PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1TD9WMW
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 and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1TD9WMW
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 43 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
FOXM1 transcription factor network 233
Glypican 2 network 177
Angiopoietin receptor Tie2-mediated signaling 153
Aurora B signaling 126
HIF-1-alpha transcription factor network 122
Signaling events mediated by the Hedgehog family 113
Endothelins 82
PLK1 signaling events 76
Aurora C signaling 70
Signaling mediated by p38-alpha and p38-beta 64
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 515 . 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 ( 515 ).

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
FOXM1 transcription factor network 0.4524 233 11908 51 -0.034 0.78 1000 -1000 -0.084 -1000
Glypican 2 network 0.3437 177 711 4 0.092 0.14 1000 -1000 0.016 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2971 153 13507 88 -0.59 0.12 1000 -1000 -0.055 -1000
Aurora B signaling 0.2447 126 8477 67 -0.14 0.28 1000 -1000 -0.028 -1000
HIF-1-alpha transcription factor network 0.2369 122 9304 76 -0.06 0.43 1000 -1000 -0.031 -1000
Signaling events mediated by the Hedgehog family 0.2194 113 5882 52 -0.22 0.1 1000 -1000 -0.022 -1000
Endothelins 0.1592 82 7878 96 -0.31 0.2 1000 -1000 -0.037 -1000
PLK1 signaling events 0.1476 76 6503 85 -0.049 0.2 1000 -1000 -0.021 -1000
Aurora C signaling 0.1359 70 493 7 0 0.16 1000 -1000 -0.008 -1000
Signaling mediated by p38-alpha and p38-beta 0.1243 64 2855 44 -0.1 0.021 1000 -1000 -0.021 -1000
Visual signal transduction: Cones 0.1165 60 2307 38 -0.08 0.12 1000 -1000 -0.018 -1000
Signaling events regulated by Ret tyrosine kinase 0.1165 60 4998 82 -0.076 0.059 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 0.1087 56 2599 46 -0.2 0.16 1000 -1000 -0.082 -1000
Osteopontin-mediated events 0.1049 54 2076 38 0 0.23 1000 -1000 -0.032 -1000
Fc-epsilon receptor I signaling in mast cells 0.1049 54 5293 97 -0.095 0.021 1000 -1000 -0.044 -1000
BMP receptor signaling 0.1029 53 4310 81 -0.19 0.22 1000 -1000 -0.027 -1000
IL4-mediated signaling events 0.1010 52 4734 91 -0.62 0.34 1000 -1000 -0.11 -1000
amb2 Integrin signaling 0.1010 52 4323 82 -0.29 0.084 1000 -1000 -0.024 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0932 48 2502 52 -0.14 0.045 1000 -1000 -0.033 -1000
Ephrin B reverse signaling 0.0932 48 2336 48 -0.079 0.076 1000 -1000 -0.023 -1000
Visual signal transduction: Rods 0.0874 45 2350 52 -0.08 0.1 1000 -1000 -0.031 -1000
Syndecan-1-mediated signaling events 0.0796 41 1405 34 0 0.21 1000 -1000 -0.023 -1000
p75(NTR)-mediated signaling 0.0777 40 5074 125 -0.15 0.13 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0718 37 2566 68 -0.16 0.07 1000 -1000 -0.073 -1000
Thromboxane A2 receptor signaling 0.0699 36 3787 105 -0.12 0.071 1000 -1000 -0.041 -1000
TCGA08_retinoblastoma 0.0699 36 288 8 -0.023 0.098 1000 -1000 -0.003 -1000
IL23-mediated signaling events 0.0699 36 2192 60 -0.21 0.025 1000 -1000 -0.086 -1000
Integrins in angiogenesis 0.0680 35 3011 84 -0.069 0.23 1000 -1000 -0.032 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0680 35 4300 120 -0.16 0.14 1000 -1000 -0.048 -1000
LPA4-mediated signaling events 0.0660 34 416 12 -0.071 0 1000 -1000 -0.015 -1000
Arf6 signaling events 0.0660 34 2164 62 -0.11 0.071 1000 -1000 -0.033 -1000
Canonical Wnt signaling pathway 0.0660 34 1769 51 -0.21 0.095 1000 -1000 -0.034 -1000
HIF-2-alpha transcription factor network 0.0641 33 1423 43 -0.13 0.14 1000 -1000 -0.037 -1000
Presenilin action in Notch and Wnt signaling 0.0621 32 1996 61 -0.21 0.095 1000 -1000 -0.028 -1000
Glucocorticoid receptor regulatory network 0.0621 32 3698 114 -0.25 0.17 1000 -1000 -0.038 -1000
Reelin signaling pathway 0.0621 32 1816 56 -0.038 0.049 1000 -1000 -0.023 -1000
Aurora A signaling 0.0583 30 1819 60 -0.028 0.18 1000 -1000 -0.02 -1000
Effects of Botulinum toxin 0.0583 30 787 26 0 0.045 1000 -1000 -0.009 -1000
IL6-mediated signaling events 0.0583 30 2252 75 -0.15 0.057 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 0.0583 30 635 21 -0.027 0.071 1000 -1000 -0.029 -1000
Glypican 1 network 0.0563 29 1430 48 -0.066 0.037 1000 -1000 -0.024 -1000
TCGA08_p53 0.0563 29 204 7 -0.023 0.019 1000 -1000 -0.009 -1000
Wnt signaling 0.0544 28 197 7 -0.02 0.04 1000 -1000 -0.009 -1000
Noncanonical Wnt signaling pathway 0.0485 25 652 26 -0.042 0.04 1000 -1000 -0.033 -1000
Nectin adhesion pathway 0.0466 24 1515 63 -0.047 0.051 1000 -1000 -0.04 -1000
Nongenotropic Androgen signaling 0.0466 24 1279 52 -0.056 0.041 1000 -1000 -0.019 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0447 23 802 34 -0.035 0.06 1000 -1000 -0.022 -1000
IL1-mediated signaling events 0.0447 23 1454 62 -0.08 0.042 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.0447 23 2384 102 -0.056 0.085 1000 -1000 -0.063 -1000
PDGFR-alpha signaling pathway 0.0427 22 978 44 -0.19 0.04 1000 -1000 -0.03 -1000
FoxO family signaling 0.0427 22 1426 64 -0.001 0.2 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 0.0427 22 1486 67 -0.041 0.12 1000 -1000 -0.03 -1000
Regulation of Androgen receptor activity 0.0427 22 1575 70 -0.14 0.12 1000 -1000 -0.042 -1000
Syndecan-2-mediated signaling events 0.0408 21 1498 69 -0.047 0.053 1000 -1000 -0.03 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0408 21 723 33 -0.07 0.096 1000 -1000 -0.028 -1000
ErbB2/ErbB3 signaling events 0.0388 20 1309 65 -0.051 0.03 1000 -1000 -0.055 -1000
FAS signaling pathway (CD95) 0.0388 20 968 47 -0.24 0.034 1000 -1000 -0.029 -1000
S1P4 pathway 0.0388 20 516 25 -0.019 0.027 1000 -1000 -0.014 -1000
ErbB4 signaling events 0.0369 19 1353 69 -0.11 0.15 1000 -1000 -0.026 -1000
EPHB forward signaling 0.0369 19 1677 85 -0.032 0.084 1000 -1000 -0.045 -1000
Class IB PI3K non-lipid kinase events 0.0369 19 57 3 -0.008 0.008 1000 -1000 -0.018 -1000
Coregulation of Androgen receptor activity 0.0350 18 1387 76 -0.059 0.096 1000 -1000 -0.02 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0350 18 1010 54 -0.034 0.1 1000 -1000 -0.032 -1000
Ceramide signaling pathway 0.0350 18 1437 76 -0.019 0.071 1000 -1000 -0.024 -1000
S1P5 pathway 0.0350 18 307 17 -0.016 0.022 1000 -1000 -0.004 -1000
Caspase cascade in apoptosis 0.0330 17 1287 74 -0.03 0.088 1000 -1000 -0.023 -1000
IL12-mediated signaling events 0.0330 17 1496 87 -0.13 0.057 1000 -1000 -0.065 -1000
PLK2 and PLK4 events 0.0330 17 52 3 -0.007 0.036 1000 -1000 -0.015 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0330 17 1485 85 -0.044 0.035 1000 -1000 -0.046 -1000
Signaling events mediated by PTP1B 0.0330 17 1347 76 -0.056 0.072 1000 -1000 -0.025 -1000
Calcium signaling in the CD4+ TCR pathway 0.0330 17 535 31 -0.038 0.028 1000 -1000 -0.038 -1000
TCR signaling in naïve CD8+ T cells 0.0311 16 1568 93 -0.041 0.033 1000 -1000 -0.033 -1000
BCR signaling pathway 0.0311 16 1668 99 -0.053 0.085 1000 -1000 -0.053 -1000
Plasma membrane estrogen receptor signaling 0.0311 16 1445 86 -0.062 0.059 1000 -1000 -0.036 -1000
S1P1 pathway 0.0291 15 568 36 -0.086 0.021 1000 -1000 -0.029 -1000
Regulation of p38-alpha and p38-beta 0.0291 15 814 54 -0.036 0.065 1000 -1000 -0.039 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0291 15 1202 78 -0.042 0.023 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class III 0.0252 13 552 40 -0.062 0.059 1000 -1000 -0.033 -1000
Syndecan-3-mediated signaling events 0.0252 13 488 35 -0.12 0.047 1000 -1000 -0.022 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0252 13 1749 125 -0.19 0.042 1000 -1000 -0.042 -1000
Class I PI3K signaling events 0.0233 12 898 73 -0.033 0.065 1000 -1000 -0.026 -1000
IL27-mediated signaling events 0.0214 11 605 51 -0.047 0.03 1000 -1000 -0.043 -1000
Signaling events mediated by PRL 0.0214 11 401 34 -0.02 0.085 1000 -1000 -0.035 -1000
BARD1 signaling events 0.0194 10 609 57 -0.046 0.12 1000 -1000 -0.034 -1000
IL2 signaling events mediated by STAT5 0.0194 10 226 22 -0.024 0.089 1000 -1000 -0.027 -1000
PDGFR-beta signaling pathway 0.0194 10 1004 97 -0.032 0.052 1000 -1000 -0.036 -1000
Ephrin A reverse signaling 0.0175 9 64 7 -0.012 0.028 1000 -1000 -0.009 -1000
Insulin Pathway 0.0175 9 702 74 -0.096 0.051 1000 -1000 -0.032 -1000
VEGFR1 specific signals 0.0175 9 523 56 -0.19 0.049 1000 -1000 -0.026 -1000
Regulation of nuclear SMAD2/3 signaling 0.0155 8 1182 136 -0.17 0.072 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 0.0155 8 149 17 -0.012 0.047 1000 -1000 -0.018 -1000
Cellular roles of Anthrax toxin 0.0155 8 323 39 -0.032 0.028 1000 -1000 -0.016 -1000
Hedgehog signaling events mediated by Gli proteins 0.0155 8 570 65 -0.14 0.049 1000 -1000 -0.031 -1000
mTOR signaling pathway 0.0155 8 444 53 -0.058 0.025 1000 -1000 -0.036 -1000
ceramide signaling pathway 0.0155 8 419 49 -0.007 0.029 1000 -1000 -0.022 -1000
Retinoic acid receptors-mediated signaling 0.0155 8 499 58 -0.091 0.049 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0155 8 381 45 -0.016 0.05 1000 -1000 -0.031 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0155 8 624 74 -0.087 0.071 1000 -1000 -0.042 -1000
Regulation of Telomerase 0.0155 8 822 102 -0.02 0.1 1000 -1000 -0.032 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0136 7 197 28 -0.015 0.034 1000 -1000 -0.014 -1000
EPO signaling pathway 0.0136 7 418 55 -0.026 0.045 1000 -1000 -0.036 -1000
IFN-gamma pathway 0.0136 7 498 68 -0.029 0.064 1000 -1000 -0.036 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0136 7 611 83 -0.057 0.049 1000 -1000 -0.026 -1000
Arf6 trafficking events 0.0136 7 508 71 -0.037 0.038 1000 -1000 -0.029 -1000
Ras signaling in the CD4+ TCR pathway 0.0136 7 127 17 -0.002 0.032 1000 -1000 -0.014 -1000
IL2 signaling events mediated by PI3K 0.0117 6 367 58 -0.014 0.081 1000 -1000 -0.035 -1000
TCGA08_rtk_signaling 0.0117 6 162 26 -0.012 0.047 1000 -1000 -0.006 -1000
E-cadherin signaling in the nascent adherens junction 0.0117 6 523 76 -0.031 0.051 1000 -1000 -0.037 -1000
IGF1 pathway 0.0117 6 367 57 -0.032 0.049 1000 -1000 -0.029 -1000
E-cadherin signaling in keratinocytes 0.0117 6 265 43 -0.015 0.039 1000 -1000 -0.018 -1000
p38 MAPK signaling pathway 0.0117 6 297 44 -0.005 0.064 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class I 0.0097 5 598 104 -0.035 0.048 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 0.0097 5 81 15 -0.018 0.022 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 0.0078 4 360 75 -0.02 0.057 1000 -1000 -0.024 -1000
Circadian rhythm pathway 0.0078 4 90 22 -0.004 0.046 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 0.0078 4 283 68 -0.028 0.044 1000 -1000 -0.021 -1000
S1P3 pathway 0.0078 4 179 42 -0.021 0.034 1000 -1000 -0.027 -1000
Arf6 downstream pathway 0.0058 3 162 43 -0.046 0.047 1000 -1000 -0.022 -1000
Canonical NF-kappaB pathway 0.0039 2 99 39 -0.016 0.042 1000 -1000 -0.022 -1000
Insulin-mediated glucose transport 0.0039 2 76 32 -0.016 0.038 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0039 2 101 37 -0.024 0.05 1000 -1000 -0.015 -1000
TRAIL signaling pathway 0.0039 2 123 48 -0.018 0.046 1000 -1000 -0.024 -1000
Rapid glucocorticoid signaling 0.0039 2 50 20 -0.008 0.026 1000 -1000 -0.008 -1000
Arf1 pathway 0.0039 2 113 54 -0.008 0.034 1000 -1000 -0.013 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 28 23 0 0.036 1000 -1000 -0.011 -1000
a4b1 and a4b7 Integrin signaling 0.0019 1 7 5 0.02 0.03 1000 -1000 0.018 -1000
Paxillin-dependent events mediated by a4b1 0.0019 1 68 36 -0.037 0.039 1000 -1000 -0.026 -1000
Atypical NF-kappaB pathway 0.0019 1 38 31 -0.017 0.029 1000 -1000 -0.017 -1000
E-cadherin signaling events 0.0019 1 6 5 0.019 0.039 1000 -1000 0.02 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 23 27 -0.019 0.045 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.056 1000 -1000 0 -1000
Total NA 3521 207894 7203 -9.6 11 131000 -131000 -3.8 -131000
FOXM1 transcription factor network

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
NFATC3 0.63 0.48 1 281 -10000 0 281
PLK1 0.36 0.32 0.67 243 -0.68 2 245
BIRC5 0.4 0.32 0.69 249 -0.72 2 251
HSPA1B 0.64 0.49 1 282 -10000 0 282
MAP2K1 0.19 0.15 0.32 255 -10000 0 255
BRCA2 0.63 0.48 1 280 -10000 0 280
FOXM1 0.78 0.63 1.3 292 -0.83 1 293
XRCC1 0.64 0.48 1 283 -10000 0 283
FOXM1B/p19 0.2 0.35 0.84 102 -0.84 1 103
Cyclin D1/CDK4 0.53 0.43 0.92 258 -10000 0 258
CDC2 0.71 0.55 1.1 293 -10000 0 293
TGFA 0.57 0.45 0.94 280 -0.7 1 281
SKP2 0.69 0.53 1.1 287 -10000 0 287
CCNE1 0.15 0.16 0.38 173 -10000 0 173
CKS1B 0.63 0.48 1 293 -0.73 1 294
RB1 0.37 0.36 0.73 233 -0.61 3 236
FOXM1C/SP1 0.56 0.42 0.92 267 -0.79 1 268
AURKB 0.34 0.37 0.68 237 -0.68 18 255
CENPF 0.72 0.56 1.1 295 -10000 0 295
CDK4 0.087 0.068 0.2 69 -10000 0 69
MYC 0.42 0.42 0.86 221 -10000 0 221
CHEK2 0.19 0.15 0.32 257 -10000 0 257
ONECUT1 0.61 0.48 1 276 -10000 0 276
CDKN2A -0.034 0.15 0.27 49 -0.22 138 187
LAMA4 0.62 0.49 1 280 -1.1 5 285
FOXM1B/HNF6 0.62 0.49 1 269 -10000 0 269
FOS 0.59 0.51 1 264 -0.94 2 266
SP1 0.022 0.005 -10000 0 -10000 0 0
CDC25B 0.63 0.48 1 282 -10000 0 282
response to radiation 0.13 0.11 0.23 262 -10000 0 262
CENPB 0.63 0.48 1 282 -10000 0 282
CENPA 0.72 0.56 1.2 293 -10000 0 293
NEK2 0.74 0.56 1.2 298 -10000 0 298
HIST1H2BA 0.63 0.48 1 281 -10000 0 281
CCNA2 0.13 0.15 0.39 116 -10000 0 116
EP300 0.02 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.68 0.53 1.1 281 -10000 0 281
CCNB2 0.71 0.55 1.1 288 -10000 0 288
CCNB1 0.73 0.57 1.2 289 -10000 0 289
ETV5 0.62 0.5 1 273 -1.1 2 275
ESR1 0.62 0.5 1 273 -1.1 4 277
CCND1 0.6 0.48 0.99 282 -10000 0 282
GSK3A 0.15 0.11 0.26 233 -10000 0 233
Cyclin A-E1/CDK1-2 0.26 0.21 0.43 274 -10000 0 274
CDK2 0.06 0.039 0.18 1 -10000 0 1
G2/M transition of mitotic cell cycle 0.17 0.14 0.28 285 -10000 0 285
FOXM1B/Cbp/p300 0.16 0.26 0.69 61 -0.77 1 62
GAS1 0.61 0.51 1 275 -1 6 281
MMP2 0.63 0.48 1 279 -10000 0 279
RB1/FOXM1C 0.5 0.44 0.92 244 -10000 0 244
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.11 0.14 0.32 151 -9999 0 151
GPC2 0.092 0.13 0.32 122 -9999 0 122
GPC2/Midkine 0.14 0.14 0.28 219 -9999 0 219
neuron projection morphogenesis 0.14 0.14 0.28 219 -9999 0 219
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.46 0.48 -10000 0 -0.94 246 246
NCK1/PAK1/Dok-R -0.22 0.21 -10000 0 -0.43 245 245
NCK1/Dok-R -0.51 0.58 -10000 0 -1.1 244 244
PIK3CA 0.022 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.063 0.096 0.23 127 -10000 0 127
RELA 0.021 0.004 -10000 0 -10000 0 0
SHC1 0.017 0.015 0.32 1 -10000 0 1
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
F2 0.12 0.16 0.32 174 -10000 0 174
TNIP2 0.021 0.003 -10000 0 -10000 0 0
NF kappa B/RelA -0.46 0.54 -10000 0 -0.99 244 244
FN1 0.019 0.033 0.32 1 -0.32 4 5
PLD2 -0.53 0.6 -10000 0 -1.1 244 244
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB14 0.034 0.078 0.32 28 -0.32 5 33
ELK1 -0.48 0.52 -10000 0 -0.99 245 245
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PAK1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.48 0.57 -10000 0 -1 244 244
CDKN1A -0.33 0.32 -10000 0 -0.65 243 243
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.51 0.58 -10000 0 -1.1 244 244
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:NO -0.33 0.34 -10000 0 -0.68 244 244
PLG -0.53 0.6 -10000 0 -1.1 244 244
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.43 0.44 -10000 0 -0.88 245 245
GRB2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.012 0.021 -10000 0 -0.33 1 1
ANGPT2 -0.3 0.32 -10000 0 -0.69 173 173
BMX -0.58 0.62 -10000 0 -1.2 244 244
ANGPT1 -0.32 0.49 -10000 0 -1.2 127 127
tube development -0.37 0.36 -10000 0 -0.73 246 246
ANGPT4 -0.16 0.16 -10000 0 -0.33 248 248
response to hypoxia -0.032 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.54 0.63 -10000 0 -1.1 244 244
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
STAT5A (dimer) -0.43 0.42 -10000 0 -0.85 244 244
mol:L-citrulline -0.33 0.34 -10000 0 -0.68 244 244
AGTR1 -0.088 0.16 -10000 0 -0.32 161 161
MAPK14 -0.59 0.64 -10000 0 -1.2 247 247
Tie2/SHP2 -0.46 0.53 -10000 0 -1 222 222
TEK -0.51 0.58 -10000 0 -1.1 221 221
RPS6KB1 -0.44 0.46 -10000 0 -0.9 247 247
Angiotensin II/AT1 -0.058 0.11 -10000 0 -0.22 161 161
Tie2/Ang1/GRB2 -0.54 0.63 -10000 0 -1.1 244 244
MAPK3 -0.49 0.53 -10000 0 -1 244 244
MAPK1 -0.48 0.53 -10000 0 -1 242 242
Tie2/Ang1/GRB7 -0.54 0.63 -10000 0 -1.1 244 244
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.53 0.6 -10000 0 -1.1 244 244
PI3K -0.54 0.57 -10000 0 -1.1 246 246
FES -0.59 0.64 -10000 0 -1.2 247 247
Crk/Dok-R -0.51 0.58 -10000 0 -1.1 244 244
Tie2/Ang1/ABIN2 -0.54 0.63 -10000 0 -1.1 244 244
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.41 0.42 -10000 0 -0.83 246 246
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.43 0.46 -10000 0 -0.88 247 247
Tie2/Ang2 -0.53 0.53 -10000 0 -1 246 246
Tie2/Ang1 -0.58 0.67 -10000 0 -1.2 244 244
FOXO1 -0.41 0.42 -10000 0 -0.84 246 246
ELF1 -0.034 0.067 -10000 0 -10000 0 0
ELF2 -0.53 0.6 -10000 0 -1.1 243 243
mol:Choline -0.5 0.56 -10000 0 -1 244 244
cell migration -0.12 0.11 -10000 0 -0.24 246 246
FYN -0.43 0.42 -10000 0 -0.85 246 246
DOK2 -0.004 0.083 -10000 0 -0.32 32 32
negative regulation of cell cycle -0.3 0.29 -10000 0 -0.59 243 243
ETS1 -0.055 0.11 -10000 0 -0.25 117 117
PXN -0.35 0.37 -10000 0 -0.72 247 247
ITGB1 0.021 0.004 -10000 0 -10000 0 0
NOS3 -0.38 0.39 -10000 0 -0.78 244 244
RAC1 0.019 0.007 -10000 0 -10000 0 0
TNF -0.064 0.12 -10000 0 -0.26 129 129
MAPKKK cascade -0.5 0.56 -10000 0 -1 244 244
RASA1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.54 0.62 -10000 0 -1.1 244 244
NCK1 0.021 0.003 -10000 0 -10000 0 0
vasculogenesis -0.3 0.3 -10000 0 -0.6 244 244
mol:Phosphatidic acid -0.5 0.56 -10000 0 -1 244 244
mol:Angiotensin II 0 0.002 -10000 0 -10000 0 0
mol:NADP -0.33 0.34 -10000 0 -0.68 244 244
Rac1/GTP -0.4 0.42 -10000 0 -0.82 246 246
MMP2 -0.53 0.6 -10000 0 -1.1 243 243
Aurora B signaling

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
Condensin I complex 0.11 0.12 0.24 211 -0.18 6 217
STMN1 0.069 0.087 0.16 244 -10000 0 244
Aurora B/RasGAP/Survivin 0.21 0.17 0.36 280 -10000 0 280
Chromosomal passenger complex/Cul3 protein complex 0.088 0.11 0.2 214 -0.21 9 223
BIRC5 0.19 0.16 0.33 275 -10000 0 275
DES -0.14 0.28 -10000 0 -0.56 102 102
Aurora C/Aurora B/INCENP 0.12 0.096 0.22 237 -0.15 3 240
Aurora B/TACC1 0.089 0.1 0.21 201 -0.15 16 217
Aurora B/PP2A 0.12 0.1 0.23 232 -10000 0 232
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.035 0.036 0.14 19 -10000 0 19
mitotic metaphase/anaphase transition -0.004 0.007 -10000 0 -10000 0 0
NDC80 0.14 0.15 0.27 273 -10000 0 273
Cul3 protein complex 0.028 0.049 0.22 3 -0.19 20 23
KIF2C 0.16 0.13 0.25 304 -0.32 1 305
PEBP1 0.023 0.005 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 265 -10000 0 265
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.1 0.23 239 -10000 0 239
SEPT1 0.02 0.016 -10000 0 -0.32 1 1
SMC2 0.021 0.004 -10000 0 -10000 0 0
SMC4 0.021 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.1 0.19 0.3 123 -0.43 34 157
PSMA3 0.021 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.075 0.072 0.15 248 -10000 0 248
AURKB 0.17 0.16 0.33 247 -10000 0 247
AURKC 0.02 0.035 0.32 3 -0.32 3 6
CDCA8 0.13 0.15 0.34 167 -10000 0 167
cytokinesis 0.14 0.15 0.3 221 -0.31 3 224
Aurora B/Septin1 0.18 0.18 0.36 226 -0.26 9 235
AURKA 0.053 0.12 0.32 85 -10000 0 85
INCENP 0.028 0.01 -10000 0 -10000 0 0
KLHL13 0.009 0.071 0.32 3 -0.32 20 23
BUB1 0.085 0.14 0.32 128 -10000 0 128
hSgo1/Aurora B/Survivin 0.28 0.24 0.46 289 -10000 0 289
EVI5 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.16 0.15 0.34 183 -0.32 1 184
SGOL1 0.15 0.15 0.32 226 -10000 0 226
CENPA 0.16 0.16 0.29 270 -0.2 13 283
NCAPG 0.14 0.15 0.32 205 -10000 0 205
Aurora B/HC8 Proteasome 0.12 0.1 0.23 239 -10000 0 239
NCAPD2 0.02 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.12 0.1 0.23 242 -10000 0 242
RHOA 0.021 0.004 -10000 0 -10000 0 0
NCAPH 0.15 0.15 0.32 217 -10000 0 217
NPM1 0.071 0.13 0.2 80 -0.34 24 104
RASA1 0.02 0.005 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 0.23 239 -10000 0 239
PPP1CC 0.021 0.003 -10000 0 -10000 0 0
Centraspindlin 0.18 0.17 0.35 219 -0.34 1 220
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
NSUN2 0.088 0.13 0.27 64 -0.3 19 83
MYLK 0.066 0.077 0.14 236 -0.15 14 250
KIF23 0.087 0.13 0.34 103 -10000 0 103
VIM 0.07 0.092 0.16 241 -10000 0 241
RACGAP1 0.03 0.03 0.34 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.075 0.12 0.2 83 -0.3 26 109
Chromosomal passenger complex 0.16 0.15 0.28 274 -0.21 5 279
Chromosomal passenger complex/EVI5 0.27 0.22 0.46 269 -10000 0 269
TACC1 0.008 0.06 -10000 0 -0.32 16 16
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
CUL3 0.021 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.26 0.24 0.5 184 -0.62 5 189
HDAC7 0.031 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.32 0.31 0.64 183 -0.83 3 186
SMAD4 0.019 0.01 -10000 0 -10000 0 0
ID2 0.28 0.24 0.54 151 -0.62 6 157
AP1 0.002 0.071 -10000 0 -0.24 30 30
ABCG2 0.26 0.25 0.54 143 -0.61 7 150
HIF1A 0.1 0.09 0.26 73 -0.25 1 74
TFF3 0.31 0.28 0.6 182 -0.7 4 186
GATA2 -0.017 0.098 -10000 0 -0.33 42 42
AKT1 0.098 0.099 0.27 64 -0.24 4 68
response to hypoxia 0.079 0.095 0.2 137 -0.22 8 145
MCL1 0.23 0.23 0.54 122 -0.73 2 124
NDRG1 0.25 0.24 0.54 129 -0.63 4 133
SERPINE1 0.27 0.24 0.54 145 -0.67 4 149
FECH 0.26 0.24 0.54 144 -0.67 4 148
FURIN 0.28 0.24 0.56 152 -0.67 4 156
NCOA2 0.016 0.035 -10000 0 -0.32 5 5
EP300 0.12 0.14 0.29 127 -0.3 13 140
HMOX1 0.28 0.24 0.54 149 -0.63 4 153
BHLHE40 0.28 0.24 0.54 151 -0.67 4 155
BHLHE41 0.26 0.24 0.55 135 -0.65 6 141
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.14 0.36 80 -0.32 1 81
ENG 0.11 0.098 0.28 44 -0.31 3 47
JUN 0.009 0.037 -10000 0 -0.34 3 3
RORA 0.27 0.24 0.54 147 -0.7 4 151
ABCB1 0.006 0.18 0.37 24 -0.73 21 45
TFRC 0.27 0.24 0.54 141 -0.67 4 145
CXCR4 0.28 0.23 0.54 149 -0.67 4 153
TF 0.32 0.28 0.63 179 -0.63 5 184
CITED2 0.27 0.24 0.54 148 -0.67 4 152
HIF1A/ARNT 0.43 0.4 0.85 194 -0.8 3 197
LDHA 0.053 0.11 0.42 11 -0.54 2 13
ETS1 0.28 0.23 0.54 150 -0.59 4 154
PGK1 0.28 0.23 0.54 152 -0.67 4 156
NOS2 0.27 0.26 0.55 149 -0.73 4 153
ITGB2 0.28 0.24 0.54 151 -0.77 4 155
ALDOA 0.28 0.23 0.54 150 -0.67 4 154
Cbp/p300/CITED2 0.28 0.28 0.6 143 -0.87 4 147
FOS -0.007 0.082 -10000 0 -0.34 27 27
HK2 0.28 0.24 0.54 153 -0.69 5 158
SP1 0.015 0.036 -10000 0 -0.16 15 15
GCK 0.16 0.25 0.51 57 -1 12 69
HK1 0.28 0.23 0.54 151 -0.67 4 155
NPM1 0.27 0.24 0.54 147 -0.67 4 151
EGLN1 0.26 0.24 0.54 143 -0.81 2 145
CREB1 0.023 0.009 -10000 0 -10000 0 0
PGM1 0.28 0.23 0.54 147 -0.67 4 151
SMAD3 0.02 0.008 -10000 0 -10000 0 0
EDN1 -0.06 0.41 0.42 6 -0.98 79 85
IGFBP1 0.29 0.26 0.6 153 -0.67 4 157
VEGFA 0.26 0.23 0.51 163 -0.68 3 166
HIF1A/JAB1 0.081 0.067 0.22 31 -0.17 1 32
CP 0.38 0.29 0.62 241 -0.66 4 245
CXCL12 0.27 0.25 0.54 150 -0.73 5 155
COPS5 0.02 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.027 0.014 -10000 0 -10000 0 0
BNIP3 0.28 0.23 0.54 150 -0.67 4 154
EGLN3 0.31 0.28 0.63 171 -0.59 4 175
CA9 0.4 0.29 0.62 277 -0.66 4 281
TERT 0.29 0.29 0.62 176 -0.67 3 179
ENO1 0.28 0.23 0.54 150 -0.67 4 154
PFKL 0.28 0.23 0.54 151 -0.67 4 155
NCOA1 0.021 0.003 -10000 0 -10000 0 0
ADM 0.28 0.24 0.55 147 -0.7 4 151
ARNT 0.091 0.086 0.23 86 -10000 0 86
HNF4A 0.069 0.13 0.32 96 -0.29 13 109
ADFP 0.26 0.24 0.5 184 -0.62 5 189
SLC2A1 0.33 0.28 0.59 215 -0.59 4 219
LEP 0.29 0.26 0.57 164 -0.67 4 168
HIF1A/ARNT/Cbp/p300 0.32 0.32 0.67 182 -0.76 4 186
EPO 0.23 0.23 0.52 125 -0.69 3 128
CREBBP 0.12 0.13 0.29 126 -0.27 12 138
HIF1A/ARNT/Cbp/p300/HDAC7 0.35 0.33 0.69 191 -0.79 3 194
PFKFB3 0.27 0.24 0.54 148 -0.66 4 152
NT5E 0.28 0.25 0.56 150 -0.67 4 154
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.092 0.18 0.32 7 -0.5 46 53
IHH -0.015 0.13 0.27 7 -0.39 45 52
SHH Np/Cholesterol/GAS1 -0.036 0.058 0.12 1 -0.18 65 66
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.058 0.18 65 -0.11 1 66
SMO/beta Arrestin2 -0.15 0.18 0.3 2 -0.32 212 214
SMO -0.15 0.19 0.34 1 -0.34 211 212
AKT1 -0.081 0.14 0.27 1 -0.47 36 37
ARRB2 0.02 0.006 -10000 0 -10000 0 0
BOC 0.02 0.016 -10000 0 -0.32 1 1
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
heart looping -0.15 0.18 0.34 1 -0.33 211 212
STIL -0.088 0.14 0.26 11 -0.32 68 79
DHH N/PTCH2 0.013 0.066 -10000 0 -0.23 36 36
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.36 65 65
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DHH -0.003 0.088 -10000 0 -0.32 36 36
PTHLH -0.12 0.22 0.38 7 -0.56 44 51
determination of left/right symmetry -0.15 0.18 0.34 1 -0.33 211 212
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
skeletal system development -0.12 0.22 0.38 7 -0.56 44 51
IHH N/Hhip -0.22 0.18 0.21 3 -0.32 371 374
DHH N/Hhip -0.12 0.14 -10000 0 -0.24 280 280
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.15 0.18 0.34 1 -0.33 211 212
pancreas development -0.16 0.17 -10000 0 -0.32 273 273
HHAT 0.018 0.022 -10000 0 -0.32 2 2
PI3K 0.029 0.014 -10000 0 -0.23 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.012 0.054 -10000 0 -0.32 13 13
somite specification -0.15 0.18 0.34 1 -0.33 211 212
SHH Np/Cholesterol/PTCH1 -0.099 0.14 -10000 0 -0.34 72 72
SHH Np/Cholesterol/PTCH2 -0.034 0.052 0.12 1 -0.18 60 61
SHH Np/Cholesterol/Megalin -0.069 0.087 0.12 1 -0.19 159 160
SHH -0.039 0.07 0.16 1 -0.23 60 61
catabolic process -0.11 0.16 0.23 3 -0.25 248 251
SMO/Vitamin D3 -0.12 0.17 0.37 2 -0.29 213 215
SHH Np/Cholesterol/Hhip -0.1 0.1 0.12 1 -0.2 251 252
LRP2 -0.072 0.16 0.32 1 -0.32 139 140
receptor-mediated endocytosis -0.17 0.18 0.3 2 -0.41 136 138
SHH Np/Cholesterol/BOC -0.033 0.052 0.12 1 -0.18 59 60
SHH Np/Cholesterol/CDO -0.035 0.056 0.12 1 -0.18 64 65
mesenchymal cell differentiation 0.1 0.1 0.2 251 -0.11 1 252
mol:Vitamin D3 -0.093 0.15 0.36 6 -0.34 69 75
IHH N/PTCH2 -0.097 0.13 0.21 4 -0.21 279 283
CDON 0.013 0.048 -10000 0 -0.32 10 10
IHH N/PTCH1 -0.1 0.17 0.27 3 -0.26 251 254
Megalin/LRPAP1 -0.038 0.12 0.23 1 -0.23 136 137
PTCH2 0.02 0.015 -10000 0 -0.32 1 1
SHH Np/Cholesterol -0.029 0.052 -10000 0 -0.17 60 60
PTCH1 -0.11 0.16 0.23 3 -0.25 248 251
HHIP -0.16 0.17 -10000 0 -0.32 273 273
Endothelins

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
AKT1 -0.084 0.12 0.23 1 -0.33 55 56
PTK2B 0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -10000 0 -0.82 60 60
EDN1 -0.078 0.14 -10000 0 -0.34 83 83
EDN3 -0.07 0.15 0.32 1 -0.32 131 132
EDN2 0.1 0.14 0.32 139 -0.32 2 141
HRAS/GDP -0.15 0.19 -10000 0 -0.41 126 126
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.071 0.13 -10000 0 -0.34 71 71
ADCY4 -0.07 0.11 0.22 3 -0.28 63 66
ADCY5 -0.08 0.13 0.24 3 -0.3 80 83
ADCY6 -0.066 0.1 0.24 3 -0.28 52 55
ADCY7 -0.066 0.1 0.24 4 -0.28 53 57
ADCY1 -0.061 0.1 0.3 1 -0.28 49 50
ADCY2 -0.064 0.11 0.23 7 -0.3 58 65
ADCY3 -0.066 0.11 0.26 3 -0.28 55 58
ADCY8 -0.1 0.12 0.27 3 -0.26 123 126
ADCY9 -0.068 0.11 0.24 4 -0.28 62 66
arachidonic acid secretion -0.12 0.19 -10000 0 -0.48 84 84
ETB receptor/Endothelin-1/Gq/GTP -0.15 0.16 -10000 0 -0.27 269 269
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.052 0.12 0.31 1 -0.3 49 50
ETA receptor/Endothelin-1/Gs/GTP -0.055 0.12 0.29 1 -0.28 59 60
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.052 0.16 0.3 29 -0.34 50 79
EDNRB -0.16 0.17 -10000 0 -0.32 265 265
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.088 0.13 0.23 1 -0.37 53 54
CYSLTR1 -0.093 0.14 0.23 1 -0.4 53 54
SLC9A1 -0.052 0.081 -10000 0 -0.22 57 57
mol:GDP -0.16 0.2 -10000 0 -0.43 132 132
SLC9A3 -0.31 0.35 -10000 0 -0.69 176 176
RAF1 -0.15 0.19 -10000 0 -0.46 106 106
JUN -0.11 0.21 -10000 0 -0.69 40 40
JAK2 -0.08 0.12 0.23 1 -0.34 51 52
mol:IP3 -0.12 0.17 -10000 0 -0.38 117 117
ETA receptor/Endothelin-1 -0.084 0.15 0.35 1 -0.34 78 79
PLCB1 0.018 0.023 0.32 1 -0.33 1 2
PLCB2 0.011 0.047 -10000 0 -0.33 9 9
ETA receptor/Endothelin-3 -0.075 0.11 0.18 1 -0.24 138 139
FOS -0.14 0.22 -10000 0 -0.71 49 49
Gai/GDP -0.052 0.2 -10000 0 -0.81 31 31
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.19 -10000 0 -0.44 126 126
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
PRKCB1 -0.12 0.16 -10000 0 -0.35 126 126
GNAQ 0.015 0.022 -10000 0 -0.33 1 1
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
GNAL 0.017 0.047 0.32 3 -0.32 7 10
Gs family/GDP -0.14 0.18 -10000 0 -0.39 128 128
ETA receptor/Endothelin-1/Gq/GTP -0.072 0.13 -10000 0 -0.32 80 80
MAPK14 -0.14 0.16 0.2 1 -0.34 140 141
TRPC6 -0.14 0.3 -10000 0 -0.88 60 60
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.17 -10000 0 -0.36 145 145
ETB receptor/Endothelin-2 -0.074 0.15 0.24 49 -0.21 264 313
ETB receptor/Endothelin-3 -0.15 0.16 0.24 1 -0.27 309 310
ETB receptor/Endothelin-1 -0.16 0.16 0.21 7 -0.3 269 276
MAPK3 -0.15 0.23 -10000 0 -0.64 67 67
MAPK1 -0.16 0.23 -10000 0 -0.64 71 71
Rac1/GDP -0.14 0.18 -10000 0 -0.4 119 119
cAMP biosynthetic process -0.078 0.14 0.28 8 -0.34 62 70
MAPK8 -0.12 0.25 -10000 0 -0.69 63 63
SRC 0.02 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.13 0.14 -10000 0 -0.33 130 130
p130Cas/CRK/Src/PYK2 -0.16 0.22 -10000 0 -0.54 100 100
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.18 -10000 0 -0.4 119 119
COL1A2 -0.16 0.18 0.32 7 -0.37 170 177
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.043 0.12 0.22 128 -0.19 15 143
mol:DAG -0.12 0.17 -10000 0 -0.37 118 118
MAP2K2 -0.15 0.2 -10000 0 -0.53 83 83
MAP2K1 -0.15 0.2 -10000 0 -0.53 82 82
EDNRA -0.036 0.076 0.21 2 -0.24 19 21
positive regulation of muscle contraction -0.059 0.11 0.21 18 -0.29 47 65
Gq family/GDP -0.11 0.18 0.35 1 -0.41 92 93
HRAS/GTP -0.14 0.19 -10000 0 -0.42 123 123
PRKCH -0.12 0.16 -10000 0 -0.37 115 115
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.12 0.16 -10000 0 -0.36 113 113
PRKCB -0.13 0.17 0.19 1 -0.37 125 126
PRKCE -0.13 0.16 -10000 0 -0.37 118 118
PRKCD -0.12 0.16 -10000 0 -0.37 111 111
PRKCG -0.12 0.16 -10000 0 -0.37 108 108
regulation of vascular smooth muscle contraction -0.17 0.26 -10000 0 -0.84 50 50
PRKCQ -0.14 0.18 -10000 0 -0.39 124 124
PLA2G4A -0.13 0.21 -10000 0 -0.53 84 84
GNA14 0.009 0.052 -10000 0 -0.33 11 11
GNA15 0.015 0.015 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.021 -10000 0 -0.32 1 1
Rac1/GTP -0.052 0.12 0.31 1 -0.29 52 53
MMP1 0.2 0.17 0.33 256 -0.68 2 258
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.049 0.064 0.12 15 -0.12 226 241
BUB1B 0.07 0.076 0.14 217 -0.11 10 227
PLK1 0.03 0.039 0.092 104 -0.077 3 107
PLK1S1 0.014 0.038 0.12 2 -0.16 15 17
KIF2A 0.023 0.041 0.16 18 -10000 0 18
regulation of mitotic centrosome separation 0.03 0.039 0.092 104 -0.077 3 107
GOLGA2 0.021 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.17 0.17 0.34 235 -10000 0 235
WEE1 0.029 0.059 0.18 2 -0.27 11 13
cytokinesis 0.086 0.096 0.2 139 -0.2 4 143
PP2A-alpha B56 0.077 0.095 -10000 0 -0.49 6 6
AURKA 0.036 0.057 0.14 101 -0.19 6 107
PICH/PLK1 0.076 0.11 0.22 176 -10000 0 176
CENPE 0.034 0.054 0.14 78 -10000 0 78
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.041 0.15 18 -10000 0 18
PPP2CA 0.02 0.005 -10000 0 -10000 0 0
FZR1 0.02 0.006 -10000 0 -10000 0 0
TPX2 0.073 0.069 0.13 276 -0.16 5 281
PAK1 0.02 0.005 -10000 0 -10000 0 0
SPC24 0.1 0.14 0.32 141 -10000 0 141
FBXW11 0.02 0.005 -10000 0 -10000 0 0
CLSPN 0.059 0.074 0.15 172 -0.23 5 177
GORASP1 0.021 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.016 11 -0.011 1 12
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.014 0.019 0.044 90 -0.041 2 92
G2 phase of mitotic cell cycle 0 0.003 0.014 12 -10000 0 12
STAG2 0.021 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.098 -10000 0 -0.51 18 18
spindle elongation 0.03 0.039 0.092 104 -0.077 3 107
ODF2 0.021 0.006 -10000 0 -10000 0 0
BUB1 0.067 0.11 -10000 0 -0.51 7 7
TPT1 0.009 0.043 0.11 2 -0.16 26 28
CDC25C 0.099 0.096 0.16 313 -0.22 17 330
CDC25B 0.022 0.011 -10000 0 -10000 0 0
SGOL1 0.049 0.064 0.12 226 -0.12 15 241
RHOA 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.074 0.086 0.22 127 -10000 0 127
CDC14B -0.008 0.004 -10000 0 -10000 0 0
CDC20 0.2 0.15 0.32 294 -10000 0 294
PLK1/PBIP1 0.01 0.041 0.14 38 -10000 0 38
mitosis -0.003 0.006 0.021 8 -0.016 68 76
FBXO5 0.014 0.039 0.12 11 -0.1 2 13
CDC2 0.003 0.005 0.011 130 -0.009 13 143
NDC80 0.15 0.15 0.32 223 -10000 0 223
metaphase plate congression 0.021 0.042 0.12 1 -0.22 10 11
ERCC6L 0.078 0.1 0.22 163 -10000 0 163
NLP/gamma Tubulin 0.016 0.022 0.075 21 -0.086 3 24
microtubule cytoskeleton organization 0.009 0.043 0.11 2 -0.16 26 28
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 2 -10000 0 2
PPP1R12A 0.022 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 0.16 0.15 0.29 262 -10000 0 262
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.03 -10000 0 -10000 0 0
RAB1A 0.021 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.024 0.035 0.082 103 -0.067 3 106
mitotic prometaphase 0.001 0.003 0.018 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.055 0.2 2 -0.39 1 3
microtubule-based process 0.14 0.12 0.25 265 -10000 0 265
Golgi organization 0.03 0.039 0.092 104 -0.077 3 107
Cohesin/SA2 0.037 0.031 0.12 8 -10000 0 8
PPP1CB/MYPT1 0.031 0.007 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 265 -10000 0 265
APC/C/CDC20 0.15 0.12 0.25 295 -10000 0 295
PPP2R1A 0.021 0.004 -10000 0 -10000 0 0
chromosome segregation 0.009 0.04 0.14 38 -10000 0 38
PRC1 0.062 0.1 0.32 70 -10000 0 70
ECT2 0.031 0.059 0.18 44 -10000 0 44
C13orf34 0.024 0.033 0.077 105 -0.067 2 107
NUDC 0.021 0.043 0.12 1 -0.22 10 11
regulation of attachment of spindle microtubules to kinetochore 0.07 0.075 0.14 217 -0.11 10 227
spindle assembly 0.023 0.031 0.088 42 -0.07 2 44
spindle stabilization 0.014 0.038 0.12 2 -0.16 15 17
APC/C/HCDH1 0.016 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.14 0.12 0.25 265 -10000 0 265
CCNB1 0.1 0.14 0.33 137 -10000 0 137
PPP1CB 0.022 0.003 -10000 0 -10000 0 0
BTRC 0.021 0.003 -10000 0 -10000 0 0
ROCK2 0.025 0.038 0.17 2 -0.18 2 4
TUBG1 0.018 0.026 0.13 2 -0.2 3 5
G2/M transition of mitotic cell cycle 0.03 0.056 0.13 95 -10000 0 95
MLF1IP 0.005 0.043 0.16 35 -10000 0 35
INCENP 0.021 0.004 -10000 0 -10000 0 0
Aurora C 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
INCENP 0.021 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.094 0.21 237 -0.16 3 240
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.016 0.014 -10000 0 -10000 0 0
AURKB 0.16 0.15 0.32 247 -10000 0 247
AURKC 0.02 0.035 0.32 3 -0.32 3 6
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.084 0.26 -10000 0 -0.86 46 46
MKNK1 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.023 0.12 -10000 0 -0.3 79 79
ATF2/c-Jun -0.036 0.11 -10000 0 -0.36 21 21
MAPK11 -0.022 0.12 -10000 0 -0.31 74 74
MITF -0.047 0.15 -10000 0 -0.37 84 84
MAPKAPK5 -0.039 0.14 -10000 0 -0.36 76 76
KRT8 -0.041 0.14 0.27 2 -0.35 80 82
MAPKAPK3 0.021 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.038 0.18 -10000 0 -0.43 81 81
CEBPB -0.038 0.14 -10000 0 -0.36 72 72
SLC9A1 -0.041 0.14 -10000 0 -0.36 78 78
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.041 0.14 0.25 1 -0.35 79 80
p38alpha-beta/MNK1 -0.017 0.15 -10000 0 -0.36 71 71
JUN -0.035 0.1 -10000 0 -0.36 21 21
PPARGC1A -0.1 0.19 -10000 0 -0.34 169 169
USF1 -0.032 0.13 0.32 1 -0.35 66 67
RAB5/GDP/GDI1 -0.028 0.1 -10000 0 -0.26 77 77
NOS2 -0.086 0.27 0.34 7 -0.67 76 83
DDIT3 -0.039 0.14 0.23 2 -0.36 76 78
RAB5A 0.021 0.004 -10000 0 -10000 0 0
HSPB1 -0.039 0.12 0.26 11 -0.3 72 83
p38alpha-beta/HBP1 -0.018 0.15 -10000 0 -0.35 76 76
CREB1 -0.046 0.15 0.24 2 -0.38 79 81
RAB5/GDP 0.015 0.003 -10000 0 -10000 0 0
EIF4E -0.059 0.12 0.18 1 -0.33 70 71
RPS6KA4 -0.042 0.14 -10000 0 -0.36 79 79
PLA2G4A -0.035 0.13 0.18 53 -0.32 67 120
GDI1 -0.039 0.14 0.28 1 -0.35 76 77
TP53 -0.066 0.16 0.26 1 -0.44 74 75
RPS6KA5 -0.041 0.14 0.3 3 -0.36 78 81
ESR1 -0.045 0.15 0.28 1 -0.38 78 79
HBP1 0.02 0.005 -10000 0 -10000 0 0
MEF2C -0.04 0.14 -10000 0 -0.36 77 77
MEF2A -0.042 0.14 -10000 0 -0.36 78 78
EIF4EBP1 -0.049 0.16 0.24 2 -0.4 79 81
KRT19 -0.042 0.14 -10000 0 -0.36 79 79
ELK4 -0.037 0.13 -10000 0 -0.35 73 73
ATF6 -0.033 0.13 0.32 1 -0.35 67 68
ATF1 -0.046 0.15 0.24 3 -0.38 81 84
p38alpha-beta/MAPKAPK2 -0.017 0.14 -10000 0 -0.34 76 76
p38alpha-beta/MAPKAPK3 -0.018 0.15 -10000 0 -0.35 78 78
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.039 0.049 0.2 29 -0.16 10 39
RGS9BP -0.029 0.12 -10000 0 -0.32 73 73
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.037 0.074 0.32 32 -10000 0 32
mol:Na + 0.11 0.11 0.23 202 -10000 0 202
mol:ADP -0.005 0.045 0.16 33 -10000 0 33
GNAT2 0.02 0.014 0.32 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.058 0.13 -10000 0 -0.21 193 193
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.014 0.21 2 -10000 0 2
GRK7 0.02 0.003 -10000 0 -10000 0 0
CNGB3 0.063 0.11 0.32 77 -10000 0 77
Cone Metarhodopsin II/X-Arrestin 0.015 0.016 0.22 3 -10000 0 3
mol:Ca2+ 0.055 0.09 0.21 101 -10000 0 101
Cone PDE6 -0.039 0.12 -10000 0 -0.19 182 182
Cone Metarhodopsin II 0.034 0.042 0.2 31 -10000 0 31
Na + (4 Units) 0.11 0.12 0.24 202 -10000 0 202
GNAT2/GDP -0.044 0.11 -10000 0 -0.18 192 192
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.015 0.019 0.17 4 -10000 0 4
Cone Transducin 0.042 0.053 0.21 29 -0.18 10 39
SLC24A2 0.04 0.08 0.32 37 -10000 0 37
GNB3/GNGT2 0.036 0.061 0.23 29 -0.23 10 39
GNB3 0.037 0.073 0.32 30 -0.32 1 31
GNAT2/GTP 0.015 0.01 0.22 1 -10000 0 1
CNGA3 0.12 0.14 0.32 173 -10000 0 173
ARR3 0.02 0.023 0.32 3 -10000 0 3
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.11 0.11 0.24 202 -10000 0 202
mol:Pi -0.058 0.12 -10000 0 -0.21 193 193
Cone CNG Channel 0.094 0.091 0.34 25 -10000 0 25
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.04 0.079 0.32 37 -10000 0 37
RGS9 -0.08 0.16 -10000 0 -0.32 149 149
PDE6C 0.018 0.003 -10000 0 -10000 0 0
GNGT2 0.014 0.048 -10000 0 -0.32 10 10
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.018 0.014 0.32 1 -10000 0 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.006 0.058 -10000 0 -0.35 11 11
Crk/p130 Cas/Paxillin -0.056 0.086 -10000 0 -0.23 86 86
JUN -0.034 0.088 0.16 8 -0.19 96 104
HRAS 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.012 0.11 0.23 44 -0.17 97 141
RAP1A 0.02 0.005 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.01 0.11 0.23 46 -0.17 110 156
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.013 0.088 0.21 5 -0.17 112 117
RHOA 0.021 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.008 0.1 0.19 46 -0.17 93 139
GRB7 0.019 0.022 -10000 0 -0.32 2 2
RET51/GFRalpha1/GDNF 0.009 0.11 0.23 45 -0.17 111 156
MAPKKK cascade -0.031 0.092 0.18 6 -0.2 87 93
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.012 0.089 0.21 6 -0.17 112 118
lamellipodium assembly -0.034 0.088 -10000 0 -0.21 76 76
RET51/GFRalpha1/GDNF/SHC 0.013 0.11 0.23 42 -0.17 90 132
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.081 0.21 5 -0.17 90 95
RET9/GFRalpha1/GDNF/Shank3 -0.014 0.09 0.21 6 -0.17 113 119
MAPK3 -0.019 0.1 0.18 62 -0.29 1 63
DOK1 0.021 0.002 -10000 0 -10000 0 0
DOK6 -0.01 0.095 -10000 0 -0.32 43 43
PXN 0.021 0.003 -10000 0 -10000 0 0
neurite development -0.029 0.094 0.23 7 -0.24 23 30
DOK5 0.059 0.1 0.32 67 -10000 0 67
GFRA1 -0.076 0.16 0.32 1 -0.32 144 145
MAPK8 -0.038 0.086 0.16 6 -0.19 98 104
HRAS/GTP -0.003 0.12 0.34 2 -0.21 94 96
tube development -0.011 0.086 0.2 13 -0.17 104 117
MAPK1 -0.019 0.094 0.18 55 -0.29 1 56
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.029 0.081 0.15 2 -0.19 98 100
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
PDLIM7 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.001 0.12 0.23 40 -0.2 113 153
SHC1 0.019 0.016 0.32 1 -10000 0 1
RET51/GFRalpha1/GDNF/Dok4 0.011 0.11 0.23 46 -0.17 107 153
RET51/GFRalpha1/GDNF/Dok5 0.024 0.12 0.24 73 -0.17 99 172
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
CREB1 -0.022 0.091 0.23 1 -0.22 72 73
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.078 0.16 2 -0.19 83 85
RET51/GFRalpha1/GDNF/Grb7 0.009 0.12 0.23 48 -0.17 112 160
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.059 0.11 0.32 68 -0.32 3 71
DOK4 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.032 0.088 0.24 2 -0.18 96 98
RET9/GFRalpha1/GDNF/FRS2 -0.012 0.087 0.21 6 -0.17 106 112
SHANK3 0.018 0.027 -10000 0 -0.32 3 3
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.075 0.16 2 -0.19 82 84
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.093 0.18 10 -0.19 92 102
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.023 0.096 0.18 7 -0.2 100 107
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.011 0.086 0.19 11 -0.19 72 83
PI3K -0.044 0.13 0.25 5 -0.29 88 93
SOS1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.005 0.089 0.21 6 -0.17 106 112
GRB10 0.019 0.007 -10000 0 -10000 0 0
activation of MAPKK activity -0.021 0.083 0.16 8 -0.18 88 96
RET51/GFRalpha1/GDNF/FRS2 0.009 0.11 0.23 44 -0.17 108 152
GAB1 0.02 0.022 -10000 0 -0.32 2 2
IRS1 0.02 0.015 -10000 0 -0.32 1 1
IRS2 0.019 0.016 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.089 0.19 11 -0.2 75 86
RET51/GFRalpha1/GDNF/PKC alpha 0.01 0.11 0.23 45 -0.17 108 153
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GDNF 0.02 0.037 0.32 7 -10000 0 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.01 0.11 0.23 45 -0.17 111 156
Rac1/GTP -0.032 0.11 0.22 1 -0.25 75 76
RET9/GFRalpha1/GDNF -0.023 0.09 0.21 6 -0.19 112 118
GFRalpha1/GDNF -0.029 0.11 0.23 6 -0.23 112 118
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.019 0.29 0.55 34 -0.65 19 53
PCK1 0.067 0.24 0.56 57 -0.55 3 60
HNF4A -0.094 0.47 0.71 53 -0.79 99 152
KCNJ11 0.026 0.29 0.62 33 -0.77 12 45
AKT1 0.048 0.18 0.42 47 -0.4 1 48
response to starvation -0.027 0.075 0.15 4 -0.19 51 55
DLK1 0.048 0.29 0.62 42 -0.7 5 47
NKX2-1 0.031 0.17 0.39 46 -0.4 7 53
ACADM -0.021 0.28 0.53 34 -0.65 20 54
TAT 0.06 0.23 0.55 52 -0.52 1 53
CEBPB 0.027 0.02 0.15 3 -10000 0 3
CEBPA 0.016 0.077 0.22 3 -0.32 22 25
TTR 0.07 0.28 0.63 58 -0.7 10 68
PKLR 0.008 0.3 0.61 40 -0.65 19 59
APOA1 -0.2 0.61 0.79 39 -1.1 134 173
CPT1C -0.017 0.29 0.55 37 -0.64 20 57
ALAS1 0.036 0.18 0.46 27 -0.49 4 31
TFRC 0.093 0.3 0.62 69 -0.84 9 78
FOXF1 -0.049 0.14 -10000 0 -0.32 102 102
NF1 0.022 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.11 0.16 0.39 111 -0.32 1 112
CPT1A -0.017 0.29 0.54 35 -0.65 19 54
HMGCS1 0.008 0.29 0.6 40 -0.66 16 56
NR3C1 0.045 0.048 0.22 12 -10000 0 12
CPT1B -0.021 0.29 0.54 35 -0.64 22 57
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.042 0.041 -10000 0 -10000 0 0
GCK -0.011 0.3 0.57 37 -0.67 24 61
CREB1 0.036 0.037 0.18 6 -10000 0 6
IGFBP1 0.033 0.21 0.55 32 -0.66 2 34
PDX1 0.11 0.28 0.66 70 -0.54 1 71
UCP2 -0.016 0.29 0.54 36 -0.65 20 56
ALDOB 0.044 0.3 0.67 45 -0.77 7 52
AFP 0.078 0.1 0.34 35 -10000 0 35
BDH1 -0.019 0.29 0.55 35 -0.64 20 55
HADH 0.029 0.28 0.58 38 -0.7 5 43
F2 -0.01 0.42 0.82 50 -0.86 20 70
HNF1A 0.11 0.16 0.39 111 -0.32 1 112
G6PC 0.083 0.13 0.48 20 -10000 0 20
SLC2A2 0.091 0.29 0.68 61 -0.67 3 64
INS -0.032 0.035 -10000 0 -0.14 1 1
FOXA1 0.057 0.078 0.26 40 -0.32 1 41
FOXA3 0.16 0.18 0.42 145 -0.29 3 148
FOXA2 0.072 0.38 0.83 59 -0.77 6 65
ABCC8 -0.013 0.37 0.62 41 -0.79 53 94
ALB 0.09 0.12 0.33 64 -10000 0 64
Osteopontin-mediated events

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
IKK alpha homodimer 0.074 0.078 0.2 83 -10000 0 83
NF kappa B1 p50/RelA/I kappa B alpha 0.083 0.092 0.28 31 -10000 0 31
alphaV/beta3 Integrin/Osteopontin/Src 0.18 0.099 0.24 346 -10000 0 346
AP1 0.078 0.11 0.25 84 -10000 0 84
ILK 0.066 0.07 0.23 26 -10000 0 26
bone resorption 0.043 0.072 0.23 18 -10000 0 18
PTK2B 0.018 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.14 0.11 0.28 77 -0.17 4 81
ITGAV 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.027 0.029 -10000 0 -0.23 6 6
alphaV/beta3 Integrin/Osteopontin 0.18 0.11 0.25 339 -0.19 4 343
MAP3K1 0.065 0.069 0.21 36 -0.18 4 40
JUN 0.019 0.027 -10000 0 -0.32 3 3
MAPK3 0.061 0.083 0.22 85 -10000 0 85
MAPK1 0.06 0.081 0.22 80 -10000 0 80
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.045 0.061 0.22 23 -10000 0 23
ITGB3 0.035 0.074 0.34 23 -0.32 5 28
NFKBIA 0.056 0.084 0.23 79 -10000 0 79
FOS 0.003 0.077 -10000 0 -0.32 27 27
CD44 0.015 0.046 -10000 0 -0.32 9 9
CHUK 0.021 0.003 -10000 0 -10000 0 0
PLAU 0.088 0.13 0.42 18 -10000 0 18
NF kappa B1 p50/RelA 0.086 0.1 0.26 85 -10000 0 85
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
RELA 0.021 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.046 0.055 0.26 23 -0.23 5 28
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.064 0.069 0.21 36 -0.18 5 41
VAV3 0.042 0.063 0.21 25 -0.21 6 31
MAP3K14 0.074 0.079 0.2 95 -0.18 4 99
ROCK2 0.021 0.003 -10000 0 -10000 0 0
SPP1 0.23 0.14 0.33 351 -10000 0 351
RAC1 0.019 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.037 0.06 0.18 20 -0.26 2 22
MMP2 0.034 0.076 0.3 8 -10000 0 8
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.014 0.32 1 -10000 0 1
LAT2 -0.072 0.13 -10000 0 -0.32 84 84
AP1 -0.08 0.2 -10000 0 -0.46 82 82
mol:PIP3 -0.081 0.17 0.3 16 -0.36 97 113
IKBKB -0.034 0.11 0.25 25 -0.23 60 85
AKT1 -0.039 0.14 0.32 46 -0.27 45 91
IKBKG -0.042 0.11 0.23 19 -0.23 69 88
MS4A2 -0.059 0.14 -10000 0 -0.32 110 110
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.006 -10000 0 -10000 0 0
MAP3K1 -0.066 0.14 0.22 8 -0.35 69 77
mol:Ca2+ -0.06 0.14 0.26 20 -0.29 78 98
LYN 0.014 0.018 -10000 0 -10000 0 0
CBLB -0.073 0.12 -10000 0 -0.31 86 86
SHC1 0.019 0.016 0.32 1 -10000 0 1
RasGAP/p62DOK 0.02 0.059 -10000 0 -0.17 42 42
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
PLD2 -0.045 0.15 0.3 50 -0.24 109 159
PTPN13 -0.088 0.17 -10000 0 -0.5 31 31
PTPN11 0.011 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.049 0.12 0.28 11 -0.28 43 54
SYK 0.014 0.027 -10000 0 -0.33 2 2
GRB2 0.02 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.084 0.16 0.18 1 -0.35 102 103
LAT -0.073 0.13 -10000 0 -0.31 86 86
PAK2 -0.073 0.16 0.24 7 -0.39 72 79
NFATC2 -0.036 0.1 -10000 0 -0.51 18 18
HRAS -0.075 0.17 0.25 7 -0.42 71 78
GAB2 0.017 0.034 -10000 0 -0.32 5 5
PLA2G1B -0.052 0.17 -10000 0 -0.92 18 18
Fc epsilon R1 -0.054 0.14 0.22 1 -0.26 157 158
Antigen/IgE/Fc epsilon R1 -0.046 0.13 0.21 1 -0.23 156 157
mol:GDP -0.088 0.18 -10000 0 -0.45 73 73
JUN 0.019 0.027 -10000 0 -0.32 3 3
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.016 -10000 0 -0.33 1 1
FOS 0.002 0.077 -10000 0 -0.32 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.069 0.14 -10000 0 -0.32 89 89
CHUK -0.047 0.11 0.23 16 -0.22 71 87
KLRG1 -0.064 0.11 0.14 1 -0.32 59 60
VAV1 -0.07 0.12 -10000 0 -0.32 80 80
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.071 0.12 -10000 0 -0.31 84 84
negative regulation of mast cell degranulation -0.055 0.12 -10000 0 -0.31 58 58
BTK -0.095 0.2 -10000 0 -0.49 78 78
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.079 0.15 -10000 0 -0.31 124 124
GAB2/PI3K/SHP2 -0.078 0.085 -10000 0 -0.23 106 106
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.065 0.13 -10000 0 -0.25 142 142
RAF1 -0.016 0.18 -10000 0 -0.97 18 18
Fc epsilon R1/FcgammaRIIB/SHIP -0.032 0.14 0.22 1 -0.22 152 153
FCER1G 0.011 0.044 -10000 0 -0.32 7 7
FCER1A -0.067 0.15 0.32 1 -0.34 119 120
Antigen/IgE/Fc epsilon R1/Fyn -0.039 0.12 0.21 1 -0.22 153 154
MAPK3 -0.018 0.17 -10000 0 -0.88 18 18
MAPK1 -0.022 0.18 -10000 0 -0.91 18 18
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.065 0.22 -10000 0 -0.66 48 48
DUSP1 -0.008 0.095 -10000 0 -0.32 42 42
NF-kappa-B/RelA -0.032 0.062 0.14 5 -0.15 48 53
actin cytoskeleton reorganization -0.073 0.16 -10000 0 -0.43 43 43
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.065 0.15 -10000 0 -0.37 66 66
FER -0.071 0.12 -10000 0 -0.31 85 85
RELA 0.021 0.004 -10000 0 -10000 0 0
ITK -0.024 0.066 -10000 0 -0.31 19 19
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG1 -0.089 0.18 0.26 3 -0.44 77 80
cytokine secretion -0.028 0.039 -10000 0 -0.16 2 2
SPHK1 -0.07 0.12 -10000 0 -0.31 82 82
PTK2 -0.076 0.16 -10000 0 -0.52 20 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.085 0.16 0.22 1 -0.36 104 105
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.078 0.17 0.29 16 -0.37 81 97
MAP2K2 -0.022 0.17 -10000 0 -0.9 18 18
MAP2K1 -0.021 0.17 -10000 0 -0.9 18 18
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.049 0.11 0.17 1 -0.29 58 59
MAP2K4 -0.093 0.32 -10000 0 -0.92 64 64
Fc epsilon R1/FcgammaRIIB -0.04 0.14 0.22 1 -0.23 155 156
mol:Choline -0.044 0.15 0.29 50 -0.23 109 159
SHC/Grb2/SOS1 -0.041 0.13 -10000 0 -0.3 73 73
FYN 0.019 0.016 -10000 0 -0.32 1 1
DOK1 0.021 0.002 -10000 0 -10000 0 0
PXN -0.074 0.15 -10000 0 -0.42 43 43
HCLS1 -0.073 0.13 -10000 0 -0.32 85 85
PRKCB -0.062 0.14 0.26 17 -0.29 82 99
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
IGHE -0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.056 0.12 -10000 0 -0.32 58 58
LCP2 0.018 0.027 -10000 0 -0.32 3 3
PLA2G4A -0.066 0.12 0.19 1 -0.31 80 81
RASA1 0.02 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.044 0.15 0.29 50 -0.23 109 159
IKK complex -0.024 0.096 0.24 24 -0.18 42 66
WIPF1 0.021 0.003 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.021 0.11 0.24 29 -0.18 86 115
SMAD6-7/SMURF1 0.01 0.075 -10000 0 -0.2 57 57
NOG 0.01 0.085 0.32 10 -0.32 24 34
SMAD9 -0.11 0.22 -10000 0 -0.46 137 137
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD5 -0.038 0.1 -10000 0 -0.33 35 35
BMP7/USAG1 -0.13 0.14 0.23 8 -0.24 292 300
SMAD5/SKI -0.03 0.12 0.26 3 -0.35 31 34
SMAD1 -0.003 0.057 -10000 0 -0.28 9 9
BMP2 -0.024 0.12 -10000 0 -0.32 66 66
SMAD1/SMAD1/SMAD4 -0.009 0.075 -10000 0 -0.37 5 5
BMPR1A 0.021 0.003 -10000 0 -10000 0 0
BMPR1B -0.011 0.11 0.32 3 -0.32 50 53
BMPR1A-1B/BAMBI 0.022 0.08 0.22 15 -0.2 50 65
AHSG 0.038 0.075 0.32 33 -10000 0 33
CER1 0.02 0.031 0.32 5 -10000 0 5
BMP2-4/CER1 0.003 0.085 0.22 3 -0.2 70 73
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.029 0.1 -10000 0 -0.33 33 33
BMP2-4 (homodimer) -0.009 0.094 -10000 0 -0.24 72 72
RGMB 0.02 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.001 0.11 0.23 3 -0.2 102 105
RGMA 0.023 0.039 0.32 6 -0.32 2 8
SMURF1 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.024 0.084 -10000 0 -0.29 25 25
BMP2-4/USAG1 -0.12 0.13 -10000 0 -0.22 302 302
SMAD6/SMURF1/SMAD5 -0.028 0.11 0.26 3 -0.37 25 28
SOSTDC1 -0.19 0.17 -10000 0 -0.32 304 304
BMP7/BMPR2/BMPR1A-1B 0.015 0.096 0.23 14 -0.19 82 96
SKI 0.021 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) -0.026 0.12 0.32 2 -0.32 71 73
HFE2 0.022 0.041 0.32 9 -10000 0 9
ZFYVE16 0.02 0.005 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD 0.013 0.091 0.22 18 -0.2 68 86
SMAD5/SMAD5/SMAD4 -0.029 0.11 0.26 3 -0.36 29 32
MAPK1 0.02 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.01 0.089 -10000 0 -0.27 25 25
BMP7 (homodimer) 0.001 0.11 0.32 17 -0.32 43 60
NUP214 0.021 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.008 0.1 0.23 33 -0.23 66 99
SMAD1/SKI 0.008 0.067 0.23 1 -0.31 8 9
SMAD6 -0.023 0.11 -10000 0 -0.32 64 64
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.016 0.096 0.22 29 -0.2 68 97
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.22 0.15 0.32 333 -10000 0 333
BMPR2 (homodimer) 0.021 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.038 0.02 -10000 0 -0.2 2 2
BMPR1A-1B (homodimer) 0.007 0.078 0.23 3 -0.23 49 52
CHRDL1 -0.1 0.17 -10000 0 -0.32 184 184
ENDOFIN/SMAD1 0.008 0.065 0.23 1 -0.34 5 6
SMAD6-7/SMURF1/SMAD1 -0.001 0.085 -10000 0 -0.4 5 5
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI 0.026 0.062 0.32 15 -0.32 5 20
SMURF2 0.021 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.069 0.14 -10000 0 -0.23 202 202
BMP2-4/GREM1 0.1 0.14 0.22 265 -0.16 70 335
SMAD7 0.019 0.016 -10000 0 -0.32 1 1
SMAD8A/SMAD8A/SMAD4 -0.1 0.21 -10000 0 -0.43 141 141
SMAD1/SMAD6 0.007 0.067 0.23 1 -0.3 10 11
TAK1/SMAD6 0.027 0.011 -10000 0 -10000 0 0
BMP7 0.001 0.11 0.32 17 -0.32 43 60
BMP6 -0.026 0.12 0.32 2 -0.32 71 73
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.028 0.093 -10000 0 -0.33 29 29
PPM1A 0.021 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.006 0.067 0.23 1 -0.32 7 8
SMAD7/SMURF1 0.026 0.016 -10000 0 -0.23 1 1
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
PPP1CA 0.021 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
PPP1R15A 0.019 0.022 -10000 0 -0.32 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.027 0.1 0.22 1 -0.32 31 32
CHRD 0.033 0.065 0.32 23 -0.32 1 24
BMPR2 0.021 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.09 -10000 0 -0.31 26 26
BMP4 0.014 0.058 0.32 3 -0.32 12 15
FST 0.025 0.089 0.32 25 -0.32 15 40
BMP2-4/NOG -0.001 0.1 0.22 7 -0.22 82 89
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.023 0.093 -10000 0 -0.18 71 71
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.3 0.56 0.79 2 -1.2 89 91
STAT6 (cleaved dimer) -0.32 0.55 -10000 0 -1.2 98 98
IGHG1 -0.084 0.24 0.44 15 -0.66 15 30
IGHG3 -0.3 0.53 0.61 3 -1.2 101 104
AKT1 -0.14 0.32 0.5 3 -0.89 38 41
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.3 0.47 3 -0.91 35 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.32 0.48 7 -0.87 35 42
THY1 -0.3 0.56 0.73 3 -1.2 90 93
MYB 0.02 0.029 0.32 3 -0.32 1 4
HMGA1 0.045 0.083 0.32 41 -10000 0 41
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.16 0.36 0.55 9 -0.76 72 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.32 0.48 7 -0.89 35 42
SP1 0.026 0.024 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
SOCS5 0.011 0.036 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.3 0.55 0.61 1 -1.2 94 95
SOCS1 -0.19 0.36 0.53 3 -0.75 87 90
SOCS3 -0.14 0.3 0.52 1 -0.81 33 34
FCER2 -0.24 0.49 0.72 9 -1.1 75 84
PARP14 0.023 0.012 -10000 0 -10000 0 0
CCL17 -0.35 0.62 0.78 5 -1.4 106 111
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.27 0.46 7 -0.72 35 42
T cell proliferation -0.31 0.56 0.63 1 -1.3 93 94
IL4R/JAK1 -0.31 0.55 0.63 2 -1.2 91 93
EGR2 -0.32 0.6 0.77 4 -1.3 94 98
JAK2 -0.007 0.065 -10000 0 -0.36 2 2
JAK3 0.02 0.016 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.003 0.034 -10000 0 -10000 0 0
COL1A2 -0.064 0.22 0.49 3 -1.3 4 7
CCL26 -0.29 0.56 0.76 6 -1.3 85 91
IL4R -0.32 0.6 0.77 7 -1.3 91 98
PTPN6 0.015 0.03 -10000 0 -10000 0 0
IL13RA2 -0.34 0.61 0.73 4 -1.3 101 105
IL13RA1 -0.006 0.064 0.18 7 -10000 0 7
IRF4 -0.057 0.26 0.54 2 -0.98 25 27
ARG1 -0.093 0.25 0.47 6 -0.68 39 45
CBL -0.16 0.33 0.5 6 -0.72 68 74
GTF3A 0.063 0.06 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 0 0.089 0.24 11 -0.27 2 13
IRF4/BCL6 -0.062 0.23 -10000 0 -0.91 25 25
CD40LG 0.011 0.076 -10000 0 -0.33 23 23
MAPK14 -0.15 0.33 0.51 6 -0.77 55 61
mitosis -0.13 0.3 0.48 4 -0.82 38 42
STAT6 -0.35 0.68 0.88 6 -1.5 97 103
SPI1 0.006 0.074 -10000 0 -0.32 24 24
RPS6KB1 -0.13 0.29 0.47 3 -0.8 35 38
STAT6 (dimer) -0.35 0.67 0.88 6 -1.5 97 103
STAT6 (dimer)/PARP14 -0.34 0.6 0.67 4 -1.3 100 104
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.36 0.48 6 -0.89 61 67
FRAP1 -0.14 0.32 0.5 3 -0.88 38 41
LTA -0.3 0.56 0.75 3 -1.3 87 90
FES 0.02 0.016 -10000 0 -0.32 1 1
T-helper 1 cell differentiation 0.34 0.64 1.4 98 -0.88 6 104
CCL11 -0.32 0.56 -10000 0 -1.2 99 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.33 0.48 6 -0.97 36 42
IL2RG 0.017 0.036 -10000 0 -0.3 5 5
IL10 -0.3 0.56 0.77 4 -1.3 86 90
IRS1 0.02 0.015 -10000 0 -0.32 1 1
IRS2 0.019 0.016 -10000 0 -0.32 1 1
IL4 -0.071 0.27 0.52 6 -1.1 22 28
IL5 -0.31 0.55 0.7 2 -1.3 89 91
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.25 0.5 0.71 8 -1 95 103
COL1A1 -0.013 0.29 0.58 16 -0.88 15 31
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.32 0.56 -10000 0 -1.3 91 91
IL2R gamma/JAK3 0.028 0.029 -10000 0 -0.19 5 5
TFF3 -0.31 0.59 0.73 7 -1.3 97 104
ALOX15 -0.62 0.72 0.69 3 -1.3 239 242
MYBL1 0.023 0.033 0.32 6 -10000 0 6
T-helper 2 cell differentiation -0.24 0.47 0.63 6 -0.99 95 101
SHC1 0.019 0.016 0.32 1 -10000 0 1
CEBPB 0.021 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.31 0.47 6 -0.81 36 42
mol:PI-3-4-5-P3 -0.14 0.32 0.5 3 -0.88 38 41
PI3K -0.15 0.34 0.52 2 -0.97 38 40
DOK2 -0.004 0.083 -10000 0 -0.32 32 32
ETS1 0.011 0.039 -10000 0 -0.22 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.091 0.24 0.44 8 -0.64 31 39
ITGB3 -0.3 0.57 0.68 6 -1.3 92 98
PIGR -0.43 0.69 0.74 6 -1.4 148 154
IGHE 0.008 0.073 0.2 22 -0.19 10 32
MAPKKK cascade -0.089 0.24 0.44 8 -0.62 31 39
BCL6 0.017 0.015 -10000 0 -10000 0 0
OPRM1 -0.31 0.55 0.7 2 -1.2 90 92
RETNLB -0.31 0.56 0.69 3 -1.2 91 94
SELP -0.41 0.68 0.72 5 -1.4 136 141
AICDA -0.32 0.56 0.7 2 -1.2 100 102
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.008 0.074 0.22 1 -0.28 19 20
alphaM/beta2 Integrin/GPIbA 0.006 0.079 0.22 3 -0.27 25 28
alphaM/beta2 Integrin/proMMP-9 0.048 0.11 0.22 104 -0.25 17 121
PLAUR 0.02 0.005 -10000 0 -10000 0 0
HMGB1 0.005 0.03 -10000 0 -0.12 1 1
alphaM/beta2 Integrin/Talin 0.008 0.075 -10000 0 -0.28 20 20
AGER -0.29 0.12 -10000 0 -0.34 443 443
RAP1A 0.02 0.005 -10000 0 -10000 0 0
SELPLG 0.009 0.062 -10000 0 -0.32 17 17
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.19 0.12 -10000 0 -0.23 422 422
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.084 0.12 0.32 109 -10000 0 109
CYR61 0.005 0.072 -10000 0 -0.32 23 23
TLN1 0.019 0.016 -10000 0 -0.32 1 1
Rap1/GTP -0.05 0.13 -10000 0 -0.35 54 54
RHOA 0.021 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.049 0.14 -10000 0 -0.32 101 101
MYH2 -0.1 0.16 0.22 2 -0.37 90 92
MST1R 0.02 0.016 -10000 0 -0.32 1 1
leukocyte activation during inflammatory response 0.008 0.084 0.19 19 -0.21 42 61
APOB 0.018 0.1 0.32 24 -0.32 25 49
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.014 0.32 1 -10000 0 1
JAM3 0.019 0.022 -10000 0 -0.32 2 2
GP1BA 0.017 0.047 0.32 3 -0.32 7 10
alphaM/beta2 Integrin/CTGF 0 0.086 -10000 0 -0.26 36 36
alphaM/beta2 Integrin -0.066 0.14 0.21 2 -0.37 59 61
JAM3 homodimer 0.019 0.022 -10000 0 -0.32 2 2
ICAM2 0.018 0.027 -10000 0 -0.32 3 3
ICAM1 0.017 0.034 -10000 0 -0.32 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.066 0.14 0.21 2 -0.37 60 62
cell adhesion 0.005 0.079 0.22 3 -0.27 25 28
NFKB1 -0.22 0.16 -10000 0 -0.47 128 128
THY1 0.028 0.048 0.32 13 -10000 0 13
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.022 0.063 0.21 25 -0.19 26 51
alphaM/beta2 Integrin/LRP/tPA 0.033 0.094 0.23 29 -0.28 17 46
IL6 -0.24 0.25 -10000 0 -0.65 122 122
ITGB2 -0.001 0.055 -10000 0 -0.34 9 9
elevation of cytosolic calcium ion concentration 0.044 0.1 0.22 74 -0.27 16 90
alphaM/beta2 Integrin/JAM2/JAM3 -0.003 0.098 -10000 0 -0.24 55 55
JAM2 -0.012 0.1 -10000 0 -0.32 48 48
alphaM/beta2 Integrin/ICAM1 0.025 0.084 -10000 0 -0.26 20 20
alphaM/beta2 Integrin/uPA/Plg 0.048 0.11 0.23 80 -0.26 18 98
RhoA/GTP -0.078 0.16 0.23 2 -0.31 106 108
positive regulation of phagocytosis -0.052 0.13 -10000 0 -0.35 54 54
Ron/MSP 0.037 0.042 0.23 19 -0.23 2 21
alphaM/beta2 Integrin/uPAR/uPA 0.046 0.1 0.23 74 -0.27 16 90
alphaM/beta2 Integrin/uPAR 0.008 0.072 -10000 0 -0.29 17 17
PLAU 0.075 0.12 0.32 91 -10000 0 91
PLAT 0.047 0.092 0.32 49 -0.32 1 50
actin filament polymerization -0.1 0.15 0.21 2 -0.36 88 90
MST1 0.031 0.06 0.32 19 -0.32 1 20
alphaM/beta2 Integrin/lipoprotein(a) 0.011 0.087 0.21 19 -0.21 42 61
TNF -0.21 0.17 -10000 0 -0.49 111 111
RAP1B 0.02 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.041 0.11 0.22 87 -0.29 18 105
fibrinolysis 0.046 0.1 0.22 80 -0.26 18 98
HCK 0.006 0.07 -10000 0 -0.32 22 22
dendritic cell antigen processing and presentation -0.066 0.14 0.21 2 -0.37 60 62
VTN -0.032 0.14 0.32 7 -0.32 85 92
alphaM/beta2 Integrin/CYR61 -0.001 0.088 -10000 0 -0.26 39 39
LPA 0.018 0.025 0.32 2 -0.32 1 3
LRP1 0.018 0.031 -10000 0 -0.32 4 4
cell migration 0.023 0.077 0.24 2 -0.24 16 18
FN1 0.019 0.033 0.32 1 -0.32 4 5
alphaM/beta2 Integrin/Thy1 0.012 0.079 0.22 13 -0.27 20 33
MPO 0.012 0.056 0.32 1 -0.32 13 14
KNG1 0.039 0.077 0.32 35 -10000 0 35
RAP1/GDP 0.026 0.009 -10000 0 -10000 0 0
ROCK1 -0.072 0.15 0.24 5 -0.36 67 72
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.023 0.045 0.32 11 -10000 0 11
CTGF 0.005 0.07 -10000 0 -0.32 22 22
alphaM/beta2 Integrin/Hck 0.001 0.091 -10000 0 -0.31 28 28
ITGAM -0.008 0.073 -10000 0 -0.33 20 20
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.025 0.12 -10000 0 -0.23 102 102
HP -0.041 0.16 0.32 23 -0.32 111 134
leukocyte adhesion -0.19 0.13 -10000 0 -0.35 137 137
SELP -0.049 0.14 -10000 0 -0.32 101 101
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.096 0.8 4 -10000 0 4
VDR 0.021 0.021 0.32 1 -0.32 1 2
FAM120B 0.019 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.087 0.11 -10000 0 -0.32 31 31
RXRs/LXRs/DNA/Oxysterols -0.087 0.12 -10000 0 -0.48 22 22
MED1 0.021 0.004 -10000 0 -10000 0 0
mol:9cRA -0.001 0.009 -10000 0 -0.093 1 1
RARs/THRs/DNA/Src-1 -0.009 0.066 -10000 0 -0.19 45 45
RXRs/NUR77 -0.095 0.13 -10000 0 -0.21 275 275
RXRs/PPAR -0.11 0.13 -10000 0 -0.22 253 253
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.014 0.22 1 -0.22 1 2
RARs/VDR/DNA/Vit D3 0.045 0.024 0.21 1 -0.17 3 4
RARA 0.021 0.004 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.021 0.32 1 -0.32 1 2
RARs/RARs/DNA/9cRA 0.032 0.021 -10000 0 -0.17 2 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.032 0.12 0.62 18 -10000 0 18
RARs/THRs/DNA/SMRT -0.01 0.067 -10000 0 -0.19 47 47
THRA 0.021 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.014 0.22 1 -0.22 1 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.066 0.11 -10000 0 -0.21 24 24
NR1H4 0.041 0.078 0.32 36 -10000 0 36
RXRs/LXRs/DNA -0.056 0.12 -10000 0 -0.31 7 7
NR1H2 0.019 0.014 -10000 0 -10000 0 0
NR1H3 0.019 0.015 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.058 0.1 -10000 0 -0.17 232 232
NR4A1 -0.047 0.14 -10000 0 -0.32 100 100
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.071 0.095 0.18 1 -0.17 218 219
RXRG -0.14 0.17 -10000 0 -0.32 238 238
RXR alpha/CCPG 0.026 0.016 -10000 0 -10000 0 0
RXRA 0.019 0.015 -10000 0 -10000 0 0
RXRB 0.019 0.015 -10000 0 -10000 0 0
THRB -0.011 0.1 -10000 0 -0.32 47 47
PPARG -0.023 0.11 -10000 0 -0.32 64 64
PPARD 0.021 0.004 -10000 0 -10000 0 0
TNF -0.095 0.18 -10000 0 -0.86 19 19
mol:Oxysterols 0 0.009 -10000 0 -10000 0 0
cholesterol transport -0.086 0.12 -10000 0 -0.48 22 22
PPARA 0.02 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.022 -10000 0 -0.32 2 2
RXRs/NUR77/BCL2 -0.12 0.13 -10000 0 -0.23 273 273
SREBF1 -0.075 0.12 -10000 0 -0.54 10 10
RXRs/RXRs/DNA/9cRA -0.066 0.11 -10000 0 -0.18 225 225
ABCA1 -0.081 0.12 -10000 0 -0.62 10 10
RARs/THRs 0.037 0.069 -10000 0 -0.18 44 44
RXRs/FXR -0.056 0.12 -10000 0 -0.18 218 218
BCL2 0.019 0.021 0.32 1 -0.32 1 2
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.015 0.043 -10000 0 -0.32 8 8
EPHB2 0.054 0.094 0.32 55 -10000 0 55
EFNB1 -0.011 0.03 0.18 8 -0.23 2 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.08 0.22 76 -0.23 6 82
Ephrin B2/EPHB1-2 0.066 0.083 0.23 91 -0.16 10 101
neuron projection morphogenesis 0.043 0.063 0.21 19 -0.22 6 25
Ephrin B1/EPHB1-2/Tiam1 0.069 0.088 0.24 87 -0.22 8 95
DNM1 0.025 0.036 0.33 7 -10000 0 7
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.061 0.16 -10000 0 -0.5 59 59
YES1 -0.074 0.24 -10000 0 -0.72 60 60
Ephrin B1/EPHB1-2/NCK2 0.076 0.085 0.24 95 -0.2 5 100
PI3K -0.03 0.17 -10000 0 -0.49 61 61
mol:GDP 0.067 0.086 0.23 87 -0.22 8 95
ITGA2B -0.008 0.1 0.32 5 -0.32 47 52
endothelial cell proliferation 0.022 0.028 -10000 0 -0.19 8 8
FYN -0.078 0.24 -10000 0 -0.72 60 60
MAP3K7 -0.06 0.17 -10000 0 -0.52 59 59
FGR -0.079 0.24 -10000 0 -0.72 60 60
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RGS3 0.02 0.004 -10000 0 -10000 0 0
cell adhesion -0.05 0.17 0.24 1 -0.49 58 59
LYN -0.071 0.23 -10000 0 -0.71 59 59
Ephrin B1/EPHB1-2/Src Family Kinases -0.07 0.21 -10000 0 -0.65 61 61
Ephrin B1/EPHB1-2 -0.06 0.18 -10000 0 -0.56 59 59
SRC -0.071 0.23 -10000 0 -0.7 61 61
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
EPHB1 0.052 0.099 0.33 55 -0.33 3 58
EPHB4 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.028 -10000 0 -0.19 8 8
alphaIIb/beta3 Integrin 0.015 0.095 0.23 28 -0.23 51 79
BLK -0.068 0.24 -10000 0 -0.71 60 60
HCK -0.078 0.24 -10000 0 -0.72 61 61
regulation of stress fiber formation -0.074 0.083 0.2 5 -0.23 95 100
MAPK8 -0.06 0.15 0.23 1 -0.47 60 61
Ephrin B1/EPHB1-2/RGS3 0.073 0.083 0.23 91 -0.2 5 96
endothelial cell migration -0.044 0.14 0.19 17 -0.42 55 72
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTPN13 -0.024 0.14 -10000 0 -0.44 51 51
regulation of focal adhesion formation -0.074 0.083 0.2 5 -0.23 95 100
chemotaxis -0.071 0.081 0.2 5 -0.23 91 96
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.054 0.072 0.22 36 -0.23 6 42
angiogenesis -0.06 0.18 -10000 0 -0.56 59 59
LCK -0.071 0.24 -10000 0 -0.71 61 61
Visual signal transduction: Rods

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
mol:K + 0.021 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.028 0.22 10 -10000 0 10
Metarhodopsin II/Arrestin 0.025 0.009 0.21 1 -10000 0 1
PDE6G/GNAT1/GTP 0.028 0.034 0.23 10 -0.17 3 13
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.043 0.32 10 -10000 0 10
GRK1 0.037 0.074 0.32 32 -10000 0 32
CNG Channel 0.043 0.084 0.26 17 -0.17 31 48
mol:Na + 0.081 0.082 0.28 33 -0.17 3 36
mol:ADP 0.037 0.074 0.32 32 -10000 0 32
RGS9-1/Gbeta5/R9AP -0.058 0.13 -10000 0 -0.21 193 193
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.1 0.096 0.33 34 -0.17 3 37
CNGB1 0.072 0.12 0.32 88 -0.32 1 89
RDH5 0.025 0.035 0.32 7 -10000 0 7
SAG 0.019 0.014 0.32 1 -10000 0 1
mol:Ca2+ 0.015 0.089 0.3 31 -10000 0 31
Na + (4 Units) 0.024 0.081 0.21 30 -10000 0 30
RGS9 -0.08 0.16 -10000 0 -0.32 149 149
GNB1/GNGT1 0.063 0.078 0.23 88 -10000 0 88
GNAT1/GDP -0.042 0.12 0.21 5 -0.18 187 192
GUCY2D 0.021 0.043 0.32 6 -0.32 3 9
GNGT1 0.077 0.12 0.32 97 -10000 0 97
GUCY2F 0.02 0.019 0.32 2 -10000 0 2
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.029 0.049 0.18 2 -0.18 40 42
mol:11-cis-retinal 0.025 0.035 0.32 7 -10000 0 7
mol:cGMP 0.061 0.075 0.22 82 -0.18 4 86
GNB1 0.021 0.004 -10000 0 -10000 0 0
Rhodopsin 0.032 0.024 0.23 7 -10000 0 7
SLC24A1 0.021 0.003 -10000 0 -10000 0 0
CNGA1 0.057 0.099 0.32 62 -10000 0 62
Metarhodopsin II 0.033 0.042 0.2 31 -10000 0 31
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.073 0.078 0.23 86 -0.18 4 90
RGS9BP -0.029 0.12 -10000 0 -0.32 73 73
Metarhodopsin II/Transducin 0.026 0.04 0.16 9 -10000 0 9
GCAP Family/Ca ++ 0.065 0.07 0.22 85 -0.15 2 87
PDE6A/B 0.008 0.073 0.23 1 -0.23 44 45
mol:Pi -0.058 0.12 -10000 0 -0.21 193 193
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.066 0.072 0.22 90 -10000 0 90
PDE6B 0.016 0.04 -10000 0 -0.32 7 7
PDE6A -0.005 0.093 0.32 1 -0.32 39 40
PDE6G 0.02 0.033 0.32 2 -0.32 3 5
RHO 0.019 0.003 -10000 0 -10000 0 0
PDE6 -0.048 0.13 -10000 0 -0.21 190 190
GUCA1A 0.071 0.11 0.32 86 -10000 0 86
GC2/GCAP Family 0.076 0.072 0.23 86 -0.18 1 87
GUCA1C 0.018 0.014 0.32 1 -10000 0 1
GUCA1B 0.021 0.032 0.32 3 -0.32 2 5
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CCL5 0.017 0.034 -10000 0 -0.32 5 5
SDCBP 0.019 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.081 0.08 0.23 45 -0.34 1 46
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.073 0.088 0.22 36 -0.32 5 41
Syndecan-1/Syntenin 0.072 0.091 0.23 36 -0.32 6 42
MAPK3 0.057 0.088 0.21 41 -0.28 6 47
HGF/MET 0.013 0.078 0.23 10 -0.23 40 50
TGFB1/TGF beta receptor Type II 0.021 0.004 -10000 0 -10000 0 0
BSG 0.02 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.072 0.087 0.22 36 -0.31 5 41
Syndecan-1/RANTES 0.077 0.092 0.23 40 -0.29 7 47
Syndecan-1/CD147 0.083 0.091 0.23 39 -0.29 6 45
Syndecan-1/Syntenin/PIP2 0.067 0.086 0.21 35 -0.31 6 41
LAMA5 0.018 0.027 -10000 0 -0.32 3 3
positive regulation of cell-cell adhesion 0.065 0.084 0.21 35 -0.3 6 41
MMP7 0.063 0.13 0.32 85 -0.32 11 96
HGF 0.007 0.078 0.32 4 -0.32 24 28
Syndecan-1/CASK 0.06 0.086 0.19 45 -0.31 6 51
Syndecan-1/HGF/MET 0.068 0.11 0.24 39 -0.33 9 48
regulation of cell adhesion 0.049 0.081 0.19 41 -0.27 6 47
HPSE 0.022 0.019 0.32 2 -10000 0 2
positive regulation of cell migration 0.081 0.08 0.23 45 -0.34 1 46
SDC1 0.08 0.08 0.23 44 -0.34 1 45
Syndecan-1/Collagen 0.081 0.08 0.23 45 -0.34 1 46
PPIB 0.021 0.014 0.32 1 -10000 0 1
MET 0.011 0.072 0.32 6 -0.32 18 24
PRKACA 0.02 0.005 -10000 0 -10000 0 0
MMP9 0.084 0.12 0.32 109 -10000 0 109
MAPK1 0.058 0.083 0.2 38 -0.27 6 44
homophilic cell adhesion 0.078 0.089 0.24 41 -0.34 1 42
MMP1 0.21 0.15 0.32 325 -0.32 2 327
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.029 0.018 -10000 0 -0.23 2 2
Necdin/E2F1 0.029 0.031 0.23 5 -0.22 4 9
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.048 0.07 -10000 0 -0.17 28 28
NGF (dimer)/p75(NTR)/BEX1 -0.009 0.13 0.24 35 -0.2 132 167
NT-4/5 (dimer)/p75(NTR) 0.017 0.071 0.26 7 -0.23 32 39
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.018 0.053 0.18 20 -10000 0 20
IKBKG 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 258 258
MGDIs/NGR/p75(NTR)/LINGO1 0.056 0.071 0.23 60 -0.18 10 70
FURIN 0.029 0.05 0.32 14 -10000 0 14
proBDNF (dimer)/p75(NTR)/Sortilin -0.076 0.12 0.22 5 -0.2 253 258
LINGO1 0.059 0.1 0.32 64 -10000 0 64
Sortilin/TRAF6/NRIF -0.029 0.019 -10000 0 -0.17 2 2
proBDNF (dimer) -0.15 0.17 -10000 0 -0.32 258 258
NTRK1 0.01 0.056 0.32 1 -0.32 13 14
RTN4R 0.019 0.016 -10000 0 -0.32 1 1
neuron apoptosis -0.099 0.14 0.28 4 -0.37 49 53
IRAK1 0.02 0.004 -10000 0 -10000 0 0
SHC1 -0.015 0.041 0.1 26 -0.2 14 40
ARHGDIA 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.047 0.031 -10000 0 -0.17 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.048 0.066 0.23 27 -0.18 24 51
MAGEH1 0.021 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.044 0.07 0.23 26 -0.19 26 52
Mammalian IAPs/DIABLO 0.051 0.027 0.23 5 -0.18 2 7
proNGF (dimer) 0.025 0.085 0.32 23 -0.32 13 36
MAGED1 0.021 0.014 0.32 1 -10000 0 1
APP 0.02 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.076 -10000 0 -0.32 26 26
ZNF274 0.02 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.02 0.045 0.19 1 -0.16 22 23
NGF 0.025 0.085 0.32 23 -0.32 13 36
cell cycle arrest 0.002 0.071 0.22 21 -10000 0 21
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.006 0.057 0.18 6 -0.27 3 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.028 0.065 0.24 7 -0.2 32 39
NCSTN 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.039 0.065 0.22 28 -0.19 21 49
PSENEN 0.02 0.005 -10000 0 -10000 0 0
mol:ceramide -0.016 0.05 0.2 11 -0.18 18 29
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.004 0.051 0.16 8 -0.28 3 11
p75(NTR)/beta APP 0.027 0.042 0.23 7 -0.23 9 16
BEX1 -0.051 0.16 0.32 19 -0.32 123 142
mol:GDP -0.014 0.046 0.21 1 -0.19 22 23
NGF (dimer) 0.073 0.096 0.23 109 -0.18 18 127
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.065 0.069 0.23 59 -0.17 10 69
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RAC1/GTP 0.03 0.054 0.2 22 -0.16 21 43
MYD88 0.021 0.004 -10000 0 -10000 0 0
CHUK 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.04 0.065 0.22 28 -0.19 21 49
RHOB 0.02 0.015 -10000 0 -0.32 1 1
RHOA 0.021 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.03 0.02 0.23 4 -10000 0 4
NT3 (dimer) 0.006 0.074 0.32 2 -0.32 23 25
TP53 -0.084 0.089 0.26 7 -0.3 6 13
PRDM4 -0.018 0.054 0.2 13 -0.18 21 34
BDNF (dimer) -0.01 0.17 0.26 107 -0.18 136 243
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SORT1 0.019 0.022 -10000 0 -0.32 2 2
activation of caspase activity 0.043 0.066 -10000 0 -0.17 28 28
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.048 0.066 0.23 27 -0.18 24 51
RHOC 0.02 0.005 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
MAPK10 -0.077 0.12 0.29 13 -0.32 51 64
DIABLO 0.021 0.003 -10000 0 -10000 0 0
SMPD2 -0.016 0.051 0.2 11 -0.18 18 29
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.067 0.22 27 -0.19 24 51
PSEN1 0.021 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.017 0.072 0.29 7 -0.23 31 38
MAPK8 -0.062 0.1 0.31 11 -0.28 28 39
MAPK9 -0.061 0.1 0.3 11 -0.29 25 36
APAF1 0.021 0.003 -10000 0 -10000 0 0
NTF3 0.006 0.074 0.32 2 -0.32 23 25
NTF4 0.003 0.076 -10000 0 -0.32 26 26
NDN 0.017 0.034 -10000 0 -0.32 5 5
RAC1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.047 0.057 -10000 0 -0.16 21 21
p75 CTF/Sortilin/TRAF6/NRIF 0.049 0.022 -10000 0 -0.18 2 2
RhoA-B-C/GTP 0.039 0.064 0.22 28 -0.19 21 49
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.058 0.12 0.22 3 -0.18 245 248
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.064 0.12 0.23 5 -0.18 250 255
PRKACB 0.021 0.014 0.32 1 -10000 0 1
proBDNF (dimer)/p75 ECD -0.099 0.13 -10000 0 -0.23 255 255
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BIRC2 0.02 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.007 0.072 0.22 14 -0.2 15 29
BAD -0.072 0.11 0.31 13 -0.31 33 46
RIPK2 0.019 0.007 -10000 0 -10000 0 0
NGFR 0.019 0.058 0.32 7 -0.32 9 16
CYCS -0.021 0.052 0.21 11 -10000 0 11
ADAM17 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.044 0.064 0.23 24 -0.18 21 45
BCL2L11 -0.072 0.11 0.32 12 -0.31 33 45
BDNF (dimer)/p75(NTR) -0.098 0.13 0.23 5 -0.23 254 259
PI3K 0.046 0.065 0.23 26 -0.18 22 48
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.047 0.066 0.23 27 -0.18 23 50
NDNL2 0.02 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.029 0.072 0.23 28 -0.23 22 50
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.048 0.066 0.23 27 -0.18 23 50
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
PLG 0.023 0.045 0.32 11 -10000 0 11
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.098 0.096 -10000 0 -0.19 245 245
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
NGFRAP1 0.018 0.034 -10000 0 -0.32 5 5
CASP3 -0.068 0.11 0.3 13 -0.3 35 48
E2F1 0.023 0.03 0.32 5 -10000 0 5
CASP9 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.031 0.067 -10000 0 -0.27 8 8
NGF (dimer)/TRKA 0.023 0.066 0.23 19 -0.22 22 41
MMP7 0.063 0.13 0.32 85 -0.32 11 96
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 0.065 0.22 25 -0.17 22 47
MMP3 0.13 0.15 0.32 187 -10000 0 187
APAF-1/Caspase 9 -0.039 0.035 -10000 0 -0.17 17 17
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.069 0.11 0.34 74 -0.22 2 76
NFATC2 0.004 0.14 -10000 0 -0.5 16 16
NFATC3 -0.007 0.085 -10000 0 -0.26 34 34
CD40LG -0.092 0.29 -10000 0 -0.79 62 62
ITCH -0.024 0.077 -10000 0 -0.24 1 1
CBLB -0.027 0.08 -10000 0 -0.2 84 84
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.032 0.25 0.48 15 -0.75 32 47
JUNB 0.018 0.027 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.099 -10000 0 -0.23 94 94
T cell anergy -0.056 0.14 0.28 4 -0.34 85 89
TLE4 -0.01 0.1 -10000 0 -0.46 12 12
Jun/NFAT1-c-4/p21SNFT -0.039 0.29 0.52 1 -0.77 57 58
AP-1/NFAT1-c-4 -0.052 0.34 0.76 1 -0.86 62 63
IKZF1 -0.005 0.086 -10000 0 -0.37 12 12
T-helper 2 cell differentiation -0.032 0.19 -10000 0 -0.72 22 22
AP-1/NFAT1 0.014 0.12 0.33 3 -0.36 16 19
CALM1 -0.009 0.067 -10000 0 -0.15 94 94
EGR2 -0.096 0.33 -10000 0 -1.1 39 39
EGR3 -0.13 0.41 -10000 0 -1.2 62 62
NFAT1/FOXP3 0.054 0.14 0.42 21 -0.34 12 33
EGR1 0.003 0.073 -10000 0 -0.32 24 24
JUN 0.012 0.037 -10000 0 -0.33 3 3
EGR4 0.05 0.092 0.32 52 -10000 0 52
mol:Ca2+ -0.024 0.054 -10000 0 -0.14 96 96
GBP3 -0.017 0.12 -10000 0 -0.52 22 22
FOSL1 0.028 0.059 0.32 16 -0.32 3 19
NFAT1-c-4/MAF/IRF4 -0.037 0.28 -10000 0 -0.76 58 58
DGKA -0.006 0.09 0.5 1 -0.38 10 11
CREM 0.02 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.074 0.3 -10000 0 -0.8 63 63
CTLA4 0.015 0.1 0.34 12 -0.3 8 20
NFAT1-c-4 (dimer)/EGR1 -0.06 0.3 -10000 0 -0.82 61 61
NFAT1-c-4 (dimer)/EGR4 -0.036 0.3 -10000 0 -0.79 61 61
FOS -0.004 0.081 -10000 0 -0.33 27 27
IFNG -0.039 0.22 0.37 3 -0.81 25 28
T cell activation -0.039 0.17 -10000 0 -0.7 12 12
MAF 0.02 0.016 -10000 0 -0.32 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.07 0.24 0.69 55 -10000 0 55
TNF -0.081 0.28 0.48 1 -0.76 62 63
FASLG -0.16 0.45 -10000 0 -1.2 68 68
TBX21 0.015 0.075 0.32 2 -0.28 24 26
BATF3 0.019 0.006 -10000 0 -10000 0 0
PRKCQ -0.022 0.11 -10000 0 -0.33 63 63
PTPN1 -0.008 0.091 0.34 1 -0.38 10 11
NFAT1-c-4/ICER1 -0.051 0.28 -10000 0 -0.77 61 61
GATA3 0.02 0.021 0.32 1 -0.32 1 2
T-helper 1 cell differentiation -0.038 0.22 0.37 3 -0.79 25 28
IL2RA -0.021 0.26 0.49 23 -0.75 32 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.008 0.089 -10000 0 -0.35 15 15
E2F1 0.025 0.031 0.33 5 -10000 0 5
PPARG -0.023 0.11 -10000 0 -0.32 64 64
SLC3A2 -0.007 0.088 -10000 0 -0.36 13 13
IRF4 0.026 0.055 0.32 13 -0.32 3 16
PTGS2 -0.093 0.29 0.5 1 -0.79 58 59
CSF2 -0.093 0.3 0.48 3 -0.79 62 65
JunB/Fra1/NFAT1-c-4 -0.039 0.29 0.5 2 -0.74 63 65
IL4 -0.034 0.2 -10000 0 -0.75 22 22
IL5 -0.088 0.28 -10000 0 -0.77 61 61
IL2 -0.04 0.17 -10000 0 -0.72 12 12
IL3 -0.029 0.14 -10000 0 -0.86 10 10
RNF128 -0.071 0.17 -10000 0 -0.43 94 94
NFATC1 -0.071 0.24 -10000 0 -0.7 55 55
CDK4 0.051 0.16 0.58 22 -10000 0 22
PTPRK -0.005 0.084 -10000 0 -0.37 11 11
IL8 -0.081 0.29 0.47 5 -0.76 62 67
POU2F1 0.019 0.006 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.017 0.027 -10000 0 -0.33 3 3
GNB1/GNG2 -0.051 0.071 -10000 0 -0.19 101 101
AKT1 -0.039 0.1 0.29 1 -0.28 20 21
EGF 0.071 0.12 0.32 91 -0.32 5 96
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.029 0.059 -10000 0 -0.23 17 17
mol:Ca2+ -0.064 0.14 -10000 0 -0.32 78 78
LYN -0.021 0.041 -10000 0 -0.2 4 4
RhoA/GTP -0.026 0.057 -10000 0 -0.13 67 67
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.074 0.15 -10000 0 -0.34 100 100
GNG2 0.019 0.022 -10000 0 -0.32 2 2
ARRB2 0.02 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.033 0.15 -10000 0 -0.6 30 30
G beta5/gamma2 -0.064 0.093 -10000 0 -0.24 99 99
PRKCH -0.074 0.16 0.31 1 -0.36 98 99
DNM1 0.025 0.035 0.32 7 -10000 0 7
TXA2/TP beta/beta Arrestin3 0.008 0.045 -10000 0 -0.53 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.013 0.05 -10000 0 -0.32 11 11
G12 family/GTP -0.063 0.13 -10000 0 -0.3 95 95
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
ADRBK2 0.02 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.026 0.008 -10000 0 -10000 0 0
mol:GDP 0.044 0.11 0.37 28 -10000 0 28
mol:NADP 0.022 0.047 0.32 7 -0.32 4 11
RAB11A 0.021 0.003 -10000 0 -10000 0 0
PRKG1 -0.021 0.11 -10000 0 -0.32 62 62
mol:IP3 -0.082 0.17 -10000 0 -0.39 98 98
cell morphogenesis 0.026 0.008 -10000 0 -10000 0 0
PLCB2 -0.12 0.23 -10000 0 -0.53 102 102
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.074 0.21 7 -0.19 4 11
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.025 0.052 0.16 1 -0.23 10 11
RHOA 0.021 0.004 -10000 0 -10000 0 0
PTGIR 0.016 0.037 -10000 0 -0.32 6 6
PRKCB1 -0.08 0.17 -10000 0 -0.38 98 98
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
mol:L-citrulline 0.022 0.047 0.32 7 -0.32 4 11
TXA2/TXA2-R family -0.11 0.22 -10000 0 -0.52 104 104
LCK -0.022 0.047 -10000 0 -0.22 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.01 0.048 0.18 3 -0.2 13 16
TXA2-R family/G12 family/GDP/G beta/gamma 0.009 0.062 -10000 0 -0.42 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.012 0.045 -10000 0 -0.19 13 13
MAPK14 -0.047 0.11 0.27 7 -0.24 41 48
TGM2/GTP -0.091 0.18 -10000 0 -0.43 85 85
MAPK11 -0.051 0.1 -10000 0 -0.23 79 79
ARHGEF1 -0.043 0.074 -10000 0 -0.19 34 34
GNAI2 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.081 0.17 -10000 0 -0.38 101 101
RAB11/GDP 0.021 0.005 -10000 0 -10000 0 0
ICAM1 -0.059 0.13 -10000 0 -0.29 83 83
cAMP biosynthetic process -0.077 0.16 -10000 0 -0.36 86 86
Gq family/GTP/EBP50 0 0.043 0.23 1 -0.19 20 21
actin cytoskeleton reorganization 0.026 0.008 -10000 0 -10000 0 0
SRC -0.021 0.042 -10000 0 -0.2 4 4
GNB5 0.021 0.004 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.007 0.08 0.19 12 -0.25 16 28
VCAM1 -0.06 0.13 -10000 0 -0.29 100 100
TP beta/Gq family/GDP/G beta5/gamma2 -0.033 0.15 -10000 0 -0.6 30 30
platelet activation -0.063 0.14 0.3 5 -0.31 80 85
PGI2/IP 0.012 0.026 -10000 0 -0.22 6 6
PRKACA 0.002 0.041 -10000 0 -0.22 15 15
Gq family/GDP/G beta5/gamma2 -0.019 0.12 -10000 0 -0.52 22 22
TXA2/TP beta/beta Arrestin2 -0.004 0.059 -10000 0 -0.36 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.033 -10000 0 -0.2 13 13
mol:DAG -0.09 0.19 -10000 0 -0.43 98 98
EGFR 0.014 0.045 0.32 1 -0.32 8 9
TXA2/TP alpha -0.11 0.21 -10000 0 -0.49 97 97
Gq family/GTP -0.015 0.066 0.22 1 -0.22 43 44
YES1 -0.02 0.044 -10000 0 -0.2 4 4
GNAI2/GTP -0.005 0.042 -10000 0 -0.2 9 9
PGD2/DP 0.01 0.035 -10000 0 -0.22 11 11
SLC9A3R1 0.021 0.014 0.32 1 -10000 0 1
FYN -0.02 0.042 -10000 0 -0.2 4 4
mol:NO 0.022 0.047 0.32 7 -0.32 4 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
PGK/cGMP 0.003 0.075 0.21 7 -0.19 60 67
RhoA/GDP 0.02 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.02 0.051 -10000 0 -0.2 15 15
NOS3 0.022 0.047 0.32 7 -0.32 4 11
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.074 0.16 0.31 1 -0.36 96 97
PRKCB -0.078 0.16 -10000 0 -0.37 98 98
PRKCE -0.075 0.16 -10000 0 -0.36 94 94
PRKCD -0.081 0.16 -10000 0 -0.38 103 103
PRKCG -0.08 0.17 -10000 0 -0.39 93 93
muscle contraction -0.11 0.21 -10000 0 -0.48 105 105
PRKCZ -0.075 0.15 -10000 0 -0.34 102 102
ARR3 0.02 0.023 0.32 3 -10000 0 3
TXA2/TP beta 0.007 0.048 -10000 0 -0.2 11 11
PRKCQ -0.086 0.16 -10000 0 -0.38 105 105
MAPKKK cascade -0.1 0.2 -10000 0 -0.46 99 99
SELE -0.074 0.15 -10000 0 -0.36 102 102
TP beta/GNAI2/GDP/G beta/gamma 0.021 0.05 -10000 0 -0.2 13 13
ROCK1 0.02 0.005 -10000 0 -10000 0 0
GNA14 0.013 0.05 -10000 0 -0.32 11 11
chemotaxis -0.12 0.25 -10000 0 -0.59 102 102
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
Rac1/GTP 0.014 0.005 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.012 0.04 -10000 0 -0.29 7 7
CDKN2C 0.001 0.032 0.33 1 -10000 0 1
CDKN2A 0.098 0.14 0.33 135 -10000 0 135
CCND2 -0.021 0.048 0.15 6 -0.2 11 17
RB1 0.021 0.053 0.26 8 -0.17 5 13
CDK4 -0.023 0.052 0.17 6 -0.26 6 12
CDK6 -0.023 0.052 0.17 5 -0.26 7 12
G1/S progression 0.006 0.092 0.18 82 -0.28 9 91
IL23-mediated signaling events

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
CCL2 -0.11 0.45 0.7 1 -1.2 49 50
IL23A -0.1 0.47 0.75 4 -1.2 50 54
NF kappa B1 p50/RelA/I kappa B alpha -0.1 0.45 0.64 3 -1.2 50 53
positive regulation of T cell mediated cytotoxicity -0.13 0.52 0.74 3 -1.3 54 57
ITGA3 -0.11 0.45 0.69 2 -1.1 55 57
IL17F -0.073 0.3 0.53 8 -0.72 53 61
IL12B 0.018 0.06 0.28 5 -0.34 1 6
STAT1 (dimer) -0.13 0.49 0.65 1 -1.3 54 55
CD4 -0.11 0.45 0.69 4 -1.2 52 56
IL23 -0.091 0.45 0.71 3 -1.1 49 52
IL23R 0.004 0.17 -10000 0 -0.98 9 9
IL1B -0.12 0.5 0.74 3 -1.3 57 60
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.097 0.44 0.71 4 -1.1 51 55
TYK2 0.014 0.042 -10000 0 -10000 0 0
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP 0.008 0.068 -10000 0 -0.32 20 20
IL12RB1 0.007 0.07 -10000 0 -0.36 12 12
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.017 0.065 0.2 1 -0.26 11 12
IL23R/JAK2 0.014 0.17 -10000 0 -0.96 8 8
positive regulation of chronic inflammatory response -0.13 0.52 0.74 3 -1.3 54 57
natural killer cell activation 0 0.01 -10000 0 -0.047 2 2
JAK2 0.015 0.055 -10000 0 -0.34 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
NFKB1 0.013 0.021 -10000 0 -10000 0 0
RELA 0.013 0.021 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.083 0.43 0.69 4 -1.1 49 53
ALOX12B -0.1 0.44 0.82 1 -1.1 49 50
CXCL1 -0.13 0.47 0.73 3 -1.2 61 64
T cell proliferation -0.13 0.52 0.74 3 -1.3 54 57
NFKBIA 0.011 0.02 -10000 0 -10000 0 0
IL17A -0.027 0.26 0.49 23 -0.56 47 70
PI3K -0.12 0.47 0.62 1 -1.2 54 55
IFNG 0.006 0.047 0.13 31 -0.12 15 46
STAT3 (dimer) -0.11 0.45 0.62 3 -1.2 53 56
IL18R1 0.007 0.071 -10000 0 -0.32 22 22
IL23/IL23R/JAK2/TYK2/SOCS3 -0.067 0.34 0.56 4 -0.86 46 50
IL18/IL18R 0.025 0.086 0.19 1 -0.24 39 40
macrophage activation -0.004 0.024 0.051 30 -0.046 10 40
TNF -0.11 0.48 0.73 4 -1.2 54 58
STAT3/STAT4 -0.12 0.47 0.62 1 -1.2 54 55
STAT4 (dimer) -0.13 0.49 0.65 1 -1.3 54 55
IL18 0.013 0.049 -10000 0 -0.32 10 10
IL19 -0.095 0.44 0.74 2 -1.1 51 53
STAT5A (dimer) -0.13 0.49 0.65 1 -1.3 54 55
STAT1 0.021 0.002 -10000 0 -10000 0 0
SOCS3 0.018 0.031 -10000 0 -0.32 4 4
CXCL9 -0.11 0.46 0.74 2 -1.2 57 59
MPO -0.12 0.46 0.67 2 -1.2 60 62
positive regulation of humoral immune response -0.13 0.52 0.74 3 -1.3 54 57
IL23/IL23R/JAK2/TYK2 -0.15 0.56 0.74 3 -1.5 54 57
IL6 -0.21 0.58 0.69 2 -1.2 123 125
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
IL2 0.013 0.027 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.01 -10000 0 -0.047 2 2
CD3E -0.11 0.44 0.7 1 -1.1 54 55
keratinocyte proliferation -0.13 0.52 0.74 3 -1.3 54 57
NOS2 -0.16 0.5 0.69 4 -1.1 81 85
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.024 0.04 -10000 0 -0.23 12 12
alphaV beta3 Integrin 0.016 0.093 0.22 21 -0.2 69 90
PTK2 -0.042 0.12 0.33 10 -0.36 26 36
IGF1R 0.02 0.004 -10000 0 -10000 0 0
PI4KB 0.018 0.008 -10000 0 -10000 0 0
MFGE8 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
CDKN1B -0.057 0.16 0.18 6 -0.41 80 86
VEGFA 0.021 0.004 -10000 0 -10000 0 0
ILK -0.06 0.16 0.18 6 -0.4 84 90
ROCK1 0.02 0.005 -10000 0 -10000 0 0
AKT1 -0.067 0.14 -10000 0 -0.38 83 83
PTK2B -0.013 0.053 0.17 27 -0.18 13 40
alphaV/beta3 Integrin/JAM-A -0.003 0.11 0.22 25 -0.19 105 130
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.054 0.059 0.22 47 -0.19 5 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.046 0.04 0.23 1 -0.19 11 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.023 0.084 0.16 2 -0.31 16 18
alphaV/beta3 Integrin/Syndecan-1 0.047 0.046 0.22 23 -0.2 5 28
PI4KA 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.016 0.091 -10000 0 -0.2 65 65
PI4 Kinase 0.026 0.013 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.17 0.11 0.24 339 -0.18 5 344
RPS6KB1 -0.045 0.072 0.29 4 -0.36 7 11
TLN1 0.019 0.016 -10000 0 -0.32 1 1
MAPK3 -0.057 0.14 0.28 1 -0.42 62 63
GPR124 0.017 0.023 -10000 0 -0.32 2 2
MAPK1 -0.056 0.14 0.28 1 -0.42 62 63
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
alphaV/beta3 Integrin/Tumstatin -0.014 0.11 0.22 19 -0.2 133 152
cell adhesion 0.04 0.053 0.22 23 -0.2 7 30
ANGPTL3 0.034 0.066 0.32 25 -10000 0 25
VEGFR2 homodimer/VEGFA homodimer/Src 0.034 0.036 -10000 0 -0.2 11 11
IGF-1R heterotetramer 0.02 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.048 -10000 0 -0.32 10 10
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
IGF1 0.014 0.052 0.32 1 -0.32 11 12
RAC1 0.019 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.04 0.05 0.22 21 -0.22 6 27
apoptosis 0.021 0.002 -10000 0 -10000 0 0
CD47 0.02 0.022 -10000 0 -0.32 2 2
alphaV/beta3 Integrin/CD47 0.046 0.049 0.22 23 -0.2 7 30
VCL 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.026 0.082 0.23 20 -0.21 43 63
CSF1 0.018 0.027 -10000 0 -0.32 3 3
PIK3C2A -0.06 0.16 0.18 6 -0.4 84 90
PI4 Kinase/Pyk2 -0.053 0.073 0.18 1 -0.28 17 18
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.059 0.23 22 -0.19 16 38
FAK1/Vinculin -0.033 0.11 0.31 10 -0.3 23 33
alphaV beta3/Integrin/ppsTEM5 0.041 0.05 0.22 21 -0.22 6 27
RHOA 0.021 0.004 -10000 0 -10000 0 0
VTN -0.032 0.14 0.32 7 -0.32 85 92
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
F11R -0.035 0.063 -10000 0 -0.23 49 49
alphaV/beta3 Integrin/Lactadherin 0.047 0.046 0.22 23 -0.2 5 28
alphaV/beta3 Integrin/TGFBR2 0.042 0.056 0.22 23 -0.2 14 37
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.027 -10000 0 -0.18 4 4
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.042 0.045 0.21 22 -0.2 5 27
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.033 0.32 1 -0.32 4 5
alphaV/beta3 Integrin/Pyk2 0.031 0.058 0.21 20 -0.18 15 35
SDC1 0.021 0.002 -10000 0 -10000 0 0
VAV3 -0.02 0.045 0.17 21 -0.32 1 22
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.015 -10000 0 -0.32 1 1
FAK1/Paxillin -0.034 0.11 0.3 9 -0.3 24 33
cell migration -0.035 0.1 0.27 12 -0.28 22 34
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.004 0.1 0.28 1 -0.19 88 89
SPP1 0.23 0.14 0.32 351 -10000 0 351
KDR 0.013 0.052 -10000 0 -0.32 12 12
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.002 -10000 0 -10000 0 0
COL4A3 -0.069 0.15 -10000 0 -0.32 133 133
angiogenesis -0.055 0.16 0.28 2 -0.43 61 63
Rac1/GTP -0.02 0.041 0.16 18 -0.28 1 19
EDIL3 -0.007 0.096 0.32 1 -0.32 42 43
cell proliferation 0.041 0.056 0.22 23 -0.2 14 37
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.023 0.07 -10000 0 -0.24 25 25
NT3 (dimer)/TRKC -0.025 0.11 0.23 2 -0.25 102 104
NT3 (dimer)/TRKB -0.044 0.13 0.3 7 -0.21 179 186
SHC/Grb2/SOS1/GAB1/PI3K 0.008 0.027 -10000 0 -0.19 2 2
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 258 258
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
NTRK1 0.01 0.056 0.32 1 -0.32 13 14
NTRK2 -0.095 0.17 0.32 3 -0.32 173 176
NTRK3 -0.045 0.14 -10000 0 -0.32 97 97
NT-4/5 (dimer)/TRKB -0.047 0.13 0.28 6 -0.21 185 191
neuron apoptosis 0.14 0.16 0.4 111 -10000 0 111
SHC 2-3/Grb2 -0.16 0.18 -10000 0 -0.43 112 112
SHC1 0.019 0.016 0.32 1 -10000 0 1
SHC2 -0.11 0.15 -10000 0 -0.43 64 64
SHC3 -0.16 0.21 -10000 0 -0.52 110 110
STAT3 (dimer) 0.018 0.038 -10000 0 -0.3 7 7
NT3 (dimer)/TRKA 0.023 0.069 0.27 7 -0.2 32 39
RIN/GDP -0.02 0.073 0.22 3 -0.23 14 17
GIPC1 0.02 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
DNAJA3 -0.014 0.056 0.18 5 -0.21 23 28
RIN/GTP 0.013 0.013 0.22 2 -10000 0 2
CCND1 -0.022 0.067 -10000 0 -0.59 7 7
MAGED1 0.021 0.014 0.32 1 -10000 0 1
PTPN11 0.021 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.076 -10000 0 -0.32 26 26
SHC/GRB2/SOS1 0.035 0.017 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.025 0.071 0.22 16 -0.2 34 50
TRKA/NEDD4-2 0.019 0.043 0.23 1 -0.23 13 14
ELMO1 0.018 0.022 -10000 0 -0.32 2 2
RhoG/GTP/ELMO1/DOCK1 0.025 0.016 -10000 0 -0.19 2 2
NGF 0.025 0.085 0.32 23 -0.32 13 36
HRAS 0.021 0.004 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
GAB2 0.017 0.034 -10000 0 -0.32 5 5
RIT2 0.017 0.02 0.32 2 -10000 0 2
RIT1 0.018 0.008 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
DNM1 0.025 0.035 0.32 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.011 0.063 0.18 2 -0.21 25 27
mol:GDP -0.034 0.1 0.27 3 -0.32 18 21
NGF (dimer) 0.025 0.085 0.32 23 -0.32 13 36
RhoG/GDP 0.014 0.015 -10000 0 -0.22 2 2
RIT1/GDP -0.025 0.065 0.22 1 -0.23 13 14
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
BDNF (dimer)/TRKB -0.14 0.15 0.22 1 -0.24 329 330
KIDINS220/CRKL/C3G 0.029 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.026 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.039 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.044 0.025 -10000 0 -0.18 1 1
RIT1/GTP 0.013 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.006 0.074 0.32 2 -0.32 23 25
RAP1/GDP -0.023 0.061 -10000 0 -0.19 16 16
KIDINS220/CRKL 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.15 0.17 -10000 0 -0.32 258 258
ubiquitin-dependent protein catabolic process 0.029 0.06 0.22 17 -0.19 22 39
Schwann cell development -0.037 0.025 -10000 0 -10000 0 0
EHD4 0.02 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.048 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.004 0.049 -10000 0 -0.23 6 6
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.14 -10000 0 -0.24 310 310
ABL1 0.021 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.076 0.1 -10000 0 -0.41 27 27
STAT3 0.018 0.038 -10000 0 -0.3 7 7
axon guidance -0.16 0.12 -10000 0 -0.24 305 305
MAPK3 -0.012 0.073 0.18 40 -0.2 26 66
MAPK1 -0.011 0.071 0.18 38 -0.19 23 61
CDC42/GDP -0.021 0.074 0.22 3 -0.23 12 15
NTF3 0.006 0.074 0.32 2 -0.32 23 25
NTF4 0.003 0.076 -10000 0 -0.32 26 26
NGF (dimer)/TRKA/FAIM 0.033 0.061 0.22 19 -0.19 21 40
PI3K 0.029 0.014 -10000 0 -0.23 1 1
FRS3 0.02 0.004 -10000 0 -10000 0 0
FAIM 0.021 0.003 -10000 0 -10000 0 0
GAB1 0.02 0.022 -10000 0 -0.32 2 2
RASGRF1 -0.059 0.088 0.15 1 -0.26 37 38
SOS1 0.021 0.003 -10000 0 -10000 0 0
MCF2L -0.052 0.081 0.2 2 -0.21 93 95
RGS19 0.019 0.006 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
RAS family/GTP 0 0.076 0.31 2 -0.39 4 6
Rac1/GDP -0.023 0.07 -10000 0 -0.23 15 15
NGF (dimer)/TRKA/GRIT 0.022 0.057 0.21 19 -0.18 22 41
neuron projection morphogenesis 0.005 0.1 -10000 0 -0.88 3 3
NGF (dimer)/TRKA/NEDD4-2 0.029 0.061 0.22 17 -0.19 22 39
MAP2K1 0.012 0.091 0.2 87 -10000 0 87
NGFR 0.019 0.058 0.32 7 -0.32 9 16
NGF (dimer)/TRKA/GIPC/GAIP 0.001 0.061 0.18 7 -0.22 19 26
RAS family/GTP/PI3K 0.01 0.02 0.15 1 -0.17 5 6
FRS2 family/SHP2/GRB2/SOS1 0.054 0.025 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
MAPKKK cascade -0.065 0.18 -10000 0 -0.56 54 54
RASA1 0.02 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.021 0.043 0.23 1 -0.23 13 14
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.14 0.23 2 -0.22 329 331
NGF (dimer)/TRKA/p62/Atypical PKCs 0.043 0.063 0.22 16 -0.18 21 37
MATK 0.009 0.06 -10000 0 -0.32 16 16
NEDD4L 0.019 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.029 0.045 -10000 0 -0.17 19 19
NGF (dimer)/TRKA 0 0.061 0.18 5 -0.21 25 30
Rac1/GTP -0.061 0.069 -10000 0 -0.21 60 60
FRS2 family/SHP2/CRK family 0.049 0.029 -10000 0 -10000 0 0
LPA4-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
ADCY4 -0.02 0.037 -10000 0 -0.2 21 21
ADCY5 -0.033 0.063 0.091 8 -0.2 61 69
ADCY6 -0.015 0.017 -10000 0 -0.19 5 5
ADCY7 -0.015 0.018 -10000 0 -0.19 5 5
ADCY1 -0.012 0.027 0.16 6 -0.19 5 11
ADCY2 -0.02 0.051 0.12 12 -0.19 36 48
ADCY3 -0.015 0.017 -10000 0 -0.19 5 5
ADCY8 -0.071 0.085 0.091 1 -0.19 172 173
PRKCE -0.011 0.021 -10000 0 -0.22 5 5
ADCY9 -0.017 0.028 -10000 0 -0.19 13 13
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.005 0.1 0.21 49 -0.24 12 61
Arf6 signaling events

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
CENTA1/KIF3B 0.021 0.015 -10000 0 -0.17 1 1
ARNO/beta Arrestin1-2 -0.052 0.17 -10000 0 -0.82 19 19
EGFR 0.014 0.045 0.32 1 -0.32 8 9
EPHA2 0.014 0.048 -10000 0 -0.32 10 10
USP6 0.02 0.006 -10000 0 -10000 0 0
IQSEC1 0.02 0.016 -10000 0 -0.32 1 1
EGFR/EGFR/EGF/EGF 0.051 0.087 0.24 75 -0.23 12 87
ARRB2 0.017 0.038 0.14 42 -10000 0 42
mol:GTP 0.005 0.039 0.14 11 -0.15 7 18
ARRB1 0.017 0.034 -10000 0 -0.32 5 5
FBXO8 0.021 0.004 -10000 0 -10000 0 0
TSHR 0.052 0.093 0.32 54 -10000 0 54
EGF 0.071 0.12 0.32 91 -0.32 5 96
somatostatin receptor activity 0 0 0.001 13 -0.001 63 76
ARAP2 0.011 0.056 -10000 0 -0.32 14 14
mol:GDP -0.065 0.14 0.18 7 -0.29 105 112
mol:PI-3-4-5-P3 0 0 0.001 11 -0.001 28 39
ITGA2B -0.008 0.1 0.32 5 -0.32 47 52
ARF6 0.02 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.041 0.034 -10000 0 -0.18 7 7
ADAP1 0.018 0.017 -10000 0 -0.32 1 1
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET 0.013 0.078 0.23 10 -0.23 40 50
PXN 0.021 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.047 0.12 0.24 11 -0.26 63 74
EGFR/EGFR/EGF/EGF/ARFGEP100 0.055 0.077 0.23 67 -0.2 11 78
ADRB2 -0.11 0.17 -10000 0 -0.32 187 187
receptor agonist activity 0 0 0 4 0 61 65
actin filament binding 0 0 0.001 9 0 83 92
SRC 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
EFA6/PI-4-5-P2 0 0 0.001 15 -0.001 41 56
ARF6/GDP -0.037 0.14 0.29 2 -0.39 49 51
ARF6/GDP/GULP/ACAP1 -0.048 0.14 -10000 0 -0.33 65 65
alphaIIb/beta3 Integrin/paxillin/GIT1 0.037 0.083 0.23 26 -0.18 50 76
ACAP1 0.019 0.016 -10000 0 -0.32 1 1
ACAP2 0.02 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.032 0.071 0.25 44 -10000 0 44
EFNA1 0.017 0.017 -10000 0 -0.32 1 1
HGF 0.006 0.078 0.32 4 -0.32 24 28
CYTH3 -0.007 0.015 0.21 2 -10000 0 2
CYTH2 -0.023 0.19 -10000 0 -1 19 19
NCK1 0.021 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 12 0 45 57
endosomal lumen acidification 0 0 0 34 0 30 64
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.018 0.031 -10000 0 -0.32 4 4
GNAQ/ARNO -0.009 0.18 -10000 0 -0.92 19 19
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 6 0 11 17
MET 0.011 0.072 0.32 6 -0.32 18 24
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 45 55
GNA11 0.019 0.016 -10000 0 -0.32 1 1
LHCGR 0.044 0.086 0.32 44 -10000 0 44
AGTR1 -0.088 0.16 -10000 0 -0.32 161 161
desensitization of G-protein coupled receptor protein signaling pathway 0.032 0.071 0.25 44 -10000 0 44
IPCEF1/ARNO 0.017 0.18 -10000 0 -0.84 19 19
alphaIIb/beta3 Integrin 0.015 0.095 0.23 28 -0.23 51 79
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.017 0.19 1 -10000 0 1
AES 0.021 0.014 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.029 0.01 -10000 0 -10000 0 0
SMAD4 0.019 0.007 -10000 0 -10000 0 0
DKK2 -0.049 0.14 -10000 0 -0.32 104 104
TLE1 0.022 0.014 -10000 0 -10000 0 0
MACF1 0.019 0.031 -10000 0 -0.32 4 4
CTNNB1 0.078 0.11 0.3 22 -0.33 9 31
WIF1 -0.21 0.16 -10000 0 -0.32 336 336
beta catenin/RanBP3 0.045 0.11 0.44 20 -0.35 3 23
KREMEN2 0.095 0.13 0.32 126 -10000 0 126
DKK1 0.037 0.16 0.32 82 -0.32 48 130
beta catenin/beta TrCP1 0.08 0.1 0.3 17 -0.31 8 25
FZD1 0.021 0.005 -10000 0 -10000 0 0
AXIN2 -0.028 0.25 0.59 19 -1.2 18 37
AXIN1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.022 0.014 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin 0.027 0.096 -10000 0 -0.66 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.017 0.18 0.32 1 -0.57 31 32
Axin1/APC/GSK3 0.05 0.073 0.23 21 -0.3 6 27
Axin1/APC/GSK3/beta catenin/Macf1 0.033 0.084 0.25 16 -0.35 10 26
HNF1A 0.081 0.12 0.32 101 -0.32 1 102
CTBP1 0.023 0.015 0.18 1 -10000 0 1
MYC 0.072 0.23 0.56 81 -1.3 2 83
RANBP3 0.02 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.027 0.12 0.22 80 -0.17 98 178
NKD1 -0.016 0.11 0.32 4 -0.32 57 61
TCF4 0.019 0.026 0.17 1 -0.32 2 3
TCF3 0.022 0.015 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.051 0.029 0.23 7 -10000 0 7
Ran/GTP 0.016 0.009 0.22 1 -10000 0 1
CtBP/CBP/TCF/TLE1/AES 0.008 0.12 0.43 16 -0.47 10 26
LEF1 0.024 0.02 0.25 2 -10000 0 2
DVL1 0.039 0.055 -10000 0 -0.31 5 5
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.025 0.16 -10000 0 -0.59 23 23
DKK1/LRP6/Kremen 2 0.084 0.13 0.25 156 -0.17 46 202
LRP6 0.021 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.016 -10000 0 -10000 0 0
NLK 0.019 0.011 -10000 0 -10000 0 0
CCND1 -0.004 0.19 0.58 21 -1.3 7 28
WNT1 0.028 0.044 0.32 11 -10000 0 11
GSK3A 0.021 0.005 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D 0.048 0.077 0.24 43 -0.24 6 49
APC -0.003 0.061 0.19 43 -10000 0 43
WNT1/LRP6/FZD1 0.094 0.088 0.22 28 -0.19 3 31
CREBBP 0.023 0.015 0.18 1 -10000 0 1
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.023 0.06 0.42 2 -0.57 3 5
oxygen homeostasis 0.009 0.014 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.071 0.098 0.29 9 -0.3 5 14
EPO 0.098 0.15 0.4 52 -0.47 1 53
FIH (dimer) 0.025 0.021 -10000 0 -10000 0 0
APEX1 0.028 0.026 -10000 0 -10000 0 0
SERPINE1 0.11 0.16 0.41 62 -0.5 1 63
FLT1 -0.007 0.13 -10000 0 -0.53 22 22
ADORA2A 0.096 0.15 0.36 74 -0.49 1 75
germ cell development 0.11 0.17 0.39 80 -0.41 3 83
SLC11A2 0.11 0.15 0.4 63 -0.5 1 64
BHLHE40 0.11 0.16 0.4 65 -0.5 1 66
HIF1AN 0.025 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.083 0.12 0.34 33 -0.33 2 35
ETS1 0.019 0.025 -10000 0 -0.15 7 7
CITED2 -0.017 0.15 -10000 0 -0.54 32 32
KDR -0.008 0.16 -10000 0 -0.76 20 20
PGK1 0.11 0.16 0.4 65 -0.5 1 66
SIRT1 0.021 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.14 0.19 0.53 48 -0.57 1 49
EPAS1 0.051 0.097 0.26 41 -0.29 5 46
SP1 0.023 0.01 -10000 0 -10000 0 0
ABCG2 0.096 0.18 0.4 65 -0.44 10 75
EFNA1 0.093 0.15 0.4 51 -0.5 1 52
FXN 0.097 0.15 0.36 72 -0.49 1 73
POU5F1 0.11 0.17 0.41 68 -0.42 3 71
neuron apoptosis -0.13 0.19 0.55 1 -0.52 48 49
EP300 0.02 0.005 -10000 0 -10000 0 0
EGLN3 0.089 0.13 0.34 110 -0.32 1 111
EGLN2 0.026 0.022 -10000 0 -10000 0 0
EGLN1 0.024 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.037 0.016 -10000 0 -10000 0 0
VHL 0.02 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.026 -10000 0 -10000 0 0
SLC2A1 0.14 0.18 0.41 114 -0.49 1 115
TWIST1 0.11 0.17 0.42 80 -10000 0 80
ELK1 0.021 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.089 0.12 0.36 31 -0.34 2 33
VEGFA 0.11 0.16 0.4 63 -0.5 1 64
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.006 0.097 -10000 0 -0.41 22 22
HDAC1 0.021 0.006 -10000 0 -10000 0 0
AES 0.02 0.006 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
DTX1 0.022 0.019 0.32 2 -10000 0 2
LRP6/FZD1 0.028 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.005 -10000 0 -10000 0 0
AP1 -0.022 0.084 -10000 0 -0.23 59 59
NCSTN 0.019 0.007 -10000 0 -10000 0 0
ADAM10 0.021 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.1 -10000 0 -0.62 9 9
NICD/RBPSUH 0.016 0.1 -10000 0 -0.41 22 22
WIF1 -0.21 0.16 -10000 0 -0.32 336 336
NOTCH1 -0.003 0.087 -10000 0 -0.43 20 20
PSENEN 0.02 0.005 -10000 0 -10000 0 0
KREMEN2 0.095 0.13 0.32 126 -10000 0 126
DKK1 0.037 0.16 0.32 82 -0.32 48 130
beta catenin/beta TrCP1 0.012 0.075 0.3 1 -0.28 5 6
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
AXIN1 0 0.071 -10000 0 -0.42 7 7
CtBP/CBP/TCF1/TLE1/AES 0.022 0.055 0.26 2 -0.19 1 3
PSEN1 0.021 0.004 -10000 0 -10000 0 0
FOS 0.002 0.077 -10000 0 -0.32 27 27
JUN 0.019 0.027 -10000 0 -0.32 3 3
MAP3K7 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.008 0.075 0.27 2 -0.28 6 8
MAPK3 0.021 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.027 0.12 0.22 80 -0.17 98 178
HNF1A 0.079 0.12 0.32 100 -0.32 1 101
CTBP1 0.021 0.005 -10000 0 -10000 0 0
MYC 0.008 0.079 -10000 0 -1.2 2 2
NKD1 -0.016 0.11 0.32 4 -0.32 57 61
FZD1 0.02 0.005 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.018 0.1 -10000 0 -0.42 21 21
apoptosis -0.022 0.084 -10000 0 -0.23 59 59
Delta 1/NOTCHprecursor 0.013 0.1 -10000 0 -0.41 22 22
DLL1 0.015 0.04 -10000 0 -0.32 7 7
PPARD 0.016 0.041 -10000 0 -0.85 1 1
Gamma Secretase 0.047 0.031 -10000 0 -0.17 1 1
APC -0.009 0.093 -10000 0 -0.42 17 17
DVL1 -0.033 0.073 -10000 0 -0.3 29 29
CSNK2A1 0.02 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.083 0.13 0.25 156 -0.17 46 202
LRP6 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.006 -10000 0 -10000 0 0
NLK 0.007 0.006 -10000 0 -10000 0 0
CCND1 -0.002 0.15 -10000 0 -1.1 9 9
WNT1 0.027 0.044 0.32 11 -10000 0 11
Axin1/APC/beta catenin 0.004 0.11 0.3 7 -0.43 12 19
DKK2 -0.049 0.14 -10000 0 -0.32 104 104
NOTCH1 precursor/DVL1 -0.032 0.11 -10000 0 -0.45 25 25
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.097 -10000 0 -0.42 21 21
PPP2R5D 0.01 0.073 0.21 2 -0.32 8 10
MAPK1 0.02 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.093 0.11 0.23 3 -0.18 311 314
RBPJ 0.021 0.004 -10000 0 -10000 0 0
CREBBP 0.021 0.005 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.026 0.083 -10000 0 -0.33 1 1
SMARCC2 0.021 0.009 -10000 0 -0.17 1 1
SMARCC1 0.021 0.007 -10000 0 -10000 0 0
TBX21 -0.039 0.16 0.37 7 -0.46 44 51
SUMO2 0.019 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.002 -10000 0 -10000 0 0
FKBP4 0.02 0.005 -10000 0 -10000 0 0
FKBP5 0.021 0.004 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.047 0.11 0.28 32 -10000 0 32
PRL -0.019 0.11 0.45 2 -0.57 1 3
cortisol/GR alpha (dimer)/TIF2 0.059 0.21 0.49 56 -0.35 9 65
RELA -0.038 0.1 -10000 0 -0.21 85 85
FGG 0.026 0.28 0.51 73 -0.4 69 142
GR beta/TIF2 0.034 0.11 0.28 33 -0.24 2 35
IFNG -0.055 0.26 0.42 14 -0.65 47 61
apoptosis 0.011 0.13 0.47 12 -0.48 8 20
CREB1 0.04 0.046 0.2 1 -10000 0 1
histone acetylation -0.071 0.12 -10000 0 -0.32 52 52
BGLAP -0.018 0.1 -10000 0 -0.36 9 9
GR/PKAc 0.049 0.11 0.29 27 -10000 0 27
NF kappa B1 p50/RelA -0.067 0.18 0.29 1 -0.32 136 137
SMARCD1 0.021 0.006 -10000 0 -10000 0 0
MDM2 0.035 0.086 0.21 60 -10000 0 60
GATA3 0.022 0.021 0.33 1 -0.32 1 2
AKT1 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.13 0.27 -10000 0 -0.87 49 49
GSK3B 0.019 0.012 -10000 0 -10000 0 0
NR1I3 0.024 0.13 0.48 9 -0.5 2 11
CSN2 0.052 0.18 0.37 61 -0.31 12 73
BRG1/BAF155/BAF170/BAF60A 0.049 0.027 -10000 0 -0.26 2 2
NFATC1 0.018 0.027 -10000 0 -0.32 3 3
POU2F1 0.022 0.017 -10000 0 -10000 0 0
CDKN1A -0.006 0.068 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 9 -0.32 1 10
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.056 0.1 0.28 26 -10000 0 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.01 0.19 0.46 9 -0.68 26 35
JUN -0.013 0.18 0.33 32 -0.38 38 70
IL4 -0.034 0.12 -10000 0 -0.49 11 11
CDK5R1 0.027 0.049 0.32 13 -10000 0 13
PRKACA 0.02 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.041 0.065 0.17 3 -0.23 26 29
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.051 0.1 0.28 26 -10000 0 26
cortisol/GR alpha (monomer) 0.086 0.27 0.59 69 -0.4 11 80
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.012 0.11 0.23 12 -0.3 22 34
AP-1/NFAT1-c-4 -0.01 0.27 0.42 37 -0.47 68 105
AFP -0.014 0.17 0.44 8 -0.49 3 11
SUV420H1 0.021 0.004 -10000 0 -10000 0 0
IRF1 0.052 0.14 0.39 26 -10000 0 26
TP53 0.021 0.042 -10000 0 -0.91 1 1
PPP5C 0.02 0.005 -10000 0 -10000 0 0
KRT17 -0.061 0.3 0.44 24 -0.74 51 75
KRT14 0.037 0.18 0.4 16 -0.43 3 19
TBP 0.021 0.007 -10000 0 -10000 0 0
CREBBP -0.019 0.07 -10000 0 -0.27 1 1
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.023 0.023 -10000 0 -10000 0 0
AP-1 -0.01 0.27 0.42 37 -0.47 69 106
MAPK14 0.019 0.012 -10000 0 -10000 0 0
MAPK10 -0.017 0.11 -10000 0 -0.32 55 55
MAPK11 0.017 0.025 -10000 0 -0.32 2 2
KRT5 -0.2 0.45 0.45 17 -0.91 137 154
interleukin-1 receptor activity 0.005 0.021 -10000 0 -10000 0 0
NCOA1 0.022 0.003 -10000 0 -10000 0 0
STAT1 0.023 0.002 -10000 0 -10000 0 0
CGA -0.001 0.13 0.34 15 -0.37 13 28
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.005 0.17 0.44 39 -0.32 12 51
MAPK3 0.02 0.012 -10000 0 -10000 0 0
MAPK1 0.019 0.012 -10000 0 -10000 0 0
ICAM1 -0.1 0.21 -10000 0 -0.6 44 44
NFKB1 -0.039 0.1 0.18 1 -0.21 93 94
MAPK8 -0.019 0.16 0.3 15 -0.36 44 59
MAPK9 0.019 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.01 0.14 0.47 12 -0.5 8 20
BAX -0.009 0.058 -10000 0 -10000 0 0
POMC -0.12 0.28 -10000 0 -0.84 42 42
EP300 -0.019 0.071 -10000 0 -0.27 1 1
cortisol/GR alpha (dimer)/p53 0.071 0.22 0.53 52 -0.38 2 54
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.074 0.2 42 -10000 0 42
SGK1 -0.027 0.11 -10000 0 -0.77 3 3
IL13 -0.051 0.2 -10000 0 -0.58 24 24
IL6 -0.21 0.37 -10000 0 -0.81 127 127
PRKACG 0.017 0.004 -10000 0 -10000 0 0
IL5 -0.049 0.17 -10000 0 -0.62 10 10
IL2 -0.06 0.23 0.38 6 -0.59 39 45
CDK5 0.019 0.01 -10000 0 -10000 0 0
PRKACB 0.021 0.014 0.32 1 -10000 0 1
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 -0.09 0.2 0.35 2 -0.51 51 53
CDK5R1/CDK5 0.033 0.034 0.24 12 -10000 0 12
NF kappa B1 p50/RelA/PKAc -0.029 0.15 -10000 0 -0.28 77 77
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.07 0.21 0.48 61 -0.34 6 67
SMARCA4 0.02 0.016 -10000 0 -0.32 1 1
chromatin remodeling 0.042 0.13 0.35 35 -10000 0 35
NF kappa B1 p50/RelA/Cbp -0.073 0.16 0.37 1 -0.36 68 69
JUN (dimer) -0.013 0.18 0.33 32 -0.39 37 69
YWHAH 0.02 0.004 -10000 0 -10000 0 0
VIPR1 -0.25 0.34 -10000 0 -0.67 197 197
NR3C1 0.056 0.17 0.4 56 -0.26 1 57
NR4A1 -0.058 0.16 -10000 0 -0.35 111 111
TIF2/SUV420H1 0.025 0.027 -10000 0 -0.23 5 5
MAPKKK cascade 0.011 0.13 0.47 12 -0.48 8 20
cortisol/GR alpha (dimer)/Src-1 0.079 0.23 0.5 67 -0.35 9 76
PBX1 0.014 0.055 -10000 0 -0.32 12 12
POU1F1 0.021 0.023 0.43 1 -10000 0 1
SELE -0.18 0.35 -10000 0 -0.84 104 104
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.042 0.13 0.35 35 -10000 0 35
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.07 0.21 0.48 61 -0.34 6 67
mol:cortisol 0.049 0.15 0.34 72 -0.21 12 84
MMP1 0.17 0.2 0.38 76 -0.73 8 84
Reelin signaling pathway

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
CDK5R1/CDK5 0.034 0.032 0.23 12 -10000 0 12
VLDLR 0.014 0.043 -10000 0 -0.32 8 8
CRKL 0.02 0.005 -10000 0 -10000 0 0
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
ITGA3 0.017 0.034 -10000 0 -0.32 5 5
RELN/VLDLR/Fyn 0.007 0.083 0.22 5 -0.2 66 71
MAPK8IP1/MKK7/MAP3K11/JNK1 0.049 0.029 -10000 0 -0.17 1 1
AKT1 -0.034 0.074 0.2 3 -0.21 58 61
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
DAB1 0.023 0.036 0.32 7 -10000 0 7
RELN/LRP8/DAB1 0.018 0.079 0.22 18 -0.17 61 79
LRPAP1/LRP8 0.034 0.028 0.23 9 -10000 0 9
RELN/LRP8/DAB1/Fyn 0.022 0.078 0.22 16 -0.17 60 76
DAB1/alpha3/beta1 Integrin 0.014 0.077 0.27 1 -0.18 56 57
long-term memory 0.009 0.1 0.24 16 -0.18 86 102
DAB1/LIS1 0.022 0.083 0.35 1 -0.18 57 58
DAB1/CRLK/C3G 0.014 0.075 0.27 1 -0.18 54 55
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.026 0.084 0.35 1 -0.17 58 59
ARHGEF2 0.018 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.009 0.14 0.32 42 -0.32 53 95
CDK5R1 0.028 0.048 0.32 13 -10000 0 13
RELN -0.018 0.12 0.32 6 -0.32 62 68
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RELN/LRP8/Fyn 0.013 0.084 0.22 13 -0.19 63 76
GRIN2A/RELN/LRP8/DAB1/Fyn 0.02 0.11 0.23 42 -0.18 90 132
MAPK8 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.011 0.079 0.23 10 -0.18 64 74
ITGB1 0.021 0.004 -10000 0 -10000 0 0
MAP1B -0.026 0.075 0.17 27 -0.19 55 82
RELN/LRP8 0.016 0.084 0.22 13 -0.19 62 75
GRIN2B/RELN/LRP8/DAB1/Fyn 0.029 0.088 0.26 20 -0.17 59 79
PI3K 0.029 0.014 -10000 0 -0.23 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.027 0.027 -10000 0 -0.23 5 5
RAP1A -0.028 0.078 0.26 7 -0.28 3 10
PAFAH1B1 0.019 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.021 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.029 0.01 -10000 0 -10000 0 0
GRIN2B 0.023 0.041 0.32 9 -10000 0 9
NCK2 0.021 0.002 -10000 0 -10000 0 0
neuron differentiation -0.007 0.073 0.21 3 -0.26 17 20
neuron adhesion -0.03 0.089 0.31 12 -0.28 4 16
LRP8 0.027 0.042 0.32 10 -10000 0 10
GSK3B -0.036 0.071 0.18 3 -0.21 59 62
RELN/VLDLR/DAB1/Fyn 0.016 0.078 0.23 8 -0.17 63 71
MAP3K11 0.02 0.016 -10000 0 -0.32 1 1
RELN/VLDLR/DAB1/P13K -0.016 0.081 0.18 3 -0.22 64 67
CDK5 0.02 0.005 -10000 0 -10000 0 0
MAPT -0.003 0.12 0.78 9 -0.29 19 28
neuron migration -0.038 0.099 0.23 13 -0.27 53 66
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.069 0.21 3 -0.25 14 17
RELN/VLDLR 0.02 0.086 0.23 12 -0.18 65 77
Aurora A signaling

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
Aurora A/GADD45A -0.006 0.056 -10000 0 -10000 0 0
BIRC5 0.18 0.15 0.32 275 -10000 0 275
NFKBIA 0.003 0.079 0.28 29 -10000 0 29
CPEB1 -0.025 0.12 0.32 2 -0.32 70 72
AKT1 -0.013 0.046 0.28 3 -10000 0 3
NDEL1 0.019 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.004 0.051 0.24 1 -10000 0 1
NDEL1/TACC3 0.002 0.055 0.28 1 -10000 0 1
GADD45A 0.021 0.003 -10000 0 -10000 0 0
GSK3B -0.015 0.031 -10000 0 -10000 0 0
PAK1/Aurora A -0.006 0.055 -10000 0 -10000 0 0
MDM2 0.02 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.082 0.096 0.17 275 -10000 0 275
TP53 -0.003 0.054 0.21 1 -0.22 19 20
DLG7 -0.011 0.037 0.15 2 -10000 0 2
AURKAIP1 0.02 0.016 -10000 0 -0.32 1 1
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.002 0.059 0.3 1 -10000 0 1
G2/M transition of mitotic cell cycle -0.004 0.05 0.24 1 -10000 0 1
AURKA -0.005 0.055 0.19 2 -10000 0 2
AURKB 0.096 0.087 0.19 223 -10000 0 223
CDC25B -0.002 0.043 0.15 1 -0.23 4 5
G2/M transition checkpoint -0.013 0.038 -10000 0 -0.13 4 4
mRNA polyadenylation -0.028 0.078 0.35 1 -0.2 53 54
Aurora A/CPEB -0.028 0.078 0.36 1 -0.2 53 54
Aurora A/TACC1/TRAP/chTOG 0.002 0.066 -10000 0 -0.22 7 7
BRCA1 0.021 0.014 0.32 1 -10000 0 1
centrosome duplication -0.006 0.055 -10000 0 -10000 0 0
regulation of centrosome cycle 0.001 0.054 0.27 1 -10000 0 1
spindle assembly 0.001 0.065 -10000 0 -0.21 7 7
TDRD7 0.021 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.11 0.098 0.24 104 -10000 0 104
CENPA 0.11 0.09 0.19 259 -10000 0 259
Aurora A/PP2A -0.006 0.055 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.007 0.047 0.19 3 -0.18 3 6
negative regulation of DNA binding -0.003 0.054 0.21 1 -0.22 19 20
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.029 0.009 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.013 0.039 -10000 0 -0.13 4 4
mitotic prometaphase -0.014 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.055 0.19 2 -10000 0 2
TACC1 0.008 0.06 -10000 0 -0.32 16 16
TACC3 0.022 0.019 0.32 2 -10000 0 2
Aurora A/Antizyme1 0.002 0.058 -10000 0 -0.17 1 1
Aurora A/RasGAP -0.005 0.054 -10000 0 -10000 0 0
OAZ1 0.02 0.006 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.015 0.031 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.038 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.082 0.096 0.17 275 -10000 0 275
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.05 0.082 0.19 90 -10000 0 90
PAK1 0.02 0.005 -10000 0 -10000 0 0
CKAP5 0.021 0.003 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.036 0.077 0.16 133 -10000 0 133
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.016 0.075 0.23 15 -0.23 35 50
STXBP1 0.019 0.027 -10000 0 -0.32 3 3
ACh/CHRNA1 0.028 0.067 0.24 34 -0.15 11 45
RAB3GAP2/RIMS1/UNC13B 0.025 0.066 0.22 13 -0.2 32 45
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.006 0.1 0.32 17 -0.32 34 51
mol:ACh 0.004 0.031 0.08 30 -0.11 10 40
RAB3GAP2 0.019 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.025 0.068 0.18 10 -0.15 30 40
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.028 0.067 0.24 34 -0.15 11 45
UNC13B 0.02 0.016 -10000 0 -0.32 1 1
CHRNA1 0.034 0.089 0.32 33 -0.32 9 42
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.031 0.071 0.25 39 -0.14 8 47
SNAP25 0.004 0.032 0.12 20 -0.22 5 25
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.039 0.091 0.32 39 -0.32 7 46
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.045 0.054 0.13 131 -0.19 3 134
STX1A/SNAP25 fragment 1/VAMP2 0.025 0.068 0.18 10 -0.15 30 40
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.012 0.28 0.59 20 -0.7 5 25
CRP 0.028 0.29 0.61 30 -0.73 6 36
cell cycle arrest 0.001 0.3 0.58 26 -0.63 29 55
TIMP1 0.018 0.26 0.54 25 -0.61 13 38
IL6ST 0.004 0.072 -10000 0 -0.32 20 20
Rac1/GDP -0.004 0.14 0.31 19 -0.32 35 54
AP1 0.057 0.13 0.38 8 -0.46 7 15
GAB2 0.019 0.035 -10000 0 -0.32 5 5
TNFSF11 0.036 0.3 0.59 39 -0.65 10 49
HSP90B1 0.022 0.15 -10000 0 -0.74 9 9
GAB1 0.021 0.022 -10000 0 -0.32 2 2
MAPK14 -0.027 0.1 0.29 3 -0.42 14 17
AKT1 0.013 0.086 0.29 1 -0.64 5 6
FOXO1 0.01 0.083 0.38 1 -0.61 5 6
MAP2K6 -0.018 0.12 0.29 10 -0.3 35 45
mol:GTP 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.001 0.18 0.35 29 -0.37 32 61
MITF -0.008 0.13 0.28 21 -0.3 38 59
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.005 -10000 0 -10000 0 0
A2M -0.12 0.38 -10000 0 -1.2 59 59
CEBPB 0.024 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.019 0.088 0.28 4 -0.38 6 10
STAT3 -0.003 0.31 0.59 26 -0.66 29 55
STAT1 0.023 0.037 -10000 0 -10000 0 0
CEBPD 0.017 0.29 0.59 27 -0.73 10 37
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.015 -10000 0 -0.23 1 1
JUN 0.019 0.027 -10000 0 -0.32 3 3
PIAS3/MITF -0.007 0.13 0.28 14 -0.3 33 47
MAPK11 -0.026 0.1 0.27 3 -0.44 12 15
STAT3 (dimer)/FOXO1 -0.018 0.26 0.54 17 -0.64 14 31
GRB2/SOS1/GAB family 0.005 0.12 0.28 4 -0.31 20 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.021 0.11 0.24 4 -0.26 67 71
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.022 -10000 0 -0.32 2 2
LBP 0.053 0.27 0.56 50 -0.61 9 59
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.013 0.025 -10000 0 -10000 0 0
MYC 0.031 0.29 0.61 30 -0.7 9 39
FGG -0.15 0.51 0.6 31 -0.9 149 180
macrophage differentiation 0.001 0.3 0.58 26 -0.63 29 55
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.002 0.099 0.26 1 -0.22 36 37
JUNB 0.002 0.27 0.55 21 -0.67 12 33
FOS 0.003 0.077 -10000 0 -0.32 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.005 0.14 0.3 23 -0.31 41 64
STAT1/PIAS1 0.013 0.16 0.34 31 -0.32 32 63
GRB2/SOS1/GAB family/SHP2/PI3K 0.016 0.086 -10000 0 -0.66 5 5
STAT3 (dimer) -0.003 0.31 0.59 26 -0.65 29 55
PRKCD 0.017 0.23 0.43 45 -0.44 29 74
IL6R 0.005 0.049 -10000 0 -0.32 9 9
SOCS3 -0.026 0.13 0.34 1 -0.79 7 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.073 0.24 2 -0.19 16 18
Rac1/GTP -0.003 0.16 0.31 27 -0.34 35 62
HCK 0.006 0.069 -10000 0 -0.32 22 22
MAPKKK cascade 0.035 0.11 0.34 1 -0.51 7 8
bone resorption 0.039 0.3 0.58 40 -0.62 10 50
IRF1 0.005 0.28 0.57 21 -0.7 7 28
mol:GDP -0.002 0.13 0.27 28 -0.31 36 64
SOS1 0.023 0.007 -10000 0 -10000 0 0
VAV1 -0.005 0.13 0.28 28 -0.31 36 64
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.023 0.11 -10000 0 -0.43 20 20
PTPN11 0.011 0.1 -10000 0 -0.7 9 9
IL6/IL6RA -0.018 0.1 0.17 1 -0.23 81 82
gp130 (dimer)/TYK2/TYK2/LMO4 0.026 0.063 0.2 1 -0.18 20 21
gp130 (dimer)/JAK2/JAK2/LMO4 0.024 0.061 0.2 1 -0.18 19 20
IL6 -0.049 0.14 -10000 0 -0.32 102 102
PIAS3 0.018 0.008 -10000 0 -10000 0 0
PTPRE -0.002 0.043 -10000 0 -0.24 4 4
PIAS1 0.021 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.021 0.11 0.25 3 -0.26 61 64
LMO4 0.017 0.035 -10000 0 -0.29 1 1
STAT3 (dimer)/PIAS3 -0.026 0.27 0.56 13 -0.63 27 40
MCL1 0.037 0.11 0.43 3 -0.58 4 7
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.045 0.32 1 -0.32 8 9
EGF/EGFR 0.024 0.088 0.18 58 -0.16 70 128
EGF/EGFR dimer/SHC/GRB2/SOS1 0.061 0.073 0.23 56 -0.19 8 64
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.02 0.016 -10000 0 -0.32 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.071 0.12 0.32 91 -0.32 5 96
EGF/EGFR dimer/SHC 0.048 0.074 0.23 57 -0.2 10 67
mol:GDP 0.056 0.068 0.33 1 -0.19 8 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.027 0.12 -10000 0 -0.32 71 71
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP 0.035 0.048 0.22 1 -0.18 7 8
SHC1 0.019 0.016 0.32 1 -10000 0 1
HRAS/GDP 0.049 0.06 0.28 1 -0.19 7 8
FRAP1 -0.013 0.036 0.16 6 -0.18 8 14
EGF/EGFR dimer 0.051 0.087 0.24 75 -0.23 12 87
SOS1 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.006 0.09 -10000 0 -0.23 72 72
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.008 0.08 -10000 0 -0.2 65 65
fibroblast growth factor receptor signaling pathway 0.007 0.079 -10000 0 -0.2 65 65
LAMA1 0.024 0.066 0.32 15 -0.32 7 22
PRNP 0.019 0.022 -10000 0 -0.32 2 2
GPC1/SLIT2 -0.034 0.11 -10000 0 -0.23 127 127
SMAD2 -0.022 0.026 0.17 2 -0.18 8 10
GPC1/PrPc/Cu2+ 0.025 0.02 -10000 0 -0.18 4 4
GPC1/Laminin alpha1 0.029 0.05 0.23 14 -0.22 10 24
TDGF1 0.023 0.073 0.32 17 -0.32 10 27
CRIPTO/GPC1 0.03 0.056 0.23 17 -0.23 13 30
APP/GPC1 0.028 0.022 -10000 0 -0.23 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.034 -10000 0 -0.2 11 11
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.035 0.038 0.22 1 -0.19 12 13
SERPINC1 0.023 0.038 0.32 8 -10000 0 8
FYN -0.018 0.037 0.1 16 -0.21 11 27
FGR -0.03 0.057 0.1 15 -0.2 41 56
positive regulation of MAPKKK cascade -0.019 0.098 0.23 5 -0.32 33 38
SLIT2 -0.066 0.15 -10000 0 -0.32 128 128
GPC1/NRG -0.017 0.097 -10000 0 -0.23 84 84
NRG1 -0.039 0.13 -10000 0 -0.32 84 84
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.037 0.022 -10000 0 -0.2 3 3
LYN -0.017 0.034 -10000 0 -0.2 10 10
mol:Spermine -0.01 0.016 -10000 0 -0.22 3 3
cell growth 0.007 0.079 -10000 0 -0.2 65 65
BMP signaling pathway -0.019 0.027 0.32 3 -10000 0 3
SRC -0.019 0.034 -10000 0 -0.2 11 11
TGFBR1 0.021 0.014 0.32 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.012 0.13 0.32 17 -0.32 63 80
GPC1 0.019 0.027 -10000 0 -0.32 3 3
TGFBR1 (dimer) 0.021 0.014 0.32 1 -10000 0 1
VEGFA 0.021 0.004 -10000 0 -10000 0 0
BLK 0.013 0.076 0.17 81 -0.2 11 92
HCK -0.025 0.047 0.1 15 -0.2 29 44
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
FGFR1 0.018 0.017 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.048 -10000 0 -0.32 10 10
cell death 0.027 0.022 -10000 0 -0.23 3 3
ATIII/GPC1 0.029 0.034 0.23 8 -0.23 3 11
PLA2G2A/GPC1 0.005 0.096 0.23 17 -0.23 63 80
LCK -0.02 0.038 0.17 1 -0.2 14 15
neuron differentiation -0.017 0.097 -10000 0 -0.23 84 84
PrPc/Cu2+ 0.014 0.015 -10000 0 -0.22 2 2
APP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.014 0.048 -10000 0 -0.32 10 10
TCGA08_p53

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
CDKN2A 0.04 0.075 0.16 140 -10000 0 140
TP53 0.011 0.037 -10000 0 -0.12 13 13
Senescence 0.011 0.037 -10000 0 -0.12 12 12
Apoptosis 0.011 0.037 -10000 0 -0.12 12 12
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.023 0.075 0.25 22 -0.19 5 27
MDM4 0.019 0.006 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.02 0.092 0.18 2 -0.23 65 67
FZD6 0.018 0.017 -10000 0 -0.32 1 1
WNT6 0.04 0.073 0.32 32 -10000 0 32
WNT4 0.01 0.078 0.32 6 -0.32 22 28
FZD3 0.018 0.016 0.32 1 -10000 0 1
WNT5A 0.017 0.037 -10000 0 -0.32 6 6
WNT11 -0.02 0.11 0.32 1 -0.32 61 62
Noncanonical Wnt signaling pathway

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
NFATC2 0.008 0.064 -10000 0 -0.32 18 18
GNB1/GNG2 -0.004 0.1 0.23 1 -0.3 22 23
mol:DAG -0.034 0.08 0.19 3 -0.28 20 23
PLCG1 -0.035 0.082 0.19 3 -0.29 20 23
YES1 -0.031 0.085 0.22 5 -0.22 62 67
FZD3 0.018 0.016 0.32 1 -10000 0 1
FZD6 0.018 0.017 -10000 0 -0.32 1 1
G protein -0.002 0.1 0.25 4 -0.29 21 25
MAP3K7 -0.04 0.085 0.18 6 -0.27 32 38
mol:Ca2+ -0.033 0.078 0.18 4 -0.27 20 24
mol:IP3 -0.034 0.08 0.19 3 -0.28 20 23
NLK -0.001 0.087 -10000 0 -0.8 6 6
GNB1 0.021 0.004 -10000 0 -10000 0 0
CAMK2A -0.042 0.092 0.19 5 -0.28 37 42
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.02 0.092 0.18 2 -0.23 65 67
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
GNAS -0.032 0.081 0.16 2 -0.29 23 25
GO:0007205 -0.032 0.08 0.18 3 -0.28 21 24
WNT6 0.04 0.073 0.32 32 -10000 0 32
WNT4 0.01 0.078 0.32 6 -0.32 22 28
NFAT1/CK1 alpha -0.012 0.1 0.27 5 -0.3 21 26
GNG2 0.019 0.022 -10000 0 -0.32 2 2
WNT5A 0.017 0.037 -10000 0 -0.32 6 6
WNT11 -0.02 0.11 0.32 1 -0.32 61 62
CDC42 -0.03 0.085 0.21 6 -0.22 60 66
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.037 0.05 0.23 23 -0.23 5 28
PTK2 -0.022 0.11 -10000 0 -0.34 33 33
positive regulation of JNK cascade -0.023 0.11 -10000 0 -0.29 45 45
CDC42/GDP -0.022 0.15 -10000 0 -0.38 50 50
Rac1/GDP -0.024 0.15 -10000 0 -0.37 50 50
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.023 0.14 -10000 0 -0.35 44 44
nectin-3/I-afadin 0.009 0.069 0.23 1 -0.23 39 40
RAPGEF1 -0.039 0.14 0.28 1 -0.37 69 70
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.045 0.15 -10000 0 -0.4 70 70
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
TLN1 -0.025 0.055 -10000 0 -0.19 36 36
Rap1/GTP -0.028 0.11 -10000 0 -0.28 67 67
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.009 0.069 0.23 1 -0.23 39 40
PVR 0.02 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.04 0.18 -10000 0 -0.43 66 66
MLLT4 0.019 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.037 0.063 0.22 1 -0.17 35 36
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.031 0.031 0.23 10 -10000 0 10
positive regulation of lamellipodium assembly -0.024 0.12 -10000 0 -0.29 68 68
PVRL1 0.026 0.042 0.32 10 -10000 0 10
PVRL3 -0.005 0.093 0.32 1 -0.32 39 40
PVRL2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CDH1 0.019 0.022 -10000 0 -0.32 2 2
CLDN1 0.023 0.055 0.32 10 -0.32 5 15
JAM-A/CLDN1 0.032 0.068 0.23 11 -0.19 31 42
SRC -0.047 0.17 -10000 0 -0.44 72 72
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
nectin-1(dimer)/I-afadin/I-afadin 0.031 0.031 0.23 10 -10000 0 10
FARP2 -0.036 0.18 -10000 0 -0.47 40 40
RAC1 0.019 0.007 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.021 0.062 0.22 1 -0.19 37 38
nectin-1/I-afadin 0.031 0.031 0.23 10 -10000 0 10
nectin-2/I-afadin 0.028 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.025 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.024 0.066 0.22 9 -0.19 36 45
CDC42/GTP/IQGAP1/filamentous actin 0.028 0.006 -10000 0 -10000 0 0
F11R 0.018 0.017 -10000 0 -0.32 1 1
positive regulation of filopodium formation -0.023 0.11 -10000 0 -0.29 45 45
alphaV/beta3 Integrin/Talin -0.025 0.08 0.2 24 -0.3 15 39
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
PIP5K1C -0.021 0.06 -10000 0 -0.2 40 40
VAV2 -0.041 0.19 -10000 0 -0.48 49 49
RAP1/GDP -0.02 0.14 -10000 0 -0.34 62 62
ITGAV 0.021 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.021 0.063 0.22 1 -0.19 38 39
nectin-3(dimer)/I-afadin/I-afadin 0.009 0.069 0.23 1 -0.23 39 40
Rac1/GTP -0.026 0.14 -10000 0 -0.37 49 49
PTPRM -0.014 0.072 -10000 0 -0.22 45 45
E-cadherin/beta catenin/alpha catenin 0.051 0.036 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 -0.007 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.01 0.074 0.21 1 -0.18 67 68
regulation of S phase of mitotic cell cycle -0.017 0.076 0.16 1 -0.2 67 68
GNAO1 0.021 0.035 0.32 4 -0.32 2 6
HRAS 0.019 0.009 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.004 -10000 0 -10000 0 0
PELP1 0.018 0.009 -10000 0 -10000 0 0
AKT1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.039 0.063 0.18 2 -0.26 11 13
T-DHT/AR -0.017 0.082 0.21 1 -0.22 69 70
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.006 27 27
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
mol:GDP -0.051 0.11 0.19 2 -0.31 72 74
cell proliferation -0.056 0.12 0.23 1 -0.42 37 38
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FOS -0.054 0.17 -10000 0 -0.71 30 30
mol:Ca2+ -0.008 0.019 0.051 1 -0.056 49 50
MAPK3 -0.048 0.093 0.24 2 -0.33 32 34
MAPK1 -0.033 0.11 -10000 0 -0.39 29 29
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 0 0.001 -10000 0 -0.004 25 25
cAMP biosynthetic process 0.001 0.018 0.23 1 -10000 0 1
GNG2 0.019 0.022 -10000 0 -0.32 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 25 25
HRAS/GTP 0.007 0.07 -10000 0 -0.16 66 66
actin cytoskeleton reorganization 0.027 0.016 -10000 0 -0.16 1 1
SRC 0.019 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 25 25
PI3K 0.026 0.012 -10000 0 -0.19 1 1
apoptosis 0.041 0.12 0.44 33 -10000 0 33
T-DHT/AR/PELP1 -0.004 0.074 0.2 1 -0.19 69 70
HRAS/GDP -0.052 0.1 0.18 2 -0.3 71 73
CREB1 -0.044 0.12 -10000 0 -0.47 33 33
RAC1-CDC42/GTP 0.033 0.019 -10000 0 -0.16 1 1
AR -0.026 0.12 0.32 1 -0.33 69 70
GNB1 0.021 0.004 -10000 0 -10000 0 0
RAF1 -0.034 0.063 0.18 2 -0.24 11 13
RAC1-CDC42/GDP -0.019 0.11 0.2 1 -0.3 64 65
T-DHT/AR/PELP1/Src 0.007 0.073 0.2 1 -0.18 67 68
MAP2K2 -0.039 0.062 0.15 1 -0.26 11 12
T-DHT/AR/PELP1/Src/PI3K -0.017 0.076 0.16 1 -0.21 67 68
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
SHBG 0.019 0.006 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.022 0.097 -10000 0 -0.39 20 20
mol:T-DHT 0 0 -10000 0 -0.003 6 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
GNRH1 -0.009 0.017 -10000 0 -0.22 3 3
Gi family/GTP -0.025 0.068 0.15 1 -0.2 49 50
CDC42 0.021 0.003 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.035 0.061 0.24 8 -0.23 30 38
KIRREL 0.016 0.045 -10000 0 -0.33 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.036 0.061 0.23 30 -0.24 8 38
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARRB2 0.02 0.006 -10000 0 -10000 0 0
WASL 0.02 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.051 0.057 0.22 30 -0.18 8 38
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.041 0.16 2 -0.21 8 10
FYN 0.016 0.084 0.21 67 -0.17 8 75
mol:Ca2+ 0.048 0.055 0.21 29 -0.18 8 37
mol:DAG 0.049 0.056 0.22 29 -0.18 8 37
NPHS2 -0.004 0.023 -10000 0 -10000 0 0
mol:IP3 0.049 0.056 0.22 29 -0.18 8 37
regulation of endocytosis 0.036 0.05 0.2 26 -0.17 8 34
Nephrin/NEPH1/podocin/Cholesterol 0.041 0.054 0.2 30 -0.18 8 38
establishment of cell polarity 0.035 0.061 0.23 30 -0.24 8 38
Nephrin/NEPH1/podocin/NCK1-2 0.06 0.058 0.28 1 -0.17 8 9
Nephrin/NEPH1/beta Arrestin2 0.038 0.051 0.2 26 -0.17 8 34
NPHS1 0.041 0.083 0.33 36 -10000 0 36
Nephrin/NEPH1/podocin 0.04 0.052 0.2 30 -0.17 8 38
TJP1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.05 0.057 0.22 29 -0.18 8 37
CD2AP 0.021 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.05 0.057 0.22 29 -0.18 8 37
GRB2 0.02 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.006 0.093 0.22 61 -0.18 30 91
cytoskeleton organization -0.003 0.054 0.22 12 -0.22 8 20
Nephrin/NEPH1 0.03 0.048 0.19 30 -0.16 8 38
Nephrin/NEPH1/ZO-1 0.04 0.053 0.22 26 -0.19 8 34
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.016 0.002 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.061 -10000 0 -0.26 17 17
IRAK/TOLLIP 0.019 0.009 0.18 1 -10000 0 1
IKBKB 0.018 0.007 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.038 0.13 0.24 22 -0.23 153 175
IL1A -0.08 0.16 0.32 3 -0.32 153 156
IL1B -0.031 0.054 -10000 0 -0.23 36 36
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.028 -10000 0 -0.17 3 3
IL1R2 0.032 0.067 0.32 22 -0.32 3 25
IL1R1 0.02 0.022 -10000 0 -0.32 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.05 -10000 0 -0.26 10 10
TOLLIP 0.021 0.004 -10000 0 -10000 0 0
TICAM2 0.018 0.031 -10000 0 -0.32 4 4
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
TAK1/TAB1/TAB2 0.013 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.001 0.057 -10000 0 -0.36 2 2
JUN -0.02 0.029 0.14 9 -0.15 4 13
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.033 0.06 -10000 0 -0.17 33 33
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.016 0.11 0.23 2 -0.18 152 154
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.009 0.11 0.22 2 -0.17 146 148
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.055 -10000 0 -0.18 36 36
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.015 0.031 0.16 10 -0.15 2 12
IRAK1 -0.012 0.01 0.2 1 -10000 0 1
IL1RN/IL1R1 0.026 0.036 -10000 0 -0.23 10 10
IRAK4 0.021 0.003 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.061 -10000 0 -0.3 11 11
CHUK 0.021 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.055 -10000 0 -0.18 36 36
IL1 beta/IL1R2 0.015 0.071 0.22 19 -0.2 36 55
IRAK/TRAF6/TAK1/TAB1/TAB2 0.024 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.022 0.055 -10000 0 -0.17 26 26
IRAK3 0.012 0.054 -10000 0 -0.32 13 13
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.031 0.061 -10000 0 -0.17 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.048 0.1 -10000 0 -0.2 144 144
IL1 alpha/IL1R1/IL1RAP -0.028 0.11 0.22 3 -0.2 152 155
RELA 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
MYD88 0.021 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.031 0.015 0.17 3 -10000 0 3
IL1RAP 0.02 0.005 -10000 0 -10000 0 0
UBE2N 0.021 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.044 0.034 -10000 0 -0.28 1 1
CASP1 0.016 0.037 -10000 0 -0.32 6 6
IL1RN/IL1R2 0.035 0.058 0.23 22 -0.25 10 32
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.024 0.057 -10000 0 -0.17 36 36
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.042 0.097 -10000 0 -0.33 24 24
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL1RN 0.016 0.043 -10000 0 -0.32 8 8
TRAF6/TAK1/TAB1/TAB2 0.028 0.01 -10000 0 -10000 0 0
MAP2K6 -0.008 0.041 0.17 23 -0.16 2 25
LPA receptor mediated events

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 0.037 0.023 0.18 1 -0.17 3 4
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.11 0.26 2 -0.27 49 51
AP1 0.006 0.071 -10000 0 -0.16 66 66
mol:PIP3 -0.036 0.044 -10000 0 -0.17 40 40
AKT1 -0.01 0.07 0.25 8 -0.28 8 16
PTK2B -0.041 0.12 0.24 2 -0.25 81 83
RHOA -0.007 0.075 0.18 8 -0.36 16 24
PIK3CB 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.085 0.2 11 -0.23 46 57
MAGI3 0.017 0.034 -10000 0 -0.32 5 5
RELA 0.021 0.004 -10000 0 -10000 0 0
apoptosis -0.011 0.06 -10000 0 -0.19 48 48
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.046 0.11 0.2 9 -0.32 35 44
NF kappa B1 p50/RelA -0.051 0.082 -10000 0 -0.25 53 53
endothelial cell migration -0.009 0.015 0.3 1 -10000 0 1
ADCY4 -0.013 0.054 0.24 1 -0.26 8 9
ADCY5 -0.023 0.07 0.22 2 -0.25 22 24
ADCY6 -0.009 0.048 0.24 1 -0.26 6 7
ADCY7 -0.01 0.045 -10000 0 -0.23 6 6
ADCY1 -0.009 0.048 0.24 1 -0.24 8 9
ADCY2 -0.015 0.058 0.24 1 -0.24 12 13
ADCY3 -0.007 0.043 0.24 1 -0.2 5 6
ADCY8 -0.056 0.082 -10000 0 -0.25 23 23
ADCY9 -0.012 0.054 0.24 1 -0.25 10 11
GSK3B -0.041 0.11 0.21 7 -0.33 39 46
arachidonic acid secretion -0.015 0.051 -10000 0 -0.3 8 8
GNG2 0.019 0.022 -10000 0 -0.32 2 2
TRIP6 0.01 0.025 0.14 1 -0.3 3 4
GNAO1 -0.009 0.021 0.16 5 -0.19 2 7
HRAS 0.021 0.004 -10000 0 -10000 0 0
NFKBIA -0.028 0.11 0.24 7 -0.29 53 60
GAB1 0.02 0.022 -10000 0 -0.32 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.024 0.22 -10000 0 -0.84 33 33
JUN 0.019 0.027 -10000 0 -0.32 3 3
LPA/LPA2/NHERF2 0.026 0.022 -10000 0 -0.18 5 5
TIAM1 -0.04 0.26 -10000 0 -1 33 33
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 -0.022 0.072 0.2 11 -0.21 40 51
PLCB3 -0.014 0.031 0.18 10 -0.17 5 15
FOS 0.002 0.077 -10000 0 -0.32 27 27
positive regulation of mitosis -0.015 0.051 -10000 0 -0.3 8 8
LPA/LPA1-2-3 0.022 0.065 0.22 4 -0.17 48 52
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
stress fiber formation -0.022 0.091 0.23 4 -0.31 24 28
GNAZ -0.023 0.048 0.12 1 -0.19 39 40
EGFR/PI3K-beta/Gab1 -0.036 0.047 -10000 0 -0.21 8 8
positive regulation of dendritic cell cytokine production 0.02 0.064 0.21 4 -0.17 48 52
LPA/LPA2/MAGI-3 0.025 0.023 -10000 0 -0.19 5 5
ARHGEF1 0.007 0.074 0.2 60 -10000 0 60
GNAI2 -0.011 0.011 0.12 1 -0.19 1 2
GNAI3 -0.01 0.011 0.12 1 -0.19 1 2
GNAI1 -0.011 0.014 0.12 1 -0.19 2 3
LPA/LPA3 -0.004 0.071 0.22 4 -0.22 47 51
LPA/LPA2 0.016 0.005 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.014 0.18 1 -0.22 1 2
HB-EGF/EGFR -0.014 0.088 0.13 80 -0.2 55 135
HBEGF -0.011 0.1 0.16 93 -0.22 70 163
mol:DAG -0.022 0.072 0.2 11 -0.21 40 51
cAMP biosynthetic process -0.019 0.062 0.3 2 -0.25 7 9
NFKB1 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.006 -10000 0 -10000 0 0
LYN -0.033 0.11 0.3 4 -0.28 56 60
GNAQ -0.011 0.061 0.17 1 -0.2 44 45
LPAR2 0.02 0.005 -10000 0 -10000 0 0
LPAR3 -0.009 0.1 0.32 4 -0.32 47 51
LPAR1 0.021 0.017 -10000 0 -0.32 1 1
IL8 -0.02 0.12 0.29 15 -0.36 25 40
PTK2 -0.024 0.053 0.19 9 -0.17 1 10
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
CASP3 -0.012 0.06 -10000 0 -0.19 48 48
EGFR 0.014 0.045 0.32 1 -0.32 8 9
PLCG1 -0.016 0.07 0.14 6 -0.23 43 49
PLD2 -0.024 0.055 0.19 13 -0.17 1 14
G12/G13 0.037 0.018 -10000 0 -10000 0 0
PI3K-beta -0.024 0.049 -10000 0 -0.29 11 11
cell migration -0.012 0.07 0.19 1 -0.25 30 31
SLC9A3R2 0.017 0.034 -10000 0 -0.32 5 5
PXN -0.023 0.093 0.23 4 -0.32 24 28
HRAS/GTP -0.015 0.051 -10000 0 -0.32 7 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
MMP9 0.085 0.12 0.32 109 -10000 0 109
PRKCE 0.017 0.034 -10000 0 -0.32 5 5
PRKCD -0.035 0.085 0.19 10 -0.34 17 27
Gi(beta/gamma) -0.005 0.045 -10000 0 -0.25 4 4
mol:LPA 0.001 0.004 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.01 0.084 0.3 1 -0.34 13 14
MAPKKK cascade -0.015 0.051 -10000 0 -0.3 8 8
contractile ring contraction involved in cytokinesis -0.005 0.077 0.19 9 -0.35 17 26
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.014 0.067 0.17 1 -0.2 52 53
GNA15 -0.009 0.057 0.17 1 -0.2 42 43
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.047 0.11 0.22 6 -0.34 35 41
GNA11 -0.01 0.057 -10000 0 -0.2 42 42
Rac1/GTP -0.026 0.23 -10000 0 -0.9 33 33
MMP2 -0.009 0.015 0.3 1 -10000 0 1
PDGFR-alpha signaling pathway

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
PDGFRA 0.015 0.034 -10000 0 -0.31 4 4
PDGF/PDGFRA/CRKL 0.025 0.026 -10000 0 -0.21 4 4
positive regulation of JUN kinase activity 0.038 0.028 -10000 0 -0.17 1 1
CRKL 0.02 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.028 0.1 -10000 0 -0.23 104 104
AP1 -0.054 0.17 0.27 1 -0.73 27 28
mol:IP3 -0.019 0.023 -10000 0 -0.22 3 3
PLCG1 -0.019 0.023 -10000 0 -0.22 3 3
PDGF/PDGFRA/alphaV Integrin 0.025 0.027 -10000 0 -0.21 4 4
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.023 -10000 0 -0.22 3 3
CAV3 -0.049 0.14 -10000 0 -0.32 101 101
CAV1 -0.19 0.17 -10000 0 -0.32 309 309
SHC/Grb2/SOS1 0.04 0.029 -10000 0 -0.17 1 1
PDGF/PDGFRA/Shf 0.026 0.029 0.24 2 -0.21 4 6
FOS -0.055 0.16 0.31 2 -0.73 26 28
JUN -0.023 0.023 -10000 0 -0.22 3 3
oligodendrocyte development 0.025 0.027 -10000 0 -0.21 4 4
GRB2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:DAG -0.019 0.023 -10000 0 -0.22 3 3
PDGF/PDGFRA 0.015 0.034 -10000 0 -0.31 4 4
actin cytoskeleton reorganization 0.024 0.026 -10000 0 -0.21 4 4
SRF -0.014 0.011 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
PI3K 0.034 0.029 -10000 0 -0.17 5 5
PDGF/PDGFRA/Crk/C3G 0.032 0.028 -10000 0 -0.17 4 4
JAK1 -0.017 0.018 -10000 0 -0.21 3 3
ELK1/SRF -0.021 0.036 0.15 18 -0.19 2 20
SHB 0.02 0.006 -10000 0 -10000 0 0
SHF 0.021 0.02 0.32 2 -10000 0 2
CSNK2A1 0.021 0.016 -10000 0 -10000 0 0
GO:0007205 -0.015 0.024 -10000 0 -0.25 3 3
SOS1 0.021 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.038 0.028 -10000 0 -0.17 1 1
PDGF/PDGFRA/SHB 0.024 0.026 -10000 0 -0.21 4 4
PDGF/PDGFRA/Caveolin-1 -0.13 0.13 -10000 0 -0.24 302 302
ITGAV 0.021 0.002 -10000 0 -10000 0 0
ELK1 -0.019 0.025 -10000 0 -0.23 2 2
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.023 0.027 -10000 0 -0.21 4 4
JAK-STAT cascade -0.017 0.018 -10000 0 -0.21 3 3
cell proliferation 0.026 0.029 0.23 2 -0.21 4 6
FoxO family 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
G6PC 0.013 0.063 -10000 0 -10000 0 0
PLK1 0.2 0.26 0.56 140 -10000 0 140
CDKN1B 0.13 0.17 0.41 78 -0.34 7 85
FOXO3 0.19 0.23 0.52 138 -10000 0 138
KAT2B 0.054 0.044 0.19 4 -10000 0 4
FOXO1/SIRT1 0.009 0.041 -10000 0 -0.25 2 2
CAT 0.15 0.24 0.55 60 -0.76 7 67
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.055 0.043 0.18 2 -10000 0 2
FOXO1 0.016 0.057 0.24 9 -0.26 2 11
MAPK10 0.015 0.063 0.2 37 -0.16 14 51
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.033 0.072 0.31 5 -10000 0 5
response to oxidative stress 0.036 0.042 0.12 52 -10000 0 52
FOXO3A/SIRT1 0.16 0.2 0.44 133 -0.43 3 136
XPO1 0.021 0.002 -10000 0 -10000 0 0
EP300 0.022 0.007 -10000 0 -10000 0 0
BCL2L11 0.063 0.061 -10000 0 -10000 0 0
FOXO1/SKP2 0.023 0.041 -10000 0 -10000 0 0
mol:GDP 0.036 0.042 0.12 50 -10000 0 50
RAN 0.022 0.014 0.32 1 -10000 0 1
GADD45A 0.11 0.17 0.42 31 -0.63 8 39
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.001 0.13 -10000 0 -0.49 23 23
MST1 0.065 0.073 0.3 28 -10000 0 28
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.004 0.089 -10000 0 -0.4 13 13
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.026 0.061 0.2 47 -10000 0 47
MAPK9 0.026 0.062 0.2 46 -10000 0 46
YWHAG 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
SIRT1 0.002 0.023 0.14 1 -10000 0 1
SOD2 0.12 0.18 0.44 48 -0.44 3 51
RBL2 0.13 0.21 0.51 38 -0.65 8 46
RAL/GDP 0.047 0.031 0.17 1 -10000 0 1
CHUK 0.054 0.043 0.18 10 -10000 0 10
Ran/GTP 0.016 0.009 0.22 1 -10000 0 1
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
RAL/GTP 0.046 0.03 0.19 1 -10000 0 1
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
FASLG 0.048 0.14 -10000 0 -1.1 6 6
SKP2 0.018 0.016 0.32 1 -10000 0 1
USP7 0.021 0.003 -10000 0 -10000 0 0
IKBKB 0.046 0.042 0.17 5 -10000 0 5
CCNB1 0.19 0.26 0.57 125 -10000 0 125
FOXO1-3a-4/beta catenin 0.12 0.15 0.4 56 -10000 0 56
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.041 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
SGK1 0.052 0.045 0.18 12 -10000 0 12
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.01 0.21 1 -10000 0 1
ZFAND5 0.028 0.067 0.44 1 -10000 0 1
SFN 0.025 0.043 0.32 9 -0.32 1 10
CDK2 0.012 0.02 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.046 0.11 0.26 17 -0.39 10 27
CREBBP 0.012 0.02 -10000 0 -10000 0 0
FBXO32 0.2 0.26 0.63 86 -0.53 1 87
BCL6 0.13 0.22 0.52 34 -0.75 10 44
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.02 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.018 0.096 0.23 1 -0.58 8 9
Syndecan-4/Syndesmos 0.038 0.16 0.33 1 -0.75 13 14
positive regulation of JNK cascade 0.036 0.15 0.31 1 -0.69 13 14
Syndecan-4/ADAM12 0.097 0.19 0.33 93 -0.75 13 106
CCL5 0.017 0.034 -10000 0 -0.32 5 5
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DNM2 0.02 0.005 -10000 0 -10000 0 0
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
SDCBP 0.019 0.006 -10000 0 -10000 0 0
PLG 0.012 0.05 0.32 11 -10000 0 11
ADAM12 0.12 0.14 0.32 171 -10000 0 171
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.035 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.04 0.16 0.32 6 -0.73 13 19
Syndecan-4/CXCL12/CXCR4 0.038 0.16 0.32 1 -0.74 13 14
Syndecan-4/Laminin alpha3 0.02 0.15 0.33 1 -0.72 15 16
MDK 0.11 0.14 0.32 151 -10000 0 151
Syndecan-4/FZD7 0.038 0.15 0.33 1 -0.75 13 14
Syndecan-4/Midkine 0.091 0.18 0.34 54 -0.74 13 67
FZD7 0.02 0.015 -10000 0 -0.32 1 1
Syndecan-4/FGFR1/FGF 0.022 0.16 -10000 0 -0.63 18 18
THBS1 0.019 0.022 -10000 0 -0.32 2 2
integrin-mediated signaling pathway 0.046 0.16 0.32 9 -0.67 15 24
positive regulation of MAPKKK cascade 0.036 0.15 0.31 1 -0.69 13 14
Syndecan-4/TACI 0.049 0.17 0.33 24 -0.74 13 37
CXCR4 0.021 0.002 -10000 0 -10000 0 0
cell adhesion 0.008 0.039 0.19 11 -0.24 5 16
Syndecan-4/Dynamin 0.038 0.15 0.33 1 -0.74 13 14
Syndecan-4/TSP1 0.036 0.15 0.33 1 -0.72 14 15
Syndecan-4/GIPC 0.039 0.15 0.33 1 -0.74 13 14
Syndecan-4/RANTES 0.038 0.16 0.33 1 -0.76 13 14
ITGB1 0.021 0.004 -10000 0 -10000 0 0
LAMA1 0.024 0.066 0.32 15 -0.32 7 22
LAMA3 -0.041 0.13 0.32 1 -0.32 91 92
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA 0.008 0.16 0.78 19 -0.32 1 20
Syndecan-4/alpha-Actinin 0.037 0.15 0.33 1 -0.75 13 14
TFPI 0.006 0.07 -10000 0 -0.32 22 22
F2 0.063 0.11 0.33 72 -10000 0 72
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
positive regulation of cell adhesion 0.003 0.15 0.32 1 -0.66 16 17
ACTN1 0.021 0.004 -10000 0 -10000 0 0
TNC 0.032 0.081 0.32 28 -0.32 7 35
Syndecan-4/CXCL12 0.034 0.16 0.33 1 -0.77 13 14
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CXCL12 0 0.082 -10000 0 -0.32 31 31
TNFRSF13B 0.041 0.09 0.32 41 -0.32 5 46
FGF2 -0.026 0.12 -10000 0 -0.32 70 70
FGFR1 0.018 0.017 -10000 0 -0.32 1 1
Syndecan-4/PI-4-5-P2 0.022 0.15 0.29 4 -0.75 13 17
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.038 0.32 1 -0.32 4 5
cell migration -0.021 0.013 -10000 0 -10000 0 0
PRKCD 0.015 0.019 -10000 0 -10000 0 0
vasculogenesis 0.036 0.15 0.3 4 -0.68 14 18
SDC4 0.032 0.15 0.32 4 -0.85 10 14
Syndecan-4/Tenascin C 0.046 0.16 0.32 9 -0.7 15 24
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.034 0.15 0.33 1 -0.74 13 14
MMP9 0.085 0.13 0.33 109 -10000 0 109
Rac1/GTP 0.008 0.039 0.19 11 -0.25 5 16
cytoskeleton organization 0.038 0.15 0.32 1 -0.71 13 14
GIPC1 0.02 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.033 0.16 0.33 1 -0.73 14 15
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.016 0.005 -10000 0 -10000 0 0
SMARCC1 0.002 0.013 -10000 0 -10000 0 0
REL 0.02 0.007 -10000 0 -10000 0 0
HDAC7 -0.035 0.076 0.29 6 -0.27 20 26
JUN 0.019 0.027 -10000 0 -0.32 3 3
EP300 0.02 0.005 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
KAT5 0.021 0.004 -10000 0 -10000 0 0
MAPK14 -0.012 0.036 0.16 15 -0.24 2 17
FOXO1 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.032 0.078 0.28 3 -0.28 19 22
MAP2K6 0.024 0.057 0.32 14 -0.33 2 16
BRM/BAF57 0.027 0.023 -10000 0 -0.23 3 3
MAP2K4 0.016 0.015 -10000 0 -10000 0 0
SMARCA2 0.017 0.027 -10000 0 -0.32 3 3
PDE9A -0.032 0.16 -10000 0 -0.8 16 16
NCOA2 0.016 0.035 -10000 0 -0.32 5 5
CEBPA 0.004 0.072 -10000 0 -0.32 23 23
EHMT2 0.021 0.004 -10000 0 -10000 0 0
cell proliferation -0.026 0.13 0.34 18 -0.37 27 45
NR0B1 0.08 0.12 0.32 104 -10000 0 104
EGR1 0.005 0.073 -10000 0 -0.32 24 24
RXRs/9cRA -0.064 0.1 -10000 0 -0.17 236 236
AR/RACK1/Src -0.012 0.079 0.29 12 -0.29 2 14
AR/GR -0.014 0.085 0.2 5 -0.22 56 61
GNB2L1 0.021 0.005 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
RCHY1 0.021 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 0.012 2 -10000 0 2
MAPK8 -0.014 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.017 0.07 0.27 4 -0.28 3 7
SRC -0.022 0.032 0.19 4 -0.2 2 6
NR3C1 0.021 0.004 -10000 0 -10000 0 0
KLK3 0.014 0.09 0.33 2 -0.39 2 4
APPBP2 0.016 0.015 -10000 0 -10000 0 0
TRIM24 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.02 0.065 0.24 10 -0.3 2 12
TMPRSS2 -0.08 0.27 -10000 0 -0.89 47 47
RXRG -0.14 0.17 -10000 0 -0.32 238 238
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.021 0.004 -10000 0 -10000 0 0
RXRB 0.021 0.004 -10000 0 -10000 0 0
CARM1 0.021 0.006 -10000 0 -10000 0 0
NR2C2 0.021 0.004 -10000 0 -10000 0 0
KLK2 -0.003 0.085 0.3 26 -0.26 1 27
AR -0.028 0.077 0.18 3 -0.23 59 62
SENP1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.019 0.009 -10000 0 -10000 0 0
SRY 0 0.003 -10000 0 -0.027 7 7
GATA2 -0.006 0.093 -10000 0 -0.32 40 40
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.12 0.14 0.32 173 -10000 0 173
T-DHT/AR/RACK1/Src -0.017 0.073 0.3 9 -0.3 2 11
positive regulation of transcription -0.006 0.093 -10000 0 -0.32 40 40
DNAJA1 0.016 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.011 0.17 2 -10000 0 2
NCOA1 0.023 0.015 -10000 0 -10000 0 0
SPDEF 0.11 0.14 0.32 159 -0.32 3 162
T-DHT/AR/TIF2 -0.009 0.075 0.23 7 -0.34 9 16
T-DHT/AR/Hsp90 -0.021 0.062 0.25 6 -0.3 2 8
GSK3B 0.018 0.012 -10000 0 -10000 0 0
NR2C1 0.02 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.021 0.029 0.16 2 -0.21 2 4
SIRT1 0.021 0.003 -10000 0 -10000 0 0
ZMIZ2 0.018 0.01 -10000 0 -10000 0 0
POU2F1 0.01 0.038 -10000 0 -0.17 4 4
T-DHT/AR/DAX-1 0.019 0.11 0.22 83 -0.31 2 85
CREBBP 0.021 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.013 0.031 0.22 1 -0.21 8 9
EPHB2 0.053 0.094 0.32 55 -10000 0 55
Syndecan-2/TACI 0.028 0.064 0.22 41 -0.18 9 50
LAMA1 0.024 0.066 0.32 15 -0.32 7 22
Syndecan-2/alpha2 ITGB1 0.007 0.081 0.23 11 -0.17 72 83
HRAS 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.017 -10000 0 -0.18 5 5
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
BAX -0.013 0.013 -10000 0 -10000 0 0
EPB41 0.021 0.003 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.019 -10000 0 -0.17 5 5
LAMA3 -0.041 0.13 0.32 1 -0.32 91 92
EZR 0.019 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.047 0.14 -10000 0 -0.32 100 100
Syndecan-2/MMP2 0.014 0.023 0.22 1 -0.18 5 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.037 0.23 13 -0.23 2 15
dendrite morphogenesis 0.037 0.071 0.23 55 -0.19 5 60
Syndecan-2/GM-CSF 0.007 0.059 0.23 9 -0.19 30 39
determination of left/right symmetry -0.008 0.021 -10000 0 -0.22 5 5
Syndecan-2/PKC delta 0.014 0.021 -10000 0 -0.19 5 5
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.005 0.071 0.18 44 -0.18 29 73
MAPK1 -0.004 0.069 0.18 43 -0.18 24 67
Syndecan-2/RACK1 0.024 0.019 -10000 0 -0.15 4 4
NF1 0.021 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.008 0.021 -10000 0 -0.22 5 5
ITGA2 0.026 0.053 0.32 13 -0.32 2 15
MAPK8 -0.011 0.016 -10000 0 -0.19 4 4
Syndecan-2/alpha2/beta1 Integrin 0.041 0.059 0.25 24 -0.19 7 31
Syndecan-2/Kininogen 0.027 0.057 0.22 35 -0.18 5 40
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC 0.001 0.06 0.17 54 -0.16 2 56
Syndecan-2/CASK/Protein 4.1 0.013 0.019 -10000 0 -0.17 5 5
extracellular matrix organization 0.014 0.021 -10000 0 -0.19 5 5
actin cytoskeleton reorganization 0.013 0.031 0.22 1 -0.21 8 9
Syndecan-2/Caveolin-2/Ras -0.007 0.074 -10000 0 -0.17 83 83
Syndecan-2/Laminin alpha3 -0.017 0.075 0.22 1 -0.19 81 82
Syndecan-2/RasGAP 0.032 0.022 -10000 0 -0.15 4 4
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
PRKCD 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.037 0.071 0.23 55 -0.19 5 60
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.018 0.024 0.16 6 -10000 0 6
RHOA 0.021 0.004 -10000 0 -10000 0 0
SDCBP 0.019 0.006 -10000 0 -10000 0 0
TNFRSF13B 0.041 0.09 0.32 41 -0.32 5 46
RASA1 0.02 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.037 0.23 13 -0.23 2 15
Syndecan-2/Synbindin 0.015 0.019 -10000 0 -0.18 4 4
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CASP3 0.002 0.061 0.18 49 -0.17 5 54
FN1 0.019 0.033 0.32 1 -0.32 4 5
Syndecan-2/IL8 0.021 0.045 0.23 17 -0.18 6 23
SDC2 -0.008 0.021 -10000 0 -0.22 5 5
KNG1 0.039 0.077 0.32 35 -10000 0 35
Syndecan-2/Neurofibromin 0.015 0.019 -10000 0 -0.18 4 4
TRAPPC4 0.02 0.004 -10000 0 -10000 0 0
CSF2 0.003 0.095 0.32 9 -0.32 33 42
Syndecan-2/TGFB1 0.014 0.021 -10000 0 -0.19 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.019 -10000 0 -0.17 5 5
Syndecan-2/Ezrin 0.023 0.023 -10000 0 -0.17 5 5
PRKACA 0.004 0.06 0.18 51 -0.17 2 53
angiogenesis 0.021 0.045 0.23 17 -0.18 6 23
MMP2 0.021 0.014 0.32 1 -10000 0 1
IL8 0.029 0.059 0.32 17 -0.32 2 19
calcineurin-NFAT signaling pathway 0.028 0.064 0.22 41 -0.18 9 50
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.07 0.15 -10000 0 -0.32 133 133
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.019 0.006 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.053 0.24 2 -0.24 8 10
HIF1A 0.01 0.041 -10000 0 -0.25 8 8
COPS5 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.051 0.027 -10000 0 -10000 0 0
FIH (dimer) 0.021 0.003 -10000 0 -10000 0 0
CDKN2A 0.096 0.14 0.32 135 -10000 0 135
ARNT/IPAS -0.033 0.11 -10000 0 -0.23 114 114
HIF1AN 0.021 0.003 -10000 0 -10000 0 0
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.023 0.043 0.21 2 -0.23 5 7
CUL2 0.021 0.004 -10000 0 -10000 0 0
OS9 0.02 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.037 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.029 0.051 -10000 0 -0.25 8 8
PHD1-3/OS9 0.078 0.079 0.23 94 -10000 0 94
HIF1A/RACK1/Elongin B/Elongin C 0.042 0.05 0.24 2 -0.24 6 8
VHL 0.02 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.027 0.052 0.24 2 -0.25 8 10
EGLN3 0.083 0.13 0.32 110 -0.32 1 111
EGLN2 0.02 0.004 -10000 0 -10000 0 0
EGLN1 0.02 0.006 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.009 0.1 -10000 0 -0.5 19 19
ARNT 0.018 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.07 0.099 0.25 60 -0.22 6 66
ErbB2/ErbB3 signaling events

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.014 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.085 0.22 1 -0.23 6 7
NFATC4 -0.04 0.068 0.24 11 -0.18 1 12
ERBB2IP 0.02 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.02 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.049 0.066 -10000 0 -0.19 69 69
JUN -0.006 0.062 0.26 2 -10000 0 2
HRAS 0.02 0.006 -10000 0 -10000 0 0
DOCK7 -0.051 0.066 -10000 0 -0.2 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.071 -10000 0 -0.18 62 62
AKT1 -0.008 0.006 -10000 0 -10000 0 0
BAD -0.013 0.005 -10000 0 -10000 0 0
MAPK10 -0.032 0.067 0.18 12 -0.18 21 33
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.051 0.071 -10000 0 -0.22 7 7
RAF1 -0.012 0.094 0.25 16 -0.25 6 22
ErbB2/ErbB3/neuregulin 2 -0.012 0.066 0.19 2 -0.19 53 55
STAT3 0.003 0.13 -10000 0 -0.88 11 11
cell migration -0.025 0.075 0.21 19 -0.2 14 33
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.028 0.18 0.42 2 -0.57 27 29
FOS -0.022 0.15 0.33 5 -0.42 39 44
NRAS 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.066 -10000 0 -0.19 69 69
MAPK3 -0.016 0.15 0.39 3 -0.51 18 21
MAPK1 -0.028 0.17 0.37 4 -0.58 25 29
JAK2 -0.048 0.067 -10000 0 -0.22 8 8
NF2 -0.027 0.13 -10000 0 -0.61 24 24
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.018 0.071 0.2 3 -0.2 60 63
NRG1 -0.039 0.13 -10000 0 -0.33 84 84
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
MAPK8 -0.048 0.088 0.19 1 -0.23 60 61
MAPK9 -0.023 0.058 0.18 15 -10000 0 15
ERBB2 -0.019 0.02 0.26 2 -10000 0 2
ERBB3 0.014 0.025 -10000 0 -0.32 2 2
SHC1 0.019 0.016 0.32 1 -10000 0 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.004 0.13 -10000 0 -0.85 11 11
RNF41 -0.018 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.045 -10000 0 -0.15 59 59
ErbB2/ErbB2/HSP90 (dimer) -0.02 0.017 0.2 2 -10000 0 2
CHRNA1 -0.006 0.14 0.3 21 -0.49 19 40
myelination -0.031 0.085 0.26 21 -10000 0 21
PPP3CB -0.049 0.061 -10000 0 -0.19 6 6
KRAS 0.019 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.002 0.079 0.22 1 -0.19 52 53
NRG2 -0.018 0.11 -10000 0 -0.32 56 56
mol:GDP -0.018 0.071 0.2 3 -0.2 60 63
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K2 -0.014 0.094 0.26 14 -0.28 6 20
SRC 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.051 0.066 -10000 0 -0.2 6 6
MAP2K1 -0.034 0.17 0.37 2 -0.56 25 27
heart morphogenesis -0.049 0.066 -10000 0 -0.19 69 69
RAS family/GDP 0.003 0.086 0.23 1 -0.22 6 7
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA -0.026 0.14 -10000 0 -0.65 26 26
CHRNE 0.002 0.02 0.18 3 -10000 0 3
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.006 -10000 0 -10000 0 0
nervous system development -0.049 0.066 -10000 0 -0.19 69 69
CDC42 0.021 0.003 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.012 0.036 0.19 3 -0.2 13 16
RFC1 -0.01 0.041 0.21 8 -0.2 11 19
PRKDC -0.002 0.055 0.21 25 -0.19 10 35
RIPK1 0.023 0.006 -10000 0 -10000 0 0
CASP7 -0.012 0.092 -10000 0 -0.63 9 9
FASLG/FAS/FADD/FAF1 0.004 0.054 0.16 26 -0.25 4 30
MAP2K4 -0.063 0.14 0.24 3 -0.31 101 104
mol:ceramide -0.021 0.078 -10000 0 -0.26 15 15
GSN -0.013 0.035 0.18 2 -0.2 13 15
FASLG/FAS/FADD/FAF1/Caspase 8 -0.004 0.06 0.19 2 -0.29 3 5
FAS 0.005 0.043 -10000 0 -0.33 6 6
BID -0.021 0.027 0.5 1 -0.18 2 3
MAP3K1 -0.032 0.1 0.25 3 -0.44 12 15
MAP3K7 0.011 0.018 -10000 0 -10000 0 0
RB1 -0.012 0.027 -10000 0 -0.19 11 11
CFLAR 0.023 0.005 -10000 0 -10000 0 0
HGF/MET 0.007 0.1 0.22 10 -0.23 69 79
ARHGDIB -0.01 0.038 0.2 6 -0.2 11 17
FADD 0.009 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.036 0.2 15 -0.18 2 17
NFKB1 -0.025 0.11 -10000 0 -0.62 7 7
MAPK8 -0.1 0.2 0.25 1 -0.46 118 119
DFFA -0.012 0.033 0.19 3 -0.19 12 15
DNA fragmentation during apoptosis -0.012 0.038 0.2 5 -0.18 15 20
FAS/FADD/MET 0.015 0.06 0.22 6 -0.21 20 26
CFLAR/RIP1 0.034 0.01 -10000 0 -10000 0 0
FAIM3 0.02 0.03 0.32 2 -0.32 2 4
FAF1 0.008 0.026 -10000 0 -10000 0 0
PARP1 -0.012 0.036 0.19 3 -0.2 13 16
DFFB -0.011 0.036 0.2 5 -0.19 12 17
CHUK -0.031 0.099 -10000 0 -0.64 6 6
FASLG 0.006 0.035 -10000 0 -0.33 3 3
FAS/FADD 0.012 0.041 -10000 0 -0.24 6 6
HGF 0.007 0.078 0.32 4 -0.32 24 28
LMNA -0.008 0.052 0.18 23 -0.23 4 27
CASP6 -0.012 0.034 0.19 3 -0.2 11 14
CASP10 0.007 0.032 -10000 0 -0.33 2 2
CASP3 -0.005 0.024 0.19 1 -0.27 3 4
PTPN13 -0.014 0.1 -10000 0 -0.32 51 51
CASP8 -0.021 0.026 0.29 2 -0.23 3 5
IL6 -0.24 0.48 -10000 0 -1.1 120 120
MET 0.011 0.072 0.32 6 -0.32 18 24
ICAD/CAD -0.014 0.041 0.3 4 -0.18 12 16
FASLG/FAS/FADD/FAF1/Caspase 10 -0.021 0.079 -10000 0 -0.26 15 15
activation of caspase activity by cytochrome c -0.021 0.027 0.5 1 -0.18 2 3
PAK2 -0.008 0.044 0.21 11 -0.2 11 22
BCL2 0.02 0.021 0.32 1 -0.32 1 2
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
CDC42/GTP -0.01 0.075 -10000 0 -0.21 27 27
PLCG1 -0.018 0.064 0.27 1 -0.21 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
cell migration -0.011 0.074 -10000 0 -0.21 27 27
S1PR5 0.001 0.081 0.32 1 -0.32 29 30
S1PR4 0.008 0.062 -10000 0 -0.32 17 17
MAPK3 -0.019 0.063 -10000 0 -0.18 59 59
MAPK1 -0.015 0.057 -10000 0 -0.17 52 52
S1P/S1P5/Gi -0.015 0.075 -10000 0 -0.19 66 66
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
CDC42/GDP 0.015 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.014 0.049 0.21 1 -0.19 26 27
RHOA -0.002 0.074 0.19 53 -0.17 14 67
S1P/S1P4/Gi -0.012 0.069 -10000 0 -0.19 59 59
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
S1P/S1P4/G12/G13 0.027 0.038 -10000 0 -0.17 15 15
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.047 0.1 -10000 0 -0.3 27 27
epithelial cell differentiation -0.028 0.089 -10000 0 -0.33 3 3
ITCH 0.031 0.018 -10000 0 -10000 0 0
WWP1 -0.018 0.068 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
EGFR 0.014 0.045 0.32 1 -0.32 8 9
PRL 0.025 0.045 0.32 11 -10000 0 11
neuron projection morphogenesis -0.03 0.093 0.35 6 -10000 0 6
PTPRZ1 0.03 0.14 0.32 64 -0.32 41 105
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.019 0.082 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.042 0.082 -10000 0 -0.26 31 31
ADAM17 0.033 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.032 0.065 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.086 0.12 -10000 0 -0.3 69 69
NCOR1 0.02 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.038 0.084 -10000 0 -0.3 3 3
GRIN2B -0.047 0.078 0.26 3 -0.3 2 5
ErbB4/ErbB2/betacellulin -0.012 0.065 -10000 0 -0.3 1 1
STAT1 0.021 0.002 -10000 0 -10000 0 0
HBEGF -0.032 0.12 -10000 0 -0.32 78 78
PRLR 0.021 0.095 0.32 27 -0.32 18 45
E4ICDs/ETO2 -0.029 0.085 -10000 0 -0.3 11 11
axon guidance -0.028 0.069 -10000 0 -0.37 3 3
NEDD4 0.03 0.023 -10000 0 -0.3 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.029 0.074 0.24 34 -0.23 18 52
CBFA2T3 0.002 0.076 -10000 0 -0.32 26 26
ErbB4/ErbB2/HBEGF -0.032 0.084 -10000 0 -0.31 1 1
MAPK3 -0.036 0.079 0.22 1 -10000 0 1
STAT1 (dimer) -0.023 0.076 -10000 0 -0.33 2 2
MAPK1 -0.036 0.078 0.23 2 -10000 0 2
JAK2 0.018 0.022 -10000 0 -0.32 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.052 0.074 -10000 0 -0.31 1 1
NRG1 -0.04 0.083 -10000 0 -0.22 84 84
NRG3 -0.11 0.17 0.32 1 -0.32 195 196
NRG2 -0.018 0.11 -10000 0 -0.32 56 56
NRG4 0.036 0.09 0.32 36 -0.32 8 44
heart development -0.028 0.069 -10000 0 -0.37 3 3
neural crest cell migration -0.051 0.073 -10000 0 -0.31 1 1
ERBB2 0 0.031 0.3 3 -10000 0 3
WWOX/E4ICDs -0.021 0.074 -10000 0 -0.32 2 2
SHC1 0.019 0.016 0.32 1 -10000 0 1
ErbB4/EGFR/neuregulin 4 -0.004 0.091 0.29 1 -0.28 11 12
apoptosis 0.15 0.2 0.39 174 -10000 0 174
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.04 0.097 -10000 0 -0.3 24 24
ErbB4/ErbB2/epiregulin -0.002 0.11 0.33 3 -0.3 3 6
ErbB4/ErbB4/betacellulin/betacellulin -0.025 0.082 -10000 0 -0.31 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.015 0.11 0.32 1 -0.32 5 6
MDM2 -0.02 0.076 0.24 17 -10000 0 17
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.033 0.076 -10000 0 -0.26 1 1
STAT5A -0.029 0.069 -10000 0 -0.44 1 1
ErbB4/EGFR/neuregulin 1 beta -0.035 0.083 -10000 0 -0.32 6 6
DLG4 0.02 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.026 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.021 0.069 -10000 0 -0.3 2 2
STAT5A (dimer) -0.025 0.098 -10000 0 -0.37 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.021 0.081 -10000 0 -0.36 3 3
LRIG1 0.019 0.022 -10000 0 -0.32 2 2
EREG 0.012 0.18 0.32 78 -0.32 82 160
BTC 0.013 0.054 0.32 1 -0.32 12 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.028 0.067 -10000 0 -0.39 2 2
ERBB4 -0.032 0.065 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
YAP1 -0.005 0.068 -10000 0 -0.46 10 10
GRB2 0.02 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.002 0.078 -10000 0 -10000 0 0
glial cell differentiation 0.021 0.068 0.3 2 -10000 0 2
WWOX 0.02 0.006 -10000 0 -10000 0 0
cell proliferation -0.06 0.11 0.32 3 -0.39 13 16
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.045 0.061 0.22 52 -0.17 3 55
cell-cell adhesion 0.021 0.035 0.18 11 -10000 0 11
Ephrin B/EPHB2/RasGAP 0.062 0.068 0.22 48 -0.18 12 60
ITSN1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
Ephrin B1/EPHB3 0.029 0.028 0.21 7 -0.19 3 10
Ephrin B1/EPHB1 0.044 0.062 0.21 54 -0.22 5 59
HRAS/GDP 0.013 0.073 0.28 1 -0.23 18 19
Ephrin B/EPHB1/GRB7 0.059 0.069 0.22 41 -0.19 14 55
Endophilin/SYNJ1 -0.011 0.049 0.18 16 -0.3 1 17
KRAS 0.02 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.06 0.066 0.22 41 -0.19 11 52
endothelial cell migration 0.035 0.032 -10000 0 -0.17 9 9
GRB2 0.02 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PAK1 -0.015 0.053 0.2 8 -0.3 2 10
HRAS 0.021 0.004 -10000 0 -10000 0 0
RRAS -0.013 0.051 0.18 15 -0.3 2 17
DNM1 0.025 0.035 0.32 7 -10000 0 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.014 0.048 0.18 15 -0.26 2 17
lamellipodium assembly -0.021 0.035 -10000 0 -0.18 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.012 0.055 0.19 7 -0.21 10 17
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
EPHB2 0.053 0.094 0.32 55 -10000 0 55
EPHB3 0.025 0.036 0.32 7 -10000 0 7
EPHB1 0.051 0.098 0.32 55 -0.32 3 58
EPHB4 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.009 0.055 0.22 6 -0.27 10 16
Ephrin B/EPHB2 0.054 0.064 0.21 50 -0.18 12 62
Ephrin B/EPHB3 0.04 0.043 0.21 6 -0.18 12 18
JNK cascade -0.004 0.057 0.23 12 -0.31 1 13
Ephrin B/EPHB1 0.051 0.063 0.21 42 -0.18 12 54
RAP1/GDP -0.014 0.08 0.23 17 -0.26 14 31
EFNB2 0.015 0.043 -10000 0 -0.32 8 8
EFNB3 0.019 0.026 0.32 1 -0.32 2 3
EFNB1 0.019 0.026 -10000 0 -0.32 3 3
Ephrin B2/EPHB1-2 0.066 0.083 0.23 91 -0.16 11 102
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.038 0.067 0.2 5 -0.23 10 15
Rap1/GTP -0.021 0.045 0.098 5 -0.25 2 7
axon guidance 0.044 0.061 0.21 52 -0.17 3 55
MAPK3 -0.003 0.047 0.23 4 -0.28 2 6
MAPK1 -0.003 0.043 0.22 3 -0.25 1 4
Rac1/GDP -0.017 0.07 0.22 7 -0.26 14 21
actin cytoskeleton reorganization -0.027 0.045 0.091 4 -0.2 8 12
CDC42/GDP -0.014 0.08 0.23 17 -0.26 14 31
PI3K 0.039 0.033 -10000 0 -0.17 9 9
EFNA5 0.019 0.033 0.32 2 -0.32 3 5
Ephrin B2/EPHB4 0.022 0.028 -10000 0 -0.19 8 8
Ephrin B/EPHB2/Intersectin/N-WASP 0.007 0.062 0.18 4 -0.31 3 7
CDC42 0.021 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.024 0.04 -10000 0 -0.18 8 8
PTK2 0.055 0.18 0.53 67 -10000 0 67
MAP4K4 -0.004 0.057 0.23 12 -0.31 1 13
SRC 0.02 0.004 -10000 0 -10000 0 0
KALRN 0.019 0.027 -10000 0 -0.32 3 3
Intersectin/N-WASP 0.029 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis 0 0.086 0.26 28 -0.29 3 31
MAP2K1 0.004 0.05 0.19 8 -0.29 2 10
WASL 0.02 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.084 0.083 0.24 98 -0.21 5 103
cell migration 0.011 0.079 0.25 13 -0.26 5 18
NRAS 0.02 0.005 -10000 0 -10000 0 0
SYNJ1 -0.011 0.049 0.18 16 -0.3 1 17
PXN 0.021 0.003 -10000 0 -10000 0 0
TF 0.007 0.069 0.2 20 -0.29 1 21
HRAS/GTP 0.039 0.052 0.18 6 -0.18 11 17
Ephrin B1/EPHB1-2 0.072 0.082 0.22 98 -0.2 5 103
cell adhesion mediated by integrin 0.015 0.04 0.18 11 -0.19 9 20
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.046 0.059 0.22 7 -0.18 11 18
RAC1-CDC42/GTP -0.024 0.037 -10000 0 -0.18 11 11
RASA1 0.02 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.017 0.071 0.22 7 -0.26 14 21
ruffle organization 0.005 0.092 0.31 21 -0.25 2 23
NCK1 0.021 0.003 -10000 0 -10000 0 0
receptor internalization -0.015 0.047 0.18 16 -0.29 1 17
Ephrin B/EPHB2/KALRN 0.062 0.071 0.22 50 -0.19 14 64
ROCK1 -0.011 0.033 0.18 12 -0.18 2 14
RAS family/GDP -0.032 0.04 -10000 0 -0.2 10 10
Rac1/GTP -0.019 0.043 0.11 5 -0.18 11 16
Ephrin B/EPHB1/Src/Paxillin 0.005 0.061 -10000 0 -0.22 12 12
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.008 0.065 0.32 19 -10000 0 19
PI3K Class IB/PDE3B 0.008 0.065 -10000 0 -0.32 19 19
PDE3B 0.008 0.065 -10000 0 -0.32 19 19
Coregulation of Androgen receptor activity

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
NRIP1 0.02 0.006 -10000 0 -10000 0 0
SVIL 0.021 0.005 -10000 0 -10000 0 0
ZNF318 0.019 0.009 -10000 0 -10000 0 0
JMJD2C 0.007 0.028 0.13 26 -10000 0 26
T-DHT/AR/Ubc9 0.003 0.087 0.17 6 -0.2 70 76
CARM1 0.02 0.005 -10000 0 -10000 0 0
PRDX1 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.019 0.008 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.007 -10000 0 -10000 0 0
PTK2B 0.018 0.008 -10000 0 -10000 0 0
MED1 0.02 0.007 -10000 0 -10000 0 0
MAK 0.008 0.062 -10000 0 -0.32 17 17
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.019 0.027 -10000 0 -0.32 3 3
GSN 0.021 0.005 -10000 0 -10000 0 0
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
NCOA6 0.021 0.005 -10000 0 -10000 0 0
DNA-PK 0.036 0.018 -10000 0 -10000 0 0
NCOA4 0.021 0.003 -10000 0 -10000 0 0
PIAS3 0.018 0.008 -10000 0 -10000 0 0
cell proliferation -0.015 0.12 -10000 0 -0.58 19 19
XRCC5 0.02 0.006 -10000 0 -10000 0 0
UBE3A 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.005 0.093 0.19 2 -0.2 84 86
FHL2 0.038 0.1 0.32 49 -10000 0 49
RANBP9 0.021 0.004 -10000 0 -10000 0 0
JMJD1A -0.008 0.034 -10000 0 -0.12 40 40
CDK6 0.02 0.016 -10000 0 -0.32 1 1
TGFB1I1 0.019 0.027 -10000 0 -0.32 3 3
T-DHT/AR/CyclinD1 0.002 0.088 0.17 6 -0.2 68 74
XRCC6 0.02 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.013 0.11 0.28 9 -0.21 72 81
CTDSP1 0.021 0.003 -10000 0 -10000 0 0
CTDSP2 0.019 0.009 -10000 0 -10000 0 0
BRCA1 0.022 0.014 0.32 1 -10000 0 1
TCF4 0.017 0.023 -10000 0 -0.32 2 2
CDKN2A 0.096 0.14 0.32 135 -10000 0 135
SRF 0.038 0.044 0.16 6 -10000 0 6
NKX3-1 -0.023 0.069 0.09 5 -0.22 42 47
KLK3 -0.006 0.059 -10000 0 -10000 0 0
TMF1 0.021 0.004 -10000 0 -10000 0 0
HNRNPA1 0.02 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 -0.016 0.006 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.003 0.087 0.17 5 -0.2 70 75
AR -0.025 0.12 0.32 1 -0.33 69 70
UBA3 0.021 0.004 -10000 0 -10000 0 0
PATZ1 0.02 0.007 -10000 0 -10000 0 0
PAWR 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.008 -10000 0 -10000 0 0
PA2G4 0.02 0.007 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.004 0.078 0.16 5 -0.18 68 73
RPS6KA3 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.003 0.086 0.17 6 -0.2 69 75
LATS2 0.019 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.005 0.078 0.16 5 -0.18 68 73
Cyclin D3/CDK11 p58 0.015 0.004 -10000 0 -10000 0 0
VAV3 0.018 0.037 0.32 1 -0.32 5 6
KLK2 0.007 0.082 0.31 22 -0.35 4 26
CASP8 0.02 0.016 -10000 0 -0.32 1 1
T-DHT/AR/TIF2/CARM1 0.012 0.083 0.21 1 -0.18 62 63
TMPRSS2 -0.059 0.22 -10000 0 -0.74 44 44
CCND1 0.016 0.04 -10000 0 -0.32 7 7
PIAS1 0.021 0.005 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.018 0.055 9 -0.057 18 27
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.02 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.004 0.085 0.17 5 -0.2 66 71
CMTM2 -0.04 0.13 -10000 0 -0.32 89 89
SNURF 0.009 0.06 -10000 0 -0.32 16 16
ZMIZ1 0.02 0.025 -10000 0 -10000 0 0
CCND3 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.019 0.008 -10000 0 -10000 0 0
FKBP4 0.02 0.006 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.014 0.043 -10000 0 -0.32 8 8
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
NUDC 0.021 0.003 -10000 0 -10000 0 0
RELN/LRP8 0.016 0.084 0.22 13 -0.19 62 75
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.019 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.029 0.071 0.18 23 -0.18 56 79
IQGAP1/CaM 0.03 0.008 -10000 0 -10000 0 0
DAB1 0.023 0.036 0.32 7 -10000 0 7
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
PLA2G7 0.024 0.044 0.32 8 -0.32 2 10
CALM1 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.028 0.23 9 -10000 0 9
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.003 -10000 0 -10000 0 0
CDK5R1 0.028 0.048 0.32 13 -10000 0 13
LIS1/Poliovirus Protein 3A -0.012 0.004 -10000 0 -10000 0 0
CDK5R2 0.1 0.14 0.32 140 -10000 0 140
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.01 0.086 0.24 10 -0.2 64 74
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.003 0.094 0.3 21 -0.22 1 22
MAP1B 0.003 0.013 -10000 0 -0.22 1 1
RAC1 0.005 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.029 0.074 0.2 26 -10000 0 26
RELN -0.018 0.12 0.32 6 -0.32 62 68
PAFAH/LIS1 -0.014 0.035 0.24 8 -0.2 2 10
LIS1/CLIP170 -0.017 0.007 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.021 0.062 0.16 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.023 0.094 0.26 2 -0.31 23 25
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.001 0.083 0.25 21 -0.22 4 25
LIS1/IQGAP1 -0.018 0.007 -10000 0 -10000 0 0
RHOA 0.005 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.015 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.032 0.058 0.32 19 -10000 0 19
PAFAH1B2 0.02 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.009 0.032 -10000 0 -0.19 3 3
NDEL1/Katanin 60/Dynein heavy chain -0.001 0.095 0.3 19 -10000 0 19
LRP8 0.027 0.042 0.32 10 -10000 0 10
NDEL1/Katanin 60 0.001 0.095 0.3 22 -0.22 2 24
P39/CDK5 0.019 0.12 0.21 129 -10000 0 129
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.017 0.007 -10000 0 -10000 0 0
CDK5 -0.034 0.062 0.18 14 -0.17 55 69
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.014 0.006 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.011 0.078 0.25 9 -0.18 57 66
RELN/VLDLR 0.02 0.086 0.23 12 -0.18 65 77
CDC42 0.005 0.002 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.018 0.029 -10000 0 -0.23 9 9
MAP4K4 -0.008 0.042 0.14 1 -0.26 5 6
BAG4 0.019 0.007 -10000 0 -10000 0 0
PKC zeta/ceramide 0.003 0.062 -10000 0 -0.18 51 51
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BAX -0.008 0.074 -10000 0 -0.35 20 20
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.003 0.11 0.72 11 -10000 0 11
BAD -0.012 0.06 0.2 4 -0.18 52 56
SMPD1 0.006 0.053 0.21 9 -0.21 5 14
RB1 -0.013 0.057 0.12 1 -0.18 52 53
FADD/Caspase 8 0.002 0.054 -10000 0 -0.28 6 6
MAP2K4 -0.014 0.059 0.18 8 -0.17 50 58
NSMAF 0.019 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.013 0.062 0.19 12 -0.17 51 63
EGF 0.071 0.12 0.32 91 -0.32 5 96
mol:ceramide -0.008 0.062 0.12 5 -0.18 52 57
MADD 0.021 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.026 -10000 0 -0.23 7 7
ASAH1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.056 0.12 2 -0.17 52 54
cell proliferation 0.002 0.066 0.23 2 -0.21 5 7
BID -0.009 0.13 -10000 0 -0.58 22 22
MAP3K1 -0.01 0.062 0.18 9 -0.18 51 60
EIF2A -0.014 0.066 0.2 17 -0.18 36 53
TRADD 0.021 0.004 -10000 0 -10000 0 0
CRADD 0.021 0.021 0.32 1 -0.32 1 2
MAPK3 -0.013 0.06 0.18 11 -0.17 34 45
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.063 0.18 11 -0.18 33 44
Cathepsin D/ceramide 0.003 0.063 -10000 0 -0.18 52 52
FADD -0.006 0.041 0.15 2 -0.26 5 7
KSR1 -0.009 0.066 0.21 11 -0.18 52 63
MAPK8 -0.009 0.065 -10000 0 -0.26 7 7
PRKRA -0.011 0.061 0.23 5 -0.18 50 55
PDGFA 0.014 0.043 -10000 0 -0.32 8 8
TRAF2 0.021 0.004 -10000 0 -10000 0 0
IGF1 0.014 0.052 0.32 1 -0.32 11 12
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.061 0.12 5 -0.18 52 57
CTSD 0.021 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.03 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.003 0.071 0.24 2 -0.23 5 7
PRKCD 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.026 -10000 0 -0.23 7 7
RelA/NF kappa B1 0.03 0.007 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.001 0.042 0.16 2 -0.28 3 5
TNFR1A/BAG4/TNF-alpha 0.029 0.042 0.22 1 -0.19 14 15
mol:Sphingosine-1-phosphate -0.018 0.029 -10000 0 -0.23 9 9
MAP2K1 -0.015 0.061 0.18 14 -0.17 48 62
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
CYCS 0.004 0.051 0.18 3 -0.18 16 19
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.061 0.2 10 -0.17 47 57
TNF-alpha/TNFR1A/FAN 0.031 0.041 0.22 1 -0.2 13 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.045 -10000 0 -0.27 7 7
MAP2K2 -0.016 0.059 0.18 11 -0.17 45 56
SMPD3 0.008 0.055 0.19 5 -0.28 8 13
TNF 0.011 0.06 0.32 1 -0.32 15 16
PKC zeta/PAR4 0.028 0.021 -10000 0 -0.23 3 3
mol:PHOSPHOCHOLINE -0.019 0.063 0.18 8 -0.15 50 58
NF kappa B1/RelA/I kappa B alpha 0.049 0.03 -10000 0 -0.17 2 2
AIFM1 -0.002 0.06 0.17 4 -0.19 16 20
BCL2 0.019 0.021 0.32 1 -0.32 1 2
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.013 0.078 0.21 35 -10000 0 35
GNAI2 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.014 0.049 0.21 1 -0.19 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
RhoA/GTP -0.013 0.08 -10000 0 -0.21 35 35
negative regulation of cAMP metabolic process -0.016 0.075 -10000 0 -0.19 68 68
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
S1PR5 0.001 0.081 0.32 1 -0.32 29 30
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.015 0.075 -10000 0 -0.19 66 66
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
Caspase cascade in apoptosis

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
TOP1 -0.015 0.1 0.28 2 -0.35 25 27
ACTA1 -0.02 0.093 0.29 4 -0.3 31 35
NUMA1 -0.009 0.085 0.28 2 -0.32 20 22
SPTAN1 -0.025 0.093 0.32 3 -0.3 35 38
LIMK1 -0.021 0.095 0.21 15 -0.3 33 48
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BIRC2 0.02 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
CASP10 -0.03 0.049 -10000 0 -0.22 31 31
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
PTK2 -0.011 0.084 0.26 2 -0.35 17 19
DIABLO 0.021 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.025 0.092 0.32 3 -0.29 35 38
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.021 0.021 0.32 1 -0.32 1 2
GSN -0.026 0.093 0.33 3 -0.3 35 38
MADD 0.021 0.003 -10000 0 -10000 0 0
TFAP2A 0.088 0.14 0.38 1 -0.49 20 21
BID -0.012 0.037 -10000 0 -0.15 29 29
MAP3K1 -0.014 0.089 0.21 1 -0.42 19 20
TRADD 0.021 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.023 0.093 0.22 9 -0.3 34 43
CASP9 0.021 0.004 -10000 0 -10000 0 0
DNA repair 0 0.04 0.17 6 -0.21 2 8
neuron apoptosis -0.013 0.13 -10000 0 -0.63 21 21
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.017 0.094 0.29 3 -0.35 21 24
APAF1 0.021 0.004 -10000 0 -10000 0 0
CASP6 -0.006 0.11 -10000 0 -0.84 7 7
TRAF2 0.021 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.027 0.094 0.33 6 -0.3 32 38
CASP7 -0.004 0.064 0.24 2 -0.27 10 12
KRT18 0.013 0.028 -10000 0 -10000 0 0
apoptosis -0.022 0.095 0.4 2 -0.38 19 21
DFFA -0.025 0.092 0.25 5 -0.3 35 40
DFFB -0.025 0.093 0.24 6 -0.3 34 40
PARP1 0 0.04 0.21 2 -0.18 6 8
actin filament polymerization 0.003 0.11 0.27 30 -0.28 26 56
TNF 0.011 0.06 0.32 1 -0.32 15 16
CYCS 0 0.045 0.15 11 -0.19 6 17
SATB1 -0.011 0.11 -10000 0 -0.75 8 8
SLK -0.026 0.092 0.29 3 -0.3 35 38
p15 BID/BAX 0.004 0.053 0.19 2 -0.26 7 9
CASP2 0.003 0.051 0.19 14 -0.22 5 19
JNK cascade 0.014 0.089 0.41 19 -0.21 1 20
CASP3 -0.023 0.096 0.31 2 -0.31 35 37
LMNB2 -0.011 0.12 0.21 2 -0.39 35 37
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CASP4 0.02 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.051 0.028 0.23 5 -0.18 2 7
negative regulation of DNA binding 0.088 0.14 0.38 1 -0.48 20 21
stress fiber formation -0.026 0.09 0.29 3 -0.29 35 38
GZMB -0.03 0.059 -10000 0 -0.25 31 31
CASP1 0.004 0.027 -10000 0 -0.25 6 6
LMNB1 0 0.11 0.25 4 -0.43 19 23
APP -0.013 0.13 -10000 0 -0.64 21 21
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.009 -10000 0 -0.22 1 1
VIM -0.017 0.095 0.34 2 -0.38 19 21
LMNA 0.006 0.067 0.25 1 -0.34 7 8
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.046 -10000 0 -0.25 6 6
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.024 0.092 0.21 6 -0.3 35 41
APAF-1/Caspase 9 0.003 0.091 -10000 0 -0.64 9 9
nuclear fragmentation during apoptosis -0.009 0.084 0.28 2 -0.32 20 22
CFL2 -0.003 0.11 0.3 23 -0.28 30 53
GAS2 -0.027 0.096 0.24 6 -0.3 36 42
positive regulation of apoptosis -0.001 0.11 0.21 3 -0.43 17 20
PRF1 0.005 0.072 -10000 0 -0.32 23 23
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.011 0.092 -10000 0 -0.3 28 28
TBX21 -0.098 0.31 -10000 0 -1.1 31 31
B2M 0.02 0.009 -10000 0 -10000 0 0
TYK2 0.011 0.027 -10000 0 -10000 0 0
IL12RB1 0.003 0.06 -10000 0 -0.35 12 12
GADD45B -0.091 0.28 -10000 0 -1 28 28
IL12RB2 0.033 0.091 0.32 39 -0.34 3 42
GADD45G -0.082 0.27 -10000 0 -1 25 25
natural killer cell activation -0.003 0.013 -10000 0 -0.048 6 6
RELB 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL18 0.007 0.051 -10000 0 -0.33 10 10
IL2RA 0.04 0.078 0.32 35 -0.32 1 36
IFNG 0.033 0.085 0.32 31 -0.32 8 39
STAT3 (dimer) -0.072 0.23 -10000 0 -0.72 36 36
HLA-DRB5 -0.001 0.005 -10000 0 -0.023 17 17
FASLG -0.07 0.27 -10000 0 -1 22 22
NF kappa B2 p52/RelB -0.068 0.27 -10000 0 -0.9 29 29
CD4 0.012 0.047 -10000 0 -0.33 9 9
SOCS1 0.022 0.019 0.32 2 -10000 0 2
EntrezGene:6955 -0.001 0.008 0.025 1 -0.03 30 31
CD3D 0.015 0.032 -10000 0 -0.34 3 3
CD3E 0.014 0.037 -10000 0 -0.33 5 5
CD3G 0.01 0.051 -10000 0 -0.33 10 10
IL12Rbeta2/JAK2 0.03 0.069 0.24 30 -0.24 5 35
CCL3 -0.083 0.27 -10000 0 -1 23 23
CCL4 -0.084 0.27 -10000 0 -1.1 23 23
HLA-A 0 0.006 0.024 1 -0.05 6 7
IL18/IL18R 0.015 0.089 -10000 0 -0.24 39 39
NOS2 -0.13 0.38 -10000 0 -1.1 60 60
IL12/IL12R/TYK2/JAK2/SPHK2 -0.012 0.096 -10000 0 -0.31 30 30
IL1R1 -0.084 0.26 -10000 0 -1.1 21 21
IL4 0.003 0.027 -10000 0 -10000 0 0
JAK2 0.009 0.034 -10000 0 -0.32 2 2
EntrezGene:6957 -0.001 0.008 0.025 1 -0.038 13 14
TCR/CD3/MHC I/CD8 -0.018 0.14 -10000 0 -0.82 10 10
RAB7A -0.073 0.23 -10000 0 -0.8 23 23
lysosomal transport -0.069 0.22 -10000 0 -0.76 23 23
FOS -0.085 0.29 -10000 0 -0.98 42 42
STAT4 (dimer) -0.07 0.25 -10000 0 -0.84 29 29
STAT5A (dimer) -0.064 0.27 -10000 0 -0.88 31 31
GZMA -0.081 0.27 -10000 0 -1.1 21 21
GZMB -0.092 0.3 -10000 0 -1.2 26 26
HLX 0.017 0.031 -10000 0 -0.32 4 4
LCK -0.083 0.28 -10000 0 -0.99 29 29
TCR/CD3/MHC II/CD4 -0.012 0.069 -10000 0 -0.25 30 30
IL2/IL2R 0.057 0.057 0.23 35 -0.25 4 39
MAPK14 -0.088 0.28 -10000 0 -0.92 32 32
CCR5 -0.081 0.26 -10000 0 -1 23 23
IL1B -0.009 0.088 -10000 0 -0.34 31 31
STAT6 -0.009 0.076 -10000 0 -0.32 2 2
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
NFKB2 0.021 0.003 -10000 0 -10000 0 0
IL12B 0.013 0.042 0.31 5 -0.34 1 6
CD8A 0.019 0.035 0.32 1 -0.33 4 5
CD8B 0.019 0.043 0.32 3 -0.33 5 8
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.011 0.092 0.3 28 -10000 0 28
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.062 0.23 -10000 0 -0.76 28 28
IL2RG 0.018 0.034 -10000 0 -0.32 5 5
IL12 0.019 0.048 0.24 3 -0.25 4 7
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
CD247 0.015 0.026 -10000 0 -0.32 2 2
IL2 0.019 0.003 -10000 0 -10000 0 0
SPHK2 0.02 0.016 -10000 0 -0.32 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.008 0.046 0.33 1 -0.34 5 6
IL12/IL12R/TYK2/JAK2 -0.082 0.31 -10000 0 -1.1 28 28
MAP2K3 -0.095 0.29 -10000 0 -0.93 34 34
RIPK2 0.019 0.007 -10000 0 -10000 0 0
MAP2K6 -0.084 0.28 -10000 0 -0.85 39 39
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.006 -10000 0 -0.025 24 24
IL18RAP 0.001 0.07 -10000 0 -0.33 20 20
IL12Rbeta1/TYK2 0.013 0.053 -10000 0 -0.25 11 11
EOMES -0.015 0.16 -10000 0 -0.76 17 17
STAT1 (dimer) -0.059 0.24 -10000 0 -0.76 29 29
T cell proliferation -0.058 0.19 -10000 0 -0.6 31 31
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0 0.072 -10000 0 -0.33 22 22
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.063 0.22 -10000 0 -0.63 38 38
ATF2 -0.082 0.26 0.45 2 -0.84 32 34
PLK2 and PLK4 events

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.02 0.005 -10000 0 -9999 0 0
PLK4 0.036 0.067 0.32 26 -9999 0 26
regulation of centriole replication -0.007 0.039 0.16 26 -9999 0 26
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.023 0.052 0.23 6 -0.23 17 23
CRKL -0.002 0.095 0.29 5 -0.42 12 17
mol:PIP3 0.008 0.038 -10000 0 -0.83 1 1
AKT1 0.002 0.05 -10000 0 -0.73 1 1
PTK2B 0.018 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.006 0.09 0.27 5 -0.4 11 16
RANBP10 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.026 0.067 0.22 10 -0.19 36 46
MAP3K5 -0.004 0.096 0.27 6 -0.42 13 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.035 0.069 0.22 13 -0.18 37 50
AP1 -0.021 0.056 -10000 0 -0.2 24 24
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
apoptosis -0.044 0.22 -10000 0 -0.71 47 47
STAT3 (dimer) -0.012 0.077 0.19 2 -0.24 34 36
GAB1/CRKL/SHP2/PI3K 0.021 0.093 0.29 2 -0.38 12 14
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
CBL/CRK 0.005 0.091 0.35 2 -0.38 12 14
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
ELK1 0.005 0.093 0.3 38 -10000 0 38
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.045 0.14 1 -0.24 6 7
PAK1 0.005 0.062 0.39 2 -0.7 1 3
HGF/MET/RANBP10 0.025 0.069 0.22 10 -0.2 37 47
HRAS -0.011 0.12 0.28 1 -0.48 24 25
DOCK1 -0.006 0.093 0.28 7 -0.42 11 18
GAB1 -0.003 0.088 0.23 3 -0.39 12 15
CRK -0.007 0.093 0.37 2 -0.4 13 15
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.13 -10000 0 -0.41 43 43
JUN 0.019 0.027 -10000 0 -0.32 3 3
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.005 0.054 0.13 11 -0.18 38 49
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
cell morphogenesis -0.013 0.098 0.31 12 -0.31 15 27
GRB2/SHC 0.018 0.053 0.21 1 -0.17 26 27
FOS 0.002 0.077 -10000 0 -0.32 27 27
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.005 0.093 0.3 38 -10000 0 38
HGF/MET/MUC20 0.013 0.066 0.21 10 -0.19 40 50
cell migration 0.017 0.053 0.2 1 -0.17 26 27
GRB2 0.02 0.005 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.022 0.054 0.23 6 -0.23 18 24
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.01 0.068 0.15 7 -0.22 33 40
MET/MUC20 0.009 0.049 0.22 6 -0.22 18 24
RAP1B 0 0.092 0.27 9 -0.38 11 20
RAP1A -0.009 0.086 0.26 6 -0.38 11 17
HGF/MET/RANBP9 0.025 0.07 0.22 10 -0.2 38 48
RAF1 -0.01 0.12 0.27 1 -0.46 25 26
STAT3 -0.012 0.078 0.19 2 -0.24 34 36
cell proliferation -0.001 0.11 0.3 17 -0.3 30 47
RPS6KB1 0.003 0.03 -10000 0 -0.25 2 2
MAPK3 -0.006 0.077 0.42 4 -10000 0 4
MAPK1 0.018 0.15 0.64 21 -10000 0 21
RANBP9 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0 0.09 0.27 5 -0.36 14 19
SRC -0.023 0.059 0.14 6 -0.21 32 38
PI3K 0.017 0.061 0.21 1 -0.18 34 35
MET/Glomulin 0.009 0.05 0.24 6 -0.19 18 24
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K1 -0.012 0.11 0.25 1 -0.43 25 26
MET 0.011 0.072 0.32 6 -0.32 18 24
MAP4K1 -0.002 0.1 0.29 6 -0.45 13 19
PTK2 0.018 0.007 -10000 0 -10000 0 0
MAP2K2 -0.013 0.11 0.25 1 -0.43 24 25
BAD -0.001 0.052 0.4 1 -0.7 1 2
MAP2K4 -0.007 0.089 0.26 6 -0.38 13 19
SHP2/GRB2/SOS1/GAB1 0.009 0.088 -10000 0 -0.33 20 20
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PXN 0.021 0.003 -10000 0 -10000 0 0
SH3KBP1 0.02 0.004 -10000 0 -10000 0 0
HGS -0.013 0.047 0.14 5 -0.17 35 40
PLCgamma1/PKC 0.015 0.004 -10000 0 -10000 0 0
HGF 0.007 0.078 0.32 4 -0.32 24 28
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.017 0.061 0.21 1 -0.18 35 36
PDPK1 0.004 0.045 -10000 0 -0.77 1 1
HGF/MET/SHIP 0.024 0.074 0.22 9 -0.21 39 48
Signaling events mediated by PTP1B

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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.008 0.13 0.24 1 -0.37 38 39
PTP1B/AKT1 0.013 0.074 0.19 1 -0.31 11 12
FYN 0.019 0.016 -10000 0 -0.32 1 1
p210 bcr-abl/PTP1B 0.006 0.078 0.23 3 -0.32 12 15
EGFR 0.014 0.047 0.33 1 -0.33 8 9
EGF/EGFR 0.035 0.097 0.23 24 -0.35 8 32
CSF1 0.018 0.027 -10000 0 -0.32 3 3
AKT1 0.019 0.009 -10000 0 -10000 0 0
INSR 0.02 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.03 0.094 0.23 37 -0.29 13 50
Insulin Receptor/Insulin 0.023 0.073 -10000 0 -0.34 7 7
HCK 0.006 0.07 -10000 0 -0.32 22 22
CRK 0.019 0.006 -10000 0 -10000 0 0
TYK2 0.002 0.074 0.32 2 -0.37 7 9
EGF 0.072 0.12 0.32 91 -0.33 5 96
YES1 0.02 0.005 -10000 0 -10000 0 0
CAV1 -0.056 0.11 0.24 4 -0.32 30 34
TXN 0.022 0.02 0.33 2 -10000 0 2
PTP1B/IRS1/GRB2 0.022 0.075 0.25 1 -0.32 8 9
cell migration -0.006 0.078 0.32 12 -0.23 3 15
STAT3 0.021 0.003 -10000 0 -10000 0 0
PRLR 0.022 0.096 0.32 27 -0.32 18 45
ITGA2B -0.008 0.11 0.32 5 -0.33 47 52
CSF1R 0.016 0.04 -10000 0 -0.32 7 7
Prolactin Receptor/Prolactin 0.029 0.075 0.24 34 -0.23 18 52
FGR -0.003 0.087 -10000 0 -0.32 35 35
PTP1B/p130 Cas 0.014 0.076 0.22 2 -0.3 12 14
Crk/p130 Cas 0.021 0.077 0.25 1 -0.34 8 9
DOK1 0.002 0.083 0.24 2 -0.32 16 18
JAK2 -0.006 0.13 0.23 1 -0.37 37 38
Jak2/Leptin Receptor/Leptin 0.025 0.096 0.24 8 -0.34 10 18
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
PTPN1 0.006 0.078 0.23 3 -0.32 12 15
LYN 0.02 0.006 -10000 0 -10000 0 0
CDH2 0.043 0.096 0.32 46 -0.32 6 52
SRC 0.007 0.091 -10000 0 -0.43 17 17
ITGB3 0.028 0.073 0.32 23 -0.33 5 28
CAT1/PTP1B -0.024 0.14 0.28 5 -0.4 41 46
CAPN1 0.021 0.005 -10000 0 -10000 0 0
CSK 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.027 0.07 -10000 0 -0.29 7 7
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.089 0.23 3 -0.29 13 16
negative regulation of transcription -0.006 0.13 0.23 1 -0.36 37 38
FCGR2A 0.016 0.031 -10000 0 -0.32 4 4
FER 0.021 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.015 0.096 0.23 28 -0.23 51 79
BLK 0.065 0.11 0.32 81 -0.32 1 82
Insulin Receptor/Insulin/Shc 0.033 0.017 -10000 0 -10000 0 0
RHOA 0.021 0.005 -10000 0 -10000 0 0
LEPR -0.016 0.11 -10000 0 -0.32 55 55
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
p210 bcr-abl/Grb2 0.02 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.039 0.16 0.22 4 -0.38 64 68
PRL 0.024 0.045 0.33 11 -10000 0 11
SOCS3 0.002 0.13 -10000 0 -1.1 7 7
SPRY2 0.018 0.023 -10000 0 -0.33 2 2
Insulin Receptor/Insulin/IRS1 0.038 0.015 -10000 0 -0.18 1 1
CSF1/CSF1R 0.021 0.082 -10000 0 -0.34 11 11
Ras protein signal transduction 0.009 0.12 0.56 21 -10000 0 21
IRS1 0.02 0.015 -10000 0 -0.32 1 1
INS 0.011 0.015 -10000 0 -10000 0 0
LEP 0.048 0.09 0.32 49 -10000 0 49
STAT5B 0.007 0.09 0.22 4 -0.32 19 23
STAT5A 0.006 0.091 0.21 5 -0.31 22 27
GRB2 0.02 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.075 0.22 2 -0.3 12 14
CSN2 0.018 0.063 0.56 1 -10000 0 1
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
LAT 0.015 0.066 -10000 0 -0.4 9 9
YBX1 0.024 0.005 -10000 0 -10000 0 0
LCK 0.02 0.026 0.32 1 -0.32 2 3
SHC1 0.019 0.016 0.32 1 -10000 0 1
NOX4 0.029 0.05 0.32 14 -10000 0 14
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.01 0.028 0.11 1 -0.21 3 4
NFATC2 -0.015 0.043 0.11 1 -0.21 18 19
NFATC3 -0.01 0.024 0.11 1 -10000 0 1
CD40LG -0.037 0.14 0.29 20 -0.4 33 53
PTGS2 -0.038 0.15 0.33 12 -0.39 38 50
JUNB 0.018 0.027 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.02 -10000 0 -10000 0 0
CALM1 0.013 0.02 -10000 0 -10000 0 0
JUN 0.012 0.034 -10000 0 -0.33 3 3
mol:Ca2+ -0.001 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.011 -10000 0 -10000 0 0
FOSL1 0.028 0.059 0.32 16 -0.32 3 19
CREM 0.02 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.016 0.093 0.28 15 -0.3 9 24
FOS -0.004 0.079 -10000 0 -0.33 27 27
IFNG -0.022 0.15 0.35 30 -0.37 26 56
AP-1/NFAT1-c-4 0.013 0.17 0.47 15 -0.41 23 38
FASLG -0.029 0.13 0.34 8 -0.37 22 30
NFAT1-c-4/ICER1 0.006 0.064 0.26 1 -0.24 7 8
IL2RA -0.019 0.15 0.34 38 -0.37 21 59
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSF2 -0.038 0.15 0.35 15 -0.39 41 56
JunB/Fra1/NFAT1-c-4 0.016 0.081 0.26 14 -0.24 10 24
IL4 -0.033 0.13 0.35 7 -0.36 22 29
IL2 0.001 0.1 -10000 0 -0.82 8 8
IL3 -0.015 0.14 -10000 0 -0.62 24 24
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
BATF3 0.019 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.006 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.03 0.1 0.25 32 -0.33 15 47
FYN -0.004 0.11 0.24 11 -0.39 21 32
LAT/GRAP2/SLP76 0.009 0.1 0.26 3 -0.35 22 25
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.008 0.093 0.24 8 -0.3 26 34
B2M 0.018 0.013 -10000 0 -10000 0 0
IKBKG -0.003 0.033 0.1 13 -0.1 8 21
MAP3K8 0.02 0.016 -10000 0 -0.32 1 1
mol:Ca2+ -0.017 0.014 0.039 9 -0.055 12 21
integrin-mediated signaling pathway 0.024 0.016 -10000 0 -0.19 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.014 0.12 0.24 5 -0.42 25 30
TRPV6 0.006 0.26 1.2 20 -0.51 1 21
CD28 0.019 0.017 -10000 0 -0.33 1 1
SHC1 0.016 0.12 0.26 42 -0.38 18 60
receptor internalization -0.008 0.11 -10000 0 -0.4 26 26
PRF1 -0.041 0.24 -10000 0 -0.95 30 30
KRAS 0.02 0.006 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
COT/AKT1 0.003 0.08 0.23 7 -0.26 22 29
LAT -0.008 0.11 0.27 5 -0.38 24 29
EntrezGene:6955 -0.001 0.005 -10000 0 -0.031 3 3
CD3D 0.017 0.03 -10000 0 -0.34 3 3
CD3E 0.016 0.037 -10000 0 -0.34 5 5
CD3G 0.012 0.05 -10000 0 -0.33 10 10
RASGRP2 -0.009 0.037 -10000 0 -0.15 29 29
RASGRP1 -0.017 0.099 0.24 6 -0.31 27 33
HLA-A -0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.018 0.022 -10000 0 -0.32 2 2
RAP1A/GTP/RAPL 0.025 0.016 -10000 0 -0.19 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.047 0.12 31 -0.12 8 39
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.035 -10000 0 -0.15 17 17
PRKCA -0.011 0.051 0.17 4 -0.19 13 17
GRAP2 0.011 0.056 -10000 0 -0.32 14 14
mol:IP3 0.012 0.085 0.17 40 -0.28 20 60
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.012 0.084 -10000 0 -0.37 17 17
ORAI1 -0.024 0.21 0.4 5 -0.98 20 25
CSK -0.005 0.11 0.28 2 -0.38 22 24
B7 family/CD28 0.014 0.12 0.24 1 -0.43 23 24
CHUK 0.021 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.008 0.12 -10000 0 -0.41 24 24
PTPN6 -0.01 0.1 0.21 4 -0.37 21 25
VAV1 -0.009 0.11 0.23 1 -0.38 24 25
Monovalent TCR/CD3 0.002 0.047 -10000 0 -0.27 11 11
CBL 0.02 0.005 -10000 0 -10000 0 0
LCK -0.002 0.11 0.25 7 -0.41 17 24
PAG1 0 0.11 0.24 9 -0.37 22 31
RAP1A 0.02 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.008 0.11 0.2 1 -0.41 22 23
CD80 0.012 0.053 -10000 0 -0.33 12 12
CD86 0.013 0.049 -10000 0 -0.33 10 10
PDK1/CARD11/BCL10/MALT1 0.002 0.049 0.13 5 -0.18 14 19
HRAS 0.021 0.004 -10000 0 -10000 0 0
GO:0035030 -0.019 0.097 0.19 4 -0.34 28 32
CD8A 0.017 0.036 0.33 1 -0.33 4 5
CD8B 0.018 0.044 0.32 3 -0.34 5 8
PTPRC 0.012 0.051 -10000 0 -0.33 11 11
PDK1/PKC theta -0.018 0.11 0.3 8 -0.35 28 36
CSK/PAG1 0 0.11 0.23 16 -0.39 17 33
SOS1 0.021 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 0.012 0.11 0.23 1 -0.39 23 24
STIM1 -0.003 0.069 1.2 1 -10000 0 1
RAS family/GTP 0.01 0.053 0.17 6 -0.16 11 17
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.009 0.12 -10000 0 -0.42 26 26
mol:DAG -0.021 0.062 0.092 5 -0.24 24 29
RAP1A/GDP 0.007 0.022 0.069 9 -0.062 4 13
PLCG1 0.02 0.005 -10000 0 -10000 0 0
CD247 0.016 0.024 -10000 0 -0.32 2 2
cytotoxic T cell degranulation -0.038 0.23 -10000 0 -0.9 30 30
RAP1A/GTP -0.005 0.014 -10000 0 -0.06 28 28
mol:PI-3-4-5-P3 -0.01 0.1 0.23 6 -0.36 24 30
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.016 0.1 0.22 13 -0.36 18 31
NRAS 0.02 0.005 -10000 0 -10000 0 0
ZAP70 0.017 0.037 -10000 0 -0.33 6 6
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.015 0.094 0.26 2 -0.34 21 23
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.027 0.048 0.31 3 -0.29 7 10
CARD11 0.033 0.065 0.32 24 -10000 0 24
PRKCB -0.015 0.058 0.15 2 -0.22 20 22
PRKCE -0.013 0.055 0.17 5 -0.2 15 20
PRKCQ -0.02 0.12 0.26 4 -0.38 30 34
LCP2 0.018 0.027 -10000 0 -0.32 3 3
BCL10 0.021 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.006 0.083 0.22 9 -0.27 24 33
IKK complex 0.005 0.048 0.2 13 -0.12 4 17
RAS family/GDP -0.004 0.008 -10000 0 -0.039 3 3
MAP3K14 -0.008 0.061 0.18 8 -0.2 20 28
PDPK1 -0.009 0.091 0.26 10 -0.3 22 32
TCR/CD3/MHC I/CD8/Fyn -0.016 0.12 -10000 0 -0.47 20 20
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.035 0.1 0.27 18 -0.38 9 27
IKBKB 0.024 0.092 0.25 7 -0.28 17 24
AKT1 0.033 0.076 0.21 43 -0.2 2 45
IKBKG 0.03 0.069 0.24 5 -0.26 7 12
CALM1 0.018 0.081 0.25 7 -0.41 7 14
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 0.042 0.12 0.27 29 -0.45 9 38
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.085 0.22 1 -0.46 7 8
DOK1 0.021 0.002 -10000 0 -10000 0 0
AP-1 0.022 0.073 0.22 11 -0.25 5 16
LYN 0.019 0.006 -10000 0 -10000 0 0
BLNK 0.02 0.022 -10000 0 -0.32 2 2
SHC1 0.019 0.016 0.32 1 -10000 0 1
BCR complex 0.073 0.097 0.25 106 -0.32 2 108
CD22 0.012 0.072 0.24 14 -0.4 4 18
CAMK2G 0.014 0.077 0.25 6 -0.39 7 13
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
SHC/GRB2/SOS1 -0.004 0.049 0.15 8 -10000 0 8
GO:0007205 0.019 0.087 0.22 1 -0.47 7 8
SYK 0.019 0.022 -10000 0 -0.32 2 2
ELK1 0.015 0.082 0.23 3 -0.46 6 9
NFATC1 0.036 0.093 0.25 21 -0.36 6 27
B-cell antigen/BCR complex 0.073 0.097 0.25 106 -0.32 2 108
PAG1/CSK 0.027 0.011 -10000 0 -10000 0 0
NFKBIB 0.023 0.04 0.14 6 -0.13 9 15
HRAS 0.022 0.073 0.23 10 -0.35 4 14
NFKBIA 0.022 0.04 0.14 6 -0.13 8 14
NF-kappa-B/RelA/I kappa B beta 0.025 0.036 0.14 6 -10000 0 6
RasGAP/Csk 0.083 0.084 0.24 102 -0.16 1 103
mol:GDP 0.018 0.088 0.22 1 -0.46 7 8
PTEN 0.021 0.003 -10000 0 -10000 0 0
CD79B 0.025 0.043 0.32 9 -0.32 1 10
NF-kappa-B/RelA/I kappa B alpha 0.025 0.035 0.14 6 -10000 0 6
GRB2 0.02 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.051 0.12 0.3 11 -0.48 7 18
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 0.019 0.086 0.22 1 -0.47 7 8
CSK 0.021 0.004 -10000 0 -10000 0 0
FOS 0.007 0.086 0.25 6 -0.39 8 14
CHUK 0.027 0.076 0.24 5 -0.27 11 16
IBTK 0.019 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.037 0.076 -10000 0 -0.32 6 6
PTPN6 0.006 0.068 0.22 14 -0.37 5 19
RELA 0.021 0.004 -10000 0 -10000 0 0
BCL2A1 0.016 0.027 0.12 1 -10000 0 1
VAV2 0.049 0.089 0.25 18 -0.4 4 22
ubiquitin-dependent protein catabolic process 0.023 0.04 0.14 6 -0.13 10 16
BTK -0.053 0.27 -10000 0 -0.98 39 39
CD19 0.047 0.088 0.26 24 -0.34 3 27
MAP4K1 0.017 0.031 -10000 0 -0.32 4 4
CD72 0.02 0.005 -10000 0 -10000 0 0
PAG1 0.019 0.007 -10000 0 -10000 0 0
MAPK14 0.042 0.12 0.27 34 -0.39 8 42
SH3BP5 0.018 0.031 -10000 0 -0.32 4 4
PIK3AP1 0.02 0.087 0.23 1 -0.45 8 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.018 0.13 -10000 0 -0.57 13 13
RAF1 0.018 0.07 0.22 10 -0.34 4 14
RasGAP/p62DOK/SHIP 0.079 0.077 0.35 8 -0.24 2 10
CD79A 0.081 0.13 0.32 105 -0.32 3 108
re-entry into mitotic cell cycle 0.021 0.072 0.22 12 -0.25 5 17
RASA1 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.012 0.066 0.21 8 -0.32 3 11
MAPK1 0.014 0.065 0.24 11 -0.35 2 13
CD72/SHP1 0.021 0.086 0.24 23 -0.35 5 28
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.038 0.11 0.26 31 -0.39 8 39
actin cytoskeleton organization 0.062 0.1 0.27 44 -0.36 3 47
NF-kappa-B/RelA 0.049 0.07 0.25 6 -0.23 3 9
Calcineurin 0.031 0.073 -10000 0 -0.36 5 5
PI3K 0.005 0.066 0.19 7 -0.28 5 12
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.024 0.078 0.25 1 -0.48 6 7
SOS1 0.021 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.037 0.12 -10000 0 -0.6 12 12
DAPP1 0.026 0.13 -10000 0 -0.66 12 12
cytokine secretion 0.036 0.09 0.24 23 -0.34 6 29
mol:DAG 0.019 0.086 0.22 1 -0.47 7 8
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
MAP2K1 0.013 0.067 0.22 8 -0.34 3 11
B-cell antigen/BCR complex/FcgammaRIIB 0.074 0.088 0.24 103 -0.17 2 105
mol:PI-3-4-5-P3 0.017 0.068 0.18 26 -0.22 4 30
ETS1 0.011 0.073 0.24 8 -0.34 6 14
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.085 0.085 0.39 8 -0.24 2 10
B-cell antigen/BCR complex/LYN 0.031 0.065 0.28 8 -0.36 4 12
MALT1 0.019 0.006 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.058 0.098 0.27 38 -0.38 3 41
B-cell antigen/BCR complex/LYN/SYK 0.06 0.1 0.36 15 -0.31 5 20
CARD11 0.033 0.094 0.27 13 -0.43 6 19
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
PPP3CA 0.021 0.003 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.022 0.047 0.14 27 -0.12 5 32
PTPRC 0.012 0.05 -10000 0 -0.32 11 11
PDPK1 0.021 0.069 0.18 44 -0.17 3 47
PPP3CB 0.021 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.008 -10000 0 -10000 0 0
POU2F2 0.019 0.026 0.12 6 -10000 0 6
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.041 0.041 0.21 7 -0.18 9 16
ER alpha/Gai/GDP/Gbeta gamma -0.032 0.14 -10000 0 -0.46 30 30
AKT1 -0.062 0.24 -10000 0 -0.7 59 59
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.059 0.24 -10000 0 -0.71 59 59
mol:Ca2+ -0.02 0.066 -10000 0 -0.32 19 19
IGF1R 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.025 0.039 0.21 9 -0.19 9 18
SHC1 0.019 0.016 0.32 1 -10000 0 1
apoptosis 0.059 0.23 0.66 59 -10000 0 59
RhoA/GTP -0.023 0.022 -10000 0 -0.15 6 6
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.015 0.12 0.24 2 -0.39 29 31
regulation of stress fiber formation 0.014 0.053 0.24 1 -0.21 3 4
E2/ERA-ERB (dimer) 0.025 0.039 0.21 9 -0.19 9 18
KRAS 0.02 0.006 -10000 0 -10000 0 0
G13/GTP 0.024 0.033 0.2 9 -0.17 7 16
pseudopodium formation -0.014 0.053 0.21 3 -0.24 1 4
E2/ER alpha (dimer)/PELP1 0.025 0.037 0.21 9 -0.18 8 17
GRB2 0.02 0.005 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.038 0.16 0.26 1 -0.44 57 58
E2/ER beta (dimer) 0.015 0.011 -10000 0 -0.22 1 1
mol:GDP -0.003 0.063 0.18 11 -0.26 10 21
mol:NADP -0.038 0.16 0.26 1 -0.44 57 58
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.021 0.068 -10000 0 -0.34 19 19
IGF-1R heterotetramer 0.02 0.004 -10000 0 -10000 0 0
PLCB1 -0.006 0.063 -10000 0 -0.35 14 14
PLCB2 -0.008 0.067 -10000 0 -0.35 15 15
IGF1 0.014 0.052 0.32 1 -0.32 11 12
mol:L-citrulline -0.038 0.16 0.26 1 -0.44 57 58
RHOA 0.021 0.004 -10000 0 -10000 0 0
Gai/GDP -0.022 0.16 -10000 0 -0.62 28 28
JNK cascade 0.015 0.011 -10000 0 -0.22 1 1
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
ESR2 0.02 0.016 -10000 0 -0.32 1 1
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
ESR1 0.019 0.059 0.32 9 -0.32 8 17
Gq family/GDP/Gbeta gamma -0.045 0.2 -10000 0 -0.72 40 40
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.013 0.06 -10000 0 -0.51 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.012 0.11 0.23 1 -0.38 24 25
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
E2/ER alpha (dimer) 0.014 0.04 0.22 9 -0.22 8 17
STRN 0.02 0.015 -10000 0 -0.32 1 1
GNAL 0.017 0.047 0.32 3 -0.32 7 10
PELP1 0.02 0.006 -10000 0 -10000 0 0
MAPK11 -0.013 0.017 0.22 1 -0.19 3 4
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
HBEGF -0.04 0.15 0.33 11 -0.43 40 51
cAMP biosynthetic process 0.018 0.038 0.14 11 -0.17 14 25
SRC -0.032 0.13 0.28 1 -0.45 28 29
PI3K 0.029 0.014 -10000 0 -0.23 1 1
GNB1 0.021 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.019 0.063 -10000 0 -0.29 5 5
SOS1 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.023 0.09 -10000 0 -0.33 24 24
Gs family/GTP 0.023 0.041 0.17 11 -0.17 14 25
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.015 -10000 0 -10000 0 0
vasodilation -0.036 0.15 0.26 1 -0.42 57 58
mol:DAG -0.021 0.068 -10000 0 -0.34 19 19
Gs family/GDP/Gbeta gamma 0.002 0.061 -10000 0 -0.27 9 9
MSN -0.015 0.055 0.22 3 -0.26 1 4
Gq family/GTP 0.002 0.068 -10000 0 -0.35 16 16
mol:PI-3-4-5-P3 -0.056 0.23 -10000 0 -0.68 59 59
NRAS 0.02 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.036 0.15 0.42 57 -0.26 1 58
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.067 0.19 9 -0.26 8 17
NOS3 -0.041 0.17 0.26 1 -0.46 57 58
GNA11 0.019 0.016 -10000 0 -0.32 1 1
MAPKKK cascade -0.032 0.16 0.32 2 -0.47 54 56
E2/ER alpha (dimer)/PELP1/Src -0.018 0.13 0.25 5 -0.4 28 33
ruffle organization -0.014 0.053 0.21 3 -0.24 1 4
ROCK2 -0.01 0.059 0.23 3 -10000 0 3
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MMP9 -0.019 0.13 0.35 7 -0.42 27 34
MMP2 -0.032 0.13 0.26 8 -0.44 26 34
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.043 -10000 0 -0.23 12 12
PDGFRB 0.015 0.015 -10000 0 -10000 0 0
SPHK1 0.002 0.049 -10000 0 -0.64 2 2
mol:S1P -0.006 0.048 -10000 0 -0.55 2 2
S1P1/S1P/Gi -0.037 0.13 0.32 1 -0.37 52 53
GNAO1 0.017 0.037 0.32 4 -0.33 2 6
PDGFB-D/PDGFRB/PLCgamma1 -0.031 0.13 0.27 6 -0.35 47 53
PLCG1 -0.044 0.12 0.22 7 -0.36 50 57
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.015 -10000 0 -10000 0 0
GNAI2 0.016 0.015 -10000 0 -10000 0 0
GNAI3 0.017 0.015 -10000 0 -10000 0 0
GNAI1 0.016 0.021 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.029 -10000 0 -0.2 12 12
S1P1/S1P -0.019 0.058 0.21 1 -0.31 6 7
negative regulation of cAMP metabolic process -0.036 0.13 0.22 6 -0.36 52 58
MAPK3 -0.06 0.17 0.28 8 -0.54 48 56
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
KDR 0.009 0.054 -10000 0 -0.33 12 12
PLCB2 -0.015 0.063 0.22 5 -0.27 8 13
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.023 0.045 -10000 0 -0.27 6 6
receptor internalization -0.02 0.052 -10000 0 -0.29 6 6
PTGS2 -0.086 0.28 0.4 1 -0.91 48 49
Rac1/GTP -0.022 0.044 -10000 0 -0.28 5 5
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFA 0.017 0.014 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.036 0.13 0.22 6 -0.36 52 58
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.01 0.092 -10000 0 -0.33 39 39
MAPK1 -0.057 0.17 0.26 6 -0.54 47 53
S1P1/S1P/PDGFB-D/PDGFRB -0.008 0.07 0.28 2 -0.31 6 8
ABCC1 0.017 0.014 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0.012 -10000 0 -0.19 1 1
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.054 0.32 14 -0.32 2 16
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.032 0.15 9 -0.16 2 11
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
FYN 0.019 0.016 -10000 0 -0.32 1 1
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR -0.003 0.087 -10000 0 -0.32 35 35
p38 alpha/TAB1 -0.036 0.086 -10000 0 -0.29 38 38
PRKG1 -0.021 0.11 -10000 0 -0.32 62 62
DUSP8 0.015 0.046 -10000 0 -0.32 9 9
PGK/cGMP/p38 alpha -0.018 0.12 -10000 0 -0.31 46 46
apoptosis -0.035 0.082 -10000 0 -0.28 38 38
RAL/GTP 0.026 0.009 -10000 0 -10000 0 0
LYN 0.02 0.006 -10000 0 -10000 0 0
DUSP1 -0.008 0.095 -10000 0 -0.32 42 42
PAK1 0.02 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.043 0.024 -10000 0 -0.16 1 1
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.025 0.01 -10000 0 -10000 0 0
MAPK11 -0.002 0.12 0.25 13 -0.3 40 53
BLK 0.065 0.11 0.32 81 -0.32 1 82
HCK 0.006 0.07 -10000 0 -0.32 22 22
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
DUSP16 0.02 0.005 -10000 0 -10000 0 0
DUSP10 0.018 0.022 -10000 0 -0.32 2 2
TRAF6/MEKK3 0.025 0.011 -10000 0 -0.17 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.12 0.23 12 -0.36 26 38
positive regulation of innate immune response -0.003 0.14 0.28 13 -0.37 36 49
LCK 0.02 0.026 0.32 1 -0.32 2 3
p38alpha-beta/MKP7 0.005 0.14 0.29 12 -0.36 33 45
p38alpha-beta/MKP5 0.004 0.13 0.3 9 -0.36 31 40
PGK/cGMP -0.013 0.077 -10000 0 -0.22 62 62
PAK2 0.02 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.002 0.14 0.3 11 -0.36 40 51
CDC42 0.021 0.003 -10000 0 -10000 0 0
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.019 0.006 -10000 0 -10000 0 0
PAK3 0.053 0.1 0.32 60 -0.32 5 65
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.014 0.089 0.42 2 -0.38 19 21
CRKL -0.018 0.087 0.36 2 -0.4 21 23
HRAS -0.006 0.079 -10000 0 -0.37 13 13
mol:PIP3 0.003 0.1 0.37 2 -0.41 18 20
SPRED1 0.02 0.005 -10000 0 -10000 0 0
SPRED2 0.021 0.001 -10000 0 -10000 0 0
GAB1 -0.014 0.093 0.32 1 -0.41 23 24
FOXO3 -0.003 0.11 0.33 1 -0.39 25 26
AKT1 0 0.12 -10000 0 -0.42 25 25
BAD -0.002 0.11 -10000 0 -0.39 25 25
megakaryocyte differentiation -0.025 0.1 -10000 0 -0.4 26 26
GSK3B -0.001 0.11 -10000 0 -0.39 25 25
RAF1 -0.007 0.074 0.23 2 -0.3 13 15
SHC1 0.019 0.016 0.32 1 -10000 0 1
STAT3 -0.016 0.095 0.32 1 -0.41 24 25
STAT1 -0.042 0.21 0.44 1 -0.93 24 25
HRAS/SPRED1 0.008 0.075 -10000 0 -0.3 13 13
cell proliferation -0.015 0.091 -10000 0 -0.4 23 23
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
TEC 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.002 0.11 -10000 0 -0.42 24 24
HRAS/SPRED2 0.008 0.076 -10000 0 -0.31 13 13
LYN/TEC/p62DOK 0.02 0.096 0.31 1 -0.41 18 19
MAPK3 -0.001 0.066 0.29 3 -0.24 5 8
STAP1 -0.018 0.097 0.32 1 -0.42 23 24
GRAP2 0.011 0.056 -10000 0 -0.32 14 14
JAK2 -0.037 0.19 0.42 1 -0.8 24 25
STAT1 (dimer) -0.04 0.2 0.44 1 -0.91 24 25
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.018 0.097 -10000 0 -0.4 17 17
actin filament polymerization -0.013 0.084 0.32 1 -0.39 18 19
LYN 0.02 0.006 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.032 0.14 0.36 1 -0.56 25 26
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CBL/CRKL/GRB2 0.007 0.087 0.41 2 -0.37 16 18
PI3K 0.015 0.1 -10000 0 -0.41 21 21
PTEN 0.021 0.003 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.023 0.23 -10000 0 -1.1 23 23
MAPK8 -0.016 0.092 -10000 0 -0.41 23 23
STAT3 (dimer) -0.015 0.093 0.32 1 -0.4 24 25
positive regulation of transcription 0.001 0.058 0.23 5 -0.2 4 9
mol:GDP 0 0.08 -10000 0 -0.39 13 13
PIK3C2B -0.014 0.094 0.44 2 -0.43 19 21
CBL/CRKL -0.002 0.091 0.42 2 -0.38 19 21
FER -0.015 0.093 0.32 1 -0.41 23 24
SH2B3 -0.015 0.093 0.32 1 -0.41 24 25
PDPK1 0.001 0.099 0.34 3 -0.38 18 21
SNAI2 -0.012 0.089 0.32 1 -0.42 20 21
positive regulation of cell proliferation -0.033 0.16 0.4 1 -0.68 25 26
KITLG 0.014 0.037 -10000 0 -0.35 4 4
cell motility -0.033 0.16 0.4 1 -0.68 25 26
PTPN6 0.019 0.011 -10000 0 -10000 0 0
EPOR -0.018 0.16 -10000 0 -0.8 10 10
STAT5A (dimer) -0.024 0.14 0.38 1 -0.56 26 27
SOCS1 0.022 0.019 0.32 2 -10000 0 2
cell migration 0.019 0.094 0.41 24 -10000 0 24
SOS1 0.021 0.003 -10000 0 -10000 0 0
EPO 0.02 0.029 0.32 4 -10000 0 4
VAV1 0.018 0.027 -10000 0 -0.32 3 3
GRB10 -0.014 0.09 0.33 1 -0.42 19 20
PTPN11 0.019 0.01 -10000 0 -10000 0 0
SCF/KIT -0.01 0.1 0.35 1 -0.42 24 25
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.005 0.066 0.22 6 -0.24 11 17
CBL 0.02 0.005 -10000 0 -10000 0 0
KIT -0.035 0.25 0.47 1 -1.1 25 26
MAP2K2 -0.004 0.064 0.22 6 -0.24 13 19
SHC/Grb2/SOS1 0.016 0.089 -10000 0 -0.42 13 13
STAT5A -0.023 0.14 0.38 1 -0.57 26 27
GRB2 0.02 0.005 -10000 0 -10000 0 0
response to radiation -0.012 0.087 0.32 1 -0.41 20 21
SHC/GRAP2 0.023 0.028 -10000 0 -0.23 5 5
PTPRO -0.025 0.1 -10000 0 -0.41 26 26
SH2B2 -0.013 0.085 0.32 1 -0.4 18 19
DOK1 0.021 0.002 -10000 0 -10000 0 0
MATK -0.019 0.095 -10000 0 -0.42 24 24
CREBBP 0.02 0.033 0.29 1 -10000 0 1
BCL2 -0.038 0.19 0.47 1 -0.71 22 23
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.005 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.004 0.05 -10000 0 -0.2 27 27
CDKN1A -0.011 0.004 -10000 0 -10000 0 0
KAT2B 0.02 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
FOXO3 -0.003 0.002 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
FOXO4 0.006 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
TAT 0.047 0.086 0.32 45 -10000 0 45
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.014 0.16 3 -10000 0 3
PPARGC1A -0.062 0.15 0.32 1 -0.32 123 124
FHL2 0.059 0.1 0.32 64 -10000 0 64
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.03 0.012 0.25 1 -10000 0 1
HIST2H4A -0.004 0.05 0.2 27 -10000 0 27
SIRT1/FOXO3a 0.013 0.028 0.24 1 -0.2 4 5
SIRT1 0.021 0.015 0.35 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.036 0.019 0.24 1 -10000 0 1
SIRT1/Histone H1b 0.024 0.04 0.24 2 -0.22 4 6
apoptosis -0.039 0.015 -10000 0 -0.23 1 1
SIRT1/PGC1A -0.023 0.093 0.22 2 -0.19 120 122
p53/SIRT1 0.027 0.025 0.55 1 -10000 0 1
SIRT1/FOXO4 0.016 0.034 0.24 1 -0.22 4 5
FOXO1/FHL2/SIRT1 0.058 0.058 0.21 62 -10000 0 62
HIST1H1E 0.015 0.031 0.23 1 -10000 0 1
SIRT1/p300 0.029 0.012 0.25 1 -10000 0 1
muscle cell differentiation -0.024 0.018 -10000 0 -0.21 4 4
TP53 0.019 0.016 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.039 0.015 0.24 1 -10000 0 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
MEF2D 0.018 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.046 0.057 0.23 43 -10000 0 43
ACSS2 -0.016 0.016 0.27 1 -0.23 1 2
SIRT1/PCAF/MYOD 0.024 0.018 0.21 4 -10000 0 4
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.072 0.29 2 -0.38 1 3
Syndecan-3/Neurocan 0.025 0.047 0.28 6 -0.28 3 9
POMC 0.014 0.072 0.32 7 -0.32 17 24
EGFR 0.014 0.045 0.32 1 -0.32 8 9
Syndecan-3/EGFR 0.016 0.035 0.3 1 -0.29 3 4
AGRP -0.12 0.17 -10000 0 -0.32 209 209
NCSTN 0.019 0.007 -10000 0 -10000 0 0
PSENEN 0.02 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
NCAN 0.029 0.053 0.32 16 -10000 0 16
long-term memory 0.037 0.037 -10000 0 -0.36 1 1
Syndecan-3/IL8 0.025 0.047 0.26 4 -0.29 3 7
PSEN1 0.021 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.029 0.009 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
limb bud formation 0.005 0.018 -10000 0 -0.4 1 1
MC4R 0.038 0.075 0.32 33 -10000 0 33
SRC 0.02 0.004 -10000 0 -10000 0 0
PTN -0.017 0.12 0.32 6 -0.32 61 67
FGFR/FGF/Syndecan-3 0.005 0.018 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.01 0.072 0.36 6 -0.37 1 7
Syndecan-3/AgRP -0.036 0.08 -10000 0 -0.31 4 4
Syndecan-3/AgRP/MC4R -0.022 0.099 0.28 3 -0.33 3 6
Fyn/Cortactin 0.028 0.011 -10000 0 -10000 0 0
SDC3 0.005 0.019 -10000 0 -0.41 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.025 0.047 0.26 4 -0.29 3 7
IL8 0.029 0.059 0.32 17 -0.32 2 19
Syndecan-3/Fyn/Cortactin 0.038 0.038 -10000 0 -0.37 1 1
Syndecan-3/CASK 0.003 0.024 -10000 0 -0.29 3 3
alpha-MSH/MC4R 0.034 0.07 0.23 35 -0.21 17 52
Gamma Secretase 0.047 0.031 -10000 0 -0.17 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.037 0.05 0.23 23 -0.23 5 28
AKT1 -0.026 0.1 0.35 4 -0.41 17 21
PTK2B -0.03 0.09 0.33 2 -0.43 13 15
VEGFR2 homodimer/Frs2 -0.012 0.094 -10000 0 -0.48 12 12
CAV1 -0.19 0.17 -10000 0 -0.32 309 309
CALM1 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.002 0.09 -10000 0 -0.44 12 12
endothelial cell proliferation -0.024 0.12 0.37 9 -0.4 20 29
mol:Ca2+ -0.039 0.078 -10000 0 -0.41 12 12
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.009 0.091 -10000 0 -0.44 12 12
RP11-342D11.1 -0.035 0.079 -10000 0 -0.43 12 12
CDH5 -0.018 0.11 -10000 0 -0.32 58 58
VEGFA homodimer 0.042 0.024 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
SHC2 0.016 0.043 0.32 1 -0.32 7 8
HRAS/GDP 0.005 0.076 -10000 0 -0.36 12 12
SH2D2A 0.019 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.018 0.12 -10000 0 -0.41 34 34
VEGFR2 homodimer/VEGFA homodimer/TsAd 0 0.092 -10000 0 -0.47 12 12
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.018 0.086 -10000 0 -0.39 12 12
GRB10 -0.037 0.078 -10000 0 -0.44 11 11
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
PAK1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.003 0.12 -10000 0 -0.4 26 26
HRAS 0.021 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.012 0.078 0.2 1 -0.3 22 23
HIF1A 0.021 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.008 0.09 -10000 0 -0.43 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.012 0.054 -10000 0 -0.32 13 13
Nck/Pak 0.03 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.001 0.093 -10000 0 -0.46 12 12
mol:GDP 0.011 0.081 -10000 0 -0.38 12 12
mol:NADP -0.025 0.12 0.36 6 -0.38 36 42
eNOS/Hsp90 -0.016 0.12 0.36 4 -0.37 33 37
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.039 0.078 -10000 0 -0.41 12 12
HIF1A/ARNT 0.025 0.013 -10000 0 -10000 0 0
SHB 0.02 0.006 -10000 0 -10000 0 0
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFC 0.02 0.029 0.32 2 -0.32 2 4
FAK1/Vinculin -0.013 0.12 0.29 8 -0.45 18 26
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.018 0.11 0.32 1 -0.45 13 14
PTPN6 0.02 0.005 -10000 0 -10000 0 0
EPAS1 -0.022 0.12 -10000 0 -0.34 64 64
mol:L-citrulline -0.025 0.12 0.36 6 -0.38 36 42
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.012 0.089 -10000 0 -0.41 12 12
VEGFR2 homodimer/VEGFA homodimer 0.002 0.094 -10000 0 -0.47 12 12
VEGFR2/3 heterodimer -0.016 0.11 -10000 0 -0.5 16 16
VEGFB 0.021 0.003 -10000 0 -10000 0 0
MAPK11 -0.029 0.093 0.33 4 -0.45 12 16
VEGFR2 homodimer -0.046 0.1 -10000 0 -0.58 12 12
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.02 0.016 -10000 0 -0.32 1 1
MAPK3 -0.028 0.092 0.32 8 -0.42 11 19
MAPK1 -0.027 0.09 0.28 10 -0.4 11 21
VEGFA145/NRP2 0.029 0.02 -10000 0 -0.22 3 3
VEGFR1/2 heterodimer -0.012 0.097 -10000 0 -0.51 12 12
KDR -0.046 0.1 -10000 0 -0.58 12 12
VEGFA165/NRP1/VEGFR2 homodimer 0.003 0.089 -10000 0 -0.44 12 12
SRC 0.02 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.026 0.097 0.3 11 -0.4 12 23
PI3K -0.04 0.085 -10000 0 -0.47 12 12
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.002 0.094 -10000 0 -0.47 12 12
FES -0.04 0.081 -10000 0 -0.45 12 12
GAB1 -0.027 0.098 -10000 0 -0.47 13 13
VEGFR2 homodimer/VEGFA homodimer/Src 0.001 0.093 -10000 0 -0.46 12 12
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.089 0.13 -10000 0 -0.44 38 38
VEGFR2 homodimer/VEGFA homodimer/Yes 0.001 0.093 -10000 0 -0.47 12 12
PI3K/GAB1 -0.015 0.1 -10000 0 -0.44 14 14
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.022 0.092 -10000 0 -0.41 12 12
PRKACA 0.02 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.005 0.1 -10000 0 -0.46 16 16
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 -0.039 0.081 -10000 0 -0.45 12 12
actin cytoskeleton reorganization 0 0.092 -10000 0 -0.47 12 12
PTK2 -0.026 0.11 0.32 2 -0.48 19 21
EDG1 -0.035 0.079 -10000 0 -0.43 12 12
mol:DAG -0.039 0.078 -10000 0 -0.41 12 12
CaM/Ca2+ -0.035 0.077 -10000 0 -0.39 12 12
MAP2K3 -0.034 0.078 -10000 0 -0.39 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.012 0.1 -10000 0 -0.44 12 12
PLCG1 -0.039 0.079 -10000 0 -0.42 12 12
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.01 0.091 -10000 0 -0.42 12 12
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0 0.094 -10000 0 -0.47 12 12
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.001 0.092 -10000 0 -0.46 12 12
cell migration -0.022 0.12 0.3 7 -0.43 20 27
mol:PI-3-4-5-P3 -0.038 0.08 -10000 0 -0.44 12 12
FYN 0.019 0.016 -10000 0 -0.32 1 1
VEGFB/NRP1 -0.038 0.075 -10000 0 -0.42 12 12
mol:NO -0.025 0.12 0.36 6 -0.38 36 42
PXN 0.021 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.043 0.062 -10000 0 -0.36 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.074 -10000 0 -0.45 11 11
VHL 0.02 0.005 -10000 0 -10000 0 0
ITGB3 0.031 0.072 0.32 23 -0.32 5 28
NOS3 -0.029 0.14 0.37 6 -0.43 36 42
VEGFR2 homodimer/VEGFA homodimer/Sck -0.002 0.099 -10000 0 -0.45 15 15
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.037 0.077 -10000 0 -0.41 11 11
PRKCB -0.04 0.085 0.33 1 -0.43 12 13
VCL 0.021 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.035 0.08 -10000 0 -0.43 12 12
VEGFR1/2 heterodimer/VEGFA homodimer 0 0.094 -10000 0 -0.47 12 12
VEGFA165/NRP2 0.029 0.02 -10000 0 -0.22 3 3
MAPKKK cascade -0.028 0.086 0.31 3 -0.41 8 11
NRP2 0.019 0.026 -10000 0 -0.32 3 3
VEGFC homodimer 0.02 0.029 0.32 2 -0.32 2 4
NCK1 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0.02 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.014 0.12 0.28 7 -0.46 18 25
MAP3K13 -0.037 0.078 -10000 0 -0.42 12 12
PDPK1 -0.038 0.075 0.24 2 -0.39 12 14
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.012 0.061 0.24 3 -10000 0 3
DAPP1 -0.018 0.12 0.21 5 -0.34 39 44
Src family/SYK family/BLNK-LAT/BTK-ITK -0.033 0.17 -10000 0 -0.48 46 46
mol:DAG -0.013 0.071 0.18 9 -0.21 22 31
HRAS 0.021 0.007 -10000 0 -10000 0 0
RAP1A 0.021 0.007 -10000 0 -10000 0 0
ARF5/GDP -0.004 0.092 -10000 0 -0.31 24 24
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.004 -10000 0 -10000 0 0
mol:GTP -0.016 0.048 0.15 34 -10000 0 34
ARF1/GTP -0.01 0.045 0.25 5 -0.18 2 7
RHOA 0.021 0.004 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.016 0.047 0.16 31 -10000 0 31
ADAP1 -0.018 0.048 0.19 9 -0.28 1 10
ARAP3 -0.016 0.048 0.15 34 -10000 0 34
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PREX1 0.017 0.031 -10000 0 -0.32 4 4
ARHGEF6 0.008 0.065 -10000 0 -0.32 19 19
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.006 -10000 0 -10000 0 0
NRAS 0.02 0.007 -10000 0 -10000 0 0
FYN 0.019 0.016 -10000 0 -0.32 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
FGR -0.003 0.087 -10000 0 -0.32 35 35
mol:Ca2+ -0.01 0.039 0.14 4 -0.13 7 11
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
ZAP70 0.017 0.037 -10000 0 -0.32 6 6
mol:IP3 -0.015 0.052 0.15 9 -0.17 14 23
LYN 0.02 0.006 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.085 -10000 0 -0.31 19 19
RhoA/GDP -0.01 0.063 0.21 7 -0.25 4 11
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
BLNK 0.02 0.022 -10000 0 -0.32 2 2
actin cytoskeleton reorganization -0.007 0.083 0.26 7 -0.29 16 23
SRC 0.02 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PTEN 0.019 0.014 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.022 0.048 0.28 2 -10000 0 2
RhoA/GTP -0.019 0.049 0.22 6 -10000 0 6
Src family/SYK family/BLNK-LAT -0.015 0.11 -10000 0 -0.32 39 39
BLK 0.065 0.11 0.32 81 -0.32 1 82
PDPK1 0.021 0.003 -10000 0 -10000 0 0
CYTH1 -0.019 0.048 0.21 8 -10000 0 8
HCK 0.006 0.07 -10000 0 -0.32 22 22
CYTH3 -0.017 0.047 0.18 10 -10000 0 10
CYTH2 -0.019 0.049 0.2 9 -10000 0 9
KRAS 0.019 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.047 -10000 0 -0.33 6 6
SGK1 -0.013 0.095 -10000 0 -0.33 37 37
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
mol:GDP -0.014 0.093 0.18 3 -0.29 34 37
SOS1 0.021 0.003 -10000 0 -10000 0 0
SYK 0.019 0.022 -10000 0 -0.32 2 2
ARF6/GDP -0.012 0.061 0.2 9 -0.22 5 14
mol:PI-3-4-5-P3 -0.018 0.043 0.17 6 -10000 0 6
ARAP3/RAP1A/GTP -0.017 0.048 0.16 31 -10000 0 31
VAV1 0.018 0.027 -10000 0 -0.32 3 3
mol:PI-3-4-P2 -0.017 0.014 -10000 0 -0.23 2 2
RAS family/GTP/PI3K Class I -0.022 0.034 0.18 8 -10000 0 8
PLEKHA1 -0.02 0.012 -10000 0 -0.2 2 2
Rac1/GDP -0.004 0.088 0.18 1 -0.28 32 33
LAT 0.022 0.014 0.32 1 -10000 0 1
Rac1/GTP -0.006 0.096 0.21 1 -0.36 26 27
ITK -0.023 0.047 0.18 7 -0.17 7 14
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.022 0.09 0.22 6 -0.29 25 31
LCK 0.02 0.026 0.32 1 -0.32 2 3
BTK -0.027 0.056 0.18 9 -0.18 23 32
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 0.024 0.018 -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 0.021 0.11 0.43 12 -10000 0 12
IL27/IL27R/JAK1 0.03 0.092 -10000 0 -0.88 1 1
TBX21 -0.024 0.11 0.9 1 -0.58 4 5
IL12B 0.024 0.034 0.32 5 -0.32 1 6
IL12A -0.009 0.023 0.16 1 -0.22 5 6
IL6ST 0.006 0.069 -10000 0 -0.33 20 20
IL27RA/JAK1 0.008 0.057 0.38 1 -1.1 1 2
IL27 0.009 0.059 -10000 0 -0.33 14 14
TYK2 0.021 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.016 0.12 0.42 3 -0.38 5 8
T-helper 2 cell differentiation 0.021 0.11 0.43 12 -10000 0 12
T cell proliferation during immune response 0.021 0.11 0.43 12 -10000 0 12
MAPKKK cascade -0.021 0.11 -10000 0 -0.43 12 12
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT2 0.021 0.004 -10000 0 -10000 0 0
STAT1 0.02 0.009 -10000 0 -10000 0 0
IL12RB1 0.012 0.053 -10000 0 -0.32 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.014 0.11 0.38 10 -0.5 4 14
IL27/IL27R/JAK2/TYK2 -0.022 0.11 -10000 0 -0.44 12 12
positive regulation of T cell mediated cytotoxicity -0.021 0.11 -10000 0 -0.43 12 12
STAT1 (dimer) 0.026 0.12 -10000 0 -0.58 5 5
JAK2 0.019 0.025 -10000 0 -0.32 2 2
JAK1 0.02 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.014 0.12 0.45 1 -0.4 17 18
T cell proliferation -0.046 0.12 0.32 1 -0.42 26 27
IL12/IL12R/TYK2/JAK2 -0.035 0.24 -10000 0 -0.8 41 41
IL17A -0.019 0.12 0.44 2 -0.38 7 9
mast cell activation 0.021 0.11 0.43 12 -10000 0 12
IFNG 0.001 0.042 0.11 33 -0.11 20 53
T cell differentiation -0.001 0.005 0.013 9 -0.02 14 23
STAT3 (dimer) -0.014 0.12 0.45 1 -0.41 15 16
STAT5A (dimer) -0.015 0.12 0.45 1 -0.42 15 16
STAT4 (dimer) -0.014 0.12 0.45 1 -0.4 16 17
STAT4 0.021 0.002 -10000 0 -10000 0 0
T cell activation -0.003 0.006 0.11 1 -10000 0 1
IL27R/JAK2/TYK2 0.027 0.077 -10000 0 -0.61 2 2
GATA3 -0.002 0.094 0.63 7 -1.1 1 8
IL18 -0.011 0.03 -10000 0 -0.22 10 10
positive regulation of mast cell cytokine production -0.014 0.12 0.45 1 -0.4 15 16
IL27/EBI3 0.023 0.048 -10000 0 -0.23 15 15
IL27RA -0.001 0.056 -10000 0 -1.1 1 1
IL6 -0.047 0.14 -10000 0 -0.32 102 102
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.008 0.032 0.4 2 -10000 0 2
IL1B -0.021 0.051 -10000 0 -0.22 31 31
EBI3 0.02 0.021 -10000 0 -0.32 1 1
TNF -0.013 0.037 0.16 1 -0.22 15 16
Signaling events mediated by PRL

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
CCNE1 0.12 0.14 0.32 163 -10000 0 163
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.019 0.022 -10000 0 -0.32 2 2
CDKN1A 0.005 0.025 -10000 0 -0.32 2 2
PRL-3/alpha Tubulin 0.028 0.014 0.23 1 -10000 0 1
mol:Ca2+ 0.001 0.064 0.16 60 -0.23 6 66
AGT 0.059 0.11 0.32 72 -0.32 5 77
CCNA2 -0.006 0.055 0.35 6 -10000 0 6
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
EGR1 -0.016 0.045 -10000 0 -0.22 24 24
CDK2/Cyclin E1 0.085 0.095 0.32 10 -0.3 3 13
MAPK3 -0.014 0.016 0.21 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.03 0.007 -10000 0 -10000 0 0
MAPK1 -0.013 0.016 0.21 2 -10000 0 2
PTP4A1 -0.02 0.031 -10000 0 -10000 0 0
PTP4A3 0.019 0.015 0.32 1 -10000 0 1
PTP4A2 0.021 0.002 -10000 0 -10000 0 0
ITGB1 -0.014 0.01 0.16 1 -10000 0 1
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.004 0.032 -10000 0 -0.45 2 2
Rab GGTase beta/Rab GGTase alpha 0.029 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.018 0.044 -10000 0 -10000 0 0
RABGGTA 0.02 0.005 -10000 0 -10000 0 0
BCAR1 -0.019 0.015 -10000 0 -0.23 2 2
RHOC 0.002 0.044 -10000 0 -0.36 6 6
RHOA 0 0.048 -10000 0 -0.34 9 9
cell motility 0.005 0.062 0.27 3 -0.31 8 11
PRL-1/alpha Tubulin -0.019 0.043 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.019 0.23 1 -0.23 1 2
ROCK1 0.003 0.052 0.27 3 -0.33 5 8
RABGGTB 0.021 0.004 -10000 0 -10000 0 0
CDK2 0.021 0.004 -10000 0 -10000 0 0
mitosis -0.02 0.031 -10000 0 -10000 0 0
ATF5 0.021 0.014 0.32 1 -10000 0 1
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 0.028 0.021 0.23 1 -0.23 2 3
ATM 0.02 0.004 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
UBE2L3 0.02 0.005 -10000 0 -10000 0 0
FANCD2 0.011 0.013 0.17 3 -10000 0 3
protein ubiquitination 0.099 0.078 0.34 3 -0.17 1 4
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.017 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
DNA-PK 0.038 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.001 0.089 -10000 0 -0.47 12 12
FANCF 0.021 0.003 -10000 0 -10000 0 0
BRCA1 0.021 0.014 0.32 1 -10000 0 1
CCNE1 0.12 0.14 0.32 163 -10000 0 163
CDK2/Cyclin E1 0.091 0.096 0.23 157 -10000 0 157
FANCG 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.03 0.021 0.23 2 -0.23 2 4
FANCE 0.021 0.004 -10000 0 -10000 0 0
FANCC 0.02 0.005 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
FANCA 0.032 0.059 0.32 20 -10000 0 20
DNA repair 0.004 0.068 0.22 6 -0.36 5 11
BRCA1/BARD1/ubiquitin 0.03 0.021 0.23 2 -0.23 2 4
BARD1/DNA-PK 0.047 0.024 -10000 0 -0.18 2 2
FANCL 0.021 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.021 0.23 2 -0.23 1 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.038 -10000 0 -0.22 6 6
BRCA1/BACH1/BARD1/TopBP1 0.041 0.021 0.22 2 -0.2 2 4
BRCA1/BARD1/P53 0.048 0.025 0.23 1 -0.18 2 3
BARD1/CSTF1/BRCA1 0.038 0.023 0.22 2 -0.2 2 4
BRCA1/BACH1 0.021 0.014 0.32 1 -10000 0 1
BARD1 0.02 0.026 0.32 1 -0.32 2 3
PCNA 0.021 0.014 0.32 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.041 0.021 0.22 2 -0.2 2 4
BRCA1/BARD1/UbcH7 0.038 0.019 -10000 0 -0.2 2 2
BRCA1/BARD1/RAD51/PCNA 0.075 0.072 0.23 78 -0.18 2 80
BARD1/DNA-PK/P53 0.05 0.03 -10000 0 -0.17 2 2
BRCA1/BARD1/Ubiquitin 0.03 0.021 0.23 2 -0.23 2 4
BRCA1/BARD1/CTIP 0.028 0.02 0.21 2 -0.17 2 4
FA complex 0.01 0.043 0.22 2 -0.27 3 5
BARD1/EWS 0.029 0.02 0.23 1 -0.23 2 3
RBBP8 -0.015 0.005 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
TOPBP1 0.021 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.024 0.18 2 -0.22 1 3
BRCA1/BARD1 0.11 0.084 0.37 3 -0.17 1 4
CSTF1 0.02 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.015 0.017 0.22 1 -0.22 2 3
CDK2 0.021 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.069 0.11 0.32 82 -10000 0 82
RAD50 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.03 0.021 0.23 2 -0.23 2 4
EWSR1 0.02 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0.034 -10000 0 -0.32 5 5
ELF1 0.032 0.039 -10000 0 -10000 0 0
CCNA2 0.089 0.13 0.32 115 -10000 0 115
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
JAK3 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.021 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.07 -10000 0 -0.4 4 4
SHC1 0.019 0.016 0.32 1 -10000 0 1
SP1 0.017 0.043 -10000 0 -0.3 9 9
IL2RA 0.008 0.08 0.3 35 -10000 0 35
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
SOS1 0.021 0.003 -10000 0 -10000 0 0
IL2RG 0.018 0.034 -10000 0 -0.32 5 5
G1/S transition of mitotic cell cycle 0.029 0.1 0.3 21 -0.42 11 32
PTPN11 0.021 0.004 -10000 0 -10000 0 0
CCND2 -0.024 0.076 -10000 0 -0.59 9 9
LCK 0.02 0.026 0.32 1 -0.32 2 3
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL2 0.02 0.003 -10000 0 -10000 0 0
CDK6 0.02 0.016 -10000 0 -0.32 1 1
CCND3 0.019 0.077 0.42 2 -0.39 2 4
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.001 0.078 0.26 2 -0.3 20 22
PDGFB-D/PDGFRB/SLAP 0.022 0.034 -10000 0 -0.23 8 8
PDGFB-D/PDGFRB/APS/CBL 0.038 0.018 -10000 0 -0.2 1 1
AKT1 -0.012 0.078 0.34 12 -10000 0 12
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.095 0.28 5 -0.35 21 26
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FGR -0.029 0.14 0.32 2 -0.48 43 45
mol:Ca2+ -0.003 0.1 0.27 6 -0.39 24 30
MYC 0.034 0.13 0.38 16 -0.51 5 21
SHC1 0.019 0.016 0.32 1 -10000 0 1
HRAS/GDP -0.012 0.042 0.16 29 -10000 0 29
LRP1/PDGFRB/PDGFB 0.036 0.03 -10000 0 -0.19 7 7
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 -0.004 0.1 0.27 6 -0.39 24 30
PTEN 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PDGFB-D/PDGFRB/SHP2 0.03 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.028 0.011 -10000 0 -10000 0 0
cell cycle arrest 0.022 0.034 -10000 0 -0.22 8 8
HRAS 0.021 0.004 -10000 0 -10000 0 0
HIF1A -0.015 0.072 0.32 12 -10000 0 12
GAB1 -0.001 0.098 0.29 4 -0.35 20 24
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.001 0.086 0.28 7 -0.32 13 20
PDGFB-D/PDGFRB 0.038 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.03 0.008 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.057 -10000 0 -0.27 7 7
positive regulation of MAPKKK cascade 0.03 0.009 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.004 0.11 0.27 6 -0.4 24 30
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.019 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.018 -10000 0 -0.23 2 2
SHB 0.02 0.006 -10000 0 -10000 0 0
BLK -0.026 0.17 0.32 4 -0.4 72 76
PTPN2 0.019 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.03 0.009 -10000 0 -10000 0 0
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
VAV2 -0.004 0.11 0.28 6 -0.38 21 27
CBL 0.02 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.008 -10000 0 -10000 0 0
LCK 0.007 0.06 0.32 2 -0.42 4 6
PDGFRB 0.02 0.009 -10000 0 -10000 0 0
ACP1 0.021 0.002 -10000 0 -10000 0 0
HCK -0.017 0.13 0.33 2 -0.54 27 29
ABL1 -0.005 0.1 0.25 7 -0.35 23 30
PDGFB-D/PDGFRB/CBL -0.005 0.11 0.31 2 -0.4 26 28
PTPN1 0.019 0.009 -10000 0 -10000 0 0
SNX15 0.021 0.004 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
cell proliferation 0.034 0.12 0.37 18 -0.46 5 23
SLA 0.012 0.046 -10000 0 -0.32 9 9
actin cytoskeleton reorganization -0.014 0.06 0.32 6 -10000 0 6
SRC 0.001 0.091 0.32 2 -0.59 9 11
PI3K -0.032 0.02 -10000 0 -0.17 6 6
PDGFB-D/PDGFRB/GRB7/SHC 0.034 0.023 -10000 0 -0.2 2 2
SH2B2 0.019 0.016 -10000 0 -0.32 1 1
PLCgamma1/SPHK1 0.006 0.097 0.28 5 -0.36 21 26
LYN 0.007 0.053 0.31 1 -0.41 3 4
LRP1 0.018 0.031 -10000 0 -0.32 4 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
NCK1-2/p130 Cas 0.052 0.03 -10000 0 -0.17 1 1
SPHK1 0.023 0.031 0.32 5 -10000 0 5
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.004 0.11 0.27 6 -0.4 24 30
PLCG1 -0.004 0.11 0.27 6 -0.4 24 30
NHERF/PDGFRB 0.038 0.028 0.22 1 -0.2 5 6
YES1 -0.011 0.12 0.34 1 -0.58 18 19
cell migration 0.037 0.028 0.22 1 -0.2 5 6
SHC/Grb2/SOS1 0.046 0.032 -10000 0 -10000 0 0
SLC9A3R2 0.017 0.034 -10000 0 -0.32 5 5
SLC9A3R1 0.021 0.014 0.32 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.047 0.03 0.23 1 -0.18 5 6
FYN -0.027 0.13 0.32 2 -0.42 44 46
DOK1 -0.011 0.042 0.16 27 -10000 0 27
HRAS/GTP 0.015 0.003 -10000 0 -10000 0 0
PDGFB 0.018 0.031 -10000 0 -0.32 4 4
RAC1 0.011 0.12 0.34 9 -0.4 14 23
PRKCD -0.01 0.044 0.17 30 -10000 0 30
FER -0.01 0.044 0.17 29 -10000 0 29
MAPKKK cascade 0.016 0.1 0.39 19 -10000 0 19
RASA1 -0.01 0.043 0.17 28 -10000 0 28
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.014 0.044 0.16 30 -10000 0 30
PDGFB-D/PDGFRB/SHB 0.029 0.01 -10000 0 -10000 0 0
chemotaxis -0.005 0.099 0.25 7 -0.34 23 30
STAT1-3-5/STAT1-3-5 0.043 0.026 -10000 0 -0.18 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.006 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.028 0.03 0.21 10 -0.17 3 13
EFNA5 0.019 0.033 0.32 2 -0.32 3 5
FYN -0.012 0.03 0.18 9 -0.18 2 11
neuron projection morphogenesis 0.028 0.03 0.21 10 -0.17 3 13
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.028 0.031 0.21 10 -0.17 3 13
EPHA5 0.025 0.04 0.32 9 -10000 0 9
Insulin 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
CBL/APS/CAP 0.027 0.045 -10000 0 -0.16 21 21
TC10/GTP 0.023 0.043 -10000 0 -0.16 20 20
Insulin Receptor/Insulin/IRS1/Shp2 0.049 0.02 -10000 0 -0.15 1 1
HRAS 0.021 0.004 -10000 0 -10000 0 0
APS homodimer 0.019 0.016 -10000 0 -0.32 1 1
GRB14 0.034 0.078 0.32 28 -0.32 5 33
FOXO3 -0.048 0.19 -10000 0 -0.62 52 52
AKT1 -0.02 0.053 0.28 5 -10000 0 5
INSR 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.007 -10000 0 -10000 0 0
SORBS1 0.002 0.079 -10000 0 -0.32 28 28
CRK 0.019 0.006 -10000 0 -10000 0 0
PTPN1 -0.013 0.019 -10000 0 -10000 0 0
CAV1 -0.096 0.08 -10000 0 -0.17 263 263
CBL/APS/CAP/Crk-II/C3G 0.04 0.052 -10000 0 -0.17 21 21
Insulin Receptor/Insulin/IRS1/NCK2 0.05 0.02 -10000 0 -0.15 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.021 -10000 0 -0.17 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.001 0.07 -10000 0 -0.32 17 17
RPS6KB1 -0.023 0.048 0.27 5 -10000 0 5
PARD6A 0.02 0.016 -10000 0 -0.32 1 1
CBL 0.02 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.012 0.037 -10000 0 -0.57 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.026 0.042 0.16 1 -10000 0 1
HRAS/GTP -0.027 0.019 -10000 0 -0.16 1 1
Insulin Receptor 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.049 0.029 -10000 0 -10000 0 0
PRKCI 0.003 0.074 -10000 0 -0.3 23 23
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.033 -10000 0 -0.17 4 4
SHC1 0.019 0.016 0.32 1 -10000 0 1
negative regulation of MAPKKK cascade 0.029 0.039 -10000 0 -0.48 2 2
PI3K 0.046 0.024 -10000 0 -0.17 1 1
NCK2 0.021 0.002 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
AKT2 -0.02 0.052 0.27 6 -10000 0 6
PRKCZ -0.002 0.085 -10000 0 -0.33 24 24
SH2B2 0.019 0.016 -10000 0 -0.32 1 1
SHC/SHIP -0.018 0.025 0.16 4 -0.17 2 6
F2RL2 0.036 0.079 0.32 31 -0.32 4 35
TRIP10 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.033 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.049 0.029 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.034 0.051 -10000 0 -0.18 23 23
TC10/GDP 0.016 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.04 0.025 -10000 0 -10000 0 0
INPP5D -0.019 0.019 0.15 2 -0.17 2 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
SGK1 -0.051 0.19 -10000 0 -0.66 47 47
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.015 -10000 0 -0.32 1 1
p62DOK/RasGAP 0.03 0.04 -10000 0 -0.49 2 2
INS -0.014 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.019 0.15 2 -0.17 2 4
GRB2 0.02 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.052 0.21 11 -10000 0 11
PTPRA 0.022 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.027 0.008 -10000 0 -10000 0 0
PDPK1 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.023 -10000 0 -0.19 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.016 -10000 0 -0.14 1 1
Insulin Receptor/Insulin/IRS3 0.03 0.012 -10000 0 -10000 0 0
Par3/Par6 0.051 0.044 0.21 26 -0.16 4 30
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.018 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.011 0.003 -10000 0 -10000 0 0
mol:DAG -0.014 0.033 0.23 5 -10000 0 5
VEGFR1 homodimer/NRP1/VEGFR 121 0.017 0.006 -10000 0 -10000 0 0
CaM/Ca2+ -0.018 0.027 0.19 3 -10000 0 3
HIF1A 0.023 0.004 -10000 0 -10000 0 0
GAB1 0.02 0.022 -10000 0 -0.32 2 2
AKT1 -0.014 0.046 0.41 3 -10000 0 3
PLCG1 -0.014 0.033 0.23 5 -10000 0 5
NOS3 -0.007 0.085 0.44 7 -0.43 4 11
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:NO -0.003 0.094 0.47 9 -0.42 4 13
FLT1 -0.014 0.004 -10000 0 -10000 0 0
PGF 0.029 0.051 0.32 15 -10000 0 15
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.016 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 -0.012 0.083 0.36 5 -0.43 6 11
endothelial cell proliferation -0.006 0.058 0.34 7 -0.24 1 8
mol:Ca2+ -0.014 0.033 0.23 5 -10000 0 5
MAPK3 -0.019 0.041 0.26 9 -10000 0 9
MAPK1 -0.02 0.037 0.28 6 -10000 0 6
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
PLGF homodimer 0.029 0.051 0.32 15 -10000 0 15
PRKACA 0.02 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.19 0.17 -10000 0 -0.32 309 309
VEGFA homodimer 0.021 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.018 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.021 0.05 0.36 6 -10000 0 6
PI3K 0.042 0.035 -10000 0 -10000 0 0
PRKCA -0.018 0.028 0.23 4 -10000 0 4
PRKCB -0.02 0.037 0.22 6 -10000 0 6
VEGFR1 homodimer/PLGF homodimer 0.024 0.035 0.22 15 -10000 0 15
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFB 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 -0.014 0.033 0.23 5 -10000 0 5
RASA1 -0.016 0.027 0.18 9 -10000 0 9
NRP2 0.019 0.026 -10000 0 -0.32 3 3
VEGFR1 homodimer -0.014 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.09 0.1 0.44 2 -0.39 22 24
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.034 -10000 0 -10000 0 0
mol:L-citrulline -0.003 0.094 0.47 9 -0.42 4 13
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.038 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.011 -10000 0 -10000 0 0
CD2AP 0.021 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.049 0.04 -10000 0 -10000 0 0
PDPK1 -0.016 0.05 0.38 4 -10000 0 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.011 -10000 0 -10000 0 0
mol:NADP -0.003 0.094 0.47 9 -0.42 4 13
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.018 0.015 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.016 0.017 -10000 0 -10000 0 0
HSPA8 0.019 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.025 0.06 0.23 7 -0.23 7 14
AKT1 0.014 0.028 -10000 0 -10000 0 0
GSC 0.038 0.11 0.8 2 -10000 0 2
NKX2-5 0 0 -10000 0 -10000 0 0
muscle cell differentiation -0.012 0.076 0.28 4 -10000 0 4
SMAD2-3/SMAD4/SP1 0.047 0.065 -10000 0 -0.25 1 1
SMAD4 0.016 0.032 -10000 0 -0.17 1 1
CBFB 0.021 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.025 0.06 0.23 7 -0.2 24 31
SMAD3/SMAD4/VDR 0.042 0.049 -10000 0 -0.23 1 1
MYC 0.019 0.026 -10000 0 -0.33 2 2
CDKN2B -0.17 0.4 -10000 0 -1.2 57 57
AP1 0.007 0.057 -10000 0 -0.24 9 9
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.022 0.096 -10000 0 -0.32 31 31
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.022 0.1 0.18 1 -0.32 38 39
SP3 0.021 0.003 -10000 0 -10000 0 0
CREB1 0.021 0.003 -10000 0 -10000 0 0
FOXH1 0.052 0.093 0.33 51 -10000 0 51
SMAD3/SMAD4/GR 0.03 0.042 -10000 0 -0.18 1 1
GATA3 0.02 0.025 0.32 1 -0.32 1 2
SKI/SIN3/HDAC complex/NCoR1 -0.014 0.074 -10000 0 -0.34 15 15
MEF2C/TIF2 0.007 0.061 0.33 2 -0.23 1 3
endothelial cell migration -0.014 0.077 0.72 4 -10000 0 4
MAX 0.02 0.009 -10000 0 -10000 0 0
RBBP7 0.021 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
RUNX2 0.025 0.035 0.32 7 -10000 0 7
RUNX3 0.019 0.027 -10000 0 -0.32 3 3
RUNX1 0.02 0.005 -10000 0 -10000 0 0
CTBP1 0.021 0.004 -10000 0 -10000 0 0
NR3C1 0.02 0.009 -10000 0 -10000 0 0
VDR 0.021 0.021 0.32 1 -0.32 1 2
CDKN1A -0.001 0.052 -10000 0 -0.84 1 1
KAT2B 0.017 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.059 0.076 0.25 40 -10000 0 40
DCP1A 0.021 0.004 -10000 0 -10000 0 0
SKI 0.021 0.004 -10000 0 -10000 0 0
SERPINE1 0.013 0.077 -10000 0 -0.72 4 4
SMAD3/SMAD4/ATF2 0.031 0.041 -10000 0 -0.18 1 1
SMAD3/SMAD4/ATF3 0.021 0.059 -10000 0 -0.21 18 18
SAP30 0.021 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.03 0.03 -10000 0 -10000 0 0
JUN -0.01 0.054 0.22 1 -0.26 6 7
SMAD3/SMAD4/IRF7 0.034 0.047 0.29 4 -10000 0 4
TFE3 0.022 0.007 -10000 0 -10000 0 0
COL1A2 0.019 0.075 0.31 18 -0.51 4 22
mesenchymal cell differentiation -0.033 0.046 0.18 1 -0.23 5 6
DLX1 0.038 0.072 0.32 30 -10000 0 30
TCF3 0.02 0.006 -10000 0 -10000 0 0
FOS -0.002 0.079 -10000 0 -0.33 26 26
SMAD3/SMAD4/Max 0.03 0.042 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.034 0.024 -10000 0 -10000 0 0
ZBTB17 0.022 0.009 -10000 0 -10000 0 0
LAMC1 -0.012 0.031 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.031 0.041 -10000 0 -0.18 1 1
IRF7 0.023 0.025 0.34 3 -10000 0 3
ESR1 0.016 0.061 0.32 9 -0.32 8 17
HNF4A 0.07 0.13 0.32 97 -0.32 10 107
MEF2C 0.02 0.077 0.31 11 -10000 0 11
SMAD2-3/SMAD4 0.034 0.053 -10000 0 -0.24 1 1
Cbp/p300/Src-1 0.034 0.026 -10000 0 -10000 0 0
IGHV3OR16-13 0.004 0.016 -10000 0 -0.32 1 1
TGIF2/HDAC complex 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.017 0.015 -10000 0 -10000 0 0
SKIL 0.02 0.005 -10000 0 -10000 0 0
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.019 0.006 -10000 0 -10000 0 0
SNIP1 0.02 0.006 -10000 0 -10000 0 0
GCN5L2 0 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.035 0.042 -10000 0 -10000 0 0
MSG1/HSC70 0.021 0.061 0.23 8 -0.22 24 32
SMAD2 0.018 0.027 -10000 0 -10000 0 0
SMAD3 0.009 0.033 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.046 -10000 0 -0.22 4 4
SMAD2/SMAD2/SMAD4 -0.008 0.077 0.21 3 -0.3 17 20
NCOR1 0.02 0.006 -10000 0 -10000 0 0
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
NCOA1 0.021 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.027 0.012 0.23 1 -10000 0 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.052 0.069 -10000 0 -0.27 1 1
IFNB1 -0.013 0.036 0.33 3 -10000 0 3
SMAD3/SMAD4/MEF2C 0.048 0.066 0.27 2 -10000 0 2
CITED1 0.009 0.083 0.32 8 -0.32 24 32
SMAD2-3/SMAD4/ARC105 0.043 0.053 -10000 0 -0.21 1 1
RBL1 0.02 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.042 0.15 -10000 0 -0.52 40 40
RUNX1-3/PEBPB2 0.038 0.021 -10000 0 -0.18 3 3
SMAD7 0 0.077 -10000 0 -0.44 5 5
MYC/MIZ-1 0.028 0.025 0.2 1 -0.23 1 2
SMAD3/SMAD4 -0.004 0.065 -10000 0 -0.35 2 2
IL10 -0.016 0.051 0.3 3 -0.34 6 9
PIASy/HDAC complex 0.018 0.013 -10000 0 -10000 0 0
PIAS3 0.015 0.013 -10000 0 -10000 0 0
CDK2 0.017 0.014 -10000 0 -10000 0 0
IL5 -0.017 0.035 -10000 0 -0.25 1 1
CDK4 0.016 0.015 -10000 0 -10000 0 0
PIAS4 0.018 0.013 -10000 0 -10000 0 0
ATF3 0.007 0.064 -10000 0 -0.32 18 18
SMAD3/SMAD4/SP1 0.036 0.052 -10000 0 -0.2 1 1
FOXG1 0.046 0.09 0.32 49 -10000 0 49
FOXO3 -0.02 0.023 -10000 0 -0.14 2 2
FOXO1 -0.021 0.024 -10000 0 -0.14 1 1
FOXO4 -0.021 0.023 -10000 0 -0.14 1 1
heart looping 0.02 0.077 0.31 11 -10000 0 11
CEBPB 0.014 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.041 0.056 0.24 19 -0.18 1 20
MYOD1 0.019 0.024 0.32 3 -10000 0 3
SMAD3/SMAD4/HNF4 0.058 0.091 0.24 76 -0.2 11 87
SMAD3/SMAD4/GATA3 0.031 0.049 -10000 0 -0.23 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.045 0.048 -10000 0 -0.2 1 1
SMAD3/SMAD4/SP1-3 0.045 0.053 -10000 0 -10000 0 0
MED15 0.02 0.005 -10000 0 -10000 0 0
SP1 0.019 0.021 -10000 0 -10000 0 0
SIN3B 0.02 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.057 0.072 0.26 17 -10000 0 17
ITGB5 -0.014 0.044 0.26 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP -0.011 0.063 -10000 0 -0.32 11 11
SMAD3/SMAD4/AR 0.001 0.091 -10000 0 -0.22 64 64
AR -0.025 0.12 0.32 1 -0.32 69 70
negative regulation of cell growth -0.005 0.066 -10000 0 -0.26 17 17
SMAD3/SMAD4/MYOD 0.03 0.043 0.24 2 -0.18 1 3
E2F5 0.019 0.007 -10000 0 -10000 0 0
E2F4 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.072 0.074 0.3 7 -10000 0 7
SMAD2-3/SMAD4/FOXO1-3a-4 -0.02 0.1 -10000 0 -0.37 35 35
TFDP1 0.019 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.024 0.063 -10000 0 -0.25 9 9
SMAD3/SMAD4/RUNX2 0.033 0.046 0.24 5 -0.18 1 6
TGIF2 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.02 0.006 -10000 0 -10000 0 0
ATF2 0.021 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.041 0.048 0.23 1 -0.21 14 15
MAP4K1 0.017 0.031 -10000 0 -0.32 4 4
MAP3K8 0.02 0.016 -10000 0 -0.32 1 1
PRKCB 0.011 0.056 -10000 0 -0.32 14 14
DBNL 0.019 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.005 -10000 0 -10000 0 0
MAP3K1 0 0.05 -10000 0 -0.3 7 7
JUN -0.012 0.13 -10000 0 -0.56 24 24
MAP3K7 0.001 0.044 -10000 0 -0.23 10 10
GRAP2 0.011 0.056 -10000 0 -0.32 14 14
CRK 0.019 0.006 -10000 0 -10000 0 0
MAP2K4 -0.003 0.069 0.2 2 -0.39 8 10
LAT 0.022 0.014 0.32 1 -10000 0 1
LCP2 0.018 0.027 -10000 0 -0.32 3 3
MAPK8 -0.007 0.13 -10000 0 -0.57 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.058 -10000 0 -0.28 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 0.047 0.042 0.22 1 -0.21 7 8
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.015 -10000 0 -0.32 1 1
ANTXR2 0.021 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.002 -10000 0 -0.046 1 1
monocyte activation -0.01 0.098 -10000 0 -0.36 34 34
MAP2K2 -0.03 0.15 -10000 0 -0.57 37 37
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.007 0.002 -10000 0 -10000 0 0
MAP2K6 -0.006 0.018 0.072 15 -0.16 2 17
CYAA -0.011 0.007 -10000 0 -0.16 1 1
MAP2K4 -0.007 0.002 -10000 0 -10000 0 0
IL1B -0.014 0.036 0.14 4 -0.16 25 29
Channel 0.027 0.01 -10000 0 -0.17 1 1
NLRP1 -0.007 0.007 -10000 0 -0.16 1 1
CALM1 0.02 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.057 -10000 0 -0.39 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.002 0.046 1 -10000 0 1
MAPK3 -0.008 0.002 -10000 0 -10000 0 0
MAPK1 -0.007 0.002 -10000 0 -10000 0 0
PGR -0.032 0.055 -10000 0 -0.16 84 84
PA/Cellular Receptors 0.028 0.011 -10000 0 -0.19 1 1
apoptosis -0.003 0.002 -10000 0 -0.046 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.009 -10000 0 -0.16 1 1
macrophage activation -0.012 0.004 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
VCAM1 -0.009 0.096 -10000 0 -0.37 31 31
platelet activation -0.001 0.057 -10000 0 -0.39 11 11
MAPKKK cascade 0.004 0.017 -10000 0 -0.071 18 18
IL18 -0.009 0.024 0.14 2 -0.21 5 7
negative regulation of macrophage activation -0.003 0.002 -10000 0 -0.046 1 1
LEF -0.003 0.002 -10000 0 -0.046 1 1
CASP1 -0.004 0.011 -10000 0 -0.12 4 4
mol:cAMP -0.002 0.058 -10000 0 -0.39 11 11
necrosis -0.003 0.002 -10000 0 -0.046 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.009 -10000 0 -0.16 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.02 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.025 0.22 1 -0.2 3 4
forebrain development -0.037 0.14 -10000 0 -0.57 20 20
GNAO1 0.015 0.038 0.32 4 -0.32 2 6
SMO/beta Arrestin2 0.021 0.029 0.23 3 -0.2 1 4
SMO 0.015 0.033 0.32 3 -0.32 1 4
ARRB2 0.013 0.016 -10000 0 -10000 0 0
GLI3/SPOP 0.002 0.087 -10000 0 -0.36 16 16
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
GNAI2 0.014 0.015 -10000 0 -10000 0 0
SIN3/HDAC complex 0.049 0.02 -10000 0 -10000 0 0
GNAI1 0.014 0.021 -10000 0 -0.33 1 1
XPO1 0.013 0.02 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.14 -10000 0 -0.53 22 22
SAP30 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.015 0.033 0.32 3 -0.32 1 4
MIM/GLI2A 0.001 0.047 -10000 0 -0.23 2 2
IFT88 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.014 0.016 -10000 0 -10000 0 0
GLI2 -0.005 0.072 -10000 0 -0.38 11 11
GLI3 -0.009 0.088 -10000 0 -0.36 17 17
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.005 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.006 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
Gi family/GTP -0.014 0.067 -10000 0 -0.19 49 49
SIN3B 0.021 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) -0.007 0.087 -10000 0 -0.37 17 17
GLI2/Su(fu) -0.006 0.085 -10000 0 -0.38 18 18
FOXA2 -0.14 0.34 -10000 0 -0.85 93 93
neural tube patterning -0.037 0.14 -10000 0 -0.57 20 20
SPOP 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.014 0.037 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
MTSS1 0.001 0.047 -10000 0 -0.33 1 1
embryonic limb morphogenesis -0.037 0.14 -10000 0 -0.57 20 20
SUFU 0.007 0.014 -10000 0 -10000 0 0
LGALS3 0.02 0.004 -10000 0 -10000 0 0
catabolic process -0.003 0.12 -10000 0 -0.47 23 23
GLI3A/CBP 0.006 0.06 -10000 0 -0.32 14 14
KIF3A 0.02 0.005 -10000 0 -10000 0 0
GLI1 -0.038 0.15 -10000 0 -0.59 20 20
RAB23 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
IFT172 0.021 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.012 0.038 -10000 0 -10000 0 0
GNAZ -0.012 0.092 -10000 0 -0.33 39 39
RBBP4 0.021 0.003 -10000 0 -10000 0 0
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
PIAS1 0.021 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0 0.085 -10000 0 -0.39 16 16
STK36 0.013 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.013 0.063 -10000 0 -0.29 8 8
PTCH1 -0.046 0.18 -10000 0 -0.84 17 17
MIM/GLI1 -0.051 0.19 -10000 0 -0.46 72 72
CREBBP 0.006 0.06 -10000 0 -0.32 14 14
Su(fu)/SIN3/HDAC complex 0 0.066 -10000 0 -0.29 16 16
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.021 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.013 0.025 -10000 0 -0.2 7 7
FRAP1 -0.006 0.084 -10000 0 -0.42 18 18
AKT1 -0.008 0.037 0.15 15 -0.21 6 21
INSR 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.012 0.044 0.21 2 -0.2 4 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.015 0.026 -10000 0 -0.2 5 5
TSC2 0.021 0.003 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.025 -10000 0 -0.18 3 3
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.026 -10000 0 -0.21 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.036 -10000 0 -0.22 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.021 0.002 -10000 0 -10000 0 0
RPS6KB1 0.006 0.058 0.21 3 -0.36 5 8
MAP3K5 -0.012 0.054 0.18 4 -0.18 45 49
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
apoptosis -0.012 0.054 0.18 4 -0.18 45 49
mol:LY294002 0 0 -10000 0 -0.001 3 3
EIF4B 0.004 0.057 0.25 3 -0.32 5 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.05 0.2 1 -0.3 4 5
eIF4E/eIF4G1/eIF4A1 0.004 0.052 -10000 0 -0.26 17 17
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.03 -10000 0 -0.2 7 7
mTOR/RHEB/GTP/Raptor/GBL -0.004 0.033 0.14 11 -0.15 3 14
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
RHEB/GTP -0.016 0.037 -10000 0 -0.19 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 3 3
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.018 0.021 -10000 0 -0.19 6 6
EIF4E 0.021 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.032 0.18 -10000 0 -0.53 54 54
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.039 -10000 0 -0.24 1 1
TSC1/TSC2 -0.012 0.047 0.22 2 -0.22 3 5
tumor necrosis factor receptor activity 0 0 0.001 3 -10000 0 3
RPS6 0.019 0.006 -10000 0 -10000 0 0
PPP5C 0.02 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.004 -10000 0 -10000 0 0
IRS1 0.002 0.027 -10000 0 -0.24 6 6
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.021 0.004 -10000 0 -10000 0 0
PDK2 -0.018 0.024 0.17 1 -0.19 7 8
EIF4EBP1 -0.058 0.29 -10000 0 -1 41 41
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D -0.004 0.081 0.21 3 -0.38 17 20
peptide biosynthetic process -0.016 0.013 0.17 2 -10000 0 2
RHEB 0.02 0.005 -10000 0 -10000 0 0
EIF4A1 0.02 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 17 -0.002 1 18
EEF2 -0.016 0.013 0.17 2 -10000 0 2
eIF4E/4E-BP1 -0.046 0.27 -10000 0 -0.96 41 41
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.003 0.069 0.23 4 -0.37 8 12
BAG4 0.019 0.007 -10000 0 -10000 0 0
BAD -0.001 0.037 0.25 4 -0.13 5 9
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.037 0.32 5 -0.32 2 7
BAX -0.001 0.031 0.16 4 -0.13 5 9
EnzymeConsortium:3.1.4.12 0.001 0.02 0.081 3 -0.083 8 11
IKBKB 0.008 0.082 0.28 9 -0.36 8 17
MAP2K2 -0.005 0.036 0.16 12 -10000 0 12
MAP2K1 -0.005 0.04 0.16 15 -0.15 1 16
SMPD1 0 0.025 0.11 2 -0.12 7 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.006 0.074 0.25 5 -0.37 8 13
MAP2K4 -0.002 0.037 0.19 10 -0.15 1 11
protein ubiquitination 0.003 0.078 0.28 7 -0.36 8 15
EnzymeConsortium:2.7.1.37 -0.007 0.043 0.16 13 -0.17 1 14
response to UV 0 0 0.002 14 -0.002 1 15
RAF1 -0.002 0.039 0.16 13 -0.15 1 14
CRADD 0.021 0.021 0.32 1 -0.32 1 2
mol:ceramide 0.002 0.032 0.12 5 -0.12 9 14
I-kappa-B-alpha/RELA/p50/ubiquitin 0.024 0.011 -10000 0 -10000 0 0
MADD 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 0.001 0.039 0.19 10 -0.14 4 14
TRADD 0.021 0.004 -10000 0 -10000 0 0
RELA/p50 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.003 0.039 0.16 12 -10000 0 12
MAPK1 -0.006 0.043 0.16 12 -0.18 4 16
p50/RELA/I-kappa-B-alpha 0.026 0.012 -10000 0 -10000 0 0
FADD 0.001 0.071 0.22 4 -0.37 8 12
KSR1 0.001 0.039 0.17 12 -0.13 5 17
MAPK8 -0.005 0.042 0.19 15 -10000 0 15
TRAF2 0.021 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.004 0.071 0.33 3 -0.36 8 11
TNF R/SODD 0.026 0.012 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
CYCS 0.008 0.042 0.16 10 -0.13 4 14
IKBKG 0.001 0.075 0.28 5 -0.34 8 13
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.002 0.068 -10000 0 -0.38 8 8
RELA 0.021 0.004 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AIFM1 0.003 0.038 0.16 6 -0.13 4 10
TNF/TNF R/SODD 0.029 0.041 0.22 1 -0.19 14 15
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.011 0.085 -10000 0 -0.57 10 10
NSMAF 0.008 0.08 0.24 7 -0.36 8 15
response to hydrogen peroxide 0 0 0.002 14 -0.002 1 15
BCL2 0.019 0.021 0.32 1 -0.32 1 2
Retinoic acid receptors-mediated signaling

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
HDAC1 0.021 0.002 -10000 0 -10000 0 0
HDAC3 0.021 0.004 -10000 0 -10000 0 0
VDR 0.021 0.021 0.32 1 -0.32 1 2
Cbp/p300/PCAF 0.039 0.013 -10000 0 -10000 0 0
EP300 0.02 0.005 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.013 0.039 0.16 1 -0.34 2 3
KAT2B 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.007 0.042 0.23 2 -0.19 6 8
RAR alpha/9cRA/Cyclin H 0.035 0.047 -10000 0 -0.23 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.008 0.053 -10000 0 -0.22 17 17
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.021 0.034 -10000 0 -0.19 5 5
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.014 0.22 1 -0.22 1 2
RXRs/RARs/NRIP1/9cRA -0.01 0.098 0.32 4 -0.42 13 17
NCOA2 0.016 0.034 -10000 0 -0.32 5 5
NCOA3 0.02 0.006 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.021 0.32 1 -0.32 1 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.006 0.086 0.28 1 -0.36 13 14
RARA 0.017 0.034 0.19 3 -0.2 2 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.048 -10000 0 -0.21 17 17
PRKCA 0.02 0.022 -10000 0 -0.32 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.016 0.11 0.33 2 -0.46 13 15
RXRG -0.091 0.13 0.25 2 -0.25 192 194
RXRA 0.01 0.029 0.18 4 -0.18 2 6
RXRB 0.023 0.045 0.24 3 -0.25 2 5
VDR/Vit D3/DNA 0.015 0.014 0.22 1 -0.22 1 2
RBP1 0.023 0.031 0.32 4 -0.32 1 5
CRBP1/9-cic-RA 0.017 0.021 0.22 4 -0.22 1 5
RARB 0.02 0.022 -10000 0 -0.32 2 2
PRKCG 0.049 0.09 0.32 49 -10000 0 49
MNAT1 0.021 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.012 0.086 0.27 1 -0.38 15 16
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.005 0.083 0.25 5 -0.36 12 17
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.077 0.23 4 -0.34 11 15
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.017 0.11 0.33 2 -0.44 15 17
positive regulation of DNA binding 0.025 0.039 -10000 0 -0.22 2 2
NRIP1 -0.015 0.11 0.46 1 -0.5 8 9
RXRs/RARs -0.018 0.11 0.28 1 -0.4 22 23
RXRs/RXRs/DNA/9cRA -0.016 0.08 0.28 1 -0.36 14 15
PRKACA 0.02 0.005 -10000 0 -10000 0 0
CDK7 0.02 0.005 -10000 0 -10000 0 0
TFIIH 0.04 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.043 0.04 -10000 0 -0.22 1 1
CCNH 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.035 0.017 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.007 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.021 0.047 -10000 0 -0.27 3 3
NEF -0.001 0.018 -10000 0 -0.17 6 6
NFKBIA 0.019 0.009 -10000 0 -10000 0 0
BIRC3 0.006 0.068 0.18 65 -10000 0 65
CYCS -0.003 0.047 0.16 25 -0.29 2 27
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CD247 0.018 0.026 -10000 0 -0.22 5 5
MAP2K7 -0.016 0.17 -10000 0 -0.64 30 30
protein ubiquitination 0.002 0.065 0.29 2 -0.29 5 7
CRADD 0.021 0.021 0.32 1 -0.32 1 2
DAXX 0.021 0.004 -10000 0 -10000 0 0
FAS 0.017 0.037 -10000 0 -0.32 6 6
BID 0.006 0.048 0.16 27 -0.28 3 30
NF-kappa-B/RelA/I kappa B alpha 0.039 0.025 0.22 5 -10000 0 5
TRADD 0.021 0.004 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
CFLAR 0.021 0.002 -10000 0 -10000 0 0
FADD 0.02 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.025 0.22 5 -10000 0 5
MAPK8 -0.016 0.16 0.35 2 -0.59 30 32
APAF1 0.021 0.003 -10000 0 -10000 0 0
TRAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.034 -10000 0 -0.25 5 5
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.003 0.065 -10000 0 -0.32 8 8
CHUK 0.001 0.067 0.3 2 -0.31 5 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.05 0.032 -10000 0 -0.17 3 3
TCRz/NEF 0.014 0.025 -10000 0 -0.23 5 5
TNF 0.011 0.06 0.32 1 -0.32 15 16
FASLG -0.014 0.034 -10000 0 -0.33 5 5
NFKB1 0.021 0.011 -10000 0 -0.13 2 2
TNFR1A/BAG4/TNF-alpha 0.029 0.042 0.22 1 -0.19 14 15
CASP6 0.028 0.07 -10000 0 -0.48 4 4
CASP7 0.026 0.095 0.31 20 -0.3 2 22
RELA 0.021 0.011 -10000 0 -0.13 2 2
CASP2 0.02 0.004 -10000 0 -10000 0 0
CASP3 0.023 0.092 0.32 17 -0.29 1 18
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
CASP8 0.02 0.015 -10000 0 -0.32 1 1
CASP9 0.021 0.004 -10000 0 -10000 0 0
MAP3K14 0.003 0.065 0.2 1 -0.34 5 6
APAF-1/Caspase 9 -0.011 0.052 0.22 5 -0.28 1 6
BCL2 -0.015 0.15 0.34 3 -0.54 30 33
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.009 0.027 -10000 0 -0.18 9 9
epithelial cell differentiation 0.041 0.018 -10000 0 -0.16 2 2
CYFIP2 0.016 0.04 -10000 0 -0.32 7 7
ENAH -0.02 0.055 0.29 5 -0.23 1 6
EGFR 0.014 0.045 0.32 1 -0.32 8 9
EPHA2 0.014 0.048 -10000 0 -0.32 10 10
MYO6 -0.018 0.038 0.43 2 -10000 0 2
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.039 0.022 -10000 0 -0.2 3 3
AQP5 -0.061 0.17 0.4 4 -0.38 98 102
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.019 0.038 0.22 9 -10000 0 9
regulation of calcium-dependent cell-cell adhesion -0.086 0.074 -10000 0 -0.3 1 1
EGF 0.071 0.12 0.32 91 -0.32 5 96
NCKAP1 0.021 0.003 -10000 0 -10000 0 0
AQP3 -0.022 0.072 0.24 1 -0.32 25 26
cortical microtubule organization 0.041 0.018 -10000 0 -0.16 2 2
GO:0000145 -0.018 0.036 0.21 9 -10000 0 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.02 -10000 0 -0.16 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.033 0.023 -10000 0 -0.16 5 5
ARF6 0.02 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.041 0.034 -10000 0 -0.18 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.037 0.42 2 -0.21 1 3
PVRL2 0.02 0.005 -10000 0 -10000 0 0
ZYX -0.019 0.039 0.43 2 -10000 0 2
ARF6/GTP 0.044 0.035 -10000 0 -0.17 6 6
CDH1 0.019 0.022 -10000 0 -0.32 2 2
EGFR/EGFR/EGF/EGF 0.041 0.055 0.24 1 -0.18 11 12
RhoA/GDP 0.042 0.019 -10000 0 -0.16 2 2
actin cytoskeleton organization -0.02 0.036 0.41 2 -10000 0 2
IGF-1R heterotetramer 0.02 0.004 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
IGF1R 0.02 0.004 -10000 0 -10000 0 0
IGF1 0.014 0.052 0.32 1 -0.32 11 12
DIAPH1 0.015 0.12 -10000 0 -0.54 13 13
Wnt receptor signaling pathway -0.041 0.018 0.16 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.034 0.025 -10000 0 -0.18 6 6
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
VCL -0.021 0.036 0.42 2 -10000 0 2
EFNA1 0.017 0.017 -10000 0 -0.32 1 1
LPP -0.022 0.037 0.42 2 -10000 0 2
Ephrin A1/EPHA2 0.028 0.034 -10000 0 -0.18 9 9
SEC6/SEC8 -0.025 0.018 -10000 0 -10000 0 0
MGAT3 -0.087 0.075 -10000 0 -0.3 1 1
HGF/MET 0.021 0.056 -10000 0 -0.16 37 37
HGF 0.007 0.078 0.32 4 -0.32 24 28
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.027 -10000 0 -0.18 9 9
actin cable formation 0.009 0.085 0.29 19 -0.25 3 22
KIAA1543 -0.02 0.028 0.18 8 -10000 0 8
KIFC3 -0.023 0.02 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ACTN1 -0.019 0.038 0.43 2 -10000 0 2
NCK1/GIT1 0.03 0.007 -10000 0 -10000 0 0
mol:GDP 0.041 0.018 -10000 0 -0.16 2 2
EXOC4 0.02 0.005 -10000 0 -10000 0 0
STX4 -0.021 0.029 0.19 7 -10000 0 7
PIP5K1C -0.019 0.038 0.22 9 -10000 0 9
LIMA1 0.021 0.003 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
ROCK1 -0.008 0.078 0.31 11 -0.26 1 12
adherens junction assembly -0.026 0.09 0.35 6 -0.46 10 16
IGF-1R heterotetramer/IGF1 0.031 0.034 -10000 0 -0.16 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
MET 0.011 0.072 0.32 6 -0.32 18 24
PLEKHA7 -0.021 0.029 0.19 8 -10000 0 8
mol:GTP 0.039 0.034 -10000 0 -0.18 7 7
establishment of epithelial cell apical/basal polarity 0.018 0.096 0.32 17 -10000 0 17
cortical actin cytoskeleton stabilization 0.009 0.027 -10000 0 -0.18 9 9
regulation of cell-cell adhesion -0.02 0.036 0.41 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.027 -10000 0 -0.18 9 9
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 0.098 0.16 0.38 50 -0.42 2 52
RAD9A 0.021 0.004 -10000 0 -10000 0 0
AP1 0.023 0.062 -10000 0 -0.22 29 29
IFNAR2 0.028 0.014 -10000 0 -10000 0 0
AKT1 0.022 0.034 0.2 1 -0.34 1 2
ER alpha/Oestrogen 0.018 0.041 0.22 9 -0.21 8 17
NFX1/SIN3/HDAC complex 0.012 0.05 -10000 0 -0.29 5 5
EGF 0.074 0.12 0.33 91 -0.32 5 96
SMG5 0.018 0.008 -10000 0 -10000 0 0
SMG6 0.019 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.04 0.025 -10000 0 -10000 0 0
TERT/c-Abl 0.09 0.14 0.36 26 -0.39 2 28
SAP18 0.021 0.006 -10000 0 -10000 0 0
MRN complex 0.036 0.017 -10000 0 -10000 0 0
WT1 0.012 0.096 0.34 10 -0.32 31 41
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.031 0.019 -10000 0 -10000 0 0
SP3 0.024 0.008 -10000 0 -10000 0 0
TERF2IP 0.02 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.054 0.11 -10000 0 -0.39 2 2
Mad/Max 0.039 0.017 -10000 0 -10000 0 0
TERT 0.099 0.16 0.39 36 -0.42 2 38
CCND1 0.087 0.18 0.46 11 -0.84 7 18
MAX 0.024 0.008 -10000 0 -10000 0 0
RBBP7 0.022 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
TERF2 -0.017 0.015 -10000 0 -10000 0 0
PTGES3 0.021 0.004 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
Telomerase/911 0.053 0.062 0.23 4 -0.31 1 5
CDKN1B 0.001 0.04 0.22 2 -0.19 4 6
RAD1 0.018 0.008 -10000 0 -10000 0 0
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.028 0.01 -10000 0 -10000 0 0
UBE3A 0.023 0.008 -10000 0 -10000 0 0
JUN 0.022 0.027 -10000 0 -0.32 3 3
E6 0.003 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.014 -10000 0 -10000 0 0
FOS 0.006 0.077 -10000 0 -0.32 27 27
IFN-gamma/IRF1 0.046 0.063 0.25 31 -0.22 8 39
PARP2 0.02 0.005 -10000 0 -10000 0 0
BLM 0.049 0.088 0.32 48 -10000 0 48
Telomerase 0.037 0.087 0.29 3 -0.6 3 6
IRF1 0.025 0.009 -10000 0 -10000 0 0
ESR1 0.021 0.059 0.33 9 -0.32 8 17
KU/TER 0.03 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.011 0.058 -10000 0 -0.28 9 9
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.011 0.058 -10000 0 -0.29 8 8
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.028 0.018 -10000 0 -10000 0 0
ATM 0.009 0.008 -10000 0 -10000 0 0
SMAD3 -0.02 0.009 -10000 0 -10000 0 0
ABL1 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.025 0.008 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
HUS1 0.019 0.006 -10000 0 -10000 0 0
RPS6KB1 0.02 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.094 0.14 0.38 16 -0.44 1 17
NR2F2 0.004 0.026 -10000 0 -10000 0 0
MAPK3 -0.004 0.02 -10000 0 -10000 0 0
MAPK1 -0.005 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.02 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
HNRNPC 0.02 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.008 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.045 0.33 1 -0.32 8 9
mol:Oestrogen 0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.057 0.088 0.24 75 -0.22 12 87
MYC 0.02 0.024 -10000 0 -0.32 2 2
IL2 0.03 0.019 -10000 0 -10000 0 0
KU 0.03 0.007 -10000 0 -10000 0 0
RAD50 0.02 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.008 0.02 -10000 0 -10000 0 0
TRF2/BLM 0.046 0.056 0.22 45 -10000 0 45
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.1 0.14 0.38 22 -0.4 2 24
SP1/HDAC2 0.047 0.036 -10000 0 -10000 0 0
PINX1 0.018 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.051 0.1 -10000 0 -0.38 2 2
Smad3/Myc -0.019 0.015 -10000 0 -0.19 2 2
911 complex 0.032 0.019 -10000 0 -10000 0 0
IFNG 0.037 0.086 0.33 31 -0.32 8 39
Telomerase/PinX1 0.045 0.1 -10000 0 -0.38 2 2
Telomerase/AKT1/mTOR/p70S6K 0.051 0.088 0.26 11 -0.44 5 16
SIN3B 0.022 0.006 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1B 0.048 0.1 -10000 0 -0.38 1 1
response to DNA damage stimulus 0.002 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.048 0.026 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.012 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.053 0.11 -10000 0 -0.39 2 2
E2F1 0.031 0.032 0.32 5 -10000 0 5
ZNFX1 0.021 0.006 -10000 0 -10000 0 0
PIF1 0.064 0.11 0.32 73 -10000 0 73
NCL 0.021 0.003 -10000 0 -10000 0 0
DKC1 0.02 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.02 0.016 -10000 0 -0.32 1 1
SPHK1 0.023 0.03 0.32 5 -10000 0 5
GNAI2 0.021 0.004 -10000 0 -10000 0 0
mol:S1P 0.007 0.015 -10000 0 -0.22 1 1
GNAO1 0.022 0.035 0.32 4 -0.32 2 6
mol:Sphinganine-1-P -0.015 0.02 0.16 5 -0.23 1 6
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.033 -10000 0 -0.2 2 2
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
S1PR3 0.021 0.014 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.028 -10000 0 -0.23 3 3
S1PR5 0.001 0.081 0.32 1 -0.32 29 30
S1PR4 0.008 0.062 -10000 0 -0.32 17 17
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
S1P/S1P5/G12 0.017 0.051 0.22 1 -0.17 22 23
S1P/S1P3/Gq 0.004 0.067 -10000 0 -0.28 22 22
S1P/S1P4/Gi -0.013 0.083 -10000 0 -0.26 27 27
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
ABCC1 0.021 0.003 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0.018 0.057 0.34 2 -10000 0 2
CRKL -0.01 0.047 0.25 6 -10000 0 6
mol:DAG 0.01 0.032 0.24 1 -0.22 1 2
HRAS -0.001 0.074 0.24 15 -10000 0 15
MAPK8 -0.001 0.058 0.18 35 -10000 0 35
RAP1A -0.01 0.048 0.2 11 -10000 0 11
GAB1 -0.011 0.049 0.22 9 -0.25 1 10
MAPK14 -0.002 0.057 0.17 49 -10000 0 49
EPO 0.011 0.034 0.32 4 -10000 0 4
PLCG1 0.01 0.032 0.24 1 -0.23 1 2
EPOR/TRPC2/IP3 Receptors 0.022 0.009 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.037 0.03 0.21 3 -0.2 4 7
GAB1/SHC/GRB2/SOS1 -0.017 0.046 0.24 4 -10000 0 4
EPO/EPOR (dimer) 0.031 0.022 0.22 4 -10000 0 4
IRS2 -0.01 0.047 0.25 6 -10000 0 6
STAT1 0.011 0.036 0.32 1 -10000 0 1
STAT5B 0.011 0.034 0.28 1 -0.23 1 2
cell proliferation -0.004 0.061 0.17 50 -10000 0 50
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.035 -10000 0 -0.28 1 1
TEC -0.01 0.049 0.2 11 -10000 0 11
SOCS3 0.018 0.031 -10000 0 -0.32 4 4
STAT1 (dimer) 0.011 0.035 0.32 1 -10000 0 1
JAK2 0.019 0.023 -10000 0 -0.32 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
EPO/EPOR (dimer)/JAK2 0.045 0.038 0.36 1 -0.16 2 3
EPO/EPOR 0.031 0.022 0.22 4 -10000 0 4
LYN 0.02 0.006 -10000 0 -10000 0 0
TEC/VAV2 -0.013 0.047 0.2 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.022 0.009 -10000 0 -10000 0 0
SHC1 0.019 0.016 0.32 1 -10000 0 1
EPO/EPOR (dimer)/LYN 0.038 0.024 0.22 3 -10000 0 3
mol:IP3 0.01 0.032 0.24 1 -0.22 1 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.053 0.26 4 -0.29 1 5
SH2B3 0.021 0.023 -10000 0 -0.33 2 2
NFKB1 -0.001 0.059 0.17 52 -10000 0 52
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.043 0.19 2 -0.23 12 14
PTPN6 -0.008 0.044 0.15 33 -10000 0 33
TEC/VAV2/GRB2 -0.016 0.047 0.26 4 -10000 0 4
EPOR 0.022 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
mol:GDP -0.017 0.046 0.24 4 -10000 0 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
CRKL/CBL/C3G -0.016 0.046 0.26 4 -10000 0 4
VAV2 -0.01 0.048 0.21 10 -10000 0 10
CBL -0.009 0.049 0.2 11 -10000 0 11
SHC/Grb2/SOS1 0.024 0.023 -10000 0 -10000 0 0
STAT5A 0.01 0.037 0.28 1 -0.37 1 2
GRB2 0.02 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.022 0.039 0.38 1 -0.34 1 2
LYN/PLCgamma2 0.026 0.022 -10000 0 -0.23 3 3
PTPN11 0.021 0.004 -10000 0 -10000 0 0
BTK -0.017 0.059 0.22 8 -0.28 3 11
BCL2 0.009 0.074 0.39 2 -0.46 1 3
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.044 0.058 -10000 0 -0.16 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.01 0.056 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.028 -10000 0 -0.18 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.019 0.038 -10000 0 -0.28 1 1
CaM/Ca2+ 0.041 0.054 -10000 0 -0.16 8 8
RAP1A 0.02 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.01 0.048 0.16 2 -10000 0 2
AKT1 -0.011 0.06 0.27 9 -10000 0 9
MAP2K1 -0.013 0.051 0.24 5 -10000 0 5
MAP3K11 -0.01 0.052 0.25 5 -10000 0 5
IFNGR1 0.019 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.002 0.12 0.23 4 -0.32 46 50
Rap1/GTP -0.029 0.025 -10000 0 -10000 0 0
CRKL/C3G 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.053 0.059 -10000 0 -0.17 6 6
CEBPB -0.007 0.11 0.3 3 -0.42 17 20
STAT3 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.052 0.08 -10000 0 -0.67 3 3
STAT1 -0.009 0.052 0.27 4 -10000 0 4
CALM1 0.02 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.031 0.087 0.32 31 -0.33 8 39
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.01 0.057 0.27 5 -10000 0 5
CEBPB/PTGES2/Cbp/p300 0.005 0.069 -10000 0 -0.31 11 11
mol:Ca2+ 0.041 0.056 -10000 0 -0.16 9 9
MAPK3 0.002 0.068 -10000 0 -0.48 3 3
STAT1 (dimer) -0.021 0.053 -10000 0 -0.39 1 1
MAPK1 -0.022 0.14 -10000 0 -0.68 20 20
JAK2 0.018 0.024 -10000 0 -0.32 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.02 0.011 -10000 0 -10000 0 0
CAMK2D 0.021 0.003 -10000 0 -10000 0 0
DAPK1 -0.009 0.1 0.28 2 -0.5 14 16
SMAD7 -0.003 0.038 0.19 6 -0.16 2 8
CBL/CRKL/C3G -0.012 0.055 0.27 3 -10000 0 3
PI3K 0.038 0.051 -10000 0 -10000 0 0
IFNG 0.031 0.087 0.32 31 -0.33 8 39
apoptosis -0.006 0.098 0.3 1 -0.42 20 21
CAMK2G 0.021 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.003 -10000 0 -10000 0 0
CAMK2A -0.011 0.1 0.32 1 -0.32 48 49
CAMK2B 0.064 0.11 0.32 75 -10000 0 75
FRAP1 -0.012 0.056 0.26 9 -10000 0 9
PRKCD -0.012 0.062 0.28 9 -10000 0 9
RAP1B 0.02 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.019 0.038 -10000 0 -0.28 1 1
PTPN2 0.02 0.005 -10000 0 -10000 0 0
EP300 0.02 0.005 -10000 0 -10000 0 0
IRF1 -0.011 0.049 0.24 5 -10000 0 5
STAT1 (dimer)/PIASy -0.01 0.057 0.27 5 -10000 0 5
SOCS1 0.014 0.081 -10000 0 -1 3 3
mol:GDP -0.012 0.052 0.25 3 -10000 0 3
CASP1 -0.005 0.043 0.18 7 -0.19 6 13
PTGES2 0.021 0.004 -10000 0 -10000 0 0
IRF9 -0.003 0.036 -10000 0 -0.16 1 1
mol:PI-3-4-5-P3 0.026 0.042 -10000 0 -0.16 8 8
RAP1/GDP -0.026 0.034 -10000 0 -10000 0 0
CBL -0.009 0.051 0.25 5 -10000 0 5
MAP3K1 -0.01 0.051 0.27 4 -10000 0 4
PIAS1 0.021 0.004 -10000 0 -10000 0 0
PIAS4 0.02 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.019 0.038 -10000 0 -0.28 1 1
PTPN11 -0.006 0.051 0.22 4 -10000 0 4
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.005 -10000 0 -10000 0 0
NFATC1 -0.013 0.096 0.25 2 -0.4 14 16
NFATC2 -0.012 0.06 0.18 6 -0.25 13 19
NFATC3 0.006 0.021 -10000 0 -0.3 2 2
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.019 0.094 0.26 1 -0.35 21 22
Exportin 1/Ran/NUP214 0.04 0.013 0.22 1 -10000 0 1
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.001 0.085 -10000 0 -0.32 18 18
BCL2/BAX 0.028 0.018 0.23 1 -0.23 1 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.015 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.015 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.013 0.016 -10000 0 -10000 0 0
BAD 0.021 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.004 0.084 0.24 1 -0.34 17 18
Calcineurin A alpha-beta B1/BCL2 0.019 0.021 0.32 1 -0.32 1 2
FKBP8 0.02 0.016 -10000 0 -0.32 1 1
activation-induced cell death of T cells 0.004 0.083 0.33 17 -0.24 1 18
KPNB1 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.023 0.03 0.32 5 -10000 0 5
XPO1 0.021 0.002 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 9 -0.32 1 10
MAP3K8 0.012 0.022 -10000 0 -0.32 1 1
NFAT4/CK1 alpha 0.007 0.026 -10000 0 -0.16 2 2
MEF2D/NFAT1/Cbp/p300 -0.018 0.1 -10000 0 -0.23 82 82
CABIN1 -0.019 0.094 0.26 1 -0.35 21 22
CALM1 0.012 0.017 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
CAMK4 0.016 0.043 0.32 1 -0.32 7 8
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.022 -10000 0 -0.23 3 3
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.017 -10000 0 -10000 0 0
MAPK9 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.014 0.1 0.26 2 -0.4 17 19
PRKCH 0.021 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.017 0.028 -10000 0 -10000 0 0
CASP3 0.013 0.016 -10000 0 -10000 0 0
PIM1 0.021 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.011 -10000 0 -10000 0 0
apoptosis 0.012 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.04 -10000 0 -0.3 3 3
PRKCB 0.011 0.056 -10000 0 -0.32 14 14
PRKCE 0.018 0.034 -10000 0 -0.32 5 5
JNK2/NFAT4 0.016 0.036 -10000 0 -0.27 2 2
BAD/BCL-XL 0.029 0.008 -10000 0 -10000 0 0
PRKCD 0.021 0.004 -10000 0 -10000 0 0
NUP214 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.011 0.031 -10000 0 -0.33 3 3
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
PRKCG 0.049 0.09 0.32 49 -10000 0 49
PRKCQ -0.022 0.11 -10000 0 -0.32 63 63
FKBP38/BCL2 0.027 0.021 0.23 1 -0.23 2 3
EP300 0.011 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
NFATc/JNK1 -0.006 0.096 0.26 1 -0.38 14 15
CaM/Ca2+/FKBP38 0.017 0.023 -10000 0 -0.2 1 1
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.015 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.015 0.033 0.21 1 -0.19 7 8
NFATc/ERK1 -0.002 0.096 0.26 1 -0.39 13 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.001 0.094 -10000 0 -0.32 22 22
NR4A1 -0.057 0.15 0.23 7 -0.35 92 99
GSK3B 0.013 0.017 -10000 0 -10000 0 0
positive T cell selection 0.006 0.021 -10000 0 -0.3 2 2
NFAT1/CK1 alpha -0.01 0.042 0.13 2 -0.2 8 10
RCH1/ KPNB1 0.032 0.021 0.23 5 -10000 0 5
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.013 0.016 -10000 0 -10000 0 0
AKAP5 0.019 0.027 -10000 0 -0.32 3 3
MEF2D 0.009 0.019 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha -0.009 0.093 -10000 0 -0.38 14 14
CREBBP 0.011 0.02 -10000 0 -10000 0 0
BCL2 0.019 0.021 0.32 1 -0.32 1 2
Arf6 trafficking events

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
SLC2A4 0.017 0.031 -10000 0 -0.32 4 4
CLTC 0.016 0.054 0.23 2 -0.44 4 6
calcium ion-dependent exocytosis 0.01 0.03 0.19 3 -0.16 4 7
Dynamin 2/GTP -0.005 0.04 0.12 40 -10000 0 40
EXOC4 0.02 0.005 -10000 0 -10000 0 0
CD59 0.011 0.034 -10000 0 -0.31 3 3
CPE -0.005 0.041 0.19 19 -10000 0 19
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
membrane fusion 0.01 0.025 -10000 0 -10000 0 0
CTNND1 -0.003 0.051 0.19 27 -10000 0 27
DNM2 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.043 0.18 6 -0.26 3 9
TSHR 0.007 0.056 0.17 54 -10000 0 54
INS 0.001 0.074 -10000 0 -0.51 10 10
BIN1 0.021 0.001 -10000 0 -10000 0 0
mol:Choline 0.01 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.006 0.06 0.19 47 -10000 0 47
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.039 0.12 40 -10000 0 40
JUP 0.011 0.029 -10000 0 -0.3 2 2
ASAP2/amphiphysin II 0.038 0.014 -10000 0 -0.18 1 1
ARF6/GTP 0.015 0.003 -10000 0 -10000 0 0
CDH1 0.011 0.035 -10000 0 -0.31 3 3
clathrin-independent pinocytosis 0.015 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.014 0.32 1 -10000 0 1
positive regulation of endocytosis 0.015 0.003 -10000 0 -10000 0 0
EXOC2 0.02 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.007 0.019 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.032 0.044 0.3 3 -10000 0 3
positive regulation of phagocytosis -0.013 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.027 0.011 0.21 1 -10000 0 1
ACAP1 0.013 0.029 -10000 0 -0.15 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.009 0.06 -10000 0 -0.31 3 3
clathrin heavy chain/ACAP1 0.015 0.047 0.22 6 -0.33 3 9
JIP4/KLC1 0.037 0.012 -10000 0 -10000 0 0
EXOC1 0.021 0.003 -10000 0 -10000 0 0
exocyst 0.007 0.02 -10000 0 -10000 0 0
RALA/GTP 0.014 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.007 -10000 0 -10000 0 0
receptor recycling 0.015 0.003 -10000 0 -10000 0 0
CTNNA1 -0.003 0.05 0.19 26 -10000 0 26
NME1 0.006 0.06 0.19 47 -10000 0 47
clathrin coat assembly 0.016 0.057 0.23 2 -0.4 5 7
IL2RA 0.015 0.038 -10000 0 -0.34 3 3
VAMP3 -0.013 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.045 -10000 0 -0.31 4 4
EXOC6 0.021 0.003 -10000 0 -10000 0 0
PLD1 0.005 0.005 -10000 0 -10000 0 0
PLD2 0.005 0.004 -10000 0 -10000 0 0
EXOC5 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.041 0.18 5 -0.26 3 8
SDC1 0.012 0.034 -10000 0 -0.31 3 3
ARF6/GDP 0.027 0.034 0.14 44 -10000 0 44
EXOC7 0.02 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.034 0.045 -10000 0 -0.31 3 3
mol:Phosphatidic acid 0.01 0.025 -10000 0 -10000 0 0
endocytosis -0.037 0.013 0.17 1 -10000 0 1
SCAMP2 0.021 0.004 -10000 0 -10000 0 0
ADRB2 -0.037 0.087 0.21 1 -0.46 5 6
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ASAP2 0.02 0.016 -10000 0 -0.32 1 1
Dynamin 2/GDP 0.031 0.044 0.17 43 -10000 0 43
KLC1 0.02 0.005 -10000 0 -10000 0 0
AVPR2 -0.013 0.085 0.27 8 -0.41 5 13
RALA 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.048 0.33 2 -0.29 3 5
Ras signaling in the CD4+ TCR pathway

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.012 0.1 -9999 0 -0.41 15 15
MAP3K8 0.018 0.018 -9999 0 -0.32 1 1
FOS 0.008 0.084 -9999 0 -0.37 12 12
PRKCA 0.017 0.024 -9999 0 -0.33 2 2
PTPN7 0.017 0.014 -9999 0 -10000 0 0
HRAS 0.02 0.006 -9999 0 -10000 0 0
PRKCB 0.009 0.057 -9999 0 -0.33 14 14
NRAS 0.02 0.007 -9999 0 -10000 0 0
RAS family/GTP 0.032 0.02 -9999 0 -10000 0 0
MAPK3 0.014 0.041 -9999 0 -0.34 1 1
MAP2K1 -0.001 0.078 -9999 0 -0.37 15 15
ELK1 0.018 0.014 -9999 0 -10000 0 0
BRAF 0 0.054 -9999 0 -0.35 11 11
mol:GTP 0 0.001 -9999 0 -0.004 27 27
MAPK1 0 0.092 -9999 0 -0.44 16 16
RAF1 -0.002 0.062 -9999 0 -0.36 13 13
KRAS 0.019 0.007 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.002 0.062 -10000 0 -0.5 1 1
UGCG -0.002 0.11 -10000 0 -0.62 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.053 0.082 0.28 7 -0.38 4 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.001 0.11 -10000 0 -0.61 15 15
mol:DAG 0.002 0.081 -10000 0 -0.79 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.025 0.078 0.29 2 -0.36 8 10
FRAP1 0.019 0.085 0.31 2 -0.4 8 10
FOXO3 0.015 0.08 0.31 1 -0.41 7 8
AKT1 0.018 0.086 0.33 1 -0.44 7 8
GAB2 0.017 0.034 -10000 0 -0.32 5 5
SMPD1 0.006 0.083 -10000 0 -0.6 9 9
SGMS1 0.011 0.059 -10000 0 -0.56 5 5
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 -0.012 0.009 -10000 0 -0.19 1 1
CALM1 0.02 0.004 -10000 0 -10000 0 0
cell proliferation 0.024 0.087 0.27 3 -0.36 14 17
EIF3A 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.029 0.015 -10000 0 -0.23 1 1
RPS6KB1 0.014 0.059 -10000 0 -0.84 2 2
mol:sphingomyelin 0.002 0.081 -10000 0 -0.79 5 5
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.021 0.006 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MYC 0.04 0.12 0.4 5 -0.76 3 8
MYB 0.002 0.11 -10000 0 -1 5 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.066 -10000 0 -0.36 5 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.058 -10000 0 -0.77 2 2
mol:PI-3-4-5-P3 0.016 0.067 -10000 0 -0.36 5 5
Rac1/GDP -0.014 0.01 -10000 0 -0.17 1 1
T cell proliferation 0.012 0.066 -10000 0 -0.32 4 4
SHC1 0.019 0.016 0.32 1 -10000 0 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.009 0.088 3 -0.066 4 7
PRKCZ 0.012 0.065 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA 0.034 0.082 0.3 2 -0.37 7 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.053 -10000 0 -0.37 5 5
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL2RA 0.04 0.079 0.32 35 -0.32 1 36
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
TERT 0.081 0.13 0.32 109 -10000 0 109
E2F1 0.011 0.078 0.24 1 -0.44 12 13
SOS1 0.021 0.004 -10000 0 -10000 0 0
RPS6 0.019 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 4 -0.047 3 7
PTPN11 0.021 0.005 -10000 0 -10000 0 0
IL2RG 0.018 0.034 -10000 0 -0.32 5 5
actin cytoskeleton organization 0.012 0.066 -10000 0 -0.32 4 4
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL2 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.019 -10000 0 -0.16 1 1
LCK 0.021 0.026 0.32 1 -0.32 2 3
BCL2 0.017 0.083 0.47 1 -0.6 2 3
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.018 0.031 -10000 0 -0.32 4 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.045 0.32 1 -0.32 8 9
AKT 0.029 0.064 0.24 12 -0.22 4 16
FOXO3 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
AKT3 0.018 0.027 -10000 0 -0.32 3 3
FOXO4 0.021 0.002 -10000 0 -10000 0 0
MET 0.011 0.072 0.32 6 -0.32 18 24
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PIK3CB 0.021 0.003 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
PIK3CG 0.01 0.058 -10000 0 -0.32 15 15
PIK3R3 0.02 0.015 -10000 0 -0.32 1 1
PIK3R2 0.02 0.005 -10000 0 -10000 0 0
NF1 0.021 0.004 -10000 0 -10000 0 0
RAS 0.017 0.042 0.19 6 -0.13 14 20
ERBB2 0.021 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.012 0.075 0.3 16 -0.21 1 17
PI3K 0.02 0.062 0.21 23 -0.15 17 40
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
KRAS 0.02 0.006 -10000 0 -10000 0 0
FOXO 0.047 0.048 0.23 12 -10000 0 12
AKT2 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.006 0.071 -10000 0 -0.31 24 24
KLHL20 -0.003 0.051 0.16 1 -0.21 11 12
CYFIP2 0.016 0.04 -10000 0 -0.32 7 7
Rac1/GDP -0.011 0.061 0.33 3 -0.25 9 12
ENAH -0.006 0.071 -10000 0 -0.31 24 24
AP1M1 0.02 0.005 -10000 0 -10000 0 0
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.026 0.023 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.027 -10000 0 -0.14 16 16
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.046 0.026 -10000 0 -0.18 3 3
RAPGEF1 -0.01 0.06 0.21 2 -0.29 15 17
CTNND1 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.004 0.075 -10000 0 -0.32 25 25
CRK -0.01 0.054 -10000 0 -0.3 15 15
E-cadherin/gamma catenin/alpha catenin 0.039 0.019 -10000 0 -0.2 2 2
alphaE/beta7 Integrin 0.028 0.015 -10000 0 -0.23 1 1
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
NCKAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
DLG1 -0.004 0.068 -10000 0 -0.31 22 22
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.026 0.016 -10000 0 -0.13 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.047 0.053 0.21 38 -0.16 6 44
PI3K -0.031 0.02 -10000 0 -0.17 2 2
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.029 0.018 -10000 0 -0.23 2 2
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
E-cadherin(dimer)/Ca2+ 0.045 0.02 -10000 0 -0.16 2 2
AKT1 -0.017 0.026 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CDH1 0.019 0.022 -10000 0 -0.32 2 2
RhoA/GDP -0.011 0.064 0.3 4 -0.25 9 13
actin cytoskeleton organization 0.001 0.045 0.17 9 -0.16 10 19
CDC42/GDP -0.012 0.064 0.3 4 -0.25 10 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.009 0.013 -10000 0 -0.19 2 2
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.049 0.021 -10000 0 -0.17 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.016 -10000 0 -0.15 2 2
mol:GDP -0.012 0.07 0.32 4 -0.29 10 14
CDC42/GTP/IQGAP1 0.028 0.006 -10000 0 -10000 0 0
JUP 0.021 0.004 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.005 0.061 0.23 2 -0.25 6 8
RAC1/GTP/IQGAP1 0.025 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.029 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.003 0.039 0.14 12 -0.15 5 17
NME1 0.046 0.084 0.32 43 -10000 0 43
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.001 0.056 -10000 0 -0.31 14 14
regulation of cell-cell adhesion -0.024 0.019 -10000 0 -0.15 2 2
WASF2 -0.004 0.023 -10000 0 -0.093 1 1
Rap1/GTP -0.023 0.03 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.031 -10000 0 -0.18 3 3
CCND1 0.002 0.042 0.15 10 -0.17 7 17
VAV2 -0.01 0.13 -10000 0 -0.57 20 20
RAP1/GDP -0.02 0.045 -10000 0 -0.23 4 4
adherens junction assembly 0 0.055 -10000 0 -0.3 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.02 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.027 -10000 0 -0.17 3 3
E-cadherin/beta catenin 0.004 0.019 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.006 0.071 -10000 0 -0.31 24 24
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.066 -10000 0 -0.33 15 15
E-cadherin/beta catenin/alpha catenin 0.039 0.019 -10000 0 -0.18 2 2
ITGAE 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.001 0.075 -10000 0 -0.32 25 25
IGF1 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
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTK2 0.018 0.007 -10000 0 -10000 0 0
CRKL -0.018 0.026 0.15 2 -0.19 8 10
GRB2/SOS1/SHC 0.035 0.017 -10000 0 -10000 0 0
HRAS 0.021 0.004 -10000 0 -10000 0 0
IRS1/Crk 0.009 0.032 -10000 0 -0.18 11 11
IGF-1R heterotetramer/IGF1/PTP1B 0.034 0.034 0.21 1 -0.19 9 10
AKT1 -0.023 0.039 0.15 11 -0.18 7 18
BAD -0.027 0.037 0.14 11 -0.23 1 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.027 0.15 2 -0.19 9 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.036 0.19 4 -0.19 11 15
RAF1 -0.018 0.074 0.26 1 -0.4 15 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.041 0.038 -10000 0 -0.19 7 7
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.035 0.2 1 -0.2 11 12
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.022 0.039 0.15 13 -0.24 1 14
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.007 0.071 0.27 6 -0.31 9 15
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.024 0.016 -10000 0 -0.17 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.049 0.032 -10000 0 -0.16 2 2
IGF-1R heterotetramer 0.02 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.032 0.039 0.2 1 -0.19 11 12
Crk/p130 Cas/Paxillin 0.036 0.04 -10000 0 -0.17 11 11
IGF1R 0.02 0.016 -10000 0 -10000 0 0
IGF1 0.014 0.056 0.33 1 -0.34 11 12
IRS2/Crk -0.021 0.028 0.14 2 -0.18 10 12
PI3K 0.039 0.041 -10000 0 -0.18 11 11
apoptosis 0.023 0.041 0.21 1 -0.28 1 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
PRKCD -0.003 0.04 -10000 0 -0.24 9 9
RAF1/14-3-3 E -0.013 0.075 0.25 2 -0.34 16 18
BAD/14-3-3 -0.024 0.043 0.28 1 -0.22 1 2
PRKCZ -0.024 0.04 0.15 11 -0.24 1 12
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.032 -10000 0 -0.22 1 1
PTPN1 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0 0.043 -10000 0 -0.26 8 8
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.039 0.032 0.21 1 -0.16 4 5
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.016 0.036 -10000 0 -0.19 11 11
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 -0.019 0.03 0.15 3 -0.19 11 14
IRS1 -0.015 0.033 0.12 8 -0.2 11 19
IRS2 -0.019 0.029 0.15 3 -0.19 10 13
IGF-1R heterotetramer/IGF1 0.024 0.043 0.23 1 -0.25 11 12
GRB2 0.02 0.005 -10000 0 -10000 0 0
PDPK1 -0.021 0.041 0.16 12 -0.18 8 20
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKD1 -0.007 0.044 -10000 0 -0.29 5 5
SHC1 0.019 0.016 0.32 1 -10000 0 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.006 0.044 0.3 2 -0.23 9 11
adherens junction organization -0.006 0.055 -10000 0 -0.38 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.051 0.22 1 -0.22 3 4
FMN1 -0.012 0.055 -10000 0 -0.27 13 13
mol:IP3 -0.013 0.03 -10000 0 -0.21 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.058 -10000 0 -0.27 15 15
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 -0.015 0.039 0.2 2 -0.24 5 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.003 0.11 -10000 0 -0.54 13 13
CTNND1 0.021 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.045 -10000 0 -0.27 10 10
VASP -0.006 0.043 -10000 0 -0.32 6 6
ZYX -0.01 0.053 -10000 0 -0.27 13 13
JUB -0.003 0.055 -10000 0 -0.26 15 15
EGFR(dimer) 0.006 0.062 0.2 1 -0.27 15 16
E-cadherin/beta catenin-gamma catenin 0.039 0.018 -10000 0 -0.16 2 2
mol:PI-3-4-5-P3 0.02 0.05 0.22 2 -0.24 6 8
PIK3CA 0.019 0.009 -10000 0 -10000 0 0
PI3K 0.02 0.051 0.23 2 -0.25 6 8
FYN -0.015 0.063 0.33 2 -0.27 9 11
mol:Ca2+ -0.013 0.029 -10000 0 -0.2 4 4
JUP 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.33 1 1
mol:DAG -0.013 0.03 -10000 0 -0.21 4 4
CDH1 0.019 0.022 -10000 0 -0.32 2 2
RhoA/GDP -0.005 0.063 0.22 1 -0.22 2 3
establishment of polarity of embryonic epithelium -0.005 0.042 -10000 0 -0.31 6 6
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.045 0.32 1 -0.32 8 9
CASR -0.007 0.045 0.3 2 -0.2 4 6
RhoA/GTP 0.01 0.038 -10000 0 -0.19 4 4
AKT2 -0.013 0.038 0.2 2 -0.24 5 7
actin cable formation -0.012 0.046 -10000 0 -0.32 6 6
apoptosis -0.002 0.053 0.24 10 -0.25 5 15
CTNNA1 0.02 0.006 -10000 0 -10000 0 0
mol:GDP -0.015 0.04 0.17 4 -0.21 5 9
PIP5K1A -0.008 0.045 -10000 0 -0.27 10 10
PLCG1 -0.014 0.03 -10000 0 -0.21 4 4
Rac1/GTP 0.013 0.059 -10000 0 -0.26 12 12
homophilic cell adhesion -0.001 0.002 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.013 0.012 -10000 0 -10000 0 0
TRAF2/ASK1 0.025 0.01 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
MAP2K3 -0.005 0.091 0.29 2 -0.33 22 24
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.002 0.082 0.28 2 -0.37 12 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.036 0.32 2 -0.32 4 6
TXN 0.005 0.012 0.16 3 -10000 0 3
CALM1 0.02 0.004 -10000 0 -10000 0 0
GADD45A 0.021 0.003 -10000 0 -10000 0 0
GADD45B 0.018 0.022 -10000 0 -0.32 2 2
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
MAP3K6 0.021 0.003 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
MAP3K4 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.028 0.01 -10000 0 -10000 0 0
TAK1/TAB family 0 0.018 0.13 2 -0.13 1 3
RAC1/OSM/MEKK3 0.035 0.017 -10000 0 -0.16 1 1
TRAF2 0.021 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.005 0.074 -10000 0 -0.29 16 16
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.064 0.11 0.32 75 -10000 0 75
CCM2 0.019 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.051 0.065 0.21 72 -10000 0 72
MAPK11 0.018 0.022 -10000 0 -0.32 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.055 0.063 0.21 66 -10000 0 66
OSM/MEKK3 0.027 0.015 -10000 0 -0.23 1 1
TAOK1 0.007 0.011 -10000 0 -0.25 1 1
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAP3K10 0.018 0.027 -10000 0 -0.32 3 3
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
TRX/ASK1 0.015 0.019 0.15 1 -10000 0 1
GADD45/MTK1/MTK1 0.041 0.032 0.21 2 -0.2 4 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.031 0.062 0.22 1 -0.25 14 15
Ran/GTP/Exportin 1/HDAC1 -0.018 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.063 -10000 0 -0.27 15 15
SUMO1 0.021 0.003 -10000 0 -10000 0 0
ZFPM1 0.021 0.014 0.32 1 -10000 0 1
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.004 -10000 0 -10000 0 0
Histones 0.035 0.051 -10000 0 -0.29 1 1
YY1/LSF 0.013 0.046 -10000 0 -0.24 8 8
SMG5 0.018 0.008 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
I kappa B alpha/HDAC3 0.006 0.033 -10000 0 -0.2 12 12
I kappa B alpha/HDAC1 0.015 0.038 -10000 0 -10000 0 0
SAP18 0.02 0.005 -10000 0 -10000 0 0
RELA 0.007 0.045 -10000 0 -0.21 12 12
HDAC1/Smad7 0.036 0.019 -10000 0 -0.2 1 1
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.016 0.047 -10000 0 -0.31 1 1
NuRD/MBD3 Complex -0.005 0.053 -10000 0 -0.3 9 9
NF kappa B1 p50/RelA 0.012 0.068 -10000 0 -0.28 14 14
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.006 0.093 -10000 0 -0.32 40 40
GATA1 -0.014 0.1 -10000 0 -0.32 50 50
Mad/Max 0.03 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.018 0.091 -10000 0 -0.31 26 26
RBBP7 0.021 0.004 -10000 0 -10000 0 0
NPC 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
MAX 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.024 -10000 0 -10000 0 0
KAT2B 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.009 0.053 -10000 0 -0.37 4 4
SIN3 complex 0.048 0.019 -10000 0 -10000 0 0
SMURF1 0.02 0.005 -10000 0 -10000 0 0
CHD3 0.019 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.02 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.005 0.048 -10000 0 -0.27 9 9
YY1/HDAC2 0.014 0.042 -10000 0 -0.24 8 8
YY1/HDAC1 0.013 0.046 -10000 0 -0.24 8 8
NuRD/MBD2 Complex (MeCP1) -0.008 0.058 -10000 0 -0.31 10 10
PPARG -0.022 0.1 -10000 0 -0.28 60 60
HDAC8/hEST1B 0.035 0.017 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.016 0.047 -10000 0 -0.31 1 1
MBD3L2 0.017 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.019 -10000 0 -0.2 1 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.079 -10000 0 -0.3 24 24
HDAC1 0.021 0.002 -10000 0 -10000 0 0
HDAC3 0.007 0.028 -10000 0 -0.34 1 1
HDAC2 0.019 0.006 -10000 0 -10000 0 0
YY1 0.008 0.003 -10000 0 -10000 0 0
HDAC8 0.021 0.002 -10000 0 -10000 0 0
SMAD7 0.019 0.016 -10000 0 -0.32 1 1
NCOR2 0.021 0.003 -10000 0 -10000 0 0
MXD1 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.01 0.003 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.046 -10000 0 -0.22 8 8
YY1/SAP30/HDAC1 0.024 0.046 -10000 0 -0.22 8 8
EP300 0.02 0.005 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.01 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.024 -10000 0 -10000 0 0
histone deacetylation -0.001 0.062 -10000 0 -0.31 10 10
STAT3 (dimer non-phopshorylated)/HDAC3 0.006 0.038 -10000 0 -0.22 7 7
nuclear export -0.035 0.017 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GATAD2B 0.018 0.008 -10000 0 -10000 0 0
GATAD2A 0.02 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.004 0.066 -10000 0 -0.27 7 7
GATA1/HDAC1 0.005 0.077 -10000 0 -0.23 50 50
GATA1/HDAC3 0 0.07 -10000 0 -0.28 8 8
CHD4 0.02 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.022 0.044 0.23 1 -0.23 14 15
SIN3/HDAC complex/Mad/Max -0.008 0.057 -10000 0 -0.3 9 9
NuRD Complex -0.004 0.075 -10000 0 -0.3 19 19
positive regulation of chromatin silencing 0.033 0.05 -10000 0 -0.29 1 1
SIN3B 0.02 0.005 -10000 0 -10000 0 0
MTA2 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.027 0.031 -10000 0 -0.21 3 3
HDAC complex 0.048 0.019 -10000 0 -10000 0 0
GATA1/Fog1 0.004 0.076 -10000 0 -0.22 50 50
FKBP25/HDAC1/HDAC2 0.038 0.015 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
negative regulation of cell growth -0.007 0.058 -10000 0 -0.3 9 9
NuRD/MBD2/PRMT5 Complex -0.008 0.058 -10000 0 -0.31 10 10
Ran/GTP/Exportin 1 0.028 0.03 -10000 0 -0.19 4 4
NF kappa B/RelA/I kappa B alpha -0.002 0.056 -10000 0 -0.27 15 15
SIN3/HDAC complex/NCoR1 -0.011 0.073 -10000 0 -0.35 14 14
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.003 -10000 0 -10000 0 0
MBD3 0.018 0.022 -10000 0 -0.32 2 2
MBD2 0.019 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 0.007 -10000 0 -10000 0 0
SNTA1 0.022 0.024 0.32 3 -10000 0 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.028 0.41 2 -10000 0 2
MAPK12 -0.009 0.017 0.2 1 -0.17 2 3
CCND1 -0.003 0.051 -10000 0 -0.38 9 9
p38 gamma/SNTA1 -0.008 0.044 0.18 19 -0.16 2 21
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.009 0.017 0.2 1 -0.16 2 3
MAP2K6 -0.004 0.02 0.24 1 -0.18 2 3
MAPT -0.007 0.071 0.22 12 -0.25 25 37
MAPK13 -0.015 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.004 0.001 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.021 -10000 0 -0.18 1 1
HDAC3 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.005 -10000 0 -10000 0 0
GATA1/HDAC4 0.005 0.076 -10000 0 -0.23 49 49
GATA1/HDAC5 0.005 0.076 -10000 0 -0.23 48 48
GATA2/HDAC5 0.01 0.069 -10000 0 -0.23 39 39
HDAC5/BCL6/BCoR 0.039 0.013 -10000 0 -10000 0 0
HDAC9 0.019 0.046 0.32 5 -0.32 5 10
Glucocorticoid receptor/Hsp90/HDAC6 0.039 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC5/YWHAB 0.029 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
GATA2 -0.006 0.093 -10000 0 -0.32 40 40
HDAC4/RFXANK 0.03 0.008 -10000 0 -10000 0 0
BCOR 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.016 -10000 0 -0.32 1 1
HDAC5 0.021 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.018 -10000 0 -0.23 2 2
Histones 0.009 0.05 -10000 0 -0.26 5 5
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.03 0.007 -10000 0 -10000 0 0
HDAC7 0.021 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
HDAC6 0.021 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.029 0.008 -10000 0 -10000 0 0
CAMK4 0.016 0.043 0.32 1 -0.32 7 8
Tubulin/HDAC6 0.044 0.03 0.22 12 -10000 0 12
SUMO1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
GATA1 -0.014 0.1 -10000 0 -0.32 50 50
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.021 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.027 0.03 -10000 0 -0.2 3 3
SRF 0.021 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.029 0.009 -10000 0 -10000 0 0
Tubulin 0.036 0.033 0.23 13 -10000 0 13
HDAC4/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.029 0.008 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.04 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.036 0.031 0.22 1 -0.2 7 8
HDAC4/ER alpha 0.027 0.042 0.23 8 -0.23 8 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.009 0.05 -10000 0 -0.26 5 5
cell motility 0.044 0.03 0.22 12 -10000 0 12
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.03 0.007 -10000 0 -10000 0 0
BCL6 0.02 0.004 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.021 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.03 0.008 -10000 0 -10000 0 0
ESR1 0.019 0.059 0.32 9 -0.32 8 17
HDAC6/HDAC11 0.03 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.03 -10000 0 -0.19 4 4
NPC 0.013 0.001 -10000 0 -10000 0 0
MEF2C 0.02 0.005 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
HDAC4/MEF2C 0.057 0.022 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
NCOR2 0.021 0.003 -10000 0 -10000 0 0
TUBB2A 0.029 0.05 0.32 14 -10000 0 14
HDAC11 0.02 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
ANKRA2 0.02 0.004 -10000 0 -10000 0 0
RFXANK 0.02 0.005 -10000 0 -10000 0 0
nuclear import -0.02 0.009 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.054 0.41 5 -10000 0 5
CLOCK 0.022 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.026 0.031 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.008 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.02 -10000 0 -10000 0 0
ARNTL 0.022 0.005 -10000 0 -10000 0 0
TIMELESS 0.01 0.037 0.38 2 -10000 0 2
NPAS2 0.024 0.023 0.32 3 -10000 0 3
CRY2 0.021 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.012 -10000 0 -0.1 7 7
CHEK1 0.037 0.07 0.32 29 -10000 0 29
mol:HEME 0.004 0.012 0.1 7 -10000 0 7
PER1 0.008 0.062 -10000 0 -0.32 17 17
BMAL/CLOCK/NPAS2 0.046 0.022 0.23 3 -10000 0 3
BMAL1/CLOCK 0.01 0.042 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.044 0.054 0.41 5 -10000 0 5
TIMELESS/CHEK1/ATR 0.045 0.054 0.42 5 -10000 0 5
mol:NADPH 0.004 0.012 0.1 7 -10000 0 7
PER1/TIMELESS 0.019 0.041 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.015 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.013 -10000 0 -10000 0 0
CDKN1B 0.008 0.042 -10000 0 -0.29 6 6
CDKN1A 0.007 0.043 -10000 0 -0.29 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
FOXO3 0.008 0.031 -10000 0 -0.29 3 3
AKT1 0.002 0.035 -10000 0 -0.29 7 7
BAD 0.021 0.003 -10000 0 -10000 0 0
AKT3 0.006 0.016 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.042 -10000 0 -0.29 7 7
AKT1/ASK1 0.024 0.053 -10000 0 -0.27 7 7
BAD/YWHAZ 0.036 0.017 -10000 0 -10000 0 0
RICTOR 0.017 0.008 -10000 0 -10000 0 0
RAF1 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.023 0.05 0.26 7 -10000 0 7
TSC1 0.008 0.034 -10000 0 -0.29 4 4
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.028 0.056 0.23 2 -0.27 9 11
EP300 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0.003 0.036 -10000 0 -0.29 7 7
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.006 0.039 -10000 0 -0.29 7 7
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAPKAP1 0.021 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.016 0.067 0.28 9 -0.23 8 17
YWHAH 0.02 0.004 -10000 0 -10000 0 0
AKT1S1 0.007 0.039 -10000 0 -0.29 6 6
CASP9 0.009 0.039 -10000 0 -0.29 5 5
YWHAB 0.02 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.062 0.27 7 -0.27 7 14
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.009 0.048 0.23 6 -0.24 7 13
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.036 0.18 1 -0.32 4 5
CHUK 0.007 0.041 -10000 0 -0.29 7 7
BAD/BCL-XL 0.026 0.052 -10000 0 -0.28 7 7
mTORC2 0.022 0.011 -10000 0 -10000 0 0
AKT2 0.007 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.018 0.083 0.3 6 -0.36 8 14
PDPK1 0.021 0.003 -10000 0 -10000 0 0
MDM2 0.015 0.054 -10000 0 -0.29 6 6
MAPKKK cascade -0.028 0.056 0.26 9 -0.22 2 11
MDM2/Cbp/p300 0.044 0.069 0.32 5 -0.27 7 12
TSC1/TSC2 0.004 0.048 0.25 8 -0.28 7 15
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.066 0.31 5 -0.26 7 12
glucose import -0.009 0.025 0.2 5 -0.17 4 9
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.037 0.22 1 -0.21 6 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.014 -10000 0 -0.17 4 4
GSK3A 0.008 0.043 -10000 0 -0.29 7 7
FOXO1 0.007 0.035 -10000 0 -0.28 5 5
GSK3B 0.007 0.038 -10000 0 -0.29 6 6
SFN 0.025 0.043 0.32 9 -0.32 1 10
G1/S transition of mitotic cell cycle 0.006 0.052 0.24 5 -0.28 7 12
p27Kip1/14-3-3 family 0.012 0.055 -10000 0 -0.4 4 4
PRKACA 0.02 0.005 -10000 0 -10000 0 0
KPNA1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
RHEB 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
mol:S1P 0 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.01 0.062 -10000 0 -0.19 50 50
GNAO1 0.022 0.035 0.32 4 -0.33 2 6
S1P/S1P3/G12/G13 0.034 0.017 -10000 0 -10000 0 0
AKT1 0.004 0.068 -10000 0 -0.4 12 12
AKT3 -0.005 0.1 -10000 0 -0.97 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
GNAI2 0.02 0.007 -10000 0 -10000 0 0
GNAI3 0.02 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.017 -10000 0 -0.32 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.021 0.015 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.064 -10000 0 -0.45 2 2
MAPK3 -0.012 0.057 -10000 0 -0.59 1 1
MAPK1 -0.01 0.054 -10000 0 -0.57 1 1
JAK2 -0.021 0.077 0.2 2 -0.34 11 13
CXCR4 -0.013 0.059 -10000 0 -0.44 2 2
FLT1 0.02 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC -0.012 0.061 0.27 2 -0.44 2 4
S1P/S1P3/Gi -0.005 0.064 -10000 0 -0.46 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.069 -10000 0 -0.33 4 4
VEGFA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.006 0.064 -10000 0 -0.29 6 6
VEGFR1 homodimer/VEGFA homodimer 0.029 0.013 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.007 0.037 -10000 0 -0.22 12 12
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
GNAZ -0.006 0.092 -10000 0 -0.32 39 39
G12/G13 0.027 0.011 -10000 0 -10000 0 0
GNA14 0.013 0.05 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
Rac1/GTP -0.002 0.066 -10000 0 -0.29 6 6
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.01 0.013 -10000 0 -10000 0 0
regulation of axonogenesis -0.001 0.012 0.25 1 -10000 0 1
myoblast fusion -0.012 0.021 -10000 0 -10000 0 0
mol:GTP 0.016 0.013 -10000 0 -0.16 2 2
regulation of calcium-dependent cell-cell adhesion -0.046 0.056 0.2 4 -0.21 37 41
ARF1/GTP 0.025 0.017 -10000 0 -10000 0 0
mol:GM1 0.005 0.008 -10000 0 -10000 0 0
mol:Choline -0.01 0.008 -10000 0 -10000 0 0
lamellipodium assembly 0.005 0.023 -10000 0 -0.34 1 1
MAPK3 0.012 0.011 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.047 0.056 0.22 37 -0.2 4 41
ARF1 0.02 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.012 0.021 -10000 0 -10000 0 0
ARF1/GDP 0.015 0.027 -10000 0 -0.21 2 2
ARF6 0.026 0.008 -10000 0 -10000 0 0
RAB11A 0.021 0.003 -10000 0 -10000 0 0
TIAM1 0.015 0.04 -10000 0 -0.32 7 7
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.009 -10000 0 -10000 0 0
actin filament bundle formation -0.019 0.028 0.21 2 -10000 0 2
KALRN 0.004 0.016 -10000 0 -0.18 2 2
RAB11FIP3/RAB11A 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.028 -10000 0 -0.22 2 2
NME1 0.045 0.085 0.32 43 -10000 0 43
Rac1/GDP 0.017 0.027 -10000 0 -0.22 2 2
substrate adhesion-dependent cell spreading 0.016 0.013 -10000 0 -0.16 2 2
cortical actin cytoskeleton organization 0.005 0.023 -10000 0 -0.34 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
liver development 0.016 0.013 -10000 0 -0.16 2 2
ARF6/GTP 0.016 0.013 -10000 0 -0.16 2 2
RhoA/GTP 0.025 0.016 -10000 0 -0.12 2 2
mol:GDP 0.005 0.014 -10000 0 -0.21 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.038 0.018 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
PLD1 0.01 0.011 -10000 0 -10000 0 0
RAB11FIP3 0.021 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.005 0.023 -10000 0 -0.34 1 1
ruffle organization 0.001 0.012 -10000 0 -0.25 1 1
regulation of epithelial cell migration 0.016 0.013 -10000 0 -0.16 2 2
PLD2 0.01 0.01 -10000 0 -10000 0 0
PIP5K1A 0.001 0.012 -10000 0 -0.25 1 1
mol:Phosphatidic acid -0.01 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.023 -10000 0 -0.34 1 1
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 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.06 0.22 3 -0.34 4 7
ERC1 0.02 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.027 0.011 -10000 0 -10000 0 0
NFKBIA -0.016 0.021 0.2 4 -10000 0 4
BIRC2 0.02 0.004 -10000 0 -10000 0 0
IKBKB 0.018 0.007 -10000 0 -10000 0 0
RIPK2 0.019 0.007 -10000 0 -10000 0 0
IKBKG 0.003 0.047 -10000 0 -0.33 7 7
IKK complex/A20 0.028 0.073 -10000 0 -0.38 7 7
NEMO/A20/RIP2 0.019 0.007 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.023 0.072 -10000 0 -0.37 10 10
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
Exportin 1/RanGTP 0.028 0.01 0.21 1 -10000 0 1
IKK complex/ELKS 0.023 0.066 -10000 0 -0.35 9 9
BCL10/MALT1/TRAF6 0.037 0.016 -10000 0 -10000 0 0
NOD2 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
MALT1 0.019 0.007 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.03 0.007 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.022 0.044 0.23 1 -0.23 14 15
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
CHUK 0.021 0.003 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
TNF 0.011 0.06 0.32 1 -0.32 15 16
NF kappa B1 p50/RelA 0.042 0.013 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.021 0.2 4 -10000 0 4
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.071 -10000 0 -0.37 9 9
CYLD 0.02 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.032 0.069 -10000 0 -0.38 7 7
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.009 0.1 -10000 0 -0.36 16 16
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
AKT2 0.02 0.005 -10000 0 -10000 0 0
STXBP4 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.008 0.1 0.24 1 -0.39 18 19
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
YWHAQ 0.021 0.003 -10000 0 -10000 0 0
TBC1D4 -0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.015 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
ASIP 0.02 0.014 0.32 1 -10000 0 1
PRKCI 0.02 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
GYS1 -0.005 0.011 0.23 1 -10000 0 1
PRKCZ 0.019 0.027 -10000 0 -0.32 3 3
TRIP10 0.02 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.004 0.05 -10000 0 -0.27 6 6
VAMP2 0.019 0.006 -10000 0 -10000 0 0
SLC2A4 -0.011 0.11 0.24 1 -0.42 19 20
STX4 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.01 0.003 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 9 -0.32 1 10
LNPEP 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.009 0.016 -10000 0 -0.23 2 2
CRKL 0.02 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.022 -10000 0 -0.32 2 2
alpha4/beta7 Integrin/MAdCAM1 0.049 0.031 0.23 6 -0.17 3 9
EPO 0.021 0.027 0.32 4 -10000 0 4
alpha4/beta7 Integrin 0.029 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.013 -10000 0 -0.23 1 1
EPO/EPOR (dimer) 0.029 0.021 0.23 4 -10000 0 4
lamellipodium assembly 0.004 0.042 -10000 0 -0.43 2 2
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
JAK2 0.011 0.017 0.18 1 -0.29 1 2
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
MADCAM1 0.024 0.036 0.32 7 -10000 0 7
cell adhesion 0.047 0.031 0.22 6 -0.17 3 9
CRKL/CBL 0.028 0.01 -10000 0 -10000 0 0
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC -0.017 0.033 0.17 13 -0.18 2 15
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.039 0.023 0.22 1 -0.2 3 4
p130Cas/Crk/Dock1 -0.024 0.038 0.18 13 -10000 0 13
VCAM1 0.02 0.026 0.32 1 -0.32 2 3
RHOA 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0.019 -10000 0 -0.18 1 1
BCAR1 -0.02 0.036 0.18 12 -0.17 3 15
EPOR 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.043 -10000 0 -0.45 2 2
TRAIL 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
TNFSF10 0.017 0.034 -10000 0 -0.32 5 5
positive regulation of NF-kappaB transcription factor activity 0.023 0.027 -10000 0 -0.22 5 5
MAP2K4 0.005 0.026 -10000 0 -0.25 2 2
IKBKB 0.018 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.008 -10000 0 -10000 0 0
SMPD1 0.004 0.015 -10000 0 -0.14 5 5
IKBKG 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.017 -10000 0 -0.32 1 1
TRAIL/TRAILR2 0.023 0.027 -10000 0 -0.21 5 5
TRAIL/TRAILR3 0.021 0.035 -10000 0 -0.22 9 9
TRAIL/TRAILR1 0.023 0.027 -10000 0 -0.22 5 5
TRAIL/TRAILR4 0.023 0.027 -10000 0 -0.22 5 5
TRAIL/TRAILR1/DAP3/GTP 0.028 0.026 -10000 0 -0.17 4 4
IKK complex 0.001 0.046 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.006 -10000 0 -10000 0 0
MAPK3 -0.018 0.025 0.27 1 -0.23 5 6
MAP3K1 0.013 0.022 -10000 0 -0.28 1 1
TRAILR4 (trimer) 0.017 0.017 -10000 0 -0.32 1 1
TRADD 0.021 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0 0.04 -10000 0 -0.27 1 1
CFLAR 0.021 0.002 -10000 0 -10000 0 0
MAPK1 -0.016 0.021 0.27 1 -0.23 3 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.034 -10000 0 -0.17 3 3
mol:ceramide 0.004 0.015 -10000 0 -0.14 5 5
FADD 0.02 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 0.042 -10000 0 -0.26 4 4
TRAF2 0.021 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.035 -10000 0 -0.32 5 5
CHUK 0.021 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.032 0.028 -10000 0 -0.18 5 5
DAP3 0.018 0.008 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.26 2 -0.22 2 4
JNK cascade 0.023 0.027 -10000 0 -0.22 5 5
TRAIL (trimer) 0.017 0.034 -10000 0 -0.32 5 5
TNFRSF10C 0.014 0.035 -10000 0 -0.32 5 5
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.03 -10000 0 -0.16 4 4
TRAIL/TRAILR2/FADD 0.032 0.028 -10000 0 -0.18 5 5
cell death 0.004 0.016 0.14 1 -0.14 5 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0.04 -10000 0 -0.22 3 3
TRAILR2 (trimer) 0.018 0.008 -10000 0 -10000 0 0
CASP8 0.009 0.05 -10000 0 -0.66 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.034 -10000 0 -0.17 3 3
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.031 0.03 0.2 3 -0.16 8 11
MAPK9 0.004 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.013 0.16 3 -10000 0 3
GNB1/GNG2 0.026 0.015 -10000 0 -0.19 2 2
GNB1 0.021 0.004 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.004 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.011 0.025 0.18 3 -0.16 7 10
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 0.002 0.005 0.047 7 -10000 0 7
GNAL 0.017 0.047 0.32 3 -0.32 7 10
GNG2 0.019 0.022 -10000 0 -0.32 2 2
CRH 0.019 0.024 0.32 3 -10000 0 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.001 -10000 0 -10000 0 0
MAPK11 0.003 0.016 -10000 0 -0.25 2 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0.041 0.15 37 -0.16 2 39
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.037 -10000 0 -0.16 2 2
AP2 0.029 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.022 0.016 -10000 0 -10000 0 0
CLTB 0.02 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.006 -10000 0 -10000 0 0
CD4 0.014 0.046 -10000 0 -0.32 9 9
CLTA 0.02 0.006 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.022 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.003 0.012 -10000 0 -10000 0 0
mol:Choline -0.002 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.009 -10000 0 -10000 0 0
DDEF1 -0.001 0.008 -10000 0 -10000 0 0
ARF1/GDP 0 0.016 -10000 0 -0.095 8 8
AP2M1 0.02 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.011 -10000 0 -10000 0 0
Rac/GTP 0.015 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.013 -10000 0 -10000 0 0
ARFIP2 0.01 0.02 -10000 0 -10000 0 0
COPA 0.019 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0 0.034 -10000 0 -0.18 8 8
ARF1/GTP/ARHGAP10 0.012 0.007 -10000 0 -10000 0 0
GGA3 0.02 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.025 -10000 0 -0.27 3 3
AP2A1 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.001 0.026 -10000 0 -0.17 8 8
ARF1/GDP/Membrin 0.016 0.029 -10000 0 -0.3 3 3
Arfaptin 2/Rac/GDP 0.02 0.018 -10000 0 -10000 0 0
CYTH2 0.024 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.012 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.004 0.039 -10000 0 -0.2 12 12
PLD2 -0.002 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.002 -10000 0 -10000 0 0
PIP5K1A -0.002 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.008 0.02 -10000 0 -0.13 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.002 -10000 0 -10000 0 0
GOSR2 0.006 0.015 -10000 0 -0.31 1 1
USO1 0.004 0.029 -10000 0 -0.31 4 4
GBF1 0.004 0.029 -10000 0 -0.31 4 4
ARF1/GTP/Arfaptin 2 0.026 0.013 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.034 0.033 -10000 0 -0.19 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD2 0 0.043 0.25 2 -0.22 4 6
SMAD3 0.01 0.036 -10000 0 -10000 0 0
SMAD3/SMAD4 0.022 0.037 -10000 0 -0.4 2 2
SMAD4/Ubc9/PIASy 0.036 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.05 0.23 1 -0.21 3 4
PPM1A 0.021 0.004 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.005 0.041 -10000 0 -0.21 7 7
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.019 -10000 0 -0.23 2 2
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
KPNB1 0.021 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.02 0.022 -10000 0 -0.32 2 2
UBE2I 0.021 0.004 -10000 0 -10000 0 0
NUP153 0.021 0.003 -10000 0 -10000 0 0
KPNA2 0.023 0.03 0.32 5 -10000 0 5
PIAS4 0.02 0.006 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.021 0.004 -9999 0 -10000 0 0
ITGB7 0.02 0.016 -9999 0 -0.32 1 1
ITGA4 0.02 0.022 -9999 0 -0.32 2 2
alpha4/beta7 Integrin 0.029 0.021 -9999 0 -0.23 3 3
alpha4/beta1 Integrin 0.03 0.013 -9999 0 -0.23 1 1
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.01 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.022 -10000 0 -0.32 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.016 -10000 0 -0.2 1 1
alpha4/beta7 Integrin/Paxillin 0.028 0.018 -10000 0 -0.18 3 3
lamellipodium assembly -0.007 0.082 -10000 0 -0.37 18 18
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
TLN1 0.019 0.016 -10000 0 -0.32 1 1
PXN -0.016 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
ARF6/GTP 0.036 0.019 -10000 0 -0.16 1 1
cell adhesion 0.036 0.02 -10000 0 -0.16 2 2
CRKL/CBL 0.028 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.028 0.013 -10000 0 -0.18 1 1
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.037 0.024 0.22 1 -0.17 3 4
p130Cas/Crk/Dock1 0.037 0.018 -10000 0 -0.2 1 1
VCAM1 0.02 0.026 0.32 1 -0.32 2 3
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.02 -10000 0 -0.16 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.038 0.018 -10000 0 -0.17 1 1
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
mol:GDP -0.037 0.017 0.17 1 -10000 0 1
CBL 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.02 -10000 0 -0.16 2 2
Rac1/GTP -0.008 0.089 -10000 0 -0.41 18 18
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.029 0.014 -10000 0 -0.23 1 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.017 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.042 0.23 1 -0.18 2 3
NFKBIA 0.002 0.011 -10000 0 -0.17 2 2
MAPK14 0.021 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.016 0.008 -10000 0 -10000 0 0
ARRB2 0.007 0.002 -10000 0 -10000 0 0
REL 0.021 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.017 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.017 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.014 0.014 0.24 1 -10000 0 1
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
NFKB1 -0.015 0.006 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.008 0.034 -10000 0 -0.19 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.018 0.04 -10000 0 -0.19 1 1
SRC 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
NF kappa B1 p50/RelA 0.008 0.033 -10000 0 -0.18 4 4
IKBKB 0.018 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
SYK 0.019 0.022 -10000 0 -0.32 2 2
I kappa B alpha/PIK3R1 0.026 0.053 0.25 10 -0.18 2 12
cell death 0.017 0.039 -10000 0 -0.18 1 1
NF kappa B1 p105/c-Rel -0.017 0.007 -10000 0 -10000 0 0
LCK 0.02 0.026 0.32 1 -0.32 2 3
BCL3 0.02 0.016 -10000 0 -0.32 1 1
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 0.039 0.019 -9999 0 -0.18 2 2
E-cadherin/beta catenin 0.029 0.017 -9999 0 -0.22 2 2
CTNNB1 0.021 0.004 -9999 0 -10000 0 0
JUP 0.021 0.004 -9999 0 -10000 0 0
CDH1 0.019 0.022 -9999 0 -0.32 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.008 -10000 0 -10000 0 0
MDM2/SUMO1 0.026 0.031 -10000 0 -0.21 3 3
HDAC4 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.019 0.009 -10000 0 -10000 0 0
SUMO1 0.021 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.006 0.016 -10000 0 -0.16 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.027 0.03 -10000 0 -0.2 3 3
SUMO1/HDAC1 0.027 0.031 -10000 0 -0.21 3 3
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.045 0.023 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.006 0.002 -10000 0 -10000 0 0
Ran/GTP 0.017 0.029 -10000 0 -0.19 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.005 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.014 0.033 0.21 4 -0.19 4 8
NPC 0.013 0.001 -10000 0 -10000 0 0
PIAS2 0.019 0.006 -10000 0 -10000 0 0
PIAS1 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.03 0.007 -9999 0 -9999 0 0
FBXW11 0.02 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -9999 0 0
CHUK 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.056 0.021 -9999 0 -9999 0 0
NFKB1 0.021 0.003 -9999 0 -9999 0 0
MAP3K14 0.021 0.003 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.03 0.007 -9999 0 -9999 0 0
RELB 0.02 0.004 -9999 0 -9999 0 0
NFKB2 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.027 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.027 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 512 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.S2.AA1A TCGA.O1.A52J TCGA.NJ.A7XG TCGA.NJ.A55R
109_MAP3K5 0.0086 -0.02 -0.12 0.0086
47_PPARGC1A 0.021 0.021 -0.32 0.021
105_BMP4 0.021 0.021 0.021 0.021
105_BMP6 0.021 -0.32 -0.32 0.021
105_BMP7 0.32 0 0.021 0.021
105_BMP2 0.021 0.021 0.021 0.021
131_RELN/VLDLR 0.055 -0.18 -0.16 0.055
30_TGFB1/TGF beta receptor Type II 0.021 0.021 0.021 -0.024
84_STAT5B 0.015 0.074 -0.19 0.016
84_STAT5A 0.015 0.074 -0.19 0.016
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/LUAD-TP/19438942/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LUAD-TP/19775358/GDAC_Gistic2Report_19782105/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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