PARADIGM pathway analysis of mRNA expression and copy number data
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C12Z13WM
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C12Z13WM
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 43 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 316
TCGA08_retinoblastoma 107
Effects of Botulinum toxin 99
PLK1 signaling events 98
Osteopontin-mediated events 97
S1P3 pathway 96
Signaling events regulated by Ret tyrosine kinase 91
Endothelins 81
PLK2 and PLK4 events 80
Circadian rhythm pathway 79
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 570 . 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 ( 570 ).

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 0.5544 316 16125 51 -0.013 1.7 1000 -1000 -0.003 -1000
TCGA08_retinoblastoma 0.1877 107 861 8 -0.084 0.075 1000 -1000 -0.001 -1000
Effects of Botulinum toxin 0.1737 99 2581 26 -0.13 0.058 1000 -1000 -0.028 -1000
PLK1 signaling events 0.1719 98 8346 85 -0.11 0.23 1000 -1000 -0.022 -1000
Osteopontin-mediated events 0.1702 97 3709 38 -0.086 0.21 1000 -1000 -0.045 -1000
S1P3 pathway 0.1684 96 4061 42 -0.6 0.043 1000 -1000 -0.022 -1000
Signaling events regulated by Ret tyrosine kinase 0.1596 91 7500 82 -0.18 0.031 1000 -1000 -0.054 -1000
Endothelins 0.1421 81 7787 96 -0.22 0.071 1000 -1000 -0.046 -1000
PLK2 and PLK4 events 0.1404 80 241 3 0.016 0.071 1000 -1000 -0.027 -1000
Circadian rhythm pathway 0.1386 79 1754 22 -0.098 0.27 1000 -1000 -0.026 -1000
IGF1 pathway 0.1351 77 4392 57 -0.097 0.057 1000 -1000 -0.05 -1000
Nongenotropic Androgen signaling 0.1228 70 3643 52 -0.19 0.14 1000 -1000 -0.034 -1000
IL4-mediated signaling events 0.1140 65 5919 91 -0.78 0.19 1000 -1000 -0.061 -1000
PDGFR-alpha signaling pathway 0.1140 65 2885 44 -0.18 0.034 1000 -1000 -0.037 -1000
Thromboxane A2 receptor signaling 0.1105 63 6682 105 -0.13 0.042 1000 -1000 -0.043 -1000
IL2 signaling events mediated by STAT5 0.1105 63 1402 22 -0.41 0.032 1000 -1000 -0.028 -1000
mTOR signaling pathway 0.1070 61 3268 53 -0.15 0.031 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.1070 61 6246 102 -0.071 0.031 1000 -1000 -0.054 -1000
Ephrin B reverse signaling 0.1018 58 2819 48 -0.18 0.063 1000 -1000 -0.043 -1000
Syndecan-1-mediated signaling events 0.1000 57 1970 34 -0.052 0.031 1000 -1000 -0.031 -1000
Insulin Pathway 0.0947 54 4045 74 -0.14 0.066 1000 -1000 -0.053 -1000
HIF-2-alpha transcription factor network 0.0930 53 2289 43 -0.043 0.22 1000 -1000 -0.037 -1000
Coregulation of Androgen receptor activity 0.0895 51 3945 76 -0.5 0.043 1000 -1000 -0.024 -1000
IL23-mediated signaling events 0.0895 51 3119 60 -0.13 0.1 1000 -1000 -0.028 -1000
FoxO family signaling 0.0877 50 3252 64 -0.018 0.38 1000 -1000 -0.021 -1000
Cellular roles of Anthrax toxin 0.0807 46 1815 39 -0.25 0.031 1000 -1000 -0.023 -1000
Signaling mediated by p38-alpha and p38-beta 0.0789 45 2011 44 -0.088 0.031 1000 -1000 -0.035 -1000
Signaling events mediated by the Hedgehog family 0.0737 42 2209 52 -0.042 0.073 1000 -1000 -0.042 -1000
Aurora B signaling 0.0719 41 2768 67 -0.19 0.18 1000 -1000 -0.027 -1000
Integrins in angiogenesis 0.0684 39 3278 84 -0.14 0.054 1000 -1000 -0.06 -1000
Reelin signaling pathway 0.0667 38 2153 56 -0.068 0.079 1000 -1000 -0.034 -1000
Plasma membrane estrogen receptor signaling 0.0667 38 3323 86 -0.15 0.11 1000 -1000 -0.052 -1000
FAS signaling pathway (CD95) 0.0649 37 1751 47 -0.1 0.043 1000 -1000 -0.023 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0632 36 1908 52 -0.22 0.11 1000 -1000 -0.015 -1000
Nectin adhesion pathway 0.0614 35 2230 63 -0.12 0.054 1000 -1000 -0.045 -1000
Signaling mediated by p38-gamma and p38-delta 0.0614 35 525 15 -0.085 0.029 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0614 35 2086 58 -0.3 0.054 1000 -1000 -0.021 -1000
TCGA08_rtk_signaling 0.0596 34 896 26 -0.14 0.031 1000 -1000 -0.015 -1000
HIF-1-alpha transcription factor network 0.0526 30 2285 76 -0.027 0.42 1000 -1000 -0.069 -1000
Insulin-mediated glucose transport 0.0526 30 963 32 -0.18 0.039 1000 -1000 -0.027 -1000
amb2 Integrin signaling 0.0526 30 2491 82 -0.099 0.061 1000 -1000 -0.035 -1000
TRAIL signaling pathway 0.0526 30 1478 48 -0.083 0.031 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0526 30 1360 45 -0.11 0.07 1000 -1000 -0.042 -1000
Regulation of Androgen receptor activity 0.0491 28 1962 70 -0.59 0.046 1000 -1000 -0.027 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0474 27 2354 85 -0.13 0.054 1000 -1000 -0.04 -1000
Aurora A signaling 0.0474 27 1639 60 -0.19 0.17 1000 -1000 -0.027 -1000
IL6-mediated signaling events 0.0474 27 2075 75 -0.29 0.035 1000 -1000 -0.02 -1000
Arf6 signaling events 0.0456 26 1617 62 -0.066 0.058 1000 -1000 -0.009 -1000
Class I PI3K signaling events 0.0456 26 1907 73 -0.03 0.075 1000 -1000 -0.028 -1000
Fc-epsilon receptor I signaling in mast cells 0.0439 25 2436 97 -0.061 0.052 1000 -1000 -0.06 -1000
IL1-mediated signaling events 0.0439 25 1577 62 -0.047 0.061 1000 -1000 -0.059 -1000
PDGFR-beta signaling pathway 0.0439 25 2493 97 -0.071 0.058 1000 -1000 -0.059 -1000
Caspase cascade in apoptosis 0.0421 24 1840 74 -0.068 0.044 1000 -1000 -0.033 -1000
Signaling events mediated by PTP1B 0.0421 24 1866 76 -0.14 0.041 1000 -1000 -0.031 -1000
Canonical Wnt signaling pathway 0.0421 24 1271 51 -0.33 0.14 1000 -1000 -0.051 -1000
E-cadherin signaling in keratinocytes 0.0421 24 1074 43 -0.036 0.046 1000 -1000 -0.03 -1000
Syndecan-2-mediated signaling events 0.0404 23 1640 69 -0.037 0.044 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 0.0404 23 1366 58 -0.13 0.031 1000 -1000 -0.031 -1000
p75(NTR)-mediated signaling 0.0386 22 2773 125 -0.14 0.081 1000 -1000 -0.063 -1000
ceramide signaling pathway 0.0386 22 1126 49 -0.071 0.042 1000 -1000 -0.031 -1000
E-cadherin signaling in the nascent adherens junction 0.0386 22 1700 76 -0.086 0.06 1000 -1000 -0.059 -1000
Ras signaling in the CD4+ TCR pathway 0.0386 22 382 17 -0.03 0.021 1000 -1000 -0.01 -1000
LPA4-mediated signaling events 0.0368 21 252 12 -0.051 0.002 1000 -1000 -0.023 -1000
TCR signaling in naïve CD8+ T cells 0.0368 21 1953 93 -0.095 0.078 1000 -1000 -0.047 -1000
Presenilin action in Notch and Wnt signaling 0.0351 20 1267 61 -0.3 0.061 1000 -1000 -0.03 -1000
Glypican 1 network 0.0351 20 973 48 -0.16 0.055 1000 -1000 -0.033 -1000
Glucocorticoid receptor regulatory network 0.0351 20 2323 114 -0.32 0.16 1000 -1000 -0.064 -1000
Syndecan-3-mediated signaling events 0.0351 20 706 35 -0.023 0.049 1000 -1000 -0.029 -1000
EGFR-dependent Endothelin signaling events 0.0351 20 429 21 -0.047 0.058 1000 -1000 -0.04 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0351 20 1595 78 -0.14 0.041 1000 -1000 -0.029 -1000
EPO signaling pathway 0.0333 19 1058 55 -0.058 0.048 1000 -1000 -0.042 -1000
ErbB2/ErbB3 signaling events 0.0316 18 1197 65 -0.038 0.061 1000 -1000 -0.07 -1000
BMP receptor signaling 0.0316 18 1476 81 -0.12 0.057 1000 -1000 -0.028 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0316 18 683 37 -0.019 0.062 1000 -1000 -0.039 -1000
TCGA08_p53 0.0316 18 128 7 -0.006 0.03 1000 -1000 -0.019 -1000
IL27-mediated signaling events 0.0316 18 967 51 -0.058 0.067 1000 -1000 -0.038 -1000
EPHB forward signaling 0.0298 17 1465 85 -0.068 0.14 1000 -1000 -0.066 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0298 17 1298 74 -0.14 0.076 1000 -1000 -0.066 -1000
BCR signaling pathway 0.0298 17 1700 99 -0.062 0.073 1000 -1000 -0.061 -1000
ErbB4 signaling events 0.0281 16 1126 69 -0.19 0.16 1000 -1000 -0.038 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0281 16 874 54 -0.057 0.042 1000 -1000 -0.049 -1000
IFN-gamma pathway 0.0281 16 1113 68 -0.085 0.065 1000 -1000 -0.052 -1000
Ceramide signaling pathway 0.0281 16 1245 76 -0.048 0.066 1000 -1000 -0.03 -1000
Regulation of p38-alpha and p38-beta 0.0281 16 902 54 -0.063 0.067 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0281 16 1119 68 -0.09 0.044 1000 -1000 -0.057 -1000
Regulation of Telomerase 0.0281 16 1660 102 -0.26 0.068 1000 -1000 -0.044 -1000
Arf1 pathway 0.0281 16 893 54 -0.026 0.037 1000 -1000 -0.023 -1000
IL12-mediated signaling events 0.0263 15 1360 87 -0.22 0.042 1000 -1000 -0.055 -1000
Arf6 downstream pathway 0.0263 15 667 43 -0.047 0.061 1000 -1000 -0.031 -1000
FOXA2 and FOXA3 transcription factor networks 0.0263 15 715 46 0 0.23 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class III 0.0263 15 603 40 -0.06 0.065 1000 -1000 -0.032 -1000
S1P1 pathway 0.0263 15 571 36 -0.091 0.031 1000 -1000 -0.04 -1000
Signaling events mediated by PRL 0.0263 15 535 34 -0.087 0.042 1000 -1000 -0.034 -1000
BARD1 signaling events 0.0246 14 800 57 -0.034 0.19 1000 -1000 -0.037 -1000
Calcium signaling in the CD4+ TCR pathway 0.0246 14 462 31 -0.092 0.032 1000 -1000 -0.024 -1000
Regulation of nuclear SMAD2/3 signaling 0.0228 13 1868 136 -0.11 0.12 1000 -1000 -0.028 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0228 13 1137 83 -0.13 0.067 1000 -1000 -0.028 -1000
Noncanonical Wnt signaling pathway 0.0211 12 330 26 -0.018 0.055 1000 -1000 -0.04 -1000
Paxillin-dependent events mediated by a4b1 0.0211 12 461 36 -0.057 0.06 1000 -1000 -0.027 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0211 12 1535 120 -0.16 0.08 1000 -1000 -0.052 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0193 11 401 34 -0.032 0.084 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0193 11 760 68 -0.12 0.057 1000 -1000 -0.023 -1000
Ephrin A reverse signaling 0.0175 10 73 7 -0.037 0.037 1000 -1000 -0.022 -1000
E-cadherin signaling events 0.0175 10 52 5 0.022 0.046 1000 -1000 0.022 -1000
Canonical NF-kappaB pathway 0.0158 9 376 39 -0.055 0.055 1000 -1000 -0.027 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0158 9 267 28 -0.066 0.043 1000 -1000 -0.024 -1000
Atypical NF-kappaB pathway 0.0158 9 292 31 -0.037 0.031 1000 -1000 -0.034 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0158 9 1171 125 -0.08 0.065 1000 -1000 -0.069 -1000
JNK signaling in the CD4+ TCR pathway 0.0140 8 144 17 -0.022 0.06 1000 -1000 -0.025 -1000
Syndecan-4-mediated signaling events 0.0140 8 571 67 -0.04 0.074 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class I 0.0123 7 786 104 -0.049 0.063 1000 -1000 -0.036 -1000
Hedgehog signaling events mediated by Gli proteins 0.0105 6 432 65 -0.032 0.058 1000 -1000 -0.031 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0105 6 163 27 -0.036 0.067 1000 -1000 -0.039 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0105 6 211 33 -0.008 0.075 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 0.0088 5 396 75 -0.031 0.065 1000 -1000 -0.037 -1000
S1P5 pathway 0.0088 5 88 17 -0.012 0.031 1000 -1000 -0.011 -1000
Arf6 trafficking events 0.0088 5 402 71 -0.036 0.055 1000 -1000 -0.029 -1000
S1P4 pathway 0.0088 5 132 25 -0.027 0.043 1000 -1000 -0.022 -1000
p38 MAPK signaling pathway 0.0088 5 242 44 -0.018 0.055 1000 -1000 -0.015 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0070 4 94 23 -0.019 0.055 1000 -1000 -0.018 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0070 4 423 88 -0.048 0.044 1000 -1000 -0.067 -1000
Visual signal transduction: Cones 0.0053 3 123 38 -0.016 0.063 1000 -1000 -0.021 -1000
VEGFR1 specific signals 0.0053 3 207 56 -0.055 0.05 1000 -1000 -0.043 -1000
Wnt signaling 0.0035 2 17 7 0.011 0.031 1000 -1000 -0.016 -1000
Visual signal transduction: Rods 0.0035 2 116 52 -0.064 0.073 1000 -1000 -0.055 -1000
Alternative NF-kappaB pathway 0.0035 2 30 13 0 0.079 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 0.0018 1 9 5 0.028 0.042 1000 -1000 0.019 -1000
Aurora C signaling 0.0018 1 8 7 0 0.043 1000 -1000 -0.017 -1000
Glypican 2 network 0.0000 0 0 4 0.03 0.045 1000 -1000 0.019 -1000
Rapid glucocorticoid signaling 0.0000 0 16 20 -0.015 0.038 1000 -1000 -0.019 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.031 0.031 1000 -1000 -0.023 -1000
Total NA 3956 224917 7203 -14 11 131000 -131000 -4.5 -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 1.1 0.45 1.3 435 -0.93 1 436
PLK1 0.24 0.34 0.91 76 -10000 0 76
BIRC5 0.23 0.34 0.94 68 -0.71 1 69
HSPA1B 1.1 0.44 1.3 457 -0.91 2 459
MAP2K1 0.45 0.18 0.51 481 -10000 0 481
BRCA2 1.3 0.57 1.5 447 -0.92 2 449
FOXM1 1.7 0.98 2.2 425 -1.1 2 427
XRCC1 1.2 0.46 1.4 449 -0.92 2 451
FOXM1B/p19 0.28 0.48 1.1 129 -0.95 2 131
Cyclin D1/CDK4 0.64 0.51 1.1 297 -1 2 299
CDC2 1.4 0.55 1.7 466 -0.96 2 468
TGFA 0.71 0.52 1.1 332 -0.9 2 334
SKP2 1.3 0.57 1.5 451 -10000 0 451
CCNE1 0.01 0.033 0.14 22 -10000 0 22
CKS1B 1.4 0.62 1.6 450 -0.93 1 451
RB1 0.029 0.17 0.84 18 -0.88 2 20
FOXM1C/SP1 0.85 0.47 1.1 399 -1 1 400
AURKB 0.26 0.38 1 87 -0.84 2 89
CENPF 1.6 0.62 1.8 473 -0.93 1 474
CDK4 0.13 0.074 0.19 294 -10000 0 294
MYC 0.55 0.53 1.1 274 -0.83 1 275
CHEK2 0.38 0.18 0.46 451 -10000 0 451
ONECUT1 0.74 0.56 1.2 333 -0.98 2 335
CDKN2A -0.013 0.088 -10000 0 -0.32 37 37
LAMA4 1 0.59 1.3 408 -1.1 4 412
FOXM1B/HNF6 0.74 0.56 1.2 325 -1.1 2 327
FOS 0.95 0.62 1.4 367 -1.1 3 370
SP1 0.002 0.1 -10000 0 -0.29 56 56
CDC25B 1.2 0.48 1.4 446 -0.93 1 447
response to radiation 0.24 0.082 0.27 475 -10000 0 475
CENPB 1.2 0.48 1.4 444 -0.93 1 445
CENPA 1.2 0.46 1.4 442 -0.93 1 443
NEK2 1.5 0.63 1.8 451 -10000 0 451
HIST1H2BA 1.2 0.47 1.4 445 -0.93 1 446
CCNA2 0.012 0.035 0.14 16 -10000 0 16
EP300 0.027 0.024 -10000 0 -0.28 3 3
CCNB1/CDK1 1.3 0.65 1.6 417 -1 2 419
CCNB2 1.6 0.6 1.8 481 -10000 0 481
CCNB1 1.7 0.7 1.9 462 -0.96 2 464
ETV5 1.3 0.61 1.5 448 -10000 0 448
ESR1 1 0.56 1.3 400 -1.1 3 403
CCND1 0.76 0.56 1.2 332 -1 2 334
GSK3A 0.26 0.11 0.31 443 -0.3 1 444
Cyclin A-E1/CDK1-2 0.026 0.09 0.35 38 -10000 0 38
CDK2 0.068 0.069 0.14 230 -10000 0 230
G2/M transition of mitotic cell cycle 0.41 0.16 0.46 493 -10000 0 493
FOXM1B/Cbp/p300 0.12 0.3 0.89 45 -0.98 2 47
GAS1 1 0.53 1.3 413 -1.1 2 415
MMP2 0.98 0.61 1.3 383 -1.1 7 390
RB1/FOXM1C 0.51 0.56 1.1 241 -1 2 243
CREBBP 0.026 0.033 -10000 0 -0.28 6 6
TCGA08_retinoblastoma

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
CDKN2B -0.044 0.033 -10000 0 -10000 0 0
CDKN2C -0.017 0.048 -10000 0 -0.096 1 1
CDKN2A 0.014 0.024 -10000 0 -10000 0 0
CCND2 -0.084 0.074 -10000 0 -0.17 201 201
RB1 0.075 0.089 0.18 202 -0.2 6 208
CDK4 -0.015 0.035 -10000 0 -0.14 30 30
CDK6 -0.075 0.073 -10000 0 -0.16 201 201
G1/S progression -0.084 0.094 0.2 6 -0.18 214 220
Effects of Botulinum toxin

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
STX1A -0.016 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.044 0.011 -10000 0 -10000 0 0
STXBP1 -0.004 0.098 -10000 0 -0.28 61 61
ACh/CHRNA1 -0.042 0.046 -10000 0 -0.076 354 354
RAB3GAP2/RIMS1/UNC13B 0.058 0.019 -10000 0 -10000 0 0
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 0.03 0.006 -10000 0 -10000 0 0
mol:ACh -0.057 0.041 0.083 1 -0.086 351 352
RAB3GAP2 0.03 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.1 0.1 -10000 0 -0.18 333 333
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.042 0.046 -10000 0 -0.076 354 354
UNC13B 0.031 0.005 -10000 0 -10000 0 0
CHRNA1 0.03 0.008 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.042 0.047 -10000 0 -0.076 354 354
SNAP25 0.002 0.001 -10000 0 -10000 0 0
VAMP2 -0.13 0.091 -10000 0 -0.19 379 379
SYT1 0.03 0.007 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.039 0.045 -10000 0 -0.17 61 61
STX1A/SNAP25 fragment 1/VAMP2 -0.1 0.1 -10000 0 -0.18 333 333
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.11 0.043 0.14 1 -0.13 476 477
BUB1B 0.15 0.068 0.18 450 -0.14 1 451
PLK1 0.066 0.028 0.08 380 -10000 0 380
PLK1S1 0.033 0.016 0.052 162 -10000 0 162
KIF2A 0.046 0.03 0.17 7 -10000 0 7
regulation of mitotic centrosome separation 0.066 0.028 0.08 374 -10000 0 374
GOLGA2 0.031 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.006 0.021 -10000 0 -10000 0 0
WEE1 0.078 0.066 0.17 7 -0.25 12 19
cytokinesis 0.21 0.091 0.25 444 -10000 0 444
PP2A-alpha B56 0.12 0.08 -10000 0 -0.5 6 6
AURKA 0.074 0.034 0.11 96 -10000 0 96
PICH/PLK1 0.1 0.082 0.17 306 -10000 0 306
CENPE 0.06 0.059 0.25 42 -10000 0 42
RhoA/GTP 0.023 0.009 -10000 0 -0.19 1 1
positive regulation of microtubule depolymerization 0.048 0.029 0.17 7 -10000 0 7
PPP2CA 0.031 0.005 -10000 0 -10000 0 0
FZR1 0.029 0.009 -10000 0 -10000 0 0
TPX2 0.1 0.033 0.12 447 -10000 0 447
PAK1 0.031 0.01 -10000 0 -10000 0 0
SPC24 0.022 0.015 -10000 0 -10000 0 0
FBXW11 0.031 0.006 -10000 0 -10000 0 0
CLSPN 0.047 0.036 0.13 33 -0.22 4 37
GORASP1 0.031 0.003 -10000 0 -10000 0 0
metaphase 0.002 0.005 0.013 72 -0.01 1 73
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.033 0.016 0.052 162 -10000 0 162
G2 phase of mitotic cell cycle 0.005 0.003 0.017 21 -10000 0 21
STAG2 0.029 0.015 -10000 0 -0.28 1 1
GRASP65/GM130/RAB1/GTP 0.027 0.033 -10000 0 -0.41 2 2
spindle elongation 0.066 0.028 0.08 374 -10000 0 374
ODF2 0.037 0.006 -10000 0 -10000 0 0
BUB1 -0.001 0.052 -10000 0 -0.59 4 4
TPT1 0.03 0.042 0.095 2 -0.14 26 28
CDC25C 0.073 0.055 0.15 67 -0.22 6 73
CDC25B 0.032 0.019 -10000 0 -10000 0 0
SGOL1 0.11 0.043 0.13 476 -0.14 1 477
RHOA 0.031 0.014 -10000 0 -0.28 1 1
CCNB1/CDK1 0.011 0.029 -10000 0 -0.15 2 2
CDC14B -0.013 0.003 -10000 0 -10000 0 0
CDC20 0.007 0.013 -10000 0 -10000 0 0
PLK1/PBIP1 0.039 0.025 0.073 105 -10000 0 105
mitosis 0 0.001 -10000 0 -10000 0 0
FBXO5 0.1 0.079 0.18 271 -0.14 4 275
CDC2 0.006 0.004 0.01 48 -0.011 1 49
NDC80 0.003 0.01 -10000 0 -10000 0 0
metaphase plate congression 0.044 0.043 -10000 0 -0.2 14 14
ERCC6L 0.088 0.077 0.16 300 -0.15 1 301
NLP/gamma Tubulin 0.029 0.026 0.07 38 -0.083 9 47
microtubule cytoskeleton organization 0.03 0.042 0.095 2 -0.14 26 28
G2/M transition DNA damage checkpoint 0.001 0.002 0.014 5 -10000 0 5
PPP1R12A 0.033 0.006 -10000 0 -10000 0 0
interphase 0.001 0.002 0.014 5 -10000 0 5
PLK1/PRC1-2 0.01 0.026 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.093 0.03 0.16 2 -10000 0 2
RAB1A 0.031 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.069 0.025 0.079 423 -10000 0 423
mitotic prometaphase 0.002 0.004 0.023 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.03 -10000 0 -0.25 2 2
microtubule-based process 0.011 0.026 0.1 8 -10000 0 8
Golgi organization 0.066 0.028 0.08 374 -10000 0 374
Cohesin/SA2 0.065 0.028 0.11 65 -10000 0 65
PPP1CB/MYPT1 0.048 0.016 -10000 0 -0.21 1 1
KIF20A 0.006 0.013 -10000 0 -10000 0 0
APC/C/CDC20 0.014 0.028 0.1 4 -10000 0 4
PPP2R1A 0.03 0.006 -10000 0 -10000 0 0
chromosome segregation 0.039 0.025 0.072 105 -10000 0 105
PRC1 0.009 0.014 -10000 0 -10000 0 0
ECT2 0.23 0.072 0.25 514 -10000 0 514
C13orf34 0.059 0.024 0.071 383 -10000 0 383
NUDC 0.044 0.043 -10000 0 -0.2 14 14
regulation of attachment of spindle microtubules to kinetochore 0.15 0.068 0.18 450 -0.14 1 451
spindle assembly 0.047 0.025 0.08 130 -10000 0 130
spindle stabilization 0.033 0.016 0.052 162 -10000 0 162
APC/C/HCDH1 0.022 0.013 -10000 0 -10000 0 0
MKLP2/PLK1 0.011 0.026 0.1 8 -10000 0 8
CCNB1 0.007 0.014 -10000 0 -10000 0 0
PPP1CB 0.032 0.015 -10000 0 -0.29 1 1
BTRC 0.031 0.005 -10000 0 -10000 0 0
ROCK2 0.055 0.031 -10000 0 -0.22 3 3
TUBG1 0.031 0.047 0.11 7 -0.16 25 32
G2/M transition of mitotic cell cycle 0.11 0.079 0.17 346 -10000 0 346
MLF1IP -0.013 0.005 -10000 0 -10000 0 0
INCENP 0.036 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.15 0.2 0.41 170 -0.34 3 173
NF kappa B1 p50/RelA/I kappa B alpha 0.14 0.24 0.46 164 -0.37 7 171
alphaV/beta3 Integrin/Osteopontin/Src 0.008 0.036 0.2 2 -0.25 4 6
AP1 0.076 0.26 0.46 136 -0.41 20 156
ILK 0.12 0.17 0.34 161 -0.35 3 164
bone resorption 0.025 0.16 0.26 114 -0.31 24 138
PTK2B 0.025 0.022 -10000 0 -0.28 2 2
PYK2/p130Cas 0.068 0.13 0.31 18 -0.22 16 34
ITGAV 0.033 0.054 0.16 14 -0.29 3 17
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.045 0.12 -10000 0 -0.2 200 200
alphaV/beta3 Integrin/Osteopontin -0.004 0.069 0.26 6 -0.21 40 46
MAP3K1 0.11 0.17 0.34 159 -0.36 3 162
JUN 0.024 0.034 0.13 1 -0.29 2 3
MAPK3 0.16 0.25 0.52 160 -0.31 8 168
MAPK1 0.17 0.25 0.51 171 -0.34 3 174
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
MAPK8 0.11 0.18 0.34 161 -0.36 3 164
ITGB3 -0.001 0.12 0.16 14 -0.29 69 83
NFKBIA 0.16 0.26 0.51 169 -0.34 5 174
FOS -0.03 0.12 -10000 0 -0.28 103 103
CD44 -0.086 0.15 -10000 0 -0.28 208 208
CHUK 0.03 0.007 -10000 0 -10000 0 0
PLAU 0.21 0.36 0.78 148 -0.61 3 151
NF kappa B1 p50/RelA 0.16 0.26 0.52 161 -0.39 2 163
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
RELA 0.03 0.019 -10000 0 -0.28 2 2
alphaV beta3 Integrin 0.032 0.12 0.19 119 -0.22 69 188
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.12 0.16 0.32 163 -0.35 3 166
VAV3 0.1 0.16 0.31 160 -0.34 3 163
MAP3K14 0.16 0.22 0.44 173 -0.35 3 176
ROCK2 0.031 0.005 -10000 0 -10000 0 0
SPP1 0.004 0.03 -10000 0 -0.29 3 3
RAC1 0.03 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.095 0.15 0.27 171 -0.32 3 174
MMP2 0.031 0.22 0.36 122 -0.4 43 165
S1P3 pathway

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
PDGFRB 0.02 0.059 -10000 0 -0.28 20 20
mol:S1P -0.017 0.016 0.073 4 -0.034 65 69
S1P1/S1P/Gi -0.07 0.094 0.25 4 -0.23 65 69
GNAO1 -0.021 0.048 0.13 1 -0.29 2 3
S1P/S1P3/G12/G13 -0.015 0.047 0.16 4 -0.065 3 7
AKT1 -0.064 0.14 0.29 1 -0.52 38 39
AKT3 -0.6 0.52 0.67 3 -1 330 333
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.058 -10000 0 -0.28 20 20
GNAI2 -0.022 0.047 -10000 0 -10000 0 0
GNAI3 -0.019 0.043 -10000 0 -10000 0 0
GNAI1 -0.024 0.058 -10000 0 -0.3 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.019 0.019 0.086 4 -0.034 289 293
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.16 0.42 4 -0.28 312 316
MAPK3 -0.16 0.15 0.37 4 -0.28 309 313
MAPK1 -0.15 0.14 0.37 4 -0.27 305 309
JAK2 -0.15 0.15 0.36 4 -0.28 269 273
CXCR4 -0.15 0.14 0.34 3 -0.27 295 298
FLT1 -0.025 0.052 0.17 4 -10000 0 4
RhoA/GDP 0.023 0.009 -10000 0 -0.19 1 1
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
SRC -0.15 0.14 0.37 4 -0.27 286 290
S1P/S1P3/Gi -0.15 0.16 0.42 4 -0.28 312 316
RAC1 0.03 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.14 0.15 0.35 4 -0.26 310 314
VEGFA -0.023 0.05 0.17 4 -10000 0 4
S1P/S1P2/Gi -0.091 0.11 0.3 4 -0.26 66 70
VEGFR1 homodimer/VEGFA homodimer -0.03 0.076 0.35 4 -10000 0 4
RHOA 0.031 0.014 -10000 0 -0.28 1 1
S1P/S1P3/Gq -0.075 0.1 -10000 0 -0.21 176 176
GNAQ 0.022 0.051 -10000 0 -0.28 15 15
GNAZ -0.02 0.051 0.12 1 -0.27 6 7
G12/G13 0.043 0.012 -10000 0 -10000 0 0
GNA14 0.029 0.02 -10000 0 -0.28 2 2
GNA15 0.028 0.021 -10000 0 -0.28 2 2
GNA12 0.03 0.007 -10000 0 -10000 0 0
GNA13 0.031 0.005 -10000 0 -10000 0 0
GNA11 -0.066 0.14 -10000 0 -0.28 168 168
Rac1/GTP -0.14 0.15 0.35 4 -0.26 310 314
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.002 0.052 -10000 0 -0.4 6 6
Crk/p130 Cas/Paxillin -0.15 0.11 -10000 0 -0.27 202 202
JUN -0.065 0.094 0.19 3 -0.27 20 23
HRAS 0.03 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.015 0.12 -10000 0 -0.17 190 190
RAP1A 0.031 0.004 -10000 0 -10000 0 0
FRS2 0.03 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.023 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.015 0.12 -10000 0 -0.17 191 191
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.031 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.023 0.1 -10000 0 -0.16 194 194
RHOA 0.031 0.014 -10000 0 -0.28 1 1
RAP1A/GTP -0.013 0.11 -10000 0 -0.16 188 188
GRB7 0.028 0.024 -10000 0 -0.28 3 3
RET51/GFRalpha1/GDNF -0.011 0.11 -10000 0 -0.17 164 164
MAPKKK cascade -0.087 0.084 0.11 2 -0.2 162 164
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.12 -10000 0 -0.2 362 362
lamellipodium assembly -0.14 0.11 -10000 0 -0.25 193 193
RET51/GFRalpha1/GDNF/SHC -0.014 0.11 -10000 0 -0.17 186 186
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.022 0.1 -10000 0 -0.16 190 190
RET9/GFRalpha1/GDNF/Shank3 -0.031 0.098 -10000 0 -0.16 194 194
MAPK3 -0.081 0.092 0.28 4 -0.27 23 27
DOK1 0.031 0.014 -10000 0 -0.28 1 1
DOK6 0.029 0.009 -10000 0 -10000 0 0
PXN 0.024 0.046 -10000 0 -0.28 12 12
neurite development -0.086 0.11 0.24 7 -0.32 47 54
DOK5 0.009 0.048 -10000 0 -0.28 13 13
GFRA1 -0.086 0.15 -10000 0 -0.28 206 206
MAPK8 -0.063 0.097 0.18 1 -0.28 20 21
HRAS/GTP -0.028 0.13 -10000 0 -0.21 168 168
tube development -0.034 0.095 0.22 5 -0.16 190 195
MAPK1 -0.07 0.084 0.31 3 -10000 0 3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.05 0.095 -10000 0 -0.18 177 177
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
SRC 0.03 0.007 -10000 0 -10000 0 0
PDLIM7 0.029 0.023 -10000 0 -0.28 3 3
RET51/GFRalpha1/GDNF/Dok6 -0.01 0.12 -10000 0 -0.17 183 183
SHC1 0.03 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.017 0.11 -10000 0 -0.17 190 190
RET51/GFRalpha1/GDNF/Dok5 -0.012 0.087 -10000 0 -0.18 107 107
PRKCA 0.028 0.027 -10000 0 -0.28 4 4
HRAS/GDP 0.022 0.005 -10000 0 -10000 0 0
CREB1 -0.053 0.11 0.21 1 -0.21 170 171
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.055 0.1 -10000 0 -0.19 187 187
RET51/GFRalpha1/GDNF/Grb7 -0.016 0.11 -10000 0 -0.17 188 188
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.031 0.005 -10000 0 -10000 0 0
DOK4 0.03 0.008 -10000 0 -10000 0 0
JNK cascade -0.064 0.093 0.19 3 -0.27 20 23
RET9/GFRalpha1/GDNF/FRS2 -0.021 0.1 -10000 0 -0.16 185 185
SHANK3 0.024 0.013 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.28 3 3
NCK1 0.028 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.047 0.093 -10000 0 -0.18 173 173
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.047 0.097 -10000 0 -0.19 173 173
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.05 0.1 -10000 0 -0.19 172 172
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.044 0.097 -10000 0 -0.18 169 169
PI3K -0.18 0.16 0.31 2 -0.36 193 195
SOS1 0.03 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.025 0.1 -10000 0 -0.16 190 190
GRB10 0.031 0.005 -10000 0 -10000 0 0
activation of MAPKK activity -0.042 0.094 -10000 0 -0.29 5 5
RET51/GFRalpha1/GDNF/FRS2 -0.014 0.11 -10000 0 -0.17 181 181
GAB1 0.029 0.02 -10000 0 -0.28 2 2
IRS1 -0.14 0.16 -10000 0 -0.28 297 297
IRS2 0.03 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.051 0.1 -10000 0 -0.19 183 183
RET51/GFRalpha1/GDNF/PKC alpha -0.017 0.12 -10000 0 -0.17 191 191
GRB2 0.03 0.006 -10000 0 -10000 0 0
PRKACA 0.027 0.011 -10000 0 -10000 0 0
GDNF 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.11 0.14 -10000 0 -0.21 359 359
Rac1/GTP -0.16 0.13 -10000 0 -0.3 193 193
RET9/GFRalpha1/GDNF -0.035 0.098 -10000 0 -0.17 195 195
GFRalpha1/GDNF -0.045 0.12 -10000 0 -0.2 195 195
Endothelins

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
AKT1 0.027 0.21 0.4 116 -0.38 7 123
PTK2B 0.025 0.022 -10000 0 -0.28 2 2
mol:Ca2+ -0.013 0.2 0.56 9 -0.62 10 19
EDN1 0.007 0.14 0.26 108 -0.26 9 117
EDN3 0.029 0.009 -10000 0 -10000 0 0
EDN2 0.029 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.037 0.21 0.38 23 -0.43 49 72
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.16 0.26 54 -0.34 54 108
ADCY4 0.068 0.2 0.31 197 -0.32 8 205
ADCY5 0.067 0.2 0.31 193 -0.32 8 201
ADCY6 0.07 0.2 0.31 191 -0.32 8 199
ADCY7 0.065 0.2 0.31 183 -0.32 8 191
ADCY1 0.069 0.2 0.31 198 -0.32 8 206
ADCY2 0.065 0.19 0.31 184 -0.32 6 190
ADCY3 0.069 0.2 0.31 195 -0.32 8 203
ADCY8 -0.014 0.15 0.31 58 -0.31 25 83
ADCY9 0.056 0.2 0.31 179 -0.31 16 195
arachidonic acid secretion -0.15 0.28 0.55 10 -0.57 113 123
ETB receptor/Endothelin-1/Gq/GTP -0.012 0.16 0.24 62 -0.29 62 124
GNAO1 0.028 0.02 -10000 0 -0.28 2 2
HRAS 0.026 0.016 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.023 0.11 0.35 11 -0.23 75 86
ETA receptor/Endothelin-1/Gs/GTP 0.015 0.15 0.35 67 -0.21 73 140
mol:GTP 0.001 0.012 0.11 4 -10000 0 4
COL3A1 -0.04 0.14 0.38 30 -0.48 12 42
EDNRB 0.071 0.098 0.22 159 -0.12 2 161
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.006 0.25 0.4 108 -0.43 83 191
CYSLTR1 0.011 0.2 0.4 95 -0.38 8 103
SLC9A1 0.018 0.13 0.26 107 -0.26 11 118
mol:GDP -0.04 0.21 0.37 23 -0.45 49 72
SLC9A3 0.046 0.2 0.43 5 -0.6 17 22
RAF1 -0.061 0.24 0.45 17 -0.45 87 104
JUN -0.02 0.22 0.67 8 -0.75 11 19
JAK2 0.021 0.21 0.4 109 -0.37 8 117
mol:IP3 -0.031 0.17 0.3 55 -0.38 44 99
ETA receptor/Endothelin-1 -0.038 0.12 0.36 6 -0.28 80 86
PLCB1 0.018 0.025 -10000 0 -10000 0 0
PLCB2 0.019 0.026 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 0.029 0.11 0.23 73 -0.18 13 86
FOS -0.18 0.38 0.72 8 -0.87 113 121
Gai/GDP -0.021 0.2 -10000 0 -0.71 39 39
CRK 0.03 0.008 -10000 0 -10000 0 0
mol:Ca ++ 0.019 0.25 0.4 126 -0.42 32 158
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
PRKCB1 -0.017 0.18 0.28 60 -0.38 45 105
GNAQ 0.012 0.057 0.14 3 -0.29 15 18
GNAZ 0.026 0.031 -10000 0 -0.28 5 5
GNAL 0.031 0.006 -10000 0 -10000 0 0
Gs family/GDP -0.036 0.2 0.34 24 -0.42 47 71
ETA receptor/Endothelin-1/Gq/GTP -0.041 0.17 0.29 56 -0.35 60 116
MAPK14 -0.018 0.14 0.25 17 -0.32 39 56
TRPC6 -0.016 0.21 0.59 7 -0.65 10 17
GNAI2 0.031 0.003 -10000 0 -10000 0 0
GNAI3 0.03 0.007 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.28 11 11
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.01 0.15 0.22 59 -0.33 40 99
ETB receptor/Endothelin-2 0.071 0.066 0.18 145 -0.096 1 146
ETB receptor/Endothelin-3 0.071 0.066 0.18 139 -10000 0 139
ETB receptor/Endothelin-1 -0.004 0.085 0.31 11 -0.23 10 21
MAPK3 -0.17 0.37 0.68 8 -0.81 116 124
MAPK1 -0.16 0.36 0.68 8 -0.77 117 125
Rac1/GDP -0.038 0.21 0.37 20 -0.43 48 68
cAMP biosynthetic process 0.04 0.19 0.3 115 -0.33 18 133
MAPK8 -0.026 0.22 0.55 8 -0.65 20 28
SRC 0.03 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.038 0.11 0.2 130 -0.3 8 138
p130Cas/CRK/Src/PYK2 -0.044 0.22 0.5 11 -0.51 34 45
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.038 0.21 0.37 20 -0.43 49 69
COL1A2 -0.028 0.15 0.55 13 -0.56 9 22
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.027 0.11 0.23 68 -0.17 14 82
mol:DAG -0.031 0.17 0.3 55 -0.38 44 99
MAP2K2 -0.14 0.29 0.54 11 -0.59 117 128
MAP2K1 -0.098 0.28 0.55 12 -0.55 113 125
EDNRA 0.01 0.15 0.27 117 -0.24 15 132
positive regulation of muscle contraction 0.013 0.17 0.32 112 -0.34 7 119
Gq family/GDP -0.086 0.18 0.39 6 -0.42 61 67
HRAS/GTP -0.033 0.21 0.37 25 -0.42 60 85
PRKCH -0.019 0.18 0.27 62 -0.39 42 104
RAC1 0.03 0.007 -10000 0 -10000 0 0
PRKCA -0.019 0.18 0.28 60 -0.39 42 102
PRKCB -0.015 0.18 0.28 61 -0.38 46 107
PRKCE -0.018 0.18 0.28 60 -0.39 40 100
PRKCD -0.02 0.18 0.28 58 -0.39 44 102
PRKCG -0.017 0.18 0.28 58 -0.39 43 101
regulation of vascular smooth muscle contraction -0.22 0.45 0.7 8 -1 113 121
PRKCQ -0.017 0.18 0.28 58 -0.39 45 103
PLA2G4A -0.16 0.3 0.56 10 -0.62 115 125
GNA14 0.019 0.035 -10000 0 -0.28 2 2
GNA15 0.019 0.033 0.14 2 -0.29 2 4
GNA12 0.03 0.007 -10000 0 -10000 0 0
GNA11 -0.07 0.14 -10000 0 -0.28 164 164
Rac1/GTP -0.023 0.11 0.35 11 -0.23 73 84
MMP1 0.037 0.11 0.39 42 -10000 0 42
PLK2 and PLK4 events

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
PLK2 0.02 0.023 -10000 0 -0.28 2 2
PLK4 0.016 0.016 -10000 0 -10000 0 0
regulation of centriole replication 0.071 0.1 0.19 238 -0.2 1 239
Circadian rhythm pathway

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
chromatin modification 0.007 0.051 0.43 7 -10000 0 7
CLOCK 0.053 0.035 -10000 0 -10000 0 0
TIMELESS/CRY2 0.21 0.22 0.46 242 -10000 0 242
DEC1/BMAL1 0.062 0.028 -10000 0 -10000 0 0
ATR 0.021 0.015 -10000 0 -10000 0 0
NR1D1 0.14 0.25 0.48 4 -0.84 14 18
ARNTL 0.054 0.035 -10000 0 -10000 0 0
TIMELESS 0.27 0.32 0.65 231 -10000 0 231
NPAS2 0.053 0.038 -10000 0 -0.28 1 1
CRY2 0.031 0.003 -10000 0 -10000 0 0
mol:CO -0.098 0.11 0.13 3 -0.22 245 248
CHEK1 0.003 0.009 -10000 0 -10000 0 0
mol:HEME 0.098 0.11 0.22 245 -0.13 3 248
PER1 0.029 0.015 -10000 0 -0.28 1 1
BMAL/CLOCK/NPAS2 0.15 0.13 0.3 225 -0.17 4 229
BMAL1/CLOCK 0.14 0.21 0.41 30 -0.68 5 35
S phase of mitotic cell cycle 0.007 0.051 0.43 7 -10000 0 7
TIMELESS/CHEK1/ATR 0.007 0.051 0.44 7 -10000 0 7
mol:NADPH 0.098 0.11 0.22 245 -0.13 3 248
PER1/TIMELESS 0.2 0.22 0.46 232 -10000 0 232
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.031 0.005 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.031 0.004 -10000 0 -10000 0 0
PTK2 0.022 0.014 -10000 0 -10000 0 0
CRKL -0.091 0.091 0.12 7 -0.24 125 132
GRB2/SOS1/SHC 0.057 0.021 -10000 0 -10000 0 0
HRAS 0.03 0.007 -10000 0 -10000 0 0
IRS1/Crk -0.092 0.089 0.097 4 -0.24 125 129
IGF-1R heterotetramer/IGF1/PTP1B 0.003 0.11 -10000 0 -0.2 117 117
AKT1 -0.054 0.12 0.16 39 -0.26 76 115
BAD -0.062 0.11 0.2 10 -0.26 67 77
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.09 0.09 0.12 6 -0.24 123 129
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.095 0.09 0.17 4 -0.24 128 132
RAF1 -0.037 0.12 0.26 4 -0.35 12 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.054 0.12 -10000 0 -0.24 120 120
YWHAZ 0.027 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.071 0.12 0.17 3 -0.25 130 133
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
RPS6KB1 -0.055 0.12 0.17 26 -0.26 65 91
GNB2L1 0.031 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.032 0.11 0.27 6 -0.3 11 17
PXN 0.024 0.046 -10000 0 -0.28 12 12
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.097 0.08 -10000 0 -0.24 115 115
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.031 0.11 -10000 0 -0.18 112 112
IGF-1R heterotetramer -0.059 0.13 -10000 0 -0.14 292 292
IGF-1R heterotetramer/IGF1/IRS/Nck -0.062 0.12 0.18 3 -0.24 130 133
Crk/p130 Cas/Paxillin -0.066 0.12 0.23 2 -0.24 133 135
IGF1R -0.059 0.13 -10000 0 -0.14 292 292
IGF1 -0.024 0.063 -10000 0 -0.072 304 304
IRS2/Crk -0.092 0.087 0.16 2 -0.24 121 123
PI3K -0.055 0.11 -10000 0 -0.23 122 122
apoptosis 0.048 0.11 0.24 60 -0.22 10 70
HRAS/GDP 0.022 0.005 -10000 0 -10000 0 0
PRKCD -0.081 0.12 -10000 0 -0.3 104 104
RAF1/14-3-3 E -0.03 0.11 0.26 3 -0.38 4 7
BAD/14-3-3 -0.051 0.11 0.23 10 -0.25 60 70
PRKCZ -0.055 0.12 0.16 38 -0.26 75 113
Crk/p130 Cas/Paxillin/FAK1 -0.057 0.1 0.14 13 -0.27 43 56
PTPN1 0.029 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.074 0.12 -10000 0 -0.3 105 105
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.02 0.11 -10000 0 -0.18 117 117
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.03 0.007 -10000 0 -10000 0 0
IRS1/NCK2 -0.093 0.092 0.13 11 -0.24 129 140
GRB10 0.031 0.005 -10000 0 -10000 0 0
PTPN11 -0.093 0.09 0.12 7 -0.24 128 135
IRS1 -0.065 0.11 0.12 11 -0.26 124 135
IRS2 -0.091 0.091 0.12 7 -0.24 124 131
IGF-1R heterotetramer/IGF1 -0.015 0.13 -10000 0 -0.26 124 124
GRB2 0.03 0.006 -10000 0 -10000 0 0
PDPK1 -0.051 0.13 0.23 10 -0.27 68 78
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
PRKD1 -0.076 0.12 0.2 3 -0.3 100 103
SHC1 0.03 0.006 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.007 -10000 0 -10000 0 0
GNB1/GNG2 -0.04 0.11 -10000 0 -0.16 240 240
regulation of S phase of mitotic cell cycle -0.061 0.11 -10000 0 -0.21 172 172
GNAO1 0.028 0.02 -10000 0 -0.28 2 2
HRAS 0.019 0.024 -10000 0 -10000 0 0
SHBG/T-DHT 0.02 0.004 -10000 0 -10000 0 0
PELP1 0.019 0.024 -10000 0 -10000 0 0
AKT1 -0.015 0.003 -10000 0 -10000 0 0
MAP2K1 -0.097 0.091 0.25 6 -0.26 41 47
T-DHT/AR -0.074 0.1 -10000 0 -0.19 243 243
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 0.01 8 -0.007 40 48
GNAI2 0.031 0.003 -10000 0 -10000 0 0
GNAI3 0.03 0.007 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.28 11 11
mol:GDP -0.13 0.14 -10000 0 -0.28 239 239
cell proliferation -0.19 0.18 0.37 7 -0.47 113 120
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
FOS -0.19 0.29 0.56 7 -0.74 109 116
mol:Ca2+ -0.016 0.022 0.058 5 -0.066 38 43
MAPK3 -0.16 0.15 0.3 7 -0.39 105 112
MAPK1 -0.095 0.14 0.3 8 -0.36 77 85
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
mol:IP3 -0.001 0.003 0.017 8 -10000 0 8
cAMP biosynthetic process 0.002 0.025 0.27 3 -10000 0 3
GNG2 0.029 0.027 -10000 0 -0.28 4 4
potassium channel inhibitor activity -0.001 0.003 0.017 8 -10000 0 8
HRAS/GTP -0.049 0.1 0.22 5 -0.16 224 229
actin cytoskeleton reorganization 0.014 0.052 -10000 0 -0.15 37 37
SRC 0.019 0.024 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.003 0.017 8 -10000 0 8
PI3K 0.012 0.052 -10000 0 -0.17 37 37
apoptosis 0.14 0.18 0.45 117 -0.44 7 124
T-DHT/AR/PELP1 -0.056 0.1 -10000 0 -0.17 241 241
HRAS/GDP -0.12 0.16 0.13 1 -0.3 207 208
CREB1 -0.16 0.18 -10000 0 -0.48 120 120
RAC1-CDC42/GTP 0.021 0.057 -10000 0 -0.15 37 37
AR -0.11 0.15 -10000 0 -0.28 240 240
GNB1 0.03 0.015 -10000 0 -0.28 1 1
RAF1 -0.087 0.088 0.23 6 -0.23 39 45
RAC1-CDC42/GDP -0.12 0.16 -10000 0 -0.32 161 161
T-DHT/AR/PELP1/Src -0.047 0.1 -10000 0 -0.16 228 228
MAP2K2 -0.13 0.11 0.26 2 -0.27 128 130
T-DHT/AR/PELP1/Src/PI3K -0.061 0.11 -10000 0 -0.21 172 172
GNAZ 0.026 0.031 -10000 0 -0.28 5 5
SHBG 0.03 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.04 0.11 -10000 0 -0.41 23 23
mol:T-DHT 0 0.001 -10000 0 -0.007 1 1
RAC1 0.03 0.007 -10000 0 -10000 0 0
GNRH1 -0.013 0.006 -10000 0 -10000 0 0
Gi family/GTP -0.054 0.071 -10000 0 -0.22 42 42
CDC42 0.031 0.004 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.17 0.66 1.1 10 -1.2 91 101
STAT6 (cleaved dimer) -0.28 0.6 0.69 1 -1.2 124 125
IGHG1 0.004 0.32 0.69 25 -1.1 4 29
IGHG3 -0.19 0.61 -10000 0 -1.2 104 104
AKT1 -0.13 0.4 0.67 1 -0.96 47 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.076 0.36 0.62 3 -1 42 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.18 0.43 0.67 3 -0.93 79 82
THY1 -0.12 0.71 1.2 37 -1.3 86 123
MYB 0.006 0.084 -10000 0 -0.28 43 43
HMGA1 0.029 0.02 -10000 0 -0.28 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.078 0.45 0.79 18 -0.93 46 64
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.089 0.43 0.67 3 -1.1 40 43
SP1 0.11 0.13 0.31 164 -0.15 5 169
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.001 0.058 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.24 0.64 -10000 0 -1.2 117 117
SOCS1 -0.13 0.43 0.65 4 -0.78 100 104
SOCS3 -0.078 0.39 0.88 1 -0.92 38 39
FCER2 -0.11 0.53 0.96 5 -1.1 44 49
PARP14 0.022 0.026 -10000 0 -0.28 3 3
CCL17 -0.19 0.65 0.98 2 -1.3 92 94
GRB2 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.045 0.34 0.62 5 -0.73 38 43
T cell proliferation -0.26 0.69 -10000 0 -1.3 124 124
IL4R/JAK1 -0.29 0.72 -10000 0 -1.4 131 131
EGR2 -0.18 0.65 1.4 2 -1.3 89 91
JAK2 0.02 0.1 0.26 21 -0.32 1 22
JAK3 0.015 0.032 -10000 0 -10000 0 0
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
JAK1 0.013 0.059 0.18 2 -0.28 2 4
COL1A2 0.088 0.4 0.75 62 -1.1 12 74
CCL26 -0.19 0.65 -10000 0 -1.3 89 89
IL4R -0.27 0.81 1.1 17 -1.5 123 140
PTPN6 0.003 0.049 -10000 0 -0.13 1 1
IL13RA2 -0.18 0.65 1.1 7 -1.3 91 98
IL13RA1 0.016 0.12 0.26 27 -0.32 12 39
IRF4 0.02 0.21 0.61 1 -0.76 7 8
ARG1 0.012 0.27 0.7 5 -0.74 8 13
CBL -0.084 0.42 0.71 3 -0.87 48 51
GTF3A 0.15 0.15 0.32 227 -0.12 1 228
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
IL13RA1/JAK2 0.039 0.15 0.36 30 -0.24 12 42
IRF4/BCL6 0.009 0.18 -10000 0 -0.7 8 8
CD40LG 0.033 0.019 0.35 2 -10000 0 2
MAPK14 -0.083 0.42 0.72 2 -0.92 45 47
mitosis -0.12 0.38 0.65 2 -0.89 45 47
STAT6 -0.22 0.79 1.4 23 -1.5 97 120
SPI1 0.029 0.032 0.28 1 -0.28 5 6
RPS6KB1 -0.12 0.37 0.65 2 -0.87 44 46
STAT6 (dimer) -0.22 0.78 1.4 23 -1.5 97 120
STAT6 (dimer)/PARP14 -0.24 0.64 -10000 0 -1.3 102 102
mast cell activation -0.003 0.027 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.11 0.43 0.71 2 -1 49 51
FRAP1 -0.13 0.4 0.67 1 -0.96 47 48
LTA -0.19 0.65 1 3 -1.2 94 97
FES 0.03 0.006 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.19 0.77 1.4 94 -1.4 23 117
CCL11 -0.18 0.63 1 15 -1.2 96 111
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.086 0.42 0.66 3 -1.1 41 44
IL2RG -0.004 0.072 -10000 0 -0.27 31 31
IL10 -0.19 0.65 0.97 4 -1.2 97 101
IRS1 -0.14 0.16 -10000 0 -0.28 297 297
IRS2 0.03 0.007 -10000 0 -10000 0 0
IL4 0.035 0.31 0.82 21 -1.1 9 30
IL5 -0.19 0.65 0.98 2 -1.3 90 92
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.13 0.63 1.1 22 -1.2 72 94
COL1A1 0.17 0.53 1 81 -1.2 19 100
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.31 0.73 -10000 0 -1.4 126 126
IL2R gamma/JAK3 0.027 0.058 0.18 2 -0.19 30 32
TFF3 -0.78 0.62 1.1 1 -1.4 225 226
ALOX15 -0.19 0.65 1.1 4 -1.2 97 101
MYBL1 0.026 0.012 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.2 0.61 0.89 6 -1.1 111 117
SHC1 0.03 0.006 -10000 0 -10000 0 0
CEBPB 0.027 0.03 0.28 1 -0.28 4 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.084 0.42 0.66 3 -1.1 42 45
mol:PI-3-4-5-P3 -0.13 0.4 0.68 1 -0.96 46 47
PI3K -0.14 0.43 0.68 1 -1 49 50
DOK2 0.026 0.012 -10000 0 -10000 0 0
ETS1 -0.006 0.062 -10000 0 -0.16 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.039 0.32 0.6 6 -0.7 38 44
ITGB3 -0.25 0.74 1.4 3 -1.4 119 122
PIGR -0.39 0.76 1.1 8 -1.4 147 155
IGHE -0.027 0.12 0.21 19 -0.32 31 50
MAPKKK cascade -0.037 0.32 0.6 7 -0.68 38 45
BCL6 0.019 0.048 -10000 0 -0.28 13 13
OPRM1 -0.19 0.65 0.98 2 -1.3 92 94
RETNLB -0.18 0.65 1.1 4 -1.3 93 97
SELP -0.22 0.68 1.1 3 -1.3 105 108
AICDA -0.18 0.61 1 3 -1.2 91 94
PDGFR-alpha signaling pathway

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
PDGFRA -0.029 0.11 0.13 2 -0.3 75 77
PDGF/PDGFRA/CRKL -0.013 0.094 -10000 0 -0.2 96 96
positive regulation of JUN kinase activity 0.026 0.089 -10000 0 -0.17 86 86
CRKL 0.03 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.014 0.095 -10000 0 -0.2 97 97
AP1 -0.18 0.29 0.56 5 -0.74 108 113
mol:IP3 -0.061 0.08 0.18 11 -0.22 86 97
PLCG1 -0.061 0.08 0.18 11 -0.22 86 97
PDGF/PDGFRA/alphaV Integrin -0.015 0.094 -10000 0 -0.21 95 95
RAPGEF1 0.031 0.005 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.06 0.08 0.18 11 -0.22 86 97
CAV3 0.03 0.014 -10000 0 -0.28 1 1
CAV1 -0.024 0.12 -10000 0 -0.28 96 96
SHC/Grb2/SOS1 0.028 0.09 -10000 0 -0.17 86 86
PDGF/PDGFRA/Shf -0.014 0.094 -10000 0 -0.2 96 96
FOS -0.18 0.29 0.68 5 -0.73 107 112
JUN -0.04 0.042 0.16 9 -0.24 2 11
oligodendrocyte development -0.015 0.094 -10000 0 -0.21 95 95
GRB2 0.03 0.006 -10000 0 -10000 0 0
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
mol:DAG -0.061 0.08 0.18 11 -0.22 86 97
PDGF/PDGFRA -0.06 0.099 0.12 5 -0.3 75 80
actin cytoskeleton reorganization -0.014 0.094 -10000 0 -0.2 96 96
SRF -0.021 0.028 -10000 0 -0.2 5 5
SHC1 0.03 0.006 -10000 0 -10000 0 0
PI3K -0.015 0.095 -10000 0 -0.2 93 93
PDGF/PDGFRA/Crk/C3G 0.001 0.091 -10000 0 -0.18 94 94
JAK1 -0.059 0.07 0.17 5 -0.21 91 96
ELK1/SRF -0.061 0.074 0.14 25 -0.21 71 96
SHB 0.031 0.004 -10000 0 -10000 0 0
SHF 0.03 0.007 -10000 0 -10000 0 0
CSNK2A1 0.034 0.031 -10000 0 -0.1 3 3
GO:0007205 -0.059 0.092 0.2 12 -0.25 86 98
SOS1 0.03 0.007 -10000 0 -10000 0 0
Ras protein signal transduction 0.026 0.089 -10000 0 -0.17 86 86
PDGF/PDGFRA/SHB -0.013 0.094 -10000 0 -0.2 96 96
PDGF/PDGFRA/Caveolin-1 -0.047 0.13 -10000 0 -0.24 157 157
ITGAV 0.027 0.024 -10000 0 -0.28 3 3
ELK1 -0.065 0.088 0.2 12 -0.23 81 93
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.013 0.093 -10000 0 -0.2 95 95
JAK-STAT cascade -0.058 0.07 0.17 5 -0.21 91 96
cell proliferation -0.014 0.094 -10000 0 -0.2 96 96
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.12 0.16 -10000 0 -0.28 270 270
GNB1/GNG2 -0.066 0.068 -10000 0 -0.19 104 104
AKT1 -0.005 0.23 0.46 86 -0.37 9 95
EGF 0.029 0.008 -10000 0 -10000 0 0
mol:TXA2 0 0.002 -10000 0 -10000 0 0
FGR -0.018 0.062 0.21 6 -10000 0 6
mol:Ca2+ -0.047 0.29 0.54 86 -0.36 58 144
LYN -0.023 0.062 0.2 6 -10000 0 6
RhoA/GTP -0.025 0.13 0.27 74 -0.2 1 75
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.045 0.3 0.55 85 -0.38 58 143
GNG2 0.029 0.027 -10000 0 -0.28 4 4
ARRB2 0.03 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.13 0.2 -10000 0 -0.36 190 190
G beta5/gamma2 -0.069 0.11 0.25 24 -0.25 102 126
PRKCH -0.053 0.31 0.56 86 -0.43 61 147
DNM1 0.031 0.005 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.042 0.04 -10000 0 -0.5 1 1
mol:GTP 0.001 0.008 0.063 1 -10000 0 1
PTGDR 0.031 0.014 -10000 0 -0.28 1 1
G12 family/GTP -0.13 0.13 -10000 0 -0.31 118 118
ADRBK1 0.031 0.004 -10000 0 -10000 0 0
ADRBK2 0.023 0.046 -10000 0 -0.28 12 12
RhoA/GTP/ROCK1 0.041 0.013 -10000 0 -0.17 1 1
mol:GDP 0.021 0.22 0.47 34 -0.4 84 118
mol:NADP 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.031 0.005 -10000 0 -10000 0 0
PRKG1 0.031 0.003 -10000 0 -10000 0 0
mol:IP3 -0.075 0.33 0.57 85 -0.45 81 166
cell morphogenesis 0.041 0.013 -10000 0 -0.17 1 1
PLCB2 -0.13 0.39 0.6 83 -0.62 91 174
mol:cGMP 0 0.002 -10000 0 -10000 0 0
BLK -0.015 0.058 0.21 7 -10000 0 7
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK -0.019 0.059 0.21 4 -10000 0 4
RHOA 0.031 0.014 -10000 0 -0.28 1 1
PTGIR 0.029 0.02 -10000 0 -0.28 2 2
PRKCB1 -0.066 0.32 0.57 86 -0.45 65 151
GNAQ 0.022 0.051 -10000 0 -0.28 15 15
mol:L-citrulline 0.03 0.008 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.092 0.38 0.62 86 -0.57 90 176
LCK -0.017 0.062 0.21 7 -10000 0 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.016 0.053 0.18 5 -10000 0 5
TXA2-R family/G12 family/GDP/G beta/gamma -0.014 0.12 -10000 0 -0.43 41 41
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.05 0.14 4 -10000 0 4
MAPK14 -0.017 0.23 0.46 85 -10000 0 85
TGM2/GTP -0.11 0.36 0.61 82 -0.53 80 162
MAPK11 -0.02 0.23 0.46 85 -10000 0 85
ARHGEF1 -0.02 0.19 0.38 83 -10000 0 83
GNAI2 0.031 0.003 -10000 0 -10000 0 0
JNK cascade -0.049 0.32 0.59 86 -0.43 63 149
RAB11/GDP 0.02 0.029 -10000 0 -0.1 6 6
ICAM1 -0.018 0.28 0.55 86 -0.38 15 101
cAMP biosynthetic process -0.08 0.31 0.53 86 -0.41 81 167
Gq family/GTP/EBP50 -0.11 0.15 -10000 0 -0.25 251 251
actin cytoskeleton reorganization 0.041 0.013 -10000 0 -0.17 1 1
SRC -0.019 0.059 0.21 4 -10000 0 4
GNB5 0.026 0.035 -10000 0 -0.28 7 7
GNB1 0.03 0.015 -10000 0 -0.28 1 1
EGF/EGFR -0.028 0.08 0.24 6 -0.26 11 17
VCAM1 -0.024 0.3 0.59 86 -0.37 79 165
TP beta/Gq family/GDP/G beta5/gamma2 -0.13 0.2 -10000 0 -0.36 190 190
platelet activation -0.043 0.28 0.53 85 -0.35 4 89
PGI2/IP 0.022 0.014 -10000 0 -0.19 2 2
PRKACA 0.006 0.023 -10000 0 -0.17 2 2
Gq family/GDP/G beta5/gamma2 -0.11 0.17 -10000 0 -0.31 188 188
TXA2/TP beta/beta Arrestin2 0.032 0.052 -10000 0 -0.35 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.022 -10000 0 -0.16 3 3
mol:DAG -0.08 0.34 0.59 85 -0.49 82 167
EGFR 0.002 0.091 -10000 0 -0.28 51 51
TXA2/TP alpha -0.13 0.38 0.59 86 -0.58 86 172
Gq family/GTP -0.068 0.097 -10000 0 -0.18 202 202
YES1 -0.019 0.062 0.21 7 -10000 0 7
GNAI2/GTP -0.016 0.058 0.14 11 -0.17 2 13
PGD2/DP 0.023 0.01 -10000 0 -0.19 1 1
SLC9A3R1 -0.053 0.14 -10000 0 -0.28 148 148
FYN -0.027 0.07 0.22 6 -0.23 6 12
mol:NO 0.03 0.008 -10000 0 -10000 0 0
GNA15 0.028 0.021 -10000 0 -0.28 2 2
PGK/cGMP 0.04 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.032 -10000 0 -0.13 7 7
TP alpha/TGM2/GDP/G beta/gamma -0.056 0.092 -10000 0 -0.22 20 20
NOS3 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
PRKCA -0.053 0.31 0.56 86 -0.43 59 145
PRKCB -0.048 0.31 0.56 86 -0.42 62 148
PRKCE -0.046 0.31 0.56 86 -0.42 58 144
PRKCD -0.053 0.32 0.57 86 -0.44 63 149
PRKCG -0.065 0.32 0.57 85 -0.46 62 147
muscle contraction -0.089 0.36 0.6 86 -0.53 89 175
PRKCZ -0.043 0.3 0.55 86 -0.38 55 141
ARR3 0.031 0.003 -10000 0 -10000 0 0
TXA2/TP beta -0.002 0.066 0.22 7 -10000 0 7
PRKCQ -0.047 0.31 0.56 86 -0.42 55 141
MAPKKK cascade -0.088 0.36 0.58 86 -0.52 85 171
SELE -0.018 0.27 0.53 86 -10000 0 86
TP beta/GNAI2/GDP/G beta/gamma 0.033 0.061 0.22 5 -0.24 1 6
ROCK1 0.031 0.005 -10000 0 -10000 0 0
GNA14 0.029 0.02 -10000 0 -0.28 2 2
chemotaxis -0.091 0.4 0.65 86 -0.62 85 171
GNA12 0.03 0.007 -10000 0 -10000 0 0
GNA13 0.031 0.005 -10000 0 -10000 0 0
GNA11 -0.066 0.14 -10000 0 -0.28 168 168
Rac1/GTP 0.023 0.008 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.021 0.048 -10000 0 -0.28 13 13
ELF1 0.032 0.025 -10000 0 -0.29 3 3
CCNA2 0.005 0.011 -10000 0 -10000 0 0
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
JAK3 0.029 0.009 -10000 0 -10000 0 0
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
JAK1 0.03 0.019 -10000 0 -0.28 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.002 0.11 -10000 0 -0.43 12 12
SHC1 0.031 0.006 -10000 0 -10000 0 0
SP1 -0.23 0.15 -10000 0 -0.31 433 433
IL2RA -0.023 0.039 0.4 4 -10000 0 4
IL2RB 0.026 0.031 -10000 0 -0.28 5 5
SOS1 0.03 0.007 -10000 0 -10000 0 0
IL2RG 0.01 0.076 -10000 0 -0.28 35 35
G1/S transition of mitotic cell cycle -0.36 0.29 0.32 19 -0.51 411 430
PTPN11 0.031 0.004 -10000 0 -10000 0 0
CCND2 -0.41 0.26 0.4 2 -0.57 396 398
LCK 0.03 0.007 -10000 0 -10000 0 0
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.03 0.007 -10000 0 -10000 0 0
CDK6 0.025 0.04 -10000 0 -0.28 9 9
CCND3 0.002 0.1 0.39 1 -0.47 4 5
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.031 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.11 0.12 0.14 22 -0.26 185 207
FRAP1 0.002 0.067 -10000 0 -0.44 7 7
AKT1 -0.081 0.12 0.16 20 -0.23 178 198
INSR 0.011 0.074 -10000 0 -0.28 33 33
Insulin Receptor/Insulin 0.026 0.05 -10000 0 -0.17 32 32
mol:GTP -0.072 0.11 0.2 6 -0.26 32 38
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.042 0.05 -10000 0 -0.2 11 11
TSC2 0.03 0.006 -10000 0 -10000 0 0
RHEB/GDP -0.071 0.092 0.11 15 -0.19 147 162
TSC1 0.03 0.014 -10000 0 -0.28 1 1
Insulin Receptor/IRS1 -0.14 0.16 -10000 0 -0.28 293 293
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.038 0.061 0.14 1 -0.23 11 12
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.031 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.024 0.09 0.21 5 -0.31 13 18
MAP3K5 -0.008 0.052 0.18 5 -0.21 30 35
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
apoptosis -0.008 0.052 0.18 5 -0.21 30 35
mol:LY294002 -0.001 0.001 -10000 0 -0.001 285 285
EIF4B -0.027 0.084 0.26 3 -0.29 12 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.008 0.092 0.21 5 -0.28 11 16
eIF4E/eIF4G1/eIF4A1 -0.022 0.044 -10000 0 -0.26 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.1 0.14 -10000 0 -0.27 201 201
mTOR/RHEB/GTP/Raptor/GBL -0.02 0.06 0.18 8 -0.18 4 12
FKBP1A 0.03 0.008 -10000 0 -10000 0 0
RHEB/GTP -0.064 0.1 0.19 4 -0.26 20 24
mol:Amino Acids -0.001 0.001 -10000 0 -0.001 285 285
FKBP12/Rapamycin 0.022 0.007 -10000 0 -10000 0 0
PDPK1 -0.1 0.12 0.15 15 -0.25 180 195
EIF4E 0.03 0.008 -10000 0 -10000 0 0
ASK1/PP5C 0.004 0.15 -10000 0 -0.55 34 34
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.001 0.069 -10000 0 -0.24 38 38
TSC1/TSC2 -0.076 0.12 0.21 6 -0.28 32 38
tumor necrosis factor receptor activity 0.001 0.001 0.001 285 -10000 0 285
RPS6 0.03 0.007 -10000 0 -10000 0 0
PPP5C 0.03 0.007 -10000 0 -10000 0 0
EIF4G1 0.026 0.012 -10000 0 -10000 0 0
IRS1 -0.15 0.14 -10000 0 -0.28 302 302
INS 0.03 0.006 -10000 0 -10000 0 0
PTEN 0.028 0.021 -10000 0 -0.28 2 2
PDK2 -0.1 0.12 0.15 15 -0.25 183 198
EIF4EBP1 -0.047 0.27 -10000 0 -1 39 39
PIK3CA 0.021 0.015 -10000 0 -10000 0 0
PPP2R5D 0.001 0.068 0.24 5 -0.38 7 12
peptide biosynthetic process -0.035 0.045 0.18 9 -0.16 39 48
RHEB 0.029 0.009 -10000 0 -10000 0 0
EIF4A1 0.03 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 11 -10000 0 11
EEF2 -0.036 0.045 0.18 9 -0.16 39 48
eIF4E/4E-BP1 -0.031 0.26 -10000 0 -0.96 39 39
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.005 0.079 -10000 0 -0.17 86 86
NF kappa B1 p50/RelA/I kappa B alpha -0.068 0.098 0.21 1 -0.31 29 30
AP1 -0.022 0.1 0.22 37 -0.16 150 187
mol:PIP3 -0.062 0.073 -10000 0 -0.18 132 132
AKT1 -0.037 0.095 0.25 4 -0.26 19 23
PTK2B -0.065 0.11 0.19 15 -0.21 164 179
RHOA -0.014 0.055 0.18 16 -0.32 4 20
PIK3CB 0.027 0.017 -10000 0 -0.28 1 1
mol:Ca2+ -0.057 0.063 0.19 1 -0.19 42 43
MAGI3 0.031 0.005 -10000 0 -10000 0 0
RELA 0.03 0.019 -10000 0 -0.28 2 2
apoptosis -0.015 0.08 0.25 15 -0.18 83 98
HRAS/GDP 0.022 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.069 0.1 0.16 17 -0.23 113 130
NF kappa B1 p50/RelA -0.069 0.11 0.23 43 -0.24 57 100
endothelial cell migration -0.065 0.13 -10000 0 -0.38 85 85
ADCY4 -0.036 0.095 0.24 15 -0.22 81 96
ADCY5 -0.034 0.093 0.24 15 -0.22 83 98
ADCY6 -0.035 0.094 0.24 15 -0.22 83 98
ADCY7 -0.035 0.096 0.24 14 -0.22 84 98
ADCY1 -0.035 0.094 0.24 15 -0.22 82 97
ADCY2 -0.034 0.092 0.25 15 -0.22 75 90
ADCY3 -0.035 0.094 0.24 15 -0.22 85 100
ADCY8 -0.069 0.1 0.27 5 -0.25 80 85
ADCY9 -0.049 0.11 0.24 15 -0.25 88 103
GSK3B -0.065 0.11 0.17 26 -0.24 116 142
arachidonic acid secretion -0.046 0.093 0.22 15 -0.22 84 99
GNG2 0.028 0.028 -10000 0 -0.28 4 4
TRIP6 0.008 0.032 -10000 0 -0.29 3 3
GNAO1 -0.029 0.084 0.3 15 -0.18 84 99
HRAS 0.03 0.007 -10000 0 -10000 0 0
NFKBIA -0.067 0.09 -10000 0 -0.3 37 37
GAB1 0.029 0.02 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.03 0.14 -10000 0 -0.81 14 14
JUN 0.029 0.02 -10000 0 -0.28 2 2
LPA/LPA2/NHERF2 -0.002 0.051 -10000 0 -0.099 104 104
TIAM1 0.017 0.16 -10000 0 -0.94 14 14
PIK3R1 -0.002 0.091 -10000 0 -0.28 53 53
mol:IP3 -0.051 0.062 0.16 2 -0.19 38 40
PLCB3 -0.028 0.049 0.14 20 -0.16 26 46
FOS -0.029 0.12 -10000 0 -0.28 106 106
positive regulation of mitosis -0.046 0.093 0.22 15 -0.22 84 99
LPA/LPA1-2-3 -0.019 0.058 0.058 7 -0.15 85 92
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
stress fiber formation -0.037 0.1 0.23 15 -0.28 42 57
GNAZ -0.027 0.08 0.3 14 -0.18 74 88
EGFR/PI3K-beta/Gab1 -0.062 0.077 0.051 11 -0.18 132 143
positive regulation of dendritic cell cytokine production -0.02 0.058 0.062 3 -0.15 85 88
LPA/LPA2/MAGI-3 0.006 0.035 -10000 0 -0.075 80 80
ARHGEF1 -0.039 0.074 0.24 20 -0.18 11 31
GNAI2 -0.031 0.083 0.3 15 -0.18 84 99
GNAI3 -0.03 0.083 0.3 15 -0.18 83 98
GNAI1 -0.029 0.083 0.3 15 -0.19 78 93
LPA/LPA3 -0.013 0.029 -10000 0 -0.08 85 85
LPA/LPA2 -0.013 0.029 -10000 0 -0.079 85 85
LPA/LPA1 -0.031 0.076 -10000 0 -0.21 85 85
HB-EGF/EGFR -0.014 0.077 0.16 63 -0.18 34 97
HBEGF 0.001 0.075 0.19 72 -10000 0 72
mol:DAG -0.051 0.062 0.19 1 -0.19 38 39
cAMP biosynthetic process -0.047 0.096 0.22 16 -0.24 62 78
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
SRC 0.03 0.007 -10000 0 -10000 0 0
GNB1 0.029 0.016 -10000 0 -0.28 1 1
LYN -0.06 0.088 0.21 2 -0.25 52 54
GNAQ -0.004 0.044 0.13 15 -0.084 91 106
LPAR2 0 0.002 -10000 0 -10000 0 0
LPAR3 0 0.001 -10000 0 -10000 0 0
LPAR1 -0.021 0.045 -10000 0 -0.13 85 85
IL8 -0.004 0.23 0.61 46 -0.37 53 99
PTK2 -0.005 0.067 0.27 12 -0.15 65 77
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
CASP3 -0.016 0.081 0.26 15 -0.18 83 98
EGFR 0.003 0.091 -10000 0 -0.28 51 51
PLCG1 -0.03 0.057 0.13 10 -0.11 145 155
PLD2 -0.004 0.074 0.27 15 -0.15 79 94
G12/G13 0.006 0.078 -10000 0 -0.17 83 83
PI3K-beta -0.058 0.071 -10000 0 -0.26 32 32
cell migration -0.005 0.059 -10000 0 -0.25 14 14
SLC9A3R2 0.016 0.066 -10000 0 -0.28 26 26
PXN -0.038 0.1 0.23 15 -0.28 42 57
HRAS/GTP -0.047 0.095 0.22 15 -0.22 85 100
RAC1 0.03 0.007 -10000 0 -10000 0 0
MMP9 0.025 0.013 -10000 0 -10000 0 0
PRKCE 0.03 0.007 -10000 0 -10000 0 0
PRKCD -0.062 0.064 0.18 1 -0.2 30 31
Gi(beta/gamma) -0.038 0.096 0.25 14 -0.22 83 97
mol:LPA -0.021 0.045 -10000 0 -0.13 85 85
TRIP6/p130 Cas/FAK1/Paxillin -0.017 0.091 0.24 11 -0.22 47 58
MAPKKK cascade -0.046 0.093 0.22 15 -0.22 84 99
contractile ring contraction involved in cytokinesis -0.014 0.056 0.18 16 -0.32 4 20
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0 0.037 0.13 15 -0.087 7 22
GNA15 0.001 0.037 0.13 15 -0.14 3 18
GNA12 0.03 0.007 -10000 0 -10000 0 0
GNA13 0.031 0.005 -10000 0 -10000 0 0
MAPT -0.071 0.1 0.16 17 -0.23 114 131
GNA11 -0.042 0.084 0.13 10 -0.15 177 187
Rac1/GTP 0.03 0.14 -10000 0 -0.86 14 14
MMP2 -0.065 0.13 -10000 0 -0.38 85 85
Ephrin B reverse signaling

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
EFNB2 0.011 0.074 -10000 0 -0.28 33 33
EPHB2 0.032 0.008 -10000 0 -10000 0 0
EFNB1 -0.027 0.022 -10000 0 -0.2 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.045 -10000 0 -0.16 3 3
Ephrin B2/EPHB1-2 0.042 0.054 -10000 0 -0.16 31 31
neuron projection morphogenesis -0.018 0.053 0.088 1 -10000 0 1
Ephrin B1/EPHB1-2/Tiam1 0.056 0.038 0.2 1 -0.16 6 7
DNM1 0.032 0.006 -10000 0 -10000 0 0
cell-cell signaling 0.001 0.005 -10000 0 -10000 0 0
MAP2K4 -0.13 0.22 -10000 0 -0.5 141 141
YES1 -0.17 0.32 -10000 0 -0.72 143 143
Ephrin B1/EPHB1-2/NCK2 0.057 0.036 0.2 1 -0.16 5 6
PI3K -0.11 0.23 -10000 0 -0.49 143 143
mol:GDP 0.054 0.038 -10000 0 -0.16 6 6
ITGA2B 0.03 0.006 -10000 0 -10000 0 0
endothelial cell proliferation 0.026 0.05 -10000 0 -0.17 33 33
FYN -0.18 0.33 -10000 0 -0.74 142 142
MAP3K7 -0.13 0.23 0.23 4 -0.53 138 142
FGR -0.16 0.32 -10000 0 -0.71 143 143
TIAM1 0.03 0.014 -10000 0 -0.28 1 1
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
RGS3 0.031 0.005 -10000 0 -10000 0 0
cell adhesion -0.13 0.22 0.22 1 -0.49 141 142
LYN -0.17 0.33 -10000 0 -0.72 143 143
Ephrin B1/EPHB1-2/Src Family Kinases -0.16 0.3 -10000 0 -0.66 143 143
Ephrin B1/EPHB1-2 -0.13 0.25 -10000 0 -0.56 138 138
SRC -0.16 0.32 -10000 0 -0.71 142 142
ITGB3 -0.01 0.1 -10000 0 -0.28 71 71
EPHB1 0.031 0.009 -10000 0 -10000 0 0
EPHB4 0.031 0.006 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.05 -10000 0 -0.17 33 33
alphaIIb/beta3 Integrin 0.012 0.083 -10000 0 -0.2 71 71
BLK -0.18 0.32 -10000 0 -0.72 143 143
HCK -0.16 0.32 -10000 0 -0.71 142 142
regulation of stress fiber formation -0.055 0.035 0.16 5 -0.19 1 6
MAPK8 -0.13 0.21 -10000 0 -0.48 142 142
Ephrin B1/EPHB1-2/RGS3 0.057 0.037 0.2 1 -0.16 5 6
endothelial cell migration -0.11 0.2 0.25 5 -0.44 139 144
NCK2 0.031 0.004 -10000 0 -10000 0 0
PTPN13 0.007 0.086 -10000 0 -0.41 22 22
regulation of focal adhesion formation -0.055 0.035 0.16 5 -0.19 1 6
chemotaxis -0.055 0.036 0.16 5 -10000 0 5
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
Rac1/GTP 0.053 0.04 -10000 0 -0.16 3 3
angiogenesis -0.13 0.25 -10000 0 -0.56 141 141
LCK -0.16 0.32 -10000 0 -0.71 143 143
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.037 0.13 -10000 0 -0.28 118 118
CCL5 -0.003 0.096 -10000 0 -0.28 58 58
SDCBP 0.029 0.015 -10000 0 -0.28 1 1
FGFR/FGF2/Syndecan-1 -0.016 0.14 0.22 48 -0.34 49 97
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 -0.01 0.14 0.24 25 -0.33 44 69
Syndecan-1/Syntenin -0.006 0.15 0.25 34 -0.33 43 77
MAPK3 -0.039 0.14 0.21 31 -0.32 56 87
HGF/MET 0.022 0.068 -10000 0 -0.2 44 44
TGFB1/TGF beta receptor Type II -0.036 0.13 -10000 0 -0.28 118 118
BSG 0.029 0.009 -10000 0 -10000 0 0
keratinocyte migration -0.01 0.14 0.24 25 -0.33 44 69
Syndecan-1/RANTES -0.018 0.17 0.25 34 -0.33 76 110
Syndecan-1/CD147 -0.002 0.16 0.25 33 -0.32 51 84
Syndecan-1/Syntenin/PIP2 -0.008 0.14 0.23 33 -0.32 43 76
LAMA5 0.028 0.01 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.008 0.14 0.22 33 -0.32 43 76
MMP7 -0.052 0.13 -10000 0 -0.28 140 140
HGF 0.031 0.005 -10000 0 -10000 0 0
Syndecan-1/CASK -0.034 0.13 0.18 33 -0.31 54 87
Syndecan-1/HGF/MET -0.011 0.16 0.26 30 -0.32 59 89
regulation of cell adhesion -0.047 0.14 0.22 14 -0.32 56 70
HPSE 0.029 0.008 -10000 0 -10000 0 0
positive regulation of cell migration -0.016 0.14 0.22 48 -0.34 49 97
SDC1 -0.008 0.14 0.22 47 -0.36 36 83
Syndecan-1/Collagen -0.016 0.14 0.22 48 -0.34 49 97
PPIB 0.031 0.005 -10000 0 -10000 0 0
MET 0.004 0.084 -10000 0 -0.28 44 44
PRKACA 0.027 0.011 -10000 0 -10000 0 0
MMP9 0.025 0.013 -10000 0 -10000 0 0
MAPK1 -0.03 0.14 0.22 31 -0.32 50 81
homophilic cell adhesion -0.014 0.15 0.23 48 -0.33 50 98
MMP1 0.024 0.014 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.076 0.11 -10000 0 -0.17 303 303
TC10/GTP 0.026 0.056 -10000 0 -0.16 39 39
Insulin Receptor/Insulin/IRS1/Shp2 -0.064 0.13 -10000 0 -0.18 293 293
HRAS 0.03 0.007 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.03 0.007 -10000 0 -10000 0 0
FOXO3 -0.033 0.15 -10000 0 -0.61 33 33
AKT1 -0.06 0.11 0.33 4 -0.27 25 29
INSR 0.028 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.043 0.066 0.21 24 -0.16 28 52
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.031 0.005 -10000 0 -10000 0 0
SORBS1 0.005 0.086 -10000 0 -0.28 45 45
CRK 0.03 0.008 -10000 0 -10000 0 0
PTPN1 -0.033 0.047 -10000 0 -10000 0 0
CAV1 -0.11 0.094 0.16 7 -0.28 70 77
CBL/APS/CAP/Crk-II/C3G 0.046 0.067 -10000 0 -0.16 42 42
Insulin Receptor/Insulin/IRS1/NCK2 -0.064 0.13 -10000 0 -0.18 293 293
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.053 0.1 -10000 0 -0.18 203 203
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.092 0.15 -10000 0 -0.46 57 57
RPS6KB1 -0.065 0.1 0.3 4 -0.26 24 28
PARD6A 0.028 0.016 -10000 0 -0.28 1 1
CBL 0.031 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.025 0.033 -10000 0 -0.72 1 1
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.075 0.1 0.18 9 -0.28 23 32
HRAS/GTP -0.1 0.067 -10000 0 -0.17 237 237
Insulin Receptor 0.028 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.056 0.13 -10000 0 -0.18 274 274
PRKCI -0.003 0.076 -10000 0 -0.36 19 19
Insulin Receptor/Insulin/GRB14/PDK1 -0.083 0.082 -10000 0 -0.19 157 157
SHC1 0.03 0.006 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.047 0.042 -10000 0 -0.63 1 1
PI3K -0.046 0.11 -10000 0 -0.18 203 203
NCK2 0.031 0.004 -10000 0 -10000 0 0
RHOQ 0.031 0.006 -10000 0 -10000 0 0
mol:H2O2 -0.006 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.005 -10000 0 -10000 0 0
AKT2 -0.062 0.11 0.34 2 -0.27 25 27
PRKCZ -0.011 0.1 -10000 0 -0.36 38 38
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.092 0.074 0.15 5 -0.25 25 30
F2RL2 0.029 0.009 -10000 0 -10000 0 0
TRIP10 0.03 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.041 0.056 -10000 0 -0.15 32 32
TC10/GTP/CIP4/Exocyst 0.039 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.066 0.071 -10000 0 -0.16 29 29
RAPGEF1 0.031 0.005 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.28 3 3
NCK1 0.028 0.01 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.036 0.061 -10000 0 -0.16 43 43
TC10/GDP 0.023 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.055 0.067 -10000 0 -0.16 32 32
INPP5D -0.095 0.071 -10000 0 -0.16 288 288
SOS1 0.03 0.007 -10000 0 -10000 0 0
SGK1 -0.01 0.009 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.031 0.004 -10000 0 -10000 0 0
IRS1 -0.14 0.16 -10000 0 -0.28 297 297
p62DOK/RasGAP 0.047 0.042 -10000 0 -0.64 1 1
INS 0.027 0.024 0.092 1 -0.048 28 29
mol:PI-3-4-P2 -0.094 0.07 -10000 0 -0.16 288 288
GRB2 0.03 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.067 0.097 0.22 1 -0.26 25 26
PTPRA 0.023 0.025 -10000 0 -0.048 27 27
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.039 0.012 -10000 0 -10000 0 0
PDPK1 0.031 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.093 0.11 -10000 0 -0.29 55 55
Insulin Receptor/Insulin/IRS1 -0.066 0.12 -10000 0 -0.17 295 295
Insulin Receptor/Insulin/IRS3 0.031 0.063 -10000 0 -0.21 32 32
Par3/Par6 0.05 0.045 -10000 0 -0.16 1 1
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.006 0.11 0.66 8 -0.72 6 14
oxygen homeostasis 0.051 0.079 0.2 102 -10000 0 102
TCEB2 0.031 0.006 -10000 0 -10000 0 0
TCEB1 0.03 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.12 0.27 0.57 95 -0.36 7 102
EPO 0.16 0.36 0.85 73 -10000 0 73
FIH (dimer) 0.058 0.097 0.23 96 -10000 0 96
APEX1 0.047 0.063 0.18 62 -10000 0 62
SERPINE1 0.11 0.35 0.88 53 -10000 0 53
FLT1 -0.023 0.14 -10000 0 -0.67 21 21
ADORA2A 0.22 0.41 0.9 98 -10000 0 98
germ cell development 0.19 0.4 0.87 94 -0.57 1 95
SLC11A2 0.16 0.39 0.89 78 -10000 0 78
BHLHE40 0.15 0.38 0.86 78 -10000 0 78
HIF1AN 0.058 0.097 0.23 96 -10000 0 96
HIF2A/ARNT/SIRT1 0.047 0.22 0.5 30 -0.41 1 31
ETS1 0.032 0.021 0.27 2 -0.28 1 3
CITED2 -0.043 0.2 -10000 0 -0.82 32 32
KDR -0.014 0.11 -10000 0 -0.62 16 16
PGK1 0.029 0.29 0.9 30 -10000 0 30
SIRT1 0.031 0.004 -10000 0 -10000 0 0
response to hypoxia -0.001 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.045 0.28 0.71 13 -0.61 2 15
EPAS1 0.16 0.37 0.86 93 -0.39 1 94
SP1 0.045 0.061 0.3 27 -0.17 2 29
ABCG2 0.14 0.4 0.88 79 -0.62 10 89
EFNA1 0.15 0.38 0.88 78 -10000 0 78
FXN 0.21 0.4 0.84 114 -10000 0 114
POU5F1 0.16 0.39 0.88 84 -0.59 1 85
neuron apoptosis -0.043 0.27 0.59 2 -0.7 12 14
EP300 0.027 0.024 -10000 0 -0.28 3 3
EGLN3 0.042 0.11 0.23 85 -0.29 19 104
EGLN2 0.054 0.099 0.23 93 -10000 0 93
EGLN1 0.056 0.096 0.23 94 -10000 0 94
VHL/Elongin B/Elongin C 0.057 0.02 -10000 0 -10000 0 0
VHL 0.031 0.004 -10000 0 -10000 0 0
ARNT 0.049 0.064 0.18 65 -10000 0 65
SLC2A1 0.19 0.4 0.88 96 -10000 0 96
TWIST1 0.21 0.4 0.88 102 -10000 0 102
ELK1 0.025 0.031 -10000 0 -0.14 17 17
HIF2A/ARNT/Cbp/p300 0.052 0.24 0.54 35 -0.43 1 36
VEGFA 0.16 0.38 0.88 75 -10000 0 75
CREBBP 0.026 0.033 -10000 0 -0.28 6 6
Coregulation of Androgen receptor activity

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
NRIP1 -0.048 0.14 -10000 0 -0.28 139 139
SVIL 0.022 0.053 -10000 0 -0.28 16 16
ZNF318 0.03 0.007 -10000 0 -10000 0 0
JMJD2C 0.001 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.12 0.094 -10000 0 -0.21 246 246
CARM1 0.028 0.01 -10000 0 -10000 0 0
PRDX1 0.031 0.005 -10000 0 -10000 0 0
PELP1 0.03 0.007 -10000 0 -10000 0 0
CTNNB1 0.031 0.003 -10000 0 -10000 0 0
AKT1 0.03 0.007 -10000 0 -10000 0 0
PTK2B 0.025 0.022 -10000 0 -0.28 2 2
MED1 0.03 0.008 -10000 0 -10000 0 0
MAK -0.039 0.13 -10000 0 -0.28 120 120
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.031 0.005 -10000 0 -10000 0 0
GSN 0 0.094 -10000 0 -0.28 55 55
NCOA2 0.029 0.009 -10000 0 -10000 0 0
NCOA6 0.03 0.008 -10000 0 -10000 0 0
DNA-PK 0.043 0.03 -10000 0 -10000 0 0
NCOA4 0.031 0.003 -10000 0 -10000 0 0
PIAS3 0.031 0.005 -10000 0 -10000 0 0
cell proliferation -0.17 0.26 -10000 0 -0.64 128 128
XRCC5 0.028 0.01 -10000 0 -10000 0 0
UBE3A 0.03 0.008 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.12 0.094 -10000 0 -0.21 246 246
FHL2 -0.069 0.079 0.55 1 -0.44 13 14
RANBP9 0.029 0.008 -10000 0 -10000 0 0
JMJD1A -0.074 0.06 -10000 0 -0.13 211 211
CDK6 0.025 0.04 -10000 0 -0.28 9 9
TGFB1I1 0.004 0.089 -10000 0 -0.28 49 49
T-DHT/AR/CyclinD1 -0.15 0.12 -10000 0 -0.24 307 307
XRCC6 0.029 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.16 0.11 -10000 0 -0.29 136 136
CTDSP1 0.029 0.023 -10000 0 -0.28 3 3
CTDSP2 0.029 0.019 -10000 0 -0.28 2 2
BRCA1 0.028 0.01 -10000 0 -10000 0 0
TCF4 0.028 0.024 -10000 0 -0.28 3 3
CDKN2A 0.012 0.015 -10000 0 -10000 0 0
SRF 0.029 0.033 0.31 1 -0.28 5 6
NKX3-1 -0.21 0.14 -10000 0 -0.52 61 61
KLK3 -0.02 0.069 -10000 0 -10000 0 0
TMF1 0.031 0.004 -10000 0 -10000 0 0
HNRNPA1 0.031 0.005 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 -0.029 0.008 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.12 0.094 -10000 0 -0.2 246 246
AR -0.16 0.14 -10000 0 -0.31 243 243
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.029 0.008 -10000 0 -10000 0 0
PAWR 0.031 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.013 -10000 0 -10000 0 0
PA2G4 0.03 0.006 -10000 0 -10000 0 0
UBE2I 0.03 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.1 0.087 -10000 0 -0.18 241 241
RPS6KA3 0.028 0.027 -10000 0 -0.28 4 4
T-DHT/AR/ARA70 -0.12 0.095 -10000 0 -0.21 247 247
LATS2 0.03 0.007 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.1 0.086 -10000 0 -0.19 241 241
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 0.028 0.01 -10000 0 -10000 0 0
KLK2 -0.079 0.059 -10000 0 -0.4 9 9
CASP8 0.031 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.098 0.094 -10000 0 -0.2 209 209
TMPRSS2 -0.5 0.35 -10000 0 -0.76 352 352
CCND1 -0.049 0.14 -10000 0 -0.28 142 142
PIAS1 0.031 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.032 0.024 -10000 0 -0.077 9 9
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.029 0.009 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.12 0.097 -10000 0 -0.21 244 244
CMTM2 0.028 0.01 -10000 0 -10000 0 0
SNURF 0.029 0.015 -10000 0 -0.28 1 1
ZMIZ1 -0.038 0.055 -10000 0 -0.29 4 4
CCND3 0.03 0.007 -10000 0 -10000 0 0
TGIF1 0.03 0.007 -10000 0 -10000 0 0
FKBP4 0.027 0.011 -10000 0 -10000 0 0
IL23-mediated 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
CCL2 0.026 0.58 1.2 47 -1.2 40 87
IL23A 0.032 0.52 1.1 34 -1.1 22 56
NF kappa B1 p50/RelA/I kappa B alpha -0.013 0.46 0.76 33 -0.96 52 85
positive regulation of T cell mediated cytotoxicity 0.045 0.6 1.3 47 -1.2 29 76
ITGA3 -0.027 0.56 1 32 -1.2 50 82
IL17F 0.03 0.38 0.75 47 -0.72 24 71
IL12B 0.062 0.13 0.36 60 -10000 0 60
STAT1 (dimer) -0.1 0.37 0.89 12 -1.1 32 44
CD4 0.052 0.53 1.1 47 -1.1 27 74
IL23 0.022 0.48 0.95 33 -1 25 58
IL23R 0.093 0.26 0.83 33 -0.81 4 37
IL1B 0.039 0.53 1.2 35 -1.1 25 60
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.03 0.5 1 47 -1 28 75
TYK2 0.04 0.089 0.26 48 -10000 0 48
STAT4 0.031 0.005 -10000 0 -10000 0 0
STAT3 0.024 0.04 -10000 0 -0.28 9 9
IL18RAP 0.02 0.033 -10000 0 -10000 0 0
IL12RB1 0.04 0.09 0.26 48 -10000 0 48
PIK3CA 0.021 0.015 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.05 0.1 0.27 57 -10000 0 57
IL23R/JAK2 0.1 0.26 0.73 44 -0.81 3 47
positive regulation of chronic inflammatory response 0.045 0.6 1.3 47 -1.2 29 76
natural killer cell activation -0.007 0.022 -10000 0 -0.065 49 49
JAK2 0.059 0.13 0.36 60 -0.3 2 62
PIK3R1 -0.002 0.092 -10000 0 -0.28 53 53
NFKB1 0.011 0.053 -10000 0 -0.29 10 10
RELA 0.015 0.039 -10000 0 -0.29 2 2
positive regulation of dendritic cell antigen processing and presentation 0.026 0.47 0.95 33 -1 24 57
ALOX12B 0.029 0.5 1 34 -1 27 61
CXCL1 -0.13 0.7 1.1 38 -1.2 128 166
T cell proliferation 0.045 0.6 1.3 47 -1.2 29 76
NFKBIA 0.009 0.06 -10000 0 -0.29 15 15
IL17A 0.035 0.34 0.7 47 -0.58 16 63
PI3K -0.058 0.42 0.81 26 -1 41 67
IFNG 0.035 0.097 0.37 32 -10000 0 32
STAT3 (dimer) -0.055 0.41 0.79 28 -0.97 41 69
IL18R1 0.02 0.033 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.065 0.39 0.89 48 -0.82 13 61
IL18/IL18R 0.053 0.069 0.32 24 -10000 0 24
macrophage activation -0.003 0.025 0.067 22 -10000 0 22
TNF 0.032 0.52 1.1 35 -1.1 25 60
STAT3/STAT4 -0.016 0.46 0.79 30 -0.97 49 79
STAT4 (dimer) 0.01 0.5 0.89 45 -1.1 33 78
IL18 0.017 0.028 0.12 1 -10000 0 1
IL19 0.031 0.51 1.1 35 -1 27 62
STAT5A (dimer) 0.012 0.51 0.89 46 -1.1 39 85
STAT1 0.015 0.016 -10000 0 -10000 0 0
SOCS3 0.026 0.038 -10000 0 -0.28 8 8
CXCL9 0.071 0.57 1.2 62 -1 27 89
MPO 0.029 0.5 1 46 -1 28 74
positive regulation of humoral immune response 0.045 0.6 1.3 47 -1.2 29 76
IL23/IL23R/JAK2/TYK2 0.034 0.61 1.3 49 -1.3 29 78
IL6 -0.016 0.57 1 35 -1.2 53 88
STAT5A 0.027 0.033 -10000 0 -0.28 6 6
IL2 0.02 0.06 0.23 27 -10000 0 27
positive regulation of tyrosine phosphorylation of STAT protein -0.007 0.022 -10000 0 -0.065 49 49
CD3E 0.023 0.54 1.1 36 -1.2 33 69
keratinocyte proliferation 0.045 0.6 1.3 47 -1.2 29 76
NOS2 0.033 0.5 1 46 -1 29 75
FoxO family 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
G6PC 0.036 0.084 -10000 0 -10000 0 0
PLK1 0.29 0.39 0.88 82 -0.87 13 95
CDKN1B 0.21 0.3 0.66 82 -0.46 2 84
FOXO3 0.27 0.41 0.62 269 -0.86 18 287
KAT2B 0.065 0.068 0.12 313 -0.077 2 315
FOXO1/SIRT1 0.021 0.087 0.33 2 -0.27 8 10
CAT 0.26 0.38 0.75 72 -0.9 18 90
CTNNB1 0.031 0.004 -10000 0 -10000 0 0
AKT1 0.089 0.084 0.23 65 -10000 0 65
FOXO1 0.048 0.096 0.53 1 -0.3 4 5
MAPK10 0.017 0.064 0.19 30 -10000 0 30
mol:GTP 0 0.008 -10000 0 -10000 0 0
FOXO4 0.023 0.16 0.47 28 -0.5 5 33
response to oxidative stress 0.065 0.07 0.17 94 -0.084 1 95
FOXO3A/SIRT1 0.25 0.35 0.57 171 -0.75 23 194
XPO1 0.026 0.016 -10000 0 -10000 0 0
EP300 0.021 0.033 -10000 0 -0.28 3 3
BCL2L11 0.097 0.13 0.7 2 -0.97 3 5
FOXO1/SKP2 0.036 0.082 0.4 1 -0.28 5 6
mol:GDP 0.065 0.069 0.17 94 -0.084 1 95
RAN 0.022 0.025 -10000 0 -10000 0 0
GADD45A 0.21 0.29 0.73 72 -0.63 5 77
YWHAQ 0.031 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.013 0.14 -10000 0 -0.47 27 27
MST1 0.091 0.08 0.22 68 -10000 0 68
CSNK1D 0.03 0.007 -10000 0 -10000 0 0
CSNK1E 0.029 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.011 0.12 -10000 0 -0.51 17 17
YWHAB 0.029 0.009 -10000 0 -10000 0 0
MAPK8 0.019 0.065 0.2 31 -10000 0 31
MAPK9 0.019 0.064 0.2 20 -10000 0 20
YWHAG 0.029 0.023 -10000 0 -0.28 3 3
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
YWHAZ 0.027 0.011 -10000 0 -10000 0 0
SIRT1 -0.007 0.055 0.17 24 -0.16 1 25
SOD2 0.058 0.47 0.64 59 -0.75 112 171
RBL2 0.18 0.35 0.66 56 -0.79 26 82
RAL/GDP 0.074 0.068 0.19 57 -0.14 1 58
CHUK 0.09 0.08 0.21 75 -0.11 1 76
Ran/GTP 0.017 0.025 -10000 0 -10000 0 0
CSNK1G2 0.029 0.009 -10000 0 -10000 0 0
RAL/GTP 0.071 0.078 0.27 27 -0.13 1 28
CSNK1G1 0.031 0.005 -10000 0 -10000 0 0
FASLG 0.1 0.095 -10000 0 -10000 0 0
SKP2 0.024 0.014 -10000 0 -10000 0 0
USP7 0.022 0.027 -10000 0 -0.28 1 1
IKBKB 0.086 0.08 0.22 62 -10000 0 62
CCNB1 0.38 0.43 0.73 297 -0.96 9 306
FOXO1-3a-4/beta catenin 0.15 0.3 0.63 63 -0.44 3 66
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.081 0.39 1 -0.28 5 6
CSNK1A1 0.031 0.005 -10000 0 -10000 0 0
SGK1 0.065 0.068 0.12 313 -0.077 2 315
CSNK1G3 0.03 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0.036 0.15 1 -10000 0 1
ZFAND5 0.021 0.15 0.48 10 -0.65 2 12
SFN 0.03 0.008 -10000 0 -10000 0 0
CDK2 -0.004 0.025 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.093 0.14 0.31 50 -0.43 13 63
CREBBP -0.018 0.042 -10000 0 -0.29 6 6
FBXO32 0.17 0.6 0.8 130 -0.85 112 242
BCL6 0.2 0.34 0.65 53 -0.89 22 75
RALB 0.021 0.029 -10000 0 -0.29 1 1
RALA 0.021 0.026 -10000 0 -10000 0 0
YWHAH 0.029 0.008 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.048 -10000 0 -0.28 13 13
ANTXR2 0.011 0.075 -10000 0 -0.28 34 34
negative regulation of myeloid dendritic cell antigen processing and presentation -0.008 0.011 -10000 0 -0.044 42 42
monocyte activation -0.028 0.14 -10000 0 -0.37 82 82
MAP2K2 -0.25 0.33 -10000 0 -0.66 223 223
MAP2K1 -0.016 0.012 0.16 1 -10000 0 1
MAP2K7 -0.016 0.01 -10000 0 -10000 0 0
MAP2K6 -0.001 0.051 0.16 51 -0.072 4 55
CYAA -0.029 0.036 -10000 0 -0.15 42 42
MAP2K4 -0.016 0.015 -10000 0 -0.14 4 4
IL1B -0.011 0.054 0.15 41 -0.12 7 48
Channel 0.022 0.055 -10000 0 -0.16 42 42
NLRP1 -0.016 0.012 0.12 1 -10000 0 1
CALM1 0.022 0.053 -10000 0 -0.28 16 16
negative regulation of phagocytosis -0.015 0.098 -10000 0 -0.46 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.008 0.011 0.044 42 -10000 0 42
MAPK3 -0.025 0.032 -10000 0 -0.14 38 38
MAPK1 -0.015 0.01 -10000 0 -10000 0 0
PGR -0.11 0.053 -10000 0 -0.14 452 452
PA/Cellular Receptors 0.023 0.06 -10000 0 -0.18 42 42
apoptosis -0.008 0.011 -10000 0 -0.044 42 42
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.053 -10000 0 -0.16 42 42
macrophage activation -0.031 0.033 0.14 1 -0.14 40 41
TNF 0.031 0.005 -10000 0 -10000 0 0
VCAM1 -0.04 0.14 -10000 0 -0.37 82 82
platelet activation -0.015 0.098 -10000 0 -0.46 25 25
MAPKKK cascade 0.029 0.04 0.1 18 -0.098 6 24
IL18 0.007 0.071 0.15 97 -0.12 7 104
negative regulation of macrophage activation -0.008 0.011 -10000 0 -0.044 42 42
LEF -0.008 0.011 -10000 0 -0.044 42 42
CASP1 -0.015 0.027 0.042 8 -0.09 52 60
mol:cAMP -0.015 0.099 -10000 0 -0.47 25 25
necrosis -0.008 0.011 -10000 0 -0.044 42 42
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.052 -10000 0 -0.15 42 42
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.062 0.26 0.54 4 -0.87 49 53
MKNK1 0.031 0.005 -10000 0 -10000 0 0
MAPK14 0.01 0.095 0.21 12 -0.28 48 60
ATF2/c-Jun -0.052 0.079 -10000 0 -0.26 46 46
MAPK11 0.007 0.087 0.2 10 -0.3 37 47
MITF -0.017 0.1 0.25 4 -0.34 48 52
MAPKAPK5 -0.017 0.1 0.25 4 -0.34 48 52
KRT8 -0.018 0.1 0.25 4 -0.34 49 53
MAPKAPK3 0.031 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.03 0.014 -10000 0 -0.28 1 1
p38alpha-beta/CK2 0.001 0.13 0.32 4 -0.39 49 53
CEBPB -0.015 0.1 0.25 4 -0.35 42 46
SLC9A1 -0.017 0.1 0.22 9 -0.34 47 56
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.014 0.11 0.38 10 -0.34 46 56
p38alpha-beta/MNK1 0.016 0.11 0.29 4 -0.32 48 52
JUN -0.051 0.079 -10000 0 -0.26 46 46
PPARGC1A -0.017 0.1 0.25 3 -0.35 47 50
USF1 -0.017 0.11 0.27 5 -0.34 49 54
RAB5/GDP/GDI1 -0.023 0.098 -10000 0 -0.25 56 56
NOS2 -0.02 0.1 0.22 9 -0.34 49 58
DDIT3 -0.002 0.11 0.24 9 -0.34 41 50
RAB5A 0.031 0.004 -10000 0 -10000 0 0
HSPB1 -0.033 0.088 0.26 4 -0.3 48 52
p38alpha-beta/HBP1 0.014 0.11 0.29 3 -0.32 48 51
CREB1 -0.053 0.13 0.26 4 -0.38 48 52
RAB5/GDP 0.023 0.003 -10000 0 -10000 0 0
EIF4E -0.055 0.086 0.19 10 -0.32 35 45
RPS6KA4 -0.018 0.1 0.25 4 -0.34 49 53
PLA2G4A -0.088 0.11 0.19 6 -0.39 42 48
GDI1 -0.019 0.1 0.22 9 -0.34 50 59
TP53 -0.055 0.12 0.23 10 -0.43 48 58
RPS6KA5 -0.017 0.1 0.25 4 -0.34 47 51
ESR1 -0.04 0.13 0.25 3 -0.3 93 96
HBP1 0.029 0.008 -10000 0 -10000 0 0
MEF2C -0.022 0.11 0.22 7 -0.37 50 57
MEF2A -0.018 0.1 0.22 8 -0.34 47 55
EIF4EBP1 -0.048 0.13 0.26 4 -0.4 46 50
KRT19 -0.03 0.13 0.23 8 -0.35 65 73
ELK4 -0.018 0.1 0.28 4 -0.34 49 53
ATF6 -0.018 0.1 0.24 9 -0.34 49 58
ATF1 -0.053 0.13 0.26 4 -0.37 49 53
p38alpha-beta/MAPKAPK2 0.015 0.11 0.29 3 -0.32 50 53
p38alpha-beta/MAPKAPK3 0.017 0.11 0.29 4 -0.32 49 53
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.033 0.067 -10000 0 -0.5 5 5
IHH 0.056 0.063 0.23 7 -0.15 15 22
SHH Np/Cholesterol/GAS1 -0.041 0.04 0.14 1 -0.16 49 50
LRPAP1 0.029 0.02 -10000 0 -0.28 2 2
dorsoventral neural tube patterning 0.04 0.04 0.16 49 -0.14 1 50
SMO/beta Arrestin2 0.07 0.14 0.31 108 -0.43 10 118
SMO 0.049 0.15 0.32 111 -0.44 10 121
AKT1 0.011 0.13 0.27 16 -0.42 13 29
ARRB2 0.03 0.007 -10000 0 -10000 0 0
BOC -0.001 0.094 -10000 0 -0.28 56 56
ADRBK1 0.031 0.004 -10000 0 -10000 0 0
heart looping 0.048 0.15 0.32 111 -0.44 10 121
STIL 0.007 0.077 0.28 29 -10000 0 29
DHH N/PTCH2 0.045 0.01 -10000 0 -10000 0 0
DHH N/PTCH1 0.073 0.14 0.32 106 -0.31 15 121
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
DHH 0.031 0.003 -10000 0 -10000 0 0
PTHLH 0.06 0.22 0.51 94 -0.46 5 99
determination of left/right symmetry 0.048 0.15 0.32 111 -0.44 10 121
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
skeletal system development 0.06 0.22 0.51 94 -0.46 5 99
IHH N/Hhip 0.054 0.05 0.18 3 -0.19 6 9
DHH N/Hhip 0.044 0.011 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.048 0.15 0.32 111 -0.44 10 121
pancreas development 0.03 0.007 -10000 0 -10000 0 0
HHAT 0.027 0.033 -10000 0 -0.28 6 6
PI3K 0.012 0.062 -10000 0 -0.2 37 37
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.004 0.088 -10000 0 -0.28 48 48
somite specification 0.048 0.15 0.32 111 -0.44 10 121
SHH Np/Cholesterol/PTCH1 0.017 0.13 0.28 102 -0.31 10 112
SHH Np/Cholesterol/PTCH2 -0.03 0.018 0.14 1 -0.16 6 7
SHH Np/Cholesterol/Megalin -0.023 0.02 -10000 0 -0.16 5 5
SHH -0.03 0.022 0.19 1 -0.2 6 7
catabolic process 0.049 0.18 0.39 111 -0.37 10 121
SMO/Vitamin D3 0.022 0.14 0.26 102 -0.41 10 112
SHH Np/Cholesterol/Hhip -0.03 0.019 0.14 1 -0.16 6 7
LRP2 0.023 0.014 -10000 0 -10000 0 0
receptor-mediated endocytosis 0.047 0.14 0.29 103 -0.43 10 113
SHH Np/Cholesterol/BOC -0.042 0.042 0.14 1 -0.16 58 59
SHH Np/Cholesterol/CDO -0.03 0.02 0.14 1 -0.16 8 9
mesenchymal cell differentiation 0.03 0.019 0.16 6 -0.14 1 7
mol:Vitamin D3 -0.018 0.084 0.21 45 -0.31 10 55
IHH N/PTCH2 0.055 0.049 0.18 4 -0.19 6 10
CDON 0.028 0.02 -10000 0 -0.28 2 2
IHH N/PTCH1 0.011 0.066 -10000 0 -0.34 15 15
Megalin/LRPAP1 0.032 0.026 -10000 0 -0.2 2 2
PTCH2 0.03 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.021 0.017 0.16 1 -0.15 6 7
PTCH1 0.049 0.18 0.39 111 -0.37 10 121
HHIP 0.03 0.007 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.006 0.032 -10000 0 -0.31 2 2
STMN1 0.024 0.083 0.19 105 -10000 0 105
Aurora B/RasGAP/Survivin 0.054 0.042 -10000 0 -0.16 2 2
Chromosomal passenger complex/Cul3 protein complex 0.001 0.09 0.19 25 -0.21 13 38
BIRC5 0.044 0.019 -10000 0 -10000 0 0
DES -0.07 0.16 -10000 0 -0.5 42 42
Aurora C/Aurora B/INCENP 0.058 0.036 -10000 0 -10000 0 0
Aurora B/TACC1 -0.079 0.091 -10000 0 -0.16 302 302
Aurora B/PP2A 0.04 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.006 0.015 0.12 5 -0.12 3 8
mitotic metaphase/anaphase transition -0.004 0.005 -10000 0 -10000 0 0
NDC80 0.13 0.1 0.21 351 -10000 0 351
Cul3 protein complex -0.01 0.11 -10000 0 -0.18 157 157
KIF2C 0.11 0.091 0.19 290 -10000 0 290
PEBP1 0.044 0.009 -10000 0 -10000 0 0
KIF20A 0.005 0.013 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.037 0.03 -10000 0 -0.2 3 3
SEPT1 0.031 0.005 -10000 0 -10000 0 0
SMC2 0.022 0.014 -10000 0 -10000 0 0
SMC4 0.002 0.008 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.001 0.042 -10000 0 -0.4 5 5
PSMA3 0.03 0.014 -10000 0 -0.28 1 1
G2/M transition of mitotic cell cycle 0 0.002 -10000 0 -10000 0 0
H3F3B 0.011 0.018 -10000 0 -0.22 3 3
AURKB 0.031 0.019 -10000 0 -10000 0 0
AURKC 0.03 0.007 -10000 0 -10000 0 0
CDCA8 0.045 0.019 -10000 0 -10000 0 0
cytokinesis 0.002 0.026 0.22 5 -0.24 1 6
Aurora B/Septin1 0.18 0.13 0.28 314 -0.25 1 315
AURKA 0.002 0.008 -10000 0 -10000 0 0
INCENP 0.053 0.011 -10000 0 -10000 0 0
KLHL13 -0.058 0.14 -10000 0 -0.28 158 158
BUB1 0.003 0.009 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.009 0.026 -10000 0 -10000 0 0
EVI5 0.041 0.016 -10000 0 -0.28 1 1
RhoA/GTP 0.004 0.021 -10000 0 -10000 0 0
SGOL1 0.004 0.011 -10000 0 -10000 0 0
CENPA 0.021 0.053 0.18 29 -10000 0 29
NCAPG 0.003 0.01 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.04 0.026 -10000 0 -0.2 1 1
NCAPD2 0.015 0.016 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.04 0.026 -10000 0 -0.2 1 1
RHOA 0.031 0.014 -10000 0 -0.28 1 1
NCAPH 0.013 0.016 -10000 0 -10000 0 0
NPM1 -0.001 0.016 -10000 0 -0.27 2 2
RASA1 0.027 0.024 -10000 0 -0.28 3 3
KLHL9 0.03 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.012 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.026 -10000 0 -0.2 1 1
PPP1CC 0.03 0.014 -10000 0 -0.28 1 1
Centraspindlin 0.004 0.02 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.009 -10000 0 -0.19 1 1
NSUN2 0 0.013 -10000 0 -0.29 1 1
MYLK -0.01 0.068 -10000 0 -0.22 51 51
KIF23 0.002 0.008 -10000 0 -10000 0 0
VIM -0.018 0.096 0.18 62 -0.2 78 140
RACGAP1 0.007 0.015 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0.013 -10000 0 -0.29 1 1
Chromosomal passenger complex 0.15 0.11 0.22 356 -10000 0 356
Chromosomal passenger complex/EVI5 0.076 0.061 -10000 0 -0.17 1 1
TACC1 -0.19 0.14 -10000 0 -0.28 389 389
PPP2R5D 0.03 0.007 -10000 0 -10000 0 0
CUL3 0.031 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.041 0.015 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.022 0.082 -10000 0 -0.18 71 71
PTK2 -0.018 0.14 0.29 15 -0.32 49 64
IGF1R -0.033 0.12 -10000 0 -0.28 111 111
PI4KB 0.03 0.008 -10000 0 -10000 0 0
MFGE8 0.018 0.059 -10000 0 -0.28 20 20
SRC 0.03 0.007 -10000 0 -10000 0 0
CDKN1B -0.002 0.063 -10000 0 -0.3 16 16
VEGFA 0.029 0.009 -10000 0 -10000 0 0
ILK -0.001 0.062 -10000 0 -0.28 16 16
ROCK1 0.031 0.005 -10000 0 -10000 0 0
AKT1 -0.019 0.059 -10000 0 -0.27 19 19
PTK2B -0.021 0.091 0.22 31 -0.28 2 33
alphaV/beta3 Integrin/JAM-A 0.021 0.08 -10000 0 -0.17 67 67
CBL 0.031 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.024 0.081 -10000 0 -0.18 69 69
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.087 0.14 -10000 0 -0.21 310 310
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.006 0.084 0.18 4 -0.3 15 19
alphaV/beta3 Integrin/Syndecan-1 0.024 0.08 -10000 0 -0.18 67 67
PI4KA 0.03 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.077 0.14 -10000 0 -0.22 209 209
PI4 Kinase 0.042 0.015 -10000 0 -10000 0 0
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.002 0.06 -10000 0 -0.19 40 40
RPS6KB1 -0.08 0.14 0.29 13 -0.29 81 94
TLN1 0.03 0.019 -10000 0 -0.28 2 2
MAPK3 -0.08 0.17 -10000 0 -0.42 88 88
GPR124 0.016 0.061 -10000 0 -0.28 22 22
MAPK1 -0.069 0.16 -10000 0 -0.42 87 87
PXN 0.024 0.046 -10000 0 -0.28 12 12
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
alphaV/beta3 Integrin/Tumstatin 0.024 0.082 -10000 0 -0.18 71 71
cell adhesion 0.007 0.094 -10000 0 -0.21 74 74
ANGPTL3 0.031 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.054 0.024 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.033 0.12 -10000 0 -0.28 111 111
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
TGFBR2 0.024 0.046 -10000 0 -0.28 12 12
ITGB3 -0.01 0.1 -10000 0 -0.28 71 71
IGF1 0.022 0.053 -10000 0 -0.28 16 16
RAC1 0.03 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.013 0.089 -10000 0 -0.19 82 82
apoptosis 0.027 0.024 -10000 0 -0.28 3 3
CD47 0.028 0.016 -10000 0 -0.28 1 1
alphaV/beta3 Integrin/CD47 0.022 0.079 -10000 0 -0.18 64 64
VCL 0.031 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.015 0.08 -10000 0 -0.18 68 68
CSF1 0.019 0.06 -10000 0 -0.28 21 21
PIK3C2A 0.001 0.057 -10000 0 -0.27 13 13
PI4 Kinase/Pyk2 -0.063 0.064 0.1 20 -0.28 2 22
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.032 0.083 -10000 0 -0.17 64 64
FAK1/Vinculin -0.008 0.13 0.27 16 -0.3 26 42
alphaV beta3/Integrin/ppsTEM5 0.013 0.089 -10000 0 -0.19 82 82
RHOA 0.031 0.014 -10000 0 -0.28 1 1
VTN 0.03 0.007 -10000 0 -10000 0 0
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
FGF2 0.03 0.007 -10000 0 -10000 0 0
F11R -0.028 0.013 0.19 1 -10000 0 1
alphaV/beta3 Integrin/Lactadherin 0.015 0.091 -10000 0 -0.19 83 83
alphaV/beta3 Integrin/TGFBR2 0.021 0.088 -10000 0 -0.19 76 76
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.052 0.062 -10000 0 -0.18 24 24
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.022 0.076 -10000 0 -0.16 71 71
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.013 0.046 -10000 0 -0.28 12 12
alphaV/beta3 Integrin/Pyk2 -0.045 0.068 0.17 28 -0.28 2 30
SDC1 0.031 0.005 -10000 0 -10000 0 0
VAV3 -0.032 0.066 0.2 17 -0.28 1 18
PTPN11 0.031 0.004 -10000 0 -10000 0 0
IRS1 -0.14 0.16 -10000 0 -0.28 297 297
FAK1/Paxillin -0.01 0.13 0.27 16 -0.3 28 44
cell migration -0.018 0.12 0.25 18 -0.28 27 45
ITGAV 0.027 0.024 -10000 0 -0.28 3 3
PI3K 0.017 0.094 -10000 0 -0.19 69 69
SPP1 0.008 0.026 -10000 0 -0.28 3 3
KDR 0.03 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.024 -10000 0 -0.28 3 3
COL4A3 0.031 0.004 -10000 0 -10000 0 0
angiogenesis -0.08 0.18 0.32 2 -0.45 90 92
Rac1/GTP -0.037 0.065 0.19 20 -0.27 1 21
EDIL3 0.025 0.018 -10000 0 -0.28 1 1
cell proliferation 0.02 0.088 -10000 0 -0.19 76 76
Reelin signaling pathway

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.019 -10000 0 -10000 0 0
VLDLR 0.021 0.048 -10000 0 -0.28 13 13
CRKL 0.03 0.007 -10000 0 -10000 0 0
LRPAP1 0.029 0.02 -10000 0 -0.28 2 2
FYN -0.002 0.095 -10000 0 -0.28 57 57
ITGA3 0.004 0.086 -10000 0 -0.28 46 46
RELN/VLDLR/Fyn -0.005 0.1 -10000 0 -0.19 128 128
MAPK8IP1/MKK7/MAP3K11/JNK1 0.079 0.041 -10000 0 -0.17 1 1
AKT1 -0.032 0.087 0.18 3 -0.28 20 23
MAP2K7 0.03 0.008 -10000 0 -10000 0 0
RAPGEF1 0.031 0.005 -10000 0 -10000 0 0
DAB1 0.031 0.005 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.022 0.077 -10000 0 -0.16 80 80
LRPAP1/LRP8 0.042 0.02 -10000 0 -0.2 2 2
RELN/LRP8/DAB1/Fyn 0.008 0.099 -10000 0 -0.17 124 124
DAB1/alpha3/beta1 Integrin 0.005 0.1 -10000 0 -0.18 112 112
long-term memory 0.02 0.11 -10000 0 -0.18 110 110
DAB1/LIS1 0.034 0.097 -10000 0 -0.17 81 81
DAB1/CRLK/C3G 0.018 0.092 -10000 0 -0.18 83 83
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
DAB1/NCK2 0.035 0.099 -10000 0 -0.17 84 84
ARHGEF2 0.03 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.029 0.009 -10000 0 -10000 0 0
CDK5R1 0.03 0.008 -10000 0 -10000 0 0
RELN -0.016 0.11 -10000 0 -0.28 81 81
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
RELN/LRP8/Fyn -0.001 0.1 -10000 0 -0.19 124 124
GRIN2A/RELN/LRP8/DAB1/Fyn 0.025 0.11 -10000 0 -0.18 119 119
MAPK8 0.031 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.015 0.08 -10000 0 -0.16 88 88
ITGB1 0.031 0.006 -10000 0 -10000 0 0
MAP1B -0.049 0.089 0.2 15 -0.29 12 27
RELN/LRP8 0.02 0.084 -10000 0 -0.18 78 78
GRIN2B/RELN/LRP8/DAB1/Fyn 0.021 0.11 -10000 0 -0.18 115 115
PI3K 0.012 0.062 -10000 0 -0.2 37 37
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.023 0.069 -10000 0 -0.2 46 46
RAP1A -0.054 0.097 0.34 11 -0.27 1 12
PAFAH1B1 0.03 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.031 0.004 -10000 0 -10000 0 0
CRLK/C3G 0.043 0.012 -10000 0 -10000 0 0
GRIN2B 0.028 0.01 -10000 0 -10000 0 0
NCK2 0.031 0.004 -10000 0 -10000 0 0
neuron differentiation -0.025 0.089 0.17 1 -0.29 24 25
neuron adhesion -0.068 0.1 0.32 15 -0.28 5 20
LRP8 0.03 0.006 -10000 0 -10000 0 0
GSK3B -0.034 0.091 0.17 9 -0.28 21 30
RELN/VLDLR/DAB1/Fyn 0.004 0.1 -10000 0 -0.17 127 127
MAP3K11 0.031 0.014 -10000 0 -0.28 1 1
RELN/VLDLR/DAB1/P13K -0.021 0.094 -10000 0 -0.22 55 55
CDK5 0.027 0.011 -10000 0 -10000 0 0
MAPT -0.014 0.016 -10000 0 -10000 0 0
neuron migration -0.046 0.12 0.26 11 -0.29 49 60
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.026 0.089 0.17 1 -0.29 24 25
RELN/VLDLR 0.023 0.091 -10000 0 -0.17 84 84
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.037 0.078 -10000 0 -0.16 62 62
ER alpha/Gai/GDP/Gbeta gamma -0.042 0.15 -10000 0 -0.48 26 26
AKT1 -0.11 0.26 -10000 0 -0.68 90 90
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.1 0.27 -10000 0 -0.69 90 90
mol:Ca2+ -0.07 0.11 -10000 0 -0.37 26 26
IGF1R -0.033 0.12 -10000 0 -0.28 111 111
E2/ER alpha (dimer)/Striatin 0.017 0.064 -10000 0 -0.17 58 58
SHC1 0.03 0.006 -10000 0 -10000 0 0
apoptosis 0.11 0.25 0.65 90 -10000 0 90
RhoA/GTP -0.029 0.036 -10000 0 -0.16 21 21
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.024 0.15 0.25 2 -0.34 71 73
regulation of stress fiber formation -0.02 0.1 0.24 3 -0.24 46 49
E2/ERA-ERB (dimer) 0.017 0.065 -10000 0 -0.17 60 60
KRAS 0.026 0.012 -10000 0 -10000 0 0
G13/GTP 0.016 0.059 -10000 0 -0.15 60 60
pseudopodium formation 0.02 0.1 0.24 46 -0.24 3 49
E2/ER alpha (dimer)/PELP1 0.016 0.065 -10000 0 -0.17 60 60
GRB2 0.03 0.006 -10000 0 -10000 0 0
GNG2 0.029 0.027 -10000 0 -0.28 4 4
GNAO1 0.028 0.02 -10000 0 -0.28 2 2
HRAS 0.03 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.06 0.17 -10000 0 -0.4 90 90
E2/ER beta (dimer) 0.023 0.004 -10000 0 -10000 0 0
mol:GDP -0.035 0.071 -10000 0 -0.22 62 62
mol:NADP -0.06 0.17 -10000 0 -0.4 90 90
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
mol:IP3 -0.075 0.11 -10000 0 -0.39 25 25
IGF-1R heterotetramer -0.033 0.12 -10000 0 -0.28 111 111
PLCB1 -0.064 0.11 -10000 0 -0.41 23 23
PLCB2 -0.075 0.1 -10000 0 -0.41 26 26
IGF1 0.022 0.053 -10000 0 -0.28 16 16
mol:L-citrulline -0.06 0.17 -10000 0 -0.4 90 90
RHOA 0.031 0.014 -10000 0 -0.28 1 1
Gai/GDP -0.014 0.17 -10000 0 -0.61 37 37
JNK cascade 0.023 0.004 -10000 0 -10000 0 0
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
ESR2 0.031 0.005 -10000 0 -10000 0 0
GNAQ 0.022 0.051 -10000 0 -0.28 15 15
ESR1 -0.004 0.097 -10000 0 -0.28 60 60
Gq family/GDP/Gbeta gamma -0.15 0.25 -10000 0 -0.5 132 132
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.001 0.12 -10000 0 -0.78 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.022 0.15 0.25 2 -0.35 69 71
GNAZ 0.026 0.031 -10000 0 -0.28 5 5
E2/ER alpha (dimer) -0.001 0.066 -10000 0 -0.19 60 60
STRN 0.031 0.005 -10000 0 -10000 0 0
GNAL 0.031 0.006 -10000 0 -10000 0 0
PELP1 0.03 0.007 -10000 0 -10000 0 0
MAPK11 -0.019 0.011 -10000 0 -10000 0 0
GNAI2 0.031 0.003 -10000 0 -10000 0 0
GNAI3 0.03 0.007 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.28 11 11
HBEGF -0.032 0.15 0.29 15 -0.44 28 43
cAMP biosynthetic process 0.013 0.055 -10000 0 -0.14 59 59
SRC -0.043 0.14 -10000 0 -0.5 22 22
PI3K 0.012 0.062 -10000 0 -0.2 37 37
GNB1 0.03 0.015 -10000 0 -0.28 1 1
G13/GDP/Gbeta gamma 0.022 0.095 -10000 0 -0.25 35 35
SOS1 0.03 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.062 0.12 -10000 0 -0.31 72 72
Gs family/GTP 0.02 0.059 -10000 0 -0.14 59 59
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.027 0.031 -10000 0 -10000 0 0
vasodilation -0.057 0.16 -10000 0 -0.39 90 90
mol:DAG -0.075 0.11 -10000 0 -0.39 25 25
Gs family/GDP/Gbeta gamma -0.031 0.081 -10000 0 -0.25 35 35
MSN 0.02 0.1 0.25 46 -0.26 3 49
Gq family/GTP -0.061 0.12 -10000 0 -0.35 41 41
mol:PI-3-4-5-P3 -0.099 0.26 -10000 0 -0.67 90 90
NRAS 0.018 0.016 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.057 0.16 0.39 90 -10000 0 90
GRB2/SOS1 0.043 0.013 -10000 0 -10000 0 0
RhoA/GDP 0.005 0.091 -10000 0 -0.22 61 61
NOS3 -0.063 0.18 -10000 0 -0.42 90 90
GNA11 -0.066 0.14 -10000 0 -0.28 168 168
MAPKKK cascade -0.058 0.2 -10000 0 -0.49 91 91
E2/ER alpha (dimer)/PELP1/Src -0.027 0.15 0.26 2 -0.35 71 73
ruffle organization 0.02 0.1 0.24 46 -0.24 3 49
ROCK2 0.034 0.11 0.28 43 -10000 0 43
GNA14 0.029 0.02 -10000 0 -0.28 2 2
GNA15 0.028 0.021 -10000 0 -0.28 2 2
GNA13 0.031 0.005 -10000 0 -10000 0 0
MMP9 -0.02 0.16 0.32 21 -0.47 22 43
MMP2 -0.059 0.14 0.26 3 -0.45 31 34
FAS signaling pathway (CD95)

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
SPTAN1 -0.006 0.069 0.27 4 -0.2 29 33
RFC1 0.002 0.078 0.23 20 -0.2 25 45
PRKDC 0.028 0.11 0.22 91 -0.21 27 118
RIPK1 0.029 0.013 -10000 0 -0.088 1 1
CASP7 0.006 0.066 -10000 0 -0.54 6 6
FASLG/FAS/FADD/FAF1 0.022 0.078 0.25 1 -0.2 15 16
MAP2K4 -0.013 0.11 0.33 5 -0.32 37 42
mol:ceramide -0.001 0.076 0.32 3 -0.29 11 14
GSN -0.017 0.075 0.22 4 -0.22 29 33
FASLG/FAS/FADD/FAF1/Caspase 8 0.012 0.075 0.2 7 -0.26 6 13
FAS 0.016 0.057 -10000 0 -0.29 17 17
BID -0.034 0.033 0.27 5 -10000 0 5
MAP3K1 0.01 0.087 0.28 7 -0.31 9 16
MAP3K7 0.025 0.018 -10000 0 -10000 0 0
RB1 -0.001 0.074 0.22 17 -0.2 26 43
CFLAR 0.031 0.011 -10000 0 -0.082 4 4
HGF/MET -0.009 0.11 -10000 0 -0.2 131 131
ARHGDIB 0.003 0.094 0.23 37 -0.22 28 65
FADD 0.025 0.021 -10000 0 -10000 0 0
actin filament polymerization 0.017 0.076 0.22 30 -0.22 4 34
NFKB1 -0.04 0.2 0.4 4 -0.66 46 50
MAPK8 -0.032 0.14 0.36 7 -0.44 46 53
DFFA -0.007 0.071 0.27 4 -0.2 33 37
DNA fragmentation during apoptosis -0.006 0.069 0.22 6 -0.2 31 37
FAS/FADD/MET 0.024 0.08 -10000 0 -0.2 54 54
CFLAR/RIP1 0.043 0.02 -10000 0 -0.12 4 4
FAIM3 0.029 0.027 -10000 0 -0.28 4 4
FAF1 0.025 0.023 -10000 0 -10000 0 0
PARP1 0.009 0.091 0.22 44 -0.2 30 74
DFFB -0.006 0.07 0.22 6 -0.2 31 37
CHUK -0.046 0.19 0.32 4 -0.63 45 49
FASLG 0.025 0.023 -10000 0 -0.064 1 1
FAS/FADD 0.029 0.051 -10000 0 -0.21 17 17
HGF 0.031 0.005 -10000 0 -10000 0 0
LMNA 0.032 0.11 0.29 40 -0.21 2 42
CASP6 0.039 0.11 0.22 112 -0.2 14 126
CASP10 0.024 0.028 -10000 0 -0.28 2 2
CASP3 0.003 0.081 0.18 59 -0.22 34 93
PTPN13 -0.036 0.12 -10000 0 -0.28 114 114
CASP8 -0.032 0.024 0.28 3 -10000 0 3
IL6 -0.1 0.35 0.68 4 -0.97 65 69
MET 0.004 0.084 -10000 0 -0.28 44 44
ICAD/CAD -0.014 0.067 0.25 6 -0.2 28 34
FASLG/FAS/FADD/FAF1/Caspase 10 -0.001 0.076 0.32 3 -0.29 11 14
activation of caspase activity by cytochrome c -0.034 0.033 0.27 5 -10000 0 5
PAK2 0.023 0.11 0.26 67 -0.2 25 92
BCL2 -0.005 0.097 -10000 0 -0.28 60 60
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.22 0.41 -10000 0 -1 120 120
VDR 0.031 0.004 -10000 0 -10000 0 0
FAM120B 0.029 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.034 0.12 0.42 36 -0.35 3 39
RXRs/LXRs/DNA/Oxysterols 0.037 0.14 0.51 36 -0.4 5 41
MED1 0.03 0.008 -10000 0 -10000 0 0
mol:9cRA 0.011 0.029 0.11 41 -10000 0 41
RARs/THRs/DNA/Src-1 -0.017 0.093 -10000 0 -0.24 25 25
RXRs/NUR77 0.012 0.14 0.31 24 -0.18 125 149
RXRs/PPAR 0.008 0.079 0.25 4 -0.24 8 12
NCOR2 0.026 0.04 -10000 0 -0.28 9 9
VDR/VDR/Vit D3 0.023 0.003 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.062 0.032 -10000 0 -10000 0 0
RARA 0.03 0.008 -10000 0 -10000 0 0
NCOA1 0.029 0.023 -10000 0 -0.28 3 3
VDR/VDR/DNA 0.031 0.004 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.053 0.031 -10000 0 -10000 0 0
RARG 0.03 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.099 0.19 0.54 10 -0.43 121 131
RARs/THRs/DNA/SMRT -0.019 0.096 -10000 0 -0.2 112 112
THRA -0.023 0.12 -10000 0 -0.28 94 94
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.003 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.11 0.13 0.41 47 -10000 0 47
NR1H4 0.031 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.1 0.13 0.46 36 -0.26 6 42
NR1H2 0.028 0.06 0.15 1 -0.28 15 16
NR1H3 0.037 0.039 0.16 1 -0.23 4 5
RXRs/VDR/DNA/Vit D3 0.088 0.088 0.3 40 -0.16 15 55
NR4A1 -0.08 0.15 -10000 0 -0.28 197 197
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.022 0.072 0.2 39 -0.21 5 44
RXRG 0.04 0.033 0.14 39 -0.28 1 40
RXR alpha/CCPG 0.04 0.054 -10000 0 -0.2 20 20
RXRA 0.033 0.06 0.16 2 -0.28 14 16
RXRB 0.042 0.032 0.17 2 -10000 0 2
THRB 0.03 0.008 -10000 0 -10000 0 0
PPARG 0.031 0.005 -10000 0 -10000 0 0
PPARD 0.031 0.005 -10000 0 -10000 0 0
TNF 0.022 0.14 0.47 36 -0.45 1 37
mol:Oxysterols 0.007 0.027 0.1 41 -10000 0 41
cholesterol transport 0.037 0.14 0.51 36 -0.4 5 41
PPARA 0.026 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.03 0.006 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.072 0.12 0.17 1 -0.21 202 203
SREBF1 0.012 0.16 0.46 33 -0.82 8 41
RXRs/RXRs/DNA/9cRA 0.11 0.13 0.4 47 -10000 0 47
ABCA1 0.032 0.17 0.64 36 -0.45 1 37
RARs/THRs 0.046 0.099 -10000 0 -0.17 85 85
RXRs/FXR 0.095 0.095 0.32 41 -0.17 15 56
BCL2 -0.005 0.097 -10000 0 -0.28 60 60
Nectin adhesion pathway

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
PDGFRB 0.02 0.059 -10000 0 -0.28 20 20
alphaV beta3 Integrin 0.008 0.084 -10000 0 -0.21 71 71
PTK2 -0.038 0.11 -10000 0 -0.36 40 40
positive regulation of JNK cascade -0.012 0.11 -10000 0 -0.31 41 41
CDC42/GDP -0.012 0.15 -10000 0 -0.41 45 45
Rac1/GDP -0.015 0.15 -10000 0 -0.41 45 45
RAP1B 0.03 0.015 -10000 0 -0.28 1 1
RAP1A 0.031 0.004 -10000 0 -10000 0 0
CTNNB1 0.031 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.013 0.14 -10000 0 -0.38 41 41
nectin-3/I-afadin 0.028 0.049 -10000 0 -0.2 21 21
RAPGEF1 -0.037 0.14 -10000 0 -0.42 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.037 0.15 -10000 0 -0.46 50 50
PDGFB-D/PDGFRB 0.02 0.058 -10000 0 -0.28 20 20
TLN1 -0.094 0.12 -10000 0 -0.27 170 170
Rap1/GTP -0.026 0.11 -10000 0 -0.32 49 49
IQGAP1 0.029 0.02 -10000 0 -0.28 2 2
Rap1/GTP/I-afadin 0.046 0.041 -10000 0 -0.16 13 13
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.028 0.049 -10000 0 -0.2 21 21
PVR 0.03 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.03 0.007 -10000 0 -10000 0 0
mol:GDP -0.032 0.17 -10000 0 -0.5 45 45
MLLT4 0.022 0.046 -10000 0 -0.28 12 12
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
PI3K 0.034 0.095 -10000 0 -0.18 65 65
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.039 -10000 0 -0.2 12 12
positive regulation of lamellipodium assembly -0.013 0.12 -10000 0 -0.33 43 43
PVRL1 0.031 0.005 -10000 0 -10000 0 0
PVRL3 0.022 0.043 -10000 0 -0.28 10 10
PVRL2 0.029 0.015 -10000 0 -0.28 1 1
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
CDH1 0.023 0.04 -10000 0 -0.28 9 9
CLDN1 -0.036 0.12 -10000 0 -0.28 110 110
JAM-A/CLDN1 0.007 0.098 -10000 0 -0.18 104 104
SRC -0.038 0.16 -10000 0 -0.5 50 50
ITGB3 -0.01 0.1 -10000 0 -0.28 71 71
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.039 -10000 0 -0.2 12 12
FARP2 -0.028 0.17 -10000 0 -0.49 46 46
RAC1 0.03 0.007 -10000 0 -10000 0 0
CTNNA1 0.03 0.014 -10000 0 -0.28 1 1
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.04 0.05 -10000 0 -0.18 20 20
nectin-1/I-afadin 0.036 0.039 -10000 0 -0.2 12 12
nectin-2/I-afadin 0.035 0.04 -10000 0 -0.2 13 13
RAC1/GTP/IQGAP1/filamentous actin 0.038 0.017 -10000 0 -0.17 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.04 0.051 -10000 0 -0.18 21 21
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.016 -10000 0 -0.17 2 2
F11R 0.031 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.012 0.11 -10000 0 -0.31 41 41
alphaV/beta3 Integrin/Talin -0.12 0.13 0.2 5 -0.28 178 183
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.035 0.04 -10000 0 -0.2 13 13
nectin-2(dimer)/I-afadin/I-afadin 0.035 0.04 -10000 0 -0.2 13 13
PIP5K1C -0.095 0.13 -10000 0 -0.28 175 175
VAV2 -0.03 0.18 -10000 0 -0.53 43 43
RAP1/GDP -0.009 0.14 -10000 0 -0.39 45 45
ITGAV 0.027 0.024 -10000 0 -0.28 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.04 0.051 -10000 0 -0.18 21 21
nectin-3(dimer)/I-afadin/I-afadin 0.028 0.049 -10000 0 -0.2 21 21
Rac1/GTP -0.014 0.14 -10000 0 -0.41 43 43
PTPRM -0.1 0.15 -10000 0 -0.3 194 194
E-cadherin/beta catenin/alpha catenin 0.054 0.073 -10000 0 -0.18 21 21
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.031 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.032 0.018 0.17 2 -0.18 1 3
SNTA1 0.029 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.004 0.072 0.17 79 -0.18 1 80
MAPK12 -0.004 0.059 0.16 47 -0.2 14 61
CCND1 -0.085 0.16 -10000 0 -0.37 134 134
p38 gamma/SNTA1 -0.001 0.078 0.17 61 -0.2 17 78
MAP2K3 0.029 0.016 -10000 0 -0.28 1 1
PKN1 0.027 0.017 -10000 0 -0.28 1 1
G2/M transition checkpoint -0.005 0.06 0.16 47 -0.2 15 62
MAP2K6 0.002 0.071 0.2 52 -0.21 16 68
MAPT -0.008 0.059 0.2 4 -0.28 12 16
MAPK13 -0.028 0.018 0.19 2 -0.2 1 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0 0.043 -10000 0 -0.23 18 18
Retinoic acid receptors-mediated signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.029 0.009 -10000 0 -10000 0 0
HDAC3 0.031 0.004 -10000 0 -10000 0 0
VDR 0.031 0.004 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.034 0.031 -10000 0 -0.21 7 7
EP300 0.027 0.024 -10000 0 -0.28 3 3
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.02 0.082 0.17 2 -0.32 22 24
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.031 0.006 -10000 0 -10000 0 0
AKT1 0.022 0.091 0.22 13 -0.28 5 18
RAR alpha/9cRA/Cyclin H -0.062 0.14 -10000 0 -0.33 49 49
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.021 0.074 0.18 1 -0.26 31 32
CDC2 -0.004 0.006 -10000 0 -10000 0 0
response to UV -0.007 0.011 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.012 0.068 -10000 0 -0.23 20 20
NCOR2 0.026 0.04 -10000 0 -0.28 9 9
VDR/VDR/Vit D3 0.023 0.003 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.15 0.26 -10000 0 -0.53 156 156
NCOA2 0.029 0.009 -10000 0 -10000 0 0
NCOA3 0.028 0.01 -10000 0 -10000 0 0
NCOA1 0.029 0.023 -10000 0 -0.28 3 3
VDR/VDR/DNA 0.031 0.004 -10000 0 -10000 0 0
RARG 0.011 0.031 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.019 0.031 -10000 0 -10000 0 0
MAPK3 -0.015 0.089 -10000 0 -0.29 47 47
MAPK1 0.029 0.008 -10000 0 -10000 0 0
MAPK8 0.008 0.037 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.094 0.17 -10000 0 -0.35 151 151
RARA -0.018 0.05 -10000 0 -0.21 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.02 0.072 0.18 1 -0.28 26 27
PRKCA -0.002 0.055 -10000 0 -0.15 12 12
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.17 0.28 -10000 0 -0.59 162 162
RXRG -0.014 0.058 -10000 0 -0.24 6 6
RXRA -0.075 0.11 -10000 0 -0.34 36 36
RXRB -0.015 0.05 -10000 0 -0.24 4 4
VDR/Vit D3/DNA 0.023 0.003 -10000 0 -10000 0 0
RBP1 -0.06 0.14 -10000 0 -0.28 158 158
CRBP1/9-cic-RA -0.039 0.095 -10000 0 -0.19 158 158
RARB 0.007 0.038 -10000 0 -10000 0 0
PRKCG 0 0.049 -10000 0 -10000 0 0
MNAT1 0.031 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.079 0.19 -10000 0 -0.39 112 112
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.075 0.16 -10000 0 -0.41 44 44
proteasomal ubiquitin-dependent protein catabolic process -0.026 0.089 -10000 0 -0.33 22 22
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.17 0.28 -10000 0 -0.6 162 162
positive regulation of DNA binding -0.062 0.13 -10000 0 -0.24 157 157
NRIP1 -0.3 0.49 -10000 0 -1.1 162 162
RXRs/RARs -0.11 0.2 -10000 0 -0.42 156 156
RXRs/RXRs/DNA/9cRA -0.11 0.16 -10000 0 -0.35 155 155
PRKACA 0.027 0.011 -10000 0 -10000 0 0
CDK7 0.028 0.011 -10000 0 -10000 0 0
TFIIH 0.054 0.024 -10000 0 -10000 0 0
RAR alpha/9cRA 0.006 0.08 -10000 0 -0.23 17 17
CCNH 0.029 0.009 -10000 0 -10000 0 0
CREBBP 0.026 0.033 -10000 0 -0.28 6 6
RAR gamma2/9cRA 0.016 0.052 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.026 0.12 -10000 0 -0.28 99 99
HRAS 0.03 0.007 -10000 0 -10000 0 0
EGFR 0.002 0.091 -10000 0 -0.28 51 51
AKT -0.07 0.14 0.22 19 -0.28 93 112
FOXO3 0.026 0.033 -10000 0 -0.28 6 6
AKT1 0.03 0.007 -10000 0 -10000 0 0
FOXO1 0.025 0.038 -10000 0 -0.28 8 8
AKT3 -0.14 0.15 -10000 0 -0.28 304 304
FOXO4 0.031 0.004 -10000 0 -10000 0 0
MET 0.004 0.084 -10000 0 -0.28 44 44
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
PIK3CB 0.027 0.017 -10000 0 -0.28 1 1
NRAS 0.018 0.016 -10000 0 -10000 0 0
PIK3CG 0.03 0.008 -10000 0 -10000 0 0
PIK3R3 0.023 0.014 -10000 0 -10000 0 0
PIK3R2 0.029 0.009 -10000 0 -10000 0 0
NF1 0.024 0.038 -10000 0 -0.28 8 8
RAS 0.022 0.083 0.17 32 -0.25 16 48
ERBB2 0.027 0.028 -10000 0 -0.28 4 4
proliferation/survival/translation 0.021 0.12 0.27 49 -0.22 5 54
PI3K 0.021 0.098 0.19 54 -0.24 29 83
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
KRAS 0.026 0.012 -10000 0 -10000 0 0
FOXO 0.011 0.082 0.22 19 -10000 0 19
AKT2 0.029 0.009 -10000 0 -10000 0 0
PTEN 0.029 0.02 -10000 0 -0.28 2 2
HIF-1-alpha transcription factor network

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
PKM2 0.4 0.42 0.9 3 -0.97 7 10
HDAC7 -0.003 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.03 0.24 0.71 29 -0.74 9 38
SMAD4 0.025 0.02 -10000 0 -0.083 10 10
ID2 0.41 0.42 -10000 0 -0.97 7 7
AP1 0.001 0.1 0.25 13 -0.2 105 118
ABCG2 0.32 0.43 0.9 3 -0.93 10 13
HIF1A 0.14 0.14 0.33 87 -10000 0 87
TFF3 0.038 0.33 0.9 1 -0.96 12 13
GATA2 0.034 0.036 0.22 14 -0.28 2 16
AKT1 0.18 0.16 0.41 102 -10000 0 102
response to hypoxia 0.087 0.15 0.32 140 -10000 0 140
MCL1 0.38 0.42 -10000 0 -0.97 7 7
NDRG1 0.26 0.41 0.9 2 -1 6 8
SERPINE1 0.32 0.41 0.9 1 -0.97 7 8
FECH 0.39 0.42 0.89 7 -0.97 7 14
FURIN 0.4 0.42 -10000 0 -0.95 8 8
NCOA2 0.03 0.009 -10000 0 -10000 0 0
EP300 0.26 0.29 0.68 127 -0.42 2 129
HMOX1 0.38 0.42 -10000 0 -0.98 7 7
BHLHE40 0.14 0.36 0.81 64 -0.96 7 71
BHLHE41 0.14 0.36 0.81 64 -0.96 7 71
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.16 0.18 0.42 50 -10000 0 50
ENG 0.15 0.16 0.49 1 -10000 0 1
JUN 0.032 0.026 0.15 8 -0.28 2 10
RORA 0.41 0.42 0.9 5 -0.97 7 12
ABCB1 0.002 0.06 0.64 1 -10000 0 1
TFRC 0.22 0.39 0.9 1 -0.94 7 8
CXCR4 0.39 0.42 0.9 3 -0.97 7 10
TF 0.39 0.42 0.89 5 -0.97 7 12
CITED2 0.39 0.42 0.9 3 -0.97 8 11
HIF1A/ARNT -0.023 0.23 0.89 7 -0.98 10 17
LDHA 0.014 0.11 0.67 11 -0.67 2 13
ETS1 0.39 0.42 0.89 8 -0.97 7 15
PGK1 0.2 0.37 0.9 2 -0.97 7 9
NOS2 0.14 0.36 0.81 64 -0.96 7 71
ITGB2 0.4 0.42 -10000 0 -1 7 7
ALDOA 0.41 0.42 0.9 3 -0.97 7 10
Cbp/p300/CITED2 0.28 0.42 0.88 70 -0.96 9 79
FOS -0.027 0.12 0.15 9 -0.28 106 115
HK2 0.42 0.42 0.9 3 -0.97 7 10
SP1 0.03 0.026 0.25 3 -10000 0 3
GCK 0.34 0.33 0.86 94 -10000 0 94
HK1 0.41 0.42 0.9 5 -0.97 7 12
NPM1 0.41 0.42 -10000 0 -0.97 7 7
EGLN1 0.4 0.42 0.9 6 -0.99 6 12
CREB1 0.076 0.091 0.26 106 -10000 0 106
PGM1 0.36 0.42 -10000 0 -0.97 7 7
SMAD3 0.024 0.033 -10000 0 -0.28 4 4
EDN1 0.21 0.26 0.8 35 -1.1 1 36
IGFBP1 0.41 0.42 -10000 0 -0.97 7 7
VEGFA 0.34 0.38 0.88 82 -0.68 4 86
HIF1A/JAB1 0.088 0.1 0.26 9 -10000 0 9
CP 0.007 0.26 -10000 0 -0.98 8 8
CXCL12 0.34 0.44 0.9 6 -0.95 10 16
COPS5 0.028 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.036 -10000 0 -0.14 18 18
BNIP3 0.34 0.42 0.9 4 -0.97 7 11
EGLN3 0.36 0.42 0.9 2 -0.99 8 10
CA9 0.33 0.42 0.9 3 -0.97 7 10
TERT 0.36 0.42 -10000 0 -0.97 7 7
ENO1 0.41 0.42 -10000 0 -0.97 7 7
PFKL 0.4 0.42 0.9 1 -0.97 7 8
NCOA1 0.029 0.023 -10000 0 -0.28 3 3
ADM 0.34 0.41 -10000 0 -0.97 7 7
ARNT 0.14 0.14 0.34 42 -10000 0 42
HNF4A 0.03 0.008 -10000 0 -10000 0 0
ADFP 0.14 0.36 0.81 64 -0.96 7 71
SLC2A1 0.3 0.36 0.84 63 -0.68 4 67
LEP 0.4 0.42 -10000 0 -0.99 6 6
HIF1A/ARNT/Cbp/p300 0.017 0.23 0.74 21 -0.76 9 30
EPO 0.31 0.34 0.78 55 -0.77 3 58
CREBBP 0.27 0.29 0.68 133 -10000 0 133
HIF1A/ARNT/Cbp/p300/HDAC7 0.013 0.22 0.68 19 -0.74 9 28
PFKFB3 0.37 0.43 0.9 4 -1 8 12
NT5E 0.33 0.43 0.9 3 -0.99 9 12
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.089 0.13 -10000 0 -0.37 47 47
CaM/Ca2+ 0.017 0.036 -10000 0 -0.19 16 16
AKT1 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.029 0.009 -10000 0 -10000 0 0
STXBP4 0.031 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.043 0.12 -10000 0 -0.37 43 43
YWHAZ 0.027 0.011 -10000 0 -10000 0 0
CALM1 0.022 0.053 -10000 0 -0.28 16 16
YWHAQ 0.031 0.005 -10000 0 -10000 0 0
TBC1D4 -0.028 0.013 0.19 1 -10000 0 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.029 0.008 -10000 0 -10000 0 0
YWHAB 0.029 0.009 -10000 0 -10000 0 0
SNARE/Synip -0.1 0.11 -10000 0 -0.18 374 374
YWHAG 0.029 0.023 -10000 0 -0.28 3 3
ASIP 0.028 0.024 -10000 0 -0.28 3 3
PRKCI 0.013 0.016 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.017 0.036 -10000 0 -0.19 16 16
RHOQ 0.031 0.006 -10000 0 -10000 0 0
GYS1 -0.011 0.012 0.24 1 -10000 0 1
PRKCZ 0.03 0.006 -10000 0 -10000 0 0
TRIP10 0.03 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.012 -10000 0 -10000 0 0
AS160/14-3-3 0 0.07 0.16 4 -0.31 15 19
VAMP2 -0.18 0.14 -10000 0 -0.28 379 379
SLC2A4 -0.048 0.14 -10000 0 -0.41 43 43
STX4 0.031 0.004 -10000 0 -10000 0 0
GSK3B 0.012 0.005 -10000 0 -10000 0 0
SFN 0.03 0.008 -10000 0 -10000 0 0
LNPEP 0.028 0.016 -10000 0 -0.28 1 1
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
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 0.009 0.093 0.18 4 -0.18 89 93
alphaM/beta2 Integrin/GPIbA 0.045 0.051 0.18 5 -0.17 9 14
alphaM/beta2 Integrin/proMMP-9 0.037 0.048 0.18 3 -0.17 6 9
PLAUR 0.029 0.008 -10000 0 -10000 0 0
HMGB1 0.024 0.027 -10000 0 -0.088 3 3
alphaM/beta2 Integrin/Talin 0.045 0.052 0.18 5 -0.18 11 16
AGER 0.024 0.026 -10000 0 -10000 0 0
RAP1A 0.031 0.004 -10000 0 -10000 0 0
SELPLG 0.019 0.061 -10000 0 -0.28 22 22
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.052 0.085 0.37 5 -0.2 36 41
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.025 0.013 -10000 0 -10000 0 0
CYR61 0.002 0.09 -10000 0 -0.28 50 50
TLN1 0.03 0.019 -10000 0 -0.28 2 2
Rap1/GTP -0.015 0.13 0.2 17 -0.3 45 62
RHOA 0.031 0.014 -10000 0 -0.28 1 1
P-selectin oligomer 0.01 0.079 -10000 0 -0.28 38 38
MYH2 -0.036 0.14 0.23 14 -0.34 42 56
MST1R 0.031 0.004 -10000 0 -10000 0 0
leukocyte activation during inflammatory response 0.043 0.053 -10000 0 -0.16 7 7
APOB 0.031 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.019 0.11 -10000 0 -0.28 85 85
JAM3 0.029 0.008 -10000 0 -10000 0 0
GP1BA 0.03 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.006 0.1 0.18 5 -0.19 104 109
alphaM/beta2 Integrin -0.027 0.12 0.23 3 -0.33 43 46
JAM3 homodimer 0.029 0.008 -10000 0 -10000 0 0
ICAM2 0.027 0.033 -10000 0 -0.28 6 6
ICAM1 0.018 0.05 -10000 0 -0.28 14 14
phagocytosis triggered by activation of immune response cell surface activating receptor -0.025 0.13 0.23 6 -0.32 44 50
cell adhesion 0.044 0.05 0.18 5 -0.17 9 14
NFKB1 -0.06 0.1 0.41 7 -0.34 33 40
THY1 0.021 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.009 -10000 0 -0.19 1 1
Lipoprotein(a) 0.038 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.007 0.11 -10000 0 -0.18 115 115
IL6 -0.081 0.14 0.36 2 -0.55 41 43
ITGB2 0.019 0.045 -10000 0 -0.26 9 9
elevation of cytosolic calcium ion concentration 0.034 0.056 -10000 0 -0.17 7 7
alphaM/beta2 Integrin/JAM2/JAM3 -0.017 0.12 -10000 0 -0.18 179 179
JAM2 -0.079 0.15 -10000 0 -0.28 194 194
alphaM/beta2 Integrin/ICAM1 0.061 0.073 -10000 0 -0.2 16 16
alphaM/beta2 Integrin/uPA/Plg 0.029 0.064 -10000 0 -0.18 15 15
RhoA/GTP -0.039 0.14 0.18 41 -0.35 49 90
positive regulation of phagocytosis -0.013 0.11 0.22 4 -0.32 25 29
Ron/MSP 0.046 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.057 -10000 0 -0.17 7 7
alphaM/beta2 Integrin/uPAR 0.044 0.049 0.18 3 -0.17 8 11
PLAU 0.022 0.014 -10000 0 -10000 0 0
PLAT -0.031 0.12 -10000 0 -0.28 107 107
actin filament polymerization -0.031 0.14 0.23 21 -0.33 43 64
MST1 0.031 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.048 0.056 -10000 0 -0.16 7 7
TNF -0.064 0.089 0.4 6 -0.32 33 39
RAP1B 0.03 0.015 -10000 0 -0.28 1 1
alphaM/beta2 Integrin/uPA 0.029 0.05 0.18 1 -0.17 9 10
fibrinolysis 0.027 0.062 -10000 0 -0.17 15 15
HCK 0.029 0.009 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.025 0.13 0.23 6 -0.32 44 50
VTN 0.03 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.027 0.08 0.18 4 -0.19 54 58
LPA 0.029 0.009 -10000 0 -10000 0 0
LRP1 0.025 0.044 -10000 0 -0.28 11 11
cell migration -0.027 0.091 0.17 76 -0.21 8 84
FN1 0.013 0.046 -10000 0 -0.28 12 12
alphaM/beta2 Integrin/Thy1 0.031 0.046 0.18 2 -0.17 6 8
MPO 0.031 0.005 -10000 0 -10000 0 0
KNG1 0.027 0.012 -10000 0 -10000 0 0
RAP1/GDP 0.04 0.013 -10000 0 -0.17 1 1
ROCK1 -0.04 0.15 0.23 16 -0.34 47 63
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.024 0.04 -10000 0 -0.28 9 9
CTGF -0.028 0.12 -10000 0 -0.28 103 103
alphaM/beta2 Integrin/Hck 0.045 0.048 0.18 5 -0.17 6 11
ITGAM 0.024 0.027 -10000 0 -0.088 3 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.038 0.092 -10000 0 -0.2 57 57
HP -0.099 0.15 -10000 0 -0.28 218 218
leukocyte adhesion -0.015 0.13 0.31 2 -0.27 26 28
SELP 0.01 0.079 -10000 0 -0.28 38 38
TRAIL signaling pathway

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
TNFSF10 0.002 0.076 -10000 0 -0.28 36 36
positive regulation of NF-kappaB transcription factor activity 0.012 0.06 -10000 0 -0.2 36 36
MAP2K4 -0.019 0.086 -10000 0 -0.31 21 21
IKBKB 0.029 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.012 -10000 0 -10000 0 0
TNFRSF10A 0.025 0.012 -10000 0 -10000 0 0
SMPD1 -0.011 0.038 -10000 0 -0.14 36 36
IKBKG 0.03 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.026 0.012 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.012 0.061 -10000 0 -0.2 36 36
TRAIL/TRAILR3 -0.049 0.11 -10000 0 -0.22 160 160
TRAIL/TRAILR1 0.011 0.061 -10000 0 -0.2 36 36
TRAIL/TRAILR4 0.012 0.061 -10000 0 -0.2 36 36
TRAIL/TRAILR1/DAP3/GTP 0.018 0.057 -10000 0 -0.16 35 35
IKK complex 0.012 0.069 -10000 0 -0.27 18 18
RIPK1 0.029 0.008 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.022 0.005 -10000 0 -10000 0 0
MAPK3 -0.032 0.08 0.19 30 -0.2 66 96
MAP3K1 -0.02 0.089 0.18 1 -0.31 28 29
TRAILR4 (trimer) 0.026 0.012 -10000 0 -10000 0 0
TRADD 0.026 0.028 -10000 0 -0.28 4 4
TRAILR1 (trimer) 0.025 0.012 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.018 0.08 -10000 0 -0.27 22 22
CFLAR 0.031 0.004 -10000 0 -10000 0 0
MAPK1 -0.019 0.07 0.19 34 -0.2 32 66
TRAIL/TRAILR1/FADD/TRADD/RIP 0.031 0.078 -10000 0 -0.17 37 37
mol:ceramide -0.011 0.038 -10000 0 -0.13 36 36
FADD 0.031 0.006 -10000 0 -10000 0 0
MAPK8 -0.029 0.091 -10000 0 -0.31 27 27
TRAF2 0.03 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.082 0.14 -10000 0 -0.28 192 192
CHUK 0.03 0.007 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.022 0.059 -10000 0 -0.18 33 33
DAP3 0.03 0.006 -10000 0 -10000 0 0
CASP10 0.008 0.089 0.31 4 -0.22 30 34
JNK cascade 0.012 0.06 -10000 0 -0.2 36 36
TRAIL (trimer) 0.002 0.076 -10000 0 -0.28 36 36
TNFRSF10C -0.083 0.15 -10000 0 -0.28 192 192
TRAIL/TRAILR1/DAP3/GTP/FADD 0.024 0.062 -10000 0 -0.16 32 32
TRAIL/TRAILR2/FADD 0.023 0.059 -10000 0 -0.18 33 33
cell death -0.011 0.038 -10000 0 -0.13 36 36
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.018 0.079 -10000 0 -0.22 47 47
TRAILR2 (trimer) 0.026 0.012 -10000 0 -10000 0 0
CASP8 -0.004 0.059 -10000 0 -0.51 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.031 0.078 -10000 0 -0.17 37 37
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.029 0.068 -10000 0 -0.31 5 5
NEF -0.003 0.001 -10000 0 -10000 0 0
NFKBIA -0.003 0.077 0.17 12 -0.13 102 114
BIRC3 -0.11 0.14 0.17 8 -0.38 117 125
CYCS -0.021 0.049 0.25 1 -0.36 3 4
RIPK1 0.029 0.008 -10000 0 -10000 0 0
CD247 0.031 0.008 -10000 0 -10000 0 0
MAP2K7 -0.022 0.16 -10000 0 -0.58 31 31
protein ubiquitination -0.038 0.099 0.24 1 -0.32 30 31
CRADD 0.031 0.005 -10000 0 -10000 0 0
DAXX 0.031 0.005 -10000 0 -10000 0 0
FAS 0.021 0.054 -10000 0 -0.28 17 17
BID -0.017 0.043 0.15 5 -0.37 2 7
NF-kappa-B/RelA/I kappa B alpha -0.01 0.13 -10000 0 -0.24 123 123
TRADD 0.026 0.028 -10000 0 -0.28 4 4
MAP3K5 0.027 0.03 -10000 0 -0.28 5 5
CFLAR 0.031 0.004 -10000 0 -10000 0 0
FADD 0.031 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.01 0.13 -10000 0 -0.24 123 123
MAPK8 -0.027 0.14 -10000 0 -0.55 30 30
APAF1 0.03 0.006 -10000 0 -10000 0 0
TRAF1 0.031 0.005 -10000 0 -10000 0 0
TRAF2 0.03 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.006 0.045 -10000 0 -0.43 2 2
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.034 0.12 0.23 1 -0.38 35 36
CHUK -0.041 0.11 0.24 1 -0.34 33 34
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.07 0.061 -10000 0 -0.18 16 16
TCRz/NEF 0.026 0.004 -10000 0 -10000 0 0
TNF 0.031 0.005 -10000 0 -10000 0 0
FASLG -0.026 0.004 -10000 0 -10000 0 0
NFKB1 0 0.071 0.17 12 -0.12 99 111
TNFR1A/BAG4/TNF-alpha 0.042 0.049 -10000 0 -0.18 19 19
CASP6 0.003 0.15 -10000 0 -0.53 36 36
CASP7 -0.1 0.19 0.39 12 -0.44 118 130
RELA 0.004 0.06 0.17 13 -0.27 3 16
CASP2 0.029 0.008 -10000 0 -10000 0 0
CASP3 -0.11 0.2 0.39 12 -0.44 123 135
TNFRSF1A 0.015 0.063 -10000 0 -0.28 23 23
TNFR1A/BAG4 0.029 0.047 -10000 0 -0.2 19 19
CASP8 0.031 0.004 -10000 0 -10000 0 0
CASP9 0.031 0.005 -10000 0 -10000 0 0
MAP3K14 -0.04 0.11 -10000 0 -0.36 35 35
APAF-1/Caspase 9 -0.098 0.11 0.17 1 -0.3 97 98
BCL2 -0.043 0.13 -10000 0 -0.5 31 31
Regulation of Androgen receptor activity

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
HDAC1 -0.016 0.053 0.19 34 -10000 0 34
SMARCC1 -0.013 0.024 -10000 0 -10000 0 0
REL 0.031 0.005 -10000 0 -10000 0 0
HDAC7 -0.17 0.11 0.26 1 -0.29 160 161
JUN 0.029 0.02 -10000 0 -0.28 2 2
EP300 0.027 0.024 -10000 0 -0.28 3 3
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.034 0.054 0.19 28 -10000 0 28
FOXO1 0.025 0.038 -10000 0 -0.28 8 8
T-DHT/AR -0.17 0.12 -10000 0 -0.34 55 55
MAP2K6 -0.017 0.033 -10000 0 -10000 0 0
BRM/BAF57 -0.007 0.097 -10000 0 -0.2 108 108
MAP2K4 -0.019 0.042 -10000 0 -0.3 4 4
SMARCA2 -0.032 0.12 -10000 0 -0.28 108 108
PDE9A -0.2 0.31 -10000 0 -0.97 71 71
NCOA2 0.029 0.009 -10000 0 -10000 0 0
CEBPA 0.029 0.009 -10000 0 -10000 0 0
EHMT2 0.031 0.005 -10000 0 -10000 0 0
cell proliferation -0.17 0.14 0.31 1 -0.38 54 55
NR0B1 0.029 0.008 -10000 0 -10000 0 0
EGR1 -0.09 0.15 -10000 0 -0.28 214 214
RXRs/9cRA 0.046 0.046 -10000 0 -0.16 21 21
AR/RACK1/Src -0.087 0.096 0.27 3 -0.32 2 5
AR/GR -0.11 0.11 -10000 0 -0.23 219 219
GNB2L1 0.031 0.005 -10000 0 -10000 0 0
PKN1 0.027 0.017 -10000 0 -0.28 1 1
RCHY1 0.029 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.046 0.024 -10000 0 -0.22 4 4
T-DHT/AR/TIF2/CARM1 -0.084 0.091 0.32 1 -0.33 2 3
SRC -0.063 0.063 -10000 0 -0.22 3 3
NR3C1 0.026 0.042 -10000 0 -0.28 10 10
KLK3 -0.057 0.086 -10000 0 -10000 0 0
APPBP2 -0.017 0.036 -10000 0 -10000 0 0
TRIM24 0.03 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.093 0.07 0.14 1 -0.21 34 35
TMPRSS2 -0.59 0.46 -10000 0 -0.94 350 350
RXRG 0.029 0.02 -10000 0 -0.28 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.019 0.059 -10000 0 -0.28 20 20
RXRB 0.031 0.005 -10000 0 -10000 0 0
CARM1 0.028 0.01 -10000 0 -10000 0 0
NR2C2 0.031 0.004 -10000 0 -10000 0 0
KLK2 -0.068 0.079 0.28 1 -0.33 6 7
AR -0.11 0.11 -10000 0 -0.25 212 212
SENP1 0.03 0.007 -10000 0 -10000 0 0
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
MDM2 0.029 0.015 -10000 0 -0.28 1 1
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.029 0.024 -10000 0 -0.28 3 3
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.03 0.006 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.087 0.1 0.28 4 -0.29 5 9
positive regulation of transcription 0.029 0.024 -10000 0 -0.28 3 3
DNAJA1 -0.017 0.036 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.049 -10000 0 -0.22 17 17
NCOA1 0.036 0.013 -10000 0 -10000 0 0
SPDEF -0.008 0.1 -10000 0 -0.28 69 69
T-DHT/AR/TIF2 -0.059 0.086 0.26 3 -0.28 30 33
T-DHT/AR/Hsp90 -0.093 0.089 0.27 4 -0.27 7 11
GSK3B -0.01 0.03 -10000 0 -10000 0 0
NR2C1 0.03 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.059 0.066 0.15 5 -0.23 3 8
SIRT1 0.031 0.004 -10000 0 -10000 0 0
ZMIZ2 0.031 0.004 -10000 0 -10000 0 0
POU2F1 -0.072 0.08 -10000 0 -0.19 49 49
T-DHT/AR/DAX-1 -0.089 0.089 0.25 5 -0.27 5 10
CREBBP 0.026 0.033 -10000 0 -0.28 6 6
SMARCE1 0.03 0.007 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.021 0.066 -10000 0 -0.2 41 41
CRKL -0.019 0.12 0.23 1 -0.4 32 33
mol:PIP3 0.015 0.073 -10000 0 -0.8 4 4
AKT1 -0.001 0.07 -10000 0 -0.67 4 4
PTK2B 0.025 0.022 -10000 0 -0.28 2 2
RAPGEF1 -0.026 0.11 0.22 1 -0.42 25 26
RANBP10 0.028 0.01 -10000 0 -10000 0 0
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.038 0.065 -10000 0 -0.18 41 41
MAP3K5 -0.018 0.12 0.25 1 -0.43 26 27
HGF/MET/CIN85/CBL/ENDOPHILINS 0.048 0.071 -10000 0 -0.17 43 43
AP1 -0.037 0.089 0.14 25 -0.2 78 103
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.03 0.006 -10000 0 -10000 0 0
apoptosis -0.13 0.32 -10000 0 -0.71 127 127
STAT3 (dimer) -0.015 0.094 0.17 2 -0.3 28 30
GAB1/CRKL/SHP2/PI3K -0.012 0.12 -10000 0 -0.41 27 27
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.003 0.12 0.28 3 -0.39 29 32
PTPN11 0.031 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.03 0.007 -10000 0 -10000 0 0
PTEN 0.029 0.02 -10000 0 -0.28 2 2
ELK1 0.033 0.15 0.41 45 -0.28 1 46
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.001 0.056 0.14 5 -0.18 14 19
PAK1 0.005 0.086 0.38 1 -0.65 4 5
HGF/MET/RANBP10 0.032 0.067 -10000 0 -0.18 44 44
HRAS -0.027 0.16 -10000 0 -0.49 54 54
DOCK1 -0.024 0.11 0.24 7 -0.42 26 33
GAB1 -0.012 0.12 -10000 0 -0.41 32 32
CRK -0.016 0.12 0.28 3 -0.44 25 28
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.14 -10000 0 -0.42 55 55
JUN 0.029 0.02 -10000 0 -0.28 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.01 0.056 -10000 0 -0.19 46 46
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
cell morphogenesis -0.006 0.14 0.26 21 -0.37 24 45
GRB2/SHC 0.028 0.071 0.2 1 -0.19 43 44
FOS -0.03 0.12 -10000 0 -0.28 107 107
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.033 0.15 0.4 46 -0.28 1 47
HGF/MET/MUC20 0.021 0.057 -10000 0 -0.17 44 44
cell migration 0.028 0.07 0.2 1 -0.18 43 44
GRB2 0.03 0.006 -10000 0 -10000 0 0
CBL 0.031 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.019 0.067 -10000 0 -0.2 44 44
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.075 -10000 0 -0.22 45 45
MET/MUC20 0.004 0.057 -10000 0 -0.19 44 44
RAP1B -0.028 0.11 0.22 1 -0.42 23 24
RAP1A -0.033 0.1 0.25 1 -0.41 24 25
HGF/MET/RANBP9 0.035 0.065 -10000 0 -0.18 41 41
RAF1 -0.031 0.15 -10000 0 -0.47 54 54
STAT3 -0.015 0.095 0.17 2 -0.3 28 30
cell proliferation -0.022 0.12 0.27 7 -0.34 41 48
RPS6KB1 0.012 0.049 -10000 0 -0.25 8 8
MAPK3 0.054 0.23 0.67 59 -10000 0 59
MAPK1 0.028 0.19 0.67 37 -10000 0 37
RANBP9 0.029 0.008 -10000 0 -10000 0 0
MAPK8 -0.014 0.11 0.26 1 -0.41 21 22
SRC -0.02 0.075 -10000 0 -0.28 15 15
PI3K 0.006 0.076 0.2 1 -0.17 64 65
MET/Glomulin 0.027 0.037 0.097 66 -0.088 23 89
SOS1 0.03 0.007 -10000 0 -10000 0 0
MAP2K1 -0.036 0.14 -10000 0 -0.45 54 54
MET 0.004 0.084 -10000 0 -0.28 44 44
MAP4K1 -0.012 0.12 0.27 1 -0.46 25 26
PTK2 0.022 0.014 -10000 0 -10000 0 0
MAP2K2 -0.069 0.14 -10000 0 -0.47 54 54
BAD -0.009 0.067 -10000 0 -0.65 4 4
MAP2K4 -0.025 0.11 0.23 1 -0.4 25 26
SHP2/GRB2/SOS1/GAB1 0.006 0.12 -10000 0 -0.33 55 55
INPPL1 0.03 0.006 -10000 0 -10000 0 0
PXN 0.024 0.046 -10000 0 -0.28 12 12
SH3KBP1 0.031 0.005 -10000 0 -10000 0 0
HGS -0.021 0.055 -10000 0 -0.18 45 45
PLCgamma1/PKC 0.022 0.005 -10000 0 -10000 0 0
HGF 0.031 0.005 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.28 3 3
NCK1 0.028 0.01 -10000 0 -10000 0 0
PTPRJ 0.031 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.068 0.2 1 -0.18 42 43
PDPK1 0.004 0.066 -10000 0 -0.7 4 4
HGF/MET/SHIP 0.021 0.057 -10000 0 -0.17 44 44
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.073 0.051 0.19 2 -10000 0 2
BIRC5 0.027 0.011 -10000 0 -10000 0 0
NFKBIA 0.064 0.048 0.2 4 -10000 0 4
CPEB1 0.031 0.006 -10000 0 -10000 0 0
AKT1 0.064 0.051 0.29 3 -10000 0 3
NDEL1 0.03 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.065 0.045 0.16 1 -10000 0 1
NDEL1/TACC3 0.048 0.054 -10000 0 -10000 0 0
GADD45A 0.029 0.009 -10000 0 -10000 0 0
GSK3B 0.029 0.01 -10000 0 -10000 0 0
PAK1/Aurora A 0.074 0.05 0.19 1 -10000 0 1
MDM2 0.03 0.015 -10000 0 -0.28 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.17 0.067 0.19 485 -10000 0 485
TP53 0.054 0.052 0.17 2 -0.25 4 6
DLG7 0.06 0.054 0.2 3 -10000 0 3
AURKAIP1 0.022 0.051 -10000 0 -0.28 15 15
ARHGEF7 0.03 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.051 0.057 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.064 0.045 0.16 1 -10000 0 1
AURKA 0.09 0.061 0.25 3 -10000 0 3
AURKB 0.026 0.025 -10000 0 -0.15 2 2
CDC25B 0.069 0.048 0.18 3 -10000 0 3
G2/M transition checkpoint 0 0.001 -10000 0 -10000 0 0
mRNA polyadenylation 0.069 0.043 0.16 1 -10000 0 1
Aurora A/CPEB 0.069 0.043 0.16 1 -10000 0 1
Aurora A/TACC1/TRAP/chTOG -0.012 0.072 -10000 0 -0.18 1 1
BRCA1 0.028 0.01 -10000 0 -10000 0 0
centrosome duplication 0.074 0.05 0.19 1 -10000 0 1
regulation of centrosome cycle 0.047 0.052 -10000 0 -10000 0 0
spindle assembly -0.012 0.07 -10000 0 -0.18 1 1
TDRD7 0.03 0.015 -10000 0 -0.28 1 1
Aurora A/RasGAP/Survivin 0.085 0.062 -10000 0 -10000 0 0
CENPA 0.039 0.034 -10000 0 -10000 0 0
Aurora A/PP2A 0.077 0.049 0.19 2 -10000 0 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.038 0.051 0.2 5 -0.21 1 6
negative regulation of DNA binding 0.054 0.052 0.17 2 -0.25 4 6
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.013 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.28 3 3
Ajuba/Aurora A 0 0.001 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.09 0.061 0.25 3 -10000 0 3
TACC1 -0.19 0.14 -10000 0 -0.28 389 389
TACC3 0.018 0.016 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.038 0.08 -10000 0 -0.19 8 8
Aurora A/RasGAP 0.074 0.05 -10000 0 -10000 0 0
OAZ1 -0.075 0.15 -10000 0 -0.28 185 185
RAN 0.031 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.013 -10000 0 -10000 0 0
GIT1 0.03 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.054 0.023 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.17 0.067 0.19 485 -10000 0 485
PPP2R5D 0.03 0.007 -10000 0 -10000 0 0
Aurora A/TPX2 0.004 0.025 0.15 15 -10000 0 15
PAK1 0.028 0.016 -10000 0 -0.28 1 1
CKAP5 0.025 0.013 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.2 0.31 -10000 0 -0.86 62 62
CRP -0.2 0.31 -10000 0 -0.9 53 53
cell cycle arrest -0.24 0.37 -10000 0 -1 72 72
TIMP1 -0.2 0.31 -10000 0 -0.83 74 74
IL6ST -0.004 0.063 -10000 0 -0.29 18 18
Rac1/GDP -0.059 0.13 -10000 0 -0.45 20 20
AP1 -0.001 0.14 0.44 4 -0.55 17 21
GAB2 0.023 0.047 -10000 0 -0.28 12 12
TNFSF11 -0.21 0.3 -10000 0 -0.89 56 56
HSP90B1 -0.022 0.13 -10000 0 -0.86 9 9
GAB1 0.03 0.021 -10000 0 -0.28 2 2
MAPK14 -0.044 0.12 0.38 1 -0.57 14 15
AKT1 0.001 0.082 0.6 1 -0.44 2 3
FOXO1 -0.007 0.08 0.55 1 -0.43 2 3
MAP2K6 -0.045 0.11 -10000 0 -0.47 16 16
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.11 0.16 0.56 1 -0.56 21 22
MITF -0.065 0.11 0.4 1 -0.44 19 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.028 0.01 -10000 0 -10000 0 0
A2M -0.086 0.33 0.68 2 -1.2 43 45
CEBPB 0.027 0.028 -10000 0 -0.28 4 4
GRB2/SOS1/GAB family/SHP2 0.006 0.1 -10000 0 -0.43 18 18
STAT3 -0.26 0.41 -10000 0 -1.1 74 74
STAT1 0.032 0.06 -10000 0 -0.88 1 1
CEBPD -0.22 0.34 -10000 0 -0.97 67 67
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
PI3K 0.012 0.062 -10000 0 -0.2 37 37
JUN 0.029 0.02 -10000 0 -0.28 2 2
PIAS3/MITF -0.048 0.12 0.37 1 -0.41 21 22
MAPK11 -0.039 0.12 0.38 1 -0.59 13 14
STAT3 (dimer)/FOXO1 -0.2 0.3 -10000 0 -0.82 66 66
GRB2/SOS1/GAB family 0.008 0.12 -10000 0 -0.34 10 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.029 0.089 -10000 0 -0.33 18 18
GRB2 0.031 0.009 -10000 0 -10000 0 0
JAK2 0.028 0.021 -10000 0 -0.28 2 2
LBP -0.14 0.24 -10000 0 -0.7 28 28
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
JAK1 0.007 0.039 0.14 1 -0.29 2 3
MYC -0.19 0.38 -10000 0 -0.99 76 76
FGG -0.21 0.3 -10000 0 -0.9 53 53
macrophage differentiation -0.24 0.37 -10000 0 -1 72 72
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.006 0.1 -10000 0 -0.23 31 31
JUNB -0.29 0.44 -10000 0 -0.95 157 157
FOS -0.03 0.12 -10000 0 -0.28 107 107
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.053 0.12 -10000 0 -0.46 20 20
STAT1/PIAS1 -0.044 0.14 -10000 0 -0.47 12 12
GRB2/SOS1/GAB family/SHP2/PI3K 0.012 0.079 0.49 1 -0.38 6 7
STAT3 (dimer) -0.26 0.41 -10000 0 -1.1 74 74
PRKCD -0.15 0.22 0.64 1 -0.62 49 50
IL6R 0.007 0.037 0.14 1 -0.29 1 2
SOCS3 -0.033 0.15 0.49 1 -1.1 8 9
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.075 -10000 0 -0.2 19 19
Rac1/GTP -0.071 0.15 -10000 0 -0.49 21 21
HCK 0.029 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0.006 0.12 0.45 1 -0.54 16 17
bone resorption -0.2 0.29 -10000 0 -0.83 54 54
IRF1 -0.22 0.34 -10000 0 -0.93 72 72
mol:GDP -0.068 0.12 -10000 0 -0.45 20 20
SOS1 0.031 0.01 -10000 0 -10000 0 0
VAV1 -0.069 0.12 -10000 0 -0.46 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.008 0.11 -10000 0 -0.52 16 16
PTPN11 0.006 0.078 -10000 0 -0.78 5 5
IL6/IL6RA 0 0.075 0.25 1 -0.22 38 39
gp130 (dimer)/TYK2/TYK2/LMO4 0.013 0.064 -10000 0 -0.18 15 15
gp130 (dimer)/JAK2/JAK2/LMO4 0.014 0.066 -10000 0 -0.19 18 18
IL6 -0.014 0.086 0.16 1 -0.29 41 42
PIAS3 0.031 0.005 -10000 0 -10000 0 0
PTPRE 0.035 0.022 -10000 0 -0.15 1 1
PIAS1 0.031 0.005 -10000 0 -10000 0 0
RAC1 0.013 0.028 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.032 0.088 -10000 0 -0.3 26 26
LMO4 0.006 0.04 0.16 1 -0.29 1 2
STAT3 (dimer)/PIAS3 -0.22 0.38 -10000 0 -1 75 75
MCL1 0.006 0.094 0.72 1 -10000 0 1
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.004 0.048 -10000 0 -0.16 45 45
ARNO/beta Arrestin1-2 0.027 0.032 -10000 0 -0.14 9 9
EGFR 0.002 0.091 -10000 0 -0.28 51 51
EPHA2 0.031 0.005 -10000 0 -10000 0 0
USP6 0.03 0.007 -10000 0 -10000 0 0
IQSEC1 0.031 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.02 0.072 -10000 0 -0.2 51 51
ARRB2 0.008 0.002 -10000 0 -10000 0 0
mol:GTP 0.004 0.021 0.11 4 -10000 0 4
ARRB1 0.025 0.04 -10000 0 -0.28 9 9
FBXO8 0.029 0.008 -10000 0 -10000 0 0
TSHR 0.03 0.008 -10000 0 -10000 0 0
EGF 0.029 0.008 -10000 0 -10000 0 0
somatostatin receptor activity 0 0 0 4 -0.001 36 40
ARAP2 0 0 0 3 0 28 31
mol:GDP -0.038 0.086 0.19 1 -0.25 38 39
mol:PI-3-4-5-P3 0 0 0.001 2 -0.001 35 37
ITGA2B 0.03 0.006 -10000 0 -10000 0 0
ARF6 0.031 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.04 -10000 0 -10000 0 0
ADAP1 0 0 0 2 0 16 18
KIF13B 0.001 0.085 -10000 0 -0.28 45 45
HGF/MET 0.022 0.068 -10000 0 -0.2 44 44
PXN 0.024 0.046 -10000 0 -0.28 12 12
ARF6/GTP -0.04 0.089 0.21 2 -0.26 36 38
EGFR/EGFR/EGF/EGF/ARFGEP100 0.037 0.069 -10000 0 -0.18 48 48
ADRB2 0.031 0.004 -10000 0 -10000 0 0
receptor agonist activity 0 0 0 4 0 33 37
actin filament binding 0 0 0 4 0 38 42
SRC 0.03 0.007 -10000 0 -10000 0 0
ITGB3 -0.01 0.1 -10000 0 -0.28 71 71
GNAQ 0.022 0.051 -10000 0 -0.28 15 15
EFA6/PI-4-5-P2 0 0 0.001 6 -0.001 24 30
ARF6/GDP -0.009 0.074 0.17 8 -0.29 20 28
ARF6/GDP/GULP/ACAP1 -0.043 0.11 0.19 1 -0.25 57 58
alphaIIb/beta3 Integrin/paxillin/GIT1 0.035 0.091 -10000 0 -0.17 80 80
ACAP1 0 0 0 1 -10000 0 1
ACAP2 0 0 0 1 0 28 29
LHCGR/beta Arrestin2 0.023 0.019 -10000 0 -10000 0 0
EFNA1 0.029 0.009 -10000 0 -10000 0 0
HGF 0.031 0.005 -10000 0 -10000 0 0
CYTH3 0 0 0.001 6 -0.001 31 37
CYTH2 -0.001 0.001 0.003 1 -0.004 41 42
NCK1 0.028 0.01 -10000 0 -10000 0 0
fibronectin binding 0 0 0 4 0 33 37
endosomal lumen acidification 0 0 0 3 0 25 28
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.016 0.11 -10000 0 -0.28 82 82
GNAQ/ARNO 0.019 0.006 -10000 0 -0.002 38 38
mol:Phosphatidic acid 0 0 0 1 0 28 29
PIP3-E 0 0 0 1 0 41 42
MET 0.004 0.084 -10000 0 -0.28 44 44
GNA14 0.029 0.02 -10000 0 -0.28 2 2
GNA15 0.028 0.021 -10000 0 -0.28 2 2
GIT1 0.03 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 3 -0.001 29 32
GNA11 -0.066 0.14 -10000 0 -0.28 168 168
LHCGR 0.03 0.006 -10000 0 -10000 0 0
AGTR1 0.029 0.009 -10000 0 -10000 0 0
desensitization of G-protein coupled receptor protein signaling pathway 0.023 0.019 -10000 0 -10000 0 0
IPCEF1/ARNO 0.018 0.047 -10000 0 -0.13 51 51
alphaIIb/beta3 Integrin 0.012 0.083 -10000 0 -0.2 71 71
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.049 0.1 0.26 43 -10000 0 43
DAPP1 -0.024 0.098 0.2 8 -0.31 23 31
Src family/SYK family/BLNK-LAT/BTK-ITK -0.005 0.12 -10000 0 -0.41 20 20
mol:DAG 0.019 0.089 0.2 51 -0.2 8 59
HRAS 0.036 0.012 -10000 0 -10000 0 0
RAP1A 0.037 0.012 -10000 0 -10000 0 0
ARF5/GDP 0.051 0.066 0.2 2 -0.25 8 10
PLCG2 0.028 0.01 -10000 0 -10000 0 0
PLCG1 0.03 0.007 -10000 0 -10000 0 0
ARF5 0.03 0.007 -10000 0 -10000 0 0
mol:GTP 0.048 0.098 0.27 46 -10000 0 46
ARF1/GTP 0.044 0.088 0.25 44 -10000 0 44
RHOA 0.031 0.014 -10000 0 -0.28 1 1
YES1 0.03 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.059 0.11 0.16 268 -10000 0 268
ADAP1 0.043 0.091 0.25 45 -10000 0 45
ARAP3 0.048 0.097 0.27 46 -10000 0 46
INPPL1 0.03 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.016 -10000 0 -0.28 1 1
ARHGEF6 0.03 0.019 -10000 0 -0.28 2 2
ARHGEF7 0.03 0.007 -10000 0 -10000 0 0
ARF1 0.011 0.074 -10000 0 -0.28 33 33
NRAS 0.018 0.018 -10000 0 -10000 0 0
FYN -0.002 0.095 -10000 0 -0.28 57 57
ARF6 0.031 0.004 -10000 0 -10000 0 0
FGR 0.031 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.006 0.052 0.14 29 -10000 0 29
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.03 0.014 -10000 0 -0.28 1 1
ZAP70 0.031 0.004 -10000 0 -10000 0 0
mol:IP3 0.004 0.064 0.17 26 -0.16 3 29
LYN 0.021 0.051 -10000 0 -0.28 15 15
ARF1/GDP 0.046 0.068 0.2 2 -0.25 9 11
RhoA/GDP 0.075 0.11 0.21 118 -10000 0 118
PDK1/Src/Hsp90 0.057 0.02 -10000 0 -10000 0 0
BLNK 0.015 0.067 -10000 0 -0.28 27 27
actin cytoskeleton reorganization 0.063 0.095 0.24 55 -0.3 1 56
SRC 0.03 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.022 0.01 -10000 0 -0.17 1 1
RAC1 0.03 0.007 -10000 0 -10000 0 0
PTEN -0.004 0.039 -10000 0 -0.26 2 2
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.051 0.1 0.26 47 -10000 0 47
RhoA/GTP 0.05 0.1 0.27 46 -10000 0 46
Src family/SYK family/BLNK-LAT -0.03 0.093 -10000 0 -0.3 30 30
BLK 0.026 0.012 -10000 0 -10000 0 0
PDPK1 0.031 0.006 -10000 0 -10000 0 0
CYTH1 0.043 0.091 0.25 45 -10000 0 45
HCK 0.029 0.009 -10000 0 -10000 0 0
CYTH3 0.043 0.091 0.25 45 -10000 0 45
CYTH2 0.043 0.091 0.25 45 -10000 0 45
KRAS 0.029 0.016 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.03 0.058 0.17 39 -10000 0 39
SGK1 0.041 0.062 0.18 40 -0.19 3 43
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.064 0.18 6 -0.25 8 14
SOS1 0.03 0.007 -10000 0 -10000 0 0
SYK 0.027 0.033 -10000 0 -0.28 6 6
ARF6/GDP 0.059 0.098 0.23 68 -10000 0 68
mol:PI-3-4-5-P3 0.047 0.096 0.26 43 -10000 0 43
ARAP3/RAP1A/GTP 0.059 0.11 0.16 268 -10000 0 268
VAV1 0.029 0.008 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.015 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.022 0.035 0.2 11 -10000 0 11
PLEKHA1 -0.022 0.016 0.18 3 -10000 0 3
Rac1/GDP 0.052 0.065 0.2 2 -0.25 8 10
LAT 0.031 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.056 0.19 1 -0.27 9 10
ITK 0.038 0.093 0.25 42 -10000 0 42
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.015 0.11 0.23 44 -0.27 9 53
LCK 0.03 0.007 -10000 0 -10000 0 0
BTK 0.037 0.094 0.25 44 -10000 0 44
Fc-epsilon receptor I signaling in mast cells

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.028 0.016 -10000 0 -0.28 1 1
LAT2 -0.014 0.082 0.16 1 -0.28 31 32
AP1 0.015 0.12 -10000 0 -0.38 21 21
mol:PIP3 -0.024 0.1 0.29 5 -0.34 25 30
IKBKB -0.013 0.076 0.22 18 -0.21 19 37
AKT1 -0.009 0.13 0.3 35 -0.29 9 44
IKBKG -0.015 0.071 0.22 13 -0.21 18 31
MS4A2 0.026 0.022 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.018 0.019 -10000 0 -10000 0 0
MAP3K1 0.013 0.11 0.27 26 -0.32 17 43
mol:Ca2+ -0.018 0.084 0.22 11 -0.26 23 34
LYN 0.017 0.052 -10000 0 -0.3 13 13
CBLB -0.012 0.081 0.16 3 -0.27 30 33
SHC1 0.03 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK -0.011 0.099 -10000 0 -0.16 164 164
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.043 0.086 0.34 10 -0.24 7 17
PTPN13 -0.039 0.13 -10000 0 -0.5 12 12
PTPN11 0.027 0.023 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.017 0.11 0.28 17 -0.32 7 24
SYK 0.023 0.036 -10000 0 -0.3 5 5
GRB2 0.031 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.007 0.093 -10000 0 -0.31 32 32
LAT -0.013 0.08 0.16 1 -0.27 31 32
PAK2 0.02 0.12 0.24 58 -0.32 20 78
NFATC2 -0.014 0.061 -10000 0 -0.43 11 11
HRAS 0 0.1 0.26 5 -0.34 23 28
GAB2 0.021 0.048 -10000 0 -0.28 13 13
PLA2G1B -0.022 0.075 -10000 0 -0.91 2 2
Fc epsilon R1 0.04 0.061 -10000 0 -0.16 43 43
Antigen/IgE/Fc epsilon R1 0.038 0.054 -10000 0 -0.13 41 41
mol:GDP 0.007 0.1 0.21 2 -0.36 20 22
JUN 0.029 0.02 -10000 0 -0.28 2 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.001 0.091 -10000 0 -0.28 52 52
FOS -0.03 0.12 -10000 0 -0.28 107 107
Antigen/IgE/Fc epsilon R1/LYN/SYK 0 0.083 -10000 0 -0.27 34 34
CHUK -0.016 0.068 0.2 9 -0.21 19 28
KLRG1 -0.02 0.063 0.14 2 -0.24 28 30
VAV1 -0.01 0.081 0.15 3 -0.28 27 30
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.013 0.082 0.16 1 -0.28 31 32
negative regulation of mast cell degranulation -0.021 0.059 0.12 2 -0.24 22 24
BTK 0.007 0.095 -10000 0 -0.37 17 17
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.005 0.061 -10000 0 -0.2 19 19
GAB2/PI3K/SHP2 -0.061 0.067 -10000 0 -0.21 60 60
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.007 0.068 -10000 0 -0.22 34 34
RAF1 0.023 0.063 -10000 0 -0.96 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.048 0.06 -10000 0 -0.14 41 41
FCER1G 0.004 0.073 -10000 0 -0.29 30 30
FCER1A 0.024 0.022 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/Fyn 0.027 0.086 -10000 0 -0.16 82 82
MAPK3 -0.026 0.084 -10000 0 -0.89 2 2
MAPK1 -0.019 0.077 -10000 0 -0.95 2 2
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
MAPK8 -0.002 0.16 -10000 0 -0.48 42 42
DUSP1 -0.061 0.14 -10000 0 -0.28 163 163
NF-kappa-B/RelA -0.016 0.057 0.14 16 -0.18 16 32
actin cytoskeleton reorganization -0.02 0.12 -10000 0 -0.5 9 9
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.007 0.1 0.23 2 -0.36 21 23
FER -0.012 0.08 0.15 1 -0.28 29 30
RELA 0.03 0.019 -10000 0 -0.28 2 2
ITK 0.002 0.044 0.12 7 -0.23 12 19
SOS1 0.03 0.007 -10000 0 -10000 0 0
PLCG1 0.003 0.1 0.29 6 -0.34 19 25
cytokine secretion -0.015 0.036 0.092 2 -0.13 13 15
SPHK1 -0.012 0.08 0.16 2 -0.27 29 31
PTK2 -0.021 0.12 -10000 0 -0.56 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs 0 0.1 -10000 0 -0.32 35 35
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.027 0.11 0.25 8 -0.33 29 37
MAP2K2 -0.034 0.082 -10000 0 -0.91 2 2
MAP2K1 0.009 0.061 -10000 0 -0.91 2 2
MAP2K7 0.03 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 -0.002 0.079 0.18 40 -0.26 15 55
MAP2K4 -0.061 0.3 -10000 0 -0.87 64 64
Fc epsilon R1/FcgammaRIIB 0.052 0.065 -10000 0 -0.15 41 41
mol:Choline -0.043 0.085 0.34 10 -0.24 7 17
SHC/Grb2/SOS1 0.044 0.094 -10000 0 -0.26 27 27
FYN -0.002 0.095 -10000 0 -0.28 57 57
DOK1 0.031 0.014 -10000 0 -0.28 1 1
PXN -0.029 0.11 -10000 0 -0.49 9 9
HCLS1 -0.012 0.086 0.16 8 -0.29 29 37
PRKCB -0.019 0.084 0.22 9 -0.26 28 37
FCGR2B 0.028 0.016 -10000 0 -0.28 1 1
IGHE -0.001 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.021 0.06 0.12 2 -0.24 22 24
LCP2 0.017 0.064 -10000 0 -0.28 24 24
PLA2G4A -0.041 0.1 0.16 7 -0.31 36 43
RASA1 0.027 0.024 -10000 0 -0.28 3 3
mol:Phosphatidic acid -0.043 0.085 0.34 10 -0.24 7 17
IKK complex -0.012 0.069 0.22 17 -0.18 6 23
WIPF1 0.03 0.014 -10000 0 -0.28 1 1
IL1-mediated signaling events

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
UBC13/UEV1A 0.023 0.01 -10000 0 -0.19 1 1
PRKCZ 0.03 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.017 -10000 0 -0.28 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.015 0.053 -10000 0 -0.3 4 4
IRAK/TOLLIP -0.029 0.016 0.17 2 -0.16 1 3
IKBKB 0.029 0.008 -10000 0 -10000 0 0
IKBKG 0.03 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.04 0.03 -10000 0 -0.2 7 7
IL1A 0.03 0.006 -10000 0 -10000 0 0
IL1B -0.028 0.083 0.19 45 -0.2 54 99
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.05 -10000 0 -10000 0 0
IL1R2 0.026 0.035 -10000 0 -0.28 7 7
IL1R1 -0.037 0.13 -10000 0 -0.28 120 120
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.02 0.11 0.17 6 -0.28 29 35
TOLLIP 0.03 0.007 -10000 0 -10000 0 0
TICAM2 0.029 0.015 -10000 0 -0.28 1 1
MAP3K3 0.031 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.02 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.018 0.066 0.23 1 -0.29 6 7
JUN -0.026 0.057 0.16 17 -10000 0 17
MAP3K7 0.03 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.008 0.11 0.28 2 -0.2 87 89
IL1 alpha/IL1R1/IL1RAP/MYD88 0.009 0.078 -10000 0 -0.17 71 71
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.046 0.096 -10000 0 -0.17 68 68
IL1 beta fragment/IL1R1/IL1RAP -0.009 0.085 0.16 22 -0.18 86 108
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
MAPK8 -0.032 0.037 0.15 13 -10000 0 13
IRAK1 -0.023 0.009 -10000 0 -0.17 1 1
IL1RN/IL1R1 -0.009 0.1 -10000 0 -0.2 117 117
IRAK4 0.029 0.008 -10000 0 -10000 0 0
PRKCI 0.013 0.016 -10000 0 -10000 0 0
TRAF6 0.031 0.005 -10000 0 -10000 0 0
PI3K 0.012 0.062 -10000 0 -0.2 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.11 0.2 23 -0.28 22 45
CHUK 0.03 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.009 0.085 0.16 22 -0.18 86 108
IL1 beta/IL1R2 -0.034 0.076 0.2 35 -0.18 59 94
IRAK/TRAF6/TAK1/TAB1/TAB2 0.032 0.022 0.16 2 -0.15 1 3
NF kappa B1 p50/RelA -0.035 0.098 0.13 15 -0.3 27 42
IRAK3 0.029 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.023 0.1 0.28 1 -0.19 77 78
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.089 -10000 0 -0.26 6 6
IL1 alpha/IL1R1/IL1RAP 0.002 0.075 -10000 0 -0.18 70 70
RELA 0.03 0.019 -10000 0 -0.28 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.03 0.006 -10000 0 -10000 0 0
MYD88 0.031 0.014 -10000 0 -0.28 1 1
IRAK/TRAF6/MEKK3 0.042 0.021 0.18 2 -0.16 1 3
IL1RAP 0.017 0.016 -10000 0 -10000 0 0
UBE2N 0.03 0.014 -10000 0 -0.28 1 1
IRAK/TRAF6 -0.047 0.069 0.089 19 -0.27 11 30
CASP1 -0.002 0.094 -10000 0 -0.28 56 56
IL1RN/IL1R2 0.039 0.031 -10000 0 -0.2 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.003 0.09 -10000 0 -0.19 82 82
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.019 0.13 -10000 0 -0.29 66 66
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
IL1RN 0.03 0.007 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.041 0.02 -10000 0 -0.14 1 1
MAP2K6 -0.025 0.038 0.17 13 -10000 0 13
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.003 0.11 0.28 4 -0.37 25 29
PDGFB-D/PDGFRB/SLAP 0.022 0.048 -10000 0 -0.2 19 19
PDGFB-D/PDGFRB/APS/CBL 0.033 0.04 -10000 0 -0.17 19 19
AKT1 -0.036 0.12 0.29 18 -0.27 19 37
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0.11 0.27 4 -0.4 25 29
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
FGR -0.006 0.1 0.32 1 -0.49 12 13
mol:Ca2+ -0.008 0.11 0.26 2 -0.43 25 27
MYC -0.031 0.26 0.38 5 -0.69 62 67
SHC1 0.03 0.006 -10000 0 -10000 0 0
HRAS/GDP -0.036 0.061 0.16 41 -10000 0 41
LRP1/PDGFRB/PDGFB 0.044 0.058 -10000 0 -0.18 30 30
GRB10 0.031 0.005 -10000 0 -10000 0 0
PTPN11 0.031 0.004 -10000 0 -10000 0 0
GO:0007205 -0.009 0.11 0.26 2 -0.44 25 27
PTEN 0.029 0.02 -10000 0 -0.28 2 2
GRB2 0.03 0.006 -10000 0 -10000 0 0
GRB7 0.028 0.024 -10000 0 -0.28 3 3
PDGFB-D/PDGFRB/SHP2 0.034 0.049 -10000 0 -0.2 20 20
PDGFB-D/PDGFRB/GRB10 0.034 0.048 -10000 0 -0.2 19 19
cell cycle arrest 0.022 0.048 -10000 0 -0.2 19 19
HRAS 0.03 0.007 -10000 0 -10000 0 0
HIF1A -0.041 0.11 0.25 20 -0.25 19 39
GAB1 -0.016 0.12 0.3 1 -0.39 29 30
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.015 0.12 0.29 9 -0.36 27 36
PDGFB-D/PDGFRB 0.037 0.06 -10000 0 -0.19 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.049 -10000 0 -0.2 20 20
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.015 0.12 0.27 5 -0.33 35 40
positive regulation of MAPKKK cascade 0.034 0.049 -10000 0 -0.2 20 20
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
mol:IP3 -0.009 0.11 0.26 2 -0.44 25 27
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.025 0.019 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.031 0.052 -10000 0 -0.2 23 23
SHB 0.031 0.004 -10000 0 -10000 0 0
BLK -0.062 0.17 0.32 1 -0.41 86 87
PTPN2 0.022 0.024 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.049 -10000 0 -0.2 20 20
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
VAV2 -0.028 0.14 0.33 1 -0.39 42 43
CBL 0.031 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.049 -10000 0 -0.2 20 20
LCK -0.005 0.092 0.32 1 -0.47 9 10
PDGFRB 0.012 0.062 -10000 0 -0.29 20 20
ACP1 0.028 0.01 -10000 0 -10000 0 0
HCK -0.001 0.064 0.32 1 -10000 0 1
ABL1 -0.015 0.1 0.28 3 -0.33 29 32
PDGFB-D/PDGFRB/CBL -0.017 0.13 -10000 0 -0.46 27 27
PTPN1 0.019 0.025 -10000 0 -10000 0 0
SNX15 0.031 0.003 -10000 0 -10000 0 0
STAT3 0.025 0.04 -10000 0 -0.28 9 9
STAT1 0.015 0.016 -10000 0 -10000 0 0
cell proliferation -0.023 0.24 0.38 5 -0.61 62 67
SLA 0.022 0.015 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.02 0.1 0.33 15 -0.28 1 16
SRC -0.002 0.074 0.32 1 -0.88 1 2
PI3K -0.071 0.073 -10000 0 -0.22 49 49
PDGFB-D/PDGFRB/GRB7/SHC 0.046 0.051 -10000 0 -0.18 23 23
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0 0.12 0.27 4 -0.41 25 29
LYN -0.015 0.1 0.32 1 -0.49 15 16
LRP1 0.025 0.044 -10000 0 -0.28 11 11
SOS1 0.03 0.007 -10000 0 -10000 0 0
STAT5B 0.027 0.033 -10000 0 -0.28 6 6
STAT5A 0.027 0.033 -10000 0 -0.28 6 6
NCK1-2/p130 Cas 0.051 0.078 -10000 0 -0.18 19 19
SPHK1 0.023 0.022 -10000 0 -10000 0 0
EDG1 -0.001 0.003 -10000 0 -10000 0 0
mol:DAG -0.009 0.11 0.26 2 -0.44 25 27
PLCG1 -0.009 0.12 0.27 1 -0.45 25 26
NHERF/PDGFRB -0.02 0.12 -10000 0 -0.19 173 173
YES1 -0.005 0.094 0.32 1 -0.58 7 8
cell migration -0.021 0.12 -10000 0 -0.19 173 173
SHC/Grb2/SOS1 0.058 0.071 -10000 0 -0.18 16 16
SLC9A3R2 0.016 0.066 -10000 0 -0.28 26 26
SLC9A3R1 -0.053 0.14 -10000 0 -0.28 148 148
NHERF1-2/PDGFRB/PTEN -0.011 0.12 -10000 0 -0.18 173 173
FYN -0.065 0.18 0.32 1 -0.46 78 79
DOK1 -0.029 0.066 0.16 50 -0.18 1 51
HRAS/GTP 0.022 0.005 -10000 0 -10000 0 0
PDGFB 0.029 0.009 -10000 0 -10000 0 0
RAC1 -0.064 0.21 0.31 1 -0.52 72 73
PRKCD -0.029 0.067 0.16 50 -0.19 2 52
FER -0.028 0.064 0.16 47 -10000 0 47
MAPKKK cascade -0.026 0.083 0.33 9 -10000 0 9
RASA1 -0.029 0.063 0.16 43 -0.18 1 44
NCK1 0.028 0.01 -10000 0 -10000 0 0
NCK2 0.031 0.004 -10000 0 -10000 0 0
p62DOK/Csk -0.031 0.069 0.17 52 -10000 0 52
PDGFB-D/PDGFRB/SHB 0.034 0.049 -10000 0 -0.2 20 20
chemotaxis -0.014 0.1 0.28 3 -0.32 29 32
STAT1-3-5/STAT1-3-5 0.052 0.073 -10000 0 -0.18 20 20
Bovine Papilomavirus E5/PDGFRB 0.01 0.042 -10000 0 -0.19 20 20
PTPRJ 0.031 0.004 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.01 0.11 0.28 5 -0.39 20 25
ACTA1 -0.002 0.09 0.23 14 -0.24 19 33
NUMA1 0.012 0.11 0.28 5 -0.38 22 27
SPTAN1 -0.003 0.088 0.26 8 -0.26 9 17
LIMK1 -0.001 0.09 0.26 11 -0.26 9 20
BIRC3 -0.037 0.13 -10000 0 -0.28 118 118
BIRC2 0.026 0.012 -10000 0 -10000 0 0
BAX 0.03 0.006 -10000 0 -10000 0 0
CASP10 -0.032 0.055 0.18 23 -0.18 26 49
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 4 -0.001 36 40
PTK2 -0.005 0.12 0.28 5 -0.39 28 33
DIABLO 0.017 0.016 -10000 0 -10000 0 0
apoptotic nuclear changes -0.003 0.087 0.26 8 -0.25 9 17
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.031 0.005 -10000 0 -10000 0 0
GSN -0.014 0.094 0.27 8 -0.27 14 22
MADD 0.031 0.004 -10000 0 -10000 0 0
TFAP2A 0.025 0.12 -10000 0 -0.8 9 9
BID -0.016 0.043 0.11 20 -0.14 27 47
MAP3K1 -0.017 0.12 -10000 0 -0.38 49 49
TRADD 0.026 0.028 -10000 0 -0.28 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.044 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.007 0.11 0.26 39 -0.25 15 54
CASP9 0.031 0.005 -10000 0 -10000 0 0
DNA repair -0.031 0.069 0.26 3 -0.18 25 28
neuron apoptosis -0.006 0.15 -10000 0 -0.72 21 21
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.005 0.1 0.28 5 -0.35 19 24
APAF1 0.03 0.006 -10000 0 -10000 0 0
CASP6 -0.024 0.24 -10000 0 -0.9 35 35
TRAF2 0.03 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.009 0.085 0.25 9 -0.26 8 17
CASP7 0.042 0.11 0.21 118 -0.25 22 140
KRT18 0.014 0.067 -10000 0 -0.67 3 3
apoptosis -0.019 0.14 0.32 9 -0.45 30 39
DFFA -0.001 0.086 0.26 8 -0.24 12 20
DFFB -0.001 0.087 0.24 9 -0.26 9 18
PARP1 0.031 0.069 0.18 25 -0.26 3 28
actin filament polymerization 0.009 0.087 0.25 7 -0.29 9 16
TNF 0.031 0.005 -10000 0 -10000 0 0
CYCS -0.01 0.055 0.17 5 -0.24 14 19
SATB1 -0.068 0.22 -10000 0 -0.88 35 35
SLK -0.003 0.088 0.28 8 -0.24 13 21
p15 BID/BAX -0.022 0.051 0.2 2 -0.21 6 8
CASP2 -0.036 0.095 0.19 15 -0.29 34 49
JNK cascade 0.017 0.12 0.38 49 -10000 0 49
CASP3 0.007 0.092 0.29 7 -0.23 19 26
LMNB2 -0.034 0.18 0.25 5 -0.49 57 62
RIPK1 0.029 0.008 -10000 0 -10000 0 0
CASP4 0.024 0.044 -10000 0 -0.28 11 11
Mammalian IAPs/DIABLO 0.004 0.064 -10000 0 -0.16 61 61
negative regulation of DNA binding 0.025 0.12 -10000 0 -0.78 9 9
stress fiber formation -0.003 0.088 0.28 8 -0.25 10 18
GZMB -0.03 0.055 0.19 19 -0.2 24 43
CASP1 -0.021 0.091 -10000 0 -0.27 58 58
LMNB1 0 0.14 0.24 14 -0.42 36 50
APP -0.006 0.16 -10000 0 -0.74 21 21
TNFRSF1A 0.015 0.063 -10000 0 -0.28 23 23
response to stress 0 0 0.001 11 -0.001 10 21
CASP8 -0.016 0.002 -10000 0 -10000 0 0
VIM -0.009 0.15 0.29 13 -0.46 31 44
LMNA -0.01 0.13 0.23 11 -0.4 37 48
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.032 0.097 -10000 0 -0.3 37 37
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.004 0.087 0.26 7 -0.26 10 17
APAF-1/Caspase 9 0.015 0.14 -10000 0 -0.6 9 9
nuclear fragmentation during apoptosis 0.012 0.11 0.28 5 -0.38 22 27
CFL2 -0.009 0.088 0.29 9 -0.26 8 17
GAS2 0.001 0.092 0.27 14 -0.25 10 24
positive regulation of apoptosis -0.012 0.15 0.24 14 -0.46 40 54
PRF1 0.017 0.065 -10000 0 -0.28 25 25
Signaling events mediated by PTP1B

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
PDGFRB 0.02 0.059 -10000 0 -0.28 20 20
Jak2/Leptin Receptor 0.007 0.12 -10000 0 -0.37 31 31
PTP1B/AKT1 -0.005 0.098 -10000 0 -0.32 12 12
FYN -0.002 0.095 -10000 0 -0.28 57 57
p210 bcr-abl/PTP1B -0.016 0.098 -10000 0 -0.34 12 12
EGFR 0.006 0.077 -10000 0 -0.29 32 32
EGF/EGFR -0.004 0.11 -10000 0 -0.31 24 24
CSF1 0.019 0.06 -10000 0 -0.28 21 21
AKT1 0.022 0.022 -10000 0 -10000 0 0
INSR 0.008 0.074 -10000 0 -0.29 32 32
PTP1B/N-cadherin -0.015 0.1 -10000 0 -0.31 27 27
Insulin Receptor/Insulin 0 0.11 -10000 0 -0.31 16 16
HCK 0.029 0.009 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
TYK2 -0.007 0.11 0.27 18 -0.33 10 28
EGF 0.021 0.026 -10000 0 -10000 0 0
YES1 0.03 0.007 -10000 0 -10000 0 0
CAV1 -0.041 0.12 0.22 1 -0.34 36 37
TXN 0.008 0.071 -10000 0 -0.29 28 28
PTP1B/IRS1/GRB2 -0.075 0.12 -10000 0 -0.32 49 49
cell migration 0.016 0.098 0.34 12 -10000 0 12
STAT3 0.025 0.038 -10000 0 -0.28 8 8
PRLR 0.029 0.011 0.15 1 -10000 0 1
ITGA2B 0.022 0.021 -10000 0 -10000 0 0
CSF1R 0.016 0.066 -10000 0 -0.28 26 26
Prolactin Receptor/Prolactin 0.041 0.021 0.29 1 -10000 0 1
FGR 0.031 0.005 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.006 0.1 -10000 0 -0.32 14 14
Crk/p130 Cas -0.002 0.11 -10000 0 -0.32 13 13
DOK1 -0.026 0.099 0.28 1 -0.34 15 16
JAK2 -0.006 0.11 -10000 0 -0.38 32 32
Jak2/Leptin Receptor/Leptin -0.008 0.13 0.27 2 -0.36 18 20
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
PTPN1 -0.016 0.099 -10000 0 -0.34 12 12
LYN 0.021 0.051 -10000 0 -0.28 15 15
CDH2 -0.016 0.1 -10000 0 -0.28 71 71
SRC 0.007 0.097 -10000 0 -0.52 13 13
ITGB3 -0.011 0.1 -10000 0 -0.28 71 71
CAT1/PTP1B -0.024 0.12 0.27 8 -0.4 18 26
CAPN1 0.024 0.031 -10000 0 -0.29 4 4
CSK 0.03 0.006 -10000 0 -10000 0 0
PI3K -0.01 0.1 -10000 0 -0.31 16 16
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.008 0.12 0.32 2 -0.34 19 21
negative regulation of transcription -0.005 0.11 -10000 0 -0.38 32 32
FCGR2A 0.023 0.049 -10000 0 -0.28 14 14
FER 0.022 0.021 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.011 0.084 -10000 0 -0.21 71 71
BLK 0.026 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.041 0.06 -10000 0 -0.18 32 32
RHOA 0.026 0.022 -10000 0 -0.29 1 1
LEPR 0.03 0.02 -10000 0 -0.28 2 2
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
p210 bcr-abl/Grb2 0.03 0.006 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.027 0.13 0.25 3 -0.4 27 30
PRL 0.03 0.01 0.15 1 -10000 0 1
SOCS3 -0.011 0.2 0.67 2 -1.2 15 17
SPRY2 -0.022 0.11 -10000 0 -0.29 78 78
Insulin Receptor/Insulin/IRS1 -0.076 0.13 -10000 0 -0.19 295 295
CSF1/CSF1R -0.008 0.12 -10000 0 -0.33 24 24
Ras protein signal transduction -0.005 0.089 0.56 12 -10000 0 12
IRS1 -0.14 0.16 -10000 0 -0.28 297 297
INS 0.023 0.022 -10000 0 -10000 0 0
LEP 0.029 0.016 -10000 0 -0.28 1 1
STAT5B -0.014 0.12 -10000 0 -0.38 25 25
STAT5A -0.014 0.12 -10000 0 -0.37 25 25
GRB2 0.03 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.009 0.11 -10000 0 -0.34 14 14
CSN2 0.012 0.076 0.64 1 -10000 0 1
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
LAT 0.004 0.11 -10000 0 -0.5 21 21
YBX1 0.031 0.018 -10000 0 -10000 0 0
LCK 0.03 0.007 -10000 0 -10000 0 0
SHC1 0.03 0.006 -10000 0 -10000 0 0
NOX4 0.017 0.018 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.056 0.054 0.24 27 -10000 0 27
AES 0.019 0.1 0.21 20 -0.28 47 67
FBXW11 0.031 0.006 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.018 -10000 0 -10000 0 0
SMAD4 0.03 0.007 -10000 0 -10000 0 0
DKK2 0.03 0.008 -10000 0 -10000 0 0
TLE1 0.054 0.045 0.21 26 -10000 0 26
MACF1 0.028 0.016 -10000 0 -0.28 1 1
CTNNB1 0.033 0.08 0.28 17 -0.41 1 18
WIF1 0.03 0.01 -10000 0 -10000 0 0
beta catenin/RanBP3 0.14 0.2 0.42 165 -0.35 1 166
KREMEN2 0.031 0.007 -10000 0 -10000 0 0
DKK1 0.031 0.006 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.054 0.08 0.28 17 -0.38 1 18
FZD1 0.03 0.009 -10000 0 -10000 0 0
AXIN2 -0.078 0.18 0.63 6 -0.76 18 24
AXIN1 0.03 0.007 -10000 0 -10000 0 0
RAN 0.032 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.023 0.11 -10000 0 -0.51 12 12
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.039 0.18 0.3 7 -0.56 36 43
Axin1/APC/GSK3 0.018 0.065 0.21 13 -0.55 1 14
Axin1/APC/GSK3/beta catenin/Macf1 0.008 0.082 0.29 7 -0.38 6 13
HNF1A 0.056 0.048 0.21 29 -10000 0 29
CTBP1 0.053 0.049 0.22 27 -10000 0 27
MYC 0.004 0.5 0.6 129 -1.2 60 189
RANBP3 0.031 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.05 0.028 -10000 0 -10000 0 0
NKD1 0.028 0.01 -10000 0 -10000 0 0
TCF4 0.053 0.054 0.22 27 -0.28 2 29
TCF3 0.052 0.048 0.21 25 -10000 0 25
WNT1/LRP6/FZD1/Axin1 0.062 0.039 -10000 0 -10000 0 0
Ran/GTP 0.025 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.12 0.28 0.55 116 -0.56 12 128
LEF1 0.047 0.049 0.23 21 -10000 0 21
DVL1 0.022 0.055 0.2 3 -0.32 4 7
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.12 0.2 -10000 0 -0.51 82 82
DKK1/LRP6/Kremen 2 0.05 0.027 -10000 0 -10000 0 0
LRP6 0.026 0.012 -10000 0 -10000 0 0
CSNK1A1 0.06 0.054 0.24 28 -10000 0 28
NLK 0.008 0.032 -10000 0 -10000 0 0
CCND1 -0.33 0.57 0.64 15 -1.2 151 166
WNT1 0.031 0.007 -10000 0 -10000 0 0
GSK3A 0.025 0.034 -10000 0 -0.28 6 6
GSK3B 0.029 0.012 -10000 0 -10000 0 0
FRAT1 0.027 0.022 -10000 0 -0.28 2 2
PPP2R5D 0.031 0.051 -10000 0 -0.31 7 7
APC -0.011 0.087 0.2 60 -10000 0 60
WNT1/LRP6/FZD1 0.02 0.048 0.18 5 -0.22 2 7
CREBBP 0.052 0.053 0.21 26 -0.28 3 29
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.011 0.089 -10000 0 -0.29 18 18
adherens junction organization -0.024 0.1 -10000 0 -0.31 42 42
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.1 0.25 4 -0.27 14 18
FMN1 -0.026 0.095 -10000 0 -0.29 42 42
mol:IP3 -0.021 0.072 -10000 0 -0.24 13 13
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.1 -10000 0 -0.29 43 43
CTNNB1 0.033 0.006 -10000 0 -10000 0 0
AKT1 -0.024 0.077 0.2 1 -0.23 26 27
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.1 -10000 0 -0.33 23 23
CTNND1 0.029 0.017 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.016 0.096 0.18 21 -0.28 40 61
VASP -0.024 0.094 -10000 0 -0.29 42 42
ZYX -0.036 0.1 -10000 0 -0.3 46 46
JUB -0.014 0.096 -10000 0 -0.28 43 43
EGFR(dimer) -0.01 0.11 -10000 0 -0.29 49 49
E-cadherin/beta catenin-gamma catenin 0.046 0.05 -10000 0 -0.18 20 20
mol:PI-3-4-5-P3 -0.007 0.079 -10000 0 -0.24 29 29
PIK3CA 0.013 0.023 -10000 0 -10000 0 0
PI3K -0.007 0.081 -10000 0 -0.24 29 29
FYN -0.033 0.12 0.18 1 -0.3 65 66
mol:Ca2+ -0.02 0.071 -10000 0 -0.24 13 13
JUP 0.024 0.048 -10000 0 -0.28 13 13
PIK3R1 0.01 0.075 -10000 0 -0.29 33 33
mol:DAG -0.021 0.072 -10000 0 -0.24 13 13
CDH1 0.024 0.039 -10000 0 -0.28 8 8
RhoA/GDP -0.018 0.1 0.25 3 -0.27 14 17
establishment of polarity of embryonic epithelium -0.024 0.093 -10000 0 -0.28 42 42
SRC 0.03 0.007 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
RHOA 0.031 0.014 -10000 0 -0.28 1 1
EGFR 0.002 0.091 -10000 0 -0.28 51 51
CASR -0.012 0.084 0.19 1 -0.24 14 15
RhoA/GTP -0.008 0.088 0.18 1 -0.23 14 15
AKT2 -0.026 0.078 0.2 1 -0.24 29 30
actin cable formation -0.031 0.092 0.18 6 -0.29 39 45
apoptosis 0.016 0.088 0.28 19 -0.2 5 24
CTNNA1 0.028 0.022 -10000 0 -0.29 1 1
mol:GDP -0.021 0.094 0.19 1 -0.26 20 21
PIP5K1A -0.017 0.097 0.17 20 -0.28 40 60
PLCG1 -0.021 0.073 -10000 0 -0.25 13 13
Rac1/GTP -0.003 0.11 -10000 0 -0.28 48 48
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.006 0.04 -10000 0 -0.17 24 24
EPHB2 0.03 0.006 -10000 0 -10000 0 0
Syndecan-2/TACI 0.016 0.032 -10000 0 -0.17 15 15
LAMA1 0.025 0.013 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.023 0.094 -10000 0 -0.18 81 81
HRAS 0.03 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK -0.015 0.024 -10000 0 -0.16 15 15
ITGA5 0.031 0.006 -10000 0 -10000 0 0
BAX -0.024 0.032 -10000 0 -10000 0 0
EPB41 0.03 0.008 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.03 -10000 0 -0.16 15 15
LAMA3 0.007 0.081 -10000 0 -0.28 40 40
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.015 0.067 -10000 0 -0.28 27 27
Syndecan-2/MMP2 -0.01 0.075 -10000 0 -0.18 82 82
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.017 0.074 -10000 0 -0.2 55 55
dendrite morphogenesis 0.016 0.032 -10000 0 -0.17 15 15
Syndecan-2/GM-CSF 0.017 0.031 -10000 0 -0.17 14 14
determination of left/right symmetry -0.018 0.029 -10000 0 -0.19 15 15
Syndecan-2/PKC delta 0.016 0.034 -10000 0 -0.17 17 17
GNB2L1 0.031 0.005 -10000 0 -10000 0 0
MAPK3 -0.022 0.081 0.18 58 -0.28 4 62
MAPK1 -0.01 0.069 0.18 59 -10000 0 59
Syndecan-2/RACK1 0.029 0.037 -10000 0 -0.15 15 15
NF1 0.024 0.038 -10000 0 -0.28 8 8
FGFR/FGF/Syndecan-2 -0.018 0.029 -10000 0 -0.19 15 15
ITGA2 -0.005 0.098 -10000 0 -0.28 61 61
MAPK8 -0.022 0.034 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.031 0.076 -10000 0 -0.17 46 46
Syndecan-2/Kininogen 0.014 0.032 -10000 0 -0.17 15 15
ITGB1 0.031 0.006 -10000 0 -10000 0 0
SRC -0.016 0.069 0.18 53 -10000 0 53
Syndecan-2/CASK/Protein 4.1 0.015 0.027 -10000 0 -0.15 13 13
extracellular matrix organization -0.02 0.08 -10000 0 -0.17 116 116
actin cytoskeleton reorganization 0.006 0.04 -10000 0 -0.17 24 24
Syndecan-2/Caveolin-2/Ras 0.025 0.054 -10000 0 -0.17 32 32
Syndecan-2/Laminin alpha3 0.004 0.055 -10000 0 -0.17 49 49
Syndecan-2/RasGAP 0.036 0.047 -10000 0 -0.15 17 17
alpha5/beta1 Integrin 0.044 0.011 -10000 0 -10000 0 0
PRKCD 0.03 0.019 -10000 0 -0.28 2 2
Syndecan-2 dimer 0.016 0.032 -10000 0 -0.17 15 15
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.037 0.034 0.15 6 -10000 0 6
RHOA 0.031 0.014 -10000 0 -0.28 1 1
SDCBP 0.029 0.015 -10000 0 -0.28 1 1
TNFRSF13B 0.03 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.28 3 3
alpha2/beta1 Integrin 0.017 0.074 -10000 0 -0.2 55 55
Syndecan-2/Synbindin 0.015 0.031 -10000 0 -0.17 14 14
TGFB1 -0.037 0.13 -10000 0 -0.28 118 118
CASP3 -0.011 0.068 0.18 56 -10000 0 56
FN1 0.013 0.046 -10000 0 -0.28 12 12
Syndecan-2/IL8 0.014 0.031 -10000 0 -0.17 14 14
SDC2 -0.019 0.029 -10000 0 -0.19 15 15
KNG1 0.027 0.012 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.014 0.036 -10000 0 -0.17 19 19
TRAPPC4 0.029 0.009 -10000 0 -10000 0 0
CSF2 0.031 0.006 -10000 0 -10000 0 0
Syndecan-2/TGFB1 -0.02 0.081 -10000 0 -0.18 116 116
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.03 -10000 0 -0.16 15 15
Syndecan-2/Ezrin 0.015 0.03 -10000 0 -0.15 16 16
PRKACA -0.011 0.064 0.18 48 -10000 0 48
angiogenesis 0.014 0.031 -10000 0 -0.17 14 14
MMP2 -0.019 0.11 -10000 0 -0.28 85 85
IL8 0.027 0.011 -10000 0 -10000 0 0
calcineurin-NFAT signaling pathway 0.016 0.032 -10000 0 -0.17 15 15
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.013 0.097 -10000 0 -0.47 5 5
UGCG -0.011 0.12 -10000 0 -0.68 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT -0.057 0.18 0.38 1 -0.5 47 48
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.011 0.12 -10000 0 -0.67 16 16
mol:DAG -0.001 0.12 -10000 0 -0.84 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.088 0.23 -10000 0 -0.53 87 87
FRAP1 -0.11 0.27 -10000 0 -0.62 87 87
FOXO3 -0.087 0.23 -10000 0 -0.65 55 55
AKT1 -0.088 0.26 0.35 1 -0.67 62 63
GAB2 0.01 0.052 -10000 0 -0.29 13 13
SMPD1 -0.019 0.14 -10000 0 -0.69 22 22
SGMS1 -0.005 0.099 -10000 0 -0.65 11 11
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 -0.027 0.041 -10000 0 -0.17 37 37
CALM1 0.022 0.053 -10000 0 -0.28 16 16
cell proliferation -0.004 0.15 -10000 0 -0.52 19 19
EIF3A 0.031 0.004 -10000 0 -10000 0 0
PI3K 0.004 0.063 -10000 0 -0.21 37 37
RPS6KB1 -0.015 0.13 -10000 0 -0.92 8 8
mol:sphingomyelin -0.001 0.12 -10000 0 -0.84 11 11
natural killer cell activation -0.002 0.004 -10000 0 -10000 0 0
JAK3 0.016 0.027 0.17 1 -10000 0 1
PIK3R1 -0.012 0.092 0.17 1 -0.28 53 54
JAK1 0.017 0.033 0.17 1 -0.28 2 3
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
MYC -0.06 0.32 -10000 0 -0.86 63 63
MYB -0.077 0.3 0.55 1 -1.1 45 46
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.045 0.15 0.36 1 -0.44 38 39
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.008 0.13 -10000 0 -0.86 8 8
mol:PI-3-4-5-P3 -0.044 0.15 0.36 1 -0.43 39 40
Rac1/GDP -0.016 0.068 0.15 60 -0.16 37 97
T cell proliferation -0.045 0.14 0.34 1 -0.41 37 38
SHC1 0.017 0.027 -10000 0 -10000 0 0
RAC1 0.03 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.004 0.02 0.24 1 -0.066 1 2
PRKCZ -0.048 0.14 0.34 1 -0.43 37 38
NF kappa B1 p50/RelA -0.081 0.24 0.43 1 -0.54 84 85
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.018 0.099 -10000 0 -0.39 15 15
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
RELA 0.03 0.019 -10000 0 -0.28 2 2
IL2RA 0.017 0.026 -10000 0 -10000 0 0
IL2RB 0.014 0.039 0.17 1 -0.28 5 6
TERT 0.028 0.01 -10000 0 -10000 0 0
E2F1 -0.017 0.12 0.47 1 -0.41 45 46
SOS1 0.017 0.026 -10000 0 -10000 0 0
RPS6 0.03 0.007 -10000 0 -10000 0 0
mol:cAMP 0.002 0.009 0.036 5 -0.081 1 6
PTPN11 0.017 0.028 -10000 0 -10000 0 0
IL2RG -0.002 0.077 0.17 1 -0.28 34 35
actin cytoskeleton organization -0.045 0.14 0.34 1 -0.41 37 38
GRB2 0.017 0.027 -10000 0 -10000 0 0
IL2 0.017 0.028 0.17 1 -10000 0 1
PIK3CA 0.013 0.023 -10000 0 -10000 0 0
Rac1/GTP 0.006 0.058 0.31 1 -0.15 37 38
LCK 0.017 0.028 0.17 1 -10000 0 1
BCL2 -0.13 0.29 -10000 0 -0.74 92 92
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.045 0.009 -10000 0 -10000 0 0
Necdin/E2F1 -0.085 0.12 -10000 0 -0.2 282 282
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.064 0.034 -10000 0 -0.16 3 3
NGF (dimer)/p75(NTR)/BEX1 -0.01 0.087 -10000 0 -0.17 127 127
NT-4/5 (dimer)/p75(NTR) 0.023 0.004 -10000 0 -10000 0 0
IKBKB 0.029 0.008 -10000 0 -10000 0 0
AKT1 0.017 0.1 0.18 92 -10000 0 92
IKBKG 0.03 0.007 -10000 0 -10000 0 0
BDNF 0.031 0.005 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.058 0.019 -10000 0 -10000 0 0
FURIN 0.028 0.03 -10000 0 -0.28 5 5
proBDNF (dimer)/p75(NTR)/Sortilin 0.06 0.016 -10000 0 -10000 0 0
LINGO1 0.03 0.006 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.068 0.046 -10000 0 -0.18 47 47
proBDNF (dimer) 0.031 0.005 -10000 0 -10000 0 0
NTRK1 0.031 0.005 -10000 0 -10000 0 0
RTN4R 0.03 0.007 -10000 0 -10000 0 0
neuron apoptosis -0.031 0.13 0.3 3 -0.54 18 21
IRAK1 0.03 0.007 -10000 0 -10000 0 0
SHC1 -0.023 0.01 0.17 1 -10000 0 1
ARHGDIA -0.034 0.13 -10000 0 -0.28 115 115
RhoA/GTP 0.023 0.009 -10000 0 -0.19 1 1
Gamma Secretase 0.049 0.084 -10000 0 -0.17 56 56
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.052 0.034 -10000 0 -0.16 10 10
MAGEH1 0.025 0.044 -10000 0 -0.28 11 11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.063 0.11 -10000 0 -0.16 297 297
Mammalian IAPs/DIABLO 0.004 0.064 -10000 0 -0.16 61 61
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.029 0.02 -10000 0 -0.28 2 2
APP 0.027 0.035 -10000 0 -0.28 7 7
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.03 0.008 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.001 0.076 0.17 2 -0.15 112 114
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.005 0.054 0.22 10 -10000 0 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.028 0.047 -10000 0 -0.19 2 2
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.04 0.01 -10000 0 -10000 0 0
NCSTN 0.031 0.006 -10000 0 -10000 0 0
mol:GTP 0.04 0.01 -10000 0 -10000 0 0
PSENEN 0.018 0.056 -10000 0 -0.28 18 18
mol:ceramide -0.026 0.035 0.18 13 -0.16 2 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.026 0.048 -10000 0 -0.23 3 3
p75(NTR)/beta APP 0.041 0.03 -10000 0 -0.2 7 7
BEX1 -0.043 0.13 -10000 0 -0.28 127 127
mol:GDP -0.012 0.002 -10000 0 -10000 0 0
NGF (dimer) -0.012 0.093 -10000 0 -0.16 145 145
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.02 0.1 -10000 0 -0.17 112 112
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
RAC1/GTP 0.034 0.013 -10000 0 -10000 0 0
MYD88 0.031 0.014 -10000 0 -0.28 1 1
CHUK 0.03 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.04 0.01 -10000 0 -10000 0 0
RHOB 0.017 0.064 -10000 0 -0.28 24 24
RHOA 0.031 0.014 -10000 0 -0.28 1 1
MAGE-G1/E2F1 0.04 0.019 -10000 0 -0.2 1 1
NT3 (dimer) 0.025 0.013 -10000 0 -10000 0 0
TP53 -0.057 0.061 0.32 3 -10000 0 3
PRDM4 -0.028 0.031 0.18 11 -10000 0 11
BDNF (dimer) -0.003 0.1 -10000 0 -0.17 142 142
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
SORT1 0.031 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.058 0.032 -10000 0 -0.16 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.056 0.019 -10000 0 -10000 0 0
RHOC 0.031 0.014 -10000 0 -0.28 1 1
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.04 0.064 0.24 7 -0.24 7 14
DIABLO 0.017 0.016 -10000 0 -10000 0 0
SMPD2 -0.026 0.035 0.18 13 -0.16 2 15
APH1B 0.005 0.086 -10000 0 -0.28 46 46
APH1A 0.03 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.009 -10000 0 -10000 0 0
PSEN1 0.031 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.044 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.036 0.02 -10000 0 -10000 0 0
MAPK8 -0.035 0.058 0.24 7 -0.24 7 14
MAPK9 -0.036 0.056 0.24 6 -0.24 5 11
APAF1 0.03 0.006 -10000 0 -10000 0 0
NTF3 0.025 0.013 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.14 0.16 -10000 0 -0.28 305 305
RAC1/GDP 0.022 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.05 -10000 0 -0.16 23 23
p75 CTF/Sortilin/TRAF6/NRIF 0.055 0.041 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.039 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.081 0.039 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.074 0.026 -10000 0 -10000 0 0
PRKACB 0.03 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.036 0.02 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.037 0.13 -10000 0 -0.28 118 118
BIRC2 0.026 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.055 0.071 0.18 8 -0.24 17 25
BAD -0.04 0.063 0.23 6 -0.28 6 12
RIPK2 0.022 0.015 -10000 0 -10000 0 0
NGFR 0.031 0.006 -10000 0 -10000 0 0
CYCS -0.028 0.049 0.18 26 -10000 0 26
ADAM17 0.025 0.013 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.038 0.031 -10000 0 -10000 0 0
BCL2L11 -0.04 0.063 0.23 6 -0.28 6 12
BDNF (dimer)/p75(NTR) 0.045 0.01 -10000 0 -10000 0 0
PI3K 0.02 0.058 -10000 0 -0.16 37 37
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.052 0.026 -10000 0 -0.16 1 1
NDNL2 0.029 0.015 -10000 0 -0.28 1 1
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
PRKCI 0.013 0.016 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.023 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.055 0.023 -10000 0 -0.16 2 2
TRAF6 0.031 0.005 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
PRKCZ 0.03 0.006 -10000 0 -10000 0 0
PLG 0.024 0.04 -10000 0 -0.28 9 9
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.018 0.021 0.14 6 -10000 0 6
SQSTM1 0.03 0.006 -10000 0 -10000 0 0
NGFRAP1 0.03 0.019 -10000 0 -0.28 2 2
CASP3 -0.041 0.068 0.22 6 -0.3 13 19
E2F1 0.029 0.008 -10000 0 -10000 0 0
CASP9 0.031 0.005 -10000 0 -10000 0 0
IKK complex 0.071 0.063 -10000 0 -0.24 3 3
NGF (dimer)/TRKA 0.023 0.004 -10000 0 -10000 0 0
MMP7 -0.052 0.13 -10000 0 -0.28 140 140
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.065 0.031 -10000 0 -10000 0 0
MMP3 0.03 0.008 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.045 0.053 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.065 0.14 0.24 1 -0.42 42 43
BAG4 0.028 0.01 -10000 0 -10000 0 0
BAD -0.034 0.048 0.19 1 -0.16 30 31
NFKBIA 0.022 0.051 -10000 0 -0.28 15 15
BIRC3 -0.037 0.13 -10000 0 -0.28 118 118
BAX -0.032 0.05 0.18 4 -0.16 29 33
EnzymeConsortium:3.1.4.12 -0.017 0.033 0.068 1 -0.094 40 41
IKBKB -0.063 0.14 0.22 3 -0.42 38 41
MAP2K2 -0.071 0.065 0.16 1 -0.2 36 37
MAP2K1 -0.044 0.048 -10000 0 -0.19 9 9
SMPD1 -0.021 0.04 -10000 0 -0.14 29 29
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.059 0.14 0.23 4 -0.42 38 42
MAP2K4 -0.038 0.045 -10000 0 -0.19 10 10
protein ubiquitination -0.066 0.14 0.22 1 -0.42 39 40
EnzymeConsortium:2.7.1.37 -0.064 0.054 -10000 0 -0.21 13 13
response to UV -0.001 0 -10000 0 -0.002 5 5
RAF1 -0.04 0.048 0.15 5 -0.19 13 18
CRADD 0.03 0.005 -10000 0 -10000 0 0
mol:ceramide -0.026 0.049 -10000 0 -0.15 38 38
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.037 -10000 0 -0.17 17 17
MADD 0.031 0.004 -10000 0 -10000 0 0
MAP3K1 -0.032 0.046 -10000 0 -0.17 25 25
TRADD 0.026 0.028 -10000 0 -0.28 4 4
RELA/p50 0.03 0.019 -10000 0 -0.28 2 2
MAPK3 -0.068 0.062 -10000 0 -0.22 30 30
MAPK1 -0.064 0.063 -10000 0 -0.24 23 23
p50/RELA/I-kappa-B-alpha 0.038 0.044 -10000 0 -0.2 17 17
FADD -0.064 0.14 0.24 4 -0.43 39 43
KSR1 -0.033 0.049 0.16 4 -0.17 24 28
MAPK8 -0.045 0.043 0.22 1 -0.19 7 8
TRAF2 0.03 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.068 0.14 0.22 1 -0.42 38 39
TNF R/SODD 0.029 0.047 -10000 0 -0.2 19 19
TNF 0.03 0.005 -10000 0 -10000 0 0
CYCS -0.022 0.056 0.14 7 -0.16 18 25
IKBKG -0.066 0.14 0.24 4 -0.41 38 42
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.059 0.15 -10000 0 -0.43 44 44
RELA 0.03 0.019 -10000 0 -0.28 2 2
RIPK1 0.03 0.008 -10000 0 -10000 0 0
AIFM1 -0.01 0.061 0.13 19 -0.16 18 37
TNF/TNF R/SODD 0.042 0.049 -10000 0 -0.18 19 19
TNFRSF1A 0.015 0.063 -10000 0 -0.28 23 23
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.074 -10000 0 -0.67 5 5
NSMAF -0.058 0.14 0.24 7 -0.43 39 46
response to hydrogen peroxide -0.001 0 -10000 0 -0.002 5 5
BCL2 -0.005 0.097 -10000 0 -0.28 60 60
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.037 0.11 -10000 0 -0.32 64 64
KLHL20 -0.055 0.083 0.51 1 -0.27 17 18
CYFIP2 0.026 0.038 -10000 0 -0.28 8 8
Rac1/GDP -0.042 0.08 0.24 5 -0.26 16 21
ENAH -0.038 0.11 -10000 0 -0.32 66 66
AP1M1 0.028 0.01 -10000 0 -10000 0 0
RAP1B 0.03 0.015 -10000 0 -0.28 1 1
RAP1A 0.031 0.004 -10000 0 -10000 0 0
CTNNB1 0.031 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.054 0.051 0.12 25 -0.26 1 26
ABI1/Sra1/Nap1 -0.051 0.047 -10000 0 -0.17 33 33
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.058 0.054 -10000 0 -0.17 13 13
RAPGEF1 -0.043 0.1 0.24 4 -0.31 55 59
CTNND1 0.031 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.02 0.12 -10000 0 -0.32 68 68
CRK -0.043 0.1 -10000 0 -0.32 61 61
E-cadherin/gamma catenin/alpha catenin 0.045 0.054 -10000 0 -0.2 21 21
alphaE/beta7 Integrin 0.042 0.026 -10000 0 -0.2 5 5
IQGAP1 0.029 0.02 -10000 0 -0.28 2 2
NCKAP1 0.031 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.045 0.041 -10000 0 -0.16 13 13
DLG1 -0.026 0.1 -10000 0 -0.32 54 54
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.04 0.04 -10000 0 -0.17 7 7
MLLT4 0.022 0.046 -10000 0 -0.28 12 12
ARF6/GTP/NME1/Tiam1 0.051 0.026 -10000 0 -0.16 1 1
PI3K -0.05 0.05 -10000 0 -0.21 7 7
ARF6 0.031 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.031 0.053 -10000 0 -0.23 20 20
TIAM1 0.03 0.014 -10000 0 -0.28 1 1
E-cadherin(dimer)/Ca2+ 0.055 0.047 -10000 0 -0.16 10 10
AKT1 -0.006 0.07 0.14 58 -0.16 1 59
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
CDH1 0.023 0.04 -10000 0 -0.28 9 9
RhoA/GDP -0.04 0.079 0.24 4 -0.26 16 20
actin cytoskeleton organization -0.041 0.062 0.44 1 -0.22 7 8
CDC42/GDP -0.04 0.08 0.24 5 -0.26 15 20
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.063 -10000 0 -0.2 37 37
ITGB7 0.028 0.03 -10000 0 -0.28 5 5
RAC1 0.03 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.06 0.051 -10000 0 -0.17 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin 0.042 0.037 -10000 0 -0.15 10 10
mol:GDP -0.039 0.086 0.24 5 -0.28 18 23
CDC42/GTP/IQGAP1 0.04 0.016 -10000 0 -0.17 2 2
JUP 0.022 0.049 -10000 0 -0.28 14 14
p120 catenin/RhoA/GDP -0.041 0.083 0.25 4 -0.26 14 18
RAC1/GTP/IQGAP1 0.038 0.017 -10000 0 -0.17 2 2
PIP5K1C/AP1M1 0.039 0.018 -10000 0 -10000 0 0
RHOA 0.031 0.014 -10000 0 -0.28 1 1
CDC42 0.031 0.004 -10000 0 -10000 0 0
CTNNA1 0.03 0.014 -10000 0 -0.28 1 1
positive regulation of S phase of mitotic cell cycle -0.047 0.065 0.12 1 -0.15 143 144
NME1 0.029 0.009 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.038 0.11 -10000 0 -0.32 68 68
regulation of cell-cell adhesion -0.05 0.041 0.087 22 -0.2 2 24
WASF2 -0.038 0.04 0.094 4 -0.11 42 46
Rap1/GTP -0.05 0.059 0.16 26 -0.29 1 27
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.059 0.073 -10000 0 -0.18 25 25
CCND1 -0.057 0.079 0.14 1 -0.18 146 147
VAV2 -0.034 0.16 -10000 0 -0.67 22 22
RAP1/GDP -0.042 0.067 0.26 3 -0.27 2 5
adherens junction assembly -0.037 0.11 -10000 0 -0.31 68 68
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.031 0.005 -10000 0 -10000 0 0
PIP5K1C 0.029 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.011 0.069 -10000 0 -0.18 24 24
E-cadherin/beta catenin -0.008 0.053 -10000 0 -0.18 42 42
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.036 0.11 -10000 0 -0.33 62 62
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.086 0.12 -10000 0 -0.39 35 35
E-cadherin/beta catenin/alpha catenin 0.051 0.038 -10000 0 -0.18 10 10
ITGAE 0.03 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.021 0.12 -10000 0 -0.33 68 68
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.03 0.15 -10000 0 -0.35 58 58
MAP3K8 0.019 0.026 -10000 0 -10000 0 0
FOS -0.013 0.12 0.48 8 -0.37 22 30
PRKCA 0.016 0.039 0.12 1 -0.28 4 5
PTPN7 0.018 0.035 0.16 7 -10000 0 7
HRAS 0.019 0.025 -10000 0 -10000 0 0
PRKCB -0.002 0.011 0.074 8 -0.023 2 10
NRAS 0.013 0.02 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.037 0.16 5 -10000 0 5
MAPK3 -0.015 0.15 0.34 8 -0.42 55 63
MAP2K1 0.014 0.07 0.27 9 -0.29 11 20
ELK1 0.016 0.033 -10000 0 -10000 0 0
BRAF 0.011 0.046 0.2 8 -0.25 8 16
mol:GTP -0.001 0.003 0.012 8 -0.005 106 114
MAPK1 0.004 0.12 0.34 8 -0.41 30 38
RAF1 0.011 0.051 0.2 8 -0.29 8 16
KRAS 0.017 0.023 -10000 0 -10000 0 0
LPA4-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
ADCY4 -0.023 0.011 0.18 1 -10000 0 1
ADCY5 -0.023 0.013 0.18 2 -10000 0 2
ADCY6 -0.024 0.005 -10000 0 -10000 0 0
ADCY7 -0.023 0.007 -10000 0 -10000 0 0
ADCY1 -0.024 0.005 -10000 0 -10000 0 0
ADCY2 -0.022 0.008 -10000 0 -10000 0 0
ADCY3 -0.024 0.01 0.18 1 -10000 0 1
ADCY8 -0.051 0.074 0.18 8 -0.17 148 156
PRKCE -0.015 0.003 -10000 0 -10000 0 0
ADCY9 -0.035 0.041 -10000 0 -0.17 47 47
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.002 0.093 0.2 44 -0.25 1 45
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.002 0.13 0.32 10 -0.38 25 35
FYN -0.038 0.15 0.32 10 -0.45 36 46
LAT/GRAP2/SLP76 -0.031 0.13 0.28 6 -0.41 26 32
IKBKB 0.029 0.008 -10000 0 -10000 0 0
AKT1 -0.032 0.12 0.28 6 -0.34 38 44
B2M 0.024 0.035 -10000 0 -0.29 5 5
IKBKG -0.021 0.044 0.12 9 -0.13 14 23
MAP3K8 0.031 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.027 0.014 0.081 1 -0.074 3 4
integrin-mediated signaling pathway 0.039 0.021 -10000 0 -0.17 5 5
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.042 0.15 0.33 6 -0.46 40 46
TRPV6 0.078 0.33 1.3 37 -10000 0 37
CD28 0.028 0.015 -10000 0 -10000 0 0
SHC1 -0.027 0.13 0.3 9 -0.45 27 36
receptor internalization -0.022 0.12 0.3 4 -0.4 30 34
PRF1 -0.053 0.25 0.81 1 -1 31 32
KRAS 0.026 0.012 -10000 0 -10000 0 0
GRB2 0.03 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.025 0.1 0.25 9 -0.3 31 40
LAT -0.03 0.13 0.3 6 -0.44 28 34
EntrezGene:6955 -0.001 0.005 0.072 1 -10000 0 1
CD3D -0.019 0.12 -10000 0 -0.29 85 85
CD3E 0.015 0.05 -10000 0 -0.29 11 11
CD3G 0.024 0.023 -10000 0 -0.3 1 1
RASGRP2 -0.003 0.016 -10000 0 -0.14 2 2
RASGRP1 -0.054 0.14 0.3 5 -0.4 47 52
HLA-A 0.015 0.052 -10000 0 -0.29 12 12
RASSF5 0.028 0.03 -10000 0 -0.28 5 5
RAP1A/GTP/RAPL 0.04 0.021 -10000 0 -0.17 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.002 0.053 0.19 7 -0.13 15 22
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.038 0.054 -10000 0 -0.18 37 37
PRKCA -0.03 0.073 0.23 8 -0.23 17 25
GRAP2 0.029 0.009 -10000 0 -10000 0 0
mol:IP3 -0.038 0.093 -10000 0 -0.3 29 29
EntrezGene:6957 -0.001 0.006 0.079 1 -10000 0 1
TCR/CD3/MHC I/CD8 -0.028 0.12 0.53 1 -0.37 36 37
ORAI1 -0.095 0.29 -10000 0 -1.2 37 37
CSK -0.028 0.13 0.35 5 -0.46 25 30
B7 family/CD28 -0.002 0.14 0.66 1 -0.45 29 30
CHUK 0.03 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.027 0.14 0.3 6 -0.47 30 36
PTPN6 -0.025 0.13 0.31 7 -0.45 27 34
VAV1 -0.027 0.13 0.32 6 -0.45 27 33
Monovalent TCR/CD3 -0.019 0.092 0.38 1 -0.21 84 85
CBL 0.031 0.005 -10000 0 -10000 0 0
LCK -0.026 0.14 0.31 9 -0.47 28 37
PAG1 -0.024 0.13 0.31 7 -0.45 26 33
RAP1A 0.031 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.026 0.14 0.3 7 -0.47 30 37
CD80 0.027 0.016 -10000 0 -10000 0 0
CD86 0.026 0.016 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.036 0.07 -10000 0 -0.22 36 36
HRAS 0.03 0.007 -10000 0 -10000 0 0
GO:0035030 -0.043 0.11 0.32 3 -0.38 30 33
CD8A 0.027 0.019 -10000 0 -10000 0 0
CD8B 0.021 0.025 -10000 0 -10000 0 0
PTPRC 0.002 0.084 -10000 0 -0.29 43 43
PDK1/PKC theta -0.042 0.13 0.31 8 -0.42 31 39
CSK/PAG1 -0.028 0.13 0.32 7 -0.45 25 32
SOS1 0.03 0.007 -10000 0 -10000 0 0
peptide-MHC class I 0.032 0.052 0.18 1 -0.23 16 17
GRAP2/SLP76 -0.004 0.15 0.33 5 -0.44 30 35
STIM1 -0.041 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.072 0.19 20 -0.18 8 28
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.023 0.12 0.3 4 -0.42 30 34
mol:DAG -0.047 0.074 -10000 0 -0.27 33 33
RAP1A/GDP 0.003 0.027 0.093 7 -0.065 5 12
PLCG1 0.03 0.007 -10000 0 -10000 0 0
CD247 0.026 0.019 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.049 0.24 0.81 1 -0.97 31 32
RAP1A/GTP -0.003 0.008 -10000 0 -0.057 2 2
mol:PI-3-4-5-P3 -0.034 0.13 0.3 7 -0.39 39 46
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.041 0.12 0.21 2 -0.4 25 27
NRAS 0.018 0.016 -10000 0 -10000 0 0
ZAP70 0.031 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.039 0.12 0.26 7 -0.4 27 34
MALT1 0.028 0.01 -10000 0 -10000 0 0
TRAF6 0.031 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.042 0.024 0.19 1 -10000 0 1
CARD11 0.03 0.008 -10000 0 -10000 0 0
PRKCB -0.038 0.051 -10000 0 -0.19 36 36
PRKCE -0.03 0.071 0.23 7 -0.23 17 24
PRKCQ -0.041 0.14 0.31 8 -0.44 36 44
LCP2 0.017 0.064 -10000 0 -0.28 24 24
BCL10 0.031 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.027 0.1 0.26 7 -0.3 34 41
IKK complex -0.006 0.043 0.16 14 -0.12 2 16
RAS family/GDP -0.004 0.009 -10000 0 -10000 0 0
MAP3K14 -0.027 0.08 0.2 9 -0.24 26 35
PDPK1 -0.033 0.11 0.27 8 -0.33 37 45
TCR/CD3/MHC I/CD8/Fyn -0.034 0.15 0.48 1 -0.5 33 34
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.01 0.14 -10000 0 -0.44 45 45
HDAC1 0.04 0.022 -10000 0 -10000 0 0
AES 0.001 0.094 -10000 0 -0.28 54 54
FBXW11 0.031 0.006 -10000 0 -10000 0 0
DTX1 0.031 0.004 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.018 -10000 0 -10000 0 0
TLE1 0.032 0.011 -10000 0 -10000 0 0
AP1 -0.037 0.099 0.18 4 -0.21 116 120
NCSTN 0.03 0.006 -10000 0 -10000 0 0
ADAM10 0.031 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.12 0.21 -10000 0 -0.57 66 66
NICD/RBPSUH 0.005 0.14 -10000 0 -0.44 44 44
WIF1 0.03 0.006 -10000 0 -10000 0 0
NOTCH1 -0.011 0.13 -10000 0 -0.47 41 41
PSENEN 0.018 0.056 -10000 0 -0.28 18 18
KREMEN2 0.03 0.006 -10000 0 -10000 0 0
DKK1 0.03 0.006 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.002 0.068 -10000 0 -0.32 1 1
APH1B 0.005 0.086 -10000 0 -0.28 46 46
APH1A 0.03 0.007 -10000 0 -10000 0 0
AXIN1 -0.012 0.1 -10000 0 -0.44 21 21
CtBP/CBP/TCF1/TLE1/AES 0.01 0.11 0.26 20 -0.29 13 33
PSEN1 0.031 0.005 -10000 0 -10000 0 0
FOS -0.03 0.12 -10000 0 -0.28 107 107
JUN 0.029 0.02 -10000 0 -0.28 2 2
MAP3K7 0.035 0.012 -10000 0 -10000 0 0
CTNNB1 -0.008 0.061 0.22 1 -0.33 1 2
MAPK3 0.005 0.087 -10000 0 -0.28 47 47
DKK2/LRP6/Kremen 2 0.049 0.027 -10000 0 -10000 0 0
HNF1A 0.035 0.01 -10000 0 -10000 0 0
CTBP1 0.033 0.012 -10000 0 -10000 0 0
MYC -0.16 0.37 -10000 0 -1.2 60 60
NKD1 0.031 0.009 -10000 0 -10000 0 0
FZD1 0.03 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.005 0.14 -10000 0 -0.44 45 45
apoptosis -0.037 0.099 0.18 4 -0.21 116 120
Delta 1/NOTCHprecursor 0.004 0.14 -10000 0 -0.44 45 45
DLL1 0.029 0.009 -10000 0 -10000 0 0
PPARD -0.017 0.1 -10000 0 -0.99 5 5
Gamma Secretase 0.047 0.083 -10000 0 -0.17 56 56
APC -0.017 0.12 -10000 0 -0.45 29 29
DVL1 0 0.056 -10000 0 -0.37 5 5
CSNK2A1 0.011 0.028 -10000 0 -10000 0 0
MAP3K7IP1 0.005 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.05 0.027 -10000 0 -10000 0 0
LRP6 0.026 0.012 -10000 0 -10000 0 0
CSNK1A1 0.011 0.029 -10000 0 -10000 0 0
NLK 0.019 0.019 -10000 0 -10000 0 0
CCND1 -0.3 0.52 -10000 0 -1.2 143 143
WNT1 0.031 0.003 -10000 0 -10000 0 0
Axin1/APC/beta catenin -0.019 0.1 -10000 0 -0.42 17 17
DKK2 0.029 0.008 -10000 0 -10000 0 0
NOTCH1 precursor/DVL1 -0.007 0.13 -10000 0 -0.45 39 39
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.032 0.02 -10000 0 -0.28 2 2
NOTCH/Deltex homolog 1 0.013 0.14 -10000 0 -0.44 45 45
PPP2R5D 0.013 0.046 -10000 0 -0.36 6 6
MAPK1 0.029 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.061 0.036 -10000 0 -10000 0 0
RBPJ 0.031 0.006 -10000 0 -10000 0 0
CREBBP 0.012 0.033 -10000 0 -0.28 3 3
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.049 0.04 -10000 0 -0.18 11 11
fibroblast growth factor receptor signaling pathway 0.048 0.04 -10000 0 -0.18 11 11
LAMA1 0.025 0.013 -10000 0 -10000 0 0
PRNP 0.025 0.04 -10000 0 -0.28 9 9
GPC1/SLIT2 0.027 0.06 -10000 0 -0.2 33 33
SMAD2 -0.041 0.03 0.17 6 -10000 0 6
GPC1/PrPc/Cu2+ 0.036 0.029 -10000 0 -0.17 9 9
GPC1/Laminin alpha1 0.036 0.02 -10000 0 -10000 0 0
TDGF1 0.031 0.003 -10000 0 -10000 0 0
CRIPTO/GPC1 0.045 0.009 -10000 0 -10000 0 0
APP/GPC1 0.041 0.03 -10000 0 -0.2 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.034 0.011 -10000 0 -10000 0 0
FLT1 0.03 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.055 0.038 -10000 0 -0.18 12 12
SERPINC1 0.031 0.005 -10000 0 -10000 0 0
FYN -0.047 0.044 -10000 0 -0.18 53 53
FGR -0.035 0.009 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.025 0.075 0.24 8 -0.27 10 18
SLIT2 0.01 0.074 -10000 0 -0.28 33 33
GPC1/NRG 0.039 0.017 -10000 0 -10000 0 0
NRG1 0.027 0.011 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.054 0.024 -10000 0 -10000 0 0
LYN -0.037 0.026 -10000 0 -0.18 14 14
mol:Spermine -0.015 0.003 -10000 0 -10000 0 0
cell growth 0.048 0.04 -10000 0 -0.18 11 11
BMP signaling pathway -0.031 0.005 -10000 0 -10000 0 0
SRC -0.034 0.011 -10000 0 -10000 0 0
TGFBR1 0.031 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.16 0.15 -10000 0 -0.28 345 345
GPC1 0.031 0.005 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.031 0.005 -10000 0 -10000 0 0
VEGFA 0.029 0.009 -10000 0 -10000 0 0
BLK -0.03 0.015 -10000 0 -10000 0 0
HCK -0.033 0.012 -10000 0 -10000 0 0
FGF2 0.03 0.007 -10000 0 -10000 0 0
FGFR1 0.022 0.044 -10000 0 -0.28 11 11
VEGFR1 homodimer 0.03 0.007 -10000 0 -10000 0 0
TGFBR2 0.024 0.046 -10000 0 -0.28 12 12
cell death 0.041 0.03 -10000 0 -0.2 7 7
ATIII/GPC1 0.044 0.01 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.11 0.12 -10000 0 -0.2 343 343
LCK -0.034 0.01 -10000 0 -10000 0 0
neuron differentiation 0.039 0.017 -10000 0 -10000 0 0
PrPc/Cu2+ 0.018 0.027 -10000 0 -0.19 9 9
APP 0.027 0.035 -10000 0 -0.28 7 7
TGFBR2 (dimer) 0.024 0.046 -10000 0 -0.28 12 12
Glucocorticoid receptor regulatory network

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
PCK2 -0.058 0.079 -10000 0 -0.42 11 11
SMARCC2 0.03 0.006 -10000 0 -10000 0 0
SMARCC1 0.031 0.004 -10000 0 -10000 0 0
TBX21 0.043 0.083 0.37 5 -10000 0 5
SUMO2 0.008 0.032 -10000 0 -10000 0 0
STAT1 (dimer) 0.008 0.046 0.27 3 -0.18 21 24
FKBP4 0.027 0.011 -10000 0 -10000 0 0
FKBP5 -0.013 0.11 -10000 0 -0.28 78 78
GR alpha/HSP90/FKBP51/HSP90 -0.056 0.11 -10000 0 -0.28 30 30
PRL 0.048 0.067 0.72 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.12 0.14 -10000 0 -0.48 8 8
RELA 0.03 0.092 0.28 13 -0.22 23 36
FGG -0.13 0.13 -10000 0 -0.44 18 18
GR beta/TIF2 -0.074 0.072 -10000 0 -0.29 5 5
IFNG 0.11 0.18 0.6 36 -10000 0 36
apoptosis -0.18 0.23 0.58 3 -0.64 36 39
CREB1 0.033 0.004 -10000 0 -10000 0 0
histone acetylation 0.042 0.077 -10000 0 -0.35 5 5
BGLAP 0.059 0.072 0.6 2 -10000 0 2
GR/PKAc -0.013 0.092 -10000 0 -0.24 2 2
NF kappa B1 p50/RelA 0.04 0.16 0.32 65 -0.34 48 113
SMARCD1 0.031 0.003 -10000 0 -10000 0 0
MDM2 -0.035 0.043 -10000 0 -0.25 2 2
GATA3 0.031 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.007 -10000 0 -10000 0 0
CSF2 0.017 0.054 -10000 0 -0.38 1 1
GSK3B 0.008 0.032 -10000 0 -10000 0 0
NR1I3 -0.16 0.2 0.71 1 -0.67 9 10
CSN2 -0.12 0.12 -10000 0 -0.43 10 10
BRG1/BAF155/BAF170/BAF60A 0.068 0.035 -10000 0 -0.17 2 2
NFATC1 0.03 0.01 -10000 0 -10000 0 0
POU2F1 0.032 0.009 0.21 1 -10000 0 1
CDKN1A -0.09 0.31 -10000 0 -1.2 33 33
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.008 0.11 1 -10000 0 1
SFN 0.03 0.008 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.038 0.11 -10000 0 -0.26 28 28
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.32 0.36 0.68 3 -0.75 222 225
JUN 0.099 0.17 0.54 38 -10000 0 38
IL4 0.055 0.062 -10000 0 -10000 0 0
CDK5R1 0.008 0.03 -10000 0 -10000 0 0
PRKACA 0.027 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.076 0.085 -10000 0 -0.27 27 27
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.041 0.11 -10000 0 -0.26 28 28
cortisol/GR alpha (monomer) -0.15 0.16 -10000 0 -0.52 11 11
NCOA2 0.029 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.032 0.14 0.29 33 -0.29 72 105
AP-1/NFAT1-c-4 0.095 0.22 0.62 35 -10000 0 35
AFP 0.069 0.12 -10000 0 -10000 0 0
SUV420H1 0.031 0.004 -10000 0 -10000 0 0
IRF1 -0.04 0.18 0.49 1 -0.75 25 26
TP53 -0.035 0.16 -10000 0 -0.52 31 31
PPP5C 0.03 0.007 -10000 0 -10000 0 0
KRT17 0.098 0.2 0.63 39 -0.5 1 40
KRT14 0.068 0.12 0.67 16 -10000 0 16
TBP 0.031 0.014 0.21 2 -10000 0 2
CREBBP 0.02 0.051 -10000 0 -0.24 20 20
HDAC1 0.029 0.008 -10000 0 -10000 0 0
HDAC2 0.029 0.008 -10000 0 -10000 0 0
AP-1 0.095 0.22 0.62 35 -10000 0 35
MAPK14 0.008 0.033 -10000 0 -10000 0 0
MAPK10 -0.002 0.06 0.14 1 -0.28 17 18
MAPK11 0.006 0.029 -10000 0 -10000 0 0
KRT5 0.16 0.27 0.67 105 -10000 0 105
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.029 0.023 -10000 0 -0.28 3 3
STAT1 0.008 0.046 0.27 3 -0.18 21 24
CGA 0.06 0.063 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.084 0.11 -10000 0 -0.42 28 28
MAPK3 -0.015 0.087 0.14 1 -0.29 46 47
MAPK1 0.007 0.032 -10000 0 -10000 0 0
ICAM1 0.06 0.24 0.67 37 -0.85 17 54
NFKB1 0.028 0.1 0.28 13 -0.22 51 64
MAPK8 0.085 0.15 0.43 36 -10000 0 36
MAPK9 0.008 0.033 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.19 0.24 0.58 3 -0.65 44 47
BAX -0.041 0.12 -10000 0 -10000 0 0
POMC 0.008 0.13 0.58 2 -10000 0 2
EP300 0.021 0.045 -10000 0 -0.23 16 16
cortisol/GR alpha (dimer)/p53 -0.16 0.15 -10000 0 -0.51 18 18
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.054 0.23 13 -0.22 1 14
SGK1 -0.033 0.092 -10000 0 -0.3 40 40
IL13 0.078 0.13 0.52 8 -10000 0 8
IL6 0.002 0.28 0.47 13 -0.86 44 57
PRKACG 0.031 0.006 -10000 0 -10000 0 0
IL5 0.067 0.12 -10000 0 -10000 0 0
IL2 0.081 0.18 0.55 16 -0.52 3 19
CDK5 0.009 0.028 -10000 0 -10000 0 0
PRKACB 0.03 0.006 -10000 0 -10000 0 0
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
IL8 0.08 0.2 0.64 44 -0.46 3 47
CDK5R1/CDK5 0.013 0.039 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.065 0.14 0.4 13 -0.3 22 35
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.085 0.15 -10000 0 -0.44 11 11
SMARCA4 0.027 0.021 -10000 0 -0.28 2 2
chromatin remodeling -0.07 0.087 -10000 0 -0.36 4 4
NF kappa B1 p50/RelA/Cbp 0.047 0.15 0.42 11 -0.3 35 46
JUN (dimer) 0.098 0.17 0.54 38 -10000 0 38
YWHAH 0.029 0.008 -10000 0 -10000 0 0
VIPR1 0.044 0.085 0.41 4 -10000 0 4
NR3C1 -0.11 0.095 -10000 0 -0.37 8 8
NR4A1 -0.079 0.15 -10000 0 -0.28 196 196
TIF2/SUV420H1 0.042 0.014 -10000 0 -10000 0 0
MAPKKK cascade -0.18 0.23 0.58 3 -0.64 36 39
cortisol/GR alpha (dimer)/Src-1 -0.13 0.14 -10000 0 -0.48 6 6
PBX1 0.026 0.045 0.21 1 -0.28 11 12
POU1F1 0.032 0.009 0.21 1 -10000 0 1
SELE 0.06 0.13 0.46 6 -10000 0 6
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.071 0.087 -10000 0 -0.36 4 4
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.085 0.15 -10000 0 -0.44 11 11
mol:cortisol -0.078 0.079 -10000 0 -0.27 6 6
MMP1 0.14 0.25 0.64 102 -0.5 5 107
Syndecan-3-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
CTTN 0.03 0.006 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.011 0.12 -10000 0 -0.45 27 27
Syndecan-3/Neurocan 0 0.12 -10000 0 -0.48 28 28
POMC 0.031 0.005 -10000 0 -10000 0 0
EGFR 0.002 0.091 -10000 0 -0.28 51 51
Syndecan-3/EGFR -0.003 0.12 -10000 0 -0.5 29 29
AGRP 0.028 0.009 -10000 0 -10000 0 0
NCSTN 0.031 0.006 -10000 0 -10000 0 0
PSENEN 0.018 0.056 -10000 0 -0.28 18 18
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.005 0.086 -10000 0 -0.28 46 46
APH1A 0.03 0.007 -10000 0 -10000 0 0
NCAN 0.029 0.009 -10000 0 -10000 0 0
long-term memory 0 0.13 -10000 0 -0.47 29 29
Syndecan-3/IL8 -0.002 0.12 -10000 0 -0.48 29 29
PSEN1 0.031 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.043 0.014 -10000 0 -10000 0 0
FYN -0.002 0.095 -10000 0 -0.28 57 57
limb bud formation -0.022 0.11 -10000 0 -0.51 28 28
MC4R 0 0 -10000 0 -10000 0 0
SRC 0.03 0.007 -10000 0 -10000 0 0
PTN 0.014 0.059 -10000 0 -0.28 20 20
FGFR/FGF/Syndecan-3 -0.023 0.11 -10000 0 -0.51 28 28
neuron projection morphogenesis -0.006 0.13 0.26 8 -0.45 25 33
Syndecan-3/AgRP 0 0.12 -10000 0 -0.48 29 29
Syndecan-3/AgRP/MC4R 0 0.11 -10000 0 -0.47 29 29
Fyn/Cortactin 0.018 0.074 -10000 0 -0.2 54 54
SDC3 -0.023 0.12 -10000 0 -0.52 28 28
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.002 0.11 -10000 0 -0.47 29 29
IL8 0.027 0.011 -10000 0 -10000 0 0
Syndecan-3/Fyn/Cortactin 0.001 0.13 -10000 0 -0.49 29 29
Syndecan-3/CASK -0.023 0.11 -10000 0 -0.48 29 29
alpha-MSH/MC4R 0.023 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.049 0.084 -10000 0 -0.17 56 56
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.03 0.007 -10000 0 -10000 0 0
EGFR 0.002 0.091 -10000 0 -0.28 51 51
EGF/EGFR 0.031 0.063 -10000 0 -0.15 48 48
EGF/EGFR dimer/SHC/GRB2/SOS1 0.058 0.078 -10000 0 -0.17 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.03 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.029 0.008 -10000 0 -10000 0 0
EGF/EGFR dimer/SHC 0.036 0.07 -10000 0 -0.18 49 49
mol:GDP 0.052 0.074 -10000 0 -0.17 43 43
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.028 0.016 -10000 0 -0.28 1 1
GRB2/SOS1 0.043 0.013 -10000 0 -10000 0 0
HRAS/GTP 0.028 0.065 -10000 0 -0.16 43 43
SHC1 0.03 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.047 0.076 -10000 0 -0.17 43 43
FRAP1 -0.047 0.043 0.11 16 -0.16 40 56
EGF/EGFR dimer 0.02 0.072 -10000 0 -0.2 51 51
SOS1 0.03 0.007 -10000 0 -10000 0 0
GRB2 0.03 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.04 0.019 -10000 0 -0.2 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.005 0.12 0.39 21 -0.32 1 22
CRKL -0.006 0.12 0.4 16 -0.29 7 23
HRAS -0.006 0.12 0.39 11 -0.35 7 18
mol:PIP3 0.024 0.13 0.42 17 -0.36 5 22
SPRED1 0.027 0.03 -10000 0 -0.28 5 5
SPRED2 0.031 0.004 -10000 0 -10000 0 0
GAB1 0.004 0.12 0.44 17 -0.32 7 24
FOXO3 0.003 0.13 0.4 18 -0.43 9 27
AKT1 0.01 0.14 0.42 18 -0.45 9 27
BAD 0.003 0.13 0.4 17 -0.43 9 26
megakaryocyte differentiation 0.007 0.12 0.47 16 -0.32 7 23
GSK3B 0.008 0.13 0.41 18 -0.44 8 26
RAF1 -0.009 0.11 0.33 17 -0.31 5 22
SHC1 0.03 0.006 -10000 0 -10000 0 0
STAT3 0.002 0.12 0.44 15 -0.32 7 22
STAT1 0.011 0.23 0.63 17 -0.59 25 42
HRAS/SPRED1 0.007 0.11 0.35 12 -0.31 5 17
cell proliferation 0.004 0.12 0.46 17 -0.32 8 25
PIK3CA 0.021 0.015 -10000 0 -10000 0 0
TEC 0.027 0.011 -10000 0 -10000 0 0
RPS6KB1 0.015 0.14 0.44 19 -0.35 8 27
HRAS/SPRED2 0.008 0.11 0.36 11 -0.31 5 16
LYN/TEC/p62DOK 0.027 0.12 0.4 9 -0.32 8 17
MAPK3 -0.038 0.1 0.31 11 -0.27 20 31
STAP1 0.006 0.12 0.44 17 -0.31 9 26
GRAP2 0.029 0.009 -10000 0 -10000 0 0
JAK2 0.002 0.21 0.6 17 -0.55 20 37
STAT1 (dimer) 0.014 0.23 0.62 18 -0.59 25 43
mol:Gleevec -0.001 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.026 0.14 0.42 12 -0.32 10 22
actin filament polymerization 0.012 0.12 0.45 17 -0.3 9 26
LYN 0.021 0.051 -10000 0 -0.28 15 15
STAP1/STAT5A (dimer) -0.01 0.17 0.49 16 -0.49 19 35
PIK3R1 0 0.091 -10000 0 -0.28 52 52
CBL/CRKL/GRB2 0.012 0.13 0.38 18 -0.3 4 22
PI3K 0.003 0.12 0.43 11 -0.34 11 22
PTEN 0.029 0.02 -10000 0 -0.28 2 2
SCF/KIT/EPO/EPOR 0.033 0.22 0.66 12 -0.67 5 17
MAPK8 0.004 0.13 0.46 17 -0.32 9 26
STAT3 (dimer) 0.002 0.12 0.44 15 -0.32 7 22
positive regulation of transcription -0.03 0.087 0.29 12 -0.23 13 25
mol:GDP 0.002 0.12 0.38 7 -0.33 6 13
PIK3C2B 0.003 0.12 0.45 17 -0.32 8 25
CBL/CRKL -0.002 0.12 0.37 21 -0.31 2 23
FER 0.004 0.12 0.44 16 -0.33 6 22
SH2B3 0.005 0.12 0.44 17 -0.3 8 25
PDPK1 0.017 0.12 0.4 18 -0.39 2 20
SNAI2 0.001 0.13 0.44 16 -0.32 11 27
positive regulation of cell proliferation 0.005 0.2 0.55 19 -0.53 16 35
KITLG 0.028 0.038 0.15 10 -10000 0 10
cell motility 0.005 0.2 0.55 19 -0.53 16 35
PTPN6 0 0.036 -10000 0 -0.13 2 2
EPOR -0.009 0.2 0.76 4 -0.7 19 23
STAT5A (dimer) -0.001 0.18 0.52 18 -0.5 18 36
SOCS1 0.017 0.064 -10000 0 -0.28 24 24
cell migration -0.003 0.12 0.32 6 -0.44 15 21
SOS1 0.03 0.007 -10000 0 -10000 0 0
EPO 0.026 0.03 0.14 2 -10000 0 2
VAV1 0.029 0.008 -10000 0 -10000 0 0
GRB10 0.005 0.12 0.44 17 -0.32 8 25
PTPN11 0.004 0.034 -10000 0 -0.11 2 2
SCF/KIT 0.016 0.13 0.49 17 -0.32 9 26
GO:0007205 -0.002 0.013 -10000 0 -0.1 2 2
MAP2K1 -0.01 0.097 0.32 16 -0.26 3 19
CBL 0.031 0.005 -10000 0 -10000 0 0
KIT 0.008 0.21 0.72 17 -0.66 15 32
MAP2K2 -0.04 0.095 0.32 11 -0.27 7 18
SHC/Grb2/SOS1 0.033 0.13 0.42 13 -0.32 7 20
STAT5A 0 0.18 0.52 18 -0.51 18 36
GRB2 0.03 0.006 -10000 0 -10000 0 0
response to radiation 0.004 0.13 0.43 18 -0.32 11 29
SHC/GRAP2 0.041 0.015 -10000 0 -10000 0 0
PTPRO 0.005 0.12 0.47 16 -0.33 7 23
SH2B2 0.012 0.12 0.45 17 -0.31 9 26
DOK1 0.031 0.014 -10000 0 -0.28 1 1
MATK 0.003 0.12 0.44 15 -0.32 7 22
CREBBP 0.025 0.089 0.36 19 -0.3 6 25
BCL2 -0.14 0.44 0.99 2 -1.1 90 92
EPO signaling 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
BCL2L1 0.007 0.12 0.61 1 -0.46 2 3
CRKL -0.018 0.09 0.27 12 -10000 0 12
mol:DAG -0.025 0.074 0.37 2 -0.28 8 10
HRAS -0.025 0.1 0.27 29 -10000 0 29
MAPK8 -0.012 0.082 0.16 81 -0.19 1 82
RAP1A -0.017 0.093 0.28 14 -10000 0 14
GAB1 -0.017 0.093 0.28 14 -10000 0 14
MAPK14 -0.012 0.082 0.17 74 -0.2 2 76
EPO 0.023 0.03 0.11 1 -0.052 49 50
PLCG1 -0.026 0.075 0.37 2 -0.29 8 10
EPOR/TRPC2/IP3 Receptors 0.02 0.029 -10000 0 -0.052 47 47
RAPGEF1 0.031 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.042 0.049 -10000 0 -0.19 6 6
GAB1/SHC/GRB2/SOS1 -0.03 0.097 0.26 12 -10000 0 12
EPO/EPOR (dimer) 0.03 0.04 -10000 0 -10000 0 0
IRS2 -0.016 0.092 0.28 14 -10000 0 14
STAT1 -0.019 0.077 0.5 2 -0.37 3 5
STAT5B -0.033 0.094 0.46 2 -0.33 6 8
cell proliferation -0.019 0.083 0.16 83 -0.19 1 84
GAB1/SHIP/PIK3R1/SHP2/SHC -0.054 0.078 0.12 27 -0.24 9 36
TEC -0.014 0.087 0.28 11 -10000 0 11
SOCS3 0.026 0.038 -10000 0 -0.28 8 8
STAT1 (dimer) -0.018 0.076 0.5 2 -0.36 3 5
JAK2 0.023 0.028 0.093 1 -0.054 4 5
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
EPO/EPOR (dimer)/JAK2 0.048 0.09 0.45 3 -0.21 5 8
EPO/EPOR 0.03 0.04 -10000 0 -10000 0 0
LYN 0.013 0.054 -10000 0 -0.27 15 15
TEC/VAV2 -0.025 0.08 0.26 5 -10000 0 5
elevation of cytosolic calcium ion concentration 0.02 0.029 -10000 0 -0.052 47 47
SHC1 0.03 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.036 0.061 0.31 2 -0.19 12 14
mol:IP3 -0.025 0.074 0.37 2 -0.28 8 10
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.033 0.095 0.26 14 -0.27 5 19
SH2B3 0.024 0.03 0.093 1 -0.053 6 7
NFKB1 -0.013 0.083 0.17 69 -0.27 6 75
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.034 0.2 1 -0.18 8 9
PTPN6 -0.025 0.075 0.27 7 -10000 0 7
TEC/VAV2/GRB2 -0.02 0.095 0.3 8 -10000 0 8
EPOR 0.02 0.029 -10000 0 -0.052 47 47
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.098 0.27 12 -10000 0 12
SOS1 0.03 0.007 -10000 0 -10000 0 0
PLCG2 0.028 0.01 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.03 0.095 0.26 11 -10000 0 11
VAV2 -0.018 0.092 0.28 13 -10000 0 13
CBL -0.016 0.094 0.28 14 -10000 0 14
SHC/Grb2/SOS1 -0.048 0.059 0.27 1 -10000 0 1
STAT5A -0.033 0.097 0.46 2 -0.36 8 10
GRB2 0.03 0.006 -10000 0 -10000 0 0
STAT5 (dimer) -0.058 0.13 0.58 2 -0.41 32 34
LYN/PLCgamma2 0.024 0.048 -10000 0 -0.2 15 15
PTPN11 0.031 0.004 -10000 0 -10000 0 0
BTK -0.016 0.094 0.28 14 -10000 0 14
BCL2 -0.048 0.25 0.52 1 -0.67 68 69
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.021 0.018 0.18 3 -10000 0 3
RAS family/GTP 0.021 0.095 0.38 19 -0.25 3 22
NFATC4 -0.027 0.087 0.25 25 -10000 0 25
ERBB2IP 0.02 0.027 -10000 0 -0.28 1 1
HSP90 (dimer) 0.03 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.033 0.087 0.34 11 -10000 0 11
JUN 0.008 0.13 0.45 26 -10000 0 26
HRAS 0.029 0.012 -10000 0 -10000 0 0
DOCK7 -0.028 0.085 0.27 14 -10000 0 14
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.025 0.077 0.2 9 -0.18 29 38
AKT1 -0.014 0.009 -10000 0 -10000 0 0
BAD -0.023 0.007 -10000 0 -10000 0 0
MAPK10 -0.017 0.077 0.21 28 -10000 0 28
mol:GTP 0 0.003 0.017 14 -10000 0 14
ErbB2/ErbB3/neuregulin 1 beta -0.035 0.093 0.36 11 -10000 0 11
RAF1 0.061 0.16 0.4 59 -10000 0 59
ErbB2/ErbB3/neuregulin 2 -0.023 0.068 0.16 31 -0.18 29 60
STAT3 -0.026 0.23 -10000 0 -0.9 36 36
cell migration -0.015 0.077 0.24 21 -10000 0 21
mol:PI-3-4-5-P3 -0.001 0.002 0.012 2 -10000 0 2
cell proliferation -0.011 0.25 0.7 30 -0.61 7 37
FOS -0.038 0.26 0.66 31 -0.44 100 131
NRAS 0.018 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.033 0.087 0.34 11 -10000 0 11
MAPK3 -0.012 0.23 0.65 29 -0.55 14 43
MAPK1 0.001 0.22 0.62 32 -0.59 9 41
JAK2 -0.03 0.085 0.26 16 -0.21 2 18
NF2 -0.001 0.065 -10000 0 -0.66 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.005 0.062 0.17 11 -0.21 29 40
NRG1 0.02 0.023 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.014 -10000 0 -10000 0 0
MAPK8 -0.024 0.098 0.31 11 -0.25 19 30
MAPK9 -0.015 0.078 0.21 30 -10000 0 30
ERBB2 -0.03 0.025 0.28 1 -0.21 4 5
ERBB3 0.006 0.069 -10000 0 -0.28 26 26
SHC1 0.03 0.01 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
apoptosis 0.015 0.012 -10000 0 -0.16 1 1
STAT3 (dimer) -0.024 0.23 -10000 0 -0.87 37 37
RNF41 -0.027 0.02 0.15 4 -10000 0 4
FRAP1 -0.012 0.005 0.003 48 -10000 0 48
RAC1-CDC42/GTP -0.038 0.058 0.18 2 -0.18 3 5
ErbB2/ErbB2/HSP90 (dimer) -0.032 0.026 0.21 1 -0.18 3 4
CHRNA1 0.015 0.2 0.65 34 -0.43 1 35
myelination -0.021 0.096 0.24 37 -10000 0 37
PPP3CB -0.03 0.083 0.25 16 -10000 0 16
KRAS 0.026 0.014 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.02 0.085 0.21 2 -0.2 29 31
NRG2 0.031 0.004 -10000 0 -10000 0 0
mol:GDP -0.005 0.062 0.17 11 -0.2 29 40
SOS1 0.03 0.009 -10000 0 -10000 0 0
MAP2K2 0.016 0.16 0.42 44 -0.36 1 45
SRC 0.03 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.032 0.084 0.25 14 -10000 0 14
MAP2K1 0.047 0.21 0.64 29 -0.61 6 35
heart morphogenesis -0.033 0.087 0.34 11 -10000 0 11
RAS family/GDP 0.017 0.077 0.34 7 -0.24 4 11
GRB2 0.031 0.008 -10000 0 -10000 0 0
PRKACA 0.006 0.066 -10000 0 -0.68 5 5
CHRNE 0.004 0.048 0.2 19 -10000 0 19
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
activation of caspase activity 0.014 0.009 -10000 0 -10000 0 0
nervous system development -0.033 0.087 0.34 11 -10000 0 11
CDC42 0.031 0.004 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.044 0.094 -10000 0 -0.18 59 59
SMAD6-7/SMURF1 0.057 0.02 -10000 0 -10000 0 0
NOG 0.03 0.014 -10000 0 -0.28 1 1
SMAD9 -0.019 0.14 -10000 0 -0.47 48 48
SMAD4 0.03 0.007 -10000 0 -10000 0 0
SMAD5 -0.015 0.083 0.21 3 -0.34 17 20
BMP7/USAG1 0.013 0.061 -10000 0 -0.21 34 34
SMAD5/SKI -0.003 0.092 -10000 0 -0.34 18 18
SMAD1 -0.016 0.089 -10000 0 -0.42 16 16
BMP2 0.029 0.015 -10000 0 -0.28 1 1
SMAD1/SMAD1/SMAD4 0.009 0.092 -10000 0 -0.37 16 16
BMPR1A 0.03 0.006 -10000 0 -10000 0 0
BMPR1B 0.012 0.072 -10000 0 -0.28 31 31
BMPR1A-1B/BAMBI 0.04 0.055 -10000 0 -0.18 27 27
AHSG 0.027 0.012 -10000 0 -10000 0 0
CER1 0.029 0.008 -10000 0 -10000 0 0
BMP2-4/CER1 0.054 0.025 -10000 0 -0.18 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.033 0.11 -10000 0 -0.32 39 39
BMP2-4 (homodimer) 0.042 0.018 -10000 0 -0.2 1 1
RGMB 0.03 0.008 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.051 0.064 -10000 0 -0.17 27 27
RGMA 0.019 0.06 -10000 0 -0.28 21 21
SMURF1 0.03 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.013 0.072 -10000 0 -0.28 18 18
BMP2-4/USAG1 0.043 0.034 -10000 0 -0.18 3 3
SMAD6/SMURF1/SMAD5 -0.003 0.092 -10000 0 -0.33 19 19
SOSTDC1 0.023 0.023 -10000 0 -0.28 2 2
BMP7/BMPR2/BMPR1A-1B 0.026 0.084 -10000 0 -0.18 60 60
SKI 0.03 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.029 0.009 -10000 0 -10000 0 0
HFE2 0.031 0.005 -10000 0 -10000 0 0
ZFYVE16 0.028 0.009 -10000 0 -10000 0 0
MAP3K7 0.03 0.008 -10000 0 -10000 0 0
BMP2-4/CHRD 0.048 0.029 -10000 0 -0.18 1 1
SMAD5/SMAD5/SMAD4 -0.003 0.093 -10000 0 -0.33 19 19
MAPK1 0.029 0.008 -10000 0 -10000 0 0
TAK1/TAB family 0.006 0.081 -10000 0 -0.26 20 20
BMP7 (homodimer) 0.003 0.079 -10000 0 -0.28 39 39
NUP214 0.031 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.036 0.02 -10000 0 -10000 0 0
SMAD1/SKI 0.001 0.091 -10000 0 -0.39 16 16
SMAD6 0.031 0.005 -10000 0 -10000 0 0
CTDSP2 0.03 0.019 -10000 0 -0.28 2 2
BMP2-4/FETUA 0.048 0.029 -10000 0 -0.18 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.028 0.009 -10000 0 -10000 0 0
BMPR2 (homodimer) 0.031 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.034 0.07 -10000 0 -0.18 50 50
BMPR1A-1B (homodimer) 0.028 0.058 -10000 0 -0.2 31 31
CHRDL1 -0.12 0.16 -10000 0 -0.28 264 264
ENDOFIN/SMAD1 0 0.092 -10000 0 -0.4 16 16
SMAD6-7/SMURF1/SMAD1 0.024 0.099 -10000 0 -0.39 16 16
SMAD6/SMURF1 0.03 0.006 -10000 0 -10000 0 0
BAMBI 0.027 0.021 -10000 0 -0.28 2 2
SMURF2 0.031 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.047 0.12 -10000 0 -0.18 239 239
BMP2-4/GREM1 0.052 0.027 -10000 0 -0.18 1 1
SMAD7 0.03 0.007 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.01 0.15 -10000 0 -0.45 52 52
SMAD1/SMAD6 0.001 0.091 -10000 0 -0.39 16 16
TAK1/SMAD6 0.043 0.013 -10000 0 -10000 0 0
BMP7 0.003 0.079 -10000 0 -0.28 39 39
BMP6 0.029 0.009 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.011 0.078 -10000 0 -0.3 19 19
PPM1A 0.031 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.001 0.092 -10000 0 -0.4 16 16
SMAD7/SMURF1 0.043 0.013 -10000 0 -10000 0 0
CTDSPL 0.031 0.003 -10000 0 -10000 0 0
PPP1CA 0.031 0.004 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.029 0.023 -10000 0 -0.28 3 3
PPP1R15A 0.002 0.09 -10000 0 -0.28 51 51
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.012 0.084 -10000 0 -0.31 21 21
CHRD 0.026 0.012 -10000 0 -10000 0 0
BMPR2 0.031 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.012 0.077 0.18 1 -0.29 18 19
BMP4 0.03 0.006 -10000 0 -10000 0 0
FST 0.027 0.011 -10000 0 -10000 0 0
BMP2-4/NOG 0.055 0.026 -10000 0 -0.18 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.046 0.092 -10000 0 -0.18 59 59
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.009 0.032 0.14 18 -0.19 3 21
CRKL 0.03 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
DOCK1 0.03 0.014 -10000 0 -0.28 1 1
ITGA4 0.029 0.008 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.062 0.044 -10000 0 -0.17 4 4
EPO 0.031 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.024 -10000 0 -0.2 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.014 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.041 0.016 -10000 0 -10000 0 0
lamellipodium assembly 0.009 0.11 -10000 0 -0.37 17 17
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
PI3K 0.012 0.062 -10000 0 -0.2 37 37
ARF6 0.031 0.004 -10000 0 -10000 0 0
JAK2 0.015 0.03 -10000 0 -0.26 1 1
PXN 0.024 0.046 -10000 0 -0.28 12 12
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
MADCAM1 0.029 0.009 -10000 0 -10000 0 0
cell adhesion 0.06 0.043 -10000 0 -0.17 4 4
CRKL/CBL 0.043 0.012 -10000 0 -10000 0 0
ITGB1 0.031 0.006 -10000 0 -10000 0 0
SRC -0.009 0.11 0.17 119 -10000 0 119
ITGB7 0.028 0.03 -10000 0 -0.28 5 5
RAC1 0.03 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.017 0.081 -10000 0 -0.18 74 74
p130Cas/Crk/Dock1 -0.019 0.11 0.17 110 -10000 0 110
VCAM1 -0.019 0.11 -10000 0 -0.28 80 80
RHOA 0.031 0.014 -10000 0 -0.28 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.047 -10000 0 -0.17 10 10
BCAR1 -0.016 0.098 0.15 113 -10000 0 113
EPOR 0.028 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.031 0.005 -10000 0 -10000 0 0
GIT1 0.03 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.11 -10000 0 -0.38 17 17
TCGA08_p53

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
CDKN2A -0.006 0.008 -10000 0 -10000 0 0
TP53 0.024 0.077 -10000 0 -0.22 39 39
Senescence 0.024 0.077 -10000 0 -0.22 39 39
Apoptosis 0.024 0.077 -10000 0 -0.22 39 39
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.043 0.3 10 -0.19 1 11
MDM4 0.03 0.007 -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 -0.036 0.13 -10000 0 -0.28 118 118
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.007 0.14 0.49 7 -0.41 27 34
IL27/IL27R/JAK1 0.067 0.13 0.56 7 -0.97 2 9
TBX21 0.05 0.15 0.44 31 -0.58 2 33
IL12B 0.034 0.015 -10000 0 -10000 0 0
IL12A -0.011 0.014 0.045 4 -0.19 1 5
IL6ST 0.023 0.058 0.15 1 -0.29 16 17
IL27RA/JAK1 0.037 0.1 0.38 4 -1.1 2 6
IL27 0.035 0.019 0.15 1 -10000 0 1
TYK2 0.033 0.031 0.16 25 -10000 0 25
T-helper cell lineage commitment -0.058 0.13 -10000 0 -0.49 14 14
T-helper 2 cell differentiation -0.007 0.14 0.49 7 -0.41 27 34
T cell proliferation during immune response -0.007 0.14 0.49 7 -0.41 27 34
MAPKKK cascade 0.007 0.14 0.41 27 -0.49 7 34
STAT3 0.025 0.04 -10000 0 -0.28 9 9
STAT2 0.027 0.011 -10000 0 -10000 0 0
STAT1 0.015 0.016 -10000 0 -10000 0 0
IL12RB1 0.03 0.012 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.046 0.15 0.46 27 -0.58 2 29
IL27/IL27R/JAK2/TYK2 0.007 0.14 0.41 27 -0.5 7 34
positive regulation of T cell mediated cytotoxicity 0.007 0.14 0.41 27 -0.49 7 34
STAT1 (dimer) 0.061 0.11 0.56 1 -0.82 2 3
JAK2 0.03 0.031 0.13 25 -0.29 1 26
JAK1 0.03 0.02 -10000 0 -0.28 2 2
STAT2 (dimer) 0.015 0.13 0.38 20 -0.45 7 27
T cell proliferation -0.012 0.14 0.44 9 -0.5 8 17
IL12/IL12R/TYK2/JAK2 0.026 0.19 0.53 9 -0.7 24 33
IL17A -0.057 0.12 -10000 0 -0.49 14 14
mast cell activation -0.007 0.14 0.49 7 -0.41 27 34
IFNG 0.019 0.068 0.29 29 -0.12 1 30
T cell differentiation -0.001 0.007 0.028 22 -0.023 2 24
STAT3 (dimer) 0.02 0.14 0.37 27 -0.47 8 35
STAT5A (dimer) 0.022 0.14 0.37 28 -0.46 8 36
STAT4 (dimer) 0.022 0.14 0.37 27 -0.44 8 35
STAT4 0.031 0.005 -10000 0 -10000 0 0
T cell activation -0.003 0.015 0.12 1 -0.24 2 3
IL27R/JAK2/TYK2 0.052 0.12 0.43 27 -0.98 2 29
GATA3 0.01 0.13 0.61 21 -10000 0 21
IL18 -0.012 0.008 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production 0.02 0.14 0.37 27 -0.46 8 35
IL27/EBI3 0.049 0.033 0.2 5 -10000 0 5
IL27RA 0.024 0.11 0.46 6 -1.1 2 8
IL6 0.006 0.083 -10000 0 -0.28 42 42
STAT5A 0.027 0.033 -10000 0 -0.28 6 6
monocyte differentiation 0.001 0.004 0.019 28 -10000 0 28
IL2 -0.012 0.051 0.45 2 -0.66 1 3
IL1B -0.013 0.008 -10000 0 -10000 0 0
EBI3 0.029 0.024 0.16 1 -10000 0 1
TNF -0.014 0.007 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.037 0.02 -10000 0 -0.17 3 3
cell-cell adhesion 0.063 0.037 0.26 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.056 0.08 -10000 0 -0.17 41 41
ITSN1 0.031 0.004 -10000 0 -10000 0 0
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
SHC1 0.03 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.025 -10000 0 -0.17 5 5
Ephrin B1/EPHB1 0.038 0.023 -10000 0 -0.17 5 5
HRAS/GDP -0.016 0.1 -10000 0 -0.23 41 41
Ephrin B/EPHB1/GRB7 0.059 0.076 -10000 0 -0.17 37 37
Endophilin/SYNJ1 -0.039 0.063 0.32 3 -0.27 1 4
KRAS 0.026 0.012 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.06 0.074 -10000 0 -0.17 35 35
endothelial cell migration 0.013 0.071 -10000 0 -0.17 58 58
GRB2 0.03 0.006 -10000 0 -10000 0 0
GRB7 0.028 0.024 -10000 0 -0.28 3 3
PAK1 -0.039 0.073 0.32 5 -0.28 1 6
HRAS 0.03 0.007 -10000 0 -10000 0 0
RRAS -0.051 0.071 0.22 6 -0.27 7 13
DNM1 0.031 0.005 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.029 0.073 0.25 6 -0.27 1 7
lamellipodium assembly -0.063 0.037 -10000 0 -0.26 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.003 0.061 -10000 0 -0.25 9 9
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
EPHB2 0.03 0.006 -10000 0 -10000 0 0
EPHB3 0.026 0.012 -10000 0 -10000 0 0
EPHB1 0.03 0.008 -10000 0 -10000 0 0
EPHB4 0.031 0.006 -10000 0 -10000 0 0
mol:GDP -0.047 0.086 0.22 6 -0.25 33 39
Ephrin B/EPHB2 0.046 0.065 -10000 0 -0.16 38 38
Ephrin B/EPHB3 0.036 0.065 -10000 0 -0.16 37 37
JNK cascade -0.009 0.1 0.29 37 -10000 0 37
Ephrin B/EPHB1 0.045 0.064 -10000 0 -0.16 36 36
RAP1/GDP -0.058 0.094 0.23 8 -0.26 7 15
EFNB2 0.011 0.074 -10000 0 -0.28 33 33
EFNB3 0.028 0.024 -10000 0 -0.28 3 3
EFNB1 0.028 0.03 -10000 0 -0.28 5 5
Ephrin B2/EPHB1-2 0.039 0.054 -10000 0 -0.16 31 31
RAP1B 0.03 0.015 -10000 0 -0.28 1 1
RAP1A 0.031 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.031 0.084 -10000 0 -0.21 37 37
Rap1/GTP -0.068 0.042 0.075 2 -10000 0 2
axon guidance 0.037 0.02 -10000 0 -0.17 3 3
MAPK3 -0.033 0.066 0.17 1 -0.28 12 13
MAPK1 -0.02 0.055 0.17 6 -0.25 3 9
Rac1/GDP -0.054 0.094 0.27 5 -0.26 9 14
actin cytoskeleton reorganization -0.041 0.053 -10000 0 -0.19 16 16
CDC42/GDP -0.055 0.095 0.24 9 -0.24 36 45
PI3K 0.016 0.074 -10000 0 -0.17 58 58
EFNA5 0.028 0.024 -10000 0 -0.28 3 3
Ephrin B2/EPHB4 0.026 0.05 -10000 0 -0.17 33 33
Ephrin B/EPHB2/Intersectin/N-WASP -0.002 0.066 -10000 0 -0.2 45 45
CDC42 0.031 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.035 0.045 -10000 0 -0.27 1 1
PTK2 0.14 0.26 0.56 151 -10000 0 151
MAP4K4 -0.01 0.1 0.29 37 -10000 0 37
SRC 0.03 0.007 -10000 0 -10000 0 0
KALRN 0.03 0.006 -10000 0 -10000 0 0
Intersectin/N-WASP 0.044 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.042 0.092 0.25 27 -10000 0 27
MAP2K1 -0.018 0.058 0.16 5 -0.25 6 11
WASL 0.03 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.064 0.038 -10000 0 -0.17 3 3
cell migration -0.027 0.083 0.26 4 -0.3 10 14
NRAS 0.018 0.016 -10000 0 -10000 0 0
SYNJ1 -0.04 0.064 0.33 3 -0.27 1 4
PXN 0.024 0.046 -10000 0 -0.28 12 12
TF -0.045 0.059 0.31 3 -0.27 1 4
HRAS/GTP -0.053 0.056 0.12 38 -0.27 1 39
Ephrin B1/EPHB1-2 0.052 0.029 -10000 0 -0.16 5 5
cell adhesion mediated by integrin 0.023 0.069 0.2 14 -0.22 15 29
RAC1 0.03 0.007 -10000 0 -10000 0 0
mol:GTP 0.036 0.071 -10000 0 -0.17 39 39
RAC1-CDC42/GTP -0.063 0.045 -10000 0 -0.27 1 1
RASA1 0.027 0.024 -10000 0 -0.28 3 3
RAC1-CDC42/GDP -0.059 0.095 0.25 8 -0.26 8 16
ruffle organization -0.047 0.086 0.29 13 -0.28 1 14
NCK1 0.028 0.01 -10000 0 -10000 0 0
receptor internalization -0.046 0.061 0.21 8 -0.27 1 9
Ephrin B/EPHB2/KALRN 0.062 0.075 -10000 0 -0.17 37 37
ROCK1 0.006 0.083 0.18 104 -0.16 5 109
RAS family/GDP -0.044 0.055 -10000 0 -0.21 18 18
Rac1/GTP -0.066 0.039 -10000 0 -0.28 1 1
Ephrin B/EPHB1/Src/Paxillin -0.005 0.067 -10000 0 -0.26 6 6
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization -0.015 0.073 -10000 0 -0.22 46 46
epithelial cell differentiation 0.051 0.045 -10000 0 -0.16 10 10
CYFIP2 0.026 0.038 -10000 0 -0.28 8 8
ENAH -0.044 0.063 0.22 7 -10000 0 7
EGFR 0.002 0.091 -10000 0 -0.28 51 51
EPHA2 0.031 0.005 -10000 0 -10000 0 0
MYO6 -0.046 0.028 0.16 4 -0.27 1 5
CTNNB1 0.031 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.055 0.033 -10000 0 -0.18 8 8
AQP5 -0.016 0.039 -10000 0 -0.3 4 4
CTNND1 0.031 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.043 0.027 0.16 4 -10000 0 4
regulation of calcium-dependent cell-cell adhesion -0.044 0.031 0.16 4 -10000 0 4
EGF 0.029 0.008 -10000 0 -10000 0 0
NCKAP1 0.031 0.006 -10000 0 -10000 0 0
AQP3 -0.14 0.18 -10000 0 -0.41 170 170
cortical microtubule organization 0.051 0.045 -10000 0 -0.16 10 10
GO:0000145 -0.041 0.025 0.14 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.056 0.047 -10000 0 -0.16 10 10
MLLT4 0.022 0.046 -10000 0 -0.28 12 12
ARF6/GDP -0.061 0.033 -10000 0 -10000 0 0
ARF6 0.031 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.04 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.054 0.075 -10000 0 -0.24 60 60
PVRL2 0.029 0.015 -10000 0 -0.28 1 1
ZYX -0.06 0.046 0.16 1 -0.27 1 2
ARF6/GTP 0.076 0.044 -10000 0 -10000 0 0
CDH1 0.023 0.04 -10000 0 -0.28 9 9
EGFR/EGFR/EGF/EGF 0.022 0.075 -10000 0 -0.17 56 56
RhoA/GDP 0.051 0.048 -10000 0 -0.16 11 11
actin cytoskeleton organization -0.048 0.029 0.14 3 -0.27 1 4
IGF-1R heterotetramer -0.033 0.12 -10000 0 -0.28 111 111
GIT1 0.03 0.007 -10000 0 -10000 0 0
IGF1R -0.033 0.12 -10000 0 -0.28 111 111
IGF1 0.022 0.053 -10000 0 -0.28 16 16
DIAPH1 0.034 0.13 -10000 0 -0.54 22 22
Wnt receptor signaling pathway -0.051 0.045 0.16 10 -10000 0 10
RHOA 0.031 0.014 -10000 0 -0.28 1 1
RhoA/GTP -0.061 0.034 -10000 0 -10000 0 0
CTNNA1 0.03 0.014 -10000 0 -0.28 1 1
VCL -0.049 0.029 0.14 3 -0.28 1 4
EFNA1 0.029 0.009 -10000 0 -10000 0 0
LPP -0.05 0.039 0.14 3 -0.38 1 4
Ephrin A1/EPHA2 0.039 0.047 -10000 0 -0.16 8 8
SEC6/SEC8 -0.06 0.034 -10000 0 -0.28 1 1
MGAT3 -0.045 0.031 0.16 4 -10000 0 4
HGF/MET 0.022 0.072 -10000 0 -0.17 50 50
HGF 0.031 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.015 0.073 -10000 0 -0.22 46 46
actin cable formation -0.028 0.088 0.28 13 -0.29 7 20
KIAA1543 -0.044 0.023 0.14 4 -10000 0 4
KIFC3 -0.045 0.024 0.16 2 -10000 0 2
NCK1 0.028 0.01 -10000 0 -10000 0 0
EXOC3 0.028 0.01 -10000 0 -10000 0 0
ACTN1 -0.047 0.029 0.16 4 -0.27 1 5
NCK1/GIT1 0.039 0.018 -10000 0 -10000 0 0
mol:GDP 0.051 0.045 -10000 0 -0.16 10 10
EXOC4 0.03 0.008 -10000 0 -10000 0 0
STX4 -0.046 0.025 0.16 4 -10000 0 4
PIP5K1C -0.044 0.027 0.16 4 -10000 0 4
LIMA1 0.012 0.076 -10000 0 -0.28 35 35
ABI1 0.031 0.005 -10000 0 -10000 0 0
ROCK1 -0.04 0.078 0.24 12 -10000 0 12
adherens junction assembly -0.059 0.1 0.23 1 -0.58 13 14
IGF-1R heterotetramer/IGF1 -0.007 0.096 -10000 0 -0.17 132 132
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.035 0.04 -10000 0 -0.2 13 13
MET 0.004 0.084 -10000 0 -0.28 44 44
PLEKHA7 -0.046 0.025 0.16 4 -10000 0 4
mol:GTP 0.056 0.039 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.039 0.09 0.29 13 -0.27 1 14
cortical actin cytoskeleton stabilization -0.015 0.073 -10000 0 -0.22 46 46
regulation of cell-cell adhesion -0.048 0.029 0.14 3 -0.27 1 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.015 0.073 -10000 0 -0.22 46 46
BCR signaling pathway

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
JUN -0.031 0.12 0.26 2 -0.37 31 33
IKBKB 0.01 0.082 0.3 6 -0.31 7 13
AKT1 0.006 0.1 0.29 32 -0.23 4 36
IKBKG 0.008 0.067 0.28 2 -0.26 7 9
CALM1 -0.014 0.076 0.2 1 -0.28 20 21
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
MAP3K1 -0.024 0.15 0.37 1 -0.47 35 36
MAP3K7 0.03 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.079 0.21 1 -0.28 24 25
DOK1 0.031 0.014 -10000 0 -0.28 1 1
AP-1 -0.031 0.077 0.28 2 -0.23 25 27
LYN 0.021 0.051 -10000 0 -0.28 15 15
BLNK 0.015 0.067 -10000 0 -0.28 27 27
SHC1 0.03 0.006 -10000 0 -10000 0 0
BCR complex 0.043 0.013 -10000 0 -10000 0 0
CD22 -0.038 0.093 0.2 1 -0.34 25 26
CAMK2G -0.021 0.079 -10000 0 -0.29 17 17
CSNK2A1 0.029 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.062 0.042 -10000 0 -0.2 25 25
GO:0007205 -0.006 0.08 0.21 1 -0.29 24 25
SYK 0.027 0.033 -10000 0 -0.28 6 6
ELK1 -0.009 0.085 0.25 7 -0.29 20 27
NFATC1 -0.029 0.096 0.22 6 -0.34 24 30
B-cell antigen/BCR complex 0.043 0.013 -10000 0 -10000 0 0
PAG1/CSK 0.042 0.015 -10000 0 -10000 0 0
NFKBIB 0.011 0.05 0.16 2 -0.14 14 16
HRAS -0.017 0.077 0.2 1 -0.29 20 21
NFKBIA 0.012 0.049 0.16 2 -0.13 25 27
NF-kappa-B/RelA/I kappa B beta 0.016 0.046 0.15 3 -0.13 12 15
RasGAP/Csk 0.073 0.053 -10000 0 -0.17 4 4
mol:GDP -0.006 0.078 0.21 1 -0.28 22 23
PTEN 0.029 0.02 -10000 0 -0.28 2 2
CD79B 0.031 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.016 0.045 0.15 3 -0.12 11 14
GRB2 0.03 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.048 0.15 0.3 2 -0.42 35 37
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
mol:IP3 -0.005 0.08 0.22 1 -0.29 24 25
CSK 0.03 0.006 -10000 0 -10000 0 0
FOS -0.032 0.096 0.25 5 -0.31 23 28
CHUK 0.004 0.083 0.25 3 -0.3 17 20
IBTK 0.03 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.013 0.089 -10000 0 -0.3 13 13
PTPN6 -0.035 0.094 0.21 3 -0.34 23 26
RELA 0.03 0.019 -10000 0 -0.28 2 2
BCL2A1 0.009 0.033 0.1 6 -0.1 6 12
VAV2 -0.02 0.1 0.25 2 -0.39 23 25
ubiquitin-dependent protein catabolic process 0.012 0.05 0.16 2 -0.12 51 53
BTK 0.018 0.044 -10000 0 -0.99 1 1
CD19 -0.016 0.087 0.2 1 -0.34 21 22
MAP4K1 0.028 0.01 -10000 0 -10000 0 0
CD72 0.031 0.005 -10000 0 -10000 0 0
PAG1 0.029 0.009 -10000 0 -10000 0 0
MAPK14 -0.023 0.13 0.3 4 -0.4 34 38
SH3BP5 0.029 0.023 -10000 0 -0.28 3 3
PIK3AP1 -0.009 0.08 0.26 3 -0.31 21 24
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.002 0.097 -10000 0 -0.34 31 31
RAF1 -0.024 0.074 0.24 2 -0.29 17 19
RasGAP/p62DOK/SHIP 0.06 0.047 -10000 0 -0.16 5 5
CD79A 0.03 0.008 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.03 0.077 0.24 3 -0.23 24 27
RASA1 0.027 0.024 -10000 0 -0.28 3 3
MAPK3 -0.044 0.07 0.3 1 -0.28 16 17
MAPK1 -0.031 0.07 0.26 3 -0.28 13 16
CD72/SHP1 -0.02 0.12 0.27 22 -0.33 22 44
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
MAPK8 -0.026 0.13 0.29 2 -0.42 32 34
actin cytoskeleton organization -0.022 0.1 0.26 6 -0.36 21 27
NF-kappa-B/RelA 0.026 0.093 0.27 3 -0.24 25 28
Calcineurin 0.007 0.093 -10000 0 -0.29 17 17
PI3K -0.05 0.083 -10000 0 -0.3 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.001 0.076 0.24 1 -0.3 21 22
SOS1 0.03 0.007 -10000 0 -10000 0 0
Bam32/HPK1 -0.019 0.21 -10000 0 -0.64 50 50
DAPP1 -0.038 0.23 -10000 0 -0.72 49 49
cytokine secretion -0.027 0.092 0.22 6 -0.32 24 30
mol:DAG -0.005 0.08 0.22 1 -0.29 24 25
PLCG2 0.028 0.01 -10000 0 -10000 0 0
MAP2K1 -0.029 0.071 0.27 1 -0.3 14 15
B-cell antigen/BCR complex/FcgammaRIIB 0.053 0.026 -10000 0 -0.18 1 1
mol:PI-3-4-5-P3 -0.006 0.11 0.26 36 -0.26 8 44
ETS1 -0.023 0.08 0.23 2 -0.28 17 19
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.06 0.076 -10000 0 -0.19 33 33
B-cell antigen/BCR complex/LYN 0.003 0.091 -10000 0 -0.35 22 22
MALT1 0.028 0.01 -10000 0 -10000 0 0
TRAF6 0.031 0.005 -10000 0 -10000 0 0
RAC1 -0.025 0.1 0.24 4 -0.37 23 27
B-cell antigen/BCR complex/LYN/SYK 0.006 0.12 0.33 5 -0.32 17 22
CARD11 -0.014 0.078 0.2 2 -0.3 19 21
FCGR2B 0.028 0.016 -10000 0 -0.28 1 1
PPP3CA 0.027 0.028 -10000 0 -0.28 4 4
BCL10 0.031 0.004 -10000 0 -10000 0 0
IKK complex 0.014 0.047 0.16 20 -0.12 5 25
PTPRC 0.004 0.083 -10000 0 -0.28 43 43
PDPK1 -0.002 0.097 0.26 36 -0.2 5 41
PPP3CB 0.031 0.005 -10000 0 -10000 0 0
PPP3CC 0.026 0.012 -10000 0 -10000 0 0
POU2F2 0.009 0.032 0.17 3 -0.13 3 6
ErbB4 signaling 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
ErbB4/ErbB4/HBEGF/HBEGF 0.028 0.081 0.41 2 -0.61 3 5
epithelial cell differentiation 0.021 0.075 -10000 0 -0.6 3 3
ITCH 0.016 0.036 0.21 1 -0.13 3 4
WWP1 0.006 0.11 0.93 1 -1.1 3 4
FYN -0.002 0.095 -10000 0 -0.28 57 57
EGFR 0.002 0.091 -10000 0 -0.28 51 51
PRL 0.029 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.022 0.09 0.31 7 -0.49 3 10
PTPRZ1 0.03 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.047 0.085 0.35 1 -0.52 3 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.01 0.056 0.39 1 -0.55 3 4
ADAM17 0.02 0.029 0.21 1 -0.13 3 4
ErbB4/ErbB4 0.006 0.074 -10000 0 -0.66 3 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.016 0.095 -10000 0 -0.64 3 3
NCOR1 0.027 0.028 -10000 0 -0.28 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.012 0.083 -10000 0 -0.53 3 3
GRIN2B -0.014 0.081 0.29 1 -0.52 3 4
ErbB4/ErbB2/betacellulin 0.03 0.074 0.35 1 -0.53 3 4
STAT1 0.015 0.016 -10000 0 -10000 0 0
HBEGF 0.031 0.004 -10000 0 -10000 0 0
PRLR 0.029 0.009 -10000 0 -10000 0 0
E4ICDs/ETO2 0.022 0.078 0.37 1 -0.61 3 4
axon guidance 0.011 0.072 0.46 1 -0.68 3 4
NEDD4 0.014 0.038 0.21 1 -0.13 3 4
Prolactin receptor/Prolactin receptor/Prolactin 0.04 0.017 -10000 0 -10000 0 0
CBFA2T3 0.028 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.032 0.075 0.35 1 -0.53 3 4
MAPK3 -0.01 0.096 0.32 8 -0.5 3 11
STAT1 (dimer) 0.008 0.064 0.37 1 -0.56 3 4
MAPK1 -0.002 0.09 0.33 7 -0.5 3 10
JAK2 0.028 0.021 -10000 0 -0.28 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.016 0.056 0.35 1 -0.53 3 4
NRG1 0.008 0.073 0.18 81 -10000 0 81
NRG3 -0.19 0.14 -10000 0 -0.28 388 388
NRG2 0.031 0.004 -10000 0 -10000 0 0
NRG4 0.026 0.033 -10000 0 -0.28 6 6
heart development 0.011 0.072 0.46 1 -0.68 3 4
neural crest cell migration -0.015 0.056 0.35 1 -0.53 3 4
ERBB2 0.008 0.078 0.18 88 -0.21 3 91
WWOX/E4ICDs 0.023 0.077 0.37 1 -0.61 3 4
SHC1 0.03 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.022 0.094 0.37 2 -0.59 3 5
apoptosis 0.16 0.18 0.33 247 -10000 0 247
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.028 0.081 0.41 2 -0.61 3 5
ErbB4/ErbB2/epiregulin 0.031 0.074 0.35 1 -0.53 3 4
ErbB4/ErbB4/betacellulin/betacellulin 0.026 0.08 0.41 2 -0.61 3 5
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.051 0.088 0.4 1 -0.56 3 4
MDM2 -0.001 0.075 0.31 2 -0.61 3 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.025 0.065 0.37 1 -0.49 3 4
STAT5A 0.002 0.071 0.4 1 -0.66 3 4
ErbB4/EGFR/neuregulin 1 beta 0.016 0.082 0.35 1 -0.53 3 4
DLG4 0.03 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.044 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.02 0.073 -10000 0 -0.57 3 3
STAT5A (dimer) 0.031 0.085 0.36 1 -0.66 3 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.029 0.081 0.4 2 -0.66 3 5
LRIG1 0.028 0.024 -10000 0 -0.28 3 3
EREG 0.029 0.008 -10000 0 -10000 0 0
BTC 0.027 0.028 -10000 0 -0.28 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.009 0.069 -10000 0 -0.68 3 3
ERBB4 0.006 0.074 -10000 0 -0.67 3 3
STAT5B 0.027 0.033 -10000 0 -0.28 6 6
YAP1 0.019 0.053 -10000 0 -0.45 5 5
GRB2 0.03 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.03 0.076 0.35 1 -0.53 3 4
glial cell differentiation -0.02 0.072 0.57 3 -10000 0 3
WWOX 0.028 0.01 -10000 0 -10000 0 0
cell proliferation 0.004 0.083 0.33 1 -0.59 3 4
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.031 0.006 -10000 0 -10000 0 0
VLDLR 0.021 0.048 -10000 0 -0.28 13 13
LRPAP1 0.029 0.02 -10000 0 -0.28 2 2
NUDC 0.031 0.006 -10000 0 -10000 0 0
RELN/LRP8 0.02 0.084 -10000 0 -0.18 78 78
CaM/Ca2+ 0.017 0.036 -10000 0 -0.19 16 16
KATNA1 0.03 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.039 0.086 0.17 57 -0.29 1 58
IQGAP1/CaM 0.036 0.045 -10000 0 -0.2 18 18
DAB1 0.031 0.005 -10000 0 -10000 0 0
IQGAP1 0.029 0.02 -10000 0 -0.28 2 2
PLA2G7 0.026 0.028 -10000 0 -0.28 4 4
CALM1 0.022 0.053 -10000 0 -0.28 16 16
DYNLT1 0.002 0.088 -10000 0 -0.28 48 48
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.042 0.02 -10000 0 -0.2 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.031 0.004 -10000 0 -10000 0 0
CDK5R1 0.03 0.008 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.022 0.008 -10000 0 -10000 0 0
CDK5R2 0.031 0.004 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.015 0.087 -10000 0 -0.18 88 88
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
NDEL1/14-3-3 E -0.031 0.1 0.29 16 -0.25 3 19
MAP1B -0.015 0.061 0.12 1 -0.21 49 50
RAC1 -0.003 0.042 -10000 0 -0.26 14 14
p35/CDK5 -0.034 0.093 0.21 25 -0.28 1 26
RELN -0.016 0.11 -10000 0 -0.28 81 81
PAFAH/LIS1 -0.029 0.019 -10000 0 -0.18 3 3
LIS1/CLIP170 -0.032 0.012 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.057 0.091 0.2 7 -0.27 4 11
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.02 0.093 0.2 1 -0.28 19 20
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.026 0.093 0.27 13 -0.24 7 20
LIS1/IQGAP1 -0.032 0.016 -10000 0 -0.18 2 2
RHOA 0.002 0.024 -10000 0 -0.29 3 3
PAFAH1B1 -0.028 0.01 -10000 0 -10000 0 0
PAFAH1B3 0.029 0.009 -10000 0 -10000 0 0
PAFAH1B2 0.03 0.014 -10000 0 -0.28 1 1
MAP1B/LIS1/Dynein heavy chain -0.041 0.046 -10000 0 -0.23 4 4
NDEL1/Katanin 60/Dynein heavy chain -0.035 0.11 0.27 21 -0.26 2 23
LRP8 0.03 0.006 -10000 0 -10000 0 0
NDEL1/Katanin 60 -0.032 0.1 0.28 16 -0.26 2 18
P39/CDK5 -0.034 0.095 0.21 27 -0.28 1 28
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.032 0.013 -10000 0 -10000 0 0
CDK5 -0.041 0.076 0.16 41 -0.28 1 42
PPP2R5D 0.03 0.007 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.029 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.084 -10000 0 -0.17 76 76
RELN/VLDLR 0.023 0.091 -10000 0 -0.17 84 84
CDC42 0.002 0.021 -10000 0 -0.26 3 3
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.051 0.071 0.39 2 -0.2 15 17
positive regulation of NF-kappaB transcription factor activity 0 0.002 -10000 0 -10000 0 0
CRKL 0.03 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.009 0.09 0.23 2 -0.29 15 17
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.057 0.22 3 -0.21 16 19
antigen processing and presentation of peptide antigen via MHC class I -0.028 0.076 0.14 3 -0.25 32 35
CaM/Ca2+ 0.046 0.077 0.31 1 -0.18 24 25
RAP1A 0.031 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.02 0.052 0.21 3 -0.27 5 8
AKT1 0.005 0.12 0.27 28 -0.29 11 39
MAP2K1 -0.036 0.068 0.29 6 -0.27 4 10
MAP3K11 -0.029 0.075 0.32 7 -0.27 4 11
IFNGR1 -0.019 0.042 0.079 6 -0.3 6 12
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.016 0.11 -10000 0 -0.33 40 40
Rap1/GTP -0.06 0.048 -10000 0 -0.22 7 7
CRKL/C3G 0.043 0.012 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.065 0.07 0.33 1 -0.2 14 15
CEBPB -0.051 0.15 0.42 2 -0.55 26 28
STAT3 0.025 0.04 -10000 0 -0.28 9 9
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.015 0.26 -10000 0 -0.96 36 36
STAT1 -0.02 0.055 0.37 2 -0.27 5 7
CALM1 0.022 0.053 -10000 0 -0.28 16 16
IFN-gamma (dimer) -0.022 0.025 0.079 2 -10000 0 2
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.022 0.058 0.37 2 -0.28 4 6
CEBPB/PTGES2/Cbp/p300 -0.056 0.11 -10000 0 -0.36 33 33
mol:Ca2+ 0.045 0.069 0.37 2 -0.2 15 17
MAPK3 -0.085 0.23 0.49 1 -0.71 59 60
STAT1 (dimer) -0.03 0.11 0.45 4 -0.38 20 24
MAPK1 -0.054 0.19 0.42 2 -0.71 36 38
JAK2 -0.019 0.034 0.082 5 -0.31 2 7
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
JAK1 -0.019 0.033 0.082 5 -0.31 1 6
CAMK2D 0.019 0.056 -10000 0 -0.28 18 18
DAPK1 -0.033 0.11 0.52 2 -0.43 17 19
SMAD7 0.025 0.11 0.35 31 -0.2 2 33
CBL/CRKL/C3G -0.036 0.082 0.3 6 -0.28 3 9
PI3K 0.025 0.088 0.26 2 -0.22 32 34
IFNG -0.022 0.025 0.079 2 -10000 0 2
apoptosis -0.005 0.1 0.44 4 -0.41 4 8
CAMK2G 0.031 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.04 -10000 0 -0.28 9 9
CAMK2A 0.031 0.004 -10000 0 -10000 0 0
CAMK2B 0.031 0.005 -10000 0 -10000 0 0
FRAP1 0 0.1 0.25 28 -0.27 11 39
PRKCD 0.005 0.12 0.28 30 -0.29 11 41
RAP1B 0.03 0.015 -10000 0 -0.28 1 1
negative regulation of cell growth -0.028 0.076 0.14 3 -0.25 32 35
PTPN2 0.03 0.006 -10000 0 -10000 0 0
EP300 0.022 0.03 -10000 0 -0.28 3 3
IRF1 -0.013 0.13 0.21 24 -0.35 32 56
STAT1 (dimer)/PIASy -0.02 0.057 0.27 1 -0.29 3 4
SOCS1 -0.063 0.3 -10000 0 -1.2 36 36
mol:GDP -0.036 0.077 0.3 5 -0.26 4 9
CASP1 0 0.088 0.22 6 -0.23 31 37
PTGES2 0.031 0.005 -10000 0 -10000 0 0
IRF9 -0.03 0.055 0.33 3 -0.19 11 14
mol:PI-3-4-5-P3 -0.036 0.065 0.14 10 -0.26 16 26
RAP1/GDP -0.052 0.065 0.16 3 -0.25 4 7
CBL -0.029 0.073 0.33 6 -0.26 5 11
MAP3K1 -0.027 0.072 0.31 6 -0.27 4 10
PIAS1 0.031 0.005 -10000 0 -10000 0 0
PIAS4 0.029 0.009 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.028 0.076 0.14 3 -0.25 32 35
PTPN11 -0.022 0.075 0.3 8 -0.25 6 14
CREBBP 0.021 0.037 -10000 0 -0.28 6 6
RAPGEF1 0.031 0.005 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.036 0.037 -10000 0 -0.2 24 24
MAP4K4 -0.043 0.097 0.17 3 -0.3 38 41
BAG4 0.028 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide 0.032 0.033 -10000 0 -0.18 9 9
NFKBIA 0.022 0.051 -10000 0 -0.28 15 15
BIRC3 -0.037 0.13 -10000 0 -0.28 118 118
BAX 0.009 0.058 -10000 0 -0.32 15 15
RIPK1 0.029 0.008 -10000 0 -10000 0 0
AKT1 -0.008 0.11 0.67 15 -10000 0 15
BAD 0.003 0.033 0.22 2 -0.19 9 11
SMPD1 -0.012 0.068 0.18 6 -0.23 24 30
RB1 0.007 0.046 0.18 18 -0.19 9 27
FADD/Caspase 8 -0.04 0.11 0.25 4 -0.34 36 40
MAP2K4 -0.007 0.031 -10000 0 -0.2 1 1
NSMAF 0.03 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.04 0.19 10 -0.2 1 11
EGF 0.029 0.008 -10000 0 -10000 0 0
mol:ceramide 0.014 0.033 -10000 0 -0.19 10 10
MADD 0.031 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.032 0.037 -10000 0 -0.2 22 22
ASAH1 0.026 0.018 -10000 0 -0.28 1 1
negative regulation of cell cycle 0.008 0.046 0.18 18 -0.18 9 27
cell proliferation -0.046 0.07 0.19 2 -0.24 21 23
BID -0.044 0.19 -10000 0 -0.66 40 40
MAP3K1 0.002 0.03 -10000 0 -0.19 6 6
EIF2A 0.057 0.1 0.28 41 -10000 0 41
TRADD 0.026 0.028 -10000 0 -0.28 4 4
CRADD 0.031 0.005 -10000 0 -10000 0 0
MAPK3 -0.041 0.064 0.19 2 -0.26 19 21
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.036 0.057 0.21 2 -0.26 9 11
Cathepsin D/ceramide 0.031 0.035 -10000 0 -0.18 10 10
FADD -0.045 0.097 0.19 4 -0.3 38 42
KSR1 0.004 0.037 0.23 5 -0.19 9 14
MAPK8 0.003 0.043 -10000 0 -10000 0 0
PRKRA 0.009 0.047 0.22 16 -0.19 9 25
PDGFA 0.015 0.066 -10000 0 -0.28 26 26
TRAF2 0.03 0.006 -10000 0 -10000 0 0
IGF1 0.022 0.053 -10000 0 -0.28 16 16
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.014 0.033 -10000 0 -0.18 10 10
CTSD 0.025 0.042 -10000 0 -0.28 10 10
regulation of nitric oxide biosynthetic process 0.038 0.038 -10000 0 -0.2 12 12
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.048 0.075 0.2 2 -0.26 21 23
PRKCD 0.03 0.019 -10000 0 -0.28 2 2
PRKCZ 0.03 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.032 0.037 -10000 0 -0.2 22 22
RelA/NF kappa B1 0.038 0.038 -10000 0 -0.2 12 12
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.031 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.033 0.1 -10000 0 -0.31 36 36
TNFR1A/BAG4/TNF-alpha 0.042 0.049 -10000 0 -0.18 19 19
mol:Sphingosine-1-phosphate -0.036 0.037 -10000 0 -0.2 24 24
MAP2K1 -0.011 0.04 0.23 1 -10000 0 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.03 0.019 -10000 0 -0.28 2 2
CYCS 0.023 0.058 0.17 16 -0.17 7 23
TNFRSF1A 0.015 0.063 -10000 0 -0.28 23 23
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
TNFR1A/BAG4 0.029 0.047 -10000 0 -0.2 19 19
EIF2AK2 0.05 0.089 0.23 40 -0.2 1 41
TNF-alpha/TNFR1A/FAN 0.044 0.049 -10000 0 -0.18 19 19
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.024 0.12 -10000 0 -0.43 36 36
MAP2K2 -0.047 0.064 0.2 3 -0.3 3 6
SMPD3 -0.029 0.11 0.19 4 -0.32 57 61
TNF 0.031 0.005 -10000 0 -10000 0 0
PKC zeta/PAR4 0.044 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.011 0.038 0.14 3 -0.15 7 10
NF kappa B1/RelA/I kappa B alpha 0.066 0.069 -10000 0 -0.18 24 24
AIFM1 0.04 0.068 0.19 40 -0.17 4 44
BCL2 -0.005 0.097 -10000 0 -0.28 60 60
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.039 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.029 0.008 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.028 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.028 -10000 0 -0.28 4 4
RAC1-CDC42/GTP/PAK family -0.032 0.071 -10000 0 -0.16 114 114
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.03 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.005 -10000 0 -10000 0 0
FYN -0.002 0.095 -10000 0 -0.28 57 57
MAP3K12 0.031 0.003 -10000 0 -10000 0 0
FGR 0.031 0.005 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.047 0.093 -10000 0 -0.3 46 46
PRKG1 0.031 0.003 -10000 0 -10000 0 0
DUSP8 0.03 0.007 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.022 0.11 0.19 1 -0.35 32 33
apoptosis -0.045 0.089 -10000 0 -0.29 46 46
RAL/GTP 0.041 0.012 -10000 0 -0.17 1 1
LYN 0.021 0.051 -10000 0 -0.28 15 15
DUSP1 -0.061 0.14 -10000 0 -0.28 163 163
PAK1 0.028 0.016 -10000 0 -0.28 1 1
SRC 0.03 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.067 0.038 -10000 0 -0.17 1 1
TRAF6 0.031 0.005 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.031 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.04 0.011 -10000 0 -10000 0 0
MAPK11 -0.047 0.12 0.21 2 -0.34 40 42
BLK 0.026 0.012 -10000 0 -10000 0 0
HCK 0.029 0.009 -10000 0 -10000 0 0
MAP2K3 0.029 0.016 -10000 0 -0.28 1 1
DUSP16 0.028 0.01 -10000 0 -10000 0 0
DUSP10 0.029 0.008 -10000 0 -10000 0 0
TRAF6/MEKK3 0.038 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.029 0.12 0.19 3 -0.38 33 36
positive regulation of innate immune response -0.047 0.13 0.24 2 -0.4 40 42
LCK 0.03 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP7 -0.04 0.13 -10000 0 -0.39 38 38
p38alpha-beta/MKP5 -0.038 0.13 0.27 1 -0.39 39 40
PGK/cGMP 0.023 0.002 -10000 0 -10000 0 0
PAK2 0.026 0.012 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.063 0.15 0.27 1 -0.39 58 59
CDC42 0.031 0.004 -10000 0 -10000 0 0
RALB 0.03 0.014 -10000 0 -0.28 1 1
RALA 0.031 0.005 -10000 0 -10000 0 0
PAK3 -0.06 0.14 -10000 0 -0.28 162 162
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.025 0.032 0.24 6 -10000 0 6
NFATC2 0.013 0.2 0.51 3 -0.55 17 20
NFATC3 0 0.073 0.36 2 -10000 0 2
CD40LG -0.036 0.23 0.68 7 -0.77 2 9
ITCH -0.029 0.053 0.31 10 -10000 0 10
CBLB -0.032 0.046 0.3 7 -10000 0 7
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.025 0.19 0.73 6 -0.66 7 13
JUNB -0.049 0.13 -10000 0 -0.28 137 137
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.04 -10000 0 -0.21 15 15
T cell anergy -0.01 0.083 0.49 10 -0.32 1 11
TLE4 -0.074 0.22 -10000 0 -0.59 69 69
Jun/NFAT1-c-4/p21SNFT 0.032 0.17 0.62 2 -0.72 2 4
AP-1/NFAT1-c-4 0.008 0.23 0.85 2 -0.85 2 4
IKZF1 -0.03 0.13 -10000 0 -0.41 13 13
T-helper 2 cell differentiation -0.004 0.15 -10000 0 -0.6 6 6
AP-1/NFAT1 0.004 0.18 0.47 4 -0.4 28 32
CALM1 -0.036 0.055 0.2 12 -0.3 15 27
EGR2 -0.002 0.16 0.86 2 -0.74 1 3
EGR3 -0.012 0.16 0.88 1 -0.71 2 3
NFAT1/FOXP3 0.028 0.15 0.5 5 -0.4 16 21
EGR1 -0.09 0.15 -10000 0 -0.28 213 213
JUN -0.014 0.051 0.18 6 -0.29 2 8
EGR4 0.031 0.006 0.15 1 -10000 0 1
mol:Ca2+ -0.009 0.002 -10000 0 -10000 0 0
GBP3 -0.044 0.2 0.43 18 -0.58 38 56
FOSL1 0.031 0.003 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 0.036 0.17 -10000 0 -0.72 1 1
DGKA -0.027 0.14 0.41 5 -0.4 13 18
CREM 0.031 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.036 0.16 -10000 0 -0.74 2 2
CTLA4 -0.027 0.13 0.51 6 -0.35 14 20
NFAT1-c-4 (dimer)/EGR1 -0.039 0.18 -10000 0 -0.75 4 4
NFAT1-c-4 (dimer)/EGR4 0.038 0.17 0.61 1 -0.75 1 2
FOS -0.057 0.11 0.18 5 -0.29 89 94
IFNG 0.002 0.19 0.58 26 -0.58 12 38
T cell activation -0.017 0.16 -10000 0 -10000 0 0
MAF 0.026 0.025 -10000 0 -0.28 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.001 0.13 1 1 -0.7 2 3
TNF -0.074 0.16 0.57 1 -0.7 3 4
FASLG -0.01 0.17 -10000 0 -0.84 1 1
TBX21 0.044 0.057 0.29 28 -10000 0 28
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.023 0.044 -10000 0 -0.28 11 11
PTPN1 -0.032 0.13 -10000 0 -0.41 14 14
NFAT1-c-4/ICER1 0.036 0.16 -10000 0 -0.74 2 2
GATA3 0.03 0.008 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.008 0.19 0.59 27 -0.58 12 39
IL2RA -0.017 0.18 0.74 4 -0.62 9 13
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.026 0.14 0.42 8 -0.42 12 20
E2F1 0.032 0.019 0.18 7 -10000 0 7
PPARG 0.031 0.005 -10000 0 -10000 0 0
SLC3A2 -0.031 0.13 0.42 2 -0.41 14 16
IRF4 0.029 0.008 -10000 0 -10000 0 0
PTGS2 -0.052 0.23 0.64 5 -0.74 3 8
CSF2 -0.038 0.23 0.69 6 -0.77 2 8
JunB/Fra1/NFAT1-c-4 -0.003 0.18 -10000 0 -0.77 3 3
IL4 -0.006 0.16 -10000 0 -0.62 6 6
IL5 -0.039 0.23 0.68 7 -0.77 2 9
IL2 -0.018 0.16 -10000 0 -10000 0 0
IL3 -0.01 0.091 -10000 0 -0.56 13 13
RNF128 -0.034 0.043 0.33 5 -10000 0 5
NFATC1 0.001 0.13 0.7 2 -1 1 3
CDK4 0.011 0.15 0.84 5 -10000 0 5
PTPRK -0.036 0.15 0.41 3 -0.48 22 25
IL8 -0.074 0.16 0.64 2 -0.77 2 4
POU2F1 0.032 0.004 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.11 0.2 0.6 1 -0.62 17 18
RAD9A 0.031 0.004 -10000 0 -10000 0 0
AP1 -0.022 0.097 -10000 0 -0.21 106 106
IFNAR2 0.013 0.032 -10000 0 -10000 0 0
AKT1 -0.016 0.052 -10000 0 -0.2 16 16
ER alpha/Oestrogen -0.012 0.066 -10000 0 -0.19 60 60
NFX1/SIN3/HDAC complex -0.008 0.074 0.2 3 -0.34 13 16
EGF 0.015 0.028 -10000 0 -10000 0 0
SMG5 0.03 0.006 -10000 0 -10000 0 0
SMG6 0.03 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.02 0.043 0.16 1 -10000 0 1
TERT/c-Abl -0.1 0.2 0.54 1 -0.58 22 23
SAP18 0.018 0.024 -10000 0 -10000 0 0
MRN complex 0.041 0.031 -10000 0 -10000 0 0
WT1 -0.005 0.077 -10000 0 -0.28 34 34
WRN 0.023 0.014 -10000 0 -10000 0 0
SP1 0.011 0.036 0.14 1 -10000 0 1
SP3 0.014 0.029 -10000 0 -10000 0 0
TERF2IP 0.028 0.01 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.098 0.19 -10000 0 -0.54 22 22
Mad/Max 0.022 0.04 -10000 0 -10000 0 0
TERT -0.12 0.21 -10000 0 -0.64 17 17
CCND1 -0.26 0.44 0.78 1 -1 143 144
MAX 0.014 0.029 -10000 0 -10000 0 0
RBBP7 0.016 0.029 -10000 0 -0.28 1 1
RBBP4 0.019 0.023 -10000 0 -10000 0 0
TERF2 -0.03 0.018 0.079 7 -10000 0 7
PTGES3 0.004 0.088 -10000 0 -0.28 48 48
SIN3A 0.018 0.024 -10000 0 -10000 0 0
Telomerase/911 0.013 0.082 -10000 0 -0.33 3 3
CDKN1B -0.031 0.059 0.17 26 -0.42 2 28
RAD1 0.029 0.009 -10000 0 -10000 0 0
XRCC5 0.028 0.01 -10000 0 -10000 0 0
XRCC6 0.029 0.009 -10000 0 -10000 0 0
SAP30 0.016 0.025 -10000 0 -10000 0 0
TRF2/PARP2 0.033 0.021 -10000 0 -10000 0 0
UBE3A 0.015 0.028 -10000 0 -10000 0 0
JUN 0.013 0.033 -10000 0 -0.28 2 2
E6 -0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.01 0.023 0.098 1 -10000 0 1
FOS -0.043 0.12 -10000 0 -0.28 107 107
IFN-gamma/IRF1 0.012 0.062 -10000 0 -0.22 22 22
PARP2 0.027 0.011 -10000 0 -10000 0 0
BLM 0.022 0.015 -10000 0 -10000 0 0
Telomerase 0.004 0.084 -10000 0 -0.36 9 9
IRF1 -0.004 0.07 0.19 5 -0.28 25 30
ESR1 -0.018 0.096 -10000 0 -0.28 60 60
KU/TER 0.038 0.018 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.021 -10000 0 -0.081 7 7
ubiquitin-dependent protein catabolic process -0.009 0.074 0.18 1 -0.33 13 14
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.009 0.076 0.19 1 -0.33 14 15
HDAC1 0.018 0.024 -10000 0 -10000 0 0
HDAC2 0.011 0.034 0.12 1 -10000 0 1
ATM 0.021 0.025 0.23 2 -10000 0 2
SMAD3 -0.062 0.072 -10000 0 -0.2 116 116
ABL1 0.027 0.035 -10000 0 -0.28 7 7
MXD1 0.014 0.029 -10000 0 -10000 0 0
MRE11A 0.024 0.014 -10000 0 -10000 0 0
HUS1 0.031 0.005 -10000 0 -10000 0 0
RPS6KB1 0.03 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.096 0.21 -10000 0 -0.62 22 22
NR2F2 0.032 0.022 -10000 0 -0.28 2 2
MAPK3 -0.046 0.049 -10000 0 -0.21 44 44
MAPK1 -0.031 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II -0.033 0.13 -10000 0 -0.28 114 114
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
HNRNPC 0.03 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.02 0.025 0.23 2 -10000 0 2
NBN 0.027 0.011 -10000 0 -10000 0 0
EGFR -0.011 0.091 -10000 0 -0.29 51 51
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.004 0.076 -10000 0 -0.21 51 51
MYC -0.015 0.085 -10000 0 -0.28 47 47
IL2 0.011 0.035 -10000 0 -10000 0 0
KU 0.038 0.018 -10000 0 -10000 0 0
RAD50 0.031 0.005 -10000 0 -10000 0 0
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
TGFB1 -0.034 0.13 -10000 0 -0.28 114 114
TRF2/BLM 0.026 0.023 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.095 0.21 0.54 1 -0.59 20 21
SP1/HDAC2 0.018 0.048 0.24 1 -10000 0 1
PINX1 0.025 0.013 -10000 0 -10000 0 0
Telomerase/EST1A -0.099 0.19 -10000 0 -0.54 22 22
Smad3/Myc -0.047 0.082 -10000 0 -0.2 106 106
911 complex 0.057 0.021 -10000 0 -10000 0 0
IFNG 0.008 0.039 0.2 6 -0.17 3 9
Telomerase/PinX1 -0.1 0.18 -10000 0 -0.54 22 22
Telomerase/AKT1/mTOR/p70S6K -0.035 0.14 -10000 0 -0.43 31 31
SIN3B 0.016 0.025 -10000 0 -10000 0 0
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
Telomerase/EST1B -0.096 0.18 -10000 0 -0.54 22 22
response to DNA damage stimulus 0.008 0.02 0.13 2 -0.1 7 9
MRN complex/TRF2/Rap1 0.068 0.05 -10000 0 -10000 0 0
TRF2/WRN 0.029 0.022 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.098 0.18 -10000 0 -0.55 21 21
E2F1 0.012 0.031 -10000 0 -10000 0 0
ZNFX1 0.018 0.024 -10000 0 -10000 0 0
PIF1 0.031 0.005 -10000 0 -10000 0 0
NCL 0.031 0.004 -10000 0 -10000 0 0
DKC1 0.023 0.014 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Arf1 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
coatomer protein complex 0.008 0.043 0.14 53 -10000 0 53
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.002 0.062 0.12 1 -0.21 38 39
AP2 0.024 0.057 -10000 0 -0.2 30 30
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.034 0.024 -10000 0 -10000 0 0
CLTB 0.031 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein -0.002 0.049 -10000 0 -0.19 31 31
CD4 0.026 0.021 -10000 0 -0.28 2 2
CLTA 0.031 0.005 -10000 0 -10000 0 0
mol:GTP -0.004 0.005 -10000 0 -0.024 30 30
ARFGAP1 -0.014 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.031 0.089 23 -0.17 1 24
ARF1/GTP -0.026 0.038 -10000 0 -0.18 31 31
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.015 0.037 0.1 1 -0.17 28 29
mol:Choline -0.002 0.03 0.089 23 -0.16 1 24
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.03 0.011 0.055 1 0 63 64
DDEF1 0 0.03 -10000 0 -0.17 1 1
ARF1/GDP 0.004 0.013 -10000 0 -0.098 4 4
AP2M1 0.026 0.012 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.025 0.034 0.039 1 -0.15 32 33
Rac/GTP 0.02 0.013 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.045 -10000 0 -0.15 31 31
ARFIP2 0.02 0.024 -10000 0 -10000 0 0
COPA 0.031 0.006 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0 0.046 -10000 0 -0.17 28 28
ARF1/GTP/ARHGAP10 0.009 0.043 -10000 0 -0.16 33 33
GGA3 0.031 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.005 0.057 -10000 0 -0.18 46 46
AP2A1 0.009 0.079 -10000 0 -0.28 38 38
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.005 0.042 -10000 0 -0.16 31 31
ARF1/GDP/Membrin 0.013 0.063 -10000 0 -0.26 17 17
Arfaptin 2/Rac/GDP 0.037 0.018 -10000 0 -10000 0 0
CYTH2 -0.004 0.005 -10000 0 -0.024 30 30
ARF1/GTP/GGA3 0.026 0.051 -10000 0 -0.17 33 33
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.022 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.006 0.054 -10000 0 -0.24 9 9
PLD2 -0.002 0.03 0.089 23 -0.16 1 24
ARF-GAP1/v-SNARE -0.014 0.005 -10000 0 -10000 0 0
PIP5K1A -0.002 0.031 0.09 23 -0.17 1 24
ARF1/GTP/Membrin/GBF1/p115 0.002 0.044 -10000 0 -0.15 37 37
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.03 0.089 23 -0.16 1 24
KDEL Receptor/Ligand/ARF-GAP1 -0.014 0.005 -10000 0 -10000 0 0
GOSR2 0.004 0.053 -10000 0 -0.35 11 11
USO1 0.004 0.051 -10000 0 -0.35 10 10
GBF1 0.002 0.057 -10000 0 -0.35 13 13
ARF1/GTP/Arfaptin 2 0.025 0.053 -10000 0 -0.18 33 33
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.034 0.055 -10000 0 -0.18 26 26
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.11 0.38 11 -0.29 10 21
TBX21 -0.055 0.25 0.89 5 -0.78 6 11
B2M 0.027 0.03 -10000 0 -0.28 5 5
TYK2 0.011 0.048 0.22 5 -10000 0 5
IL12RB1 0.009 0.049 0.2 6 -10000 0 6
GADD45B -0.035 0.24 0.95 7 -0.73 10 17
IL12RB2 0.01 0.052 0.22 6 -10000 0 6
GADD45G -0.022 0.22 0.91 5 -0.72 4 9
natural killer cell activation -0.002 0.031 0.16 8 -10000 0 8
RELB 0.029 0.02 -10000 0 -0.28 2 2
RELA 0.03 0.019 -10000 0 -0.28 2 2
IL18 0.01 0.029 -10000 0 -10000 0 0
IL2RA 0.029 0.008 -10000 0 -10000 0 0
IFNG 0.029 0.009 -10000 0 -10000 0 0
STAT3 (dimer) -0.058 0.24 0.72 7 -0.69 20 27
HLA-DRB5 0.006 0.054 -10000 0 -0.28 14 14
FASLG -0.053 0.25 0.89 5 -0.76 7 12
NF kappa B2 p52/RelB -0.047 0.23 0.52 4 -0.6 30 34
CD4 0.014 0.035 -10000 0 -0.28 2 2
SOCS1 0.017 0.064 -10000 0 -0.28 24 24
EntrezGene:6955 -0.003 0.013 -10000 0 -10000 0 0
CD3D -0.028 0.11 -10000 0 -0.29 84 84
CD3E 0.011 0.053 -10000 0 -0.29 12 12
CD3G 0.016 0.034 -10000 0 -0.28 1 1
IL12Rbeta2/JAK2 0.017 0.073 0.32 6 -0.22 2 8
CCL3 -0.05 0.26 0.9 12 -0.78 6 18
CCL4 -0.051 0.25 0.79 8 -0.62 24 32
HLA-A 0.023 0.048 -10000 0 -0.28 13 13
IL18/IL18R 0.04 0.071 0.44 9 -10000 0 9
NOS2 -0.035 0.23 0.8 9 -0.62 9 18
IL12/IL12R/TYK2/JAK2/SPHK2 0.004 0.1 0.39 10 -0.29 4 14
IL1R1 -0.2 0.48 0.82 7 -1 122 129
IL4 0.027 0.046 -10000 0 -0.21 6 6
JAK2 0.009 0.053 0.22 5 -0.3 2 7
EntrezGene:6957 -0.003 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.028 0.1 -10000 0 -0.49 8 8
RAB7A -0.017 0.22 0.84 6 -0.71 3 9
lysosomal transport -0.015 0.21 0.83 6 -0.68 3 9
FOS -0.22 0.5 0.72 11 -1.1 119 130
STAT4 (dimer) -0.01 0.24 0.77 9 -0.69 6 15
STAT5A (dimer) -0.053 0.23 0.52 4 -0.6 28 32
GZMA -0.061 0.26 0.86 6 -0.99 8 14
GZMB -0.051 0.26 0.84 8 -0.85 4 12
HLX 0.03 0.006 -10000 0 -10000 0 0
LCK -0.06 0.25 0.81 7 -0.65 25 32
TCR/CD3/MHC II/CD4 -0.068 0.18 0.33 8 -0.43 85 93
IL2/IL2R 0.042 0.071 -10000 0 -0.18 36 36
MAPK14 -0.024 0.24 0.89 7 -0.72 9 16
CCR5 -0.015 0.21 0.82 6 -0.67 4 10
IL1B 0.008 0.048 0.23 3 -10000 0 3
STAT6 -0.004 0.14 0.55 7 -0.6 7 14
STAT4 0.031 0.005 -10000 0 -10000 0 0
STAT3 0.025 0.04 -10000 0 -0.28 9 9
STAT1 0.015 0.016 -10000 0 -10000 0 0
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
NFKB2 0.031 0.005 -10000 0 -10000 0 0
IL12B 0.01 0.052 0.23 5 -10000 0 5
CD8A 0.031 0.004 -10000 0 -10000 0 0
CD8B 0.031 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.003 0.11 0.29 10 -0.38 11 21
IL2RB 0.026 0.031 -10000 0 -0.28 5 5
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.23 0.76 9 -0.64 6 15
IL2RG 0.01 0.076 -10000 0 -0.28 35 35
IL12 0.018 0.07 0.32 6 -0.21 1 7
STAT5A 0.027 0.033 -10000 0 -0.28 6 6
CD247 0.018 0.031 -10000 0 -10000 0 0
IL2 0.03 0.007 -10000 0 -10000 0 0
SPHK2 0.03 0.006 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.009 0.05 0.22 5 -0.29 1 6
IL12/IL12R/TYK2/JAK2 -0.064 0.27 1 7 -0.68 23 30
MAP2K3 -0.035 0.25 0.88 7 -0.78 11 18
RIPK2 0.022 0.015 -10000 0 -10000 0 0
MAP2K6 -0.02 0.23 0.88 7 -0.76 6 13
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.05 0.13 -10000 0 -0.28 128 128
IL18RAP 0.016 0.033 0.16 3 -10000 0 3
IL12Rbeta1/TYK2 0.016 0.062 0.26 6 -10000 0 6
EOMES -0.001 0.072 -10000 0 -10000 0 0
STAT1 (dimer) -0.012 0.21 0.71 7 -0.65 7 14
T cell proliferation 0.003 0.2 0.7 9 -0.53 4 13
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.016 0.033 0.16 3 -10000 0 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.041 0.16 0.44 1 -0.51 8 9
ATF2 -0.026 0.23 0.81 7 -0.7 8 15
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.003 0.1 0.61 12 -10000 0 12
regulation of axonogenesis -0.001 0.05 0.27 6 -0.21 13 19
myoblast fusion -0.02 0.064 0.33 1 -0.36 13 14
mol:GTP 0.03 0.039 0.23 12 -0.18 7 19
regulation of calcium-dependent cell-cell adhesion -0.047 0.057 0.15 1 -0.31 13 14
ARF1/GTP 0.031 0.06 0.21 10 -0.16 38 48
mol:GM1 0.012 0.034 0.21 13 -0.13 7 20
mol:Choline -0.008 0.042 0.17 26 -10000 0 26
lamellipodium assembly 0.005 0.07 0.35 12 -0.37 6 18
MAPK3 -0.011 0.076 0.39 13 -10000 0 13
ARF6/GTP/NME1/Tiam1 0.048 0.058 0.32 13 -0.15 1 14
ARF1 0.011 0.074 -10000 0 -0.28 33 33
ARF6/GDP 0.02 0.064 0.36 13 -0.33 1 14
ARF1/GDP 0.015 0.066 0.32 11 -0.2 14 25
ARF6 0.046 0.022 0.18 13 -10000 0 13
RAB11A 0.031 0.005 -10000 0 -10000 0 0
TIAM1 0.021 0.028 -10000 0 -0.28 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.001 0.064 0.39 13 -10000 0 13
actin filament bundle formation -0.025 0.062 0.22 7 -0.31 12 19
KALRN 0.003 0.027 0.14 6 -0.28 1 7
RAB11FIP3/RAB11A 0.044 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.063 0.31 12 -0.23 7 19
NME1 0.021 0.025 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.062 0.31 12 -0.23 7 19
substrate adhesion-dependent cell spreading 0.03 0.038 0.23 12 -0.18 7 19
cortical actin cytoskeleton organization 0.005 0.07 0.35 12 -0.38 6 18
RAC1 0.03 0.007 -10000 0 -10000 0 0
liver development 0.03 0.038 0.23 12 -0.18 7 19
ARF6/GTP 0.03 0.039 0.23 12 -0.18 7 19
RhoA/GTP 0.046 0.036 0.21 12 -0.15 8 20
mol:GDP 0.007 0.067 0.41 12 -0.22 6 18
ARF6/GTP/RAB11FIP3/RAB11A 0.061 0.037 0.22 12 -0.13 7 19
RHOA 0.031 0.014 -10000 0 -0.28 1 1
PLD1 0.013 0.033 0.22 10 -0.14 6 16
RAB11FIP3 0.03 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.005 0.07 0.35 12 -0.37 6 18
ruffle organization 0.001 0.05 0.21 13 -0.27 6 19
regulation of epithelial cell migration 0.03 0.038 0.23 12 -0.18 7 19
PLD2 0.018 0.036 0.22 13 -0.14 6 19
PIP5K1A 0.001 0.05 0.21 13 -0.27 6 19
mol:Phosphatidic acid -0.008 0.042 0.17 26 -10000 0 26
Rac1/GTP 0.005 0.07 0.35 12 -0.38 6 18
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.12 0.24 0.66 8 -0.81 1 9
PCK1 0.16 0.24 0.65 46 -0.75 4 50
HNF4A 0.16 0.29 0.79 30 -0.81 1 31
KCNJ11 0.13 0.26 -10000 0 -0.86 1 1
AKT1 0.12 0.17 0.44 11 -0.4 1 12
response to starvation 0.001 0.007 0.16 1 -10000 0 1
DLK1 0.14 0.29 0.87 15 -0.86 1 16
NKX2-1 0.11 0.17 -10000 0 -10000 0 0
ACADM 0.12 0.25 0.66 9 -0.81 1 10
TAT 0.12 0.18 0.52 13 -10000 0 13
CEBPB 0.028 0.03 0.19 2 -0.28 4 6
CEBPA 0.03 0.013 0.19 1 -10000 0 1
TTR 0.14 0.18 0.76 8 -10000 0 8
PKLR 0.13 0.25 0.69 14 -0.81 1 15
APOA1 0.21 0.36 0.96 46 -1 1 47
CPT1C 0.12 0.25 0.75 15 -0.81 1 16
ALAS1 0.092 0.18 0.87 3 -0.61 1 4
TFRC 0.23 0.32 0.78 101 -10000 0 101
FOXF1 0.028 0.01 -10000 0 -10000 0 0
NF1 0.026 0.042 0.24 4 -0.28 8 12
HNF1A (dimer) 0.031 0.023 -10000 0 -0.28 3 3
CPT1A 0.12 0.25 0.68 6 -0.82 2 8
HMGCS1 0.14 0.27 0.7 35 -0.81 1 36
NR3C1 0.027 0.042 -10000 0 -0.28 10 10
CPT1B 0.11 0.24 0.63 5 -0.81 1 6
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -0.26 1 1
GCK 0.12 0.24 0.63 5 -0.81 1 6
CREB1 0.059 0.087 0.24 83 -0.4 5 88
IGFBP1 0.1 0.16 0.52 3 -10000 0 3
PDX1 0.099 0.17 -10000 0 -1 1 1
UCP2 0.059 0.36 0.68 12 -0.8 44 56
ALDOB 0.13 0.26 -10000 0 -0.86 1 1
AFP 0.038 0.055 -10000 0 -10000 0 0
BDH1 0.15 0.28 0.74 31 -0.73 2 33
HADH 0.1 0.3 -10000 0 -0.96 9 9
F2 0.18 0.3 0.85 13 -0.99 1 14
HNF1A 0.031 0.023 -10000 0 -0.28 3 3
G6PC 0.046 0.083 -10000 0 -10000 0 0
SLC2A2 0.13 0.2 0.58 3 -10000 0 3
INS 0.028 0.023 -10000 0 -0.24 4 4
FOXA1 0.035 0.023 0.35 1 -0.29 1 2
FOXA3 0.11 0.12 0.38 36 -0.28 2 38
FOXA2 0.21 0.34 0.84 34 -0.96 1 35
ABCC8 0.13 0.26 -10000 0 -0.86 1 1
ALB 0.039 0.058 0.48 1 -10000 0 1
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.024 -10000 0 -0.28 3 3
HDAC4 0.031 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.01 0.032 -10000 0 -0.12 32 32
CDKN1A -0.032 0.12 0.38 1 -0.52 30 31
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.03 0.006 -10000 0 -10000 0 0
FOXO3 0.002 0.024 0.29 2 -0.15 5 7
FOXO1 0.025 0.038 -10000 0 -0.28 8 8
FOXO4 0.002 0.034 -10000 0 -0.28 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.029 0.009 -10000 0 -10000 0 0
TAT 0.028 0.01 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.002 -10000 0 -10000 0 0
PPARGC1A 0.03 0.006 -10000 0 -10000 0 0
FHL2 0.031 0.004 -10000 0 -10000 0 0
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.048 0.029 0.16 25 -10000 0 25
HIST2H4A -0.01 0.032 0.12 32 -10000 0 32
SIRT1/FOXO3a 0.036 0.044 0.22 6 -10000 0 6
SIRT1 0.035 0.041 0.19 27 -10000 0 27
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.065 0.028 0.18 1 -10000 0 1
SIRT1/Histone H1b 0.013 0.075 0.2 4 -0.25 18 22
apoptosis -0.06 0.032 -10000 0 -0.18 1 1
SIRT1/PGC1A 0.045 0.024 0.14 25 -10000 0 25
p53/SIRT1 0.032 0.11 0.35 27 -0.21 62 89
SIRT1/FOXO4 0.012 0.072 -10000 0 -0.25 17 17
FOXO1/FHL2/SIRT1 0.055 0.038 0.16 21 -0.16 4 25
HIST1H1E 0.003 0.037 0.13 7 -0.28 7 14
SIRT1/p300 0.046 0.035 0.16 26 -0.21 3 29
muscle cell differentiation 0.018 0.034 -10000 0 -0.12 28 28
TP53 -0.001 0.11 0.19 27 -0.29 63 90
KU70/SIRT1/BAX 0.061 0.032 0.18 1 -10000 0 1
CREBBP 0.026 0.033 -10000 0 -0.28 6 6
MEF2D 0.031 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.046 0.028 0.16 22 -10000 0 22
ACSS2 -0.023 0.036 0.12 26 -0.21 1 27
SIRT1/PCAF/MYOD -0.018 0.034 0.12 28 -10000 0 28
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.035 0.029 -10000 0 -10000 0 0
PDGFRB 0.012 0.06 -10000 0 -0.29 19 19
SPHK1 -0.001 0.089 -10000 0 -0.71 8 8
mol:S1P -0.009 0.084 0.24 1 -0.62 8 9
S1P1/S1P/Gi -0.036 0.13 0.53 6 -0.38 43 49
GNAO1 0.021 0.03 0.12 1 -0.29 2 3
PDGFB-D/PDGFRB/PLCgamma1 -0.039 0.13 0.5 6 -0.37 38 44
PLCG1 -0.042 0.13 0.44 8 -0.38 40 48
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.06 -10000 0 -0.29 19 19
GNAI2 0.023 0.024 -10000 0 -10000 0 0
GNAI3 0.022 0.024 -10000 0 -10000 0 0
GNAI1 0.017 0.049 -10000 0 -0.29 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.022 0.02 0.13 6 -10000 0 6
S1P1/S1P -0.027 0.076 0.32 5 -0.45 8 13
negative regulation of cAMP metabolic process -0.035 0.13 0.53 6 -0.37 43 49
MAPK3 -0.065 0.18 0.6 6 -0.55 50 56
calcium-dependent phospholipase C activity -0.001 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.009 -10000 0 -0.19 1 1
KDR 0.025 0.02 -10000 0 -10000 0 0
PLCB2 -0.017 0.087 0.28 10 -0.41 8 18
RAC1 0.03 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.059 -10000 0 -0.39 8 8
receptor internalization -0.025 0.072 0.26 7 -0.42 8 15
PTGS2 -0.091 0.28 0.7 6 -0.92 50 56
Rac1/GTP -0.033 0.058 -10000 0 -0.39 8 8
RHOA 0.031 0.014 -10000 0 -0.28 1 1
VEGFA 0.023 0.02 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.035 0.13 0.53 6 -0.37 43 49
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.037 -10000 0 -0.28 5 5
MAPK1 -0.056 0.17 0.57 5 -0.53 51 56
S1P1/S1P/PDGFB-D/PDGFRB -0.026 0.096 0.32 11 -0.38 9 20
ABCC1 0.022 0.023 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.003 0.009 -10000 0 -10000 0 0
mol:Halofuginone 0 0.018 -10000 0 -0.17 6 6
ITGA1 0.025 0.013 -10000 0 -10000 0 0
CDKN1A -0.038 0.12 -10000 0 -0.44 40 40
PRL-3/alpha Tubulin 0.03 0.034 -10000 0 -0.2 7 7
mol:Ca2+ -0.028 0.054 0.28 7 -0.21 25 32
AGT 0.012 0.072 -10000 0 -0.28 31 31
CCNA2 0.042 0.11 0.31 2 -0.62 6 8
TUBA1B 0.031 0.003 -10000 0 -10000 0 0
EGR1 -0.087 0.091 -10000 0 -0.2 219 219
CDK2/Cyclin E1 -0.013 0.059 -10000 0 -0.32 12 12
MAPK3 -0.034 0.052 0.19 2 -0.2 42 44
PRL-2 /Rab GGTase beta 0.026 0.023 -10000 0 -10000 0 0
MAPK1 -0.022 0.028 0.19 2 -0.2 7 9
PTP4A1 -0.077 0.09 -10000 0 -0.65 6 6
PTP4A3 0.019 0.037 -10000 0 -0.28 7 7
PTP4A2 0.03 0.007 -10000 0 -10000 0 0
ITGB1 -0.023 0.027 0.19 2 -0.2 6 8
SRC 0.03 0.007 -10000 0 -10000 0 0
RAC1 -0.02 0.085 -10000 0 -0.42 19 19
Rab GGTase beta/Rab GGTase alpha 0.026 0.023 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.072 0.1 0.35 2 -0.62 6 8
RABGGTA 0.03 0.006 -10000 0 -10000 0 0
BCAR1 -0.019 0.039 0.28 7 -0.21 2 9
RHOC -0.015 0.073 -10000 0 -0.45 11 11
RHOA -0.017 0.079 -10000 0 -0.44 14 14
cell motility -0.02 0.084 0.29 2 -0.44 10 12
PRL-1/alpha Tubulin -0.072 0.1 0.35 2 -0.62 6 8
PRL-3/alpha1 Integrin 0.024 0.034 -10000 0 -0.2 7 7
ROCK1 -0.016 0.08 0.27 1 -0.44 10 11
RABGGTB 0.018 0.016 -10000 0 -10000 0 0
CDK2 0.017 0.016 -10000 0 -10000 0 0
mitosis -0.076 0.09 -10000 0 -0.64 6 6
ATF5 0.03 0.014 -10000 0 -0.28 1 1
BARD1 signaling events

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
BARD1/CSTF1 0.034 0.021 -10000 0 -10000 0 0
ATM 0.03 0.007 -10000 0 -10000 0 0
UBE2D3 0.029 0.008 -10000 0 -10000 0 0
PRKDC 0.025 0.013 -10000 0 -10000 0 0
ATR 0.021 0.015 -10000 0 -10000 0 0
UBE2L3 0.03 0.007 -10000 0 -10000 0 0
FANCD2 0.05 0.06 0.14 183 -10000 0 183
protein ubiquitination 0.046 0.059 -10000 0 -10000 0 0
XRCC5 0.028 0.01 -10000 0 -10000 0 0
XRCC6 0.029 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.031 -10000 0 -10000 0 0
MRE11A 0.024 0.014 -10000 0 -10000 0 0
DNA-PK 0.043 0.03 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.029 0.074 0.23 2 -0.46 6 8
FANCF 0.031 0.005 -10000 0 -10000 0 0
BRCA1 0.028 0.01 -10000 0 -10000 0 0
CCNE1 0.003 0.009 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.003 0.011 -10000 0 -10000 0 0
FANCG 0.031 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.034 0.021 -10000 0 -10000 0 0
FANCE 0.031 0.006 -10000 0 -10000 0 0
FANCC 0.03 0.006 -10000 0 -10000 0 0
NBN 0.027 0.011 -10000 0 -10000 0 0
FANCA 0.027 0.011 -10000 0 -10000 0 0
DNA repair 0.19 0.19 0.38 231 -0.36 2 233
BRCA1/BARD1/ubiquitin 0.034 0.021 -10000 0 -10000 0 0
BARD1/DNA-PK 0.045 0.044 -10000 0 -10000 0 0
FANCL 0.029 0.008 -10000 0 -10000 0 0
mRNA polyadenylation -0.034 0.021 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.022 0.068 0.19 29 -0.32 4 33
BRCA1/BACH1/BARD1/TopBP1 0.026 0.032 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.024 0.066 -10000 0 -0.17 36 36
BARD1/CSTF1/BRCA1 0.042 0.031 -10000 0 -10000 0 0
BRCA1/BACH1 0.028 0.01 -10000 0 -10000 0 0
BARD1 0.025 0.013 -10000 0 -10000 0 0
PCNA 0.025 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.045 0.029 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.046 0.029 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.031 0.043 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.054 0.082 -10000 0 -0.17 41 41
BRCA1/BARD1/Ubiquitin 0.034 0.021 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.041 0.045 0.16 53 -10000 0 53
FA complex 0.036 0.052 0.19 15 -0.2 5 20
BARD1/EWS 0.035 0.021 -10000 0 -10000 0 0
RBBP8 0.007 0.081 0.19 90 -10000 0 90
TP53 -0.008 0.1 -10000 0 -0.28 67 67
TOPBP1 0.016 0.016 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.023 0.065 0.17 36 -10000 0 36
BRCA1/BARD1 0.05 0.064 -10000 0 -10000 0 0
CSTF1 0.028 0.01 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.019 0.009 -10000 0 -10000 0 0
CDK2 0.017 0.016 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.017 0.016 -10000 0 -10000 0 0
RAD50 0.031 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.034 0.021 -10000 0 -10000 0 0
EWSR1 0.029 0.008 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.024 0.054 0.34 4 -10000 0 4
NFATC2 -0.025 0.058 0.31 5 -0.19 6 11
NFATC3 -0.023 0.055 0.31 5 -10000 0 5
CD40LG -0.069 0.17 0.72 5 -10000 0 5
PTGS2 -0.085 0.17 0.72 5 -0.51 3 8
JUNB -0.049 0.13 -10000 0 -0.28 137 137
CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.043 0.12 2 -0.18 15 17
CaM/Ca2+ 0.004 0.043 0.12 2 -0.18 15 17
CALM1 0.008 0.056 0.16 2 -0.29 13 15
JUN 0.016 0.036 0.16 2 -0.29 2 4
mol:Ca2+ -0.004 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.013 0.1 2 -10000 0 2
FOSL1 0.031 0.003 -10000 0 -10000 0 0
CREM 0.031 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.049 0.1 0.36 21 -10000 0 21
FOS -0.034 0.12 0.16 2 -0.29 93 95
IFNG -0.089 0.11 -10000 0 -10000 0 0
AP-1/NFAT1-c-4 -0.092 0.14 0.52 12 -0.48 2 14
FASLG -0.071 0.16 0.72 5 -10000 0 5
NFAT1-c-4/ICER1 -0.041 0.092 0.32 14 -10000 0 14
IL2RA -0.07 0.15 0.62 2 -10000 0 2
FKBP12/FK506 0.022 0.006 -10000 0 -10000 0 0
CSF2 -0.07 0.17 0.78 4 -10000 0 4
JunB/Fra1/NFAT1-c-4 -0.068 0.1 0.35 11 -0.3 12 23
IL4 -0.07 0.17 0.55 15 -10000 0 15
IL2 -0.035 0.21 -10000 0 -0.92 30 30
IL3 0.002 0.11 -10000 0 -0.67 14 14
FKBP1A 0.029 0.008 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.032 0.004 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.033 0.027 -10000 0 -0.28 2 2
HSPA8 0.022 0.024 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.014 0.1 0.29 3 -0.26 16 19
AKT1 0.026 0.017 -10000 0 -10000 0 0
GSC 0.003 0.06 -10000 0 -0.51 1 1
NKX2-5 0.025 0.021 -10000 0 -0.089 3 3
muscle cell differentiation -0.024 0.11 0.36 5 -0.31 2 7
SMAD2-3/SMAD4/SP1 0.064 0.14 0.38 6 -0.34 2 8
SMAD4 -0.007 0.082 0.21 13 -10000 0 13
CBFB 0.028 0.01 -10000 0 -10000 0 0
SAP18 0.022 0.021 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.061 0.048 -10000 0 -0.21 6 6
SMAD3/SMAD4/VDR 0.056 0.11 0.32 6 -0.29 3 9
MYC -0.006 0.085 -10000 0 -0.28 47 47
CDKN2B -0.054 0.12 -10000 0 -0.69 3 3
AP1 -0.034 0.1 0.25 2 -0.36 3 5
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.021 0.11 0.21 4 -0.39 23 27
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.018 0.076 -10000 0 -0.33 12 12
SP3 0.033 0.03 0.18 19 -10000 0 19
CREB1 0.031 0.004 -10000 0 -10000 0 0
FOXH1 0.019 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.002 0.11 0.28 5 -0.25 17 22
GATA3 -0.03 0.008 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.008 0.089 0.24 1 -0.41 16 17
MEF2C/TIF2 0 0.11 0.27 10 -0.34 10 20
endothelial cell migration -0.1 0.22 0.62 2 -0.67 68 70
MAX 0.009 0.058 -10000 0 -0.14 69 69
RBBP7 0.023 0.024 -10000 0 -0.29 1 1
RBBP4 0.022 0.021 -10000 0 -10000 0 0
RUNX2 0.03 0.007 -10000 0 -10000 0 0
RUNX3 0.031 0.005 -10000 0 -10000 0 0
RUNX1 0.03 0.014 -10000 0 -0.28 1 1
CTBP1 0.029 0.008 -10000 0 -10000 0 0
NR3C1 0.004 0.069 -10000 0 -0.16 79 79
VDR 0.031 0.004 -10000 0 -10000 0 0
CDKN1A -0.028 0.3 -10000 0 -1 37 37
KAT2B 0.002 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.027 0.066 -10000 0 -10000 0 0
DCP1A 0.031 0.004 -10000 0 -10000 0 0
SKI 0.023 0.021 -10000 0 -10000 0 0
SERPINE1 0.1 0.22 0.67 68 -0.62 2 70
SMAD3/SMAD4/ATF2 0.026 0.091 0.28 8 -0.31 1 9
SMAD3/SMAD4/ATF3 0.026 0.091 0.28 7 -0.3 2 9
SAP30 0.022 0.021 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.066 0.059 0.19 65 -0.21 7 72
JUN -0.037 0.1 0.25 2 -0.36 3 5
SMAD3/SMAD4/IRF7 0.025 0.094 0.28 10 -0.31 1 11
TFE3 0.047 0.055 0.2 44 -0.29 1 45
COL1A2 0.12 0.24 0.52 136 -0.63 10 146
mesenchymal cell differentiation -0.026 0.09 0.26 2 -0.27 10 12
DLX1 0.031 0.005 -10000 0 -10000 0 0
TCF3 0.029 0.009 -10000 0 -10000 0 0
FOS -0.01 0.057 0.18 5 -0.32 10 15
SMAD3/SMAD4/Max 0.004 0.1 0.3 3 -0.26 8 11
Cbp/p300/SNIP1 0.053 0.043 -10000 0 -0.21 7 7
ZBTB17 0.031 0.005 -10000 0 -10000 0 0
LAMC1 -0.015 0.085 0.3 8 -0.28 1 9
TGIF2/HDAC complex/SMAD3/SMAD4 0.025 0.091 0.28 9 -0.27 2 11
IRF7 0.024 0.018 -10000 0 -10000 0 0
ESR1 -0.026 0.099 0.14 1 -0.28 61 62
HNF4A 0.029 0.008 -10000 0 -10000 0 0
MEF2C 0.009 0.11 0.28 12 -0.34 12 24
SMAD2-3/SMAD4 0.023 0.094 0.32 2 -0.31 1 3
Cbp/p300/Src-1 0.059 0.05 -10000 0 -0.2 10 10
IGHV3OR16-13 -0.005 0.028 -10000 0 -0.41 2 2
TGIF2/HDAC complex 0.029 0.015 -10000 0 -0.28 1 1
CREBBP 0.031 0.036 -10000 0 -0.28 6 6
SKIL 0.013 0.016 -10000 0 -10000 0 0
HDAC1 0.022 0.021 -10000 0 -10000 0 0
HDAC2 0.022 0.021 -10000 0 -10000 0 0
SNIP1 0.022 0.022 -10000 0 -10000 0 0
GCN5L2 0.005 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.037 0.098 0.34 5 -0.27 2 7
MSG1/HSC70 0.033 0.031 -10000 0 -10000 0 0
SMAD2 0.021 0.025 -10000 0 -10000 0 0
SMAD3 -0.011 0.083 0.21 9 -0.37 2 11
SMAD3/E2F4-5/DP1/p107/SMAD4 0.017 0.076 0.25 11 -0.26 3 14
SMAD2/SMAD2/SMAD4 -0.005 0.062 0.19 4 -0.19 23 27
NCOR1 0.02 0.033 -10000 0 -0.28 4 4
NCOA2 0.029 0.009 -10000 0 -10000 0 0
NCOA1 0.029 0.023 -10000 0 -0.28 3 3
MYOD/E2A 0.042 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.081 0.15 0.38 15 -0.32 2 17
IFNB1 -0.022 0.086 0.25 7 -0.28 1 8
SMAD3/SMAD4/MEF2C 0.014 0.13 0.34 9 -0.36 10 19
CITED1 0.03 0.008 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.04 0.099 0.32 1 -0.28 1 2
RBL1 0.028 0.01 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.015 0.079 -10000 0 -0.46 4 4
RUNX1-3/PEBPB2 0.056 0.024 -10000 0 -0.18 1 1
SMAD7 -0.002 0.16 0.42 17 -0.51 2 19
MYC/MIZ-1 0.009 0.068 -10000 0 -0.2 47 47
SMAD3/SMAD4 0.056 0.13 0.36 57 -0.4 5 62
IL10 -0.015 0.096 0.28 5 -0.28 1 6
PIASy/HDAC complex 0.018 0.032 -10000 0 -10000 0 0
PIAS3 0.033 0.008 -10000 0 -10000 0 0
CDK2 0.019 0.019 -10000 0 -10000 0 0
IL5 -0.013 0.097 0.29 6 -0.28 1 7
CDK4 0.035 0.015 -10000 0 -10000 0 0
PIAS4 0.018 0.032 -10000 0 -10000 0 0
ATF3 0.03 0.015 -10000 0 -0.28 1 1
SMAD3/SMAD4/SP1 0.047 0.13 0.38 5 -0.3 10 15
FOXG1 0.031 0.008 -10000 0 -10000 0 0
FOXO3 -0.03 0.019 -10000 0 -0.2 5 5
FOXO1 -0.031 0.024 -10000 0 -0.21 8 8
FOXO4 -0.03 0.008 -10000 0 -10000 0 0
heart looping 0.01 0.11 0.28 12 -0.33 12 24
CEBPB 0.027 0.028 -10000 0 -0.28 4 4
SMAD3/SMAD4/DLX1 0.026 0.091 0.28 9 -0.31 1 10
MYOD1 0.031 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.026 0.09 0.27 10 -0.31 1 11
SMAD3/SMAD4/GATA3 0.029 0.094 0.28 10 -0.32 1 11
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.05 0.1 0.32 2 -0.25 2 4
SMAD3/SMAD4/SP1-3 0.062 0.14 0.36 10 -0.32 3 13
MED15 0.029 0.02 -10000 0 -0.28 2 2
SP1 0.047 0.08 0.19 41 -0.17 7 48
SIN3B 0.021 0.021 -10000 0 -10000 0 0
SIN3A 0.023 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.043 0.075 -10000 0 -0.23 10 10
ITGB5 0.001 0.12 0.33 21 -0.32 2 23
TGIF/SIN3/HDAC complex/CtBP -0.002 0.081 0.24 1 -0.34 17 18
SMAD3/SMAD4/AR -0.062 0.13 0.28 5 -0.26 56 61
AR -0.11 0.16 -10000 0 -0.28 243 243
negative regulation of cell growth 0.012 0.092 0.27 10 -0.29 15 25
SMAD3/SMAD4/MYOD 0.026 0.092 0.28 9 -0.27 2 11
E2F5 0.027 0.012 -10000 0 -10000 0 0
E2F4 0.028 0.01 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.05 0.076 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.016 0.067 -10000 0 -0.37 2 2
TFDP1 0.029 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.011 0.12 -10000 0 -0.29 11 11
SMAD3/SMAD4/RUNX2 0.026 0.09 0.27 10 -0.27 2 12
TGIF2 0.029 0.015 -10000 0 -0.28 1 1
TGIF1 0.03 0.007 -10000 0 -10000 0 0
ATF2 0.031 0.005 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.029 0.009 -10000 0 -10000 0 0
NFATC1 0.06 0.094 0.26 9 -0.34 12 21
NFATC2 -0.011 0.062 0.26 5 -0.24 6 11
NFATC3 0 0.03 -10000 0 -0.18 4 4
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.004 0.062 0.25 1 -0.25 17 18
Exportin 1/Ran/NUP214 0.054 0.022 -10000 0 -10000 0 0
mol:DAG -0.001 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.002 0.081 0.22 1 -0.26 17 18
BCL2/BAX 0.016 0.076 -10000 0 -0.2 58 58
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.043 0.13 5 -0.19 16 21
CaM/Ca2+ 0 0.043 0.13 5 -0.19 16 21
BAX 0.03 0.006 -10000 0 -10000 0 0
MAPK14 0.01 0.029 -10000 0 -10000 0 0
BAD 0.031 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D 0.01 0.066 0.23 1 -0.25 17 18
Calcineurin A alpha-beta B1/BCL2 -0.005 0.097 -10000 0 -0.28 60 60
FKBP8 0.02 0.053 -10000 0 -0.28 16 16
activation-induced cell death of T cells -0.01 0.066 0.24 17 -0.23 1 18
KPNB1 0.03 0.006 -10000 0 -10000 0 0
KPNA2 0.004 0.011 -10000 0 -10000 0 0
XPO1 0.028 0.01 -10000 0 -10000 0 0
SFN 0.03 0.008 -10000 0 -10000 0 0
MAP3K8 0.009 0.03 -10000 0 -10000 0 0
NFAT4/CK1 alpha -0.046 0.039 0.16 4 -0.21 15 19
MEF2D/NFAT1/Cbp/p300 -0.05 0.13 -10000 0 -0.24 128 128
CABIN1 -0.004 0.062 0.25 1 -0.25 16 17
CALM1 0 0.058 -10000 0 -0.28 16 16
RAN 0.03 0.005 -10000 0 -10000 0 0
MAP3K1 0.028 0.016 -10000 0 -0.28 1 1
CAMK4 0.029 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.009 0.075 1 -10000 0 1
MAPK3 0.005 0.087 -10000 0 -0.28 47 47
YWHAH 0.029 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.038 0.017 -10000 0 -10000 0 0
YWHAB 0.029 0.009 -10000 0 -10000 0 0
MAPK8 0.009 0.03 -10000 0 -10000 0 0
MAPK9 0.03 0.014 -10000 0 -0.28 1 1
YWHAG 0.029 0.023 -10000 0 -0.28 3 3
FKBP1A 0.029 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.043 0.11 0.28 5 -0.37 12 17
PRKCH 0.03 0.019 -10000 0 -0.28 2 2
CABIN1/Cbp/p300 0.007 0.054 -10000 0 -0.25 7 7
CASP3 0.009 0.028 -10000 0 -10000 0 0
PIM1 0.03 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.019 -10000 0 -10000 0 0
apoptosis 0.01 0.034 0.21 1 -0.15 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.059 -10000 0 -0.24 13 13
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.031 0.006 -10000 0 -10000 0 0
JNK2/NFAT4 0.002 0.072 -10000 0 -0.18 62 62
BAD/BCL-XL 0.043 0.014 -10000 0 -10000 0 0
PRKCD 0.03 0.019 -10000 0 -0.28 2 2
NUP214 0.03 0.005 -10000 0 -10000 0 0
PRKCZ 0.009 0.03 -10000 0 -10000 0 0
PRKCA 0.028 0.027 -10000 0 -0.28 4 4
PRKCG 0.03 0.006 -10000 0 -10000 0 0
PRKCQ 0.023 0.044 -10000 0 -0.28 11 11
FKBP38/BCL2 0.007 0.084 -10000 0 -0.21 72 72
EP300 0.004 0.039 -10000 0 -0.28 3 3
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.029 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.067 0.098 0.27 6 -0.33 12 18
CaM/Ca2+/FKBP38 0.004 0.055 0.14 5 -0.17 29 34
FKBP12/FK506 0.022 0.006 -10000 0 -10000 0 0
CSNK1A1 -0.031 0.029 0.12 5 -0.17 15 20
CaM/Ca2+/CAMK IV 0.009 0.047 0.14 5 -0.17 15 20
NFATc/ERK1 0.061 0.099 0.26 6 -0.32 12 18
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.021 0.077 0.22 1 -0.25 17 18
NR4A1 -0.13 0.15 0.18 3 -0.33 192 195
GSK3B 0.009 0.03 -10000 0 -10000 0 0
positive T cell selection 0 0.03 -10000 0 -0.18 4 4
NFAT1/CK1 alpha -0.022 0.055 0.23 5 -0.21 11 16
RCH1/ KPNB1 0.006 0.016 -10000 0 -10000 0 0
YWHAQ 0.031 0.005 -10000 0 -10000 0 0
PRKACA 0.009 0.028 -10000 0 -10000 0 0
AKAP5 0.031 0.005 -10000 0 -10000 0 0
MEF2D 0.007 0.034 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.066 0.096 0.26 4 -0.33 11 15
CREBBP 0.003 0.045 -10000 0 -0.28 6 6
BCL2 -0.005 0.097 -10000 0 -0.28 60 60
Noncanonical Wnt 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
NFATC2 0.022 0.044 -10000 0 -0.28 11 11
GNB1/GNG2 0.049 0.085 -10000 0 -0.24 5 5
mol:DAG -0.001 0.079 0.17 30 -0.26 3 33
PLCG1 -0.001 0.081 0.18 30 -0.26 3 33
YES1 0.002 0.067 0.2 8 -0.23 10 18
FZD3 0.021 0.027 -10000 0 -0.28 3 3
FZD6 0.025 0.018 -10000 0 -0.28 1 1
G protein 0.055 0.098 0.27 22 -0.27 3 25
MAP3K7 -0.016 0.071 0.23 8 -0.24 3 11
mol:Ca2+ 0 0.078 0.17 30 -0.25 3 33
mol:IP3 -0.001 0.079 0.17 30 -0.26 3 33
NLK -0.018 0.16 -10000 0 -0.79 24 24
GNB1 0.03 0.015 -10000 0 -0.28 1 1
CAMK2A -0.009 0.075 0.21 12 -0.25 3 15
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.011 0.066 -10000 0 -0.23 11 11
CSNK1A1 0.031 0.005 -10000 0 -10000 0 0
GNAS 0 0.065 0.18 6 -0.22 11 17
GO:0007205 0.001 0.076 0.21 12 -0.26 3 15
WNT6 0.031 0.004 -10000 0 -10000 0 0
WNT4 0.031 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.033 0.088 0.28 11 -0.28 5 16
GNG2 0.029 0.027 -10000 0 -0.28 4 4
WNT5A 0.03 0.019 -10000 0 -0.28 2 2
WNT11 0.027 0.011 -10000 0 -10000 0 0
CDC42 -0.001 0.066 0.18 17 -0.27 2 19
Paxillin-dependent events mediated by a4b1

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
CRKL 0.03 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.028 -10000 0 -10000 0 0
DOCK1 0.03 0.014 -10000 0 -0.28 1 1
ITGA4 0.029 0.008 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.024 -10000 0 -0.2 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.05 0.027 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.029 0.037 -10000 0 -0.18 12 12
lamellipodium assembly -0.038 0.14 -10000 0 -0.37 60 60
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
PI3K 0.012 0.062 -10000 0 -0.2 37 37
ARF6 0.031 0.004 -10000 0 -10000 0 0
TLN1 0.03 0.019 -10000 0 -0.28 2 2
PXN -0.03 0.027 -10000 0 -0.2 11 11
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
ARF6/GTP 0.055 0.051 -10000 0 -0.16 9 9
cell adhesion 0.058 0.055 -10000 0 -0.18 10 10
CRKL/CBL 0.043 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.03 0.033 -10000 0 -0.17 9 9
ITGB1 0.031 0.006 -10000 0 -10000 0 0
ITGB7 0.028 0.03 -10000 0 -0.28 5 5
ARF6/GDP 0.024 0.028 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.027 0.085 -10000 0 -0.17 65 65
p130Cas/Crk/Dock1 0.052 0.029 -10000 0 -0.18 3 3
VCAM1 -0.019 0.11 -10000 0 -0.28 80 80
alpha4/beta1 Integrin/Paxillin/Talin 0.06 0.057 -10000 0 -0.18 10 10
alpha4/beta1 Integrin/Paxillin/GIT1 0.059 0.055 -10000 0 -0.17 9 9
BCAR1 0.027 0.021 -10000 0 -0.28 2 2
mol:GDP -0.057 0.054 0.17 9 -10000 0 9
CBL 0.031 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.011 -10000 0 -10000 0 0
GIT1 0.03 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.06 0.057 -10000 0 -0.18 10 10
Rac1/GTP -0.043 0.15 -10000 0 -0.41 60 60
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.03 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.033 0.048 -10000 0 -0.24 2 2
NT3 (dimer)/TRKC 0.036 0.02 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.048 0.028 -10000 0 -10000 0 0
SHC/Grb2/SOS1/GAB1/PI3K -0.001 0.072 -10000 0 -0.19 45 45
RAPGEF1 0.031 0.005 -10000 0 -10000 0 0
BDNF 0.031 0.005 -10000 0 -10000 0 0
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
DYNLT1 0.002 0.088 -10000 0 -0.28 48 48
NTRK1 0.031 0.005 -10000 0 -10000 0 0
NTRK2 0.031 0.006 -10000 0 -10000 0 0
NTRK3 0.03 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.04 0.01 -10000 0 -10000 0 0
neuron apoptosis 0.004 0.11 0.3 37 -10000 0 37
SHC 2-3/Grb2 -0.005 0.12 -10000 0 -0.32 37 37
SHC1 0.03 0.006 -10000 0 -10000 0 0
SHC2 -0.028 0.14 -10000 0 -0.4 65 65
SHC3 0.01 0.089 -10000 0 -0.41 16 16
STAT3 (dimer) -0.055 0.15 -10000 0 -0.3 147 147
NT3 (dimer)/TRKA 0.048 0.028 -10000 0 -10000 0 0
RIN/GDP 0.047 0.079 0.22 27 -0.26 11 38
GIPC1 0.027 0.011 -10000 0 -10000 0 0
KRAS 0.026 0.012 -10000 0 -10000 0 0
DNAJA3 -0.005 0.053 0.15 1 -0.29 1 2
RIN/GTP 0.022 0.005 -10000 0 -10000 0 0
CCND1 -0.16 0.23 -10000 0 -0.57 137 137
MAGED1 0.029 0.02 -10000 0 -0.28 2 2
PTPN11 0.031 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.057 0.021 -10000 0 -10000 0 0
GRB2 0.03 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.038 0.013 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.042 0.018 -10000 0 -0.2 1 1
ELMO1 0.03 0.007 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.039 0.015 -10000 0 -0.17 1 1
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.03 0.007 -10000 0 -10000 0 0
DOCK1 0.03 0.014 -10000 0 -0.28 1 1
GAB2 0.021 0.048 -10000 0 -0.28 13 13
RIT2 0.03 0.007 -10000 0 -10000 0 0
RIT1 0.029 0.009 -10000 0 -10000 0 0
FRS2 0.03 0.007 -10000 0 -10000 0 0
DNM1 0.031 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.021 0.06 -10000 0 -0.22 3 3
mol:GDP 0.048 0.1 0.27 22 -0.39 11 33
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.022 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.043 0.074 0.22 19 -0.25 10 29
TIAM1 0.03 0.014 -10000 0 -0.28 1 1
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
BDNF (dimer)/TRKB 0.057 0.02 -10000 0 -10000 0 0
KIDINS220/CRKL/C3G 0.043 0.012 -10000 0 -10000 0 0
SHC/RasGAP 0.04 0.023 -10000 0 -0.2 3 3
FRS2 family/SHP2 0.057 0.02 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.067 0.036 -10000 0 -0.17 2 2
RIT1/GTP 0.021 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.025 0.013 -10000 0 -10000 0 0
RAP1/GDP 0.036 0.064 0.17 18 -0.22 12 30
KIDINS220/CRKL 0.03 0.007 -10000 0 -10000 0 0
BDNF (dimer) 0.031 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.016 -10000 0 -0.17 1 1
Schwann cell development -0.009 0.012 -10000 0 -10000 0 0
EHD4 0.029 0.008 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.066 0.033 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.007 0.06 -10000 0 -0.25 16 16
RAP1B 0.03 0.015 -10000 0 -0.28 1 1
RAP1A 0.031 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.024 0.076 0.14 92 -10000 0 92
ABL1 0.027 0.035 -10000 0 -0.28 7 7
SH2B family/GRB2/SOS1 0.043 0.013 -10000 0 -10000 0 0
Rap1/GTP 0.007 0.074 -10000 0 -0.28 11 11
STAT3 -0.055 0.15 -10000 0 -0.3 147 147
axon guidance -0.036 0.05 0.11 53 -10000 0 53
MAPK3 -0.036 0.047 0.18 12 -0.16 41 53
MAPK1 -0.026 0.031 0.18 12 -10000 0 12
CDC42/GDP 0.05 0.08 0.21 30 -0.26 11 41
NTF3 0.025 0.013 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.039 0.012 -10000 0 -10000 0 0
PI3K 0.012 0.062 -10000 0 -0.2 37 37
FRS3 0.03 0.007 -10000 0 -10000 0 0
FAIM 0.03 0.008 -10000 0 -10000 0 0
GAB1 0.029 0.02 -10000 0 -0.28 2 2
RASGRF1 -0.005 0.053 0.15 1 -0.19 1 2
SOS1 0.03 0.007 -10000 0 -10000 0 0
MCF2L -0.01 0.061 0.17 57 -10000 0 57
RGS19 0.028 0.01 -10000 0 -10000 0 0
CDC42 0.031 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.078 0.28 3 -0.39 5 8
Rac1/GDP 0.048 0.08 0.22 28 -0.26 11 39
NGF (dimer)/TRKA/GRIT 0.021 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.088 0.24 -10000 0 -0.88 37 37
NGF (dimer)/TRKA/NEDD4-2 0.038 0.016 -10000 0 -0.17 1 1
MAP2K1 -0.027 0.067 0.17 41 -10000 0 41
NGFR 0.031 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.058 -10000 0 -0.19 42 42
RAS family/GTP/PI3K 0.018 0.061 -10000 0 -0.19 18 18
FRS2 family/SHP2/GRB2/SOS1 0.08 0.038 -10000 0 -10000 0 0
NRAS 0.018 0.016 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.013 -10000 0 -10000 0 0
PRKCI 0.013 0.016 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.03 0.007 -10000 0 -10000 0 0
PRKCZ 0.03 0.006 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.036 -10000 0 -10000 0 0
RASA1 0.027 0.024 -10000 0 -0.28 3 3
TRKA/c-Abl 0.041 0.03 -10000 0 -0.2 7 7
SQSTM1 0.03 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.041 0.071 -10000 0 -0.17 40 40
NGF (dimer)/TRKA/p62/Atypical PKCs 0.027 0.037 -10000 0 -10000 0 0
MATK 0.029 0.009 -10000 0 -10000 0 0
NEDD4L 0.029 0.016 -10000 0 -0.28 1 1
RAS family/GDP -0.01 0.033 -10000 0 -0.19 11 11
NGF (dimer)/TRKA 0.002 0.051 0.17 1 -0.22 3 4
Rac1/GTP -0.007 0.042 -10000 0 -0.2 5 5
FRS2 family/SHP2/CRK family 0.074 0.046 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.032 0.036 0.24 1 -10000 0 1
KIRREL 0.025 0.03 -10000 0 -0.053 51 51
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.032 0.037 -10000 0 -0.24 1 1
PLCG1 0.03 0.007 -10000 0 -10000 0 0
ARRB2 0.03 0.007 -10000 0 -10000 0 0
WASL 0.03 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.067 0.039 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.018 0.034 -10000 0 -0.21 1 1
FYN -0.002 0.065 0.15 78 -0.27 1 79
mol:Ca2+ 0.063 0.039 -10000 0 -0.2 1 1
mol:DAG 0.065 0.04 -10000 0 -0.2 1 1
NPHS2 0.027 0.027 -10000 0 -0.049 51 51
mol:IP3 0.065 0.04 -10000 0 -0.2 1 1
regulation of endocytosis 0.034 0.056 -10000 0 -0.26 1 1
Nephrin/NEPH1/podocin/Cholesterol 0.052 0.03 -10000 0 -0.19 1 1
establishment of cell polarity 0.032 0.036 -10000 0 -0.24 1 1
Nephrin/NEPH1/podocin/NCK1-2 0.084 0.047 -10000 0 -0.2 1 1
Nephrin/NEPH1/beta Arrestin2 0.036 0.058 -10000 0 -0.26 1 1
NPHS1 0.024 0.026 -10000 0 -0.049 51 51
Nephrin/NEPH1/podocin 0.034 0.054 0.19 3 -0.11 51 54
TJP1 0.029 0.008 -10000 0 -10000 0 0
NCK1 0.028 0.01 -10000 0 -10000 0 0
NCK2 0.031 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.066 0.041 -10000 0 -0.2 1 1
CD2AP 0.029 0.02 -10000 0 -0.28 2 2
Nephrin/NEPH1/podocin/GRB2 0.067 0.04 -10000 0 -0.2 1 1
GRB2 0.03 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.009 0.072 0.15 84 -0.18 1 85
cytoskeleton organization -0.012 0.049 0.2 12 -0.23 1 13
Nephrin/NEPH1 0.035 0.019 -10000 0 -0.16 1 1
Nephrin/NEPH1/ZO-1 0.052 0.031 -10000 0 -0.2 1 1
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.025 0.013 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.022 -10000 0 -10000 0 0
CDKN1B 0.021 0.068 0.19 35 -0.31 8 43
CDKN1A 0.008 0.063 0.19 8 -0.3 9 17
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.013 -10000 0 -10000 0 0
FOXO3 0.011 0.055 0.19 3 -0.3 8 11
AKT1 0.018 0.056 -10000 0 -0.33 9 9
BAD 0.031 0.003 -10000 0 -10000 0 0
AKT3 -0.12 0.12 -10000 0 -0.23 292 292
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.012 0.058 -10000 0 -0.31 9 9
AKT1/ASK1 0.037 0.063 0.21 2 -0.3 11 13
BAD/YWHAZ 0.047 0.029 -10000 0 -10000 0 0
RICTOR 0.029 0.008 -10000 0 -10000 0 0
RAF1 0.031 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.061 0.29 11 -0.2 2 13
TSC1 0.012 0.05 -10000 0 -0.29 7 7
YWHAZ 0.027 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.042 0.065 0.22 2 -0.31 11 13
EP300 0.027 0.024 -10000 0 -0.28 3 3
mol:GDP 0.018 0.056 -10000 0 -0.33 9 9
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.01 0.055 -10000 0 -0.3 10 10
YWHAQ 0.031 0.005 -10000 0 -10000 0 0
TBC1D4 -0.012 0.01 0.2 1 -10000 0 1
MAP3K5 0.027 0.03 -10000 0 -0.28 5 5
MAPKAP1 0.031 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.022 0.065 0.3 7 -0.17 4 11
YWHAH 0.029 0.008 -10000 0 -10000 0 0
AKT1S1 0.01 0.059 0.19 1 -0.31 11 12
CASP9 0.012 0.055 0.19 1 -0.3 9 10
YWHAB 0.029 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.08 0.27 15 -0.31 9 24
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.057 0.02 -10000 0 -10000 0 0
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
SRC 0.03 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.004 0.062 0.22 11 -0.3 8 19
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.033 -10000 0 -0.28 3 3
CHUK 0.014 0.059 0.24 4 -0.3 9 13
BAD/BCL-XL 0.028 0.056 -10000 0 -0.32 8 8
mTORC2 0.036 0.014 -10000 0 -10000 0 0
AKT2 0.008 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.022 0.082 0.25 2 -0.38 9 11
PDPK1 0.031 0.006 -10000 0 -10000 0 0
MDM2 0.015 0.063 0.19 14 -0.31 10 24
MAPKKK cascade -0.042 0.064 0.3 11 -0.22 2 13
MDM2/Cbp/p300 0.045 0.076 0.3 6 -0.3 12 18
TSC1/TSC2 -0.001 0.056 0.23 3 -0.32 10 13
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.072 0.29 6 -0.29 12 18
glucose import -0.018 0.034 0.19 11 -10000 0 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.017 0.045 0.21 3 -0.2 7 10
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.015 0.031 0.19 11 -10000 0 11
GSK3A 0.011 0.057 0.19 5 -0.3 9 14
FOXO1 0.009 0.051 -10000 0 -0.3 7 7
GSK3B 0.012 0.061 0.19 9 -0.31 10 19
SFN 0.03 0.008 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.011 0.076 0.29 14 -0.32 9 23
p27Kip1/14-3-3 family 0.021 0.047 0.23 1 -0.33 2 3
PRKACA 0.027 0.011 -10000 0 -10000 0 0
KPNA1 0.031 0.006 -10000 0 -10000 0 0
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
YWHAG 0.029 0.023 -10000 0 -0.28 3 3
RHEB 0.028 0.009 -10000 0 -10000 0 0
CREBBP 0.026 0.033 -10000 0 -0.28 6 6
Ephrin A reverse signaling

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.036 0.02 -10000 0 -0.17 3 3
EFNA5 0.028 0.024 -10000 0 -0.28 3 3
FYN -0.037 0.05 0.17 12 -0.16 49 61
neuron projection morphogenesis 0.036 0.02 -10000 0 -0.17 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.037 0.02 -10000 0 -0.17 3 3
EPHA5 0.03 0.007 -10000 0 -10000 0 0
E-cadherin signaling 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
E-cadherin/beta catenin-gamma catenin 0.046 0.053 -9999 0 -0.2 20 20
E-cadherin/beta catenin 0.037 0.034 -9999 0 -0.2 9 9
CTNNB1 0.031 0.003 -9999 0 -10000 0 0
JUP 0.022 0.049 -9999 0 -0.28 14 14
CDH1 0.023 0.04 -9999 0 -0.28 9 9
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.023 -10000 0 -0.096 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.12 0.24 10 -0.34 19 29
ERC1 0.027 0.017 -10000 0 -0.28 1 1
RIP2/NOD2 0.03 0.023 -10000 0 -10000 0 0
NFKBIA -0.055 0.059 -10000 0 -0.38 15 15
BIRC2 0.026 0.012 -10000 0 -10000 0 0
IKBKB 0.029 0.008 -10000 0 -10000 0 0
RIPK2 0.022 0.015 -10000 0 -10000 0 0
IKBKG 0.014 0.11 -10000 0 -0.42 25 25
IKK complex/A20 0.039 0.13 0.25 4 -0.39 31 35
NEMO/A20/RIP2 0.021 0.015 -10000 0 -10000 0 0
XPO1 0.028 0.01 -10000 0 -10000 0 0
NEMO/ATM 0.027 0.13 0.24 3 -0.4 34 37
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.031 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.038 0.014 -10000 0 -10000 0 0
IKK complex/ELKS 0.03 0.12 -10000 0 -0.37 33 33
BCL10/MALT1/TRAF6 0.055 0.023 -10000 0 -10000 0 0
NOD2 0.029 0.008 -10000 0 -10000 0 0
NFKB1 0.019 0.049 -10000 0 -0.19 22 22
RELA 0.025 0.029 -10000 0 -0.29 2 2
MALT1 0.028 0.01 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.036 0.02 -10000 0 -10000 0 0
ATM 0.03 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.031 0.049 -10000 0 -0.2 21 21
TRAF6 0.031 0.005 -10000 0 -10000 0 0
PRKCA 0.028 0.027 -10000 0 -0.28 4 4
CHUK 0.03 0.007 -10000 0 -10000 0 0
UBE2D3 0.029 0.008 -10000 0 -10000 0 0
TNF 0.031 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.044 0.065 -10000 0 -0.22 24 24
BCL10 0.031 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.055 0.058 -10000 0 -0.38 15 15
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.023 -10000 0 -0.096 12 12
TNFRSF1A 0.015 0.063 -10000 0 -0.28 23 23
IKK complex 0.038 0.13 0.25 4 -0.39 33 37
CYLD 0.029 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.045 0.13 -10000 0 -0.4 29 29
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.03 0.006 -10000 0 -10000 0 0
SPHK1 0.031 0.006 -10000 0 -10000 0 0
GNAI2 0.031 0.003 -10000 0 -10000 0 0
mol:S1P 0.007 0.009 0.13 3 -10000 0 3
GNAO1 0.028 0.02 -10000 0 -0.28 2 2
mol:Sphinganine-1-P -0.029 0.012 0.19 1 -10000 0 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.037 0.039 0.17 1 -0.26 3 4
GNAI3 0.03 0.007 -10000 0 -10000 0 0
G12/G13 0.043 0.012 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.001 0.03 -10000 0 -0.28 3 3
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.024 0.044 -10000 0 -0.28 11 11
S1P/S1P5/G12 0.02 0.036 0.16 1 -0.26 3 4
S1P/S1P3/Gq -0.051 0.11 -10000 0 -0.35 35 35
S1P/S1P4/Gi 0 0.066 0.18 1 -0.29 11 12
GNAQ 0.022 0.051 -10000 0 -0.28 15 15
GNAZ 0.026 0.031 -10000 0 -0.28 5 5
GNA14 0.029 0.02 -10000 0 -0.28 2 2
GNA15 0.028 0.021 -10000 0 -0.28 2 2
GNA12 0.03 0.007 -10000 0 -10000 0 0
GNA13 0.031 0.005 -10000 0 -10000 0 0
GNA11 -0.066 0.14 -10000 0 -0.28 168 168
ABCC1 0.031 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.035 0.05 -10000 0 -0.22 19 19
FBXW11 0.031 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.033 0.023 0.16 1 -0.18 8 9
NF kappa B1 p50/RelA/I kappa B alpha -0.025 0.057 0.2 2 -0.25 8 10
NFKBIA -0.003 0.041 -10000 0 -0.16 15 15
MAPK14 0.031 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.034 0.024 0.16 1 -0.18 9 10
ARRB2 0.009 0.002 -10000 0 -10000 0 0
REL 0.031 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.037 0.035 0.16 1 -0.18 26 27
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.035 0.025 0.16 1 -0.18 11 12
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.031 0.024 -10000 0 -0.2 9 9
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
NFKB1 -0.03 0.026 0.19 1 -0.2 9 10
RELA 0.03 0.019 -10000 0 -0.28 2 2
positive regulation of anti-apoptosis -0.004 0.042 -10000 0 -0.21 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.029 0.058 0.17 1 -0.25 10 11
SRC 0.03 0.007 -10000 0 -10000 0 0
PI3K 0.012 0.062 -10000 0 -0.2 37 37
NF kappa B1 p50/RelA -0.004 0.042 -10000 0 -0.21 4 4
IKBKB 0.029 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.006 -10000 0 -10000 0 0
SYK 0.027 0.033 -10000 0 -0.28 6 6
I kappa B alpha/PIK3R1 0.01 0.058 0.18 1 -0.22 15 16
cell death -0.029 0.056 0.16 1 -0.24 9 10
NF kappa B1 p105/c-Rel -0.033 0.023 0.16 1 -0.18 8 9
LCK 0.03 0.007 -10000 0 -10000 0 0
BCL3 0.019 0.057 -10000 0 -0.28 19 19
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.008 0.084 -10000 0 -0.21 71 71
AKT1 -0.042 0.12 0.51 1 -0.38 11 12
PTK2B -0.059 0.12 0.3 14 -0.29 33 47
VEGFR2 homodimer/Frs2 -0.068 0.066 0.21 1 -10000 0 1
CAV1 -0.024 0.12 -10000 0 -0.28 96 96
CALM1 0.022 0.053 -10000 0 -0.28 16 16
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.015 0.092 0.31 1 -10000 0 1
endothelial cell proliferation -0.027 0.11 0.35 5 -0.39 5 10
mol:Ca2+ -0.055 0.088 0.32 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.001 0.1 0.28 2 -0.29 1 3
RP11-342D11.1 -0.059 0.073 0.31 3 -10000 0 3
CDH5 0.028 0.01 -10000 0 -10000 0 0
VEGFA homodimer 0.065 0.036 -10000 0 -0.17 1 1
SHC1 0.03 0.006 -10000 0 -10000 0 0
SHC2 0.015 0.065 -10000 0 -0.28 25 25
HRAS/GDP -0.075 0.069 -10000 0 -10000 0 0
SH2D2A 0.031 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.007 0.099 0.42 1 -0.5 3 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.016 0.093 0.31 1 -10000 0 1
VEGFR1 homodimer 0.03 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.015 0.11 0.26 2 -10000 0 2
GRB10 -0.058 0.087 0.28 3 -10000 0 3
PTPN11 0.031 0.004 -10000 0 -10000 0 0
GRB2 0.03 0.006 -10000 0 -10000 0 0
PAK1 0.028 0.016 -10000 0 -0.28 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.005 0.11 0.28 2 -0.29 1 3
HRAS 0.03 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.033 0.1 0.21 1 -0.3 40 41
HIF1A 0.03 0.014 -10000 0 -0.28 1 1
FRS2 0.03 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.002 0.1 0.27 2 -0.29 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.031 0.005 -10000 0 -10000 0 0
Nck/Pak 0.037 0.021 -10000 0 -0.2 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.032 0.1 -10000 0 -0.3 17 17
mol:GDP 0.004 0.1 -10000 0 -10000 0 0
mol:NADP -0.021 0.093 0.35 2 -0.48 3 5
eNOS/Hsp90 -0.021 0.094 0.32 4 -0.46 3 7
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
mol:IP3 -0.055 0.088 0.32 4 -10000 0 4
HIF1A/ARNT 0.042 0.017 -10000 0 -0.2 1 1
SHB 0.031 0.004 -10000 0 -10000 0 0
VEGFA 0.028 0.011 0.13 1 -10000 0 1
VEGFC 0.018 0.057 -10000 0 -0.28 19 19
FAK1/Vinculin -0.046 0.14 0.3 8 -0.36 32 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.031 0.014 -10000 0 -0.28 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.02 0.12 0.28 2 -0.3 32 34
PTPN6 0.028 0.01 -10000 0 -10000 0 0
EPAS1 -0.049 0.14 -10000 0 -0.29 143 143
mol:L-citrulline -0.021 0.093 0.35 2 -0.48 3 5
ITGAV 0.027 0.024 -10000 0 -0.28 3 3
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.003 0.1 0.29 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer -0.013 0.096 -10000 0 -10000 0 0
VEGFR2/3 heterodimer -0.072 0.066 -10000 0 -10000 0 0
VEGFB 0.027 0.037 -10000 0 -0.28 8 8
MAPK11 -0.054 0.098 0.33 6 -0.35 2 8
VEGFR2 homodimer -0.072 0.085 0.36 3 -10000 0 3
FLT1 0.03 0.007 -10000 0 -10000 0 0
NEDD4 0.03 0.008 0.13 1 -10000 0 1
MAPK3 -0.054 0.096 0.34 7 -10000 0 7
MAPK1 -0.048 0.094 0.33 7 -10000 0 7
VEGFA145/NRP2 0.04 0.017 -10000 0 -10000 0 0
VEGFR1/2 heterodimer -0.071 0.067 0.21 1 -10000 0 1
KDR -0.072 0.085 0.36 3 -10000 0 3
VEGFA165/NRP1/VEGFR2 homodimer -0.063 0.074 0.31 3 -10000 0 3
SRC 0.03 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.051 0.098 0.33 9 -10000 0 9
PI3K -0.047 0.093 0.25 2 -0.32 1 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.017 0.091 0.31 1 -10000 0 1
FES -0.058 0.09 0.32 4 -10000 0 4
GAB1 -0.057 0.1 0.28 3 -0.34 10 13
VEGFR2 homodimer/VEGFA homodimer/Src -0.014 0.089 -10000 0 -10000 0 0
CTNNB1 0.031 0.003 -10000 0 -10000 0 0
SOS1 0.03 0.007 -10000 0 -10000 0 0
ARNT 0.03 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.03 0.1 0.32 3 -0.45 4 7
VEGFR2 homodimer/VEGFA homodimer/Yes -0.014 0.091 0.31 1 -10000 0 1
PI3K/GAB1 -0.045 0.14 0.3 1 -0.38 23 24
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.015 0.11 0.29 3 -0.29 1 4
PRKACA 0.027 0.011 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.022 0.099 -10000 0 -0.3 6 6
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
CDC42 -0.059 0.092 0.32 4 -10000 0 4
actin cytoskeleton reorganization -0.016 0.093 0.31 1 -10000 0 1
PTK2 -0.058 0.12 0.32 3 -0.37 33 36
EDG1 -0.059 0.073 0.31 3 -10000 0 3
mol:DAG -0.055 0.088 0.32 4 -10000 0 4
CaM/Ca2+ -0.06 0.087 0.3 3 -0.28 5 8
MAP2K3 -0.051 0.081 0.28 3 -0.29 1 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.068 0.073 0.24 4 -10000 0 4
PLCG1 -0.055 0.089 0.32 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.004 0.1 0.28 2 -10000 0 2
IQGAP1 0.029 0.02 -10000 0 -0.28 2 2
YES1 0.03 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.017 0.094 0.31 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.011 0.087 0.31 1 -10000 0 1
cell migration -0.053 0.13 0.3 6 -0.39 17 23
mol:PI-3-4-5-P3 -0.045 0.089 0.24 3 -0.3 1 4
FYN -0.002 0.095 -10000 0 -0.28 57 57
VEGFB/NRP1 -0.057 0.087 0.3 4 -0.28 3 7
mol:NO -0.021 0.093 0.35 2 -0.48 3 5
PXN 0.024 0.046 -10000 0 -0.28 12 12
HRAS/GTP -0.08 0.057 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.071 0.066 0.26 2 -10000 0 2
VHL 0.031 0.004 -10000 0 -10000 0 0
ITGB3 -0.01 0.1 -10000 0 -0.28 71 71
NOS3 -0.024 0.099 0.42 1 -0.54 3 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.026 0.099 0.31 1 -0.3 5 6
RAC1 0.03 0.007 -10000 0 -10000 0 0
PRKCA -0.057 0.09 0.31 7 -0.28 2 9
PRKCB -0.051 0.085 0.31 6 -10000 0 6
VCL 0.031 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.059 0.073 0.18 19 -10000 0 19
VEGFR1/2 heterodimer/VEGFA homodimer -0.018 0.094 0.31 1 -10000 0 1
VEGFA165/NRP2 0.04 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.075 0.083 0.26 6 -10000 0 6
NRP2 0.03 0.008 -10000 0 -10000 0 0
VEGFC homodimer 0.018 0.057 -10000 0 -0.28 19 19
NCK1 0.028 0.01 -10000 0 -10000 0 0
ROCK1 0.031 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.048 0.14 0.29 9 -0.36 34 43
MAP3K13 -0.049 0.084 0.29 3 -10000 0 3
PDPK1 -0.046 0.087 0.24 1 -10000 0 1
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.052 0.058 -10000 0 -0.17 19 19
MAP4K1 0.028 0.01 -10000 0 -10000 0 0
MAP3K8 0.031 0.005 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.031 0.004 -10000 0 -10000 0 0
CRKL 0.03 0.007 -10000 0 -10000 0 0
MAP3K1 -0.014 0.055 -10000 0 -0.29 9 9
JUN 0 0.063 0.24 1 -0.56 4 5
MAP3K7 -0.012 0.056 0.16 6 -0.24 10 16
GRAP2 0.029 0.009 -10000 0 -10000 0 0
CRK 0.03 0.008 -10000 0 -10000 0 0
MAP2K4 -0.022 0.086 0.26 1 -0.37 18 19
LAT 0.031 0.004 -10000 0 -10000 0 0
LCP2 0.017 0.064 -10000 0 -0.28 24 24
MAPK8 0.006 0.056 -10000 0 -0.58 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.065 -10000 0 -0.23 29 29
LAT/GRAP2/SLP76/HPK1/HIP-55 0.06 0.064 -10000 0 -0.17 19 19
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.072 0.11 0.26 13 -0.42 12 25
Syndecan-4/Syndesmos 0.072 0.099 0.36 2 -0.47 1 3
positive regulation of JNK cascade 0.055 0.12 0.34 3 -0.44 1 4
Syndecan-4/ADAM12 0.039 0.084 -10000 0 -0.47 1 1
CCL5 -0.003 0.096 -10000 0 -0.28 58 58
Rac1/GDP 0.022 0.005 -10000 0 -10000 0 0
DNM2 0.028 0.009 -10000 0 -10000 0 0
ITGA5 0.031 0.006 -10000 0 -10000 0 0
SDCBP 0.029 0.015 -10000 0 -0.28 1 1
PLG -0.01 0.051 -10000 0 -0.25 11 11
ADAM12 0.023 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.03 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.02 0.035 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.061 0.094 0.36 2 -0.47 1 3
Syndecan-4/CXCL12/CXCR4 0.058 0.12 0.37 2 -0.46 1 3
Syndecan-4/Laminin alpha3 0.064 0.099 0.36 2 -0.47 1 3
MDK 0.031 0.004 -10000 0 -10000 0 0
Syndecan-4/FZD7 0.071 0.098 0.36 2 -0.47 1 3
Syndecan-4/Midkine 0.074 0.098 0.36 2 -0.47 1 3
FZD7 0.03 0.007 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.072 0.1 0.36 2 -0.45 1 3
THBS1 -0.005 0.097 -10000 0 -0.28 60 60
integrin-mediated signaling pathway 0.045 0.084 -10000 0 -0.45 1 1
positive regulation of MAPKKK cascade 0.055 0.12 0.34 3 -0.44 1 4
Syndecan-4/TACI 0.073 0.097 0.35 3 -0.47 1 4
CXCR4 0.029 0.015 -10000 0 -0.28 1 1
cell adhesion -0.007 0.044 0.19 9 -0.2 13 22
Syndecan-4/Dynamin 0.07 0.096 0.36 2 -0.47 1 3
Syndecan-4/TSP1 0.063 0.1 0.36 2 -0.47 1 3
Syndecan-4/GIPC 0.065 0.095 0.36 2 -0.47 1 3
Syndecan-4/RANTES 0.064 0.1 0.36 2 -0.47 1 3
ITGB1 0.031 0.006 -10000 0 -10000 0 0
LAMA1 0.025 0.013 -10000 0 -10000 0 0
LAMA3 0.007 0.081 -10000 0 -0.28 40 40
RAC1 0.03 0.007 -10000 0 -10000 0 0
PRKCA -0.026 0.092 0.62 9 -10000 0 9
Syndecan-4/alpha-Actinin 0.073 0.099 0.35 3 -0.47 1 4
TFPI -0.04 0.13 -10000 0 -0.28 125 125
F2 0.02 0.032 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.044 0.011 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.039 0.088 0.34 2 -0.46 1 3
ACTN1 0.026 0.038 -10000 0 -0.28 8 8
TNC 0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/CXCL12 0.063 0.11 0.36 2 -0.47 1 3
FGF6 0.028 0.01 -10000 0 -10000 0 0
RHOA 0.031 0.014 -10000 0 -0.28 1 1
CXCL12 -0.019 0.12 -10000 0 -0.28 89 89
TNFRSF13B 0.03 0.008 -10000 0 -10000 0 0
FGF2 0.03 0.007 -10000 0 -10000 0 0
FGFR1 0.022 0.044 -10000 0 -0.28 11 11
Syndecan-4/PI-4-5-P2 0.04 0.086 0.33 1 -0.46 1 2
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.006 0.048 -10000 0 -0.26 12 12
cell migration -0.013 0.014 -10000 0 -10000 0 0
PRKCD -0.006 0.044 -10000 0 -0.18 5 5
vasculogenesis 0.062 0.1 0.34 3 -0.46 1 4
SDC4 0.049 0.089 0.36 1 -0.49 1 2
Syndecan-4/Tenascin C 0.046 0.086 -10000 0 -0.47 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.018 0.025 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.07 0.097 0.36 2 -0.47 1 3
MMP9 0.01 0.027 -10000 0 -10000 0 0
Rac1/GTP -0.009 0.037 0.17 6 -0.22 10 16
cytoskeleton organization 0.071 0.097 0.34 3 -0.45 1 4
GIPC1 0.027 0.011 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.055 0.11 0.36 2 -0.47 2 4
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.028 0.096 -10000 0 -0.27 33 33
Ran/GTP/Exportin 1/HDAC1 -0.029 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.1 0.2 1 -0.34 32 33
SUMO1 0.031 0.004 -10000 0 -10000 0 0
ZFPM1 0.028 0.01 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 -0.003 0.035 -10000 0 -0.25 4 4
FKBP3 0.03 0.006 -10000 0 -10000 0 0
Histones 0.049 0.065 -10000 0 -0.25 8 8
YY1/LSF 0.003 0.066 -10000 0 -0.24 20 20
SMG5 0.03 0.006 -10000 0 -10000 0 0
RAN 0.031 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.001 0.06 -10000 0 -0.23 30 30
I kappa B alpha/HDAC1 0.017 0.075 -10000 0 -0.25 28 28
SAP18 0.03 0.007 -10000 0 -10000 0 0
RELA -0.005 0.086 0.26 1 -0.4 12 13
HDAC1/Smad7 0.055 0.023 -10000 0 -10000 0 0
RANGAP1 0.029 0.009 -10000 0 -10000 0 0
HDAC3/TR2 0.028 0.054 -10000 0 -0.22 13 13
NuRD/MBD3 Complex 0.008 0.064 0.24 1 -0.24 15 16
NF kappa B1 p50/RelA 0.003 0.1 0.22 1 -0.33 28 29
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.029 0.024 -10000 0 -0.28 3 3
GATA1 0.03 0.007 -10000 0 -10000 0 0
Mad/Max 0.045 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.004 0.084 0.24 1 -0.33 18 19
RBBP7 0.03 0.014 -10000 0 -0.28 1 1
NPC 0.018 0.002 -10000 0 -10000 0 0
RBBP4 0.029 0.008 -10000 0 -10000 0 0
MAX 0.031 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.031 0.006 -10000 0 -10000 0 0
NFKBIA -0.001 0.065 -10000 0 -0.34 16 16
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.003 0.067 0.18 4 -0.3 10 14
SIN3 complex 0.058 0.043 -10000 0 -10000 0 0
SMURF1 0.03 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.035 -10000 0 -0.28 7 7
SAP30 0.029 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.028 -10000 0 -0.28 4 4
YY1/HDAC3 -0.009 0.068 -10000 0 -0.29 18 18
YY1/HDAC2 0.006 0.066 -10000 0 -0.26 18 18
YY1/HDAC1 0.005 0.065 -10000 0 -0.24 19 19
NuRD/MBD2 Complex (MeCP1) 0.01 0.064 0.24 1 -0.27 11 12
PPARG -0.001 0.086 0.28 1 -0.27 29 30
HDAC8/hEST1B 0.049 0.027 -10000 0 -10000 0 0
UBE2I 0.03 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.015 0.063 -10000 0 -0.28 23 23
HDAC3/SMRT (N-CoR2) 0.026 0.06 -10000 0 -0.22 15 15
MBD3L2 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.054 0.022 -10000 0 -10000 0 0
CREBBP 0.026 0.033 -10000 0 -0.28 6 6
NuRD/MBD3/MBD3L2 Complex 0.003 0.086 0.25 1 -0.32 20 21
HDAC1 0.029 0.009 -10000 0 -10000 0 0
HDAC3 0.006 0.038 -10000 0 -0.34 3 3
HDAC2 0.029 0.008 -10000 0 -10000 0 0
YY1 0.002 0.033 -10000 0 -0.29 6 6
HDAC8 0.029 0.008 -10000 0 -10000 0 0
SMAD7 0.03 0.007 -10000 0 -10000 0 0
NCOR2 0.026 0.04 -10000 0 -0.28 9 9
MXD1 0.031 0.004 -10000 0 -10000 0 0
STAT3 0.005 0.048 -10000 0 -0.29 12 12
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.031 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.017 0.069 -10000 0 -0.24 18 18
YY1/SAP30/HDAC1 0.018 0.069 -10000 0 -0.25 16 16
EP300 0.027 0.024 -10000 0 -0.28 3 3
STAT3 (dimer non-phopshorylated) 0.005 0.048 -10000 0 -0.29 12 12
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.065 -10000 0 -0.34 16 16
histone deacetylation 0.01 0.064 0.24 1 -0.27 11 12
STAT3 (dimer non-phopshorylated)/HDAC3 0.001 0.076 -10000 0 -0.32 16 16
nuclear export -0.049 0.027 -10000 0 -10000 0 0
PRKACA 0.027 0.011 -10000 0 -10000 0 0
GATAD2B 0.03 0.014 -10000 0 -0.28 1 1
GATAD2A 0.029 0.016 -10000 0 -0.28 1 1
GATA2/HDAC3 0.026 0.057 -10000 0 -0.22 14 14
GATA1/HDAC1 0.041 0.016 -10000 0 -10000 0 0
GATA1/HDAC3 0.027 0.056 -10000 0 -0.22 14 14
CHD4 0.028 0.01 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.031 0.049 -10000 0 -0.2 21 21
SIN3/HDAC complex/Mad/Max 0.003 0.074 0.24 1 -0.3 14 15
NuRD Complex 0 0.083 0.25 1 -0.33 16 17
positive regulation of chromatin silencing 0.047 0.063 -10000 0 -0.25 8 8
SIN3B 0.028 0.01 -10000 0 -10000 0 0
MTA2 0.031 0.003 -10000 0 -10000 0 0
SIN3A 0.031 0.006 -10000 0 -10000 0 0
XPO1 0.028 0.01 -10000 0 -10000 0 0
SUMO1/HDAC1 0.026 0.052 -10000 0 -0.22 11 11
HDAC complex 0.063 0.039 -10000 0 -0.17 1 1
GATA1/Fog1 0.039 0.017 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.053 0.024 -10000 0 -10000 0 0
TNF 0.031 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.004 0.073 0.24 1 -0.3 14 15
NuRD/MBD2/PRMT5 Complex 0.01 0.064 0.24 1 -0.27 11 12
Ran/GTP/Exportin 1 0.026 0.052 -10000 0 -0.22 12 12
NF kappa B/RelA/I kappa B alpha -0.018 0.087 -10000 0 -0.31 36 36
SIN3/HDAC complex/NCoR1 -0.004 0.083 0.17 3 -0.38 16 19
TFCP2 0.027 0.025 -10000 0 -0.28 3 3
NR2C1 0.03 0.007 -10000 0 -10000 0 0
MBD3 0.029 0.009 -10000 0 -10000 0 0
MBD2 0.03 0.008 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.029 0.009 -10000 0 -10000 0 0
HDAC2 0.03 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.054 0.031 -10000 0 -0.18 5 5
forebrain development -0.003 0.089 -10000 0 -0.44 9 9
GNAO1 0.023 0.026 -10000 0 -0.28 2 2
SMO/beta Arrestin2 0.036 0.026 -10000 0 -10000 0 0
SMO 0.025 0.019 -10000 0 -10000 0 0
ARRB2 0.026 0.017 -10000 0 -10000 0 0
GLI3/SPOP 0.026 0.089 0.26 4 -0.34 13 17
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.031 0.006 -10000 0 -10000 0 0
GNAI2 0.026 0.017 -10000 0 -10000 0 0
SIN3/HDAC complex 0.058 0.044 -10000 0 -10000 0 0
GNAI1 0.019 0.046 -10000 0 -0.28 11 11
XPO1 0.024 0.02 -10000 0 -10000 0 0
GLI1/Su(fu) 0 0.092 -10000 0 -0.56 5 5
SAP30 0.029 0.009 -10000 0 -10000 0 0
mol:GDP 0.025 0.019 -10000 0 -10000 0 0
MIM/GLI2A 0.015 0.036 -10000 0 -0.13 27 27
IFT88 0.024 0.042 -10000 0 -0.28 10 10
GNAI3 0.026 0.017 -10000 0 -10000 0 0
GLI2 -0.003 0.076 0.22 1 -0.34 14 15
GLI3 0.011 0.086 0.25 5 -0.35 13 18
CSNK1D 0.03 0.007 -10000 0 -10000 0 0
CSNK1E 0.029 0.009 -10000 0 -10000 0 0
SAP18 0.03 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.024 0.042 -10000 0 -0.28 10 10
GNG2 0.029 0.027 -10000 0 -0.28 4 4
Gi family/GTP -0.001 0.056 -10000 0 -0.24 10 10
SIN3B 0.028 0.01 -10000 0 -10000 0 0
SIN3A 0.031 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.008 0.095 0.24 2 -0.41 13 15
GLI2/Su(fu) -0.002 0.087 0.2 1 -0.38 18 19
FOXA2 -0.032 0.21 -10000 0 -0.83 34 34
neural tube patterning -0.003 0.089 -10000 0 -0.44 9 9
SPOP 0.031 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.023 0.044 -10000 0 -0.22 3 3
GNB1 0.03 0.015 -10000 0 -0.28 1 1
CSNK1G2 0.029 0.009 -10000 0 -10000 0 0
CSNK1G3 0.03 0.006 -10000 0 -10000 0 0
MTSS1 0.015 0.036 -10000 0 -0.13 27 27
embryonic limb morphogenesis -0.003 0.089 -10000 0 -0.44 9 9
SUFU 0.01 0.018 -10000 0 -10000 0 0
LGALS3 -0.004 0.099 -10000 0 -0.28 62 62
catabolic process 0.017 0.11 -10000 0 -0.43 17 17
GLI3A/CBP 0.024 0.039 -10000 0 -0.29 6 6
KIF3A 0.031 0.006 -10000 0 -10000 0 0
GLI1 -0.004 0.091 -10000 0 -0.46 9 9
RAB23 0.03 0.006 -10000 0 -10000 0 0
CSNK1A1 0.031 0.005 -10000 0 -10000 0 0
IFT172 0.03 0.019 -10000 0 -0.28 2 2
RBBP7 0.03 0.014 -10000 0 -0.28 1 1
Su(fu)/Galectin3 0.006 0.066 -10000 0 -0.21 5 5
GNAZ 0.022 0.034 -10000 0 -0.28 5 5
RBBP4 0.029 0.008 -10000 0 -10000 0 0
CSNK1G1 0.031 0.005 -10000 0 -10000 0 0
PIAS1 0.031 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.011 -10000 0 -10000 0 0
GLI2/SPOP 0.012 0.085 0.21 1 -0.36 15 16
STK36 0.025 0.02 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.007 0.07 -10000 0 -0.34 9 9
PTCH1 -0.018 0.15 -10000 0 -0.95 11 11
MIM/GLI1 -0.005 0.12 -10000 0 -0.59 5 5
CREBBP 0.024 0.04 -10000 0 -0.29 6 6
Su(fu)/SIN3/HDAC complex 0.003 0.098 0.21 2 -0.45 16 18
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.029 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.036 0.019 -10000 0 -0.14 2 2
MDM2/SUMO1 0.026 0.054 -10000 0 -0.22 13 13
HDAC4 0.031 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.034 0.02 -10000 0 -0.14 2 2
SUMO1 0.031 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.004 0.02 0.09 2 -0.18 6 8
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.004 0.051 0.16 36 -0.26 3 39
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.031 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.031 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.027 0.055 -10000 0 -0.22 13 13
SUMO1/HDAC1 0.026 0.052 -10000 0 -0.22 11 11
RANGAP1 0.029 0.009 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.067 0.037 -10000 0 -0.17 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.003 0.035 -10000 0 -0.25 4 4
Ran/GTP 0.012 0.049 -10000 0 -0.21 13 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.03 0.015 -10000 0 -0.28 1 1
UBE2I 0.03 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 -0.009 0.065 0.16 44 -0.22 12 56
NPC 0.018 0.002 -10000 0 -10000 0 0
PIAS2 0.029 0.008 -10000 0 -10000 0 0
PIAS1 0.031 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.03 0.007 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.031 0.006 -9999 0 -10000 0 0
TCEB1 0.03 0.008 -9999 0 -10000 0 0
HIF1A/p53 0.007 0.068 -9999 0 -0.32 17 17
HIF1A -0.005 0.051 -9999 0 -0.3 12 12
COPS5 0.028 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.075 0.05 -9999 0 -10000 0 0
FIH (dimer) 0.03 0.006 -9999 0 -10000 0 0
CDKN2A 0.012 0.015 -9999 0 -10000 0 0
ARNT/IPAS 0.042 0.015 -9999 0 -10000 0 0
HIF1AN 0.03 0.006 -9999 0 -10000 0 0
GNB2L1 0.031 0.005 -9999 0 -10000 0 0
HIF1A/ARNT 0.011 0.066 -9999 0 -0.32 15 15
CUL2 0.028 0.01 -9999 0 -10000 0 0
OS9 0.03 0.014 -9999 0 -0.28 1 1
RACK1/Elongin B/Elongin C 0.057 0.02 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.013 0.066 -9999 0 -0.32 15 15
PHD1-3/OS9 0.054 0.056 -9999 0 -0.17 19 19
HIF1A/RACK1/Elongin B/Elongin C 0.036 0.073 -9999 0 -0.32 14 14
VHL 0.031 0.004 -9999 0 -10000 0 0
HSP90AA1 0.03 0.006 -9999 0 -10000 0 0
HIF1A/JAB1 0.01 0.064 -9999 0 -0.32 14 14
EGLN3 0.016 0.063 -9999 0 -0.28 23 23
EGLN2 0.029 0.008 -9999 0 -10000 0 0
EGLN1 0.03 0.007 -9999 0 -10000 0 0
TP53 -0.008 0.1 -9999 0 -0.28 67 67
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.022 0.067 -9999 0 -0.62 5 5
ARNT 0.03 0.008 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.029 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF 0.002 0.05 -9999 0 -0.31 9 9
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.067 0.045 -10000 0 -0.17 9 9
HDAC3 0.031 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.031 0.011 -10000 0 -10000 0 0
GATA1/HDAC4 0.043 0.013 -10000 0 -10000 0 0
GATA1/HDAC5 0.041 0.025 -10000 0 -0.2 4 4
GATA2/HDAC5 0.04 0.03 -10000 0 -0.2 7 7
HDAC5/BCL6/BCoR 0.043 0.046 -10000 0 -0.18 16 16
HDAC9 0.029 0.009 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.053 0.037 -10000 0 -0.18 10 10
HDAC4/ANKRA2 0.041 0.015 -10000 0 -10000 0 0
HDAC5/YWHAB 0.039 0.026 -10000 0 -0.2 4 4
NPC/RanGAP1/SUMO1/Ubc9 -0.003 0.035 -10000 0 -0.25 4 4
GATA2 0.029 0.024 -10000 0 -0.28 3 3
HDAC4/RFXANK 0.041 0.015 -10000 0 -10000 0 0
BCOR 0.031 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.024 0.013 -10000 0 -10000 0 0
HDAC5 0.028 0.027 -10000 0 -0.28 4 4
GNB1/GNG2 0.042 0.026 -10000 0 -0.2 5 5
Histones -0.016 0.069 -10000 0 -0.23 28 28
ADRBK1 0.031 0.004 -10000 0 -10000 0 0
HDAC4 0.031 0.005 -10000 0 -10000 0 0
XPO1 0.028 0.01 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.026 -10000 0 -0.2 4 4
HDAC4/Ubc9 0.044 0.012 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.04 0.027 -10000 0 -0.2 5 5
TUBA1B 0.031 0.003 -10000 0 -10000 0 0
HDAC6 0.03 0.007 -10000 0 -10000 0 0
HDAC5/RFXANK 0.039 0.026 -10000 0 -0.2 4 4
CAMK4 0.029 0.008 -10000 0 -10000 0 0
Tubulin/HDAC6 0.056 0.022 -10000 0 -10000 0 0
SUMO1 0.031 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.029 0.009 -10000 0 -10000 0 0
GATA1 0.03 0.007 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.029 0.015 -10000 0 -0.28 1 1
NR3C1 0.026 0.042 -10000 0 -0.28 10 10
SUMO1/HDAC4 0.027 0.055 -10000 0 -0.22 13 13
SRF 0.027 0.03 -10000 0 -0.28 5 5
HDAC4/YWHAB 0.042 0.014 -10000 0 -10000 0 0
Tubulin 0.043 0.013 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.042 0.017 -10000 0 -0.2 1 1
GNB1 0.03 0.015 -10000 0 -0.28 1 1
RANGAP1 0.029 0.009 -10000 0 -10000 0 0
BCL6/BCoR 0.033 0.041 -10000 0 -0.2 13 13
HDAC4/HDAC3/SMRT (N-CoR2) 0.057 0.033 -10000 0 -0.18 9 9
HDAC4/SRF 0.054 0.031 -10000 0 -0.18 5 5
HDAC4/ER alpha 0.016 0.077 -10000 0 -0.2 59 59
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.016 0.069 -10000 0 -0.23 28 28
cell motility 0.055 0.022 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.03 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.023 0.003 -10000 0 -10000 0 0
BCL6 0.019 0.048 -10000 0 -0.28 13 13
HDAC4/CaMK II delta B 0.031 0.005 -10000 0 -10000 0 0
Hsp90/HDAC6 0.043 0.013 -10000 0 -10000 0 0
ESR1 -0.004 0.097 -10000 0 -0.28 60 60
HDAC6/HDAC11 0.044 0.012 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.052 -10000 0 -0.22 12 12
NPC 0.018 0.002 -10000 0 -10000 0 0
MEF2C 0.02 0.053 -10000 0 -0.28 16 16
RAN 0.031 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.065 0.068 -10000 0 -0.17 25 25
GNG2 0.029 0.027 -10000 0 -0.28 4 4
NCOR2 0.026 0.04 -10000 0 -0.28 9 9
TUBB2A 0.029 0.008 -10000 0 -10000 0 0
HDAC11 0.031 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
RANBP2 0.031 0.004 -10000 0 -10000 0 0
ANKRA2 0.028 0.009 -10000 0 -10000 0 0
RFXANK 0.029 0.009 -10000 0 -10000 0 0
nuclear import -0.019 0.04 0.21 5 -10000 0 5
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.012 0.06 0.22 11 -10000 0 11
GNAI2 0.031 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.028 0.02 -10000 0 -0.28 2 2
RhoA/GTP 0.012 0.061 -10000 0 -0.22 11 11
negative regulation of cAMP metabolic process 0.001 0.054 -10000 0 -0.19 23 23
GNAZ 0.026 0.031 -10000 0 -0.28 5 5
GNAI3 0.03 0.007 -10000 0 -10000 0 0
GNA12 0.03 0.007 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.054 -10000 0 -0.2 23 23
RhoA/GDP 0.023 0.009 -10000 0 -0.19 1 1
RHOA 0.031 0.014 -10000 0 -0.28 1 1
GNAI1 0.024 0.044 -10000 0 -0.28 11 11
Arf6 trafficking events

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
SLC2A4 0.03 0.007 -10000 0 -10000 0 0
CLTC 0.015 0.067 0.19 2 -0.37 11 13
calcium ion-dependent exocytosis 0.002 0.03 -10000 0 -0.2 7 7
Dynamin 2/GTP -0.021 0.037 0.14 25 -10000 0 25
EXOC4 0.03 0.008 -10000 0 -10000 0 0
CD59 0.002 0.045 0.19 1 -0.36 6 7
CPE -0.028 0.03 -10000 0 -0.17 22 22
CTNNB1 0.031 0.003 -10000 0 -10000 0 0
membrane fusion 0.002 0.028 -10000 0 -0.18 7 7
CTNND1 -0.025 0.047 0.16 32 -10000 0 32
DNM2 0.028 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.05 -10000 0 -0.24 11 11
TSHR -0.023 0.006 -10000 0 -10000 0 0
INS -0.001 0.098 -10000 0 -0.47 22 22
BIN1 0.03 0.019 -10000 0 -0.28 2 2
mol:Choline 0.002 0.028 -10000 0 -0.18 7 7
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.007 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.037 0.14 25 -10000 0 25
JUP -0.001 0.05 -10000 0 -0.39 6 6
ASAP2/amphiphysin II 0.038 0.015 -10000 0 -0.15 2 2
ARF6/GTP 0.023 0.003 -10000 0 -10000 0 0
CDH1 -0.003 0.055 -10000 0 -0.45 6 6
clathrin-independent pinocytosis 0.023 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.03 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.003 -10000 0 -10000 0 0
EXOC2 0.029 0.009 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.049 0.18 1 -0.26 8 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.031 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.065 0.33 7 -0.21 1 8
positive regulation of phagocytosis -0.024 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.04 0.01 -10000 0 -10000 0 0
ACAP1 0.003 0.026 -10000 0 -0.18 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.004 0.047 -10000 0 -0.35 7 7
clathrin heavy chain/ACAP1 0.002 0.061 0.2 4 -0.32 10 14
JIP4/KLC1 0.055 0.021 -10000 0 -10000 0 0
EXOC1 0.03 0.006 -10000 0 -10000 0 0
exocyst 0.009 0.049 0.18 1 -0.26 8 9
RALA/GTP 0.023 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.009 -10000 0 -10000 0 0
receptor recycling 0.023 0.003 -10000 0 -10000 0 0
CTNNA1 -0.025 0.048 0.16 32 -10000 0 32
NME1 -0.023 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0.013 0.072 0.19 2 -0.35 14 16
IL2RA 0.005 0.052 -10000 0 -0.37 7 7
VAMP3 -0.024 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.032 0.066 0.19 2 -0.31 10 12
EXOC6 0.031 0.006 -10000 0 -10000 0 0
PLD1 0.004 0.01 -10000 0 -0.12 1 1
PLD2 0.005 0.013 -10000 0 -0.22 1 1
EXOC5 0.031 0.005 -10000 0 -10000 0 0
PIP5K1C -0.001 0.04 -10000 0 -0.23 8 8
SDC1 0.003 0.046 -10000 0 -0.35 7 7
ARF6/GDP -0.022 0.007 -10000 0 -10000 0 0
EXOC7 0.031 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.068 0.22 1 -0.34 7 8
mol:Phosphatidic acid 0.002 0.028 -10000 0 -0.18 7 7
endocytosis -0.036 0.015 0.15 2 -10000 0 2
SCAMP2 0.03 0.014 -10000 0 -0.28 1 1
ADRB2 0.006 0.069 0.22 4 -0.35 13 17
EXOC3 0.028 0.01 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.026 0.017 0.17 2 -10000 0 2
KLC1 0.03 0.006 -10000 0 -10000 0 0
AVPR2 0.011 0.077 0.22 12 -0.36 13 25
RALA 0.031 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.018 0.066 0.19 1 -0.34 7 8
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.028 0.02 -10000 0 -0.28 2 2
CDC42/GTP 0.012 0.061 -10000 0 -0.22 12 12
PLCG1 -0.016 0.05 0.16 1 -0.22 12 13
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.031 0.003 -10000 0 -10000 0 0
GNAI3 0.03 0.007 -10000 0 -10000 0 0
G12/G13 0.043 0.012 -10000 0 -10000 0 0
cell migration 0.011 0.06 -10000 0 -0.21 12 12
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.024 0.058 -10000 0 -0.24 14 14
MAPK1 -0.013 0.044 -10000 0 -0.24 8 8
S1P/S1P5/Gi 0.001 0.054 -10000 0 -0.2 23 23
GNAI1 0.024 0.044 -10000 0 -0.28 11 11
CDC42/GDP 0.023 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.02 0.005 -10000 0 -10000 0 0
RHOA -0.027 0.029 0.2 8 -0.15 1 9
S1P/S1P4/Gi 0.001 0.054 -10000 0 -0.2 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.031 -10000 0 -0.28 5 5
S1P/S1P4/G12/G13 0.037 0.014 -10000 0 -10000 0 0
GNA12 0.03 0.007 -10000 0 -10000 0 0
GNA13 0.031 0.005 -10000 0 -10000 0 0
CDC42 0.031 0.004 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.02 -9999 0 -0.11 11 11
TRAF2/ASK1 0.038 0.023 -9999 0 -0.17 5 5
ATM 0.03 0.007 -9999 0 -10000 0 0
MAP2K3 -0.018 0.1 -9999 0 -0.31 39 39
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.014 0.09 -9999 0 -0.36 19 19
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.03 0.014 -9999 0 -0.28 1 1
TXN -0.007 0.051 -9999 0 -0.23 28 28
CALM1 0.022 0.053 -9999 0 -0.28 16 16
GADD45A 0.029 0.009 -9999 0 -10000 0 0
GADD45B 0.029 0.009 -9999 0 -10000 0 0
MAP3K1 0.028 0.016 -9999 0 -0.28 1 1
MAP3K6 0.031 0.005 -9999 0 -10000 0 0
MAP3K7 0.03 0.008 -9999 0 -10000 0 0
MAP3K4 0.029 0.009 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.041 0.026 -9999 0 -0.2 5 5
TAK1/TAB family 0.015 0.028 -9999 0 -0.13 2 2
RAC1/OSM/MEKK3 0.055 0.021 -9999 0 -10000 0 0
TRAF2 0.03 0.006 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.007 0.098 -9999 0 -0.27 38 38
TRAF6 0.004 0.001 -9999 0 -10000 0 0
RAC1 0.03 0.007 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.031 0.005 -9999 0 -10000 0 0
CCM2 0.031 0.005 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.035 0.035 -9999 0 -0.17 15 15
MAPK11 0.024 0.013 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.046 0.046 -9999 0 -0.16 20 20
OSM/MEKK3 0.045 0.01 -9999 0 -10000 0 0
TAOK1 0.008 0.003 -9999 0 -10000 0 0
TAOK2 0.009 0.002 -9999 0 -10000 0 0
TAOK3 0.009 0.002 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.031 0.006 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.027 0.03 -9999 0 -0.28 5 5
MAP3K10 0.029 0.009 -9999 0 -10000 0 0
MAP3K3 0.031 0.005 -9999 0 -10000 0 0
TRX/ASK1 0.011 0.055 -9999 0 -0.19 37 37
GADD45/MTK1/MTK1 0.052 0.042 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.03 0.007 -10000 0 -10000 0 0
SMAD2 0.005 0.053 0.18 3 -0.23 2 5
SMAD3 -0.019 0.061 -10000 0 -0.26 7 7
SMAD3/SMAD4 0.053 0.088 -10000 0 -0.5 10 10
SMAD4/Ubc9/PIASy 0.055 0.023 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.009 0.034 -10000 0 -0.22 1 1
PPM1A 0.031 0.005 -10000 0 -10000 0 0
CALM1 0.022 0.053 -10000 0 -0.28 16 16
SMAD2/SMAD4 0.019 0.051 -10000 0 -0.22 2 2
MAP3K1 0.028 0.016 -10000 0 -0.28 1 1
TRAP-1/SMAD4 0.044 0.012 -10000 0 -10000 0 0
MAPK3 0.005 0.087 -10000 0 -0.28 47 47
MAPK1 0.029 0.008 -10000 0 -10000 0 0
NUP214 0.031 0.005 -10000 0 -10000 0 0
CTDSP1 0.029 0.023 -10000 0 -0.28 3 3
CTDSP2 0.03 0.019 -10000 0 -0.28 2 2
CTDSPL 0.031 0.003 -10000 0 -10000 0 0
KPNB1 0.03 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.031 0.004 -10000 0 -10000 0 0
UBE2I 0.03 0.006 -10000 0 -10000 0 0
NUP153 0.029 0.009 -10000 0 -10000 0 0
KPNA2 0.004 0.011 -10000 0 -10000 0 0
PIAS4 0.029 0.009 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.025 0.13 0.77 4 -0.83 1 5
NCK1/PAK1/Dok-R -0.038 0.058 -10000 0 -0.37 2 2
NCK1/Dok-R 0.025 0.08 0.71 1 -0.84 1 2
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.021 -10000 0 -0.18 7 7
RELA 0.03 0.019 -10000 0 -0.28 2 2
SHC1 0.028 0.014 -10000 0 -10000 0 0
Rac/GDP 0.022 0.005 -10000 0 -10000 0 0
F2 0.013 0.047 -10000 0 -0.23 13 13
TNIP2 0.03 0.008 -10000 0 -10000 0 0
NF kappa B/RelA 0.04 0.089 0.69 1 -0.81 1 2
FN1 0.013 0.046 -10000 0 -0.28 12 12
PLD2 -0.006 0.069 0.81 1 -0.86 1 2
PTPN11 0.031 0.004 -10000 0 -10000 0 0
GRB14 0.03 0.007 -10000 0 -10000 0 0
ELK1 -0.015 0.077 0.72 1 -0.82 1 2
GRB7 0.028 0.024 -10000 0 -0.28 3 3
PAK1 0.028 0.016 -10000 0 -0.28 1 1
Tie2/Ang1/alpha5/beta1 Integrin 0.018 0.077 -10000 0 -0.83 1 1
CDKN1A -0.048 0.21 0.73 6 -0.73 34 40
ITGA5 0.031 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.027 0.082 0.71 1 -0.84 1 2
CRK 0.03 0.008 -10000 0 -10000 0 0
mol:NO -0.019 0.12 0.61 7 -0.63 1 8
PLG -0.007 0.068 0.81 1 -0.86 1 2
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.013 0.12 0.71 4 -0.79 1 5
GRB2 0.03 0.006 -10000 0 -10000 0 0
PIK3R1 -0.003 0.091 -10000 0 -0.28 52 52
ANGPT2 -0.02 0.15 0.74 8 -0.65 2 10
BMX -0.007 0.07 0.81 1 -0.86 1 2
ANGPT1 0.004 0.064 0.53 6 -10000 0 6
tube development -0.041 0.14 0.71 7 -0.65 1 8
ANGPT4 0.027 0.017 -10000 0 -10000 0 0
response to hypoxia -0.001 0.009 0.13 1 -10000 0 1
Tie2/Ang1/GRB14 0.018 0.077 0.75 1 -0.87 1 2
alpha5/beta1 Integrin 0.044 0.011 -10000 0 -10000 0 0
FGF2 0.029 0.014 -10000 0 -0.083 3 3
STAT5A (dimer) -0.032 0.19 0.74 6 -0.67 6 12
mol:L-citrulline -0.019 0.12 0.61 7 -0.63 1 8
AGTR1 0.026 0.019 0.13 1 -10000 0 1
MAPK14 0.005 0.1 0.81 2 -0.88 2 4
Tie2/SHP2 0.008 0.098 -10000 0 -0.55 3 3
TEK 0.002 0.1 0.88 1 -0.99 1 2
RPS6KB1 -0.025 0.13 0.72 4 -0.8 1 5
Angiotensin II/AT1 0.021 0.025 0.21 7 -10000 0 7
Tie2/Ang1/GRB2 0.02 0.077 0.75 1 -0.87 1 2
MAPK3 -0.023 0.076 0.73 1 -0.82 1 2
MAPK1 -0.01 0.072 0.73 1 -0.82 1 2
Tie2/Ang1/GRB7 0.018 0.067 -10000 0 -0.87 1 1
NFKB1 0.024 0.042 -10000 0 -0.28 10 10
MAPK8 -0.006 0.071 0.81 1 -0.86 1 2
PI3K -0.024 0.13 0.92 2 -0.93 1 3
FES 0.001 0.12 0.81 2 -0.78 4 6
Crk/Dok-R 0.029 0.082 0.71 1 -0.84 1 2
Tie2/Ang1/ABIN2 0.019 0.076 0.75 1 -0.87 1 2
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.023 0.13 0.65 7 -0.75 1 8
STAT5A 0.023 0.036 -10000 0 -0.28 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.014 0.15 0.72 4 -0.67 1 5
Tie2/Ang2 -0.034 0.15 0.77 5 -0.84 1 6
Tie2/Ang1 0.01 0.075 0.96 1 -0.9 1 2
FOXO1 -0.026 0.14 0.68 7 -0.76 1 8
ELF1 0.026 0.033 0.27 1 -0.24 4 5
ELF2 0.003 0.072 0.91 1 -0.86 1 2
mol:Choline -0.005 0.072 0.81 1 -0.83 1 2
cell migration -0.022 0.037 -10000 0 -0.21 2 2
FYN -0.044 0.15 0.72 7 -0.73 1 8
DOK2 0.026 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle -0.043 0.19 0.72 6 -0.65 34 40
ETS1 0.031 0.025 0.2 6 -0.3 1 7
PXN 0.012 0.14 0.64 5 -0.58 1 6
ITGB1 0.031 0.006 -10000 0 -10000 0 0
NOS3 -0.022 0.13 0.65 6 -0.72 1 7
RAC1 0.03 0.007 -10000 0 -10000 0 0
TNF 0.031 0.027 0.22 7 -10000 0 7
MAPKKK cascade -0.005 0.072 0.81 1 -0.83 1 2
RASA1 0.027 0.024 -10000 0 -0.28 3 3
Tie2/Ang1/Shc 0.022 0.081 0.8 1 -0.87 1 2
NCK1 0.028 0.01 -10000 0 -10000 0 0
vasculogenesis -0.017 0.12 0.6 7 -0.56 1 8
mol:Phosphatidic acid -0.005 0.072 0.81 1 -0.83 1 2
mol:Angiotensin II 0.001 0.011 0.1 2 -10000 0 2
mol:NADP -0.019 0.12 0.61 7 -0.63 1 8
Rac1/GTP -0.02 0.11 0.56 2 -0.64 2 4
MMP2 -0.014 0.084 0.81 1 -0.86 1 2
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.048 0.022 -10000 0 -10000 0 0
RGS9BP 0.028 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.038 0.013 -10000 0 -10000 0 0
mol:ADP -0.015 0.004 -10000 0 -10000 0 0
GNAT2 0.031 0.003 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.051 0.035 -10000 0 -0.18 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.038 0.013 -10000 0 -10000 0 0
GRK7 0.029 0.008 -10000 0 -10000 0 0
CNGB3 0.029 0.009 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.023 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.054 0.18 40 -10000 0 40
Cone PDE6 0.063 0.054 -10000 0 -0.17 6 6
Cone Metarhodopsin II 0.019 0.005 -10000 0 -10000 0 0
Na + (4 Units) 0.05 0.025 -10000 0 -10000 0 0
GNAT2/GDP 0.057 0.041 -10000 0 -0.16 7 7
GNB5 0.026 0.035 -10000 0 -0.28 7 7
mol:GMP (4 units) -0.013 0.06 0.18 49 -10000 0 49
Cone Transducin 0.052 0.023 -10000 0 -10000 0 0
SLC24A2 0.03 0.007 -10000 0 -10000 0 0
GNB3/GNGT2 0.041 0.016 -10000 0 -10000 0 0
GNB3 0.028 0.01 -10000 0 -10000 0 0
GNAT2/GTP 0.023 0.002 -10000 0 -10000 0 0
CNGA3 0.031 0.004 -10000 0 -10000 0 0
ARR3 0.031 0.003 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.038 0.013 -10000 0 -10000 0 0
mol:Pi 0.05 0.035 -10000 0 -0.18 7 7
Cone CNG Channel 0.06 0.037 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.03 0.007 -10000 0 -10000 0 0
RGS9 0.031 0.005 -10000 0 -10000 0 0
PDE6C 0.031 0.006 -10000 0 -10000 0 0
GNGT2 0.031 0.006 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.028 0.009 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.036 0.02 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.022 0.009 -10000 0 -10000 0 0
mol:DAG -0.037 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 -0.028 0.011 -10000 0 -10000 0 0
CaM/Ca2+ -0.046 0.032 -10000 0 -10000 0 0
HIF1A 0.034 0.015 -10000 0 -0.3 1 1
GAB1 0.029 0.02 -10000 0 -0.28 2 2
AKT1 -0.012 0.086 0.28 1 -10000 0 1
PLCG1 -0.037 0.022 -10000 0 -10000 0 0
NOS3 -0.008 0.059 -10000 0 -10000 0 0
CBL 0.031 0.005 -10000 0 -10000 0 0
mol:NO -0.001 0.069 0.4 2 -10000 0 2
FLT1 -0.027 0.008 -10000 0 -10000 0 0
PGF 0.031 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.035 0.025 -10000 0 -10000 0 0
CALM1 0.022 0.053 -10000 0 -0.28 16 16
PIK3CA 0.022 0.015 -10000 0 -10000 0 0
eNOS/Hsp90 0.002 0.077 0.31 1 -10000 0 1
endothelial cell proliferation -0.016 0.047 0.33 1 -0.3 1 2
mol:Ca2+ -0.037 0.022 -10000 0 -10000 0 0
MAPK3 -0.055 0.048 0.33 1 -0.28 1 2
MAPK1 -0.043 0.038 0.33 1 -10000 0 1
PIK3R1 -0.001 0.092 -10000 0 -0.28 53 53
PLGF homodimer 0.031 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.011 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.024 0.12 -10000 0 -0.28 96 96
VEGFA homodimer 0.029 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.031 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.055 0.057 0.31 1 -0.28 1 2
PI3K 0.02 0.062 -10000 0 -10000 0 0
PRKCA -0.041 0.03 -10000 0 -10000 0 0
PRKCB -0.034 0.02 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer -0.033 0.011 -10000 0 -10000 0 0
VEGFA 0.029 0.009 -10000 0 -10000 0 0
VEGFB 0.027 0.037 -10000 0 -0.28 8 8
mol:IP3 -0.037 0.022 -10000 0 -10000 0 0
RASA1 -0.038 0.029 -10000 0 -10000 0 0
NRP2 0.03 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer -0.027 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.037 -10000 0 -0.28 8 8
NCK1 0.028 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.013 0.091 0.4 2 -0.36 3 5
PTPN11 0.031 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.019 0.061 -10000 0 -10000 0 0
mol:L-citrulline -0.001 0.069 0.4 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.05 0.038 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.033 0.026 -10000 0 -10000 0 0
CD2AP 0.029 0.02 -10000 0 -0.28 2 2
PI3K/GAB1 0.038 0.075 -10000 0 -10000 0 0
PDPK1 -0.005 0.092 0.32 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.037 0.024 -10000 0 -10000 0 0
mol:NADP -0.001 0.069 0.4 2 -10000 0 2
HSP90AA1 0.03 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.048 0.037 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.032 0.013 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD 0.011 0.066 -9999 0 -0.23 11 11
FZD6 0.025 0.018 -9999 0 -0.28 1 1
WNT6 0.031 0.004 -9999 0 -10000 0 0
WNT4 0.031 0.004 -9999 0 -10000 0 0
FZD3 0.021 0.027 -9999 0 -0.28 3 3
WNT5A 0.03 0.019 -9999 0 -0.28 2 2
WNT11 0.027 0.011 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.031 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.023 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.041 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.041 0.009 -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 0.031 0.004 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.043 0.049 -10000 0 -0.16 13 13
mol:Na + 0.041 0.051 -10000 0 -0.17 13 13
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.051 0.035 -10000 0 -0.18 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.053 0.057 -10000 0 -0.17 13 13
CNGB1 0.029 0.008 -10000 0 -10000 0 0
RDH5 0.03 0.006 -10000 0 -10000 0 0
SAG 0.031 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.045 0.086 0.31 20 -10000 0 20
Na + (4 Units) -0.064 0.028 -10000 0 -10000 0 0
RGS9 0.031 0.005 -10000 0 -10000 0 0
GNB1/GNGT1 0.043 0.016 -10000 0 -0.2 1 1
GNAT1/GDP 0.057 0.041 -10000 0 -0.16 7 7
GUCY2D 0.03 0.007 -10000 0 -10000 0 0
GNGT1 0.03 0.006 -10000 0 -10000 0 0
GUCY2F 0.031 0.002 -10000 0 -10000 0 0
GNB5 0.026 0.035 -10000 0 -0.28 7 7
mol:GMP (4 units) -0.035 0.017 0.14 2 -10000 0 2
mol:11-cis-retinal 0.03 0.006 -10000 0 -10000 0 0
mol:cGMP 0.052 0.029 -10000 0 -10000 0 0
GNB1 0.03 0.015 -10000 0 -0.28 1 1
Rhodopsin 0.043 0.013 -10000 0 -10000 0 0
SLC24A1 0.031 0.005 -10000 0 -10000 0 0
CNGA1 0.022 0.051 -10000 0 -0.28 15 15
Metarhodopsin II 0.02 0.004 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.069 0.033 -10000 0 -10000 0 0
RGS9BP 0.028 0.01 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.008 0.026 -10000 0 -0.19 2 2
GCAP Family/Ca ++ 0.055 0.018 -10000 0 -10000 0 0
PDE6A/B 0.042 0.014 -10000 0 -10000 0 0
mol:Pi 0.05 0.035 -10000 0 -0.18 7 7
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.054 0.023 -10000 0 -0.16 1 1
PDE6B 0.029 0.008 -10000 0 -10000 0 0
PDE6A 0.031 0.005 -10000 0 -10000 0 0
PDE6G 0.03 0.006 -10000 0 -10000 0 0
RHO 0.031 0.006 -10000 0 -10000 0 0
PDE6 0.066 0.055 -10000 0 -0.17 7 7
GUCA1A 0.03 0.007 -10000 0 -10000 0 0
GC2/GCAP Family 0.073 0.025 -10000 0 -10000 0 0
GUCA1C 0.03 0.007 -10000 0 -10000 0 0
GUCA1B 0.03 0.007 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.043 0.013 -9999 0 -10000 0 0
FBXW11 0.031 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.006 -9999 0 -10000 0 0
CHUK 0.03 0.007 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.079 0.045 -9999 0 -0.17 2 2
NFKB1 0.024 0.042 -9999 0 -0.28 10 10
MAP3K14 0.03 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.037 0.038 -9999 0 -0.2 12 12
RELB 0.029 0.02 -9999 0 -0.28 2 2
NFKB2 0.031 0.005 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.039 0.016 -9999 0 -0.17 2 2
regulation of B cell activation 0.039 0.016 -9999 0 -0.17 2 2
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.031 0.006 -9999 0 -10000 0 0
ITGB7 0.028 0.03 -9999 0 -0.28 5 5
ITGA4 0.029 0.008 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.024 -9999 0 -0.2 4 4
alpha4/beta1 Integrin 0.042 0.014 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0.031 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.043 0.03 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0 0.046 -9999 0 -0.38 8 8
AURKB 0.024 0.013 -9999 0 -10000 0 0
AURKC 0.03 0.007 -9999 0 -10000 0 0
Glypican 2 network

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
MDK 0.031 0.004 -9999 0 -9999 0 0
GPC2 0.03 0.006 -9999 0 -9999 0 0
GPC2/Midkine 0.045 0.01 -9999 0 -9999 0 0
neuron projection morphogenesis 0.045 0.01 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.048 0.028 -9999 0 -0.15 5 5
MAPK9 0.004 0.01 -9999 0 -0.23 1 1
adrenocorticotropin secretion -0.015 0.004 -9999 0 -10000 0 0
GNB1/GNG2 0.038 0.022 -9999 0 -0.17 5 5
GNB1 0.03 0.015 -9999 0 -0.28 1 1
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.004 0.001 -9999 0 -10000 0 0
Gs family/GTP 0.02 0.004 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.003 0 -9999 0 -10000 0 0
GNAL 0.031 0.006 -9999 0 -10000 0 0
GNG2 0.029 0.027 -9999 0 -0.28 4 4
CRH 0.029 0.009 -9999 0 -10000 0 0
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.004 0.001 -9999 0 -10000 0 0
MAPK11 0.004 0.002 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.031 0.005 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.031 0.005 -9999 0 -9999 0 0
PDE3B 0.031 0.005 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 558 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.61.2614 TCGA.61.2613 TCGA.61.2612 TCGA.61.2113
109_MAP3K5 0.065 0.0049 0.015 -0.022
47_PPARGC1A 0.032 0.032 0.032 0.032
105_BMP4 0.032 0.032 0.032 0.032
105_BMP6 0.032 0.032 0.032 0.032
105_BMP7 0 0.032 0.032 0.032
105_BMP2 0 0.032 0.032 0.032
131_RELN/VLDLR 0.081 0.081 0.081 0
30_TGFB1/TGF beta receptor Type II 0.032 0.032 0 0.032
84_STAT5B 0.032 -0.031 -0.031 0.07
84_STAT5A 0.032 -0.031 -0.031 0.07
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV-TP/4393852/GDAC_MergeDataFiles_4397232/OV-TP.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/OV-TP/4466803/GDAC_Gistic2Report_4469340/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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