 -10000 0 -10000 0 0
AURKA -0.007 0.03 -10000 0 -10000 0 0
PICH/PLK1 -0.12 0.17 -10000 0 -0.46 59 59
CENPE -0.039 0.11 -10000 0 -0.36 52 52
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.005 0.033 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 -0.061 0.049 -10000 0 -0.12 21 21
PAK1 0.003 0.026 -10000 0 -0.57 1 1
SPC24 -0.16 0.26 -10000 0 -0.57 138 138
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN -0.012 0.038 -10000 0 -0.14 8 8
GORASP1 0 0 -10000 0 -10000 0 0
metaphase -0.001 0.003 -10000 0 -0.012 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.02 -10000 0 -0.067 5 5
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -10000 0 0
STAG2 0 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.011 -10000 0 -10000 0 0
spindle elongation -0.014 0.037 -10000 0 -0.13 10 10
ODF2 0.004 0.005 -10000 0 -10000 0 0
BUB1 -0.006 0.033 -10000 0 -10000 0 0
TPT1 -0.003 0.02 -10000 0 -10000 0 0
CDC25C -0.078 0.058 -10000 0 -0.16 15 15
CDC25B 0.009 0.003 -10000 0 -10000 0 0
SGOL1 -0.072 0.075 -10000 0 -0.14 261 261
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.031 0.082 -10000 0 -10000 0 0
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.38 0.27 -10000 0 -0.57 331 331
PLK1/PBIP1 -0.028 0.059 -10000 0 -0.33 15 15
mitosis -0.001 0.005 0.022 14 -10000 0 14
FBXO5 -0.004 0.032 -10000 0 -10000 0 0
CDC2 -0.001 0.004 -10000 0 -0.013 5 5
NDC80 -0.2 0.27 -10000 0 -0.57 175 175
metaphase plate congression -0.007 0.026 -10000 0 -10000 0 0
ERCC6L -0.12 0.17 -10000 0 -0.49 40 40
NLP/gamma Tubulin -0.005 0.022 -10000 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.02 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.003 0.005 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.2 0.2 -10000 0 -0.37 267 267
GRASP65/GM130/RAB1/GTP/PLK1 -0.009 0.016 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.029 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.045 0.035 -10000 0 -10000 0 0
microtubule-based process -0.18 0.17 -10000 0 -0.34 259 259
Golgi organization -0.014 0.037 -10000 0 -0.13 10 10
Cohesin/SA2 -0.019 0.025 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.3 0.29 -10000 0 -0.57 259 259
APC/C/CDC20 -0.23 0.16 -10000 0 -0.34 331 331
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation -0.028 0.058 -10000 0 -0.32 15 15
PRC1 -0.055 0.17 -10000 0 -0.57 48 48
ECT2 -0.016 0.073 -10000 0 -0.35 18 18
C13orf34 -0.003 0.029 -10000 0 -10000 0 0
NUDC -0.007 0.026 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.13 0.099 -10000 0 -0.22 200 200
spindle assembly -0.009 0.03 -10000 0 -10000 0 0
spindle stabilization -0.003 0.02 -10000 0 -10000 0 0
APC/C/HCDH1 0 0 -10000 0 -10000 0 0
MKLP2/PLK1 -0.18 0.17 -10000 0 -0.35 259 259
CCNB1 -0.063 0.19 -10000 0 -0.57 63 63
PPP1CB 0.003 0.005 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 0.001 0.025 -10000 0 -10000 0 0
TUBG1 -0.003 0.02 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.033 0.079 -10000 0 -10000 0 0
MLF1IP -0.007 0.075 -10000 0 -0.43 15 15
INCENP 0.005 0.006 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.032 0.03 -9999 0 -10000 0 0
VDR -0.001 0.033 -9999 0 -0.74 1 1
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.13 0.18 -9999 0 -0.54 10 10
RXRs/LXRs/DNA/Oxysterols -0.097 0.16 -9999 0 -0.58 13 13
MED1 0 0 -9999 0 -10000 0 0
mol:9cRA 0.004 0.006 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.013 0.061 -9999 0 -0.3 21 21
RXRs/NUR77 -0.28 0.26 -9999 0 -0.48 289 289
RXRs/PPAR -0.18 0.2 -9999 0 -0.56 43 43
NCOR2 -0.001 0.033 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.025 -9999 0 -0.56 1 1
RARs/VDR/DNA/Vit D3 -0.003 0.036 -9999 0 -0.41 4 4
RARA 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.001 0.033 -9999 0 -0.74 1 1
RARs/RARs/DNA/9cRA -0.002 0.032 -9999 0 -0.41 3 3
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.057 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.013 0.063 -9999 0 -10000 0 0
THRA 0 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.025 -9999 0 -0.56 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.23 0.21 -9999 0 -0.43 265 265
NR1H4 -0.005 0.051 -9999 0 -0.57 4 4
RXRs/LXRs/DNA -0.21 0.19 -9999 0 -0.56 10 10
NR1H2 0.015 0.004 -9999 0 -10000 0 0
NR1H3 0.014 0.005 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.21 0.2 -9999 0 -0.4 266 266
NR4A1 -0.096 0.25 -9999 0 -0.74 65 65
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.12 0.14 -9999 0 -0.33 11 11
RXRG -0.38 0.37 -9999 0 -0.73 265 265
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.015 0.004 -9999 0 -10000 0 0
RXRB 0.014 0.005 -9999 0 -10000 0 0
THRB -0.026 0.14 -9999 0 -0.74 18 18
PPARG -0.084 0.23 -9999 0 -0.74 57 57
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.1 0.23 -9999 0 -1.2 13 13
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.097 0.16 -9999 0 -0.58 13 13
PPARA 0 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.004 0.057 -9999 0 -0.74 3 3
RXRs/NUR77/BCL2 -0.2 0.19 -9999 0 -0.35 289 289
SREBF1 -0.082 0.15 -9999 0 -0.6 9 9
RXRs/RXRs/DNA/9cRA -0.23 0.21 -9999 0 -0.43 265 265
ABCA1 -0.082 0.15 -9999 0 -0.6 9 9
RARs/THRs -0.017 0.08 -9999 0 -0.4 21 21
RXRs/FXR -0.23 0.22 -9999 0 -0.43 265 265
BCL2 -0.001 0.026 -9999 0 -0.57 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.18 0.21 -9999 0 -0.56 76 76
SMAD6-7/SMURF1 -0.047 0.14 -9999 0 -0.48 49 49
NOG -0.031 0.15 -9999 0 -0.73 21 21
SMAD9 -0.1 0.21 -9999 0 -0.59 73 73
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.022 0.13 -9999 0 -0.47 22 22
BMP7/USAG1 -0.24 0.27 -9999 0 -0.5 242 242
SMAD5/SKI -0.049 0.11 -9999 0 -0.44 22 22
SMAD1 0.033 0.029 -9999 0 -10000 0 0
BMP2 -0.093 0.24 -9999 0 -0.74 63 63
SMAD1/SMAD1/SMAD4 -0.031 0.091 -9999 0 -10000 0 0
BMPR1A 0 0 -9999 0 -10000 0 0
BMPR1B -0.056 0.2 -9999 0 -0.74 38 38
BMPR1A-1B/BAMBI -0.04 0.13 -9999 0 -0.47 43 43
AHSG -0.02 0.1 -9999 0 -0.57 17 17
CER1 -0.002 0.036 -9999 0 -0.57 2 2
BMP2-4/CER1 -0.073 0.18 -9999 0 -0.5 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.066 0.13 -9999 0 -0.49 29 29
BMP2-4 (homodimer) -0.082 0.2 -9999 0 -0.57 72 72
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.043 0.13 -9999 0 -0.45 48 48
RGMA -0.065 0.18 -9999 0 -0.58 56 56
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.062 0.12 -9999 0 -0.44 29 29
BMP2-4/USAG1 -0.16 0.26 -9999 0 -0.54 146 146
SMAD6/SMURF1/SMAD5 -0.049 0.11 -9999 0 -0.48 15 15
SOSTDC1 -0.14 0.29 -9999 0 -0.74 95 95
BMP7/BMPR2/BMPR1A-1B -0.14 0.19 -9999 0 -0.52 44 44
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.018 0.11 -9999 0 -0.74 12 12
HFE2 -0.002 0.036 -9999 0 -0.57 2 2
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.073 0.18 -9999 0 -0.5 72 72
SMAD5/SMAD5/SMAD4 -0.049 0.11 -9999 0 -0.44 22 22
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.05 0.1 -9999 0 -0.45 16 16
BMP7 (homodimer) -0.2 0.28 -9999 0 -0.58 170 170
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.027 0.11 -9999 0 -0.48 29 29
SMAD1/SKI 0.037 0.028 -9999 0 -10000 0 0
SMAD6 -0.072 0.22 -9999 0 -0.74 49 49
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.083 0.19 -9999 0 -0.5 71 71
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.35 0.28 -9999 0 -0.57 303 303
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.042 0.15 -9999 0 -0.56 38 38
CHRDL1 -0.39 0.37 -9999 0 -0.74 263 263
ENDOFIN/SMAD1 0.037 0.028 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.036 0.1 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.007 0.067 -9999 0 -0.67 5 5
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.3 -9999 0 -0.55 288 288
BMP2-4/GREM1 -0.28 0.22 -9999 0 -0.62 71 71
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.094 0.2 -9999 0 -0.55 73 73
SMAD1/SMAD6 0.037 0.028 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.2 0.28 -9999 0 -0.58 170 170
BMP6 -0.018 0.11 -9999 0 -0.74 12 12
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.057 0.11 -9999 0 -0.4 29 29
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.037 0.028 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL -0.001 0.033 -9999 0 -0.74 1 1
PPP1CA 0 0 -9999 0 -10000 0 0
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 -0.084 0.14 -9999 0 -0.46 43 43
CHRD -0.004 0.053 -9999 0 -0.68 3 3
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.071 0.14 -9999 0 -0.49 29 29
BMP4 -0.017 0.11 -9999 0 -0.72 12 12
FST -0.097 0.22 -9999 0 -0.58 84 84
BMP2-4/NOG -0.09 0.21 -9999 0 -0.53 83 83
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.13 0.17 -9999 0 -0.7 13 13
Nectin adhesion 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
PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
alphaV beta3 Integrin -0.012 0.081 -9999 0 -0.56 11 11
PTK2 -0.11 0.17 -9999 0 -0.58 44 44
positive regulation of JNK cascade -0.035 0.092 -9999 0 -0.34 40 40
CDC42/GDP -0.023 0.14 -9999 0 -0.47 40 40
Rac1/GDP -0.021 0.14 -9999 0 -0.46 40 40
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 -0.043 0.11 -9999 0 -0.42 40 40
nectin-3/I-afadin -0.044 0.15 -9999 0 -0.56 40 40
RAPGEF1 -0.034 0.15 -9999 0 -0.54 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.048 0.18 -9999 0 -0.62 40 40
PDGFB-D/PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
TLN1 -0.021 0.15 -9999 0 -0.52 33 33
Rap1/GTP -0.036 0.099 -9999 0 -0.37 40 40
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.044 0.15 -9999 0 -0.56 40 40
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.035 0.17 -9999 0 -0.58 40 40
MLLT4 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K -0.033 0.11 -9999 0 -0.4 41 41
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.42 238 238
positive regulation of lamellipodium assembly -0.038 0.098 -9999 0 -0.36 43 43
PVRL1 -0.27 0.29 -9999 0 -0.57 238 238
PVRL3 -0.059 0.2 -9999 0 -0.74 40 40
PVRL2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
CLDN1 -0.1 0.22 -9999 0 -0.58 88 88
JAM-A/CLDN1 -0.089 0.17 -9999 0 -0.48 41 41
SRC -0.079 0.19 -9999 0 -0.71 40 40
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
nectin-1(dimer)/I-afadin/I-afadin -0.2 0.21 -9999 0 -0.42 238 238
FARP2 -0.039 0.16 -9999 0 -0.57 40 40
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) -0.038 0.13 -9999 0 -0.48 40 40
nectin-1/I-afadin -0.2 0.21 -9999 0 -0.42 238 238
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
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 -0.2 0.21 -9999 0 -0.39 258 258
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 -0.035 0.092 -9999 0 -0.34 40 40
alphaV/beta3 Integrin/Talin -0.051 0.15 -9999 0 -0.52 38 38
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.052 0.16 -9999 0 -0.56 33 33
VAV2 -0.043 0.17 -9999 0 -0.58 43 43
RAP1/GDP -0.04 0.12 -9999 0 -0.43 40 40
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.038 0.13 -9999 0 -0.48 40 40
nectin-3(dimer)/I-afadin/I-afadin -0.044 0.15 -9999 0 -0.56 40 40
Rac1/GTP -0.046 0.12 -9999 0 -0.44 43 43
PTPRM -0.057 0.17 -9999 0 -0.45 64 64
E-cadherin/beta catenin/alpha catenin -0.12 0.13 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Arf6 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
CENTA1/KIF3B -0.015 0.089 -9999 0 -0.51 15 15
ARNO/beta Arrestin1-2 -0.17 0.24 -9999 0 -0.7 50 50
EGFR -0.023 0.12 -9999 0 -0.63 18 18
EPHA2 -0.004 0.057 -9999 0 -0.74 3 3
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.027 0.12 -9999 0 -0.5 27 27
ARRB2 0.008 0.011 -9999 0 -0.22 1 1
mol:GTP 0.015 0.024 -9999 0 -0.15 7 7
ARRB1 -0.14 0.29 -9999 0 -0.74 98 98
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.017 0.098 -9999 0 -0.57 15 15
EGF -0.014 0.097 -9999 0 -0.69 10 10
somatostatin receptor activity 0 0 -9999 0 -0.001 128 128
ARAP2 -0.001 0.033 -9999 0 -0.74 1 1
mol:GDP -0.12 0.15 -9999 0 -0.33 139 139
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 81 81
ITGA2B -0.022 0.13 -9999 0 -0.74 15 15
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.033 -9999 0 -0.43 3 3
ADAP1 -0.012 0.092 -9999 0 -0.74 8 8
KIF13B -0.012 0.092 -9999 0 -0.74 8 8
HGF/MET -0.12 0.23 -9999 0 -0.56 111 111
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.32 129 129
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.023 0.099 -9999 0 -0.42 27 27
ADRB2 -0.21 0.33 -9999 0 -0.74 143 143
receptor agonist activity 0 0 -9999 0 0 154 154
actin filament binding 0 0 -9999 0 -0.001 147 147
SRC 0 0 -9999 0 -10000 0 0
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
GNAQ 0 0.033 -9999 0 -0.74 1 1
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 106 106
ARF6/GDP -0.013 0.07 -9999 0 -0.35 3 3
ARF6/GDP/GULP/ACAP1 -0.11 0.14 -9999 0 -0.42 46 46
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.022 0.096 -9999 0 -0.43 26 26
ACAP1 -0.003 0.042 -9999 0 -0.66 2 2
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.014 -9999 0 -0.32 1 1
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.16 0.3 -9999 0 -0.74 108 108
CYTH3 0.01 0 -9999 0 -10000 0 0
CYTH2 0.005 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 110 110
endosomal lumen acidification 0 0 0 1 -0.001 91 92
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.013 0.098 -9999 0 -0.74 9 9
GNAQ/ARNO 0.004 0.02 -9999 0 -0.41 1 1
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 9 9
MET -0.004 0.053 -9999 0 -0.68 3 3
GNA14 -0.18 0.32 -9999 0 -0.74 123 123
GNA15 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 110 110
GNA11 0 0 -9999 0 -10000 0 0
LHCGR -0.001 0.026 -9999 0 -0.57 1 1
AGTR1 -0.3 0.36 -9999 0 -0.74 205 205
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.014 -9999 0 -0.32 1 1
IPCEF1/ARNO -0.017 0.078 -9999 0 -0.74 1 1
alphaIIb/beta3 Integrin -0.029 0.12 -9999 0 -0.56 26 26
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.009 0.14 -10000 0 -10000 0 0
CRKL -0.014 0.15 -10000 0 -0.41 63 63
HRAS -0.06 0.14 -10000 0 -0.62 14 14
mol:PIP3 -0.025 0.14 -10000 0 -0.39 61 61
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.022 0.16 -10000 0 -0.43 63 63
FOXO3 -0.007 0.14 -10000 0 -0.37 61 61
AKT1 -0.016 0.14 -10000 0 -0.4 61 61
BAD -0.007 0.14 -10000 0 -0.37 61 61
megakaryocyte differentiation -0.051 0.21 -10000 0 -0.49 84 84
GSK3B -0.007 0.14 -10000 0 -0.37 61 61
RAF1 0.004 0.14 -10000 0 -0.48 14 14
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.022 0.16 -10000 0 -0.43 63 63
STAT1 -0.075 0.36 -10000 0 -1 63 63
HRAS/SPRED1 -0.048 0.11 -10000 0 -0.48 14 14
cell proliferation -0.021 0.15 -10000 0 -0.42 63 63
PIK3CA 0 0 -10000 0 -10000 0 0
TEC -0.003 0.046 -10000 0 -0.74 2 2
RPS6KB1 -0.022 0.16 -10000 0 -0.43 63 63
HRAS/SPRED2 -0.048 0.11 -10000 0 -0.48 14 14
LYN/TEC/p62DOK -0.053 0.14 -10000 0 -0.41 63 63
MAPK3 0.018 0.1 -10000 0 -0.32 13 13
STAP1 -0.044 0.2 -10000 0 -0.5 76 76
GRAP2 -0.044 0.18 -10000 0 -0.74 30 30
JAK2 -0.11 0.28 -10000 0 -0.85 63 63
STAT1 (dimer) -0.072 0.35 -10000 0 -0.99 63 63
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.054 0.14 -10000 0 -0.4 63 63
actin filament polymerization -0.021 0.15 -10000 0 -0.42 63 63
LYN -0.003 0.046 -10000 0 -0.74 2 2
STAP1/STAT5A (dimer) -0.049 0.25 -10000 0 -0.67 63 63
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.045 0.12 -10000 0 -10000 0 0
PI3K -0.05 0.13 -10000 0 -0.4 61 61
PTEN -0.003 0.046 -10000 0 -0.74 2 2
SCF/KIT/EPO/EPOR -0.1 0.44 -10000 0 -1.3 63 63
MAPK8 -0.022 0.16 -10000 0 -0.43 63 63
STAT3 (dimer) -0.021 0.15 -10000 0 -0.42 63 63
positive regulation of transcription 0.019 0.085 -10000 0 -0.3 1 1
mol:GDP -0.064 0.15 -10000 0 -0.66 14 14
PIK3C2B -0.022 0.16 -10000 0 -0.43 63 63
CBL/CRKL -0.007 0.14 -10000 0 -0.38 61 61
FER -0.022 0.16 -10000 0 -0.43 63 63
SH2B3 -0.024 0.16 -10000 0 -0.43 65 65
PDPK1 -0.016 0.13 -10000 0 -0.36 61 61
SNAI2 -0.022 0.16 -10000 0 -0.43 63 63
positive regulation of cell proliferation -0.045 0.26 -10000 0 -0.74 63 63
KITLG 0.013 0.005 -10000 0 -10000 0 0
cell motility -0.045 0.26 -10000 0 -0.74 63 63
PTPN6 0.004 0.011 -10000 0 -10000 0 0
EPOR 0.01 0.1 -10000 0 -10000 0 0
STAT5A (dimer) -0.032 0.22 -10000 0 -0.61 63 63
SOCS1 -0.001 0.033 -10000 0 -0.74 1 1
cell migration 0.036 0.18 0.44 76 -10000 0 76
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.002 0.063 -10000 0 -0.57 6 6
VAV1 -0.007 0.073 -10000 0 -0.74 5 5
GRB10 -0.022 0.16 -10000 0 -0.43 63 63
PTPN11 0.003 0.009 -10000 0 -10000 0 0
SCF/KIT -0.058 0.15 -10000 0 -0.46 63 63
GO:0007205 0 0.008 -10000 0 -10000 0 0
MAP2K1 0.015 0.11 -10000 0 -0.36 13 13
CBL 0 0 -10000 0 -10000 0 0
KIT -0.13 0.47 -10000 0 -1.4 63 63
MAP2K2 0.015 0.11 -10000 0 -0.36 13 13
SHC/Grb2/SOS1 -0.05 0.13 -10000 0 -0.4 61 61
STAT5A -0.035 0.22 -10000 0 -0.63 63 63
GRB2 0 0 -10000 0 -10000 0 0
response to radiation -0.021 0.15 -10000 0 -0.42 63 63
SHC/GRAP2 -0.033 0.13 -10000 0 -0.56 30 30
PTPRO -0.053 0.21 -10000 0 -0.5 84 84
SH2B2 -0.022 0.16 -10000 0 -0.43 63 63
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.037 0.18 -10000 0 -0.46 76 76
CREBBP 0.028 0.011 -10000 0 -10000 0 0
BCL2 0.01 0.1 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.44 -9999 0 -1.2 43 43
HDAC7 -0.006 0.013 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.34 -9999 0 -0.88 47 47
SMAD4 0 0.002 -9999 0 -10000 0 0
ID2 -0.2 0.44 -9999 0 -1.2 44 44
AP1 -0.07 0.18 -9999 0 -0.56 61 61
ABCG2 -0.25 0.5 -9999 0 -1.3 64 64
HIF1A -0.024 0.071 -9999 0 -10000 0 0
TFF3 -0.24 0.48 -9999 0 -1.2 52 52
GATA2 -0.073 0.23 -9999 0 -0.74 55 55
AKT1 -0.033 0.059 -9999 0 -10000 0 0
response to hypoxia -0.047 0.065 -9999 0 -10000 0 0
MCL1 -0.2 0.44 -9999 0 -1.2 43 43
NDRG1 -0.21 0.44 -9999 0 -1.2 45 45
SERPINE1 -0.2 0.44 -9999 0 -1.2 44 44
FECH -0.2 0.44 -9999 0 -1.2 43 43
FURIN -0.2 0.44 -9999 0 -1.2 43 43
NCOA2 0.008 0.034 -9999 0 -0.74 1 1
EP300 -0.024 0.09 -9999 0 -10000 0 0
HMOX1 -0.21 0.44 -9999 0 -1.2 44 44
BHLHE40 -0.2 0.44 -9999 0 -1.2 43 43
BHLHE41 -0.21 0.45 -9999 0 -1.2 45 45
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.033 0.084 -9999 0 -0.49 8 8
ENG 0.001 0.14 -9999 0 -0.83 9 9
JUN 0.008 0.005 -9999 0 -10000 0 0
RORA -0.2 0.44 -9999 0 -1.2 43 43
ABCB1 -0.2 0.44 -9999 0 -1.4 59 59
TFRC -0.2 0.44 -9999 0 -1.2 44 44
CXCR4 -0.2 0.44 -9999 0 -1.2 43 43
TF -0.23 0.46 -9999 0 -1.2 51 51
CITED2 -0.21 0.45 -9999 0 -1.2 43 43
HIF1A/ARNT -0.25 0.5 -9999 0 -1.4 50 50
LDHA -0.034 0.047 -9999 0 -10000 0 0
ETS1 -0.21 0.45 -9999 0 -1.2 45 45
PGK1 -0.2 0.44 -9999 0 -1.2 44 44
NOS2 -0.25 0.48 -9999 0 -1.2 58 58
ITGB2 -0.22 0.46 -9999 0 -1.3 48 48
ALDOA -0.2 0.44 -9999 0 -1.2 43 43
Cbp/p300/CITED2 -0.25 0.44 -9999 0 -1.2 48 48
FOS -0.082 0.25 -9999 0 -0.74 61 61
HK2 -0.2 0.44 -9999 0 -1.2 43 43
SP1 0.011 0.025 -9999 0 -10000 0 0
GCK -0.03 0.14 -9999 0 -0.74 1 1
HK1 -0.2 0.44 -9999 0 -1.2 43 43
NPM1 -0.2 0.44 -9999 0 -1.2 44 44
EGLN1 -0.2 0.44 -9999 0 -1.2 43 43
CREB1 0.017 0 -9999 0 -10000 0 0
PGM1 -0.2 0.44 -9999 0 -1.2 44 44
SMAD3 0 0.002 -9999 0 -10000 0 0
EDN1 -0.17 0.4 -9999 0 -1.2 53 53
IGFBP1 -0.21 0.44 -9999 0 -1.2 47 47
VEGFA -0.24 0.32 -9999 0 -0.83 40 40
HIF1A/JAB1 -0.018 0.029 -9999 0 -10000 0 0
CP -0.23 0.47 -9999 0 -1.3 47 47
CXCL12 -0.23 0.49 -9999 0 -1.3 52 52
COPS5 0.009 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.004 -9999 0 -10000 0 0
BNIP3 -0.2 0.44 -9999 0 -1.2 43 43
EGLN3 -0.25 0.47 -9999 0 -1.2 55 55
CA9 -0.43 0.47 -9999 0 -1.2 76 76
TERT -0.31 0.49 -9999 0 -1.2 62 62
ENO1 -0.2 0.44 -9999 0 -1.2 43 43
PFKL -0.2 0.44 -9999 0 -1.2 44 44
NCOA1 0.003 0.005 -9999 0 -10000 0 0
ADM -0.21 0.44 -9999 0 -1.2 44 44
ARNT -0.024 0.07 -9999 0 -10000 0 0
HNF4A 0.002 0.074 -9999 0 -0.58 8 8
ADFP -0.21 0.44 -9999 0 -1.2 47 47
SLC2A1 -0.44 0.36 -9999 0 -0.92 106 106
LEP -0.26 0.48 -9999 0 -1.2 60 60
HIF1A/ARNT/Cbp/p300 -0.21 0.35 -9999 0 -0.9 50 50
EPO -0.084 0.25 -9999 0 -0.83 3 3
CREBBP -0.024 0.09 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.26 0.38 -9999 0 -0.92 70 70
PFKFB3 -0.2 0.44 -9999 0 -1.2 43 43
NT5E -0.21 0.44 -9999 0 -1.2 43 43
TCGA08_p53

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
CDKN2A -0.19 0.22 -10000 0 -0.43 233 233
TP53 -0.052 0.058 -10000 0 -0.38 1 1
Senescence -0.051 0.058 -10000 0 -0.38 1 1
Apoptosis -0.051 0.058 -10000 0 -0.38 1 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.097 0.11 0.31 5 -0.43 1 6
MDM4 0 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.031 0.13 -9999 0 -0.56 28 28
alphaV beta3 Integrin -0.024 0.11 -9999 0 -0.49 24 24
PTK2 -0.19 0.23 -9999 0 -0.7 43 43
IGF1R 0 0 -9999 0 -10000 0 0
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
CDKN1B -0.22 0.29 -9999 0 -0.58 189 189
VEGFA 0 0 -9999 0 -10000 0 0
ILK -0.22 0.29 -9999 0 -0.58 189 189
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.21 0.27 -9999 0 -0.54 189 189
PTK2B 0.002 0.13 -9999 0 -0.8 7 7
alphaV/beta3 Integrin/JAM-A -0.17 0.22 -9999 0 -0.43 200 200
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.013 0.076 -9999 0 -0.48 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.016 0.081 -9999 0 -0.43 18 18
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.12 0.16 -9999 0 -0.66 20 20
alphaV/beta3 Integrin/Syndecan-1 -0.011 0.073 -9999 0 -0.48 12 12
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.041 0.14 -9999 0 -0.78 11 11
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.19 0.18 -9999 0 -0.59 11 11
RPS6KB1 -0.038 0.13 -9999 0 -0.72 11 11
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.1 0.18 -9999 0 -0.75 24 24
GPR124 -0.001 0.033 -9999 0 -0.74 1 1
MAPK1 -0.1 0.18 -9999 0 -0.75 24 24
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.31 0.25 -9999 0 -0.49 313 313
cell adhesion -0.014 0.073 -9999 0 -0.44 11 11
ANGPTL3 -0.005 0.051 -9999 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.027 0.11 -9999 0 -0.48 28 28
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.054 0.19 -9999 0 -0.74 37 37
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
IGF1 -0.028 0.14 -9999 0 -0.73 19 19
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.011 0.072 -9999 0 -0.47 12 12
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.004 0.057 -9999 0 -0.74 3 3
alphaV/beta3 Integrin/CD47 -0.013 0.078 -9999 0 -0.48 14 14
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.04 0.14 -9999 0 -0.5 40 40
CSF1 -0.006 0.066 -9999 0 -0.74 4 4
PIK3C2A -0.22 0.29 -9999 0 -0.58 189 189
PI4 Kinase/Pyk2 -0.16 0.21 -9999 0 -0.76 25 25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.033 0.14 -9999 0 -0.52 32 32
FAK1/Vinculin -0.14 0.18 -9999 0 -0.52 43 43
alphaV beta3/Integrin/ppsTEM5 -0.011 0.073 -9999 0 -0.48 12 12
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.28 0.36 -9999 0 -0.74 191 191
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.021 0.12 -9999 0 -0.74 14 14
F11R 0.004 0.095 -9999 0 -0.56 14 14
alphaV/beta3 Integrin/Lactadherin -0.01 0.07 -9999 0 -0.48 11 11
alphaV/beta3 Integrin/TGFBR2 -0.045 0.16 -9999 0 -0.55 41 41
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.038 -9999 0 -0.43 4 4
HSP90AA1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.01 0.064 -9999 0 -0.44 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.019 0.12 -9999 0 -0.74 13 13
alphaV/beta3 Integrin/Pyk2 -0.031 0.13 -9999 0 -0.8 7 7
SDC1 -0.001 0.033 -9999 0 -0.74 1 1
VAV3 0.031 0.043 -9999 0 -0.4 5 5
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.14 0.18 -9999 0 -0.53 39 39
cell migration -0.13 0.16 -9999 0 -0.49 32 32
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.15 0.2 -9999 0 -0.76 13 13
SPP1 -0.29 0.29 -9999 0 -0.57 255 255
KDR -0.041 0.17 -9999 0 -0.74 28 28
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 -0.46 0.36 -9999 0 -0.74 313 313
angiogenesis -0.11 0.22 -9999 0 -0.74 26 26
Rac1/GTP -0.004 0.036 -9999 0 -0.36 1 1
EDIL3 -0.046 0.18 -9999 0 -0.74 31 31
cell proliferation -0.045 0.16 -9999 0 -0.55 41 41
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.39 -9999 0 -1.2 51 51
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.036 0.12 -9999 0 -0.43 8 8
ATF2/c-Jun -0.01 0.098 -9999 0 -0.43 3 3
MAPK11 -0.036 0.12 -9999 0 -0.43 8 8
MITF -0.041 0.16 -9999 0 -0.37 86 86
MAPKAPK5 -0.032 0.15 -9999 0 -0.36 75 75
KRT8 -0.032 0.15 -9999 0 -0.36 75 75
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.054 0.18 -9999 0 -0.46 75 75
CEBPB -0.032 0.15 -9999 0 -0.36 75 75
SLC9A1 -0.032 0.15 -9999 0 -0.53 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.026 0.15 -9999 0 -0.52 8 8
p38alpha-beta/MNK1 -0.065 0.13 -9999 0 -0.58 8 8
JUN -0.009 0.098 -9999 0 -0.42 3 3
PPARGC1A -0.13 0.28 -9999 0 -0.56 102 102
USF1 -0.032 0.15 -9999 0 -0.36 75 75
RAB5/GDP/GDI1 -0.045 0.095 -9999 0 -0.4 8 8
NOS2 -0.097 0.32 -9999 0 -1.2 32 32
DDIT3 -0.032 0.15 -9999 0 -0.53 8 8
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.018 0.12 -9999 0 -0.44 8 8
p38alpha-beta/HBP1 -0.065 0.13 -9999 0 -0.58 8 8
CREB1 -0.03 0.15 -9999 0 -0.38 75 75
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.021 0.13 -9999 0 -0.52 8 8
RPS6KA4 -0.032 0.15 -9999 0 -0.53 8 8
PLA2G4A -0.025 0.14 -9999 0 -0.53 13 13
GDI1 -0.032 0.15 -9999 0 -0.36 75 75
TP53 -0.044 0.19 -9999 0 -0.46 75 75
RPS6KA5 -0.032 0.15 -9999 0 -0.36 75 75
ESR1 -0.055 0.2 -9999 0 -0.43 90 90
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.044 0.18 -9999 0 -0.4 84 84
MEF2A -0.032 0.15 -9999 0 -0.53 8 8
EIF4EBP1 -0.032 0.16 -9999 0 -0.38 75 75
KRT19 -0.038 0.17 -9999 0 -0.4 77 77
ELK4 -0.032 0.15 -9999 0 -0.53 8 8
ATF6 -0.032 0.15 -9999 0 -0.53 8 8
ATF1 -0.03 0.15 -9999 0 -0.38 75 75
p38alpha-beta/MAPKAPK2 -0.065 0.13 -9999 0 -0.58 8 8
p38alpha-beta/MAPKAPK3 -0.065 0.13 -9999 0 -0.58 8 8
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.011 0.037 -9999 0 -0.53 1 1
NFATC2 -0.06 0.18 -9999 0 -0.51 70 70
NFATC3 0.012 0.028 -9999 0 -10000 0 0
CD40LG -0.17 0.38 -9999 0 -0.78 115 115
PTGS2 -0.14 0.34 -9999 0 -0.71 102 102
JUNB -0.001 0.033 -9999 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.011 -9999 0 -10000 0 0
CALM1 -0.001 0.003 -9999 0 -10000 0 0
JUN -0.001 0.003 -9999 0 -10000 0 0
mol:Ca2+ -0.006 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.003 0.044 -9999 0 -0.57 3 3
CREM 0 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.1 0.17 -9999 0 -0.56 46 46
FOS -0.091 0.24 -9999 0 -0.74 61 61
IFNG -0.11 0.29 -9999 0 -0.63 80 80
AP-1/NFAT1-c-4 -0.21 0.3 -9999 0 -0.75 93 93
FASLG -0.12 0.31 -9999 0 -0.69 79 79
NFAT1-c-4/ICER1 -0.082 0.16 -9999 0 -0.5 47 47
IL2RA -0.11 0.29 -9999 0 -0.64 81 81
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.14 0.34 -9999 0 -0.7 98 98
JunB/Fra1/NFAT1-c-4 -0.08 0.15 -9999 0 -0.49 45 45
IL4 -0.11 0.29 -9999 0 -0.63 77 77
IL2 -0.004 0.014 -9999 0 -10000 0 0
IL3 -0.019 0.023 -9999 0 -10000 0 0
FKBP1A 0 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0 0.003 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.034 0.11 -10000 0 -0.48 15 15
fibroblast growth factor receptor signaling pathway -0.033 0.11 -10000 0 -0.47 15 15
LAMA1 -0.17 0.26 -10000 0 -0.58 146 146
PRNP 0 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.14 0.25 -10000 0 -0.56 130 130
SMAD2 -0.023 0.14 -10000 0 -0.43 37 37
GPC1/PrPc/Cu2+ -0.02 0.081 -10000 0 -0.35 28 28
GPC1/Laminin alpha1 -0.14 0.22 -10000 0 -0.45 158 158
TDGF1 -0.003 0.044 -10000 0 -0.57 3 3
CRIPTO/GPC1 -0.026 0.1 -10000 0 -0.42 31 31
APP/GPC1 -0.023 0.095 -10000 0 -0.42 28 28
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.089 -10000 0 -10000 0 0
FLT1 0 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.055 0.14 -10000 0 -0.42 65 65
SERPINC1 -0.007 0.063 -10000 0 -0.57 6 6
FYN -0.002 0.092 -10000 0 -0.48 1 1
FGR -0.037 0.16 -10000 0 -0.48 43 43
positive regulation of MAPKKK cascade -0.001 0.12 -10000 0 -0.6 6 6
SLIT2 -0.16 0.3 -10000 0 -0.74 110 110
GPC1/NRG -0.04 0.13 -10000 0 -0.46 43 43
NRG1 -0.022 0.13 -10000 0 -0.74 15 15
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.019 0.08 -10000 0 -10000 0 0
LYN -0.003 0.094 -10000 0 -0.48 2 2
mol:Spermine -0.014 0.1 -10000 0 -0.42 28 28
cell growth -0.033 0.11 -10000 0 -0.47 15 15
BMP signaling pathway 0.032 0.13 0.57 28 -10000 0 28
SRC -0.001 0.089 -10000 0 -10000 0 0
TGFBR1 0 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.22 0.34 -10000 0 -0.74 152 152
GPC1 -0.032 0.13 -10000 0 -0.57 28 28
TGFBR1 (dimer) 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.024 0.13 -10000 0 -0.44 26 26
HCK -0.007 0.1 -10000 0 -0.48 6 6
FGF2 -0.021 0.12 -10000 0 -0.74 14 14
FGFR1 -0.001 0.033 -10000 0 -0.74 1 1
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
TGFBR2 -0.054 0.19 -10000 0 -0.74 37 37
cell death -0.023 0.095 -10000 0 -0.41 28 28
ATIII/GPC1 -0.028 0.1 -10000 0 -0.42 34 34
PLA2G2A/GPC1 -0.19 0.27 -10000 0 -0.56 169 169
LCK -0.002 0.092 -10000 0 -0.48 1 1
neuron differentiation -0.04 0.13 -10000 0 -0.46 43 43
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.054 0.19 -10000 0 -0.74 37 37
Nongenotropic Androgen signaling

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
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.095 0.18 -10000 0 -0.44 109 109
regulation of S phase of mitotic cell cycle -0.062 0.13 -10000 0 -0.32 18 18
GNAO1 -0.004 0.049 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
MAP2K1 -0.049 0.16 -10000 0 -0.46 18 18
T-DHT/AR -0.12 0.23 -10000 0 -0.56 103 103
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 61 61
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.033 -10000 0 -0.74 1 1
mol:GDP -0.11 0.22 -10000 0 -0.55 103 103
cell proliferation -0.058 0.2 -10000 0 -0.65 18 18
PIK3CA 0 0 -10000 0 -10000 0 0
FOS -0.09 0.3 -10000 0 -0.86 61 61
mol:Ca2+ -0.012 0.022 -10000 0 -0.069 26 26
MAPK3 -0.052 0.18 -10000 0 -0.58 18 18
MAPK1 -0.022 0.096 -10000 0 -0.3 18 18
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 61 61
cAMP biosynthetic process 0.011 0.021 -10000 0 -10000 0 0
GNG2 -0.007 0.073 -10000 0 -0.74 5 5
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 61 61
HRAS/GTP -0.084 0.16 -10000 0 -0.4 103 103
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 61 61
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.048 0.18 0.45 61 -10000 0 61
T-DHT/AR/PELP1 -0.1 0.2 -10000 0 -0.49 103 103
HRAS/GDP -0.11 0.21 -10000 0 -0.52 103 103
CREB1 -0.053 0.19 -10000 0 -0.48 61 61
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.15 0.3 -10000 0 -0.74 103 103
GNB1 -0.001 0.033 -10000 0 -0.74 1 1
RAF1 -0.056 0.17 -10000 0 -0.46 18 18
RAC1-CDC42/GDP -0.1 0.2 -10000 0 -0.5 103 103
T-DHT/AR/PELP1/Src -0.091 0.18 -10000 0 -0.44 103 103
MAP2K2 -0.049 0.16 -10000 0 -0.46 18 18
T-DHT/AR/PELP1/Src/PI3K -0.063 0.13 -10000 0 -0.32 18 18
GNAZ -0.009 0.08 -10000 0 -0.74 6 6
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.023 0.064 -10000 0 -0.62 3 3
mol:T-DHT 0 0.001 0.001 18 -0.003 43 61
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.007 0.036 -10000 0 -0.56 2 2
Gi family/GTP -0.042 0.084 -10000 0 -0.36 8 8
CDC42 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.26 0.34 -10000 0 -0.83 52 52
PCK1 -0.13 0.21 -10000 0 -0.76 15 15
HNF4A -0.31 0.4 -10000 0 -1.1 48 48
KCNJ11 -0.27 0.38 -10000 0 -1 37 37
AKT1 0 0.088 -10000 0 -10000 0 0
response to starvation -0.01 0.034 -10000 0 -10000 0 0
DLK1 -0.29 0.37 -10000 0 -0.95 46 46
NKX2-1 -0.77 0.79 -10000 0 -1.5 260 260
ACADM -0.26 0.34 -10000 0 -0.83 53 53
TAT -0.12 0.19 -10000 0 -0.73 10 10
CEBPB 0.003 0.006 -10000 0 -10000 0 0
CEBPA 0.002 0.034 -10000 0 -0.74 1 1
TTR -0.052 0.19 -10000 0 -0.79 16 16
PKLR -0.27 0.34 -10000 0 -0.85 54 54
APOA1 -0.43 0.56 -10000 0 -1.4 87 87
CPT1C -0.26 0.34 -10000 0 -0.84 48 48
ALAS1 -0.11 0.18 -10000 0 -10000 0 0
TFRC -0.16 0.25 -10000 0 -0.87 11 11
FOXF1 0 0.24 0.28 5 -0.62 58 63
NF1 0.016 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.012 0.081 -10000 0 -0.6 8 8
CPT1A -0.26 0.34 -10000 0 -0.84 51 51
HMGCS1 -0.26 0.34 -10000 0 -0.83 53 53
NR3C1 0.017 0.012 -10000 0 -10000 0 0
CPT1B -0.26 0.34 -10000 0 -0.83 53 53
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.005 0.029 -10000 0 -10000 0 0
GCK -0.26 0.34 -10000 0 -0.84 55 55
CREB1 0.007 0.017 -10000 0 -10000 0 0
IGFBP1 -0.12 0.17 -10000 0 -0.65 4 4
PDX1 -0.17 0.24 -10000 0 -0.69 19 19
UCP2 -0.26 0.34 -10000 0 -0.85 43 43
ALDOB -0.26 0.36 -10000 0 -0.91 32 32
AFP 0.017 0.14 -10000 0 -0.68 5 5
BDH1 -0.26 0.34 -10000 0 -0.84 52 52
HADH -0.26 0.36 -10000 0 -0.89 32 32
F2 -0.34 0.42 -10000 0 -1 59 59
HNF1A -0.012 0.082 -10000 0 -0.6 8 8
G6PC 0.01 0.088 -10000 0 -0.74 1 1
SLC2A2 -0.17 0.23 -10000 0 -0.87 2 2
INS -0.009 0.011 -10000 0 -10000 0 0
FOXA1 0.072 0.14 0.37 9 -0.57 11 20
FOXA3 -0.009 0.15 -10000 0 -0.72 17 17
FOXA2 -0.31 0.41 -10000 0 -0.9 70 70
ABCC8 -0.28 0.38 -10000 0 -1 33 33
ALB 0.025 0.13 -10000 0 -0.66 5 5
IL23-mediated signaling events

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
CCL2 -0.14 0.44 -10000 0 -1.1 57 57
IL23A -0.14 0.43 -10000 0 -1.2 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.21 0.36 -10000 0 -1.1 52 52
positive regulation of T cell mediated cytotoxicity -0.15 0.46 -10000 0 -1.2 52 52
ITGA3 -0.13 0.41 -10000 0 -1.1 54 54
IL17F -0.064 0.28 -10000 0 -0.74 30 30
IL12B 0.016 0.025 -10000 0 -10000 0 0
STAT1 (dimer) -0.21 0.38 -10000 0 -1.1 52 52
CD4 -0.13 0.43 -10000 0 -1.1 54 54
IL23 -0.15 0.41 -10000 0 -1.2 38 38
IL23R 0.003 0.085 -10000 0 -10000 0 0
IL1B -0.14 0.44 -10000 0 -1.2 40 40
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.13 0.4 -10000 0 -1 52 52
TYK2 0.011 0.019 -10000 0 -10000 0 0
STAT4 -0.012 0.092 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
IL18RAP -0.023 0.15 -10000 0 -0.74 21 21
IL12RB1 -0.038 0.19 -10000 0 -0.77 32 32
PIK3CA 0 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.026 0.15 -10000 0 -0.59 32 32
IL23R/JAK2 0.002 0.1 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.15 0.46 -10000 0 -1.2 52 52
natural killer cell activation 0 0.007 -10000 0 -10000 0 0
JAK2 0.018 0.023 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
NFKB1 0.006 0.006 -10000 0 -10000 0 0
RELA 0.006 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.14 0.39 -10000 0 -1.1 38 38
ALOX12B -0.17 0.42 -10000 0 -1.1 53 53
CXCL1 -0.15 0.46 -10000 0 -1.2 59 59
T cell proliferation -0.15 0.46 -10000 0 -1.2 52 52
NFKBIA 0.006 0.006 -10000 0 -10000 0 0
IL17A -0.043 0.24 -10000 0 -0.59 22 22
PI3K -0.21 0.36 -10000 0 -1.1 52 52
IFNG 0 0.028 0.099 1 -0.11 16 17
STAT3 (dimer) -0.2 0.34 -10000 0 -1 51 51
IL18R1 0 0.074 -10000 0 -0.73 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.062 0.28 -10000 0 -0.79 27 27
IL18/IL18R -0.026 0.12 -10000 0 -0.54 25 25
macrophage activation -0.012 0.017 -10000 0 -0.045 25 25
TNF -0.15 0.45 -10000 0 -1.2 49 49
STAT3/STAT4 -0.21 0.36 -10000 0 -1.1 53 53
STAT4 (dimer) -0.22 0.39 -10000 0 -1.2 53 53
IL18 0.003 0.058 -10000 0 -0.74 3 3
IL19 -0.13 0.4 -10000 0 -1 53 53
STAT5A (dimer) -0.21 0.38 -10000 0 -1.1 52 52
STAT1 0 0 -10000 0 -10000 0 0
SOCS3 -0.003 0.046 -10000 0 -0.74 2 2
CXCL9 -0.14 0.43 -10000 0 -1.1 54 54
MPO -0.15 0.46 -10000 0 -1.2 65 65
positive regulation of humoral immune response -0.15 0.46 -10000 0 -1.2 52 52
IL23/IL23R/JAK2/TYK2 -0.16 0.52 -10000 0 -1.3 52 52
IL6 -0.24 0.58 -10000 0 -1.3 98 98
STAT5A 0 0 -10000 0 -10000 0 0
IL2 0.006 0.008 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.007 -10000 0 -10000 0 0
CD3E -0.12 0.41 -10000 0 -1.1 43 43
keratinocyte proliferation -0.15 0.46 -10000 0 -1.2 52 52
NOS2 -0.17 0.48 -10000 0 -1.2 65 65
Canonical Wnt signaling pathway

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
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.003 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 -10000 0 -10000 0 0
SMAD4 0 0 -10000 0 -10000 0 0
DKK2 -0.14 0.29 -10000 0 -0.74 93 93
TLE1 0.002 0.031 -10000 0 -0.61 1 1
MACF1 0.004 0.047 -10000 0 -0.74 2 2
CTNNB1 0.066 0.099 0.29 10 -10000 0 10
WIF1 -0.47 0.36 -10000 0 -0.74 318 318
beta catenin/RanBP3 0.002 0.091 0.44 15 -10000 0 15
KREMEN2 -0.37 0.28 -10000 0 -0.57 325 325
DKK1 -0.039 0.15 -10000 0 -0.62 31 31
beta catenin/beta TrCP1 0.068 0.093 0.28 10 -10000 0 10
FZD1 0.004 0.005 -10000 0 -10000 0 0
AXIN2 -0.036 0.28 -10000 0 -1.5 17 17
AXIN1 0.008 0.005 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.092 0.054 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.02 0.063 0.24 30 -10000 0 30
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.042 -10000 0 -10000 0 0
HNF1A -0.006 0.075 -10000 0 -0.58 8 8
CTBP1 0.004 0.017 -10000 0 -10000 0 0
MYC 0.008 0.048 -10000 0 -10000 0 0
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.31 0.25 -10000 0 -0.71 94 94
NKD1 -0.071 0.22 -10000 0 -0.72 49 49
TCF4 -0.001 0.058 -10000 0 -0.72 3 3
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.002 0.023 -10000 0 -10000 0 0
Ran/GTP 0 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.017 0.094 0.45 21 -10000 0 21
LEF1 0.002 0.031 -10000 0 -0.58 1 1
DVL1 0.08 0.061 -10000 0 -10000 0 0
CSNK2A1 0.003 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.097 0.071 -10000 0 -0.56 1 1
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.68 25 25
LRP6 0.007 0.005 -10000 0 -10000 0 0
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.01 0.002 -10000 0 -10000 0 0
CCND1 -0.008 0.17 -10000 0 -1.5 6 6
WNT1 0.003 0.045 -10000 0 -0.57 3 3
GSK3A 0.008 0.005 -10000 0 -10000 0 0
GSK3B 0.003 0.004 -10000 0 -10000 0 0
FRAT1 -0.001 0.033 -10000 0 -0.74 1 1
PPP2R5D 0.076 0.1 0.37 49 -10000 0 49
APC 0 0.023 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.16 0.12 0.26 315 -10000 0 315
CREBBP 0.004 0.017 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.002 0.004 -9999 0 -10000 0 0
SVIL 0.002 0.004 -9999 0 -10000 0 0
ZNF318 0 0.005 -9999 0 -10000 0 0
JMJD2C -0.004 0.026 -9999 0 -0.081 50 50
T-DHT/AR/Ubc9 -0.13 0.2 -9999 0 -0.52 103 103
CARM1 0 0 -9999 0 -10000 0 0
PRDX1 0 0.001 -9999 0 -10000 0 0
PELP1 0 0.001 -9999 0 -10000 0 0
CTNNB1 0.001 0.004 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
PTK2B 0.001 0.004 -9999 0 -10000 0 0
MED1 0 0.002 -9999 0 -10000 0 0
MAK -0.066 0.21 -9999 0 -0.74 45 45
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.002 0.004 -9999 0 -10000 0 0
GSN 0.002 0.004 -9999 0 -10000 0 0
NCOA2 -0.001 0.033 -9999 0 -0.74 1 1
NCOA6 0.002 0.004 -9999 0 -10000 0 0
DNA-PK 0 0.006 -9999 0 -10000 0 0
NCOA4 0 0 -9999 0 -10000 0 0
PIAS3 0.001 0.004 -9999 0 -10000 0 0
cell proliferation -0.11 0.27 -9999 0 -0.94 45 45
XRCC5 0 0.002 -9999 0 -10000 0 0
UBE3A 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.14 0.22 -9999 0 -0.54 114 114
FHL2 -0.054 0.08 -9999 0 -0.56 2 2
RANBP9 0.002 0.004 -9999 0 -10000 0 0
JMJD1A -0.034 0.07 -9999 0 -0.13 162 162
CDK6 -0.002 0.036 -9999 0 -0.57 2 2
TGFB1I1 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.14 0.21 -9999 0 -0.53 108 108
XRCC6 0 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.24 -9999 0 -0.55 104 104
CTDSP1 0.001 0.004 -9999 0 -10000 0 0
CTDSP2 0 0.004 -9999 0 -10000 0 0
BRCA1 0.002 0.004 -9999 0 -10000 0 0
TCF4 -0.004 0.057 -9999 0 -0.74 3 3
CDKN2A -0.27 0.29 -9999 0 -0.58 233 233
SRF 0.016 0.007 -9999 0 -10000 0 0
NKX3-1 -0.11 0.14 -9999 0 -0.95 2 2
KLK3 0.031 0.054 -9999 0 -10000 0 0
TMF1 0.001 0.003 -9999 0 -10000 0 0
HNRNPA1 0 0.002 -9999 0 -10000 0 0
AOF2 0 0.002 -9999 0 -10000 0 0
APPL1 0.02 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.13 0.21 -9999 0 -0.52 103 103
AR -0.16 0.31 -9999 0 -0.76 103 103
UBA3 0.001 0.004 -9999 0 -10000 0 0
PATZ1 0 0.002 -9999 0 -10000 0 0
PAWR 0.001 0.003 -9999 0 -10000 0 0
PRKDC 0 0.002 -9999 0 -10000 0 0
PA2G4 0 0.003 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.12 0.19 -9999 0 -0.48 103 103
RPS6KA3 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.13 0.2 -9999 0 -0.52 103 103
LATS2 0 0.002 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.12 0.19 -9999 0 -0.48 103 103
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0 0.033 -9999 0 -0.74 1 1
KLK2 -0.093 0.14 -9999 0 -0.51 28 28
CASP8 0 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.48 104 104
TMPRSS2 -0.4 0.54 -9999 0 -1.2 161 161
CCND1 -0.01 0.084 -9999 0 -0.71 7 7
PIAS1 0.002 0.004 -9999 0 -10000 0 0
mol:T-DHT -0.019 0.036 -9999 0 -0.078 118 118
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.002 0.005 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.21 -9999 0 -0.52 105 105
CMTM2 -0.09 0.24 -9999 0 -0.74 61 61
SNURF -0.024 0.13 -9999 0 -0.74 16 16
ZMIZ1 -0.007 0.047 -9999 0 -0.8 1 1
CCND3 0 0.001 -9999 0 -10000 0 0
TGIF1 0 0.002 -9999 0 -10000 0 0
FKBP4 0 0.026 -9999 0 -0.57 1 1
IL6-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
BCL2L1 -0.14 0.25 -10000 0 -0.76 12 12
CRP -0.15 0.25 -10000 0 -0.74 15 15
cell cycle arrest -0.17 0.28 -10000 0 -0.66 57 57
TIMP1 -0.11 0.21 -10000 0 -0.66 8 8
IL6ST -0.018 0.14 -10000 0 -0.74 18 18
Rac1/GDP -0.064 0.19 -10000 0 -0.69 21 21
AP1 -0.007 0.16 -10000 0 -0.55 15 15
GAB2 -0.004 0.12 -10000 0 -0.73 14 14
TNFSF11 -0.16 0.26 -10000 0 -0.71 23 23
HSP90B1 0 0.05 -10000 0 -10000 0 0
GAB1 0.014 0.008 -10000 0 -10000 0 0
MAPK14 -0.028 0.17 -10000 0 -0.72 17 17
AKT1 0.042 0.057 -10000 0 -10000 0 0
FOXO1 0.049 0.053 -10000 0 -10000 0 0
MAP2K6 -0.051 0.18 -10000 0 -0.52 38 38
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.075 0.2 -10000 0 -0.71 18 18
MITF -0.069 0.19 -10000 0 -0.47 67 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0 0 -10000 0 -10000 0 0
A2M -0.47 0.69 -10000 0 -1.5 165 165
CEBPB 0.016 0.004 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.029 0.12 0.22 30 -0.62 6 36
STAT3 -0.18 0.29 -10000 0 -0.69 57 57
STAT1 -0.007 0.016 -10000 0 -10000 0 0
CEBPD -0.14 0.25 -10000 0 -0.82 13 13
PIK3CA 0.01 0.003 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
JUN 0.006 0.005 -10000 0 -10000 0 0
PIAS3/MITF -0.085 0.17 -10000 0 -0.61 27 27
MAPK11 -0.028 0.17 -10000 0 -0.72 17 17
STAT3 (dimer)/FOXO1 -0.19 0.31 -10000 0 -0.76 58 58
GRB2/SOS1/GAB family -0.03 0.17 -10000 0 -0.67 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.051 0.19 -10000 0 -0.46 62 62
GRB2 0.014 0.008 -10000 0 -10000 0 0
JAK2 0 0 -10000 0 -10000 0 0
LBP -0.11 0.21 -10000 0 -0.68 7 7
PIK3R1 0.008 0.005 -10000 0 -10000 0 0
JAK1 0.011 0.005 -10000 0 -10000 0 0
MYC -0.14 0.25 -10000 0 -0.75 13 13
FGG -0.48 0.57 -10000 0 -1.1 234 234
macrophage differentiation -0.17 0.28 -10000 0 -0.66 57 57
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.089 0.2 -10000 0 -0.52 66 66
JUNB -0.14 0.24 -10000 0 -0.74 14 14
FOS -0.084 0.24 -10000 0 -0.74 61 61
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.07 0.19 -10000 0 -0.49 63 63
STAT1/PIAS1 -0.084 0.18 -10000 0 -0.47 57 57
GRB2/SOS1/GAB family/SHP2/PI3K 0.02 0.061 -10000 0 -0.31 1 1
STAT3 (dimer) -0.18 0.29 -10000 0 -0.68 57 57
PRKCD -0.09 0.22 -10000 0 -0.74 16 16
IL6R -0.004 0.1 -10000 0 -0.74 10 10
SOCS3 -0.014 0.17 -10000 0 -0.7 17 17
gp130 (dimer)/JAK1/JAK1/LMO4 -0.011 0.092 -10000 0 -0.46 19 19
Rac1/GTP -0.1 0.17 -10000 0 -0.55 41 41
HCK -0.004 0.081 -10000 0 -0.74 6 6
MAPKKK cascade 0.044 0.13 -10000 0 -0.56 14 14
bone resorption -0.15 0.25 -10000 0 -0.64 33 33
IRF1 -0.14 0.25 -10000 0 -0.76 12 12
mol:GDP -0.065 0.19 -10000 0 -0.49 60 60
SOS1 0.015 0.013 -10000 0 -10000 0 0
VAV1 -0.068 0.2 -10000 0 -0.5 60 60
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.043 0.18 -10000 0 -0.77 19 19
PTPN11 -0.006 0.014 -10000 0 -10000 0 0
IL6/IL6RA -0.098 0.23 -10000 0 -0.59 86 86
gp130 (dimer)/TYK2/TYK2/LMO4 -0.014 0.091 -10000 0 -0.47 19 19
gp130 (dimer)/JAK2/JAK2/LMO4 -0.014 0.091 -10000 0 -0.47 19 19
IL6 -0.11 0.28 -10000 0 -0.74 82 82
PIAS3 0 0 -10000 0 -10000 0 0
PTPRE 0.011 0.049 -10000 0 -0.73 2 2
PIAS1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.075 0.18 -10000 0 -0.43 76 76
LMO4 0.007 0.029 -10000 0 -0.6 1 1
STAT3 (dimer)/PIAS3 -0.21 0.23 -10000 0 -0.66 57 57
MCL1 0.05 0.051 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.016 0.13 -9999 0 -0.5 33 33
ADCY5 -0.028 0.15 -9999 0 -0.49 45 45
ADCY6 0.015 0.039 -9999 0 -0.48 3 3
ADCY7 0.017 0.022 -9999 0 -0.48 1 1
ADCY1 0.016 0.032 -9999 0 -0.48 2 2
ADCY2 -0.025 0.13 -9999 0 -0.41 50 50
ADCY3 0.017 0.022 -9999 0 -0.48 1 1
ADCY8 -0.14 0.23 -9999 0 -0.48 158 158
PRKCE 0.009 0.026 -9999 0 -0.56 1 1
ADCY9 0.016 0.032 -9999 0 -0.48 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.069 0.13 -9999 0 -0.44 27 27
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0 0 -10000 0 -10000 0 0
HDAC1 0.001 0.005 -10000 0 -10000 0 0
AES 0 0.002 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.002 0.036 -10000 0 -0.57 2 2
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 -0.001 0.032 -10000 0 -0.73 1 1
AP1 -0.08 0.19 -10000 0 -0.43 92 92
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 0 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.002 0.042 -10000 0 -0.55 1 1
NICD/RBPSUH 0 0 -10000 0 -10000 0 0
WIF1 -0.47 0.36 -10000 0 -0.74 318 318
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0 0 -10000 0 -10000 0 0
KREMEN2 -0.37 0.28 -10000 0 -0.57 325 325
DKK1 -0.039 0.15 -10000 0 -0.62 31 31
beta catenin/beta TrCP1 0.016 0.06 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 -0.004 0.026 0.3 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES -0.001 0.027 -10000 0 -10000 0 0
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.09 0.24 -10000 0 -0.74 61 61
JUN 0 0 -10000 0 -10000 0 0
MAP3K7 0 0.003 -10000 0 -10000 0 0
CTNNB1 0.01 0.065 0.22 16 -10000 0 16
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.31 0.25 -10000 0 -0.71 94 94
HNF1A -0.009 0.072 -10000 0 -0.58 8 8
CTBP1 0 0.002 -10000 0 -10000 0 0
MYC 0.002 0.012 -10000 0 -10000 0 0
NKD1 -0.071 0.22 -10000 0 -0.72 49 49
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
apoptosis -0.079 0.19 -10000 0 -0.42 92 92
Delta 1/NOTCHprecursor 0 0 -10000 0 -10000 0 0
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.002 0.012 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.004 0.026 0.3 1 -10000 0 1
DVL1 -0.045 0.043 -10000 0 -0.67 1 1
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.25 0.19 -10000 0 -0.68 25 25
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.001 0.006 -10000 0 -10000 0 0
CCND1 -0.015 0.16 -10000 0 -1.4 6 6
WNT1 -0.003 0.044 -10000 0 -0.58 3 3
Axin1/APC/beta catenin 0.011 0.045 0.27 1 -0.36 1 2
DKK2 -0.14 0.29 -10000 0 -0.74 93 93
NOTCH1 precursor/DVL1 -0.022 0.028 -10000 0 -0.55 1 1
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 -0.001 0.033 -10000 0 -0.74 1 1
NOTCH/Deltex homolog 1 -0.001 0.018 -10000 0 -10000 0 0
PPP2R5D 0.01 0.1 0.31 49 -0.25 1 50
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.28 0.21 -10000 0 -0.43 317 317
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.01 0.059 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.02 0.073 -9999 0 -10000 0 0
POMC -0.055 0.17 -9999 0 -0.59 47 47
EGFR -0.023 0.12 -9999 0 -0.63 18 18
Syndecan-3/EGFR -0.012 0.061 -9999 0 -0.4 6 6
AGRP -0.34 0.37 -9999 0 -0.74 233 233
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.04 0.15 -9999 0 -0.57 35 35
long-term memory -0.001 0.017 -9999 0 -0.38 1 1
Syndecan-3/IL8 -0.011 0.059 -9999 0 -0.4 4 4
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN -0.001 0.033 -9999 0 -0.74 1 1
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R -0.024 0.12 -9999 0 -0.57 21 21
SRC 0 0 -9999 0 -10000 0 0
PTN -0.021 0.12 -9999 0 -0.7 15 15
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.027 0.082 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.19 0.2 -9999 0 -0.4 233 233
Syndecan-3/AgRP/MC4R -0.19 0.2 -9999 0 -0.39 233 233
Fyn/Cortactin -0.001 0.025 -9999 0 -0.56 1 1
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.011 0.058 -9999 0 -0.4 4 4
IL8 -0.022 0.11 -9999 0 -0.61 18 18
Syndecan-3/Fyn/Cortactin -0.001 0.017 -9999 0 -0.38 1 1
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.057 0.15 -9999 0 -0.43 67 67
Gamma Secretase 0 0 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.001 0.093 -10000 0 -0.59 12 12
NFATC2 -0.054 0.3 -10000 0 -0.73 72 72
NFATC3 0.013 0.054 -10000 0 -10000 0 0
CD40LG -0.17 0.45 -10000 0 -1.1 70 70
ITCH -0.008 0.11 -10000 0 -10000 0 0
CBLB -0.008 0.11 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.28 -10000 0 -1 30 30
JUNB -0.001 0.033 -10000 0 -0.74 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.053 0.12 -10000 0 -0.33 3 3
T cell anergy -0.061 0.18 -10000 0 -0.46 77 77
TLE4 -0.021 0.23 -10000 0 -0.74 27 27
Jun/NFAT1-c-4/p21SNFT -0.12 0.27 -10000 0 -1.1 24 24
AP-1/NFAT1-c-4 -0.23 0.39 -10000 0 -1.3 38 38
IKZF1 -0.031 0.28 -10000 0 -0.94 27 27
T-helper 2 cell differentiation -0.045 0.28 -10000 0 -0.8 46 46
AP-1/NFAT1 -0.14 0.24 -10000 0 -0.6 74 74
CALM1 -0.028 0.064 -10000 0 -10000 0 0
EGR2 -0.022 0.33 -10000 0 -1.4 17 17
EGR3 -0.024 0.33 -10000 0 -1.5 17 17
NFAT1/FOXP3 -0.09 0.21 -10000 0 -0.73 26 26
EGR1 -0.007 0.11 -10000 0 -0.74 11 11
JUN 0.003 0.022 -10000 0 -10000 0 0
EGR4 -0.005 0.086 -10000 0 -0.58 11 11
mol:Ca2+ -0.032 0.073 -10000 0 -10000 0 0
GBP3 -0.038 0.28 -10000 0 -0.89 32 32
FOSL1 -0.003 0.044 -10000 0 -0.57 3 3
NFAT1-c-4/MAF/IRF4 -0.099 0.27 -10000 0 -1.1 22 22
DGKA -0.018 0.23 -10000 0 -0.76 22 22
CREM 0 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.3 -10000 0 -1.1 29 29
CTLA4 -0.017 0.21 -10000 0 -0.78 16 16
NFAT1-c-4 (dimer)/EGR1 -0.11 0.29 -10000 0 -1.2 22 22
NFAT1-c-4 (dimer)/EGR4 -0.11 0.27 -10000 0 -1.1 24 24
FOS -0.088 0.25 -10000 0 -0.74 61 61
IFNG -0.16 0.35 -10000 0 -0.89 71 71
T cell activation -0.04 0.24 -10000 0 -0.79 22 22
MAF 0 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.003 0.2 0.82 15 -10000 0 15
TNF -0.037 0.3 -10000 0 -1 26 26
FASLG -0.089 0.46 -10000 0 -1.6 36 36
TBX21 -0.062 0.23 -10000 0 -0.74 51 51
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.059 0.22 -10000 0 -0.74 47 47
PTPN1 -0.018 0.23 -10000 0 -0.76 22 22
NFAT1-c-4/ICER1 -0.1 0.27 -10000 0 -1.1 23 23
GATA3 -0.023 0.13 -10000 0 -0.71 17 17
T-helper 1 cell differentiation -0.15 0.34 -10000 0 -0.83 78 78
IL2RA -0.15 0.28 -10000 0 -0.82 55 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.23 -10000 0 -0.76 22 22
E2F1 0.015 0.004 -10000 0 -10000 0 0
PPARG -0.084 0.23 -10000 0 -0.74 57 57
SLC3A2 -0.018 0.23 -10000 0 -0.74 24 24
IRF4 -0.009 0.08 -10000 0 -0.74 6 6
PTGS2 -0.15 0.41 -10000 0 -1.1 54 54
CSF2 -0.14 0.41 -10000 0 -1.1 46 46
JunB/Fra1/NFAT1-c-4 -0.097 0.25 -10000 0 -1.1 21 21
IL4 -0.049 0.3 -10000 0 -0.85 46 46
IL5 -0.11 0.36 -10000 0 -1.1 35 35
IL2 -0.041 0.24 -10000 0 -0.81 22 22
IL3 -0.037 0.048 -10000 0 -10000 0 0
RNF128 -0.097 0.31 -10000 0 -0.8 81 81
NFATC1 0.002 0.2 -10000 0 -0.83 15 15
CDK4 0.008 0.16 0.68 5 -10000 0 5
PTPRK -0.018 0.23 -10000 0 -0.72 26 26
IL8 -0.12 0.37 -10000 0 -1.1 36 36
POU2F1 0 0.003 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.08 0.12 -10000 0 -0.52 19 19
epithelial cell differentiation -0.036 0.1 -10000 0 -0.57 9 9
ITCH 0.023 0.027 -10000 0 -10000 0 0
WWP1 -0.038 0.088 -10000 0 -10000 0 0
FYN -0.001 0.033 -10000 0 -0.74 1 1
EGFR -0.023 0.12 -10000 0 -0.63 18 18
PRL -0.009 0.072 -10000 0 -0.57 8 8
neuron projection morphogenesis 0.002 0.089 -10000 0 -10000 0 0
PTPRZ1 -0.38 0.27 -10000 0 -0.58 332 332
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.043 0.077 -10000 0 -0.48 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.057 0.097 -10000 0 -0.49 15 15
ADAM17 0.023 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.058 0.11 -10000 0 -0.49 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.18 0.22 -10000 0 -0.53 131 131
NCOR1 0 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.053 0.091 -10000 0 -0.47 16 16
GRIN2B -0.028 0.1 -10000 0 -0.52 8 8
ErbB4/ErbB2/betacellulin -0.072 0.13 -10000 0 -0.54 21 21
STAT1 0 0 -10000 0 -10000 0 0
HBEGF -0.026 0.14 -10000 0 -0.74 18 18
PRLR -0.04 0.16 -10000 0 -0.63 32 32
E4ICDs/ETO2 -0.071 0.1 -10000 0 -0.6 8 8
axon guidance 0.054 0.073 -10000 0 -10000 0 0
NEDD4 0.021 0.042 -10000 0 -0.71 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.036 0.13 -10000 0 -0.47 39 39
CBFA2T3 -0.012 0.092 -10000 0 -0.74 8 8
ErbB4/ErbB2/HBEGF -0.056 0.093 -10000 0 -0.46 18 18
MAPK3 -0.038 0.071 -10000 0 -10000 0 0
STAT1 (dimer) -0.064 0.079 -10000 0 -0.42 1 1
MAPK1 -0.038 0.071 -10000 0 -10000 0 0
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.053 0.088 -10000 0 -0.46 15 15
NRG1 0.013 0.1 -10000 0 -0.56 15 15
NRG3 -0.19 0.32 -10000 0 -0.74 130 130
NRG2 -0.078 0.23 -10000 0 -0.74 53 53
NRG4 -0.07 0.19 -10000 0 -0.57 61 61
heart development 0.054 0.073 -10000 0 -10000 0 0
neural crest cell migration -0.053 0.087 -10000 0 -0.45 15 15
ERBB2 0.029 0.032 -10000 0 -0.42 2 2
WWOX/E4ICDs -0.064 0.079 -10000 0 -0.43 1 1
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.1 0.14 -10000 0 -0.48 33 33
apoptosis 0.2 0.26 0.56 131 -10000 0 131
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.16 -10000 0 -0.53 53 53
ErbB4/ErbB2/epiregulin -0.12 0.18 -10000 0 -0.46 98 98
ErbB4/ErbB4/betacellulin/betacellulin -0.098 0.15 -10000 0 -0.55 38 38
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.085 0.14 -10000 0 -0.62 17 17
MDM2 -0.042 0.098 -10000 0 -0.43 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.041 0.081 -10000 0 -0.46 15 15
STAT5A 0.057 0.068 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.064 0.12 -10000 0 -0.53 20 20
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.058 0.072 -10000 0 -0.4 1 1
STAT5A (dimer) -0.039 0.11 -10000 0 -0.63 9 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.045 0.068 -10000 0 -10000 0 0
LRIG1 -0.001 0.033 -10000 0 -0.74 1 1
EREG -0.15 0.29 -10000 0 -0.72 104 104
BTC -0.056 0.2 -10000 0 -0.74 38 38
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.054 0.074 -10000 0 -10000 0 0
ERBB4 -0.076 0.098 -10000 0 -0.49 1 1
STAT5B 0 0 -10000 0 -10000 0 0
YAP1 -0.02 0.025 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.077 0.11 -10000 0 -0.42 27 27
glial cell differentiation 0.058 0.072 0.4 1 -10000 0 1
WWOX 0 0 -10000 0 -10000 0 0
cell proliferation -0.02 0.15 -10000 0 -0.6 12 12
Reelin signaling pathway

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
CDK5R1/CDK5 -0.008 0.058 -9999 0 -0.42 10 10
VLDLR -0.003 0.046 -9999 0 -0.74 2 2
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.033 -9999 0 -0.74 1 1
ITGA3 -0.006 0.066 -9999 0 -0.74 4 4
RELN/VLDLR/Fyn -0.086 0.19 -9999 0 -0.49 87 87
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.001 0.022 -9999 0 -0.4 1 1
AKT1 -0.035 0.13 -9999 0 -0.49 3 3
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.033 0.13 -9999 0 -0.57 29 29
RELN/LRP8/DAB1 -0.098 0.18 -9999 0 -0.45 88 88
LRPAP1/LRP8 -0.002 0.032 -9999 0 -0.42 3 3
RELN/LRP8/DAB1/Fyn -0.092 0.17 -9999 0 -0.43 88 88
DAB1/alpha3/beta1 Integrin -0.085 0.16 -9999 0 -0.69 6 6
long-term memory -0.12 0.19 -9999 0 -0.73 16 16
DAB1/LIS1 -0.085 0.16 -9999 0 -0.64 5 5
DAB1/CRLK/C3G -0.082 0.15 -9999 0 -0.62 5 5
PIK3CA 0 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.086 0.16 -9999 0 -0.64 5 5
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.065 0.2 -9999 0 -0.66 50 50
CDK5R1 -0.011 0.08 -9999 0 -0.57 10 10
RELN -0.13 0.28 -9999 0 -0.73 89 89
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.087 0.18 -9999 0 -0.48 86 86
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.2 -9999 0 -0.51 50 50
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.097 0.18 -9999 0 -0.42 115 115
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.092 0.17 -9999 0 -0.42 90 90
RELN/LRP8 -0.086 0.18 -9999 0 -0.48 86 86
GRIN2B/RELN/LRP8/DAB1/Fyn -0.094 0.17 -9999 0 -0.42 88 88
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.004 0.049 -9999 0 -0.56 4 4
RAP1A -0.076 0.14 -9999 0 -0.58 5 5
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.003 0.042 -9999 0 -0.66 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.006 0.057 -9999 0 -0.57 5 5
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.013 0.097 -9999 0 -0.4 3 3
neuron adhesion -0.073 0.14 -9999 0 -0.62 5 5
LRP8 -0.003 0.044 -9999 0 -0.57 3 3
GSK3B -0.026 0.12 -9999 0 -0.46 3 3
RELN/VLDLR/DAB1/Fyn -0.091 0.17 -9999 0 -0.43 89 89
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.065 0.12 -9999 0 -0.32 89 89
CDK5 0 0 -9999 0 -10000 0 0
MAPT 0.003 0.083 -9999 0 -0.66 7 7
neuron migration -0.03 0.17 -9999 0 -0.55 6 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.043 0.082 -9999 0 -0.4 3 3
RELN/VLDLR -0.079 0.17 -9999 0 -0.44 87 87
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.012 0.081 -9999 0 -0.56 11 11
AKT1 -0.012 0.2 -9999 0 -0.65 28 28
PTK2B -0.06 0.26 -9999 0 -0.89 31 31
VEGFR2 homodimer/Frs2 -0.12 0.27 -9999 0 -0.61 95 95
CAV1 -0.2 0.33 -9999 0 -0.74 137 137
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.11 0.25 -9999 0 -0.93 28 28
endothelial cell proliferation -0.009 0.2 -9999 0 -0.62 30 30
mol:Ca2+ -0.054 0.24 -9999 0 -0.84 28 28
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.1 0.23 -9999 0 -0.88 28 28
RP11-342D11.1 -0.061 0.24 -9999 0 -0.84 28 28
CDH5 -0.15 0.3 -9999 0 -0.74 102 102
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.004 0.057 -9999 0 -0.74 3 3
HRAS/GDP -0.08 0.19 -9999 0 -0.71 28 28
SH2D2A -0.001 0.033 -9999 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.077 0.18 -9999 0 -0.67 29 29
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.11 0.25 -9999 0 -0.91 29 29
VEGFR1 homodimer 0 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.09 0.21 -9999 0 -0.81 28 28
GRB10 -0.054 0.24 -9999 0 -0.84 28 28
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.17 0.32 -9999 0 -0.95 57 57
HRAS 0 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.057 0.13 -9999 0 -0.46 31 31
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.098 0.23 -9999 0 -0.86 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.038 0.16 -9999 0 -0.74 26 26
Nck/Pak -0.001 0.019 -9999 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.11 0.25 -9999 0 -0.94 28 28
mol:GDP -0.087 0.2 -9999 0 -0.77 28 28
mol:NADP -0.01 0.18 -9999 0 -0.56 30 30
eNOS/Hsp90 -0.005 0.17 -9999 0 -0.52 29 29
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.056 0.24 -9999 0 -0.86 28 28
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0 0 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFC -0.003 0.046 -9999 0 -0.74 2 2
FAK1/Vinculin -0.045 0.25 -9999 0 -0.85 31 31
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.26 -9999 0 -0.96 31 31
PTPN6 0 0 -9999 0 -10000 0 0
EPAS1 -0.13 0.29 -9999 0 -0.71 95 95
mol:L-citrulline -0.01 0.18 -9999 0 -0.56 30 30
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.1 0.23 -9999 0 -0.88 28 28
VEGFR2 homodimer/VEGFA homodimer -0.11 0.25 -9999 0 -0.94 28 28
VEGFR2/3 heterodimer -0.14 0.31 -9999 0 -0.66 106 106
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 -0.053 0.25 -9999 0 -0.87 28 28
VEGFR2 homodimer -0.11 0.31 -9999 0 -0.7 95 95
FLT1 0 0 -9999 0 -10000 0 0
NEDD4 -0.001 0.033 -9999 0 -0.74 1 1
MAPK3 -0.048 0.23 -9999 0 -0.78 30 30
MAPK1 -0.048 0.23 -9999 0 -0.78 30 30
VEGFA145/NRP2 -0.004 0.049 -9999 0 -0.56 4 4
VEGFR1/2 heterodimer -0.12 0.27 -9999 0 -0.61 95 95
KDR -0.11 0.31 -9999 0 -0.7 95 95
VEGFA165/NRP1/VEGFR2 homodimer -0.099 0.24 -9999 0 -0.9 28 28
SRC 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.049 0.24 -9999 0 -0.8 30 30
PI3K -0.09 0.21 -9999 0 -0.82 28 28
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.25 -9999 0 -0.93 28 28
FES -0.058 0.25 -9999 0 -0.89 28 28
GAB1 -0.094 0.22 -9999 0 -0.84 28 28
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.25 -9999 0 -0.93 28 28
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 -0.095 0.24 -9999 0 -0.57 63 63
VEGFR2 homodimer/VEGFA homodimer/Yes -0.11 0.25 -9999 0 -0.93 28 28
PI3K/GAB1 -0.013 0.2 -9999 0 -0.67 28 28
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.096 0.22 -9999 0 -0.86 28 28
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.13 0.29 -9999 0 -1.1 31 31
HSP90AA1 0 0 -9999 0 -10000 0 0
CDC42 -0.057 0.25 -9999 0 -0.88 28 28
actin cytoskeleton reorganization -0.11 0.24 -9999 0 -0.9 29 29
PTK2 -0.056 0.28 -9999 0 -0.95 31 31
EDG1 -0.061 0.24 -9999 0 -0.84 28 28
mol:DAG -0.056 0.24 -9999 0 -0.86 28 28
CaM/Ca2+ -0.088 0.21 -9999 0 -0.78 28 28
MAP2K3 -0.046 0.24 -9999 0 -0.82 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.1 0.24 -9999 0 -0.89 28 28
PLCG1 -0.057 0.25 -9999 0 -0.88 28 28
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.1 0.23 -9999 0 -0.88 28 28
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.11 0.25 -9999 0 -0.93 28 28
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.11 0.25 -9999 0 -0.93 28 28
cell migration -0.041 0.24 -9999 0 -0.75 31 31
mol:PI-3-4-5-P3 -0.083 0.19 -9999 0 -0.73 28 28
FYN -0.001 0.033 -9999 0 -0.74 1 1
VEGFB/NRP1 -0.091 0.21 -9999 0 -0.79 28 28
mol:NO -0.01 0.18 -9999 0 -0.56 30 30
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.08 0.19 -9999 0 -0.71 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.1 0.24 -9999 0 -0.89 28 28
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.016 0.11 -9999 0 -0.74 11 11
NOS3 -0.017 0.2 -9999 0 -0.65 30 30
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.25 -9999 0 -0.94 29 29
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.045 0.23 -9999 0 -0.8 29 29
PRKCB -0.065 0.26 -9999 0 -0.89 29 29
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.097 0.22 -9999 0 -0.85 28 28
VEGFR1/2 heterodimer/VEGFA homodimer -0.11 0.25 -9999 0 -0.93 28 28
VEGFA165/NRP2 -0.004 0.049 -9999 0 -0.56 4 4
MAPKKK cascade -0.08 0.19 -9999 0 -0.71 28 28
NRP2 -0.006 0.066 -9999 0 -0.74 4 4
VEGFC homodimer -0.003 0.046 -9999 0 -0.74 2 2
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.045 0.25 -9999 0 -0.85 31 31
MAP3K13 -0.057 0.25 -9999 0 -0.88 28 28
PDPK1 -0.014 0.19 -9999 0 -0.63 28 28
Aurora A 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
Aurora A/GADD45A 0.015 0.042 -9999 0 -10000 0 0
BIRC5 -0.49 0.2 -9999 0 -0.57 426 426
NFKBIA 0.018 0.042 -9999 0 -10000 0 0
CPEB1 -0.05 0.18 -9999 0 -0.74 34 34
AKT1 0.018 0.042 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.014 0.037 -9999 0 -10000 0 0
NDEL1/TACC3 0.017 0.04 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.013 0.006 -9999 0 -10000 0 0
PAK1/Aurora A 0.015 0.045 -9999 0 -0.35 1 1
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.28 0.2 -9999 0 -0.42 349 349
TP53 0.018 0.033 -9999 0 -0.35 1 1
DLG7 0.01 0.042 -9999 0 -10000 0 0
AURKAIP1 0 0 -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 0.018 0.043 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.014 0.037 -9999 0 -10000 0 0
AURKA 0.016 0.052 -9999 0 -10000 0 0
AURKB -0.088 0.051 -9999 0 -0.16 23 23
CDC25B 0.019 0.036 -9999 0 -10000 0 0
G2/M transition checkpoint 0.014 0.037 -9999 0 -10000 0 0
mRNA polyadenylation -0.018 0.12 -9999 0 -0.44 34 34
Aurora A/CPEB -0.018 0.12 -9999 0 -0.44 34 34
Aurora A/TACC1/TRAP/chTOG 0.022 0.045 -9999 0 -0.4 2 2
BRCA1 0 0 -9999 0 -10000 0 0
centrosome duplication 0.015 0.045 -9999 0 -0.35 1 1
regulation of centrosome cycle 0.017 0.04 -9999 0 -10000 0 0
spindle assembly 0.015 0.044 -9999 0 -0.4 2 2
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.24 0.1 -9999 0 -0.42 24 24
CENPA -0.076 0.043 -9999 0 -0.18 23 23
Aurora A/PP2A 0.015 0.042 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.028 0.033 -9999 0 -10000 0 0
negative regulation of DNA binding 0.018 0.033 -9999 0 -0.35 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.014 0.037 -9999 0 -10000 0 0
mitotic prometaphase 0.025 0.017 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.052 -9999 0 -10000 0 0
TACC1 -0.003 0.046 -9999 0 -0.74 2 2
TACC3 -0.002 0.036 -9999 0 -0.57 2 2
Aurora A/Antizyme1 0.02 0.038 -9999 0 -10000 0 0
Aurora A/RasGAP 0.015 0.042 -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 0.013 0.006 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.015 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.28 0.2 -9999 0 -0.42 349 349
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.22 0.16 -9999 0 -0.46 24 24
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
CKAP5 0 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.02 0 -9999 0 -10000 0 0
SMARCC1 0.006 0.008 -9999 0 -10000 0 0
REL 0 0.002 -9999 0 -10000 0 0
HDAC7 -0.029 0.12 -9999 0 -10000 0 0
JUN 0.001 0.004 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.033 -9999 0 -0.74 1 1
KAT5 0 0.001 -9999 0 -10000 0 0
MAPK14 0.012 0.026 -9999 0 -0.45 1 1
FOXO1 0 0 -9999 0 -10000 0 0
T-DHT/AR -0.036 0.13 -9999 0 -0.44 1 1
MAP2K6 0.006 0.028 -9999 0 -0.6 1 1
BRM/BAF57 -0.001 0.025 -9999 0 -0.56 1 1
MAP2K4 0.007 0.007 -9999 0 -10000 0 0
SMARCA2 0 0.033 -9999 0 -0.74 1 1
PDE9A -0.11 0.23 -9999 0 -0.99 19 19
NCOA2 0.005 0.034 -9999 0 -0.74 1 1
CEBPA -0.001 0.033 -9999 0 -0.74 1 1
EHMT2 0.001 0.004 -9999 0 -10000 0 0
cell proliferation -0.047 0.17 -9999 0 -0.52 24 24
NR0B1 -0.18 0.27 -9999 0 -0.57 161 161
EGR1 -0.015 0.11 -9999 0 -0.74 11 11
RXRs/9cRA -0.23 0.22 -9999 0 -0.44 265 265
AR/RACK1/Src -0.014 0.074 -9999 0 -10000 0 0
AR/GR -0.063 0.12 -9999 0 -0.34 42 42
GNB2L1 0.005 0.005 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.013 0.016 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.013 0.074 -9999 0 -0.45 1 1
SRC 0.018 0.04 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
KLK3 -0.13 0.15 -9999 0 -0.59 17 17
APPBP2 0.008 0.006 -9999 0 -10000 0 0
TRIM24 0.001 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.037 0.053 -9999 0 -10000 0 0
TMPRSS2 -0.42 0.57 -9999 0 -1.2 161 161
RXRG -0.39 0.37 -9999 0 -0.74 265 265
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.006 0.005 -9999 0 -10000 0 0
NR2C2 0 0 -9999 0 -10000 0 0
KLK2 -0.019 0.13 -9999 0 -0.48 3 3
AR -0.052 0.15 -9999 0 -0.33 103 103
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
SRY -0.005 0.051 -9999 0 -0.57 4 4
GATA2 -0.081 0.23 -9999 0 -0.74 55 55
MYST2 0 0.001 -9999 0 -10000 0 0
HOXB13 -0.34 0.28 -9999 0 -0.57 294 294
T-DHT/AR/RACK1/Src -0.014 0.07 -9999 0 -10000 0 0
positive regulation of transcription -0.081 0.23 -9999 0 -0.74 55 55
DNAJA1 0.008 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.006 -9999 0 -10000 0 0
NCOA1 0.014 0.004 -9999 0 -10000 0 0
SPDEF -0.096 0.25 -9999 0 -0.73 67 67
T-DHT/AR/TIF2 0.013 0.056 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 -0.037 0.053 -9999 0 -10000 0 0
GSK3B 0.007 0.006 -9999 0 -10000 0 0
NR2C1 0 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.012 0.043 -9999 0 -0.38 1 1
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0 0.002 -9999 0 -10000 0 0
POU2F1 -0.001 0.042 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.13 0.15 -9999 0 -0.44 34 34
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0.001 0.004 -9999 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0 -9999 0 -10000 0 0
CCL5 -0.013 0.098 -9999 0 -0.74 9 9
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.09 0.1 -9999 0 -0.43 4 4
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 -0.093 0.079 -9999 0 -0.43 3 3
Syndecan-1/Syntenin -0.092 0.078 -9999 0 -0.46 2 2
MAPK3 -0.059 0.087 -9999 0 -0.48 1 1
HGF/MET -0.12 0.23 -9999 0 -0.56 111 111
TGFB1/TGF beta receptor Type II 0 0 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.092 0.078 -9999 0 -0.43 3 3
Syndecan-1/RANTES -0.1 0.1 -9999 0 -0.55 10 10
Syndecan-1/CD147 -0.084 0.072 -9999 0 -0.51 1 1
Syndecan-1/Syntenin/PIP2 -0.089 0.075 -9999 0 -0.39 4 4
LAMA5 -0.001 0.033 -9999 0 -0.74 1 1
positive regulation of cell-cell adhesion -0.087 0.074 -9999 0 -0.38 4 4
MMP7 -0.039 0.15 -9999 0 -0.62 31 31
HGF -0.16 0.3 -9999 0 -0.74 108 108
Syndecan-1/CASK -0.086 0.094 -9999 0 -0.41 4 4
Syndecan-1/HGF/MET -0.17 0.17 -9999 0 -0.54 61 61
regulation of cell adhesion -0.05 0.086 -9999 0 -0.46 1 1
HPSE 0 0 -9999 0 -10000 0 0
positive regulation of cell migration -0.09 0.1 -9999 0 -0.43 4 4
SDC1 -0.09 0.1 -9999 0 -0.43 4 4
Syndecan-1/Collagen -0.09 0.1 -9999 0 -0.43 4 4
PPIB 0 0 -9999 0 -10000 0 0
MET -0.004 0.053 -9999 0 -0.68 3 3
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.032 0.13 -9999 0 -0.57 28 28
MAPK1 -0.059 0.087 -9999 0 -0.48 1 1
homophilic cell adhesion -0.089 0.1 -9999 0 -0.42 4 4
MMP1 -0.36 0.28 -9999 0 -0.57 310 310
HIF-2-alpha transcription factor network

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
MMP14 -0.013 0.03 -10000 0 -10000 0 0
oxygen homeostasis -0.01 0.013 -10000 0 -10000 0 0
TCEB2 0 0 -10000 0 -10000 0 0
TCEB1 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.1 0.12 -10000 0 -0.43 18 18
EPO -0.15 0.22 -10000 0 -0.67 17 17
FIH (dimer) 0.003 0.009 -10000 0 -10000 0 0
APEX1 0.004 0.013 -10000 0 -10000 0 0
SERPINE1 -0.2 0.25 -10000 0 -0.74 28 28
FLT1 -0.038 0.16 -10000 0 -1 12 12
ADORA2A -0.19 0.24 -10000 0 -0.76 18 18
germ cell development -0.2 0.24 -10000 0 -0.77 21 21
SLC11A2 -0.2 0.25 -10000 0 -0.75 24 24
BHLHE40 -0.2 0.25 -10000 0 -0.75 24 24
HIF1AN 0.003 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.14 0.16 -10000 0 -0.48 47 47
ETS1 0.004 0.12 -10000 0 -0.75 12 12
CITED2 -0.037 0.18 -10000 0 -1.3 10 10
KDR -0.096 0.34 -10000 0 -1.3 34 34
PGK1 -0.2 0.25 -10000 0 -0.69 39 39
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.21 0.3 -10000 0 -0.81 45 45
EPAS1 -0.12 0.16 -10000 0 -0.41 78 78
SP1 0.017 0 -10000 0 -10000 0 0
ABCG2 -0.25 0.34 -10000 0 -0.95 65 65
EFNA1 -0.2 0.25 -10000 0 -0.75 24 24
FXN -0.19 0.24 -10000 0 -0.72 24 24
POU5F1 -0.2 0.25 -10000 0 -0.81 21 21
neuron apoptosis 0.21 0.29 0.78 45 -10000 0 45
EP300 0 0 -10000 0 -10000 0 0
EGLN3 -0.087 0.21 -10000 0 -0.59 76 76
EGLN2 0.003 0.01 -10000 0 -10000 0 0
EGLN1 0.003 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.004 0.013 -10000 0 -10000 0 0
SLC2A1 -0.38 0.29 -10000 0 -0.76 101 101
TWIST1 -0.27 0.31 -10000 0 -0.76 75 75
ELK1 0.016 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.14 0.16 -10000 0 -0.48 44 44
VEGFA -0.2 0.25 -10000 0 -0.75 24 24
CREBBP 0 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.053 -9999 0 -0.42 8 8
Metarhodopsin II/Arrestin -0.001 0.023 -9999 0 -0.36 2 2
PDE6G/GNAT1/GTP -0.015 0.081 -9999 0 -0.43 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.009 0.072 -9999 0 -0.57 8 8
GRK1 -0.002 0.036 -9999 0 -0.57 2 2
CNG Channel -0.054 0.13 -9999 0 -0.6 7 7
mol:Na + -0.096 0.15 -9999 0 -0.53 23 23
mol:ADP -0.002 0.036 -9999 0 -0.57 2 2
RGS9-1/Gbeta5/R9AP -0.059 0.16 -9999 0 -0.49 60 60
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.098 0.15 -9999 0 -0.54 23 23
CNGB1 -0.051 0.16 -9999 0 -0.57 44 44
RDH5 -0.003 0.046 -9999 0 -0.74 2 2
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.091 0.14 -9999 0 -0.51 23 23
Na + (4 Units) -0.089 0.14 -9999 0 -0.49 23 23
RGS9 -0.078 0.23 -9999 0 -0.74 53 53
GNB1/GNGT1 -0.13 0.19 -9999 0 -0.42 157 157
GNAT1/GDP -0.055 0.14 -9999 0 -0.43 60 60
GUCY2D 0 0 -9999 0 -10000 0 0
GNGT1 -0.18 0.27 -9999 0 -0.57 156 156
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.031 0.11 -9999 0 -0.43 30 30
mol:11-cis-retinal -0.003 0.046 -9999 0 -0.74 2 2
mol:cGMP -0.081 0.13 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
Rhodopsin -0.004 0.044 -9999 0 -0.49 4 4
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.007 0.063 -9999 0 -0.57 6 6
Metarhodopsin II -0.003 0.029 -9999 0 -0.32 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.086 0.14 -9999 0 -10000 0 0
RGS9BP -0.013 0.098 -9999 0 -0.74 9 9
Metarhodopsin II/Transducin -0.052 0.077 -9999 0 -0.37 2 2
GCAP Family/Ca ++ -0.088 0.14 -9999 0 -0.32 137 137
PDE6A/B -0.025 0.11 -9999 0 -0.54 23 23
mol:Pi -0.058 0.16 -9999 0 -0.49 60 60
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.1 0.15 -9999 0 -0.56 3 3
PDE6B -0.016 0.11 -9999 0 -0.72 11 11
PDE6A -0.017 0.11 -9999 0 -0.71 12 12
PDE6G -0.015 0.1 -9999 0 -0.74 10 10
RHO -0.002 0.036 -9999 0 -0.57 2 2
PDE6 -0.071 0.17 -9999 0 -0.8 11 11
GUCA1A -0.16 0.26 -9999 0 -0.57 137 137
GC2/GCAP Family -0.088 0.14 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0 0.13 -10000 0 -0.4 22 22
TBX21 -0.093 0.5 -10000 0 -1.4 57 57
B2M 0.006 0.058 -10000 0 -0.74 3 3
TYK2 0.016 0.017 -10000 0 -10000 0 0
IL12RB1 -0.033 0.19 -10000 0 -0.77 32 32
GADD45B -0.028 0.36 -10000 0 -1.1 39 39
IL12RB2 -0.046 0.18 -10000 0 -0.57 54 54
GADD45G -0.015 0.33 -10000 0 -1 32 32
natural killer cell activation 0.006 0.019 -10000 0 -10000 0 0
RELB -0.001 0.026 -10000 0 -0.57 1 1
RELA 0 0 -10000 0 -10000 0 0
IL18 0.009 0.059 -10000 0 -0.75 3 3
IL2RA -0.008 0.072 -10000 0 -0.66 6 6
IFNG -0.008 0.075 -10000 0 -0.68 6 6
STAT3 (dimer) -0.003 0.29 -10000 0 -0.8 40 40
HLA-DRB5 -0.062 0.22 -10000 0 -0.74 48 48
FASLG -0.047 0.41 -10000 0 -1.2 41 41
NF kappa B2 p52/RelB -0.13 0.3 -10000 0 -1 39 39
CD4 -0.013 0.13 -10000 0 -0.74 15 15
SOCS1 -0.001 0.033 -10000 0 -0.74 1 1
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D -0.006 0.11 -10000 0 -0.74 11 11
CD3E -0.003 0.1 -10000 0 -0.74 9 9
CD3G -0.037 0.18 -10000 0 -0.74 32 32
IL12Rbeta2/JAK2 -0.02 0.14 -10000 0 -0.41 54 54
CCL3 -0.027 0.35 -10000 0 -1.1 37 37
CCL4 -0.03 0.36 -10000 0 -1.1 37 37
HLA-A 0.009 0.034 -10000 0 -0.74 1 1
IL18/IL18R 0.019 0.14 -10000 0 -0.57 25 25
NOS2 -0.077 0.44 -10000 0 -1.2 52 52
IL12/IL12R/TYK2/JAK2/SPHK2 0.001 0.13 -10000 0 -0.4 20 20
IL1R1 -0.025 0.34 -10000 0 -1 37 37
IL4 -0.004 0.019 -10000 0 -10000 0 0
JAK2 0.016 0.017 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.03 0.31 -10000 0 -1.1 26 26
RAB7A 0.01 0.28 -10000 0 -0.79 33 33
lysosomal transport 0.014 0.26 -10000 0 -0.75 33 33
FOS -0.16 0.5 -10000 0 -1.2 86 86
STAT4 (dimer) -0.006 0.34 -10000 0 -0.96 39 39
STAT5A (dimer) -0.13 0.3 -10000 0 -1 41 41
GZMA -0.033 0.37 -10000 0 -1.1 37 37
GZMB -0.033 0.37 -10000 0 -1.2 30 30
HLX 0 0 -10000 0 -10000 0 0
LCK -0.036 0.39 -10000 0 -1.1 39 39
TCR/CD3/MHC II/CD4 -0.089 0.33 -10000 0 -0.9 50 50
IL2/IL2R -0.013 0.1 -10000 0 -0.69 8 8
MAPK14 -0.012 0.34 -10000 0 -0.99 37 37
CCR5 -0.023 0.35 -10000 0 -1.1 32 32
IL1B -0.001 0.12 -10000 0 -0.76 11 11
STAT6 0.018 0.1 -10000 0 -0.26 13 13
STAT4 -0.012 0.092 -10000 0 -0.74 8 8
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B 0.017 0.016 -10000 0 -10000 0 0
CD8A 0 0.088 -10000 0 -0.74 7 7
CD8B -0.013 0.13 -10000 0 -0.7 17 17
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0 0.13 0.4 22 -10000 0 22
IL2RB -0.004 0.057 -10000 0 -0.74 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.003 0.3 -10000 0 -0.85 39 39
IL2RG -0.01 0.087 -10000 0 -0.74 7 7
IL12 0.017 0.08 -10000 0 -0.57 8 8
STAT5A 0 0 -10000 0 -10000 0 0
CD247 -0.008 0.12 -10000 0 -0.74 12 12
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.098 -10000 0 -0.75 8 8
IL12/IL12R/TYK2/JAK2 -0.051 0.44 -10000 0 -1.2 44 44
MAP2K3 -0.016 0.34 -10000 0 -0.99 38 38
RIPK2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.016 0.34 -10000 0 -0.99 38 38
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.059 0.22 -10000 0 -0.74 46 46
IL18RAP -0.018 0.15 -10000 0 -0.75 21 21
IL12Rbeta1/TYK2 -0.015 0.15 -10000 0 -0.59 32 32
EOMES -0.028 0.23 -10000 0 -1.4 13 13
STAT1 (dimer) -0.001 0.29 -10000 0 -0.81 36 36
T cell proliferation 0.008 0.25 -10000 0 -0.69 37 37
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.006 0.076 -10000 0 -0.75 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.1 0.22 -10000 0 -0.76 39 39
ATF2 0 0.31 -10000 0 -0.89 37 37
Osteopontin-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
IKK alpha homodimer -0.14 0.14 -9999 0 -0.58 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.11 -9999 0 -0.58 4 4
alphaV/beta3 Integrin/Osteopontin/Src -0.21 0.2 -9999 0 -0.4 255 255
AP1 -0.16 0.16 -9999 0 -0.61 33 33
ILK -0.14 0.17 -9999 0 -0.62 6 6
bone resorption -0.12 0.12 -9999 0 -0.59 5 5
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.14 0.14 -9999 0 -0.65 4 4
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.001 0.025 -9999 0 -0.56 1 1
alphaV/beta3 Integrin/Osteopontin -0.18 0.18 -9999 0 -0.58 11 11
MAP3K1 -0.14 0.18 -9999 0 -0.53 11 11
JUN 0 0 -9999 0 -10000 0 0
MAPK3 -0.12 0.17 -9999 0 -0.58 6 6
MAPK1 -0.12 0.17 -9999 0 -0.58 6 6
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.12 0.17 -9999 0 -0.6 6 6
ITGB3 -0.016 0.11 -9999 0 -0.73 11 11
NFKBIA -0.1 0.16 -9999 0 -0.64 4 4
FOS -0.09 0.24 -9999 0 -0.74 61 61
CD44 -0.001 0.033 -9999 0 -0.74 1 1
CHUK 0 0 -9999 0 -10000 0 0
PLAU -0.099 0.17 -9999 0 -0.56 19 19
NF kappa B1 p50/RelA -0.12 0.12 -9999 0 -0.56 4 4
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.012 0.081 -9999 0 -0.55 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.14 0.18 -9999 0 -0.52 12 12
VAV3 -0.12 0.17 -9999 0 -0.65 6 6
MAP3K14 -0.14 0.18 -9999 0 -0.52 11 11
ROCK2 0 0 -9999 0 -10000 0 0
SPP1 -0.29 0.28 -9999 0 -0.57 255 255
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.13 0.13 -9999 0 -0.7 4 4
MMP2 -0.1 0.17 -9999 0 -0.64 9 9
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.25 0.35 -9999 0 -0.74 168 168
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0 0 -9999 0 -10000 0 0
TCEB1 0 0 -9999 0 -10000 0 0
HIF1A/p53 -0.01 0.03 -9999 0 -0.46 1 1
HIF1A -0.011 0.026 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.27 0.29 -9999 0 -0.58 233 233
ARNT/IPAS -0.19 0.26 -9999 0 -0.56 168 168
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.009 0.022 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.009 0.022 -9999 0 -10000 0 0
PHD1-3/OS9 -0.047 0.11 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.007 0.017 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.009 0.022 -9999 0 -10000 0 0
EGLN3 -0.087 0.21 -9999 0 -0.57 76 76
EGLN2 0 0 -9999 0 -10000 0 0
EGLN1 0 0 -9999 0 -10000 0 0
TP53 -0.001 0.033 -9999 0 -0.74 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0 -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 -0.14 0.14 -9999 0 -0.36 39 39
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.024 0.11 -10000 0 -0.45 27 27
ER alpha/Gai/GDP/Gbeta gamma -0.027 0.11 -10000 0 -0.46 25 25
AKT1 -0.007 0.18 -10000 0 -0.82 24 24
PIK3CA 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.011 0.18 -10000 0 -0.83 24 24
mol:Ca2+ -0.093 0.23 -10000 0 -0.48 124 124
IGF1R 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.023 0.1 -10000 0 -0.48 24 24
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.005 0.17 0.78 24 -10000 0 24
RhoA/GTP -0.017 0.076 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.029 0.12 -10000 0 -0.52 25 25
regulation of stress fiber formation -0.031 0.076 0.57 2 -10000 0 2
E2/ERA-ERB (dimer) -0.023 0.1 -10000 0 -0.48 24 24
KRAS 0 0 -10000 0 -10000 0 0
G13/GTP -0.021 0.095 -10000 0 -0.44 24 24
pseudopodium formation 0.031 0.076 -10000 0 -0.57 2 2
E2/ER alpha (dimer)/PELP1 -0.023 0.1 -10000 0 -0.48 24 24
GRB2 0 0 -10000 0 -10000 0 0
GNG2 -0.007 0.073 -10000 0 -0.74 5 5
GNAO1 -0.004 0.049 -10000 0 -0.63 3 3
HRAS 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.13 -10000 0 -0.54 25 25
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.024 0.11 -10000 0 -0.5 24 24
mol:NADP 0.014 0.13 -10000 0 -0.54 25 25
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.098 0.24 -10000 0 -0.5 124 124
IGF-1R heterotetramer 0 0 -10000 0 -10000 0 0
PLCB1 -0.13 0.23 -10000 0 -0.51 124 124
PLCB2 -0.13 0.23 -10000 0 -0.52 128 128
IGF1 -0.028 0.14 -10000 0 -0.73 19 19
mol:L-citrulline 0.014 0.13 -10000 0 -0.54 25 25
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.045 -10000 0 -0.67 1 1
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0 0 -10000 0 -10000 0 0
GNAQ -0.001 0.033 -10000 0 -0.74 1 1
ESR1 -0.035 0.16 -10000 0 -0.74 24 24
Gq family/GDP/Gbeta gamma -0.075 0.14 -10000 0 -0.81 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.018 0.074 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.029 0.12 -10000 0 -0.52 25 25
GNAZ -0.009 0.08 -10000 0 -0.74 6 6
E2/ER alpha (dimer) -0.027 0.12 -10000 0 -0.56 24 24
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.004 0.057 -10000 0 -0.74 3 3
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.016 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.001 0.033 -10000 0 -0.74 1 1
HBEGF 0.013 0.12 -10000 0 -0.68 6 6
cAMP biosynthetic process -0.021 0.091 -10000 0 -0.4 26 26
SRC 0.018 0.11 -10000 0 -0.64 5 5
PI3K 0 0 -10000 0 -10000 0 0
GNB1 -0.001 0.033 -10000 0 -0.74 1 1
G13/GDP/Gbeta gamma -0.025 0.11 -10000 0 -0.48 24 24
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.032 0.11 -10000 0 -0.59 10 10
Gs family/GTP -0.021 0.093 -10000 0 -0.41 26 26
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.015 0.13 -10000 0 -0.52 25 25
mol:DAG -0.098 0.24 -10000 0 -0.5 124 124
Gs family/GDP/Gbeta gamma -0.025 0.1 -10000 0 -0.45 24 24
MSN 0.031 0.082 -10000 0 -0.64 2 2
Gq family/GTP -0.14 0.24 -10000 0 -0.54 123 123
mol:PI-3-4-5-P3 -0.009 0.18 -10000 0 -0.79 24 24
NRAS 0 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.015 0.13 0.52 25 -10000 0 25
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.022 0.1 -10000 0 -0.47 24 24
NOS3 0.013 0.14 -10000 0 -0.57 25 25
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.018 0.15 -10000 0 -0.63 24 24
E2/ER alpha (dimer)/PELP1/Src -0.03 0.12 -10000 0 -0.54 25 25
ruffle organization 0.031 0.076 -10000 0 -0.57 2 2
ROCK2 -0.016 0.07 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.74 123 123
GNA15 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
MMP9 0.008 0.12 -10000 0 -0.59 5 5
MMP2 0.022 0.12 -10000 0 -0.79 5 5
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.007 0.06 -9999 0 -0.56 6 6
Necdin/E2F1 -0.009 0.07 -9999 0 -0.56 8 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.04 0.11 -9999 0 -0.45 17 17
NGF (dimer)/p75(NTR)/BEX1 -0.099 0.2 -9999 0 -0.45 111 111
NT-4/5 (dimer)/p75(NTR) -0.044 0.13 -9999 0 -0.44 51 51
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
AKT1 -0.004 0.12 -9999 0 -0.68 3 3
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.093 0.24 -9999 0 -0.74 63 63
MGDIs/NGR/p75(NTR)/LINGO1 -0.061 0.14 -9999 0 -0.38 82 82
FURIN 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.095 0.19 -9999 0 -0.51 68 68
LINGO1 -0.051 0.16 -9999 0 -0.57 44 44
Sortilin/TRAF6/NRIF -0.004 0.038 -9999 0 -10000 0 0
proBDNF (dimer) -0.093 0.24 -9999 0 -0.74 63 63
NTRK1 -0.007 0.073 -9999 0 -0.74 5 5
RTN4R -0.003 0.042 -9999 0 -0.66 2 2
neuron apoptosis -0.031 0.16 -9999 0 -0.6 10 10
IRAK1 0 0 -9999 0 -10000 0 0
SHC1 -0.021 0.13 -9999 0 -0.56 11 11
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.043 0.12 -9999 0 -0.48 17 17
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.05 0.13 -9999 0 -0.49 24 24
Mammalian IAPs/DIABLO -0.005 0.047 -9999 0 -0.43 6 6
proNGF (dimer) -0.02 0.12 -9999 0 -0.7 14 14
MAGED1 0 0 -9999 0 -10000 0 0
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.092 -9999 0 -0.74 8 8
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.035 0.11 -9999 0 -0.48 11 11
NGF -0.02 0.12 -9999 0 -0.7 14 14
cell cycle arrest -0.023 0.14 -9999 0 -0.45 17 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.02 0.064 -9999 0 -0.35 11 11
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.037 0.11 -9999 0 -0.37 51 51
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.042 0.13 -9999 0 -0.39 54 54
PSENEN 0 0 -9999 0 -10000 0 0
mol:ceramide -0.017 0.13 -9999 0 -0.48 17 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.015 0.049 -9999 0 -0.37 3 3
p75(NTR)/beta APP -0.036 0.12 -9999 0 -0.42 43 43
BEX1 -0.091 0.23 -9999 0 -0.68 67 67
mol:GDP -0.029 0.13 -9999 0 -0.4 54 54
NGF (dimer) -0.036 0.12 -9999 0 -0.51 19 19
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.055 0.13 -9999 0 -0.63 7 7
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.036 0.11 -9999 0 -0.34 54 54
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.042 0.13 -9999 0 -0.39 54 54
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0 0 -9999 0 -10000 0 0
NT3 (dimer) -0.013 0.093 -9999 0 -0.7 9 9
TP53 -0.075 0.15 -9999 0 -0.67 7 7
PRDM4 -0.017 0.13 -9999 0 -0.48 17 17
BDNF (dimer) -0.27 0.24 -9999 0 -0.65 86 86
PIK3CA 0 0 -9999 0 -10000 0 0
SORT1 -0.009 0.08 -9999 0 -0.74 6 6
activation of caspase activity -0.039 0.11 -9999 0 -0.45 17 17
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.043 0.12 -9999 0 -0.48 17 17
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.014 0.14 -9999 0 -0.56 9 9
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.017 0.13 -9999 0 -0.48 17 17
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.048 0.14 -9999 0 -0.4 60 60
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.045 0.13 -9999 0 -0.43 52 52
MAPK8 -0.01 0.14 -9999 0 -0.55 7 7
MAPK9 -0.01 0.14 -9999 0 -0.55 7 7
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.013 0.094 -9999 0 -0.7 9 9
NTF4 -0.012 0.092 -9999 0 -0.74 8 8
NDN -0.012 0.092 -9999 0 -0.74 8 8
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.032 0.097 -9999 0 -0.65 3 3
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.047 -9999 0 -0.43 6 6
RhoA-B-C/GTP -0.042 0.12 -9999 0 -0.39 54 54
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.08 0.16 -9999 0 -0.71 7 7
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.086 0.17 -9999 0 -0.46 68 68
PRKACB 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.07 0.18 -9999 0 -0.56 63 63
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.009 0.08 -9999 0 -0.74 6 6
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.015 0.13 -9999 0 -0.46 16 16
BAD -0.003 0.14 -9999 0 -0.54 7 7
RIPK2 0 0 -9999 0 -10000 0 0
NGFR -0.049 0.16 -9999 0 -0.57 43 43
CYCS -0.009 0.12 -9999 0 -0.45 17 17
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.038 0.11 -9999 0 -0.51 11 11
BCL2L11 -0.003 0.14 -9999 0 -0.54 7 7
BDNF (dimer)/p75(NTR) -0.1 0.22 -9999 0 -0.52 100 100
PI3K -0.038 0.11 -9999 0 -0.51 11 11
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.043 0.12 -9999 0 -0.48 17 17
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.05 0.15 -9999 0 -0.46 54 54
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.043 0.12 -9999 0 -0.48 17 17
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG -0.006 0.057 -9999 0 -0.57 5 5
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.084 0.17 -9999 0 -0.62 18 18
SQSTM1 0 0 -9999 0 -10000 0 0
NGFRAP1 0 0 -9999 0 -10000 0 0
CASP3 0 0.13 -9999 0 -0.49 7 7
E2F1 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.019 0.075 -9999 0 -0.51 3 3
NGF (dimer)/TRKA -0.02 0.1 -9999 0 -0.53 19 19
MMP7 -0.039 0.15 -9999 0 -0.62 31 31
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.04 0.11 -9999 0 -0.45 17 17
MMP3 -0.34 0.28 -9999 0 -0.57 300 300
APAF-1/Caspase 9 -0.031 0.087 -9999 0 -0.54 4 4
Wnt 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
Noncanonical Wnts/FZD -0.045 0.091 -9999 0 -0.68 2 2
FZD6 0 0 -9999 0 -10000 0 0
WNT6 -0.094 0.21 -9999 0 -0.57 82 82
WNT4 -0.01 0.083 -9999 0 -0.66 8 8
FZD3 0 0 -9999 0 -10000 0 0
WNT5A -0.014 0.093 -9999 0 -0.6 12 12
WNT11 -0.038 0.16 -9999 0 -0.68 28 28
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.065 0.1 -10000 0 -0.36 5 5
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.56 153 153
NT3 (dimer)/TRKB -0.12 0.19 -10000 0 -0.55 38 38
SHC/Grb2/SOS1/GAB1/PI3K 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.093 0.24 -10000 0 -0.74 63 63
PIK3CA 0 0 -10000 0 -10000 0 0
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 -0.007 0.073 -10000 0 -0.74 5 5
NTRK2 -0.14 0.26 -10000 0 -0.62 112 112
NTRK3 -0.22 0.34 -10000 0 -0.73 148 148
NT-4/5 (dimer)/TRKB -0.12 0.19 -10000 0 -0.54 39 39
neuron apoptosis 0.13 0.19 0.56 47 -10000 0 47
SHC 2-3/Grb2 -0.14 0.21 -10000 0 -0.63 47 47
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.056 0.1 -10000 0 -0.55 9 9
SHC3 -0.16 0.26 -10000 0 -0.68 90 90
STAT3 (dimer) -0.005 0.042 -10000 0 -0.37 6 6
NT3 (dimer)/TRKA -0.043 0.12 -10000 0 -0.37 57 57
RIN/GDP -0.045 0.092 -10000 0 -0.28 1 1
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
DNAJA3 -0.024 0.07 -10000 0 -0.46 3 3
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.014 0.11 -10000 0 -0.95 6 6
MAGED1 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.092 -10000 0 -0.74 8 8
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.035 0.12 -10000 0 -0.47 38 38
TRKA/NEDD4-2 -0.006 0.055 -10000 0 -0.56 5 5
ELMO1 -0.013 0.098 -10000 0 -0.74 9 9
RhoG/GTP/ELMO1/DOCK1 -0.009 0.064 -10000 0 -0.48 9 9
NGF -0.02 0.12 -10000 0 -0.7 14 14
HRAS 0 0 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.021 0.12 -10000 0 -0.74 14 14
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
DNM1 -0.002 0.036 -10000 0 -0.57 2 2
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 -0.03 0.085 -10000 0 -0.41 12 12
mol:GDP -0.067 0.13 -10000 0 -0.4 3 3
NGF (dimer) -0.02 0.12 -10000 0 -0.7 14 14
RhoG/GDP -0.01 0.075 -10000 0 -0.56 9 9
RIT1/GDP -0.041 0.092 -10000 0 -10000 0 0
TIAM1 -0.001 0.033 -10000 0 -0.74 1 1
PIK3R1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.14 0.23 -10000 0 -0.55 83 83
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.013 0.093 -10000 0 -0.7 9 9
RAP1/GDP -0.047 0.067 -10000 0 -10000 0 0
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.093 0.24 -10000 0 -0.74 63 63
ubiquitin-dependent protein catabolic process -0.017 0.087 -10000 0 -0.45 19 19
Schwann cell development -0.054 0.036 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.007 0.041 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.22 0.27 -10000 0 -0.72 77 77
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.049 0.076 -10000 0 -10000 0 0
STAT3 -0.005 0.042 -10000 0 -0.37 6 6
axon guidance -0.21 0.25 -10000 0 -0.68 77 77
MAPK3 -0.005 0.12 -10000 0 -0.43 35 35
MAPK1 -0.005 0.12 -10000 0 -0.43 35 35
CDC42/GDP -0.041 0.092 -10000 0 -0.27 2 2
NTF3 -0.013 0.094 -10000 0 -0.7 9 9
NTF4 -0.012 0.092 -10000 0 -0.74 8 8
NGF (dimer)/TRKA/FAIM -0.017 0.088 -10000 0 -0.46 19 19
PI3K 0 0 -10000 0 -10000 0 0
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 -0.27 0.2 -10000 0 -0.42 311 311
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.13 0.24 -10000 0 -0.48 155 155
RGS19 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.055 0.081 -10000 0 -10000 0 0
Rac1/GDP -0.041 0.092 -10000 0 -0.28 1 1
NGF (dimer)/TRKA/GRIT -0.018 0.089 -10000 0 -0.46 19 19
neuron projection morphogenesis 0.003 0.075 -10000 0 -0.42 4 4
NGF (dimer)/TRKA/NEDD4-2 -0.017 0.088 -10000 0 -0.46 19 19
MAP2K1 0.035 0 -10000 0 -10000 0 0
NGFR -0.049 0.16 -10000 0 -0.57 43 43
NGF (dimer)/TRKA/GIPC/GAIP -0.011 0.055 -10000 0 -0.3 16 16
RAS family/GTP/PI3K 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.048 0.12 -10000 0 -0.66 16 16
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.055 -10000 0 -0.56 5 5
SQSTM1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.21 -10000 0 -0.5 83 83
NGF (dimer)/TRKA/p62/Atypical PKCs -0.015 0.074 -10000 0 -0.4 16 16
MATK -0.028 0.14 -10000 0 -0.74 19 19
NEDD4L 0 0 -10000 0 -10000 0 0
RAS family/GDP -0.043 0.064 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.026 0.076 -10000 0 -0.34 16 16
Rac1/GTP -0.17 0.13 -10000 0 -0.32 142 142
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.018 0.079 -9999 0 -0.37 24 24
EFNA5 -0.004 0.057 -9999 0 -0.74 3 3
FYN 0.002 0.078 -9999 0 -0.33 25 25
neuron projection morphogenesis -0.018 0.079 -9999 0 -0.37 24 24
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.018 0.08 -9999 0 -0.37 24 24
EPHA5 -0.024 0.12 -9999 0 -0.57 21 21
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.041 0.14 -10000 0 -0.6 25 25
FYN 0.001 0.23 -10000 0 -0.85 28 28
LAT/GRAP2/SLP76 -0.056 0.18 -10000 0 -0.66 35 35
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
AKT1 0.022 0.14 -10000 0 -0.47 32 32
B2M 0.006 0.058 -10000 0 -0.74 3 3
IKBKG -0.01 0.031 -10000 0 -0.18 1 1
MAP3K8 -0.003 0.046 -10000 0 -0.74 2 2
mol:Ca2+ -0.006 0.021 -10000 0 -0.12 14 14
integrin-mediated signaling pathway -0.001 0.021 -10000 0 -0.48 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.008 0.21 -10000 0 -0.73 32 32
TRPV6 -0.017 0.11 -10000 0 -0.7 13 13
CD28 0.002 0.075 -10000 0 -0.74 5 5
SHC1 0.005 0.21 -10000 0 -0.77 28 28
receptor internalization -0.011 0.23 -10000 0 -0.81 32 32
PRF1 -0.037 0.32 -10000 0 -1.2 32 32
KRAS 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
COT/AKT1 0.026 0.11 -10000 0 -0.4 25 25
LAT 0.005 0.21 -10000 0 -0.77 28 28
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D -0.006 0.11 -10000 0 -0.75 11 11
CD3E -0.003 0.1 -10000 0 -0.75 9 9
CD3G -0.037 0.18 -10000 0 -0.74 32 32
RASGRP2 -0.013 0.066 -10000 0 -0.18 68 68
RASGRP1 0.022 0.15 -10000 0 -0.46 34 34
HLA-A 0.009 0.034 -10000 0 -0.75 1 1
RASSF5 -0.001 0.033 -10000 0 -0.74 1 1
RAP1A/GTP/RAPL -0.001 0.022 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.05 -10000 0 -0.13 27 27
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.018 0.055 -10000 0 -0.25 11 11
PRKCA -0.024 0.077 -10000 0 -0.31 25 25
GRAP2 -0.044 0.18 -10000 0 -0.74 30 30
mol:IP3 -0.036 0.13 0.25 9 -0.49 29 38
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.017 0.23 -10000 0 -0.83 28 28
ORAI1 0.009 0.061 0.35 13 -0.57 1 14
CSK 0.003 0.21 -10000 0 -0.8 27 27
B7 family/CD28 -0.064 0.22 -10000 0 -0.84 33 33
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.01 0.25 -10000 0 -0.94 28 28
PTPN6 0 0.21 -10000 0 -0.81 27 27
VAV1 0.002 0.21 -10000 0 -0.8 28 28
Monovalent TCR/CD3 -0.025 0.21 -10000 0 -0.62 39 39
CBL 0 0 -10000 0 -10000 0 0
LCK -0.002 0.23 -10000 0 -0.86 28 28
PAG1 0 0.22 -10000 0 -0.81 27 27
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.011 0.25 -10000 0 -0.92 29 29
CD80 -0.016 0.14 -10000 0 -0.74 17 17
CD86 0.002 0.075 -10000 0 -0.74 5 5
PDK1/CARD11/BCL10/MALT1 -0.021 0.066 -10000 0 -0.3 16 16
HRAS 0 0 -10000 0 -10000 0 0
GO:0035030 0.005 0.19 -10000 0 -0.66 32 32
CD8A 0 0.089 -10000 0 -0.75 7 7
CD8B -0.013 0.13 -10000 0 -0.7 17 17
PTPRC -0.04 0.19 -10000 0 -0.74 33 33
PDK1/PKC theta 0.016 0.18 -10000 0 -0.58 35 35
CSK/PAG1 0.006 0.2 -10000 0 -0.76 27 27
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.004 0.058 -10000 0 -0.72 3 3
GRAP2/SLP76 -0.066 0.21 -10000 0 -0.78 35 35
STIM1 0.006 0.03 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.059 -10000 0 -0.18 16 16
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.26 -10000 0 -0.91 32 32
mol:DAG -0.034 0.11 -10000 0 -0.43 29 29
RAP1A/GDP 0.01 0.022 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.008 0.12 -10000 0 -0.75 12 12
cytotoxic T cell degranulation -0.03 0.29 -10000 0 -1.1 32 32
RAP1A/GTP -0.009 0.022 -10000 0 -0.069 17 17
mol:PI-3-4-5-P3 0.016 0.17 -10000 0 -0.57 32 32
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.047 0.17 0.27 9 -0.65 29 38
NRAS 0 0 -10000 0 -10000 0 0
ZAP70 -0.011 0.093 -10000 0 -0.74 8 8
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.052 0.16 -10000 0 -0.63 33 33
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.025 0.13 -10000 0 -0.65 19 19
CARD11 -0.004 0.049 -10000 0 -0.63 3 3
PRKCB -0.035 0.1 -10000 0 -0.37 36 36
PRKCE -0.024 0.075 -10000 0 -0.3 25 25
PRKCQ 0.004 0.21 -10000 0 -0.68 36 36
LCP2 -0.008 0.08 -10000 0 -0.74 6 6
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.12 -10000 0 -0.39 32 32
IKK complex 0.035 0.047 -10000 0 -0.13 11 11
RAS family/GDP -0.003 0.008 -10000 0 -10000 0 0
MAP3K14 0.031 0.089 -10000 0 -0.31 20 20
PDPK1 0.025 0.13 -10000 0 -0.47 27 27
TCR/CD3/MHC I/CD8/Fyn -0.013 0.25 -10000 0 -0.92 28 28
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.003 0.046 -9999 0 -0.74 2 2
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.086 0.18 -9999 0 -0.48 86 86
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.053 0.18 -9999 0 -0.43 86 86
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.033 0.13 -9999 0 -0.57 29 29
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.006 0.066 -9999 0 -0.74 4 4
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 -0.002 0.032 -9999 0 -0.42 3 3
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.011 0.08 -9999 0 -0.57 10 10
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.15 0.25 -9999 0 -0.57 131 131
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.2 -9999 0 -0.46 115 115
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.093 0.14 -9999 0 -0.48 29 29
MAP1B -0.002 0.019 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.072 0.15 -9999 0 -0.62 3 3
RELN -0.13 0.28 -9999 0 -0.73 89 89
PAFAH/LIS1 -0.004 0.042 -9999 0 -0.48 4 4
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.069 0.11 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.062 0.12 -9999 0 -0.51 5 5
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.1 0.15 -9999 0 -0.51 29 29
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.02 0 -9999 0 -10000 0 0
PAFAH1B3 -0.006 0.061 -9999 0 -0.61 5 5
PAFAH1B2 0 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.001 0.012 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.087 0.14 -9999 0 -10000 0 0
LRP8 -0.003 0.044 -9999 0 -0.57 3 3
NDEL1/Katanin 60 -0.093 0.14 -9999 0 -0.48 29 29
P39/CDK5 -0.14 0.19 -9999 0 -0.66 27 27
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.042 0.16 -9999 0 -10000 0 0
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 -0.089 0.17 -9999 0 -0.42 89 89
RELN/VLDLR -0.079 0.17 -9999 0 -0.44 87 87
CDC42 0 0 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.003 0.087 -9999 0 -0.73 7 7
PDGF/PDGFRA/CRKL -0.008 0.063 -9999 0 -0.53 7 7
positive regulation of JUN kinase activity -0.006 0.047 -9999 0 -0.44 2 2
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.095 0.21 -9999 0 -0.56 83 83
AP1 -0.14 0.36 -9999 0 -1.1 61 61
mol:IP3 0.008 0.07 -9999 0 -0.55 7 7
PLCG1 0.008 0.07 -9999 0 -0.55 7 7
PDGF/PDGFRA/alphaV Integrin -0.008 0.063 -9999 0 -0.53 7 7
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.07 -9999 0 -0.55 7 7
CAV3 -0.11 0.26 -9999 0 -0.74 76 76
CAV1 -0.2 0.33 -9999 0 -0.74 137 137
SHC/Grb2/SOS1 -0.006 0.048 -9999 0 -0.45 2 2
PDGF/PDGFRA/Shf -0.008 0.063 -9999 0 -0.53 7 7
FOS -0.096 0.36 -9999 0 -1.1 61 61
JUN -0.008 0.02 -9999 0 -10000 0 0
oligodendrocyte development -0.008 0.063 -9999 0 -0.53 7 7
GRB2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG 0.008 0.07 -9999 0 -0.55 7 7
PDGF/PDGFRA -0.003 0.087 -9999 0 -0.72 7 7
actin cytoskeleton reorganization -0.008 0.063 -9999 0 -0.53 7 7
SRF 0.021 0.009 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.006 0.053 -9999 0 -0.47 6 6
PDGF/PDGFRA/Crk/C3G -0.006 0.053 -9999 0 -0.47 6 6
JAK1 0.011 0.065 -9999 0 -0.53 7 7
ELK1/SRF -0.007 0.048 -9999 0 -0.43 6 6
SHB 0 0 -9999 0 -10000 0 0
SHF 0 0 -9999 0 -10000 0 0
CSNK2A1 0.007 0.019 -9999 0 -10000 0 0
GO:0007205 0.008 0.072 -9999 0 -0.56 7 7
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.006 0.047 -9999 0 -0.44 2 2
PDGF/PDGFRA/SHB -0.008 0.063 -9999 0 -0.53 7 7
PDGF/PDGFRA/Caveolin-1 -0.16 0.26 -9999 0 -0.58 141 141
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 0.011 0.071 -9999 0 -0.53 6 6
PIK3CA 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.008 0.063 -9999 0 -0.53 7 7
JAK-STAT cascade 0.011 0.065 -9999 0 -0.53 7 7
cell proliferation -0.008 0.063 -9999 0 -0.53 7 7
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.003 0.04 -10000 0 -0.51 3 3
CRKL -0.027 0.12 -10000 0 -0.43 2 2
mol:PIP3 -0.014 0.043 0.66 2 -10000 0 2
AKT1 0.004 0.028 0.43 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.018 0.11 -10000 0 -0.4 2 2
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.1 0.2 -10000 0 -0.48 110 110
MAP3K5 -0.011 0.11 -10000 0 -0.44 4 4
HGF/MET/CIN85/CBL/ENDOPHILINS -0.097 0.18 -10000 0 -0.44 110 110
AP1 -0.061 0.16 -10000 0 -0.5 61 61
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.079 0.24 -10000 0 -0.73 61 61
STAT3 (dimer) -0.035 0.14 -10000 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K -0.045 0.086 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
CBL/CRK -0.02 0.11 -10000 0 -0.4 2 2
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 -0.003 0.046 -10000 0 -0.74 2 2
ELK1 -0.004 0.022 -10000 0 -0.24 3 3
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.04 0.076 -10000 0 -0.46 2 2
PAK1 0.01 0.029 0.4 2 -10000 0 2
HGF/MET/RANBP10 -0.1 0.2 -10000 0 -0.48 110 110
HRAS -0.081 0.16 -10000 0 -0.59 4 4
DOCK1 -0.018 0.11 -10000 0 -0.4 2 2
GAB1 -0.035 0.12 -10000 0 -0.39 4 4
CRK -0.027 0.12 -10000 0 -0.43 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.12 0.22 -10000 0 -0.54 110 110
JUN 0 0 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.055 0.1 -10000 0 -0.25 110 110
PIK3R1 0 0 -10000 0 -10000 0 0
cell morphogenesis -0.012 0.14 -10000 0 -10000 0 0
GRB2/SHC -0.046 0.088 -10000 0 -0.5 2 2
FOS -0.09 0.24 -10000 0 -0.74 61 61
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.004 0.022 -10000 0 -0.24 3 3
HGF/MET/MUC20 -0.11 0.2 -10000 0 -0.48 111 111
cell migration -0.045 0.087 -10000 0 -0.49 2 2
GRB2 0 0 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.003 0.04 -10000 0 -0.51 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.067 0.13 -10000 0 -10000 0 0
MET/MUC20 -0.003 0.04 -10000 0 -0.52 3 3
RAP1B -0.01 0.11 -10000 0 -0.37 2 2
RAP1A -0.01 0.11 -10000 0 -0.37 2 2
HGF/MET/RANBP9 -0.1 0.2 -10000 0 -0.48 110 110
RAF1 -0.045 0.16 -10000 0 -0.65 2 2
STAT3 -0.064 0.12 -10000 0 -10000 0 0
cell proliferation -0.049 0.19 -10000 0 -0.52 4 4
RPS6KB1 -0.019 0.036 -10000 0 -10000 0 0
MAPK3 -0.007 0.019 -10000 0 -10000 0 0
MAPK1 -0.007 0.019 -10000 0 -0.23 2 2
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.095 -10000 0 -0.39 1 1
SRC -0.032 0.13 -10000 0 -10000 0 0
PI3K -0.046 0.088 -10000 0 -0.5 2 2
MET/Glomulin -0.003 0.036 -10000 0 -0.46 3 3
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.035 0.15 -10000 0 -0.59 2 2
MET -0.004 0.053 -10000 0 -0.68 3 3
MAP4K1 -0.019 0.12 -10000 0 -0.47 4 4
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.035 0.15 -10000 0 -0.59 2 2
BAD 0.011 0.025 0.4 2 -10000 0 2
MAP2K4 -0.003 0.1 -10000 0 -0.45 2 2
SHP2/GRB2/SOS1/GAB1 -0.048 0.091 -10000 0 -0.44 2 2
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 -0.003 0.046 -10000 0 -0.74 2 2
HGS -0.049 0.095 -10000 0 -0.42 4 4
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.16 0.3 -10000 0 -0.74 108 108
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ -0.003 0.046 -10000 0 -0.74 2 2
NCK/PLCgamma1 -0.052 0.099 -10000 0 -0.52 2 2
PDPK1 -0.004 0.032 0.5 2 -10000 0 2
HGF/MET/SHIP -0.11 0.2 -10000 0 -0.48 110 110
Effects of Botulinum toxin

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
STX1A 0.006 0.039 -9999 0 -0.42 4 4
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.057 0.17 -9999 0 -0.56 51 51
STXBP1 -0.006 0.066 -9999 0 -0.74 4 4
ACh/CHRNA1 -0.014 0.072 -9999 0 -0.43 14 14
RAB3GAP2/RIMS1/UNC13B -0.049 0.15 -9999 0 -0.48 49 49
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 -0.071 0.22 -9999 0 -0.73 49 49
mol:ACh 0.005 0.024 -9999 0 -0.15 12 12
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.043 0.12 -9999 0 -0.36 56 56
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.014 0.072 -9999 0 -0.42 14 14
UNC13B -0.004 0.057 -9999 0 -0.74 3 3
CHRNA1 -0.018 0.1 -9999 0 -0.63 14 14
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.014 0.07 -9999 0 -0.39 16 16
SNAP25 -0.001 0.05 -9999 0 -0.32 11 11
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.018 0.1 -9999 0 -0.57 16 16
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.007 0.053 -9999 0 -0.42 8 8
STX1A/SNAP25 fragment 1/VAMP2 -0.043 0.12 -9999 0 -0.36 56 56
Regulation of nuclear SMAD2/3 signaling

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.007 0.013 -10000 0 -10000 0 0
HSPA8 0 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.027 0.11 -10000 0 -0.52 24 24
AKT1 0.006 0.022 -10000 0 -10000 0 0
GSC -0.037 0.14 -10000 0 -10000 0 0
NKX2-5 -0.3 0.29 -10000 0 -0.57 258 258
muscle cell differentiation 0.094 0.1 0.43 9 -10000 0 9
SMAD2-3/SMAD4/SP1 -0.009 0.037 -10000 0 -10000 0 0
SMAD4 0.016 0.027 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.01 0.035 -10000 0 -0.46 1 1
SMAD3/SMAD4/VDR 0.009 0.032 -10000 0 -10000 0 0
MYC 0.008 0.025 -10000 0 -10000 0 0
CDKN2B -0.1 0.43 -10000 0 -1.5 46 46
AP1 -0.038 0.12 -10000 0 -0.4 10 10
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.031 0.09 -10000 0 -0.42 4 4
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.044 0.16 -10000 0 -0.58 42 42
SMAD3/SMAD4/GR -0.003 0.015 -10000 0 -10000 0 0
GATA3 -0.025 0.13 -10000 0 -0.71 17 17
SKI/SIN3/HDAC complex/NCoR1 0 0.003 -10000 0 -10000 0 0
MEF2C/TIF2 -0.17 0.2 -10000 0 -0.7 34 34
endothelial cell migration -0.011 0.068 1.4 1 -10000 0 1
MAX 0 0.003 -10000 0 -10000 0 0
RBBP7 0 0.001 -10000 0 -10000 0 0
RBBP4 0 0.001 -10000 0 -10000 0 0
RUNX2 0 0 -10000 0 -10000 0 0
RUNX3 0 0 -10000 0 -10000 0 0
RUNX1 0 0 -10000 0 -10000 0 0
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 0 0.003 -10000 0 -10000 0 0
VDR -0.001 0.033 -10000 0 -0.74 1 1
CDKN1A 0.058 0.043 -10000 0 -10000 0 0
KAT2B 0.002 0.034 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.045 0.11 -10000 0 -0.48 12 12
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0.001 -10000 0 -10000 0 0
SERPINE1 0.01 0.069 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.001 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.003 0.039 -10000 0 -0.57 2 2
SAP30 0 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.016 0.032 -10000 0 -10000 0 0
JUN 0.004 0.14 -10000 0 -0.4 8 8
SMAD3/SMAD4/IRF7 -0.004 0.038 -10000 0 -0.54 2 2
TFE3 0.016 0.002 -10000 0 -10000 0 0
COL1A2 0.006 0.052 -10000 0 -0.4 1 1
mesenchymal cell differentiation 0.001 0.017 -10000 0 -10000 0 0
DLX1 -0.34 0.28 -10000 0 -0.57 292 292
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.076 0.24 -10000 0 -0.73 61 61
SMAD3/SMAD4/Max -0.003 0.015 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0.015 -10000 0 -10000 0 0
ZBTB17 0.006 0.019 -10000 0 -10000 0 0
LAMC1 0.047 0.029 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.017 -10000 0 -10000 0 0
IRF7 -0.003 0.047 -10000 0 -0.74 2 2
ESR1 -0.035 0.16 -10000 0 -0.74 24 24
HNF4A -0.009 0.072 -10000 0 -0.57 8 8
MEF2C -0.17 0.23 -10000 0 -0.74 34 34
SMAD2-3/SMAD4 -0.01 0.031 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.011 0.022 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.001 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.006 0.01 -10000 0 -10000 0 0
SKIL 0 0 -10000 0 -10000 0 0
HDAC1 0 0.001 -10000 0 -10000 0 0
HDAC2 0 0.001 -10000 0 -10000 0 0
SNIP1 -0.001 0.026 -10000 0 -0.58 1 1
GCN5L2 0.003 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.003 0.022 -10000 0 -10000 0 0
MSG1/HSC70 -0.002 0.031 -10000 0 -0.49 2 2
SMAD2 0.003 0.029 -10000 0 -10000 0 0
SMAD3 0.019 0.022 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.038 0.027 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.014 0.023 -10000 0 -0.42 1 1
NCOR1 0 0.001 -10000 0 -10000 0 0
NCOA2 -0.001 0.033 -10000 0 -0.74 1 1
NCOA1 0 0 -10000 0 -10000 0 0
MYOD/E2A -0.059 0.14 -10000 0 -0.42 71 71
SMAD2-3/SMAD4/SP1/MIZ-1 0.018 0.055 -10000 0 -10000 0 0
IFNB1 0.034 0.048 -10000 0 -0.48 3 3
SMAD3/SMAD4/MEF2C -0.17 0.2 -10000 0 -0.71 34 34
CITED1 -0.003 0.042 -10000 0 -0.66 2 2
SMAD2-3/SMAD4/ARC105 -0.008 0.025 -10000 0 -10000 0 0
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.008 0.16 -10000 0 -0.48 46 46
RUNX1-3/PEBPB2 0 0 -10000 0 -10000 0 0
SMAD7 -0.025 0.097 -10000 0 -10000 0 0
MYC/MIZ-1 0.014 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.076 0.3 8 -0.45 1 9
IL10 0.026 0.11 -10000 0 -0.59 9 9
PIASy/HDAC complex 0.007 0.006 -10000 0 -10000 0 0
PIAS3 0.004 0.007 -10000 0 -10000 0 0
CDK2 0.006 0.01 -10000 0 -10000 0 0
IL5 0.023 0.095 -10000 0 -0.46 14 14
CDK4 0.005 0.028 -10000 0 -0.58 1 1
PIAS4 0.007 0.006 -10000 0 -10000 0 0
ATF3 -0.003 0.046 -10000 0 -0.74 2 2
SMAD3/SMAD4/SP1 0.001 0.027 -10000 0 -10000 0 0
FOXG1 -0.064 0.18 -10000 0 -0.58 55 55
FOXO3 0.015 0.029 -10000 0 -10000 0 0
FOXO1 0.015 0.029 -10000 0 -10000 0 0
FOXO4 0.015 0.029 -10000 0 -10000 0 0
heart looping -0.16 0.22 -10000 0 -0.72 34 34
CEBPB 0.008 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.21 0.18 -10000 0 -0.36 292 292
MYOD1 -0.082 0.2 -10000 0 -0.57 71 71
SMAD3/SMAD4/HNF4 -0.007 0.047 -10000 0 -0.39 1 1
SMAD3/SMAD4/GATA3 -0.02 0.093 -10000 0 -0.51 15 15
SnoN/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.001 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.004 0.025 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.017 0.011 -10000 0 -10000 0 0
SIN3B 0 0.001 -10000 0 -10000 0 0
SIN3A 0 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.2 0.19 -10000 0 -0.64 35 35
ITGB5 0.055 0.035 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.1 0.2 -10000 0 -0.5 103 103
AR -0.15 0.3 -10000 0 -0.74 103 103
negative regulation of cell growth 0.003 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.053 0.13 -10000 0 -0.38 41 41
E2F5 0 0 -10000 0 -10000 0 0
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.03 0.086 -10000 0 -0.46 3 3
SMAD2-3/SMAD4/FOXO1-3a-4 -0.02 0.098 -10000 0 -10000 0 0
TFDP1 -0.003 0.044 -10000 0 -0.57 3 3
SMAD3/SMAD4/AP1 -0.038 0.12 -10000 0 -0.41 6 6
SMAD3/SMAD4/RUNX2 -0.001 0.017 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.001 0.12 -10000 0 -0.48 25 25
ACTA1 -0.011 0.16 -10000 0 -0.64 25 25
NUMA1 0.001 0.12 -10000 0 -0.48 25 25
SPTAN1 -0.009 0.15 -10000 0 -0.64 25 25
LIMK1 -0.009 0.15 -10000 0 -0.64 25 25
BIRC3 -0.009 0.08 -10000 0 -0.74 6 6
BIRC2 0 0.002 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.01 0.16 -10000 0 -0.63 28 28
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.001 0.12 -10000 0 -0.48 25 25
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.009 0.15 -10000 0 -0.62 25 25
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.009 0.16 -10000 0 -0.64 25 25
MADD 0 0 -10000 0 -10000 0 0
TFAP2A -0.071 0.12 -10000 0 -0.78 12 12
BID 0.005 0.073 -10000 0 -0.3 27 27
MAP3K1 0.004 0.046 -10000 0 -0.24 8 8
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.01 0.16 -10000 0 -0.63 26 26
CASP9 0.001 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.034 -10000 0 -0.21 2 2
neuron apoptosis 0.019 0.016 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.003 0.15 -10000 0 -0.61 25 25
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.018 0.072 -10000 0 -0.42 4 4
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD -0.002 0.15 -10000 0 -0.61 25 25
CASP7 -0.005 0.042 0.36 6 -10000 0 6
KRT18 0.013 0.019 -10000 0 -10000 0 0
apoptosis -0.001 0.14 -10000 0 -0.56 25 25
DFFA -0.009 0.15 -10000 0 -0.64 25 25
DFFB -0.009 0.15 -10000 0 -0.64 25 25
PARP1 0.002 0.034 0.21 2 -10000 0 2
actin filament polymerization 0.001 0.14 0.58 25 -10000 0 25
TNF -0.019 0.12 -10000 0 -0.72 13 13
CYCS 0.008 0.055 -10000 0 -0.26 12 12
SATB1 0.021 0.078 -10000 0 -0.5 4 4
SLK -0.009 0.15 -10000 0 -0.64 25 25
p15 BID/BAX -0.014 0.061 -10000 0 -0.34 10 10
CASP2 0.035 0.051 -10000 0 -0.44 1 1
JNK cascade -0.004 0.046 0.23 8 -10000 0 8
CASP3 -0.017 0.16 -10000 0 -0.68 25 25
LMNB2 0.033 0.048 -10000 0 -0.48 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.033 -10000 0 -0.74 1 1
Mammalian IAPs/DIABLO -0.005 0.047 -10000 0 -0.43 6 6
negative regulation of DNA binding -0.07 0.12 -10000 0 -0.77 12 12
stress fiber formation -0.009 0.15 -10000 0 -0.62 25 25
GZMB -0.02 0.18 -10000 0 -0.72 27 27
CASP1 0.012 0.051 -10000 0 -0.72 2 2
LMNB1 0.033 0.048 -10000 0 -0.48 1 1
APP 0.019 0.016 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
VIM -0.007 0.14 -10000 0 -0.55 25 25
LMNA 0.033 0.048 -10000 0 -0.48 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.046 -10000 0 -0.46 1 1
LRDD -0.001 0.033 -10000 0 -0.74 1 1
SREBF1 -0.009 0.15 -10000 0 -0.64 25 25
APAF-1/Caspase 9 -0.002 0.022 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.001 0.12 -10000 0 -0.47 25 25
CFL2 -0.002 0.15 -10000 0 -0.6 25 25
GAS2 -0.061 0.21 -10000 0 -0.52 71 71
positive regulation of apoptosis 0.035 0.048 -10000 0 -0.47 1 1
PRF1 -0.037 0.16 -10000 0 -0.74 25 25
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0.019 0.008 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
mol:Sphinganine-1-P 0.02 0 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.004 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.006 -9999 0 -10000 0 0
S1PR5 -0.01 0.075 -9999 0 -0.6 8 8
S1PR4 -0.065 0.21 -9999 0 -0.74 44 44
GNAI1 -0.001 0.033 -9999 0 -0.74 1 1
S1P/S1P5/G12 -0.005 0.04 -9999 0 -0.42 1 1
S1P/S1P3/Gq -0.069 0.12 -9999 0 -0.28 123 123
S1P/S1P4/Gi -0.03 0.092 -9999 0 -0.5 3 3
GNAQ -0.001 0.033 -9999 0 -0.74 1 1
GNAZ -0.009 0.08 -9999 0 -0.74 6 6
GNA14 -0.18 0.32 -9999 0 -0.74 123 123
GNA15 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.1 0.26 -9999 0 -0.74 70 70
GNB1/GNG2 -0.042 0.091 -9999 0 -0.58 5 5
mol:DAG -0.003 0.099 -9999 0 -0.56 4 4
PLCG1 -0.003 0.1 -9999 0 -0.58 4 4
YES1 -0.012 0.098 -9999 0 -0.64 2 2
FZD3 0 0 -9999 0 -10000 0 0
FZD6 0 0 -9999 0 -10000 0 0
G protein -0.039 0.086 -9999 0 -0.59 4 4
MAP3K7 -0.016 0.14 -9999 0 -0.54 14 14
mol:Ca2+ -0.002 0.097 -9999 0 -0.54 4 4
mol:IP3 -0.003 0.099 -9999 0 -0.56 4 4
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
CAMK2A -0.025 0.15 -9999 0 -0.58 15 15
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.045 0.091 -9999 0 -0.68 2 2
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.012 0.098 -9999 0 -0.64 2 2
GO:0007205 -0.002 0.098 -9999 0 -0.56 4 4
WNT6 -0.094 0.21 -9999 0 -0.57 82 82
WNT4 -0.01 0.083 -9999 0 -0.66 8 8
NFAT1/CK1 alpha -0.081 0.15 -9999 0 -0.56 18 18
GNG2 -0.007 0.073 -9999 0 -0.74 5 5
WNT5A -0.014 0.093 -9999 0 -0.6 12 12
WNT11 -0.038 0.16 -9999 0 -0.68 28 28
CDC42 -0.004 0.094 -9999 0 -0.6 2 2
Syndecan-2-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
Syndecan-2/Fibronectin -0.017 0.093 -9999 0 -0.5 17 17
EPHB2 -0.009 0.072 -9999 0 -0.57 8 8
Syndecan-2/TACI -0.015 0.079 -9999 0 -0.42 18 18
LAMA1 -0.17 0.26 -9999 0 -0.58 146 146
Syndecan-2/alpha2 ITGB1 -0.014 0.079 -9999 0 -0.43 17 17
HRAS 0 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.005 0.048 -9999 0 -0.48 5 5
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.031 0.045 -9999 0 -10000 0 0
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.004 0.043 -9999 0 -0.43 5 5
LAMA3 -0.019 0.12 -9999 0 -0.74 13 13
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.018 0.11 -9999 0 -0.74 12 12
Syndecan-2/MMP2 -0.008 0.069 -9999 0 -0.53 8 8
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0 0 -9999 0 -10000 0 0
dendrite morphogenesis -0.01 0.064 -9999 0 -0.4 13 13
Syndecan-2/GM-CSF -0.052 0.15 -9999 0 -0.48 54 54
determination of left/right symmetry 0.012 0.057 -9999 0 -0.55 5 5
Syndecan-2/PKC delta -0.005 0.047 -9999 0 -0.48 5 5
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 -0.021 0.14 -9999 0 -0.43 54 54
MAPK1 -0.021 0.14 -9999 0 -0.43 54 54
Syndecan-2/RACK1 -0.004 0.04 -9999 0 -0.41 5 5
NF1 0 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.057 -9999 0 -0.55 5 5
ITGA2 0 0 -9999 0 -10000 0 0
MAPK8 0.025 0.05 -9999 0 -0.47 5 5
Syndecan-2/alpha2/beta1 Integrin -0.087 0.14 -9999 0 -0.55 6 6
Syndecan-2/Kininogen -0.014 0.072 -9999 0 -0.38 18 18
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.028 0.041 -9999 0 -0.38 5 5
Syndecan-2/CASK/Protein 4.1 -0.004 0.043 -9999 0 -0.44 5 5
extracellular matrix organization -0.005 0.047 -9999 0 -0.47 5 5
actin cytoskeleton reorganization -0.017 0.092 -9999 0 -0.5 17 17
Syndecan-2/Caveolin-2/Ras -0.015 0.082 -9999 0 -0.46 16 16
Syndecan-2/Laminin alpha3 -0.017 0.093 -9999 0 -0.5 17 17
Syndecan-2/RasGAP -0.004 0.038 -9999 0 -0.38 5 5
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.01 0.064 -9999 0 -0.4 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.004 0.037 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.017 0.1 -9999 0 -0.64 13 13
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin -0.005 0.047 -9999 0 -0.48 5 5
TGFB1 0 0 -9999 0 -10000 0 0
CASP3 0.024 0.045 -9999 0 -0.43 5 5
FN1 -0.019 0.12 -9999 0 -0.74 13 13
Syndecan-2/IL8 -0.018 0.084 -9999 0 -0.4 23 23
SDC2 0.012 0.057 -9999 0 -0.56 5 5
KNG1 -0.015 0.091 -9999 0 -0.57 13 13
Syndecan-2/Neurofibromin -0.005 0.047 -9999 0 -0.48 5 5
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.072 0.22 -9999 0 -0.74 49 49
Syndecan-2/TGFB1 -0.005 0.047 -9999 0 -0.48 5 5
Syndecan-2/Syntenin/PI-4-5-P2 -0.004 0.043 -9999 0 -0.44 5 5
Syndecan-2/Ezrin -0.004 0.043 -9999 0 -0.43 5 5
PRKACA 0.024 0.045 -9999 0 -0.43 5 5
angiogenesis -0.018 0.084 -9999 0 -0.4 23 23
MMP2 -0.006 0.066 -9999 0 -0.74 4 4
IL8 -0.022 0.11 -9999 0 -0.61 18 18
calcineurin-NFAT signaling pathway -0.015 0.079 -9999 0 -0.42 18 18
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 0 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.054 0.42 8 -10000 0 8
CDKN1A 0 0.006 -10000 0 -10000 0 0
KAT2B -0.001 0.033 -10000 0 -0.74 1 1
BAX 0 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.02 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 -0.002 0.036 -10000 0 -0.57 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.048 0.15 -10000 0 -0.42 72 72
PPARGC1A -0.15 0.3 -10000 0 -0.74 100 100
FHL2 -0.005 0.051 -10000 0 -0.57 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0 -10000 0 -10000 0 0
HIST2H4A 0.011 0.054 -10000 0 -0.42 8 8
SIRT1/FOXO3a 0 0 -10000 0 -10000 0 0
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.011 0.037 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
SIRT1/PGC1A -0.097 0.19 -10000 0 -0.48 100 100
p53/SIRT1 -0.001 0.025 -10000 0 -0.56 1 1
SIRT1/FOXO4 0 0 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.003 0.028 -10000 0 -0.32 4 4
HIST1H1E 0.004 0.052 -10000 0 -10000 0 0
SIRT1/p300 0 0 -10000 0 -10000 0 0
muscle cell differentiation 0.05 0.12 0.35 72 -10000 0 72
TP53 -0.001 0.033 -10000 0 -0.74 1 1
KU70/SIRT1/BAX 0 0 -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 -0.002 0.026 -10000 0 -0.42 2 2
ACSS2 0.018 0 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.05 0.12 -10000 0 -0.35 72 72
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.002 0.02 -10000 0 -10000 0 0
RFC1 0.002 0.02 -10000 0 -10000 0 0
PRKDC 0.002 0.02 -10000 0 -10000 0 0
RIPK1 0 0.002 -10000 0 -10000 0 0
CASP7 -0.012 0.037 0.26 1 -10000 0 1
FASLG/FAS/FADD/FAF1 -0.018 0.074 0.24 4 -0.34 21 25
MAP2K4 -0.01 0.13 -10000 0 -0.51 7 7
mol:ceramide -0.006 0.11 -10000 0 -0.43 21 21
GSN 0.002 0.02 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.088 0.22 3 -0.42 20 23
FAS 0.006 0.048 -10000 0 -0.74 2 2
BID 0.003 0.028 0.31 4 -10000 0 4
MAP3K1 0.004 0.079 0.22 1 -0.28 6 7
MAP3K7 0.009 0.004 -10000 0 -10000 0 0
RB1 0.001 0.029 -10000 0 -0.47 1 1
CFLAR 0 0.002 -10000 0 -10000 0 0
HGF/MET -0.11 0.2 -10000 0 -0.48 112 112
ARHGDIB 0.001 0.023 -10000 0 -0.32 1 1
FADD 0.009 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.02 -10000 0 -10000 0 0
NFKB1 -0.037 0.078 -10000 0 -10000 0 0
MAPK8 -0.029 0.19 -10000 0 -0.44 80 80
DFFA 0.002 0.02 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.02 -10000 0 -10000 0 0
FAS/FADD/MET -0.005 0.045 -10000 0 -0.45 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.005 0.071 -10000 0 -0.7 5 5
FAF1 0.009 0.004 -10000 0 -10000 0 0
PARP1 0.002 0.02 -10000 0 -10000 0 0
DFFB 0.002 0.02 -10000 0 -10000 0 0
CHUK -0.032 0.069 -10000 0 -10000 0 0
FASLG -0.021 0.15 -10000 0 -0.74 20 20
FAS/FADD -0.003 0.036 -10000 0 -0.57 2 2
HGF -0.16 0.3 -10000 0 -0.74 108 108
LMNA 0.002 0.018 -10000 0 -10000 0 0
CASP6 0.002 0.02 -10000 0 -10000 0 0
CASP10 0.007 0.034 -10000 0 -0.74 1 1
CASP3 0.002 0.023 0.23 4 -10000 0 4
PTPN13 -0.004 0.057 -10000 0 -0.74 3 3
CASP8 0.004 0.04 0.43 4 -10000 0 4
IL6 -0.19 0.5 -10000 0 -1.3 82 82
MET -0.004 0.053 -10000 0 -0.68 3 3
ICAD/CAD 0.002 0.019 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.006 0.11 -10000 0 -0.43 21 21
activation of caspase activity by cytochrome c 0.003 0.028 0.31 4 -10000 0 4
PAK2 0.002 0.019 -10000 0 -10000 0 0
BCL2 0.001 0.026 -10000 0 -0.58 1 1
BCR signaling pathway

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
JUN 0.014 0.098 -10000 0 -0.47 12 12
IKBKB 0.015 0.052 -10000 0 -0.28 2 2
AKT1 0.004 0.085 0.23 1 -0.27 19 20
IKBKG 0.017 0.055 -10000 0 -0.28 5 5
CALM1 -0.011 0.1 -10000 0 -0.49 14 14
PIK3CA 0 0 -10000 0 -10000 0 0
MAP3K1 0 0.14 -10000 0 -0.68 14 14
MAP3K7 0 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.11 -10000 0 -0.52 14 14
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.002 0.083 0.18 2 -0.29 7 9
LYN -0.003 0.047 -10000 0 -0.74 2 2
BLNK -0.001 0.033 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.03 0.13 -10000 0 -0.56 27 27
CD22 -0.077 0.22 -10000 0 -0.63 53 53
CAMK2G -0.003 0.094 -10000 0 -0.62 6 6
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
SHC/GRB2/SOS1 -0.021 0.094 -10000 0 -0.73 4 4
GO:0007205 -0.019 0.11 -10000 0 -0.54 14 14
SYK -0.001 0.033 -10000 0 -0.74 1 1
ELK1 -0.011 0.1 -10000 0 -0.5 14 14
NFATC1 -0.007 0.12 -10000 0 -0.55 16 16
B-cell antigen/BCR complex -0.03 0.13 -10000 0 -0.56 27 27
PAG1/CSK -0.008 0.065 -10000 0 -0.56 7 7
NFKBIB 0.014 0.02 0.078 2 -10000 0 2
HRAS -0.003 0.097 -10000 0 -0.48 14 14
NFKBIA 0.014 0.019 0.078 2 -10000 0 2
NF-kappa-B/RelA/I kappa B beta 0.018 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.029 0.12 -10000 0 -0.51 24 24
mol:GDP -0.021 0.1 -10000 0 -0.51 14 14
PTEN -0.003 0.046 -10000 0 -0.74 2 2
CD79B -0.007 0.07 -10000 0 -0.7 5 5
NF-kappa-B/RelA/I kappa B alpha 0.018 0.016 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.015 0.15 -10000 0 -0.57 20 20
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.028 0.11 -10000 0 -0.54 14 14
CSK 0 0 -10000 0 -10000 0 0
FOS -0.05 0.16 -10000 0 -0.41 72 72
CHUK 0.017 0.055 -10000 0 -0.28 4 4
IBTK 0 0.001 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.023 0.084 -10000 0 -0.59 7 7
PTPN6 -0.071 0.2 -10000 0 -0.6 51 51
RELA 0 0.001 -10000 0 -10000 0 0
BCL2A1 0.015 0.025 -10000 0 -0.12 13 13
VAV2 -0.06 0.17 -10000 0 -0.7 22 22
ubiquitin-dependent protein catabolic process 0.018 0.019 0.081 2 -10000 0 2
BTK -0.11 0.34 -10000 0 -1.1 49 49
CD19 -0.066 0.18 -10000 0 -0.64 28 28
MAP4K1 -0.006 0.066 -10000 0 -0.74 4 4
CD72 -0.001 0.026 -10000 0 -0.57 1 1
PAG1 -0.01 0.087 -10000 0 -0.74 7 7
MAPK14 0.01 0.12 -10000 0 -0.59 12 12
SH3BP5 -0.012 0.092 -10000 0 -0.74 8 8
PIK3AP1 -0.014 0.13 -10000 0 -0.68 14 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.03 0.14 -10000 0 -0.62 21 21
RAF1 0.004 0.092 -10000 0 -0.6 6 6
RasGAP/p62DOK/SHIP -0.028 0.12 -10000 0 -0.74 8 8
CD79A -0.034 0.15 -10000 0 -0.68 25 25
re-entry into mitotic cell cycle -0.002 0.082 0.18 3 -0.29 7 10
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.018 0.077 -10000 0 -0.48 6 6
MAPK1 0.018 0.077 -10000 0 -0.48 6 6
CD72/SHP1 -0.065 0.19 -10000 0 -0.75 26 26
NFKB1 0 0.001 -10000 0 -10000 0 0
MAPK8 0.01 0.12 -10000 0 -0.57 13 13
actin cytoskeleton organization -0.014 0.15 -10000 0 -0.68 15 15
NF-kappa-B/RelA 0.04 0.032 0.16 2 -10000 0 2
Calcineurin -0.021 0.076 -10000 0 -0.55 6 6
PI3K -0.063 0.14 -10000 0 -0.55 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.024 0.1 0.26 4 -0.52 14 18
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.039 0.16 -10000 0 -0.9 14 14
DAPP1 -0.044 0.18 -10000 0 -1.1 13 13
cytokine secretion -0.005 0.12 -10000 0 -0.5 16 16
mol:DAG -0.028 0.11 -10000 0 -0.54 14 14
PLCG2 0 0.001 -10000 0 -10000 0 0
MAP2K1 0.011 0.085 -10000 0 -0.55 6 6
B-cell antigen/BCR complex/FcgammaRIIB -0.034 0.14 -10000 0 -0.53 32 32
mol:PI-3-4-5-P3 -0.045 0.1 0.32 1 -0.4 19 20
ETS1 -0.004 0.11 -10000 0 -0.5 17 17
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.025 0.11 -10000 0 -0.48 21 21
B-cell antigen/BCR complex/LYN -0.044 0.17 -10000 0 -0.74 21 21
MALT1 0 0.001 -10000 0 -10000 0 0
TRAF6 0.001 0.003 -10000 0 -10000 0 0
RAC1 -0.017 0.16 -10000 0 -0.74 15 15
B-cell antigen/BCR complex/LYN/SYK -0.068 0.2 -10000 0 -0.79 26 26
CARD11 -0.013 0.11 -10000 0 -0.54 14 14
FCGR2B -0.013 0.098 -10000 0 -0.74 9 9
PPP3CA 0 0 -10000 0 -10000 0 0
BCL10 0 0.001 -10000 0 -10000 0 0
IKK complex 0.016 0.026 -10000 0 -10000 0 0
PTPRC -0.049 0.18 -10000 0 -0.74 33 33
PDPK1 -0.03 0.068 0.21 1 -0.27 16 17
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.018 0.013 -10000 0 -0.1 1 1
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.057 0.13 -9999 0 -0.56 7 7
MAP3K8 0.006 0.047 -9999 0 -0.74 2 2
FOS 0 0.1 -9999 0 -0.46 7 7
PRKCA 0.007 0.048 -9999 0 -0.74 2 2
PTPN7 0.008 0.042 -9999 0 -0.66 2 2
HRAS 0 0 -9999 0 -10000 0 0
PRKCB -0.031 0.17 -9999 0 -0.74 27 27
NRAS 0 0 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.007 0.063 -9999 0 -0.45 1 1
MAP2K1 -0.003 0.13 -9999 0 -0.52 28 28
ELK1 -0.001 0.004 -9999 0 -10000 0 0
BRAF -0.032 0.12 -9999 0 -0.52 28 28
mol:GTP -0.001 0.002 -9999 0 -0.006 61 61
MAPK1 0.007 0.063 -9999 0 -0.45 1 1
RAF1 -0.032 0.12 -9999 0 -0.52 28 28
KRAS 0 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.034 0.12 -9999 0 -0.46 37 37
MAP4K1 -0.006 0.066 -9999 0 -0.74 4 4
MAP3K8 -0.003 0.046 -9999 0 -0.74 2 2
PRKCB -0.04 0.17 -9999 0 -0.74 27 27
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.015 0.098 -9999 0 -0.72 3 3
JUN -0.007 0.16 -9999 0 -0.66 27 27
MAP3K7 0.015 0.098 -9999 0 -0.72 3 3
GRAP2 -0.044 0.18 -9999 0 -0.74 30 30
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.022 0.1 -9999 0 -0.76 3 3
LAT 0 0 -9999 0 -10000 0 0
LCP2 -0.009 0.08 -9999 0 -0.74 6 6
MAPK8 -0.015 0.17 -9999 0 -0.7 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.025 0.095 -9999 0 -0.76 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.032 0.12 -9999 0 -0.81 3 3
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.031 0.13 -9999 0 -0.56 28 28
PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
SPHK1 -0.008 0.021 -9999 0 -10000 0 0
mol:S1P -0.01 0.029 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.001 0.14 -9999 0 -0.59 7 7
GNAO1 0.006 0.05 -9999 0 -0.64 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.04 0.1 -9999 0 -0.5 8 8
PLCG1 0.006 0.13 -9999 0 -0.54 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.034 -9999 0 -0.74 1 1
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GNAI1 0.008 0.034 -9999 0 -0.75 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.013 0.11 -9999 0 -0.48 28 28
S1P1/S1P -0.033 0.092 -9999 0 -0.38 28 28
negative regulation of cAMP metabolic process 0 0.13 -9999 0 -0.57 7 7
MAPK3 -0.011 0.19 -9999 0 -0.55 51 51
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.041 0.17 -9999 0 -0.74 28 28
PLCB2 0.003 0.11 -9999 0 -0.4 15 15
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.028 0.078 -9999 0 -0.41 7 7
receptor internalization -0.031 0.087 -9999 0 -0.35 28 28
PTGS2 -0.061 0.34 -9999 0 -1.1 51 51
Rac1/GTP -0.028 0.078 -9999 0 -0.41 7 7
RHOA 0 0 -9999 0 -10000 0 0
VEGFA 0 0.001 -9999 0 -10000 0 0
negative regulation of T cell proliferation 0 0.13 -9999 0 -0.57 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.082 -9999 0 -0.74 6 6
MAPK1 -0.011 0.19 -9999 0 -0.55 51 51
S1P1/S1P/PDGFB-D/PDGFRB 0.005 0.11 -9999 0 -0.55 7 7
ABCC1 -0.001 0.026 -9999 0 -0.57 1 1
EGFR-dependent Endothelin signaling events

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
HRAS 0 0 -9999 0 -10000 0 0
EGFR -0.023 0.12 -9999 0 -0.63 18 18
EGF/EGFR -0.058 0.15 -9999 0 -0.45 56 56
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.019 0.083 -9999 0 -0.81 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.009 0.08 -9999 0 -0.74 6 6
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.014 0.097 -9999 0 -0.69 10 10
EGF/EGFR dimer/SHC -0.023 0.098 -9999 0 -0.51 12 12
mol:GDP -0.019 0.082 -9999 0 -0.79 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.065 0.21 -9999 0 -0.74 44 44
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.017 0.075 -9999 0 -0.74 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.017 0.076 -9999 0 -0.75 1 1
FRAP1 -0.018 0.079 -9999 0 -0.77 1 1
EGF/EGFR dimer -0.027 0.12 -9999 0 -0.49 27 27
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.055 0.17 -9999 0 -0.56 50 50
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.029 0.11 0.45 32 -10000 0 32
KIRREL -0.004 0.095 -10000 0 -0.75 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.029 0.11 -10000 0 -0.45 32 32
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 -0.022 0.085 -10000 0 -0.45 9 9
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.013 0.053 -10000 0 -0.34 8 8
FYN -0.007 0.085 -10000 0 -0.46 9 9
mol:Ca2+ -0.022 0.085 -10000 0 -0.45 9 9
mol:DAG -0.022 0.085 -10000 0 -0.45 9 9
NPHS2 -0.003 0.047 -10000 0 -0.58 3 3
mol:IP3 -0.022 0.085 -10000 0 -0.45 9 9
regulation of endocytosis -0.019 0.075 -10000 0 -0.42 9 9
Nephrin/NEPH1/podocin/Cholesterol -0.023 0.087 -10000 0 -0.46 9 9
establishment of cell polarity -0.029 0.11 -10000 0 -0.45 32 32
Nephrin/NEPH1/podocin/NCK1-2 -0.02 0.077 -10000 0 -0.51 2 2
Nephrin/NEPH1/beta Arrestin2 -0.019 0.076 -10000 0 -0.43 9 9
NPHS1 -0.021 0.12 -10000 0 -0.57 24 24
Nephrin/NEPH1/podocin -0.021 0.082 -10000 0 -0.46 9 9
TJP1 0 0 -10000 0 -10000 0 0
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 -0.022 0.085 -10000 0 -0.45 9 9
CD2AP 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.022 0.085 -10000 0 -0.45 9 9
GRB2 0 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.024 0.14 -10000 0 -0.5 31 31
cytoskeleton organization -0.016 0.066 -10000 0 -0.5 1 1
Nephrin/NEPH1 -0.021 0.08 -10000 0 -0.32 32 32
Nephrin/NEPH1/ZO-1 -0.023 0.088 -10000 0 -0.46 9 9
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.007 0.1 -9999 0 -0.61 13 13
Syndecan-4/Syndesmos 0.01 0.075 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.048 0.12 -9999 0 -0.59 12 12
Syndecan-4/ADAM12 -0.06 0.14 -9999 0 -0.57 2 2
CCL5 -0.013 0.098 -9999 0 -0.74 9 9
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.007 0.058 -9999 0 -0.58 5 5
ADAM12 -0.14 0.25 -9999 0 -0.57 121 121
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.012 0.035 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.075 0.15 -9999 0 -0.62 2 2
Syndecan-4/CXCL12/CXCR4 -0.051 0.13 -9999 0 -0.63 12 12
Syndecan-4/Laminin alpha3 0 0.099 -9999 0 -0.6 2 2
MDK -0.01 0.076 -9999 0 -0.57 9 9
Syndecan-4/FZD7 0.01 0.076 -9999 0 -10000 0 0
Syndecan-4/Midkine 0.005 0.086 -9999 0 -0.57 1 1
FZD7 -0.001 0.026 -9999 0 -0.57 1 1
Syndecan-4/FGFR1/FGF -0.03 0.089 -9999 0 -0.59 3 3
THBS1 -0.013 0.098 -9999 0 -0.74 9 9
integrin-mediated signaling pathway -0.01 0.08 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.048 0.12 -9999 0 -0.59 12 12
Syndecan-4/TACI 0.001 0.091 -9999 0 -10000 0 0
CXCR4 -0.001 0.033 -9999 0 -0.74 1 1
cell adhesion -0.008 0.062 -9999 0 -0.36 15 15
Syndecan-4/Dynamin 0.01 0.075 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.003 0.11 -9999 0 -0.66 8 8
Syndecan-4/GIPC 0.01 0.075 -9999 0 -10000 0 0
Syndecan-4/RANTES 0.003 0.095 -9999 0 -0.68 2 2
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.17 0.26 -9999 0 -0.58 146 146
LAMA3 -0.019 0.12 -9999 0 -0.74 13 13
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.005 0.05 -9999 0 -0.69 2 2
Syndecan-4/alpha-Actinin 0.01 0.075 -9999 0 -10000 0 0
TFPI -0.054 0.19 -9999 0 -0.74 37 37
F2 -0.015 0.1 -9999 0 -0.57 16 16
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.076 0.16 -9999 0 -0.64 7 7
ACTN1 0 0 -9999 0 -10000 0 0
TNC -0.013 0.087 -9999 0 -0.59 11 11
Syndecan-4/CXCL12 -0.023 0.15 -9999 0 -0.65 11 11
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.062 0.2 -9999 0 -0.74 42 42
TNFRSF13B -0.017 0.1 -9999 0 -0.64 13 13
FGF2 -0.021 0.12 -9999 0 -0.74 14 14
FGFR1 -0.001 0.033 -9999 0 -0.74 1 1
Syndecan-4/PI-4-5-P2 0.004 0.075 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.017 0.12 -9999 0 -0.72 13 13
cell migration -0.005 0.014 -9999 0 -10000 0 0
PRKCD 0.002 0.006 -9999 0 -10000 0 0
vasculogenesis -0.01 0.1 -9999 0 -0.63 8 8
SDC4 0.005 0.078 -9999 0 -10000 0 0
Syndecan-4/Tenascin C 0.004 0.085 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2/PKC alpha -0.01 0.027 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.01 0.075 -9999 0 -10000 0 0
MMP9 -0.022 0.14 -9999 0 -0.58 28 28
Rac1/GTP -0.009 0.064 -9999 0 -0.37 15 15
cytoskeleton organization -0.004 0.07 -9999 0 -10000 0 0
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.019 0.14 -9999 0 -0.64 7 7
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.006 0.006 -9999 0 -10000 0 0
GNB1/GNG2 -0.007 0.057 -9999 0 -0.46 7 7
forebrain development -0.086 0.14 -9999 0 -0.54 6 6
GNAO1 0.001 0.05 -9999 0 -0.63 3 3
SMO/beta Arrestin2 -0.002 0.027 -9999 0 -0.42 2 2
SMO 0.003 0.038 -9999 0 -0.58 2 2
ARRB2 0.005 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.015 -9999 0 -10000 0 0
mol:GTP -0.003 0.004 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.005 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.004 -9999 0 -10000 0 0
GNAI1 0.004 0.034 -9999 0 -0.74 1 1
XPO1 0.006 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.1 0.11 -9999 0 -0.58 3 3
SAP30 0.006 0.006 -9999 0 -10000 0 0
mol:GDP 0.003 0.037 -9999 0 -0.58 2 2
MIM/GLI2A -0.033 0.05 -9999 0 -10000 0 0
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.005 0.005 -9999 0 -10000 0 0
GLI2 0.037 0.023 -9999 0 -10000 0 0
GLI3 0.04 0.016 -9999 0 -10000 0 0
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.006 0.006 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.007 0.073 -9999 0 -0.74 5 5
Gi family/GTP 0.002 0.049 -9999 0 -0.32 5 5
SIN3B 0.006 0.006 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
GLI3/Su(fu) -0.001 0.009 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.033 -9999 0 -10000 0 0
FOXA2 -0.6 0.6 -9999 0 -1.2 250 250
neural tube patterning -0.086 0.14 -9999 0 -0.54 6 6
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.009 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 -0.033 0.05 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.086 0.14 -9999 0 -0.54 6 6
SUFU 0.012 0.017 -9999 0 -10000 0 0
LGALS3 0 0 -9999 0 -10000 0 0
catabolic process -0.001 0.013 -9999 0 -10000 0 0
GLI3A/CBP 0.005 0.033 -9999 0 -0.38 1 1
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.088 0.15 -9999 0 -0.55 6 6
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.006 0.006 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.001 0.009 -9999 0 -10000 0 0
GNAZ -0.004 0.081 -9999 0 -0.74 6 6
RBBP4 0.006 0.006 -9999 0 -10000 0 0
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 0.039 0.021 -9999 0 -10000 0 0
STK36 0.006 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.009 0.054 -9999 0 -0.62 2 2
PTCH1 -0.079 0.16 -9999 0 -1 6 6
MIM/GLI1 -0.23 0.29 -9999 0 -0.51 250 250
CREBBP 0.005 0.032 -9999 0 -0.38 1 1
Su(fu)/SIN3/HDAC complex 0.029 0.029 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 -0.01 0.12 -9999 0 -0.74 14 14
ELF1 -0.004 0.033 -9999 0 -0.37 3 3
CCNA2 -0.15 0.25 -9999 0 -0.57 129 129
PIK3CA 0.01 0 -9999 0 -10000 0 0
JAK3 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
JAK1 0.01 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.056 0.073 -9999 0 -0.68 3 3
SHC1 0.01 0 -9999 0 -10000 0 0
SP1 -0.003 0.033 -9999 0 -0.37 4 4
IL2RA 0.018 0.083 -9999 0 -0.69 6 6
IL2RB 0.006 0.058 -9999 0 -0.74 3 3
SOS1 0.01 0 -9999 0 -10000 0 0
IL2RG 0 0.088 -9999 0 -0.74 7 7
G1/S transition of mitotic cell cycle -0.016 0.12 -9999 0 -0.9 4 4
PTPN11 0.01 0 -9999 0 -10000 0 0
CCND2 0.018 0.087 -9999 0 -0.95 4 4
LCK 0.009 0.033 -9999 0 -0.74 1 1
GRB2 0.01 0 -9999 0 -10000 0 0
IL2 0.005 0.005 -9999 0 -10000 0 0
CDK6 -0.002 0.036 -9999 0 -0.57 2 2
CCND3 0.06 0.063 -9999 0 -0.56 3 3
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
CDC42/GTP -0.028 0.086 -9999 0 -0.47 3 3
PLCG1 0.003 0.099 -9999 0 -0.48 3 3
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 -0.028 0.084 -9999 0 -0.46 3 3
S1PR5 -0.01 0.075 -9999 0 -0.6 8 8
S1PR4 -0.065 0.21 -9999 0 -0.74 44 44
MAPK3 0.003 0.099 -9999 0 -0.48 3 3
MAPK1 0.003 0.099 -9999 0 -0.48 3 3
S1P/S1P5/Gi -0.007 0.04 -9999 0 -0.31 2 2
GNAI1 -0.001 0.033 -9999 0 -0.74 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.047 -9999 0 -0.37 8 8
RHOA -0.01 0.12 -9999 0 -0.4 44 44
S1P/S1P4/Gi -0.032 0.096 -9999 0 -0.32 45 45
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.009 0.08 -9999 0 -0.74 6 6
S1P/S1P4/G12/G13 -0.038 0.12 -9999 0 -0.44 44 44
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.001 0.033 -10000 0 -0.74 1 1
Jak2/Leptin Receptor -0.026 0.097 -10000 0 -0.38 28 28
PTP1B/AKT1 -0.006 0.023 -10000 0 -10000 0 0
FYN -0.001 0.033 -10000 0 -0.74 1 1
p210 bcr-abl/PTP1B 0.024 0.036 -10000 0 -0.31 1 1
EGFR -0.013 0.12 -10000 0 -0.63 18 18
EGF/EGFR -0.02 0.084 -10000 0 -0.48 12 12
CSF1 -0.006 0.066 -10000 0 -0.74 4 4
AKT1 0.009 0.003 -10000 0 -10000 0 0
INSR 0.009 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.01 0.085 -10000 0 -0.36 15 15
Insulin Receptor/Insulin -0.004 0.018 -10000 0 -10000 0 0
HCK -0.009 0.08 -10000 0 -0.74 6 6
CRK 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.034 -10000 0 -0.29 1 1
EGF -0.004 0.099 -10000 0 -0.69 10 10
YES1 0 0 -10000 0 -10000 0 0
CAV1 -0.024 0.11 -10000 0 -0.46 10 10
TXN 0.008 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.005 0.021 -10000 0 -10000 0 0
cell migration -0.024 0.036 0.31 1 -10000 0 1
STAT3 0.007 0.005 -10000 0 -10000 0 0
PRLR -0.04 0.16 -10000 0 -0.63 32 32
ITGA2B -0.022 0.13 -10000 0 -0.74 15 15
CSF1R -0.015 0.1 -10000 0 -0.74 10 10
Prolactin Receptor/Prolactin -0.036 0.13 -10000 0 -0.47 39 39
FGR -0.054 0.19 -10000 0 -0.74 37 37
PTP1B/p130 Cas 0.027 0.033 -10000 0 -0.29 1 1
Crk/p130 Cas -0.005 0.021 -10000 0 -10000 0 0
DOK1 0.033 0.035 -10000 0 -0.33 1 1
JAK2 0.014 0.05 -10000 0 -0.32 2 2
Jak2/Leptin Receptor/Leptin -0.045 0.084 -10000 0 -0.47 3 3
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 0.024 0.036 -10000 0 -0.31 1 1
LYN -0.003 0.046 -10000 0 -0.74 2 2
CDH2 -0.033 0.14 -10000 0 -0.59 28 28
SRC 0.023 0.015 -10000 0 -10000 0 0
ITGB3 -0.016 0.11 -10000 0 -0.74 11 11
CAT1/PTP1B 0.015 0.12 -10000 0 -0.6 11 11
CAPN1 0.007 0.005 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.014 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.041 0.077 -10000 0 -0.54 2 2
negative regulation of transcription 0.014 0.05 -10000 0 -0.31 2 2
FCGR2A -0.015 0.1 -10000 0 -0.74 10 10
FER 0.008 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.029 0.12 -10000 0 -0.56 26 26
BLK -0.036 0.15 -10000 0 -0.66 27 27
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.007 0.005 -10000 0 -10000 0 0
LEPR -0.038 0.17 -10000 0 -0.74 28 28
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.003 0.14 -10000 0 -0.64 16 16
PRL -0.009 0.072 -10000 0 -0.58 8 8
SOCS3 0.003 0.091 -10000 0 -1.4 2 2
SPRY2 0.004 0.048 -10000 0 -0.74 2 2
Insulin Receptor/Insulin/IRS1 0 0 -10000 0 -10000 0 0
CSF1/CSF1R -0.016 0.075 -10000 0 -0.45 12 12
Ras protein signal transduction 0.005 0.012 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.1 0.23 -10000 0 -0.57 94 94
STAT5B 0.022 0.037 -10000 0 -0.25 1 1
STAT5A 0.022 0.037 -10000 0 -0.25 1 1
GRB2 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.04 -10000 0 -0.38 2 2
CSN2 -0.012 0.041 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
LAT 0.013 0.073 -10000 0 -0.48 10 10
YBX1 0.012 0.007 -10000 0 -10000 0 0
LCK -0.001 0.033 -10000 0 -0.74 1 1
SHC1 0 0 -10000 0 -10000 0 0
NOX4 0.004 0.037 -10000 0 -0.57 2 2
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0 0 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity -0.029 0.12 -10000 0 -0.55 26 26
MAP2K4 0.041 0.011 -10000 0 -10000 0 0
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.003 0.046 -10000 0 -0.74 2 2
SMPD1 0 0 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.038 0.16 -10000 0 -0.74 26 26
TRAIL/TRAILR2 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.072 0.19 -10000 0 -0.56 65 65
TRAIL/TRAILR1 -0.002 0.035 -10000 0 -0.56 2 2
TRAIL/TRAILR4 -0.029 0.12 -10000 0 -0.56 26 26
TRAIL/TRAILR1/DAP3/GTP -0.002 0.028 -10000 0 -0.44 2 2
IKK complex -0.001 0.009 -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 -10000 0 -10000 0 0
MAPK3 0.02 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.009 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.038 0.16 -10000 0 -0.74 26 26
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.003 0.046 -10000 0 -0.74 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.019 -10000 0 -0.3 2 2
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.025 -10000 0 -0.4 2 2
mol:ceramide 0 0 -10000 0 -10000 0 0
FADD 0 0 -10000 0 -10000 0 0
MAPK8 0.046 0.01 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.095 0.25 -10000 0 -0.74 65 65
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.03 -10000 0 -0.48 2 2
DAP3 0 0 -10000 0 -10000 0 0
CASP10 0.014 0.067 0.29 25 -0.39 1 26
JNK cascade -0.029 0.12 -10000 0 -0.55 26 26
TRAIL (trimer) 0 0 -10000 0 -10000 0 0
TNFRSF10C -0.096 0.25 -10000 0 -0.74 65 65
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.026 -10000 0 -0.41 2 2
TRAIL/TRAILR2/FADD 0 0 -10000 0 -10000 0 0
cell death 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0 -10000 0 -10000 0 0
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0 0.003 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0 0 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 -0.026 0.14 -9999 0 -0.74 18 18
ENAH 0.058 0.023 -9999 0 -10000 0 0
EGFR -0.023 0.12 -9999 0 -0.63 18 18
EPHA2 -0.004 0.057 -9999 0 -0.74 3 3
MYO6 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.017 0.089 -9999 0 -0.48 18 18
AQP5 -0.17 0.25 -9999 0 -0.55 157 157
CTNND1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.11 0.17 -9999 0 -0.38 141 141
EGF -0.014 0.097 -9999 0 -0.69 10 10
NCKAP1 0 0 -9999 0 -10000 0 0
AQP3 -0.076 0.19 -9999 0 -0.55 70 70
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.033 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GDP -0.002 0.025 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.033 -9999 0 -0.43 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.044 0 -9999 0 -10000 0 0
PVRL2 0 0 -9999 0 -10000 0 0
ZYX 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.03 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.017 0.076 -9999 0 -0.75 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.039 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
IGF1R 0 0 -9999 0 -10000 0 0
IGF1 -0.028 0.14 -9999 0 -0.73 19 19
DIAPH1 -0.023 0.12 -9999 0 -0.64 18 18
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.024 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
VCL 0.04 0 -9999 0 -10000 0 0
EFNA1 0 0 -9999 0 -10000 0 0
LPP 0.04 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.002 0.028 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.11 0.17 -9999 0 -10000 0 0
HGF/MET -0.081 0.15 -9999 0 -10000 0 0
HGF -0.16 0.3 -9999 0 -0.74 108 108
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0 -9999 0 -10000 0 0
actin cable formation 0.068 0.029 -9999 0 -10000 0 0
KIAA1543 0.039 0.018 -9999 0 -10000 0 0
KIFC3 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
EXOC3 0 0 -9999 0 -10000 0 0
ACTN1 0 0 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0 0 -9999 0 -10000 0 0
STX4 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
LIMA1 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
ROCK1 -0.002 0.021 -9999 0 -10000 0 0
adherens junction assembly 0.053 0.018 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.014 0.069 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.004 0.053 -9999 0 -0.68 3 3
PLEKHA7 0 0 -9999 0 -10000 0 0
mol:GTP -0.003 0.033 -9999 0 -0.43 3 3
establishment of epithelial cell apical/basal polarity 0 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.046 -10000 0 -0.74 2 2
ANTXR2 -0.01 0.087 -10000 0 -0.74 7 7
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.013 -10000 0 -0.1 7 7
monocyte activation -0.002 0.082 -10000 0 -0.45 16 16
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.011 -10000 0 -10000 0 0
MAP2K7 -0.001 0.011 -10000 0 -10000 0 0
MAP2K6 -0.002 0.017 -10000 0 -0.31 1 1
CYAA 0.006 0.067 -10000 0 -0.53 7 7
MAP2K4 -0.001 0.011 -10000 0 -10000 0 0
IL1B 0.004 0.072 -10000 0 -0.44 12 12
Channel -0.008 0.07 -10000 0 -0.56 7 7
NLRP1 -0.004 0.037 -10000 0 -0.47 3 3
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.013 0.1 7 -10000 0 7
MAPK3 -0.001 0.011 -10000 0 -10000 0 0
MAPK1 -0.001 0.011 -10000 0 -10000 0 0
PGR -0.092 0.18 -10000 0 -0.43 106 106
PA/Cellular Receptors -0.008 0.075 -10000 0 -0.61 7 7
apoptosis -0.001 0.013 -10000 0 -0.1 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.007 0.066 -10000 0 -0.53 7 7
macrophage activation 0.017 0.012 -10000 0 -10000 0 0
TNF -0.019 0.12 -10000 0 -0.72 13 13
VCAM1 -0.016 0.08 -10000 0 -0.45 16 16
platelet activation -0.002 0.015 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.013 0.12 2 -10000 0 2
IL18 0.011 0.045 -10000 0 -0.36 6 6
negative regulation of macrophage activation -0.001 0.013 -10000 0 -0.1 7 7
LEF -0.001 0.013 -10000 0 -0.1 7 7
CASP1 -0.003 0.031 -10000 0 -0.28 4 4
mol:cAMP -0.002 0.015 -10000 0 -10000 0 0
necrosis -0.001 0.013 -10000 0 -0.1 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.067 -10000 0 -0.54 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 0 0 -9999 0 -10000 0 0
VDR -0.001 0.033 -9999 0 -0.74 1 1
Cbp/p300/PCAF -0.001 0.021 -9999 0 -0.48 1 1
EP300 0 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.028 -9999 0 -0.31 1 1
KAT2B -0.001 0.033 -9999 0 -0.74 1 1
MAPK14 0 0 -9999 0 -10000 0 0
AKT1 0.02 0.037 -9999 0 -0.31 3 3
RAR alpha/9cRA/Cyclin H -0.007 0.029 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.032 0.033 -9999 0 -0.41 1 1
CDC2 0.001 0 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.008 0.03 -9999 0 -10000 0 0
NCOR2 -0.001 0.033 -9999 0 -0.74 1 1
VDR/VDR/Vit D3 -0.001 0.025 -9999 0 -0.56 1 1
RXRs/RARs/NRIP1/9cRA -0.024 0.083 -9999 0 -0.6 2 2
NCOA2 -0.001 0.033 -9999 0 -0.74 1 1
NCOA3 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.001 0.033 -9999 0 -0.74 1 1
RARG 0.01 0 -9999 0 -10000 0 0
RAR gamma1/9cRA 0 0 -9999 0 -10000 0 0
MAPK3 0.01 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.065 0.072 -9999 0 -0.66 2 2
RARA 0.014 0.043 -9999 0 -0.29 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.031 0.035 -9999 0 -0.41 1 1
PRKCA 0.01 0.047 -9999 0 -0.74 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.041 0.091 -9999 0 -0.63 2 2
RXRG -0.22 0.22 -9999 0 -0.42 266 266
RXRA 0.021 0.041 -9999 0 -0.31 2 2
RXRB 0.006 0.065 -9999 0 -0.41 2 2
VDR/Vit D3/DNA -0.001 0.025 -9999 0 -0.56 1 1
RBP1 -0.021 0.11 -9999 0 -0.57 18 18
CRBP1/9-cic-RA -0.015 0.079 -9999 0 -0.42 18 18
RARB 0.007 0.058 -9999 0 -0.74 3 3
PRKCG -0.031 0.15 -9999 0 -0.57 36 36
MNAT1 0 0 -9999 0 -10000 0 0
RAR alpha/RXRs -0.031 0.082 -9999 0 -0.66 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.013 0.071 -9999 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.038 -9999 0 -0.4 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.041 0.091 -9999 0 -0.63 2 2
positive regulation of DNA binding -0.006 0.027 -9999 0 -10000 0 0
NRIP1 -0.037 0.085 -9999 0 -0.69 1 1
RXRs/RARs -0.048 0.092 -9999 0 -0.49 4 4
RXRs/RXRs/DNA/9cRA -0.07 0.075 -9999 0 -0.69 2 2
PRKACA 0 0 -9999 0 -10000 0 0
CDK7 0 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.005 0.018 -9999 0 -10000 0 0
CCNH 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 -0.001 0.026 -9999 0 -0.57 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.001 0.018 -9999 0 -0.26 2 2
response to UV 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
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 0.033 -9999 0 -0.74 1 1
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.054 0.19 -9999 0 -0.74 37 37
p38 alpha/TAB1 -0.013 0.05 -9999 0 -0.42 3 3
PRKG1 -0.068 0.21 -9999 0 -0.74 46 46
DUSP8 -0.015 0.1 -9999 0 -0.74 10 10
PGK/cGMP/p38 alpha -0.043 0.12 -9999 0 -0.38 46 46
apoptosis -0.013 0.048 -9999 0 -0.4 3 3
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN -0.003 0.046 -9999 0 -0.74 2 2
DUSP1 -0.087 0.24 -9999 0 -0.74 59 59
PAK1 -0.001 0.026 -9999 0 -0.57 1 1
SRC 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -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 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.03 0.087 -9999 0 -0.38 12 12
BLK -0.036 0.15 -9999 0 -0.66 27 27
HCK -0.009 0.08 -9999 0 -0.74 6 6
MAP2K3 0 0 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.033 -9999 0 -0.74 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.032 0.067 -9999 0 -0.45 3 3
positive regulation of innate immune response 0.036 0.094 -9999 0 -0.41 12 12
LCK -0.001 0.033 -9999 0 -0.74 1 1
p38alpha-beta/MKP7 -0.02 0.072 -9999 0 -0.64 2 2
p38alpha-beta/MKP5 -0.021 0.075 -9999 0 -0.61 3 3
PGK/cGMP -0.052 0.16 -9999 0 -0.56 46 46
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.056 0.13 -9999 0 -0.52 17 17
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 -0.004 0.053 -9999 0 -0.68 3 3
IL27-mediated signaling 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
TGFB1 0.004 0.026 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.003 0.07 0.36 1 -10000 0 1
IL27/IL27R/JAK1 -0.028 0.097 -10000 0 -0.52 5 5
TBX21 -0.028 0.22 -10000 0 -0.6 53 53
IL12B 0.009 0.004 -10000 0 -10000 0 0
IL12A 0.001 0.072 -10000 0 -0.56 8 8
IL6ST -0.018 0.14 -10000 0 -0.74 18 18
IL27RA/JAK1 -0.003 0.013 -10000 0 -10000 0 0
IL27 0.008 0.007 -10000 0 -10000 0 0
TYK2 0.011 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.06 0.14 -10000 0 -0.7 3 3
T-helper 2 cell differentiation -0.003 0.07 0.36 1 -10000 0 1
T cell proliferation during immune response -0.003 0.07 0.36 1 -10000 0 1
MAPKKK cascade 0.003 0.07 -10000 0 -0.36 1 1
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 0.001 0.003 -10000 0 -10000 0 0
IL12RB1 -0.038 0.18 -10000 0 -0.74 32 32
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.019 0.19 -10000 0 -0.63 13 13
IL27/IL27R/JAK2/TYK2 0.002 0.071 -10000 0 -0.36 1 1
positive regulation of T cell mediated cytotoxicity 0.003 0.07 -10000 0 -0.36 1 1
STAT1 (dimer) -0.058 0.16 0.51 4 -0.69 12 16
JAK2 0.006 0.006 -10000 0 -10000 0 0
JAK1 0.001 0.003 -10000 0 -10000 0 0
STAT2 (dimer) 0.004 0.066 -10000 0 -10000 0 0
T cell proliferation -0.049 0.18 -10000 0 -0.5 30 30
IL12/IL12R/TYK2/JAK2 0.008 0.092 -10000 0 -0.59 2 2
IL17A -0.06 0.14 -10000 0 -0.7 3 3
mast cell activation -0.003 0.07 0.36 1 -10000 0 1
IFNG 0.006 0.02 -10000 0 -0.13 4 4
T cell differentiation -0.003 0.005 -10000 0 -0.021 6 6
STAT3 (dimer) 0.004 0.066 -10000 0 -10000 0 0
STAT5A (dimer) 0.004 0.066 -10000 0 -10000 0 0
STAT4 (dimer) -0.003 0.087 -10000 0 -0.46 7 7
STAT4 -0.012 0.092 -10000 0 -0.74 8 8
T cell activation -0.007 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.019 0.08 -10000 0 -0.47 4 4
GATA3 -0.033 0.24 -10000 0 -1.4 14 14
IL18 0.007 0.044 -10000 0 -0.56 3 3
positive regulation of mast cell cytokine production -0.012 0.058 -10000 0 -10000 0 0
IL27/EBI3 -0.002 0.041 -10000 0 -0.52 3 3
IL27RA 0.007 0.017 -10000 0 -10000 0 0
IL6 -0.12 0.28 -10000 0 -0.74 82 82
STAT5A 0 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.001 0.006 -10000 0 -10000 0 0
IL1B -0.003 0.084 -10000 0 -0.56 11 11
EBI3 0.001 0.054 -10000 0 -0.69 3 3
TNF -0.005 0.09 -10000 0 -0.55 13 13
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.006 0.039 -9999 0 -0.31 7 7
GNAO1 0.007 0.05 -9999 0 -0.63 3 3
S1P/S1P3/G12/G13 0 0.001 -9999 0 -10000 0 0
AKT1 -0.003 0.024 -9999 0 -0.46 1 1
AKT3 0.036 0.1 -9999 0 -1.3 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.033 -9999 0 -0.74 1 1
GNAI2 0.011 0.002 -9999 0 -10000 0 0
GNAI3 0.011 0.002 -9999 0 -10000 0 0
GNAI1 0.01 0.033 -9999 0 -0.74 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.011 0.002 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.043 -9999 0 -0.3 1 1
MAPK3 0.038 0.041 -9999 0 -10000 0 0
MAPK1 0.038 0.041 -9999 0 -10000 0 0
JAK2 0.041 0.044 -9999 0 -0.43 1 1
CXCR4 0.038 0.049 -9999 0 -0.63 1 1
FLT1 0.012 0.001 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.038 0.041 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.033 0.043 -9999 0 -0.3 1 1
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.033 -9999 0 -10000 0 0
VEGFA 0.012 0.001 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.03 0.04 -9999 0 -0.3 1 1
VEGFR1 homodimer/VEGFA homodimer 0.022 0.005 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.078 0.14 -9999 0 -0.32 123 123
GNAQ -0.001 0.033 -9999 0 -0.74 1 1
GNAZ 0.002 0.081 -9999 0 -0.74 6 6
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.32 -9999 0 -0.74 123 123
GNA15 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.005 0.033 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0 0 -10000 0 -10000 0 0
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC 0 0 -10000 0 -10000 0 0
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 0.022 0 -10000 0 -10000 0 0
protein ubiquitination -0.062 0.12 -10000 0 -10000 0 0
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 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -10000 0 -10000 0 0
FANCF 0 0 -10000 0 -10000 0 0
BRCA1 0 0 -10000 0 -10000 0 0
CCNE1 -0.13 0.24 -10000 0 -0.57 111 111
CDK2/Cyclin E1 -0.092 0.17 -10000 0 -0.42 111 111
FANCG -0.002 0.036 -10000 0 -0.57 2 2
BRCA1/BACH1/BARD1 0 0 -10000 0 -10000 0 0
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 -0.002 0.036 -10000 0 -0.57 2 2
DNA repair 0.007 0.1 -10000 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0 0 -10000 0 -10000 0 0
BARD1/DNA-PK 0 0 -10000 0 -10000 0 0
FANCL -0.001 0.026 -10000 0 -0.57 1 1
mRNA polyadenylation 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/P53 -0.001 0.019 -10000 0 -0.43 1 1
BARD1/CSTF1/BRCA1 0 0 -10000 0 -10000 0 0
BRCA1/BACH1 0 0 -10000 0 -10000 0 0
BARD1 0 0 -10000 0 -10000 0 0
PCNA 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.044 0.11 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 -0.001 0.018 -10000 0 -0.4 1 1
BRCA1/BARD1/Ubiquitin 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP -0.001 0.014 -10000 0 -10000 0 0
FA complex -0.001 0.016 -10000 0 -10000 0 0
BARD1/EWS 0 0 -10000 0 -10000 0 0
RBBP8 0.019 0.019 -10000 0 -0.42 1 1
TP53 -0.001 0.033 -10000 0 -0.74 1 1
TOPBP1 0 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.001 0.019 0.43 1 -10000 0 1
BRCA1/BARD1 -0.063 0.12 -10000 0 -10000 0 0
CSTF1 0 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0 0 -10000 0 -10000 0 0
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.083 0.2 -10000 0 -0.57 72 72
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0 0 -10000 0 -10000 0 0
EWSR1 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.034 -10000 0 -10000 0 0
IRAK/TOLLIP 0 0 -10000 0 -10000 0 0
IKBKB -0.001 0.026 -10000 0 -0.57 1 1
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.061 0.16 -10000 0 -0.47 65 65
IL1A -0.051 0.18 -10000 0 -0.65 39 39
IL1B 0.005 0.092 -10000 0 -0.56 13 13
IRAK/TRAF6/p62/Atypical PKCs 0 0 -10000 0 -10000 0 0
IL1R2 -0.033 0.13 -10000 0 -0.57 29 29
IL1R1 -0.001 0.033 -10000 0 -0.74 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.041 0.22 9 -10000 0 9
TOLLIP 0 0 -10000 0 -10000 0 0
TICAM2 -0.009 0.08 -10000 0 -0.74 6 6
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.042 0.012 -10000 0 -10000 0 0
MAP3K7 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.011 0.062 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.029 0.1 -10000 0 -0.45 18 18
PIK3R1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.027 0.097 -10000 0 -0.42 18 18
IL1 beta fragment/IL1R1/IL1RAP -0.012 0.071 -10000 0 -0.43 14 14
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.037 0.013 -10000 0 -10000 0 0
IRAK1 0.022 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.004 0.055 -10000 0 -0.66 3 3
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.039 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.012 0.071 -10000 0 -0.43 14 14
IL1 beta/IL1R2 -0.032 0.11 -10000 0 -0.5 13 13
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.009 0.056 -10000 0 -10000 0 0
IRAK3 -0.019 0.12 -10000 0 -0.74 13 13
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.015 0.078 -10000 0 -0.78 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.018 0.067 -10000 0 -0.32 18 18
IL1 alpha/IL1R1/IL1RAP -0.032 0.12 -10000 0 -0.42 39 39
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.012 0.064 -10000 0 -0.63 1 1
CASP1 -0.003 0.046 -10000 0 -0.74 2 2
IL1RN/IL1R2 -0.027 0.1 -10000 0 -0.42 32 32
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.011 0.066 -10000 0 -0.4 14 14
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.052 -10000 0 -0.61 1 1
PIK3CA 0 0 -10000 0 -10000 0 0
IL1RN -0.004 0.053 -10000 0 -0.68 3 3
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.001 0.012 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.05 0.056 -10000 0 -0.82 1 1
UGCG -0.002 0.009 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.034 0.067 -10000 0 -0.41 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.024 0.015 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.042 -10000 0 -0.48 3 3
FRAP1 0.072 0.066 -10000 0 -0.56 3 3
FOXO3 0.074 0.063 -10000 0 -0.55 3 3
AKT1 0.069 0.067 -10000 0 -0.6 3 3
GAB2 -0.01 0.12 -10000 0 -0.74 14 14
SMPD1 -0.002 0.009 -10000 0 -10000 0 0
SGMS1 -0.002 0.009 -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 0.02 0.001 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.045 0.029 -10000 0 -0.23 1 1
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.026 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0.001 0 -10000 0 -10000 0 0
JAK3 0.013 0.001 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
JAK1 0.013 0.001 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.072 0.058 -10000 0 -0.6 1 1
MYB 0.015 0.1 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.059 0.074 -10000 0 -0.68 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.059 0.072 -10000 0 -0.65 3 3
Rac1/GDP 0 0 -10000 0 -10000 0 0
T cell proliferation 0.065 0.067 -10000 0 -0.6 3 3
SHC1 0.01 0.002 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.008 -10000 0 -0.04 17 17
PRKCZ 0.065 0.069 -10000 0 -0.63 3 3
NF kappa B1 p50/RelA -0.007 0.042 -10000 0 -0.47 3 3
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.044 0.061 -10000 0 -0.64 3 3
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA 0.002 0.073 -10000 0 -0.66 6 6
IL2RB 0.008 0.058 -10000 0 -0.74 3 3
TERT -0.23 0.28 -10000 0 -0.57 197 197
E2F1 0.019 0.047 -10000 0 -0.45 2 2
SOS1 0.01 0.002 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.019 17 -10000 0 17
PTPN11 0.011 0.002 -10000 0 -10000 0 0
IL2RG 0.002 0.088 -10000 0 -0.74 7 7
actin cytoskeleton organization 0.065 0.067 -10000 0 -0.6 3 3
GRB2 0.01 0.002 -10000 0 -10000 0 0
IL2 0.007 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
Rac1/GTP 0.029 0.005 -10000 0 -10000 0 0
LCK 0.011 0.033 -10000 0 -0.74 1 1
BCL2 0.074 0.056 -10000 0 -0.53 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.009 0.079 -9999 0 -0.66 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.046 -9999 0 -10000 0 0
AP1 -0.056 0.14 -9999 0 -0.72 3 3
mol:PIP3 -0.02 0.077 -9999 0 -0.58 3 3
AKT1 -0.006 0.05 -9999 0 -0.57 3 3
PTK2B 0.017 0.037 -9999 0 -0.34 2 2
RHOA 0.027 0.02 -9999 0 -10000 0 0
PIK3CB 0 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0 0.081 -9999 0 -0.45 3 3
MAGI3 -0.001 0.033 -9999 0 -0.74 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.011 0.057 -9999 0 -0.41 6 6
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.06 -9999 0 -0.39 8 8
NF kappa B1 p50/RelA -0.023 0.065 -9999 0 -0.64 1 1
endothelial cell migration 0.016 0.087 -9999 0 -0.82 5 5
ADCY4 0.017 0.097 -9999 0 -0.61 6 6
ADCY5 0.012 0.094 -9999 0 -0.66 4 4
ADCY6 0.031 0.069 -9999 0 -0.59 4 4
ADCY7 0.032 0.067 -9999 0 -0.66 3 3
ADCY1 0.032 0.068 -9999 0 -0.66 3 3
ADCY2 0.018 0.081 -9999 0 -0.6 4 4
ADCY3 0.032 0.067 -9999 0 -0.66 3 3
ADCY8 -0.036 0.12 -9999 0 -0.65 5 5
ADCY9 0.031 0.072 -9999 0 -0.65 4 4
GSK3B 0.024 0.035 -9999 0 -0.38 1 1
arachidonic acid secretion 0.035 0.069 -9999 0 -0.58 4 4
GNG2 -0.007 0.073 -9999 0 -0.74 5 5
TRIP6 0 0.004 -9999 0 -10000 0 0
GNAO1 0.018 0.062 -9999 0 -0.54 5 5
HRAS 0 0 -9999 0 -10000 0 0
NFKBIA 0.017 0.073 -9999 0 -10000 0 0
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.058 -9999 0 -0.92 2 2
JUN 0 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.003 0.038 -9999 0 -0.48 3 3
TIAM1 -0.004 0.069 -9999 0 -1.1 2 2
PIK3R1 0 0.001 -9999 0 -10000 0 0
mol:IP3 -0.001 0.082 -9999 0 -0.46 3 3
PLCB3 0.022 0.036 -9999 0 -0.43 3 3
FOS -0.09 0.24 -9999 0 -0.74 61 61
positive regulation of mitosis 0.035 0.069 -9999 0 -0.58 4 4
LPA/LPA1-2-3 -0.013 0.071 -9999 0 -0.48 6 6
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 0.025 0.047 -9999 0 -0.42 2 2
GNAZ 0.014 0.073 -9999 0 -0.52 8 8
EGFR/PI3K-beta/Gab1 -0.02 0.08 -9999 0 -0.61 3 3
positive regulation of dendritic cell cytokine production -0.013 0.071 -9999 0 -0.48 6 6
LPA/LPA2/MAGI-3 -0.002 0.023 -9999 0 -0.48 1 1
ARHGEF1 -0.003 0.04 -9999 0 -0.7 1 1
GNAI2 0.02 0.049 -9999 0 -0.64 2 2
GNAI3 0.02 0.049 -9999 0 -0.64 2 2
GNAI1 0.019 0.064 -9999 0 -0.84 2 2
LPA/LPA3 -0.014 0.077 -9999 0 -0.46 14 14
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.005 0.054 -9999 0 -0.5 5 5
HB-EGF/EGFR -0.05 0.14 -9999 0 -0.52 24 24
HBEGF -0.025 0.14 -9999 0 -0.48 45 45
mol:DAG -0.001 0.082 -9999 0 -0.46 3 3
cAMP biosynthetic process 0.02 0.075 -9999 0 -0.66 4 4
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
LYN 0.015 0.084 -9999 0 -0.64 2 2
GNAQ -0.009 0.05 -9999 0 -0.38 5 5
LPAR2 0 0.001 -9999 0 -10000 0 0
LPAR3 -0.017 0.1 -9999 0 -0.62 14 14
LPAR1 -0.004 0.055 -9999 0 -0.83 2 2
IL8 0.001 0.13 -9999 0 -0.52 9 9
PTK2 0.021 0.072 -9999 0 -0.55 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.011 0.058 -9999 0 -0.41 6 6
EGFR -0.015 0.12 -9999 0 -0.63 18 18
PLCG1 -0.016 0.084 -9999 0 -0.36 10 10
PLD2 0.021 0.072 -9999 0 -0.7 1 1
G12/G13 -0.004 0.043 -9999 0 -0.58 2 2
PI3K-beta -0.007 0.061 -9999 0 -0.69 3 3
cell migration 0.002 0.032 -9999 0 -10000 0 0
SLC9A3R2 -0.004 0.057 -9999 0 -0.74 3 3
PXN 0.025 0.048 -9999 0 -0.43 2 2
HRAS/GTP -0.009 0.066 -9999 0 -0.61 4 4
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.032 0.13 -9999 0 -0.57 28 28
PRKCE 0.008 0.033 -9999 0 -0.74 1 1
PRKCD 0.006 0.079 -9999 0 -0.47 2 2
Gi(beta/gamma) -0.01 0.078 -9999 0 -0.65 5 5
mol:LPA -0.001 0.016 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.001 0.059 -9999 0 -0.64 1 1
MAPKKK cascade 0.035 0.069 -9999 0 -0.58 4 4
contractile ring contraction involved in cytokinesis 0.027 0.019 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.1 0.17 -9999 0 -0.39 127 127
GNA15 -0.008 0.047 -9999 0 -0.38 4 4
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT 0.024 0.061 -9999 0 -0.4 8 8
GNA11 -0.008 0.047 -9999 0 -0.38 4 4
Rac1/GTP -0.004 0.062 -9999 0 -0.98 2 2
MMP2 0.016 0.088 -9999 0 -0.83 5 5
IGF1 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
NCK2 0 0 -9999 0 -10000 0 0
PTK2 0 0 -9999 0 -10000 0 0
CRKL 0.008 0.076 -9999 0 -0.38 18 18
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
IRS1/Crk -0.014 0.072 -9999 0 -0.38 18 18
IGF-1R heterotetramer/IGF1/PTP1B -0.017 0.084 -9999 0 -0.45 18 18
AKT1 0.028 0.067 -9999 0 -10000 0 0
BAD 0.034 0.064 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.008 0.076 -9999 0 -0.38 18 18
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.014 0.072 -9999 0 -0.39 18 18
RAF1 0.037 0.061 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.013 0.068 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.016 0.079 -9999 0 -0.42 18 18
PIK3CA 0 0 -9999 0 -10000 0 0
RPS6KB1 0.028 0.067 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.032 0.054 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.012 0.06 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.013 0.066 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.007 0.017 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.014 0.072 -9999 0 -0.39 18 18
Crk/p130 Cas/Paxillin -0.013 0.064 -9999 0 -10000 0 0
IGF1R 0.007 0.017 -9999 0 -10000 0 0
IGF1 -0.018 0.14 -9999 0 -0.74 19 19
IRS2/Crk -0.016 0.074 -9999 0 -0.4 3 3
PI3K -0.013 0.067 -9999 0 -10000 0 0
apoptosis 0.009 0.047 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.019 0.092 -9999 0 -0.46 18 18
RAF1/14-3-3 E 0.04 0.055 -9999 0 -10000 0 0
BAD/14-3-3 0.038 0.06 -9999 0 -10000 0 0
PRKCZ 0.028 0.067 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.01 0.049 -9999 0 -10000 0 0
PTPN1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.018 0.091 -9999 0 -0.49 18 18
BCAR1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.014 0.073 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.014 0.072 -9999 0 -0.38 18 18
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0.008 0.076 -9999 0 -0.38 18 18
IRS1 0.001 0.082 -9999 0 -0.42 18 18
IRS2 0.006 0.084 -9999 0 -0.39 21 21
IGF-1R heterotetramer/IGF1 -0.021 0.11 -9999 0 -0.56 19 19
GRB2 0 0 -9999 0 -10000 0 0
PDPK1 -0.012 0.063 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKD1 0.006 0.13 -9999 0 -0.48 30 30
SHC1 0 0 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.044 0.12 -9999 0 -10000 0 0
TC10/GTP -0.042 0.12 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.044 0.17 -9999 0 -0.73 30 30
FOXO3 -0.003 0.014 -9999 0 -10000 0 0
AKT1 -0.02 0.078 -9999 0 -10000 0 0
INSR 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.085 0.24 -9999 0 -0.74 58 58
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.032 0 -9999 0 -10000 0 0
CAV1 -0.098 0.2 -9999 0 -0.42 137 137
CBL/APS/CAP/Crk-II/C3G -0.046 0.13 -9999 0 -0.4 58 58
Insulin Receptor/Insulin/IRS1/NCK2 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.084 -9999 0 -10000 0 0
PARD6A -0.001 0.033 -9999 0 -0.74 1 1
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.017 0.069 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.015 -9999 0 -10000 0 0
Insulin Receptor 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0 0 -9999 0 -10000 0 0
PRKCI -0.005 0.021 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.021 0.085 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 -0.02 0.078 -9999 0 -10000 0 0
PRKCZ -0.005 0.021 -9999 0 -10000 0 0
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.001 0.018 -9999 0 -0.39 1 1
F2RL2 -0.1 0.22 -9999 0 -0.58 91 91
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -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 -0.05 0.14 -9999 0 -0.43 58 58
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D 0.023 0.02 -9999 0 -0.42 1 1
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.002 0.006 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 0 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.023 0.02 -9999 0 -0.42 1 1
GRB2 0 0 -9999 0 -10000 0 0
EIF4EBP1 0.015 0.1 -9999 0 -10000 0 0
PTPRA 0.011 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
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 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.054 0.12 -9999 0 -0.48 4 4
Signaling events mediated by PRL

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
CCNE1 -0.13 0.24 -9999 0 -0.57 111 111
mol:Halofuginone 0 0 -9999 0 -10000 0 0
ITGA1 -0.009 0.08 -9999 0 -0.74 6 6
CDKN1A -0.004 0.024 -9999 0 -10000 0 0
PRL-3/alpha Tubulin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.028 0.12 -9999 0 -0.56 25 25
AGT -0.036 0.16 -9999 0 -0.73 25 25
CCNA2 -0.054 0.16 -9999 0 -0.69 4 4
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 0.008 0.084 -9999 0 -0.55 11 11
CDK2/Cyclin E1 -0.063 0.12 -9999 0 -0.43 3 3
MAPK3 0.02 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.02 0 -9999 0 -10000 0 0
PTP4A1 0.023 0.067 -9999 0 -10000 0 0
PTP4A3 0 0 -9999 0 -10000 0 0
PTP4A2 0 0 -9999 0 -10000 0 0
ITGB1 0.02 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 -0.004 0.024 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.012 0.065 -9999 0 -10000 0 0
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC -0.004 0.024 -9999 0 -10000 0 0
RHOA -0.004 0.024 -9999 0 -10000 0 0
cell motility 0.028 0.031 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.009 0.057 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.007 0.06 -9999 0 -0.56 6 6
ROCK1 0.028 0.031 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis 0.023 0.066 -9999 0 -10000 0 0
ATF5 -0.008 0.068 -9999 0 -0.57 7 7
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.018 0.003 -9999 0 -10000 0 0
RAS family/GTP -0.008 0.045 -9999 0 -10000 0 0
NFATC4 0.031 0.056 -9999 0 -10000 0 0
ERBB2IP 0.002 0.004 -9999 0 -10000 0 0
HSP90 (dimer) 0 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.011 0.061 -9999 0 -10000 0 0
JUN 0.043 0.059 -9999 0 -0.49 1 1
HRAS 0 0 -9999 0 -10000 0 0
DOCK7 0.028 0.067 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.014 0.073 -9999 0 -0.41 15 15
AKT1 0.01 0.002 -9999 0 -10000 0 0
BAD 0.018 0.001 -9999 0 -10000 0 0
MAPK10 -0.009 0.045 -9999 0 -0.33 4 4
mol:GTP 0 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.012 0.066 -9999 0 -10000 0 0
RAF1 0.047 0.059 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.048 0.14 -9999 0 -0.44 53 53
STAT3 0 0 -9999 0 -10000 0 0
cell migration 0.04 0.046 -9999 0 -0.3 2 2
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation 0.036 0.15 -9999 0 -0.61 5 5
FOS 0.005 0.2 -9999 0 -0.5 66 66
NRAS 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.061 -9999 0 -10000 0 0
MAPK3 0.044 0.11 -9999 0 -0.64 1 1
MAPK1 0.044 0.11 -9999 0 -0.64 1 1
JAK2 0.028 0.067 -9999 0 -10000 0 0
NF2 -0.001 0.018 -9999 0 -0.4 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.013 0.062 -9999 0 -0.33 15 15
NRG1 -0.013 0.13 -9999 0 -0.74 15 15
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 0.031 0.062 -9999 0 -0.32 4 4
MAPK9 -0.005 0.029 -9999 0 -10000 0 0
ERBB2 -0.002 0.027 -9999 0 -0.43 2 2
ERBB3 0.009 0.004 -9999 0 -10000 0 0
SHC1 0.008 0.004 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.003 0.008 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
RNF41 0.025 0.005 -9999 0 -10000 0 0
FRAP1 0.009 0.002 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.008 0.041 -9999 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.001 0.022 -9999 0 -0.36 2 2
CHRNA1 0.041 0.12 -9999 0 -0.68 5 5
myelination 0.036 0.054 -9999 0 -10000 0 0
PPP3CB 0.026 0.063 -9999 0 -10000 0 0
KRAS 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.009 0.048 -9999 0 -10000 0 0
NRG2 -0.078 0.23 -9999 0 -0.74 53 53
mol:GDP 0.014 0.062 -9999 0 -0.33 15 15
SOS1 0.008 0.004 -9999 0 -10000 0 0
MAP2K2 0.054 0.06 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.026 0.067 -9999 0 -10000 0 0
MAP2K1 0.034 0.11 -9999 0 -0.5 4 4
heart morphogenesis -0.011 0.061 -9999 0 -10000 0 0
RAS family/GDP -0.008 0.046 -9999 0 -10000 0 0
GRB2 0.008 0.004 -9999 0 -10000 0 0
PRKACA -0.001 0.005 -9999 0 -10000 0 0
CHRNE 0.02 0.018 -9999 0 -0.24 1 1
HSP90AA1 0 0 -9999 0 -10000 0 0
activation of caspase activity -0.01 0.002 -9999 0 -10000 0 0
nervous system development -0.011 0.061 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.005 0.047 -9999 0 -0.43 6 6
HDAC3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.05 0.16 -9999 0 -0.56 45 45
GATA1/HDAC5 -0.05 0.16 -9999 0 -0.56 45 45
GATA2/HDAC5 -0.061 0.17 -9999 0 -0.56 55 55
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.005 0.055 -9999 0 -0.62 4 4
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
GATA2 -0.081 0.23 -9999 0 -0.74 55 55
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0 0 -9999 0 -10000 0 0
HDAC5 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.007 0.06 -9999 0 -0.56 6 6
Histones -0.001 0.014 -9999 0 -10000 0 0
ADRBK1 0 0 -9999 0 -10000 0 0
HDAC4 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0 0 -9999 0 -10000 0 0
HDAC6 0 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 -0.004 0.057 -9999 0 -0.74 3 3
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
GATA1 -0.066 0.21 -9999 0 -0.74 45 45
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 -0.001 0.033 -9999 0 -0.74 1 1
RANGAP1 0 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.021 -9999 0 -0.48 1 1
HDAC4/SRF -0.003 0.037 -9999 0 -0.48 3 3
HDAC4/ER alpha -0.027 0.12 -9999 0 -0.56 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.001 0.013 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.035 0.16 -9999 0 -0.74 24 24
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.019 0.12 -9999 0 -0.74 13 13
RAN 0 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.011 0.066 -9999 0 -0.4 14 14
GNG2 -0.007 0.073 -9999 0 -0.74 5 5
NCOR2 -0.001 0.033 -9999 0 -0.74 1 1
TUBB2A 0 0 -9999 0 -10000 0 0
HDAC11 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
ANKRA2 0 0 -9999 0 -10000 0 0
RFXANK 0 0 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.001 0.033 -9999 0 -0.74 1 1
ITGA4 -0.009 0.08 -9999 0 -0.74 6 6
alpha4/beta7 Integrin -0.008 0.065 -9999 0 -0.56 7 7
alpha4/beta1 Integrin -0.007 0.06 -9999 0 -0.56 6 6
Ephrin B reverse signaling

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
EFNB2 -0.001 0.033 -10000 0 -0.74 1 1
EPHB2 -0.001 0.073 -10000 0 -0.57 8 8
EFNB1 0.018 0.027 -10000 0 -0.41 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.038 0.094 -10000 0 -0.54 1 1
Ephrin B2/EPHB1-2 -0.045 0.11 -10000 0 -0.5 3 3
neuron projection morphogenesis -0.036 0.09 -10000 0 -0.51 1 1
Ephrin B1/EPHB1-2/Tiam1 -0.041 0.1 -10000 0 -0.47 3 3
DNM1 -0.002 0.036 -10000 0 -0.57 2 2
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.016 0.059 -10000 0 -0.72 3 3
YES1 -0.005 0.074 -10000 0 -0.95 3 3
Ephrin B1/EPHB1-2/NCK2 -0.041 0.1 -10000 0 -0.5 2 2
PI3K -0.005 0.057 -10000 0 -0.73 3 3
mol:GDP -0.041 0.1 -10000 0 -0.46 3 3
ITGA2B -0.022 0.13 -10000 0 -0.74 15 15
endothelial cell proliferation -0.001 0.022 -10000 0 -0.48 1 1
FYN -0.005 0.074 -10000 0 -0.95 3 3
MAP3K7 -0.005 0.06 -10000 0 -0.77 3 3
FGR -0.018 0.089 -10000 0 -0.99 3 3
TIAM1 -0.001 0.033 -10000 0 -0.74 1 1
PIK3R1 0 0 -10000 0 -10000 0 0
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.023 0.098 -10000 0 -0.66 3 3
LYN -0.006 0.075 -10000 0 -0.95 3 3
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.07 -10000 0 -0.9 3 3
Ephrin B1/EPHB1-2 -0.008 0.065 -10000 0 -0.83 3 3
SRC -0.005 0.073 -10000 0 -0.94 3 3
ITGB3 -0.016 0.11 -10000 0 -0.74 11 11
EPHB1 -0.071 0.19 -10000 0 -0.58 62 62
EPHB4 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.022 -10000 0 -0.48 1 1
alphaIIb/beta3 Integrin -0.029 0.12 -10000 0 -0.56 26 26
BLK -0.012 0.08 -10000 0 -0.95 3 3
HCK -0.008 0.076 -10000 0 -0.95 3 3
regulation of stress fiber formation 0.04 0.1 0.49 2 -10000 0 2
MAPK8 0.023 0.056 -10000 0 -0.68 3 3
Ephrin B1/EPHB1-2/RGS3 -0.041 0.1 -10000 0 -0.5 2 2
endothelial cell migration -0.004 0.056 -10000 0 -0.6 4 4
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.001 0.067 -10000 0 -0.85 3 3
regulation of focal adhesion formation 0.04 0.1 0.49 2 -10000 0 2
chemotaxis 0.04 0.1 0.49 2 -10000 0 2
PIK3CA 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.037 0.092 -10000 0 -0.53 1 1
angiogenesis -0.008 0.064 -10000 0 -0.82 3 3
LCK -0.006 0.077 -10000 0 -0.99 3 3
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.046 0.019 -10000 0 -10000 0 0
NFATC2 0.002 0.069 -10000 0 -0.22 15 15
NFATC3 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.013 0.12 -10000 0 -0.5 20 20
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.035 0.1 -10000 0 -0.48 19 19
BCL2/BAX -0.001 0.019 -10000 0 -0.42 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.004 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.004 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.003 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.016 0.11 -10000 0 -0.48 20 20
Calcineurin A alpha-beta B1/BCL2 -0.001 0.026 -10000 0 -0.57 1 1
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.015 0.11 0.47 20 -10000 0 20
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 0 0 -10000 0 -10000 0 0
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.58 49 49
MAP3K8 0.006 0.047 -10000 0 -0.74 2 2
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.053 0.12 -10000 0 -0.45 14 14
CABIN1 -0.014 0.12 -10000 0 -0.51 20 20
CALM1 0.009 0.003 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.057 -10000 0 -0.74 3 3
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 -0.002 0.035 -10000 0 -0.56 2 2
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.003 -10000 0 -10000 0 0
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.003 0.017 -10000 0 -10000 0 0
PRKCH 0 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.004 -10000 0 -10000 0 0
CASP3 0.009 0.003 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0.007 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.024 -10000 0 -10000 0 0
PRKCB -0.04 0.17 -10000 0 -0.74 27 27
PRKCE -0.001 0.033 -10000 0 -0.74 1 1
JNK2/NFAT4 0 0 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.003 -10000 0 -10000 0 0
PRKCA -0.003 0.046 -10000 0 -0.74 2 2
PRKCG -0.041 0.15 -10000 0 -0.57 36 36
PRKCQ -0.069 0.22 -10000 0 -0.74 47 47
FKBP38/BCL2 -0.001 0.019 -10000 0 -0.42 1 1
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 0.046 0.024 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.003 0.038 -10000 0 -0.49 3 3
NFATc/ERK1 0.05 0.018 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.035 0.1 -10000 0 -0.48 19 19
NR4A1 -0.049 0.25 -10000 0 -0.68 65 65
GSK3B 0.009 0.003 -10000 0 -10000 0 0
positive T cell selection 0.018 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.021 0.045 -10000 0 -0.28 1 1
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0.009 0.003 -10000 0 -10000 0 0
AKAP5 -0.003 0.046 -10000 0 -0.74 2 2
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.046 0.024 -10000 0 -10000 0 0
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.001 0.026 -10000 0 -0.57 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.011 0.069 -9999 0 -0.44 12 12
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.059 -9999 0 -0.38 12 12
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.001 0.033 -9999 0 -0.74 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.005 0.03 -9999 0 -10000 0 0
YY1/LSF -0.001 0.013 -9999 0 -10000 0 0
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.008 0.052 -9999 0 -0.34 12 12
I kappa B alpha/HDAC1 -0.006 0.035 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.007 0.046 -9999 0 -0.3 12 12
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.006 0.035 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.007 0.041 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.081 0.23 -9999 0 -0.74 55 55
GATA1 -0.066 0.21 -9999 0 -0.74 45 45
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.019 0.062 -9999 0 -0.45 1 1
RBBP7 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
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 -0.007 0.04 -9999 0 -10000 0 0
KAT2B -0.001 0.033 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.005 0.033 -9999 0 -10000 0 0
YY1/HDAC2 -0.001 0.013 -9999 0 -10000 0 0
YY1/HDAC1 -0.001 0.013 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0 -9999 0 -10000 0 0
PPARG -0.05 0.13 -9999 0 -0.36 68 68
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) -0.007 0.04 -9999 0 -0.43 1 1
MBD3L2 0 0 -9999 0 -10000 0 0
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 0.009 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.007 0.04 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0.025 0.016 -9999 0 -0.34 1 1
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 -0.001 0.033 -9999 0 -0.74 1 1
MXD1 0 0 -9999 0 -10000 0 0
STAT3 0.022 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 0.011 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.022 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.04 -9999 0 -10000 0 0
histone deacetylation 0.041 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.005 0.031 -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 -0.053 0.14 -9999 0 -0.44 55 55
GATA1/HDAC1 -0.05 0.16 -9999 0 -0.56 45 45
GATA1/HDAC3 -0.044 0.13 -9999 0 -0.44 45 45
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.014 0.087 -9999 0 -0.55 13 13
SIN3/HDAC complex/Mad/Max 0 0 -9999 0 -10000 0 0
NuRD Complex 0 0.009 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.005 0.029 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.051 0.16 -9999 0 -0.56 46 46
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.019 0.12 -9999 0 -0.72 13 13
negative regulation of cell growth 0.041 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.01 0.062 -9999 0 -0.4 12 12
SIN3/HDAC complex/NCoR1 0 0 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 -0.001 0.033 -9999 0 -0.74 1 1
MBD2 0 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.031 0.28 2 -10000 0 2
DAPP1 0.007 0.12 -10000 0 -0.58 15 15
Src family/SYK family/BLNK-LAT/BTK-ITK 0.002 0.17 -10000 0 -0.65 24 24
mol:DAG 0.025 0.089 0.2 1 -0.28 20 21
HRAS 0.01 0.002 -10000 0 -10000 0 0
RAP1A 0 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.026 0.057 -10000 0 -0.31 8 8
PLCG2 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.032 0.25 2 -10000 0 2
ARF1/GTP -0.001 0.031 0.26 2 -10000 0 2
RHOA 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
RAP1A/GTP -0.001 0.031 0.24 2 -10000 0 2
ADAP1 -0.007 0.056 0.25 2 -10000 0 2
ARAP3 -0.001 0.032 0.25 2 -0.35 3 5
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.012 0.092 -10000 0 -0.74 8 8
ARHGEF6 -0.028 0.14 -10000 0 -0.74 19 19
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS 0.01 0.002 -10000 0 -10000 0 0
FYN -0.001 0.033 -10000 0 -0.74 1 1
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.054 0.19 -10000 0 -0.74 37 37
mol:Ca2+ 0.023 0.048 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.033 -10000 0 -0.74 1 1
ZAP70 -0.012 0.092 -10000 0 -0.74 8 8
mol:IP3 0.026 0.066 -10000 0 -10000 0 0
LYN -0.003 0.046 -10000 0 -0.74 2 2
ARF1/GDP 0.026 0.057 -10000 0 -0.31 8 8
RhoA/GDP -0.005 0.038 0.26 2 -10000 0 2
PDK1/Src/Hsp90 0 0 -10000 0 -10000 0 0
BLNK -0.001 0.033 -10000 0 -0.74 1 1
actin cytoskeleton reorganization 0.046 0.068 -10000 0 -0.49 3 3
SRC 0 0 -10000 0 -10000 0 0
PLEKHA2 0.026 0.022 -10000 0 -0.48 1 1
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.003 0.045 -10000 0 -0.71 2 2
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.031 0.28 2 -10000 0 2
RhoA/GTP -0.001 0.03 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.034 0.11 -10000 0 -0.53 17 17
BLK -0.036 0.15 -10000 0 -0.66 27 27
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.001 0.03 0.25 2 -10000 0 2
HCK -0.009 0.08 -10000 0 -0.74 6 6
CYTH3 -0.001 0.03 0.25 2 -10000 0 2
CYTH2 -0.001 0.03 0.25 2 -10000 0 2
KRAS 0.01 0.002 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.018 -10000 0 -10000 0 0
SGK1 0 0.02 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
mol:GDP 0.022 0.06 -10000 0 -0.33 8 8
SOS1 0 0 -10000 0 -10000 0 0
SYK -0.001 0.033 -10000 0 -0.74 1 1
ARF6/GDP -0.005 0.038 0.27 2 -10000 0 2
mol:PI-3-4-5-P3 -0.001 0.035 0.34 2 -10000 0 2
ARAP3/RAP1A/GTP -0.001 0.031 0.24 2 -10000 0 2
VAV1 -0.007 0.073 -10000 0 -0.74 5 5
mol:PI-3-4-P2 0.019 0.026 -10000 0 -0.56 1 1
RAS family/GTP/PI3K Class I -0.002 0.027 -10000 0 -10000 0 0
PLEKHA1 0.026 0.022 -10000 0 -0.48 1 1
Rac1/GDP 0.026 0.057 -10000 0 -0.31 8 8
LAT 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.02 0.1 -10000 0 -0.46 21 21
ITK -0.029 0.1 0.25 2 -0.38 38 40
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.023 0.12 0.22 1 -0.4 24 25
LCK -0.001 0.033 -10000 0 -0.74 1 1
BTK -0.038 0.11 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.006 0.066 -10000 0 -0.74 4 4
CLTC 0.027 0.009 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.023 0.008 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.014 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.007 -10000 0 -10000 0 0
CPE 0.014 0.028 -10000 0 -0.42 2 2
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.007 -10000 0 -10000 0 0
CTNND1 0.028 0.014 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.006 -10000 0 -10000 0 0
TSHR 0.005 0.063 -10000 0 -0.36 15 15
INS 0.01 0.002 -10000 0 -10000 0 0
BIN1 -0.003 0.046 -10000 0 -0.74 2 2
mol:Choline -0.001 0.007 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.016 -10000 0 -0.35 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.014 -10000 0 -10000 0 0
JUP 0.025 0.007 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.002 0.028 -10000 0 -0.44 2 2
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.025 0.007 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -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 0.01 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.001 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.039 0.12 -10000 0 -0.36 3 3
clathrin heavy chain/ACAP1 0.032 0.01 -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 -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 0.028 0.014 -10000 0 -10000 0 0
NME1 0.015 0.017 -10000 0 -0.36 1 1
clathrin coat assembly 0.027 0.009 -10000 0 -10000 0 0
IL2RA 0.022 0.025 -10000 0 -10000 0 0
VAMP3 0.016 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.003 0.032 -10000 0 -0.35 4 4
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.001 0.01 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.028 0.006 -10000 0 -10000 0 0
SDC1 0.024 0.014 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.016 -10000 0 -0.35 1 1
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0.01 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.007 -10000 0 -10000 0 0
endocytosis 0.002 0.027 0.44 2 -10000 0 2
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.085 0.19 -10000 0 -0.38 143 143
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.001 0.014 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.065 0.18 -10000 0 -0.38 118 118
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.009 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.092 0.19 -9999 0 -0.69 7 7
RAD9A 0 0 -9999 0 -10000 0 0
AP1 -0.068 0.18 -9999 0 -0.56 61 61
IFNAR2 0.007 0.006 -9999 0 -10000 0 0
AKT1 -0.005 0.064 -9999 0 -0.3 12 12
ER alpha/Oestrogen -0.027 0.12 -9999 0 -0.57 24 24
NFX1/SIN3/HDAC complex 0.025 0.021 -9999 0 -10000 0 0
EGF -0.008 0.098 -9999 0 -0.69 10 10
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0.001 -9999 0 -10000 0 0
TERT/c-Abl -0.12 0.15 -9999 0 -0.72 5 5
SAP18 0.006 0.005 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.025 0.13 -9999 0 -0.58 27 27
WRN -0.001 0.033 -9999 0 -0.74 1 1
SP1 0.008 0.006 -9999 0 -10000 0 0
SP3 0.007 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.1 0.14 -9999 0 -0.64 5 5
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.094 0.2 -9999 0 -0.71 7 7
CCND1 -0.085 0.22 -9999 0 -1.2 7 7
MAX 0.007 0.005 -9999 0 -10000 0 0
RBBP7 0.006 0.005 -9999 0 -10000 0 0
RBBP4 0.006 0.005 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0.006 0.005 -9999 0 -10000 0 0
Telomerase/911 0.016 0.032 -9999 0 -10000 0 0
CDKN1B 0.015 0.051 -9999 0 -0.46 4 4
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 0.006 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.006 0.005 -9999 0 -10000 0 0
JUN 0.006 0.005 -9999 0 -10000 0 0
E6 -0.003 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0.001 -9999 0 -10000 0 0
FOS -0.084 0.24 -9999 0 -0.74 61 61
IFN-gamma/IRF1 -0.006 0.055 -9999 0 -0.5 6 6
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.011 0.08 -9999 0 -0.57 10 10
Telomerase -0.028 0.055 -9999 0 -10000 0 0
IRF1 0.009 0.007 -9999 0 -10000 0 0
ESR1 -0.03 0.16 -9999 0 -0.74 24 24
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 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
HDAC1 0.006 0.005 -9999 0 -10000 0 0
HDAC2 0.007 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.023 0.005 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.007 0.005 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 0 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.15 -9999 0 -0.68 6 6
NR2F2 0.01 0.012 -9999 0 -10000 0 0
MAPK3 0.01 0.009 -9999 0 -10000 0 0
MAPK1 0.01 0.009 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.005 0.007 -9999 0 -10000 0 0
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 -0.017 0.12 -9999 0 -0.63 18 18
mol:Oestrogen -0.002 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.027 0.12 -9999 0 -0.5 27 27
MYC 0.007 0.005 -9999 0 -10000 0 0
IL2 0 0.012 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
TGFB1 0.005 0.007 -9999 0 -10000 0 0
TRF2/BLM -0.008 0.054 -9999 0 -0.38 10 10
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.12 0.15 -9999 0 -0.71 5 5
SP1/HDAC2 0 0.002 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.14 -9999 0 -0.64 5 5
Smad3/Myc 0.011 0.015 -9999 0 -10000 0 0
911 complex 0 0 -9999 0 -10000 0 0
IFNG 0.001 0.076 -9999 0 -0.68 6 6
Telomerase/PinX1 -0.1 0.14 -9999 0 -0.64 5 5
Telomerase/AKT1/mTOR/p70S6K -0.003 0.063 -9999 0 -10000 0 0
SIN3B 0.006 0.005 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.1 0.14 -9999 0 -0.64 5 5
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 -0.001 0.023 -9999 0 -0.52 1 1
Telomerase/hnRNP C1/C2 -0.1 0.14 -9999 0 -0.64 5 5
E2F1 0.007 0.006 -9999 0 -10000 0 0
ZNFX1 0.006 0.005 -9999 0 -10000 0 0
PIF1 -0.059 0.17 -9999 0 -0.57 51 51
NCL 0 0 -9999 0 -10000 0 0
DKC1 0 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
MAP2K3 0.027 0.024 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.034 0.022 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.009 0.08 -9999 0 -0.74 6 6
TXN 0.007 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GADD45B -0.019 0.12 -9999 0 -0.74 13 13
MAP3K1 0 0 -9999 0 -10000 0 0
MAP3K6 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
MAP3K4 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.005 -9999 0 -10000 0 0
TRAF6 0.007 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.069 0.19 -9999 0 -0.57 60 60
CCM2 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.042 0.12 -9999 0 -0.35 60 60
MAPK11 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.038 0.1 -9999 0 -0.32 60 60
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.014 0.019 -9999 0 -0.42 1 1
TAOK2 0.015 0 -9999 0 -10000 0 0
TAOK3 0.015 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAP3K10 -0.001 0.026 -9999 0 -0.57 1 1
MAP3K3 0 0 -9999 0 -10000 0 0
TRX/ASK1 0 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.015 0.082 -9999 0 -0.43 18 18
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.005 0.041 -9999 0 -0.38 5 5
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 -0.004 0.033 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.002 0.022 -9999 0 -0.48 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.013 0.044 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.038 -9999 0 -0.37 2 2
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.004 0.039 -9999 0 -10000 0 0
AKT1 -0.004 0.034 -9999 0 -10000 0 0
MAP2K1 0.042 0.044 -9999 0 -10000 0 0
MAP3K11 0.034 0.045 -9999 0 -10000 0 0
IFNGR1 0.009 0.034 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.051 0.13 -9999 0 -0.48 39 39
Rap1/GTP -0.003 0.028 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.005 0.043 -9999 0 -0.41 1 1
CEBPB 0.039 0.13 -9999 0 -0.72 2 2
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.007 0.066 -9999 0 -1.2 1 1
STAT1 -0.004 0.038 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) 0.002 0.075 -9999 0 -0.68 6 6
PIK3CA 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.004 0.036 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.02 0.068 -9999 0 -0.41 2 2
mol:Ca2+ -0.005 0.041 -9999 0 -0.38 5 5
MAPK3 0.042 0.064 -9999 0 -10000 0 0
STAT1 (dimer) -0.016 0.058 -9999 0 -10000 0 0
MAPK1 0.042 0.064 -9999 0 -10000 0 0
JAK2 0.01 0.005 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0.01 0.005 -9999 0 -10000 0 0
CAMK2D 0 0 -9999 0 -10000 0 0
DAPK1 0.016 0.19 -9999 0 -0.64 38 38
SMAD7 0.038 0.042 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.004 0.034 -9999 0 -10000 0 0
PI3K -0.004 0.036 -9999 0 -10000 0 0
IFNG 0.002 0.076 -9999 0 -0.68 6 6
apoptosis 0.015 0.13 -9999 0 -0.44 38 38
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.057 0.2 -9999 0 -0.74 39 39
CAMK2B -0.069 0.19 -9999 0 -0.57 60 60
FRAP1 0.044 0.038 -9999 0 -10000 0 0
PRKCD -0.004 0.034 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.013 0.044 -9999 0 -10000 0 0
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.065 0.037 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.004 0.037 -9999 0 -10000 0 0
SOCS1 -0.002 0.065 -9999 0 -1.5 1 1
mol:GDP -0.004 0.033 -9999 0 -10000 0 0
CASP1 0.037 0.047 -9999 0 -0.33 2 2
PTGES2 0 0 -9999 0 -10000 0 0
IRF9 0.043 0.043 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.036 -9999 0 -10000 0 0
RAP1/GDP -0.003 0.029 -9999 0 -10000 0 0
CBL 0.033 0.044 -9999 0 -0.38 1 1
MAP3K1 0.034 0.045 -9999 0 -0.4 1 1
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.013 0.044 -9999 0 -10000 0 0
PTPN11 0.027 0.045 -9999 0 -0.38 5 5
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.001 0.026 -9999 0 -0.57 1 1
Caspase 8 (4 units) -0.011 0.048 -9999 0 -10000 0 0
NEF -0.007 0.037 -9999 0 -10000 0 0
NFKBIA -0.001 0.012 -9999 0 -10000 0 0
BIRC3 0.03 0.086 -9999 0 -0.75 6 6
CYCS 0.032 0.065 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.025 0.13 -9999 0 -0.82 12 12
MAP2K7 0.034 0.051 -9999 0 -10000 0 0
protein ubiquitination 0.057 0.038 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.003 0.046 -9999 0 -0.74 2 2
BID 0.026 0.068 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.004 0.035 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
CFLAR 0 0 -9999 0 -10000 0 0
FADD 0 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.035 -9999 0 -10000 0 0
MAPK8 0.04 0.049 -9999 0 -10000 0 0
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.015 0.062 -9999 0 -0.3 22 22
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.006 0.034 -9999 0 -10000 0 0
CHUK 0.058 0.04 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.002 0.025 -9999 0 -0.4 2 2
TCRz/NEF -0.027 0.12 -9999 0 -0.51 27 27
TNF -0.019 0.12 -9999 0 -0.72 13 13
FASLG -0.02 0.2 -9999 0 -0.8 27 27
NFKB1 -0.001 0.012 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.076 -9999 0 -0.46 14 14
CASP6 -0.007 0.029 -9999 0 -10000 0 0
CASP7 0.061 0.084 -9999 0 -0.6 6 6
RELA -0.001 0.012 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.061 0.084 -9999 0 -0.6 6 6
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.019 -9999 0 -0.42 1 1
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.054 0.042 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.013 0.061 -9999 0 -0.48 6 6
BCL2 0.045 0.048 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.009 0.058 -10000 0 -0.39 11 11
cell-cell adhesion 0.033 0.08 0.47 1 -10000 0 1
Ephrin B/EPHB2/RasGAP -0.006 0.043 -10000 0 -0.4 1 1
ITSN1 0 0 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.013 0.066 -10000 0 -0.35 18 18
Ephrin B1/EPHB1 -0.044 0.12 -10000 0 -0.36 62 62
HRAS/GDP -0.032 0.081 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.039 0.099 -10000 0 -10000 0 0
Endophilin/SYNJ1 -0.006 0.041 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.037 0.097 -10000 0 -10000 0 0
endothelial cell migration -0.001 0.018 -10000 0 -0.4 1 1
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.005 0.051 -10000 0 -0.57 4 4
PAK1 -0.011 0.058 -10000 0 -10000 0 0
HRAS 0 0 -10000 0 -10000 0 0
RRAS -0.006 0.041 -10000 0 -10000 0 0
DNM1 -0.002 0.036 -10000 0 -0.57 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.035 0.092 -10000 0 -0.38 2 2
lamellipodium assembly -0.033 0.08 -10000 0 -0.47 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.019 0.049 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPHB2 -0.009 0.072 -10000 0 -0.57 8 8
EPHB3 -0.021 0.11 -10000 0 -0.57 18 18
EPHB1 -0.072 0.19 -10000 0 -0.58 62 62
EPHB4 0 0 -10000 0 -10000 0 0
mol:GDP -0.023 0.081 -10000 0 -0.43 1 1
Ephrin B/EPHB2 -0.007 0.044 -10000 0 -0.41 1 1
Ephrin B/EPHB3 -0.012 0.059 -10000 0 -0.41 1 1
JNK cascade -0.009 0.11 -10000 0 -0.48 2 2
Ephrin B/EPHB1 -0.038 0.099 -10000 0 -0.41 2 2
RAP1/GDP -0.019 0.07 -10000 0 -10000 0 0
EFNB2 -0.001 0.033 -10000 0 -0.74 1 1
EFNB3 -0.002 0.036 -10000 0 -0.57 2 2
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.045 0.11 -10000 0 -0.5 3 3
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.033 0.081 -10000 0 -0.46 1 1
Rap1/GTP -0.032 0.079 -10000 0 -0.47 1 1
axon guidance -0.009 0.057 -10000 0 -0.39 11 11
MAPK3 0.025 0.055 -10000 0 -10000 0 0
MAPK1 0.025 0.055 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.074 -10000 0 -0.39 1 1
actin cytoskeleton reorganization -0.027 0.067 -10000 0 -10000 0 0
CDC42/GDP -0.02 0.074 -10000 0 -0.39 1 1
PI3K -0.001 0.018 -10000 0 -0.41 1 1
EFNA5 -0.004 0.057 -10000 0 -0.74 3 3
Ephrin B2/EPHB4 -0.001 0.022 -10000 0 -0.48 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.003 0.024 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.031 0.078 -10000 0 -0.46 1 1
PTK2 0.01 0.026 -10000 0 -10000 0 0
MAP4K4 -0.009 0.11 -10000 0 -0.49 2 2
SRC 0 0 -10000 0 -10000 0 0
KALRN -0.009 0.08 -10000 0 -0.74 6 6
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.026 0.064 -10000 0 -0.48 1 1
MAP2K1 0.019 0.057 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.043 0.11 -10000 0 -0.52 2 2
cell migration 0.027 0.058 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
SYNJ1 -0.006 0.041 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
TF 0.01 0.092 -10000 0 -10000 0 0
HRAS/GTP -0.035 0.087 -10000 0 -0.5 1 1
Ephrin B1/EPHB1-2 -0.044 0.11 -10000 0 -0.32 69 69
cell adhesion mediated by integrin -0.002 0.041 0.41 1 -10000 0 1
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.038 0.093 -10000 0 -0.54 1 1
RAC1-CDC42/GTP -0.04 0.087 -10000 0 -0.47 2 2
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.019 0.07 -10000 0 -10000 0 0
ruffle organization -0.032 0.08 -10000 0 -0.47 1 1
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.032 0.048 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.011 0.061 -10000 0 -10000 0 0
ROCK1 0.01 0.063 -10000 0 -0.31 18 18
RAS family/GDP -0.023 0.058 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.084 -10000 0 -0.5 1 1
Ephrin B/EPHB1/Src/Paxillin -0.019 0.05 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.01 0.084 -10000 0 -0.71 7 7
HRAS 0 0 -10000 0 -10000 0 0
EGFR -0.023 0.12 -10000 0 -0.63 18 18
AKT 0.031 0.035 -10000 0 -0.38 3 3
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 -0.004 0.057 -10000 0 -0.74 3 3
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.004 0.053 -10000 0 -0.68 3 3
PIK3CA 0 0 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
PIK3CG -0.065 0.21 -10000 0 -0.74 44 44
PIK3R3 -0.001 0.033 -10000 0 -0.74 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 0 0 -10000 0 -10000 0 0
RAS 0.015 0.036 -10000 0 -10000 0 0
ERBB2 -0.002 0.036 -10000 0 -0.57 2 2
proliferation/survival/translation -0.019 0.036 0.21 3 -10000 0 3
PI3K 0.014 0.053 -10000 0 -0.25 5 5
PIK3R1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
FOXO 0.038 0.015 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.003 0.046 -10000 0 -0.74 2 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG 0.017 0.076 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -9999 0 -10000 0 0
CaM/Ca2+ -0.015 0.062 -9999 0 -10000 0 0
HIF1A 0 0 -9999 0 -10000 0 0
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.011 0.047 -9999 0 -10000 0 0
PLCG1 0.017 0.076 -9999 0 -10000 0 0
NOS3 0.039 0.072 -9999 0 -0.58 1 1
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.039 0.07 -9999 0 -0.55 1 1
FLT1 0.026 0 -9999 0 -10000 0 0
PGF -0.031 0.13 -9999 0 -0.57 27 27
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.038 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.043 0.068 -9999 0 -0.53 1 1
endothelial cell proliferation 0.016 0.096 -9999 0 -0.61 1 1
mol:Ca2+ 0.017 0.075 -9999 0 -10000 0 0
MAPK3 0.029 0.072 -9999 0 -10000 0 0
MAPK1 0.029 0.072 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
PLGF homodimer -0.031 0.13 -9999 0 -0.57 27 27
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.2 0.33 -9999 0 -0.74 137 137
VEGFA homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.035 0.07 -9999 0 -10000 0 0
PI3K -0.015 0.063 -9999 0 -10000 0 0
PRKCA 0.023 0.076 -9999 0 -10000 0 0
PRKCB 0.001 0.12 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer -0.018 0.077 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.017 0.076 -9999 0 -10000 0 0
RASA1 0.035 0 -9999 0 -10000 0 0
NRP2 -0.006 0.066 -9999 0 -0.74 4 4
VEGFR1 homodimer 0.026 0 -9999 0 -10000 0 0
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.064 0.18 -9999 0 -0.59 7 7
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.015 0.062 -9999 0 -10000 0 0
mol:L-citrulline 0.039 0.07 -9999 0 -0.55 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -9999 0 -10000 0 0
CD2AP 0 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.014 0.058 -9999 0 -10000 0 0
PDPK1 -0.014 0.057 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -9999 0 -10000 0 0
mol:NADP 0.039 0.07 -9999 0 -0.55 1 1
HSP90AA1 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.004 0.042 -9999 0 -0.47 4 4
Circadian rhythm 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
chromatin modification -0.001 0.012 -9999 0 -10000 0 0
CLOCK 0.013 0 -9999 0 -10000 0 0
TIMELESS/CRY2 0 0 -9999 0 -10000 0 0
DEC1/BMAL1 -0.023 0.095 -9999 0 -0.41 28 28
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.038 0 -9999 0 -10000 0 0
ARNTL 0.013 0 -9999 0 -10000 0 0
TIMELESS 0.038 0 -9999 0 -10000 0 0
NPAS2 0.013 0 -9999 0 -10000 0 0
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.012 0 -9999 0 -10000 0 0
CHEK1 -0.001 0.026 -9999 0 -0.57 1 1
mol:HEME 0.012 0 -9999 0 -10000 0 0
PER1 -0.003 0.046 -9999 0 -0.74 2 2
BMAL/CLOCK/NPAS2 0.035 0 -9999 0 -10000 0 0
BMAL1/CLOCK 0.037 0.038 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.001 0.012 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.012 -9999 0 -10000 0 0
mol:NADPH 0.012 0 -9999 0 -10000 0 0
PER1/TIMELESS -0.002 0.026 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.032 0.13 -9999 0 -0.57 28 28
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.007 0.058 -9999 0 -0.49 7 7
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 -0.009 0.08 -9999 0 -0.74 6 6
alpha4/beta7 Integrin/MAdCAM1 -0.008 0.057 -9999 0 -0.43 7 7
EPO -0.007 0.063 -9999 0 -0.57 6 6
alpha4/beta7 Integrin -0.008 0.065 -9999 0 -0.56 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.007 0.06 -9999 0 -0.56 6 6
EPO/EPOR (dimer) -0.005 0.045 -9999 0 -0.42 6 6
lamellipodium assembly 0.001 0.005 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.006 0.041 -9999 0 -0.34 6 6
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
MADCAM1 -0.005 0.051 -9999 0 -0.57 4 4
cell adhesion -0.008 0.057 -9999 0 -0.43 7 7
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.018 0.079 -9999 0 -0.53 8 8
ITGB7 -0.001 0.033 -9999 0 -0.74 1 1
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.012 0.083 -9999 0 -0.5 12 12
p130Cas/Crk/Dock1 -0.009 0.063 -9999 0 -0.72 2 2
VCAM1 -0.01 0.083 -9999 0 -0.66 8 8
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.047 -9999 0 -0.43 6 6
BCAR1 0.025 0.075 -9999 0 -0.5 8 8
EPOR 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.005 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.007 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
ITGA4 -0.009 0.08 -10000 0 -0.74 6 6
RAC1 0 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.008 0.065 -10000 0 -0.56 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.052 -10000 0 -0.48 6 6
alpha4/beta7 Integrin/Paxillin -0.006 0.051 -10000 0 -0.43 7 7
lamellipodium assembly 0.001 0.006 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
TLN1 0 0 -10000 0 -10000 0 0
PXN 0.02 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.04 -10000 0 -10000 0 0
cell adhesion -0.005 0.043 -10000 0 -0.4 6 6
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.005 0.047 -10000 0 -0.43 6 6
ITGB1 0 0 -10000 0 -10000 0 0
ITGB7 -0.001 0.033 -10000 0 -0.74 1 1
ARF6/GDP 0.001 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.01 0.071 -10000 0 -0.5 8 8
p130Cas/Crk/Dock1 0 0 -10000 0 -10000 0 0
VCAM1 -0.01 0.083 -10000 0 -0.66 8 8
alpha4/beta1 Integrin/Paxillin/Talin -0.005 0.044 -10000 0 -0.4 6 6
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.044 -10000 0 -0.4 6 6
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.043 0.4 6 -10000 0 6
CBL 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.005 0.044 -10000 0 -0.4 6 6
Rac1/GTP 0.001 0.006 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.005 0.032 -9999 0 -0.62 1 1
PDGFB-D/PDGFRB/SLAP -0.031 0.13 -9999 0 -0.58 27 27
PDGFB-D/PDGFRB/APS/CBL -0.001 0.021 -9999 0 -0.48 1 1
AKT1 -0.005 0.042 -9999 0 -0.53 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.04 -9999 0 -0.66 1 1
PIK3CA 0 0 -9999 0 -10000 0 0
FGR -0.044 0.16 -9999 0 -0.6 37 37
mol:Ca2+ 0.027 0.041 -9999 0 -0.7 1 1
MYC 0.043 0.052 -9999 0 -0.46 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.017 -9999 0 -0.39 1 1
LRP1/PDGFRB/PDGFB -0.001 0.021 -9999 0 -0.48 1 1
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.027 0.042 -9999 0 -0.71 1 1
PTEN -0.003 0.046 -9999 0 -0.74 2 2
GRB2 0 0 -9999 0 -10000 0 0
GRB7 -0.005 0.051 -9999 0 -0.57 4 4
PDGFB-D/PDGFRB/SHP2 -0.001 0.025 -9999 0 -0.56 1 1
PDGFB-D/PDGFRB/GRB10 -0.001 0.025 -9999 0 -0.56 1 1
cell cycle arrest -0.031 0.13 -9999 0 -0.58 27 27
HRAS 0 0 -9999 0 -10000 0 0
HIF1A 0.054 0.044 -9999 0 -0.46 1 1
GAB1 0.027 0.055 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.032 0.051 -9999 0 -0.66 1 1
PDGFB-D/PDGFRB 0.002 0.024 -9999 0 -0.49 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.025 -9999 0 -0.56 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.006 0.036 -9999 0 -0.62 1 1
positive regulation of MAPKKK cascade -0.001 0.025 -9999 0 -0.56 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0.027 0.042 -9999 0 -0.72 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.001 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.004 0.045 -9999 0 -0.45 5 5
SHB 0 0 -9999 0 -10000 0 0
BLK -0.021 0.1 -9999 0 -0.59 16 16
PTPN2 0.01 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.025 -9999 0 -0.56 1 1
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.028 0.069 -9999 0 -0.57 2 2
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.003 0.043 -9999 0 -0.56 3 3
LCK -0.002 0.035 -9999 0 -0.55 2 2
PDGFRB 0.009 0.034 -9999 0 -0.74 1 1
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.007 0.07 -9999 0 -0.59 7 7
ABL1 0.024 0.054 -9999 0 -0.65 1 1
PDGFB-D/PDGFRB/CBL 0.025 0.06 -9999 0 -0.77 1 1
PTPN1 0.01 0.001 -9999 0 -10000 0 0
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 0 0 -9999 0 -10000 0 0
cell proliferation 0.042 0.05 -9999 0 -0.42 1 1
SLA -0.04 0.17 -9999 0 -0.74 27 27
actin cytoskeleton reorganization 0.002 0.02 -9999 0 -10000 0 0
SRC 0 0.022 -9999 0 -0.49 1 1
PI3K -0.006 0.046 -9999 0 -0.6 1 1
PDGFB-D/PDGFRB/GRB7/SHC -0.004 0.037 -9999 0 -0.48 1 1
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.031 0.041 -9999 0 -0.69 1 1
LYN -0.002 0.044 -9999 0 -0.56 3 3
LRP1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
STAT5B 0 0 -9999 0 -10000 0 0
STAT5A 0 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.018 -9999 0 -10000 0 0
SPHK1 0.01 0.003 -9999 0 -10000 0 0
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.027 0.042 -9999 0 -0.72 1 1
PLCG1 0.027 0.043 -9999 0 -0.74 1 1
NHERF/PDGFRB -0.007 0.057 -9999 0 -0.47 7 7
YES1 0 0.022 -9999 0 -0.48 1 1
cell migration -0.006 0.057 -9999 0 -0.46 7 7
SHC/Grb2/SOS1 0 0.018 -9999 0 -10000 0 0
SLC9A3R2 -0.004 0.057 -9999 0 -0.74 3 3
SLC9A3R1 -0.005 0.051 -9999 0 -0.57 4 4
NHERF1-2/PDGFRB/PTEN -0.008 0.059 -9999 0 -0.48 6 6
FYN -0.001 0.034 -9999 0 -0.53 2 2
DOK1 0.029 0.021 -9999 0 -0.44 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.039 0.065 -9999 0 -0.66 1 1
PRKCD 0.029 0.021 -9999 0 -0.44 1 1
FER 0.029 0.021 -9999 0 -0.44 1 1
MAPKKK cascade -0.001 0.017 -9999 0 -10000 0 0
RASA1 0.029 0.021 -9999 0 -0.44 1 1
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk 0.002 0.02 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.001 0.025 -9999 0 -0.56 1 1
chemotaxis 0.024 0.053 -9999 0 -0.63 1 1
STAT1-3-5/STAT1-3-5 -0.001 0.016 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.001 0.025 -9999 0 -0.57 1 1
PTPRJ -0.003 0.046 -9999 0 -0.74 2 2
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.003 0.046 0.73 2 -10000 0 2
PI3K Class IB/PDE3B -0.003 0.046 -10000 0 -0.74 2 2
PDE3B -0.003 0.046 -10000 0 -0.74 2 2
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.001 0.021 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.034 0.032 0.23 1 -10000 0 1
YWHAZ 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.02 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP -0.002 0.036 -10000 0 -0.57 2 2
PRKCI 0 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0 0 -10000 0 -10000 0 0
GYS1 0.028 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.009 0.029 -10000 0 -10000 0 0
VAMP2 0 0 -10000 0 -10000 0 0
SLC2A4 0.034 0.034 -10000 0 -10000 0 0
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.022 0 -10000 0 -10000 0 0
SFN -0.057 0.17 -10000 0 -0.58 49 49
LNPEP 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.019 0.026 -10000 0 -0.56 1 1
MAP4K4 0.033 0.056 -10000 0 -0.64 1 1
BAG4 -0.001 0.026 -10000 0 -0.57 1 1
PKC zeta/ceramide -0.002 0.016 0.17 1 -10000 0 1
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.009 0.08 -10000 0 -0.74 6 6
BAX 0.001 0.008 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.017 0.003 -10000 0 -10000 0 0
BAD -0.001 0.016 0.19 1 -10000 0 1
SMPD1 0.02 0.041 -10000 0 -0.23 12 12
RB1 -0.002 0.025 0.19 1 -0.43 1 2
FADD/Caspase 8 0.041 0.053 -10000 0 -0.61 1 1
MAP2K4 0.005 0.015 -10000 0 -10000 0 0
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.005 0.015 -10000 0 -10000 0 0
EGF -0.014 0.097 -10000 0 -0.69 10 10
mol:ceramide -0.01 0.017 0.2 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 0.019 0.026 -10000 0 -0.56 1 1
ASAH1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.002 0.025 0.19 1 -0.42 1 2
cell proliferation -0.013 0.062 -10000 0 -0.33 1 1
BID 0.024 0.038 -10000 0 -0.38 1 1
MAP3K1 -0.001 0.016 -10000 0 -10000 0 0
EIF2A 0.012 0.015 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.015 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.015 0.015 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.002 0.016 0.17 1 -10000 0 1
FADD 0.033 0.056 -10000 0 -0.64 1 1
KSR1 -0.001 0.016 0.19 1 -10000 0 1
MAPK8 0.009 0.015 -10000 0 -10000 0 0
PRKRA -0.001 0.016 0.19 1 -10000 0 1
PDGFA -0.001 0.033 -10000 0 -0.74 1 1
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.028 0.14 -10000 0 -0.73 19 19
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.01 0.017 0.2 1 -10000 0 1
CTSD 0 0 -10000 0 -10000 0 0
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 -0.014 0.066 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.019 0.026 -10000 0 -0.56 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.009 0.052 -10000 0 -0.68 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.076 -10000 0 -0.46 14 14
mol:Sphingosine-1-phosphate 0.019 0.026 -10000 0 -0.55 1 1
MAP2K1 0.012 0.015 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS 0.001 0.012 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.019 -10000 0 -0.42 1 1
EIF2AK2 0.005 0.015 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.012 0.074 -10000 0 -0.47 13 13
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.027 -10000 0 -0.32 1 1
MAP2K2 0.012 0.015 -10000 0 -10000 0 0
SMPD3 0.018 0.063 -10000 0 -0.3 16 16
TNF -0.019 0.12 -10000 0 -0.72 13 13
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.005 0.037 0.23 10 -10000 0 10
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.001 0.012 -10000 0 -10000 0 0
BCL2 -0.001 0.026 -10000 0 -0.57 1 1
S1P5 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.006 0.034 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.047 -9999 0 -0.37 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 -0.004 0.049 -9999 0 -0.63 3 3
RhoA/GTP -0.006 0.035 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.007 0.04 -9999 0 -0.3 2 2
GNAZ -0.009 0.08 -9999 0 -0.74 6 6
GNAI3 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
S1PR5 -0.01 0.075 -9999 0 -0.6 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.007 0.04 -9999 0 -0.31 2 2
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
GNAI1 -0.001 0.033 -9999 0 -0.74 1 1
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.024 0.037 -9999 0 -10000 0 0
PLK1 -0.089 0.22 -9999 0 -0.73 3 3
CDKN1B 0.05 0.087 -9999 0 -10000 0 0
FOXO3 -0.023 0.16 -9999 0 -0.64 3 3
KAT2B 0.007 0.037 -9999 0 -0.75 1 1
FOXO1/SIRT1 0.018 0.026 -9999 0 -10000 0 0
CAT -0.017 0.17 -9999 0 -1.4 2 2
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.009 0.016 -9999 0 -10000 0 0
FOXO1 0.027 0.022 -9999 0 -10000 0 0
MAPK10 0.023 0.056 -9999 0 -0.41 8 8
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.08 0.032 -9999 0 -10000 0 0
response to oxidative stress -0.003 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.064 0.1 -9999 0 -0.61 2 2
XPO1 0.01 0 -9999 0 -10000 0 0
EP300 0.006 0.006 -9999 0 -10000 0 0
BCL2L11 0.015 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 -0.003 0.028 -9999 0 -10000 0 0
mol:GDP -0.003 0.02 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
GADD45A 0.046 0.074 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.054 0.031 -9999 0 -10000 0 0
MST1 0.007 0.029 -9999 0 -0.56 1 1
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.038 0.038 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.03 0.008 -9999 0 -10000 0 0
MAPK9 0.03 0.008 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
SIRT1 0.008 0.013 -9999 0 -10000 0 0
SOD2 0.054 0.098 -9999 0 -10000 0 0
RBL2 0.018 0.11 -9999 0 -10000 0 0
RAL/GDP 0.014 0.015 -9999 0 -10000 0 0
CHUK 0.008 0.015 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.017 0.018 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG -0.042 0.29 -9999 0 -1.5 20 20
SKP2 -0.003 0.044 -9999 0 -0.57 3 3
USP7 0.011 0 -9999 0 -10000 0 0
IKBKB 0.007 0.029 -9999 0 -0.56 1 1
CCNB1 -0.034 0.18 -9999 0 -0.73 3 3
FOXO1-3a-4/beta catenin -0.015 0.04 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.028 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.008 0.015 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.081 0.028 -9999 0 -10000 0 0
SFN -0.057 0.17 -9999 0 -0.58 49 49
CDK2 0.006 0.007 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.053 -9999 0 -10000 0 0
CREBBP 0.006 0.007 -9999 0 -10000 0 0
FBXO32 -0.018 0.15 -9999 0 -0.7 1 1
BCL6 0.018 0.11 -9999 0 -10000 0 0
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.027 0 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.025 0.024 -9999 0 -10000 0 0
MAPK12 0.027 0.015 -9999 0 -0.31 1 1
CCND1 0.014 0.051 -9999 0 -0.44 6 6
p38 gamma/SNTA1 -0.001 0.013 -9999 0 -10000 0 0
MAP2K3 0 0 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.027 0.015 -9999 0 -0.3 1 1
MAP2K6 0.021 0.016 -9999 0 -0.34 1 1
MAPT 0.023 0.045 -9999 0 -0.37 6 6
MAPK13 0.02 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.007 0.061 -10000 0 -0.46 8 8
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.019 -10000 0 -0.42 1 1
GNB1/GNG2 -0.006 0.053 -10000 0 -0.48 6 6
GNB1 -0.001 0.033 -10000 0 -0.74 1 1
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.003 0.035 -10000 0 -0.45 3 3
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 0.001 0.008 0.11 3 -10000 0 3
GNAL -0.004 0.057 -10000 0 -0.74 3 3
GNG2 -0.007 0.073 -10000 0 -0.74 5 5
CRH -0.001 0.026 -10000 0 -0.57 1 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0 -10000 0 -10000 0 0
MAPK11 0.007 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0 0 -9999 0 -10000 0 0
adherens junction organization 0.032 0.033 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP -0.009 0.049 -9999 0 -10000 0 0
FMN1 0.012 0.1 -9999 0 -0.38 32 32
mol:IP3 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
CTNND1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.039 0 -9999 0 -10000 0 0
VASP 0.039 0 -9999 0 -10000 0 0
ZYX 0.039 0 -9999 0 -10000 0 0
JUB 0.039 0 -9999 0 -10000 0 0
EGFR(dimer) -0.011 0.057 -9999 0 -0.38 6 6
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
FYN 0.043 0.036 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
PIK3R1 0.011 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
RhoA/GDP -0.009 0.049 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.039 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
EGFR -0.023 0.12 -9999 0 -0.63 18 18
CASR 0.036 0.039 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
actin cable formation 0.019 0.099 -9999 0 -10000 0 0
apoptosis 0 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
mol:GDP -0.01 0.053 -9999 0 -10000 0 0
PIP5K1A 0.039 0 -9999 0 -10000 0 0
PLCG1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.01 0.052 -9999 0 -10000 0 0
homophilic cell adhesion 0.001 0 -9999 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 0 -9999 0 -10000 0 0
SMAD2 0.012 0.014 -9999 0 -0.29 1 1
SMAD3 0.036 0.013 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0.01 -9999 0 -10000 0 0
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.001 0.012 -9999 0 -10000 0 0
MAP3K1 0 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0 0 -9999 0 -10000 0 0
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 -0.001 0.033 -9999 0 -0.74 1 1
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0 -9999 0 -10000 0 0
KPNA2 0 0 -9999 0 -10000 0 0
PIAS4 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.072 0.018 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.002 0.035 -9999 0 -0.56 2 2
NFKBIA 0.042 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
RIPK2 0 0 -9999 0 -10000 0 0
IKBKG -0.001 0.015 -9999 0 -10000 0 0
IKK complex/A20 -0.01 0.055 -9999 0 -10000 0 0
NEMO/A20/RIP2 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM -0.001 0.014 -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 -0.001 0.016 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.003 0.046 -9999 0 -0.74 2 2
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 -0.014 0.087 -9999 0 -0.55 13 13
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.003 0.046 -9999 0 -0.74 2 2
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.019 0.12 -9999 0 -0.72 13 13
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 0.041 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 -0.001 0.017 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.003 0.027 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0 0 -9999 0 -10000 0 0
PLK4 -0.001 0.026 -9999 0 -0.57 1 1
regulation of centriole replication 0.019 0.019 -9999 0 -0.42 1 1
Arf6 downstream 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
PLAUR 0.038 0.004 -10000 0 -10000 0 0
regulation of axonogenesis -0.024 0.019 -10000 0 -10000 0 0
myoblast fusion 0.002 0.015 -10000 0 -10000 0 0
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.002 0.025 0.45 1 -10000 0 1
ARF1/GTP 0 0.003 -10000 0 -10000 0 0
mol:GM1 0.009 0.005 -10000 0 -10000 0 0
mol:Choline 0.023 0.028 -10000 0 -10000 0 0
lamellipodium assembly -0.001 0.018 -10000 0 -10000 0 0
MAPK3 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.002 0.025 -10000 0 -0.46 1 1
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.002 0.015 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.014 -10000 0 -10000 0 0
ARF6 0.008 0.003 -10000 0 -10000 0 0
RAB11A 0 0 -10000 0 -10000 0 0
TIAM1 0.01 0.033 -10000 0 -0.74 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.004 -10000 0 -10000 0 0
actin filament bundle formation 0.001 0.013 -10000 0 -10000 0 0
KALRN -0.005 0.048 -10000 0 -0.44 6 6
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.001 0.013 -10000 0 -10000 0 0
NME1 0.01 0.026 -10000 0 -0.57 1 1
Rac1/GDP -0.001 0.013 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.001 0.006 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.018 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.001 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.006 -10000 0 -10000 0 0
RhoA/GTP 0 0.003 -10000 0 -10000 0 0
mol:GDP -0.001 0.016 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.001 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.015 0.031 -10000 0 -0.38 3 3
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.018 -10000 0 -10000 0 0
ruffle organization 0.024 0.019 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.001 0.006 -10000 0 -10000 0 0
PLD2 0.018 0.005 -10000 0 -10000 0 0
PIP5K1A -0.001 0.016 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.023 0.028 -10000 0 -10000 0 0
Rac1/GTP -0.001 0.018 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.066 0.037 -10000 0 -10000 0 0
CRKL 0.039 0.038 -10000 0 -10000 0 0
mol:DAG -0.004 0.033 -10000 0 -10000 0 0
HRAS -0.003 0.025 -10000 0 -10000 0 0
MAPK8 0.028 0.045 -10000 0 -0.44 2 2
RAP1A 0.039 0.038 -10000 0 -10000 0 0
GAB1 0.039 0.038 -10000 0 -10000 0 0
MAPK14 0.028 0.045 -10000 0 -0.44 2 2
EPO 0.004 0.063 -10000 0 -0.57 6 6
PLCG1 -0.005 0.034 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.012 0.004 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.006 0.047 -10000 0 -0.49 2 2
GAB1/SHC/GRB2/SOS1 -0.003 0.027 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.003 0.045 -10000 0 -0.4 6 6
IRS2 0.037 0.049 -10000 0 -10000 0 0
STAT1 0.052 0.041 -10000 0 -10000 0 0
STAT5B -0.005 0.034 -10000 0 -10000 0 0
cell proliferation 0.034 0.042 -10000 0 -0.4 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.004 0.029 -10000 0 -10000 0 0
TEC 0.038 0.046 -10000 0 -10000 0 0
SOCS3 -0.003 0.046 -10000 0 -0.74 2 2
STAT1 (dimer) 0.051 0.04 -10000 0 -10000 0 0
JAK2 0.011 0.004 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.041 0.04 -10000 0 -0.37 2 2
EPO/EPOR -0.003 0.045 -10000 0 -0.4 6 6
LYN 0.009 0.047 -10000 0 -0.74 2 2
TEC/VAV2 0.041 0.064 -10000 0 -0.72 2 2
elevation of cytosolic calcium ion concentration 0.012 0.004 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.024 0.05 -10000 0 -0.49 2 2
mol:IP3 -0.004 0.033 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.006 0.041 -10000 0 -10000 0 0
SH2B3 0.009 0.047 -10000 0 -0.73 2 2
NFKB1 0.028 0.045 -10000 0 -0.44 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.002 0.031 0.3 2 -10000 0 2
PTPN6 0.033 0.039 -10000 0 -0.36 2 2
TEC/VAV2/GRB2 -0.007 0.055 -10000 0 -0.7 2 2
EPOR 0.012 0.004 -10000 0 -10000 0 0
INPP5D -0.001 0.033 -10000 0 -0.74 1 1
mol:GDP -0.003 0.027 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0 0 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.004 0.029 -10000 0 -10000 0 0
VAV2 0.037 0.055 -10000 0 -0.74 1 1
CBL 0.039 0.038 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.004 0.029 -10000 0 -10000 0 0
STAT5A -0.005 0.034 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.063 0.042 -10000 0 -10000 0 0
LYN/PLCgamma2 -0.002 0.035 -10000 0 -0.55 2 2
PTPN11 0 0 -10000 0 -10000 0 0
BTK -0.002 0.13 -10000 0 -0.74 2 2
BCL2 0.066 0.039 -10000 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 0.001 0.02 0.31 2 -10000 0 2
FRAP1 0.014 0.007 -10000 0 -10000 0 0
AKT1 0.001 0.015 0.23 2 -10000 0 2
INSR 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0 -10000 0 -10000 0 0
TSC2 0 0 -10000 0 -10000 0 0
RHEB/GDP 0 0 -10000 0 -10000 0 0
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.026 0.01 -10000 0 -10000 0 0
MAP3K5 0.009 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
apoptosis 0.009 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -10000 0 0
EIF4B 0.03 0.01 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.029 0.009 0.17 2 -10000 0 2
FKBP1A 0 0.001 -10000 0 -10000 0 0
RHEB/GTP 0 0 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -10000 0 0
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 0.001 0.016 0.25 2 -10000 0 2
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C 0 0.006 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.001 -10000 0 -10000 0 0
TSC1/TSC2 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
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 0.007 0.001 -10000 0 -10000 0 0
INS 0 0 -10000 0 -10000 0 0
PTEN -0.003 0.046 -10000 0 -0.74 2 2
PDK2 0.001 0.016 0.25 2 -10000 0 2
EIF4EBP1 0.004 0.021 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
PPP2R5D 0.02 0.006 -10000 0 -10000 0 0
peptide biosynthetic process 0.015 0 -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 0.004 2 -10000 0 2
EEF2 0.015 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.004 0.015 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.02 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.033 0 -9999 0 -10000 0 0
CDKN1A 0.033 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0 0 -9999 0 -10000 0 0
FOXO3 0.033 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0 0 -9999 0 -10000 0 0
AKT3 0.012 0.033 -9999 0 -0.42 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.033 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0 0 -9999 0 -10000 0 0
RAF1 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.033 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.033 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.022 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAPKAP1 0 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.03 0.025 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
AKT1S1 0.033 0 -9999 0 -10000 0 0
CASP9 0.033 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0 -9999 0 -10000 0 0
CHUK 0.033 0 -9999 0 -10000 0 0
BAD/BCL-XL 0 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.015 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.043 0.027 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
MDM2 0.032 0.014 -9999 0 -10000 0 0
MAPKKK cascade 0 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0 0.011 -9999 0 -10000 0 0
TSC1/TSC2 0.039 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.01 -9999 0 -10000 0 0
glucose import 0.024 0.04 -9999 0 -0.43 4 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.028 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.024 0.041 -9999 0 -0.43 4 4
GSK3A 0.033 0 -9999 0 -10000 0 0
FOXO1 0.033 0 -9999 0 -10000 0 0
GSK3B 0.033 0 -9999 0 -10000 0 0
SFN -0.057 0.17 -9999 0 -0.58 49 49
G1/S transition of mitotic cell cycle 0.039 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.029 0.039 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
KPNA1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
RHEB 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.037 0.056 -9999 0 -0.53 1 1
BAG4 -0.001 0.026 -9999 0 -0.57 1 1
BAD 0.027 0.021 -9999 0 -10000 0 0
NFKBIA 0 0 -9999 0 -10000 0 0
BIRC3 -0.009 0.08 -9999 0 -0.74 6 6
BAX 0.027 0.021 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.015 -9999 0 -0.12 1 1
IKBKB 0.042 0.055 -9999 0 -0.49 1 1
MAP2K2 0.038 0.022 -9999 0 -10000 0 0
MAP2K1 0.038 0.022 -9999 0 -10000 0 0
SMPD1 0.017 0.015 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.043 0.055 -9999 0 -0.51 1 1
MAP2K4 0.033 0.021 -9999 0 -10000 0 0
protein ubiquitination 0.044 0.054 -9999 0 -0.5 1 1
EnzymeConsortium:2.7.1.37 0.043 0.025 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
RAF1 0.033 0.022 -9999 0 -10000 0 0
CRADD 0.01 0.001 -9999 0 -10000 0 0
mol:ceramide 0.021 0.021 -9999 0 -0.16 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.01 0.001 -9999 0 -10000 0 0
MAP3K1 0.027 0.021 -9999 0 -10000 0 0
TRADD 0.01 0.001 -9999 0 -10000 0 0
RELA/p50 0 0 -9999 0 -10000 0 0
MAPK3 0.04 0.022 -9999 0 -10000 0 0
MAPK1 0.04 0.022 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.037 0.056 -9999 0 -0.53 1 1
KSR1 0.028 0.022 -9999 0 -10000 0 0
MAPK8 0.038 0.02 -9999 0 -10000 0 0
TRAF2 0 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.042 0.053 -9999 0 -0.49 1 1
TNF R/SODD -0.001 0.019 -9999 0 -0.42 1 1
TNF -0.009 0.12 -9999 0 -0.72 13 13
CYCS 0.028 0.02 -9999 0 -10000 0 0
IKBKG 0.042 0.053 -9999 0 -0.49 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.031 0.059 -9999 0 -0.56 1 1
RELA 0 0 -9999 0 -10000 0 0
RIPK1 0 0.001 -9999 0 -10000 0 0
AIFM1 0.028 0.02 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.013 0.076 -9999 0 -0.46 14 14
TNFRSF1A 0 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.023 0.015 -9999 0 -10000 0 0
NSMAF 0.037 0.055 -9999 0 -0.52 1 1
response to hydrogen peroxide 0 0 -9999 0 -10000 0 0
BCL2 -0.001 0.026 -9999 0 -0.57 1 1
Atypical NF-kappaB 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
BCL3/RelA 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.015 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.017 -9999 0 -10000 0 0
NFKBIA 0.025 0.018 -9999 0 -10000 0 0
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.015 -9999 0 -10000 0 0
ARRB2 0.015 0 -9999 0 -10000 0 0
REL 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.015 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.015 -9999 0 -0.34 1 1
PIK3CA 0 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer -0.001 0.019 -9999 0 -0.42 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0.019 0.019 -9999 0 -0.42 1 1
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.03 0.019 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.001 0.017 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.001 0.017 -9999 0 -10000 0 0
IKBKB -0.001 0.026 -9999 0 -0.57 1 1
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK -0.001 0.033 -9999 0 -0.74 1 1
I kappa B alpha/PIK3R1 -0.001 0.015 -9999 0 -10000 0 0
cell death -0.001 0.016 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.001 0.015 -9999 0 -10000 0 0
LCK -0.001 0.033 -9999 0 -0.74 1 1
BCL3 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0 0 -9999 0 -10000 0 0
KLHL20 -0.004 0.03 -9999 0 -0.38 1 1
CYFIP2 -0.026 0.14 -9999 0 -0.74 18 18
Rac1/GDP 0.053 0.011 -9999 0 -10000 0 0
ENAH 0 0 -9999 0 -10000 0 0
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 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.035 -9999 0 -0.25 5 5
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.001 0.019 -9999 0 -0.43 1 1
RAPGEF1 0.048 0.002 -9999 0 -10000 0 0
CTNND1 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.043 0.005 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.001 0.025 -9999 0 -0.56 1 1
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.002 0.024 -9999 0 -0.44 1 1
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.001 0.033 -9999 0 -0.74 1 1
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0.053 0.01 -9999 0 -10000 0 0
actin cytoskeleton organization -0.003 0.022 -9999 0 -0.26 1 1
CDC42/GDP 0.053 0.01 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
ITGB7 -0.001 0.033 -9999 0 -0.74 1 1
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.052 0.012 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.006 -9999 0 -10000 0 0
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 -0.004 0.03 -9999 0 -0.25 7 7
NME1 -0.001 0.026 -9999 0 -0.57 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
WASF2 -0.004 0.018 -9999 0 -10000 0 0
Rap1/GTP 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.001 0.018 -9999 0 -0.4 1 1
CCND1 -0.005 0.038 -9999 0 -0.32 7 7
VAV2 0.041 0.061 -9999 0 -0.74 3 3
RAP1/GDP 0 0.001 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
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 -0.001 0.017 -9999 0 -10000 0 0
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.007 0.052 -9999 0 -0.49 3 3
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 -0.001 0.013 -9999 0 -10000 0 0
HDAC4 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.025 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.014 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.026 -9999 0 -0.57 1 1
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
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0 0 -9999 0 -9999 0 0
JUP 0 0 -9999 0 -9999 0 0
CDH1 0 0 -9999 0 -9999 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 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0 -9999 0 -10000 0 0
AP2 -0.001 0.019 -9999 0 -0.42 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0 -9999 0 -10000 0 0
CD4 -0.022 0.13 -9999 0 -0.74 15 15
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0 -9999 0 -10000 0 0
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 0 -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 0 -9999 0 -10000 0 0
AP2M1 -0.001 0.026 -9999 0 -0.57 1 1
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 0 -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 0.022 0 -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 -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 -0.008 0.044 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0 -9999 0 -10000 0 0
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 -9999 0 -10000 0 0
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 -0.015 0.082 -9999 0 -0.48 15 15
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 0.013 -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 -0.001 0.019 -9999 0 -0.42 1 1
RELB -0.001 0.026 -9999 0 -0.57 1 1
NFKB2 0 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.001 0.016 -9999 0 -0.35 1 1
regulation of B cell activation -0.001 0.016 -9999 0 -0.35 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 501 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.XC.AA0X TCGA.O2.A5IB TCGA.O2.A52W TCGA.O2.A52V
109_MAP3K5 0.048 0.048 0.048 0.048
47_PPARGC1A 0 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 -0.58 0 -0.58 -0.58
105_BMP2 0 -0.74 0 0
131_RELN/VLDLR 0 0 0 0
30_TGFB1/TGF beta receptor Type II 0.014 0.016 0.014 0.014
84_STAT5B 0.023 -0.0056 0.038 0.038
84_STAT5A 0.023 -0.0056 0.038 0.038
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/LUSC-TP/19438973/LUSC-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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