PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1KS6QDM
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 55 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 320
Signaling events mediated by Stem cell factor receptor (c-Kit) 291
Class IB PI3K non-lipid kinase events 285
Signaling mediated by p38-alpha and p38-beta 275
Reelin signaling pathway 231
EGFR-dependent Endothelin signaling events 200
Aurora B signaling 195
FOXA2 and FOXA3 transcription factor networks 188
Angiopoietin receptor Tie2-mediated signaling 162
PLK1 signaling events 159
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 1091 . 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 ( 1091 ).

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 0.2933 320 16323 51 -0.052 0.69 1000 -1000 -0.04 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2667 291 22707 78 -0.57 0.18 1000 -1000 -0.039 -1000
Class IB PI3K non-lipid kinase events 0.2612 285 855 3 -0.13 -1000 1000 -1000 -0.018 -1000
Signaling mediated by p38-alpha and p38-beta 0.2521 275 12141 44 -0.32 0.024 1000 -1000 -0.017 -1000
Reelin signaling pathway 0.2117 231 12954 56 -0.32 0.054 1000 -1000 -0.033 -1000
EGFR-dependent Endothelin signaling events 0.1833 200 4215 21 -0.21 0.034 1000 -1000 -0.035 -1000
Aurora B signaling 0.1787 195 13127 67 -0.21 0.27 1000 -1000 -0.036 -1000
FOXA2 and FOXA3 transcription factor networks 0.1723 188 8648 46 -1.1 0.034 1000 -1000 -0.042 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1485 162 14306 88 -0.32 0.11 1000 -1000 -0.062 -1000
PLK1 signaling events 0.1457 159 13573 85 -0.063 0.23 1000 -1000 -0.032 -1000
Glucocorticoid receptor regulatory network 0.1421 155 17704 114 -0.73 0.28 1000 -1000 -0.048 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1412 154 10498 68 -0.34 0.16 1000 -1000 -0.048 -1000
EPHB forward signaling 0.1393 152 12940 85 -0.2 0.14 1000 -1000 -0.057 -1000
Endothelins 0.1375 150 14405 96 -0.34 0.17 1000 -1000 -0.034 -1000
HIF-1-alpha transcription factor network 0.1357 148 11277 76 -0.47 0.035 1000 -1000 -0.035 -1000
p75(NTR)-mediated signaling 0.1302 142 17854 125 -0.22 0.096 1000 -1000 -0.058 -1000
IL4-mediated signaling events 0.1201 131 12009 91 -0.67 0.25 1000 -1000 -0.068 -1000
Ephrin B reverse signaling 0.1146 125 6007 48 -0.2 0.09 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1091 119 6473 54 -0.32 0.055 1000 -1000 -0.035 -1000
Noncanonical Wnt signaling pathway 0.1091 119 3117 26 -0.095 0.024 1000 -1000 -0.031 -1000
Wnt signaling 0.1082 118 826 7 -0.095 0.017 1000 -1000 -0.008 -1000
IL23-mediated signaling events 0.1054 115 6952 60 -0.3 0.084 1000 -1000 -0.022 -1000
IGF1 pathway 0.1027 112 6425 57 -0.11 0.044 1000 -1000 -0.031 -1000
Arf6 signaling events 0.0990 108 6707 62 -0.21 0.05 1000 -1000 -0.022 -1000
Plasma membrane estrogen receptor signaling 0.0990 108 9362 86 -0.12 0.11 1000 -1000 -0.042 -1000
Nongenotropic Androgen signaling 0.0953 104 5449 52 -0.24 0.13 1000 -1000 -0.026 -1000
ErbB2/ErbB3 signaling events 0.0907 99 6476 65 -0.26 0.034 1000 -1000 -0.051 -1000
BMP receptor signaling 0.0898 98 7947 81 -0.38 0.1 1000 -1000 -0.041 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0871 95 8114 85 -0.24 0.024 1000 -1000 -0.031 -1000
Calcium signaling in the CD4+ TCR pathway 0.0871 95 2974 31 -0.19 0.027 1000 -1000 -0.033 -1000
Signaling events mediated by PTP1B 0.0852 93 7128 76 -0.43 0.082 1000 -1000 -0.03 -1000
Signaling events regulated by Ret tyrosine kinase 0.0843 92 7566 82 -0.072 0.095 1000 -1000 -0.054 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0834 91 10942 120 -0.36 0.17 1000 -1000 -0.042 -1000
S1P1 pathway 0.0788 86 3102 36 -0.34 0.024 1000 -1000 -0.031 -1000
Aurora C signaling 0.0770 84 588 7 0 0.14 1000 -1000 -0.014 -1000
Visual signal transduction: Rods 0.0770 84 4370 52 -0.33 0.055 1000 -1000 -0.025 -1000
Effects of Botulinum toxin 0.0733 80 2081 26 -0.003 0.1 1000 -1000 -0.007 -1000
Glypican 1 network 0.0724 79 3833 48 -0.2 0.045 1000 -1000 -0.018 -1000
TCR signaling in naïve CD8+ T cells 0.0715 78 7258 93 -0.09 0.084 1000 -1000 -0.044 -1000
Integrins in angiogenesis 0.0706 77 6504 84 -0.21 0.11 1000 -1000 -0.046 -1000
amb2 Integrin signaling 0.0697 76 6305 82 -0.33 0.12 1000 -1000 -0.025 -1000
Syndecan-1-mediated signaling events 0.0687 75 2564 34 -0.074 0.18 1000 -1000 -0.03 -1000
LPA receptor mediated events 0.0678 74 7649 102 -0.19 0.12 1000 -1000 -0.065 -1000
IL6-mediated signaling events 0.0669 73 5524 75 -0.18 0.053 1000 -1000 -0.036 -1000
IL12-mediated signaling events 0.0651 71 6197 87 -0.32 0.072 1000 -1000 -0.059 -1000
ErbB4 signaling events 0.0632 69 4811 69 -0.28 0.06 1000 -1000 -0.038 -1000
Ephrin A reverse signaling 0.0632 69 486 7 -0.029 0.023 1000 -1000 -0.002 -1000
Signaling events mediated by the Hedgehog family 0.0623 68 3558 52 -0.12 0.028 1000 -1000 -0.035 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0577 63 2143 34 -0.024 0.059 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 0.0559 61 2726 44 -0.3 0.036 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 0.0550 60 2283 38 -0.024 0.16 1000 -1000 -0.006 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0550 60 3140 52 -0.11 0.071 1000 -1000 -0.033 -1000
Fc-epsilon receptor I signaling in mast cells 0.0532 58 5717 97 -0.14 0.033 1000 -1000 -0.052 -1000
Canonical Wnt signaling pathway 0.0532 58 2983 51 -0.28 0.12 1000 -1000 -0.032 -1000
E-cadherin signaling in keratinocytes 0.0522 57 2470 43 -0.19 0.032 1000 -1000 -0.027 -1000
Presenilin action in Notch and Wnt signaling 0.0495 54 3322 61 -0.28 0.12 1000 -1000 -0.037 -1000
Nectin adhesion pathway 0.0495 54 3441 63 -0.058 0.046 1000 -1000 -0.045 -1000
TCGA08_rtk_signaling 0.0486 53 1385 26 -0.19 0.037 1000 -1000 -0.011 -1000
Syndecan-2-mediated signaling events 0.0477 52 3638 69 -0.12 0.11 1000 -1000 -0.027 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0467 51 1690 33 -0.38 0.06 1000 -1000 -0.024 -1000
Rapid glucocorticoid signaling 0.0467 51 1029 20 -0.11 0.027 1000 -1000 -0.001 -1000
FAS signaling pathway (CD95) 0.0458 50 2387 47 -0.43 0.04 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 0.0458 50 1779 35 -0.23 0.055 1000 -1000 -0.016 -1000
Glypican 2 network 0.0458 50 201 4 0.032 0.057 1000 -1000 0.01 -1000
Signaling events mediated by HDAC Class III 0.0431 47 1905 40 -0.32 0.045 1000 -1000 -0.024 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0422 46 3471 74 -0.19 0.049 1000 -1000 -0.059 -1000
LPA4-mediated signaling events 0.0412 45 546 12 -0.11 0.006 1000 -1000 -0.018 -1000
Syndecan-4-mediated signaling events 0.0394 43 2947 67 -0.2 0.12 1000 -1000 -0.03 -1000
Signaling events mediated by PRL 0.0394 43 1486 34 -0.12 0.035 1000 -1000 -0.032 -1000
Regulation of Androgen receptor activity 0.0394 43 3051 70 -0.16 0.11 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 0.0394 43 743 17 -0.055 0.026 1000 -1000 -0.02 -1000
Coregulation of Androgen receptor activity 0.0385 42 3233 76 -0.14 0.064 1000 -1000 -0.013 -1000
Aurora A signaling 0.0385 42 2573 60 -0.08 0.18 1000 -1000 -0.009 -1000
Insulin Pathway 0.0376 41 3064 74 -0.12 0.061 1000 -1000 -0.04 -1000
Thromboxane A2 receptor signaling 0.0357 39 4190 105 -0.19 0.036 1000 -1000 -0.036 -1000
IL27-mediated signaling events 0.0348 38 1941 51 -0.18 0.075 1000 -1000 -0.019 -1000
Regulation of Telomerase 0.0348 38 3922 102 -0.2 0.14 1000 -1000 -0.029 -1000
Regulation of p38-alpha and p38-beta 0.0339 37 2037 54 -0.24 0.053 1000 -1000 -0.045 -1000
TCGA08_retinoblastoma 0.0339 37 302 8 -0.018 0.061 1000 -1000 -0.001 -1000
Osteopontin-mediated events 0.0321 35 1358 38 -0.14 0.086 1000 -1000 -0.03 -1000
BCR signaling pathway 0.0312 34 3401 99 -0.076 0.056 1000 -1000 -0.053 -1000
IL2 signaling events mediated by STAT5 0.0293 32 712 22 0.006 0.11 1000 -1000 -0.026 -1000
Regulation of nuclear SMAD2/3 signaling 0.0266 29 3960 136 -0.2 0.078 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 0.0238 26 1801 68 -0.16 0.043 1000 -1000 -0.024 -1000
Caspase cascade in apoptosis 0.0220 24 1802 74 -0.026 0.057 1000 -1000 -0.027 -1000
HIF-2-alpha transcription factor network 0.0220 24 1032 43 -0.15 0.16 1000 -1000 -0.045 -1000
Ceramide signaling pathway 0.0211 23 1815 76 -0.1 0.063 1000 -1000 -0.025 -1000
S1P4 pathway 0.0211 23 577 25 -0.011 0.044 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 0.0202 22 1438 65 -0.085 0.056 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 0.0192 21 1247 58 -0.001 0.065 1000 -1000 -0.029 -1000
Arf6 trafficking events 0.0192 21 1501 71 -0.27 0.042 1000 -1000 -0.026 -1000
BARD1 signaling events 0.0183 20 1171 57 -0.046 0.1 1000 -1000 -0.028 -1000
Cellular roles of Anthrax toxin 0.0183 20 812 39 -0.08 0.027 1000 -1000 -0.019 -1000
mTOR signaling pathway 0.0174 19 1048 53 -0.024 0.029 1000 -1000 -0.029 -1000
S1P5 pathway 0.0174 19 330 17 -0.007 0.033 1000 -1000 -0.011 -1000
FoxO family signaling 0.0174 19 1230 64 -0.016 0.22 1000 -1000 -0.028 -1000
JNK signaling in the CD4+ TCR pathway 0.0165 18 313 17 0.003 0.063 1000 -1000 -0.021 -1000
ceramide signaling pathway 0.0165 18 907 49 -0.002 0.037 1000 -1000 -0.03 -1000
S1P3 pathway 0.0165 18 794 42 -0.014 0.042 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 0.0147 16 250 15 -0.027 0.024 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 0.0147 16 938 58 -0.05 0.052 1000 -1000 -0.035 -1000
IL1-mediated signaling events 0.0137 15 930 62 -0.015 0.061 1000 -1000 -0.028 -1000
E-cadherin signaling in the nascent adherens junction 0.0137 15 1176 76 -0.023 0.053 1000 -1000 -0.055 -1000
PLK2 and PLK4 events 0.0128 14 44 3 0.016 0.033 1000 -1000 -0.009 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0128 14 648 45 0.003 0.055 1000 -1000 -0.029 -1000
E-cadherin signaling events 0.0128 14 70 5 0.01 0.033 1000 -1000 0.013 -1000
p38 MAPK signaling pathway 0.0128 14 643 44 -0.019 0.067 1000 -1000 -0.014 -1000
PDGFR-beta signaling pathway 0.0119 13 1326 97 -0.025 0.056 1000 -1000 -0.046 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0110 12 360 28 -0.007 0.051 1000 -1000 -0.014 -1000
TRAIL signaling pathway 0.0110 12 583 48 -0.015 0.043 1000 -1000 -0.034 -1000
Class I PI3K signaling events 0.0110 12 898 73 -0.018 0.051 1000 -1000 -0.03 -1000
IFN-gamma pathway 0.0101 11 756 68 -0.006 0.076 1000 -1000 -0.046 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0101 11 413 37 -0.009 0.067 1000 -1000 -0.03 -1000
Canonical NF-kappaB pathway 0.0092 10 408 39 0 0.051 1000 -1000 -0.025 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0092 10 896 83 -0.019 0.047 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 0.0082 9 699 75 -0.037 0.063 1000 -1000 -0.032 -1000
a4b1 and a4b7 Integrin signaling 0.0082 9 48 5 0.024 0.041 1000 -1000 0.013 -1000
EPO signaling pathway 0.0082 9 544 55 0.014 0.08 1000 -1000 -0.029 -1000
Insulin-mediated glucose transport 0.0082 9 294 32 -0.12 0.039 1000 -1000 -0.021 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 9 1136 125 -0.099 0.054 1000 -1000 -0.039 -1000
VEGFR1 specific signals 0.0073 8 458 56 -0.099 0.053 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0055 6 640 104 -0.059 0.057 1000 -1000 -0.033 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0046 5 127 23 -0.004 0.043 1000 -1000 -0.021 -1000
TCGA08_p53 0.0046 5 37 7 -0.011 0.02 1000 -1000 -0.004 -1000
Atypical NF-kappaB pathway 0.0046 5 162 31 0 0.028 1000 -1000 -0.015 -1000
Circadian rhythm pathway 0.0037 4 93 22 -0.007 0.049 1000 -1000 -0.022 -1000
Arf6 downstream pathway 0.0037 4 204 43 -0.054 0.055 1000 -1000 -0.016 -1000
Paxillin-dependent events mediated by a4b1 0.0037 4 170 36 -0.048 0.052 1000 -1000 -0.031 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0009 1 27 27 -0.008 0.057 1000 -1000 -0.038 -1000
Arf1 pathway 0.0009 1 85 54 -0.001 0.045 1000 -1000 -0.013 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 0 0.067 1000 -1000 0 -1000
Total NA 8440 500899 7203 -20 -990 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 0.57 0.39 0.98 369 -1 3 372
PLK1 0.34 0.24 0.61 356 -0.9 1 357
BIRC5 0.36 0.24 0.61 377 -0.79 4 381
HSPA1B 0.57 0.39 0.98 365 -1 3 368
MAP2K1 0.16 0.11 0.3 319 -10000 0 319
BRCA2 0.57 0.4 0.99 382 -0.99 4 386
FOXM1 0.66 0.48 1.1 424 -1.1 4 428
XRCC1 0.57 0.39 0.99 367 -1 3 370
FOXM1B/p19 0.12 0.26 0.82 48 -1.1 4 52
Cyclin D1/CDK4 0.5 0.37 0.89 368 -0.99 3 371
CDC2 0.62 0.43 1 428 -0.99 4 432
TGFA 0.5 0.39 0.89 379 -0.96 8 387
SKP2 0.57 0.39 0.99 374 -1 3 377
CCNE1 0.089 0.094 0.29 179 -10000 0 179
CKS1B 0.57 0.39 0.95 424 -0.95 4 428
RB1 0.28 0.3 0.66 329 -0.67 7 336
FOXM1C/SP1 0.52 0.36 0.9 343 -1.1 6 349
AURKB 0.29 0.3 0.62 276 -0.79 21 297
CENPF 0.66 0.45 1.1 475 -0.99 3 478
CDK4 0.08 0.053 0.23 30 -10000 0 30
MYC 0.34 0.36 0.84 248 -0.96 6 254
CHEK2 0.15 0.11 0.3 325 -10000 0 325
ONECUT1 0.52 0.39 0.92 389 -1.1 3 392
CDKN2A -0.052 0.11 0.24 10 -0.24 127 137
LAMA4 0.57 0.4 0.99 374 -1.1 6 380
FOXM1B/HNF6 0.53 0.4 0.96 353 -1.3 3 356
FOS 0.27 0.64 0.99 310 -0.99 76 386
SP1 0.024 0.021 -10000 0 -0.2 6 6
CDC25B 0.57 0.39 1 363 -1 3 366
response to radiation 0.11 0.083 0.21 333 -10000 0 333
CENPB 0.57 0.39 0.98 377 -1 3 380
CENPA 0.62 0.43 1.1 418 -1 3 421
NEK2 0.69 0.44 1.1 479 -0.97 3 482
HIST1H2BA 0.57 0.39 0.98 361 -1 3 364
CCNA2 0.14 0.12 0.3 400 -10000 0 400
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.6 0.42 1.1 360 -1.2 3 363
CCNB2 0.63 0.43 1.1 428 -1 3 431
CCNB1 0.62 0.44 1.1 403 -1.1 3 406
ETV5 0.57 0.4 1 371 -1 3 374
ESR1 0.43 0.55 1 358 -0.99 19 377
CCND1 0.52 0.41 0.95 394 -1 3 397
GSK3A 0.13 0.088 0.27 203 -10000 0 203
Cyclin A-E1/CDK1-2 0.23 0.16 0.4 435 -10000 0 435
CDK2 0.056 0.028 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.14 0.11 0.25 441 -10000 0 441
FOXM1B/Cbp/p300 0.26 0.3 0.73 76 -0.99 4 80
GAS1 0.52 0.48 0.98 367 -1.1 36 403
MMP2 0.56 0.41 0.98 368 -1.2 10 378
RB1/FOXM1C 0.46 0.38 0.88 353 -1 3 356
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.34 3 -0.38 471 474
CRKL -0.18 0.21 0.26 1 -0.4 484 485
HRAS -0.13 0.18 -10000 0 -0.35 328 328
mol:PIP3 -0.14 0.2 0.29 1 -0.38 354 355
SPRED1 0.024 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 492 492
FOXO3 -0.14 0.2 0.53 1 -0.36 409 410
AKT1 -0.16 0.21 0.37 1 -0.38 451 452
BAD -0.15 0.2 0.34 2 -0.36 425 427
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 495 495
GSK3B -0.15 0.2 0.53 1 -0.36 428 429
RAF1 -0.098 0.16 0.25 4 -0.3 298 302
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 489 489
STAT1 -0.44 0.52 -10000 0 -0.99 500 500
HRAS/SPRED1 -0.095 0.16 -10000 0 -0.3 303 303
cell proliferation -0.18 0.22 -10000 0 -0.41 494 494
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.032 -10000 0 -0.57 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 497 497
HRAS/SPRED2 -0.095 0.16 -10000 0 -0.3 278 278
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.4 414 414
MAPK3 -0.066 0.12 0.33 5 -0.27 37 42
STAP1 -0.18 0.22 -10000 0 -0.42 495 495
GRAP2 0.017 0.066 0.25 3 -0.57 13 16
JAK2 -0.37 0.44 -10000 0 -0.84 497 497
STAT1 (dimer) -0.43 0.51 -10000 0 -0.97 500 500
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.15 0.22 -10000 0 -0.4 422 422
actin filament polymerization -0.18 0.22 0.33 1 -0.41 492 493
LYN 0.021 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.59 500 500
PIK3R1 0.017 0.063 -10000 0 -0.57 12 12
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 437 437
PI3K -0.15 0.22 -10000 0 -0.4 467 467
PTEN 0.023 0.019 -10000 0 -0.57 1 1
SCF/KIT/EPO/EPOR -0.51 0.63 -10000 0 -1.2 494 494
MAPK8 -0.19 0.22 -10000 0 -0.42 494 494
STAT3 (dimer) -0.18 0.22 0.27 1 -0.41 489 490
positive regulation of transcription -0.053 0.11 0.24 13 -0.23 25 38
mol:GDP -0.13 0.19 -10000 0 -0.37 335 335
PIK3C2B -0.17 0.21 -10000 0 -0.42 386 386
CBL/CRKL -0.16 0.2 -10000 0 -0.38 474 474
FER -0.19 0.22 -10000 0 -0.42 492 492
SH2B3 -0.18 0.22 -10000 0 -0.42 494 494
PDPK1 -0.12 0.19 0.34 9 -0.35 326 335
SNAI2 -0.18 0.22 0.28 4 -0.42 442 446
positive regulation of cell proliferation -0.32 0.38 -10000 0 -0.73 500 500
KITLG -0.004 0.058 0.25 10 -0.59 5 15
cell motility -0.32 0.38 -10000 0 -0.73 500 500
PTPN6 0.033 0.017 0.26 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -0.99 16 16
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 499 499
SOCS1 0.025 0.033 0.25 14 -0.57 1 15
cell migration 0.18 0.22 0.41 498 -10000 0 498
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.04 0.091 0.24 169 -10000 0 169
VAV1 0.023 0.033 0.25 2 -0.57 3 5
GRB10 -0.18 0.22 -10000 0 -0.42 490 490
PTPN11 0.031 0.01 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 497 497
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.076 0.13 0.27 11 -0.28 56 67
CBL 0.022 0.008 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 495 495
MAP2K2 -0.076 0.13 0.33 6 -0.28 53 59
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 361 361
STAT5A -0.27 0.33 -10000 0 -0.62 499 499
GRB2 0.023 0.009 0.25 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 442 446
SHC/GRAP2 0.024 0.048 -10000 0 -0.3 18 18
PTPRO -0.18 0.22 -10000 0 -0.42 495 495
SH2B2 -0.18 0.22 -10000 0 -0.42 492 492
DOK1 0.025 0.014 0.25 4 -10000 0 4
MATK -0.19 0.22 -10000 0 -0.42 498 498
CREBBP -0.028 0.072 -10000 0 -0.18 19 19
BCL2 -0.16 0.32 -10000 0 -1.3 60 60
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.13 0.26 0.57 285 -10000 0 285
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.57 285 285
PDE3B -0.13 0.26 -10000 0 -0.57 285 285
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.32 0.5 0.42 4 -1 358 362
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.088 0.18 -10000 0 -0.34 352 352
ATF2/c-Jun -0.082 0.16 -10000 0 -0.41 99 99
MAPK11 -0.083 0.18 -10000 0 -0.35 325 325
MITF -0.12 0.22 0.28 1 -0.41 351 352
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 359 359
KRT8 -0.11 0.21 -10000 0 -0.4 338 338
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.52 357 357
CEBPB -0.1 0.2 0.28 1 -0.4 334 335
SLC9A1 -0.12 0.21 -10000 0 -0.41 353 353
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.39 348 348
p38alpha-beta/MNK1 -0.11 0.25 -10000 0 -0.45 326 326
JUN -0.081 0.16 -10000 0 -0.41 99 99
PPARGC1A -0.2 0.33 0.26 1 -0.56 422 423
USF1 -0.1 0.19 0.31 3 -0.38 335 338
RAB5/GDP/GDI1 -0.081 0.16 -10000 0 -0.3 351 351
NOS2 -0.11 0.22 -10000 0 -0.55 92 92
DDIT3 -0.11 0.21 -10000 0 -0.4 352 352
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.094 0.17 0.28 4 -0.33 329 333
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 326 326
CREB1 -0.12 0.22 -10000 0 -0.43 354 354
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.4 323 323
RPS6KA4 -0.11 0.21 -10000 0 -0.4 350 350
PLA2G4A -0.13 0.22 -10000 0 -0.43 354 354
GDI1 -0.11 0.21 -10000 0 -0.4 359 359
TP53 -0.15 0.27 0.28 1 -0.52 337 338
RPS6KA5 -0.12 0.22 -10000 0 -0.41 362 362
ESR1 -0.16 0.24 0.28 1 -0.42 413 414
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 358 358
MEF2A -0.11 0.21 0.28 1 -0.4 352 353
EIF4EBP1 -0.12 0.22 0.28 1 -0.43 341 342
KRT19 -0.11 0.21 0.31 1 -0.4 330 331
ELK4 -0.1 0.19 0.3 3 -0.38 340 343
ATF6 -0.1 0.19 0.31 3 -0.38 340 343
ATF1 -0.12 0.22 -10000 0 -0.43 359 359
p38alpha-beta/MAPKAPK2 -0.096 0.22 -10000 0 -0.41 312 312
p38alpha-beta/MAPKAPK3 -0.11 0.25 -10000 0 -0.45 326 326
Reelin signaling pathway

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
CDK5R1/CDK5 0.037 0.027 -10000 0 -10000 0 0
VLDLR 0.008 0.093 -10000 0 -0.57 27 27
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
ITGA3 0.022 0.021 0.25 1 -0.57 1 2
RELN/VLDLR/Fyn -0.2 0.21 -10000 0 -0.37 604 604
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.044 -10000 0 -0.32 7 7
AKT1 -0.15 0.14 -10000 0 -0.27 547 547
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.25 61 -10000 0 61
RELN/LRP8/DAB1 -0.16 0.19 0.32 4 -0.32 608 612
LRPAP1/LRP8 0.048 0.047 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.14 0.18 0.31 4 -0.3 592 596
DAB1/alpha3/beta1 Integrin -0.14 0.17 -10000 0 -0.31 458 458
long-term memory -0.18 0.22 0.33 5 -0.35 583 588
DAB1/LIS1 -0.14 0.19 0.29 4 -0.3 603 607
DAB1/CRLK/C3G -0.15 0.18 -10000 0 -0.31 475 475
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.14 0.19 0.3 4 -0.31 604 608
ARHGEF2 0.021 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.033 0.18 0.25 13 -0.57 106 119
CDK5R1 0.028 0.034 0.25 23 -10000 0 23
RELN -0.32 0.29 0.25 2 -0.57 619 621
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
RELN/LRP8/Fyn -0.18 0.2 -10000 0 -0.36 596 596
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 0.33 4 -0.35 557 561
MAPK8 0.02 0.048 -10000 0 -0.57 7 7
RELN/VLDLR/DAB1 -0.17 0.19 0.32 2 -0.34 608 610
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.18 0.22 2 -0.32 611 613
RELN/LRP8 -0.18 0.2 -10000 0 -0.36 612 612
GRIN2B/RELN/LRP8/DAB1/Fyn -0.16 0.2 0.36 3 -0.32 614 617
PI3K 0.028 0.048 -10000 0 -0.4 12 12
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.032 0.021 -10000 0 -0.42 1 1
RAP1A -0.16 0.15 0.34 3 -0.51 21 24
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.029 0.25 4 -0.57 2 6
CRLK/C3G 0.034 0.01 -10000 0 -10000 0 0
GRIN2B -0.018 0.15 0.25 1 -0.57 70 71
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.087 0.12 -10000 0 -0.35 77 77
neuron adhesion -0.14 0.15 0.31 5 -0.49 21 26
LRP8 0.046 0.068 0.25 104 -10000 0 104
GSK3B -0.14 0.14 -10000 0 -0.26 537 537
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.31 2 -0.32 594 596
MAP3K11 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.15 0.16 -10000 0 -0.28 560 560
CDK5 0.025 0.015 0.25 4 -10000 0 4
MAPT -0.023 0.2 0.87 20 -0.52 108 128
neuron migration -0.18 0.18 0.27 2 -0.34 532 534
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.087 0.12 -10000 0 -0.35 77 77
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 612 612
EGFR-dependent Endothelin signaling events

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
HRAS 0.025 0.02 0.25 8 -10000 0 8
EGFR -0.19 0.28 -10000 0 -0.57 393 393
EGF/EGFR -0.16 0.22 -10000 0 -0.37 519 519
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.35 398 398
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.024 0.02 0.25 1 -0.57 1 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.084 0.23 0.25 2 -0.57 196 198
EGF/EGFR dimer/SHC -0.16 0.22 -10000 0 -0.4 425 425
mol:GDP -0.12 0.2 -10000 0 -0.35 398 398
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.017 0.15 0.25 1 -0.57 74 75
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.33 397 397
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.11 0.19 -10000 0 -0.34 397 397
FRAP1 -0.14 0.16 0.16 3 -0.34 398 401
EGF/EGFR dimer -0.21 0.26 -10000 0 -0.46 528 528
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.25 1 -10000 0 1
ETA receptor/Endothelin-1 0.002 0.12 -10000 0 -0.42 75 75
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.1 0.099 0.23 313 -0.26 2 315
STMN1 0.078 0.078 0.26 69 -10000 0 69
Aurora B/RasGAP/Survivin 0.19 0.14 0.33 505 -10000 0 505
Chromosomal passenger complex/Cul3 protein complex 0.005 0.14 0.19 185 -0.24 134 319
BIRC5 0.18 0.11 0.26 711 -10000 0 711
DES -0.15 0.32 -10000 0 -0.58 270 270
Aurora C/Aurora B/INCENP 0.11 0.078 0.32 9 -0.3 1 10
Aurora B/TACC1 0.072 0.098 0.18 16 -0.33 25 41
Aurora B/PP2A 0.11 0.082 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.031 0.026 0.14 7 -10000 0 7
mitotic metaphase/anaphase transition -0.006 0.005 -10000 0 -10000 0 0
NDC80 0.14 0.12 0.26 483 -10000 0 483
Cul3 protein complex -0.11 0.2 -10000 0 -0.36 418 418
KIF2C 0.15 0.1 0.23 591 -10000 0 591
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.25 789 -10000 0 789
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.081 -10000 0 -10000 0 0
SEPT1 0.031 0.043 0.25 37 -10000 0 37
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.021 0.25 9 -10000 0 9
NSUN2/NPM1/Nucleolin 0.074 0.19 0.32 26 -0.45 93 119
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.006 -10000 0 -10000 0 0
H3F3B 0.07 0.06 0.23 33 -10000 0 33
AURKB 0.14 0.12 0.25 560 -10000 0 560
AURKC 0.026 0.032 0.25 14 -0.57 1 15
CDCA8 0.1 0.11 0.26 352 -10000 0 352
cytokinesis 0.14 0.14 0.3 383 -0.34 6 389
Aurora B/Septin1 0.18 0.17 0.36 380 -0.32 4 384
AURKA 0.11 0.11 0.25 427 -10000 0 427
INCENP 0.03 0.008 -10000 0 -10000 0 0
KLHL13 -0.21 0.29 -10000 0 -0.57 427 427
BUB1 0.17 0.11 0.25 709 -10000 0 709
hSgo1/Aurora B/Survivin 0.27 0.18 0.41 629 -10000 0 629
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.14 0.35 343 -10000 0 343
SGOL1 0.16 0.11 0.25 655 -10000 0 655
CENPA 0.16 0.14 0.3 493 -0.28 1 494
NCAPG 0.13 0.12 0.25 498 -10000 0 498
Aurora B/HC8 Proteasome 0.11 0.081 -10000 0 -10000 0 0
NCAPD2 0.024 0.009 0.25 1 -10000 0 1
Aurora B/PP1-gamma 0.11 0.081 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.11 0.11 0.25 408 -10000 0 408
NPM1 0.067 0.12 0.26 2 -0.6 9 11
RASA1 0.024 0.004 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.081 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.2 0.15 0.36 439 -10000 0 439
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 0.073 0.12 0.27 21 -0.4 9 30
MYLK 0.02 0.14 0.23 8 -0.31 127 135
KIF23 0.098 0.11 0.26 321 -10000 0 321
VIM 0.078 0.084 0.37 32 -0.41 2 34
RACGAP1 0.04 0.046 0.27 42 -10000 0 42
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.062 0.14 -10000 0 -0.51 28 28
Chromosomal passenger complex 0.17 0.12 0.28 568 -10000 0 568
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 477 -10000 0 477
TACC1 0.006 0.089 -10000 0 -0.57 25 25
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.27 0.52 1 -0.71 138 139
PCK1 -0.92 0.63 0.44 1 -1.4 677 678
HNF4A -0.23 0.28 0.65 2 -0.78 84 86
KCNJ11 -0.28 0.3 -10000 0 -0.79 140 140
AKT1 -0.16 0.16 0.37 1 -0.42 73 74
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.45 0.48 -10000 0 -1.1 358 358
NKX2-1 -0.045 0.16 0.39 20 -0.37 51 71
ACADM -0.25 0.27 0.52 1 -0.74 123 124
TAT -1.1 0.63 -10000 0 -1.4 764 764
CEBPB 0.024 0.01 -10000 0 -10000 0 0
CEBPA 0.021 0.055 -10000 0 -0.57 9 9
TTR -0.41 0.29 0.57 1 -0.74 318 319
PKLR -0.22 0.27 0.56 6 -0.7 134 140
APOA1 -0.28 0.31 0.78 1 -0.84 109 110
CPT1C -0.24 0.27 0.55 2 -0.72 140 142
ALAS1 -0.15 0.16 -10000 0 -0.77 6 6
TFRC -0.42 0.26 -10000 0 -0.69 384 384
FOXF1 0.021 0.041 0.25 7 -0.57 4 11
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.032 0.27 8 -10000 0 8
CPT1A -0.23 0.27 0.58 2 -0.73 120 122
HMGCS1 -0.25 0.27 0.61 2 -0.72 132 134
NR3C1 -0.12 0.12 -10000 0 -0.29 171 171
CPT1B -0.25 0.27 0.52 1 -0.73 127 128
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.022 -10000 0 -10000 0 0
GCK -0.27 0.32 0.52 1 -0.83 169 170
CREB1 -0.076 0.093 -10000 0 -0.2 221 221
IGFBP1 -0.41 0.54 -10000 0 -1.4 239 239
PDX1 -0.12 0.15 -10000 0 -0.57 4 4
UCP2 -0.24 0.27 0.52 2 -0.7 147 149
ALDOB -0.28 0.29 0.67 1 -0.78 136 137
AFP -0.57 0.51 0.35 1 -0.86 669 670
BDH1 -0.24 0.26 0.52 1 -0.72 131 132
HADH -0.28 0.28 -10000 0 -0.77 136 136
F2 -0.28 0.3 0.78 1 -0.86 91 92
HNF1A 0.034 0.032 0.27 8 -10000 0 8
G6PC -0.18 0.12 -10000 0 -0.55 10 10
SLC2A2 -0.16 0.17 0.62 1 -0.78 2 3
INS 0.018 0.077 0.23 22 -10000 0 22
FOXA1 -0.22 0.23 0.27 18 -0.36 643 661
FOXA3 -0.36 0.21 0.34 2 -0.47 764 766
FOXA2 -0.32 0.33 0.77 1 -0.8 210 211
ABCC8 -0.32 0.38 -10000 0 -0.96 198 198
ALB -0.76 0.54 0.35 1 -1.1 700 701
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.16 0.38 -10000 0 -0.86 239 239
NCK1/PAK1/Dok-R -0.096 0.17 -10000 0 -0.41 239 239
NCK1/Dok-R -0.19 0.46 -10000 0 -1 238 238
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.044 0.099 0.24 211 -10000 0 211
RELA 0.024 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.047 0.11 0.27 212 -10000 0 212
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.17 0.44 -10000 0 -0.97 238 238
FN1 0.11 0.11 0.25 421 -10000 0 421
PLD2 -0.21 0.47 -10000 0 -1.1 238 238
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.012 0.18 0.25 143 -0.57 78 221
ELK1 -0.19 0.42 -10000 0 -0.96 239 239
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 0.023 0.019 0.25 6 -10000 0 6
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.49 -10000 0 -1 238 238
CDKN1A -0.11 0.26 -10000 0 -0.62 172 172
ITGA5 0.025 0.007 0.25 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.19 0.46 -10000 0 -1 238 238
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.11 0.29 -10000 0 -0.64 239 239
PLG -0.22 0.47 -10000 0 -1.1 238 238
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.16 0.36 -10000 0 -0.82 239 239
GRB2 0.023 0.009 0.25 1 -10000 0 1
PIK3R1 0.016 0.063 -10000 0 -0.57 12 12
ANGPT2 -0.15 0.28 -10000 0 -0.69 161 161
BMX -0.32 0.51 -10000 0 -1.2 240 240
ANGPT1 -0.23 0.5 -10000 0 -1.2 211 211
tube development -0.13 0.29 -10000 0 -0.67 206 206
ANGPT4 -0.15 0.26 -10000 0 -0.57 303 303
response to hypoxia -0.014 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.22 0.51 -10000 0 -1.1 238 238
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 411 411
STAT5A (dimer) -0.14 0.34 -10000 0 -0.78 200 200
mol:L-citrulline -0.11 0.29 -10000 0 -0.64 239 239
AGTR1 -0.094 0.26 0.26 63 -0.57 239 302
MAPK14 -0.21 0.47 -10000 0 -1.1 241 241
Tie2/SHP2 -0.099 0.32 -10000 0 -1.1 88 88
TEK -0.11 0.35 -10000 0 -1.2 88 88
RPS6KB1 -0.14 0.38 -10000 0 -0.82 238 238
Angiotensin II/AT1 -0.069 0.19 0.18 63 -0.41 242 305
Tie2/Ang1/GRB2 -0.21 0.49 -10000 0 -1.1 238 238
MAPK3 -0.19 0.43 -10000 0 -0.97 238 238
MAPK1 -0.2 0.43 -10000 0 -0.99 238 238
Tie2/Ang1/GRB7 -0.21 0.49 -10000 0 -1.1 238 238
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.22 0.47 -10000 0 -1.1 238 238
PI3K -0.19 0.44 -10000 0 -0.99 239 239
FES -0.21 0.47 -10000 0 -1.1 240 240
Crk/Dok-R -0.19 0.46 -10000 0 -1 238 238
Tie2/Ang1/ABIN2 -0.21 0.5 -10000 0 -1.1 238 238
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.14 0.34 -10000 0 -0.77 239 239
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.37 0.47 1 -0.8 238 239
Tie2/Ang2 -0.18 0.4 -10000 0 -0.93 203 203
Tie2/Ang1 -0.23 0.52 -10000 0 -1.2 238 238
FOXO1 -0.14 0.35 0.47 1 -0.77 239 240
ELF1 0.011 0.037 -10000 0 -10000 0 0
ELF2 -0.21 0.47 -10000 0 -1.1 238 238
mol:Choline -0.2 0.45 -10000 0 -1 238 238
cell migration -0.04 0.1 -10000 0 -0.23 239 239
FYN -0.15 0.33 -10000 0 -0.77 204 204
DOK2 0.02 0.031 0.25 4 -0.57 2 6
negative regulation of cell cycle -0.1 0.24 -10000 0 -0.56 173 173
ETS1 -0.022 0.11 -10000 0 -0.27 171 171
PXN -0.1 0.32 0.45 1 -0.67 238 239
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.13 0.32 -10000 0 -0.73 239 239
RAC1 0.024 0.003 -10000 0 -10000 0 0
TNF -0.025 0.13 0.26 21 -0.27 205 226
MAPKKK cascade -0.2 0.45 -10000 0 -1 238 238
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.21 0.48 -10000 0 -1.1 236 236
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.098 0.26 0.38 1 -0.57 239 240
mol:Phosphatidic acid -0.2 0.45 -10000 0 -1 238 238
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.11 0.29 -10000 0 -0.64 239 239
Rac1/GTP -0.14 0.35 -10000 0 -0.77 239 239
MMP2 -0.22 0.47 -10000 0 -1.1 239 239
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.063 0.048 0.11 2 -0.12 148 150
BUB1B 0.082 0.066 0.15 428 -10000 0 428
PLK1 0.048 0.038 0.11 158 -10000 0 158
PLK1S1 0.025 0.034 0.14 10 -0.17 18 28
KIF2A 0.041 0.039 0.21 12 -10000 0 12
regulation of mitotic centrosome separation 0.048 0.038 0.11 158 -10000 0 158
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.23 0.14 0.31 744 -10000 0 744
WEE1 0.043 0.06 0.23 2 -0.27 25 27
cytokinesis 0.12 0.086 0.2 353 -0.22 11 364
PP2A-alpha B56 0.11 0.12 -10000 0 -0.48 14 14
AURKA 0.063 0.052 0.12 453 -0.14 4 457
PICH/PLK1 0.095 0.087 0.23 213 -10000 0 213
CENPE 0.06 0.053 0.16 75 -10000 0 75
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.041 0.039 0.21 12 -10000 0 12
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.078 0.053 0.12 563 -0.14 2 565
PAK1 0.022 0.019 0.25 6 -10000 0 6
SPC24 0.16 0.11 0.25 655 -10000 0 655
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.07 0.069 0.14 366 -0.19 22 388
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 54 -10000 0 54
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.022 0.019 0.053 146 -10000 0 146
G2 phase of mitotic cell cycle 0.001 0.003 0.015 12 -10000 0 12
STAG2 0.024 0.018 -10000 0 -0.57 1 1
GRASP65/GM130/RAB1/GTP 0.011 0.081 -10000 0 -0.5 25 25
spindle elongation 0.048 0.038 0.11 158 -10000 0 158
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.1 0.13 -10000 0 -0.49 30 30
TPT1 0.013 0.056 0.12 2 -0.17 78 80
CDC25C 0.11 0.067 0.15 643 -0.2 17 660
CDC25B 0.029 0.031 0.26 18 -10000 0 18
SGOL1 0.063 0.048 0.12 148 -0.11 2 150
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.068 0.064 0.31 11 -10000 0 11
CDC14B -0.01 0.074 -10000 0 -0.42 33 33
CDC20 0.14 0.12 0.25 565 -10000 0 565
PLK1/PBIP1 0.037 0.046 0.14 140 -10000 0 140
mitosis -0.004 0.005 0.027 4 -10000 0 4
FBXO5 0.029 0.035 0.16 15 -10000 0 15
CDC2 0.003 0.004 0.011 187 -10000 0 187
NDC80 0.16 0.12 0.25 617 -10000 0 617
metaphase plate congression 0.028 0.054 0.15 1 -0.2 40 41
ERCC6L 0.087 0.083 0.24 165 -10000 0 165
NLP/gamma Tubulin 0.023 0.024 0.077 26 -0.086 10 36
microtubule cytoskeleton organization 0.013 0.056 0.12 2 -0.17 78 80
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 13 -10000 0 13
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 13 -10000 0 13
PLK1/PRC1-2 0.2 0.12 0.26 758 -10000 0 758
GRASP65/GM130/RAB1/GTP/PLK1 0.069 0.03 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.041 0.035 0.084 283 -10000 0 283
mitotic prometaphase 0.002 0.005 0.022 51 -10000 0 51
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.051 0.2 1 -0.31 3 4
microtubule-based process 0.17 0.088 0.22 788 -10000 0 788
Golgi organization 0.048 0.038 0.11 158 -10000 0 158
Cohesin/SA2 0.053 0.031 0.17 2 -0.3 1 3
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.25 789 -10000 0 789
APC/C/CDC20 0.14 0.098 0.23 561 -10000 0 561
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.03 0.046 0.14 140 -10000 0 140
PRC1 0.079 0.099 0.25 258 -10000 0 258
ECT2 0.049 0.057 0.26 47 -10000 0 47
C13orf34 0.04 0.033 0.091 163 -10000 0 163
NUDC 0.028 0.054 0.15 1 -0.2 40 41
regulation of attachment of spindle microtubules to kinetochore 0.082 0.066 0.15 428 -10000 0 428
spindle assembly 0.035 0.029 0.088 102 -10000 0 102
spindle stabilization 0.025 0.034 0.13 10 -0.17 18 28
APC/C/HCDH1 0.01 0.067 -10000 0 -0.35 35 35
MKLP2/PLK1 0.17 0.089 0.22 788 -10000 0 788
CCNB1 0.069 0.091 0.26 205 -10000 0 205
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.026 0.085 0.23 1 -0.37 39 40
TUBG1 0.023 0.038 0.13 3 -0.16 31 34
G2/M transition of mitotic cell cycle 0.041 0.043 0.19 12 -10000 0 12
MLF1IP 0.023 0.045 0.13 149 -10000 0 149
INCENP 0.024 0.005 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.09 0.1 0.4 6 -10000 0 6
SMARCC2 0.024 0.012 -10000 0 -0.19 1 1
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.12 0.21 0.36 9 -0.5 141 150
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.032 0.26 19 -10000 0 19
FKBP4 0.025 0.016 0.25 5 -10000 0 5
FKBP5 0.016 0.076 0.25 5 -0.57 17 22
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.3 149 -0.3 9 158
PRL -0.062 0.12 0.56 2 -10000 0 2
cortisol/GR alpha (dimer)/TIF2 0.18 0.28 0.52 340 -0.48 17 357
RELA -0.037 0.1 0.25 2 -0.24 60 62
FGG 0.21 0.24 0.46 406 -0.46 4 410
GR beta/TIF2 0.078 0.16 0.31 157 -0.4 42 199
IFNG -0.3 0.36 0.48 1 -0.7 390 391
apoptosis -0.26 0.31 0.85 1 -0.64 318 319
CREB1 0.06 0.052 -10000 0 -10000 0 0
histone acetylation 0.025 0.13 0.37 53 -0.43 15 68
BGLAP -0.081 0.14 0.37 1 -0.47 31 32
GR/PKAc 0.13 0.13 0.35 93 -0.33 3 96
NF kappa B1 p50/RelA -0.062 0.18 0.42 4 -0.33 192 196
SMARCD1 0.025 0.011 -10000 0 -10000 0 0
MDM2 0.098 0.11 0.22 345 -10000 0 345
GATA3 0.014 0.11 0.26 27 -0.57 35 62
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.025 0.1 0.46 1 -0.54 5 6
GSK3B 0.001 0.023 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.8 1 -0.6 173 174
CSN2 0.16 0.19 0.37 358 -0.42 4 362
BRG1/BAF155/BAF170/BAF60A 0.061 0.04 -10000 0 -0.47 5 5
NFATC1 0.023 0.026 -10000 0 -0.57 2 2
POU2F1 0.023 0.015 0.25 1 -10000 0 1
CDKN1A 0.016 0.086 -10000 0 -1.3 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.007 -10000 0 -10000 0 0
SFN 0.021 0.07 0.25 20 -0.57 12 32
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.32 89 -0.31 5 94
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.39 0.62 2 -0.8 412 414
JUN -0.26 0.29 0.45 6 -0.55 426 432
IL4 -0.11 0.15 -10000 0 -0.44 59 59
CDK5R1 0.022 0.036 0.25 23 -10000 0 23
PRKACA 0.024 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.48 495 495
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.12 0.31 120 -0.3 6 126
cortisol/GR alpha (monomer) 0.28 0.32 0.59 455 -0.53 4 459
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.59 312 312
AP-1/NFAT1-c-4 -0.43 0.45 0.47 7 -0.81 544 551
AFP -0.54 0.65 0.47 2 -1.4 366 368
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.43 115 -10000 0 115
TP53 0.031 0.028 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.64 0.68 0.45 1 -1.4 470 471
KRT14 -0.69 0.66 -10000 0 -1.3 556 556
TBP 0.028 0.012 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.29 478 -10000 0 478
HDAC1 0.022 0.011 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.43 0.45 0.48 6 -0.82 544 550
MAPK14 0.003 0.022 -10000 0 -10000 0 0
MAPK10 -0.083 0.2 -10000 0 -0.57 157 157
MAPK11 -0.001 0.038 -10000 0 -0.58 3 3
KRT5 -0.73 0.7 0.44 1 -1.4 563 564
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.019 -10000 0 -0.57 1 1
STAT1 0.033 0.032 0.26 19 -10000 0 19
CGA -0.054 0.17 0.42 2 -0.46 33 35
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.36 376 -10000 0 376
MAPK3 0.001 0.022 -10000 0 -10000 0 0
MAPK1 0.003 0.022 -10000 0 -10000 0 0
ICAM1 -0.18 0.24 0.6 3 -0.52 285 288
NFKB1 -0.038 0.1 0.28 1 -0.26 36 37
MAPK8 -0.19 0.22 0.39 5 -0.42 414 419
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.28 0.32 0.86 1 -0.68 318 319
BAX 0.017 0.065 -10000 0 -10000 0 0
POMC -0.16 0.29 -10000 0 -1.1 56 56
EP300 0.14 0.14 0.3 366 -10000 0 366
cortisol/GR alpha (dimer)/p53 0.21 0.26 0.52 373 -0.49 3 376
proteasomal ubiquitin-dependent protein catabolic process 0.077 0.11 0.26 171 -10000 0 171
SGK1 0.19 0.2 0.54 8 -1.1 5 13
IL13 -0.25 0.28 0.55 3 -0.68 147 150
IL6 -0.43 0.52 0.49 2 -1.1 406 408
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.52 3 -0.62 95 98
IL2 -0.33 0.35 0.45 3 -0.7 430 433
CDK5 0.018 0.019 0.25 4 -10000 0 4
PRKACB 0.032 0.06 0.25 47 -0.57 4 51
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.52 4 -0.6 240 244
CDK5R1/CDK5 0.019 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.018 0.15 0.38 3 -0.36 48 51
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 421 -0.46 3 424
SMARCA4 0.024 0.011 -10000 0 -0.15 2 2
chromatin remodeling 0.15 0.16 0.36 261 -10000 0 261
NF kappa B1 p50/RelA/Cbp 0.061 0.19 0.4 73 -0.42 17 90
JUN (dimer) -0.26 0.29 0.45 6 -0.54 430 436
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.2 -10000 0 -0.56 117 117
NR3C1 0.17 0.2 0.39 367 -0.43 4 371
NR4A1 -0.025 0.17 -10000 0 -0.55 103 103
TIF2/SUV420H1 0.008 0.094 -10000 0 -0.42 48 48
MAPKKK cascade -0.26 0.31 0.85 1 -0.64 318 319
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.52 433 -0.5 3 436
PBX1 0.023 0.015 0.25 1 -10000 0 1
POU1F1 0.022 0.015 0.26 2 -10000 0 2
SELE -0.19 0.31 0.55 3 -0.71 188 191
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.36 258 -10000 0 258
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 421 -0.46 3 424
mol:cortisol 0.16 0.19 0.34 455 -0.28 3 458
MMP1 0.029 0.31 0.42 2 -0.92 85 87
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.098 0.12 0.3 279 -0.22 2 281
NFATC2 -0.028 0.23 0.49 7 -0.6 100 107
NFATC3 -0.042 0.13 -10000 0 -0.28 177 177
CD40LG -0.3 0.5 0.68 5 -0.98 320 325
ITCH -0.002 0.083 -10000 0 -10000 0 0
CBLB -0.002 0.084 -10000 0 -0.27 3 3
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.097 0.39 0.6 49 -1 91 140
JUNB 0.025 0.01 0.25 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.1 -10000 0 -0.3 107 107
T cell anergy -0.027 0.14 0.33 1 -0.42 104 105
TLE4 -0.028 0.19 0.35 1 -0.59 70 71
Jun/NFAT1-c-4/p21SNFT -0.18 0.44 0.69 5 -0.87 254 259
AP-1/NFAT1-c-4 -0.32 0.62 0.75 13 -1.2 314 327
IKZF1 -0.019 0.16 0.47 7 -0.49 63 70
T-helper 2 cell differentiation -0.088 0.28 0.45 3 -0.79 99 102
AP-1/NFAT1 -0.099 0.26 0.45 12 -0.47 285 297
CALM1 0.01 0.064 -10000 0 -10000 0 0
EGR2 -0.26 0.57 0.69 2 -1.5 164 166
EGR3 -0.34 0.63 0.67 2 -1.3 290 292
NFAT1/FOXP3 0.047 0.22 0.46 104 -0.46 82 186
EGR1 -0.16 0.27 -10000 0 -0.57 334 334
JUN 0.015 0.053 -10000 0 -0.57 6 6
EGR4 0.039 0.058 0.26 72 -10000 0 72
mol:Ca2+ -0.011 0.055 -10000 0 -0.18 98 98
GBP3 -0.022 0.17 0.39 2 -0.52 70 72
FOSL1 0.027 0.047 0.25 24 -0.57 3 27
NFAT1-c-4/MAF/IRF4 -0.2 0.46 0.62 5 -0.89 275 280
DGKA -0.019 0.16 0.56 1 -0.48 64 65
CREM 0.023 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.49 0.64 2 -0.96 298 300
CTLA4 0.036 0.21 0.42 123 -0.52 44 167
NFAT1-c-4 (dimer)/EGR1 -0.29 0.52 0.61 4 -1 320 324
NFAT1-c-4 (dimer)/EGR4 -0.19 0.46 0.6 5 -0.87 281 286
FOS -0.15 0.27 0.19 2 -0.57 305 307
IFNG -0.057 0.27 0.51 10 -0.73 89 99
T cell activation -0.15 0.3 0.66 3 -0.68 166 169
MAF 0.021 0.008 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.34 0.68 260 -0.61 2 262
TNF -0.26 0.45 0.56 3 -0.91 309 312
FASLG -0.33 0.64 0.79 2 -1.2 320 322
TBX21 0.021 0.12 0.35 15 -0.57 36 51
BATF3 0.021 0.015 0.25 3 -10000 0 3
PRKCQ 0.005 0.12 0.28 8 -0.57 41 49
PTPN1 -0.019 0.16 0.39 3 -0.48 64 67
NFAT1-c-4/ICER1 -0.2 0.44 0.55 2 -0.86 284 286
GATA3 0.01 0.11 0.25 27 -0.57 35 62
T-helper 1 cell differentiation -0.055 0.27 0.51 10 -0.72 89 99
IL2RA -0.098 0.37 0.59 45 -0.87 113 158
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.019 0.16 0.35 1 -0.48 64 65
E2F1 0.096 0.11 0.26 323 -10000 0 323
PPARG -0.11 0.25 -10000 0 -0.57 247 247
SLC3A2 -0.02 0.16 -10000 0 -0.51 54 54
IRF4 -0.02 0.16 0.25 13 -0.57 84 97
PTGS2 -0.34 0.54 0.63 4 -1 346 350
CSF2 -0.29 0.49 0.65 8 -0.96 316 324
JunB/Fra1/NFAT1-c-4 -0.18 0.44 0.62 3 -0.84 272 275
IL4 -0.093 0.29 0.46 3 -0.83 99 102
IL5 -0.29 0.49 0.61 5 -0.96 316 321
IL2 -0.16 0.3 0.66 3 -0.71 154 157
IL3 -0.05 0.13 -10000 0 -0.83 18 18
RNF128 -0.043 0.2 0.27 4 -0.66 107 111
NFATC1 -0.16 0.34 0.61 2 -0.68 260 262
CDK4 0.12 0.24 0.6 101 -0.57 2 103
PTPRK -0.021 0.17 0.42 3 -0.52 68 71
IL8 -0.29 0.5 0.58 9 -0.97 314 323
POU2F1 0.021 0.012 0.25 1 -10000 0 1
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.003 0.11 -10000 0 -0.36 96 96
cell-cell adhesion 0.13 0.15 0.31 394 -10000 0 394
Ephrin B/EPHB2/RasGAP 0.031 0.11 -10000 0 -0.32 82 82
ITSN1 0.024 0.018 -10000 0 -0.57 1 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.12 0.19 -10000 0 -0.36 415 415
HRAS/GDP -0.12 0.18 -10000 0 -0.41 181 181
Ephrin B/EPHB1/GRB7 -0.1 0.2 -10000 0 -0.35 402 402
Endophilin/SYNJ1 -0.027 0.083 0.22 2 -0.3 81 83
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.21 -10000 0 -0.36 414 414
endothelial cell migration 0.041 0.04 -10000 0 -0.31 10 10
GRB2 0.023 0.009 0.25 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 -0.031 0.099 0.35 2 -0.33 85 87
HRAS 0.025 0.02 0.25 8 -10000 0 8
RRAS -0.027 0.084 0.23 2 -0.3 81 83
DNM1 0.021 0.048 0.25 1 -0.57 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.14 0.18 0.35 2 -0.34 433 435
lamellipodium assembly -0.13 0.15 -10000 0 -0.31 394 394
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.091 0.16 -10000 0 -0.32 322 322
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
EPHB2 0.027 0.031 0.25 19 -10000 0 19
EPHB3 0.026 0.02 0.25 8 -10000 0 8
EPHB1 -0.2 0.29 0.25 1 -0.57 415 416
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.12 0.17 -10000 0 -0.42 169 169
Ephrin B/EPHB2 0.021 0.1 -10000 0 -0.31 82 82
Ephrin B/EPHB3 0.02 0.098 -10000 0 -0.31 77 77
JNK cascade -0.12 0.15 0.36 9 -0.31 411 420
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.35 433 433
RAP1/GDP -0.093 0.16 -10000 0 -0.39 151 151
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.024 0.16 -10000 0 -0.57 83 83
EFNB1 0.024 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.099 0.18 -10000 0 -0.33 414 414
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.19 -10000 0 -0.41 163 163
Rap1/GTP -0.11 0.17 -10000 0 -0.32 353 353
axon guidance -0.003 0.11 -10000 0 -0.36 96 96
MAPK3 -0.086 0.14 -10000 0 -0.39 106 106
MAPK1 -0.09 0.14 -10000 0 -0.39 113 113
Rac1/GDP -0.1 0.16 -10000 0 -0.39 165 165
actin cytoskeleton reorganization -0.11 0.13 -10000 0 -0.34 137 137
CDC42/GDP -0.1 0.16 -10000 0 -0.39 167 167
PI3K 0.045 0.042 -10000 0 -0.31 10 10
EFNA5 -0.029 0.17 0.25 1 -0.57 96 97
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.087 -10000 0 -0.27 85 85
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.16 -10000 0 -0.31 380 380
PTK2 0.14 0.26 0.67 204 -10000 0 204
MAP4K4 -0.12 0.15 0.36 9 -0.31 411 420
SRC 0.024 0.005 -10000 0 -10000 0 0
KALRN 0.013 0.08 -10000 0 -0.57 20 20
Intersectin/N-WASP 0.035 0.016 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.1 0.14 0.29 9 -0.42 81 90
MAP2K1 -0.088 0.15 -10000 0 -0.3 302 302
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.09 0.19 -10000 0 -0.33 412 412
cell migration -0.1 0.18 0.31 5 -0.43 136 141
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.084 0.23 2 -0.3 81 83
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.32 583 585
HRAS/GTP -0.1 0.19 -10000 0 -0.32 422 422
Ephrin B1/EPHB1-2 -0.098 0.18 -10000 0 -0.33 413 413
cell adhesion mediated by integrin 0.01 0.087 0.28 79 -0.21 20 99
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:GTP -0.11 0.2 -10000 0 -0.33 429 429
RAC1-CDC42/GTP -0.13 0.15 -10000 0 -0.31 386 386
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.096 0.16 -10000 0 -0.38 158 158
ruffle organization -0.13 0.16 0.36 5 -0.49 71 76
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.087 0.22 2 -0.31 82 84
Ephrin B/EPHB2/KALRN 0.025 0.12 -10000 0 -0.34 94 94
ROCK1 0.017 0.031 0.25 1 -0.33 1 2
RAS family/GDP -0.11 0.12 -10000 0 -0.34 131 131
Rac1/GTP -0.12 0.17 -10000 0 -0.32 394 394
Ephrin B/EPHB1/Src/Paxillin -0.12 0.18 -10000 0 -0.32 419 419
Endothelins

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
AKT1 -0.072 0.13 -10000 0 -0.42 97 97
PTK2B 0.02 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.052 0.19 -10000 0 -0.76 53 53
EDN1 -0.072 0.16 -10000 0 -0.53 97 97
EDN3 -0.22 0.29 0.25 3 -0.57 443 446
EDN2 0.073 0.11 0.25 244 -0.57 5 249
HRAS/GDP -0.093 0.2 0.28 1 -0.47 157 158
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.061 0.14 -10000 0 -0.39 115 115
ADCY4 -0.13 0.2 0.28 2 -0.42 279 281
ADCY5 -0.21 0.24 -10000 0 -0.44 469 469
ADCY6 -0.12 0.18 0.28 2 -0.4 270 272
ADCY7 -0.12 0.18 0.28 2 -0.4 268 270
ADCY1 -0.12 0.2 0.26 1 -0.41 277 278
ADCY2 -0.14 0.22 0.29 6 -0.45 289 295
ADCY3 -0.12 0.18 0.26 1 -0.4 269 270
ADCY8 -0.1 0.17 0.27 2 -0.4 205 207
ADCY9 -0.11 0.18 0.26 1 -0.4 256 257
arachidonic acid secretion -0.16 0.28 0.3 3 -0.5 356 359
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.34 179 179
GNAO1 0.017 0.09 0.25 32 -0.57 20 52
HRAS 0.024 0.02 0.25 8 -10000 0 8
ETA receptor/Endothelin-1/G12/GTP -0.057 0.13 -10000 0 -0.39 97 97
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.42 271 271
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.062 0.15 0.37 10 -0.43 95 105
EDNRB -0.029 0.17 -10000 0 -0.57 99 99
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.076 0.16 -10000 0 -0.49 103 103
CYSLTR1 -0.079 0.16 -10000 0 -0.48 100 100
SLC9A1 -0.044 0.092 -10000 0 -0.29 89 89
mol:GDP -0.1 0.21 0.33 2 -0.49 169 171
SLC9A3 -0.11 0.28 -10000 0 -0.63 196 196
RAF1 -0.14 0.24 0.33 1 -0.44 324 325
JUN -0.049 0.18 -10000 0 -0.74 46 46
JAK2 -0.07 0.13 -10000 0 -0.43 94 94
mol:IP3 -0.074 0.17 -10000 0 -0.43 135 135
ETA receptor/Endothelin-1 -0.081 0.16 -10000 0 -0.48 104 104
PLCB1 -0.019 0.15 -10000 0 -0.57 74 74
PLCB2 0.014 0.026 0.25 1 -0.57 1 2
ETA receptor/Endothelin-3 -0.19 0.21 -10000 0 -0.44 446 446
FOS -0.29 0.44 -10000 0 -0.93 334 334
Gai/GDP -0.099 0.29 -10000 0 -0.75 164 164
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 0.27 2 -0.53 146 148
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.4 157 157
GNAQ 0.014 0.036 -10000 0 -0.58 3 3
GNAZ 0.018 0.054 -10000 0 -0.57 9 9
GNAL -0.11 0.24 -10000 0 -0.57 236 236
Gs family/GDP -0.15 0.24 0.26 1 -0.49 270 271
ETA receptor/Endothelin-1/Gq/GTP -0.046 0.12 -10000 0 -0.37 80 80
MAPK14 -0.066 0.16 -10000 0 -0.41 143 143
TRPC6 -0.055 0.21 -10000 0 -0.81 53 53
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.17 -10000 0 -0.39 176 176
ETB receptor/Endothelin-2 0.022 0.15 0.24 17 -0.4 103 120
ETB receptor/Endothelin-3 -0.19 0.24 0.24 1 -0.44 496 497
ETB receptor/Endothelin-1 -0.078 0.18 -10000 0 -0.46 169 169
MAPK3 -0.25 0.38 0.32 1 -0.79 338 339
MAPK1 -0.26 0.39 0.32 2 -0.8 343 345
Rac1/GDP -0.093 0.19 0.28 1 -0.47 155 156
cAMP biosynthetic process -0.15 0.22 0.53 1 -0.48 247 248
MAPK8 -0.056 0.21 -10000 0 -0.7 70 70
SRC 0.024 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.067 0.17 -10000 0 -0.36 204 204
p130Cas/CRK/Src/PYK2 -0.097 0.22 0.49 1 -0.56 132 133
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.093 0.19 0.28 1 -0.46 161 162
COL1A2 -0.088 0.19 0.37 9 -0.48 153 162
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.022 0.094 0.3 3 -0.38 8 11
mol:DAG -0.075 0.17 -10000 0 -0.43 135 135
MAP2K2 -0.19 0.3 0.33 3 -0.59 342 345
MAP2K1 -0.19 0.3 0.32 2 -0.59 343 345
EDNRA -0.034 0.064 0.28 1 -0.36 8 9
positive regulation of muscle contraction -0.062 0.12 -10000 0 -0.38 92 92
Gq family/GDP -0.058 0.19 -10000 0 -0.48 116 116
HRAS/GTP -0.1 0.2 0.3 2 -0.47 177 179
PRKCH -0.076 0.16 -10000 0 -0.43 128 128
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.073 0.18 0.27 4 -0.46 136 140
PRKCB -0.074 0.18 0.24 1 -0.44 136 137
PRKCE -0.079 0.16 -10000 0 -0.42 139 139
PRKCD -0.076 0.16 -10000 0 -0.44 123 123
PRKCG -0.078 0.17 0.27 1 -0.43 135 136
regulation of vascular smooth muscle contraction -0.34 0.51 -10000 0 -1.1 334 334
PRKCQ -0.085 0.18 -10000 0 -0.46 149 149
PLA2G4A -0.18 0.31 0.3 3 -0.55 357 360
GNA14 0.014 0.068 0.25 20 -0.57 10 30
GNA15 0.022 0.027 0.25 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.033 -10000 0 -0.57 3 3
Rac1/GTP -0.057 0.13 -10000 0 -0.39 98 98
MMP1 0.17 0.13 0.38 84 -10000 0 84
HIF-1-alpha transcription factor network

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
PKM2 -0.26 0.36 -10000 0 -0.78 223 223
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.18 0.34 0.67 2 -0.78 131 133
SMAD4 0.024 0.006 -10000 0 -10000 0 0
ID2 -0.24 0.37 -10000 0 -0.82 190 190
AP1 -0.1 0.21 -10000 0 -0.42 315 315
ABCG2 -0.26 0.39 -10000 0 -0.85 209 209
HIF1A -0.047 0.085 -10000 0 -0.24 19 19
TFF3 -0.25 0.41 0.67 4 -0.83 228 232
GATA2 0.009 0.096 0.25 14 -0.57 26 40
AKT1 -0.054 0.095 -10000 0 -0.25 41 41
response to hypoxia -0.061 0.085 0.21 1 -0.2 126 127
MCL1 -0.24 0.36 -10000 0 -0.81 187 187
NDRG1 -0.22 0.36 -10000 0 -0.79 192 192
SERPINE1 -0.24 0.38 0.66 4 -0.82 196 200
FECH -0.24 0.37 -10000 0 -0.8 205 205
FURIN -0.24 0.37 -10000 0 -0.81 196 196
NCOA2 -0.002 0.12 -10000 0 -0.57 48 48
EP300 -0.058 0.13 0.33 2 -0.35 90 92
HMOX1 -0.24 0.37 0.64 2 -0.81 196 198
BHLHE40 -0.24 0.37 -10000 0 -0.79 218 218
BHLHE41 -0.25 0.38 -10000 0 -0.81 213 213
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.018 0.11 -10000 0 -10000 0 0
ENG -0.016 0.11 0.4 2 -10000 0 2
JUN 0.018 0.046 -10000 0 -0.57 6 6
RORA -0.24 0.37 -10000 0 -0.79 218 218
ABCB1 -0.26 0.45 -10000 0 -1.1 220 220
TFRC -0.24 0.37 -10000 0 -0.8 205 205
CXCR4 -0.24 0.38 0.65 1 -0.79 220 221
TF -0.4 0.46 -10000 0 -0.88 399 399
CITED2 -0.24 0.37 -10000 0 -0.83 181 181
HIF1A/ARNT -0.27 0.42 -10000 0 -0.95 170 170
LDHA -0.037 0.12 -10000 0 -0.73 23 23
ETS1 -0.24 0.37 -10000 0 -0.84 182 182
PGK1 -0.24 0.37 -10000 0 -0.8 212 212
NOS2 -0.24 0.37 -10000 0 -0.82 187 187
ITGB2 -0.24 0.37 0.64 2 -0.8 211 213
ALDOA -0.24 0.37 -10000 0 -0.82 188 188
Cbp/p300/CITED2 -0.25 0.39 -10000 0 -0.91 164 164
FOS -0.14 0.27 -10000 0 -0.57 301 301
HK2 -0.24 0.37 -10000 0 -0.84 175 175
SP1 0.002 0.057 -10000 0 -0.18 9 9
GCK -0.12 0.33 0.54 2 -1.3 60 62
HK1 -0.24 0.37 -10000 0 -0.84 177 177
NPM1 -0.24 0.37 -10000 0 -0.81 197 197
EGLN1 -0.23 0.36 -10000 0 -0.81 184 184
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.24 0.37 -10000 0 -0.81 196 196
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.36 -10000 0 -1 131 131
IGFBP1 -0.3 0.42 -10000 0 -0.88 272 272
VEGFA -0.16 0.3 -10000 0 -0.72 96 96
HIF1A/JAB1 -0.008 0.068 -10000 0 -0.27 1 1
CP -0.3 0.45 0.64 2 -0.92 270 272
CXCL12 -0.26 0.4 -10000 0 -0.86 207 207
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.012 -10000 0 -10000 0 0
BNIP3 -0.24 0.37 0.72 1 -0.85 173 174
EGLN3 -0.23 0.38 0.67 2 -0.79 219 221
CA9 -0.2 0.4 0.67 4 -0.8 197 201
TERT -0.23 0.38 0.67 3 -0.79 208 211
ENO1 -0.24 0.37 -10000 0 -0.83 182 182
PFKL -0.24 0.37 -10000 0 -0.84 173 173
NCOA1 0.025 0.019 -10000 0 -0.57 1 1
ADM -0.26 0.4 -10000 0 -0.86 217 217
ARNT -0.034 0.072 -10000 0 -10000 0 0
HNF4A 0.02 0.041 0.26 19 -10000 0 19
ADFP -0.26 0.36 -10000 0 -0.78 223 223
SLC2A1 -0.16 0.3 0.64 2 -0.69 113 115
LEP -0.47 0.42 -10000 0 -0.86 430 430
HIF1A/ARNT/Cbp/p300 -0.2 0.34 0.66 1 -0.81 133 134
EPO -0.11 0.27 0.65 4 -0.78 42 46
CREBBP -0.049 0.12 0.33 2 -0.34 75 77
HIF1A/ARNT/Cbp/p300/HDAC7 -0.18 0.34 0.72 1 -0.81 115 116
PFKFB3 -0.24 0.37 -10000 0 -0.83 190 190
NT5E -0.24 0.38 -10000 0 -0.83 198 198
p75(NTR)-mediated 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
Sortilin/TRAF6 0.034 0.016 -10000 0 -0.42 1 1
Necdin/E2F1 0.061 0.11 -10000 0 -0.39 34 34
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.046 0.17 -10000 0 -0.32 291 291
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.24 0.34 1 -0.41 368 369
NT-4/5 (dimer)/p75(NTR) -0.22 0.29 -10000 0 -0.51 496 496
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.082 0.16 0.36 1 -0.32 277 278
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.013 0.16 0.25 24 -0.57 76 100
MGDIs/NGR/p75(NTR)/LINGO1 -0.038 0.2 0.34 7 -0.35 283 290
FURIN 0.024 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.089 0.21 -10000 0 -0.39 320 320
LINGO1 0.077 0.097 0.25 248 -10000 0 248
Sortilin/TRAF6/NRIF 0.024 0.024 -10000 0 -0.55 1 1
proBDNF (dimer) -0.013 0.16 0.25 24 -0.57 76 100
NTRK1 0.024 0.051 0.25 25 -0.57 4 29
RTN4R 0.032 0.046 0.25 43 -10000 0 43
neuron apoptosis -0.079 0.2 0.35 7 -0.52 73 80
IRAK1 0.025 0.014 0.25 4 -10000 0 4
SHC1 -0.081 0.16 -10000 0 -0.37 224 224
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.054 0.18 -10000 0 -0.34 287 287
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.065 0.19 -10000 0 -0.36 296 296
Mammalian IAPs/DIABLO 0.057 0.032 -10000 0 -0.33 2 2
proNGF (dimer) 0.017 0.075 0.25 8 -0.57 16 24
MAGED1 0.025 0.01 0.25 2 -10000 0 2
APP 0.024 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.57 364 364
ZNF274 0.024 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.065 0.15 -10000 0 -0.32 278 278
NGF 0.017 0.075 0.25 8 -0.57 16 24
cell cycle arrest -0.072 0.15 0.23 48 -0.29 287 335
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.052 0.12 -10000 0 -0.27 210 210
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.18 0.26 -10000 0 -0.46 467 467
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.068 0.19 -10000 0 -0.37 289 289
PSENEN 0.024 0.008 0.25 1 -10000 0 1
mol:ceramide -0.077 0.16 -10000 0 -0.33 287 287
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.043 0.11 -10000 0 -0.36 30 30
p75(NTR)/beta APP -0.091 0.2 -10000 0 -0.42 283 283
BEX1 -0.018 0.23 0.25 171 -0.57 142 313
mol:GDP -0.1 0.16 -10000 0 -0.36 293 293
NGF (dimer) 0.002 0.14 0.33 1 -0.34 133 134
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.022 0.18 0.33 6 -0.32 269 275
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
RAC1/GTP -0.06 0.16 -10000 0 -0.32 288 288
MYD88 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.068 0.19 -10000 0 -0.37 289 289
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.077 0.072 -10000 0 -10000 0 0
NT3 (dimer) -0.059 0.21 0.25 12 -0.57 154 166
TP53 -0.09 0.17 0.33 5 -0.33 308 313
PRDM4 -0.077 0.16 -10000 0 -0.34 287 287
BDNF (dimer) 0.022 0.2 0.33 21 -0.35 191 212
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.019 -10000 0 -0.57 1 1
activation of caspase activity -0.049 0.17 -10000 0 -0.32 291 291
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.054 0.18 -10000 0 -0.34 284 284
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.13 0.2 0.33 3 -0.41 289 292
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.078 0.16 -10000 0 -0.34 287 287
APH1B 0.023 0.019 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.07 0.18 -10000 0 -0.37 289 289
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.15 0.25 -10000 0 -0.47 373 373
MAPK8 -0.095 0.18 0.29 10 -0.37 263 273
MAPK9 -0.094 0.17 0.3 6 -0.36 260 266
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.059 0.21 0.25 12 -0.57 154 166
NTF4 -0.18 0.28 -10000 0 -0.57 364 364
NDN 0.005 0.1 -10000 0 -0.57 34 34
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.042 0.16 -10000 0 -0.3 289 289
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.022 -10000 0 -0.33 1 1
RhoA-B-C/GTP -0.068 0.19 -10000 0 -0.37 289 289
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.061 0.19 -10000 0 -0.34 312 312
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.071 0.2 -10000 0 -0.36 314 314
PRKACB 0.032 0.06 0.25 47 -0.57 4 51
proBDNF (dimer)/p75 ECD 0.006 0.12 -10000 0 -0.42 75 75
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.25 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.086 0.17 0.28 15 -0.34 280 295
BAD -0.11 0.19 0.42 6 -0.39 269 275
RIPK2 0.02 0.016 0.25 3 -10000 0 3
NGFR -0.14 0.26 -10000 0 -0.57 289 289
CYCS -0.085 0.15 0.36 2 -0.32 278 280
ADAM17 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.045 0.16 -10000 0 -0.34 210 210
BCL2L11 -0.11 0.19 0.42 6 -0.39 268 274
BDNF (dimer)/p75(NTR) -0.12 0.23 -10000 0 -0.45 328 328
PI3K -0.058 0.18 -10000 0 -0.34 280 280
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.055 0.18 -10000 0 -0.34 287 287
NDNL2 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.096 0.21 -10000 0 -0.43 293 293
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.054 0.18 -10000 0 -0.34 287 287
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
PLG 0.018 0.021 0.25 8 -10000 0 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.1 0.19 -10000 0 -0.37 326 326
SQSTM1 0.024 0.008 0.25 1 -10000 0 1
NGFRAP1 0.023 0.026 -10000 0 -0.57 2 2
CASP3 -0.1 0.18 0.38 7 -0.36 276 283
E2F1 0.093 0.11 0.25 323 -10000 0 323
CASP9 0.023 0.006 -10000 0 -10000 0 0
IKK complex -0.002 0.11 -10000 0 -0.41 18 18
NGF (dimer)/TRKA 0.026 0.066 -10000 0 -0.4 20 20
MMP7 -0.038 0.19 0.25 32 -0.57 121 153
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.044 0.17 -10000 0 -0.32 280 280
MMP3 0.096 0.13 0.25 378 -0.57 13 391
APAF-1/Caspase 9 -0.085 0.11 -10000 0 -0.44 10 10
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 -0.23 0.61 0.79 12 -1.2 196 208
STAT6 (cleaved dimer) -0.3 0.58 -10000 0 -1.2 248 248
IGHG1 -0.027 0.26 0.5 68 -0.51 12 80
IGHG3 -0.23 0.57 0.67 18 -1.1 239 257
AKT1 -0.084 0.34 0.55 32 -0.74 93 125
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.046 0.29 0.51 32 -0.71 59 91
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.086 0.36 0.55 43 -0.74 96 139
THY1 -0.23 0.61 0.78 19 -1.2 219 238
MYB 0.011 0.086 0.25 1 -0.57 23 24
HMGA1 0.034 0.048 0.25 48 -10000 0 48
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.41 0.62 62 -0.73 178 240
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.078 0.35 0.54 48 -0.69 100 148
SP1 0.033 0.025 -10000 0 -0.18 1 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.014 0.046 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.26 0.6 0.67 14 -1.2 234 248
SOCS1 -0.13 0.4 0.6 28 -0.74 190 218
SOCS3 -0.092 0.35 0.63 9 -0.82 69 78
FCER2 -0.38 0.74 0.79 26 -1.3 342 368
PARP14 0.017 0.031 0.24 3 -10000 0 3
CCL17 -0.22 0.62 0.86 39 -1.2 188 227
GRB2 0.023 0.009 0.25 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.041 0.29 0.48 60 -0.65 51 111
T cell proliferation -0.25 0.61 0.71 13 -1.2 222 235
IL4R/JAK1 -0.24 0.6 0.71 6 -1.2 223 229
EGR2 -0.36 0.74 0.86 13 -1.5 263 276
JAK2 0.011 0.075 0.23 3 -10000 0 3
JAK3 0.022 0.035 0.27 14 -10000 0 14
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
JAK1 0.017 0.041 -10000 0 -10000 0 0
COL1A2 -0.024 0.27 0.58 7 -1.1 18 25
CCL26 -0.23 0.61 0.81 17 -1.2 199 216
IL4R -0.24 0.66 0.86 31 -1.3 214 245
PTPN6 0.014 0.035 0.21 2 -10000 0 2
IL13RA2 -0.24 0.61 0.84 8 -1.2 192 200
IL13RA1 0.011 0.076 0.23 5 -10000 0 5
IRF4 -0.13 0.49 0.64 6 -1.4 118 124
ARG1 -0.006 0.22 0.57 7 -0.6 8 15
CBL -0.11 0.38 0.57 42 -0.7 166 208
GTF3A 0.055 0.048 0.26 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.024 0.11 0.29 40 -10000 0 40
IRF4/BCL6 -0.12 0.44 0.55 1 -1.3 116 117
CD40LG -0.011 0.14 0.31 11 -0.58 50 61
MAPK14 -0.11 0.38 0.59 35 -0.72 155 190
mitosis -0.077 0.33 0.54 34 -0.69 91 125
STAT6 -0.27 0.75 0.93 51 -1.4 234 285
SPI1 0.027 0.017 0.26 5 -10000 0 5
RPS6KB1 -0.06 0.32 0.54 38 -0.68 80 118
STAT6 (dimer) -0.27 0.75 0.94 50 -1.4 235 285
STAT6 (dimer)/PARP14 -0.29 0.66 0.73 14 -1.3 248 262
mast cell activation 0 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.091 0.35 0.56 37 -0.72 112 149
FRAP1 -0.085 0.34 0.55 32 -0.73 93 125
LTA -0.22 0.62 0.86 36 -1.2 190 226
FES 0.022 0.032 -10000 0 -0.57 3 3
T-helper 1 cell differentiation 0.25 0.71 1.3 235 -0.93 50 285
CCL11 -0.18 0.59 0.75 29 -1.2 196 225
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.072 0.34 0.55 38 -0.73 82 120
IL2RG 0.025 0.071 0.26 46 -0.56 7 53
IL10 -0.21 0.6 0.81 24 -1.2 188 212
IRS1 0.001 0.12 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
IL4 -0.01 0.26 0.58 32 -1.1 22 54
IL5 -0.24 0.61 0.8 14 -1.2 198 212
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.52 0.79 53 -0.91 200 253
COL1A1 0 0.36 0.67 39 -0.99 49 88
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.61 0.72 2 -1.3 196 198
IL2R gamma/JAK3 0.037 0.068 0.36 17 -0.42 6 23
TFF3 -0.29 0.7 0.84 27 -1.3 257 284
ALOX15 -0.3 0.7 0.86 12 -1.3 254 266
MYBL1 0.038 0.062 0.25 81 -10000 0 81
T-helper 2 cell differentiation -0.19 0.52 0.68 37 -0.96 227 264
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.082 0.34 0.53 46 -0.72 94 140
mol:PI-3-4-5-P3 -0.084 0.34 0.55 32 -0.73 93 125
PI3K -0.093 0.36 0.57 25 -0.79 93 118
DOK2 0.02 0.031 0.25 4 -0.57 2 6
ETS1 0.004 0.051 -10000 0 -0.53 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.031 0.27 0.47 64 -0.6 44 108
ITGB3 -0.25 0.63 0.85 5 -1.3 200 205
PIGR -0.67 0.8 0.84 14 -1.3 581 595
IGHE -0.015 0.086 0.18 32 -0.2 48 80
MAPKKK cascade -0.03 0.27 0.46 64 -0.6 42 106
BCL6 0.022 0.047 -10000 0 -0.56 6 6
OPRM1 -0.24 0.61 0.89 7 -1.2 195 202
RETNLB -0.24 0.6 0.81 8 -1.2 196 204
SELP -0.36 0.77 0.83 16 -1.5 290 306
AICDA -0.23 0.58 0.78 11 -1.2 196 207
Ephrin B reverse 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
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.031 0.25 19 -10000 0 19
EFNB1 0.002 0.036 -10000 0 -0.42 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.079 0.18 -10000 0 -0.3 403 403
Ephrin B2/EPHB1-2 -0.098 0.18 -10000 0 -0.32 414 414
neuron projection morphogenesis -0.085 0.16 -10000 0 -0.29 403 403
Ephrin B1/EPHB1-2/Tiam1 -0.09 0.18 -10000 0 -0.32 410 410
DNM1 0.02 0.049 0.26 1 -0.57 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.021 0.12 -10000 0 -0.56 45 45
YES1 -0.023 0.17 -10000 0 -0.77 50 50
Ephrin B1/EPHB1-2/NCK2 -0.09 0.18 -10000 0 -0.32 413 413
PI3K 0.006 0.13 -10000 0 -0.5 59 59
mol:GDP -0.09 0.18 -10000 0 -0.31 410 410
ITGA2B 0.033 0.06 0.25 55 -0.57 3 58
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.024 0.17 -10000 0 -0.76 49 49
MAP3K7 -0.023 0.12 0.22 3 -0.57 48 51
FGR -0.021 0.17 -10000 0 -0.77 49 49
TIAM1 0.025 0.015 0.25 4 -10000 0 4
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.009 0.14 0.25 1 -0.43 84 85
LYN -0.021 0.16 -10000 0 -0.75 49 49
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.16 -10000 0 -0.72 50 50
Ephrin B1/EPHB1-2 -0.022 0.13 -10000 0 -0.64 45 45
SRC -0.02 0.16 -10000 0 -0.75 50 50
ITGB3 0.005 0.11 0.25 4 -0.57 35 39
EPHB1 -0.2 0.29 0.26 1 -0.57 415 416
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.027 0.092 -10000 0 -0.41 38 38
BLK -0.019 0.17 -10000 0 -0.78 47 47
HCK -0.019 0.16 -10000 0 -0.75 50 50
regulation of stress fiber formation 0.09 0.18 0.31 413 -10000 0 413
MAPK8 -0.024 0.12 -10000 0 -0.51 54 54
Ephrin B1/EPHB1-2/RGS3 -0.09 0.18 -10000 0 -0.32 413 413
endothelial cell migration -0.017 0.11 0.2 1 -0.51 42 43
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.68 26 26
regulation of focal adhesion formation 0.09 0.18 0.31 413 -10000 0 413
chemotaxis 0.09 0.18 0.31 413 -10000 0 413
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.081 0.17 -10000 0 -0.29 403 403
angiogenesis -0.023 0.13 -10000 0 -0.62 47 47
LCK -0.02 0.17 -10000 0 -0.77 49 49
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.008 0.093 -10000 0 -0.57 27 27
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.18 0.2 -10000 0 -0.36 612 612
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.18 0.17 -10000 0 -0.32 609 609
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.25 61 -10000 0 61
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.023 0.067 0.25 23 -0.57 10 33
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.048 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.028 0.034 0.25 23 -10000 0 23
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.082 0.25 156 -10000 0 156
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.19 0.21 0.34 2 -0.37 608 610
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.15 0.35 3 -0.32 54 57
MAP1B -0.001 0.044 -10000 0 -0.32 20 20
RAC1 0.011 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.15 0.16 -10000 0 -0.3 485 485
RELN -0.32 0.29 0.25 2 -0.57 619 621
PAFAH/LIS1 0.023 0.045 0.32 2 -0.36 9 11
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.13 -10000 0 -0.29 8 8
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.3 512 512
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.15 0.15 0.38 2 -0.34 64 66
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.011 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.05 0.073 0.25 122 -10000 0 122
PAFAH1B2 0.019 0.041 -10000 0 -0.57 5 5
MAP1B/LIS1/Dynein heavy chain 0.014 0.043 -10000 0 -0.22 18 18
NDEL1/Katanin 60/Dynein heavy chain -0.12 0.15 0.34 3 -0.32 50 53
LRP8 0.046 0.068 0.25 104 -10000 0 104
NDEL1/Katanin 60 -0.13 0.15 0.35 3 -0.33 60 63
P39/CDK5 -0.15 0.16 0.36 5 -0.3 444 449
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.18 0.15 -10000 0 -0.31 533 533
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.16 0.19 0.32 1 -0.32 602 603
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 612 612
CDC42 0.01 0.005 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.026 0.16 -10000 0 -0.57 88 88
GNB1/GNG2 -0.073 0.21 -10000 0 -0.47 158 158
mol:DAG -0.075 0.18 0.24 1 -0.44 148 149
PLCG1 -0.078 0.19 0.24 1 -0.45 148 149
YES1 -0.094 0.19 0.2 1 -0.37 273 274
FZD3 0.015 0.055 -10000 0 -0.57 9 9
FZD6 0.014 0.055 -10000 0 -0.57 9 9
G protein -0.061 0.2 0.27 15 -0.46 144 159
MAP3K7 -0.069 0.15 0.22 3 -0.39 125 128
mol:Ca2+ -0.073 0.18 0.23 1 -0.42 148 149
mol:IP3 -0.075 0.18 0.24 1 -0.44 148 149
NLK -0.009 0.13 -10000 0 -0.84 24 24
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.071 0.17 0.23 4 -0.4 143 147
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.095 0.2 0.22 1 -0.38 294 295
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
GNAS -0.088 0.19 0.2 1 -0.38 259 260
GO:0007205 -0.079 0.18 0.22 2 -0.43 149 151
WNT6 -0.076 0.24 0.25 48 -0.57 199 247
WNT4 0.017 0.087 0.25 20 -0.57 20 40
NFAT1/CK1 alpha -0.089 0.2 0.32 2 -0.47 157 159
GNG2 0.018 0.06 -10000 0 -0.57 11 11
WNT5A 0.017 0.073 0.25 9 -0.57 15 24
WNT11 -0.082 0.23 0.25 10 -0.57 192 202
CDC42 -0.082 0.18 -10000 0 -0.47 136 136
Wnt signaling

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.095 0.2 0.22 1 -0.38 294 295
FZD6 0.014 0.055 -10000 0 -0.57 9 9
WNT6 -0.076 0.24 0.25 48 -0.57 199 247
WNT4 0.017 0.087 0.25 20 -0.57 20 40
FZD3 0.015 0.055 -10000 0 -0.57 9 9
WNT5A 0.017 0.073 0.25 9 -0.57 15 24
WNT11 -0.082 0.23 0.25 10 -0.57 192 202
IL23-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
CCL2 -0.022 0.48 0.79 49 -0.9 136 185
IL23A -0.033 0.48 0.89 24 -1.1 76 100
NF kappa B1 p50/RelA/I kappa B alpha -0.06 0.45 0.77 7 -0.87 159 166
positive regulation of T cell mediated cytotoxicity -0.025 0.54 0.87 61 -0.95 165 226
ITGA3 -0.018 0.47 0.82 32 -1.1 73 105
IL17F -0.008 0.36 0.59 71 -0.6 157 228
IL12B 0.084 0.15 0.35 220 -10000 0 220
STAT1 (dimer) -0.039 0.5 0.75 45 -0.92 164 209
CD4 -0.017 0.48 0.83 38 -1 75 113
IL23 -0.018 0.48 0.82 47 -1.1 73 120
IL23R 0.047 0.2 0.6 16 -0.89 18 34
IL1B -0.036 0.5 0.82 40 -1.1 80 120
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.016 0.48 0.84 55 -1 72 127
TYK2 0.026 0.058 0.21 6 -10000 0 6
STAT4 0.001 0.12 0.25 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.008 0.11 0.27 5 -0.57 36 41
IL12RB1 0.034 0.091 0.36 45 -0.59 2 47
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.087 0.3 48 -0.43 2 50
IL23R/JAK2 0.06 0.22 0.55 25 -0.87 15 40
positive regulation of chronic inflammatory response -0.025 0.54 0.87 61 -0.95 165 226
natural killer cell activation -0.004 0.015 -10000 0 -0.05 36 36
JAK2 0.037 0.081 0.26 34 -10000 0 34
PIK3R1 0.017 0.062 -10000 0 -0.56 12 12
NFKB1 0.026 0.009 -10000 0 -10000 0 0
RELA 0.026 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.012 0.47 0.81 48 -1 73 121
ALOX12B -0.019 0.48 0.82 43 -1 77 120
CXCL1 -0.18 0.69 0.84 43 -1.2 276 319
T cell proliferation -0.025 0.54 0.87 61 -0.95 165 226
NFKBIA 0.026 0.009 -10000 0 -10000 0 0
IL17A 0.019 0.31 0.56 78 -0.53 70 148
PI3K -0.057 0.46 0.69 23 -0.88 163 186
IFNG 0.025 0.067 0.17 134 -0.11 15 149
STAT3 (dimer) -0.055 0.44 0.7 15 -0.85 162 177
IL18R1 0.017 0.076 -10000 0 -0.57 18 18
IL23/IL23R/JAK2/TYK2/SOCS3 0.035 0.34 0.64 84 -0.61 64 148
IL18/IL18R 0.04 0.1 0.28 10 -0.36 52 62
macrophage activation 0 0.029 0.055 102 -0.044 62 164
TNF -0.032 0.5 0.84 36 -1.1 80 116
STAT3/STAT4 -0.056 0.48 0.68 24 -0.91 166 190
STAT4 (dimer) -0.051 0.51 0.74 39 -0.95 167 206
IL18 0.029 0.036 0.26 23 -10000 0 23
IL19 0.02 0.48 0.82 61 -1 72 133
STAT5A (dimer) -0.042 0.5 0.73 40 -0.91 166 206
STAT1 0.028 0.03 0.25 19 -10000 0 19
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
CXCL9 0.006 0.51 0.84 73 -1 79 152
MPO -0.049 0.54 0.8 46 -1.1 130 176
positive regulation of humoral immune response -0.025 0.54 0.87 61 -0.95 165 226
IL23/IL23R/JAK2/TYK2 -0.032 0.56 0.87 61 -0.99 165 226
IL6 -0.3 0.74 0.8 31 -1.2 398 429
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
IL2 0.021 0.037 0.3 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.015 -10000 0 -0.05 36 36
CD3E -0.029 0.5 0.85 46 -1.1 82 128
keratinocyte proliferation -0.025 0.54 0.87 61 -0.95 165 226
NOS2 -0.018 0.48 0.82 39 -1 75 114
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.067 0.16 -10000 0 -0.34 239 239
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.025 0.02 0.25 8 -10000 0 8
IRS1/Crk -0.062 0.16 -10000 0 -0.34 245 245
IGF-1R heterotetramer/IGF1/PTP1B -0.044 0.17 -10000 0 -0.36 214 214
AKT1 -0.067 0.14 0.25 2 -0.32 187 189
BAD -0.065 0.13 0.24 2 -0.45 47 49
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.16 -10000 0 -0.34 245 245
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.16 -10000 0 -0.34 245 245
RAF1 -0.048 0.13 0.28 2 -0.48 47 49
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.033 0.16 -10000 0 -0.33 214 214
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.062 0.17 -10000 0 -0.36 252 252
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.33 161 163
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.029 0.12 0.3 10 -0.4 43 53
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.13 -10000 0 -0.31 163 163
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.3 160 160
IGF-1R heterotetramer -0.011 0.099 0.25 1 -0.62 20 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.046 0.17 -10000 0 -0.34 242 242
Crk/p130 Cas/Paxillin -0.037 0.16 -10000 0 -0.32 229 229
IGF1R -0.011 0.099 0.25 1 -0.63 20 21
IGF1 -0.11 0.25 -10000 0 -0.59 232 232
IRS2/Crk -0.068 0.17 -10000 0 -0.35 244 244
PI3K -0.036 0.17 -10000 0 -0.33 235 235
apoptosis 0.044 0.11 0.38 39 -0.28 4 43
HRAS/GDP 0.019 0.014 0.18 8 -10000 0 8
PRKCD -0.078 0.17 -10000 0 -0.4 227 227
RAF1/14-3-3 E -0.024 0.13 0.3 1 -0.41 46 47
BAD/14-3-3 -0.046 0.11 0.29 4 -0.4 39 43
PRKCZ -0.067 0.14 0.25 2 -0.32 199 201
Crk/p130 Cas/Paxillin/FAK1 -0.028 0.12 -10000 0 -0.41 38 38
PTPN1 0.024 0.018 0.25 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.18 -10000 0 -0.41 240 240
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.023 0.14 -10000 0 -0.32 176 176
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.054 0.16 -10000 0 -0.34 242 242
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.34 245 245
IRS1 -0.071 0.17 -10000 0 -0.36 245 245
IRS2 -0.077 0.17 -10000 0 -0.36 255 255
IGF-1R heterotetramer/IGF1 -0.078 0.21 -10000 0 -0.45 246 246
GRB2 0.023 0.009 0.25 1 -10000 0 1
PDPK1 -0.069 0.14 0.28 1 -0.33 200 201
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.19 -10000 0 -0.42 237 237
SHC1 0.02 0.009 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.027 0.029 -10000 0 -0.39 3 3
ARNO/beta Arrestin1-2 -0.063 0.16 -10000 0 -0.55 45 45
EGFR -0.19 0.28 -10000 0 -0.57 393 393
EPHA2 0.021 0.041 -10000 0 -0.57 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.26 -10000 0 -0.46 528 528
ARRB2 -0.042 0.13 -10000 0 -0.36 146 146
mol:GTP 0.012 0.05 0.16 21 -0.2 19 40
ARRB1 0.021 0.026 -10000 0 -0.57 2 2
FBXO8 0.024 0.005 -10000 0 -10000 0 0
TSHR 0.001 0.12 0.25 4 -0.57 42 46
EGF -0.084 0.23 0.25 2 -0.57 196 198
somatostatin receptor activity 0 0 0.001 1 -0.001 266 267
ARAP2 0.021 0.041 -10000 0 -0.57 5 5
mol:GDP -0.12 0.16 -10000 0 -0.31 328 328
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 143 143
ITGA2B 0.033 0.06 0.25 55 -0.57 3 58
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
ADAP1 0.025 0.029 0.25 10 -0.57 1 11
KIF13B 0.019 0.027 -10000 0 -0.57 2 2
HGF/MET -0.066 0.2 -10000 0 -0.45 226 226
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 0.19 1 -0.28 307 308
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.17 0.23 -10000 0 -0.4 517 517
ADRB2 -0.1 0.24 -10000 0 -0.57 226 226
receptor agonist activity 0 0 0 1 0 250 251
actin filament binding 0 0 0 1 -0.001 269 270
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.25 4 -0.57 35 39
GNAQ 0.022 0.032 -10000 0 -0.57 3 3
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 155 156
ARF6/GDP -0.037 0.15 0.25 2 -0.43 91 93
ARF6/GDP/GULP/ACAP1 -0.11 0.18 -10000 0 -0.41 213 213
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.081 -10000 0 -0.33 38 38
ACAP1 0.029 0.066 0.25 47 -0.57 6 53
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.056 0.17 -10000 0 -0.48 146 146
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.012 0.14 0.25 2 -0.57 65 67
CYTH3 0.005 0.013 -10000 0 -0.42 1 1
CYTH2 0.006 0.099 -10000 0 -1 10 10
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 220 221
endosomal lumen acidification 0 0 0.001 4 0 256 260
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.014 0.14 -10000 0 -0.57 69 69
GNAQ/ARNO 0.018 0.095 -10000 0 -0.95 10 10
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 167 167
MET -0.074 0.22 -10000 0 -0.57 177 177
GNA14 0.023 0.065 0.25 20 -0.57 10 30
GNA15 0.024 0.025 0.25 6 -0.57 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 217 218
GNA11 0.022 0.032 -10000 0 -0.57 3 3
LHCGR -0.069 0.2 -10000 0 -0.57 146 146
AGTR1 -0.095 0.26 0.25 63 -0.57 239 302
desensitization of G-protein coupled receptor protein signaling pathway -0.055 0.17 -10000 0 -0.48 146 146
IPCEF1/ARNO -0.13 0.19 -10000 0 -0.59 71 71
alphaIIb/beta3 Integrin 0.026 0.092 -10000 0 -0.42 38 38
Plasma membrane estrogen 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
GNB1/GNG2 0 0.15 -10000 0 -0.32 175 175
ER alpha/Gai/GDP/Gbeta gamma -0.085 0.22 -10000 0 -0.46 222 222
AKT1 -0.12 0.33 -10000 0 -0.77 208 208
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.34 -10000 0 -0.78 207 207
mol:Ca2+ -0.024 0.11 0.26 2 -0.43 33 35
IGF1R 0.013 0.079 0.25 3 -0.57 19 22
E2/ER alpha (dimer)/Striatin -0.017 0.16 -10000 0 -0.35 175 175
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.11 0.31 0.73 208 -10000 0 208
RhoA/GTP -0.016 0.1 -10000 0 -0.28 123 123
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.068 0.21 0.31 4 -0.46 202 206
regulation of stress fiber formation 0.024 0.1 0.24 130 -0.31 8 138
E2/ERA-ERB (dimer) -0.02 0.16 0.17 105 -0.36 175 280
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.01 0.13 0.16 102 -0.31 158 260
pseudopodium formation -0.024 0.1 0.31 8 -0.24 130 138
E2/ER alpha (dimer)/PELP1 -0.015 0.15 -10000 0 -0.36 155 155
GRB2 0.023 0.009 0.25 1 -10000 0 1
GNG2 0.018 0.06 -10000 0 -0.57 11 11
GNAO1 0.017 0.09 0.25 32 -0.57 20 52
HRAS 0.025 0.02 0.25 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.089 0.23 0.25 1 -0.5 225 226
E2/ER beta (dimer) 0.008 0.062 -10000 0 -0.41 23 23
mol:GDP -0.039 0.17 0.25 13 -0.39 170 183
mol:NADP -0.089 0.23 0.25 1 -0.5 225 226
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
mol:IP3 -0.027 0.11 0.27 2 -0.45 32 34
IGF-1R heterotetramer 0.013 0.079 0.25 3 -0.57 19 22
PLCB1 -0.025 0.11 0.28 2 -0.35 79 81
PLCB2 -0.005 0.083 -10000 0 -0.5 17 17
IGF1 -0.1 0.24 -10000 0 -0.57 232 232
mol:L-citrulline -0.089 0.23 0.25 1 -0.5 225 226
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.64 159 159
JNK cascade 0.008 0.062 -10000 0 -0.41 23 23
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.011 0.084 -10000 0 -0.57 22 22
GNAQ 0.022 0.032 -10000 0 -0.57 3 3
ESR1 -0.037 0.23 0.25 116 -0.57 153 269
Gq family/GDP/Gbeta gamma -0.009 0.16 -10000 0 -0.74 38 38
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.018 0.13 -10000 0 -0.58 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.06 0.2 0.31 5 -0.46 170 175
GNAZ 0.018 0.054 -10000 0 -0.57 9 9
E2/ER alpha (dimer) -0.029 0.17 0.18 116 -0.41 159 275
STRN 0.014 0.078 -10000 0 -0.57 19 19
GNAL -0.11 0.24 -10000 0 -0.57 236 236
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.056 -10000 0 -0.36 25 25
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
HBEGF -0.056 0.21 0.34 20 -0.5 116 136
cAMP biosynthetic process -0.087 0.18 -10000 0 -0.33 350 350
SRC -0.08 0.21 0.29 7 -0.44 213 220
PI3K 0.028 0.048 -10000 0 -0.4 12 12
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.16 -10000 0 -0.36 166 166
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.42 230 230
Gs family/GTP -0.084 0.19 -10000 0 -0.33 350 350
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.018 -10000 0 -10000 0 0
vasodilation -0.084 0.22 0.24 1 -0.48 225 226
mol:DAG -0.027 0.11 0.27 2 -0.45 32 34
Gs family/GDP/Gbeta gamma -0.091 0.18 -10000 0 -0.35 295 295
MSN -0.026 0.11 0.32 8 -0.26 130 138
Gq family/GTP -0.001 0.088 -10000 0 -0.53 16 16
mol:PI-3-4-5-P3 -0.11 0.32 -10000 0 -0.75 207 207
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.084 0.22 0.48 225 -0.24 1 226
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.16 0.26 10 -0.37 169 179
NOS3 -0.095 0.25 0.25 1 -0.53 225 226
GNA11 0.022 0.032 -10000 0 -0.57 3 3
MAPKKK cascade -0.085 0.25 0.3 3 -0.56 217 220
E2/ER alpha (dimer)/PELP1/Src -0.072 0.22 0.31 8 -0.47 207 215
ruffle organization -0.024 0.1 0.31 8 -0.24 130 138
ROCK2 -0.025 0.12 0.34 8 -0.28 137 145
GNA14 0.023 0.065 0.25 20 -0.57 10 30
GNA15 0.025 0.025 0.25 6 -0.57 1 7
GNA13 0.023 0.007 -10000 0 -10000 0 0
MMP9 -0.049 0.2 0.36 23 -0.48 116 139
MMP2 -0.07 0.2 0.28 9 -0.42 209 218
Nongenotropic Androgen signaling

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.01 0.13 -10000 0 -0.33 151 151
regulation of S phase of mitotic cell cycle -0.024 0.11 -10000 0 -0.29 134 134
GNAO1 0.017 0.09 0.25 32 -0.57 20 52
HRAS 0.024 0.02 0.25 8 -10000 0 8
SHBG/T-DHT 0.015 0.005 -10000 0 -10000 0 0
PELP1 0.022 0.007 -10000 0 -10000 0 0
AKT1 0.006 0.002 -10000 0 -10000 0 0
MAP2K1 -0.068 0.11 -10000 0 -0.33 125 125
T-DHT/AR -0.042 0.15 0.17 1 -0.42 142 143
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 318 318
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.008 0.13 -10000 0 -0.57 57 57
mol:GDP -0.063 0.16 -10000 0 -0.46 146 146
cell proliferation -0.14 0.21 0.27 3 -0.44 299 302
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.24 0.38 -10000 0 -0.81 322 322
mol:Ca2+ -0.013 0.028 -10000 0 -0.073 145 145
MAPK3 -0.1 0.16 0.26 4 -0.42 115 119
MAPK1 -0.079 0.14 -10000 0 -0.39 107 107
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
mol:IP3 -0.001 0.002 -10000 0 -0.004 315 315
cAMP biosynthetic process 0.004 0.021 -10000 0 -10000 0 0
GNG2 0.018 0.06 -10000 0 -0.57 11 11
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 315 315
HRAS/GTP -0.028 0.12 -10000 0 -0.32 139 139
actin cytoskeleton reorganization 0.029 0.036 -10000 0 -0.3 11 11
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 315 315
PI3K 0.026 0.041 -10000 0 -0.34 12 12
apoptosis 0.13 0.21 0.43 324 -10000 0 324
T-DHT/AR/PELP1 -0.025 0.13 -10000 0 -0.36 141 141
HRAS/GDP -0.052 0.16 -10000 0 -0.45 143 143
CREB1 -0.14 0.23 -10000 0 -0.47 323 323
RAC1-CDC42/GTP 0.037 0.039 -10000 0 -0.3 11 11
AR -0.055 0.2 0.25 1 -0.57 141 142
GNB1 0.024 0.005 -10000 0 -10000 0 0
RAF1 -0.06 0.11 -10000 0 -0.32 133 133
RAC1-CDC42/GDP -0.028 0.16 -10000 0 -0.44 141 141
T-DHT/AR/PELP1/Src -0.022 0.13 -10000 0 -0.34 140 140
MAP2K2 -0.07 0.11 -10000 0 -0.32 126 126
T-DHT/AR/PELP1/Src/PI3K -0.024 0.11 -10000 0 -0.3 134 134
GNAZ 0.018 0.054 -10000 0 -0.57 9 9
SHBG 0.022 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.051 0.16 -10000 0 -0.47 98 98
mol:T-DHT -0.001 0.001 0.002 3 -0.003 217 220
RAC1 0.024 0.003 -10000 0 -10000 0 0
GNRH1 0.001 0.026 -10000 0 -0.42 4 4
Gi family/GTP -0.036 0.1 -10000 0 -0.28 101 101
CDC42 0.023 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3 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
USP8 -0.008 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.14 0.31 1 -0.3 61 62
NFATC4 -0.064 0.12 0.26 8 -0.26 83 91
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.069 0.15 -10000 0 -0.31 252 252
JUN -0.009 0.096 0.23 27 -0.45 3 30
HRAS 0.026 0.02 0.26 8 -10000 0 8
DOCK7 -0.079 0.14 0.28 2 -0.3 250 252
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.052 0.15 -10000 0 -0.33 206 206
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.006 -10000 0 -10000 0 0
MAPK10 -0.07 0.11 0.21 8 -0.27 138 146
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.073 0.16 -10000 0 -0.33 252 252
RAF1 -0.019 0.14 0.33 15 -0.3 58 73
ErbB2/ErbB3/neuregulin 2 -0.14 0.18 -10000 0 -0.34 437 437
STAT3 -0.001 0.16 -10000 0 -0.86 34 34
cell migration -0.055 0.1 0.23 14 -0.25 86 100
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.043 0.24 0.43 13 -0.5 104 117
FOS -0.1 0.28 0.34 28 -0.49 323 351
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.069 0.15 -10000 0 -0.31 252 252
MAPK3 -0.015 0.2 0.4 13 -0.52 24 37
MAPK1 -0.027 0.21 0.41 13 -0.56 47 60
JAK2 -0.078 0.14 0.26 1 -0.3 247 248
NF2 -0.002 0.057 -10000 0 -0.68 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.13 0.23 3 -0.29 218 221
NRG1 -0.14 0.26 0.25 4 -0.57 292 296
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.08 0.15 0.25 2 -0.3 254 256
MAPK9 -0.042 0.083 0.2 11 -0.26 3 14
ERBB2 0.001 0.071 0.24 85 -0.44 1 86
ERBB3 0.021 0.041 -10000 0 -0.57 5 5
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
apoptosis 0.019 0.025 -10000 0 -0.16 7 7
STAT3 (dimer) 0 0.15 -10000 0 -0.84 34 34
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.004 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.07 0.093 -10000 0 -0.22 245 245
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.02 -10000 0 -0.38 1 1
CHRNA1 0.017 0.18 0.36 56 -0.4 19 75
myelination -0.059 0.12 0.29 17 -0.27 22 39
PPP3CB -0.074 0.13 0.27 2 -0.28 248 250
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.26 203 203
NRG2 -0.26 0.3 -10000 0 -0.57 509 509
mol:GDP -0.053 0.13 0.23 3 -0.29 218 221
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.016 0.14 0.33 16 -0.3 55 71
SRC 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.08 0.14 0.28 2 -0.3 251 253
MAP2K1 -0.053 0.22 0.43 5 -0.51 87 92
heart morphogenesis -0.069 0.15 -10000 0 -0.31 252 252
RAS family/GDP -0.022 0.14 0.29 1 -0.29 60 61
GRB2 0.023 0.009 0.25 1 -10000 0 1
PRKACA -0.002 0.067 -10000 0 -0.68 10 10
CHRNE 0.004 0.027 0.12 4 -0.21 3 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.069 0.15 -10000 0 -0.31 252 252
CDC42 0.023 0.005 -10000 0 -10000 0 0
BMP receptor signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.057 0.16 0.31 8 -0.35 117 125
SMAD6-7/SMURF1 0.046 0.015 -10000 0 -10000 0 0
NOG 0.012 0.095 0.25 19 -0.57 25 44
SMAD9 -0.09 0.26 -10000 0 -0.59 195 195
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.021 0.14 -10000 0 -0.43 69 69
BMP7/USAG1 -0.2 0.25 -10000 0 -0.45 488 488
SMAD5/SKI -0.015 0.15 0.26 3 -0.42 79 82
SMAD1 0.013 0.062 -10000 0 -0.42 8 8
BMP2 -0.074 0.22 0.25 2 -0.57 178 180
SMAD1/SMAD1/SMAD4 0.018 0.069 -10000 0 -0.4 9 9
BMPR1A 0.023 0.026 -10000 0 -0.57 2 2
BMPR1B 0.1 0.15 0.25 426 -0.57 23 449
BMPR1A-1B/BAMBI 0.083 0.12 0.34 10 -0.33 54 64
AHSG 0.022 0.029 0.25 16 -10000 0 16
CER1 0.018 0.013 0.25 3 -10000 0 3
BMP2-4/CER1 -0.046 0.18 -10000 0 -0.39 213 213
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.16 -10000 0 -0.42 97 97
BMP2-4 (homodimer) -0.066 0.2 -10000 0 -0.45 220 220
RGMB 0.023 0.019 -10000 0 -0.57 1 1
BMP6/BMPR2/BMPR1A-1B 0.07 0.14 -10000 0 -0.31 96 96
RGMA -0.053 0.2 -10000 0 -0.57 138 138
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.036 0.16 -10000 0 -0.42 118 118
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.44 577 577
SMAD6/SMURF1/SMAD5 -0.016 0.15 0.27 1 -0.44 72 73
SOSTDC1 -0.26 0.3 0.25 3 -0.57 508 511
BMP7/BMPR2/BMPR1A-1B 0.066 0.14 0.3 4 -0.32 94 98
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.016 0.15 0.25 2 -0.57 72 74
HFE2 0.018 0.023 0.25 9 -10000 0 9
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.043 0.2 -10000 0 -0.41 219 219
SMAD5/SMAD5/SMAD4 -0.016 0.15 0.26 2 -0.42 80 82
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.022 0.15 -10000 0 -0.38 109 109
BMP7 (homodimer) -0.014 0.16 0.25 29 -0.57 77 106
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.001 0.12 -10000 0 -0.42 72 72
SMAD1/SKI 0.02 0.076 -10000 0 -0.43 11 11
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.045 0.18 0.34 1 -0.39 215 216
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.036 0.095 0.25 94 -0.57 14 108
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.085 0.11 -10000 0 -0.42 25 25
CHRDL1 -0.38 0.28 -10000 0 -0.57 729 729
ENDOFIN/SMAD1 0.019 0.078 -10000 0 -0.45 11 11
SMAD6-7/SMURF1/SMAD1 0.036 0.081 -10000 0 -0.43 10 10
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.015 0.11 0.25 39 -0.57 31 70
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.26 -10000 0 -0.45 733 733
BMP2-4/GREM1 -0.037 0.2 -10000 0 -0.4 223 223
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.082 0.25 -10000 0 -0.57 197 197
SMAD1/SMAD6 0.019 0.078 -10000 0 -0.45 11 11
TAK1/SMAD6 0.033 0.01 -10000 0 -10000 0 0
BMP7 -0.014 0.16 0.25 29 -0.57 77 106
BMP6 -0.016 0.15 0.25 2 -0.57 72 74
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.034 0.17 -10000 0 -0.42 121 121
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.075 -10000 0 -0.45 10 10
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.007 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.047 0.2 0.23 1 -0.48 132 133
CHRD 0.026 0.095 0.25 58 -0.57 19 77
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.05 0.18 -10000 0 -0.48 120 120
BMP4 -0.01 0.14 0.25 1 -0.57 62 63
FST 0 0.12 0.25 4 -0.57 44 48
BMP2-4/NOG -0.048 0.19 0.34 1 -0.41 209 210
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.07 0.14 0.33 1 -0.3 93 94
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.041 0.17 -10000 0 -0.4 185 185
CRKL -0.048 0.15 0.31 2 -0.4 89 91
mol:PIP3 0.002 0.059 0.56 1 -0.89 4 5
AKT1 0.01 0.074 0.37 3 -0.78 4 7
PTK2B 0.02 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.14 0.33 2 -0.4 75 77
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.043 0.18 -10000 0 -0.39 214 214
MAP3K5 -0.04 0.15 0.36 1 -0.43 68 69
HGF/MET/CIN85/CBL/ENDOPHILINS -0.03 0.17 -10000 0 -0.36 222 222
AP1 -0.11 0.19 -10000 0 -0.4 304 304
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.24 0.38 -10000 0 -0.77 352 352
STAT3 (dimer) -0.047 0.15 -10000 0 -0.34 178 178
GAB1/CRKL/SHP2/PI3K -0.02 0.15 -10000 0 -0.45 53 53
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.036 0.14 0.34 1 -0.39 85 86
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.023 0.019 -10000 0 -0.57 1 1
ELK1 -0.03 0.096 0.29 25 -0.21 119 144
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.027 0.092 -10000 0 -0.26 78 78
PAK1 0.024 0.087 0.38 6 -0.75 4 10
HGF/MET/RANBP10 -0.045 0.18 -10000 0 -0.38 223 223
HRAS -0.11 0.26 -10000 0 -0.64 194 194
DOCK1 -0.046 0.14 0.52 1 -0.41 73 74
GAB1 -0.05 0.16 -10000 0 -0.36 167 167
CRK -0.049 0.15 0.36 1 -0.4 95 96
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.26 -10000 0 -0.57 235 235
JUN 0.02 0.044 -10000 0 -0.57 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.053 0.12 -10000 0 -0.28 226 226
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
cell morphogenesis -0.049 0.16 0.37 6 -0.45 85 91
GRB2/SHC -0.017 0.11 -10000 0 -0.27 151 151
FOS -0.14 0.27 -10000 0 -0.57 301 301
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.03 0.096 0.29 25 -0.21 119 144
HGF/MET/MUC20 -0.055 0.17 -10000 0 -0.38 225 225
cell migration -0.017 0.11 -10000 0 -0.26 151 151
GRB2 0.023 0.009 0.25 1 -10000 0 1
CBL 0.022 0.008 -10000 0 -10000 0 0
MET/RANBP10 -0.043 0.17 -10000 0 -0.41 180 180
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.048 0.14 -10000 0 -0.33 187 187
MET/MUC20 -0.056 0.16 -10000 0 -0.41 186 186
RAP1B -0.04 0.14 0.31 5 -0.43 48 53
RAP1A -0.045 0.14 0.38 3 -0.42 49 52
HGF/MET/RANBP9 -0.043 0.18 -10000 0 -0.39 218 218
RAF1 -0.099 0.25 -10000 0 -0.6 193 193
STAT3 -0.048 0.15 -10000 0 -0.35 178 178
cell proliferation -0.043 0.19 0.28 31 -0.42 162 193
RPS6KB1 -0.015 0.063 -10000 0 -0.23 31 31
MAPK3 -0.042 0.094 0.72 6 -10000 0 6
MAPK1 -0.012 0.17 0.68 53 -10000 0 53
RANBP9 0.024 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.14 0.44 1 -0.42 58 59
SRC -0.052 0.13 0.2 1 -0.32 175 176
PI3K -0.028 0.13 -10000 0 -0.29 180 180
MET/Glomulin -0.048 0.15 -10000 0 -0.37 179 179
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.091 0.23 0.47 1 -0.56 192 193
MET -0.074 0.22 -10000 0 -0.57 177 177
MAP4K1 -0.042 0.15 0.38 1 -0.42 92 93
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.091 0.23 0.47 1 -0.56 192 193
BAD 0.008 0.071 0.36 3 -0.75 4 7
MAP2K4 -0.037 0.13 0.34 1 -0.4 61 62
SHP2/GRB2/SOS1/GAB1 -0.041 0.17 -10000 0 -0.4 178 178
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.049 0.11 -10000 0 -0.27 207 207
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 0.25 2 -0.57 65 67
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.022 0.13 -10000 0 -0.26 211 211
PDPK1 0.012 0.077 0.42 1 -0.83 4 5
HGF/MET/SHIP -0.044 0.18 -10000 0 -0.39 224 224
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.003 0.039 0.2 3 -0.37 2 5
NFATC2 -0.026 0.11 0.22 2 -0.37 88 90
NFATC3 0.005 0.034 0.22 2 -10000 0 2
CD40LG -0.14 0.29 0.47 17 -0.56 258 275
PTGS2 -0.19 0.34 0.47 13 -0.63 334 347
JUNB 0.025 0.01 0.25 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.027 0.15 2 -10000 0 2
CaM/Ca2+ 0.008 0.027 0.15 2 -10000 0 2
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.013 0.049 -10000 0 -0.58 6 6
mol:Ca2+ -0.003 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.027 0.047 0.25 24 -0.57 3 27
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.005 0.15 0.46 12 -0.4 57 69
FOS -0.15 0.27 -10000 0 -0.58 301 301
IFNG -0.11 0.28 0.46 41 -0.53 224 265
AP-1/NFAT1-c-4 -0.13 0.34 0.52 39 -0.6 267 306
FASLG -0.12 0.26 0.5 23 -0.53 211 234
NFAT1-c-4/ICER1 -0.018 0.12 0.28 9 -0.34 79 88
IL2RA -0.12 0.28 0.46 30 -0.54 238 268
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.27 0.47 20 -0.52 254 274
JunB/Fra1/NFAT1-c-4 -0.008 0.13 0.34 11 -0.34 78 89
IL4 -0.13 0.27 0.46 14 -0.52 254 268
IL2 -0.014 0.15 -10000 0 -0.94 27 27
IL3 -0.017 0.11 -10000 0 -0.72 23 23
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.015 0.25 3 -10000 0 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.25 1 -10000 0 1
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.39 275 276
PTP1B/AKT1 -0.067 0.13 0.22 1 -0.34 141 142
FYN 0.022 0.026 -10000 0 -0.57 2 2
p210 bcr-abl/PTP1B -0.082 0.14 0.22 2 -0.36 157 159
EGFR -0.2 0.29 -10000 0 -0.58 393 393
EGF/EGFR -0.2 0.24 -10000 0 -0.42 532 532
CSF1 0.022 0.036 -10000 0 -0.57 4 4
AKT1 0.024 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.048 0.16 0.24 13 -0.36 138 151
Insulin Receptor/Insulin -0.043 0.12 -10000 0 -0.36 61 61
HCK 0.027 0.026 0.25 13 -10000 0 13
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.078 0.14 0.28 3 -0.35 146 149
EGF -0.1 0.23 0.25 2 -0.58 196 198
YES1 0.023 0.019 -10000 0 -0.57 1 1
CAV1 -0.16 0.21 0.27 2 -0.42 334 336
TXN 0.017 0.017 0.25 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.073 0.15 -10000 0 -0.38 147 147
cell migration 0.082 0.14 0.36 157 -0.22 2 159
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.021 0.051 0.25 6 -0.57 7 13
ITGA2B 0.032 0.06 0.25 55 -0.57 3 58
CSF1R 0.024 0.008 0.25 1 -10000 0 1
Prolactin Receptor/Prolactin 0.031 0.044 0.31 1 -0.42 6 7
FGR 0.024 0.009 0.25 1 -10000 0 1
PTP1B/p130 Cas -0.069 0.14 0.22 1 -0.35 142 143
Crk/p130 Cas -0.062 0.14 -10000 0 -0.36 119 119
DOK1 -0.067 0.13 0.24 2 -0.35 116 118
JAK2 -0.047 0.12 -10000 0 -0.44 58 58
Jak2/Leptin Receptor/Leptin -0.26 0.16 -10000 0 -0.39 450 450
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
PTPN1 -0.083 0.14 0.22 2 -0.36 158 160
LYN 0.021 0.008 -10000 0 -10000 0 0
CDH2 0.062 0.092 0.25 187 -0.57 2 189
SRC -0.018 0.098 -10000 0 -0.62 21 21
ITGB3 0.004 0.11 0.25 4 -0.57 35 39
CAT1/PTP1B -0.093 0.19 0.35 3 -0.46 158 161
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.038 0.12 -10000 0 -0.4 51 51
mol:H2O2 -0.004 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.23 0.15 -10000 0 -0.36 415 415
negative regulation of transcription -0.047 0.12 -10000 0 -0.43 59 59
FCGR2A 0.021 0.012 0.25 1 -10000 0 1
FER 0.011 0.058 -10000 0 -0.58 10 10
alphaIIb/beta3 Integrin 0.023 0.092 -10000 0 -0.42 38 38
BLK 0.051 0.086 0.25 151 -0.57 2 153
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.006 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.57 268 268
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.009 0.25 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.042 0.17 0.34 4 -0.45 102 106
PRL 0.008 0.033 0.26 11 -10000 0 11
SOCS3 0.01 0.16 -10000 0 -1.2 16 16
SPRY2 -0.039 0.18 -10000 0 -0.58 103 103
Insulin Receptor/Insulin/IRS1 0.026 0.08 -10000 0 -0.37 41 41
CSF1/CSF1R -0.064 0.14 -10000 0 -0.36 130 130
Ras protein signal transduction 0.05 0.15 0.64 59 -10000 0 59
IRS1 0.001 0.12 -10000 0 -0.57 42 42
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.43 0.25 -10000 0 -0.57 822 822
STAT5B -0.069 0.14 0.2 3 -0.35 144 147
STAT5A -0.07 0.14 0.2 3 -0.35 149 152
GRB2 0.023 0.009 0.25 1 -10000 0 1
PDGFB-D/PDGFRB -0.073 0.14 0.22 1 -0.36 148 149
CSN2 0.025 0.057 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.009 0.072 -10000 0 -0.59 8 8
YBX1 0.027 0.015 0.22 1 -10000 0 1
LCK 0.027 0.075 0.25 41 -0.57 11 52
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.019 0.036 0.25 10 -0.58 2 12
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.002 0.082 -10000 0 -0.55 14 14
Crk/p130 Cas/Paxillin -0.057 0.12 -10000 0 -0.35 118 118
JUN -0.016 0.12 0.25 1 -0.41 26 27
HRAS 0.025 0.02 0.25 8 -10000 0 8
RET51/GFRalpha1/GDNF/GRB10 0.039 0.19 0.34 51 -0.34 178 229
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.25 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.04 0.19 0.34 50 -0.34 177 227
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.012 0.15 0.32 5 -0.33 181 186
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.16 0.28 36 -0.31 178 214
GRB7 0.019 0.032 -10000 0 -0.57 3 3
RET51/GFRalpha1/GDNF 0.038 0.19 0.34 51 -0.34 177 228
MAPKKK cascade -0.002 0.15 0.28 10 -0.32 129 139
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.025 0.18 0.32 4 -0.38 193 197
lamellipodium assembly -0.034 0.13 -10000 0 -0.31 144 144
RET51/GFRalpha1/GDNF/SHC 0.034 0.18 0.34 42 -0.34 140 182
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.009 0.14 0.32 5 -0.33 136 141
RET9/GFRalpha1/GDNF/Shank3 -0.014 0.15 0.32 5 -0.33 181 186
MAPK3 -0.033 0.13 0.37 1 -0.31 136 137
DOK1 0.025 0.014 0.25 4 -10000 0 4
DOK6 0.017 0.07 0.25 7 -0.57 14 21
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.032 0.12 -10000 0 -0.44 20 20
DOK5 0.011 0.087 0.25 5 -0.57 23 28
GFRA1 -0.072 0.24 0.25 51 -0.57 193 244
MAPK8 -0.01 0.13 0.22 1 -0.45 25 26
HRAS/GTP 0.026 0.18 0.29 51 -0.34 168 219
tube development -0.007 0.15 0.34 10 -0.31 172 182
MAPK1 -0.032 0.13 0.34 2 -0.31 139 141
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.11 0.25 1 -0.27 167 168
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.035 0.19 0.33 47 -0.33 180 227
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.025 0.19 0.34 37 -0.34 180 217
RET51/GFRalpha1/GDNF/Dok5 0.022 0.2 0.34 46 -0.35 188 234
PRKCA 0.01 0.084 0.25 1 -0.57 22 23
HRAS/GDP 0.019 0.014 0.18 8 -10000 0 8
CREB1 -0.014 0.13 0.23 7 -0.31 105 112
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.02 0.1 0.25 1 -0.26 128 129
RET51/GFRalpha1/GDNF/Grb7 0.039 0.18 0.33 64 -0.34 146 210
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.095 0.13 0.25 366 -0.57 13 379
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.015 0.12 0.24 1 -0.4 26 27
RET9/GFRalpha1/GDNF/FRS2 -0.013 0.15 0.32 5 -0.33 181 186
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.021 0.1 0.25 1 -0.27 124 125
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.004 0.14 0.25 10 -0.28 140 150
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.001 0.14 0.25 4 -0.29 142 146
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.009 0.13 0.25 15 -0.3 106 121
PI3K -0.03 0.2 0.3 5 -0.47 143 148
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.005 0.14 0.31 4 -0.31 172 176
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.006 0.12 0.25 4 -0.4 12 16
RET51/GFRalpha1/GDNF/FRS2 0.036 0.19 0.34 54 -0.34 179 233
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.008 0.13 0.25 15 -0.3 106 121
RET51/GFRalpha1/GDNF/PKC alpha 0.022 0.19 0.34 41 -0.34 186 227
GRB2 0.023 0.009 0.25 1 -10000 0 1
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.052 0.25 55 -10000 0 55
RAC1 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.025 0.22 0.34 48 -0.39 189 237
Rac1/GTP -0.023 0.16 0.25 1 -0.38 138 139
RET9/GFRalpha1/GDNF -0.027 0.16 0.32 5 -0.35 192 197
GFRalpha1/GDNF -0.034 0.18 0.36 5 -0.41 193 198
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.069 0.11 -10000 0 -0.28 94 94
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.46 445 445
NT3 (dimer)/TRKB -0.29 0.31 -10000 0 -0.52 614 614
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.034 -10000 0 -0.26 8 8
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.013 0.16 0.25 24 -0.57 76 100
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.024 0.051 0.25 25 -0.57 4 29
NTRK2 -0.28 0.3 -10000 0 -0.57 552 552
NTRK3 -0.17 0.28 0.25 5 -0.57 346 351
NT-4/5 (dimer)/TRKB -0.36 0.33 -10000 0 -0.57 691 691
neuron apoptosis 0.17 0.22 0.47 291 -10000 0 291
SHC 2-3/Grb2 -0.18 0.24 -10000 0 -0.52 291 291
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.18 0.25 -10000 0 -0.54 289 289
SHC3 -0.18 0.24 -10000 0 -0.52 277 277
STAT3 (dimer) 0.033 0.043 -10000 0 -0.36 4 4
NT3 (dimer)/TRKA -0.1 0.21 -10000 0 -0.42 295 295
RIN/GDP -0.045 0.12 0.3 4 -0.27 60 64
GIPC1 0.024 0.011 0.25 2 -10000 0 2
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.079 0.15 -10000 0 -0.34 250 250
RIN/GTP 0.014 0.008 0.18 2 -10000 0 2
CCND1 0.025 0.094 0.43 39 -0.82 4 43
MAGED1 0.025 0.01 0.25 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.57 364 364
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.25 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.035 0.083 0.34 3 -0.38 29 32
TRKA/NEDD4-2 0.031 0.04 -10000 0 -0.37 5 5
ELMO1 0.024 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.008 -10000 0 -10000 0 0
NGF 0.017 0.075 0.25 8 -0.57 16 24
HRAS 0.025 0.02 0.25 8 -10000 0 8
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.021 0.02 -10000 0 -0.57 1 1
RIT2 0.018 0.011 0.25 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.25 2 -10000 0 2
DNM1 0.021 0.048 0.25 1 -0.57 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.072 0.16 -10000 0 -0.34 220 220
mol:GDP -0.074 0.16 0.35 5 -0.39 81 86
NGF (dimer) 0.017 0.075 0.25 8 -0.57 16 24
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.044 0.11 0.38 2 -0.26 65 67
TIAM1 0.025 0.015 0.25 4 -10000 0 4
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
BDNF (dimer)/TRKB -0.19 0.23 -10000 0 -0.39 573 573
KIDINS220/CRKL/C3G 0.034 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.048 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.059 0.21 0.25 12 -0.57 154 166
RAP1/GDP -0.041 0.093 -10000 0 -0.23 64 64
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.013 0.16 0.25 24 -0.57 76 100
ubiquitin-dependent protein catabolic process 0.036 0.061 -10000 0 -0.36 18 18
Schwann cell development -0.049 0.038 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.049 -10000 0 -0.34 1 1
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.28 -10000 0 -0.47 634 634
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.078 0.13 -10000 0 -0.46 51 51
STAT3 0.033 0.043 -10000 0 -0.36 4 4
axon guidance -0.26 0.26 -10000 0 -0.44 646 646
MAPK3 0.024 0.086 0.24 3 -0.35 27 30
MAPK1 0.026 0.088 0.24 4 -0.35 28 32
CDC42/GDP -0.043 0.12 0.28 6 -0.27 60 66
NTF3 -0.059 0.21 0.25 12 -0.57 154 166
NTF4 -0.18 0.28 -10000 0 -0.57 364 364
NGF (dimer)/TRKA/FAIM 0.037 0.061 -10000 0 -0.36 18 18
PI3K 0.028 0.048 -10000 0 -0.4 12 12
FRS3 0.024 0.005 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.024 0.004 -10000 0 -10000 0 0
RASGRF1 -0.078 0.16 0.25 3 -0.34 271 274
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.41 422 423
RGS19 0.023 0.01 0.25 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.095 0.33 3 -0.44 9 12
Rac1/GDP -0.044 0.12 0.31 4 -0.26 68 72
NGF (dimer)/TRKA/GRIT 0.024 0.057 -10000 0 -0.34 20 20
neuron projection morphogenesis -0.069 0.22 -10000 0 -0.73 52 52
NGF (dimer)/TRKA/NEDD4-2 0.036 0.062 -10000 0 -0.36 18 18
MAP2K1 0.029 0.085 0.36 16 -10000 0 16
NGFR -0.14 0.26 -10000 0 -0.57 289 289
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.05 -10000 0 -0.29 21 21
RAS family/GTP/PI3K 0.017 0.03 -10000 0 -0.26 9 9
FRS2 family/SHP2/GRB2/SOS1 0.063 0.026 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAPKKK cascade -0.039 0.14 -10000 0 -0.65 41 41
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.039 -10000 0 -0.42 4 4
SQSTM1 0.024 0.008 0.25 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.36 567 567
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.062 -10000 0 -0.32 18 18
MATK 0.02 0.086 0.25 30 -0.57 18 48
NEDD4L 0.023 0.019 -10000 0 -0.57 1 1
RAS family/GDP -0.055 0.07 -10000 0 -0.21 50 50
NGF (dimer)/TRKA -0.086 0.16 -10000 0 -0.34 289 289
Rac1/GTP -0.084 0.12 -10000 0 -0.28 216 216
FRS2 family/SHP2/CRK family 0.06 0.029 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.018 0.042 -10000 0 -0.38 5 5
PDGFRB 0.018 0.038 -10000 0 -0.57 4 4
SPHK1 -0.018 0.097 -10000 0 -0.75 14 14
mol:S1P -0.021 0.095 0.38 1 -0.66 14 15
S1P1/S1P/Gi -0.13 0.23 0.31 2 -0.44 349 351
GNAO1 0.005 0.092 0.24 32 -0.58 20 52
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.37 3 -0.41 315 318
PLCG1 -0.13 0.22 0.35 2 -0.42 318 320
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.038 -10000 0 -0.57 4 4
GNAI2 0.009 0.023 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.021 0.13 -10000 0 -0.58 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.028 -10000 0 -0.38 4 4
S1P1/S1P -0.034 0.097 0.34 1 -0.46 18 19
negative regulation of cAMP metabolic process -0.13 0.23 0.31 2 -0.42 349 351
MAPK3 -0.18 0.3 0.3 13 -0.58 358 371
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
KDR 0.012 0.041 -10000 0 -0.58 4 4
PLCB2 -0.024 0.097 0.29 7 -0.41 19 26
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.081 -10000 0 -0.39 18 18
receptor internalization -0.035 0.088 -10000 0 -0.43 18 18
PTGS2 -0.34 0.5 0.38 2 -1 368 370
Rac1/GTP -0.032 0.081 -10000 0 -0.39 18 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.25 7 -10000 0 7
negative regulation of T cell proliferation -0.13 0.23 0.31 2 -0.42 349 351
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.058 -10000 0 -0.58 9 9
MAPK1 -0.2 0.33 0.34 2 -0.62 373 375
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.31 4 -0.48 17 21
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.078 0.31 10 -0.3 1 11
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.019 -10000 0 -0.3 2 2
AURKB 0.14 0.12 0.25 560 -10000 0 560
AURKC 0.026 0.032 0.25 14 -0.57 1 15
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.18 14 -10000 0 14
Metarhodopsin II/Arrestin 0.037 0.037 0.32 2 -10000 0 2
PDE6G/GNAT1/GTP 0.036 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.027 0.25 14 -10000 0 14
GRK1 0.019 0.016 0.25 4 -10000 0 4
CNG Channel -0.048 0.16 -10000 0 -0.3 284 284
mol:Na + -0.048 0.16 -10000 0 -0.3 272 272
mol:ADP 0.019 0.016 0.25 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 87 88
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.042 0.17 0.28 5 -0.31 267 272
CNGB1 0.03 0.051 0.25 52 -10000 0 52
RDH5 -0.33 0.29 -10000 0 -0.57 639 639
SAG 0.032 0.051 0.25 54 -10000 0 54
mol:Ca2+ -0.081 0.14 0.36 18 -0.54 4 22
Na + (4 Units) -0.051 0.15 -10000 0 -0.29 213 213
RGS9 -0.024 0.17 0.25 11 -0.57 89 100
GNB1/GNGT1 0.054 0.059 -10000 0 -10000 0 0
GNAT1/GDP 0.025 0.11 0.3 5 -0.31 87 92
GUCY2D 0.024 0.048 0.25 18 -0.57 4 22
GNGT1 0.055 0.086 0.25 169 -10000 0 169
GUCY2F 0.018 0.011 0.25 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.019 0.051 0.2 3 -0.31 17 20
mol:11-cis-retinal -0.33 0.29 -10000 0 -0.57 639 639
mol:cGMP 0.042 0.046 -10000 0 -0.32 8 8
GNB1 0.024 0.005 -10000 0 -10000 0 0
Rhodopsin -0.24 0.22 -10000 0 -0.42 639 639
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.14 0.26 0.25 4 -0.57 294 298
Metarhodopsin II 0.026 0.019 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.051 -10000 0 -0.34 8 8
RGS9BP 0.036 0.053 0.25 59 -10000 0 59
Metarhodopsin II/Transducin 0.024 0.031 0.17 8 -0.17 1 9
GCAP Family/Ca ++ 0.044 0.037 -10000 0 -0.33 4 4
PDE6A/B 0.028 0.066 -10000 0 -0.42 19 19
mol:Pi 0.016 0.12 0.33 1 -0.36 87 88
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.058 0.053 0.32 2 -10000 0 2
PDE6B 0.014 0.079 0.25 3 -0.57 19 22
PDE6A 0.028 0.031 0.25 20 -10000 0 20
PDE6G 0.032 0.046 0.25 43 -10000 0 43
RHO 0.024 0.028 0.25 15 -10000 0 15
PDE6 0.035 0.12 0.3 8 -0.31 99 107
GUCA1A 0.031 0.045 0.25 42 -10000 0 42
GC2/GCAP Family 0.054 0.039 -10000 0 -0.34 4 4
GUCA1C 0.017 0.008 0.25 1 -10000 0 1
GUCA1B 0.022 0.036 -10000 0 -0.57 4 4
Effects of Botulinum toxin

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
STX1A 0.01 0.024 0.13 40 -10000 0 40
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.11 -10000 0 -0.42 45 45
STXBP1 0.021 0.044 -10000 0 -0.57 6 6
ACh/CHRNA1 0.072 0.09 0.19 351 -0.16 8 359
RAB3GAP2/RIMS1/UNC13B 0.035 0.088 -10000 0 -0.36 34 34
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 0.022 0.14 0.25 116 -0.57 46 162
mol:ACh -0.003 0.036 0.089 12 -0.14 43 55
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.021 0.082 0.23 1 -0.28 38 39
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.072 0.089 0.19 351 -0.15 8 359
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.25 362 -10000 0 362
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.032 0.11 0.19 196 -0.36 43 239
SNAP25 0 0.058 0.094 59 -0.3 34 93
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.046 0.15 0.25 204 -0.57 39 243
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.034 -10000 0 -0.36 6 6
STX1A/SNAP25 fragment 1/VAMP2 0.021 0.082 0.23 1 -0.28 38 39
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.36 329 329
fibroblast growth factor receptor signaling pathway -0.1 0.19 -10000 0 -0.36 329 329
LAMA1 -0.036 0.18 0.25 3 -0.57 108 111
PRNP 0.015 0.07 -10000 0 -0.57 15 15
GPC1/SLIT2 -0.015 0.14 -10000 0 -0.41 121 121
SMAD2 -0.001 0.068 0.24 1 -0.33 41 42
GPC1/PrPc/Cu2+ 0.026 0.049 -10000 0 -0.36 16 16
GPC1/Laminin alpha1 -0.013 0.14 -10000 0 -0.4 117 117
TDGF1 0.017 0.058 0.25 1 -0.57 10 11
CRIPTO/GPC1 0.03 0.048 -10000 0 -0.42 11 11
APP/GPC1 0.035 0.02 -10000 0 -0.42 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.04 -10000 0 -0.36 11 11
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.032 0.081 -10000 0 -0.36 42 42
SERPINC1 0.031 0.05 0.25 50 -10000 0 50
FYN 0.004 0.042 -10000 0 -0.36 13 13
FGR 0.005 0.039 -10000 0 -0.36 11 11
positive regulation of MAPKKK cascade 0.01 0.082 0.28 3 -0.36 26 29
SLIT2 -0.04 0.18 -10000 0 -0.57 115 115
GPC1/NRG -0.11 0.2 -10000 0 -0.42 293 293
NRG1 -0.14 0.26 0.25 4 -0.57 292 296
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.026 -10000 0 -0.36 1 1
LYN 0.005 0.035 -10000 0 -0.36 8 8
mol:Spermine 0.006 0.016 -10000 0 -0.42 1 1
cell growth -0.1 0.19 -10000 0 -0.36 329 329
BMP signaling pathway -0.025 0.025 0.57 1 -0.25 6 7
SRC 0.005 0.039 -10000 0 -0.36 11 11
TGFBR1 0.024 0.008 0.25 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.27 0.25 27 -0.57 307 334
GPC1 0.025 0.025 0.25 6 -0.57 1 7
TGFBR1 (dimer) 0.024 0.008 0.25 1 -10000 0 1
VEGFA 0.025 0.019 0.25 7 -10000 0 7
BLK 0.02 0.065 -10000 0 -0.37 13 13
HCK 0.007 0.042 -10000 0 -0.36 11 11
FGF2 -0.2 0.29 -10000 0 -0.57 411 411
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 41 41
cell death 0.035 0.02 -10000 0 -0.42 1 1
ATIII/GPC1 0.037 0.04 -10000 0 -0.42 1 1
PLA2G2A/GPC1 -0.098 0.21 -10000 0 -0.42 307 307
LCK 0.006 0.06 -10000 0 -0.36 22 22
neuron differentiation -0.11 0.2 -10000 0 -0.42 293 293
PrPc/Cu2+ 0.011 0.051 -10000 0 -0.42 15 15
APP 0.024 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.001 0.11 -10000 0 -0.57 41 41
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.043 0.17 0.3 131 -0.48 50 181
FYN 0.019 0.19 0.32 61 -0.53 67 128
LAT/GRAP2/SLP76 0.026 0.17 0.34 50 -0.51 55 105
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.022 0.16 0.3 85 -0.36 80 165
B2M 0.025 0.008 -10000 0 -10000 0 0
IKBKG 0.016 0.058 0.16 75 -0.14 27 102
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
mol:Ca2+ -0.022 0.032 -10000 0 -0.092 160 160
integrin-mediated signaling pathway 0.026 0.022 -10000 0 -0.29 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.2 0.35 52 -0.52 81 133
TRPV6 -0.09 0.27 1.2 15 -0.57 196 211
CD28 0.024 0.05 0.26 9 -0.57 6 15
SHC1 0.028 0.21 0.31 156 -0.45 102 258
receptor internalization -0.013 0.22 0.35 37 -0.47 145 182
PRF1 -0.012 0.24 0.55 7 -0.99 41 48
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.25 1 -10000 0 1
COT/AKT1 0.03 0.14 0.28 78 -0.31 70 148
LAT 0.012 0.2 0.32 69 -0.56 67 136
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.023 0.095 0.26 48 -0.58 19 67
CD3E 0.023 0.087 0.26 37 -0.58 16 53
CD3G 0.012 0.11 0.26 39 -0.57 33 72
RASGRP2 0 0.05 0.13 16 -0.17 69 85
RASGRP1 0.024 0.15 0.32 57 -0.41 58 115
HLA-A 0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.019 0.033 0.25 1 -0.57 3 4
RAP1A/GTP/RAPL 0.026 0.022 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.079 0.17 169 -0.13 23 192
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.055 -10000 0 -0.22 37 37
PRKCA 0.014 0.098 0.22 54 -0.28 50 104
GRAP2 0.017 0.066 0.25 3 -0.57 13 16
mol:IP3 0.014 0.14 0.26 130 -0.39 48 178
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.17 0.3 36 -0.66 48 84
ORAI1 0.037 0.17 0.64 4 -0.96 15 19
CSK 0.006 0.2 0.36 37 -0.55 72 109
B7 family/CD28 0.061 0.21 0.39 58 -0.61 50 108
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.001 0.22 0.37 39 -0.51 112 151
PTPN6 0.003 0.19 0.33 45 -0.55 69 114
VAV1 0.003 0.2 0.35 42 -0.53 79 121
Monovalent TCR/CD3 -0.001 0.14 0.27 34 -0.5 56 90
CBL 0.022 0.008 -10000 0 -10000 0 0
LCK 0.017 0.2 0.32 63 -0.58 64 127
PAG1 0.019 0.2 0.31 74 -0.46 98 172
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.22 0.36 37 -0.51 107 144
CD80 0.084 0.1 0.26 279 -10000 0 279
CD86 0.026 0.018 0.26 6 -10000 0 6
PDK1/CARD11/BCL10/MALT1 -0.006 0.071 0.19 4 -0.26 37 41
HRAS 0.025 0.02 0.25 8 -10000 0 8
GO:0035030 0.021 0.16 0.32 44 -0.49 52 96
CD8A 0.029 0.058 0.27 29 -0.58 5 34
CD8B 0.014 0.11 0.26 30 -0.58 32 62
PTPRC 0.021 0.041 0.26 11 -0.57 3 14
PDK1/PKC theta 0.023 0.19 0.36 81 -0.46 72 153
CSK/PAG1 0.021 0.19 0.31 69 -0.56 60 129
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.01 -10000 0 -10000 0 0
GRAP2/SLP76 0.019 0.2 0.38 35 -0.54 70 105
STIM1 0.025 0.095 1.3 4 -10000 0 4
RAS family/GTP 0.044 0.091 0.21 100 -0.19 37 137
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.23 0.35 37 -0.5 145 182
mol:DAG -0.017 0.096 0.13 16 -0.34 52 68
RAP1A/GDP 0.021 0.036 0.1 77 -10000 0 77
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.017 0.077 0.26 16 -0.57 15 31
cytotoxic T cell degranulation -0.009 0.22 0.55 7 -0.92 42 49
RAP1A/GTP -0.001 0.017 -10000 0 -0.064 67 67
mol:PI-3-4-5-P3 0.016 0.17 0.32 58 -0.43 80 138
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.021 0.17 0.29 118 -0.51 49 167
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.026 0.098 0.26 61 -0.57 20 81
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.006 0.16 0.35 16 -0.51 52 68
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.032 0.11 0.37 21 -0.48 32 53
CARD11 0.027 0.04 0.25 19 -0.57 2 21
PRKCB 0.014 0.1 0.26 50 -0.28 41 91
PRKCE 0.019 0.095 0.22 62 -0.26 41 103
PRKCQ 0.012 0.2 0.35 55 -0.51 79 134
LCP2 0.024 0.008 0.25 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.14 0.29 87 -0.31 78 165
IKK complex 0.035 0.08 0.2 133 -0.12 20 153
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.025 0.11 0.24 85 -0.26 49 134
PDPK1 0.027 0.15 0.33 84 -0.35 74 158
TCR/CD3/MHC I/CD8/Fyn -0.029 0.24 0.39 29 -0.73 72 101
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.034 0.032 -10000 0 -0.42 4 4
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.38 407 407
PTK2 -0.056 0.15 0.32 2 -0.52 42 44
IGF1R 0.013 0.079 0.25 3 -0.57 19 22
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.065 0.25 6 -0.57 12 18
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.044 0.12 -10000 0 -0.53 35 35
VEGFA 0.025 0.019 0.25 7 -10000 0 7
ILK -0.042 0.12 -10000 0 -0.49 32 32
ROCK1 0.023 0.019 -10000 0 -0.57 1 1
AKT1 -0.044 0.1 -10000 0 -0.49 28 28
PTK2B -0.014 0.071 0.36 2 -0.33 35 37
alphaV/beta3 Integrin/JAM-A -0.077 0.18 0.3 1 -0.33 296 297
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.031 0.075 -10000 0 -0.36 35 35
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.19 -10000 0 -0.38 245 245
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.013 0.068 -10000 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 0.042 0.083 -10000 0 -0.36 35 35
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.46 359 359
PI4 Kinase 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.068 0.1 0.34 3 -0.35 35 38
RPS6KB1 -0.16 0.22 0.42 3 -0.55 187 190
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.58 350 350
GPR124 0.016 0.048 -10000 0 -0.57 7 7
MAPK1 -0.21 0.29 -10000 0 -0.58 365 365
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
alphaV/beta3 Integrin/Tumstatin -0.032 0.16 -10000 0 -0.37 199 199
cell adhesion 0.023 0.084 -10000 0 -0.36 44 44
ANGPTL3 0.021 0.015 0.25 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.03 -10000 0 -0.36 3 3
IGF-1R heterotetramer 0.013 0.079 0.25 3 -0.57 19 22
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 41 41
ITGB3 0.005 0.11 0.25 4 -0.57 35 39
IGF1 -0.1 0.24 -10000 0 -0.57 232 232
RAC1 0.024 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.079 -10000 0 -0.39 31 31
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.018 -10000 0 -0.57 1 1
alphaV/beta3 Integrin/CD47 0.033 0.075 -10000 0 -0.36 35 35
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.013 0.14 -10000 0 -0.46 73 73
CSF1 0.022 0.036 -10000 0 -0.57 4 4
PIK3C2A -0.04 0.11 -10000 0 -0.5 28 28
PI4 Kinase/Pyk2 -0.077 0.15 -10000 0 -0.31 246 246
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.044 0.08 -10000 0 -0.36 35 35
FAK1/Vinculin -0.037 0.13 0.31 6 -0.41 41 47
alphaV beta3/Integrin/ppsTEM5 0.025 0.079 -10000 0 -0.4 31 31
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.033 0.077 0.25 69 -0.57 8 77
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 411 411
F11R -0.12 0.2 -10000 0 -0.42 311 311
alphaV/beta3 Integrin/Lactadherin 0.029 0.089 0.34 1 -0.38 44 45
alphaV/beta3 Integrin/TGFBR2 0.02 0.12 -10000 0 -0.45 57 57
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.034 -10000 0 -0.33 4 4
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.032 0.067 -10000 0 -0.33 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.11 0.25 421 -10000 0 421
alphaV/beta3 Integrin/Pyk2 0.026 0.074 -10000 0 -0.33 35 35
SDC1 0.038 0.059 0.25 68 -0.57 1 69
VAV3 -0.011 0.039 -10000 0 -0.32 11 11
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.57 42 42
FAK1/Paxillin -0.037 0.13 0.34 4 -0.42 39 43
cell migration -0.036 0.12 0.29 8 -0.38 37 45
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.067 0.17 -10000 0 -0.32 262 262
SPP1 0.084 0.1 0.25 279 -10000 0 279
KDR 0.022 0.036 -10000 0 -0.57 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.074 0.22 0.25 4 -0.57 178 182
angiogenesis -0.19 0.3 0.3 1 -0.58 335 336
Rac1/GTP 0.021 0.036 -10000 0 -0.29 10 10
EDIL3 -0.007 0.14 0.25 15 -0.57 61 76
cell proliferation 0.019 0.12 -10000 0 -0.45 57 57
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.007 0.07 0.34 1 -0.33 10 11
alphaM/beta2 Integrin/GPIbA 0.01 0.075 0.33 4 -0.4 6 10
alphaM/beta2 Integrin/proMMP-9 0.074 0.11 0.34 17 -0.41 1 18
PLAUR 0.041 0.06 0.25 80 -10000 0 80
HMGB1 -0.003 0.04 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.01 0.063 0.34 1 -10000 0 1
AGER -0.006 0.05 0.26 1 -0.47 3 4
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.025 0.14 0.32 4 -0.36 14 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.25 454 -0.57 1 455
CYR61 -0.004 0.12 -10000 0 -0.57 50 50
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.36 36 36
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.093 0.23 -10000 0 -0.57 206 206
MYH2 -0.013 0.14 0.29 8 -0.47 36 44
MST1R 0.022 0.053 0.25 10 -0.57 7 17
leukocyte activation during inflammatory response -0.18 0.17 0.29 1 -0.33 584 585
APOB -0.33 0.29 -10000 0 -0.57 643 643
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.049 0.25 1 -0.57 7 8
JAM3 0.019 0.041 -10000 0 -0.57 5 5
GP1BA 0.024 0.057 0.25 26 -0.57 6 32
alphaM/beta2 Integrin/CTGF 0.005 0.076 0.34 1 -0.39 13 14
alphaM/beta2 Integrin -0.013 0.12 0.21 5 -0.39 43 48
JAM3 homodimer 0.019 0.041 -10000 0 -0.57 5 5
ICAM2 0.019 0.041 -10000 0 -0.57 5 5
ICAM1 0.027 0.027 0.25 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.12 0.22 6 -0.38 45 51
cell adhesion 0.01 0.075 0.33 4 -0.4 6 10
NFKB1 -0.098 0.2 0.41 5 -0.37 339 344
THY1 0.024 0.021 0.25 8 -10000 0 8
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.21 0.19 -10000 0 -0.36 642 642
alphaM/beta2 Integrin/LRP/tPA 0.008 0.09 0.34 1 -0.35 31 32
IL6 -0.26 0.39 0.36 4 -0.76 390 394
ITGB2 -0.002 0.052 0.26 16 -10000 0 16
elevation of cytosolic calcium ion concentration 0.031 0.084 0.33 20 -10000 0 20
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 0.34 1 -0.38 46 47
JAM2 -0.006 0.13 -10000 0 -0.57 54 54
alphaM/beta2 Integrin/ICAM1 0.024 0.086 0.32 4 -0.33 17 21
alphaM/beta2 Integrin/uPA/Plg 0.019 0.07 0.33 1 -10000 0 1
RhoA/GTP -0.018 0.15 0.24 15 -0.45 48 63
positive regulation of phagocytosis -0.002 0.1 0.3 5 -0.36 20 25
Ron/MSP 0.03 0.062 0.36 1 -0.4 18 19
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.086 0.34 20 -10000 0 20
alphaM/beta2 Integrin/uPAR 0.02 0.079 0.29 10 -10000 0 10
PLAU 0.03 0.037 0.25 28 -10000 0 28
PLAT 0.006 0.091 0.25 1 -0.57 26 27
actin filament polymerization -0.011 0.14 0.29 9 -0.45 36 45
MST1 0.021 0.055 0.25 7 -0.57 8 15
alphaM/beta2 Integrin/lipoprotein(a) -0.18 0.17 0.31 1 -0.33 584 585
TNF -0.099 0.2 0.39 3 -0.76 17 20
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.014 0.068 0.34 1 -10000 0 1
fibrinolysis 0.018 0.069 0.32 1 -10000 0 1
HCK 0.027 0.026 0.25 13 -10000 0 13
dendritic cell antigen processing and presentation -0.011 0.12 0.22 6 -0.38 45 51
VTN 0.033 0.077 0.25 69 -0.57 8 77
alphaM/beta2 Integrin/CYR61 -0.007 0.1 0.34 1 -0.38 53 54
LPA 0.018 0.017 0.25 5 -10000 0 5
LRP1 0.018 0.06 -10000 0 -0.57 11 11
cell migration 0.043 0.083 0.28 15 -0.36 8 23
FN1 0.11 0.11 0.25 421 -10000 0 421
alphaM/beta2 Integrin/Thy1 0.01 0.063 0.25 4 -10000 0 4
MPO -0.011 0.14 0.25 2 -0.57 61 63
KNG1 0.023 0.032 0.25 20 -10000 0 20
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.012 0.15 0.29 12 -0.47 38 50
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.021 0.25 8 -10000 0 8
CTGF 0.017 0.066 0.25 3 -0.57 13 16
alphaM/beta2 Integrin/Hck 0.011 0.067 0.35 5 -10000 0 5
ITGAM -0.003 0.043 0.24 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.044 0.16 0.34 1 -0.36 186 187
HP -0.069 0.23 0.25 36 -0.57 176 212
leukocyte adhesion -0.038 0.14 0.28 4 -0.37 60 64
SELP -0.093 0.23 -10000 0 -0.57 206 206
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.013 0.25 3 -10000 0 3
CCL5 0.029 0.056 0.25 37 -0.57 4 41
SDCBP 0.021 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.063 0.12 0.25 35 -0.39 10 45
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 0.049 0.12 0.26 4 -0.38 16 20
Syndecan-1/Syntenin 0.05 0.12 0.28 9 -0.39 13 22
MAPK3 0.047 0.11 0.26 9 -0.36 13 22
HGF/MET -0.066 0.2 -10000 0 -0.44 226 226
TGFB1/TGF beta receptor Type II 0.025 0.013 0.25 3 -10000 0 3
BSG 0.024 0.009 0.25 1 -10000 0 1
keratinocyte migration 0.048 0.12 0.26 4 -0.37 16 20
Syndecan-1/RANTES 0.057 0.13 0.29 42 -0.4 18 60
Syndecan-1/CD147 0.062 0.13 0.3 9 -0.36 16 25
Syndecan-1/Syntenin/PIP2 0.047 0.11 0.26 9 -0.38 13 22
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.045 0.11 0.25 8 -0.37 13 21
MMP7 -0.038 0.19 0.25 32 -0.57 121 153
HGF -0.011 0.14 0.25 2 -0.57 65 67
Syndecan-1/CASK 0.041 0.12 0.19 61 -0.34 20 81
Syndecan-1/HGF/MET -0.006 0.2 0.3 7 -0.45 114 121
regulation of cell adhesion 0.041 0.11 0.25 12 -0.38 9 21
HPSE 0.027 0.034 0.25 17 -0.57 1 18
positive regulation of cell migration 0.063 0.12 0.25 35 -0.39 10 45
SDC1 0.064 0.12 0.27 23 -0.3 22 45
Syndecan-1/Collagen 0.063 0.12 0.25 35 -0.39 10 45
PPIB 0.024 0.013 0.25 3 -10000 0 3
MET -0.074 0.22 -10000 0 -0.57 177 177
PRKACA 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.25 454 -0.57 1 455
MAPK1 0.048 0.11 0.26 10 -0.34 15 25
homophilic cell adhesion 0.061 0.12 0.27 24 -0.37 15 39
MMP1 0.18 0.11 0.25 738 -10000 0 738
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.033 0.074 -10000 0 -0.32 42 42
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.12 -10000 0 -0.41 17 17
AP1 -0.093 0.19 -10000 0 -0.33 387 387
mol:PIP3 -0.13 0.18 -10000 0 -0.34 423 423
AKT1 0.007 0.079 0.32 3 -0.4 12 15
PTK2B -0.027 0.1 -10000 0 -0.31 73 73
RHOA 0.003 0.061 0.26 2 -0.3 27 29
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.11 0.31 2 -0.28 101 103
MAGI3 0.023 0.018 -10000 0 -0.57 1 1
RELA 0.024 0.005 -10000 0 -10000 0 0
apoptosis -0.026 0.12 -10000 0 -0.32 143 143
HRAS/GDP 0.019 0.014 0.18 8 -10000 0 8
positive regulation of microtubule depolymerization -0.051 0.12 0.26 3 -0.3 149 152
NF kappa B1 p50/RelA -0.012 0.12 -10000 0 -0.33 95 95
endothelial cell migration 0.002 0.081 0.26 1 -0.43 33 34
ADCY4 -0.022 0.12 0.24 1 -0.47 49 50
ADCY5 -0.076 0.16 0.24 1 -0.44 99 100
ADCY6 -0.014 0.1 0.24 1 -0.46 35 36
ADCY7 -0.013 0.099 0.24 1 -0.47 34 35
ADCY1 -0.016 0.11 0.24 1 -0.48 40 41
ADCY2 -0.029 0.13 -10000 0 -0.47 57 57
ADCY3 -0.014 0.099 0.24 1 -0.46 35 36
ADCY8 -0.012 0.091 -10000 0 -0.44 31 31
ADCY9 -0.015 0.099 0.24 1 -0.45 37 38
GSK3B -0.026 0.099 0.23 8 -0.33 55 63
arachidonic acid secretion -0.019 0.11 -10000 0 -0.37 69 69
GNG2 0.018 0.06 -10000 0 -0.57 11 11
TRIP6 0.018 0.015 -10000 0 -0.4 1 1
GNAO1 0.002 0.084 -10000 0 -0.36 47 47
HRAS 0.025 0.02 0.25 8 -10000 0 8
NFKBIA -0.02 0.13 0.28 3 -0.34 100 103
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.026 0.12 -10000 0 -0.81 23 23
JUN 0.021 0.044 -10000 0 -0.57 6 6
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.011 0.14 -10000 0 -0.95 23 23
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
mol:IP3 -0.013 0.11 0.28 3 -0.29 101 104
PLCB3 0.025 0.045 0.2 3 -10000 0 3
FOS -0.14 0.27 -10000 0 -0.57 301 301
positive regulation of mitosis -0.019 0.11 -10000 0 -0.37 69 69
LPA/LPA1-2-3 0.002 0.14 -10000 0 -0.33 142 142
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
stress fiber formation -0.016 0.1 -10000 0 -0.37 45 45
GNAZ 0.003 0.069 -10000 0 -0.34 39 39
EGFR/PI3K-beta/Gab1 -0.13 0.2 -10000 0 -0.35 423 423
positive regulation of dendritic cell cytokine production 0 0.14 -10000 0 -0.33 142 142
LPA/LPA2/MAGI-3 0.033 0.02 -10000 0 -0.35 1 1
ARHGEF1 0.018 0.07 -10000 0 -0.3 26 26
GNAI2 0.006 0.06 -10000 0 -0.33 32 32
GNAI3 0.006 0.061 -10000 0 -0.33 32 32
GNAI1 -0.014 0.11 -10000 0 -0.37 83 83
LPA/LPA3 -0.025 0.14 0.18 39 -0.41 123 162
LPA/LPA2 0.019 0.015 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.072 -10000 0 -0.38 34 34
HB-EGF/EGFR -0.081 0.2 0.27 2 -0.34 365 367
HBEGF 0.066 0.073 0.27 24 -0.42 3 27
mol:DAG -0.013 0.11 0.28 3 -0.29 101 104
cAMP biosynthetic process -0.033 0.12 0.29 3 -0.41 63 66
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.28 9 -0.34 83 92
GNAQ -0.02 0.11 0.19 2 -0.31 122 124
LPAR2 0.025 0.01 0.26 2 -10000 0 2
LPAR3 -0.034 0.19 0.25 39 -0.57 119 158
LPAR1 0.012 0.089 -10000 0 -0.49 29 29
IL8 -0.13 0.23 0.34 30 -0.41 365 395
PTK2 -0.022 0.1 0.24 1 -0.32 101 102
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.32 143 143
EGFR -0.19 0.29 -10000 0 -0.57 393 393
PLCG1 -0.022 0.11 0.2 4 -0.32 120 124
PLD2 -0.027 0.12 0.24 1 -0.31 140 141
G12/G13 0.036 0.061 -10000 0 -0.3 30 30
PI3K-beta 0 0.077 -10000 0 -0.33 36 36
cell migration 0.002 0.064 -10000 0 -0.26 22 22
SLC9A3R2 0.023 0.01 0.25 1 -10000 0 1
PXN -0.017 0.11 -10000 0 -0.38 45 45
HRAS/GTP -0.019 0.11 -10000 0 -0.38 69 69
RAC1 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.25 454 -0.57 1 455
PRKCE 0.024 0.003 -10000 0 -10000 0 0
PRKCD -0.014 0.1 0.36 1 -0.41 10 11
Gi(beta/gamma) -0.013 0.11 -10000 0 -0.43 49 49
mol:LPA 0.001 0.016 -10000 0 -0.18 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.013 0.12 -10000 0 -0.44 26 26
MAPKKK cascade -0.019 0.11 -10000 0 -0.37 69 69
contractile ring contraction involved in cytokinesis 0.002 0.063 0.26 2 -0.3 27 29
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.02 0.11 0.21 1 -0.31 127 128
GNA15 -0.018 0.1 0.2 2 -0.31 120 122
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
MAPT -0.052 0.13 0.26 3 -0.31 149 152
GNA11 -0.02 0.11 0.21 1 -0.31 122 123
Rac1/GTP 0.027 0.13 -10000 0 -0.86 23 23
MMP2 0.002 0.082 0.26 1 -0.43 33 34
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.028 0.22 0.53 9 -0.65 27 36
CRP -0.007 0.24 0.63 9 -0.71 18 27
cell cycle arrest -0.039 0.25 0.54 13 -0.67 47 60
TIMP1 -0.021 0.21 0.51 12 -0.6 27 39
IL6ST -0.037 0.19 -10000 0 -0.56 119 119
Rac1/GDP -0.069 0.2 0.3 9 -0.48 99 108
AP1 -0.072 0.21 0.37 1 -0.59 50 51
GAB2 0.022 0.02 -10000 0 -0.57 1 1
TNFSF11 -0.018 0.24 0.59 12 -0.66 26 38
HSP90B1 0.022 0.11 -10000 0 -0.74 13 13
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.096 0.18 -10000 0 -0.54 85 85
AKT1 0.023 0.066 -10000 0 -0.66 4 4
FOXO1 0.023 0.068 0.43 1 -0.59 4 5
MAP2K6 -0.096 0.19 0.27 2 -0.51 106 108
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.053 0.2 0.38 13 -0.49 82 95
MITF -0.09 0.19 0.26 11 -0.41 174 185
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.004 -10000 0 -10000 0 0
A2M -0.001 0.18 -10000 0 -1.2 24 24
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.018 0.13 -10000 0 -0.52 33 33
STAT3 -0.046 0.26 0.54 13 -0.73 48 61
STAT1 0.012 0.093 -10000 0 -0.83 10 10
CEBPD -0.014 0.23 0.54 17 -0.68 29 46
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.048 -10000 0 -0.4 12 12
JUN 0.02 0.044 -10000 0 -0.57 6 6
PIAS3/MITF -0.072 0.18 0.32 2 -0.46 97 99
MAPK11 -0.095 0.18 -10000 0 -0.53 89 89
STAT3 (dimer)/FOXO1 -0.025 0.22 0.51 13 -0.58 37 50
GRB2/SOS1/GAB family -0.061 0.18 -10000 0 -0.5 71 71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.19 -10000 0 -0.41 179 179
GRB2 0.023 0.009 0.25 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.17 0.45 0.54 24 -0.93 256 280
PIK3R1 0.018 0.063 -10000 0 -0.57 12 12
JAK1 0.026 0.008 -10000 0 -10000 0 0
MYC -0.004 0.27 0.56 16 -0.96 33 49
FGG -0.026 0.23 0.59 13 -0.64 32 45
macrophage differentiation -0.039 0.25 0.54 13 -0.67 47 60
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.093 0.21 -10000 0 -0.35 356 356
JUNB -0.03 0.22 0.5 10 -0.63 29 39
FOS -0.14 0.27 -10000 0 -0.57 301 301
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.093 0.2 0.29 11 -0.42 180 191
STAT1/PIAS1 -0.061 0.2 0.35 11 -0.39 168 179
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.07 -10000 0 -0.55 7 7
STAT3 (dimer) -0.044 0.26 0.54 13 -0.72 46 59
PRKCD -0.037 0.2 0.42 23 -0.53 56 79
IL6R 0.001 0.11 -10000 0 -0.57 38 38
SOCS3 -0.092 0.19 -10000 0 -0.71 37 37
gp130 (dimer)/JAK1/JAK1/LMO4 0.012 0.13 -10000 0 -0.35 119 119
Rac1/GTP -0.064 0.2 0.34 10 -0.48 96 106
HCK 0.027 0.026 0.25 13 -10000 0 13
MAPKKK cascade -0.002 0.14 -10000 0 -0.64 27 27
bone resorption -0.015 0.23 0.59 12 -0.62 27 39
IRF1 -0.031 0.22 0.52 10 -0.65 28 38
mol:GDP -0.084 0.19 0.28 12 -0.41 172 184
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.085 0.2 0.28 12 -0.41 172 184
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.2 -10000 0 -0.61 87 87
PTPN11 0.011 0.081 -10000 0 -0.84 8 8
IL6/IL6RA -0.12 0.22 -10000 0 -0.43 320 320
gp130 (dimer)/TYK2/TYK2/LMO4 0.007 0.13 -10000 0 -0.35 119 119
gp130 (dimer)/JAK2/JAK2/LMO4 0.007 0.13 -10000 0 -0.35 113 113
IL6 -0.18 0.29 0.27 1 -0.57 379 380
PIAS3 0.02 0.009 -10000 0 -10000 0 0
PTPRE 0.008 0.03 -10000 0 -0.57 1 1
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.11 0.19 0.22 2 -0.34 329 331
LMO4 0.028 0.036 0.28 2 -0.57 3 5
STAT3 (dimer)/PIAS3 -0.049 0.24 0.53 10 -0.68 48 58
MCL1 0.053 0.098 0.49 1 -0.58 4 5
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.041 0.14 0.34 72 -0.32 67 139
TBX21 0.015 0.34 0.73 24 -1.2 55 79
B2M 0.025 0.012 -10000 0 -10000 0 0
TYK2 0.024 0.036 0.19 1 -10000 0 1
IL12RB1 0.032 0.071 0.31 42 -0.6 2 44
GADD45B 0.037 0.26 0.64 21 -0.9 31 52
IL12RB2 0.028 0.15 0.26 126 -0.57 43 169
GADD45G 0.055 0.26 0.67 24 -0.9 29 53
natural killer cell activation 0.007 0.025 0.079 55 -0.042 29 84
RELB 0.026 0.022 0.25 10 -10000 0 10
RELA 0.024 0.005 -10000 0 -10000 0 0
IL18 0.033 0.038 0.27 23 -10000 0 23
IL2RA 0.027 0.088 0.25 58 -0.57 15 73
IFNG 0.054 0.08 0.25 146 -10000 0 146
STAT3 (dimer) 0.035 0.24 0.55 39 -0.67 52 91
HLA-DRB5 -0.006 0.011 -10000 0 -0.025 249 249
FASLG 0.049 0.31 0.72 33 -1 43 76
NF kappa B2 p52/RelB 0.022 0.25 0.67 5 -0.76 56 61
CD4 0.01 0.024 -10000 0 -10000 0 0
SOCS1 0.025 0.033 0.25 14 -0.57 1 15
EntrezGene:6955 -0.005 0.015 0.023 56 -0.028 280 336
CD3D 0.009 0.098 0.26 48 -0.58 19 67
CD3E 0.01 0.089 0.26 37 -0.57 16 53
CD3G 0 0.12 0.26 38 -0.58 33 71
IL12Rbeta2/JAK2 0.036 0.12 0.28 37 -0.43 44 81
CCL3 0.034 0.28 0.68 24 -0.92 38 62
CCL4 0.035 0.27 0.7 21 -0.91 35 56
HLA-A 0.002 0.008 0.023 72 -0.044 14 86
IL18/IL18R 0.065 0.12 0.38 15 -0.37 52 67
NOS2 0.032 0.28 0.68 22 -1 32 54
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.15 0.34 64 -0.33 66 130
IL1R1 0.018 0.31 0.69 21 -1.1 44 65
IL4 -0.011 0.037 -10000 0 -0.18 1 1
JAK2 0.023 0.035 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.014 0.022 58 -0.026 246 304
TCR/CD3/MHC I/CD8 -0.025 0.22 0.37 33 -0.65 76 109
RAB7A 0.052 0.24 0.64 19 -0.8 24 43
lysosomal transport 0.053 0.23 0.61 23 -0.75 24 47
FOS -0.32 0.62 0.58 15 -1.2 346 361
STAT4 (dimer) 0.062 0.28 0.6 35 -0.85 47 82
STAT5A (dimer) 0.047 0.28 0.58 56 -0.75 57 113
GZMA 0.025 0.29 0.7 27 -1.1 34 61
GZMB 0.023 0.32 0.69 30 -1.1 45 75
HLX 0.021 0.015 0.25 3 -10000 0 3
LCK 0.028 0.29 0.66 36 -0.84 59 95
TCR/CD3/MHC II/CD4 -0.054 0.17 0.24 27 -0.32 214 241
IL2/IL2R 0.065 0.098 0.4 39 -0.36 21 60
MAPK14 0.048 0.27 0.64 26 -0.9 34 60
CCR5 0.037 0.27 0.67 30 -0.83 40 70
IL1B 0.017 0.081 0.26 4 -0.58 15 19
STAT6 0.04 0.12 0.4 33 -0.6 7 40
STAT4 0.001 0.12 0.25 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.03 0.25 19 -10000 0 19
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.008 0.25 1 -10000 0 1
IL12B 0.072 0.11 0.28 228 -10000 0 228
CD8A 0.029 0.059 0.28 29 -0.57 5 34
CD8B 0.014 0.11 0.27 30 -0.57 32 62
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.041 0.14 0.32 67 -0.34 72 139
IL2RB 0.03 0.05 0.25 38 -0.57 2 40
proteasomal ubiquitin-dependent protein catabolic process 0.066 0.26 0.57 42 -0.76 47 89
IL2RG 0.03 0.067 0.25 46 -0.57 7 53
IL12 0.049 0.15 0.29 103 -0.42 61 164
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
CD247 0.006 0.079 0.26 16 -0.57 15 31
IL2 0.022 0.021 0.25 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.006 0.15 0.29 18 -0.58 60 78
IL12/IL12R/TYK2/JAK2 0.034 0.3 0.67 42 -0.86 56 98
MAP2K3 0.042 0.28 0.63 28 -0.85 44 72
RIPK2 0.02 0.016 0.25 3 -10000 0 3
MAP2K6 0.046 0.27 0.63 28 -0.86 38 66
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.013 -10000 0 -0.028 283 283
IL18RAP 0.011 0.11 0.28 5 -0.57 36 41
IL12Rbeta1/TYK2 0.041 0.068 0.28 37 -0.46 2 39
EOMES -0.021 0.18 -10000 0 -1 30 30
STAT1 (dimer) 0.067 0.26 0.6 66 -0.72 40 106
T cell proliferation 0.05 0.22 0.52 26 -0.65 42 68
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.078 -10000 0 -0.57 18 18
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.012 0.19 0.49 1 -0.73 39 40
ATF2 0.046 0.25 0.6 26 -0.82 34 60
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.081 -10000 0 -0.33 2 2
epithelial cell differentiation 0.032 0.08 0.39 1 -0.43 3 4
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.022 0.097 0.46 8 -10000 0 8
FYN 0.022 0.026 -10000 0 -0.57 2 2
EGFR -0.19 0.28 -10000 0 -0.57 393 393
PRL 0.022 0.024 0.25 11 -10000 0 11
neuron projection morphogenesis -0.042 0.14 0.35 12 -0.36 34 46
PTPRZ1 -0.28 0.3 0.25 6 -0.57 544 550
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.14 -10000 0 -0.38 42 42
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.088 0.16 -10000 0 -0.34 241 241
ADAM17 0.032 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.007 0.074 0.38 8 -0.3 6 14
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.11 -10000 0 -0.36 42 42
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.08 0.15 -10000 0 -0.33 221 221
GRIN2B -0.098 0.16 -10000 0 -0.41 83 83
ErbB4/ErbB2/betacellulin 0.013 0.097 -10000 0 -0.32 32 32
STAT1 0.028 0.03 0.25 19 -10000 0 19
HBEGF 0.023 0.026 -10000 0 -0.57 2 2
PRLR 0.021 0.051 0.25 6 -0.57 7 13
E4ICDs/ETO2 0.006 0.087 0.35 1 -0.4 11 12
axon guidance 0.054 0.11 0.39 9 -0.37 2 11
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.031 0.041 -10000 0 -0.39 7 7
CBFA2T3 0.014 0.071 0.25 4 -0.57 15 19
ErbB4/ErbB2/HBEGF 0.03 0.072 -10000 0 -0.34 3 3
MAPK3 -0.048 0.14 0.34 4 -0.37 36 40
STAT1 (dimer) 0.019 0.081 0.28 1 -10000 0 1
MAPK1 -0.048 0.14 0.36 5 -0.37 36 41
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.072 0.15 0.27 1 -0.38 64 65
NRG1 -0.1 0.19 -10000 0 -0.42 288 288
NRG3 -0.002 0.13 0.25 22 -0.57 53 75
NRG2 -0.26 0.3 -10000 0 -0.57 509 509
NRG4 0.027 0.027 0.25 15 -10000 0 15
heart development 0.054 0.11 0.39 9 -0.37 2 11
neural crest cell migration -0.071 0.15 0.27 1 -0.38 66 67
ERBB2 0.035 0.071 0.27 87 -0.41 1 88
WWOX/E4ICDs 0.011 0.076 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.099 0.16 -10000 0 -0.32 281 281
apoptosis 0.014 0.13 0.46 49 -10000 0 49
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.15 0.18 -10000 0 -0.34 386 386
ErbB4/ErbB2/epiregulin 0.005 0.13 0.35 12 -0.31 80 92
ErbB4/ErbB4/betacellulin/betacellulin -0.004 0.11 0.28 1 -0.36 42 43
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.04 0.087 0.39 1 -0.4 6 7
MDM2 0.008 0.079 0.28 8 -10000 0 8
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.083 0.15 -10000 0 -0.32 237 237
STAT5A 0.049 0.11 0.36 13 -0.37 3 16
ErbB4/EGFR/neuregulin 1 beta -0.19 0.23 -10000 0 -0.49 294 294
DLG4 0.022 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.01 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.059 0.1 0.45 1 -0.46 3 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.11 0.35 7 -0.35 3 10
LRIG1 0.022 0.032 -10000 0 -0.57 3 3
EREG -0.027 0.2 0.25 77 -0.57 120 197
BTC -0.008 0.13 0.25 2 -0.57 57 59
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.045 0.11 0.4 8 -0.38 2 10
ERBB4 -0.007 0.074 0.38 8 -0.3 6 14
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
YAP1 -0.014 0.11 0.22 3 -0.39 76 79
GRB2 0.023 0.009 0.25 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.033 0.071 0.31 1 -0.41 1 2
glial cell differentiation -0.01 0.07 -10000 0 -10000 0 0
WWOX 0.021 0.013 0.25 2 -10000 0 2
cell proliferation -0.038 0.17 0.36 13 -0.54 25 38
Ephrin A reverse signaling

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
MAPKKK cascade -0.005 0.11 -10000 0 -0.36 96 96
EFNA5 -0.029 0.17 0.25 1 -0.57 96 97
FYN -0.023 0.099 -10000 0 -0.33 96 96
neuron projection morphogenesis -0.005 0.11 -10000 0 -0.36 96 96
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.005 0.11 -10000 0 -0.36 96 96
EPHA5 0.023 0.016 0.25 5 -10000 0 5
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.04 0.22 0.43 4 -0.67 98 102
IHH 0.016 0.081 0.26 31 -0.26 1 32
SHH Np/Cholesterol/GAS1 0 0.076 -10000 0 -0.33 49 49
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0 0.075 0.33 49 -10000 0 49
SMO/beta Arrestin2 -0.018 0.21 -10000 0 -0.62 96 96
SMO -0.041 0.21 0.32 1 -0.65 96 97
AKT1 -0.003 0.13 -10000 0 -0.53 30 30
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.019 0.15 -10000 0 -0.57 77 77
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.04 0.21 0.32 1 -0.64 96 97
STIL 0.007 0.17 0.3 29 -0.48 84 113
DHH N/PTCH2 -0.01 0.14 -10000 0 -0.44 101 101
DHH N/PTCH1 -0.027 0.2 -10000 0 -0.55 121 121
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.008 0.097 0.25 2 -0.57 29 31
PTHLH -0.061 0.3 0.51 2 -0.88 105 107
determination of left/right symmetry -0.04 0.21 0.32 1 -0.64 96 97
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
skeletal system development -0.06 0.29 0.51 2 -0.86 105 107
IHH N/Hhip 0.027 0.056 0.25 1 -0.46 2 3
DHH N/Hhip 0.022 0.077 -10000 0 -0.42 31 31
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.04 0.21 0.32 1 -0.64 96 97
pancreas development 0.023 0.031 0.25 6 -0.57 2 8
HHAT 0.02 0.02 -10000 0 -0.57 1 1
PI3K 0.028 0.048 -10000 0 -0.4 12 12
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.57 60 60
somite specification -0.04 0.21 0.32 1 -0.64 96 97
SHH Np/Cholesterol/PTCH1 -0.024 0.16 0.3 1 -0.5 87 88
SHH Np/Cholesterol/PTCH2 -0.005 0.084 -10000 0 -0.33 61 61
SHH Np/Cholesterol/Megalin -0.06 0.15 0.28 3 -0.33 229 232
SHH 0 0.037 0.34 7 -0.42 1 8
catabolic process -0.033 0.21 0.31 2 -0.57 122 124
SMO/Vitamin D3 -0.009 0.2 0.35 16 -0.57 87 103
SHH Np/Cholesterol/Hhip 0.015 0.03 0.28 4 -0.34 3 7
LRP2 -0.12 0.26 0.25 26 -0.57 276 302
receptor-mediated endocytosis -0.079 0.22 0.3 10 -0.63 98 108
SHH Np/Cholesterol/BOC -0.004 0.084 -10000 0 -0.33 62 62
SHH Np/Cholesterol/CDO 0.012 0.042 -10000 0 -0.33 13 13
mesenchymal cell differentiation -0.015 0.03 0.33 3 -0.28 4 7
mol:Vitamin D3 0.002 0.18 0.34 20 -0.5 86 106
IHH N/PTCH2 -0.008 0.14 -10000 0 -0.47 79 79
CDON 0.014 0.067 -10000 0 -0.57 14 14
IHH N/PTCH1 -0.024 0.21 0.35 4 -0.57 122 126
Megalin/LRPAP1 -0.08 0.2 -10000 0 -0.42 279 279
PTCH2 -0.02 0.16 -10000 0 -0.57 79 79
SHH Np/Cholesterol 0.01 0.013 -10000 0 -0.33 1 1
PTCH1 -0.033 0.21 0.31 2 -0.57 122 124
HHIP 0.023 0.031 0.25 6 -0.57 2 8
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.014 0.14 0.42 85 -0.24 2 87
KIRREL -0.024 0.16 -10000 0 -0.57 87 87
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.014 0.14 0.24 2 -0.42 85 87
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.034 0.12 0.28 4 -0.32 84 88
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.008 0.089 0.24 1 -0.28 71 72
FYN 0.02 0.13 0.28 97 -0.31 83 180
mol:Ca2+ 0.031 0.11 0.31 1 -0.32 79 80
mol:DAG 0.032 0.11 0.31 1 -0.32 79 80
NPHS2 0.014 0.032 0.26 5 -10000 0 5
mol:IP3 0.032 0.11 0.31 1 -0.32 79 80
regulation of endocytosis 0.023 0.1 0.24 4 -0.29 83 87
Nephrin/NEPH1/podocin/Cholesterol 0.023 0.11 0.25 9 -0.32 84 93
establishment of cell polarity 0.014 0.14 0.24 2 -0.42 85 87
Nephrin/NEPH1/podocin/NCK1-2 0.043 0.11 0.32 1 -0.3 82 83
Nephrin/NEPH1/beta Arrestin2 0.026 0.11 0.25 4 -0.29 83 87
NPHS1 0.059 0.09 0.26 168 -10000 0 168
Nephrin/NEPH1/podocin 0.025 0.11 0.3 4 -0.31 83 87
TJP1 0.023 0.019 -10000 0 -0.57 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.033 0.12 0.32 1 -0.32 79 80
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.031 0.12 0.3 4 -0.32 81 85
GRB2 0.023 0.009 0.25 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.012 0.13 0.29 94 -0.31 89 183
cytoskeleton organization 0.003 0.11 0.27 16 -0.33 67 83
Nephrin/NEPH1 0.016 0.1 0.2 2 -0.3 85 87
Nephrin/NEPH1/ZO-1 0.025 0.12 -10000 0 -0.34 85 85
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 -0.033 0.15 -10000 0 -0.59 66 66
PDGF/PDGFRA/CRKL -0.011 0.11 -10000 0 -0.42 65 65
positive regulation of JUN kinase activity 0.024 0.084 -10000 0 -0.33 47 47
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.014 0.11 -10000 0 -0.43 67 67
AP1 -0.3 0.44 -10000 0 -0.96 319 319
mol:IP3 -0.036 0.11 -10000 0 -0.45 63 63
PLCG1 -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA/alphaV Integrin -0.011 0.11 -10000 0 -0.43 66 66
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.11 -10000 0 -0.45 63 63
CAV3 0.02 0.011 0.25 2 -10000 0 2
CAV1 -0.099 0.24 -10000 0 -0.57 222 222
SHC/Grb2/SOS1 0.026 0.085 -10000 0 -0.33 47 47
PDGF/PDGFRA/Shf -0.011 0.11 -10000 0 -0.42 67 67
FOS -0.29 0.43 0.32 1 -0.94 319 320
JUN -0.037 0.044 -10000 0 -0.44 6 6
oligodendrocyte development -0.011 0.11 -10000 0 -0.43 66 66
GRB2 0.023 0.009 0.25 1 -10000 0 1
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
mol:DAG -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA -0.033 0.15 -10000 0 -0.59 66 66
actin cytoskeleton reorganization -0.011 0.11 -10000 0 -0.42 66 66
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.012 0.11 -10000 0 -0.38 71 71
PDGF/PDGFRA/Crk/C3G 0.015 0.098 -10000 0 -0.36 66 66
JAK1 -0.027 0.1 0.23 1 -0.43 65 66
ELK1/SRF -0.035 0.091 0.32 1 -0.35 64 65
SHB 0.024 0.008 0.25 1 -10000 0 1
SHF 0.024 0.021 0.25 2 -0.57 1 3
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.047 0.11 0.22 1 -0.47 65 66
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.084 -10000 0 -0.33 47 47
PDGF/PDGFRA/SHB -0.011 0.11 -10000 0 -0.42 66 66
PDGF/PDGFRA/Caveolin-1 -0.099 0.22 -10000 0 -0.48 253 253
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.053 0.11 0.24 1 -0.43 65 66
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.012 0.11 -10000 0 -0.42 66 66
JAK-STAT cascade -0.027 0.1 0.23 1 -0.42 65 66
cell proliferation -0.011 0.11 -10000 0 -0.42 67 67
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.033 0.043 -10000 0 -0.31 13 13
RGS9BP 0.036 0.053 0.25 59 -10000 0 59
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.016 0.25 4 -10000 0 4
mol:Na + 0.037 0.045 -10000 0 -10000 0 0
mol:ADP -0.006 0.025 0.25 5 -10000 0 5
GNAT2 0.024 0.013 0.25 3 -10000 0 3
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 87 88
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.014 -10000 0 -10000 0 0
GRK7 0.023 0.019 0.25 7 -10000 0 7
CNGB3 0.022 0.037 0.25 25 -10000 0 25
Cone Metarhodopsin II/X-Arrestin 0.015 0.014 0.18 8 -10000 0 8
mol:Ca2+ 0.12 0.1 0.26 228 -10000 0 228
Cone PDE6 0.03 0.11 0.3 3 -0.32 83 86
Cone Metarhodopsin II 0.025 0.017 -10000 0 -10000 0 0
Na + (4 Units) 0.11 0.092 0.31 69 -10000 0 69
GNAT2/GDP 0.025 0.1 0.29 2 -0.31 86 88
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.033 0.21 3 -10000 0 3
Cone Transducin 0.036 0.046 -10000 0 -0.33 13 13
SLC24A2 0.16 0.12 0.25 621 -10000 0 621
GNB3/GNGT2 0.027 0.053 -10000 0 -0.39 15 15
GNB3 0.018 0.065 0.25 5 -0.57 12 17
GNAT2/GTP 0.018 0.009 0.18 3 -10000 0 3
CNGA3 0.045 0.067 0.25 101 -10000 0 101
ARR3 0.021 0.02 0.25 8 -10000 0 8
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.038 0.045 -10000 0 -10000 0 0
mol:Pi 0.016 0.12 0.33 1 -0.36 87 88
Cone CNG Channel 0.05 0.043 0.28 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.16 0.12 0.25 621 -10000 0 621
RGS9 -0.024 0.17 0.25 11 -0.57 89 100
PDE6C 0.019 0.008 0.25 1 -10000 0 1
GNGT2 0.021 0.026 -10000 0 -0.57 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.25 5 -10000 0 5
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.035 0.1 0.99 2 -10000 0 2
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.024 0.12 -10000 0 -0.38 10 10
RXRs/LXRs/DNA/Oxysterols -0.005 0.12 -10000 0 -0.42 15 15
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.004 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0.001 0.083 -10000 0 -0.3 62 62
RXRs/NUR77 -0.047 0.18 -10000 0 -0.35 257 257
RXRs/PPAR -0.099 0.17 -10000 0 -0.32 343 343
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.048 0.042 -10000 0 -0.31 11 11
RARA 0.023 0.01 0.25 1 -10000 0 1
NCOA1 0.024 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.037 0.04 -10000 0 -0.31 11 11
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.071 0.18 0.61 99 -10000 0 99
RARs/THRs/DNA/SMRT 0.002 0.079 -10000 0 -0.29 60 60
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.028 0.15 -10000 0 -0.32 213 213
NR1H4 0.021 0.026 0.25 13 -10000 0 13
RXRs/LXRs/DNA -0.006 0.15 -10000 0 -0.31 194 194
NR1H2 0.027 0.012 -10000 0 -10000 0 0
NR1H3 0.028 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.021 0.15 -10000 0 -0.31 212 212
NR4A1 -0.023 0.16 -10000 0 -0.57 86 86
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.031 0.1 -10000 0 -0.23 188 188
RXRG -0.097 0.24 0.26 2 -0.57 217 219
RXR alpha/CCPG 0.036 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.012 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB -0.006 0.13 -10000 0 -0.57 55 55
PPARG -0.11 0.25 -10000 0 -0.57 247 247
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.009 0.14 -10000 0 -1 10 10
mol:Oxysterols 0.004 0.009 -10000 0 -10000 0 0
cholesterol transport -0.004 0.12 -10000 0 -0.42 15 15
PPARA 0.02 0.041 -10000 0 -0.57 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.017 0.065 -10000 0 -0.57 13 13
RXRs/NUR77/BCL2 -0.067 0.15 -10000 0 -0.3 274 274
SREBF1 -0.005 0.11 0.44 1 -0.57 1 2
RXRs/RXRs/DNA/9cRA -0.028 0.15 -10000 0 -0.32 213 213
ABCA1 -0.009 0.13 -10000 0 -0.85 8 8
RARs/THRs 0.04 0.096 -10000 0 -0.33 59 59
RXRs/FXR -0.024 0.16 -10000 0 -0.33 213 213
BCL2 0.008 0.095 -10000 0 -0.57 28 28
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.022 0.026 -10000 0 -0.57 2 2
LAT2 -0.02 0.1 -10000 0 -0.36 57 57
AP1 -0.057 0.18 -10000 0 -0.44 118 118
mol:PIP3 0.008 0.17 0.34 48 -0.43 53 101
IKBKB 0.033 0.13 0.28 120 -0.26 28 148
AKT1 0.012 0.17 0.32 146 -0.44 22 168
IKBKG 0.015 0.11 0.25 74 -0.27 32 106
MS4A2 -0.022 0.15 0.25 5 -0.55 82 87
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.12 0.28 34 -0.39 32 66
mol:Ca2+ 0.014 0.14 0.3 56 -0.32 51 107
LYN 0.022 0.012 -10000 0 -10000 0 0
CBLB -0.019 0.1 -10000 0 -0.36 56 56
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0.001 0.12 -10000 0 -0.33 123 123
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.005 0.17 0.33 126 -0.33 137 263
PTPN13 -0.015 0.15 -10000 0 -0.56 43 43
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.012 0.13 0.32 40 -0.34 30 70
SYK 0.025 0.01 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.25 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.027 0.13 -10000 0 -0.43 55 55
LAT -0.019 0.1 -10000 0 -0.36 57 57
PAK2 0.011 0.13 0.27 40 -0.43 31 71
NFATC2 -0.049 0.16 -10000 0 -0.61 75 75
HRAS 0.008 0.13 0.26 24 -0.45 35 59
GAB2 0.021 0.02 -10000 0 -0.57 1 1
PLA2G1B 0.003 0.098 -10000 0 -0.84 12 12
Fc epsilon R1 -0.022 0.16 -10000 0 -0.4 144 144
Antigen/IgE/Fc epsilon R1 -0.018 0.14 -10000 0 -0.37 144 144
mol:GDP -0.015 0.12 0.25 1 -0.46 34 35
JUN 0.02 0.044 -10000 0 -0.57 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.017 0.063 -10000 0 -0.57 12 12
FOS -0.14 0.27 -10000 0 -0.57 301 301
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.37 61 61
CHUK 0.015 0.11 0.25 73 -0.27 32 105
KLRG1 -0.018 0.097 -10000 0 -0.32 58 58
VAV1 -0.021 0.1 -10000 0 -0.37 57 57
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.1 -10000 0 -0.36 55 55
negative regulation of mast cell degranulation -0.007 0.099 -10000 0 -0.38 32 32
BTK -0.013 0.12 -10000 0 -0.48 32 32
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.03 0.13 -10000 0 -0.36 117 117
GAB2/PI3K/SHP2 -0.048 0.1 -10000 0 -0.34 84 84
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 -10000 0 -0.31 96 96
RAF1 0.002 0.1 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0 0.15 -10000 0 -0.35 146 146
FCER1G 0.019 0.017 0.25 1 -10000 0 1
FCER1A -0.045 0.18 -10000 0 -0.58 115 115
Antigen/IgE/Fc epsilon R1/Fyn -0.009 0.14 -10000 0 -0.35 140 140
MAPK3 0.003 0.099 -10000 0 -0.86 12 12
MAPK1 -0.002 0.1 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.18 -10000 0 -0.59 69 69
DUSP1 -0.045 0.19 -10000 0 -0.57 125 125
NF-kappa-B/RelA 0.007 0.059 0.14 6 -0.18 15 21
actin cytoskeleton reorganization -0.007 0.15 -10000 0 -0.58 36 36
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.12 -10000 0 -0.45 32 32
FER -0.021 0.11 -10000 0 -0.37 61 61
RELA 0.024 0.005 -10000 0 -10000 0 0
ITK -0.012 0.091 -10000 0 -0.4 48 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.004 0.14 0.28 9 -0.48 32 41
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.018 0.1 0.21 2 -0.36 57 59
PTK2 -0.009 0.16 -10000 0 -0.61 36 36
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.024 0.14 -10000 0 -0.44 59 59
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.006 0.16 0.32 44 -0.42 61 105
MAP2K2 -0.001 0.098 -10000 0 -0.85 12 12
MAP2K1 0 0.099 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.095 0.2 1 -0.37 31 32
MAP2K4 -0.072 0.29 -10000 0 -0.83 133 133
Fc epsilon R1/FcgammaRIIB -0.008 0.15 -10000 0 -0.37 146 146
mol:Choline -0.004 0.17 0.33 126 -0.33 137 263
SHC/Grb2/SOS1 0.011 0.11 -10000 0 -0.42 28 28
FYN 0.022 0.026 -10000 0 -0.57 2 2
DOK1 0.025 0.014 0.25 4 -10000 0 4
PXN -0.009 0.14 -10000 0 -0.55 36 36
HCLS1 -0.019 0.1 -10000 0 -0.36 57 57
PRKCB 0.013 0.14 0.28 72 -0.37 37 109
FCGR2B 0.018 0.038 0.25 1 -0.57 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.007 0.1 -10000 0 -0.38 32 32
LCP2 0.024 0.008 0.26 1 -10000 0 1
PLA2G4A -0.046 0.14 -10000 0 -0.37 131 131
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.17 0.33 126 -0.33 137 263
IKK complex 0.031 0.11 0.25 121 -0.21 15 136
WIPF1 0.024 0.003 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.022 0.021 0.24 2 -10000 0 2
AES 0.022 0.019 0.21 2 -10000 0 2
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.009 0.093 0.25 2 -0.57 27 29
TLE1 0.019 0.048 0.2 2 -0.58 6 8
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.3 42 -0.36 5 47
WIF1 -0.28 0.3 0.25 12 -0.57 547 559
beta catenin/RanBP3 0.02 0.089 0.42 37 -0.4 1 38
KREMEN2 0.12 0.12 0.25 471 -10000 0 471
DKK1 0.025 0.16 0.25 146 -0.57 55 201
beta catenin/beta TrCP1 0.11 0.094 0.3 33 -0.35 3 36
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.015 0.26 0.59 82 -1.3 22 104
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.047 0.076 -10000 0 -0.53 14 14
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.13 0.33 3 -0.58 23 26
Axin1/APC/GSK3 0.047 0.053 0.24 2 -0.31 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.044 0.063 0.31 2 -0.4 4 6
HNF1A 0.025 0.028 0.25 11 -10000 0 11
CTBP1 0.021 0.02 0.24 3 -10000 0 3
MYC 0.11 0.33 0.58 253 -1.3 24 277
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.098 0.34 1 -0.33 21 22
NKD1 0.022 0.053 0.25 16 -0.57 6 22
TCF4 0.016 0.059 0.23 2 -0.56 10 12
TCF3 0.022 0.022 0.27 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.057 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.004 0.12 0.45 36 -0.5 15 51
LEF1 0.05 0.08 0.25 132 -0.53 1 133
DVL1 0.056 0.053 0.22 1 -0.36 2 3
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.14 0.29 10 -0.6 29 39
DKK1/LRP6/Kremen 2 0.098 0.14 0.34 80 -0.34 48 128
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.24 2 -10000 0 2
NLK 0.023 0.014 0.25 2 -10000 0 2
CCND1 0.091 0.26 0.61 178 -1.2 6 184
WNT1 0.024 0.011 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.055 0.29 5 -0.3 9 14
APC 0.016 0.056 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.22 521 -0.24 1 522
CREBBP 0.021 0.018 0.27 1 -10000 0 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.001 0.064 0.22 2 -0.32 10 12
adherens junction organization -0.013 0.092 0.22 1 -0.34 51 52
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.086 0.15 0.34 3 -0.33 116 119
FMN1 -0.013 0.088 -10000 0 -0.31 57 57
mol:IP3 -0.001 0.053 -10000 0 -0.27 12 12
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.087 -10000 0 -0.32 49 49
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.002 0.063 -10000 0 -0.28 12 12
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.53 37 37
CTNND1 0.024 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.076 -10000 0 -0.3 45 45
VASP -0.009 0.081 -10000 0 -0.3 46 46
ZYX -0.009 0.081 -10000 0 -0.3 48 48
JUB -0.009 0.083 -10000 0 -0.3 49 49
EGFR(dimer) -0.11 0.18 -10000 0 -0.32 379 379
E-cadherin/beta catenin-gamma catenin 0.032 0.058 -10000 0 -0.35 20 20
mol:PI-3-4-5-P3 0.016 0.073 -10000 0 -0.28 18 18
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.016 0.074 -10000 0 -0.28 18 18
FYN -0.003 0.067 -10000 0 -0.35 7 7
mol:Ca2+ -0.001 0.052 -10000 0 -0.27 12 12
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.018 0.063 -10000 0 -0.57 12 12
mol:DAG -0.001 0.053 -10000 0 -0.27 12 12
CDH1 0.011 0.08 -10000 0 -0.57 20 20
RhoA/GDP -0.085 0.15 0.36 2 -0.34 110 112
establishment of polarity of embryonic epithelium -0.009 0.08 -10000 0 -0.3 46 46
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.57 393 393
CASR -0.003 0.055 0.23 2 -0.27 9 11
RhoA/GTP 0.014 0.057 -10000 0 -0.26 9 9
AKT2 0.001 0.063 -10000 0 -0.29 10 10
actin cable formation -0.017 0.089 0.25 2 -0.33 45 47
apoptosis -0.005 0.073 0.28 22 -0.23 10 32
CTNNA1 0.024 0.006 -10000 0 -10000 0 0
mol:GDP -0.099 0.15 -10000 0 -0.3 347 347
PIP5K1A -0.008 0.077 -10000 0 -0.31 45 45
PLCG1 -0.001 0.054 -10000 0 -0.28 12 12
Rac1/GTP -0.093 0.17 -10000 0 -0.3 370 370
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.084 -10000 0 -0.43 23 23
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.028 0.17 -10000 0 -0.57 94 94
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.045 -10000 0 -0.57 6 6
AP1 -0.073 0.15 -10000 0 -0.31 285 285
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.021 0.036 -10000 0 -0.57 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.014 0.1 -10000 0 -0.63 19 19
NICD/RBPSUH 0.02 0.081 -10000 0 -0.42 25 25
WIF1 -0.28 0.3 0.25 12 -0.57 547 559
NOTCH1 0.008 0.075 -10000 0 -0.43 29 29
PSENEN 0.024 0.008 0.25 1 -10000 0 1
KREMEN2 0.12 0.12 0.25 471 -10000 0 471
DKK1 0.025 0.16 0.25 146 -0.57 55 201
beta catenin/beta TrCP1 0.009 0.066 -10000 0 -0.34 6 6
APH1B 0.023 0.019 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.01 0.061 -10000 0 -0.45 9 9
CtBP/CBP/TCF1/TLE1/AES 0.012 0.039 -10000 0 -0.29 6 6
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 301 301
JUN 0.02 0.044 -10000 0 -0.57 6 6
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 0 0.066 0.25 1 -0.37 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.098 0.34 1 -0.33 21 22
HNF1A 0.026 0.02 0.25 8 -10000 0 8
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.013 0.21 -10000 0 -1.3 27 27
NKD1 0.022 0.053 0.25 16 -0.57 6 22
FZD1 0.024 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.006 0.12 -10000 0 -0.49 20 20
apoptosis -0.073 0.15 -10000 0 -0.31 285 285
Delta 1/NOTCHprecursor 0.019 0.083 -10000 0 -0.42 27 27
DLL1 0.021 0.037 -10000 0 -0.57 4 4
PPARD 0.015 0.092 -10000 0 -0.82 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
APC 0.004 0.083 -10000 0 -0.46 23 23
DVL1 -0.029 0.077 -10000 0 -0.36 35 35
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.098 0.14 0.34 80 -0.34 48 128
LRP6 0.023 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.009 -10000 0 -10000 0 0
CCND1 0.02 0.1 -10000 0 -1.1 7 7
WNT1 0.023 0.011 0.25 2 -10000 0 2
Axin1/APC/beta catenin 0.012 0.098 0.32 5 -0.43 18 23
DKK2 0.009 0.094 0.25 2 -0.57 27 29
NOTCH1 precursor/DVL1 -0.02 0.11 -10000 0 -0.59 24 24
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.003 0.12 -10000 0 -0.49 20 20
PPP2R5D -0.004 0.057 0.29 5 -0.36 16 21
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.19 -10000 0 -0.33 529 529
RBPJ 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
alphaV beta3 Integrin 0.02 0.082 -10000 0 -0.42 35 35
PTK2 -0.042 0.16 -10000 0 -0.47 93 93
positive regulation of JNK cascade -0.022 0.12 -10000 0 -0.32 117 117
CDC42/GDP -0.019 0.17 0.43 1 -0.43 127 128
Rac1/GDP -0.019 0.17 -10000 0 -0.43 127 127
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.023 0.16 -10000 0 -0.4 102 102
nectin-3/I-afadin -0.016 0.14 -10000 0 -0.43 116 116
RAPGEF1 -0.037 0.17 0.38 2 -0.47 114 116
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.051 0.19 -10000 0 -0.54 114 114
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
TLN1 -0.023 0.069 -10000 0 -0.38 13 13
Rap1/GTP -0.025 0.12 -10000 0 -0.34 108 108
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.016 0.14 -10000 0 -0.43 116 116
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.04 0.2 0.45 1 -0.53 128 129
MLLT4 0.021 0.033 0.25 1 -0.57 3 4
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.018 0.13 -10000 0 -0.34 117 117
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.03 -10000 0 -0.3 6 6
positive regulation of lamellipodium assembly -0.021 0.13 -10000 0 -0.34 127 127
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.039 0.18 -10000 0 -0.57 115 115
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
CDH1 0.01 0.08 -10000 0 -0.57 20 20
CLDN1 0.006 0.12 0.25 23 -0.57 41 64
JAM-A/CLDN1 0.002 0.14 -10000 0 -0.36 112 112
SRC -0.058 0.21 -10000 0 -0.58 120 120
ITGB3 0.005 0.11 0.25 4 -0.57 35 39
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.03 -10000 0 -0.3 6 6
FARP2 -0.04 0.2 0.46 1 -0.54 109 110
RAC1 0.024 0.003 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.001 0.13 -10000 0 -0.37 115 115
nectin-1/I-afadin 0.029 0.03 -10000 0 -0.3 6 6
nectin-2/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.002 0.13 -10000 0 -0.36 116 116
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.022 0.12 -10000 0 -0.32 117 117
alphaV/beta3 Integrin/Talin -0.007 0.1 0.26 2 -0.4 41 43
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
PIP5K1C -0.019 0.076 -10000 0 -0.22 114 114
VAV2 -0.039 0.21 0.44 1 -0.54 121 122
RAP1/GDP -0.015 0.16 -10000 0 -0.4 117 117
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.13 -10000 0 -0.37 115 115
nectin-3(dimer)/I-afadin/I-afadin -0.016 0.14 -10000 0 -0.43 116 116
Rac1/GTP -0.023 0.16 -10000 0 -0.41 126 126
PTPRM -0.017 0.086 -10000 0 -0.24 117 117
E-cadherin/beta catenin/alpha catenin 0.046 0.064 -10000 0 -0.32 22 22
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.012 0.14 -10000 0 -0.57 66 66
HRAS 0.025 0.02 0.25 8 -10000 0 8
EGFR -0.19 0.28 -10000 0 -0.57 393 393
AKT -0.015 0.12 0.31 6 -0.28 91 97
FOXO3 0.022 0.019 -10000 0 -0.57 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.037 -10000 0 -0.57 4 4
AKT3 0.014 0.06 -10000 0 -0.57 11 11
FOXO4 0.025 0.001 -10000 0 -10000 0 0
MET -0.074 0.22 -10000 0 -0.57 177 177
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.017 0.071 0.25 4 -0.57 15 19
PIK3R3 0.024 0.008 0.25 1 -10000 0 1
PIK3R2 0.024 0.004 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.062 0.14 0.21 4 -0.24 350 354
ERBB2 0.02 0.02 -10000 0 -0.57 1 1
proliferation/survival/translation -0.007 0.088 0.31 49 -0.26 1 50
PI3K -0.05 0.14 0.28 11 -0.32 169 180
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.037 0.058 0.27 8 -0.16 2 10
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.023 0.019 -10000 0 -0.57 1 1
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.094 0.1 0.21 421 -0.35 2 423
EPHB2 0.027 0.031 0.25 19 -10000 0 19
Syndecan-2/TACI 0.024 0.06 0.29 7 -0.36 12 19
LAMA1 -0.036 0.18 0.25 3 -0.57 108 111
Syndecan-2/alpha2 ITGB1 -0.038 0.15 -10000 0 -0.32 201 201
HRAS 0.025 0.02 0.25 8 -10000 0 8
Syndecan-2/CASK 0.005 0.016 -10000 0 -0.35 2 2
ITGA5 0.025 0.007 0.25 1 -10000 0 1
BAX 0.002 0.03 0.44 1 -10000 0 1
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.018 -10000 0 -0.32 2 2
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
EZR 0.024 0.012 0.25 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.053 0.2 -10000 0 -0.57 139 139
Syndecan-2/MMP2 0.015 0.038 -10000 0 -0.36 9 9
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.07 -10000 0 -0.42 25 25
dendrite morphogenesis 0.022 0.033 0.32 4 -0.35 2 6
Syndecan-2/GM-CSF 0.021 0.035 0.31 4 -0.36 2 6
determination of left/right symmetry 0.007 0.019 -10000 0 -0.41 2 2
Syndecan-2/PKC delta 0.02 0.022 0.31 1 -0.36 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.073 0.19 172 -0.33 2 174
MAPK1 0.037 0.076 0.19 196 -0.32 2 198
Syndecan-2/RACK1 0.03 0.026 0.24 3 -0.31 2 5
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.019 -10000 0 -0.41 2 2
ITGA2 0.009 0.093 -10000 0 -0.57 27 27
MAPK8 0.005 0.032 0.27 5 -0.35 5 10
Syndecan-2/alpha2/beta1 Integrin 0.003 0.12 -10000 0 -0.35 85 85
Syndecan-2/Kininogen 0.02 0.033 0.3 5 -0.36 2 7
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.069 0.33 7 -0.3 2 9
Syndecan-2/CASK/Protein 4.1 0.018 0.018 -10000 0 -0.32 2 2
extracellular matrix organization 0.02 0.023 0.34 1 -0.35 2 3
actin cytoskeleton reorganization 0.093 0.1 0.21 421 -0.34 2 423
Syndecan-2/Caveolin-2/Ras -0.009 0.11 0.26 3 -0.33 106 109
Syndecan-2/Laminin alpha3 -0.058 0.14 -10000 0 -0.36 190 190
Syndecan-2/RasGAP 0.038 0.031 0.26 2 -0.3 2 4
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
PRKCD 0.024 0.008 0.25 1 -10000 0 1
Syndecan-2 dimer 0.022 0.033 0.32 4 -0.36 2 6
GO:0007205 0.002 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.024 -10000 0 -0.29 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.028 0.084 0.25 62 -0.57 12 74
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.07 -10000 0 -0.42 25 25
Syndecan-2/Synbindin 0.018 0.02 -10000 0 -0.35 2 2
TGFB1 0.025 0.013 0.25 3 -10000 0 3
CASP3 0.043 0.071 0.19 190 -0.32 2 192
FN1 0.11 0.11 0.25 421 -10000 0 421
Syndecan-2/IL8 0.023 0.07 0.31 13 -0.36 19 32
SDC2 0.007 0.019 -10000 0 -0.41 2 2
KNG1 0.023 0.032 0.25 20 -10000 0 20
Syndecan-2/Neurofibromin 0.019 0.02 -10000 0 -0.36 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.025 0.036 0.25 25 -10000 0 25
Syndecan-2/TGFB1 0.02 0.023 0.35 1 -0.36 2 3
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.018 -10000 0 -0.32 2 2
Syndecan-2/Ezrin 0.03 0.025 0.29 1 -0.33 2 3
PRKACA 0.044 0.072 0.19 202 -0.32 2 204
angiogenesis 0.023 0.07 0.31 13 -0.36 19 32
MMP2 0.018 0.049 0.25 1 -0.57 7 8
IL8 0.025 0.099 0.25 60 -0.57 21 81
calcineurin-NFAT signaling pathway 0.024 0.06 0.29 7 -0.36 12 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.38 0.28 -10000 0 -0.57 725 725
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.032 0.25 20 -10000 0 20
TCEB1 0.021 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.029 0.049 -10000 0 -0.28 10 10
HIF1A 0.004 0.029 -10000 0 -0.27 11 11
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.037 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.06 0.086 0.25 174 -10000 0 174
ARNT/IPAS -0.25 0.2 -10000 0 -0.42 595 595
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.047 -10000 0 -0.32 5 5
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.05 -10000 0 -0.28 14 14
PHD1-3/OS9 0.056 0.048 -10000 0 -0.33 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.042 0.053 -10000 0 -0.3 5 5
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.049 -10000 0 -0.28 14 14
EGLN3 0.039 0.062 0.25 75 -0.57 1 76
EGLN2 0.025 0.016 0.25 5 -10000 0 5
EGLN1 0.02 0.02 -10000 0 -0.57 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.065 -10000 0 -0.51 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.053 0.073 0.29 7 -0.27 13 20
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.043 0.15 -10000 0 -0.32 238 238
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.13 9 -10000 0 9
GNB1/GNG2 0.027 0.04 -10000 0 -0.34 12 12
GNB1 0.024 0.005 -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 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.062 0.14 -10000 0 -0.31 252 252
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 0.02 0.034 0.081 252 -10000 0 252
GNAL -0.11 0.24 -10000 0 -0.57 236 236
GNG2 0.018 0.06 -10000 0 -0.57 11 11
CRH 0.017 0.023 0.25 9 -10000 0 9
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.029 -10000 0 -0.35 7 7
MAPK11 0.005 0.019 -10000 0 -0.35 3 3
FAS signaling pathway (CD95)

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
SPTAN1 -0.003 0.041 0.21 29 -10000 0 29
RFC1 -0.003 0.038 0.22 24 -10000 0 24
PRKDC 0.016 0.079 0.23 108 -0.19 6 114
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.1 -10000 0 -0.63 22 22
FASLG/FAS/FADD/FAF1 -0.005 0.059 0.22 11 -0.3 13 24
MAP2K4 -0.084 0.18 0.39 2 -0.4 127 129
mol:ceramide -0.023 0.1 -10000 0 -0.38 27 27
GSN -0.006 0.054 0.21 28 -0.29 17 45
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.077 0.28 1 -0.37 16 17
FAS 0.004 0.041 -10000 0 -0.59 3 3
BID -0.018 0.02 -10000 0 -10000 0 0
MAP3K1 -0.046 0.12 0.31 2 -0.4 42 44
MAP3K7 0.011 0.019 -10000 0 -10000 0 0
RB1 -0.003 0.038 0.22 24 -10000 0 24
CFLAR 0.027 0.006 -10000 0 -10000 0 0
HGF/MET -0.052 0.19 -10000 0 -0.4 233 233
ARHGDIB -0.001 0.044 0.22 35 -10000 0 35
FADD 0.006 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.059 0.35 11 -0.21 30 41
NFKB1 -0.045 0.12 -10000 0 -0.58 18 18
MAPK8 -0.15 0.25 0.56 2 -0.46 397 399
DFFA -0.003 0.038 0.21 24 -10000 0 24
DNA fragmentation during apoptosis -0.006 0.046 0.21 26 -10000 0 26
FAS/FADD/MET -0.038 0.14 -10000 0 -0.38 142 142
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 0.026 0.035 0.25 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.048 0.22 37 -10000 0 37
DFFB -0.004 0.039 0.21 24 -10000 0 24
CHUK -0.039 0.11 -10000 0 -0.56 15 15
FASLG 0.006 0.088 0.25 41 -0.58 15 56
FAS/FADD 0.009 0.037 -10000 0 -0.29 3 3
HGF -0.011 0.14 0.25 2 -0.57 65 67
LMNA -0.003 0.053 -10000 0 -10000 0 0
CASP6 -0.003 0.037 0.21 24 -10000 0 24
CASP10 0.004 0.041 -10000 0 -0.58 3 3
CASP3 0 0.042 0.26 24 -10000 0 24
PTPN13 0.01 0.091 -10000 0 -0.57 26 26
CASP8 -0.021 0.024 -10000 0 -10000 0 0
IL6 -0.43 0.62 -10000 0 -1.2 398 398
MET -0.074 0.22 -10000 0 -0.57 177 177
ICAD/CAD -0.006 0.032 0.22 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.1 -10000 0 -0.38 27 27
activation of caspase activity by cytochrome c -0.018 0.02 -10000 0 -10000 0 0
PAK2 -0.003 0.047 0.22 35 -10000 0 35
BCL2 0.008 0.095 -10000 0 -0.57 28 28
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.071 0.16 -10000 0 -0.48 25 25
Syndecan-3/Neurocan 0.027 0.073 0.27 18 -0.37 20 38
POMC 0.019 0.091 0.25 30 -0.57 21 51
EGFR -0.19 0.28 -10000 0 -0.57 393 393
Syndecan-3/EGFR -0.09 0.16 -10000 0 -0.3 337 337
AGRP 0.021 0.024 0.25 10 -10000 0 10
NCSTN 0.02 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.008 0.25 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.019 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.055 0.25 64 -10000 0 64
long-term memory 0.034 0.062 -10000 0 -0.35 16 16
Syndecan-3/IL8 0.021 0.081 0.28 9 -0.34 36 45
PSEN1 0.024 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
limb bud formation 0.002 0.055 -10000 0 -0.39 21 21
MC4R 0.023 0.026 0.25 13 -10000 0 13
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.23 0.29 0.25 2 -0.57 454 456
FGFR/FGF/Syndecan-3 0.002 0.056 -10000 0 -0.39 21 21
neuron projection morphogenesis -0.072 0.16 0.33 5 -0.47 23 28
Syndecan-3/AgRP 0.016 0.06 0.26 1 -0.36 22 23
Syndecan-3/AgRP/MC4R 0.038 0.068 0.3 2 -0.36 20 22
Fyn/Cortactin 0.028 0.021 -10000 0 -0.3 2 2
SDC3 0.002 0.056 -10000 0 -0.39 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.02 0.08 0.28 9 -0.34 36 45
IL8 0.025 0.099 0.25 60 -0.57 21 81
Syndecan-3/Fyn/Cortactin 0.035 0.063 -10000 0 -0.36 16 16
Syndecan-3/CASK 0 0.054 -10000 0 -0.36 23 23
alpha-MSH/MC4R 0.029 0.071 0.36 2 -0.42 21 23
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
Glypican 2 network

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
MDK 0.032 0.043 0.25 38 -10000 0 38
GPC2 0.049 0.081 0.25 126 -0.57 3 129
GPC2/Midkine 0.057 0.068 0.36 14 -0.42 3 17
neuron projection morphogenesis 0.057 0.068 0.36 14 -0.42 3 17
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.57 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.033 0.065 0.42 1 -0.26 51 52
CDKN1A -0.009 0.033 -10000 0 -0.77 2 2
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
BAX 0.025 0.016 0.25 5 -10000 0 5
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.02 0.037 -10000 0 -0.57 4 4
FOXO4 0.012 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.32 0.3 0.25 26 -0.57 635 661
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.023 -10000 0 -0.42 1 1
PPARGC1A -0.09 0.24 0.25 10 -0.57 209 219
FHL2 0.021 0.045 0.25 1 -0.57 6 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.033 0.065 0.26 51 -0.42 1 52
SIRT1/FOXO3a 0.015 0.026 -10000 0 -0.19 4 4
SIRT1 0.022 0.009 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.023 -10000 0 -0.36 1 1
SIRT1/Histone H1b 0.028 0.043 -10000 0 -0.21 6 6
apoptosis -0.044 0.017 -10000 0 -10000 0 0
SIRT1/PGC1A -0.047 0.16 -10000 0 -0.34 225 225
p53/SIRT1 0.027 0.019 0.41 2 -10000 0 2
SIRT1/FOXO4 0.022 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.037 0.04 -10000 0 -0.33 9 9
HIST1H1E 0.021 0.031 0.21 7 -10000 0 7
SIRT1/p300 0.032 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.023 0.36 1 -10000 0 1
TP53 0.02 0.011 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0.045 0.017 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.25 0.21 -10000 0 -0.42 635 635
ACSS2 0.009 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.023 -10000 0 -0.36 1 1
Stabilization and expansion of the E-cadherin adherens junction

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.012 0.043 -10000 0 -0.26 21 21
epithelial cell differentiation 0.036 0.054 -10000 0 -0.31 20 20
CYFIP2 0.028 0.048 0.25 26 -0.57 3 29
ENAH -0.003 0.06 0.3 11 -10000 0 11
EGFR -0.19 0.28 -10000 0 -0.57 393 393
EPHA2 0.021 0.041 -10000 0 -0.57 5 5
MYO6 -0.011 0.052 0.36 1 -0.3 21 22
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.034 -10000 0 -0.36 3 3
AQP5 -0.18 0.26 0.31 2 -0.5 416 418
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.051 0.36 1 -0.3 20 21
regulation of calcium-dependent cell-cell adhesion -0.022 0.075 0.36 1 -0.3 63 64
EGF -0.084 0.23 0.25 2 -0.57 196 198
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.016 0.12 0.29 1 -0.47 54 55
cortical microtubule organization 0.036 0.054 -10000 0 -0.31 20 20
GO:0000145 -0.011 0.048 0.35 1 -0.28 20 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.056 -10000 0 -0.31 20 20
MLLT4 0.021 0.033 0.25 1 -0.57 3 4
ARF6/GDP -0.02 0.039 -10000 0 -0.28 3 3
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.05 -10000 0 -0.28 20 20
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.011 0.051 0.36 1 -0.3 20 21
ARF6/GTP 0.049 0.04 -10000 0 -0.31 5 5
CDH1 0.01 0.08 -10000 0 -0.57 20 20
EGFR/EGFR/EGF/EGF -0.14 0.2 -10000 0 -0.33 522 522
RhoA/GDP 0.037 0.053 -10000 0 -0.3 20 20
actin cytoskeleton organization -0.013 0.049 0.34 1 -0.29 21 22
IGF-1R heterotetramer 0.013 0.079 0.25 3 -0.57 19 22
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.013 0.079 0.25 3 -0.57 19 22
IGF1 -0.1 0.24 -10000 0 -0.57 232 232
DIAPH1 0.026 0.1 -10000 0 -0.55 15 15
Wnt receptor signaling pathway -0.036 0.054 0.31 20 -10000 0 20
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.039 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.013 0.05 0.35 1 -0.3 21 22
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.015 0.053 -10000 0 -0.29 27 27
Ephrin A1/EPHA2 0.025 0.053 -10000 0 -0.29 22 22
SEC6/SEC8 -0.021 0.042 -10000 0 -0.3 21 21
MGAT3 -0.023 0.076 0.36 1 -0.3 63 64
HGF/MET -0.04 0.15 -10000 0 -0.32 234 234
HGF -0.011 0.14 0.25 2 -0.57 65 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.012 0.043 -10000 0 -0.26 21 21
actin cable formation 0.042 0.095 0.34 30 -0.29 1 31
KIAA1543 -0.012 0.054 0.35 1 -0.33 20 21
KIFC3 -0.012 0.049 0.36 1 -0.3 20 21
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.012 0.05 -10000 0 -0.3 20 20
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.036 0.054 -10000 0 -0.31 20 20
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.011 0.049 0.36 1 -0.3 19 20
PIP5K1C -0.011 0.051 0.36 1 -0.3 20 21
LIMA1 0.024 0.018 -10000 0 -0.57 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.018 0.089 0.31 26 -10000 0 26
adherens junction assembly -0.021 0.1 0.3 3 -0.61 17 20
IGF-1R heterotetramer/IGF1 -0.042 0.15 -10000 0 -0.31 237 237
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
MET -0.074 0.22 -10000 0 -0.57 177 177
PLEKHA7 -0.012 0.057 0.36 1 -0.34 20 21
mol:GTP 0.043 0.037 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.008 0.067 0.37 7 -0.52 1 8
cortical actin cytoskeleton stabilization 0.012 0.043 -10000 0 -0.26 21 21
regulation of cell-cell adhesion -0.013 0.049 0.34 1 -0.29 21 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.012 0.043 -10000 0 -0.26 21 21
LPA4-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
ADCY4 -0.018 0.063 -10000 0 -0.36 35 35
ADCY5 -0.11 0.16 -10000 0 -0.36 325 325
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.009 0.062 -10000 0 -0.36 28 28
ADCY2 -0.03 0.1 0.24 8 -0.36 85 93
ADCY3 -0.007 0.003 -10000 0 -10000 0 0
ADCY8 -0.004 0.023 0.23 6 -10000 0 6
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.085 0.22 19 -0.24 40 59
Syndecan-4-mediated signaling 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
PTK2 0.083 0.1 0.26 42 -0.57 6 48
Syndecan-4/Syndesmos 0.094 0.1 0.37 7 -0.7 6 13
positive regulation of JNK cascade 0.083 0.13 0.35 11 -0.64 8 19
Syndecan-4/ADAM12 0.1 0.12 0.35 38 -0.72 6 44
CCL5 0.029 0.056 0.25 37 -0.57 4 41
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.025 0.007 0.25 1 -10000 0 1
SDCBP 0.021 0.008 -10000 0 -10000 0 0
PLG -0.008 0.034 0.25 8 -10000 0 8
ADAM12 0.036 0.061 0.25 64 -0.57 2 66
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.012 0.25 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.065 0.15 0.37 5 -0.66 10 15
Syndecan-4/CXCL12/CXCR4 0.087 0.14 0.37 8 -0.69 8 16
Syndecan-4/Laminin alpha3 0.033 0.15 0.37 6 -0.74 7 13
MDK 0.032 0.043 0.25 38 -10000 0 38
Syndecan-4/FZD7 0.094 0.12 0.37 7 -0.69 7 14
Syndecan-4/Midkine 0.1 0.11 0.37 12 -0.7 6 18
FZD7 0.013 0.08 -10000 0 -0.57 20 20
Syndecan-4/FGFR1/FGF -0.01 0.16 0.35 2 -0.52 20 22
THBS1 0.021 0.041 -10000 0 -0.57 5 5
integrin-mediated signaling pathway 0.092 0.12 0.35 12 -0.69 7 19
positive regulation of MAPKKK cascade 0.083 0.13 0.35 11 -0.64 8 19
Syndecan-4/TACI 0.098 0.12 0.36 17 -0.72 6 23
CXCR4 0.029 0.034 0.25 24 -10000 0 24
cell adhesion 0.06 0.083 0.24 91 -0.25 21 112
Syndecan-4/Dynamin 0.098 0.1 0.37 5 -0.73 6 11
Syndecan-4/TSP1 0.097 0.11 0.38 6 -0.72 6 12
Syndecan-4/GIPC 0.098 0.1 0.38 4 -0.73 6 10
Syndecan-4/RANTES 0.099 0.11 0.36 9 -0.72 6 15
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.036 0.18 0.25 3 -0.57 108 111
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.024 0.22 0.7 95 -0.54 22 117
Syndecan-4/alpha-Actinin 0.098 0.1 0.38 5 -0.72 6 11
TFPI -0.004 0.13 0.25 1 -0.57 51 52
F2 0.025 0.034 0.26 13 -10000 0 13
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.001 0.18 0.36 4 -0.55 33 37
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.093 0.25 11 -0.57 25 36
Syndecan-4/CXCL12 0.076 0.14 0.37 6 -0.68 9 15
FGF6 0.015 0.026 -10000 0 -0.57 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.019 0.15 -10000 0 -0.57 77 77
TNFRSF13B 0.028 0.084 0.25 62 -0.57 12 74
FGF2 -0.2 0.29 -10000 0 -0.57 411 411
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
Syndecan-4/PI-4-5-P2 0.075 0.1 0.31 8 -0.72 6 14
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.25 420 -10000 0 420
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.012 0.025 -10000 0 -10000 0 0
vasculogenesis 0.095 0.1 0.36 7 -0.68 6 13
SDC4 0.087 0.1 0.35 9 -0.78 5 14
Syndecan-4/Tenascin C 0.093 0.12 0.36 12 -0.72 7 19
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.085 0.1 0.36 6 -0.7 6 12
MMP9 0.12 0.12 0.25 454 -0.56 1 455
Rac1/GTP 0.06 0.084 0.25 88 -0.26 21 109
cytoskeleton organization 0.092 0.1 0.36 7 -0.67 6 13
GIPC1 0.024 0.011 0.25 2 -10000 0 2
Syndecan-4/TFPI 0.086 0.13 0.37 6 -0.72 7 13
Signaling events mediated by PRL

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
CCNE1 0.062 0.086 0.25 179 -10000 0 179
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.019 0.054 -10000 0 -0.57 9 9
CDKN1A -0.031 0.094 -10000 0 -0.43 30 30
PRL-3/alpha Tubulin 0.03 0.019 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.075 0.24 44 -0.42 13 57
AGT 0.029 0.089 0.25 74 -0.57 13 87
CCNA2 -0.065 0.14 0.26 1 -10000 0 1
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.12 0.2 0.17 2 -0.41 334 336
CDK2/Cyclin E1 0.016 0.11 0.27 4 -0.4 29 33
MAPK3 0.01 0.02 0.26 5 -10000 0 5
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.02 0.26 5 -10000 0 5
PTP4A1 -0.093 0.14 -10000 0 -0.32 297 297
PTP4A3 0.021 0.02 0.25 6 -10000 0 6
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.018 0.26 4 -10000 0 4
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 -0.017 0.074 -10000 0 -0.43 14 14
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.072 0.15 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.015 -10000 0 -10000 0 0
RHOC -0.02 0.082 -10000 0 -0.43 21 21
RHOA -0.023 0.092 -10000 0 -0.47 27 27
cell motility -0.026 0.1 -10000 0 -0.38 35 35
PRL-1/alpha Tubulin -0.073 0.15 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.041 -10000 0 -0.34 9 9
ROCK1 -0.024 0.099 -10000 0 -0.38 31 31
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.093 0.14 -10000 0 -0.32 297 297
ATF5 0.025 0.013 0.25 3 -10000 0 3
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.008 0.01 -10000 0 -10000 0 0
SMARCC1 0.006 0.027 -10000 0 -0.59 1 1
REL 0.017 0.066 -10000 0 -0.57 13 13
HDAC7 -0.036 0.11 0.37 3 -0.37 59 62
JUN 0.019 0.045 -10000 0 -0.57 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.018 -10000 0 -0.57 1 1
KAT5 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.008 0.066 -10000 0 -0.43 23 23
FOXO1 0.02 0.037 -10000 0 -0.57 4 4
T-DHT/AR -0.023 0.12 0.33 1 -0.38 69 70
MAP2K6 0.002 0.088 0.24 1 -0.57 23 24
BRM/BAF57 0.026 0.027 -10000 0 -10000 0 0
MAP2K4 0.014 0.02 -10000 0 -10000 0 0
SMARCA2 0.018 0.018 -10000 0 -10000 0 0
PDE9A -0.06 0.26 -10000 0 -1.1 60 60
NCOA2 -0.008 0.12 -10000 0 -0.57 48 48
CEBPA 0.019 0.054 -10000 0 -0.57 9 9
EHMT2 0.021 0.012 -10000 0 -10000 0 0
cell proliferation 0.001 0.15 0.36 30 -0.44 27 57
NR0B1 0.026 0.045 0.25 33 -0.57 1 34
EGR1 -0.16 0.27 -10000 0 -0.57 334 334
RXRs/9cRA -0.042 0.15 -10000 0 -0.33 213 213
AR/RACK1/Src -0.016 0.11 0.32 6 -0.37 33 39
AR/GR -0.027 0.12 0.24 3 -0.29 141 144
GNB2L1 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.014 9 9
MAPK8 -0.001 0.04 -10000 0 -0.43 7 7
T-DHT/AR/TIF2/CARM1 -0.017 0.12 0.32 1 -0.37 58 59
SRC -0.019 0.068 0.19 30 -0.34 27 57
NR3C1 0.018 0.057 -10000 0 -0.57 10 10
KLK3 -0.14 0.39 0.38 1 -1.1 135 136
APPBP2 0.016 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.015 0.096 0.34 2 -0.39 29 31
TMPRSS2 -0.12 0.36 -10000 0 -1 139 139
RXRG -0.1 0.24 0.25 2 -0.57 217 219
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.024 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.004 -10000 0 -10000 0 0
CARM1 0.022 0.011 -10000 0 -10000 0 0
NR2C2 0.018 0.057 -10000 0 -0.57 10 10
KLK2 -0.051 0.2 0.32 6 -0.66 85 91
AR -0.04 0.11 0.17 1 -0.3 149 150
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.016 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 127 -0.023 42 169
GATA2 0.013 0.095 0.25 14 -0.57 26 40
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.25 447 -10000 0 447
T-DHT/AR/RACK1/Src -0.012 0.1 0.34 9 -0.38 30 39
positive regulation of transcription 0.013 0.095 0.25 14 -0.57 26 40
DNAJA1 0.017 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.022 0.029 -10000 0 -0.6 1 1
SPDEF -0.013 0.16 0.25 33 -0.57 71 104
T-DHT/AR/TIF2 -0.005 0.1 0.29 9 -0.37 31 40
T-DHT/AR/Hsp90 -0.016 0.097 0.33 3 -0.39 29 32
GSK3B 0.022 0.01 -10000 0 -10000 0 0
NR2C1 0.025 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.062 0.23 1 -0.36 28 29
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.025 0.016 -10000 0 -10000 0 0
POU2F1 0.009 0.05 -10000 0 -0.18 14 14
T-DHT/AR/DAX-1 -0.015 0.1 0.31 5 -0.39 31 36
CREBBP 0.022 0.007 -10000 0 -10000 0 0
SMARCE1 0.018 0.018 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.055 0.2 0.32 1 -0.52 68 69
MAP3K8 0.009 0.051 -10000 0 -0.57 7 7
FOS -0.019 0.14 0.32 2 -0.45 50 52
PRKCA -0.002 0.086 0.23 1 -0.58 22 23
PTPN7 0.022 0.06 0.24 62 -10000 0 62
HRAS 0.024 0.021 0.25 8 -10000 0 8
PRKCB 0.006 0.079 0.25 19 -0.58 15 34
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.036 -10000 0 -10000 0 0
MAPK3 0.009 0.09 -10000 0 -0.81 5 5
MAP2K1 -0.012 0.12 -10000 0 -0.5 45 45
ELK1 0.007 0.029 -10000 0 -10000 0 0
BRAF -0.012 0.099 -10000 0 -0.48 39 39
mol:GTP -0.002 0.003 -10000 0 -0.006 319 319
MAPK1 -0.008 0.12 -10000 0 -0.47 41 41
RAF1 -0.011 0.097 -10000 0 -0.48 39 39
KRAS 0.023 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.011 0.04 -10000 0 -0.57 1 1
SVIL 0.01 0.052 -10000 0 -0.57 5 5
ZNF318 0.039 0.055 0.19 104 -10000 0 104
JMJD2C -0.001 0.042 0.11 32 -0.13 78 110
T-DHT/AR/Ubc9 -0.034 0.14 -10000 0 -0.38 139 139
CARM1 0.019 0.015 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.014 0.029 -10000 0 -10000 0 0
AKT1 0.027 0.018 -10000 0 -10000 0 0
PTK2B 0.012 0.026 -10000 0 -10000 0 0
MED1 0.025 0.02 -10000 0 -10000 0 0
MAK 0.034 0.083 0.27 10 -0.55 11 21
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.01 0.053 -10000 0 -0.57 5 5
GSN 0.006 0.071 -10000 0 -0.57 12 12
NCOA2 -0.01 0.12 -10000 0 -0.57 48 48
NCOA6 0.013 0.033 -10000 0 -10000 0 0
DNA-PK 0.05 0.053 0.23 3 -10000 0 3
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.027 -10000 0 -10000 0 0
cell proliferation 0.004 0.11 0.35 1 -0.58 24 25
XRCC5 0.026 0.015 -10000 0 -10000 0 0
UBE3A 0.009 0.044 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.043 0.16 -10000 0 -0.38 161 161
FHL2 0.001 0.11 -10000 0 -0.68 12 12
RANBP9 0.013 0.033 -10000 0 -10000 0 0
JMJD1A -0.015 0.047 0.11 1 -0.14 131 132
CDK6 0.02 0.055 0.25 2 -0.57 9 11
TGFB1I1 0.01 0.046 -10000 0 -0.57 3 3
T-DHT/AR/CyclinD1 -0.043 0.14 -10000 0 -0.38 139 139
XRCC6 0.025 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.042 0.16 -10000 0 -0.38 151 151
CTDSP1 0.018 0.019 -10000 0 -10000 0 0
CTDSP2 0.034 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.039 -10000 0 -0.57 1 1
TCF4 0.025 0.064 -10000 0 -0.56 10 10
CDKN2A 0.064 0.089 0.26 174 -10000 0 174
SRF 0.032 0.023 -10000 0 -0.15 4 4
NKX3-1 -0.048 0.096 -10000 0 -0.21 249 249
KLK3 -0.14 0.46 -10000 0 -1.4 127 127
TMF1 0.018 0.016 -10000 0 -10000 0 0
HNRNPA1 0.029 0.021 -10000 0 -10000 0 0
AOF2 -0.007 0.023 -10000 0 -0.069 127 127
APPL1 0.019 0.032 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.029 0.15 -10000 0 -0.37 139 139
AR -0.068 0.2 -10000 0 -0.58 141 141
UBA3 0.017 0.019 -10000 0 -10000 0 0
PATZ1 0.027 0.021 -10000 0 -10000 0 0
PAWR 0.018 0.024 -10000 0 -0.57 1 1
PRKDC 0.023 0.016 -10000 0 -10000 0 0
PA2G4 0.031 0.027 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.024 0.13 -10000 0 -0.34 131 131
RPS6KA3 0.008 0.059 -10000 0 -0.57 7 7
T-DHT/AR/ARA70 -0.038 0.14 -10000 0 -0.36 150 150
LATS2 0.027 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.022 0.14 -10000 0 -0.33 148 148
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.014 0.064 0.25 17 -0.57 7 24
KLK2 -0.076 0.27 0.33 1 -0.99 81 82
CASP8 0.026 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.042 0.15 -10000 0 -0.37 150 150
TMPRSS2 -0.13 0.33 -10000 0 -0.98 136 136
CCND1 0.012 0.042 0.25 1 -0.57 4 5
PIAS1 0.01 0.044 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.028 -10000 0 -0.07 170 170
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.003 0.063 -10000 0 -0.22 2 2
T-DHT/AR/CDK6 -0.036 0.15 -10000 0 -0.38 147 147
CMTM2 0.023 0.012 0.25 1 -10000 0 1
SNURF 0.012 0.082 -10000 0 -0.57 21 21
ZMIZ1 0.01 0.039 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.021 -10000 0 -10000 0 0
FKBP4 0.014 0.036 0.25 4 -10000 0 4
Aurora A signaling

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
Aurora A/GADD45A 0.044 0.041 -10000 0 -10000 0 0
BIRC5 0.18 0.11 0.25 711 -10000 0 711
NFKBIA 0.024 0.04 0.28 8 -10000 0 8
CPEB1 -0.08 0.22 0.25 1 -0.57 188 189
AKT1 0.023 0.04 0.29 7 -10000 0 7
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.033 0.036 0.2 1 -0.2 1 2
NDEL1/TACC3 0.066 0.067 0.26 17 -10000 0 17
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.001 0.026 -10000 0 -10000 0 0
PAK1/Aurora A 0.04 0.043 0.27 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.089 0.067 0.27 26 -10000 0 26
TP53 0.022 0.051 0.19 1 -0.22 13 14
DLG7 0.022 0.03 0.17 1 -10000 0 1
AURKAIP1 0.026 0.024 0.25 11 -10000 0 11
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.07 0.071 0.28 17 -10000 0 17
G2/M transition of mitotic cell cycle 0.031 0.034 0.2 1 -0.2 1 2
AURKA 0.037 0.045 0.24 1 -10000 0 1
AURKB 0.085 0.074 0.17 416 -10000 0 416
CDC25B 0.031 0.039 0.22 3 -10000 0 3
G2/M transition checkpoint 0.019 0.028 0.13 1 -0.15 1 2
mRNA polyadenylation -0.027 0.13 -10000 0 -0.3 187 187
Aurora A/CPEB -0.025 0.13 -10000 0 -0.3 187 187
Aurora A/TACC1/TRAP/chTOG 0.044 0.07 -10000 0 -0.3 24 24
BRCA1 0.023 0.02 0.25 1 -0.57 1 2
centrosome duplication 0.04 0.043 0.27 2 -10000 0 2
regulation of centrosome cycle 0.064 0.066 0.26 17 -10000 0 17
spindle assembly 0.042 0.069 -10000 0 -0.3 24 24
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.087 0.28 29 -10000 0 29
CENPA 0.094 0.081 0.19 362 -0.21 3 365
Aurora A/PP2A 0.043 0.042 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.031 0.04 0.24 1 -10000 0 1
negative regulation of DNA binding 0.018 0.063 0.19 1 -0.2 44 45
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.028 0.13 1 -0.15 1 2
mitotic prometaphase -0.009 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.045 0.24 1 -10000 0 1
TACC1 0.006 0.089 -10000 0 -0.57 25 25
TACC3 0.058 0.083 0.25 162 -10000 0 162
Aurora A/Antizyme1 0.054 0.043 -10000 0 -10000 0 0
Aurora A/RasGAP 0.043 0.042 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.001 0.027 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.04 0.024 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.089 0.067 0.27 26 -10000 0 26
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.093 0.071 0.24 39 -10000 0 39
PAK1 0.023 0.019 0.25 6 -10000 0 6
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.049 0.17 -10000 0 -0.32 274 274
TC10/GTP -0.04 0.14 -10000 0 -0.29 256 256
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.079 -10000 0 -0.34 41 41
HRAS 0.025 0.02 0.25 8 -10000 0 8
APS homodimer 0.034 0.048 0.25 48 -10000 0 48
GRB14 0.012 0.18 0.25 143 -0.57 78 221
FOXO3 -0.022 0.16 -10000 0 -0.6 74 74
AKT1 -0.019 0.11 0.33 7 -0.28 89 96
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.055 0.046 0.35 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.12 0.26 -10000 0 -0.57 266 266
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.024 -10000 0 -10000 0 0
CAV1 -0.083 0.15 -10000 0 -0.35 236 236
CBL/APS/CAP/Crk-II/C3G -0.028 0.16 -10000 0 -0.31 261 261
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.078 -10000 0 -0.34 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.075 -10000 0 -0.3 48 48
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.014 0.065 -10000 0 -0.36 13 13
RPS6KB1 -0.018 0.096 0.33 6 -0.48 1 7
PARD6A 0.023 0.019 0.25 6 -10000 0 6
CBL 0.022 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.038 -10000 0 -0.55 4 4
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.008 0.094 -10000 0 -0.28 20 20
HRAS/GTP -0.02 0.044 -10000 0 -0.28 24 24
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.07 -10000 0 -0.32 26 26
PRKCI 0.014 0.059 -10000 0 -0.45 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.004 0.1 -10000 0 -0.29 112 112
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.035 -10000 0 -0.46 4 4
PI3K 0.037 0.078 -10000 0 -0.3 48 48
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 0.18 8 -10000 0 8
AKT2 -0.019 0.11 0.31 7 -0.28 88 95
PRKCZ 0.004 0.085 -10000 0 -0.48 16 16
SH2B2 0.034 0.048 0.25 48 -10000 0 48
SHC/SHIP 0.013 0.058 -10000 0 -0.3 28 28
F2RL2 0.046 0.12 0.25 156 -0.57 19 175
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.033 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.039 0.17 -10000 0 -0.32 265 265
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.049 0.028 -10000 0 -10000 0 0
INPP5D -0.019 0.063 -10000 0 -0.32 41 41
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.02 0.14 -10000 0 -0.68 47 47
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.57 42 42
p62DOK/RasGAP 0.042 0.035 -10000 0 -0.46 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.31 41 41
GRB2 0.023 0.009 0.25 1 -10000 0 1
EIF4EBP1 -0.02 0.089 0.31 3 -0.48 1 4
PTPRA 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.053 -10000 0 -0.27 28 28
Insulin Receptor/Insulin/IRS1 0.029 0.075 -10000 0 -0.34 41 41
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.061 0.072 -10000 0 -0.31 19 19
Thromboxane A2 receptor signaling

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
TGM2 0.027 0.028 0.26 15 -10000 0 15
GNB1/GNG2 -0.016 0.048 -10000 0 -0.19 65 65
AKT1 0.023 0.092 0.32 15 -0.26 34 49
EGF -0.084 0.23 0.25 2 -0.57 196 198
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.06 0.24 3 -0.31 6 9
mol:Ca2+ 0.022 0.12 0.38 14 -0.3 73 87
LYN 0.013 0.056 0.24 3 -0.35 3 6
RhoA/GTP 0.009 0.045 0.13 4 -0.14 37 41
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.019 0.12 0.39 15 -0.35 65 80
GNG2 0.018 0.06 -10000 0 -0.57 11 11
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.006 0.12 -10000 0 -0.58 38 38
G beta5/gamma2 -0.012 0.067 -10000 0 -0.26 64 64
PRKCH 0.017 0.12 0.42 11 -0.36 65 76
DNM1 0.021 0.048 0.25 1 -0.57 7 8
TXA2/TP beta/beta Arrestin3 0.008 0.031 -10000 0 -0.53 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.008 0.1 0.25 7 -0.57 31 38
G12 family/GTP -0.001 0.09 -10000 0 -0.3 67 67
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.02 0.041 -10000 0 -0.57 5 5
RhoA/GTP/ROCK1 0.031 0.014 -10000 0 -0.36 1 1
mol:GDP -0.012 0.1 0.37 34 -0.34 8 42
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 -0.013 0.14 -10000 0 -0.57 68 68
mol:IP3 0.019 0.14 0.45 10 -0.38 74 84
cell morphogenesis 0.031 0.014 -10000 0 -0.36 1 1
PLCB2 0.011 0.17 0.54 7 -0.52 74 81
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.026 0.071 0.25 7 -0.31 6 13
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.016 0.061 0.25 3 -0.37 3 6
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.026 0.021 0.25 9 -10000 0 9
PRKCB1 0.018 0.13 0.44 10 -0.37 71 81
GNAQ 0.022 0.032 -10000 0 -0.57 3 3
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.014 0.17 0.53 8 -0.52 69 77
LCK 0.017 0.074 0.24 3 -0.36 14 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.053 -10000 0 -0.25 25 25
TXA2-R family/G12 family/GDP/G beta/gamma 0.007 0.1 -10000 0 -0.41 53 53
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.24 21 21
MAPK14 0.019 0.09 0.32 19 -0.23 61 80
TGM2/GTP 0.014 0.15 0.49 10 -0.43 72 82
MAPK11 0.017 0.09 0.33 17 -0.24 62 79
ARHGEF1 0.012 0.067 0.27 11 -0.18 57 68
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.02 0.13 0.41 14 -0.39 68 82
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.022 0.1 0.37 15 -0.28 63 78
cAMP biosynthetic process 0.016 0.13 0.42 10 -0.36 73 83
Gq family/GTP/EBP50 0.015 0.044 0.22 5 -0.22 17 22
actin cytoskeleton reorganization 0.031 0.014 -10000 0 -0.36 1 1
SRC 0.014 0.058 0.24 3 -0.32 5 8
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.048 0.1 0.24 3 -0.29 75 78
VCAM1 0.02 0.11 0.37 14 -0.31 63 77
TP beta/Gq family/GDP/G beta5/gamma2 -0.006 0.12 -10000 0 -0.58 38 38
platelet activation 0.023 0.12 0.39 17 -0.31 64 81
PGI2/IP 0.019 0.014 0.17 9 -10000 0 9
PRKACA 0.008 0.052 -10000 0 -0.28 31 31
Gq family/GDP/G beta5/gamma2 0 0.1 -10000 0 -0.49 31 31
TXA2/TP beta/beta Arrestin2 -0.006 0.066 -10000 0 -0.44 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.047 -10000 0 -0.27 29 29
mol:DAG 0.018 0.14 0.46 10 -0.42 73 83
EGFR -0.19 0.28 -10000 0 -0.57 393 393
TXA2/TP alpha 0.014 0.17 0.52 8 -0.49 73 81
Gq family/GTP 0.002 0.049 0.25 1 -0.22 44 45
YES1 0.014 0.061 0.25 2 -0.32 5 7
GNAI2/GTP 0.014 0.052 -10000 0 -0.27 19 19
PGD2/DP 0.006 0.075 0.18 7 -0.4 34 41
SLC9A3R1 0.036 0.053 0.25 60 -10000 0 60
FYN 0.013 0.059 0.24 2 -0.34 7 9
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.025 0.025 0.25 6 -0.57 1 7
PGK/cGMP 0.007 0.096 -10000 0 -0.36 68 68
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.035 0.07 -10000 0 -0.31 28 28
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.021 0.13 0.43 11 -0.38 61 72
PRKCB 0.02 0.13 0.42 12 -0.37 63 75
PRKCE 0.018 0.12 0.44 10 -0.36 64 74
PRKCD 0.017 0.13 0.45 9 -0.38 64 73
PRKCG 0.019 0.13 0.45 10 -0.38 68 78
muscle contraction 0.015 0.16 0.5 9 -0.48 71 80
PRKCZ 0.018 0.12 0.43 10 -0.35 64 74
ARR3 0.021 0.02 0.25 8 -10000 0 8
TXA2/TP beta 0.024 0.059 -10000 0 -0.27 31 31
PRKCQ 0.015 0.14 0.4 15 -0.39 67 82
MAPKKK cascade 0.014 0.16 0.49 8 -0.46 72 80
SELE 0.016 0.12 0.37 14 -0.39 63 77
TP beta/GNAI2/GDP/G beta/gamma 0.034 0.069 -10000 0 -0.32 28 28
ROCK1 0.023 0.019 -10000 0 -0.57 1 1
GNA14 0.023 0.065 0.25 20 -0.57 10 30
chemotaxis 0.012 0.18 0.58 7 -0.61 63 70
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.032 -10000 0 -0.57 3 3
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.026 0.014 0.25 3 -10000 0 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.012 0.12 0.46 9 -0.5 4 13
IL27/IL27R/JAK1 0.037 0.16 0.73 6 -0.64 10 16
TBX21 -0.001 0.17 0.49 16 -0.5 46 62
IL12B 0.075 0.098 0.26 228 -10000 0 228
IL12A -0.015 0.1 0.14 18 -0.42 60 78
IL6ST -0.041 0.19 0.2 1 -0.57 119 120
IL27RA/JAK1 0.022 0.08 0.51 2 -1.2 3 5
IL27 0.048 0.075 0.26 111 -10000 0 111
TYK2 0.03 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.097 0.16 1.1 1 -0.79 2 3
T-helper 2 cell differentiation -0.012 0.12 0.46 9 -0.5 4 13
T cell proliferation during immune response -0.012 0.12 0.46 9 -0.5 4 13
MAPKKK cascade 0.012 0.12 0.5 4 -0.46 9 13
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.032 0.26 19 -10000 0 19
IL12RB1 0.033 0.053 0.26 41 -0.57 2 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.009 0.19 0.46 33 -0.52 52 85
IL27/IL27R/JAK2/TYK2 0.012 0.12 0.5 4 -0.46 9 13
positive regulation of T cell mediated cytotoxicity 0.012 0.12 0.5 4 -0.46 9 13
STAT1 (dimer) 0.035 0.21 0.67 23 -0.67 18 41
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.024 0.12 0.44 4 -0.46 8 12
T cell proliferation -0.091 0.18 0.37 4 -0.46 85 89
IL12/IL12R/TYK2/JAK2 0.058 0.18 0.41 17 -0.7 30 47
IL17A -0.097 0.16 1.1 1 -0.79 2 3
mast cell activation -0.012 0.12 0.46 9 -0.5 4 13
IFNG 0.021 0.044 0.12 120 -0.097 9 129
T cell differentiation 0 0.006 0.025 3 -0.022 5 8
STAT3 (dimer) 0.023 0.12 0.44 4 -0.46 8 12
STAT5A (dimer) 0.021 0.12 0.44 4 -0.44 15 19
STAT4 (dimer) 0.011 0.14 0.44 4 -0.44 25 29
STAT4 0.001 0.12 0.25 1 -0.57 43 44
T cell activation -0.005 0.011 0.12 3 -0.1 6 9
IL27R/JAK2/TYK2 0.016 0.14 -10000 0 -1.1 3 3
GATA3 -0.023 0.27 0.61 39 -1.3 35 74
IL18 0.009 0.019 0.13 23 -10000 0 23
positive regulation of mast cell cytokine production 0.023 0.11 0.43 4 -0.45 8 12
IL27/EBI3 0.052 0.072 0.25 52 -0.38 6 58
IL27RA 0.01 0.082 0.74 1 -1.3 3 4
IL6 -0.18 0.28 0.25 1 -0.57 379 380
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.041 0.45 3 -0.52 1 4
IL1B 0.001 0.05 0.13 3 -0.42 15 18
EBI3 0.025 0.053 0.26 13 -0.57 6 19
TNF 0.006 0.044 0.13 25 -0.42 9 34
Regulation of Telomerase

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
Telomerase catalytic core complex 0.056 0.13 0.46 10 -0.52 2 12
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.093 0.21 -10000 0 -0.41 310 310
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 -0.004 0.089 -10000 0 -0.23 101 101
ER alpha/Oestrogen -0.027 0.17 0.18 116 -0.4 159 275
NFX1/SIN3/HDAC complex 0.023 0.059 0.24 1 -0.33 16 17
EGF -0.083 0.23 0.26 2 -0.57 196 198
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.053 0.12 0.42 4 -0.47 3 7
SAP18 0.024 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.022 -10000 0 -10000 0 0
WT1 0.14 0.12 0.26 525 -10000 0 525
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.012 -10000 0 -10000 0 0
SP3 0.026 0.005 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.05 0.1 -10000 0 -0.46 2 2
Mad/Max 0.041 0.014 -10000 0 -10000 0 0
TERT 0.056 0.13 0.48 8 -0.53 2 10
CCND1 0.079 0.16 0.54 21 -1 4 25
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.019 0.26 7 -10000 0 7
RBBP4 0.024 0.019 -10000 0 -0.57 1 1
TERF2 0.021 0.014 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.039 0.05 -10000 0 -0.38 5 5
CDKN1B 0.029 0.05 -10000 0 -0.68 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.015 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.022 0.044 -10000 0 -0.57 6 6
E6 0.002 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 301 301
IFN-gamma/IRF1 0.064 0.062 0.38 2 -0.32 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.044 0.066 0.25 97 -10000 0 97
Telomerase 0.029 0.08 0.27 2 -0.6 6 8
IRF1 0.029 0.018 0.26 3 -0.18 3 6
ESR1 -0.036 0.23 0.26 116 -0.57 153 269
KU/TER 0.034 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.056 0.23 1 -0.33 10 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.057 0.23 1 -0.34 10 11
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.012 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.014 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.008 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.058 0.13 0.45 2 -0.59 5 7
NR2F2 0.012 0.037 -10000 0 -0.57 3 3
MAPK3 0.006 0.019 -10000 0 -10000 0 0
MAPK1 0.006 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.023 0.014 0.25 3 -10000 0 3
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.016 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.57 393 393
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.2 0.26 -10000 0 -0.45 526 526
MYC 0.008 0.084 -10000 0 -0.57 22 22
IL2 0.029 0.024 0.26 8 -10000 0 8
KU 0.034 0.009 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.023 0.014 0.25 3 -10000 0 3
TRF2/BLM 0.043 0.045 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.067 0.12 0.45 5 -0.5 2 7
SP1/HDAC2 0.046 0.025 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.048 0.1 -10000 0 -0.46 2 2
Smad3/Myc 0.007 0.054 -10000 0 -0.36 20 20
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.058 0.081 0.26 146 -0.2 1 147
Telomerase/PinX1 0.04 0.097 -10000 0 -0.45 2 2
Telomerase/AKT1/mTOR/p70S6K 0.026 0.1 0.29 5 -0.57 14 19
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.044 0.096 -10000 0 -0.42 1 1
response to DNA damage stimulus -0.002 0.028 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.05 0.1 -10000 0 -0.46 2 2
E2F1 0.097 0.11 0.26 323 -10000 0 323
ZNFX1 0.024 0.006 -10000 0 -10000 0 0
PIF1 0.068 0.091 0.25 208 -10000 0 208
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.01 0.25 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.086 0.25 1 -0.57 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.091 0.12 -10000 0 -0.24 420 420
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.009 0.25 1 -10000 0 1
p38 alpha/TAB1 -0.04 0.098 -10000 0 -0.35 70 70
PRKG1 -0.014 0.14 -10000 0 -0.57 68 68
DUSP8 0.022 0.032 -10000 0 -0.57 3 3
PGK/cGMP/p38 alpha -0.018 0.13 -10000 0 -0.34 103 103
apoptosis -0.038 0.093 -10000 0 -0.34 70 70
RAL/GTP 0.032 0.006 -10000 0 -10000 0 0
LYN 0.021 0.008 -10000 0 -10000 0 0
DUSP1 -0.045 0.19 -10000 0 -0.57 125 125
PAK1 0.023 0.019 0.25 6 -10000 0 6
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.053 0.024 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -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 0.024 0.008 0.25 1 -10000 0 1
RAC1-CDC42/GTP 0.031 0.008 -10000 0 -10000 0 0
MAPK11 -0.009 0.13 0.31 4 -0.41 51 55
BLK 0.051 0.086 0.25 151 -0.57 2 153
HCK 0.027 0.026 0.25 13 -10000 0 13
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.014 0.25 2 -10000 0 2
TRAF6/MEKK3 0.028 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.13 0.3 4 -0.39 65 69
positive regulation of innate immune response -0.011 0.15 0.35 4 -0.46 59 63
LCK 0.027 0.075 0.25 41 -0.57 11 52
p38alpha-beta/MKP7 -0.002 0.14 0.35 4 -0.45 52 56
p38alpha-beta/MKP5 -0.003 0.14 0.42 2 -0.47 45 47
PGK/cGMP -0.01 0.11 -10000 0 -0.42 68 68
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.033 0.17 0.37 3 -0.46 82 85
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.24 0.29 -10000 0 -0.57 480 480
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.025 0.26 2 -0.54 1 3
CDKN2C 0.014 0.028 -10000 0 -0.55 1 1
CDKN2A 0.061 0.086 0.26 169 -10000 0 169
CCND2 -0.016 0.036 0.2 2 -0.21 14 16
RB1 0.015 0.047 0.28 12 -0.23 8 20
CDK4 -0.017 0.037 0.21 2 -0.22 12 14
CDK6 -0.018 0.04 0.22 2 -0.2 23 25
G1/S progression -0.011 0.058 0.19 41 -0.29 13 54
Osteopontin-mediated events

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
IKK alpha homodimer 0.042 0.074 0.29 2 -0.31 29 31
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.083 0.34 13 -0.33 3 16
alphaV/beta3 Integrin/Osteopontin/Src 0.081 0.071 0.23 4 -10000 0 4
AP1 -0.036 0.18 0.34 1 -0.55 33 34
ILK 0.029 0.076 0.29 1 -0.32 29 30
bone resorption 0.018 0.089 0.27 1 -0.49 13 14
PTK2B 0.02 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.067 0.094 0.3 8 -0.3 25 33
ITGAV 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.022 0.075 -10000 0 -0.41 30 30
alphaV/beta3 Integrin/Osteopontin 0.076 0.1 0.34 4 -0.35 35 39
MAP3K1 0.029 0.079 0.26 14 -0.33 35 49
JUN 0.021 0.044 -10000 0 -0.57 6 6
MAPK3 0.02 0.071 0.28 11 -0.31 26 37
MAPK1 0.02 0.072 0.27 13 -0.3 28 41
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.015 0.084 0.26 16 -0.36 31 47
ITGB3 0.007 0.11 0.26 4 -0.57 35 39
NFKBIA 0.018 0.07 0.27 12 -0.3 23 35
FOS -0.14 0.27 -10000 0 -0.57 301 301
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.022 0.099 0.45 7 -0.55 2 9
NF kappa B1 p50/RelA 0.063 0.078 0.36 6 -10000 0 6
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.082 -10000 0 -0.42 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.029 0.077 0.25 14 -0.32 35 49
VAV3 0.016 0.076 0.26 17 -0.31 32 49
MAP3K14 0.031 0.077 0.26 11 -0.32 35 46
ROCK2 0.007 0.098 -10000 0 -0.57 30 30
SPP1 0.086 0.1 0.26 279 -10000 0 279
RAC1 0.024 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.027 0.071 0.3 3 -0.28 31 34
MMP2 -0.053 0.14 0.35 3 -0.51 32 35
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.024 0.13 0.3 15 -0.39 38 53
IKBKB 0.023 0.09 0.29 10 -0.32 12 22
AKT1 0.04 0.11 0.26 92 -0.25 15 107
IKBKG 0.028 0.073 0.35 4 -0.31 5 9
CALM1 0.002 0.096 0.26 1 -0.42 20 21
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.024 0.16 0.38 10 -0.53 43 53
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.1 -10000 0 -0.37 36 36
DOK1 0.025 0.014 0.25 4 -10000 0 4
AP-1 -0.021 0.099 0.24 9 -0.25 50 59
LYN 0.021 0.008 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
BCR complex 0.005 0.16 0.36 21 -0.44 95 116
CD22 -0.011 0.13 0.27 22 -0.45 61 83
CAMK2G 0.003 0.095 0.3 2 -0.41 18 20
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.087 -10000 0 -0.33 54 54
GO:0007205 0.002 0.1 -10000 0 -0.38 36 36
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0.002 0.1 0.26 1 -0.45 18 19
NFATC1 0.031 0.13 0.3 23 -0.46 31 54
B-cell antigen/BCR complex 0.005 0.16 0.36 21 -0.44 95 116
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.023 0.048 0.16 14 -0.13 26 40
HRAS 0.011 0.11 0.26 13 -0.41 22 35
NFKBIA 0.024 0.047 0.16 14 -0.12 25 39
NF-kappa-B/RelA/I kappa B beta 0.027 0.042 0.16 13 -10000 0 13
RasGAP/Csk 0.033 0.12 0.32 22 -0.36 68 90
mol:GDP 0.004 0.099 -10000 0 -0.42 20 20
PTEN 0.023 0.019 -10000 0 -0.57 1 1
CD79B 0.012 0.099 0.25 21 -0.57 27 48
NF-kappa-B/RelA/I kappa B alpha 0.028 0.042 0.16 13 -10000 0 13
GRB2 0.023 0.009 0.25 1 -10000 0 1
PI3K/BCAP/CD19 0.023 0.16 0.35 11 -0.49 52 63
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
mol:IP3 0.003 0.1 -10000 0 -0.36 45 45
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.076 0.16 -10000 0 -0.43 83 83
CHUK 0.024 0.082 0.32 5 -0.32 15 20
IBTK 0.023 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.018 0.095 -10000 0 -0.4 18 18
PTPN6 -0.013 0.12 0.25 22 -0.56 32 54
RELA 0.024 0.005 -10000 0 -10000 0 0
BCL2A1 0.024 0.035 0.17 9 -10000 0 9
VAV2 0.014 0.14 0.29 8 -0.6 28 36
ubiquitin-dependent protein catabolic process 0.026 0.047 0.16 14 -0.12 35 49
BTK 0.015 0.061 -10000 0 -0.97 4 4
CD19 0.006 0.14 0.28 25 -0.6 28 53
MAP4K1 0.033 0.054 0.25 48 -0.57 2 50
CD72 0.03 0.042 0.25 30 -0.57 1 31
PAG1 0.021 0.014 0.25 2 -10000 0 2
MAPK14 0.026 0.14 0.36 14 -0.45 42 56
SH3BP5 0.023 0.018 -10000 0 -0.57 1 1
PIK3AP1 0.004 0.11 -10000 0 -0.44 28 28
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.13 0.26 3 -0.42 75 78
RAF1 0.011 0.1 0.27 8 -0.42 18 26
RasGAP/p62DOK/SHIP 0.032 0.12 0.3 21 -0.35 68 89
CD79A -0.003 0.17 0.25 84 -0.57 81 165
re-entry into mitotic cell cycle -0.02 0.097 0.24 9 -0.25 47 56
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.097 0.27 25 -0.36 14 39
MAPK1 0.01 0.09 0.26 9 -0.36 17 26
CD72/SHP1 0.03 0.14 0.36 25 -0.54 31 56
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.024 0.14 0.35 15 -0.45 45 60
actin cytoskeleton organization 0.031 0.14 0.32 25 -0.51 28 53
NF-kappa-B/RelA 0.056 0.081 0.29 12 -0.21 1 13
Calcineurin 0.019 0.092 -10000 0 -0.39 16 16
PI3K -0.013 0.096 -10000 0 -0.44 27 27
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.006 0.11 -10000 0 -0.39 48 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.014 0.2 0.43 6 -0.7 51 57
DAPP1 -0.015 0.2 -10000 0 -0.79 51 51
cytokine secretion 0.032 0.13 0.28 30 -0.43 31 61
mol:DAG 0.003 0.1 -10000 0 -0.36 45 45
PLCG2 0.02 0.028 0.25 1 -0.57 2 3
MAP2K1 0.01 0.097 0.27 9 -0.4 17 26
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.13 0.34 21 -0.42 68 89
mol:PI-3-4-5-P3 0.005 0.089 0.22 16 -0.33 22 38
ETS1 0.001 0.089 0.29 2 -0.39 19 21
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.13 0.32 22 -0.36 74 96
B-cell antigen/BCR complex/LYN -0.011 0.14 0.29 5 -0.45 66 71
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.14 0.32 18 -0.55 28 46
B-cell antigen/BCR complex/LYN/SYK 0.015 0.14 0.35 24 -0.44 57 81
CARD11 0.004 0.1 0.28 5 -0.45 20 25
FCGR2B 0.018 0.038 0.25 1 -0.57 4 5
PPP3CA 0.024 0.011 0.25 2 -10000 0 2
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 55 -0.14 4 59
PTPRC 0.021 0.04 0.25 11 -0.57 3 14
PDPK1 0.02 0.082 0.22 53 -0.23 20 73
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.009 -10000 0 -10000 0 0
POU2F2 0.021 0.033 0.18 10 -10000 0 10
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.02 -10000 0 -0.57 1 1
ELF1 0.03 0.054 -10000 0 -0.36 12 12
CCNA2 0.11 0.11 0.25 400 -10000 0 400
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.027 0.026 0.26 14 -10000 0 14
PIK3R1 0.017 0.063 -10000 0 -0.57 12 12
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.046 0.1 0.32 13 -0.49 13 26
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.024 0.045 -10000 0 -0.38 12 12
IL2RA 0.02 0.12 0.43 11 -0.77 15 26
IL2RB 0.031 0.05 0.25 38 -0.57 2 40
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.067 0.25 46 -0.57 7 53
G1/S transition of mitotic cell cycle 0.042 0.14 0.35 3 -0.8 17 20
PTPN11 0.025 0.003 -10000 0 -10000 0 0
CCND2 0.006 0.087 0.43 1 -0.8 12 13
LCK 0.027 0.075 0.25 41 -0.57 11 52
GRB2 0.024 0.009 0.25 1 -10000 0 1
IL2 0.023 0.021 0.25 8 -10000 0 8
CDK6 0.019 0.055 0.25 2 -0.57 9 11
CCND3 0.047 0.1 0.42 6 -0.57 5 11
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.016 0.16 0.3 3 -0.39 148 151
AKT1 0.025 0.01 -10000 0 -10000 0 0
GSC -0.028 0.27 -10000 0 -1.1 53 53
NKX2-5 0.001 0.002 -10000 0 -10000 0 0
muscle cell differentiation -0.026 0.066 0.37 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.068 0.064 -10000 0 -0.44 1 1
SMAD4 0.013 0.044 -10000 0 -10000 0 0
CBFB 0.022 0.008 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.1 0.2 0.26 1 -0.36 384 385
SMAD3/SMAD4/VDR 0.056 0.058 -10000 0 -0.34 1 1
MYC 0.005 0.084 -10000 0 -0.57 22 22
CDKN2B -0.042 0.17 -10000 0 -1 16 16
AP1 -0.049 0.16 -10000 0 -0.33 107 107
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.01 0.086 -10000 0 -0.36 31 31
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.013 0.057 -10000 0 -0.34 11 11
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.046 0.081 0.26 127 -10000 0 127
SMAD3/SMAD4/GR 0.024 0.07 -10000 0 -0.39 10 10
GATA3 0.012 0.11 0.26 27 -0.55 36 63
SKI/SIN3/HDAC complex/NCoR1 0.005 0.077 -10000 0 -0.35 34 34
MEF2C/TIF2 0.024 0.087 0.32 4 -0.31 25 29
endothelial cell migration -0.029 0.093 0.64 8 -10000 0 8
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.019 0.25 7 -10000 0 7
RBBP4 0.023 0.019 -10000 0 -0.57 1 1
RUNX2 0.027 0.027 0.25 15 -10000 0 15
RUNX3 0.022 0.044 0.25 5 -0.57 5 10
RUNX1 0.023 0.019 -10000 0 -0.57 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.015 0.059 -10000 0 -0.57 10 10
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.016 0.078 -10000 0 -1.1 3 3
KAT2B 0.024 0.019 -10000 0 -0.57 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.078 0.3 1 -0.26 24 25
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.094 -10000 0 -0.64 8 8
SMAD3/SMAD4/ATF2 0.034 0.059 -10000 0 -0.4 2 2
SMAD3/SMAD4/ATF3 -0.013 0.14 -10000 0 -0.4 115 115
SAP30 0.024 0.015 0.25 4 -10000 0 4
Cbp/p300/PIAS3 0.041 0.031 -10000 0 -10000 0 0
JUN -0.058 0.15 -10000 0 -0.4 33 33
SMAD3/SMAD4/IRF7 0.052 0.08 0.34 13 -10000 0 13
TFE3 0.029 0.009 -10000 0 -0.2 1 1
COL1A2 0.045 0.093 0.39 4 -0.64 7 11
mesenchymal cell differentiation -0.035 0.058 -10000 0 -10000 0 0
DLX1 0.054 0.1 0.25 168 -0.57 10 178
TCF3 0.024 0.009 0.25 1 -10000 0 1
FOS -0.14 0.27 -10000 0 -0.57 302 302
SMAD3/SMAD4/Max 0.028 0.058 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.044 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.014 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.034 0.055 -10000 0 -10000 0 0
IRF7 0.048 0.072 0.27 102 -10000 0 102
ESR1 -0.042 0.23 0.25 116 -0.57 153 269
HNF4A 0.023 0.032 0.25 20 -10000 0 20
MEF2C 0.048 0.086 0.4 9 -0.47 2 11
SMAD2-3/SMAD4 0.035 0.064 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.36 1 1
IGHV3OR16-13 0.006 0.039 -10000 0 -0.34 12 12
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.023 0.25 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.005 -10000 0 -10000 0 0
GCN5L2 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.043 0.06 -10000 0 -0.46 1 1
MSG1/HSC70 -0.14 0.22 -10000 0 -0.42 405 405
SMAD2 0.022 0.03 -10000 0 -10000 0 0
SMAD3 0.015 0.04 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.042 -10000 0 -0.37 2 2
SMAD2/SMAD2/SMAD4 0.027 0.058 0.25 11 -0.51 3 14
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA1 0.024 0.018 -10000 0 -0.57 1 1
MYOD/E2A 0.032 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.078 0.063 -10000 0 -0.41 1 1
IFNB1 0.022 0.071 0.34 13 -10000 0 13
SMAD3/SMAD4/MEF2C 0.065 0.083 0.31 1 -0.44 2 3
CITED1 -0.2 0.29 0.25 15 -0.57 405 420
SMAD2-3/SMAD4/ARC105 0.043 0.065 -10000 0 -10000 0 0
RBL1 0.023 0.027 0.25 1 -0.57 2 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.017 0.065 -10000 0 -0.48 9 9
RUNX1-3/PEBPB2 0.04 0.039 -10000 0 -0.42 5 5
SMAD7 -0.031 0.14 -10000 0 -0.48 10 10
MYC/MIZ-1 0.015 0.065 -10000 0 -0.42 22 22
SMAD3/SMAD4 0.032 0.072 0.3 22 -0.37 3 25
IL10 0.007 0.081 0.34 2 -0.36 30 32
PIASy/HDAC complex 0.02 0.014 -10000 0 -10000 0 0
PIAS3 0.021 0.01 -10000 0 -10000 0 0
CDK2 0.025 0.008 -10000 0 -10000 0 0
IL5 0.004 0.083 0.32 2 -0.35 34 36
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.014 -10000 0 -10000 0 0
ATF3 -0.045 0.18 0.25 1 -0.57 118 119
SMAD3/SMAD4/SP1 0.047 0.064 -10000 0 -0.49 1 1
FOXG1 0.017 0.067 0.25 74 -10000 0 74
FOXO3 0.011 0.017 -10000 0 -0.42 1 1
FOXO1 0.01 0.028 -10000 0 -0.42 4 4
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.047 0.085 0.39 9 -0.46 2 11
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.054 0.089 0.29 5 -0.39 10 15
MYOD1 0.021 0.027 0.25 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.034 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.029 0.099 0.35 1 -0.39 36 37
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.023 0.25 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.069 -10000 0 -0.4 4 4
SMAD3/SMAD4/SP1-3 0.063 0.062 -10000 0 -0.44 1 1
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.03 0.014 -10000 0 -0.2 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.056 0.074 0.28 1 -0.24 21 22
ITGB5 0.016 0.042 -10000 0 -0.4 1 1
TGIF/SIN3/HDAC complex/CtBP 0.013 0.062 -10000 0 -0.3 24 24
SMAD3/SMAD4/AR -0.018 0.15 -10000 0 -0.39 136 136
AR -0.053 0.2 0.25 1 -0.57 141 142
negative regulation of cell growth -0.001 0.084 -10000 0 -0.34 19 19
SMAD3/SMAD4/MYOD 0.032 0.057 -10000 0 -10000 0 0
E2F5 0.022 0.021 0.25 7 -10000 0 7
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.073 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.054 -10000 0 -0.37 11 11
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.034 0.17 -10000 0 -0.4 36 36
SMAD3/SMAD4/RUNX2 0.036 0.058 -10000 0 -10000 0 0
TGIF2 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.023 0.026 -10000 0 -0.57 2 2
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.02 0.3 1 -10000 0 1
CDKN1B 0.011 0.056 -10000 0 -0.3 23 23
CDKN1A 0.01 0.061 -10000 0 -0.31 27 27
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -0.31 19 19
AKT1 0.006 0.056 -10000 0 -0.33 25 25
BAD 0.024 0.008 0.25 1 -10000 0 1
AKT3 0.007 0.035 -10000 0 -0.35 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.009 0.059 -10000 0 -0.32 27 27
AKT1/ASK1 0.031 0.067 -10000 0 -0.29 30 30
BAD/YWHAZ 0.037 0.023 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.03 0.066 0.29 30 -10000 0 30
TSC1 0.011 0.051 -10000 0 -0.34 13 13
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.07 0.25 3 -0.31 27 30
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.01 0.059 -10000 0 -0.32 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.054 0.32 1 -0.3 25 26
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.004 0.015 -10000 0 -0.34 2 2
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.075 0.3 20 -0.24 6 26
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.061 -10000 0 -0.32 25 25
CASP9 0.011 0.045 -10000 0 -0.29 17 17
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.072 0.3 8 -0.32 17 25
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.012 0.058 0.25 3 -0.32 18 21
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.051 -10000 0 -0.32 21 21
CHUK 0.01 0.055 -10000 0 -0.3 25 25
BAD/BCL-XL 0.038 0.066 0.28 3 -0.34 13 16
mTORC2 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.032 0.098 0.3 9 -0.39 24 33
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.012 0.064 0.27 2 -0.32 27 29
MAPKKK cascade -0.036 0.069 0.31 27 -0.25 3 30
MDM2/Cbp/p300 0.043 0.072 0.34 4 -0.42 6 10
TSC1/TSC2 0.014 0.068 0.26 37 -0.36 13 50
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.069 0.32 4 -0.4 6 10
glucose import -0.16 0.15 0.21 2 -0.31 520 522
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.048 0.17 4 -0.28 9 13
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 2 -0.31 520 522
GSK3A 0.01 0.059 -10000 0 -0.35 17 17
FOXO1 0.012 0.04 -10000 0 -0.28 9 9
GSK3B 0.01 0.059 0.21 1 -0.32 26 27
SFN 0.021 0.07 0.25 20 -0.57 12 32
G1/S transition of mitotic cell cycle 0.015 0.065 0.27 7 -0.34 17 24
p27Kip1/14-3-3 family 0.021 0.049 0.37 1 -0.48 2 3
PRKACA 0.024 0.004 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.009 0.11 0.26 2 -0.41 44 46
ACTA1 0.012 0.11 0.26 6 -0.48 31 37
NUMA1 0.004 0.11 0.26 2 -0.39 49 51
SPTAN1 -0.002 0.11 0.27 7 -0.49 31 38
LIMK1 -0.001 0.11 0.27 5 -0.49 31 36
BIRC3 0.023 0.04 0.25 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.016 0.25 5 -10000 0 5
CASP10 -0.011 0.09 0.2 11 -0.44 33 44
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.004 0.12 0.26 2 -0.44 45 47
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.001 0.1 0.27 7 -0.48 31 38
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.006 0.12 0.28 4 -0.47 40 44
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.013 0.13 -10000 0 -0.64 33 33
BID 0.003 0.053 0.18 3 -0.26 32 35
MAP3K1 -0.003 0.094 -10000 0 -0.38 52 52
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.002 0.11 0.26 7 -0.49 30 37
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.043 0.25 4 -0.2 5 9
neuron apoptosis 0.004 0.12 -10000 0 -0.69 26 26
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.11 0.26 2 -0.44 41 43
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 0 0.15 -10000 0 -0.88 26 26
TRAF2 0.025 0.015 0.25 4 -10000 0 4
ICAD/CAD -0.004 0.1 0.25 1 -0.5 27 28
CASP7 0.002 0.06 0.26 5 -0.31 10 15
KRT18 0.015 0.079 -10000 0 -0.72 9 9
apoptosis 0.002 0.12 0.3 6 -0.44 47 53
DFFA -0.003 0.1 0.25 3 -0.49 31 34
DFFB -0.003 0.1 0.25 3 -0.49 31 34
PARP1 0.017 0.043 0.2 5 -0.25 4 9
actin filament polymerization 0.001 0.1 0.45 32 -0.29 9 41
TNF 0.024 0.065 0.25 25 -0.57 9 34
CYCS 0.005 0.048 0.21 6 -0.23 20 26
SATB1 -0.008 0.15 -10000 0 -0.76 32 32
SLK -0.002 0.11 0.28 4 -0.49 31 35
p15 BID/BAX 0.013 0.062 0.24 2 -0.25 34 36
CASP2 0.003 0.063 0.29 2 -0.38 6 8
JNK cascade 0.003 0.094 0.38 52 -10000 0 52
CASP3 0 0.11 0.28 3 -0.5 33 36
LMNB2 0.001 0.13 0.3 3 -0.5 43 46
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.032 -10000 0 -0.33 2 2
negative regulation of DNA binding 0.014 0.13 -10000 0 -0.63 33 33
stress fiber formation -0.002 0.1 0.28 4 -0.48 31 35
GZMB 0.011 0.1 0.27 11 -0.49 32 43
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.02 0.12 0.29 8 -0.5 29 37
APP 0.004 0.12 -10000 0 -0.7 26 26
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM 0.004 0.12 0.29 5 -0.44 49 54
LMNA 0.009 0.08 0.32 2 -0.36 24 26
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.067 -10000 0 -0.3 20 20
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.001 0.1 0.27 4 -0.49 30 34
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.61 38 38
nuclear fragmentation during apoptosis 0.004 0.1 0.26 2 -0.38 49 51
CFL2 -0.001 0.11 0.29 9 -0.47 32 41
GAS2 -0.026 0.14 0.27 6 -0.38 95 101
positive regulation of apoptosis 0.014 0.11 0.27 8 -0.48 33 41
PRF1 0.016 0.077 0.25 8 -0.57 17 25
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.025 0.088 -10000 0 -0.66 7 7
oxygen homeostasis 0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.027 0.032 0.25 20 -10000 0 20
TCEB1 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.087 0.087 0.36 10 -0.35 3 13
EPO 0.15 0.17 0.52 62 -0.51 3 65
FIH (dimer) 0.032 0.02 -10000 0 -10000 0 0
APEX1 0.033 0.025 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.51 29 -0.54 5 34
FLT1 -0.017 0.17 -10000 0 -0.75 27 27
ADORA2A 0.16 0.17 0.49 67 -0.5 5 72
germ cell development 0.14 0.16 0.49 44 -0.5 5 49
SLC11A2 0.14 0.16 0.51 17 -0.54 4 21
BHLHE40 0.13 0.16 0.48 30 -0.55 5 35
HIF1AN 0.032 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.12 0.4 61 -0.39 3 64
ETS1 0.027 0.034 -10000 0 -0.57 3 3
CITED2 0.015 0.09 -10000 0 -0.68 6 6
KDR -0.017 0.17 -10000 0 -0.78 26 26
PGK1 0.14 0.16 0.47 38 -0.52 5 43
SIRT1 0.025 0.004 -10000 0 -10000 0 0
response to hypoxia 0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.6 16 -0.57 6 22
EPAS1 0.069 0.088 0.28 52 -0.37 6 58
SP1 0.03 0.013 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.52 17 -0.55 42 59
EFNA1 0.11 0.14 0.5 8 -0.53 3 11
FXN 0.15 0.16 0.45 52 -0.52 4 56
POU5F1 0.14 0.16 0.49 42 -0.52 5 47
neuron apoptosis -0.15 0.18 0.56 6 -0.58 17 23
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.047 0.066 0.27 75 -0.58 1 76
EGLN2 0.033 0.026 0.26 5 -10000 0 5
EGLN1 0.027 0.028 -10000 0 -0.58 1 1
VHL/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.028 0.024 -10000 0 -10000 0 0
SLC2A1 0.15 0.16 0.46 53 -0.53 4 57
TWIST1 0.13 0.19 0.45 50 -0.55 38 88
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.42 8 -0.38 3 11
VEGFA 0.13 0.16 0.49 29 -0.54 4 33
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0.004 0.059 -10000 0 -0.36 6 6
BAG4 0.018 0.033 -10000 0 -0.57 3 3
PKC zeta/ceramide -0.001 0.052 -10000 0 -0.25 16 16
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.25 12 -0.57 3 15
BAX 0.002 0.042 -10000 0 -0.35 11 11
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.068 0.7 10 -10000 0 10
BAD -0.015 0.046 0.19 4 -0.25 14 18
SMPD1 0.014 0.056 0.22 8 -0.24 17 25
RB1 -0.015 0.044 -10000 0 -0.25 13 13
FADD/Caspase 8 0.028 0.087 0.26 12 -0.4 6 18
MAP2K4 -0.016 0.045 0.18 5 -0.3 8 13
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.056 0.19 33 -0.3 7 40
EGF -0.084 0.23 0.25 2 -0.57 196 198
mol:ceramide -0.014 0.048 -10000 0 -0.26 15 15
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.009 -10000 0 -10000 0 0
ASAH1 0.021 0.015 0.25 3 -10000 0 3
negative regulation of cell cycle -0.016 0.044 -10000 0 -0.25 13 13
cell proliferation -0.045 0.12 0.28 1 -0.27 201 202
BID -0.02 0.17 -10000 0 -0.66 60 60
MAP3K1 -0.015 0.047 0.2 3 -0.25 16 19
EIF2A -0.014 0.049 0.29 3 -0.25 6 9
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.006 0.054 0.28 3 -0.3 6 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.059 0.26 4 -0.33 5 9
Cathepsin D/ceramide 0.004 0.057 0.18 12 -0.24 14 26
FADD 0.006 0.059 0.22 12 -0.39 4 16
KSR1 -0.009 0.055 0.2 24 -0.25 13 37
MAPK8 -0.014 0.058 -10000 0 -0.27 20 20
PRKRA -0.015 0.047 0.2 4 -0.26 12 16
PDGFA 0.024 0.008 0.25 1 -10000 0 1
TRAF2 0.025 0.015 0.25 4 -10000 0 4
IGF1 -0.1 0.24 -10000 0 -0.57 232 232
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.048 -10000 0 -0.25 15 15
CTSD 0.031 0.041 0.25 34 -10000 0 34
regulation of nitric oxide biosynthetic process 0.034 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.047 0.13 0.29 1 -0.29 198 199
PRKCD 0.024 0.008 0.25 1 -10000 0 1
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.034 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.018 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.044 -10000 0 -0.35 5 5
TNFR1A/BAG4/TNF-alpha 0.037 0.051 -10000 0 -0.36 11 11
mol:Sphingosine-1-phosphate 0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.009 0.055 0.24 5 -0.3 6 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
CYCS 0 0.049 0.22 5 -0.24 9 14
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.42 3 3
EIF2AK2 -0.017 0.043 0.19 2 -0.28 7 9
TNF-alpha/TNFR1A/FAN 0.04 0.044 -10000 0 -0.36 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.078 -10000 0 -0.37 31 31
MAP2K2 -0.01 0.055 0.24 5 -0.29 7 12
SMPD3 -0.002 0.099 0.26 4 -0.29 96 100
TNF 0.024 0.065 0.25 25 -0.57 9 34
PKC zeta/PAR4 0.033 0.022 -10000 0 -0.42 2 2
mol:PHOSPHOCHOLINE 0.042 0.097 0.24 194 -0.24 2 196
NF kappa B1/RelA/I kappa B alpha 0.063 0.03 -10000 0 -0.32 2 2
AIFM1 -0.001 0.049 0.19 11 -0.23 11 22
BCL2 0.008 0.095 -10000 0 -0.57 28 28
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.25 32 -0.57 20 52
CDC42/GTP -0.004 0.096 -10000 0 -0.3 52 52
PLCG1 -0.011 0.087 -10000 0 -0.31 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
cell migration -0.005 0.094 -10000 0 -0.3 52 52
S1PR5 0.027 0.041 0.25 20 -0.57 2 22
S1PR4 0.029 0.063 0.25 40 -0.57 6 46
MAPK3 -0.008 0.082 0.26 1 -0.31 40 41
MAPK1 -0.008 0.084 -10000 0 -0.32 44 44
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.32 47 47
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 -10000 0 -0.36 2 2
RHOA 0.006 0.058 0.24 1 -0.31 6 7
S1P/S1P4/Gi -0.004 0.094 -10000 0 -0.28 91 91
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.054 -10000 0 -0.57 9 9
S1P/S1P4/G12/G13 0.044 0.041 -10000 0 -0.33 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.057 -10000 0 -0.38 18 18
forebrain development -0.041 0.2 0.35 1 -0.52 130 131
GNAO1 0.017 0.091 0.25 32 -0.57 20 52
SMO/beta Arrestin2 0.027 0.043 -10000 0 -0.42 8 8
SMO 0.017 0.052 -10000 0 -0.57 8 8
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.024 0.081 0.32 2 -0.49 11 13
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 0.022 -10000 0 -10000 0 0
GNAI1 -0.008 0.13 -10000 0 -0.57 57 57
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.19 -10000 0 -0.6 69 69
SAP30 0.024 0.015 0.25 4 -10000 0 4
mol:GDP 0.017 0.052 -10000 0 -0.57 8 8
MIM/GLI2A 0.021 0.02 0.26 2 -10000 0 2
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.023 0.009 -10000 0 -10000 0 0
GLI2 0.01 0.066 -10000 0 -0.3 23 23
GLI3 0.013 0.084 0.34 2 -0.44 17 19
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.018 0.06 -10000 0 -0.57 11 11
Gi family/GTP -0.009 0.097 -10000 0 -0.29 96 96
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.017 0.086 0.25 1 -0.43 24 25
GLI2/Su(fu) 0.013 0.081 -10000 0 -0.38 23 23
FOXA2 0.009 0.1 -10000 0 -0.69 15 15
neural tube patterning -0.041 0.2 0.35 1 -0.52 130 131
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.042 -10000 0 -0.37 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.021 0.02 0.26 2 -10000 0 2
embryonic limb morphogenesis -0.041 0.2 0.35 1 -0.52 130 131
SUFU 0.016 0.026 -10000 0 -0.23 9 9
LGALS3 0.016 0.067 -10000 0 -0.57 14 14
catabolic process 0.027 0.1 0.32 2 -0.5 20 22
GLI3A/CBP 0.003 0.089 -10000 0 -0.36 59 59
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.043 0.21 0.35 1 -0.54 130 131
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
IFT172 0.024 0.018 -10000 0 -0.57 1 1
RBBP7 0.026 0.019 0.25 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.061 -10000 0 -0.38 15 15
GNAZ 0.017 0.055 -10000 0 -0.57 9 9
RBBP4 0.023 0.019 -10000 0 -0.57 1 1
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.018 0.07 -10000 0 -0.36 15 15
STK36 0.021 0.023 -10000 0 -0.57 1 1
Gi family/GNB1/GNG2/GDP -0.013 0.11 -10000 0 -0.41 47 47
PTCH1 -0.085 0.32 -10000 0 -1.1 87 87
MIM/GLI1 -0.03 0.19 -10000 0 -0.57 81 81
CREBBP 0.003 0.089 -10000 0 -0.36 59 59
Su(fu)/SIN3/HDAC complex 0.007 0.09 -10000 0 -0.42 33 33
IL2 signaling events mediated by PI3K

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
BCL2L1 0.022 0.077 -10000 0 -0.66 3 3
UGCG 0.009 0.12 -10000 0 -0.67 30 30
AKT1/mTOR/p70S6K/Hsp90/TERT 0.048 0.12 0.3 10 -0.42 26 36
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.12 -10000 0 -0.66 30 30
mol:DAG 0.004 0.085 -10000 0 -0.76 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.038 0.13 0.3 6 -0.42 52 58
FRAP1 0.032 0.15 0.33 6 -0.48 52 58
FOXO3 0.037 0.14 0.33 12 -0.51 30 42
AKT1 0.037 0.14 0.34 6 -0.54 33 39
GAB2 0.021 0.02 -10000 0 -0.57 1 1
SMPD1 0.01 0.11 -10000 0 -0.64 25 25
SGMS1 0.018 0.066 -10000 0 -0.54 12 12
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 0.038 -10000 0 -0.34 12 12
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.046 0.11 0.29 7 -0.46 24 31
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.049 -10000 0 -0.39 13 13
RPS6KB1 0.012 0.092 -10000 0 -0.84 10 10
mol:sphingomyelin 0.004 0.085 -10000 0 -0.76 12 12
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.028 0.027 0.26 14 -10000 0 14
PIK3R1 0.017 0.063 -10000 0 -0.57 12 12
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.065 0.2 0.42 8 -0.93 27 35
MYB 0.028 0.19 0.48 2 -1.1 24 26
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.037 0.11 0.29 16 -0.48 17 33
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.088 -10000 0 -0.75 10 10
mol:PI-3-4-5-P3 0.041 0.11 0.29 17 -0.47 17 34
Rac1/GDP 0.015 0.037 -10000 0 -0.33 11 11
T cell proliferation 0.041 0.1 0.29 12 -0.49 12 24
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.013 0.1 3 -0.076 23 26
PRKCZ 0.04 0.1 0.3 10 -0.51 12 22
NF kappa B1 p50/RelA 0.048 0.14 0.31 6 -0.44 41 47
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.075 0.29 11 -0.52 8 19
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
IL2RA 0.027 0.089 0.26 58 -0.57 15 73
IL2RB 0.031 0.051 0.26 38 -0.57 2 40
TERT 0.053 0.079 0.25 142 -10000 0 142
E2F1 0.051 0.093 0.33 2 -0.36 31 33
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.034 23 -0.049 3 26
PTPN11 0.024 0.007 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.26 46 -0.57 7 53
actin cytoskeleton organization 0.041 0.1 0.29 12 -0.49 12 24
GRB2 0.023 0.011 0.26 1 -10000 0 1
IL2 0.021 0.023 0.26 8 -10000 0 8
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.042 -10000 0 -0.31 11 11
LCK 0.027 0.076 0.26 41 -0.57 11 52
BCL2 0.019 0.19 0.42 2 -0.79 44 46
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.27 0.29 -10000 0 -0.57 523 523
CLTC 0.026 0.067 0.28 1 -0.43 12 13
calcium ion-dependent exocytosis 0.009 0.026 -10000 0 -0.23 3 3
Dynamin 2/GTP 0.022 0.013 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.016 0.046 -10000 0 -0.34 10 10
CPE 0.005 0.048 -10000 0 -0.36 18 18
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.019 -10000 0 -0.16 5 5
CTNND1 0.008 0.056 0.19 90 -10000 0 90
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.043 0.21 3 -0.33 7 10
TSHR -0.003 0.073 -10000 0 -0.36 42 42
INS -0.001 0.089 -10000 0 -0.48 34 34
BIN1 0.02 0.051 -10000 0 -0.57 8 8
mol:Choline 0.011 0.019 -10000 0 -0.16 5 5
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.017 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.013 -10000 0 -10000 0 0
JUP 0.017 0.039 0.23 1 -0.33 7 8
ASAP2/amphiphysin II 0.042 0.033 -10000 0 -0.33 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.01 0.054 -10000 0 -0.37 9 9
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.028 0.25 16 -10000 0 16
substrate adhesion-dependent cell spreading 0.016 0.039 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.037 0.064 0.34 8 -10000 0 8
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.015 0.028 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.043 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.025 0.063 0.29 5 -0.35 12 17
JIP4/KLC1 0.041 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.02 0.033 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.008 0.057 0.19 93 -10000 0 93
NME1 0.013 0.017 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.069 0.28 3 -0.42 12 15
IL2RA 0.019 0.055 -10000 0 -0.32 13 13
VAMP3 0.012 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.27 407 407
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.029 -10000 0 -0.29 9 9
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.014 0.039 0.19 1 -0.36 6 7
SDC1 0.019 0.043 -10000 0 -0.33 8 8
ARF6/GDP 0.021 0.014 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.04 0.067 -10000 0 -0.34 8 8
mol:Phosphatidic acid 0.011 0.019 -10000 0 -0.16 5 5
endocytosis -0.04 0.033 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.037 0.14 0.26 1 -0.43 35 36
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.024 0.018 -10000 0 -0.57 1 1
Dynamin 2/GDP 0.026 0.017 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.08 0.16 0.26 3 -0.43 36 39
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.066 0.32 2 -0.36 5 7
BARD1 signaling events

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
BARD1/CSTF1 0.026 0.057 -10000 0 -0.39 18 18
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.064 0.071 0.3 2 -0.3 18 20
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.022 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.014 0.086 -10000 0 -0.43 19 19
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.02 0.25 1 -0.57 1 2
CCNE1 0.062 0.086 0.25 179 -10000 0 179
CDK2/Cyclin E1 0.06 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.06 -10000 0 -0.41 19 19
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
FANCA 0.059 0.087 0.25 179 -10000 0 179
DNA repair 0.027 0.085 0.3 4 -0.37 7 11
BRCA1/BARD1/ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BARD1/DNA-PK 0.045 0.053 -10000 0 -0.33 15 15
FANCL 0.024 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.057 0.39 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.071 -10000 0 -0.27 22 22
BRCA1/BACH1/BARD1/TopBP1 0.039 0.055 -10000 0 -0.36 18 18
BRCA1/BARD1/P53 0.048 0.054 -10000 0 -0.33 18 18
BARD1/CSTF1/BRCA1 0.037 0.053 -10000 0 -0.36 16 16
BRCA1/BACH1 0.023 0.02 0.25 1 -0.57 1 2
BARD1 0.014 0.077 0.25 1 -0.57 18 19
PCNA 0.024 0.011 0.25 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.04 0.054 -10000 0 -0.36 17 17
BRCA1/BARD1/UbcH7 0.038 0.054 -10000 0 -0.36 17 17
BRCA1/BARD1/RAD51/PCNA 0.091 0.088 0.31 2 -0.32 17 19
BARD1/DNA-PK/P53 0.05 0.054 -10000 0 -0.31 15 15
BRCA1/BARD1/Ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BRCA1/BARD1/CTIP 0.028 0.05 -10000 0 -0.33 18 18
FA complex 0.035 0.037 0.24 3 -0.26 1 4
BARD1/EWS 0.026 0.059 -10000 0 -0.42 18 18
RBBP8 0.01 0.005 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.054 0.33 18 -10000 0 18
BRCA1/BARD1 0.071 0.075 0.33 2 -0.3 18 20
CSTF1 0.023 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.056 0.18 1 -0.42 18 19
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.1 0.11 0.25 372 -10000 0 372
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.06 -10000 0 -0.41 19 19
EWSR1 0.023 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.023 0.032 0.25 1 -0.57 3 4
ANTXR2 0.018 0.057 -10000 0 -0.57 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.076 13 13
monocyte activation 0.003 0.085 0.25 2 -0.35 55 57
MAP2K2 0.003 0.082 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.008 -10000 0 -0.11 1 1
MAP2K7 -0.004 0.008 0.12 1 -0.11 1 2
MAP2K6 -0.01 0.045 -10000 0 -0.31 23 23
CYAA -0.009 0.035 -10000 0 -0.33 12 12
MAP2K4 -0.004 0.008 -10000 0 -0.11 1 1
IL1B -0.008 0.047 0.18 3 -0.28 27 30
Channel 0.026 0.042 -10000 0 -0.35 12 12
NLRP1 -0.007 0.033 -10000 0 -0.32 11 11
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.066 -10000 0 -0.39 29 29
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.076 13 -10000 0 13
MAPK3 -0.004 0.008 -10000 0 -10000 0 0
MAPK1 -0.004 0.009 0.12 2 -0.11 1 3
PGR -0.08 0.14 0.2 2 -0.31 281 283
PA/Cellular Receptors 0.027 0.046 -10000 0 -0.37 13 13
apoptosis -0.002 0.008 -10000 0 -0.076 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.04 0.16 1 -0.32 13 14
macrophage activation -0.005 0.01 0.14 1 -10000 0 1
TNF 0.024 0.065 0.25 25 -0.57 9 34
VCAM1 0.003 0.085 0.25 2 -0.35 55 57
platelet activation -0.001 0.066 -10000 0 -0.39 29 29
MAPKKK cascade -0.002 0.026 0.09 17 -0.14 5 22
IL18 -0.003 0.026 -10000 0 -0.22 10 10
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.076 13 13
LEF -0.002 0.008 -10000 0 -0.076 13 13
CASP1 -0.003 0.027 -10000 0 -0.22 13 13
mol:cAMP -0.001 0.067 -10000 0 -0.39 29 29
necrosis -0.002 0.008 -10000 0 -0.076 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.04 0.16 1 -0.33 12 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
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 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.018 0.065 -10000 0 -0.29 50 50
FRAP1 -0.001 0.083 0.4 1 -0.45 26 27
AKT1 -0.011 0.065 0.19 1 -0.28 38 39
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0.024 0.07 0.23 3 -0.27 15 18
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.2 6 6
TSC2 0.023 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.006 0.048 -10000 0 -0.25 14 14
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.078 -10000 0 -0.31 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.015 0.046 -10000 0 -0.23 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.012 0.075 0.33 3 -0.31 21 24
MAP3K5 -0.001 0.046 0.2 10 -0.19 47 57
PIK3R1 0.017 0.063 -10000 0 -0.57 12 12
apoptosis -0.001 0.047 0.2 10 -0.19 48 58
mol:LY294002 0 0 -10000 0 -0.001 52 52
EIF4B 0.011 0.069 0.3 4 -0.3 14 18
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.029 0.066 -10000 0 -0.28 12 12
eIF4E/eIF4G1/eIF4A1 0.004 0.05 -10000 0 -0.28 22 22
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.081 -10000 0 -0.3 58 58
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.055 0.22 17 -0.19 3 20
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.027 0.061 -10000 0 -0.25 14 14
mol:Amino Acids 0 0 -10000 0 -0.001 52 52
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.059 0.18 2 -0.28 40 42
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.006 0.14 -10000 0 -0.52 67 67
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.048 -10000 0 -10000 0 0
TSC1/TSC2 0.027 0.075 0.26 4 -0.28 15 19
tumor necrosis factor receptor activity 0 0 0.001 52 -10000 0 52
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.011 0.08 -10000 0 -0.33 60 60
INS 0.016 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
PDK2 -0.018 0.059 0.18 5 -0.29 35 40
EIF4EBP1 -0.024 0.22 -10000 0 -1 48 48
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D 0.001 0.079 0.36 3 -0.41 24 27
peptide biosynthetic process -0.01 0.018 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 22 -0.003 3 25
EEF2 -0.01 0.018 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.013 0.21 -10000 0 -0.97 48 48
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.003 0.09 0.29 47 -10000 0 47
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.25 32 -0.57 20 52
RhoA/GTP -0.003 0.091 -10000 0 -0.29 47 47
negative regulation of cAMP metabolic process -0.004 0.088 -10000 0 -0.32 47 47
GNAZ 0.018 0.054 -10000 0 -0.57 9 9
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.027 0.041 0.25 20 -0.57 2 22
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.32 47 47
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
FoxO family 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
G6PC 0.012 0.06 -10000 0 -10000 0 0
PLK1 0.24 0.18 0.55 78 -0.57 1 79
CDKN1B 0.15 0.13 0.38 58 -0.45 5 63
FOXO3 0.2 0.16 0.45 180 -0.5 3 183
KAT2B 0.055 0.034 -10000 0 -0.58 1 1
FOXO1/SIRT1 0.012 0.054 -10000 0 -0.28 8 8
CAT 0.18 0.17 0.6 16 -1 5 21
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.056 0.028 -10000 0 -10000 0 0
FOXO1 0.017 0.062 -10000 0 -0.31 8 8
MAPK10 -0.016 0.12 0.21 9 -0.29 155 164
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.035 0.084 0.41 2 -0.42 2 4
response to oxidative stress 0.034 0.026 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.17 0.14 0.38 145 -0.5 3 148
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.061 0.084 -10000 0 -0.69 10 10
FOXO1/SKP2 0.027 0.058 -10000 0 -0.28 8 8
mol:GDP 0.034 0.026 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.13 0.13 0.45 3 -0.52 13 16
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.023 0.12 -10000 0 -0.51 35 35
MST1 0.051 0.059 0.27 7 -0.51 8 15
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.01 0.12 -10000 0 -0.54 26 26
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.036 0.2 14 -0.3 7 21
MAPK9 0.031 0.024 0.21 12 -10000 0 12
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
SIRT1 0.012 0.02 -10000 0 -10000 0 0
SOD2 0.15 0.13 0.46 15 -0.43 2 17
RBL2 0.1 0.25 0.51 3 -0.62 76 79
RAL/GDP 0.056 0.021 -10000 0 -10000 0 0
CHUK 0.055 0.028 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.057 0.021 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.055 0.18 -10000 0 -1.3 17 17
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.006 -10000 0 -10000 0 0
IKBKB 0.046 0.032 -10000 0 -10000 0 0
CCNB1 0.2 0.17 0.56 50 -0.57 1 51
FOXO1-3a-4/beta catenin 0.15 0.12 0.42 37 -0.39 6 43
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.057 -10000 0 -0.28 8 8
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
SGK1 0.051 0.047 -10000 0 -0.56 4 4
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.032 0.075 0.44 1 -0.4 1 2
SFN 0.021 0.07 0.25 20 -0.57 12 32
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.061 0.11 0.32 2 -0.42 18 20
CREBBP 0.022 0.008 -10000 0 -10000 0 0
FBXO32 0.22 0.21 0.6 116 -1.2 4 120
BCL6 0.16 0.16 0.49 5 -0.88 10 15
RALB 0.025 0.003 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.056 0.072 0.37 14 -0.38 12 26
MAP4K1 0.033 0.054 0.25 48 -0.57 2 50
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
PRKCB 0.019 0.077 0.25 19 -0.57 15 34
DBNL 0.024 0.003 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.015 0.054 0.25 1 -0.36 9 10
JUN 0.003 0.13 -10000 0 -0.6 41 41
MAP3K7 0.015 0.053 0.23 2 -0.33 8 10
GRAP2 0.017 0.066 0.25 3 -0.57 13 16
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.013 0.066 0.24 1 -0.39 12 13
LAT 0.025 0.038 0.25 15 -0.57 2 17
LCP2 0.024 0.008 0.25 1 -10000 0 1
MAPK8 0.007 0.14 -10000 0 -0.64 41 41
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.022 0.059 0.25 3 -0.31 18 21
LAT/GRAP2/SLP76/HPK1/HIP-55 0.063 0.071 0.36 14 -0.36 12 26
ceramide signaling pathway

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
MAP4K4 -0.002 0.098 0.26 2 -0.41 30 32
BAG4 0.018 0.033 -10000 0 -0.57 3 3
BAD 0.006 0.038 0.2 4 -0.19 5 9
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.25 12 -0.57 3 15
BAX 0.005 0.042 0.22 6 -0.18 6 12
EnzymeConsortium:3.1.4.12 0.002 0.026 0.082 5 -0.093 26 31
IKBKB 0.017 0.1 0.34 3 -0.43 18 21
MAP2K2 0.008 0.051 0.2 19 -0.22 3 22
MAP2K1 0.009 0.053 0.2 29 -0.22 3 32
SMPD1 0.002 0.032 0.14 3 -0.15 14 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.12 0.28 20 -0.42 25 45
MAP2K4 0.006 0.034 0.18 5 -0.22 3 8
protein ubiquitination 0.004 0.1 0.34 4 -0.4 27 31
EnzymeConsortium:2.7.1.37 0.008 0.054 0.23 15 -0.22 4 19
response to UV 0 0.001 0.002 45 -0.002 2 47
RAF1 0.009 0.052 0.19 41 -0.22 4 45
CRADD 0.024 0.004 -10000 0 -10000 0 0
mol:ceramide 0.006 0.04 0.14 5 -0.15 21 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.009 -10000 0 -10000 0 0
MADD 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.039 0.18 4 -0.19 8 12
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.052 0.22 15 -0.22 3 18
MAPK1 0.007 0.059 0.2 20 -0.23 8 28
p50/RELA/I-kappa-B-alpha 0.034 0.01 -10000 0 -10000 0 0
FADD 0.024 0.11 0.27 13 -0.42 23 36
KSR1 0.009 0.05 0.19 35 -0.2 7 42
MAPK8 0.002 0.047 0.24 8 -0.28 8 16
TRAF2 0.025 0.015 0.25 4 -10000 0 4
response to radiation 0 0 0.002 11 -10000 0 11
CHUK -0.001 0.093 0.25 1 -0.41 24 25
TNF R/SODD 0.027 0.029 -10000 0 -0.42 3 3
TNF 0.025 0.065 0.25 25 -0.57 9 34
CYCS 0.008 0.045 0.18 14 -0.18 4 18
IKBKG -0.001 0.096 0.43 1 -0.42 24 25
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.001 0.1 -10000 0 -0.44 28 28
RELA 0.024 0.005 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.008 0.044 0.17 13 -0.2 4 17
TNF/TNF R/SODD 0.037 0.051 -10000 0 -0.36 11 11
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 11 -10000 0 11
CASP8 0.003 0.13 -10000 0 -0.62 41 41
NSMAF 0.017 0.11 0.26 11 -0.41 26 37
response to hydrogen peroxide 0 0.001 0.002 45 -0.002 2 47
BCL2 0.008 0.095 -10000 0 -0.57 28 28
S1P3 pathway

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
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.014 0.096 -10000 0 -0.3 92 92
GNAO1 0.018 0.091 0.26 32 -0.57 20 52
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.091 -10000 0 -0.47 29 29
AKT3 -0.013 0.17 -10000 0 -1 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.25 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.099 -10000 0 -0.35 55 55
MAPK3 -0.009 0.09 0.27 2 -0.4 28 30
MAPK1 -0.007 0.091 0.27 1 -0.4 30 31
JAK2 -0.01 0.1 -10000 0 -0.39 40 40
CXCR4 -0.01 0.096 0.21 1 -0.34 54 55
FLT1 0.023 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.011 0.093 -10000 0 -0.4 29 29
S1P/S1P3/Gi -0.004 0.1 -10000 0 -0.35 56 56
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.1 -10000 0 -0.39 32 32
VEGFA 0.025 0.021 0.26 6 -10000 0 6
S1P/S1P2/Gi -0.004 0.093 -10000 0 -0.28 90 90
VEGFR1 homodimer/VEGFA homodimer 0.036 0.022 -10000 0 -0.19 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.019 0.041 -10000 0 -0.28 17 17
GNAQ 0.022 0.032 -10000 0 -0.57 3 3
GNAZ 0.018 0.055 -10000 0 -0.57 9 9
G12/G13 0.033 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.065 0.25 20 -0.57 10 30
GNA15 0.025 0.025 0.25 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.032 -10000 0 -0.57 3 3
Rac1/GTP -0.003 0.1 -10000 0 -0.39 32 32
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.011 0.23 2 -10000 0 2
SNTA1 0.024 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.034 0.3 8 -10000 0 8
MAPK12 -0.009 0.048 0.21 1 -0.33 22 23
CCND1 0.01 0.047 -10000 0 -0.38 7 7
p38 gamma/SNTA1 0.021 0.07 0.32 2 -0.32 22 24
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint -0.009 0.048 0.21 1 -0.33 22 23
MAP2K6 -0.006 0.051 -10000 0 -0.35 23 23
MAPT -0.027 0.12 0.26 14 -0.32 124 138
MAPK13 0.011 0.011 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.006 0.001 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.021 -10000 0 -0.36 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.061 -10000 0 -0.36 15 15
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.066 0.2 6 -0.37 16 22
RAR alpha/9cRA/Cyclin H 0.047 0.073 -10000 0 -0.34 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.065 -10000 0 -0.41 13 13
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.023 0.063 -10000 0 -0.43 11 11
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.009 0.11 -10000 0 -0.57 19 19
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.024 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARG 0.025 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.048 -10000 0 -0.57 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.1 -10000 0 -0.51 20 20
RARA 0.013 0.056 0.2 12 -0.27 27 39
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.079 -10000 0 -0.38 22 22
PRKCA 0.012 0.085 0.26 1 -0.57 22 23
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.12 0.45 1 -0.58 19 20
RXRG -0.05 0.15 0.24 12 -0.35 202 214
RXRA 0.022 0.063 0.34 1 -0.27 26 27
RXRB 0.016 0.061 0.24 11 -0.34 22 33
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.035 0.075 0.25 71 -0.57 7 78
CRBP1/9-cic-RA 0.025 0.053 0.18 71 -0.42 7 78
RARB 0.018 0.065 -10000 0 -0.57 13 13
PRKCG 0.032 0.045 0.26 41 -10000 0 41
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.54 24 24
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.009 0.099 -10000 0 -0.5 19 19
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.079 0.24 14 -0.36 17 31
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.12 0.45 1 -0.59 19 20
positive regulation of DNA binding 0.033 0.064 -10000 0 -0.32 19 19
NRIP1 0.012 0.12 0.54 1 -0.75 10 11
RXRs/RARs 0.01 0.12 -10000 0 -0.56 23 23
RXRs/RXRs/DNA/9cRA -0.013 0.091 -10000 0 -0.5 23 23
PRKACA 0.024 0.004 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.052 0.056 -10000 0 -0.31 3 3
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.044 0.015 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.018 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.05 -10000 0 -0.37 7 7
IRAK/TOLLIP 0.027 0.009 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.025 0.095 0.36 3 -0.42 40 43
IL1A 0.028 0.03 0.25 18 -10000 0 18
IL1B 0.004 0.055 0.26 1 -0.43 16 17
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.027 -10000 0 -0.3 1 1
IL1R2 0.008 0.12 0.25 29 -0.57 40 69
IL1R1 0.012 0.084 -10000 0 -0.57 22 22
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.063 0.26 5 -0.3 21 26
TOLLIP 0.024 0.004 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.057 0.27 1 -0.37 1 2
JUN -0.015 0.056 0.26 2 -0.27 35 37
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.084 -10000 0 -0.33 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88 0.053 0.061 -10000 0 -0.33 22 22
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.061 0.06 -10000 0 -0.32 22 22
IL1 beta fragment/IL1R1/IL1RAP 0.022 0.073 -10000 0 -0.35 36 36
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.011 0.054 0.34 1 -0.28 28 29
IRAK1 0.012 0.008 -10000 0 -10000 0 0
IL1RN/IL1R1 0.031 0.074 -10000 0 -0.42 24 24
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.028 0.048 -10000 0 -0.4 12 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.059 -10000 0 -0.29 25 25
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.022 0.073 -10000 0 -0.35 36 36
IL1 beta/IL1R2 0.012 0.094 -10000 0 -0.38 54 54
IRAK/TRAF6/TAK1/TAB1/TAB2 0.032 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.076 -10000 0 -0.32 42 42
IRAK3 0.002 0.11 0.25 1 -0.57 39 40
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.074 -10000 0 -0.32 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.047 -10000 0 -0.27 22 22
IL1 alpha/IL1R1/IL1RAP 0.042 0.062 -10000 0 -0.36 22 22
RELA 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.008 0.25 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.038 0.021 -10000 0 -10000 0 0
IL1RAP 0.024 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.018 0.06 -10000 0 -0.3 26 26
CASP1 0.021 0.02 -10000 0 -0.57 1 1
IL1RN/IL1R2 0.028 0.1 0.36 5 -0.42 42 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.034 0.073 -10000 0 -0.33 36 36
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.071 -10000 0 -0.34 34 34
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.049 0.25 37 -0.57 2 39
TRAF6/TAK1/TAB1/TAB2 0.033 0.011 -10000 0 -10000 0 0
MAP2K6 -0.007 0.054 0.34 2 -0.29 22 24
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.02 0.11 -10000 0 -0.41 45 45
KLHL20 0.016 0.065 0.24 8 -0.23 9 17
CYFIP2 0.028 0.048 0.25 26 -0.57 3 29
Rac1/GDP 0.001 0.085 0.26 6 -0.31 18 24
ENAH -0.015 0.1 -10000 0 -0.4 43 43
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.047 -10000 0 -0.4 1 1
ABI1/Sra1/Nap1 -0.012 0.032 -10000 0 -0.16 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.047 0.067 -10000 0 -0.33 22 22
RAPGEF1 -0.018 0.11 0.26 1 -0.4 30 31
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.12 -10000 0 -0.41 55 55
CRK -0.016 0.1 -10000 0 -0.39 43 43
E-cadherin/gamma catenin/alpha catenin 0.032 0.06 -10000 0 -0.36 20 20
alphaE/beta7 Integrin 0.037 0.034 -10000 0 -0.42 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
DLG1 -0.023 0.12 -10000 0 -0.4 52 52
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.032 -10000 0 -0.24 2 2
MLLT4 0.021 0.033 0.25 1 -0.57 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.004 0.046 -10000 0 -0.32 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.021 0.065 -10000 0 -0.42 20 20
TIAM1 0.025 0.015 0.25 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.04 0.056 -10000 0 -0.31 20 20
AKT1 -0.007 0.036 0.14 1 -0.21 1 2
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
CDH1 0.01 0.08 -10000 0 -0.57 20 20
RhoA/GDP 0.001 0.084 0.26 5 -0.31 18 23
actin cytoskeleton organization 0.015 0.053 0.18 20 -0.17 6 26
CDC42/GDP 0.002 0.083 0.26 5 -0.31 18 23
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.042 -10000 0 -0.27 20 20
ITGB7 0.03 0.046 0.25 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.044 0.06 -10000 0 -0.33 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin 0.03 0.052 -10000 0 -0.31 20 20
mol:GDP -0.012 0.091 0.27 5 -0.36 19 24
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 0.086 -10000 0 -0.32 18 18
RAC1/GTP/IQGAP1 0.032 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.047 0.18 39 -0.24 4 43
NME1 0.026 0.031 0.25 18 -10000 0 18
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.021 0.12 -10000 0 -0.41 48 48
regulation of cell-cell adhesion 0.004 0.04 -10000 0 -0.35 1 1
WASF2 0.008 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.013 0.058 0.24 1 -0.46 1 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.053 0.067 -10000 0 -0.32 21 21
CCND1 0.015 0.055 0.2 36 -0.3 4 40
VAV2 -0.019 0.15 -10000 0 -0.62 23 23
RAP1/GDP 0.007 0.07 0.26 3 -0.35 3 6
adherens junction assembly -0.021 0.11 -10000 0 -0.4 48 48
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.024 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.042 0.063 -10000 0 -0.31 21 21
E-cadherin/beta catenin 0.001 0.06 -10000 0 -0.34 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.023 0.12 -10000 0 -0.4 53 53
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.089 0.25 34 -0.34 23 57
E-cadherin/beta catenin/alpha catenin 0.033 0.06 -10000 0 -0.36 20 20
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.13 -10000 0 -0.42 55 55
PLK2 and PLK4 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
PLK2 0.024 0.009 0.25 1 -9999 0 1
PLK4 0.033 0.044 0.25 41 -9999 0 41
regulation of centriole replication 0.016 0.026 0.26 2 -9999 0 2
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.033 -10000 0 -0.57 3 3
Caspase 8 (4 units) 0.039 0.061 -10000 0 -0.5 2 2
NEF 0.003 0.023 -10000 0 -0.18 11 11
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.02 0.054 0.26 12 -0.44 7 19
CYCS 0.036 0.077 0.25 26 -0.28 16 42
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.017 0.086 0.29 16 -0.43 26 42
MAP2K7 0.041 0.12 0.37 2 -0.7 17 19
protein ubiquitination 0.015 0.082 0.31 5 -0.37 11 16
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.022 0.032 -10000 0 -0.57 3 3
BID 0.035 0.073 0.18 100 -0.29 16 116
NF-kappa-B/RelA/I kappa B alpha 0.051 0.033 -10000 0 -0.27 5 5
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.033 -10000 0 -0.27 5 5
MAPK8 0.038 0.12 0.4 5 -0.63 18 23
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.013 0.25 3 -10000 0 3
TRAF2 0.025 0.015 0.25 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.059 0.22 6 -0.31 16 22
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.015 0.091 -10000 0 -0.42 18 18
CHUK 0.015 0.085 0.31 4 -0.4 11 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.04 -10000 0 -0.34 4 4
TCRz/NEF 0.016 0.081 0.31 9 -0.42 26 35
TNF 0.024 0.065 0.25 25 -0.57 9 34
FASLG 0.011 0.11 0.28 41 -0.57 26 67
NFKB1 0.025 0.011 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.037 0.051 -10000 0 -0.36 11 11
CASP6 0.052 0.1 0.38 1 -0.48 23 24
CASP7 0.04 0.1 0.34 11 -0.43 14 25
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.34 8 -0.45 12 20
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.42 3 3
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.006 -10000 0 -10000 0 0
MAP3K14 0.016 0.087 0.29 1 -0.42 13 14
APAF-1/Caspase 9 0.033 0.061 0.24 6 -0.37 5 11
BCL2 0.031 0.12 0.42 6 -0.54 23 29
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.033 0.06 -9999 0 -0.36 20 20
E-cadherin/beta catenin 0.021 0.065 -9999 0 -0.34 30 30
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.01 0.08 -9999 0 -0.57 20 20
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.02 -10000 0 -0.3 3 3
TRAF2/ASK1 0.03 0.025 -10000 0 -0.36 3 3
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.019 0.11 0.25 2 -0.33 72 74
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.015 0.099 0.27 1 -0.34 44 45
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.054 0.077 0.25 139 -10000 0 139
TXN 0.007 0.006 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.027 -10000 0 -0.41 3 3
TAK1/TAB family 0 0.019 0.18 2 -0.14 6 8
RAC1/OSM/MEKK3 0.042 0.016 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.25 4 -10000 0 4
RAC1/OSM/MEKK3/MKK3 -0.001 0.092 -10000 0 -0.3 39 39
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.006 0.16 0.25 45 -0.57 71 116
CCM2 0.024 0.008 0.25 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.012 0.1 -10000 0 -0.36 71 71
MAPK11 0.021 0.032 -10000 0 -0.57 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.023 0.1 -10000 0 -0.33 73 73
OSM/MEKK3 0.032 0.013 -10000 0 -10000 0 0
TAOK1 -0.008 0.081 -10000 0 -0.36 54 54
TAOK2 0.011 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.025 -10000 0 -0.35 3 3
GADD45/MTK1/MTK1 0.067 0.047 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.026 0.073 0.3 4 -0.38 12 16
PDGFB-D/PDGFRB/SLAP 0.028 0.033 -10000 0 -0.36 4 4
PDGFB-D/PDGFRB/APS/CBL 0.048 0.042 -10000 0 -0.36 4 4
AKT1 0.025 0.095 0.34 38 -0.28 1 39
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.032 0.084 0.32 6 -0.4 15 21
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.44 39 39
mol:Ca2+ 0.024 0.087 0.3 6 -0.43 17 23
MYC 0.053 0.17 0.38 27 -0.78 26 53
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.3 3 3
LRP1/PDGFRB/PDGFB 0.041 0.053 -10000 0 -0.41 13 13
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.024 0.088 0.3 6 -0.44 17 23
PTEN 0.023 0.019 -10000 0 -0.57 1 1
GRB2 0.023 0.009 0.25 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PDGFB-D/PDGFRB/SHP2 0.034 0.029 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.029 -10000 0 -0.42 4 4
cell cycle arrest 0.028 0.033 -10000 0 -0.36 4 4
HRAS 0.025 0.02 0.25 8 -10000 0 8
HIF1A 0.02 0.089 0.33 37 -10000 0 37
GAB1 0.026 0.093 0.29 8 -0.42 17 25
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.026 0.086 0.32 10 -0.37 14 24
PDGFB-D/PDGFRB 0.043 0.031 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.026 -10000 0 -0.42 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.023 0.065 0.28 3 -0.38 9 12
positive regulation of MAPKKK cascade 0.034 0.028 -10000 0 -0.42 4 4
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
mol:IP3 0.024 0.089 0.3 6 -0.44 17 23
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.039 -10000 0 -0.42 7 7
SHB 0.024 0.008 0.25 1 -10000 0 1
BLK -0.025 0.16 0.29 5 -0.4 139 144
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.029 -10000 0 -0.42 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.028 0.1 0.3 9 -0.44 21 30
CBL 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.029 -10000 0 -0.42 4 4
LCK 0.006 0.11 -10000 0 -0.5 36 36
PDGFRB 0.022 0.037 -10000 0 -0.57 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.016 0.06 -10000 0 -0.53 6 6
ABL1 0.021 0.093 0.3 7 -0.38 26 33
PDGFB-D/PDGFRB/CBL 0.021 0.1 0.3 3 -0.44 28 31
PTPN1 0.024 0.019 0.25 6 -10000 0 6
SNX15 0.024 0.005 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.03 0.25 19 -10000 0 19
cell proliferation 0.054 0.15 0.35 35 -0.68 26 61
SLA 0.021 0.024 0.25 9 -10000 0 9
actin cytoskeleton reorganization 0.034 0.05 0.33 2 -0.29 3 5
SRC 0.012 0.06 -10000 0 -0.52 7 7
PI3K -0.013 0.032 -10000 0 -0.28 11 11
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.038 -10000 0 -0.36 6 6
SH2B2 0.034 0.048 0.25 48 -10000 0 48
PLCgamma1/SPHK1 0.033 0.086 0.32 6 -0.42 15 21
LYN 0.01 0.064 -10000 0 -0.46 12 12
LRP1 0.018 0.06 -10000 0 -0.57 11 11
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.3 3 3
SPHK1 0.027 0.041 0.25 20 -0.57 2 22
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.024 0.089 0.3 6 -0.44 17 23
PLCG1 0.024 0.09 0.3 6 -0.45 17 23
NHERF/PDGFRB 0.049 0.045 -10000 0 -0.36 4 4
YES1 0.001 0.11 -10000 0 -0.51 37 37
cell migration 0.048 0.044 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.05 0.042 -10000 0 -0.3 3 3
SLC9A3R2 0.023 0.01 0.25 1 -10000 0 1
SLC9A3R1 0.036 0.053 0.25 60 -10000 0 60
NHERF1-2/PDGFRB/PTEN 0.056 0.048 0.29 2 -0.33 4 6
FYN -0.003 0.1 -10000 0 -0.42 46 46
DOK1 0.021 0.049 0.33 1 -0.33 3 4
HRAS/GTP 0.019 0.014 0.18 8 -10000 0 8
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.023 0.12 0.33 4 -0.51 30 34
PRKCD 0.022 0.051 0.27 2 -0.33 3 5
FER 0.018 0.059 -10000 0 -0.34 12 12
MAPKKK cascade 0.037 0.096 0.36 34 -0.3 3 37
RASA1 0.021 0.049 0.2 6 -0.33 3 9
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.036 0.043 0.3 1 -0.31 3 4
PDGFB-D/PDGFRB/SHB 0.034 0.03 -10000 0 -0.42 4 4
chemotaxis 0.021 0.091 0.28 9 -0.37 26 35
STAT1-3-5/STAT1-3-5 0.049 0.048 -10000 0 -0.37 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.027 -10000 0 -0.42 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.026 0.041 0.25 20 -0.57 2 22
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.019 0.22 1 -0.29 2 3
GNAO1 0.017 0.09 0.25 32 -0.57 20 52
mol:Sphinganine-1-P 0.012 0.026 0.26 1 -0.42 2 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.036 -10000 0 -0.23 1 1
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.02 0.25 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.006 0.023 -10000 0 -0.24 5 5
S1PR5 0.027 0.041 0.25 20 -0.57 2 22
S1PR4 0.029 0.063 0.25 40 -0.57 6 46
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
S1P/S1P5/G12 0.046 0.041 0.24 4 -0.26 4 8
S1P/S1P3/Gq 0.026 0.064 -10000 0 -0.29 32 32
S1P/S1P4/Gi 0.001 0.097 0.26 1 -0.33 48 49
GNAQ 0.022 0.032 -10000 0 -0.57 3 3
GNAZ 0.018 0.054 -10000 0 -0.57 9 9
GNA14 0.023 0.065 0.25 20 -0.57 10 30
GNA15 0.025 0.025 0.25 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.032 -10000 0 -0.57 3 3
ABCC1 0.023 0.006 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.048 -10000 0 -0.57 7 7
positive regulation of NF-kappaB transcription factor activity -0.006 0.11 -10000 0 -0.4 71 71
MAP2K4 0.017 0.046 -10000 0 -0.38 4 4
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.033 -10000 0 -0.57 3 3
SMPD1 0.008 0.029 -10000 0 -0.34 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.015 0.14 0.25 1 -0.57 64 65
TRAIL/TRAILR2 0.026 0.038 -10000 0 -0.4 7 7
TRAIL/TRAILR3 0.027 0.043 -10000 0 -0.37 9 9
TRAIL/TRAILR1 0.024 0.047 -10000 0 -0.41 10 10
TRAIL/TRAILR4 -0.006 0.11 -10000 0 -0.41 71 71
TRAIL/TRAILR1/DAP3/GTP 0.029 0.039 -10000 0 -0.32 7 7
IKK complex 0.011 0.041 -10000 0 -0.41 1 1
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.008 0.035 0.25 1 -0.42 7 8
MAP3K1 0.018 0.061 -10000 0 -0.45 8 8
TRAILR4 (trimer) -0.015 0.14 0.25 1 -0.57 64 65
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.032 -10000 0 -0.57 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.045 -10000 0 -0.36 9 9
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.008 0.035 0.25 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.047 -10000 0 -0.3 7 7
mol:ceramide 0.008 0.029 -10000 0 -0.34 6 6
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.013 0.062 0.26 1 -0.44 7 8
TRAF2 0.025 0.015 0.25 4 -10000 0 4
TRAILR3 (trimer) 0.022 0.021 0.25 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.031 0.041 -10000 0 -0.35 7 7
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.036 0.084 0.28 61 -0.34 3 64
JNK cascade -0.006 0.11 -10000 0 -0.4 71 71
TRAIL (trimer) 0.02 0.048 -10000 0 -0.57 7 7
TNFRSF10C 0.022 0.021 0.25 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.039 -10000 0 -0.31 5 5
TRAIL/TRAILR2/FADD 0.032 0.036 -10000 0 -0.35 5 5
cell death 0.008 0.029 -10000 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.041 -10000 0 -0.41 6 6
TRAILR2 (trimer) 0.02 0.009 -10000 0 -10000 0 0
CASP8 0.012 0.049 -10000 0 -0.56 6 6
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.043 0.043 -10000 0 -0.29 5 5
Class I PI3K signaling events

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
ARF5/GTP -0.013 0.039 0.3 4 -0.28 2 6
DAPP1 0.017 0.1 0.27 7 -0.35 36 43
Src family/SYK family/BLNK-LAT/BTK-ITK 0.018 0.14 0.28 13 -0.51 33 46
mol:DAG 0.022 0.08 0.24 35 -0.25 11 46
HRAS 0.026 0.021 0.25 8 -10000 0 8
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.06 0.27 1 -0.32 10 11
PLCG2 0.02 0.028 0.25 1 -0.57 2 3
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.008 0.25 1 -10000 0 1
mol:GTP -0.01 0.038 0.34 4 -0.28 1 5
ARF1/GTP -0.003 0.033 0.27 7 -0.28 1 8
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
RAP1A/GTP -0.011 0.033 0.2 1 -0.27 1 2
ADAP1 -0.011 0.04 0.32 4 -0.28 2 6
ARAP3 -0.01 0.037 0.34 4 -0.28 1 5
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.027 0.033 0.25 21 -10000 0 21
ARHGEF6 0.017 0.067 -10000 0 -0.57 14 14
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.009 0.25 1 -10000 0 1
mol:Ca2+ 0.016 0.056 0.24 19 -10000 0 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.25 4 -10000 0 4
ZAP70 0.026 0.098 0.25 61 -0.57 20 81
mol:IP3 0.017 0.068 0.21 51 -0.19 5 56
LYN 0.021 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.058 0.36 2 -0.32 10 12
RhoA/GDP 0.03 0.041 0.25 1 -10000 0 1
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.02 0.07 0.32 12 -0.35 2 14
SRC 0.024 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.011 0.23 2 -10000 0 2
RAC1 0.024 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.02 -10000 0 -0.55 1 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.038 0.32 4 -0.27 1 5
RhoA/GTP -0.012 0.037 0.33 4 -0.27 1 5
Src family/SYK family/BLNK-LAT 0.026 0.096 0.25 18 -0.41 18 36
BLK 0.051 0.086 0.25 151 -0.57 2 153
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.037 0.32 4 -0.27 1 5
HCK 0.027 0.026 0.25 13 -10000 0 13
CYTH3 -0.012 0.038 0.33 3 -0.28 2 5
CYTH2 -0.011 0.039 0.32 4 -0.27 1 5
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.051 0.31 1 -0.48 6 7
SGK1 0.006 0.075 -10000 0 -0.35 36 36
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.062 0.38 2 -0.32 12 14
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.044 0.31 6 -10000 0 6
mol:PI-3-4-5-P3 -0.011 0.035 0.28 4 -0.28 1 5
ARAP3/RAP1A/GTP -0.011 0.033 0.2 1 -0.28 1 2
VAV1 0.023 0.033 0.25 2 -0.57 3 5
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.04 0.039 -10000 0 -0.28 1 1
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.059 0.27 1 -0.33 9 10
LAT 0.025 0.038 0.25 15 -0.57 2 17
Rac1/GTP 0.016 0.052 -10000 0 -0.34 11 11
ITK -0.018 0.062 0.32 4 -0.31 30 34
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.022 0.098 0.28 32 -0.33 15 47
LCK 0.027 0.075 0.25 41 -0.57 11 52
BTK -0.011 0.039 0.32 4 -0.27 1 5
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.069 0.051 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.055 0.046 0.33 5 -10000 0 5
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.042 -10000 0 -10000 0 0
CaM/Ca2+ 0.067 0.046 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.042 0.042 0.28 2 -10000 0 2
AKT1 0.011 0.064 0.29 11 -0.28 9 20
MAP2K1 0.007 0.045 0.29 4 -0.29 1 5
MAP3K11 0.023 0.042 0.29 4 -10000 0 4
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.018 0.097 -10000 0 -0.4 10 10
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.034 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.076 0.054 -10000 0 -10000 0 0
CEBPB 0.028 0.095 0.32 2 -0.49 7 9
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.075 0.094 -10000 0 -0.67 10 10
STAT1 0.026 0.047 0.29 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.054 0.08 0.25 146 -10000 0 146
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.045 0.28 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.028 0.062 0.3 3 -0.33 5 8
mol:Ca2+ 0.065 0.048 -10000 0 -10000 0 0
MAPK3 0.023 0.078 -10000 0 -0.59 10 10
STAT1 (dimer) 0.026 0.059 -10000 0 -10000 0 0
MAPK1 -0.006 0.16 -10000 0 -0.67 58 58
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.032 -10000 0 -0.57 3 3
DAPK1 0.027 0.069 0.29 3 -0.34 2 5
SMAD7 0.017 0.036 0.17 7 -10000 0 7
CBL/CRKL/C3G 0.045 0.038 0.29 4 -10000 0 4
PI3K 0.056 0.055 -10000 0 -0.29 10 10
IFNG 0.054 0.08 0.25 146 -10000 0 146
apoptosis 0.024 0.072 0.28 1 -0.4 10 11
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.032 0.042 0.25 36 -10000 0 36
CAMK2B -0.006 0.16 0.25 45 -0.57 71 116
FRAP1 0.008 0.059 0.28 11 -0.26 9 20
PRKCD 0.011 0.066 0.3 13 -10000 0 13
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -10000 0 0
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.022 0.057 0.29 11 -0.32 1 12
STAT1 (dimer)/PIASy 0.038 0.046 0.28 5 -10000 0 5
SOCS1 0.017 0.11 -10000 0 -1 10 10
mol:GDP 0.041 0.036 0.27 4 -10000 0 4
CASP1 0.016 0.039 0.2 7 -0.24 3 10
PTGES2 0.024 0.008 0.25 1 -10000 0 1
IRF9 0.028 0.041 0.23 9 -10000 0 9
mol:PI-3-4-5-P3 0.041 0.046 -10000 0 -0.28 11 11
RAP1/GDP 0.036 0.022 -10000 0 -10000 0 0
CBL 0.021 0.04 0.29 4 -10000 0 4
MAP3K1 0.022 0.042 0.29 4 -0.3 1 5
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.042 -10000 0 -10000 0 0
PTPN11 0.025 0.044 0.31 3 -10000 0 3
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.019 0.023 0.21 5 -0.3 1 6
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.25 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.067 0.048 0.35 10 -0.34 2 12
EPO 0.059 0.084 0.25 169 -10000 0 169
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.016 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.059 0.058 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.076 -10000 0 -0.42 22 22
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.048 -10000 0 -0.4 12 12
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.033 0.03 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
MADCAM1 0.031 0.044 0.25 39 -10000 0 39
cell adhesion 0.065 0.047 0.34 10 -0.33 2 12
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.013 0.043 -10000 0 -0.33 10 10
ITGB7 0.03 0.046 0.25 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.047 -10000 0 -0.36 11 11
p130Cas/Crk/Dock1 0.026 0.041 0.35 1 -0.28 9 10
VCAM1 0.019 0.062 0.25 6 -0.57 11 17
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.023 -10000 0 -10000 0 0
BCAR1 -0.009 0.044 0.38 2 -0.3 10 12
EPOR 0.024 0.008 0.25 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.078 -10000 0 -0.45 20 20
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.11 0.28 16 -0.32 28 44
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.034 0.36 1 -0.42 1 2
NFKBIA 0.012 0.025 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.016 0.25 3 -10000 0 3
IKBKG 0.019 0.03 -10000 0 -10000 0 0
IKK complex/A20 0.021 0.12 -10000 0 -0.4 41 41
NEMO/A20/RIP2 0.02 0.016 0.25 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.014 0.12 0.28 1 -0.37 78 79
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.032 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.11 -10000 0 -0.38 43 43
BCL10/MALT1/TRAF6 0.045 0.014 -10000 0 -10000 0 0
NOD2 0.028 0.043 0.25 30 -0.57 1 31
NFKB1 0.026 0.004 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
MALT1 0.023 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.034 0.049 -10000 0 -0.42 9 9
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.084 0.25 1 -0.57 22 23
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.065 0.25 25 -0.57 9 34
NF kappa B1 p50/RelA 0.051 0.016 -10000 0 -10000 0 0
BCL10 0.024 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.025 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.015 0.12 -10000 0 -0.4 45 45
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.42 51 51
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.021 0.084 0.31 5 -0.39 15 20
NFATC2 -0.005 0.071 0.18 4 -0.25 40 44
NFATC3 0.014 0.016 -10000 0 -0.4 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.095 0.29 2 -0.41 25 27
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.088 0.27 2 -0.44 11 13
BCL2/BAX 0.022 0.075 -10000 0 -0.42 28 28
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.013 -10000 0 -10000 0 0
BAX 0.025 0.016 0.25 5 -10000 0 5
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.008 0.25 1 -10000 0 1
CABIN1/MEF2D 0.019 0.084 -10000 0 -0.42 15 15
Calcineurin A alpha-beta B1/BCL2 0.008 0.094 -10000 0 -0.57 28 28
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.083 0.41 15 -10000 0 15
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.055 0.25 64 -10000 0 64
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.021 0.07 0.25 20 -0.57 12 32
MAP3K8 0.019 0.048 -10000 0 -0.57 7 7
NFAT4/CK1 alpha 0.018 0.028 -10000 0 -0.28 2 2
MEF2D/NFAT1/Cbp/p300 0.011 0.1 -10000 0 -0.29 75 75
CABIN1 0.012 0.094 0.29 2 -0.41 24 26
CALM1 0.021 0.012 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
CAMK4 0.031 0.046 0.25 37 -0.57 1 38
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.041 0.038 -10000 0 -0.42 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.048 -10000 0 -0.57 7 7
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.096 0.3 1 -0.44 13 14
PRKCH 0.023 0.019 -10000 0 -0.57 1 1
CABIN1/Cbp/p300 0.027 0.022 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.008 -10000 0 -10000 0 0
apoptosis 0.011 0.033 -10000 0 -0.36 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.039 -10000 0 -0.28 4 4
PRKCB 0.019 0.077 0.25 19 -0.57 15 34
PRKCE 0.024 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.008 0.059 -10000 0 -0.37 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.024 0.008 0.25 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 -10000 0 -0.57 1 1
PRKCA 0.01 0.084 0.25 1 -0.57 22 23
PRKCG 0.03 0.045 0.25 41 -10000 0 41
PRKCQ 0.002 0.12 0.25 8 -0.57 41 49
FKBP38/BCL2 0.021 0.075 -10000 0 -0.42 28 28
EP300 0.019 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.086 0.32 1 -0.37 15 16
CaM/Ca2+/FKBP38 0.028 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.033 -10000 0 -0.36 1 1
NFATc/ERK1 0.03 0.083 0.32 1 -0.4 11 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.038 0.094 0.28 1 -0.43 18 19
NR4A1 -0.009 0.16 0.25 2 -0.51 86 88
GSK3B 0.023 0.008 -10000 0 -10000 0 0
positive T cell selection 0.014 0.016 -10000 0 -0.4 1 1
NFAT1/CK1 alpha -0.001 0.056 -10000 0 -0.24 16 16
RCH1/ KPNB1 0.041 0.039 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.034 0.053 0.25 52 -0.57 1 53
MEF2D 0.018 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.082 0.32 1 -0.39 12 13
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.008 0.095 -10000 0 -0.57 28 28
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.044 -10000 0 -0.33 10 10
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.008 -10000 0 -0.28 1 1
GATA1/HDAC4 0.036 0.025 -10000 0 -0.42 1 1
GATA1/HDAC5 0.036 0.021 -10000 0 -10000 0 0
GATA2/HDAC5 0.026 0.073 -10000 0 -0.42 26 26
HDAC5/BCL6/BCoR 0.043 0.038 -10000 0 -0.36 8 8
HDAC9 0.021 0.061 0.25 10 -0.57 10 20
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.041 -10000 0 -0.36 10 10
HDAC4/ANKRA2 0.034 0.016 -10000 0 -0.42 1 1
HDAC5/YWHAB 0.033 0.01 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.005 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.25 14 -0.57 26 40
HDAC4/RFXANK 0.035 0.018 -10000 0 -0.42 1 1
BCOR 0.023 0.026 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.012 0.25 2 -10000 0 2
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.047 -10000 0 -0.4 12 12
Histones 0.016 0.049 -10000 0 -0.32 9 9
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.57 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.009 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.018 -10000 0 -0.42 1 1
HDAC7 0.024 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.035 0.012 -10000 0 -10000 0 0
CAMK4 0.031 0.046 0.25 37 -0.57 1 38
Tubulin/HDAC6 0.047 0.018 -10000 0 -0.36 1 1
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
GATA1 0.026 0.029 0.25 17 -10000 0 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.018 0.057 -10000 0 -0.57 10 10
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.23 5 5
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.017 -10000 0 -0.42 1 1
Tubulin 0.035 0.017 -10000 0 -0.42 1 1
HDAC4/14-3-3 E 0.032 0.018 -10000 0 -0.42 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.032 0.04 -10000 0 -0.42 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.017 -10000 0 -0.36 1 1
HDAC4/SRF 0.05 0.034 -10000 0 -0.36 2 2
HDAC4/ER alpha -0.016 0.17 -10000 0 -0.42 157 157
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.049 -10000 0 -0.32 9 9
cell motility 0.047 0.018 -10000 0 -0.36 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.036 0.006 -10000 0 -10000 0 0
BCL6 0.02 0.044 -10000 0 -0.57 6 6
HDAC4/CaMK II delta B 0.023 0.019 -10000 0 -0.57 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.037 0.23 0.25 116 -0.57 153 269
HDAC6/HDAC11 0.036 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.019 -10000 0 -0.57 1 1
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.063 0.03 -10000 0 -0.31 2 2
GNG2 0.018 0.06 -10000 0 -0.57 11 11
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.023 0.021 0.25 2 -0.57 1 3
HDAC11 0.024 0.008 0.25 1 -10000 0 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.025 0.013 0.25 3 -10000 0 3
nuclear import -0.027 0.016 0.33 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.03 0.046 0.25 30 -0.57 2 32
ITGA4 0.026 0.022 0.25 10 -10000 0 10
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
alpha4/beta1 Integrin 0.036 0.016 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0.051 0.081 -10000 0 -0.48 1 1
CRKL 0.025 0.047 0.31 6 -10000 0 6
mol:DAG 0.038 0.051 -10000 0 -10000 0 0
HRAS 0.034 0.078 0.3 19 -10000 0 19
MAPK8 0.04 0.07 0.24 35 -0.34 5 40
RAP1A 0.026 0.047 0.31 7 -10000 0 7
GAB1 0.026 0.046 0.32 5 -10000 0 5
MAPK14 0.042 0.065 0.24 35 -10000 0 35
EPO 0.06 0.084 0.25 169 -10000 0 169
PLCG1 0.038 0.051 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.013 0.25 1 -10000 0 1
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.063 0.061 -10000 0 -0.35 5 5
GAB1/SHC/GRB2/SOS1 0.042 0.041 0.26 2 -10000 0 2
EPO/EPOR (dimer) 0.06 0.058 -10000 0 -10000 0 0
IRS2 0.014 0.071 0.31 5 -0.31 26 31
STAT1 0.044 0.064 0.32 3 -10000 0 3
STAT5B 0.04 0.058 -10000 0 -0.34 1 1
cell proliferation 0.022 0.075 0.24 37 -0.32 5 42
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.044 -10000 0 -0.28 7 7
TEC 0.025 0.047 0.29 5 -0.3 1 6
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
STAT1 (dimer) 0.044 0.063 0.32 3 -10000 0 3
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
EPO/EPOR (dimer)/JAK2 0.08 0.062 0.33 3 -10000 0 3
EPO/EPOR 0.06 0.058 -10000 0 -10000 0 0
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.046 0.28 3 -0.29 1 4
elevation of cytosolic calcium ion concentration 0.026 0.013 0.25 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.062 0.054 -10000 0 -10000 0 0
mol:IP3 0.038 0.051 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.031 0.078 0.29 2 -0.31 16 18
SH2B3 0.026 0.009 -10000 0 -10000 0 0
NFKB1 0.042 0.065 0.25 28 -10000 0 28
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.042 -10000 0 -0.27 2 2
PTPN6 0.023 0.039 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.047 0.048 0.28 3 -10000 0 3
EPOR 0.026 0.013 0.25 1 -10000 0 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.041 0.27 2 -10000 0 2
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.028 0.25 1 -0.57 2 3
CRKL/CBL/C3G 0.046 0.047 0.28 5 -10000 0 5
VAV2 0.027 0.048 0.3 8 -10000 0 8
CBL 0.025 0.047 0.29 8 -10000 0 8
SHC/Grb2/SOS1 0.036 0.037 -10000 0 -10000 0 0
STAT5A 0.038 0.063 -10000 0 -0.33 6 6
GRB2 0.023 0.009 0.25 1 -10000 0 1
STAT5 (dimer) 0.051 0.08 0.34 1 -0.43 2 3
LYN/PLCgamma2 0.027 0.026 -10000 0 -0.42 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.028 0.048 0.3 8 -10000 0 8
BCL2 0.031 0.17 -10000 0 -0.83 35 35
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.41 67 67
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.004 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.11 0.15 0.4 1 -0.42 75 76
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.009 0.027 -10000 0 -0.42 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.021 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.024 0.024 0.25 11 -10000 0 11
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.01 0.016 0.24 5 -10000 0 5
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.063 0.26 1 -0.33 11 12
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.12 0.16 0.41 1 -0.47 77 78
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.021 0.07 0.25 20 -0.57 12 32
LNPEP 0.019 0.051 -10000 0 -0.57 8 8
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.02 0.082 -10000 0 -0.42 35 35
AKT1 0.032 0.085 0.37 3 -0.55 7 10
PTK2B 0.003 0.085 0.35 1 -0.73 6 7
VEGFR2 homodimer/Frs2 0.025 0.059 -10000 0 -0.6 8 8
CAV1 -0.099 0.24 -10000 0 -0.57 222 222
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.039 0.058 -10000 0 -0.56 8 8
endothelial cell proliferation 0.044 0.11 0.34 27 -0.57 8 35
mol:Ca2+ 0.014 0.052 -10000 0 -0.61 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.051 0.059 -10000 0 -0.51 9 9
RP11-342D11.1 0.004 0.052 -10000 0 -0.51 8 8
CDH5 0.018 0.048 -10000 0 -0.57 7 7
VEGFA homodimer 0.05 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.011 0.086 0.25 1 -0.57 23 24
HRAS/GDP 0.031 0.048 -10000 0 -0.57 4 4
SH2D2A 0.04 0.072 0.25 96 -0.57 2 98
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.044 0.085 -10000 0 -0.53 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.046 0.073 -10000 0 -0.5 9 9
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.059 -10000 0 -0.64 4 4
GRB10 0.015 0.054 -10000 0 -0.64 5 5
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.25 1 -10000 0 1
PAK1 0.023 0.019 0.25 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.072 -10000 0 -0.71 6 6
HRAS 0.025 0.02 0.25 8 -10000 0 8
VEGF/Rho/ROCK1/Integrin Complex 0.011 0.073 -10000 0 -0.52 9 9
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.25 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.049 0.058 -10000 0 -0.5 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.032 -10000 0 -0.57 3 3
Nck/Pak 0.033 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.037 0.063 -10000 0 -0.56 9 9
mol:GDP 0.039 0.053 -10000 0 -0.62 4 4
mol:NADP 0.026 0.082 0.56 1 -0.46 11 12
eNOS/Hsp90 0.037 0.078 0.55 1 -0.44 10 11
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
mol:IP3 0.014 0.053 -10000 0 -0.62 5 5
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.008 0.25 1 -10000 0 1
VEGFA 0.026 0.019 0.26 7 -10000 0 7
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.022 0.1 0.35 1 -0.69 8 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.039 0.095 -10000 0 -0.4 34 34
PTPN6 0.024 0.011 0.25 2 -10000 0 2
EPAS1 0.025 0.056 -10000 0 -0.55 9 9
mol:L-citrulline 0.026 0.082 0.56 1 -0.46 11 12
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.048 0.06 -10000 0 -0.53 8 8
VEGFR2 homodimer/VEGFA homodimer 0.041 0.059 -10000 0 -0.53 9 9
VEGFR2/3 heterodimer 0.024 0.066 -10000 0 -0.61 10 10
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.005 0.067 -10000 0 -0.66 6 6
VEGFR2 homodimer 0.012 0.064 -10000 0 -0.64 9 9
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.007 0.072 0.27 1 -0.61 5 6
MAPK1 0.01 0.073 0.27 1 -0.58 6 7
VEGFA145/NRP2 0.035 0.025 -10000 0 -0.39 2 2
VEGFR1/2 heterodimer 0.024 0.061 -10000 0 -0.58 9 9
KDR 0.012 0.065 -10000 0 -0.65 9 9
VEGFA165/NRP1/VEGFR2 homodimer 0.041 0.061 -10000 0 -0.56 8 8
SRC 0.024 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.015 0.08 0.46 1 -0.59 6 7
PI3K 0.026 0.068 -10000 0 -0.71 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.04 0.058 -10000 0 -0.53 9 9
FES 0.014 0.058 -10000 0 -0.66 5 5
GAB1 0.015 0.061 -10000 0 -0.74 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.039 0.057 -10000 0 -0.51 9 9
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.016 0.13 -10000 0 -0.48 22 22
VEGFR2 homodimer/VEGFA homodimer/Yes 0.038 0.06 -10000 0 -0.51 10 10
PI3K/GAB1 0.039 0.08 0.31 1 -0.55 7 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.054 0.059 -10000 0 -0.62 5 5
PRKACA 0.024 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.064 -10000 0 -0.57 10 10
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.014 0.056 -10000 0 -0.52 8 8
actin cytoskeleton reorganization 0.045 0.072 -10000 0 -0.5 9 9
PTK2 0.006 0.086 -10000 0 -0.76 8 8
EDG1 0.004 0.052 -10000 0 -0.51 8 8
mol:DAG 0.014 0.053 -10000 0 -0.62 5 5
CaM/Ca2+ 0.026 0.051 -10000 0 -0.57 5 5
MAP2K3 -0.006 0.059 -10000 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.04 0.058 -10000 0 -0.67 5 5
PLCG1 0.014 0.054 -10000 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.05 0.058 -10000 0 -0.49 9 9
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.04 0.058 -10000 0 -0.53 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.058 -10000 0 -0.56 8 8
cell migration 0.025 0.092 0.31 2 -0.65 7 9
mol:PI-3-4-5-P3 0.026 0.063 -10000 0 -0.64 5 5
FYN 0.022 0.026 -10000 0 -0.57 2 2
VEGFB/NRP1 0.019 0.052 -10000 0 -0.6 5 5
mol:NO 0.026 0.082 0.56 1 -0.46 11 12
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.043 -10000 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.055 -10000 0 -0.67 5 5
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.25 4 -0.57 35 39
NOS3 0.026 0.089 0.57 1 -0.53 11 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.078 -10000 0 -0.39 30 30
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.008 0.072 0.35 1 -0.69 5 6
PRKCB -0.005 0.065 -10000 0 -0.64 5 5
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.023 0.054 -10000 0 -0.48 9 9
VEGFR1/2 heterodimer/VEGFA homodimer 0.038 0.06 -10000 0 -0.54 9 9
VEGFA165/NRP2 0.035 0.025 -10000 0 -0.39 2 2
MAPKKK cascade 0.051 0.079 0.34 10 -0.58 4 14
NRP2 0.023 0.027 0.25 1 -0.57 2 3
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.019 -10000 0 -0.57 1 1
FAK1/Paxillin 0.023 0.1 0.42 2 -0.74 7 9
MAP3K13 0.013 0.058 -10000 0 -0.5 9 9
PDPK1 0.015 0.056 0.27 1 -0.57 4 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.026 0.018 -10000 0 -0.47 1 1
VEGFR1 homodimer/NRP1 0.01 0.015 -10000 0 -0.48 1 1
mol:DAG 0.013 0.03 -10000 0 -0.38 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.02 -10000 0 -0.44 1 1
CaM/Ca2+ 0.026 0.029 -10000 0 -0.37 2 2
HIF1A 0.028 0.011 -10000 0 -0.31 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.01 0.051 -10000 0 -0.42 1 1
PLCG1 0.013 0.03 -10000 0 -0.39 2 2
NOS3 0.017 0.052 -10000 0 -0.52 2 2
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:NO 0.021 0.061 0.3 1 -0.45 5 6
FLT1 0.014 0.018 -10000 0 -0.56 1 1
PGF 0.024 0.024 0.25 5 -0.57 1 6
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.03 -10000 0 -0.39 3 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.033 0.063 -10000 0 -0.43 6 6
endothelial cell proliferation 0.011 0.082 0.33 7 -0.46 8 15
mol:Ca2+ 0.013 0.03 -10000 0 -0.38 2 2
MAPK3 -0.012 0.049 -10000 0 -0.67 1 1
MAPK1 -0.012 0.048 0.22 1 -0.32 18 19
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
PLGF homodimer 0.024 0.024 0.25 5 -0.57 1 6
PRKACA 0.024 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.099 0.24 -10000 0 -0.57 222 222
VEGFA homodimer 0.025 0.019 0.25 7 -10000 0 7
VEGFR1 homodimer/VEGFA homodimer 0.027 0.022 -10000 0 -0.48 1 1
platelet activating factor biosynthetic process -0.013 0.046 -10000 0 -0.64 1 1
PI3K 0.044 0.047 -10000 0 -0.32 13 13
PRKCA -0.011 0.052 0.24 1 -0.33 20 21
PRKCB -0.008 0.049 -10000 0 -0.34 15 15
VEGFR1 homodimer/PLGF homodimer 0.027 0.024 -10000 0 -0.42 2 2
VEGFA 0.025 0.019 0.25 7 -10000 0 7
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.03 -10000 0 -0.38 2 2
RASA1 0.013 0.028 -10000 0 -0.43 1 1
NRP2 0.023 0.027 0.25 1 -0.57 2 3
VEGFR1 homodimer 0.014 0.018 -10000 0 -0.55 1 1
VEGFB homodimer 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.028 0.14 0.3 1 -0.44 25 26
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.046 -10000 0 -0.32 13 13
mol:L-citrulline 0.021 0.061 0.3 1 -0.45 5 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.028 -10000 0 -0.41 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.039 0.023 -10000 0 -0.45 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.053 0.049 -10000 0 -0.31 13 13
PDPK1 -0.004 0.052 -10000 0 -0.4 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.023 -10000 0 -0.45 1 1
mol:NADP 0.021 0.061 0.3 1 -0.45 5 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.027 -10000 0 -0.41 1 1
VEGFR1 homodimer/NRP2 0.026 0.027 -10000 0 -0.44 3 3
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.05 0.061 -10000 0 -0.37 8 8
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.061 -10000 0 -0.34 8 8
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.021 0.25 7 -10000 0 7
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.005 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.053 0.041 -10000 0 -0.4 1 1
YY1/LSF 0.024 0.05 -10000 0 -0.3 7 7
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.03 -10000 0 -0.3 7 7
I kappa B alpha/HDAC1 0.03 0.037 -10000 0 -0.42 1 1
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.02 0.036 -10000 0 -0.3 7 7
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.031 0.036 -10000 0 -0.43 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.28 12 12
NF kappa B1 p50/RelA 0.026 0.064 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.25 14 -0.57 26 40
GATA1 0.026 0.029 0.25 17 -10000 0 17
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.079 -10000 0 -0.36 20 20
RBBP7 0.026 0.019 0.25 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.019 -10000 0 -0.57 1 1
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.026 -10000 0 -0.25 7 7
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.029 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.022 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.015 0.25 4 -10000 0 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.023 0.046 -10000 0 -0.38 3 3
YY1/HDAC2 0.025 0.045 -10000 0 -0.29 5 5
YY1/HDAC1 0.025 0.047 -10000 0 -0.29 6 6
NuRD/MBD2 Complex (MeCP1) 0.024 0.054 -10000 0 -0.27 13 13
PPARG -0.059 0.16 -10000 0 -0.34 223 223
HDAC8/hEST1B 0.041 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.036 -10000 0 -0.43 1 1
MBD3L2 0.017 0.011 0.25 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.065 -10000 0 -0.35 14 14
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.019 0.027 -10000 0 -0.24 8 8
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.011 -10000 0 -0.29 1 1
HDAC8 0.025 0.001 -10000 0 -10000 0 0
SMAD7 0.024 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.007 0.25 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.036 0.049 -10000 0 -0.28 5 5
YY1/SAP30/HDAC1 0.037 0.047 -10000 0 -0.27 3 3
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.026 -10000 0 -0.25 7 7
histone deacetylation 0.024 0.053 -10000 0 -0.27 13 13
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.035 -10000 0 -0.33 2 2
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GATAD2B 0.021 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.025 0.065 -10000 0 -0.33 23 23
GATA1/HDAC1 0.036 0.02 -10000 0 -10000 0 0
GATA1/HDAC3 0.033 0.041 -10000 0 -0.45 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.049 -10000 0 -0.42 9 9
SIN3/HDAC complex/Mad/Max 0.016 0.053 -10000 0 -0.29 18 18
NuRD Complex 0.025 0.065 -10000 0 -0.38 9 9
positive regulation of chromatin silencing 0.051 0.04 -10000 0 -0.4 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.24 3 3
HDAC complex 0.057 0.022 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.025 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.016 -10000 0 -10000 0 0
TNF 0.024 0.065 0.25 25 -0.57 9 34
negative regulation of cell growth 0.016 0.053 -10000 0 -0.29 18 18
NuRD/MBD2/PRMT5 Complex 0.024 0.054 -10000 0 -0.27 13 13
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NF kappa B/RelA/I kappa B alpha 0.019 0.052 -10000 0 -0.36 8 8
SIN3/HDAC complex/NCoR1 0.008 0.066 -10000 0 -0.32 28 28
TFCP2 0.024 0.018 -10000 0 -0.57 1 1
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.009 0.25 1 -10000 0 1
MBD2 0.024 0.005 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.004 0.039 0.21 1 -0.24 9 10
SMAD3 0.022 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.063 -10000 0 -0.46 10 10
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.058 -10000 0 -0.28 1 1
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.27 8 8
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
TRAP-1/SMAD4 0.027 0.056 -10000 0 -0.41 17 17
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.015 0.072 -10000 0 -0.57 16 16
UBE2I 0.023 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.005 -10000 0 -10000 0 0
KPNA2 0.036 0.055 0.25 64 -10000 0 64
PIAS4 0.024 0.004 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.026 0.047 -10000 0 -10000 0 0
TP53 0.01 0.018 -10000 0 -0.19 2 2
Senescence 0.009 0.022 -10000 0 -0.19 2 2
Apoptosis 0.009 0.022 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.011 0.059 0.29 31 -10000 0 31
MDM4 0.02 0.009 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.034 0.011 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.043 -10000 0 -0.4 1 1
NFKBIA 0.015 0.037 -10000 0 -0.25 11 11
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.017 0.065 -10000 0 -0.57 13 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.013 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.012 0.25 2 -10000 0 2
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
NFKB1 0.01 0.011 0.26 2 -10000 0 2
RELA 0.024 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.024 0.046 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.046 -10000 0 -0.38 2 2
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.048 -10000 0 -0.4 12 12
NF kappa B1 p50/RelA 0.024 0.046 -10000 0 -0.26 10 10
IKBKB 0.02 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.057 -10000 0 -0.29 15 15
cell death 0.024 0.045 -10000 0 -0.36 2 2
NF kappa B1 p105/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
LCK 0.027 0.075 0.25 41 -0.57 11 52
BCL3 0.024 0.011 0.25 2 -10000 0 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.042 0.035 -10000 0 -10000 0 0
CLOCK 0.02 0.06 -10000 0 -0.57 11 11
TIMELESS/CRY2 0.031 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.014 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.017 -10000 0 -10000 0 0
ARNTL 0.026 0.004 -10000 0 -10000 0 0
TIMELESS 0.018 0.023 -10000 0 -10000 0 0
NPAS2 0.023 0.041 0.26 1 -0.57 5 6
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.006 -10000 0 -0.089 5 5
CHEK1 0.027 0.034 0.25 23 -10000 0 23
mol:HEME 0.007 0.006 0.089 5 -10000 0 5
PER1 0.014 0.07 -10000 0 -0.57 15 15
BMAL/CLOCK/NPAS2 0.049 0.052 -10000 0 -0.36 16 16
BMAL1/CLOCK 0.019 0.062 -10000 0 -0.48 1 1
S phase of mitotic cell cycle 0.042 0.035 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.042 0.036 -10000 0 -10000 0 0
mol:NADPH 0.007 0.006 0.089 5 -10000 0 5
PER1/TIMELESS 0.025 0.045 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.018 0.25 6 -10000 0 6
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.04 0.068 0.32 8 -10000 0 8
regulation of axonogenesis -0.011 0.026 0.23 6 -10000 0 6
myoblast fusion -0.026 0.046 -10000 0 -0.22 1 1
mol:GTP 0.022 0.031 -10000 0 -0.15 8 8
regulation of calcium-dependent cell-cell adhesion -0.054 0.044 -10000 0 -0.3 2 2
ARF1/GTP 0.03 0.029 -10000 0 -10000 0 0
mol:GM1 0.012 0.024 -10000 0 -10000 0 0
mol:Choline 0.009 0.038 -10000 0 -0.34 9 9
lamellipodium assembly 0.018 0.058 -10000 0 -0.36 7 7
MAPK3 0.032 0.045 0.21 1 -10000 0 1
ARF6/GTP/NME1/Tiam1 0.055 0.045 0.3 2 -10000 0 2
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.046 0.22 1 -10000 0 1
ARF1/GDP 0.025 0.048 -10000 0 -0.26 3 3
ARF6 0.031 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.015 0.25 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.031 0.044 0.2 9 -10000 0 9
actin filament bundle formation -0.032 0.05 0.24 5 -10000 0 5
KALRN 0.01 0.055 -10000 0 -0.31 21 21
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.051 -10000 0 -0.25 5 5
NME1 0.028 0.031 0.26 18 -10000 0 18
Rac1/GDP 0.033 0.051 -10000 0 -0.25 5 5
substrate adhesion-dependent cell spreading 0.022 0.031 -10000 0 -0.15 8 8
cortical actin cytoskeleton organization 0.018 0.058 -10000 0 -0.37 7 7
RAC1 0.024 0.003 -10000 0 -10000 0 0
liver development 0.022 0.031 -10000 0 -0.15 8 8
ARF6/GTP 0.022 0.031 -10000 0 -0.15 8 8
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.046 0.23 1 -0.21 5 6
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.016 0.045 -10000 0 -0.39 9 9
RAB11FIP3 0.023 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.018 0.058 -10000 0 -0.36 7 7
ruffle organization 0.011 0.026 -10000 0 -0.23 6 6
regulation of epithelial cell migration 0.022 0.031 -10000 0 -0.15 8 8
PLD2 0.02 0.024 -10000 0 -10000 0 0
PIP5K1A 0.011 0.026 -10000 0 -0.23 6 6
mol:Phosphatidic acid 0.009 0.038 -10000 0 -0.34 9 9
Rac1/GTP 0.018 0.058 -10000 0 -0.37 7 7
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.25 10 -10000 0 10
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.017 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.044 0.035 0.33 4 -0.33 2 6
lamellipodium assembly -0.002 0.086 -10000 0 -0.41 32 32
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.048 -10000 0 -0.4 12 12
ARF6 0.024 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.004 -10000 0 -10000 0 0
PXN 0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.017 0.062 -10000 0 -0.57 12 12
ARF6/GTP 0.047 0.021 -10000 0 -10000 0 0
cell adhesion 0.05 0.019 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.016 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.03 0.046 0.25 30 -0.57 2 32
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.048 0.043 -10000 0 -0.32 11 11
p130Cas/Crk/Dock1 0.041 0.019 -10000 0 -10000 0 0
VCAM1 0.019 0.062 0.25 6 -0.57 11 17
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.019 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.021 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.048 0.021 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.019 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.095 -10000 0 -0.46 32 32
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.011 -10000 0 -0.26 1 1
MDM2/SUMO1 0.033 0.04 -10000 0 -0.23 4 4
HDAC4 0.023 0.019 -10000 0 -0.57 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.009 0.017 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.23 5 5
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.24 3 3
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.057 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.005 -10000 0 -10000 0 0
Ran/GTP 0.023 0.036 -10000 0 -0.24 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.038 0.25 1 -0.24 4 5
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.032 0.18 3 -10000 0 3
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.047 -10000 0 -0.19 4 4
AP2 0.034 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.01 -10000 0 -10000 0 0
CLTB 0.025 0.016 0.25 5 -10000 0 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.01 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.012 0.2 3 -10000 0 3
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.02 -10000 0 -0.15 1 1
AP2M1 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.017 -10000 0 -10000 0 0
ARFIP2 0.015 0.018 -10000 0 -10000 0 0
COPA 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.011 0.023 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.041 -10000 0 -0.24 20 20
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.023 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.013 0.049 -10000 0 -0.26 27 27
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -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 0.019 0.023 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 -10000 0 -10000 0 0
PIP5K1A 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.006 -10000 0 -10000 0 0
GOSR2 0.008 0.028 -10000 0 -0.31 7 7
USO1 0.01 0.02 -10000 0 -0.32 3 3
GBF1 0.009 0.024 -10000 0 -0.31 5 5
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.015 -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 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.067 0.025 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.024 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.016 -10000 0 -9999 0 0
RELB 0.026 0.022 0.25 10 -9999 0 10
NFKB2 0.024 0.008 0.25 1 -9999 0 1
NF kappa B2 p52/RelB 0.033 0.016 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.016 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1073 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z7.A8R6 TCGA.Z7.A8R5 TCGA.XX.A89A TCGA.XX.A899
109_MAP3K5 -0.33 0.025 0.025 0.025
47_PPARGC1A -0.57 0.025 0.025 0.025
105_BMP4 0.025 0.025 0.025 0.025
105_BMP6 0.025 0.025 0.025 0.025
105_BMP7 0.025 0.025 0.025 0.025
105_BMP2 -0.57 0.025 0.025 0.025
131_RELN/VLDLR -0.33 -0.33 0.063 0.063
30_TGFB1/TGF beta receptor Type II -0.033 0.024 0.019 0.019
84_STAT5B -0.16 -0.06 0.12 0.03
84_STAT5A -0.16 -0.06 0.12 0.03
Methods & Data
Input
  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/11493679/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/11541490/Gistic2_Analysis_11541873/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)