PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C14X55TB
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C14X55TB
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 57 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 345
Signaling events mediated by Stem cell factor receptor (c-Kit) 243
Signaling mediated by p38-alpha and p38-beta 231
Class IB PI3K non-lipid kinase events 229
Reelin signaling pathway 209
Aurora B signaling 183
EGFR-dependent Endothelin signaling events 164
PLK1 signaling events 161
FOXA2 and FOXA3 transcription factor networks 149
HIF-1-alpha transcription factor network 136
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 914 . 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 ( 914 ).

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 0.3775 345 17616 51 -0.076 0.79 1000 -1000 -0.051 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2659 243 18991 78 -0.57 0.18 1000 -1000 -0.041 -1000
Signaling mediated by p38-alpha and p38-beta 0.2527 231 10199 44 -0.33 0.024 1000 -1000 -0.018 -1000
Class IB PI3K non-lipid kinase events 0.2505 229 687 3 -0.13 -1000 1000 -1000 -0.011 -1000
Reelin signaling pathway 0.2287 209 11740 56 -0.34 0.055 1000 -1000 -0.031 -1000
Aurora B signaling 0.2002 183 12277 67 -0.22 0.28 1000 -1000 -0.027 -1000
EGFR-dependent Endothelin signaling events 0.1794 164 3451 21 -0.21 0.033 1000 -1000 -0.036 -1000
PLK1 signaling events 0.1761 161 13713 85 -0.071 0.25 1000 -1000 -0.024 -1000
FOXA2 and FOXA3 transcription factor networks 0.1630 149 6899 46 -1.1 0.033 1000 -1000 -0.05 -1000
HIF-1-alpha transcription factor network 0.1488 136 10367 76 -0.5 0.034 1000 -1000 -0.046 -1000
EPHB forward signaling 0.1477 135 11491 85 -0.23 0.15 1000 -1000 -0.059 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1455 133 9073 68 -0.36 0.17 1000 -1000 -0.044 -1000
p75(NTR)-mediated signaling 0.1389 127 15885 125 -0.25 0.1 1000 -1000 -0.059 -1000
Glucocorticoid receptor regulatory network 0.1368 125 14360 114 -0.76 0.29 1000 -1000 -0.052 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1346 123 10840 88 -0.3 0.12 1000 -1000 -0.06 -1000
Endothelins 0.1324 121 11678 96 -0.35 0.18 1000 -1000 -0.047 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1269 116 6280 54 -0.34 0.055 1000 -1000 -0.031 -1000
Ephrin B reverse signaling 0.1204 110 5293 48 -0.23 0.11 1000 -1000 -0.027 -1000
IL4-mediated signaling events 0.1171 107 9787 91 -0.68 0.25 1000 -1000 -0.054 -1000
Wnt signaling 0.1116 102 715 7 -0.1 0.019 1000 -1000 -0.013 -1000
Noncanonical Wnt signaling pathway 0.1028 94 2458 26 -0.1 0.024 1000 -1000 -0.037 -1000
IL23-mediated signaling events 0.1028 94 5651 60 -0.31 0.083 1000 -1000 -0.032 -1000
Arf6 signaling events 0.1007 92 5760 62 -0.21 0.053 1000 -1000 -0.026 -1000
IGF1 pathway 0.0985 90 5145 57 -0.11 0.042 1000 -1000 -0.038 -1000
ErbB2/ErbB3 signaling events 0.0963 88 5743 65 -0.28 0.034 1000 -1000 -0.046 -1000
Plasma membrane estrogen receptor signaling 0.0919 84 7295 86 -0.11 0.095 1000 -1000 -0.053 -1000
BMP receptor signaling 0.0908 83 6778 81 -0.4 0.11 1000 -1000 -0.031 -1000
Nongenotropic Androgen signaling 0.0886 81 4251 52 -0.25 0.14 1000 -1000 -0.029 -1000
Signaling events regulated by Ret tyrosine kinase 0.0864 79 6527 82 -0.069 0.1 1000 -1000 -0.058 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0864 79 9541 120 -0.38 0.17 1000 -1000 -0.043 -1000
Signaling events mediated by PTP1B 0.0842 77 5913 76 -0.46 0.079 1000 -1000 -0.027 -1000
Visual signal transduction: Rods 0.0842 77 4054 52 -0.36 0.056 1000 -1000 -0.025 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0832 76 6502 85 -0.25 0.026 1000 -1000 -0.04 -1000
Calcium signaling in the CD4+ TCR pathway 0.0821 75 2332 31 -0.19 0.027 1000 -1000 -0.049 -1000
ErbB4 signaling events 0.0799 73 5091 69 -0.29 0.062 1000 -1000 -0.03 -1000
Aurora C signaling 0.0766 70 495 7 0 0.15 1000 -1000 -0.009 -1000
Effects of Botulinum toxin 0.0766 70 1835 26 -0.004 0.11 1000 -1000 -0.003 -1000
S1P1 pathway 0.0755 69 2495 36 -0.34 0.024 1000 -1000 -0.034 -1000
Glypican 1 network 0.0744 68 3292 48 -0.21 0.044 1000 -1000 -0.021 -1000
amb2 Integrin signaling 0.0744 68 5619 82 -0.36 0.12 1000 -1000 -0.022 -1000
IL6-mediated signaling events 0.0700 64 4812 75 -0.19 0.057 1000 -1000 -0.037 -1000
Syndecan-1-mediated signaling events 0.0689 63 2142 34 -0.076 0.19 1000 -1000 -0.027 -1000
Integrins in angiogenesis 0.0678 62 5208 84 -0.21 0.12 1000 -1000 -0.038 -1000
Ephrin A reverse signaling 0.0667 61 429 7 -0.033 0.023 1000 -1000 -0.003 -1000
Signaling events mediated by the Hedgehog family 0.0646 59 3099 52 -0.12 0.032 1000 -1000 -0.026 -1000
TCR signaling in naïve CD8+ T cells 0.0646 59 5552 93 -0.095 0.093 1000 -1000 -0.047 -1000
LPA receptor mediated events 0.0624 57 5879 102 -0.19 0.12 1000 -1000 -0.045 -1000
Visual signal transduction: Cones 0.0580 53 2022 38 -0.032 0.17 1000 -1000 -0.016 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0569 52 2713 52 -0.11 0.072 1000 -1000 -0.017 -1000
Fc-epsilon receptor I signaling in mast cells 0.0536 49 4757 97 -0.16 0.034 1000 -1000 -0.051 -1000
PDGFR-alpha signaling pathway 0.0536 49 2156 44 -0.32 0.036 1000 -1000 -0.032 -1000
E-cadherin signaling in keratinocytes 0.0536 49 2111 43 -0.19 0.03 1000 -1000 -0.03 -1000
Syndecan-2-mediated signaling events 0.0525 48 3323 69 -0.12 0.12 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 0.0525 48 1685 35 -0.24 0.053 1000 -1000 -0.019 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0514 47 1559 33 -0.4 0.058 1000 -1000 -0.024 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0503 46 1587 34 -0.022 0.062 1000 -1000 -0.02 -1000
Canonical Wnt signaling pathway 0.0503 46 2374 51 -0.29 0.13 1000 -1000 -0.039 -1000
IL12-mediated signaling events 0.0492 45 3936 87 -0.34 0.069 1000 -1000 -0.062 -1000
Presenilin action in Notch and Wnt signaling 0.0492 45 2799 61 -0.29 0.13 1000 -1000 -0.046 -1000
TCGA08_rtk_signaling 0.0470 43 1121 26 -0.19 0.037 1000 -1000 -0.006 -1000
FAS signaling pathway (CD95) 0.0460 42 1983 47 -0.44 0.039 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 0.0460 42 716 17 -0.061 0.023 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class III 0.0438 40 1602 40 -0.34 0.044 1000 -1000 -0.019 -1000
Glypican 2 network 0.0438 40 162 4 0.032 0.055 1000 -1000 0.01 -1000
Rapid glucocorticoid signaling 0.0438 40 819 20 -0.11 0.028 1000 -1000 -0.003 -1000
Nectin adhesion pathway 0.0427 39 2468 63 -0.048 0.044 1000 -1000 -0.04 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0427 39 2942 74 -0.2 0.049 1000 -1000 -0.059 -1000
Aurora A signaling 0.0416 38 2292 60 -0.086 0.18 1000 -1000 -0.012 -1000
LPA4-mediated signaling events 0.0405 37 448 12 -0.12 0.005 1000 -1000 -0.021 -1000
Signaling events mediated by PRL 0.0394 36 1246 34 -0.13 0.034 1000 -1000 -0.035 -1000
Syndecan-4-mediated signaling events 0.0383 35 2383 67 -0.21 0.12 1000 -1000 -0.043 -1000
Regulation of Androgen receptor activity 0.0372 34 2397 70 -0.18 0.11 1000 -1000 -0.044 -1000
Coregulation of Androgen receptor activity 0.0361 33 2511 76 -0.17 0.064 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 0.0350 32 3370 105 -0.19 0.036 1000 -1000 -0.037 -1000
Insulin Pathway 0.0350 32 2396 74 -0.12 0.06 1000 -1000 -0.044 -1000
Regulation of p38-alpha and p38-beta 0.0339 31 1694 54 -0.26 0.051 1000 -1000 -0.046 -1000
Regulation of Telomerase 0.0339 31 3254 102 -0.21 0.15 1000 -1000 -0.043 -1000
BCR signaling pathway 0.0339 31 3136 99 -0.085 0.058 1000 -1000 -0.049 -1000
IL2 signaling events mediated by STAT5 0.0317 29 649 22 0.008 0.12 1000 -1000 -0.028 -1000
TCGA08_retinoblastoma 0.0317 29 237 8 -0.017 0.059 1000 -1000 -0.006 -1000
Regulation of nuclear SMAD2/3 signaling 0.0306 28 3932 136 -0.22 0.075 1000 -1000 -0.029 -1000
IL27-mediated signaling events 0.0306 28 1448 51 -0.19 0.073 1000 -1000 -0.039 -1000
Osteopontin-mediated events 0.0284 26 1002 38 -0.16 0.092 1000 -1000 -0.025 -1000
TCGA08_p53 0.0263 24 168 7 -0.01 0.02 1000 -1000 -0.004 -1000
Arf6 trafficking events 0.0252 23 1655 71 -0.28 0.04 1000 -1000 -0.021 -1000
Ceramide signaling pathway 0.0230 21 1608 76 -0.1 0.063 1000 -1000 -0.026 -1000
Caspase cascade in apoptosis 0.0219 20 1495 74 -0.03 0.056 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0219 20 1372 68 -0.16 0.042 1000 -1000 -0.026 -1000
HIF-2-alpha transcription factor network 0.0219 20 891 43 -0.16 0.16 1000 -1000 -0.047 -1000
FoxO family signaling 0.0219 20 1342 64 -0.017 0.25 1000 -1000 -0.04 -1000
S1P4 pathway 0.0219 20 508 25 -0.013 0.042 1000 -1000 -0.024 -1000
S1P5 pathway 0.0208 19 329 17 -0.006 0.032 1000 -1000 -0.013 -1000
Signaling mediated by p38-gamma and p38-delta 0.0208 19 290 15 -0.025 0.024 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 0.0197 18 1178 65 -0.09 0.055 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 0.0175 16 637 39 -0.081 0.028 1000 -1000 -0.019 -1000
S1P3 pathway 0.0175 16 673 42 -0.013 0.042 1000 -1000 -0.024 -1000
mTOR signaling pathway 0.0164 15 795 53 -0.028 0.026 1000 -1000 -0.033 -1000
IL2 signaling events mediated by PI3K 0.0164 15 875 58 -0.001 0.069 1000 -1000 -0.033 -1000
BARD1 signaling events 0.0153 14 801 57 -0.049 0.11 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 0.0153 14 239 17 0.003 0.06 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0153 14 732 49 -0.004 0.035 1000 -1000 -0.03 -1000
E-cadherin signaling in the nascent adherens junction 0.0153 14 1087 76 -0.026 0.05 1000 -1000 -0.053 -1000
Retinoic acid receptors-mediated signaling 0.0142 13 772 58 -0.054 0.052 1000 -1000 -0.026 -1000
PLK2 and PLK4 events 0.0131 12 38 3 0.016 0.033 1000 -1000 -0.005 -1000
a4b1 and a4b7 Integrin signaling 0.0131 12 62 5 0.023 0.04 1000 -1000 0.014 -1000
TRAIL signaling pathway 0.0120 11 538 48 -0.015 0.041 1000 -1000 -0.034 -1000
p38 MAPK signaling pathway 0.0120 11 499 44 -0.017 0.062 1000 -1000 -0.015 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0109 10 289 28 -0.006 0.049 1000 -1000 -0.019 -1000
IL1-mediated signaling events 0.0109 10 627 62 -0.011 0.063 1000 -1000 -0.034 -1000
E-cadherin signaling events 0.0109 10 54 5 0.009 0.03 1000 -1000 0.011 -1000
IFN-gamma pathway 0.0098 9 633 68 -0.01 0.076 1000 -1000 -0.047 -1000
Class I PI3K signaling events 0.0098 9 679 73 -0.017 0.048 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 0.0098 9 958 97 -0.03 0.056 1000 -1000 -0.052 -1000
EPO signaling pathway 0.0088 8 484 55 0.011 0.08 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0088 8 329 37 -0.007 0.065 1000 -1000 -0.027 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0088 8 728 83 -0.019 0.046 1000 -1000 -0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0088 8 403 45 0.005 0.054 1000 -1000 -0.032 -1000
Canonical NF-kappaB pathway 0.0077 7 301 39 0 0.051 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 0.0077 7 554 75 -0.029 0.061 1000 -1000 -0.032 -1000
Insulin-mediated glucose transport 0.0077 7 250 32 -0.13 0.038 1000 -1000 -0.021 -1000
VEGFR1 specific signals 0.0066 6 354 56 -0.097 0.054 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 0.0055 5 536 104 -0.06 0.057 1000 -1000 -0.032 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0055 5 688 125 -0.097 0.055 1000 -1000 -0.029 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0033 3 89 23 -0.003 0.042 1000 -1000 -0.015 -1000
Circadian rhythm pathway 0.0033 3 76 22 -0.007 0.05 1000 -1000 -0.027 -1000
Arf6 downstream pathway 0.0033 3 156 43 -0.053 0.054 1000 -1000 -0.019 -1000
Paxillin-dependent events mediated by a4b1 0.0033 3 130 36 -0.046 0.05 1000 -1000 -0.034 -1000
Atypical NF-kappaB pathway 0.0022 2 92 31 0 0.032 1000 -1000 -0.013 -1000
Arf1 pathway 0.0011 1 75 54 -0.001 0.044 1000 -1000 -0.017 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 23 27 -0.009 0.055 1000 -1000 -0.038 -1000
Alternative NF-kappaB pathway 0.0000 0 7 13 0 0.066 1000 -1000 0 -1000
Total NA 7215 427569 7203 -21 -990 131000 -131000 -4 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.66 0.39 0.99 433 -0.98 2 435
PLK1 0.4 0.26 0.66 376 -0.87 1 377
BIRC5 0.42 0.27 0.62 469 -0.78 4 473
HSPA1B 0.65 0.39 0.99 430 -0.99 2 432
MAP2K1 0.19 0.12 0.33 304 -10000 0 304
BRCA2 0.66 0.41 1 428 -0.93 3 431
FOXM1 0.78 0.51 1.2 469 -1.2 2 471
XRCC1 0.66 0.4 1 430 -0.99 2 432
FOXM1B/p19 0.13 0.27 0.81 65 -1.1 2 67
Cyclin D1/CDK4 0.57 0.37 0.9 404 -0.94 2 406
CDC2 0.72 0.45 1.1 469 -1 2 471
TGFA 0.57 0.39 0.9 421 -0.96 5 426
SKP2 0.66 0.4 1 429 -0.99 2 431
CCNE1 0.093 0.097 0.31 138 -10000 0 138
CKS1B 0.7 0.43 1 457 -0.99 2 459
RB1 0.33 0.32 0.69 330 -0.65 5 335
FOXM1C/SP1 0.59 0.36 0.9 400 -1.1 3 403
AURKB 0.34 0.31 0.63 373 -0.71 17 390
CENPF 0.76 0.47 1.1 481 -0.99 2 483
CDK4 0.09 0.057 0.26 15 -10000 0 15
MYC 0.38 0.38 0.84 276 -1.1 3 279
CHEK2 0.18 0.12 0.32 337 -10000 0 337
ONECUT1 0.6 0.39 0.93 435 -1 2 437
CDKN2A -0.076 0.12 0.22 11 -0.24 219 230
LAMA4 0.66 0.4 1 427 -0.99 2 429
FOXM1B/HNF6 0.61 0.4 0.97 401 -1.2 2 403
FOS 0.33 0.65 1 308 -0.97 52 360
SP1 0.023 0.023 -10000 0 -0.22 4 4
CDC25B 0.66 0.4 1 424 -0.99 2 426
response to radiation 0.13 0.089 0.24 266 -10000 0 266
CENPB 0.66 0.39 1 414 -0.99 2 416
CENPA 0.72 0.44 1.1 446 -0.99 2 448
NEK2 0.79 0.46 1.1 511 -0.95 2 513
HIST1H2BA 0.65 0.39 0.99 427 -0.99 2 429
CCNA2 0.15 0.13 0.31 367 -10000 0 367
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.69 0.43 1.1 415 -1.1 2 417
CCNB2 0.73 0.45 1.1 457 -0.99 2 459
CCNB1 0.73 0.46 1.1 451 -1 2 453
ETV5 0.66 0.4 0.99 447 -0.99 2 449
ESR1 0.52 0.55 1 381 -0.96 12 393
CCND1 0.6 0.42 0.96 436 -0.96 2 438
GSK3A 0.15 0.094 0.28 183 -10000 0 183
Cyclin A-E1/CDK1-2 0.25 0.17 0.42 384 -10000 0 384
CDK2 0.062 0.03 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.16 0.12 0.29 360 -10000 0 360
FOXM1B/Cbp/p300 0.23 0.29 0.71 86 -1.1 2 88
GAS1 0.6 0.48 0.99 420 -1.1 27 447
MMP2 0.65 0.41 0.99 429 -1.1 7 436
RB1/FOXM1C 0.53 0.39 0.9 384 -0.98 2 386
CREBBP 0.022 0.006 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.33 2 -0.38 394 396
CRKL -0.17 0.21 -10000 0 -0.4 402 402
HRAS -0.13 0.18 -10000 0 -0.36 266 266
mol:PIP3 -0.14 0.2 0.26 1 -0.37 314 315
SPRED1 0.023 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 409 409
FOXO3 -0.14 0.2 0.51 1 -0.36 369 370
AKT1 -0.16 0.21 0.35 1 -0.38 397 398
BAD -0.15 0.2 0.33 1 -0.36 378 379
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 411 411
GSK3B -0.15 0.2 0.51 1 -0.36 374 375
RAF1 -0.098 0.16 0.24 7 -0.3 258 265
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 405 405
STAT1 -0.44 0.52 -10000 0 -1 415 415
HRAS/SPRED1 -0.094 0.16 -10000 0 -0.3 259 259
cell proliferation -0.18 0.22 -10000 0 -0.41 410 410
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.029 -10000 0 -0.59 2 2
RPS6KB1 -0.17 0.22 -10000 0 -0.41 415 415
HRAS/SPRED2 -0.094 0.16 -10000 0 -0.3 230 230
LYN/TEC/p62DOK -0.14 0.22 -10000 0 -0.4 339 339
MAPK3 -0.067 0.12 0.25 12 -0.26 38 50
STAP1 -0.18 0.22 -10000 0 -0.42 410 410
GRAP2 0.016 0.069 0.26 3 -0.59 11 14
JAK2 -0.37 0.45 -10000 0 -0.84 414 414
STAT1 (dimer) -0.43 0.51 -10000 0 -0.98 415 415
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 346 346
actin filament polymerization -0.18 0.22 0.33 1 -0.41 408 409
LYN 0.021 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 414 414
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 361 361
PI3K -0.15 0.22 -10000 0 -0.39 389 389
PTEN 0.022 0.029 -10000 0 -0.59 2 2
SCF/KIT/EPO/EPOR -0.51 0.64 -10000 0 -1.2 410 410
MAPK8 -0.18 0.22 -10000 0 -0.42 410 410
STAT3 (dimer) -0.18 0.22 -10000 0 -0.41 405 405
positive regulation of transcription -0.053 0.11 0.23 14 -0.22 28 42
mol:GDP -0.13 0.19 -10000 0 -0.37 268 268
PIK3C2B -0.16 0.2 -10000 0 -0.42 321 321
CBL/CRKL -0.16 0.2 -10000 0 -0.38 399 399
FER -0.18 0.22 -10000 0 -0.42 412 412
SH2B3 -0.18 0.22 -10000 0 -0.42 411 411
PDPK1 -0.12 0.19 0.32 8 -0.35 272 280
SNAI2 -0.17 0.21 0.28 4 -0.42 366 370
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 416 416
KITLG -0.004 0.063 0.26 10 -0.61 5 15
cell motility -0.32 0.39 -10000 0 -0.73 416 416
PTPN6 0.032 0.018 0.28 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -1 13 13
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 414 414
SOCS1 0.023 0.029 0.26 6 -0.59 1 7
cell migration 0.18 0.22 0.41 416 -10000 0 416
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.044 0.096 0.25 147 -10000 0 147
VAV1 0.024 0.024 0.26 2 -0.59 1 3
GRB10 -0.18 0.22 -10000 0 -0.42 409 409
PTPN11 0.03 0.01 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 413 413
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.076 0.13 0.25 14 -0.28 44 58
CBL 0.022 0.007 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 411 411
MAP2K2 -0.075 0.14 0.26 12 -0.28 44 56
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 297 297
STAT5A -0.27 0.33 -10000 0 -0.62 414 414
GRB2 0.023 0.01 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 366 370
SHC/GRAP2 0.023 0.05 -10000 0 -0.35 13 13
PTPRO -0.18 0.22 -10000 0 -0.42 411 411
SH2B2 -0.18 0.22 -10000 0 -0.42 408 408
DOK1 0.024 0.008 0.26 1 -10000 0 1
MATK -0.19 0.22 -10000 0 -0.42 416 416
CREBBP -0.028 0.072 -10000 0 -10000 0 0
BCL2 -0.16 0.31 -10000 0 -1.2 50 50
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.33 0.51 0.41 3 -1 300 303
MKNK1 0.023 0.004 -10000 0 -10000 0 0
MAPK14 -0.09 0.18 -10000 0 -0.34 297 297
ATF2/c-Jun -0.086 0.17 -10000 0 -0.44 82 82
MAPK11 -0.084 0.18 -10000 0 -0.35 274 274
MITF -0.12 0.21 -10000 0 -0.41 294 294
MAPKAPK5 -0.12 0.21 -10000 0 -0.4 301 301
KRT8 -0.11 0.2 -10000 0 -0.4 282 282
MAPKAPK3 0.023 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.15 0.29 -10000 0 -0.53 301 301
CEBPB -0.11 0.2 0.29 1 -0.4 278 279
SLC9A1 -0.12 0.21 -10000 0 -0.41 295 295
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.21 -10000 0 -0.4 289 289
p38alpha-beta/MNK1 -0.11 0.25 -10000 0 -0.44 294 294
JUN -0.086 0.16 -10000 0 -0.44 82 82
PPARGC1A -0.21 0.33 0.27 2 -0.56 358 360
USF1 -0.1 0.19 0.32 3 -0.39 279 282
RAB5/GDP/GDI1 -0.083 0.16 -10000 0 -0.3 294 294
NOS2 -0.11 0.22 0.36 1 -0.51 102 103
DDIT3 -0.11 0.21 -10000 0 -0.4 296 296
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.097 0.17 0.28 3 -0.34 271 274
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 273 273
CREB1 -0.12 0.22 -10000 0 -0.43 298 298
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.12 0.21 -10000 0 -0.41 271 271
RPS6KA4 -0.11 0.21 -10000 0 -0.4 295 295
PLA2G4A -0.13 0.22 -10000 0 -0.43 292 292
GDI1 -0.11 0.21 -10000 0 -0.4 300 300
TP53 -0.15 0.27 -10000 0 -0.53 281 281
RPS6KA5 -0.12 0.21 -10000 0 -0.41 303 303
ESR1 -0.15 0.24 0.29 1 -0.42 336 337
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.12 0.21 -10000 0 -0.4 298 298
MEF2A -0.12 0.21 0.29 1 -0.4 294 295
EIF4EBP1 -0.12 0.22 -10000 0 -0.44 285 285
KRT19 -0.11 0.21 0.32 1 -0.41 282 283
ELK4 -0.1 0.19 0.31 3 -0.38 283 286
ATF6 -0.1 0.19 0.32 3 -0.38 285 288
ATF1 -0.12 0.22 -10000 0 -0.42 300 300
p38alpha-beta/MAPKAPK2 -0.098 0.22 -10000 0 -0.42 259 259
p38alpha-beta/MAPKAPK3 -0.11 0.25 -10000 0 -0.45 273 273
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.13 0.27 0.59 229 -10000 0 229
PI3K Class IB/PDE3B -0.13 0.27 -10000 0 -0.59 229 229
PDE3B -0.13 0.27 -10000 0 -0.59 229 229
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.028 -10000 0 -10000 0 0
VLDLR 0.009 0.091 -10000 0 -0.59 20 20
CRKL 0.023 0.005 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.022 0.021 -10000 0 -0.59 1 1
ITGA3 0.021 0.022 -10000 0 -0.59 1 1
RELN/VLDLR/Fyn -0.21 0.21 -10000 0 -0.38 540 540
MAPK8IP1/MKK7/MAP3K11/JNK1 0.055 0.04 -10000 0 -0.33 4 4
AKT1 -0.15 0.14 -10000 0 -0.27 501 501
MAP2K7 0.024 0.003 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.036 0.057 0.26 53 -10000 0 53
RELN/LRP8/DAB1 -0.17 0.2 0.36 5 -0.34 525 530
LRPAP1/LRP8 0.05 0.05 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.16 0.19 0.32 4 -0.32 514 518
DAB1/alpha3/beta1 Integrin -0.15 0.18 -10000 0 -0.32 386 386
long-term memory -0.2 0.23 0.34 5 -0.37 512 517
DAB1/LIS1 -0.16 0.2 0.3 4 -0.32 524 528
DAB1/CRLK/C3G -0.16 0.18 -10000 0 -0.31 509 509
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.2 0.31 4 -0.32 522 526
ARHGEF2 0.02 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.033 0.18 0.26 11 -0.59 86 97
CDK5R1 0.028 0.037 0.26 21 -10000 0 21
RELN -0.34 0.3 0.26 3 -0.59 535 538
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
RELN/LRP8/Fyn -0.2 0.21 -10000 0 -0.37 517 517
GRIN2A/RELN/LRP8/DAB1/Fyn -0.18 0.23 0.34 4 -0.36 485 489
MAPK8 0.022 0.036 -10000 0 -0.59 3 3
RELN/VLDLR/DAB1 -0.19 0.2 0.33 2 -0.34 540 542
ITGB1 0.023 0.004 -10000 0 -10000 0 0
MAP1B -0.19 0.18 0.22 2 -0.34 527 529
RELN/LRP8 -0.2 0.21 -10000 0 -0.37 528 528
GRIN2B/RELN/LRP8/DAB1/Fyn -0.18 0.21 0.37 3 -0.34 538 541
PI3K 0.032 0.019 -10000 0 -0.44 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.03 0.022 -10000 0 -0.44 1 1
RAP1A -0.18 0.15 0.36 1 -0.31 402 403
PAFAH1B1 0.022 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.023 0.033 0.26 4 -0.59 2 6
CRLK/C3G 0.033 0.009 -10000 0 -10000 0 0
GRIN2B -0.028 0.16 0.26 1 -0.59 70 71
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.09 0.12 -10000 0 -0.34 55 55
neuron adhesion -0.16 0.15 0.3 3 -0.5 17 20
LRP8 0.049 0.075 0.26 96 -10000 0 96
GSK3B -0.15 0.13 -10000 0 -0.26 468 468
RELN/VLDLR/DAB1/Fyn -0.17 0.19 0.32 2 -0.33 516 518
MAP3K11 0.024 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.15 0.18 1 -0.28 510 511
CDK5 0.024 0.012 0.26 2 -10000 0 2
MAPT -0.023 0.2 0.89 14 -0.54 83 97
neuron migration -0.19 0.18 0.28 1 -0.35 467 468
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.091 0.12 -10000 0 -0.35 55 55
RELN/VLDLR -0.18 0.21 -10000 0 -0.35 528 528
Aurora B signaling

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
Condensin I complex 0.12 0.11 0.24 300 -0.26 2 302
STMN1 0.083 0.083 0.28 59 -10000 0 59
Aurora B/RasGAP/Survivin 0.2 0.14 0.34 432 -10000 0 432
Chromosomal passenger complex/Cul3 protein complex 0.01 0.14 0.2 170 -0.25 108 278
BIRC5 0.19 0.12 0.27 602 -10000 0 602
DES -0.16 0.32 0.36 2 -0.58 232 234
Aurora C/Aurora B/INCENP 0.11 0.081 0.33 6 -0.31 1 7
Aurora B/TACC1 0.077 0.098 0.19 17 -0.36 16 33
Aurora B/PP2A 0.11 0.085 0.2 178 -10000 0 178
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.028 0.14 9 -10000 0 9
mitotic metaphase/anaphase transition -0.007 0.006 -10000 0 -10000 0 0
NDC80 0.16 0.13 0.28 424 -10000 0 424
Cul3 protein complex -0.12 0.21 -10000 0 -0.38 349 349
KIF2C 0.16 0.11 0.25 532 -10000 0 532
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.2 0.1 0.26 691 -10000 0 691
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.085 0.2 216 -10000 0 216
SEPT1 0.028 0.036 0.26 20 -10000 0 20
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.026 0.26 10 -10000 0 10
NSUN2/NPM1/Nucleolin 0.081 0.19 0.3 42 -0.45 81 123
PSMA3 0.023 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.074 0.065 0.24 32 -10000 0 32
AURKB 0.15 0.12 0.26 474 -10000 0 474
AURKC 0.025 0.033 0.26 10 -0.59 1 11
CDCA8 0.11 0.12 0.27 316 -10000 0 316
cytokinesis 0.15 0.15 0.32 331 -0.35 5 336
Aurora B/Septin1 0.19 0.18 0.38 326 -0.34 4 330
AURKA 0.12 0.12 0.26 376 -10000 0 376
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.3 -10000 0 -0.59 357 357
BUB1 0.19 0.11 0.26 629 -10000 0 629
hSgo1/Aurora B/Survivin 0.28 0.19 0.43 543 -10000 0 543
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.2 0.15 0.36 320 -10000 0 320
SGOL1 0.18 0.12 0.26 590 -10000 0 590
CENPA 0.18 0.15 0.31 466 -0.23 2 468
NCAPG 0.15 0.12 0.26 469 -10000 0 469
Aurora B/HC8 Proteasome 0.12 0.085 0.21 5 -10000 0 5
NCAPD2 0.023 0.01 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.084 0.2 182 -10000 0 182
RHOA 0.023 0.005 -10000 0 -10000 0 0
NCAPH 0.13 0.12 0.26 385 -10000 0 385
NPM1 0.073 0.13 0.26 5 -0.37 31 36
RASA1 0.023 0.004 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.084 0.21 5 -10000 0 5
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.22 0.16 0.38 375 -10000 0 375
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
NSUN2 0.078 0.12 0.28 19 -0.31 27 46
MYLK 0.032 0.13 0.24 6 -0.32 88 94
KIF23 0.11 0.12 0.27 285 -10000 0 285
VIM 0.083 0.088 0.38 27 -0.42 2 29
RACGAP1 0.044 0.054 0.28 44 -10000 0 44
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.069 0.14 -10000 0 -0.46 28 28
Chromosomal passenger complex 0.19 0.13 0.28 560 -0.18 1 561
Chromosomal passenger complex/EVI5 0.25 0.17 0.41 435 -10000 0 435
TACC1 0.009 0.081 -10000 0 -0.59 16 16
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.024 0.012 0.26 2 -10000 0 2
EGFR -0.19 0.29 -10000 0 -0.59 312 312
EGF/EGFR -0.16 0.23 -10000 0 -0.39 428 428
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.21 -10000 0 -0.37 325 325
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.09 0.24 0.26 2 -0.59 167 169
EGF/EGFR dimer/SHC -0.16 0.23 -10000 0 -0.42 349 349
mol:GDP -0.12 0.2 -10000 0 -0.37 325 325
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.021 0.16 0.26 1 -0.59 65 66
GRB2/SOS1 0.033 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.34 324 324
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.12 0.19 -10000 0 -0.35 324 324
FRAP1 -0.15 0.17 0.16 3 -0.35 325 328
EGF/EGFR dimer -0.21 0.27 -10000 0 -0.48 431 431
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
ETA receptor/Endothelin-1 -0.001 0.12 -10000 0 -0.43 67 67
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.071 0.05 0.1 4 -0.11 520 524
BUB1B 0.092 0.069 0.16 384 -10000 0 384
PLK1 0.053 0.04 0.098 255 -10000 0 255
PLK1S1 0.027 0.035 0.14 8 -0.17 17 25
KIF2A 0.044 0.037 0.16 11 -10000 0 11
regulation of mitotic centrosome separation 0.053 0.04 0.097 255 -10000 0 255
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.25 0.15 0.33 645 -10000 0 645
WEE1 0.047 0.06 0.24 1 -0.28 17 18
cytokinesis 0.13 0.083 0.22 265 -0.35 1 266
PP2A-alpha B56 0.12 0.12 -10000 0 -0.44 20 20
AURKA 0.069 0.054 0.12 407 -0.15 3 410
PICH/PLK1 0.11 0.093 0.22 286 -10000 0 286
CENPE 0.068 0.058 0.14 264 -10000 0 264
RhoA/GTP 0.017 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.044 0.037 0.16 11 -10000 0 11
PPP2CA 0.023 0.004 -10000 0 -10000 0 0
FZR1 0.023 0.004 -10000 0 -10000 0 0
TPX2 0.085 0.056 0.13 498 -0.14 1 499
PAK1 0.021 0.018 0.26 4 -10000 0 4
SPC24 0.17 0.12 0.26 544 -10000 0 544
FBXW11 0.023 0.004 -10000 0 -10000 0 0
CLSPN 0.079 0.072 0.14 404 -0.19 18 422
GORASP1 0.023 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 42 -10000 0 42
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.024 0.019 0.055 130 -10000 0 130
G2 phase of mitotic cell cycle 0.001 0.003 0.014 16 -10000 0 16
STAG2 0.023 0.021 -10000 0 -0.59 1 1
GRASP65/GM130/RAB1/GTP 0.01 0.082 -10000 0 -0.5 22 22
spindle elongation 0.053 0.04 0.097 255 -10000 0 255
ODF2 0.025 0.004 -10000 0 -10000 0 0
BUB1 0.12 0.13 -10000 0 -0.47 26 26
TPT1 0.015 0.056 0.13 1 -0.16 71 72
CDC25C 0.12 0.071 0.16 569 -0.19 17 586
CDC25B 0.029 0.032 0.27 15 -10000 0 15
SGOL1 0.071 0.05 0.11 520 -0.1 4 524
RHOA 0.023 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.071 0.069 0.32 10 -10000 0 10
CDC14B -0.011 0.073 -10000 0 -0.44 25 25
CDC20 0.15 0.12 0.26 488 -10000 0 488
PLK1/PBIP1 0.042 0.051 0.15 140 -10000 0 140
mitosis -0.005 0.005 0.024 3 -10000 0 3
FBXO5 0.032 0.036 0.17 11 -10000 0 11
CDC2 0.004 0.004 0.011 185 -10000 0 185
NDC80 0.17 0.12 0.26 553 -10000 0 553
metaphase plate congression 0.031 0.054 0.15 1 -0.19 41 42
ERCC6L 0.096 0.089 0.25 157 -10000 0 157
NLP/gamma Tubulin 0.025 0.025 0.08 28 -0.087 7 35
microtubule cytoskeleton organization 0.015 0.056 0.13 1 -0.16 71 72
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 13 -10000 0 13
PPP1R12A 0.024 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 13 -10000 0 13
PLK1/PRC1-2 0.22 0.13 0.28 664 -10000 0 664
GRASP65/GM130/RAB1/GTP/PLK1 0.071 0.031 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.045 0.036 0.087 260 -10000 0 260
mitotic prometaphase 0.002 0.005 0.022 41 -10000 0 41
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.051 -10000 0 -0.34 2 2
microtubule-based process 0.18 0.089 0.23 689 -10000 0 689
Golgi organization 0.053 0.04 0.097 255 -10000 0 255
Cohesin/SA2 0.056 0.032 0.15 4 -0.32 1 5
PPP1CB/MYPT1 0.036 0.007 -10000 0 -10000 0 0
KIF20A 0.21 0.1 0.26 691 -10000 0 691
APC/C/CDC20 0.14 0.1 0.24 488 -10000 0 488
PPP2R1A 0.023 0.004 -10000 0 -10000 0 0
chromosome segregation 0.035 0.051 0.14 140 -10000 0 140
PRC1 0.085 0.11 0.26 231 -10000 0 231
ECT2 0.053 0.058 0.23 52 -10000 0 52
C13orf34 0.043 0.034 0.082 259 -10000 0 259
NUDC 0.031 0.054 0.15 1 -0.19 41 42
regulation of attachment of spindle microtubules to kinetochore 0.091 0.069 0.16 384 -10000 0 384
spindle assembly 0.038 0.031 0.092 94 -10000 0 94
spindle stabilization 0.027 0.035 0.14 8 -0.17 17 25
APC/C/HCDH1 0.01 0.066 -10000 0 -0.36 27 27
MKLP2/PLK1 0.18 0.09 0.23 689 -10000 0 689
CCNB1 0.075 0.099 0.27 191 -10000 0 191
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.036 0.067 0.23 1 -0.34 20 21
TUBG1 0.025 0.039 0.15 2 -0.17 25 27
G2/M transition of mitotic cell cycle 0.045 0.047 0.21 10 -10000 0 10
MLF1IP 0.027 0.052 0.14 147 -10000 0 147
INCENP 0.024 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.25 0.27 -10000 0 -0.73 115 115
PCK1 -0.93 0.64 -10000 0 -1.4 565 565
HNF4A -0.24 0.28 -10000 0 -0.84 53 53
KCNJ11 -0.28 0.3 -10000 0 -0.8 120 120
AKT1 -0.17 0.16 -10000 0 -0.4 105 105
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.46 0.48 -10000 0 -1.1 302 302
NKX2-1 -0.039 0.16 0.52 3 -0.54 1 4
ACADM -0.26 0.27 -10000 0 -0.74 111 111
TAT -1.1 0.64 -10000 0 -1.5 649 649
CEBPB 0.023 0.008 -10000 0 -10000 0 0
CEBPA 0.019 0.058 -10000 0 -0.59 8 8
TTR -0.41 0.29 -10000 0 -0.78 219 219
PKLR -0.23 0.27 0.56 4 -0.74 92 96
APOA1 -0.29 0.32 -10000 0 -0.9 72 72
CPT1C -0.25 0.27 0.56 2 -0.73 112 114
ALAS1 -0.16 0.16 -10000 0 -0.75 6 6
TFRC -0.42 0.27 -10000 0 -0.69 328 328
FOXF1 0.017 0.046 0.26 6 -0.59 3 9
NF1 0.026 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.033 0.031 0.26 6 -10000 0 6
CPT1A -0.24 0.27 -10000 0 -0.76 96 96
HMGCS1 -0.25 0.27 -10000 0 -0.74 108 108
NR3C1 -0.12 0.12 -10000 0 -0.31 120 120
CPT1B -0.25 0.27 -10000 0 -0.74 113 113
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.024 -10000 0 -10000 0 0
GCK -0.28 0.33 -10000 0 -0.9 128 128
CREB1 -0.074 0.092 -10000 0 -0.21 124 124
IGFBP1 -0.43 0.55 -10000 0 -1.4 214 214
PDX1 -0.13 0.16 0.51 1 -0.54 6 7
UCP2 -0.25 0.27 0.56 1 -0.75 101 102
ALDOB -0.29 0.29 -10000 0 -0.79 114 114
AFP -0.58 0.52 0.37 1 -0.9 530 531
BDH1 -0.25 0.27 -10000 0 -0.74 105 105
HADH -0.28 0.29 -10000 0 -0.76 132 132
F2 -0.29 0.31 -10000 0 -0.89 71 71
HNF1A 0.033 0.031 0.27 6 -10000 0 6
G6PC -0.18 0.12 -10000 0 -0.55 10 10
SLC2A2 -0.16 0.17 -10000 0 -0.96 1 1
INS 0.021 0.079 0.23 19 -10000 0 19
FOXA1 -0.22 0.24 0.36 3 -0.44 346 349
FOXA3 -0.36 0.21 0.29 12 -0.45 689 701
FOXA2 -0.33 0.33 -10000 0 -0.82 174 174
ABCC8 -0.33 0.4 0.59 1 -0.98 175 176
ALB -0.78 0.55 0.37 1 -1.1 615 616
HIF-1-alpha transcription factor network

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
PKM2 -0.25 0.37 -10000 0 -0.8 183 183
HDAC7 0.025 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.34 0.67 1 -0.75 133 134
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.25 0.37 -10000 0 -0.8 182 182
AP1 -0.11 0.22 -10000 0 -0.45 267 267
ABCG2 -0.27 0.39 -10000 0 -0.82 200 200
HIF1A -0.049 0.083 -10000 0 -0.24 11 11
TFF3 -0.26 0.41 0.7 6 -0.82 214 220
GATA2 0.009 0.098 0.26 11 -0.59 21 32
AKT1 -0.058 0.093 -10000 0 -0.24 47 47
response to hypoxia -0.063 0.084 -10000 0 -0.22 86 86
MCL1 -0.25 0.36 -10000 0 -0.79 177 177
NDRG1 -0.23 0.36 -10000 0 -0.8 158 158
SERPINE1 -0.24 0.38 0.69 3 -0.79 186 189
FECH -0.25 0.37 -10000 0 -0.79 185 185
FURIN -0.25 0.37 -10000 0 -0.8 182 182
NCOA2 0.013 0.082 -10000 0 -0.59 16 16
EP300 -0.063 0.13 0.3 2 -0.33 102 104
HMOX1 -0.25 0.37 -10000 0 -0.8 181 181
BHLHE40 -0.25 0.37 -10000 0 -0.8 183 183
BHLHE41 -0.25 0.38 -10000 0 -0.81 184 184
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.024 0.11 -10000 0 -10000 0 0
ENG -0.018 0.11 0.4 2 -10000 0 2
JUN 0.016 0.059 -10000 0 -0.59 8 8
RORA -0.25 0.37 -10000 0 -0.8 182 182
ABCB1 -0.26 0.44 -10000 0 -1.1 175 175
TFRC -0.25 0.37 0.63 1 -0.8 184 185
CXCR4 -0.25 0.38 -10000 0 -0.8 184 184
TF -0.42 0.46 -10000 0 -0.87 365 365
CITED2 -0.25 0.37 -10000 0 -0.8 180 180
HIF1A/ARNT -0.28 0.42 0.75 3 -0.9 176 179
LDHA -0.041 0.12 -10000 0 -0.74 21 21
ETS1 -0.25 0.37 -10000 0 -0.8 180 180
PGK1 -0.25 0.37 -10000 0 -0.8 184 184
NOS2 -0.25 0.37 -10000 0 -0.8 181 181
ITGB2 -0.25 0.38 0.68 1 -0.8 179 180
ALDOA -0.25 0.37 -10000 0 -0.8 174 174
Cbp/p300/CITED2 -0.26 0.39 -10000 0 -0.88 159 159
FOS -0.16 0.28 -10000 0 -0.59 262 262
HK2 -0.25 0.37 -10000 0 -0.8 180 180
SP1 0.002 0.057 -10000 0 -0.22 4 4
GCK -0.13 0.35 0.54 1 -1.4 58 59
HK1 -0.25 0.37 -10000 0 -0.79 185 185
NPM1 -0.25 0.37 -10000 0 -0.8 182 182
EGLN1 -0.24 0.36 -10000 0 -0.79 175 175
CREB1 0.027 0.004 -10000 0 -10000 0 0
PGM1 -0.25 0.37 -10000 0 -0.79 186 186
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.38 -10000 0 -1 117 117
IGFBP1 -0.32 0.43 -10000 0 -0.87 246 246
VEGFA -0.17 0.3 -10000 0 -0.68 109 109
HIF1A/JAB1 -0.008 0.067 -10000 0 -10000 0 0
CP -0.31 0.45 0.67 2 -0.91 246 248
CXCL12 -0.27 0.4 -10000 0 -0.83 199 199
COPS5 0.024 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 0.034 0.009 -10000 0 -10000 0 0
BNIP3 -0.25 0.37 0.77 1 -0.8 185 186
EGLN3 -0.24 0.38 0.7 2 -0.79 187 189
CA9 -0.21 0.4 0.67 8 -0.79 177 185
TERT -0.24 0.38 0.7 4 -0.8 177 181
ENO1 -0.25 0.37 -10000 0 -0.8 184 184
PFKL -0.25 0.37 -10000 0 -0.79 186 186
NCOA1 0.024 0.021 -10000 0 -0.59 1 1
ADM -0.27 0.4 -10000 0 -0.84 203 203
ARNT -0.037 0.07 -10000 0 -10000 0 0
HNF4A 0.017 0.039 0.27 10 -10000 0 10
ADFP -0.26 0.36 -10000 0 -0.79 192 192
SLC2A1 -0.17 0.29 -10000 0 -0.68 112 112
LEP -0.5 0.42 -10000 0 -0.87 387 387
HIF1A/ARNT/Cbp/p300 -0.21 0.34 0.64 1 -0.78 136 137
EPO -0.097 0.26 0.62 7 -0.69 40 47
CREBBP -0.053 0.12 0.32 1 -0.34 68 69
HIF1A/ARNT/Cbp/p300/HDAC7 -0.2 0.33 -10000 0 -0.76 126 126
PFKFB3 -0.25 0.38 -10000 0 -0.82 173 173
NT5E -0.25 0.38 -10000 0 -0.8 187 187
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.005 0.12 -10000 0 -0.36 86 86
cell-cell adhesion 0.14 0.16 0.32 366 -10000 0 366
Ephrin B/EPHB2/RasGAP 0.031 0.11 0.34 1 -0.33 65 66
ITSN1 0.022 0.029 -10000 0 -0.59 2 2
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.032 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.2 -10000 0 -0.38 373 373
HRAS/GDP -0.13 0.19 -10000 0 -0.42 156 156
Ephrin B/EPHB1/GRB7 -0.12 0.21 -10000 0 -0.37 353 353
Endophilin/SYNJ1 -0.027 0.085 0.23 2 -0.31 64 66
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.12 0.22 -10000 0 -0.37 369 369
endothelial cell migration 0.043 0.02 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.022 -10000 0 -0.59 1 1
PAK1 -0.032 0.1 0.29 4 -0.34 71 75
HRAS 0.024 0.012 0.26 2 -10000 0 2
RRAS -0.027 0.087 0.23 2 -0.31 64 66
DNM1 0.021 0.046 0.26 1 -0.59 5 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.15 0.18 0.35 2 -0.35 388 390
lamellipodium assembly -0.14 0.16 -10000 0 -0.32 366 366
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.17 -10000 0 -0.32 286 286
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
EPHB2 0.027 0.033 0.26 17 -10000 0 17
EPHB3 0.024 0.017 0.26 4 -10000 0 4
EPHB1 -0.23 0.3 0.26 1 -0.59 375 376
EPHB4 0.023 0.004 -10000 0 -10000 0 0
mol:GDP -0.13 0.17 -10000 0 -0.43 144 144
Ephrin B/EPHB2 0.021 0.1 0.32 1 -0.33 65 66
Ephrin B/EPHB3 0.019 0.099 -10000 0 -0.33 61 61
JNK cascade -0.14 0.16 0.36 6 -0.32 372 378
Ephrin B/EPHB1 -0.13 0.22 -10000 0 -0.37 388 388
RAP1/GDP -0.11 0.16 -10000 0 -0.4 127 127
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EFNB3 -0.024 0.16 -10000 0 -0.59 67 67
EFNB1 0.024 0.008 0.26 1 -10000 0 1
Ephrin B2/EPHB1-2 -0.12 0.19 -10000 0 -0.34 373 373
RAP1B 0.023 0.005 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.2 -10000 0 -0.34 377 377
Rap1/GTP -0.12 0.18 -10000 0 -0.33 324 324
axon guidance -0.005 0.12 -10000 0 -0.36 86 86
MAPK3 -0.096 0.15 -10000 0 -0.4 94 94
MAPK1 -0.1 0.15 -10000 0 -0.4 97 97
Rac1/GDP -0.12 0.16 -10000 0 -0.41 138 138
actin cytoskeleton reorganization -0.12 0.13 -10000 0 -0.34 133 133
CDC42/GDP -0.12 0.16 -10000 0 -0.4 140 140
PI3K 0.048 0.022 -10000 0 -10000 0 0
EFNA5 -0.033 0.18 0.26 1 -0.59 82 83
Ephrin B2/EPHB4 0.029 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.089 -10000 0 -0.28 65 65
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.12 0.17 -10000 0 -0.32 343 343
PTK2 0.15 0.27 0.68 182 -10000 0 182
MAP4K4 -0.14 0.16 0.36 6 -0.33 372 378
SRC 0.023 0.005 -10000 0 -10000 0 0
KALRN 0.013 0.079 -10000 0 -0.59 15 15
Intersectin/N-WASP 0.033 0.023 -10000 0 -0.44 2 2
neuron projection morphogenesis -0.12 0.15 0.29 7 -0.43 69 76
MAP2K1 -0.11 0.16 -10000 0 -0.41 99 99
WASL 0.023 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.11 0.2 0.34 1 -0.35 372 373
cell migration -0.12 0.18 0.31 5 -0.44 116 121
NRAS 0.023 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.086 0.23 2 -0.31 64 66
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.19 0.18 0.22 2 -0.34 504 506
HRAS/GTP -0.12 0.19 -10000 0 -0.33 384 384
Ephrin B1/EPHB1-2 -0.12 0.19 0.33 1 -0.34 373 374
cell adhesion mediated by integrin 0.009 0.089 0.3 62 -0.21 17 79
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.12 0.2 0.26 1 -0.34 387 388
RAC1-CDC42/GTP -0.14 0.16 -10000 0 -0.32 347 347
RASA1 0.023 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.16 -10000 0 -0.4 130 130
ruffle organization -0.14 0.17 0.37 4 -0.52 57 61
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.089 0.22 2 -0.32 64 66
Ephrin B/EPHB2/KALRN 0.025 0.12 0.34 1 -0.35 75 76
ROCK1 0.017 0.029 0.2 4 -10000 0 4
RAS family/GDP -0.12 0.12 -10000 0 -0.35 110 110
Rac1/GTP -0.13 0.18 -10000 0 -0.33 366 366
Ephrin B/EPHB1/Src/Paxillin -0.13 0.18 -10000 0 -0.33 375 375
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.1 0.13 0.32 241 -0.21 1 242
NFATC2 -0.016 0.22 0.51 8 -0.62 61 69
NFATC3 -0.049 0.13 -10000 0 -0.29 164 164
CD40LG -0.31 0.52 0.78 6 -0.99 276 282
ITCH -0.006 0.087 -10000 0 -0.26 89 89
CBLB -0.006 0.088 -10000 0 -0.28 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.083 0.38 0.65 43 -0.95 69 112
JUNB 0.024 0.009 0.26 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.11 -10000 0 -0.31 95 95
T cell anergy -0.029 0.14 -10000 0 -0.42 93 93
TLE4 -0.019 0.18 0.37 1 -0.63 46 47
Jun/NFAT1-c-4/p21SNFT -0.19 0.45 0.67 8 -0.86 229 237
AP-1/NFAT1-c-4 -0.33 0.63 0.79 15 -1.2 274 289
IKZF1 -0.009 0.15 0.5 7 -0.5 40 47
T-helper 2 cell differentiation -0.076 0.26 0.53 1 -0.85 56 57
AP-1/NFAT1 -0.1 0.27 0.48 13 -0.48 238 251
CALM1 0.008 0.066 -10000 0 -0.19 2 2
EGR2 -0.27 0.58 0.7 3 -1.5 144 147
EGR3 -0.36 0.65 0.69 3 -1.3 259 262
NFAT1/FOXP3 0.06 0.22 0.48 94 -0.47 55 149
EGR1 -0.17 0.29 -10000 0 -0.59 287 287
JUN 0.013 0.066 -10000 0 -0.6 8 8
EGR4 0.038 0.06 0.27 57 -10000 0 57
mol:Ca2+ -0.013 0.057 -10000 0 -0.18 88 88
GBP3 -0.016 0.17 0.39 2 -0.54 51 53
FOSL1 0.027 0.045 0.26 19 -0.59 2 21
NFAT1-c-4/MAF/IRF4 -0.21 0.47 0.65 7 -0.88 250 257
DGKA -0.011 0.15 0.46 2 -0.48 46 48
CREM 0.022 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.28 0.5 0.65 3 -0.95 273 276
CTLA4 0.046 0.21 0.43 117 -0.51 37 154
NFAT1-c-4 (dimer)/EGR1 -0.3 0.54 0.67 3 -1 284 287
NFAT1-c-4 (dimer)/EGR4 -0.2 0.46 0.61 7 -0.87 254 261
FOS -0.16 0.28 0.21 2 -0.59 268 270
IFNG -0.046 0.27 0.53 11 -0.76 59 70
T cell activation -0.16 0.3 0.73 3 -0.74 96 99
MAF 0.021 0.008 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.17 0.34 0.64 280 -0.59 4 284
TNF -0.27 0.46 0.57 4 -0.91 278 282
FASLG -0.34 0.64 0.8 3 -1.2 277 280
TBX21 0.019 0.13 0.37 11 -0.59 33 44
BATF3 0.021 0.017 0.26 3 -10000 0 3
PRKCQ 0.008 0.12 0.29 10 -0.59 30 40
PTPN1 -0.01 0.15 0.44 3 -0.5 39 42
NFAT1-c-4/ICER1 -0.21 0.45 0.59 3 -0.86 257 260
GATA3 0.009 0.12 0.26 25 -0.59 30 55
T-helper 1 cell differentiation -0.045 0.26 0.53 11 -0.74 60 71
IL2RA -0.084 0.36 0.63 42 -0.75 108 150
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.01 0.15 -10000 0 -0.5 39 39
E2F1 0.098 0.11 0.27 267 -10000 0 267
PPARG -0.11 0.25 -10000 0 -0.59 196 196
SLC3A2 -0.011 0.15 0.37 1 -0.48 46 47
IRF4 -0.02 0.16 0.26 11 -0.59 68 79
PTGS2 -0.36 0.56 0.65 6 -1.1 298 304
CSF2 -0.3 0.5 0.69 9 -0.96 274 283
JunB/Fra1/NFAT1-c-4 -0.19 0.45 0.58 5 -0.84 251 256
IL4 -0.08 0.27 0.53 1 -0.9 55 56
IL5 -0.3 0.5 0.63 7 -0.96 275 282
IL2 -0.16 0.31 0.73 3 -0.76 90 93
IL3 -0.054 0.13 -10000 0 -0.82 17 17
RNF128 -0.049 0.22 0.28 4 -0.68 95 99
NFATC1 -0.17 0.34 0.59 4 -0.64 280 284
CDK4 0.12 0.25 0.64 56 -0.64 1 57
PTPRK -0.012 0.16 0.43 3 -0.54 42 45
IL8 -0.3 0.51 0.6 13 -0.97 272 285
POU2F1 0.021 0.012 0.26 1 -10000 0 1
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.033 0.018 -10000 0 -0.44 1 1
Necdin/E2F1 0.062 0.11 -10000 0 -0.4 26 26
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.057 0.18 -10000 0 -0.34 253 253
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.25 0.35 1 -0.42 327 328
NT-4/5 (dimer)/p75(NTR) -0.25 0.3 -10000 0 -0.52 462 462
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.087 0.16 0.36 1 -0.34 239 240
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.021 0.17 0.26 19 -0.59 72 91
MGDIs/NGR/p75(NTR)/LINGO1 -0.049 0.2 0.35 7 -0.36 246 253
FURIN 0.023 0.009 0.26 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.1 0.22 -10000 0 -0.41 286 286
LINGO1 0.077 0.1 0.26 200 -10000 0 200
Sortilin/TRAF6/NRIF 0.023 0.025 -10000 0 -0.58 1 1
proBDNF (dimer) -0.021 0.17 0.26 19 -0.59 72 91
NTRK1 0.025 0.048 0.26 22 -0.59 2 24
RTN4R 0.03 0.042 0.26 27 -10000 0 27
neuron apoptosis -0.089 0.21 0.35 8 -0.41 177 185
IRAK1 0.025 0.014 0.26 3 -10000 0 3
SHC1 -0.09 0.16 -10000 0 -0.39 195 195
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.053 0.034 -10000 0 -0.33 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.065 0.19 -10000 0 -0.36 249 249
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.075 0.2 -10000 0 -0.38 255 255
Mammalian IAPs/DIABLO 0.056 0.033 -10000 0 -0.35 2 2
proNGF (dimer) 0.015 0.082 0.26 7 -0.59 15 22
MAGED1 0.025 0.011 0.26 2 -10000 0 2
APP 0.023 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.2 0.3 -10000 0 -0.59 330 330
ZNF274 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.074 0.16 -10000 0 -0.33 241 241
NGF 0.015 0.082 0.26 7 -0.59 15 22
cell cycle arrest -0.079 0.16 0.34 11 -0.31 249 260
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.059 0.13 -10000 0 -0.28 178 178
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.21 0.27 -10000 0 -0.45 454 454
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.078 0.2 -10000 0 -0.38 251 251
PSENEN 0.024 0.009 0.26 1 -10000 0 1
mol:ceramide -0.099 0.16 -10000 0 -0.35 250 250
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.049 0.11 -10000 0 -0.37 29 29
p75(NTR)/beta APP -0.1 0.21 -10000 0 -0.42 261 261
BEX1 -0.023 0.24 0.26 141 -0.59 124 265
mol:GDP -0.12 0.17 -10000 0 -0.38 255 255
NGF (dimer) -0.002 0.14 0.34 1 -0.35 114 115
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.033 0.19 0.34 6 -0.33 234 240
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
RAC1/GTP -0.07 0.17 -10000 0 -0.33 251 251
MYD88 0.023 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.078 0.2 -10000 0 -0.38 251 251
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.078 0.075 -10000 0 -10000 0 0
NT3 (dimer) -0.066 0.22 0.26 11 -0.59 135 146
TP53 -0.099 0.18 0.39 5 -0.34 274 279
PRDM4 -0.099 0.17 -10000 0 -0.36 249 249
BDNF (dimer) 0.017 0.21 0.34 16 -0.37 166 182
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.021 -10000 0 -0.59 1 1
activation of caspase activity -0.059 0.18 -10000 0 -0.33 253 253
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.064 0.19 -10000 0 -0.36 247 247
RHOC 0.023 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.14 0.21 0.33 3 -0.42 268 271
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.1 0.16 -10000 0 -0.35 250 250
APH1B 0.023 0.021 -10000 0 -0.59 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.081 0.2 -10000 0 -0.38 253 253
PSEN1 0.023 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.16 0.26 -10000 0 -0.47 348 348
MAPK8 -0.1 0.18 0.3 8 -0.38 240 248
MAPK9 -0.1 0.18 0.3 6 -0.38 242 248
APAF1 0.024 0.002 -10000 0 -10000 0 0
NTF3 -0.067 0.22 0.26 11 -0.59 135 146
NTF4 -0.2 0.3 -10000 0 -0.59 330 330
NDN 0.005 0.1 -10000 0 -0.59 26 26
RAC1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.051 0.17 -10000 0 -0.32 250 250
p75 CTF/Sortilin/TRAF6/NRIF 0.056 0.023 -10000 0 -0.35 1 1
RhoA-B-C/GTP -0.078 0.2 -10000 0 -0.38 251 251
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.074 0.2 -10000 0 -0.36 275 275
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.085 0.21 -10000 0 -0.38 277 277
PRKACB 0.033 0.064 0.26 44 -0.59 3 47
proBDNF (dimer)/p75 ECD 0 0.13 -10000 0 -0.43 74 74
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.039 0.26 10 -0.59 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.093 0.18 0.28 15 -0.36 241 256
BAD -0.12 0.2 0.42 6 -0.39 262 268
RIPK2 0.02 0.017 0.26 3 -10000 0 3
NGFR -0.15 0.27 -10000 0 -0.59 251 251
CYCS -0.093 0.16 0.36 2 -0.34 244 246
ADAM17 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.054 0.16 -10000 0 -0.36 177 177
BCL2L11 -0.12 0.2 0.42 6 -0.39 262 268
BDNF (dimer)/p75(NTR) -0.13 0.24 -10000 0 -0.45 306 306
PI3K -0.065 0.18 -10000 0 -0.36 242 242
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.065 0.18 -10000 0 -0.36 248 248
NDNL2 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.023 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.22 -10000 0 -0.43 270 270
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.065 0.19 -10000 0 -0.36 251 251
TRAF6 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.021 -10000 0 -0.59 1 1
PLG 0.018 0.017 0.26 4 -10000 0 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.12 0.2 -10000 0 -0.39 286 286
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
NGFRAP1 0.023 0.029 -10000 0 -0.59 2 2
CASP3 -0.12 0.18 0.4 6 -0.37 265 271
E2F1 0.095 0.11 0.26 267 -10000 0 267
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.006 0.11 -10000 0 -0.41 15 15
NGF (dimer)/TRKA 0.026 0.069 -10000 0 -0.41 17 17
MMP7 -0.042 0.2 0.26 26 -0.59 103 129
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.054 0.18 -10000 0 -0.34 244 244
MMP3 0.1 0.14 0.26 323 -0.59 11 334
APAF-1/Caspase 9 -0.093 0.12 -10000 0 -0.47 10 10
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.094 0.1 0.45 4 -10000 0 4
SMARCC2 0.024 0.012 -10000 0 -0.2 1 1
SMARCC1 0.023 0.012 -10000 0 -10000 0 0
TBX21 -0.12 0.22 0.4 5 -0.66 69 74
SUMO2 0 0.022 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.036 0.28 19 -10000 0 19
FKBP4 0.024 0.017 0.26 4 -10000 0 4
FKBP5 0.016 0.072 0.26 4 -0.59 12 16
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.33 76 -0.33 7 83
PRL -0.064 0.12 0.58 2 -10000 0 2
cortisol/GR alpha (dimer)/TIF2 0.19 0.27 0.53 278 -0.5 9 287
RELA -0.038 0.1 0.27 2 -0.25 38 40
FGG 0.22 0.24 0.48 299 -0.48 2 301
GR beta/TIF2 0.093 0.15 0.33 101 -0.45 14 115
IFNG -0.32 0.36 0.49 3 -0.72 321 324
apoptosis -0.27 0.31 0.85 1 -0.64 275 276
CREB1 0.063 0.056 -10000 0 -10000 0 0
histone acetylation 0.028 0.13 0.37 48 -0.41 13 61
BGLAP -0.085 0.14 -10000 0 -0.5 16 16
GR/PKAc 0.13 0.13 0.37 64 -0.37 2 66
NF kappa B1 p50/RelA -0.063 0.18 0.46 3 -0.35 130 133
SMARCD1 0.024 0.011 -10000 0 -0.16 1 1
MDM2 0.1 0.11 0.22 293 -10000 0 293
GATA3 0.013 0.12 0.27 25 -0.59 30 55
AKT1 0.019 0.01 -10000 0 -10000 0 0
CSF2 -0.024 0.1 0.49 1 -0.53 3 4
GSK3B 0 0.023 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.8 1 -0.62 131 132
CSN2 0.16 0.19 0.38 258 -0.42 3 261
BRG1/BAF155/BAF170/BAF60A 0.06 0.039 -10000 0 -0.48 4 4
NFATC1 0.023 0.021 -10000 0 -0.59 1 1
POU2F1 0.023 0.016 0.26 1 -10000 0 1
CDKN1A 0.016 0.077 -10000 0 -1.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN 0.02 0.071 0.26 14 -0.59 10 24
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.34 64 -0.32 5 69
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.37 0.4 0.62 2 -0.83 338 340
JUN -0.26 0.29 0.36 7 -0.56 339 346
IL4 -0.12 0.15 -10000 0 -0.54 9 9
CDK5R1 0.021 0.039 0.26 21 -10000 0 21
PRKACA 0.024 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.25 -10000 0 -0.5 419 419
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.34 60 -0.32 5 65
cortisol/GR alpha (monomer) 0.29 0.32 0.62 353 -0.52 3 356
NCOA2 0.009 0.081 -10000 0 -0.59 16 16
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.19 0.29 -10000 0 -0.61 272 272
AP-1/NFAT1-c-4 -0.45 0.46 0.47 6 -0.84 459 465
AFP -0.55 0.65 0.47 1 -1.4 304 305
SUV420H1 0.022 0.006 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.42 114 -10000 0 114
TP53 0.031 0.022 -10000 0 -0.52 1 1
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.68 0.7 -10000 0 -1.4 417 417
KRT14 -0.74 0.67 -10000 0 -1.3 489 489
TBP 0.027 0.009 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.29 411 -10000 0 411
HDAC1 0.022 0.011 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.45 0.46 0.47 6 -0.84 458 464
MAPK14 0.002 0.022 -10000 0 -10000 0 0
MAPK10 -0.088 0.21 -10000 0 -0.6 133 133
MAPK11 -0.002 0.036 -10000 0 -0.6 2 2
KRT5 -0.76 0.71 0.43 2 -1.4 482 484
interleukin-1 receptor activity -0.001 0.005 -10000 0 -10000 0 0
NCOA1 0.025 0.021 -10000 0 -0.59 1 1
STAT1 0.033 0.036 0.28 19 -10000 0 19
CGA -0.056 0.18 0.41 1 -0.49 21 22
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.16 0.18 0.36 334 -10000 0 334
MAPK3 0 0.022 -10000 0 -10000 0 0
MAPK1 0.002 0.022 -10000 0 -10000 0 0
ICAM1 -0.19 0.24 0.58 2 -0.56 182 184
NFKB1 -0.038 0.1 0.3 1 -0.26 23 24
MAPK8 -0.2 0.22 0.37 3 -0.43 319 322
MAPK9 0.002 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.28 0.33 0.86 1 -0.67 279 280
BAX 0.017 0.064 -10000 0 -10000 0 0
POMC -0.17 0.3 0.46 1 -0.91 67 68
EP300 0.15 0.14 0.29 409 -10000 0 409
cortisol/GR alpha (dimer)/p53 0.22 0.26 0.53 296 -0.48 2 298
proteasomal ubiquitin-dependent protein catabolic process 0.079 0.11 0.26 146 -10000 0 146
SGK1 0.2 0.19 0.51 13 -1.1 4 17
IL13 -0.26 0.28 0.54 2 -0.68 136 138
IL6 -0.44 0.53 0.64 1 -1.1 342 343
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.22 0.23 0.52 2 -0.55 157 159
IL2 -0.34 0.36 0.52 1 -0.75 291 292
CDK5 0.016 0.018 0.26 2 -10000 0 2
PRKACB 0.033 0.064 0.26 44 -0.59 3 47
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.52 3 -0.6 205 208
CDK5R1/CDK5 0.015 0.038 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.019 0.15 0.4 3 -0.4 25 28
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.25 0.51 334 -0.45 2 336
SMARCA4 0.024 0.01 -10000 0 -0.16 1 1
chromatin remodeling 0.15 0.16 0.36 210 -10000 0 210
NF kappa B1 p50/RelA/Cbp 0.067 0.19 0.42 51 -0.42 14 65
JUN (dimer) -0.26 0.29 0.36 7 -0.56 338 345
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.14 0.21 -10000 0 -0.56 104 104
NR3C1 0.18 0.2 0.43 233 -0.63 1 234
NR4A1 -0.032 0.18 -10000 0 -0.57 93 93
TIF2/SUV420H1 0.019 0.063 -10000 0 -0.44 16 16
MAPKKK cascade -0.27 0.31 0.85 1 -0.64 275 276
cortisol/GR alpha (dimer)/Src-1 0.26 0.27 0.53 344 -0.49 2 346
PBX1 0.023 0.016 0.26 1 -10000 0 1
POU1F1 0.021 0.014 0.26 1 -10000 0 1
SELE -0.2 0.31 0.51 3 -0.65 198 201
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.36 210 -10000 0 210
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.25 0.51 334 -0.45 2 336
mol:cortisol 0.16 0.19 0.35 373 -0.25 3 376
MMP1 0.045 0.31 0.43 3 -0.92 68 71
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.14 0.36 -10000 0 -0.86 176 176
NCK1/PAK1/Dok-R -0.085 0.16 -10000 0 -0.4 176 176
NCK1/Dok-R -0.16 0.44 -10000 0 -1 176 176
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.038 0.094 0.24 157 -10000 0 157
RELA 0.024 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
F2 0.039 0.11 0.27 151 -10000 0 151
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.14 0.42 -10000 0 -0.97 176 176
FN1 0.12 0.12 0.26 377 -10000 0 377
PLD2 -0.18 0.45 -10000 0 -1.1 175 175
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.014 0.18 0.26 123 -0.59 63 186
ELK1 -0.16 0.4 -10000 0 -0.96 176 176
GRB7 0.02 0.022 -10000 0 -0.59 1 1
PAK1 0.022 0.018 0.26 4 -10000 0 4
Tie2/Ang1/alpha5/beta1 Integrin -0.097 0.46 -10000 0 -1 176 176
CDKN1A -0.098 0.25 -10000 0 -0.61 140 140
ITGA5 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.16 0.44 -10000 0 -1 176 176
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.095 0.27 0.38 1 -0.64 176 177
PLG -0.19 0.45 -10000 0 -1.1 176 176
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.14 0.35 -10000 0 -0.83 176 176
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
ANGPT2 -0.14 0.27 -10000 0 -0.7 123 123
BMX -0.3 0.49 -10000 0 -1.2 176 176
ANGPT1 -0.2 0.48 -10000 0 -1.2 157 157
tube development -0.12 0.28 -10000 0 -0.65 167 167
ANGPT4 -0.17 0.28 -10000 0 -0.59 273 273
response to hypoxia -0.012 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.18 0.49 -10000 0 -1.1 175 175
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.59 342 342
STAT5A (dimer) -0.13 0.32 -10000 0 -0.77 150 150
mol:L-citrulline -0.095 0.27 0.38 1 -0.64 176 177
AGTR1 -0.087 0.26 0.27 57 -0.59 185 242
MAPK14 -0.18 0.45 -10000 0 -1.1 177 177
Tie2/SHP2 -0.082 0.3 -10000 0 -1.1 63 63
TEK -0.09 0.32 -10000 0 -1.2 64 64
RPS6KB1 -0.12 0.36 -10000 0 -0.82 176 176
Angiotensin II/AT1 -0.064 0.19 0.18 57 -0.43 188 245
Tie2/Ang1/GRB2 -0.18 0.46 -10000 0 -1.1 176 176
MAPK3 -0.16 0.41 -10000 0 -0.98 175 175
MAPK1 -0.17 0.41 -10000 0 -0.99 175 175
Tie2/Ang1/GRB7 -0.18 0.46 -10000 0 -1.1 176 176
NFKB1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.19 0.45 -10000 0 -1.1 176 176
PI3K -0.16 0.42 -10000 0 -0.99 176 176
FES -0.18 0.45 -10000 0 -1.1 177 177
Crk/Dok-R -0.16 0.44 -10000 0 -1 176 176
Tie2/Ang1/ABIN2 -0.18 0.47 -10000 0 -1.1 176 176
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.12 0.33 -10000 0 -0.77 176 176
STAT5A 0.02 0.046 -10000 0 -0.59 5 5
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.1 0.36 0.47 1 -0.8 175 176
Tie2/Ang2 -0.16 0.37 -10000 0 -0.91 157 157
Tie2/Ang1 -0.2 0.49 -10000 0 -1.2 176 176
FOXO1 -0.12 0.33 0.47 1 -0.77 176 177
ELF1 0.014 0.034 -10000 0 -10000 0 0
ELF2 -0.18 0.44 -10000 0 -1 176 176
mol:Choline -0.17 0.42 -10000 0 -1 175 175
cell migration -0.034 0.1 -10000 0 -0.23 176 176
FYN -0.13 0.31 -10000 0 -0.74 167 167
DOK2 0.02 0.028 0.26 4 -0.59 1 5
negative regulation of cell cycle -0.087 0.23 -10000 0 -0.55 145 145
ETS1 -0.017 0.1 -10000 0 -0.26 127 127
PXN -0.08 0.3 0.43 2 -0.67 175 177
ITGB1 0.023 0.004 -10000 0 -10000 0 0
NOS3 -0.11 0.31 -10000 0 -0.72 176 176
RAC1 0.024 0.004 -10000 0 -10000 0 0
TNF -0.022 0.13 0.27 16 -0.28 156 172
MAPKKK cascade -0.17 0.42 -10000 0 -1 175 175
RASA1 0.023 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.18 0.46 -10000 0 -1.1 176 176
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.082 0.25 0.37 2 -0.57 176 178
mol:Phosphatidic acid -0.17 0.42 -10000 0 -1 175 175
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.095 0.27 0.38 1 -0.64 176 177
Rac1/GTP -0.12 0.33 -10000 0 -0.77 176 176
MMP2 -0.19 0.45 -10000 0 -1.1 176 176
Endothelins

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
AKT1 -0.074 0.13 -10000 0 -0.43 80 80
PTK2B 0.02 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.051 0.18 -10000 0 -0.81 30 30
EDN1 -0.076 0.17 -10000 0 -0.57 78 78
EDN3 -0.23 0.3 0.26 2 -0.59 368 370
EDN2 0.079 0.11 0.26 216 -0.59 4 220
HRAS/GDP -0.095 0.19 0.28 1 -0.47 128 129
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.063 0.14 -10000 0 -0.41 82 82
ADCY4 -0.13 0.2 0.29 3 -0.44 227 230
ADCY5 -0.21 0.25 -10000 0 -0.46 381 381
ADCY6 -0.12 0.19 0.29 3 -0.42 220 223
ADCY7 -0.12 0.19 0.29 3 -0.41 219 222
ADCY1 -0.12 0.2 0.27 1 -0.43 216 217
ADCY2 -0.14 0.22 0.28 9 -0.46 239 248
ADCY3 -0.12 0.19 0.28 2 -0.42 219 221
ADCY8 -0.1 0.17 0.28 3 -0.42 165 168
ADCY9 -0.12 0.18 0.27 1 -0.42 208 209
arachidonic acid secretion -0.17 0.27 0.3 2 -0.5 293 295
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.36 133 133
GNAO1 0.017 0.098 0.26 30 -0.59 18 48
HRAS 0.023 0.012 0.26 2 -10000 0 2
ETA receptor/Endothelin-1/G12/GTP -0.06 0.13 -10000 0 -0.4 77 77
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.44 220 220
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.063 0.16 0.39 10 -0.43 79 89
EDNRB -0.021 0.16 -10000 0 -0.58 70 70
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.076 0.15 -10000 0 -0.48 86 86
CYSLTR1 -0.08 0.15 -10000 0 -0.48 80 80
SLC9A1 -0.047 0.097 -10000 0 -0.3 77 77
mol:GDP -0.1 0.2 0.33 2 -0.49 136 138
SLC9A3 -0.1 0.27 -10000 0 -0.64 147 147
RAF1 -0.14 0.23 0.32 1 -0.45 257 258
JUN -0.053 0.19 -10000 0 -0.8 34 34
JAK2 -0.073 0.13 -10000 0 -0.43 78 78
mol:IP3 -0.075 0.17 -10000 0 -0.45 100 100
ETA receptor/Endothelin-1 -0.085 0.16 -10000 0 -0.49 86 86
PLCB1 -0.015 0.14 -10000 0 -0.59 52 52
PLCB2 0.013 0.028 0.26 1 -0.59 1 2
ETA receptor/Endothelin-3 -0.2 0.22 -10000 0 -0.45 373 373
FOS -0.3 0.45 -10000 0 -0.94 290 290
Gai/GDP -0.1 0.3 -10000 0 -0.76 137 137
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 -10000 0 -0.54 114 114
BCAR1 0.021 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.42 112 112
GNAQ 0.012 0.034 -10000 0 -0.6 2 2
GNAZ 0.017 0.058 -10000 0 -0.59 8 8
GNAL -0.11 0.25 -10000 0 -0.59 191 191
Gs family/GDP -0.15 0.24 0.26 1 -0.48 244 245
ETA receptor/Endothelin-1/Gq/GTP -0.049 0.12 -10000 0 -0.4 58 58
MAPK14 -0.065 0.16 -10000 0 -0.41 113 113
TRPC6 -0.054 0.19 -10000 0 -0.89 29 29
GNAI2 0.023 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNAI1 -0.006 0.13 -10000 0 -0.59 43 43
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.065 0.17 -10000 0 -0.39 137 137
ETB receptor/Endothelin-2 0.031 0.15 0.25 16 -0.4 77 93
ETB receptor/Endothelin-3 -0.19 0.25 -10000 0 -0.46 414 414
ETB receptor/Endothelin-1 -0.075 0.18 -10000 0 -0.48 133 133
MAPK3 -0.26 0.38 -10000 0 -0.79 292 292
MAPK1 -0.26 0.4 -10000 0 -0.8 295 295
Rac1/GDP -0.095 0.19 -10000 0 -0.48 117 117
cAMP biosynthetic process -0.16 0.22 0.52 1 -0.48 222 223
MAPK8 -0.058 0.2 -10000 0 -0.73 47 47
SRC 0.023 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.067 0.17 -10000 0 -0.39 152 152
p130Cas/CRK/Src/PYK2 -0.098 0.21 0.49 1 -0.57 99 100
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.095 0.19 -10000 0 -0.48 116 116
COL1A2 -0.085 0.19 0.4 8 -0.48 121 129
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.026 0.096 0.26 12 -0.4 5 17
mol:DAG -0.076 0.17 -10000 0 -0.45 100 100
MAP2K2 -0.2 0.3 0.34 2 -0.59 296 298
MAP2K1 -0.19 0.29 0.32 2 -0.58 296 298
EDNRA -0.034 0.059 -10000 0 -0.24 11 11
positive regulation of muscle contraction -0.064 0.12 -10000 0 -0.38 76 76
Gq family/GDP -0.061 0.19 -10000 0 -0.49 84 84
HRAS/GTP -0.1 0.2 0.34 1 -0.46 146 147
PRKCH -0.077 0.16 -10000 0 -0.44 99 99
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.072 0.18 0.29 3 -0.46 109 112
PRKCB -0.074 0.18 -10000 0 -0.45 104 104
PRKCE -0.08 0.16 -10000 0 -0.44 103 103
PRKCD -0.078 0.16 -10000 0 -0.44 98 98
PRKCG -0.078 0.16 0.27 1 -0.44 108 109
regulation of vascular smooth muscle contraction -0.35 0.52 -10000 0 -1.1 287 287
PRKCQ -0.085 0.18 -10000 0 -0.48 112 112
PLA2G4A -0.18 0.3 0.33 1 -0.56 293 294
GNA14 0.014 0.071 0.26 20 -0.6 8 28
GNA15 0.022 0.029 0.26 5 -0.59 1 6
GNA12 0.023 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.03 -10000 0 -0.59 2 2
Rac1/GTP -0.06 0.13 -10000 0 -0.4 77 77
MMP1 0.18 0.13 0.4 73 -10000 0 73
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.023 0.004 -10000 0 -10000 0 0
VLDLR 0.009 0.091 -10000 0 -0.59 20 20
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.2 0.21 -10000 0 -0.37 528 528
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.2 0.17 -10000 0 -0.34 526 526
IQGAP1/CaM 0.033 0.009 -10000 0 -10000 0 0
DAB1 0.036 0.057 0.26 53 -10000 0 53
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
PLA2G7 0.025 0.067 0.26 24 -0.59 7 31
CALM1 0.023 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.05 0.05 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.028 0.037 0.26 21 -10000 0 21
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.085 0.26 126 -10000 0 126
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.21 0.22 0.35 2 -0.38 540 542
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.15 0.15 0.33 2 -0.33 59 61
MAP1B -0.001 0.043 -10000 0 -0.33 15 15
RAC1 0.01 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.17 0.16 0.22 1 -0.31 492 493
RELN -0.34 0.3 0.26 3 -0.59 535 538
PAFAH/LIS1 0.024 0.047 0.32 2 -0.38 7 9
LIS1/CLIP170 0.023 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.12 0.13 -10000 0 -0.29 18 18
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.16 0.17 -10000 0 -0.3 444 444
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.16 0.15 0.3 2 -0.3 384 386
LIS1/IQGAP1 0.022 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.009 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.045 0.069 0.26 81 -10000 0 81
PAFAH1B2 0.02 0.03 -10000 0 -0.59 2 2
MAP1B/LIS1/Dynein heavy chain 0.013 0.042 -10000 0 -0.36 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.14 0.15 0.33 2 -0.33 55 57
LRP8 0.049 0.075 0.26 96 -10000 0 96
NDEL1/Katanin 60 -0.15 0.15 0.33 2 -0.3 213 215
P39/CDK5 -0.17 0.16 0.28 7 -0.31 436 443
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.009 -10000 0 -10000 0 0
CDK5 -0.19 0.16 0.2 1 -0.32 521 522
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.18 0.19 0.34 1 -0.33 522 523
RELN/VLDLR -0.18 0.21 -10000 0 -0.35 528 528
CDC42 0.01 0.004 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.26 17 -10000 0 17
EFNB1 -0.005 0.035 -10000 0 -0.44 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.095 0.18 -10000 0 -0.31 361 361
Ephrin B2/EPHB1-2 -0.12 0.19 -10000 0 -0.34 373 373
neuron projection morphogenesis -0.1 0.17 -10000 0 -0.3 363 363
Ephrin B1/EPHB1-2/Tiam1 -0.11 0.19 0.28 1 -0.33 370 371
DNM1 0.02 0.047 0.28 1 -0.59 5 6
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.023 0.12 -10000 0 -0.56 39 39
YES1 -0.024 0.17 -10000 0 -0.77 43 43
Ephrin B1/EPHB1-2/NCK2 -0.11 0.19 0.28 1 -0.33 372 373
PI3K 0.007 0.13 -10000 0 -0.54 43 43
mol:GDP -0.11 0.19 0.27 1 -0.33 370 371
ITGA2B 0.031 0.061 0.26 38 -0.59 3 41
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.026 0.17 -10000 0 -0.76 43 43
MAP3K7 -0.024 0.13 -10000 0 -0.58 41 41
FGR -0.023 0.17 -10000 0 -0.77 42 42
TIAM1 0.025 0.016 0.26 4 -10000 0 4
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.005 0.13 -10000 0 -0.46 53 53
LYN -0.022 0.16 -10000 0 -0.76 42 42
Ephrin B1/EPHB1-2/Src Family Kinases -0.027 0.16 -10000 0 -0.71 43 43
Ephrin B1/EPHB1-2 -0.025 0.14 -10000 0 -0.64 40 40
SRC -0.021 0.17 -10000 0 -0.76 43 43
ITGB3 0.012 0.085 0.26 4 -0.59 17 21
EPHB1 -0.23 0.3 0.27 1 -0.59 375 376
EPHB4 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.031 0.079 -10000 0 -0.44 20 20
BLK -0.023 0.18 -10000 0 -0.79 41 41
HCK -0.021 0.17 -10000 0 -0.76 43 43
regulation of stress fiber formation 0.11 0.19 0.33 372 -0.27 1 373
MAPK8 -0.025 0.12 -10000 0 -0.53 42 42
Ephrin B1/EPHB1-2/RGS3 -0.11 0.19 0.28 1 -0.33 370 371
endothelial cell migration -0.019 0.11 -10000 0 -0.51 37 37
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.008 0.11 -10000 0 -0.7 22 22
regulation of focal adhesion formation 0.11 0.19 0.33 372 -0.27 1 373
chemotaxis 0.11 0.19 0.33 370 -0.27 1 371
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.097 0.18 -10000 0 -0.31 362 362
angiogenesis -0.025 0.14 -10000 0 -0.63 41 41
LCK -0.022 0.17 -10000 0 -0.77 42 42
IL4-mediated signaling events

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
BCL2L1 -0.24 0.61 0.79 13 -1.2 168 181
STAT6 (cleaved dimer) -0.3 0.57 -10000 0 -1.2 212 212
IGHG1 -0.028 0.26 0.51 54 -0.64 8 62
IGHG3 -0.24 0.57 0.68 16 -1.1 204 220
AKT1 -0.085 0.34 0.58 20 -0.76 66 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.049 0.29 0.56 19 -0.78 39 58
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.087 0.35 0.6 21 -0.81 58 79
THY1 -0.24 0.61 0.8 15 -1.2 174 189
MYB 0.013 0.08 0.26 2 -0.59 15 17
HMGA1 0.032 0.045 0.26 32 -10000 0 32
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.41 0.65 48 -0.74 139 187
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.079 0.35 0.6 21 -0.83 47 68
SP1 0.035 0.028 -10000 0 -10000 0 0
INPP5D 0.023 0.004 -10000 0 -10000 0 0
SOCS5 0.015 0.043 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.26 0.6 0.68 11 -1.2 202 213
SOCS1 -0.14 0.4 0.63 15 -0.75 149 164
SOCS3 -0.094 0.36 0.64 10 -0.83 57 67
FCER2 -0.4 0.74 0.84 18 -1.3 287 305
PARP14 0.016 0.033 0.25 3 -10000 0 3
CCL17 -0.22 0.62 0.88 32 -1.2 163 195
GRB2 0.023 0.01 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.043 0.29 0.55 26 -0.77 28 54
T cell proliferation -0.26 0.61 0.74 10 -1.2 178 188
IL4R/JAK1 -0.25 0.6 0.73 3 -1.2 186 189
EGR2 -0.37 0.75 0.86 12 -1.5 231 243
JAK2 0.01 0.077 0.26 1 -10000 0 1
JAK3 0.022 0.04 0.29 15 -10000 0 15
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
JAK1 0.016 0.041 -10000 0 -10000 0 0
COL1A2 -0.02 0.26 0.58 9 -1.1 12 21
CCL26 -0.24 0.61 0.8 16 -1.2 169 185
IL4R -0.24 0.66 0.88 26 -1.3 183 209
PTPN6 0.014 0.036 0.22 2 -10000 0 2
IL13RA2 -0.24 0.61 0.81 16 -1.2 167 183
IL13RA1 0.011 0.077 0.25 2 -10000 0 2
IRF4 -0.13 0.49 0.63 11 -1.4 95 106
ARG1 -0.004 0.22 0.58 7 -0.53 4 11
CBL -0.11 0.38 0.6 31 -0.69 140 171
GTF3A 0.056 0.051 0.27 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.023 0.11 0.29 34 -10000 0 34
IRF4/BCL6 -0.11 0.44 0.57 1 -1.3 94 95
CD40LG -0.009 0.14 0.32 14 -0.6 39 53
MAPK14 -0.11 0.38 0.62 25 -0.72 123 148
mitosis -0.079 0.33 0.58 21 -0.72 65 86
STAT6 -0.27 0.75 0.97 40 -1.4 199 239
SPI1 0.028 0.023 0.27 7 -10000 0 7
RPS6KB1 -0.061 0.32 0.57 24 -0.7 57 81
STAT6 (dimer) -0.27 0.75 0.97 39 -1.4 199 238
STAT6 (dimer)/PARP14 -0.3 0.66 0.75 8 -1.2 216 224
mast cell activation 0 0.024 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.095 0.36 0.6 24 -0.76 84 108
FRAP1 -0.086 0.34 0.59 19 -0.76 66 85
LTA -0.22 0.62 0.88 28 -1.2 165 193
FES 0.021 0.036 -10000 0 -0.59 3 3
T-helper 1 cell differentiation 0.25 0.72 1.3 199 -0.97 40 239
CCL11 -0.18 0.59 0.75 32 -1.1 166 198
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.074 0.34 0.6 22 -0.78 57 79
IL2RG 0.025 0.071 0.27 37 -0.58 5 42
IL10 -0.21 0.6 0.83 18 -1.2 155 173
IRS1 0 0.12 -10000 0 -0.59 34 34
IRS2 0.002 0.11 -10000 0 -0.59 29 29
IL4 -0.012 0.27 0.66 13 -1.1 19 32
IL5 -0.24 0.61 0.78 16 -1.2 187 203
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.52 0.82 40 -0.9 172 212
COL1A1 0.001 0.36 0.65 52 -0.97 43 95
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.26 0.61 -10000 0 -1.3 156 156
IL2R gamma/JAK3 0.037 0.071 0.4 16 -0.43 4 20
TFF3 -0.29 0.71 0.88 22 -1.3 212 234
ALOX15 -0.31 0.7 0.82 15 -1.3 224 239
MYBL1 0.04 0.069 0.26 76 -10000 0 76
T-helper 2 cell differentiation -0.19 0.52 0.71 27 -0.97 183 210
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.024 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.083 0.34 0.58 23 -0.77 61 84
mol:PI-3-4-5-P3 -0.085 0.34 0.59 20 -0.77 65 85
PI3K -0.094 0.36 0.6 18 -0.83 65 83
DOK2 0.02 0.028 0.26 4 -0.59 1 5
ETS1 0.005 0.047 -10000 0 -0.55 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.032 0.27 0.52 31 -0.68 25 56
ITGB3 -0.25 0.62 0.8 11 -1.2 171 182
PIGR -0.68 0.79 0.81 21 -1.3 513 534
IGHE -0.016 0.088 0.18 29 -0.21 43 72
MAPKKK cascade -0.031 0.27 0.51 36 -0.67 25 61
BCL6 0.023 0.038 -10000 0 -0.58 3 3
OPRM1 -0.24 0.61 0.82 12 -1.2 164 176
RETNLB -0.24 0.6 0.79 13 -1.2 172 185
SELP -0.36 0.77 0.8 25 -1.4 263 288
AICDA -0.23 0.58 0.77 13 -1.2 173 186
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.1 0.22 0.23 1 -0.4 255 256
FZD6 0.014 0.051 -10000 0 -0.59 6 6
WNT6 -0.089 0.25 0.26 31 -0.59 176 207
WNT4 0.016 0.093 0.26 19 -0.59 18 37
FZD3 0.016 0.046 -10000 0 -0.59 5 5
WNT5A 0.019 0.066 0.26 9 -0.59 9 18
WNT11 -0.096 0.24 0.26 10 -0.59 176 186
Noncanonical Wnt signaling 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
NFATC2 -0.01 0.14 -10000 0 -0.59 47 47
GNB1/GNG2 -0.082 0.22 -10000 0 -0.48 140 140
mol:DAG -0.083 0.19 0.24 1 -0.45 132 133
PLCG1 -0.086 0.2 0.24 1 -0.46 132 133
YES1 -0.1 0.2 0.21 1 -0.5 131 132
FZD3 0.016 0.046 -10000 0 -0.59 5 5
FZD6 0.014 0.051 -10000 0 -0.59 6 6
G protein -0.07 0.21 0.3 2 -0.47 128 130
MAP3K7 -0.077 0.16 -10000 0 -0.42 100 100
mol:Ca2+ -0.08 0.18 0.24 1 -0.43 132 133
mol:IP3 -0.083 0.19 0.24 1 -0.45 132 133
NLK -0.011 0.13 -10000 0 -0.84 21 21
GNB1 0.023 0.005 -10000 0 -10000 0 0
CAMK2A -0.078 0.17 0.22 2 -0.43 117 119
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.1 0.22 0.23 1 -0.4 255 256
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
GNAS -0.097 0.2 0.21 1 -0.49 131 132
GO:0007205 -0.086 0.18 0.23 1 -0.44 133 134
WNT6 -0.089 0.25 0.26 31 -0.59 176 207
WNT4 0.016 0.093 0.26 19 -0.59 18 37
NFAT1/CK1 alpha -0.091 0.21 0.33 1 -0.49 126 127
GNG2 0.019 0.05 -10000 0 -0.59 6 6
WNT5A 0.019 0.066 0.26 9 -0.59 9 18
WNT11 -0.096 0.24 0.26 10 -0.59 176 186
CDC42 -0.089 0.19 -10000 0 -0.48 123 123
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.03 0.5 0.84 34 -1.1 64 98
IL23A -0.041 0.5 0.88 27 -1.1 63 90
NF kappa B1 p50/RelA/I kappa B alpha -0.072 0.46 0.77 8 -0.98 91 99
positive regulation of T cell mediated cytotoxicity -0.033 0.56 0.91 52 -0.97 142 194
ITGA3 -0.026 0.49 0.85 29 -1.1 62 91
IL17F -0.013 0.37 0.62 57 -0.69 66 123
IL12B 0.083 0.15 0.37 166 -10000 0 166
STAT1 (dimer) -0.049 0.52 0.78 40 -0.93 144 184
CD4 -0.025 0.5 0.85 37 -1 65 102
IL23 -0.027 0.5 0.84 40 -1.1 61 101
IL23R 0.051 0.2 0.64 14 -0.96 11 25
IL1B -0.042 0.51 0.86 33 -1.1 66 99
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.011 0.5 0.86 58 -0.94 85 143
TYK2 0.026 0.06 -10000 0 -10000 0 0
STAT4 0 0.12 0.26 1 -0.59 35 36
STAT3 0.023 0.005 -10000 0 -10000 0 0
IL18RAP 0.005 0.12 0.28 3 -0.59 32 35
IL12RB1 0.035 0.094 0.4 34 -0.63 1 35
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.091 0.34 34 -0.48 1 35
IL23R/JAK2 0.063 0.22 0.59 15 -0.92 10 25
positive regulation of chronic inflammatory response -0.033 0.56 0.91 52 -0.97 142 194
natural killer cell activation -0.004 0.016 -10000 0 -0.051 35 35
JAK2 0.038 0.085 0.27 28 -10000 0 28
PIK3R1 0.023 0.021 -10000 0 -0.59 1 1
NFKB1 0.026 0.01 -10000 0 -10000 0 0
RELA 0.026 0.01 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.02 0.48 0.83 42 -1 61 103
ALOX12B -0.026 0.49 0.84 39 -1 64 103
CXCL1 -0.21 0.72 0.86 40 -1.2 250 290
T cell proliferation -0.033 0.56 0.91 52 -0.97 142 194
NFKBIA 0.025 0.011 -10000 0 -10000 0 0
IL17A 0.018 0.32 0.57 76 -0.55 52 128
PI3K -0.067 0.48 0.72 17 -0.92 131 148
IFNG 0.027 0.071 0.18 120 -0.12 8 128
STAT3 (dimer) -0.07 0.45 0.83 6 -0.98 84 90
IL18R1 0.019 0.068 -10000 0 -0.59 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 0.031 0.36 0.67 69 -0.69 35 104
IL18/IL18R 0.041 0.11 0.3 7 -0.38 41 48
macrophage activation 0 0.03 0.058 85 -0.044 51 136
TNF -0.042 0.51 0.87 32 -1.1 69 101
STAT3/STAT4 -0.067 0.5 0.71 18 -0.95 131 149
STAT4 (dimer) -0.062 0.53 0.77 32 -0.96 146 178
IL18 0.03 0.039 0.27 21 -10000 0 21
IL19 0.015 0.5 0.84 58 -1 64 122
STAT5A (dimer) -0.053 0.51 0.76 32 -0.93 143 175
STAT1 0.029 0.035 0.26 19 -10000 0 19
SOCS3 0.019 0.046 -10000 0 -0.59 5 5
CXCL9 0 0.53 0.87 65 -1.1 65 130
MPO -0.056 0.56 0.85 37 -1.2 96 133
positive regulation of humoral immune response -0.033 0.56 0.91 52 -0.97 142 194
IL23/IL23R/JAK2/TYK2 -0.042 0.58 0.93 49 -1 134 183
IL6 -0.31 0.75 0.82 30 -1.2 333 363
STAT5A 0.02 0.046 -10000 0 -0.59 5 5
IL2 0.022 0.041 0.31 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.016 -10000 0 -0.051 35 35
CD3E -0.038 0.52 0.89 38 -1.2 70 108
keratinocyte proliferation -0.033 0.56 0.91 52 -0.97 142 194
NOS2 -0.026 0.5 0.83 40 -1.1 66 106
Arf6 signaling events

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
CENTA1/KIF3B 0.025 0.035 -10000 0 -0.48 3 3
ARNO/beta Arrestin1-2 -0.073 0.17 -10000 0 -0.57 42 42
EGFR -0.19 0.29 -10000 0 -0.59 312 312
EPHA2 0.019 0.046 -10000 0 -0.59 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.023 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.27 -10000 0 -0.48 431 431
ARRB2 -0.045 0.13 -10000 0 -0.37 127 127
mol:GTP 0.01 0.051 0.16 14 -0.22 17 31
ARRB1 0.021 0.03 -10000 0 -0.59 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR -0.001 0.12 0.26 3 -0.59 36 39
EGF -0.09 0.24 0.26 2 -0.59 167 169
somatostatin receptor activity 0 0 0.001 1 -0.001 246 247
ARAP2 0.02 0.046 -10000 0 -0.59 5 5
mol:GDP -0.12 0.17 -10000 0 -0.33 263 263
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 126 126
ITGA2B 0.031 0.061 0.26 38 -0.59 3 41
ARF6 0.023 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.04 -10000 0 -0.35 5 5
ADAP1 0.023 0.033 0.26 4 -0.59 2 6
KIF13B 0.018 0.03 -10000 0 -0.59 2 2
HGF/MET -0.067 0.21 -10000 0 -0.47 182 182
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 0.18 1 -0.29 263 264
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.24 -10000 0 -0.42 425 425
ADRB2 -0.11 0.26 -10000 0 -0.59 201 201
receptor agonist activity 0 0 0 1 0 244 245
actin filament binding 0 0 0 2 -0.001 251 253
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.012 0.085 0.26 4 -0.59 17 21
GNAQ 0.022 0.029 -10000 0 -0.59 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 151 152
ARF6/GDP -0.041 0.15 0.25 2 -0.45 79 81
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.41 193 193
alphaIIb/beta3 Integrin/paxillin/GIT1 0.053 0.07 -10000 0 -0.35 20 20
ACAP1 0.026 0.067 0.26 30 -0.59 6 36
ACAP2 0.023 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.061 0.18 -10000 0 -0.5 127 127
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.59 50 50
CYTH3 0.003 0.004 -10000 0 -10000 0 0
CYTH2 0.005 0.1 -10000 0 -1 9 9
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 204 205
endosomal lumen acidification 0 0 0.001 5 0 218 223
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.013 0.15 -10000 0 -0.59 54 54
GNAQ/ARNO 0.017 0.099 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 196 196
MET -0.076 0.23 -10000 0 -0.59 145 145
GNA14 0.023 0.068 0.26 20 -0.59 8 28
GNA15 0.024 0.028 0.26 5 -0.59 1 6
GIT1 0.022 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 201 202
GNA11 0.022 0.029 -10000 0 -0.59 2 2
LHCGR -0.075 0.21 -10000 0 -0.59 127 127
AGTR1 -0.088 0.26 0.26 57 -0.59 185 242
desensitization of G-protein coupled receptor protein signaling pathway -0.061 0.18 -10000 0 -0.5 127 127
IPCEF1/ARNO -0.14 0.2 -10000 0 -0.62 57 57
alphaIIb/beta3 Integrin 0.03 0.079 -10000 0 -0.44 20 20
IGF1 pathway

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
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.068 0.16 -10000 0 -0.35 195 195
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.024 0.012 0.26 2 -10000 0 2
IRS1/Crk -0.062 0.16 -10000 0 -0.35 199 199
IGF-1R heterotetramer/IGF1/PTP1B -0.045 0.17 -10000 0 -0.38 173 173
AKT1 -0.067 0.13 0.25 2 -0.32 148 150
BAD -0.065 0.13 0.24 2 -0.48 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.069 0.16 -10000 0 -0.35 199 199
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.059 0.17 -10000 0 -0.35 199 199
RAF1 -0.049 0.14 -10000 0 -0.5 36 36
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.033 0.17 -10000 0 -0.34 183 183
YWHAZ 0.018 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.063 0.18 -10000 0 -0.37 205 205
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.33 135 137
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.029 0.12 0.32 7 -0.41 32 39
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.033 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.04 0.13 -10000 0 -0.33 130 130
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.011 0.14 -10000 0 -0.32 126 126
IGF-1R heterotetramer -0.012 0.1 0.26 1 -0.64 18 19
IGF-1R heterotetramer/IGF1/IRS/Nck -0.047 0.17 -10000 0 -0.35 196 196
Crk/p130 Cas/Paxillin -0.038 0.16 -10000 0 -0.33 185 185
IGF1R -0.012 0.1 0.26 1 -0.64 18 19
IGF1 -0.11 0.26 -10000 0 -0.61 186 186
IRS2/Crk -0.069 0.17 -10000 0 -0.36 198 198
PI3K -0.034 0.17 -10000 0 -0.34 189 189
apoptosis 0.042 0.1 0.39 24 -0.27 4 28
HRAS/GDP 0.018 0.008 0.18 2 -10000 0 2
PRKCD -0.079 0.18 -10000 0 -0.41 186 186
RAF1/14-3-3 E -0.024 0.13 0.3 1 -0.43 36 37
BAD/14-3-3 -0.044 0.11 0.28 4 -0.42 24 28
PRKCZ -0.067 0.14 0.25 2 -0.33 146 148
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.11 -10000 0 -0.42 27 27
PTPN1 0.024 0.021 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.19 -10000 0 -0.42 193 193
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.024 0.15 -10000 0 -0.34 140 140
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.055 0.17 -10000 0 -0.35 196 196
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.35 199 199
IRS1 -0.072 0.17 -10000 0 -0.38 199 199
IRS2 -0.078 0.18 -10000 0 -0.38 206 206
IGF-1R heterotetramer/IGF1 -0.079 0.21 -10000 0 -0.47 199 199
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDPK1 -0.069 0.14 0.28 1 -0.34 160 161
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.2 -10000 0 -0.44 192 192
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.009 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.14 0.29 2 -0.29 63 65
NFATC4 -0.066 0.12 0.27 4 -0.25 197 201
ERBB2IP 0.024 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.023 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.071 0.15 -10000 0 -0.32 206 206
JUN -0.008 0.099 0.24 27 -0.47 2 29
HRAS 0.024 0.012 0.27 2 -10000 0 2
DOCK7 -0.082 0.14 0.28 2 -0.31 203 205
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.055 0.16 -10000 0 -0.34 168 168
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.074 0.11 0.22 6 -0.28 116 122
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.075 0.16 -10000 0 -0.34 206 206
RAF1 -0.017 0.15 0.33 13 -0.3 49 62
ErbB2/ErbB3/neuregulin 2 -0.16 0.18 -10000 0 -0.36 378 378
STAT3 -0.003 0.16 -10000 0 -0.86 30 30
cell migration -0.058 0.1 0.25 10 -0.26 72 82
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.041 0.25 0.46 10 -0.54 73 83
FOS -0.1 0.29 0.33 44 -0.49 281 325
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.071 0.15 -10000 0 -0.32 206 206
MAPK3 -0.013 0.21 0.43 10 -0.54 23 33
MAPK1 -0.025 0.22 0.43 10 -0.59 36 46
JAK2 -0.079 0.14 0.26 1 -0.3 203 204
NF2 -0.003 0.063 -10000 0 -0.69 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.14 0.22 5 -0.28 209 214
NRG1 -0.14 0.27 0.26 3 -0.59 244 247
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.08 0.15 0.25 2 -0.3 205 207
MAPK9 -0.044 0.084 0.2 9 -0.25 1 10
ERBB2 0.003 0.072 0.24 76 -10000 0 76
ERBB3 0.022 0.029 -10000 0 -0.59 2 2
SHC1 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
apoptosis 0.021 0.026 -10000 0 -0.16 6 6
STAT3 (dimer) -0.002 0.16 -10000 0 -0.84 30 30
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.073 0.095 -10000 0 -0.23 197 197
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.016 -10000 0 -10000 0 0
CHRNA1 0.023 0.19 0.37 56 -0.43 15 71
myelination -0.062 0.12 0.32 10 -0.25 190 200
PPP3CB -0.076 0.13 0.27 2 -0.29 201 203
KRAS 0.023 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.037 0.14 -10000 0 -0.27 156 156
NRG2 -0.28 0.31 -10000 0 -0.59 451 451
mol:GDP -0.054 0.13 0.21 5 -0.28 209 214
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K2 -0.015 0.15 0.34 13 -0.31 47 60
SRC 0.023 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.081 0.14 0.28 2 -0.3 205 207
MAP2K1 -0.049 0.23 0.44 5 -0.62 35 40
heart morphogenesis -0.071 0.15 -10000 0 -0.32 206 206
RAS family/GDP -0.022 0.14 0.3 1 -0.29 63 64
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA -0.004 0.073 -10000 0 -0.68 10 10
CHRNE 0.004 0.027 0.12 3 -0.22 2 5
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.071 0.15 -10000 0 -0.32 206 206
CDC42 0.023 0.005 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.003 0.15 -10000 0 -0.33 142 142
ER alpha/Gai/GDP/Gbeta gamma -0.08 0.22 -10000 0 -0.48 169 169
AKT1 -0.1 0.32 -10000 0 -0.79 157 157
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.1 0.33 -10000 0 -0.8 157 157
mol:Ca2+ -0.025 0.1 0.27 2 -0.35 58 60
IGF1R 0.012 0.085 0.26 2 -0.59 17 19
E2/ER alpha (dimer)/Striatin -0.009 0.16 0.18 111 -0.37 130 241
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.095 0.31 0.75 157 -10000 0 157
RhoA/GTP -0.015 0.1 -10000 0 -0.3 97 97
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.062 0.21 0.32 5 -0.48 155 160
regulation of stress fiber formation 0.02 0.1 0.25 92 -0.32 7 99
E2/ERA-ERB (dimer) -0.017 0.16 -10000 0 -0.38 140 140
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.007 0.14 -10000 0 -0.33 120 120
pseudopodium formation -0.02 0.1 0.32 7 -0.25 92 99
E2/ER alpha (dimer)/PELP1 -0.01 0.15 -10000 0 -0.37 121 121
GRB2 0.023 0.01 0.26 1 -10000 0 1
GNG2 0.019 0.05 -10000 0 -0.59 6 6
GNAO1 0.017 0.098 0.26 30 -0.59 18 48
HRAS 0.024 0.012 0.26 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.081 0.23 0.25 1 -0.52 173 174
E2/ER beta (dimer) 0.006 0.069 -10000 0 -0.42 22 22
mol:GDP -0.036 0.17 0.25 12 -0.4 137 149
mol:NADP -0.081 0.23 0.25 1 -0.52 173 174
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
mol:IP3 -0.026 0.11 0.27 2 -0.5 22 24
IGF-1R heterotetramer 0.012 0.084 0.26 2 -0.59 17 19
PLCB1 -0.023 0.11 0.28 2 -0.37 57 59
PLCB2 -0.006 0.085 -10000 0 -0.53 14 14
IGF1 -0.1 0.25 -10000 0 -0.59 185 185
mol:L-citrulline -0.081 0.23 0.25 1 -0.52 173 174
RHOA 0.023 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.67 117 117
JNK cascade 0.006 0.069 -10000 0 -0.42 22 22
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.009 0.093 -10000 0 -0.59 21 21
GNAQ 0.022 0.029 -10000 0 -0.59 2 2
ESR1 -0.029 0.23 0.26 112 -0.59 120 232
Gq family/GDP/Gbeta gamma -0.009 0.16 -10000 0 -0.76 33 33
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.014 0.13 -10000 0 -0.51 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.055 0.2 0.31 5 -0.48 128 133
GNAZ 0.017 0.058 -10000 0 -0.59 8 8
E2/ER alpha (dimer) -0.024 0.17 0.18 112 -0.43 125 237
STRN 0.019 0.054 -10000 0 -0.59 7 7
GNAL -0.11 0.25 -10000 0 -0.59 191 191
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.001 0.063 -10000 0 -0.39 22 22
GNAI2 0.023 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNAI1 -0.006 0.13 -10000 0 -0.59 43 43
HBEGF -0.048 0.21 0.34 22 -0.51 93 115
cAMP biosynthetic process -0.088 0.18 -10000 0 -0.34 290 290
SRC -0.074 0.22 0.3 8 -0.46 167 175
PI3K 0.032 0.019 -10000 0 -0.44 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.017 0.16 -10000 0 -0.39 114 114
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.44 178 178
Gs family/GTP -0.084 0.19 -10000 0 -0.34 290 290
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.015 -10000 0 -10000 0 0
vasodilation -0.076 0.22 0.24 1 -0.49 173 174
mol:DAG -0.026 0.11 0.27 2 -0.5 22 24
Gs family/GDP/Gbeta gamma -0.089 0.18 -10000 0 -0.36 224 224
MSN -0.022 0.11 0.32 7 -0.27 92 99
Gq family/GTP -0.001 0.09 -10000 0 -0.55 13 13
mol:PI-3-4-5-P3 -0.094 0.32 -10000 0 -0.76 157 157
NRAS 0.023 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.076 0.22 0.49 173 -0.24 1 174
GRB2/SOS1 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.02 0.17 0.26 9 -0.39 135 144
NOS3 -0.087 0.25 -10000 0 -0.55 172 172
GNA11 0.022 0.029 -10000 0 -0.59 2 2
MAPKKK cascade -0.071 0.25 0.3 5 -0.57 162 167
E2/ER alpha (dimer)/PELP1/Src -0.065 0.22 0.32 9 -0.49 160 169
ruffle organization -0.02 0.1 0.32 7 -0.25 92 99
ROCK2 -0.021 0.12 0.35 6 -0.29 98 104
GNA14 0.023 0.068 0.26 20 -0.59 8 28
GNA15 0.024 0.028 0.26 5 -0.59 1 6
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.04 0.21 0.35 28 -0.5 94 122
MMP2 -0.065 0.2 0.28 12 -0.43 163 175
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.062 0.17 0.31 9 -0.36 91 100
SMAD6-7/SMURF1 0.045 0.015 -10000 0 -10000 0 0
NOG 0.012 0.094 0.26 14 -0.59 19 33
SMAD9 -0.086 0.25 -10000 0 -0.62 144 144
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.029 0.15 -10000 0 -0.43 65 65
BMP7/USAG1 -0.2 0.26 -10000 0 -0.44 455 455
SMAD5/SKI -0.024 0.16 0.26 1 -0.45 62 63
SMAD1 0.013 0.06 0.25 1 -0.41 5 6
BMP2 -0.08 0.23 0.26 1 -0.59 151 152
SMAD1/SMAD1/SMAD4 0.017 0.07 -10000 0 -0.4 9 9
BMPR1A 0.024 0.003 -10000 0 -10000 0 0
BMPR1B 0.11 0.16 0.26 365 -0.59 20 385
BMPR1A-1B/BAMBI 0.085 0.13 0.35 9 -0.34 45 54
AHSG 0.02 0.021 0.26 6 -10000 0 6
CER1 0.018 0.013 0.26 2 -10000 0 2
BMP2-4/CER1 -0.052 0.18 -10000 0 -0.41 182 182
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.045 0.17 -10000 0 -0.43 92 92
BMP2-4 (homodimer) -0.073 0.21 -10000 0 -0.45 196 196
RGMB 0.023 0.021 -10000 0 -0.59 1 1
BMP6/BMPR2/BMPR1A-1B 0.069 0.15 -10000 0 -0.33 84 84
RGMA -0.058 0.21 -10000 0 -0.59 119 119
SMURF1 0.023 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.044 0.17 0.24 1 -0.43 106 107
BMP2-4/USAG1 -0.24 0.27 -10000 0 -0.46 497 497
SMAD6/SMURF1/SMAD5 -0.025 0.16 -10000 0 -0.45 62 62
SOSTDC1 -0.27 0.31 0.26 2 -0.59 430 432
BMP7/BMPR2/BMPR1A-1B 0.07 0.15 0.31 7 -0.34 74 81
SKI 0.023 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.021 0.16 0.26 2 -0.59 65 67
HFE2 0.02 0.021 0.26 6 -10000 0 6
ZFYVE16 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.05 0.2 -10000 0 -0.43 184 184
SMAD5/SMAD5/SMAD4 -0.025 0.16 -10000 0 -0.44 64 64
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.031 0.16 -10000 0 -0.39 98 98
BMP7 (homodimer) -0.012 0.16 0.26 26 -0.59 60 86
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.004 0.12 -10000 0 -0.42 70 70
SMAD1/SKI 0.019 0.077 -10000 0 -0.42 10 10
SMAD6 0.023 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.052 0.19 0.35 1 -0.41 182 183
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.042 0.1 0.26 95 -0.59 10 105
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.043 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.089 0.11 -10000 0 -0.44 20 20
CHRDL1 -0.4 0.28 -10000 0 -0.59 615 615
ENDOFIN/SMAD1 0.018 0.078 -10000 0 -0.44 10 10
SMAD6-7/SMURF1/SMAD1 0.034 0.082 -10000 0 -0.44 9 9
SMAD6/SMURF1 0.023 0.004 -10000 0 -10000 0 0
BAMBI 0.014 0.12 0.26 33 -0.59 27 60
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.28 -10000 0 -0.48 615 615
BMP2-4/GREM1 -0.039 0.21 -10000 0 -0.41 189 189
SMAD7 0.023 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.079 0.25 -10000 0 -0.6 145 145
SMAD1/SMAD6 0.018 0.079 -10000 0 -0.45 10 10
TAK1/SMAD6 0.033 0.01 -10000 0 -10000 0 0
BMP7 -0.012 0.16 0.26 26 -0.59 60 86
BMP6 -0.021 0.16 0.26 2 -0.59 65 67
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.046 0.17 -10000 0 -0.44 109 109
PPM1A 0.023 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.075 -10000 0 -0.43 10 10
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.023 0.004 -10000 0 -10000 0 0
PPP1CA 0.022 0.006 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.054 0.2 0.24 1 -0.49 114 115
CHRD 0.024 0.098 0.26 45 -0.59 16 61
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.058 0.19 -10000 0 -0.5 107 107
BMP4 -0.012 0.14 0.26 1 -0.59 53 54
FST 0.002 0.12 0.26 3 -0.59 32 35
BMP2-4/NOG -0.055 0.19 -10000 0 -0.42 180 180
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.073 0.14 0.3 7 -0.32 74 81
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.002 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.004 0.13 -10000 0 -0.35 106 106
regulation of S phase of mitotic cell cycle -0.018 0.098 -10000 0 -0.29 93 93
GNAO1 0.017 0.098 0.26 30 -0.59 18 48
HRAS 0.023 0.012 0.26 2 -10000 0 2
SHBG/T-DHT 0.014 0.005 -10000 0 -10000 0 0
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.068 0.12 -10000 0 -0.34 93 93
T-DHT/AR -0.036 0.14 0.18 1 -0.44 103 104
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 277 277
GNAI2 0.023 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNAI1 -0.006 0.13 -10000 0 -0.59 43 43
mol:GDP -0.055 0.15 -10000 0 -0.47 103 103
cell proliferation -0.14 0.22 0.27 2 -0.44 262 264
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.25 0.38 -10000 0 -0.82 280 280
mol:Ca2+ -0.012 0.028 -10000 0 -0.074 115 115
MAPK3 -0.1 0.17 0.26 3 -0.42 101 104
MAPK1 -0.081 0.14 -10000 0 -0.39 90 90
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
mol:IP3 -0.001 0.002 -10000 0 -0.004 275 275
cAMP biosynthetic process 0.004 0.021 -10000 0 -10000 0 0
GNG2 0.019 0.05 -10000 0 -0.59 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 275 275
HRAS/GTP -0.026 0.12 -10000 0 -0.34 100 100
actin cytoskeleton reorganization 0.032 0.017 -10000 0 -0.31 1 1
SRC 0.022 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 275 275
PI3K 0.029 0.016 -10000 0 -0.38 1 1
apoptosis 0.14 0.22 0.44 282 -10000 0 282
T-DHT/AR/PELP1 -0.021 0.13 -10000 0 -0.38 102 102
HRAS/GDP -0.044 0.15 -10000 0 -0.46 102 102
CREB1 -0.15 0.23 -10000 0 -0.47 282 282
RAC1-CDC42/GTP 0.04 0.02 -10000 0 -0.32 1 1
AR -0.047 0.2 0.26 1 -0.59 102 103
GNB1 0.023 0.005 -10000 0 -10000 0 0
RAF1 -0.06 0.11 -10000 0 -0.34 96 96
RAC1-CDC42/GDP -0.02 0.15 -10000 0 -0.44 102 102
T-DHT/AR/PELP1/Src -0.019 0.12 -10000 0 -0.36 101 101
MAP2K2 -0.069 0.11 -10000 0 -0.34 93 93
T-DHT/AR/PELP1/Src/PI3K -0.018 0.098 -10000 0 -0.3 93 93
GNAZ 0.017 0.058 -10000 0 -0.59 8 8
SHBG 0.021 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.049 0.16 -10000 0 -0.48 78 78
mol:T-DHT -0.001 0.001 0.002 1 -0.004 69 70
RAC1 0.024 0.004 -10000 0 -10000 0 0
GNRH1 0.001 0.03 -10000 0 -0.44 4 4
Gi family/GTP -0.034 0.099 -10000 0 -0.29 78 78
CDC42 0.023 0.005 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.003 0.089 -10000 0 -0.45 24 24
Crk/p130 Cas/Paxillin -0.055 0.12 -10000 0 -0.36 92 92
JUN -0.013 0.12 0.25 1 -0.42 26 27
HRAS 0.024 0.012 0.26 2 -10000 0 2
RET51/GFRalpha1/GDNF/GRB10 0.045 0.2 0.35 49 -0.36 145 194
RAP1A 0.023 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
RAP1A/GDP 0.017 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.045 0.2 0.35 48 -0.36 144 192
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.01 0.16 0.33 4 -0.35 147 151
RHOA 0.023 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.17 0.29 34 -0.32 145 179
GRB7 0.02 0.022 -10000 0 -0.59 1 1
RET51/GFRalpha1/GDNF 0.044 0.2 0.35 48 -0.36 146 194
MAPKKK cascade 0.001 0.15 0.29 9 -0.34 108 117
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.023 0.18 0.33 3 -0.4 156 159
lamellipodium assembly -0.031 0.13 -10000 0 -0.33 103 103
RET51/GFRalpha1/GDNF/SHC 0.037 0.18 0.35 40 -0.36 113 153
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.14 0.33 4 -0.34 109 113
RET9/GFRalpha1/GDNF/Shank3 -0.013 0.16 0.33 4 -0.34 147 151
MAPK3 -0.031 0.13 0.23 2 -0.32 116 118
DOK1 0.024 0.008 0.26 1 -10000 0 1
DOK6 0.018 0.064 0.26 6 -0.59 9 15
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.031 0.13 -10000 0 -0.34 68 68
DOK5 0.012 0.086 0.26 5 -0.59 17 22
GFRA1 -0.069 0.24 0.26 52 -0.59 156 208
MAPK8 -0.007 0.13 0.22 3 -0.32 78 81
HRAS/GTP 0.03 0.19 0.3 46 -0.36 139 185
tube development -0.005 0.15 0.35 10 -0.33 140 150
MAPK1 -0.03 0.14 0.24 6 -0.32 127 133
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.022 0.12 0.26 1 -0.27 141 142
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
PDLIM7 0.023 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.04 0.2 0.34 45 -0.34 148 193
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.029 0.19 0.35 35 -0.36 147 182
RET51/GFRalpha1/GDNF/Dok5 0.029 0.2 0.35 44 -0.36 153 197
PRKCA 0.01 0.086 0.26 1 -0.59 18 19
HRAS/GDP 0.018 0.008 0.18 2 -10000 0 2
CREB1 -0.011 0.13 0.23 15 -0.33 84 99
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.018 0.1 0.26 1 -0.27 102 103
RET51/GFRalpha1/GDNF/Grb7 0.044 0.19 0.34 62 -0.36 116 178
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.14 0.26 326 -0.59 13 339
DOK4 0.021 0.008 -10000 0 -10000 0 0
JNK cascade -0.012 0.12 0.25 1 -0.41 26 27
RET9/GFRalpha1/GDNF/FRS2 -0.011 0.16 0.33 4 -0.35 148 152
SHANK3 0.022 0.006 -10000 0 -10000 0 0
RASA1 0.023 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.019 0.11 0.26 1 -0.27 101 102
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.009 0.14 0.25 16 -0.3 115 131
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.004 0.14 0.26 3 -0.31 116 119
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.013 0.14 0.26 16 -0.32 86 102
PI3K -0.024 0.21 0.3 9 -0.49 109 118
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.15 0.32 3 -0.33 140 143
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.003 0.13 0.24 10 -0.28 112 122
RET51/GFRalpha1/GDNF/FRS2 0.042 0.2 0.35 52 -0.36 147 199
GAB1 0.023 0.004 -10000 0 -10000 0 0
IRS1 0 0.12 -10000 0 -0.59 34 34
IRS2 0.002 0.11 -10000 0 -0.59 29 29
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.013 0.14 0.26 16 -0.32 86 102
RET51/GFRalpha1/GDNF/PKC alpha 0.027 0.2 0.36 40 -0.36 155 195
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.033 0.056 0.26 49 -10000 0 49
RAC1 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.03 0.23 0.35 47 -0.41 153 200
Rac1/GTP -0.018 0.17 0.24 5 -0.4 95 100
RET9/GFRalpha1/GDNF -0.025 0.16 0.33 4 -0.38 148 152
GFRalpha1/GDNF -0.031 0.19 0.38 4 -0.43 156 160
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.075 0.12 -10000 0 -0.29 83 83
NT3 (dimer)/TRKC -0.19 0.27 -10000 0 -0.48 383 383
NT3 (dimer)/TRKB -0.31 0.32 -10000 0 -0.54 534 534
SHC/Grb2/SOS1/GAB1/PI3K 0.017 0.022 -10000 0 -0.27 1 1
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.021 0.17 0.26 19 -0.59 72 91
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.025 0.048 0.26 22 -0.59 2 24
NTRK2 -0.29 0.31 -10000 0 -0.59 458 458
NTRK3 -0.18 0.29 0.26 5 -0.59 301 306
NT-4/5 (dimer)/TRKB -0.38 0.35 -10000 0 -0.6 594 594
neuron apoptosis 0.17 0.22 0.47 256 -10000 0 256
SHC 2-3/Grb2 -0.19 0.24 -10000 0 -0.52 256 256
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.19 0.26 -10000 0 -0.55 248 248
SHC3 -0.18 0.23 -10000 0 -0.52 238 238
STAT3 (dimer) 0.033 0.044 -10000 0 -0.36 3 3
NT3 (dimer)/TRKA -0.12 0.22 -10000 0 -0.43 259 259
RIN/GDP -0.05 0.12 0.29 4 -0.26 72 76
GIPC1 0.024 0.004 -10000 0 -10000 0 0
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.084 0.15 -10000 0 -0.33 221 221
RIN/GTP 0.014 0.009 0.18 2 -10000 0 2
CCND1 0.025 0.094 0.44 32 -0.84 3 35
MAGED1 0.025 0.011 0.26 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.2 0.3 -10000 0 -0.59 330 330
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.032 0.086 0.35 1 -0.39 27 28
TRKA/NEDD4-2 0.031 0.038 -10000 0 -0.36 3 3
ELMO1 0.024 0.003 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.007 -10000 0 -10000 0 0
NGF 0.015 0.082 0.26 7 -0.59 15 22
HRAS 0.024 0.012 0.26 2 -10000 0 2
DOCK1 0.023 0.004 -10000 0 -10000 0 0
GAB2 0.021 0.008 -10000 0 -10000 0 0
RIT2 0.018 0.013 0.26 2 -10000 0 2
RIT1 0.02 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
DNM1 0.021 0.046 0.26 1 -0.59 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.077 0.16 -10000 0 -0.32 245 245
mol:GDP -0.08 0.16 0.34 5 -0.38 93 98
NGF (dimer) 0.015 0.082 0.26 7 -0.59 15 22
RhoG/GDP 0.018 0.002 -10000 0 -10000 0 0
RIT1/GDP -0.048 0.11 0.37 2 -0.26 59 61
TIAM1 0.025 0.016 0.26 4 -10000 0 4
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
BDNF (dimer)/TRKB -0.2 0.24 -10000 0 -0.41 480 480
KIDINS220/CRKL/C3G 0.033 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.046 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.066 0.22 0.26 11 -0.59 135 146
RAP1/GDP -0.045 0.096 -10000 0 -0.23 63 63
KIDINS220/CRKL 0.023 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.021 0.17 0.26 19 -0.59 72 91
ubiquitin-dependent protein catabolic process 0.035 0.063 -10000 0 -0.38 15 15
Schwann cell development -0.05 0.039 -10000 0 -10000 0 0
EHD4 0.023 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.054 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.05 -10000 0 -0.27 8 8
RAP1B 0.023 0.005 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.29 0.3 -10000 0 -0.5 528 528
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.033 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.081 0.13 -10000 0 -0.46 45 45
STAT3 0.033 0.044 -10000 0 -0.36 3 3
axon guidance -0.28 0.28 -10000 0 -0.47 540 540
MAPK3 0.007 0.092 0.25 3 -0.36 25 28
MAPK1 0.008 0.094 0.25 3 -0.36 26 29
CDC42/GDP -0.047 0.12 0.29 5 -0.26 67 72
NTF3 -0.067 0.22 0.26 11 -0.59 135 146
NTF4 -0.2 0.3 -10000 0 -0.59 330 330
NGF (dimer)/TRKA/FAIM 0.036 0.064 -10000 0 -0.38 15 15
PI3K 0.032 0.019 -10000 0 -0.44 1 1
FRS3 0.023 0.004 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.023 0.004 -10000 0 -10000 0 0
RASGRF1 -0.081 0.16 0.25 2 -0.34 238 240
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.17 0.23 0.21 1 -0.43 364 365
RGS19 0.023 0.013 0.26 2 -10000 0 2
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.095 0.4 1 -0.45 8 9
Rac1/GDP -0.048 0.12 0.33 3 -0.26 65 68
NGF (dimer)/TRKA/GRIT 0.024 0.06 -10000 0 -0.35 17 17
neuron projection morphogenesis -0.075 0.22 -10000 0 -0.78 38 38
NGF (dimer)/TRKA/NEDD4-2 0.035 0.064 -10000 0 -0.38 15 15
MAP2K1 0.03 0.086 0.36 15 -10000 0 15
NGFR -0.15 0.27 -10000 0 -0.59 251 251
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.051 -10000 0 -0.3 16 16
RAS family/GTP/PI3K 0.019 0.014 -10000 0 -0.27 1 1
FRS2 family/SHP2/GRB2/SOS1 0.062 0.026 -10000 0 -10000 0 0
NRAS 0.023 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.033 0.011 -10000 0 -10000 0 0
PRKCI 0.023 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.021 -10000 0 -0.59 1 1
MAPKKK cascade -0.042 0.14 -10000 0 -0.65 36 36
RASA1 0.023 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.037 -10000 0 -0.44 2 2
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.18 0.23 -10000 0 -0.38 475 475
NGF (dimer)/TRKA/p62/Atypical PKCs 0.051 0.064 -10000 0 -0.33 15 15
MATK 0.017 0.092 0.26 21 -0.59 17 38
NEDD4L 0.022 0.021 -10000 0 -0.59 1 1
RAS family/GDP -0.059 0.072 -10000 0 -0.22 43 43
NGF (dimer)/TRKA -0.091 0.17 -10000 0 -0.34 263 263
Rac1/GTP -0.089 0.12 -10000 0 -0.29 192 192
FRS2 family/SHP2/CRK family 0.059 0.028 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.029 -10000 0 -0.59 2 2
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.4 224 225
PTP1B/AKT1 -0.063 0.13 0.22 1 -0.32 119 120
FYN 0.022 0.021 -10000 0 -0.59 1 1
p210 bcr-abl/PTP1B -0.079 0.13 0.22 2 -0.34 138 140
EGFR -0.2 0.29 -10000 0 -0.6 312 312
EGF/EGFR -0.2 0.24 -10000 0 -0.42 437 437
CSF1 0.021 0.036 -10000 0 -0.59 3 3
AKT1 0.023 0.005 -10000 0 -10000 0 0
INSR 0.023 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.043 0.16 0.24 14 -0.35 114 128
Insulin Receptor/Insulin -0.041 0.11 -10000 0 -0.35 47 47
HCK 0.027 0.028 0.26 12 -10000 0 12
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.075 0.13 0.41 1 -0.34 116 117
EGF -0.11 0.24 0.26 2 -0.6 167 169
YES1 0.022 0.021 -10000 0 -0.59 1 1
CAV1 -0.16 0.2 0.27 2 -0.43 262 264
TXN 0.016 0.017 0.26 2 -10000 0 2
PTP1B/IRS1/GRB2 -0.07 0.15 -10000 0 -0.36 132 132
cell migration 0.079 0.13 0.34 138 -0.22 2 140
STAT3 0.021 0.005 -10000 0 -10000 0 0
PRLR 0.024 0.028 0.26 5 -0.59 1 6
ITGA2B 0.029 0.061 0.26 38 -0.59 3 41
CSF1R 0.024 0.009 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.034 0.032 0.32 1 -0.44 1 2
FGR 0.023 0.01 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.065 0.13 0.21 1 -0.34 120 121
Crk/p130 Cas -0.058 0.13 -10000 0 -0.34 101 101
DOK1 -0.065 0.12 0.23 2 -0.34 97 99
JAK2 -0.046 0.12 -10000 0 -0.46 45 45
Jak2/Leptin Receptor/Leptin -0.27 0.16 -10000 0 -0.39 416 416
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
PTPN1 -0.079 0.13 0.22 2 -0.34 138 140
LYN 0.021 0.008 -10000 0 -10000 0 0
CDH2 0.065 0.098 0.26 162 -0.59 2 164
SRC -0.018 0.1 -10000 0 -0.62 19 19
ITGB3 0.011 0.086 0.26 4 -0.59 17 21
CAT1/PTP1B -0.093 0.19 0.41 2 -0.46 125 127
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.023 0.004 -10000 0 -10000 0 0
PI3K -0.033 0.11 -10000 0 -0.36 35 35
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.24 0.15 -10000 0 -0.36 366 366
negative regulation of transcription -0.046 0.12 -10000 0 -0.45 46 46
FCGR2A 0.02 0.009 -10000 0 -10000 0 0
FER 0.012 0.048 -10000 0 -0.6 5 5
alphaIIb/beta3 Integrin 0.027 0.079 -10000 0 -0.44 20 20
BLK 0.048 0.088 0.26 114 -0.59 2 116
Insulin Receptor/Insulin/Shc 0.034 0.018 -10000 0 -10000 0 0
RHOA 0.02 0.006 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.59 212 212
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.01 0.26 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.046 0.18 0.34 4 -0.46 81 85
PRL 0.009 0.035 0.27 10 -10000 0 10
SOCS3 0.008 0.16 -10000 0 -1.2 14 14
SPRY2 -0.038 0.18 -10000 0 -0.6 80 80
Insulin Receptor/Insulin/IRS1 0.025 0.081 -10000 0 -0.39 32 32
CSF1/CSF1R -0.061 0.14 -10000 0 -0.35 109 109
Ras protein signal transduction 0.051 0.15 0.63 52 -10000 0 52
IRS1 0 0.12 -10000 0 -0.59 34 34
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.46 0.25 -10000 0 -0.59 704 704
STAT5B -0.067 0.13 0.2 3 -0.34 126 129
STAT5A -0.068 0.14 0.2 3 -0.34 130 133
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.069 0.14 -10000 0 -0.35 119 119
CSN2 0.026 0.059 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.01 0.075 -10000 0 -0.59 8 8
YBX1 0.026 0.017 -10000 0 -10000 0 0
LCK 0.025 0.075 0.26 28 -0.59 9 37
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.019 0.026 0.26 8 -10000 0 8
Visual signal transduction: Rods

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
mol:K + 0.023 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.18 12 -10000 0 12
Metarhodopsin II/Arrestin 0.037 0.039 0.33 2 -10000 0 2
PDE6G/GNAT1/GTP 0.035 0.034 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.029 0.26 12 -10000 0 12
GRK1 0.019 0.018 0.26 4 -10000 0 4
CNG Channel -0.058 0.17 -10000 0 -0.32 250 250
mol:Na + -0.056 0.16 -10000 0 -0.31 249 249
mol:ADP 0.019 0.018 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.01 0.13 0.35 1 -0.38 79 80
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.05 0.17 0.29 3 -0.32 247 250
CNGB1 0.031 0.054 0.26 45 -10000 0 45
RDH5 -0.36 0.3 -10000 0 -0.59 557 557
SAG 0.032 0.054 0.26 45 -10000 0 45
mol:Ca2+ -0.089 0.14 0.36 12 -0.31 183 195
Na + (4 Units) -0.059 0.15 -10000 0 -0.3 234 234
RGS9 -0.032 0.18 0.26 7 -0.59 81 88
GNB1/GNGT1 0.054 0.061 -10000 0 -10000 0 0
GNAT1/GDP 0.019 0.11 0.32 3 -0.32 79 82
GUCY2D 0.023 0.04 0.26 11 -0.59 2 13
GNGT1 0.056 0.089 0.26 138 -10000 0 138
GUCY2F 0.018 0.012 0.26 2 -10000 0 2
GNB5 0.023 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.019 0.054 0.22 2 -0.33 15 17
mol:11-cis-retinal -0.36 0.3 -10000 0 -0.59 557 557
mol:cGMP 0.042 0.046 -10000 0 -0.34 6 6
GNB1 0.023 0.005 -10000 0 -10000 0 0
Rhodopsin -0.26 0.23 0.2 7 -0.43 562 569
SLC24A1 0.023 0.004 -10000 0 -10000 0 0
CNGA1 -0.15 0.28 0.26 4 -0.59 257 261
Metarhodopsin II 0.026 0.021 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.051 -10000 0 -0.35 6 6
RGS9BP 0.035 0.052 0.26 43 -10000 0 43
Metarhodopsin II/Transducin 0.024 0.033 0.18 7 -10000 0 7
GCAP Family/Ca ++ 0.044 0.04 -10000 0 -0.35 4 4
PDE6A/B 0.027 0.069 -10000 0 -0.41 18 18
mol:Pi 0.01 0.12 0.34 1 -0.37 79 80
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.059 0.054 0.33 1 -10000 0 1
PDE6B 0.012 0.082 0.26 1 -0.59 16 17
PDE6A 0.028 0.033 0.26 17 -10000 0 17
PDE6G 0.032 0.047 0.26 35 -10000 0 35
RHO 0.024 0.029 0.26 13 -10000 0 13
PDE6 0.029 0.13 0.3 5 -0.32 89 94
GUCA1A 0.032 0.049 0.26 38 -10000 0 38
GC2/GCAP Family 0.055 0.042 -10000 0 -0.36 4 4
GUCA1C 0.017 0.009 0.26 1 -10000 0 1
GUCA1B 0.021 0.041 -10000 0 -0.59 4 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.043 0.17 -10000 0 -0.42 153 153
CRKL -0.049 0.15 0.36 1 -0.42 75 76
mol:PIP3 0.006 0.041 0.58 2 -0.85 1 3
AKT1 0.013 0.062 0.39 3 -0.75 1 4
PTK2B 0.02 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.048 0.14 0.34 1 -0.4 75 76
RANBP10 0.021 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.044 0.18 -10000 0 -0.4 173 173
MAP3K5 -0.041 0.15 0.36 1 -0.45 54 55
HGF/MET/CIN85/CBL/ENDOPHILINS -0.032 0.18 -10000 0 -0.37 179 179
AP1 -0.12 0.2 -10000 0 -0.41 266 266
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.25 0.38 -10000 0 -0.77 305 305
STAT3 (dimer) -0.05 0.15 -10000 0 -0.47 71 71
GAB1/CRKL/SHP2/PI3K -0.02 0.15 -10000 0 -0.45 42 42
INPP5D 0.023 0.004 -10000 0 -10000 0 0
CBL/CRK -0.037 0.15 0.34 1 -0.4 73 74
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.029 -10000 0 -0.59 2 2
ELK1 -0.031 0.098 0.26 30 -0.22 114 144
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.027 0.093 -10000 0 -0.26 64 64
PAK1 0.026 0.078 0.37 8 -0.72 1 9
HGF/MET/RANBP10 -0.046 0.18 -10000 0 -0.4 181 181
HRAS -0.11 0.26 -10000 0 -0.65 161 161
DOCK1 -0.048 0.14 0.52 1 -0.4 74 75
GAB1 -0.052 0.16 -10000 0 -0.37 141 141
CRK -0.05 0.15 0.36 1 -0.41 81 82
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.26 -10000 0 -0.58 190 190
JUN 0.018 0.058 -10000 0 -0.59 8 8
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.053 0.13 -10000 0 -0.29 182 182
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
cell morphogenesis -0.05 0.16 0.38 5 -0.46 69 74
GRB2/SHC -0.018 0.11 -10000 0 -0.29 103 103
FOS -0.16 0.28 -10000 0 -0.59 262 262
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.031 0.097 0.26 30 -0.22 114 144
HGF/MET/MUC20 -0.056 0.18 -10000 0 -0.4 182 182
cell migration -0.018 0.11 -10000 0 -0.28 103 103
GRB2 0.023 0.01 0.26 1 -10000 0 1
CBL 0.022 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.045 0.17 -10000 0 -0.42 153 153
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.049 0.14 -10000 0 -0.35 146 146
MET/MUC20 -0.057 0.17 -10000 0 -0.42 153 153
RAP1B -0.041 0.14 0.28 3 -0.4 60 63
RAP1A -0.047 0.14 0.41 2 -0.4 62 64
HGF/MET/RANBP9 -0.045 0.18 -10000 0 -0.4 181 181
RAF1 -0.1 0.25 -10000 0 -0.61 160 160
STAT3 -0.05 0.16 -10000 0 -0.47 71 71
cell proliferation -0.044 0.19 0.34 8 -0.44 129 137
RPS6KB1 -0.015 0.065 -10000 0 -0.23 31 31
MAPK3 -0.042 0.097 0.72 6 -10000 0 6
MAPK1 -0.012 0.17 0.68 45 -10000 0 45
RANBP9 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.028 0.13 0.43 1 -0.43 35 36
SRC -0.054 0.13 0.2 1 -0.42 66 67
PI3K -0.026 0.13 -10000 0 -0.28 146 146
MET/Glomulin -0.049 0.15 -10000 0 -0.38 147 147
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.092 0.23 0.47 1 -0.56 159 160
MET -0.076 0.23 -10000 0 -0.59 145 145
MAP4K1 -0.044 0.16 0.38 1 -0.43 75 76
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.092 0.23 0.47 1 -0.57 159 160
BAD 0.011 0.059 0.36 3 -0.72 1 4
MAP2K4 -0.038 0.14 0.34 1 -0.42 48 49
SHP2/GRB2/SOS1/GAB1 -0.042 0.18 -10000 0 -0.41 148 148
INPPL1 0.022 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.048 0.11 -10000 0 -0.28 163 163
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.59 50 50
RASA1 0.023 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.024 0.13 -10000 0 -0.27 172 172
PDPK1 0.016 0.065 0.44 2 -0.79 1 3
HGF/MET/SHIP -0.045 0.19 -10000 0 -0.4 180 180
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.005 0.041 0.23 5 -0.37 1 6
NFATC2 -0.015 0.096 0.24 4 -0.39 47 51
NFATC3 0.007 0.037 0.23 5 -10000 0 5
CD40LG -0.13 0.3 0.54 17 -0.58 193 210
PTGS2 -0.19 0.35 0.53 13 -0.66 269 282
JUNB 0.024 0.009 0.26 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.028 0.17 4 -10000 0 4
CaM/Ca2+ 0.009 0.028 0.17 4 -10000 0 4
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.011 0.062 -10000 0 -0.6 8 8
mol:Ca2+ -0.002 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.027 0.045 0.26 19 -0.59 2 21
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.004 0.14 0.48 14 -0.38 45 59
FOS -0.16 0.28 -10000 0 -0.59 267 267
IFNG -0.11 0.29 0.51 37 -0.55 173 210
AP-1/NFAT1-c-4 -0.13 0.34 0.57 36 -0.62 210 246
FASLG -0.11 0.27 0.56 21 -0.55 155 176
NFAT1-c-4/ICER1 -0.008 0.11 0.33 8 -0.35 44 52
IL2RA -0.12 0.29 0.52 30 -0.55 187 217
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSF2 -0.12 0.28 0.53 18 -0.54 192 210
JunB/Fra1/NFAT1-c-4 0.004 0.12 0.34 17 -0.35 43 60
IL4 -0.13 0.27 0.53 13 -0.55 181 194
IL2 -0.015 0.16 -10000 0 -0.95 23 23
IL3 -0.019 0.12 -10000 0 -0.72 22 22
FKBP1A 0.023 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.017 0.26 3 -10000 0 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.017 0.08 0.26 8 -0.3 5 13
epithelial cell differentiation 0.033 0.076 -10000 0 -0.32 1 1
ITCH 0.032 0.019 -10000 0 -10000 0 0
WWP1 0.026 0.099 0.48 8 -10000 0 8
FYN 0.022 0.021 -10000 0 -0.59 1 1
EGFR -0.19 0.29 -10000 0 -0.59 312 312
PRL 0.022 0.026 0.26 10 -10000 0 10
neuron projection morphogenesis -0.052 0.14 0.35 9 -0.37 27 36
PTPRZ1 -0.29 0.31 0.26 6 -0.59 463 469
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.14 -10000 0 -0.32 136 136
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.091 0.16 0.24 1 -0.34 240 241
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.073 0.4 8 -0.3 3 11
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.003 0.12 0.26 6 -0.36 54 60
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.084 0.16 -10000 0 -0.34 201 201
GRIN2B -0.11 0.16 -10000 0 -0.34 235 235
ErbB4/ErbB2/betacellulin 0.014 0.098 -10000 0 -0.33 27 27
STAT1 0.029 0.035 0.26 19 -10000 0 19
HBEGF 0.022 0.029 -10000 0 -0.59 2 2
PRLR 0.024 0.028 0.26 5 -0.59 1 6
E4ICDs/ETO2 0.008 0.087 0.28 6 -0.36 14 20
axon guidance 0.058 0.12 0.31 51 -0.34 3 54
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.033 0.027 -10000 0 -0.44 1 1
CBFA2T3 0.013 0.075 0.26 3 -0.59 13 16
ErbB4/ErbB2/HBEGF 0.031 0.072 -10000 0 -0.32 2 2
MAPK3 -0.054 0.14 -10000 0 -0.37 33 33
STAT1 (dimer) 0.02 0.081 0.27 10 -0.27 3 13
MAPK1 -0.053 0.14 0.39 2 -0.36 41 43
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.075 0.16 -10000 0 -0.34 188 188
NRG1 -0.12 0.2 -10000 0 -0.44 241 241
NRG3 -0.009 0.15 0.26 18 -0.59 54 72
NRG2 -0.28 0.31 -10000 0 -0.59 451 451
NRG4 0.026 0.028 0.26 12 -10000 0 12
heart development 0.058 0.12 0.31 51 -0.34 3 54
neural crest cell migration -0.074 0.16 -10000 0 -0.33 188 188
ERBB2 0.036 0.072 0.27 78 -10000 0 78
WWOX/E4ICDs 0.012 0.076 0.27 5 -0.27 3 8
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.096 0.17 -10000 0 -0.33 230 230
apoptosis 0.018 0.13 0.44 50 -0.27 3 53
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.17 0.18 0.26 1 -0.36 352 353
ErbB4/ErbB2/epiregulin 0.005 0.14 0.34 14 -0.32 70 84
ErbB4/ErbB4/betacellulin/betacellulin -0.003 0.11 0.27 6 -0.34 49 55
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.041 0.083 -10000 0 -0.32 3 3
MDM2 0.011 0.08 0.26 29 -0.27 3 32
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.088 0.15 -10000 0 -0.33 235 235
STAT5A 0.052 0.11 0.36 11 -0.33 3 14
ErbB4/EGFR/neuregulin 1 beta -0.19 0.24 -10000 0 -0.45 364 364
DLG4 0.022 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.012 0.07 -10000 0 -0.25 2 2
STAT5A (dimer) 0.06 0.098 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.062 0.11 0.35 7 -0.35 3 10
LRIG1 0.022 0.021 -10000 0 -0.59 1 1
EREG -0.03 0.21 0.26 67 -0.59 103 170
BTC -0.008 0.14 0.26 2 -0.59 46 48
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.048 0.11 0.32 40 -0.34 3 43
ERBB4 -0.004 0.073 0.4 8 -0.3 3 11
STAT5B 0.022 0.029 -10000 0 -0.59 2 2
YAP1 -0.01 0.1 -10000 0 -0.38 57 57
GRB2 0.023 0.01 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.034 0.071 0.32 1 -10000 0 1
glial cell differentiation -0.01 0.067 0.25 2 -10000 0 2
WWOX 0.021 0.012 0.26 1 -10000 0 1
cell proliferation -0.04 0.18 0.33 13 -0.45 44 57
Aurora C signaling

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
INCENP 0.023 0.004 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.081 0.32 7 -0.31 1 8
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.021 -10000 0 -0.3 2 2
AURKB 0.15 0.12 0.26 474 -10000 0 474
AURKC 0.025 0.033 0.26 10 -0.59 1 11
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.01 0.025 0.14 33 -10000 0 33
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.11 -10000 0 -0.43 39 39
STXBP1 0.022 0.036 -10000 0 -0.59 3 3
ACh/CHRNA1 0.078 0.094 0.2 310 -0.16 6 316
RAB3GAP2/RIMS1/UNC13B 0.034 0.091 -10000 0 -0.33 38 38
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 0.023 0.15 0.26 98 -0.59 38 136
mol:ACh -0.004 0.038 0.088 13 -0.14 40 53
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.02 0.085 0.24 1 -0.29 35 36
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.078 0.094 0.2 310 -0.16 6 316
UNC13B 0.023 0.004 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.26 321 -10000 0 321
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.034 0.12 0.2 172 -0.38 37 209
SNAP25 -0.001 0.063 0.1 51 -0.31 31 82
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.049 0.16 0.26 180 -0.59 34 214
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.03 -10000 0 -0.38 3 3
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.085 0.24 1 -0.29 35 36
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.018 0.035 -10000 0 -0.32 2 2
PDGFRB 0.019 0.031 -10000 0 -0.6 2 2
SPHK1 -0.019 0.097 -10000 0 -0.75 12 12
mol:S1P -0.023 0.095 0.4 1 -0.66 12 13
S1P1/S1P/Gi -0.13 0.23 0.32 2 -0.44 276 278
GNAO1 0.005 0.099 0.25 30 -0.6 18 48
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.22 0.38 3 -0.42 241 244
PLCG1 -0.13 0.22 0.37 2 -0.43 265 267
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.031 -10000 0 -0.6 2 2
GNAI2 0.008 0.023 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.019 0.13 -10000 0 -0.6 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.013 0.023 0.2 1 -0.28 2 3
S1P1/S1P -0.035 0.097 0.28 2 -0.48 13 15
negative regulation of cAMP metabolic process -0.13 0.23 0.32 2 -0.43 276 278
MAPK3 -0.18 0.3 0.37 4 -0.59 297 301
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
KDR 0.013 0.028 -10000 0 -0.6 1 1
PLCB2 -0.026 0.096 0.31 6 -0.42 14 20
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.08 -10000 0 -0.4 13 13
receptor internalization -0.036 0.087 -10000 0 -0.44 13 13
PTGS2 -0.34 0.5 0.4 2 -1 306 308
Rac1/GTP -0.033 0.08 -10000 0 -0.4 13 13
RHOA 0.023 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.026 0.26 5 -10000 0 5
negative regulation of T cell proliferation -0.13 0.23 0.32 2 -0.43 276 278
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.003 0.061 -10000 0 -0.6 8 8
MAPK1 -0.2 0.33 0.36 2 -0.63 312 314
S1P1/S1P/PDGFB-D/PDGFRB -0.035 0.11 0.32 3 -0.5 11 14
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Glypican 1 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
GPC1/FGF2 dimer/FGFR1 dimer -0.11 0.19 -10000 0 -0.38 278 278
fibroblast growth factor receptor signaling pathway -0.11 0.19 -10000 0 -0.38 278 278
LAMA1 -0.04 0.19 0.26 1 -0.59 92 93
PRNP 0.015 0.071 -10000 0 -0.59 12 12
GPC1/SLIT2 -0.006 0.13 -10000 0 -0.44 73 73
SMAD2 -0.019 0.057 0.25 1 -0.35 24 25
GPC1/PrPc/Cu2+ 0.025 0.05 -10000 0 -0.38 13 13
GPC1/Laminin alpha1 -0.017 0.15 -10000 0 -0.44 93 93
TDGF1 0.016 0.065 0.26 1 -0.59 10 11
CRIPTO/GPC1 0.028 0.054 -10000 0 -0.44 11 11
APP/GPC1 0.034 0.02 -10000 0 -0.44 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.004 0.045 -10000 0 -0.38 11 11
FLT1 0.022 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.035 0.071 -10000 0 -0.38 24 24
SERPINC1 0.028 0.046 0.26 32 -10000 0 32
FYN 0.003 0.046 -10000 0 -0.38 12 12
FGR 0.004 0.044 -10000 0 -0.38 11 11
positive regulation of MAPKKK cascade 0.006 0.087 0.28 2 -0.37 25 27
SLIT2 -0.026 0.17 -10000 0 -0.59 72 72
GPC1/NRG -0.11 0.21 -10000 0 -0.38 313 313
NRG1 -0.15 0.27 0.26 3 -0.59 244 247
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.044 0.026 -10000 0 -0.38 1 1
LYN 0.004 0.039 -10000 0 -0.38 8 8
mol:Spermine 0.005 0.017 0.14 3 -0.44 1 4
cell growth -0.11 0.19 -10000 0 -0.38 278 278
BMP signaling pathway -0.024 0.025 0.59 1 -0.26 3 4
SRC 0.004 0.043 -10000 0 -0.38 10 10
TGFBR1 0.024 0.009 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.15 0.29 0.26 22 -0.59 267 289
GPC1 0.024 0.025 0.26 3 -0.59 1 4
TGFBR1 (dimer) 0.024 0.009 0.26 1 -10000 0 1
VEGFA 0.025 0.018 0.26 5 -10000 0 5
BLK 0.018 0.069 -10000 0 -0.39 13 13
HCK 0.006 0.046 -10000 0 -0.38 10 10
FGF2 -0.21 0.3 -10000 0 -0.59 342 342
FGFR1 0.015 0.051 -10000 0 -0.59 6 6
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
TGFBR2 0.008 0.097 -10000 0 -0.59 23 23
cell death 0.034 0.02 -10000 0 -0.44 1 1
ATIII/GPC1 0.034 0.038 -10000 0 -0.44 1 1
PLA2G2A/GPC1 -0.11 0.22 -10000 0 -0.42 286 286
LCK 0.004 0.063 -10000 0 -0.38 20 20
neuron differentiation -0.11 0.21 -10000 0 -0.38 313 313
PrPc/Cu2+ 0.011 0.052 -10000 0 -0.44 12 12
APP 0.023 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.008 0.097 -10000 0 -0.59 23 23
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.005 0.07 0.35 1 -0.34 7 8
alphaM/beta2 Integrin/GPIbA 0.008 0.078 0.35 4 -0.42 6 10
alphaM/beta2 Integrin/proMMP-9 0.075 0.11 0.36 13 -0.43 1 14
PLAUR 0.041 0.063 0.26 65 -10000 0 65
HMGB1 -0.004 0.04 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.008 0.063 0.35 1 -10000 0 1
AGER -0.008 0.052 -10000 0 -0.64 2 2
RAP1A 0.023 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.029 0.14 0.33 4 -0.37 13 17
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 382 -0.59 1 383
CYR61 -0.007 0.13 -10000 0 -0.59 45 45
TLN1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.12 -10000 0 -0.38 33 33
RHOA 0.023 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.1 0.24 -10000 0 -0.59 176 176
MYH2 -0.013 0.15 0.25 17 -0.36 73 90
MST1R 0.021 0.055 0.26 7 -0.59 6 13
leukocyte activation during inflammatory response -0.2 0.17 0.3 1 -0.34 513 514
APOB -0.36 0.3 -10000 0 -0.59 566 566
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.041 -10000 0 -0.59 4 4
JAM3 0.019 0.036 -10000 0 -0.59 3 3
GP1BA 0.023 0.063 0.26 21 -0.59 6 27
alphaM/beta2 Integrin/CTGF 0.003 0.077 0.35 1 -0.42 10 11
alphaM/beta2 Integrin -0.012 0.12 0.21 6 -0.39 43 49
JAM3 homodimer 0.019 0.036 -10000 0 -0.59 3 3
ICAM2 0.018 0.046 -10000 0 -0.59 5 5
ICAM1 0.027 0.028 0.26 12 -10000 0 12
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.13 0.24 7 -0.38 45 52
cell adhesion 0.008 0.077 0.34 4 -0.42 6 10
NFKB1 -0.1 0.21 0.42 4 -0.38 280 284
THY1 0.023 0.021 0.26 6 -10000 0 6
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.23 0.19 -10000 0 -0.38 572 572
alphaM/beta2 Integrin/LRP/tPA 0.006 0.09 0.35 1 -0.38 23 24
IL6 -0.27 0.4 0.35 3 -0.78 329 332
ITGB2 -0.003 0.052 0.27 12 -10000 0 12
elevation of cytosolic calcium ion concentration 0.03 0.086 0.34 17 -10000 0 17
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 0.35 1 -0.39 35 36
JAM2 -0.004 0.13 -10000 0 -0.59 40 40
alphaM/beta2 Integrin/ICAM1 0.02 0.088 0.35 3 -0.34 15 18
alphaM/beta2 Integrin/uPA/Plg 0.018 0.071 0.34 1 -10000 0 1
RhoA/GTP -0.018 0.16 0.24 17 -0.37 87 104
positive regulation of phagocytosis -0.002 0.1 0.32 4 -0.37 17 21
Ron/MSP 0.027 0.064 -10000 0 -0.43 16 16
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.088 0.35 17 -10000 0 17
alphaM/beta2 Integrin/uPAR 0.018 0.08 0.4 4 -10000 0 4
PLAU 0.031 0.041 0.26 27 -10000 0 27
PLAT 0.007 0.088 -10000 0 -0.59 19 19
actin filament polymerization -0.012 0.14 0.25 17 -0.37 63 80
MST1 0.018 0.058 0.26 1 -0.59 8 9
alphaM/beta2 Integrin/lipoprotein(a) -0.2 0.18 0.32 1 -0.35 513 514
TNF -0.1 0.2 0.39 3 -0.76 19 22
RAP1B 0.023 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.013 0.069 0.35 1 -10000 0 1
fibrinolysis 0.016 0.069 0.33 1 -10000 0 1
HCK 0.027 0.028 0.26 12 -10000 0 12
dendritic cell antigen processing and presentation -0.011 0.13 0.24 7 -0.38 45 52
VTN 0.033 0.074 0.26 53 -0.59 5 58
alphaM/beta2 Integrin/CYR61 -0.011 0.11 0.35 1 -0.4 47 48
LPA 0.018 0.017 0.26 4 -10000 0 4
LRP1 0.018 0.061 -10000 0 -0.59 9 9
cell migration 0.045 0.085 0.29 12 -0.36 6 18
FN1 0.12 0.12 0.26 377 -10000 0 377
alphaM/beta2 Integrin/Thy1 0.008 0.064 0.35 1 -10000 0 1
MPO -0.014 0.14 0.26 1 -0.59 52 53
KNG1 0.021 0.026 0.26 10 -10000 0 10
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.013 0.15 0.25 22 -0.36 78 100
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.017 0.26 4 -10000 0 4
CTGF 0.017 0.066 0.26 2 -0.59 10 12
alphaM/beta2 Integrin/Hck 0.009 0.068 0.37 4 -10000 0 4
ITGAM -0.003 0.045 0.26 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.049 0.16 0.35 1 -0.38 159 160
HP -0.07 0.23 0.26 30 -0.59 144 174
leukocyte adhesion -0.04 0.14 0.29 4 -0.38 47 51
SELP -0.1 0.24 -10000 0 -0.59 176 176
IL6-mediated signaling events

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
BCL2L1 -0.017 0.23 0.57 8 -0.65 18 26
CRP 0.004 0.24 0.56 29 -0.63 20 49
cell cycle arrest -0.026 0.25 0.58 11 -0.66 35 46
TIMP1 -0.011 0.22 0.54 10 -0.63 14 24
IL6ST -0.015 0.16 -10000 0 -0.58 64 64
Rac1/GDP -0.059 0.19 0.33 8 -0.45 80 88
AP1 -0.074 0.21 0.38 2 -0.48 93 95
GAB2 0.022 0.008 -10000 0 -10000 0 0
TNFSF11 -0.004 0.24 0.63 10 -0.69 12 22
HSP90B1 0.025 0.11 -10000 0 -0.8 9 9
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.089 0.17 -10000 0 -0.51 71 71
AKT1 0.025 0.057 0.26 1 -0.52 4 5
FOXO1 0.026 0.059 0.43 1 -0.44 4 5
MAP2K6 -0.088 0.18 0.27 3 -0.4 142 145
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.042 0.2 0.4 11 -0.47 59 70
MITF -0.08 0.19 0.28 10 -0.39 141 151
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.023 0.004 -10000 0 -10000 0 0
A2M -0.003 0.18 -10000 0 -1.2 21 21
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.014 0.12 -10000 0 -0.48 31 31
STAT3 -0.034 0.26 0.58 11 -0.72 36 47
STAT1 0.015 0.093 -10000 0 -0.82 8 8
CEBPD -0.002 0.24 0.57 15 -0.69 20 35
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.019 -10000 0 -0.44 1 1
JUN 0.018 0.058 -10000 0 -0.59 8 8
PIAS3/MITF -0.065 0.18 0.34 2 -0.44 81 83
MAPK11 -0.088 0.17 -10000 0 -0.5 74 74
STAT3 (dimer)/FOXO1 -0.013 0.22 0.48 20 -0.54 34 54
GRB2/SOS1/GAB family -0.051 0.17 -10000 0 -0.44 63 63
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.093 0.19 0.26 1 -0.33 260 261
GRB2 0.023 0.01 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.15 0.46 0.55 29 -0.93 206 235
PIK3R1 0.023 0.021 -10000 0 -0.59 1 1
JAK1 0.026 0.009 -10000 0 -10000 0 0
MYC 0.009 0.28 0.57 21 -1 22 43
FGG -0.014 0.24 0.63 11 -0.66 17 28
macrophage differentiation -0.026 0.25 0.58 11 -0.66 35 46
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.088 0.21 -10000 0 -0.36 288 288
JUNB -0.02 0.22 0.55 8 -0.66 13 21
FOS -0.16 0.28 -10000 0 -0.59 262 262
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.082 0.2 0.31 10 -0.34 247 257
STAT1/PIAS1 -0.05 0.2 0.33 16 -0.38 135 151
GRB2/SOS1/GAB family/SHP2/PI3K 0.027 0.061 -10000 0 -0.49 6 6
STAT3 (dimer) -0.032 0.26 0.58 11 -0.71 35 46
PRKCD -0.026 0.2 0.43 23 -0.51 40 63
IL6R 0.006 0.099 -10000 0 -0.59 24 24
SOCS3 -0.085 0.19 -10000 0 -0.64 45 45
gp130 (dimer)/JAK1/JAK1/LMO4 0.027 0.12 0.26 1 -0.36 64 65
Rac1/GTP -0.053 0.2 0.36 9 -0.45 78 87
HCK 0.027 0.028 0.26 12 -10000 0 12
MAPKKK cascade 0.003 0.13 -10000 0 -0.57 28 28
bone resorption -0.002 0.24 0.57 18 -0.63 14 32
IRF1 -0.02 0.23 0.57 8 -0.63 20 28
mol:GDP -0.074 0.19 0.31 10 -0.39 141 151
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.075 0.19 0.31 10 -0.4 141 151
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.096 0.19 -10000 0 -0.55 77 77
PTPN11 0.012 0.085 -10000 0 -0.85 7 7
IL6/IL6RA -0.12 0.22 0.22 1 -0.4 334 335
gp130 (dimer)/TYK2/TYK2/LMO4 0.021 0.12 -10000 0 -0.37 65 65
gp130 (dimer)/JAK2/JAK2/LMO4 0.021 0.11 -10000 0 -0.37 64 64
IL6 -0.19 0.3 0.28 1 -0.59 318 319
PIAS3 0.023 0.006 -10000 0 -10000 0 0
PTPRE 0.007 0.033 -10000 0 -0.59 1 1
PIAS1 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.098 0.18 0.24 2 -0.33 258 260
LMO4 0.028 0.041 0.29 2 -0.59 3 5
STAT3 (dimer)/PIAS3 -0.036 0.25 0.56 9 -0.66 39 48
MCL1 0.057 0.094 0.49 1 -0.51 3 4
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.009 0.26 1 -10000 0 1
CCL5 0.028 0.056 0.26 29 -0.59 3 32
SDCBP 0.021 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.067 0.13 0.3 22 -0.4 13 35
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 0.052 0.13 0.27 7 -0.38 16 23
Syndecan-1/Syntenin 0.054 0.12 0.29 13 -0.4 12 25
MAPK3 0.051 0.12 0.27 12 -0.37 12 24
HGF/MET -0.067 0.21 -10000 0 -0.46 182 182
TGFB1/TGF beta receptor Type II 0.024 0.009 0.26 1 -10000 0 1
BSG 0.023 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.051 0.12 0.27 7 -0.38 16 23
Syndecan-1/RANTES 0.062 0.14 0.32 33 -0.41 17 50
Syndecan-1/CD147 0.067 0.13 0.3 13 -0.37 15 28
Syndecan-1/Syntenin/PIP2 0.05 0.12 0.27 13 -0.39 12 25
LAMA5 0.022 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.048 0.11 0.26 12 -0.38 12 24
MMP7 -0.042 0.2 0.26 26 -0.59 103 129
HGF -0.011 0.14 -10000 0 -0.59 50 50
Syndecan-1/CASK 0.046 0.12 0.25 17 -0.37 17 34
Syndecan-1/HGF/MET -0.002 0.21 0.29 7 -0.47 93 100
regulation of cell adhesion 0.044 0.11 0.26 11 -0.4 8 19
HPSE 0.027 0.039 0.26 17 -0.59 1 18
positive regulation of cell migration 0.067 0.13 0.3 22 -0.4 13 35
SDC1 0.07 0.12 0.3 21 -0.4 10 31
Syndecan-1/Collagen 0.067 0.13 0.3 22 -0.4 13 35
PPIB 0.024 0.015 0.26 3 -10000 0 3
MET -0.076 0.23 -10000 0 -0.59 145 145
PRKACA 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 382 -0.59 1 383
MAPK1 0.052 0.12 0.28 12 -0.37 12 24
homophilic cell adhesion 0.067 0.13 0.3 22 -0.39 14 36
MMP1 0.19 0.11 0.26 627 -10000 0 627
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.034 0.023 -10000 0 -0.31 2 2
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.39 328 328
PTK2 -0.056 0.15 0.32 2 -0.49 35 37
IGF1R 0.012 0.085 0.26 2 -0.59 17 19
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.067 0.26 5 -0.59 10 15
SRC 0.023 0.005 -10000 0 -10000 0 0
CDKN1B -0.045 0.12 -10000 0 -0.53 29 29
VEGFA 0.025 0.018 0.26 5 -10000 0 5
ILK -0.042 0.11 -10000 0 -0.49 25 25
ROCK1 0.023 0.004 -10000 0 -10000 0 0
AKT1 -0.043 0.1 -10000 0 -0.48 22 22
PTK2B -0.01 0.061 0.36 2 -0.34 17 19
alphaV/beta3 Integrin/JAM-A -0.078 0.18 0.3 1 -0.34 242 243
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.036 0.061 -10000 0 -0.38 17 17
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.045 0.2 -10000 0 -0.39 199 199
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.016 0.055 -10000 0 -0.42 4 4
alphaV/beta3 Integrin/Syndecan-1 0.047 0.073 -10000 0 -0.37 18 18
PI4KA 0.023 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.47 285 285
PI4 Kinase 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.076 0.093 0.35 3 -0.37 17 20
RPS6KB1 -0.16 0.23 0.42 3 -0.57 143 146
TLN1 0.023 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.57 305 305
GPR124 0.016 0.046 -10000 0 -0.59 5 5
MAPK1 -0.2 0.3 -10000 0 -0.57 318 318
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
alphaV/beta3 Integrin/Tumstatin -0.04 0.17 -10000 0 -0.38 176 176
cell adhesion 0.026 0.072 0.26 1 -0.36 27 28
ANGPTL3 0.021 0.017 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.024 -10000 0 -0.38 1 1
IGF-1R heterotetramer 0.012 0.084 0.26 2 -0.59 17 19
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
TGFBR2 0.008 0.097 -10000 0 -0.59 23 23
ITGB3 0.012 0.085 0.26 4 -0.59 17 21
IGF1 -0.1 0.25 -10000 0 -0.59 185 185
RAC1 0.024 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.028 0.065 -10000 0 -0.38 17 17
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.023 0.021 -10000 0 -0.59 1 1
alphaV/beta3 Integrin/CD47 0.037 0.062 -10000 0 -0.38 18 18
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.025 0.11 -10000 0 -0.47 39 39
CSF1 0.021 0.036 -10000 0 -0.59 3 3
PIK3C2A -0.04 0.11 -10000 0 -0.47 23 23
PI4 Kinase/Pyk2 -0.078 0.15 -10000 0 -0.31 203 203
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.063 -10000 0 -0.37 17 17
FAK1/Vinculin -0.038 0.13 0.34 4 -0.4 30 34
alphaV beta3/Integrin/ppsTEM5 0.029 0.065 -10000 0 -0.39 17 17
RHOA 0.023 0.005 -10000 0 -10000 0 0
VTN 0.033 0.074 0.26 53 -0.59 5 58
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.59 342 342
F11R -0.12 0.2 -10000 0 -0.44 261 261
alphaV/beta3 Integrin/Lactadherin 0.033 0.077 0.35 1 -0.39 26 27
alphaV/beta3 Integrin/TGFBR2 0.028 0.097 -10000 0 -0.45 32 32
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.034 -10000 0 -0.34 3 3
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.036 0.054 -10000 0 -0.34 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 377 -10000 0 377
alphaV/beta3 Integrin/Pyk2 0.029 0.061 -10000 0 -0.34 17 17
SDC1 0.04 0.065 0.26 62 -0.59 1 63
VAV3 -0.01 0.042 -10000 0 -0.33 9 9
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0 0.12 -10000 0 -0.59 34 34
FAK1/Paxillin -0.037 0.13 0.33 5 -0.4 30 35
cell migration -0.037 0.12 0.31 5 -0.37 27 32
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.065 0.17 -10000 0 -0.32 212 212
SPP1 0.09 0.11 0.26 247 -10000 0 247
KDR 0.023 0.021 -10000 0 -0.59 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.093 0.24 0.26 4 -0.59 172 176
angiogenesis -0.19 0.3 -10000 0 -0.58 288 288
Rac1/GTP 0.021 0.038 -10000 0 -0.3 8 8
EDIL3 0.004 0.12 0.26 14 -0.59 33 47
cell proliferation 0.027 0.096 -10000 0 -0.44 32 32
Ephrin A reverse signaling

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
MAPKKK cascade -0.008 0.12 -10000 0 -0.36 87 87
EFNA5 -0.033 0.18 0.26 1 -0.59 82 83
FYN -0.025 0.1 -10000 0 -0.35 81 81
neuron projection morphogenesis -0.008 0.12 -10000 0 -0.36 87 87
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.007 0.12 -10000 0 -0.36 87 87
EPHA5 0.023 0.017 0.26 4 -10000 0 4
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.044 0.23 0.42 4 -0.65 94 98
IHH 0.015 0.082 0.27 25 -0.24 5 30
SHH Np/Cholesterol/GAS1 0 0.078 -10000 0 -0.34 41 41
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0 0.077 0.34 41 -10000 0 41
SMO/beta Arrestin2 -0.02 0.21 -10000 0 -0.62 80 80
SMO -0.044 0.21 -10000 0 -0.65 83 83
AKT1 -0.002 0.12 -10000 0 -0.52 20 20
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.02 0.16 -10000 0 -0.59 64 64
ADRBK1 0.022 0.006 -10000 0 -10000 0 0
heart looping -0.043 0.21 -10000 0 -0.63 83 83
STIL 0.007 0.18 0.3 28 -0.48 75 103
DHH N/PTCH2 -0.016 0.15 -10000 0 -0.45 95 95
DHH N/PTCH1 -0.03 0.21 0.29 1 -0.51 121 122
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.007 0.1 0.26 1 -0.59 25 26
PTHLH -0.065 0.3 0.44 10 -0.85 99 109
determination of left/right symmetry -0.043 0.21 -10000 0 -0.63 83 83
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
skeletal system development -0.064 0.3 0.44 10 -0.84 99 109
IHH N/Hhip 0.027 0.055 -10000 0 -0.48 1 1
DHH N/Hhip 0.021 0.08 -10000 0 -0.42 27 27
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.043 0.21 -10000 0 -0.63 83 83
pancreas development 0.024 0.03 0.26 7 -0.59 1 8
HHAT 0.019 0.022 -10000 0 -0.59 1 1
PI3K 0.032 0.019 -10000 0 -0.44 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.14 -10000 0 -0.59 47 47
somite specification -0.043 0.21 -10000 0 -0.63 83 83
SHH Np/Cholesterol/PTCH1 -0.027 0.16 0.26 4 -0.5 78 82
SHH Np/Cholesterol/PTCH2 -0.009 0.093 -10000 0 -0.35 58 58
SHH Np/Cholesterol/Megalin -0.061 0.15 0.28 3 -0.35 183 186
SHH -0.001 0.038 0.36 5 -0.44 1 6
catabolic process -0.034 0.21 0.31 2 -0.57 105 107
SMO/Vitamin D3 -0.01 0.2 0.34 17 -0.57 76 93
SHH Np/Cholesterol/Hhip 0.016 0.032 0.29 5 -0.35 2 7
LRP2 -0.12 0.27 0.26 22 -0.59 224 246
receptor-mediated endocytosis -0.081 0.22 0.31 8 -0.61 94 102
SHH Np/Cholesterol/BOC -0.006 0.089 -10000 0 -0.34 54 54
SHH Np/Cholesterol/CDO 0.012 0.043 -10000 0 -0.35 11 11
mesenchymal cell differentiation -0.016 0.031 0.35 2 -0.28 5 7
mol:Vitamin D3 0.002 0.18 0.35 17 -0.5 78 95
IHH N/PTCH2 -0.014 0.15 -10000 0 -0.48 75 75
CDON 0.014 0.068 -10000 0 -0.59 11 11
IHH N/PTCH1 -0.025 0.21 0.36 3 -0.57 105 108
Megalin/LRPAP1 -0.081 0.21 -10000 0 -0.44 224 224
PTCH2 -0.026 0.17 -10000 0 -0.59 72 72
SHH Np/Cholesterol 0.01 0.015 -10000 0 -0.35 1 1
PTCH1 -0.034 0.21 0.31 2 -0.57 105 107
HHIP 0.024 0.03 0.26 7 -0.59 1 8
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.046 0.18 0.31 110 -0.5 42 152
FYN 0.024 0.2 0.38 37 -0.61 46 83
LAT/GRAP2/SLP76 0.028 0.18 0.4 28 -0.53 46 74
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.025 0.16 0.33 66 -0.4 57 123
B2M 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.017 0.06 0.17 57 -0.14 23 80
MAP3K8 0.021 0.041 -10000 0 -0.59 4 4
mol:Ca2+ -0.024 0.034 -10000 0 -0.095 142 142
integrin-mediated signaling pathway 0.025 0.023 0.18 1 -0.38 2 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.014 0.2 0.42 31 -0.55 63 94
TRPV6 -0.095 0.28 1.2 14 -0.59 169 183
CD28 0.024 0.048 0.27 8 -0.59 4 12
SHC1 0.031 0.21 0.33 118 -0.63 46 164
receptor internalization -0.01 0.22 0.39 28 -0.51 104 132
PRF1 -0.009 0.24 0.61 5 -1 33 38
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
COT/AKT1 0.033 0.14 0.3 63 -0.34 47 110
LAT 0.016 0.21 0.37 42 -0.64 47 89
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.022 0.094 0.28 34 -0.6 15 49
CD3E 0.021 0.093 0.28 28 -0.6 15 43
CD3G 0.016 0.11 0.27 35 -0.59 23 58
RASGRP2 0 0.052 0.14 14 -0.17 60 74
RASGRP1 0.028 0.16 0.37 38 -0.44 44 82
HLA-A 0.026 0.019 0.27 4 -10000 0 4
RASSF5 0.019 0.031 0.26 1 -0.59 2 3
RAP1A/GTP/RAPL 0.025 0.024 0.18 1 -0.38 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.042 0.082 0.17 147 -0.13 23 170
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.055 -10000 0 -0.22 35 35
PRKCA 0.014 0.099 0.23 39 -0.27 44 83
GRAP2 0.016 0.069 0.26 3 -0.59 11 14
mol:IP3 0.016 0.14 0.27 109 -0.39 43 152
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.006 0.18 0.33 27 -0.65 45 72
ORAI1 0.039 0.17 0.65 3 -0.98 13 16
CSK 0.01 0.2 0.4 28 -0.66 46 74
B7 family/CD28 0.065 0.21 0.47 35 -0.65 39 74
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.003 0.23 0.42 28 -0.7 55 83
PTPN6 0.01 0.2 0.38 30 -0.64 47 77
VAV1 0.006 0.2 0.4 28 -0.64 49 77
Monovalent TCR/CD3 -0.001 0.14 0.29 29 -0.53 43 72
CBL 0.022 0.007 -10000 0 -10000 0 0
LCK 0.021 0.21 0.39 34 -0.66 44 78
PAG1 0.023 0.21 0.35 51 -0.65 45 96
RAP1A 0.023 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.003 0.22 0.4 29 -0.69 53 82
CD80 0.093 0.11 0.27 257 -10000 0 257
CD86 0.026 0.019 0.27 5 -10000 0 5
PDK1/CARD11/BCL10/MALT1 -0.006 0.071 0.2 1 -0.26 35 36
HRAS 0.024 0.012 0.26 2 -10000 0 2
GO:0035030 0.024 0.16 0.36 34 -0.53 39 73
CD8A 0.028 0.062 0.28 23 -0.6 5 28
CD8B 0.011 0.12 0.28 22 -0.6 29 51
PTPRC 0.023 0.038 0.27 13 -0.6 1 14
PDK1/PKC theta 0.027 0.19 0.39 66 -0.52 48 114
CSK/PAG1 0.027 0.2 0.35 47 -0.64 43 90
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.037 0.018 0.21 2 -10000 0 2
GRAP2/SLP76 0.021 0.2 0.44 24 -0.62 49 73
STIM1 0.027 0.1 1.3 4 -10000 0 4
RAS family/GTP 0.046 0.094 0.23 81 -0.18 30 111
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.014 0.24 0.39 28 -0.55 104 132
mol:DAG -0.016 0.099 0.14 18 -0.36 44 62
RAP1A/GDP 0.022 0.038 0.096 85 -0.066 8 93
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.015 0.084 0.28 15 -0.6 14 29
cytotoxic T cell degranulation -0.006 0.23 0.55 7 -0.96 33 40
RAP1A/GTP -0.001 0.018 -10000 0 -0.065 56 56
mol:PI-3-4-5-P3 0.02 0.18 0.39 36 -0.45 63 99
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.023 0.17 0.3 99 -0.51 43 142
NRAS 0.023 0.004 -10000 0 -10000 0 0
ZAP70 0.021 0.1 0.27 38 -0.59 19 57
GRB2/SOS1 0.033 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.007 0.16 0.46 9 -0.52 45 54
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.029 0.11 0.34 24 -0.51 29 53
CARD11 0.027 0.046 0.26 19 -0.59 2 21
PRKCB 0.015 0.1 0.27 41 -0.28 38 79
PRKCE 0.019 0.096 0.22 47 -0.26 37 84
PRKCQ 0.016 0.2 0.42 32 -0.58 53 85
LCP2 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.023 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.028 0.14 0.31 69 -0.34 53 122
IKK complex 0.037 0.085 0.21 109 -0.12 15 124
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.027 0.11 0.25 68 -0.27 40 108
PDPK1 0.03 0.16 0.36 66 -0.38 49 115
TCR/CD3/MHC I/CD8/Fyn -0.024 0.25 0.44 22 -0.76 59 81
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.036 0.065 -10000 0 -0.35 21 21
NF kappa B1 p50/RelA/I kappa B alpha 0 0.13 -10000 0 -0.42 16 16
AP1 -0.1 0.2 -10000 0 -0.35 328 328
mol:PIP3 -0.13 0.19 -10000 0 -0.35 337 337
AKT1 0.011 0.07 0.31 3 -0.38 6 9
PTK2B -0.029 0.1 -10000 0 -0.36 43 43
RHOA 0.003 0.064 0.24 3 -0.31 24 27
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.11 0.25 1 -0.3 86 87
MAGI3 0.023 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
apoptosis -0.027 0.12 -10000 0 -0.33 115 115
HRAS/GDP 0.018 0.008 0.18 2 -10000 0 2
positive regulation of microtubule depolymerization -0.053 0.13 0.26 3 -0.33 100 103
NF kappa B1 p50/RelA -0.014 0.13 -10000 0 -0.34 83 83
endothelial cell migration 0.004 0.071 -10000 0 -0.43 21 21
ADCY4 -0.02 0.11 -10000 0 -0.51 32 32
ADCY5 -0.075 0.16 -10000 0 -0.51 61 61
ADCY6 -0.012 0.095 -10000 0 -0.48 23 23
ADCY7 -0.011 0.096 -10000 0 -0.5 23 23
ADCY1 -0.012 0.1 -10000 0 -0.48 26 26
ADCY2 -0.025 0.12 -10000 0 -0.51 35 35
ADCY3 -0.012 0.095 -10000 0 -0.48 23 23
ADCY8 -0.01 0.088 -10000 0 -0.46 21 21
ADCY9 -0.012 0.095 -10000 0 -0.49 23 23
GSK3B -0.029 0.1 0.28 3 -0.35 41 44
arachidonic acid secretion -0.017 0.1 -10000 0 -0.42 36 36
GNG2 0.019 0.05 -10000 0 -0.59 6 6
TRIP6 0.017 0.016 -10000 0 -0.42 1 1
GNAO1 0.004 0.081 -10000 0 -0.37 34 34
HRAS 0.024 0.012 0.26 2 -10000 0 2
NFKBIA -0.023 0.13 -10000 0 -0.36 88 88
GAB1 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.12 -10000 0 -0.82 16 16
JUN 0.018 0.058 -10000 0 -0.59 8 8
LPA/LPA2/NHERF2 0.031 0.016 -10000 0 -10000 0 0
TIAM1 0.014 0.13 -10000 0 -0.96 16 16
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
mol:IP3 -0.016 0.11 0.25 1 -0.3 86 87
PLCB3 0.025 0.045 -10000 0 -10000 0 0
FOS -0.16 0.28 -10000 0 -0.59 262 262
positive regulation of mitosis -0.017 0.1 -10000 0 -0.42 36 36
LPA/LPA1-2-3 0 0.14 -10000 0 -0.35 116 116
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
stress fiber formation -0.018 0.1 -10000 0 -0.38 34 34
GNAZ 0.004 0.064 -10000 0 -0.36 24 24
EGFR/PI3K-beta/Gab1 -0.12 0.2 -10000 0 -0.36 337 337
positive regulation of dendritic cell cytokine production -0.002 0.14 -10000 0 -0.34 116 116
LPA/LPA2/MAGI-3 0.032 0.015 -10000 0 -0.15 1 1
ARHGEF1 0.02 0.065 -10000 0 -0.32 12 12
GNAI2 0.008 0.051 -10000 0 -0.34 17 17
GNAI3 0.008 0.051 -10000 0 -0.33 20 20
GNAI1 -0.01 0.1 -10000 0 -0.39 57 57
LPA/LPA3 -0.029 0.15 0.18 30 -0.42 107 137
LPA/LPA2 0.019 0.014 0.18 1 -10000 0 1
LPA/LPA1 0.013 0.061 -10000 0 -0.37 21 21
HB-EGF/EGFR -0.077 0.2 0.27 1 -0.36 288 289
HBEGF 0.07 0.078 0.27 21 -0.44 3 24
mol:DAG -0.016 0.11 0.25 1 -0.3 86 87
cAMP biosynthetic process -0.031 0.11 0.4 1 -0.42 45 46
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.009 0.13 0.27 7 -0.35 69 76
GNAQ -0.023 0.11 0.21 1 -0.32 105 106
LPAR2 0.024 0.009 0.27 1 -10000 0 1
LPAR3 -0.039 0.2 0.26 30 -0.59 103 133
LPAR1 0.015 0.075 -10000 0 -0.59 13 13
IL8 -0.13 0.24 0.36 25 -0.42 283 308
PTK2 -0.023 0.1 0.25 1 -0.33 78 79
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
CASP3 -0.027 0.12 -10000 0 -0.33 115 115
EGFR -0.19 0.29 -10000 0 -0.59 312 312
PLCG1 -0.026 0.12 0.21 3 -0.34 105 108
PLD2 -0.029 0.12 0.25 1 -0.33 112 113
G12/G13 0.037 0.053 -10000 0 -0.32 15 15
PI3K-beta 0.005 0.065 -10000 0 -0.41 8 8
cell migration 0.001 0.062 -10000 0 -0.25 16 16
SLC9A3R2 0.022 0.006 -10000 0 -10000 0 0
PXN -0.019 0.1 -10000 0 -0.38 34 34
HRAS/GTP -0.017 0.1 -10000 0 -0.42 38 38
RAC1 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 382 -0.59 1 383
PRKCE 0.023 0.021 -10000 0 -0.59 1 1
PRKCD -0.018 0.11 -10000 0 -0.43 10 10
Gi(beta/gamma) -0.01 0.1 -10000 0 -0.47 29 29
mol:LPA 0.001 0.016 -10000 0 -0.18 4 4
TRIP6/p130 Cas/FAK1/Paxillin -0.016 0.12 -10000 0 -0.46 18 18
MAPKKK cascade -0.017 0.1 -10000 0 -0.42 36 36
contractile ring contraction involved in cytokinesis 0.002 0.065 0.26 2 -0.3 25 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.023 0.12 0.21 1 -0.33 109 110
GNA15 -0.022 0.11 0.21 1 -0.32 104 105
GNA12 0.023 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.055 0.13 0.26 3 -0.34 100 103
GNA11 -0.023 0.11 0.21 1 -0.32 105 106
Rac1/GTP 0.029 0.12 -10000 0 -0.87 16 16
MMP2 0.004 0.071 -10000 0 -0.44 21 21
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.031 0.046 -10000 0 -0.33 12 12
RGS9BP 0.035 0.052 0.26 43 -10000 0 43
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.018 0.26 4 -10000 0 4
mol:Na + 0.037 0.046 -10000 0 -10000 0 0
mol:ADP -0.005 0.029 0.25 6 -10000 0 6
GNAT2 0.023 0.012 0.26 2 -10000 0 2
RGS9-1/Gbeta5/R9AP 0.01 0.13 0.35 1 -0.38 79 80
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.015 0.18 4 -10000 0 4
GRK7 0.023 0.023 0.26 8 -10000 0 8
CNGB3 0.022 0.038 0.26 20 -10000 0 20
Cone Metarhodopsin II/X-Arrestin 0.015 0.015 0.18 7 -10000 0 7
mol:Ca2+ 0.13 0.11 0.27 207 -10000 0 207
Cone PDE6 0.025 0.12 0.33 2 -0.33 75 77
Cone Metarhodopsin II 0.026 0.019 -10000 0 -10000 0 0
Na + (4 Units) 0.12 0.096 0.32 60 -10000 0 60
GNAT2/GDP 0.019 0.11 0.32 1 -0.32 78 79
GNB5 0.023 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.034 0.19 1 -10000 0 1
Cone Transducin 0.033 0.049 -10000 0 -0.34 12 12
SLC24A2 0.17 0.12 0.26 550 -10000 0 550
GNB3/GNGT2 0.024 0.057 -10000 0 -0.42 13 13
GNB3 0.015 0.072 0.26 2 -0.59 12 14
GNAT2/GTP 0.017 0.008 0.18 2 -10000 0 2
CNGA3 0.047 0.072 0.26 89 -10000 0 89
ARR3 0.021 0.022 0.26 7 -10000 0 7
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.038 0.047 -10000 0 -10000 0 0
mol:Pi 0.01 0.12 0.34 1 -0.37 79 80
Cone CNG Channel 0.049 0.045 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.17 0.12 0.26 550 -10000 0 550
RGS9 -0.032 0.18 0.26 7 -0.59 81 88
PDE6C 0.019 0.004 -10000 0 -10000 0 0
GNGT2 0.021 0.022 -10000 0 -0.59 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.26 4 -10000 0 4
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.035 0.1 0.73 2 -10000 0 2
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.022 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.031 0.12 0.25 3 -0.35 17 20
RXRs/LXRs/DNA/Oxysterols -0.021 0.12 0.3 3 -0.43 16 19
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.003 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0.003 0.08 -10000 0 -0.32 43 43
RXRs/NUR77 -0.058 0.19 -10000 0 -0.37 227 227
RXRs/PPAR -0.1 0.18 -10000 0 -0.32 308 308
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.047 0.041 -10000 0 -0.33 8 8
RARA 0.022 0.007 -10000 0 -10000 0 0
NCOA1 0.023 0.021 -10000 0 -0.59 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.037 0.039 -10000 0 -0.33 8 8
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.072 0.18 0.62 84 -10000 0 84
RARs/THRs/DNA/SMRT 0.005 0.076 -10000 0 -0.3 42 42
THRA 0.021 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.036 0.16 -10000 0 -0.34 187 187
NR1H4 0.02 0.022 0.26 7 -10000 0 7
RXRs/LXRs/DNA -0.015 0.16 -10000 0 -0.32 172 172
NR1H2 0.026 0.013 -10000 0 -10000 0 0
NR1H3 0.027 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.029 0.15 -10000 0 -0.32 186 186
NR4A1 -0.03 0.17 -10000 0 -0.59 79 79
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.034 0.11 -10000 0 -0.24 165 165
RXRG -0.11 0.25 0.27 1 -0.59 189 190
RXR alpha/CCPG 0.035 0.014 -10000 0 -10000 0 0
RXRA 0.026 0.013 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB 0 0.12 -10000 0 -0.59 35 35
PPARG -0.11 0.25 -10000 0 -0.59 196 196
PPARD 0.023 0.004 -10000 0 -10000 0 0
TNF -0.017 0.16 -10000 0 -1 11 11
mol:Oxysterols 0.003 0.009 -10000 0 -10000 0 0
cholesterol transport -0.011 0.12 0.3 3 -0.43 16 19
PPARA 0.021 0.029 -10000 0 -0.59 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.017 0.061 -10000 0 -0.59 9 9
RXRs/NUR77/BCL2 -0.076 0.16 -10000 0 -0.31 241 241
SREBF1 -0.012 0.11 -10000 0 -0.53 4 4
RXRs/RXRs/DNA/9cRA -0.036 0.16 -10000 0 -0.34 187 187
ABCA1 -0.015 0.13 -10000 0 -0.72 8 8
RARs/THRs 0.043 0.09 -10000 0 -0.35 39 39
RXRs/FXR -0.032 0.16 -10000 0 -0.34 187 187
BCL2 0.005 0.1 -10000 0 -0.59 26 26
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 0.022 0.021 -10000 0 -0.59 1 1
LAT2 -0.019 0.1 0.22 1 -0.36 43 44
AP1 -0.063 0.19 -10000 0 -0.44 105 105
mol:PIP3 0.009 0.17 0.34 37 -0.43 41 78
IKBKB 0.034 0.13 0.28 98 -0.26 19 117
AKT1 0.013 0.16 0.31 127 -0.34 45 172
IKBKG 0.015 0.11 0.24 61 -0.26 24 85
MS4A2 -0.023 0.16 0.26 4 -0.57 66 70
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.012 0.12 0.3 16 -0.4 19 35
mol:Ca2+ 0.014 0.14 0.29 47 -0.32 40 87
LYN 0.021 0.013 -10000 0 -10000 0 0
CBLB -0.018 0.1 -10000 0 -0.36 41 41
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.005 0.13 -10000 0 -0.34 108 108
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.023 0.004 -10000 0 -10000 0 0
PLD2 -0.006 0.17 0.33 108 -0.34 119 227
PTPN13 -0.015 0.16 -10000 0 -0.59 34 34
PTPN11 0.022 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.012 0.13 0.32 28 -0.34 22 50
SYK 0.024 0.011 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.028 0.13 -10000 0 -0.37 76 76
LAT -0.019 0.1 0.22 1 -0.36 42 43
PAK2 0.013 0.13 0.29 24 -0.45 19 43
NFATC2 -0.037 0.14 -10000 0 -0.54 51 51
HRAS 0.009 0.13 0.28 17 -0.38 40 57
GAB2 0.021 0.008 -10000 0 -10000 0 0
PLA2G1B 0 0.11 -10000 0 -0.85 12 12
Fc epsilon R1 -0.025 0.16 -10000 0 -0.41 125 125
Antigen/IgE/Fc epsilon R1 -0.021 0.15 -10000 0 -0.38 123 123
mol:GDP -0.015 0.11 -10000 0 -0.48 20 20
JUN 0.018 0.058 -10000 0 -0.59 8 8
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.021 -10000 0 -0.59 1 1
FOS -0.16 0.28 -10000 0 -0.59 262 262
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.016 0.11 -10000 0 -0.36 49 49
CHUK 0.015 0.11 0.24 59 -0.27 20 79
KLRG1 -0.017 0.095 -10000 0 -0.32 43 43
VAV1 -0.019 0.1 -10000 0 -0.36 42 42
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.098 -10000 0 -0.36 41 41
negative regulation of mast cell degranulation -0.007 0.097 -10000 0 -0.38 22 22
BTK -0.013 0.11 -10000 0 -0.49 21 21
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.032 0.13 -10000 0 -0.36 97 97
GAB2/PI3K/SHP2 -0.047 0.098 -10000 0 -0.32 84 84
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.1 -10000 0 -0.29 97 97
RAF1 0 0.11 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.003 0.15 -10000 0 -0.36 124 124
FCER1G 0.019 0.02 0.26 2 -10000 0 2
FCER1A -0.048 0.19 -10000 0 -0.6 97 97
Antigen/IgE/Fc epsilon R1/Fyn -0.012 0.14 -10000 0 -0.35 120 120
MAPK3 0.001 0.11 -10000 0 -0.86 12 12
MAPK1 -0.004 0.11 -10000 0 -0.86 12 12
NFKB1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.02 0.18 -10000 0 -0.59 54 54
DUSP1 -0.051 0.2 -10000 0 -0.59 109 109
NF-kappa-B/RelA 0.008 0.058 -10000 0 -0.19 1 1
actin cytoskeleton reorganization -0.007 0.15 -10000 0 -0.61 27 27
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0 0.11 -10000 0 -0.45 19 19
FER -0.019 0.1 -10000 0 -0.36 45 45
RELA 0.024 0.004 -10000 0 -10000 0 0
ITK -0.011 0.089 -10000 0 -0.4 37 37
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.006 0.13 0.28 8 -0.4 38 46
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.018 0.1 0.22 2 -0.36 43 45
PTK2 -0.009 0.16 -10000 0 -0.65 27 27
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.024 0.14 -10000 0 -0.38 85 85
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.005 0.16 0.32 35 -0.42 47 82
MAP2K2 -0.003 0.11 -10000 0 -0.86 12 12
MAP2K1 -0.002 0.11 -10000 0 -0.86 12 12
MAP2K7 0.024 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.094 -10000 0 -0.36 23 23
MAP2K4 -0.07 0.29 -10000 0 -0.84 109 109
Fc epsilon R1/FcgammaRIIB -0.012 0.16 -10000 0 -0.38 124 124
mol:Choline -0.006 0.17 0.33 108 -0.33 119 227
SHC/Grb2/SOS1 0.011 0.11 -10000 0 -0.42 19 19
FYN 0.022 0.021 -10000 0 -0.59 1 1
DOK1 0.024 0.008 0.26 1 -10000 0 1
PXN -0.009 0.14 -10000 0 -0.58 27 27
HCLS1 -0.019 0.1 -10000 0 -0.36 42 42
PRKCB 0.013 0.14 0.28 61 -0.31 47 108
FCGR2B 0.018 0.037 0.26 1 -0.59 3 4
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.007 0.099 -10000 0 -0.38 22 22
LCP2 0.024 0.009 0.27 1 -10000 0 1
PLA2G4A -0.044 0.14 -10000 0 -0.37 102 102
RASA1 0.023 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.006 0.17 0.33 108 -0.33 119 227
IKK complex 0.031 0.11 0.27 79 -0.21 10 89
WIPF1 0.024 0.003 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.032 0.14 -10000 0 -0.61 50 50
PDGF/PDGFRA/CRKL -0.011 0.11 -10000 0 -0.43 51 51
positive regulation of JUN kinase activity 0.024 0.084 -10000 0 -0.34 37 37
CRKL 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.014 0.11 -10000 0 -0.44 51 51
AP1 -0.32 0.45 -10000 0 -0.98 278 278
mol:IP3 -0.036 0.11 -10000 0 -0.47 47 47
PLCG1 -0.036 0.11 -10000 0 -0.47 47 47
PDGF/PDGFRA/alphaV Integrin -0.011 0.11 -10000 0 -0.43 52 52
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.11 -10000 0 -0.47 47 47
CAV3 0.02 0.013 0.26 2 -10000 0 2
CAV1 -0.097 0.24 -10000 0 -0.59 177 177
SHC/Grb2/SOS1 0.025 0.085 -10000 0 -0.35 37 37
PDGF/PDGFRA/Shf -0.011 0.11 -10000 0 -0.44 52 52
FOS -0.31 0.44 -10000 0 -0.96 278 278
JUN -0.039 0.047 -10000 0 -0.46 6 6
oligodendrocyte development -0.011 0.11 -10000 0 -0.43 52 52
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
mol:DAG -0.036 0.11 -10000 0 -0.47 47 47
PDGF/PDGFRA -0.032 0.14 -10000 0 -0.61 50 50
actin cytoskeleton reorganization -0.011 0.11 -10000 0 -0.44 50 50
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.004 0.098 -10000 0 -0.38 49 49
PDGF/PDGFRA/Crk/C3G 0.004 0.098 -10000 0 -0.38 50 50
JAK1 -0.026 0.1 0.23 1 -0.44 50 51
ELK1/SRF -0.035 0.09 0.32 1 -0.37 48 49
SHB 0.024 0.009 0.26 1 -10000 0 1
SHF 0.023 0.022 0.26 1 -0.59 1 2
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.046 0.11 0.22 1 -0.48 49 50
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.084 -10000 0 -0.34 37 37
PDGF/PDGFRA/SHB -0.011 0.11 -10000 0 -0.44 50 50
PDGF/PDGFRA/Caveolin-1 -0.098 0.22 -10000 0 -0.5 203 203
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.054 0.1 -10000 0 -0.45 48 48
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.012 0.11 -10000 0 -0.44 50 50
JAK-STAT cascade -0.026 0.1 0.23 1 -0.44 50 51
cell proliferation -0.011 0.11 -10000 0 -0.44 52 52
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.002 0.057 0.22 1 -0.32 2 3
adherens junction organization -0.015 0.094 -10000 0 -0.34 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.085 0.15 0.34 3 -0.34 89 92
FMN1 -0.013 0.089 -10000 0 -0.32 48 48
mol:IP3 0 0.048 -10000 0 -0.27 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.009 0.09 -10000 0 -0.32 45 45
CTNNB1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.003 0.059 -10000 0 -0.28 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.015 0.13 -10000 0 -0.53 35 35
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.078 -10000 0 -0.3 41 41
VASP -0.011 0.083 -10000 0 -0.3 43 43
ZYX -0.01 0.084 -10000 0 -0.31 43 43
JUB -0.01 0.085 -10000 0 -0.31 45 45
EGFR(dimer) -0.11 0.18 -10000 0 -0.34 307 307
E-cadherin/beta catenin-gamma catenin 0.03 0.062 -10000 0 -0.37 18 18
mol:PI-3-4-5-P3 0.016 0.07 -10000 0 -0.3 3 3
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.017 0.071 -10000 0 -0.31 3 3
FYN -0.003 0.062 0.22 1 -0.33 5 6
mol:Ca2+ 0 0.047 -10000 0 -0.27 2 2
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.021 -10000 0 -0.59 1 1
mol:DAG 0 0.048 -10000 0 -0.27 2 2
CDH1 0.009 0.086 -10000 0 -0.59 18 18
RhoA/GDP -0.085 0.15 0.36 2 -0.3 273 275
establishment of polarity of embryonic epithelium -0.011 0.082 -10000 0 -0.3 43 43
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.59 312 312
CASR -0.002 0.051 0.23 1 -0.27 1 2
RhoA/GTP 0.014 0.053 -10000 0 -0.27 1 1
AKT2 0.001 0.06 -10000 0 -0.29 2 2
actin cable formation -0.017 0.089 0.25 2 -0.34 35 37
apoptosis -0.005 0.069 0.27 14 -0.23 6 20
CTNNA1 0.024 0.005 -10000 0 -10000 0 0
mol:GDP -0.097 0.15 -10000 0 -0.31 274 274
PIP5K1A -0.011 0.079 -10000 0 -0.31 41 41
PLCG1 0 0.049 -10000 0 -0.28 2 2
Rac1/GTP -0.094 0.18 -10000 0 -0.32 295 295
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.1 0.11 0.22 377 -0.36 2 379
EPHB2 0.027 0.033 0.26 17 -10000 0 17
Syndecan-2/TACI 0.02 0.061 0.2 41 -0.34 13 54
LAMA1 -0.04 0.19 0.26 1 -0.59 92 93
Syndecan-2/alpha2 ITGB1 -0.039 0.15 -10000 0 -0.34 158 158
HRAS 0.024 0.012 0.26 2 -10000 0 2
Syndecan-2/CASK 0.005 0.018 -10000 0 -0.37 2 2
ITGA5 0.024 0.002 -10000 0 -10000 0 0
BAX -0.002 0.028 0.46 1 -10000 0 1
EPB41 0.023 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.016 0.019 -10000 0 -0.34 2 2
LAMA3 -0.12 0.26 -10000 0 -0.59 207 207
EZR 0.023 0.013 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.05 0.2 -10000 0 -0.59 108 108
Syndecan-2/MMP2 0.014 0.037 -10000 0 -0.39 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.024 0.066 -10000 0 -0.42 19 19
dendrite morphogenesis 0.022 0.036 0.22 17 -0.37 2 19
Syndecan-2/GM-CSF 0.02 0.037 0.22 20 -0.37 2 22
determination of left/right symmetry 0.006 0.021 -10000 0 -0.43 2 2
Syndecan-2/PKC delta 0.018 0.024 0.32 1 -0.37 2 3
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
MAPK3 0.034 0.076 0.19 158 -0.34 2 160
MAPK1 0.039 0.079 0.19 178 -0.33 2 180
Syndecan-2/RACK1 0.027 0.024 -10000 0 -0.32 2 2
NF1 0.023 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.021 -10000 0 -0.43 2 2
ITGA2 0.01 0.088 -10000 0 -0.59 19 19
MAPK8 0.005 0.03 0.27 5 -0.36 3 8
Syndecan-2/alpha2/beta1 Integrin 0.001 0.12 -10000 0 -0.37 69 69
Syndecan-2/Kininogen 0.018 0.031 0.23 10 -0.37 2 12
ITGB1 0.023 0.004 -10000 0 -10000 0 0
SRC 0.043 0.071 0.32 6 -0.31 2 8
Syndecan-2/CASK/Protein 4.1 0.016 0.02 -10000 0 -0.34 2 2
extracellular matrix organization 0.019 0.024 0.35 1 -0.37 2 3
actin cytoskeleton reorganization 0.1 0.11 0.22 377 -0.36 2 379
Syndecan-2/Caveolin-2/Ras -0.011 0.11 -10000 0 -0.35 82 82
Syndecan-2/Laminin alpha3 -0.06 0.15 -10000 0 -0.37 151 151
Syndecan-2/RasGAP 0.036 0.029 -10000 0 -0.31 2 2
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
PRKCD 0.023 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.022 0.036 0.22 17 -0.37 2 19
GO:0007205 0.002 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.025 -10000 0 -0.3 2 2
RHOA 0.023 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.025 0.086 0.26 41 -0.59 11 52
RASA1 0.023 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.024 0.066 -10000 0 -0.42 19 19
Syndecan-2/Synbindin 0.017 0.021 -10000 0 -0.36 2 2
TGFB1 0.024 0.009 0.26 1 -10000 0 1
CASP3 0.044 0.073 0.19 171 -0.34 2 173
FN1 0.12 0.12 0.26 377 -10000 0 377
Syndecan-2/IL8 0.024 0.074 0.22 54 -0.33 19 73
SDC2 0.007 0.021 -10000 0 -0.43 2 2
KNG1 0.021 0.026 0.26 10 -10000 0 10
Syndecan-2/Neurofibromin 0.017 0.022 -10000 0 -0.37 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.025 0.036 0.26 20 -10000 0 20
Syndecan-2/TGFB1 0.019 0.024 0.36 1 -0.37 2 3
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.019 -10000 0 -0.34 2 2
Syndecan-2/Ezrin 0.028 0.027 0.3 1 -0.34 2 3
PRKACA 0.046 0.075 0.19 183 -0.33 2 185
angiogenesis 0.024 0.074 0.22 54 -0.33 19 73
MMP2 0.018 0.041 -10000 0 -0.59 4 4
IL8 0.026 0.1 0.26 54 -0.59 17 71
calcineurin-NFAT signaling pathway 0.02 0.061 0.2 41 -0.34 13 54
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.079 0.16 -10000 0 -0.31 233 233
Syndecan-3/Neurocan 0.028 0.075 0.28 18 -0.38 16 34
POMC 0.019 0.094 0.26 26 -0.59 17 43
EGFR -0.19 0.29 -10000 0 -0.59 312 312
Syndecan-3/EGFR -0.09 0.16 -10000 0 -0.32 246 246
AGRP 0.021 0.024 0.26 8 -10000 0 8
NCSTN 0.02 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.009 0.26 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.021 -10000 0 -0.59 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.037 0.059 0.26 57 -10000 0 57
long-term memory 0.035 0.061 -10000 0 -0.36 12 12
Syndecan-3/IL8 0.021 0.084 0.28 10 -0.34 30 40
PSEN1 0.023 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.029 0.014 -10000 0 -10000 0 0
FYN 0.022 0.021 -10000 0 -0.59 1 1
limb bud formation 0.002 0.054 -10000 0 -0.39 17 17
MC4R 0.023 0.028 0.26 11 -10000 0 11
SRC 0.023 0.005 -10000 0 -10000 0 0
PTN -0.24 0.3 0.26 1 -0.59 382 383
FGFR/FGF/Syndecan-3 0.002 0.055 -10000 0 -0.39 17 17
neuron projection morphogenesis -0.077 0.16 0.34 5 -0.49 20 25
Syndecan-3/AgRP 0.015 0.059 0.27 1 -0.37 17 18
Syndecan-3/AgRP/MC4R 0.038 0.067 -10000 0 -0.36 16 16
Fyn/Cortactin 0.028 0.017 -10000 0 -0.21 1 1
SDC3 0.002 0.055 -10000 0 -0.4 17 17
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.021 0.083 0.28 10 -0.34 30 40
IL8 0.026 0.1 0.26 54 -0.59 17 71
Syndecan-3/Fyn/Cortactin 0.036 0.062 -10000 0 -0.36 12 12
Syndecan-3/CASK 0 0.054 -10000 0 -0.37 17 17
alpha-MSH/MC4R 0.029 0.074 0.2 34 -0.44 17 51
Gamma Secretase 0.053 0.034 -10000 0 -0.33 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.4 0.28 -10000 0 -0.59 618 618
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.024 0.26 8 -10000 0 8
TCEB1 0.02 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.048 -10000 0 -0.29 7 7
HIF1A 0.004 0.028 -10000 0 -0.27 8 8
COPS5 0.02 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.035 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.058 0.087 0.26 134 -10000 0 134
ARNT/IPAS -0.27 0.21 -10000 0 -0.4 624 624
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.045 -10000 0 -0.28 12 12
CUL2 0.023 0.004 -10000 0 -10000 0 0
OS9 0.024 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.039 0.024 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.049 -10000 0 -0.28 11 11
PHD1-3/OS9 0.055 0.048 -10000 0 -0.35 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.041 0.051 -10000 0 -0.3 4 4
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.048 -10000 0 -0.32 4 4
EGLN3 0.041 0.064 0.26 67 -10000 0 67
EGLN2 0.025 0.017 0.26 4 -10000 0 4
EGLN1 0.019 0.022 -10000 0 -0.59 1 1
TP53 0.022 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.028 0.068 -10000 0 -0.5 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.052 0.073 0.24 33 -0.27 10 43
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.022 0.13 0.43 56 -0.23 11 67
KIRREL -0.015 0.15 -10000 0 -0.59 57 57
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.022 0.13 0.23 11 -0.43 56 67
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.023 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.04 0.11 0.29 4 -0.33 54 58
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.012 0.082 0.24 1 -0.29 45 46
FYN 0.021 0.12 0.27 100 -0.32 53 153
mol:Ca2+ 0.037 0.11 0.28 4 -0.33 52 56
mol:DAG 0.038 0.11 0.28 4 -0.33 52 56
NPHS2 0.016 0.031 0.27 5 -10000 0 5
mol:IP3 0.038 0.11 0.28 4 -0.33 52 56
regulation of endocytosis 0.028 0.098 0.25 5 -0.3 53 58
Nephrin/NEPH1/podocin/Cholesterol 0.03 0.11 0.25 9 -0.33 54 63
establishment of cell polarity 0.022 0.13 0.23 11 -0.43 56 67
Nephrin/NEPH1/podocin/NCK1-2 0.05 0.11 0.32 1 -0.31 52 53
Nephrin/NEPH1/beta Arrestin2 0.032 0.1 0.25 5 -0.3 53 58
NPHS1 0.062 0.092 0.27 141 -10000 0 141
Nephrin/NEPH1/podocin 0.031 0.1 0.31 4 -0.32 53 57
TJP1 0.022 0.021 -10000 0 -0.59 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.039 0.11 0.29 4 -0.33 52 56
CD2AP 0.023 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.037 0.11 0.28 9 -0.33 51 60
GRB2 0.023 0.01 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.02 0.13 0.29 90 -0.32 59 149
cytoskeleton organization 0.009 0.1 0.27 15 -0.33 49 64
Nephrin/NEPH1 0.021 0.098 0.17 26 -0.31 56 82
Nephrin/NEPH1/ZO-1 0.031 0.11 0.23 1 -0.36 55 56
Canonical Wnt signaling pathway

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.021 0.25 2 -10000 0 2
AES 0.022 0.018 0.21 2 -10000 0 2
FBXW11 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.013 0.082 0.26 2 -0.59 16 18
TLE1 0.017 0.058 0.22 2 -0.6 7 9
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.11 0.1 0.31 29 -0.46 1 30
WIF1 -0.29 0.31 0.26 10 -0.59 464 474
beta catenin/RanBP3 0.018 0.085 0.41 28 -0.4 1 29
KREMEN2 0.13 0.12 0.26 387 -10000 0 387
DKK1 0.025 0.16 0.26 121 -0.59 45 166
beta catenin/beta TrCP1 0.11 0.095 0.31 20 -0.41 1 21
FZD1 0.024 0.003 -10000 0 -10000 0 0
AXIN2 0.021 0.25 0.59 74 -1.3 16 90
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.047 0.074 -10000 0 -0.54 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.065 0.13 0.3 7 -0.61 18 25
Axin1/APC/GSK3 0.046 0.055 0.24 1 -0.31 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.042 0.062 0.31 2 -0.36 3 5
HNF1A 0.024 0.027 0.26 7 -10000 0 7
CTBP1 0.021 0.019 0.24 2 -10000 0 2
MYC 0.12 0.34 0.59 197 -1.4 20 217
RANBP3 0.023 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.096 0.35 1 -0.35 13 14
NKD1 0.021 0.059 0.26 14 -0.59 6 20
TCF4 0.017 0.053 0.23 2 -0.58 6 8
TCF3 0.021 0.019 0.23 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.056 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.002 0.13 0.47 27 -0.52 14 41
LEF1 0.054 0.084 0.26 119 -10000 0 119
DVL1 0.055 0.054 -10000 0 -0.46 1 1
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.069 0.15 0.3 8 -0.67 20 28
DKK1/LRP6/Kremen 2 0.1 0.14 0.35 64 -0.36 39 103
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.022 0.021 0.25 2 -10000 0 2
NLK 0.022 0.013 0.27 1 -10000 0 1
CCND1 0.093 0.26 0.61 152 -1.2 5 157
WNT1 0.023 0.01 0.27 1 -10000 0 1
GSK3A 0.024 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.003 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.037 0.058 0.29 6 -0.29 10 16
APC 0.015 0.057 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.23 357 -0.25 1 358
CREBBP 0.021 0.018 0.23 1 -10000 0 1
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.035 0.15 0.36 52 -0.37 39 91
TBX21 0.006 0.35 0.79 18 -1.2 45 63
B2M 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.022 0.036 -10000 0 -10000 0 0
IL12RB1 0.031 0.073 0.34 34 -0.63 1 35
GADD45B 0.03 0.25 0.69 17 -0.85 29 46
IL12RB2 0.024 0.16 0.28 104 -0.6 39 143
GADD45G 0.045 0.26 0.67 22 -0.82 27 49
natural killer cell activation 0.006 0.025 0.17 1 -10000 0 1
RELB 0.025 0.022 0.26 7 -10000 0 7
RELA 0.024 0.004 -10000 0 -10000 0 0
IL18 0.033 0.041 0.28 21 -10000 0 21
IL2RA 0.03 0.087 0.26 51 -0.59 10 61
IFNG 0.056 0.085 0.26 127 -10000 0 127
STAT3 (dimer) 0.029 0.24 0.56 36 -0.66 44 80
HLA-DRB5 0.023 0.083 0.26 65 -0.6 5 70
FASLG 0.048 0.29 0.79 23 -0.98 27 50
NF kappa B2 p52/RelB 0.013 0.25 0.75 4 -0.74 47 51
CD4 0.008 0.025 -10000 0 -10000 0 0
SOCS1 0.023 0.029 0.26 6 -0.59 1 7
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D 0.007 0.097 0.27 34 -0.6 15 49
CD3E 0.007 0.095 0.28 27 -0.6 15 42
CD3G 0.002 0.11 0.27 34 -0.6 23 57
IL12Rbeta2/JAK2 0.032 0.13 0.3 27 -0.44 41 68
CCL3 0.026 0.28 0.75 18 -0.94 30 48
CCL4 0.028 0.27 0.71 22 -0.9 29 51
HLA-A 0.026 0.019 0.27 4 -10000 0 4
IL18/IL18R 0.061 0.12 0.38 13 -0.39 41 54
NOS2 0.026 0.27 0.73 18 -0.9 33 51
IL12/IL12R/TYK2/JAK2/SPHK2 0.033 0.15 0.35 53 -0.35 52 105
IL1R1 0.015 0.3 0.74 17 -1 35 52
IL4 -0.01 0.037 -10000 0 -10000 0 0
JAK2 0.021 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.005 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.024 0.23 0.41 26 -0.78 48 74
RAB7A 0.042 0.23 0.66 15 -0.79 18 33
lysosomal transport 0.044 0.23 0.63 18 -0.73 19 37
FOS -0.34 0.63 0.62 13 -1.2 301 314
STAT4 (dimer) 0.055 0.28 0.59 37 -0.85 38 75
STAT5A (dimer) 0.041 0.28 0.62 41 -0.75 46 87
GZMA 0.018 0.29 0.71 27 -1.1 26 53
GZMB 0.019 0.32 0.73 26 -1.1 34 60
HLX 0.02 0.015 0.26 2 -10000 0 2
LCK 0.021 0.29 0.68 31 -0.82 49 80
TCR/CD3/MHC II/CD4 -0.049 0.18 0.29 21 -0.43 97 118
IL2/IL2R 0.067 0.098 0.44 33 -0.37 13 46
MAPK14 0.039 0.26 0.65 23 -0.81 34 57
CCR5 0.032 0.26 0.73 24 -0.84 29 53
IL1B 0.017 0.077 0.31 3 -0.6 10 13
STAT6 0.037 0.12 0.4 32 -0.52 5 37
STAT4 0 0.12 0.26 1 -0.59 35 36
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.035 0.26 19 -10000 0 19
NFKB1 0.023 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.003 -10000 0 -10000 0 0
IL12B 0.069 0.11 0.29 175 -10000 0 175
CD8A 0.028 0.063 0.29 23 -0.59 5 28
CD8B 0.012 0.12 0.28 22 -0.59 29 51
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.035 0.15 0.37 39 -0.36 52 91
IL2RB 0.032 0.048 0.26 36 -10000 0 36
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.26 0.58 39 -0.76 38 77
IL2RG 0.031 0.067 0.26 37 -0.59 5 42
IL12 0.044 0.15 0.31 67 -0.44 50 117
STAT5A 0.02 0.046 -10000 0 -0.59 5 5
CD247 0.005 0.086 0.28 15 -0.6 14 29
IL2 0.022 0.024 0.26 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.008 0.15 0.3 13 -0.6 49 62
IL12/IL12R/TYK2/JAK2 0.028 0.3 0.71 35 -0.85 46 81
MAP2K3 0.032 0.27 0.65 23 -0.81 38 61
RIPK2 0.02 0.017 0.26 3 -10000 0 3
MAP2K6 0.037 0.26 0.64 24 -0.8 35 59
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.036 0.24 2 -0.59 1 3
IL18RAP 0.008 0.12 0.29 3 -0.59 32 35
IL12Rbeta1/TYK2 0.039 0.069 0.32 24 -0.49 1 25
EOMES -0.016 0.18 -10000 0 -1 23 23
STAT1 (dimer) 0.062 0.26 0.64 51 -0.73 30 81
T cell proliferation 0.044 0.21 0.51 26 -0.61 38 64
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.022 0.069 -10000 0 -0.59 11 11
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.012 0.19 0.4 5 -0.7 34 39
ATF2 0.037 0.25 0.62 21 -0.76 32 53
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.022 0.077 -10000 0 -0.44 8 8
HDAC1 0.02 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.023 0.004 -10000 0 -10000 0 0
DTX1 -0.034 0.18 -10000 0 -0.59 84 84
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.018 0.054 -10000 0 -0.59 7 7
AP1 -0.081 0.16 -10000 0 -0.32 252 252
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.023 0.021 -10000 0 -0.59 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.014 0.097 -10000 0 -0.65 12 12
NICD/RBPSUH 0.021 0.075 -10000 0 -0.41 11 11
WIF1 -0.29 0.31 0.26 10 -0.59 464 474
NOTCH1 0.01 0.066 -10000 0 -0.4 21 21
PSENEN 0.024 0.009 0.26 1 -10000 0 1
KREMEN2 0.13 0.12 0.26 387 -10000 0 387
DKK1 0.025 0.16 0.26 121 -0.59 45 166
beta catenin/beta TrCP1 0.006 0.07 0.25 1 -0.36 6 7
APH1B 0.023 0.021 -10000 0 -0.59 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.06 -10000 0 -0.46 7 7
CtBP/CBP/TCF1/TLE1/AES 0.011 0.042 -10000 0 -0.3 7 7
PSEN1 0.023 0.005 -10000 0 -10000 0 0
FOS -0.16 0.28 -10000 0 -0.59 262 262
JUN 0.018 0.058 -10000 0 -0.59 8 8
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 -0.003 0.069 0.24 2 -0.37 7 9
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.095 0.096 0.35 1 -0.35 13 14
HNF1A 0.025 0.02 0.26 6 -10000 0 6
CTBP1 0.022 0.006 -10000 0 -10000 0 0
MYC -0.014 0.21 -10000 0 -1.3 23 23
NKD1 0.021 0.059 0.26 14 -0.59 6 20
FZD1 0.024 0.003 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.008 0.12 -10000 0 -0.45 20 20
apoptosis -0.081 0.16 -10000 0 -0.32 252 252
Delta 1/NOTCHprecursor 0.02 0.076 -10000 0 -0.42 11 11
DLL1 0.021 0.029 -10000 0 -0.59 2 2
PPARD 0.013 0.098 -10000 0 -0.84 11 11
Gamma Secretase 0.054 0.034 -10000 0 -0.33 1 1
APC 0.003 0.085 0.25 1 -0.45 23 24
DVL1 -0.032 0.081 -10000 0 -0.38 29 29
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.099 0.14 0.35 64 -0.36 39 103
LRP6 0.023 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.009 -10000 0 -10000 0 0
CCND1 0.021 0.099 -10000 0 -1.1 5 5
WNT1 0.023 0.009 0.26 1 -10000 0 1
Axin1/APC/beta catenin 0.01 0.1 0.34 3 -0.43 17 20
DKK2 0.013 0.082 0.26 2 -0.59 16 18
NOTCH1 precursor/DVL1 -0.022 0.11 -10000 0 -0.6 19 19
GSK3B 0.023 0.003 -10000 0 -10000 0 0
FRAT1 0.023 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.12 -10000 0 -0.45 20 20
PPP2R5D -0.006 0.063 0.28 6 -0.34 20 26
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.2 -10000 0 -0.35 449 449
RBPJ 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.011 0.14 -10000 0 -0.59 50 50
HRAS 0.024 0.012 0.26 2 -10000 0 2
EGFR -0.19 0.29 -10000 0 -0.59 312 312
AKT -0.012 0.12 0.28 7 -0.27 86 93
FOXO3 0.022 0.021 -10000 0 -0.59 1 1
AKT1 0.023 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.03 -10000 0 -0.59 2 2
AKT3 0.014 0.058 -10000 0 -0.59 8 8
FOXO4 0.024 0.001 -10000 0 -10000 0 0
MET -0.076 0.23 -10000 0 -0.59 145 145
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.023 0.004 -10000 0 -10000 0 0
PIK3CG 0.018 0.063 0.26 4 -0.59 9 13
PIK3R3 0.024 0.009 0.26 1 -10000 0 1
PIK3R2 0.024 0.003 -10000 0 -10000 0 0
NF1 0.023 0.005 -10000 0 -10000 0 0
RAS -0.059 0.14 0.21 4 -0.24 285 289
ERBB2 0.02 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.005 0.093 0.34 40 -0.26 1 41
PI3K -0.048 0.14 0.25 14 -0.32 137 151
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.037 0.057 0.26 9 -0.17 1 10
AKT2 0.023 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.029 -10000 0 -0.59 2 2
FAS signaling pathway (CD95)

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
SPTAN1 -0.002 0.043 0.22 24 -10000 0 24
RFC1 -0.002 0.042 0.22 23 -10000 0 23
PRKDC 0.017 0.08 0.23 97 -10000 0 97
RIPK1 0.026 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.1 -10000 0 -0.64 18 18
FASLG/FAS/FADD/FAF1 -0.004 0.055 0.23 8 -0.29 6 14
MAP2K4 -0.083 0.17 0.39 2 -0.41 90 92
mol:ceramide -0.021 0.094 -10000 0 -0.39 14 14
GSN -0.007 0.059 0.22 27 -0.37 11 38
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.07 -10000 0 -0.39 7 7
FAS 0.003 0.039 -10000 0 -0.6 2 2
BID -0.019 0.022 -10000 0 -10000 0 0
MAP3K1 -0.048 0.12 0.32 2 -0.45 27 29
MAP3K7 0.01 0.019 -10000 0 -10000 0 0
RB1 -0.002 0.041 0.22 24 -10000 0 24
CFLAR 0.027 0.007 -10000 0 -10000 0 0
HGF/MET -0.054 0.2 -10000 0 -0.42 189 189
ARHGDIB 0 0.049 0.23 31 -10000 0 31
FADD 0.005 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.064 0.36 11 -0.22 26 37
NFKB1 -0.046 0.12 -10000 0 -0.6 16 16
MAPK8 -0.15 0.25 0.56 2 -0.46 332 334
DFFA -0.003 0.042 0.22 24 -10000 0 24
DNA fragmentation during apoptosis -0.006 0.048 0.22 21 -10000 0 21
FAS/FADD/MET -0.041 0.15 -10000 0 -0.35 149 149
CFLAR/RIP1 0.039 0.013 -10000 0 -10000 0 0
FAIM3 0.026 0.038 0.26 20 -10000 0 20
FAF1 0.002 0.029 -10000 0 -10000 0 0
PARP1 0 0.052 0.25 30 -10000 0 30
DFFB -0.003 0.041 0.22 21 -10000 0 21
CHUK -0.04 0.11 -10000 0 -0.57 14 14
FASLG 0.009 0.075 0.26 34 -0.61 6 40
FAS/FADD 0.008 0.037 -10000 0 -0.34 2 2
HGF -0.011 0.14 -10000 0 -0.59 50 50
LMNA -0.003 0.055 -10000 0 -10000 0 0
CASP6 -0.003 0.04 0.22 21 -10000 0 21
CASP10 0.003 0.039 -10000 0 -0.61 2 2
CASP3 0.001 0.047 0.27 24 -10000 0 24
PTPN13 0.008 0.095 -10000 0 -0.59 22 22
CASP8 -0.021 0.026 -10000 0 -10000 0 0
IL6 -0.44 0.62 -10000 0 -1.2 336 336
MET -0.076 0.23 -10000 0 -0.59 145 145
ICAD/CAD -0.006 0.035 0.22 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.095 -10000 0 -0.39 14 14
activation of caspase activity by cytochrome c -0.018 0.022 -10000 0 -10000 0 0
PAK2 -0.002 0.054 0.24 31 -10000 0 31
BCL2 0.006 0.1 -10000 0 -0.59 26 26
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 -0.061 0.2 0.31 1 -0.4 158 159
MAP3K8 0.009 0.045 -10000 0 -0.6 4 4
FOS -0.022 0.14 0.32 2 -0.46 39 41
PRKCA -0.003 0.088 0.24 1 -0.6 18 19
PTPN7 0.02 0.061 0.25 49 -10000 0 49
HRAS 0.023 0.013 0.26 2 -10000 0 2
PRKCB 0.005 0.08 0.26 16 -0.6 12 28
NRAS 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.035 -10000 0 -10000 0 0
MAPK3 0.006 0.093 -10000 0 -0.8 5 5
MAP2K1 -0.012 0.12 -10000 0 -0.51 35 35
ELK1 0.005 0.029 -10000 0 -10000 0 0
BRAF -0.013 0.1 -10000 0 -0.5 31 31
mol:GTP -0.002 0.003 -10000 0 -0.006 278 278
MAPK1 -0.009 0.12 -10000 0 -0.46 34 34
RAF1 -0.012 0.1 -10000 0 -0.5 31 31
KRAS 0.022 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.021 -10000 0 -0.59 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.018 0.063 0.44 1 -0.26 13 14
CDKN1A -0.009 0.027 -10000 0 -0.79 1 1
KAT2B 0.024 0.003 -10000 0 -10000 0 0
BAX 0.024 0.014 0.26 3 -10000 0 3
FOXO3 -0.004 0.009 -10000 0 -0.26 1 1
FOXO1 0.02 0.03 -10000 0 -0.59 2 2
FOXO4 0.011 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.34 0.31 0.26 24 -0.59 534 558
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.019 -10000 0 -10000 0 0
PPARGC1A -0.094 0.24 0.26 9 -0.59 174 183
FHL2 0.021 0.047 0.26 2 -0.59 5 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.01 -10000 0 -10000 0 0
HIST2H4A 0.018 0.063 0.26 13 -0.44 1 14
SIRT1/FOXO3a 0.015 0.026 -10000 0 -0.2 4 4
SIRT1 0.022 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.038 0.024 -10000 0 -0.38 1 1
SIRT1/Histone H1b 0.027 0.043 -10000 0 -10000 0 0
apoptosis -0.044 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.051 0.16 -10000 0 -0.38 174 174
p53/SIRT1 0.026 0.016 0.41 1 -10000 0 1
SIRT1/FOXO4 0.022 0.036 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.037 0.04 -10000 0 -0.35 7 7
HIST1H1E 0.02 0.031 0.21 6 -10000 0 6
SIRT1/p300 0.032 0.01 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.022 -10000 0 -10000 0 0
TP53 0.02 0.01 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.044 0.016 -10000 0 -10000 0 0
CREBBP 0.022 0.006 -10000 0 -10000 0 0
MEF2D 0.02 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.27 0.22 -10000 0 -0.4 625 625
ACSS2 -0.008 0.01 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.022 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.032 0.043 0.26 30 -10000 0 30
GPC2 0.047 0.084 0.26 97 -0.59 3 100
GPC2/Midkine 0.055 0.071 0.38 13 -0.44 3 16
neuron projection morphogenesis 0.055 0.071 0.38 13 -0.44 3 16
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.042 0.15 -10000 0 -0.33 191 191
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.14 7 -10000 0 7
GNB1/GNG2 0.028 0.034 -10000 0 -0.37 6 6
GNB1 0.023 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.063 0.14 -10000 0 -0.33 203 203
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.02 0.035 0.084 203 -10000 0 203
GNAL -0.11 0.25 -10000 0 -0.59 191 191
GNG2 0.019 0.05 -10000 0 -0.59 6 6
CRH 0.017 0.023 0.26 7 -10000 0 7
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.021 -10000 0 -0.36 3 3
MAPK11 0.005 0.017 -10000 0 -0.36 2 2
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.029 -10000 0 -0.59 2 2
alphaV beta3 Integrin 0.025 0.066 -10000 0 -0.44 17 17
PTK2 -0.034 0.14 -10000 0 -0.47 65 65
positive regulation of JNK cascade -0.017 0.12 -10000 0 -0.32 88 88
CDC42/GDP -0.011 0.16 0.43 1 -0.43 91 92
Rac1/GDP -0.012 0.16 -10000 0 -0.43 91 91
RAP1B 0.023 0.005 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
CTNNB1 0.023 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.016 0.15 -10000 0 -0.4 87 87
nectin-3/I-afadin -0.01 0.14 -10000 0 -0.45 80 80
RAPGEF1 -0.028 0.16 0.46 1 -0.48 78 79
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.041 0.17 -10000 0 -0.53 84 84
PDGFB-D/PDGFRB 0.022 0.029 -10000 0 -0.59 2 2
TLN1 -0.021 0.065 -10000 0 -0.39 9 9
Rap1/GTP -0.019 0.12 -10000 0 -0.34 76 76
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.039 0.028 -10000 0 -0.35 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.01 0.14 -10000 0 -0.45 80 80
PVR 0.024 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.003 -10000 0 -10000 0 0
mol:GDP -0.03 0.19 0.45 1 -0.53 93 94
MLLT4 0.02 0.036 -10000 0 -0.59 3 3
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.12 -10000 0 -0.33 80 80
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.032 -10000 0 -0.34 5 5
positive regulation of lamellipodium assembly -0.015 0.13 -10000 0 -0.34 94 94
PVRL1 0.022 0.007 -10000 0 -10000 0 0
PVRL3 -0.03 0.17 -10000 0 -0.59 79 79
PVRL2 0.024 0.009 0.26 1 -10000 0 1
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
CDH1 0.009 0.086 -10000 0 -0.59 18 18
CLDN1 0.005 0.12 0.26 20 -0.59 34 54
JAM-A/CLDN1 0.006 0.13 -10000 0 -0.38 79 79
SRC -0.048 0.19 -10000 0 -0.56 95 95
ITGB3 0.012 0.085 0.26 4 -0.59 17 21
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.032 -10000 0 -0.34 5 5
FARP2 -0.03 0.2 0.46 1 -0.53 91 92
RAC1 0.024 0.004 -10000 0 -10000 0 0
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.006 0.12 -10000 0 -0.39 79 79
nectin-1/I-afadin 0.029 0.032 -10000 0 -0.34 5 5
nectin-2/I-afadin 0.031 0.031 -10000 0 -0.44 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.004 0.12 -10000 0 -0.39 80 80
CDC42/GTP/IQGAP1/filamentous actin 0.03 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.017 0.12 -10000 0 -0.32 88 88
alphaV/beta3 Integrin/Talin 0 0.093 0.27 1 -0.41 22 23
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.031 -10000 0 -0.44 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.031 0.031 -10000 0 -0.44 3 3
PIP5K1C -0.016 0.072 -10000 0 -0.23 78 78
VAV2 -0.03 0.2 0.44 1 -0.55 92 93
RAP1/GDP -0.009 0.15 -10000 0 -0.4 86 86
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.007 0.12 -10000 0 -0.39 79 79
nectin-3(dimer)/I-afadin/I-afadin -0.01 0.14 -10000 0 -0.45 80 80
Rac1/GTP -0.016 0.16 -10000 0 -0.42 92 92
PTPRM -0.013 0.081 -10000 0 -0.25 80 80
E-cadherin/beta catenin/alpha catenin 0.044 0.069 -10000 0 -0.34 20 20
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.01 0.046 -10000 0 -0.27 19 19
epithelial cell differentiation 0.034 0.058 -10000 0 -0.33 18 18
CYFIP2 0.03 0.046 0.26 26 -0.59 1 27
ENAH -0.005 0.059 0.27 8 -10000 0 8
EGFR -0.19 0.29 -10000 0 -0.59 312 312
EPHA2 0.019 0.046 -10000 0 -0.59 5 5
MYO6 -0.014 0.053 -10000 0 -0.32 19 19
CTNNB1 0.023 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.032 -10000 0 -0.38 1 1
AQP5 -0.2 0.27 0.33 1 -0.51 366 367
CTNND1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.014 0.051 -10000 0 -0.31 18 18
regulation of calcium-dependent cell-cell adhesion -0.025 0.078 -10000 0 -0.32 52 52
EGF -0.09 0.24 0.26 2 -0.59 167 169
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.019 0.12 0.29 1 -0.47 47 48
cortical microtubule organization 0.034 0.058 -10000 0 -0.33 18 18
GO:0000145 -0.014 0.049 -10000 0 -0.3 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.038 0.06 -10000 0 -0.33 18 18
MLLT4 0.02 0.036 -10000 0 -0.59 3 3
ARF6/GDP -0.022 0.043 -10000 0 -0.29 20 20
ARF6 0.023 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.04 -10000 0 -0.34 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.005 0.05 -10000 0 -0.3 18 18
PVRL2 0.024 0.009 0.26 1 -10000 0 1
ZYX -0.014 0.051 -10000 0 -0.32 18 18
ARF6/GTP 0.048 0.042 -10000 0 -0.32 5 5
CDH1 0.009 0.086 -10000 0 -0.59 18 18
EGFR/EGFR/EGF/EGF -0.15 0.2 -10000 0 -0.35 433 433
RhoA/GDP 0.035 0.056 -10000 0 -0.31 18 18
actin cytoskeleton organization -0.016 0.05 -10000 0 -0.31 19 19
IGF-1R heterotetramer 0.012 0.084 0.26 2 -0.59 17 19
GIT1 0.022 0.006 -10000 0 -10000 0 0
IGF1R 0.012 0.085 0.26 2 -0.59 17 19
IGF1 -0.1 0.25 -10000 0 -0.59 185 185
DIAPH1 0.026 0.1 -10000 0 -0.56 10 10
Wnt receptor signaling pathway -0.034 0.058 0.33 18 -10000 0 18
RHOA 0.023 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.044 -10000 0 -0.29 20 20
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
VCL -0.016 0.051 -10000 0 -0.31 19 19
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.016 0.052 -10000 0 -0.3 20 20
Ephrin A1/EPHA2 0.023 0.058 -10000 0 -0.31 21 21
SEC6/SEC8 -0.023 0.046 -10000 0 -0.31 20 20
MGAT3 -0.026 0.079 -10000 0 -0.32 52 52
HGF/MET -0.042 0.16 -10000 0 -0.34 190 190
HGF -0.011 0.14 -10000 0 -0.59 50 50
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.01 0.047 -10000 0 -0.27 19 19
actin cable formation 0.039 0.094 0.3 29 -0.3 1 30
KIAA1543 -0.014 0.054 -10000 0 -0.33 18 18
KIFC3 -0.014 0.05 -10000 0 -0.32 18 18
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.023 0.005 -10000 0 -10000 0 0
ACTN1 -0.014 0.052 -10000 0 -0.32 18 18
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.034 0.058 -10000 0 -0.33 18 18
EXOC4 0.023 0.004 -10000 0 -10000 0 0
STX4 -0.013 0.051 -10000 0 -0.32 18 18
PIP5K1C -0.014 0.052 -10000 0 -0.32 18 18
LIMA1 0.023 0.021 -10000 0 -0.59 1 1
ABI1 0.023 0.004 -10000 0 -10000 0 0
ROCK1 0.014 0.088 0.3 20 -10000 0 20
adherens junction assembly -0.026 0.11 0.28 2 -0.64 14 16
IGF-1R heterotetramer/IGF1 -0.045 0.15 -10000 0 -0.32 196 196
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.031 -10000 0 -0.44 3 3
MET -0.076 0.23 -10000 0 -0.59 145 145
PLEKHA7 -0.014 0.057 -10000 0 -0.35 18 18
mol:GTP 0.042 0.04 -10000 0 -0.34 5 5
establishment of epithelial cell apical/basal polarity -0.01 0.068 0.35 5 -0.54 1 6
cortical actin cytoskeleton stabilization 0.01 0.046 -10000 0 -0.27 19 19
regulation of cell-cell adhesion -0.016 0.05 -10000 0 -0.31 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.01 0.047 -10000 0 -0.27 19 19
Aurora A signaling

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
Aurora A/GADD45A 0.045 0.044 -10000 0 -10000 0 0
BIRC5 0.18 0.12 0.26 602 -10000 0 602
NFKBIA 0.025 0.042 0.29 7 -10000 0 7
CPEB1 -0.086 0.24 0.26 1 -0.59 160 161
AKT1 0.025 0.041 0.29 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.034 0.037 0.21 1 -10000 0 1
NDEL1/TACC3 0.066 0.069 0.26 15 -10000 0 15
GADD45A 0.023 0.004 -10000 0 -10000 0 0
GSK3B -0.004 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.041 0.044 0.26 2 -10000 0 2
MDM2 0.023 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.098 0.07 0.27 23 -10000 0 23
TP53 0.022 0.053 -10000 0 -0.22 12 12
DLG7 0.023 0.032 0.18 1 -10000 0 1
AURKAIP1 0.024 0.019 0.26 5 -10000 0 5
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.07 0.073 0.27 15 -10000 0 15
G2/M transition of mitotic cell cycle 0.031 0.035 0.21 1 -10000 0 1
AURKA 0.039 0.048 0.25 1 -10000 0 1
AURKB 0.092 0.078 0.18 371 -10000 0 371
CDC25B 0.033 0.039 0.22 4 -10000 0 4
G2/M transition checkpoint 0.02 0.03 -10000 0 -10000 0 0
mRNA polyadenylation -0.03 0.14 -10000 0 -0.31 160 160
Aurora A/CPEB -0.029 0.14 -10000 0 -0.31 160 160
Aurora A/TACC1/TRAP/chTOG 0.045 0.068 -10000 0 -0.31 15 15
BRCA1 0.023 0.009 0.26 1 -10000 0 1
centrosome duplication 0.041 0.044 0.26 2 -10000 0 2
regulation of centrosome cycle 0.064 0.067 0.25 15 -10000 0 15
spindle assembly 0.043 0.067 -10000 0 -0.31 15 15
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.09 0.26 91 -10000 0 91
CENPA 0.1 0.085 0.19 387 -0.21 3 390
Aurora A/PP2A 0.044 0.044 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.032 0.041 0.24 1 -10000 0 1
negative regulation of DNA binding 0.017 0.062 -10000 0 -0.22 12 12
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.023 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.02 0.03 -10000 0 -10000 0 0
mitotic prometaphase -0.01 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.048 0.25 1 -10000 0 1
TACC1 0.009 0.081 -10000 0 -0.59 16 16
TACC3 0.059 0.086 0.26 133 -10000 0 133
Aurora A/Antizyme1 0.054 0.043 -10000 0 -10000 0 0
Aurora A/RasGAP 0.044 0.044 -10000 0 -10000 0 0
OAZ1 0.023 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.004 0.027 -10000 0 -10000 0 0
GIT1 0.022 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.038 0.023 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.098 0.07 0.27 23 -10000 0 23
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.074 0.25 26 -10000 0 26
PAK1 0.022 0.018 0.26 4 -10000 0 4
CKAP5 0.024 0.003 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.019 0.066 -10000 0 -0.38 30 30
ADCY5 -0.12 0.17 -10000 0 -0.38 270 270
ADCY6 -0.007 0.012 -10000 0 -0.38 1 1
ADCY7 -0.007 0.013 -10000 0 -0.38 1 1
ADCY1 -0.007 0.062 -10000 0 -0.38 20 20
ADCY2 -0.03 0.1 0.25 6 -0.38 67 73
ADCY3 -0.007 0.013 -10000 0 -0.38 1 1
ADCY8 -0.004 0.023 0.23 5 -10000 0 5
PRKCE 0.005 0.015 -10000 0 -0.44 1 1
ADCY9 -0.007 0.012 -10000 0 -0.38 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.01 0.089 0.23 15 -0.26 30 45
Signaling events mediated by PRL

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
CCNE1 0.06 0.087 0.26 138 -10000 0 138
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.022 0.029 -10000 0 -0.59 2 2
CDKN1A -0.033 0.094 -10000 0 -0.44 23 23
PRL-3/alpha Tubulin 0.028 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.08 0.24 38 -0.44 12 50
AGT 0.029 0.097 0.26 66 -0.59 12 78
CCNA2 -0.068 0.15 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.13 0.21 -10000 0 -0.43 287 287
CDK2/Cyclin E1 0.012 0.11 -10000 0 -0.51 12 12
MAPK3 0.01 0.022 0.26 6 -10000 0 6
PRL-2 /Rab GGTase beta 0.034 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.023 0.26 7 -10000 0 7
PTP4A1 -0.1 0.15 -10000 0 -0.34 255 255
PTP4A3 0.019 0.015 0.26 2 -10000 0 2
PTP4A2 0.023 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.022 0.26 6 -10000 0 6
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 -0.022 0.079 -10000 0 -0.41 16 16
Rab GGTase beta/Rab GGTase alpha 0.034 0.007 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.08 0.16 -10000 0 -10000 0 0
RABGGTA 0.023 0.004 -10000 0 -10000 0 0
BCAR1 -0.013 0.012 -10000 0 -10000 0 0
RHOC -0.023 0.085 -10000 0 -0.43 19 19
RHOA -0.026 0.095 -10000 0 -0.46 24 24
cell motility -0.029 0.1 -10000 0 -0.37 32 32
PRL-1/alpha Tubulin -0.081 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.025 -10000 0 -0.32 2 2
ROCK1 -0.028 0.1 -10000 0 -0.38 29 29
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.1 0.15 -10000 0 -0.34 255 255
ATF5 0.024 0.014 0.26 3 -10000 0 3
Syndecan-4-mediated signaling events

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
PTK2 0.089 0.11 0.28 37 -0.63 6 43
Syndecan-4/Syndesmos 0.098 0.11 0.39 4 -0.67 6 10
positive regulation of JNK cascade 0.088 0.14 0.37 5 -0.65 7 12
Syndecan-4/ADAM12 0.11 0.12 0.4 7 -0.7 6 13
CCL5 0.028 0.056 0.26 29 -0.59 3 32
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DNM2 0.023 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
PLG -0.01 0.032 0.26 4 -10000 0 4
ADAM12 0.039 0.069 0.26 63 -0.59 2 65
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.013 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.068 0.15 0.42 2 -0.66 8 10
Syndecan-4/CXCL12/CXCR4 0.092 0.14 0.39 5 -0.7 7 12
Syndecan-4/Laminin alpha3 0.037 0.16 0.4 3 -0.69 7 10
MDK 0.032 0.043 0.26 30 -10000 0 30
Syndecan-4/FZD7 0.098 0.12 0.39 4 -0.7 6 10
Syndecan-4/Midkine 0.11 0.11 0.39 10 -0.67 6 16
FZD7 0.012 0.084 -10000 0 -0.59 17 17
Syndecan-4/FGFR1/FGF -0.012 0.17 -10000 0 -0.56 15 15
THBS1 0.023 0.021 -10000 0 -0.59 1 1
integrin-mediated signaling pathway 0.096 0.12 0.38 6 -0.67 7 13
positive regulation of MAPKKK cascade 0.088 0.14 0.37 5 -0.65 7 12
Syndecan-4/TACI 0.1 0.12 0.38 10 -0.69 6 16
CXCR4 0.03 0.039 0.26 24 -10000 0 24
cell adhesion 0.064 0.087 0.25 72 -0.26 18 90
Syndecan-4/Dynamin 0.1 0.11 0.4 3 -0.7 6 9
Syndecan-4/TSP1 0.1 0.11 0.39 4 -0.69 6 10
Syndecan-4/GIPC 0.1 0.11 0.39 4 -0.7 6 10
Syndecan-4/RANTES 0.1 0.11 0.38 4 -0.69 6 10
ITGB1 0.023 0.004 -10000 0 -10000 0 0
LAMA1 -0.04 0.19 0.26 1 -0.59 92 93
LAMA3 -0.12 0.26 -10000 0 -0.59 207 207
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.021 0.22 0.7 79 -0.56 17 96
Syndecan-4/alpha-Actinin 0.1 0.11 0.4 3 -0.7 6 9
TFPI -0.001 0.12 -10000 0 -0.59 36 36
F2 0.024 0.031 0.27 6 -10000 0 6
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.005 0.18 0.44 1 -0.55 27 28
ACTN1 0.023 0.005 -10000 0 -10000 0 0
TNC 0.012 0.09 0.26 5 -0.59 19 24
Syndecan-4/CXCL12 0.081 0.14 0.4 3 -0.73 7 10
FGF6 0.015 0.029 -10000 0 -0.59 2 2
RHOA 0.023 0.005 -10000 0 -10000 0 0
CXCL12 -0.019 0.16 -10000 0 -0.59 62 62
TNFRSF13B 0.025 0.086 0.26 41 -0.59 11 52
FGF2 -0.21 0.3 -10000 0 -0.59 342 342
FGFR1 0.015 0.051 -10000 0 -0.59 6 6
Syndecan-4/PI-4-5-P2 0.079 0.1 0.34 1 -0.7 6 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 375 -10000 0 375
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.011 0.026 -10000 0 -10000 0 0
vasculogenesis 0.1 0.11 0.38 5 -0.66 6 11
SDC4 0.092 0.11 0.43 2 -0.78 5 7
Syndecan-4/Tenascin C 0.098 0.12 0.39 4 -0.7 7 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.089 0.11 0.37 3 -0.67 6 9
MMP9 0.12 0.12 0.26 382 -0.58 1 383
Rac1/GTP 0.065 0.088 0.26 72 -0.27 18 90
cytoskeleton organization 0.097 0.1 0.38 5 -0.64 6 11
GIPC1 0.024 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.092 0.13 0.4 3 -0.7 7 10
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0.011 -10000 0 -10000 0 0
SMARCC1 0.004 0.03 -10000 0 -0.51 2 2
REL 0.022 0.047 -10000 0 -0.59 5 5
HDAC7 -0.037 0.11 0.38 1 -0.39 41 42
JUN 0.016 0.058 -10000 0 -0.59 8 8
EP300 0.022 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.003 -10000 0 -10000 0 0
KAT5 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.01 0.068 -10000 0 -0.45 19 19
FOXO1 0.02 0.03 -10000 0 -0.59 2 2
T-DHT/AR -0.025 0.12 -10000 0 -0.39 48 48
MAP2K6 0.001 0.09 0.25 1 -0.6 19 20
BRM/BAF57 0.023 0.027 -10000 0 -10000 0 0
MAP2K4 0.013 0.021 -10000 0 -10000 0 0
SMARCA2 0.016 0.019 -10000 0 -10000 0 0
PDE9A -0.066 0.27 -10000 0 -1.1 54 54
NCOA2 0.007 0.081 -10000 0 -0.59 16 16
CEBPA 0.018 0.058 -10000 0 -0.59 8 8
EHMT2 0.02 0.013 -10000 0 -10000 0 0
cell proliferation 0 0.15 0.38 19 -0.47 19 38
NR0B1 0.028 0.044 0.26 30 -10000 0 30
EGR1 -0.18 0.28 -10000 0 -0.59 288 288
RXRs/9cRA -0.05 0.16 -10000 0 -0.35 187 187
AR/RACK1/Src -0.019 0.11 0.32 6 -0.38 23 29
AR/GR -0.024 0.11 0.28 1 -0.3 98 99
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.023 0.004 -10000 0 -10000 0 0
RCHY1 0.023 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.016 5 5
MAPK8 -0.002 0.034 -10000 0 -0.45 3 3
T-DHT/AR/TIF2/CARM1 -0.01 0.11 0.34 2 -0.37 30 32
SRC -0.02 0.065 0.19 21 -0.36 18 39
NR3C1 0.019 0.054 -10000 0 -0.59 7 7
KLK3 -0.16 0.41 -10000 0 -1.2 124 124
APPBP2 0.015 0.019 -10000 0 -10000 0 0
TRIM24 0.017 0.02 0.26 1 -10000 0 1
T-DHT/AR/TIP60 -0.014 0.096 0.32 4 -0.4 21 25
TMPRSS2 -0.13 0.37 -10000 0 -1.1 114 114
RXRG -0.11 0.25 0.26 1 -0.59 189 190
mol:9cRA -0.001 0.002 -10000 0 -0.016 1 1
RXRA 0.023 0.005 -10000 0 -10000 0 0
RXRB 0.023 0.005 -10000 0 -10000 0 0
CARM1 0.021 0.011 -10000 0 -10000 0 0
NR2C2 0.02 0.041 -10000 0 -0.59 4 4
KLK2 -0.055 0.21 0.33 5 -0.68 78 83
AR -0.037 0.1 0.17 1 -0.3 105 106
SENP1 0.023 0.004 -10000 0 -10000 0 0
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
MDM2 0.026 0.015 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 120 -0.024 21 141
GATA2 0.012 0.097 0.26 11 -0.59 21 32
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.26 367 -10000 0 367
T-DHT/AR/RACK1/Src -0.013 0.1 0.34 10 -0.39 20 30
positive regulation of transcription 0.012 0.097 0.26 11 -0.59 21 32
DNAJA1 0.016 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.02 0.032 -10000 0 -0.62 1 1
SPDEF -0.013 0.15 0.25 15 -0.59 51 66
T-DHT/AR/TIF2 0.002 0.091 0.31 4 -0.39 14 18
T-DHT/AR/Hsp90 -0.015 0.094 0.31 3 -0.4 21 24
GSK3B 0.02 0.012 -10000 0 -10000 0 0
NR2C1 0.024 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.061 0.23 1 -0.38 20 21
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.026 0.016 -10000 0 -10000 0 0
POU2F1 0.008 0.051 -10000 0 -0.19 10 10
T-DHT/AR/DAX-1 -0.014 0.099 0.31 4 -0.4 22 26
CREBBP 0.022 0.006 -10000 0 -10000 0 0
SMARCE1 0.016 0.018 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.043 -10000 0 -0.59 1 1
SVIL 0.009 0.05 -10000 0 -0.59 3 3
ZNF318 0.042 0.056 0.22 2 -10000 0 2
JMJD2C -0.003 0.043 0.12 14 -0.13 75 89
T-DHT/AR/Ubc9 -0.03 0.14 -10000 0 -0.4 100 100
CARM1 0.018 0.016 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.012 0.031 -10000 0 -10000 0 0
AKT1 0.028 0.018 -10000 0 -10000 0 0
PTK2B 0.01 0.027 -10000 0 -10000 0 0
MED1 0.026 0.02 -10000 0 -10000 0 0
MAK 0.037 0.088 0.23 20 -0.56 10 30
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.008 0.054 -10000 0 -0.59 4 4
GSN 0.002 0.079 -10000 0 -0.59 12 12
NCOA2 0.004 0.082 -10000 0 -0.59 16 16
NCOA6 0.011 0.034 -10000 0 -10000 0 0
DNA-PK 0.052 0.054 -10000 0 -10000 0 0
NCOA4 0.019 0.013 -10000 0 -10000 0 0
PIAS3 0.012 0.03 -10000 0 -10000 0 0
cell proliferation 0.006 0.11 0.31 2 -0.58 21 23
XRCC5 0.027 0.015 -10000 0 -10000 0 0
UBE3A 0.006 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.039 0.16 -10000 0 -0.39 124 124
FHL2 0.004 0.12 0.29 1 -0.7 11 12
RANBP9 0.011 0.035 -10000 0 -10000 0 0
JMJD1A -0.01 0.056 0.12 34 -0.14 123 157
CDK6 0.022 0.043 0.26 2 -0.59 4 6
TGFB1I1 0.008 0.049 -10000 0 -0.59 3 3
T-DHT/AR/CyclinD1 -0.039 0.14 -10000 0 -0.4 102 102
XRCC6 0.026 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.036 0.17 -10000 0 -0.4 115 115
CTDSP1 0.016 0.02 -10000 0 -10000 0 0
CTDSP2 0.036 0.038 -10000 0 -10000 0 0
BRCA1 0.011 0.036 -10000 0 -10000 0 0
TCF4 0.028 0.058 -10000 0 -0.58 6 6
CDKN2A 0.064 0.091 0.28 134 -10000 0 134
SRF 0.032 0.024 -10000 0 -10000 0 0
NKX3-1 -0.06 0.2 0.3 26 -0.61 72 98
KLK3 -0.17 0.48 -10000 0 -1.4 120 120
TMF1 0.017 0.017 -10000 0 -10000 0 0
HNRNPA1 0.03 0.021 -10000 0 -10000 0 0
AOF2 -0.009 0.024 -10000 0 -0.069 120 120
APPL1 0.014 0.037 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.023 0.15 -10000 0 -0.38 104 104
AR -0.061 0.2 0.22 1 -0.6 102 103
UBA3 0.016 0.02 -10000 0 -10000 0 0
PATZ1 0.028 0.021 -10000 0 -10000 0 0
PAWR 0.017 0.026 -10000 0 -0.59 1 1
PRKDC 0.024 0.016 -10000 0 -10000 0 0
PA2G4 0.032 0.027 -10000 0 -10000 0 0
UBE2I 0.022 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.02 0.13 -10000 0 -0.36 96 96
RPS6KA3 0.008 0.052 -10000 0 -0.59 3 3
T-DHT/AR/ARA70 -0.034 0.14 -10000 0 -0.39 103 103
LATS2 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.016 0.14 0.19 6 -0.34 114 120
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.013 0.067 0.26 17 -0.59 6 23
KLK2 -0.088 0.3 0.39 1 -1 77 78
CASP8 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.029 0.13 -10000 0 -0.36 97 97
TMPRSS2 -0.13 0.34 -10000 0 -1 115 115
CCND1 0.011 0.042 0.26 1 -0.59 3 4
PIAS1 0.007 0.046 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.031 0.061 2 -0.072 155 157
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.001 0.066 -10000 0 -0.17 100 100
T-DHT/AR/CDK6 -0.029 0.15 -10000 0 -0.39 108 108
CMTM2 0.023 0.013 0.26 1 -10000 0 1
SNURF 0.01 0.086 -10000 0 -0.59 18 18
ZMIZ1 0.009 0.042 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.021 -10000 0 -10000 0 0
FKBP4 0.012 0.037 0.26 3 -10000 0 3
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.027 0.03 0.27 14 -10000 0 14
GNB1/GNG2 -0.015 0.047 -10000 0 -0.19 51 51
AKT1 0.023 0.094 0.35 12 -0.27 31 43
EGF -0.09 0.24 0.26 2 -0.59 167 169
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.057 0.25 2 -0.28 4 6
mol:Ca2+ 0.023 0.11 0.41 11 -0.29 67 78
LYN 0.012 0.052 0.25 2 -10000 0 2
RhoA/GTP 0.009 0.044 0.15 3 -0.13 37 40
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.02 0.12 0.42 12 -0.34 52 64
GNG2 0.019 0.05 -10000 0 -0.59 6 6
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.58 34 34
G beta5/gamma2 -0.011 0.064 -10000 0 -0.26 49 49
PRKCH 0.019 0.12 0.4 12 -0.35 56 68
DNM1 0.021 0.046 0.26 1 -0.59 5 6
TXA2/TP beta/beta Arrestin3 0.008 0.032 -10000 0 -0.53 1 1
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
PTGDR 0.011 0.096 0.26 7 -0.59 21 28
G12 family/GTP 0.001 0.087 -10000 0 -0.3 49 49
ADRBK1 0.022 0.006 -10000 0 -10000 0 0
ADRBK2 0.021 0.036 -10000 0 -0.59 3 3
RhoA/GTP/ROCK1 0.031 0.008 -10000 0 -10000 0 0
mol:GDP -0.012 0.1 0.37 27 -0.33 9 36
mol:NADP 0.023 0.004 -10000 0 -10000 0 0
RAB11A 0.023 0.004 -10000 0 -10000 0 0
PRKG1 -0.003 0.12 -10000 0 -0.59 39 39
mol:IP3 0.021 0.13 0.44 11 -0.37 68 79
cell morphogenesis 0.031 0.008 -10000 0 -10000 0 0
PLCB2 0.014 0.17 0.54 7 -0.49 68 75
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.025 0.069 0.26 7 -0.27 4 11
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.058 0.25 4 -0.28 2 6
RHOA 0.023 0.005 -10000 0 -10000 0 0
PTGIR 0.025 0.02 0.26 6 -10000 0 6
PRKCB1 0.02 0.13 0.42 11 -0.36 59 70
GNAQ 0.022 0.029 -10000 0 -0.59 2 2
mol:L-citrulline 0.023 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.017 0.16 0.52 8 -0.52 56 64
LCK 0.016 0.071 0.25 2 -0.36 10 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.052 -10000 0 -0.34 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.1 -10000 0 -0.42 43 43
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.049 -10000 0 -0.25 18 18
MAPK14 0.02 0.089 0.37 12 -0.23 49 61
TGM2/GTP 0.017 0.15 0.5 9 -0.42 61 70
MAPK11 0.018 0.09 0.35 14 -0.24 50 64
ARHGEF1 0.012 0.066 0.28 10 -0.18 43 53
GNAI2 0.023 0.004 -10000 0 -10000 0 0
JNK cascade 0.022 0.13 0.45 11 -0.38 56 67
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.023 0.1 0.39 12 -0.28 50 62
cAMP biosynthetic process 0.018 0.12 0.42 10 -0.35 62 72
Gq family/GTP/EBP50 0.015 0.043 0.22 4 -0.23 13 17
actin cytoskeleton reorganization 0.031 0.008 -10000 0 -10000 0 0
SRC 0.013 0.055 0.25 2 -0.28 2 4
GNB5 0.023 0.004 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.048 0.11 0.24 3 -0.3 55 58
VCAM1 0.022 0.11 0.4 11 -0.3 50 61
TP beta/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.58 34 34
platelet activation 0.025 0.12 0.42 14 -0.3 53 67
PGI2/IP 0.019 0.014 0.18 6 -10000 0 6
PRKACA 0.009 0.049 -10000 0 -0.3 21 21
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.47 30 30
TXA2/TP beta/beta Arrestin2 -0.006 0.065 -10000 0 -0.43 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.003 0.044 -10000 0 -0.28 20 20
mol:DAG 0.02 0.14 0.48 9 -0.41 61 70
EGFR -0.19 0.29 -10000 0 -0.59 312 312
TXA2/TP alpha 0.017 0.16 0.52 8 -0.47 62 70
Gq family/GTP 0.001 0.05 0.25 1 -0.22 37 38
YES1 0.014 0.058 0.25 2 -0.27 4 6
GNAI2/GTP 0.014 0.047 -10000 0 -0.26 11 11
PGD2/DP 0.008 0.071 0.18 7 -0.42 23 30
SLC9A3R1 0.035 0.054 0.26 46 -10000 0 46
FYN 0.013 0.055 0.26 1 -0.28 4 5
mol:NO 0.023 0.004 -10000 0 -10000 0 0
GNA15 0.024 0.028 0.26 5 -0.59 1 6
PGK/cGMP 0.014 0.083 -10000 0 -0.38 39 39
RhoA/GDP 0.022 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.036 0.063 -10000 0 -0.37 7 7
NOS3 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.023 0.13 0.4 13 -0.37 53 66
PRKCB 0.023 0.13 0.41 12 -0.37 53 65
PRKCE 0.02 0.12 0.44 10 -0.35 54 64
PRKCD 0.019 0.12 0.45 9 -0.38 52 61
PRKCG 0.021 0.13 0.45 10 -0.37 56 66
muscle contraction 0.017 0.16 0.5 9 -0.48 58 67
PRKCZ 0.019 0.12 0.42 11 -0.34 52 63
ARR3 0.021 0.022 0.26 7 -10000 0 7
TXA2/TP beta 0.024 0.054 -10000 0 -0.27 22 22
PRKCQ 0.017 0.13 0.43 12 -0.38 57 69
MAPKKK cascade 0.017 0.15 0.47 9 -0.45 60 69
SELE 0.018 0.12 0.38 13 -0.39 50 63
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.061 -10000 0 -0.38 6 6
ROCK1 0.023 0.004 -10000 0 -10000 0 0
GNA14 0.023 0.068 0.26 20 -0.59 8 28
chemotaxis 0.015 0.18 0.61 6 -0.6 52 58
GNA12 0.023 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.029 -10000 0 -0.59 2 2
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
Insulin Pathway

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.046 0.17 -10000 0 -0.34 211 211
TC10/GTP -0.037 0.14 -10000 0 -0.3 201 201
Insulin Receptor/Insulin/IRS1/Shp2 0.042 0.08 -10000 0 -0.36 32 32
HRAS 0.024 0.012 0.26 2 -10000 0 2
APS homodimer 0.033 0.046 0.26 34 -10000 0 34
GRB14 0.014 0.18 0.26 123 -0.59 63 186
FOXO3 -0.019 0.16 -10000 0 -0.59 59 59
AKT1 -0.016 0.11 0.33 6 -0.3 52 58
INSR 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.056 0.049 0.44 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.12 0.26 -10000 0 -0.59 206 206
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.002 0.025 -10000 0 -10000 0 0
CAV1 -0.083 0.15 -10000 0 -0.36 190 190
CBL/APS/CAP/Crk-II/C3G -0.026 0.17 -10000 0 -0.32 204 204
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.079 -10000 0 -0.36 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.031 0.068 -10000 0 -0.32 30 30
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.012 0.067 -10000 0 -0.34 12 12
RPS6KB1 -0.016 0.098 0.32 6 -0.5 1 7
PARD6A 0.022 0.016 0.26 3 -10000 0 3
CBL 0.022 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.04 -10000 0 -0.56 4 4
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.009 0.095 -10000 0 -0.28 64 64
HRAS/GTP -0.021 0.047 -10000 0 -0.29 21 21
Insulin Receptor 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.04 0.073 -10000 0 -0.34 23 23
PRKCI 0.013 0.058 -10000 0 -0.46 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.002 0.1 -10000 0 -0.31 83 83
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.04 0.038 -10000 0 -0.47 4 4
PI3K 0.04 0.072 -10000 0 -0.32 30 30
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.008 0.18 2 -10000 0 2
AKT2 -0.017 0.11 0.3 5 -0.3 53 58
PRKCZ 0.005 0.082 -10000 0 -0.49 11 11
SH2B2 0.033 0.046 0.26 34 -10000 0 34
SHC/SHIP 0.011 0.061 -10000 0 -0.32 25 25
F2RL2 0.048 0.12 0.26 130 -0.59 14 144
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.052 0.033 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.023 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.035 0.17 -10000 0 -0.34 205 205
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.048 0.028 -10000 0 -10000 0 0
INPP5D -0.019 0.064 -10000 0 -0.33 32 32
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.017 0.14 -10000 0 -0.68 36 36
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0 0.12 -10000 0 -0.59 34 34
p62DOK/RasGAP 0.04 0.038 -10000 0 -0.48 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.063 -10000 0 -0.33 32 32
GRB2 0.023 0.01 0.26 1 -10000 0 1
EIF4EBP1 -0.02 0.091 0.31 2 -0.5 1 3
PTPRA 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.022 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.008 0.055 -10000 0 -0.28 24 24
Insulin Receptor/Insulin/IRS1 0.029 0.076 -10000 0 -0.35 33 33
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.06 0.072 -10000 0 -0.32 14 14
Regulation of p38-alpha and p38-beta

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.023 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.009 0.089 0.26 1 -0.59 19 20
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.021 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.098 0.13 -10000 0 -0.24 362 362
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.021 -10000 0 -0.59 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
FYN 0.022 0.021 -10000 0 -0.59 1 1
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.023 0.01 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.04 0.096 -10000 0 -0.34 59 59
PRKG1 -0.003 0.12 -10000 0 -0.59 39 39
DUSP8 0.021 0.036 -10000 0 -0.59 3 3
PGK/cGMP/p38 alpha -0.015 0.13 -10000 0 -0.35 74 74
apoptosis -0.039 0.092 -10000 0 -0.33 59 59
RAL/GTP 0.031 0.007 -10000 0 -10000 0 0
LYN 0.021 0.008 -10000 0 -10000 0 0
DUSP1 -0.051 0.2 -10000 0 -0.59 109 109
PAK1 0.022 0.018 0.26 4 -10000 0 4
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.051 0.024 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.009 0.26 1 -10000 0 1
RAC1-CDC42/GTP 0.03 0.008 -10000 0 -10000 0 0
MAPK11 -0.011 0.13 0.3 5 -0.37 52 57
BLK 0.048 0.088 0.26 114 -0.59 2 116
HCK 0.027 0.028 0.26 12 -10000 0 12
MAP2K3 0.022 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.02 0.012 0.26 1 -10000 0 1
TRAF6/MEKK3 0.027 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.006 0.13 0.31 4 -0.38 56 60
positive regulation of innate immune response -0.013 0.15 0.34 5 -0.44 51 56
LCK 0.025 0.075 0.26 28 -0.59 9 37
p38alpha-beta/MKP7 -0.005 0.14 0.37 3 -0.44 44 47
p38alpha-beta/MKP5 -0.005 0.14 0.43 2 -0.44 41 43
PGK/cGMP -0.002 0.092 -10000 0 -0.44 39 39
PAK2 0.023 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.039 0.17 0.37 3 -0.44 76 79
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.023 0.004 -10000 0 -10000 0 0
PAK3 -0.26 0.31 -10000 0 -0.59 414 414
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.058 0.14 0.51 6 -0.59 1 7
RAD9A 0.022 0.006 -10000 0 -10000 0 0
AP1 -0.1 0.22 -10000 0 -0.44 264 264
IFNAR2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.001 0.089 -10000 0 -0.25 46 46
ER alpha/Oestrogen -0.022 0.17 0.18 112 -0.42 125 237
NFX1/SIN3/HDAC complex 0.023 0.058 0.25 1 -0.32 13 14
EGF -0.089 0.24 0.27 2 -0.59 167 169
SMG5 0.02 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.04 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.055 0.12 0.44 3 -0.52 1 4
SAP18 0.023 0.007 -10000 0 -10000 0 0
MRN complex 0.035 0.022 -10000 0 -10000 0 0
WT1 0.15 0.12 0.27 461 -10000 0 461
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.006 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.045 0.1 -10000 0 -0.51 1 1
Mad/Max 0.04 0.015 -10000 0 -10000 0 0
TERT 0.058 0.14 0.53 5 -0.6 1 6
CCND1 0.082 0.17 0.54 20 -1.1 3 23
MAX 0.026 0.007 -10000 0 -10000 0 0
RBBP7 0.026 0.022 0.27 7 -10000 0 7
RBBP4 0.024 0.005 -10000 0 -10000 0 0
TERF2 0.02 0.013 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
Telomerase/911 0.039 0.053 -10000 0 -0.38 5 5
CDKN1B 0.029 0.055 -10000 0 -0.7 3 3
RAD1 0.023 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.017 0.27 4 -10000 0 4
TRF2/PARP2 0.031 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.02 0.058 -10000 0 -0.59 8 8
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.15 0.28 -10000 0 -0.59 262 262
IFN-gamma/IRF1 0.065 0.067 0.39 2 -0.33 3 5
PARP2 0.023 0.004 -10000 0 -10000 0 0
BLM 0.046 0.071 0.26 86 -10000 0 86
Telomerase 0.029 0.077 0.26 2 -0.61 4 6
IRF1 0.028 0.02 0.27 3 -0.19 3 6
ESR1 -0.028 0.23 0.27 112 -0.59 120 232
KU/TER 0.033 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.053 0.24 1 -0.32 7 8
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.054 0.24 1 -0.33 7 8
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.028 0.013 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -10000 0 0
SMAD3 0.003 0.013 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.026 0.009 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.021 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.06 0.13 0.51 1 -0.62 4 5
NR2F2 0.011 0.041 -10000 0 -0.6 3 3
MAPK3 0.006 0.021 -10000 0 -10000 0 0
MAPK1 0.006 0.021 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.02 0.014 0.26 1 -10000 0 1
NFKB1 0.023 0.004 -10000 0 -10000 0 0
HNRNPC 0.023 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.016 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.59 312 312
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.21 0.26 -10000 0 -0.47 431 431
MYC 0.007 0.086 -10000 0 -0.59 18 18
IL2 0.029 0.027 0.27 8 -10000 0 8
KU 0.033 0.009 -10000 0 -10000 0 0
RAD50 0.023 0.004 -10000 0 -10000 0 0
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
TGFB1 0.02 0.014 0.26 1 -10000 0 1
TRF2/BLM 0.044 0.048 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.067 0.13 0.47 4 -0.56 1 5
SP1/HDAC2 0.046 0.027 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.042 0.1 -10000 0 -0.5 1 1
Smad3/Myc 0.006 0.057 -10000 0 -0.38 18 18
911 complex 0.043 0.016 -10000 0 -10000 0 0
IFNG 0.06 0.087 0.27 127 -10000 0 127
Telomerase/PinX1 0.034 0.096 -10000 0 -0.5 1 1
Telomerase/AKT1/mTOR/p70S6K 0.027 0.1 0.34 2 -0.58 11 13
SIN3B 0.024 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.039 0.094 -10000 0 -10000 0 0
response to DNA damage stimulus -0.002 0.026 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.045 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.044 0.1 -10000 0 -0.51 1 1
E2F1 0.099 0.11 0.27 267 -10000 0 267
ZNFX1 0.023 0.007 -10000 0 -10000 0 0
PIF1 0.066 0.093 0.26 160 -10000 0 160
NCL 0.023 0.004 -10000 0 -10000 0 0
DKC1 0.024 0.012 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.021 0.13 0.29 17 -0.39 36 53
IKBKB 0.024 0.089 0.34 5 -0.32 7 12
AKT1 0.038 0.1 0.25 82 -0.24 17 99
IKBKG 0.028 0.074 0.32 5 -0.27 4 9
CALM1 0.001 0.1 0.26 1 -0.35 40 41
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.021 0.16 0.33 18 -0.53 40 58
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.1 -10000 0 -0.36 43 43
DOK1 0.024 0.008 0.26 1 -10000 0 1
AP-1 -0.026 0.1 0.26 6 -0.26 41 47
LYN 0.021 0.008 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
BCR complex -0.001 0.16 0.38 13 -0.47 81 94
CD22 -0.015 0.14 0.3 15 -0.47 51 66
CAMK2G 0.002 0.098 0.26 5 -0.42 17 22
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.001 0.091 -10000 0 -0.35 46 46
GO:0007205 0.001 0.11 -10000 0 -0.36 43 43
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0.001 0.1 0.26 1 -0.38 31 32
NFATC1 0.03 0.14 0.29 24 -0.45 29 53
B-cell antigen/BCR complex -0.001 0.16 0.38 13 -0.47 81 94
PAG1/CSK 0.029 0.017 -10000 0 -10000 0 0
NFKBIB 0.025 0.046 0.17 9 -0.13 25 34
HRAS 0.01 0.11 0.26 13 -0.36 35 48
NFKBIA 0.025 0.046 0.17 9 -0.12 21 30
NF-kappa-B/RelA/I kappa B beta 0.028 0.041 0.17 9 -10000 0 9
RasGAP/Csk 0.026 0.13 0.33 14 -0.38 60 74
mol:GDP 0.003 0.1 -10000 0 -0.34 42 42
PTEN 0.022 0.029 -10000 0 -0.59 2 2
CD79B 0.008 0.11 0.26 14 -0.59 25 39
NF-kappa-B/RelA/I kappa B alpha 0.028 0.041 0.17 9 -10000 0 9
GRB2 0.023 0.01 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.023 0.16 0.34 12 -0.5 43 55
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
mol:IP3 0.002 0.11 -10000 0 -0.37 42 42
CSK 0.023 0.004 -10000 0 -10000 0 0
FOS -0.085 0.16 -10000 0 -0.43 75 75
CHUK 0.025 0.081 0.32 5 -0.32 9 14
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.017 0.099 -10000 0 -0.42 16 16
PTPN6 -0.017 0.13 0.28 14 -0.59 28 42
RELA 0.024 0.004 -10000 0 -10000 0 0
BCL2A1 0.025 0.035 0.16 11 -10000 0 11
VAV2 0.012 0.15 0.29 13 -0.59 27 40
ubiquitin-dependent protein catabolic process 0.027 0.046 0.17 9 -0.12 25 34
BTK 0.015 0.067 -10000 0 -0.97 4 4
CD19 0.002 0.14 0.3 19 -0.46 48 67
MAP4K1 0.03 0.053 0.26 31 -0.59 2 33
CD72 0.029 0.043 0.26 22 -0.59 1 23
PAG1 0.02 0.015 0.26 2 -10000 0 2
MAPK14 0.023 0.14 0.32 20 -0.45 38 58
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0.002 0.11 0.25 1 -0.38 44 45
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0 0.14 0.28 3 -0.43 62 65
RAF1 0.009 0.1 0.26 12 -0.41 19 31
RasGAP/p62DOK/SHIP 0.026 0.12 0.3 13 -0.37 60 73
CD79A -0.007 0.18 0.26 60 -0.59 68 128
re-entry into mitotic cell cycle -0.025 0.099 0.26 6 -0.26 40 46
RASA1 0.023 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0.099 0.28 20 -0.38 12 32
MAPK1 0.009 0.093 0.27 8 -0.37 15 23
CD72/SHP1 0.026 0.15 0.37 20 -0.56 28 48
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.022 0.15 0.32 22 -0.45 39 61
actin cytoskeleton organization 0.029 0.14 0.31 24 -0.51 26 50
NF-kappa-B/RelA 0.058 0.078 0.3 9 -0.21 2 11
Calcineurin 0.017 0.094 -10000 0 -0.4 14 14
PI3K -0.013 0.097 -10000 0 -0.46 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.004 0.12 -10000 0 -0.4 47 47
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.009 0.2 0.45 7 -0.71 46 53
DAPP1 -0.02 0.21 -10000 0 -0.8 47 47
cytokine secretion 0.031 0.13 0.28 32 -0.42 29 61
mol:DAG 0.002 0.11 -10000 0 -0.37 42 42
PLCG2 0.02 0.023 0.26 1 -0.59 1 2
MAP2K1 0.009 0.1 0.28 8 -0.41 15 23
B-cell antigen/BCR complex/FcgammaRIIB 0.01 0.14 0.35 13 -0.43 61 74
mol:PI-3-4-5-P3 0.006 0.091 0.22 25 -0.34 19 44
ETS1 0.001 0.091 0.28 1 -0.4 16 17
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.029 0.13 0.33 14 -0.38 62 76
B-cell antigen/BCR complex/LYN -0.014 0.14 0.28 13 -0.47 56 69
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.021 0.14 0.3 20 -0.55 26 46
B-cell antigen/BCR complex/LYN/SYK 0.01 0.14 0.37 16 -0.46 50 66
CARD11 0.003 0.11 0.27 6 -0.37 38 44
FCGR2B 0.018 0.037 0.26 1 -0.59 3 4
PPP3CA 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.023 0.004 -10000 0 -10000 0 0
IKK complex 0.028 0.05 0.15 46 -0.13 2 48
PTPRC 0.023 0.037 0.26 13 -0.59 1 14
PDPK1 0.022 0.084 0.21 64 -0.23 17 81
PPP3CB 0.024 0.003 -10000 0 -10000 0 0
PPP3CC 0.019 0.01 -10000 0 -10000 0 0
POU2F2 0.022 0.032 0.17 9 -10000 0 9
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.008 -10000 0 -10000 0 0
ELF1 0.031 0.05 -10000 0 -0.36 7 7
CCNA2 0.12 0.12 0.26 367 -10000 0 367
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.031 0.26 15 -10000 0 15
PIK3R1 0.023 0.021 -10000 0 -0.59 1 1
JAK1 0.024 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.05 0.099 0.32 17 -0.53 8 25
SHC1 0.02 0.009 -10000 0 -10000 0 0
SP1 0.026 0.033 -10000 0 -0.36 6 6
IL2RA 0.022 0.11 0.3 57 -0.76 10 67
IL2RB 0.033 0.048 0.26 36 -10000 0 36
SOS1 0.024 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.067 0.26 37 -0.59 5 42
G1/S transition of mitotic cell cycle 0.052 0.12 -10000 0 -0.77 11 11
PTPN11 0.024 0.003 -10000 0 -10000 0 0
CCND2 0.008 0.074 0.44 1 -0.8 7 8
LCK 0.025 0.075 0.26 28 -0.59 9 37
GRB2 0.023 0.01 0.26 1 -10000 0 1
IL2 0.023 0.024 0.26 8 -10000 0 8
CDK6 0.021 0.043 0.26 2 -0.59 4 6
CCND3 0.049 0.099 0.39 9 -0.64 3 12
TCGA08_retinoblastoma

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
CDKN2B 0.024 0.015 0.27 1 -10000 0 1
CDKN2C 0.014 0.029 -10000 0 -0.57 1 1
CDKN2A 0.059 0.086 0.26 134 -10000 0 134
CCND2 -0.016 0.037 0.18 1 -0.24 10 11
RB1 0.015 0.048 0.29 11 -0.24 7 18
CDK4 -0.017 0.044 0.21 1 -0.31 9 10
CDK6 -0.017 0.04 0.2 1 -0.22 15 16
G1/S progression -0.009 0.059 0.19 35 -0.28 11 46
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.016 0.17 0.29 5 -0.41 119 124
AKT1 0.024 0.01 -10000 0 -10000 0 0
GSC -0.039 0.29 -10000 0 -1.4 40 40
NKX2-5 0.054 0.083 0.27 120 -10000 0 120
muscle cell differentiation -0.026 0.063 0.35 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.057 0.072 -10000 0 -10000 0 0
SMAD4 0.009 0.047 -10000 0 -10000 0 0
CBFB 0.021 0.008 -10000 0 -10000 0 0
SAP18 0.022 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.21 0.27 1 -0.38 342 343
SMAD3/SMAD4/VDR 0.049 0.063 -10000 0 -0.36 1 1
MYC 0.004 0.086 -10000 0 -0.59 18 18
CDKN2B -0.045 0.17 -10000 0 -0.94 15 15
AP1 -0.06 0.17 -10000 0 -0.32 227 227
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.008 0.086 -10000 0 -0.36 26 26
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.058 -10000 0 -0.33 12 12
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.039 0.077 0.27 82 -10000 0 82
SMAD3/SMAD4/GR 0.022 0.07 -10000 0 -0.41 7 7
GATA3 0.012 0.12 0.27 25 -0.57 31 56
SKI/SIN3/HDAC complex/NCoR1 0.005 0.076 -10000 0 -0.35 28 28
MEF2C/TIF2 0.029 0.08 0.31 3 -0.35 6 9
endothelial cell migration -0.028 0.087 0.51 13 -10000 0 13
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.025 0.021 0.26 7 -10000 0 7
RBBP4 0.023 0.004 -10000 0 -10000 0 0
RUNX2 0.026 0.027 0.26 11 -10000 0 11
RUNX3 0.022 0.031 0.26 2 -0.59 2 4
RUNX1 0.023 0.021 -10000 0 -0.59 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.015 0.056 -10000 0 -0.59 7 7
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.016 0.067 -10000 0 -0.95 2 2
KAT2B 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.049 0.079 -10000 0 -0.27 22 22
DCP1A 0.023 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.087 -10000 0 -0.51 13 13
SMAD3/SMAD4/ATF2 0.03 0.059 -10000 0 -0.39 1 1
SMAD3/SMAD4/ATF3 -0.021 0.15 -10000 0 -0.42 102 102
SAP30 0.024 0.017 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.045 0.029 -10000 0 -10000 0 0
JUN -0.069 0.16 -10000 0 -0.32 199 199
SMAD3/SMAD4/IRF7 0.046 0.079 0.34 15 -10000 0 15
TFE3 0.028 0.009 -10000 0 -0.2 1 1
COL1A2 0.049 0.087 0.41 3 -0.52 4 7
mesenchymal cell differentiation -0.032 0.059 -10000 0 -10000 0 0
DLX1 0.053 0.11 0.26 134 -0.59 9 143
TCF3 0.023 0.005 -10000 0 -10000 0 0
FOS -0.15 0.28 -10000 0 -0.59 264 264
SMAD3/SMAD4/Max 0.025 0.059 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.044 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.006 -10000 0 -10000 0 0
LAMC1 0.01 0.039 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.056 -10000 0 -10000 0 0
IRF7 0.043 0.065 0.28 62 -10000 0 62
ESR1 -0.035 0.23 0.26 112 -0.59 120 232
HNF4A 0.022 0.028 0.26 11 -10000 0 11
MEF2C 0.051 0.094 0.4 10 -0.45 2 12
SMAD2-3/SMAD4 0.03 0.066 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.026 -10000 0 -0.38 1 1
IGHV3OR16-13 0.004 0.042 -10000 0 -0.35 12 12
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.023 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.026 0.26 10 -10000 0 10
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.022 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.039 0.062 -10000 0 -0.48 1 1
MSG1/HSC70 -0.16 0.23 -10000 0 -0.44 361 361
SMAD2 0.02 0.032 -10000 0 -0.16 11 11
SMAD3 0.012 0.042 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.04 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 0.021 0.049 0.25 8 -0.34 2 10
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 0.009 0.081 -10000 0 -0.59 16 16
NCOA1 0.023 0.021 -10000 0 -0.59 1 1
MYOD/E2A 0.031 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.075 0.064 -10000 0 -10000 0 0
IFNB1 0.019 0.072 0.33 27 -10000 0 27
SMAD3/SMAD4/MEF2C 0.067 0.088 -10000 0 -0.43 2 2
CITED1 -0.22 0.3 0.26 11 -0.59 360 371
SMAD2-3/SMAD4/ARC105 0.038 0.067 -10000 0 -10000 0 0
RBL1 0.024 0.009 0.26 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.064 -10000 0 -0.4 12 12
RUNX1-3/PEBPB2 0.04 0.035 -10000 0 -0.54 2 2
SMAD7 -0.039 0.15 -10000 0 -0.46 20 20
MYC/MIZ-1 0.014 0.067 -10000 0 -0.44 18 18
SMAD3/SMAD4 0.029 0.074 0.3 22 -0.36 3 25
IL10 0.005 0.085 0.32 3 -0.38 25 28
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.023 0.006 -10000 0 -10000 0 0
CDK2 0.025 0.007 -10000 0 -10000 0 0
IL5 0.002 0.087 0.28 6 -0.37 29 35
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.05 0.19 -10000 0 -0.59 103 103
SMAD3/SMAD4/SP1 0.045 0.064 -10000 0 -10000 0 0
FOXG1 0.017 0.068 0.26 59 -10000 0 59
FOXO3 0.01 0.018 -10000 0 -0.44 1 1
FOXO1 0.01 0.023 -10000 0 -0.44 2 2
FOXO4 0.012 0.009 -10000 0 -10000 0 0
heart looping 0.051 0.093 0.4 10 -0.44 2 12
CEBPB 0.022 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.05 0.091 0.29 3 -0.4 9 12
MYOD1 0.021 0.027 0.26 11 -10000 0 11
SMAD3/SMAD4/HNF4 0.03 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.026 0.1 -10000 0 -0.41 31 31
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.026 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.041 0.069 -10000 0 -0.51 2 2
SMAD3/SMAD4/SP1-3 0.056 0.066 -10000 0 -10000 0 0
MED15 0.023 0.005 -10000 0 -10000 0 0
SP1 0.031 0.012 -10000 0 -10000 0 0
SIN3B 0.023 0.004 -10000 0 -10000 0 0
SIN3A 0.023 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.074 0.093 0.35 11 -0.39 1 12
ITGB5 0.014 0.042 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.012 0.062 -10000 0 -0.35 11 11
SMAD3/SMAD4/AR -0.017 0.15 -10000 0 -0.41 100 100
AR -0.046 0.2 0.26 1 -0.59 102 103
negative regulation of cell growth -0.002 0.083 -10000 0 -0.32 17 17
SMAD3/SMAD4/MYOD 0.029 0.059 -10000 0 -10000 0 0
E2F5 0.021 0.022 0.26 6 -10000 0 6
E2F4 0.021 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.063 0.074 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.051 -10000 0 -0.34 10 10
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.045 0.18 -10000 0 -0.32 220 220
SMAD3/SMAD4/RUNX2 0.033 0.06 -10000 0 -10000 0 0
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.023 0.021 -10000 0 -0.59 1 1
IL27-mediated signaling events

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.012 0.26 1 -10000 0 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.019 0.12 0.56 3 -0.53 3 6
IL27/IL27R/JAK1 0.048 0.16 0.73 4 -0.8 4 8
TBX21 0.004 0.17 0.48 12 -0.55 33 45
IL12B 0.073 0.099 0.27 175 -10000 0 175
IL12A -0.015 0.1 0.15 13 -0.44 49 62
IL6ST -0.02 0.16 -10000 0 -0.59 64 64
IL27RA/JAK1 0.022 0.073 0.65 1 -1.2 2 3
IL27 0.045 0.075 0.28 83 -10000 0 83
TYK2 0.03 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.1 0.16 0.76 2 -0.55 8 10
T-helper 2 cell differentiation -0.019 0.12 0.56 3 -0.53 3 6
T cell proliferation during immune response -0.019 0.12 0.56 3 -0.53 3 6
MAPKKK cascade 0.019 0.12 0.53 3 -0.56 3 6
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.027 0.038 0.27 19 -10000 0 19
IL12RB1 0.034 0.052 0.28 34 -0.59 1 35
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.014 0.19 0.46 28 -0.54 45 73
IL27/IL27R/JAK2/TYK2 0.019 0.12 0.53 3 -0.56 3 6
positive regulation of T cell mediated cytotoxicity 0.019 0.12 0.53 3 -0.56 3 6
STAT1 (dimer) 0.044 0.2 0.64 21 -0.67 14 35
JAK2 0.027 0.013 -10000 0 -10000 0 0
JAK1 0.022 0.012 -10000 0 -10000 0 0
STAT2 (dimer) 0.03 0.11 0.51 2 -0.54 3 5
T cell proliferation -0.094 0.19 0.37 3 -0.51 49 52
IL12/IL12R/TYK2/JAK2 0.056 0.18 0.46 4 -0.74 24 28
IL17A -0.1 0.16 0.76 2 -0.55 8 10
mast cell activation -0.019 0.12 0.56 3 -0.53 3 6
IFNG 0.023 0.048 0.13 109 -0.1 4 113
T cell differentiation 0 0.006 0.024 2 -0.025 2 4
STAT3 (dimer) 0.03 0.11 0.65 1 -0.54 3 4
STAT5A (dimer) 0.028 0.12 0.51 2 -0.53 6 8
STAT4 (dimer) 0.018 0.14 0.65 1 -0.52 11 12
STAT4 0 0.12 0.26 1 -0.59 35 36
T cell activation -0.005 0.011 0.12 2 -0.11 5 7
IL27R/JAK2/TYK2 0.028 0.12 -10000 0 -1.2 2 2
GATA3 -0.028 0.27 0.61 31 -1.3 30 61
IL18 0.009 0.021 0.14 21 -10000 0 21
positive regulation of mast cell cytokine production 0.029 0.11 0.65 1 -0.53 3 4
IL27/EBI3 0.05 0.073 0.26 37 -0.4 5 42
IL27RA 0.01 0.076 0.75 1 -1.3 2 3
IL6 -0.19 0.29 0.26 1 -0.59 318 319
STAT5A 0.02 0.046 -10000 0 -0.59 5 5
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.015 0.044 -10000 0 -10000 0 0
IL1B 0.002 0.047 0.14 3 -0.44 10 13
EBI3 0.024 0.055 0.27 10 -0.59 5 15
TNF 0.004 0.051 0.14 19 -0.44 10 29
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.049 0.067 0.3 2 -0.31 17 19
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.081 0.35 9 -0.34 2 11
alphaV/beta3 Integrin/Osteopontin/Src 0.084 0.076 0.24 17 -10000 0 17
AP1 -0.038 0.18 0.35 1 -0.52 23 24
ILK 0.036 0.069 0.3 1 -0.33 17 18
bone resorption 0.027 0.072 0.28 1 -0.41 7 8
PTK2B 0.02 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.071 0.088 0.31 7 -0.31 14 21
ITGAV 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.05 -10000 0 -0.44 10 10
alphaV/beta3 Integrin/Osteopontin 0.084 0.095 0.34 5 -0.36 17 22
MAP3K1 0.036 0.07 0.26 14 -0.33 17 31
JUN 0.018 0.058 -10000 0 -0.59 8 8
MAPK3 0.026 0.067 0.28 12 -0.32 13 25
MAPK1 0.027 0.068 0.28 13 -0.32 13 26
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
NFKB1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.072 0.26 15 -0.34 18 33
ITGB3 0.015 0.085 0.27 4 -0.59 17 21
NFKBIA 0.023 0.067 0.32 6 -0.32 12 18
FOS -0.16 0.28 -10000 0 -0.59 262 262
CD44 0.023 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.027 0.1 0.47 6 -0.55 2 8
NF kappa B1 p50/RelA 0.069 0.074 0.37 5 -10000 0 5
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.03 0.066 0.24 1 -0.43 17 18
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.036 0.069 0.26 13 -0.33 17 30
VAV3 0.015 0.074 0.26 17 -0.31 22 39
MAP3K14 0.038 0.07 0.27 11 -0.33 17 28
ROCK2 0.017 0.064 -10000 0 -0.59 10 10
SPP1 0.092 0.11 0.27 247 -10000 0 247
RAC1 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.033 0.066 0.3 3 -0.3 16 19
MMP2 -0.055 0.14 0.35 3 -0.5 21 24
TCGA08_p53

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
CDKN2A 0.025 0.048 0.14 134 -10000 0 134
TP53 0.009 0.019 -10000 0 -0.19 2 2
Senescence 0.009 0.019 -10000 0 -0.19 2 2
Apoptosis 0.009 0.019 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.01 0.062 0.29 28 -10000 0 28
MDM4 0.02 0.009 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.28 0.3 -10000 0 -0.59 434 434
CLTC 0.026 0.07 0.28 1 -0.44 11 12
calcium ion-dependent exocytosis 0.009 0.024 -10000 0 -0.26 2 2
Dynamin 2/GTP 0.021 0.013 -10000 0 -10000 0 0
EXOC4 0.023 0.004 -10000 0 -10000 0 0
CD59 0.016 0.047 -10000 0 -0.34 9 9
CPE 0.005 0.05 -10000 0 -0.38 15 15
CTNNB1 0.023 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.017 -10000 0 -10000 0 0
CTNND1 0.008 0.058 0.19 80 -10000 0 80
DNM2 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.046 0.22 2 -0.31 9 11
TSHR -0.005 0.077 0.15 3 -0.38 36 39
INS -0.002 0.091 -10000 0 -0.48 29 29
BIN1 0.018 0.058 -10000 0 -0.59 8 8
mol:Choline 0.011 0.017 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.016 0.15 11 -10000 0 11
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.023 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.013 -10000 0 -10000 0 0
JUP 0.017 0.04 0.23 1 -0.33 6 7
ASAP2/amphiphysin II 0.04 0.038 -10000 0 -0.35 7 7
ARF6/GTP 0.017 0.003 -10000 0 -10000 0 0
CDH1 0.008 0.057 -10000 0 -0.38 8 8
clathrin-independent pinocytosis 0.017 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.017 0.003 -10000 0 -10000 0 0
EXOC2 0.026 0.028 0.26 12 -10000 0 12
substrate adhesion-dependent cell spreading 0.016 0.04 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.036 0.067 0.33 9 -10000 0 9
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.015 0.026 -10000 0 -0.22 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.045 -10000 0 -0.34 9 9
clathrin heavy chain/ACAP1 0.024 0.066 0.28 6 -0.36 11 17
JIP4/KLC1 0.04 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.018 0.035 -10000 0 -0.34 4 4
RALA/GTP 0.017 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.01 -10000 0 -10000 0 0
receptor recycling 0.017 0.003 -10000 0 -10000 0 0
CTNNA1 0.009 0.059 0.2 36 -10000 0 36
NME1 0.012 0.016 0.15 11 -10000 0 11
clathrin coat assembly 0.028 0.072 0.28 3 -0.43 11 14
IL2RA 0.019 0.056 -10000 0 -0.32 13 13
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.15 -10000 0 -0.28 358 358
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.025 -10000 0 -0.31 5 5
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.023 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.042 0.19 1 -0.33 8 9
SDC1 0.02 0.045 -10000 0 -0.33 8 8
ARF6/GDP 0.021 0.013 -10000 0 -10000 0 0
EXOC7 0.022 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.039 0.07 -10000 0 -0.34 9 9
mol:Phosphatidic acid 0.011 0.017 -10000 0 -10000 0 0
endocytosis -0.039 0.037 0.34 7 -10000 0 7
SCAMP2 0.023 0.004 -10000 0 -10000 0 0
ADRB2 -0.045 0.15 0.26 1 -0.32 163 164
EXOC3 0.023 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.021 -10000 0 -0.59 1 1
Dynamin 2/GDP 0.025 0.016 -10000 0 -10000 0 0
KLC1 0.023 0.004 -10000 0 -10000 0 0
AVPR2 -0.096 0.16 0.28 4 -0.3 281 285
RALA 0.023 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.034 0.068 0.32 2 -0.36 5 7
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0.007 -10000 0 -0.19 1 1
MAP4K4 0.002 0.063 -10000 0 -0.39 6 6
BAG4 0.019 0.022 -10000 0 -0.59 1 1
PKC zeta/ceramide -0.003 0.055 -10000 0 -0.25 16 16
NFKBIA 0.023 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.039 0.26 10 -0.59 2 12
BAX 0 0.043 -10000 0 -0.35 10 10
RIPK1 0.023 0.004 -10000 0 -10000 0 0
AKT1 0.001 0.065 0.68 8 -10000 0 8
BAD -0.016 0.049 0.19 3 -0.3 8 11
SMPD1 0.014 0.059 0.2 12 -0.25 16 28
RB1 -0.017 0.047 -10000 0 -0.28 10 10
FADD/Caspase 8 0.025 0.089 0.28 4 -0.39 8 12
MAP2K4 -0.017 0.045 0.18 1 -0.3 7 8
NSMAF 0.021 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.057 0.2 24 -0.31 6 30
EGF -0.09 0.24 0.26 2 -0.59 167 169
mol:ceramide -0.016 0.051 0.15 1 -0.26 15 16
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.011 -10000 0 -0.19 1 1
ASAH1 0.021 0.017 0.26 3 -10000 0 3
negative regulation of cell cycle -0.017 0.047 -10000 0 -0.27 10 10
cell proliferation -0.047 0.13 0.28 1 -0.28 171 172
BID -0.023 0.17 -10000 0 -0.65 54 54
MAP3K1 -0.017 0.047 -10000 0 -0.24 15 15
EIF2A -0.015 0.05 0.29 3 -0.25 6 9
TRADD 0.021 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.009 0.055 0.28 3 -0.3 6 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.06 0.28 3 -0.35 4 7
Cathepsin D/ceramide 0.004 0.061 0.18 32 -0.24 14 46
FADD 0.004 0.063 0.22 10 -0.3 15 25
KSR1 -0.011 0.056 0.2 19 -0.25 13 32
MAPK8 -0.014 0.057 -10000 0 -0.28 13 13
PRKRA -0.016 0.049 0.2 2 -0.27 11 13
PDGFA 0.023 0.005 -10000 0 -10000 0 0
TRAF2 0.024 0.012 0.26 2 -10000 0 2
IGF1 -0.1 0.25 -10000 0 -0.59 185 185
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.016 0.051 0.15 1 -0.25 15 16
CTSD 0.033 0.047 0.26 35 -10000 0 35
regulation of nitric oxide biosynthetic process 0.034 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.049 0.14 0.3 1 -0.3 169 170
PRKCD 0.023 0.009 0.26 1 -10000 0 1
PRKCZ 0.022 0.021 -10000 0 -0.59 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.011 -10000 0 -0.19 1 1
RelA/NF kappa B1 0.034 0.007 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.021 -10000 0 -0.59 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.013 0.052 -10000 0 -0.37 8 8
TNFR1A/BAG4/TNF-alpha 0.035 0.053 -10000 0 -0.37 10 10
mol:Sphingosine-1-phosphate 0.01 0.007 -10000 0 -0.19 1 1
MAP2K1 -0.011 0.055 0.26 4 -0.31 5 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
CYCS -0.001 0.051 0.18 16 -0.25 9 25
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.023 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.022 -10000 0 -0.44 1 1
EIF2AK2 -0.018 0.045 0.18 3 -0.28 7 10
TNF-alpha/TNFR1A/FAN 0.039 0.046 -10000 0 -0.38 6 6
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.016 0.076 -10000 0 -0.38 24 24
MAP2K2 -0.012 0.055 0.32 2 -0.31 5 7
SMPD3 -0.005 0.1 0.28 4 -0.29 90 94
TNF 0.022 0.074 0.26 19 -0.59 10 29
PKC zeta/PAR4 0.033 0.024 -10000 0 -0.44 2 2
mol:PHOSPHOCHOLINE 0.044 0.1 0.24 165 -0.24 2 167
NF kappa B1/RelA/I kappa B alpha 0.063 0.029 -10000 0 -0.33 2 2
AIFM1 -0.002 0.051 0.18 17 -0.23 11 28
BCL2 0.005 0.1 -10000 0 -0.59 26 26
Caspase cascade in apoptosis

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
TOP1 0.007 0.11 0.24 1 -0.42 36 37
ACTA1 0.012 0.11 0.24 5 -0.5 26 31
NUMA1 0.002 0.11 -10000 0 -0.42 35 35
SPTAN1 -0.003 0.11 0.27 5 -0.5 26 31
LIMK1 -0.002 0.11 0.27 4 -0.5 26 30
BIRC3 0.023 0.039 0.26 10 -0.59 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.024 0.014 0.26 3 -10000 0 3
CASP10 -0.011 0.093 0.22 10 -0.46 27 37
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.001 0.12 0.24 1 -0.47 36 37
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.003 0.11 0.27 5 -0.49 26 31
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.008 0.12 0.28 3 -0.49 34 37
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.011 0.14 -10000 0 -0.68 28 28
BID 0.003 0.053 0.19 3 -0.26 26 29
MAP3K1 -0.006 0.1 -10000 0 -0.39 48 48
TRADD 0.021 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.001 0.11 0.25 4 -0.5 26 30
CASP9 0.023 0.005 -10000 0 -10000 0 0
DNA repair -0.016 0.043 0.25 4 -0.21 3 7
neuron apoptosis 0.005 0.11 -10000 0 -0.71 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.002 0.11 -10000 0 -0.5 27 27
APAF1 0.024 0.002 -10000 0 -10000 0 0
CASP6 -0.003 0.16 -10000 0 -0.92 22 22
TRAF2 0.024 0.012 0.26 2 -10000 0 2
ICAD/CAD -0.005 0.1 -10000 0 -0.5 24 24
CASP7 0.001 0.06 0.26 4 -0.42 3 7
KRT18 0.016 0.067 -10000 0 -0.65 6 6
apoptosis 0.001 0.12 0.32 2 -0.47 36 38
DFFA -0.004 0.11 0.24 2 -0.5 26 28
DFFB -0.004 0.11 0.24 2 -0.5 26 28
PARP1 0.016 0.043 0.21 3 -0.25 4 7
actin filament polymerization 0.001 0.11 0.47 27 -0.3 6 33
TNF 0.022 0.074 0.26 19 -0.59 10 29
CYCS 0.005 0.05 0.21 5 -0.23 17 22
SATB1 -0.01 0.16 -10000 0 -0.79 27 27
SLK -0.003 0.11 0.26 3 -0.5 26 29
p15 BID/BAX 0.012 0.061 -10000 0 -0.24 30 30
CASP2 0.001 0.067 0.23 7 -0.3 18 25
JNK cascade 0.006 0.099 0.38 48 -10000 0 48
CASP3 -0.001 0.11 0.27 2 -0.53 26 28
LMNB2 -0.002 0.14 0.3 3 -0.52 40 43
RIPK1 0.023 0.004 -10000 0 -10000 0 0
CASP4 0.022 0.007 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.056 0.033 -10000 0 -0.35 2 2
negative regulation of DNA binding 0.011 0.14 -10000 0 -0.67 28 28
stress fiber formation -0.003 0.1 0.26 3 -0.49 26 29
GZMB 0.01 0.11 0.29 10 -0.52 26 36
CASP1 0.011 0.013 -10000 0 -0.36 1 1
LMNB1 0.02 0.12 0.3 7 -0.53 23 30
APP 0.005 0.11 -10000 0 -0.72 18 18
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.001 -10000 0 -10000 0 0
VIM 0.003 0.12 0.3 4 -0.46 40 44
LMNA 0.007 0.085 0.32 2 -0.38 21 23
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.071 -10000 0 -0.29 27 27
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.002 0.11 0.27 3 -0.5 26 29
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.61 31 31
nuclear fragmentation during apoptosis 0.002 0.11 -10000 0 -0.42 35 35
CFL2 -0.002 0.11 0.3 6 -0.48 27 33
GAS2 -0.03 0.14 0.27 5 -0.39 84 89
positive regulation of apoptosis 0.013 0.12 0.28 6 -0.51 28 34
PRF1 0.015 0.082 0.26 7 -0.59 15 22
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.01 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.029 0.018 -10000 0 -10000 0 0
CDKN1B 0.01 0.058 -10000 0 -0.34 15 15
CDKN1A 0.008 0.063 -10000 0 -0.35 18 18
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
FOXO3 0.011 0.061 -10000 0 -0.36 14 14
AKT1 0.005 0.059 -10000 0 -0.37 17 17
BAD 0.023 0.005 -10000 0 -10000 0 0
AKT3 0.006 0.035 -10000 0 -0.36 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.062 -10000 0 -0.34 19 19
AKT1/ASK1 0.031 0.069 -10000 0 -0.32 19 19
BAD/YWHAZ 0.036 0.022 -10000 0 -10000 0 0
RICTOR 0.023 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.03 0.067 0.32 19 -10000 0 19
TSC1 0.01 0.053 -10000 0 -0.34 12 12
YWHAZ 0.018 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.073 0.27 1 -0.35 18 19
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.062 -10000 0 -0.35 19 19
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.006 0.057 0.32 1 -0.33 17 18
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.004 0.005 -10000 0 -10000 0 0
MAP3K5 0.022 0.021 -10000 0 -0.59 1 1
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.025 0.079 0.31 19 -0.25 4 23
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.064 -10000 0 -0.35 17 17
CASP9 0.011 0.047 -10000 0 -0.32 11 11
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.035 0.075 0.3 6 -0.41 6 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.017 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.061 0.25 3 -0.48 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.054 -10000 0 -0.32 19 19
CHUK 0.009 0.057 -10000 0 -0.33 16 16
BAD/BCL-XL 0.036 0.071 0.29 1 -0.58 3 4
mTORC2 0.03 0.006 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.031 0.1 0.32 6 -0.42 22 28
PDPK1 0.022 0.006 -10000 0 -10000 0 0
MDM2 0.011 0.067 0.27 2 -0.34 19 21
MAPKKK cascade -0.035 0.072 0.34 18 -0.26 1 19
MDM2/Cbp/p300 0.042 0.076 0.34 4 -0.56 3 7
TSC1/TSC2 0.013 0.07 0.26 31 -0.59 3 34
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.072 0.32 4 -0.53 3 7
glucose import -0.16 0.16 0.21 3 -0.32 430 433
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.051 -10000 0 -0.41 4 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.16 0.16 -10000 0 -0.33 430 430
GSK3A 0.009 0.062 -10000 0 -0.35 17 17
FOXO1 0.011 0.046 -10000 0 -0.35 8 8
GSK3B 0.008 0.062 -10000 0 -0.35 18 18
SFN 0.02 0.071 0.26 14 -0.59 10 24
G1/S transition of mitotic cell cycle 0.013 0.067 0.31 3 -0.43 7 10
p27Kip1/14-3-3 family 0.018 0.052 0.38 1 -0.46 3 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.023 0.004 -10000 0 -10000 0 0
CREBBP 0.022 0.006 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.088 -10000 0 -0.64 6 6
oxygen homeostasis 0.012 0.013 -10000 0 -10000 0 0
TCEB2 0.024 0.024 0.26 8 -10000 0 8
TCEB1 0.02 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.088 0.082 0.36 5 -0.32 1 6
EPO 0.16 0.17 0.53 70 -0.51 2 72
FIH (dimer) 0.032 0.019 -10000 0 -10000 0 0
APEX1 0.033 0.024 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.51 33 -0.5 4 37
FLT1 -0.011 0.16 -10000 0 -0.74 18 18
ADORA2A 0.16 0.17 0.5 74 -0.47 5 79
germ cell development 0.14 0.15 0.5 38 -0.5 3 41
SLC11A2 0.14 0.15 0.49 30 -0.5 4 34
BHLHE40 0.14 0.15 0.52 18 -0.58 3 21
HIF1AN 0.032 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.12 0.41 51 -0.37 1 52
ETS1 0.027 0.023 -10000 0 -0.61 1 1
CITED2 0.017 0.082 -10000 0 -0.68 3 3
KDR -0.006 0.15 -10000 0 -0.67 21 21
PGK1 0.14 0.15 0.49 35 -0.5 4 39
SIRT1 0.025 0.004 -10000 0 -10000 0 0
response to hypoxia 0.002 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.17 0.6 15 -0.55 5 20
EPAS1 0.074 0.085 0.3 42 -0.36 1 43
SP1 0.029 0.012 -10000 0 -10000 0 0
ABCG2 0.12 0.19 0.54 16 -0.58 26 42
EFNA1 0.12 0.14 0.51 7 -0.49 5 12
FXN 0.15 0.15 0.47 46 -0.47 5 51
POU5F1 0.14 0.16 0.51 38 -0.52 3 41
neuron apoptosis -0.16 0.17 0.54 5 -0.59 15 20
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.05 0.068 0.28 67 -10000 0 67
EGLN2 0.034 0.025 0.27 4 -10000 0 4
EGLN1 0.027 0.029 -10000 0 -0.6 1 1
VHL/Elongin B/Elongin C 0.039 0.024 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.029 0.023 -10000 0 -10000 0 0
SLC2A1 0.15 0.16 0.48 52 -0.49 4 56
TWIST1 0.14 0.18 0.47 42 -0.54 26 68
ELK1 0.027 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.11 0.11 0.42 7 -0.38 1 8
VEGFA 0.14 0.15 0.55 16 -0.5 4 20
CREBBP 0.022 0.006 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.013 0.058 -10000 0 -10000 0 0
PLK1 0.27 0.19 0.53 184 -0.58 1 185
CDKN1B 0.16 0.14 0.39 59 -0.45 5 64
FOXO3 0.22 0.17 0.48 174 -0.63 1 175
KAT2B 0.059 0.03 -10000 0 -10000 0 0
FOXO1/SIRT1 0.009 0.052 -10000 0 -0.32 4 4
CAT 0.2 0.17 0.65 13 -0.89 3 16
CTNNB1 0.023 0.004 -10000 0 -10000 0 0
AKT1 0.06 0.031 -10000 0 -10000 0 0
FOXO1 0.018 0.06 -10000 0 -0.32 5 5
MAPK10 -0.017 0.12 0.2 14 -0.31 131 145
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.036 0.085 0.39 4 -0.34 1 5
response to oxidative stress 0.038 0.028 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.18 0.14 0.4 141 -0.61 1 142
XPO1 0.024 0.003 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
BCL2L11 0.068 0.082 -10000 0 -0.65 8 8
FOXO1/SKP2 0.027 0.056 -10000 0 -0.31 4 4
mol:GDP 0.038 0.028 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
GADD45A 0.14 0.13 0.48 3 -0.54 9 12
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.021 0.12 -10000 0 -0.52 28 28
MST1 0.053 0.064 0.3 1 -0.53 8 9
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.12 -10000 0 -0.45 39 39
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.032 0.034 0.2 16 -0.32 3 19
MAPK9 0.033 0.028 0.2 17 -10000 0 17
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.018 0.01 -10000 0 -10000 0 0
SIRT1 0.009 0.021 -10000 0 -10000 0 0
SOD2 0.16 0.13 0.44 21 -0.51 1 22
RBL2 0.12 0.26 0.57 2 -0.68 34 36
RAL/GDP 0.058 0.023 -10000 0 -10000 0 0
CHUK 0.06 0.03 -10000 0 -10000 0 0
Ran/GTP 0.019 0.003 -10000 0 -10000 0 0
CSNK1G2 0.023 0.005 -10000 0 -10000 0 0
RAL/GTP 0.058 0.022 -10000 0 -10000 0 0
CSNK1G1 0.023 0.004 -10000 0 -10000 0 0
FASLG 0.071 0.14 -10000 0 -1.3 7 7
SKP2 0.023 0.004 -10000 0 -10000 0 0
USP7 0.023 0.006 -10000 0 -10000 0 0
IKBKB 0.049 0.035 -10000 0 -10000 0 0
CCNB1 0.22 0.18 0.53 158 -0.58 1 159
FOXO1-3a-4/beta catenin 0.16 0.13 0.39 68 -0.38 2 70
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.056 -10000 0 -0.31 4 4
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
SGK1 0.055 0.048 -10000 0 -0.57 3 3
CSNK1G3 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.033 0.076 0.41 2 -10000 0 2
SFN 0.02 0.071 0.26 14 -0.59 10 24
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.067 0.11 0.36 1 -0.42 14 15
CREBBP 0.021 0.007 -10000 0 -10000 0 0
FBXO32 0.25 0.22 0.62 110 -1.2 3 113
BCL6 0.18 0.15 0.53 4 -0.82 6 10
RALB 0.024 0.004 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.098 0.26 30 -0.59 18 48
CDC42/GTP -0.006 0.099 -10000 0 -0.32 42 42
PLCG1 -0.013 0.09 -10000 0 -0.32 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.023 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.011 -10000 0 -10000 0 0
cell migration -0.006 0.097 -10000 0 -0.31 42 42
S1PR5 0.026 0.042 0.26 14 -0.59 2 16
S1PR4 0.027 0.066 0.26 28 -0.59 6 34
MAPK3 -0.01 0.086 0.27 1 -0.32 36 37
MAPK1 -0.009 0.087 -10000 0 -0.33 39 39
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.29 67 67
GNAI1 -0.006 0.13 -10000 0 -0.59 43 43
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.027 -10000 0 -0.38 2 2
RHOA 0.005 0.059 0.24 1 -0.32 6 7
S1P/S1P4/Gi -0.005 0.096 -10000 0 -0.3 74 74
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.017 0.058 -10000 0 -0.59 8 8
S1P/S1P4/G12/G13 0.042 0.043 -10000 0 -0.34 6 6
GNA12 0.023 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.091 0.3 39 -10000 0 39
GNAI2 0.023 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.027 -10000 0 -0.38 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.098 0.26 30 -0.59 18 48
RhoA/GTP -0.004 0.093 -10000 0 -0.3 39 39
negative regulation of cAMP metabolic process -0.004 0.089 -10000 0 -0.29 67 67
GNAZ 0.017 0.058 -10000 0 -0.59 8 8
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNA12 0.023 0.004 -10000 0 -10000 0 0
S1PR5 0.026 0.042 0.26 14 -0.59 2 16
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.29 67 67
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
GNAI1 -0.006 0.13 -10000 0 -0.59 43 43
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.012 0.23 2 -10000 0 2
SNTA1 0.023 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.036 0.3 7 -10000 0 7
MAPK12 -0.01 0.055 0.21 1 -0.34 23 24
CCND1 0.01 0.049 -10000 0 -0.38 6 6
p38 gamma/SNTA1 0.02 0.074 0.32 2 -0.32 21 23
MAP2K3 0.022 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint 0.004 0.077 0.21 62 -0.34 23 85
MAP2K6 -0.005 0.057 -10000 0 -0.36 23 23
MAPT -0.025 0.12 0.26 13 -0.32 101 114
MAPK13 0.01 0.012 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.025 -10000 0 -0.36 4 4
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.055 -10000 0 -0.41 12 12
forebrain development -0.046 0.21 0.35 1 -0.53 114 115
GNAO1 0.016 0.098 0.26 30 -0.59 18 48
SMO/beta Arrestin2 0.026 0.045 -10000 0 -0.44 7 7
SMO 0.016 0.055 -10000 0 -0.59 7 7
ARRB2 0.02 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.021 0.083 0.27 1 -0.5 10 11
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.003 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.055 0.023 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.59 43 43
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.037 0.2 -10000 0 -0.62 62 62
SAP30 0.024 0.017 0.26 4 -10000 0 4
mol:GDP 0.016 0.055 -10000 0 -0.59 7 7
MIM/GLI2A 0.022 0.026 0.28 4 -10000 0 4
IFT88 0.022 0.006 -10000 0 -10000 0 0
GNAI3 0.022 0.009 -10000 0 -10000 0 0
GLI2 0.007 0.066 -10000 0 -0.36 9 9
GLI3 0.01 0.087 0.29 1 -0.49 12 13
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.022 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.022 0.006 -10000 0 -10000 0 0
GNG2 0.019 0.05 -10000 0 -0.59 6 6
Gi family/GTP -0.009 0.099 -10000 0 -0.34 50 50
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.089 -10000 0 -0.45 19 19
GLI2/Su(fu) 0.011 0.081 -10000 0 -0.41 16 16
FOXA2 0.009 0.11 0.43 1 -0.69 15 16
neural tube patterning -0.046 0.21 0.35 1 -0.53 114 115
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.042 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.023 0.005 -10000 0 -10000 0 0
CSNK1G3 0.023 0.004 -10000 0 -10000 0 0
MTSS1 0.022 0.026 0.28 4 -10000 0 4
embryonic limb morphogenesis -0.046 0.21 0.35 1 -0.53 114 115
SUFU 0.015 0.024 -10000 0 -0.22 7 7
LGALS3 0.017 0.064 -10000 0 -0.59 10 10
catabolic process 0.023 0.1 0.29 1 -0.55 15 16
GLI3A/CBP -0.001 0.095 -10000 0 -0.37 56 56
KIF3A 0.023 0.004 -10000 0 -10000 0 0
GLI1 -0.048 0.22 0.35 1 -0.55 114 115
RAB23 0.023 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
IFT172 0.023 0.021 -10000 0 -0.59 1 1
RBBP7 0.026 0.021 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.059 -10000 0 -0.4 10 10
GNAZ 0.016 0.058 -10000 0 -0.59 8 8
RBBP4 0.023 0.004 -10000 0 -10000 0 0
CSNK1G1 0.023 0.004 -10000 0 -10000 0 0
PIAS1 0.023 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.016 0.07 -10000 0 -0.42 8 8
STK36 0.022 0.015 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.014 0.11 -10000 0 -0.41 36 36
PTCH1 -0.09 0.33 -10000 0 -1.1 78 78
MIM/GLI1 -0.035 0.2 -10000 0 -0.62 61 61
CREBBP -0.001 0.095 -10000 0 -0.37 56 56
Su(fu)/SIN3/HDAC complex 0.007 0.09 -10000 0 -0.43 26 26
Cellular roles of Anthrax toxin

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
ANTXR1 0.024 0.008 0.26 1 -10000 0 1
ANTXR2 0.018 0.058 -10000 0 -0.59 8 8
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.007 -10000 0 -0.074 9 9
monocyte activation 0.004 0.082 0.26 2 -0.34 43 45
MAP2K2 0 0.089 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.007 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 0.12 1 -10000 0 1
MAP2K6 -0.011 0.046 -10000 0 -0.32 19 19
CYAA -0.008 0.03 -10000 0 -0.32 8 8
MAP2K4 -0.004 0.007 -10000 0 -10000 0 0
IL1B -0.007 0.043 0.22 2 -0.27 20 22
Channel 0.026 0.036 -10000 0 -0.34 8 8
NLRP1 -0.007 0.03 -10000 0 -0.32 8 8
CALM1 0.023 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.07 -10000 0 -0.39 27 27
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.007 0.074 9 -10000 0 9
MAPK3 -0.004 0.007 -10000 0 -10000 0 0
MAPK1 -0.004 0.008 0.12 1 -10000 0 1
PGR -0.081 0.14 0.2 2 -0.32 228 230
PA/Cellular Receptors 0.028 0.04 -10000 0 -0.38 8 8
apoptosis -0.002 0.007 -10000 0 -0.074 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.034 -10000 0 -0.32 8 8
macrophage activation -0.006 0.009 0.14 1 -10000 0 1
TNF 0.022 0.074 0.26 19 -0.59 10 29
VCAM1 0.004 0.082 0.26 2 -0.35 43 45
platelet activation -0.002 0.07 -10000 0 -0.39 27 27
MAPKKK cascade -0.002 0.027 0.13 3 -0.13 7 10
IL18 -0.003 0.024 -10000 0 -0.22 7 7
negative regulation of macrophage activation -0.002 0.007 -10000 0 -0.074 9 9
LEF -0.002 0.007 -10000 0 -0.074 9 9
CASP1 -0.002 0.025 -10000 0 -0.17 14 14
mol:cAMP -0.002 0.07 -10000 0 -0.4 27 27
necrosis -0.002 0.007 -10000 0 -0.074 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.034 -10000 0 -0.32 8 8
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.022 0.029 -10000 0 -0.59 2 2
mol:S1P 0 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.013 0.097 -10000 0 -0.3 74 74
GNAO1 0.017 0.098 0.27 30 -0.59 18 48
S1P/S1P3/G12/G13 0.042 0.019 -10000 0 -10000 0 0
AKT1 0.005 0.095 -10000 0 -0.47 27 27
AKT3 -0.01 0.16 -10000 0 -0.93 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.029 -10000 0 -0.59 2 2
GNAI2 0.023 0.008 -10000 0 -10000 0 0
GNAI3 0.023 0.007 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.59 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.022 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.098 -10000 0 -0.36 42 42
MAPK3 -0.009 0.092 0.27 2 -0.4 24 26
MAPK1 -0.006 0.091 0.27 1 -0.41 24 25
JAK2 -0.009 0.1 -10000 0 -0.4 33 33
CXCR4 -0.008 0.095 0.21 1 -0.35 40 41
FLT1 0.023 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC -0.011 0.094 0.21 1 -0.34 40 41
S1P/S1P3/Gi -0.002 0.099 -10000 0 -0.36 42 42
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.1 -10000 0 -0.33 42 42
VEGFA 0.025 0.02 0.27 5 -10000 0 5
S1P/S1P2/Gi -0.003 0.092 -10000 0 -0.29 69 69
VEGFR1 homodimer/VEGFA homodimer 0.035 0.022 -10000 0 -0.2 1 1
RHOA 0.023 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.019 0.041 -10000 0 -0.29 13 13
GNAQ 0.022 0.029 -10000 0 -0.59 2 2
GNAZ 0.017 0.058 -10000 0 -0.59 8 8
G12/G13 0.032 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.068 0.26 20 -0.59 8 28
GNA15 0.024 0.028 0.26 5 -0.59 1 6
GNA12 0.023 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.029 -10000 0 -0.59 2 2
Rac1/GTP -0.002 0.1 -10000 0 -0.4 25 25
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.023 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.016 0.063 0.26 1 -0.3 35 36
FRAP1 -0.003 0.082 0.26 1 -0.47 21 22
AKT1 -0.009 0.063 0.19 2 -0.29 25 27
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0.023 0.064 0.23 1 -0.3 5 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.21 4 4
TSC2 0.022 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.007 0.044 -10000 0 -0.27 5 5
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.004 0.078 -10000 0 -0.31 49 49
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.045 -10000 0 -0.23 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.023 0.004 -10000 0 -10000 0 0
RPS6KB1 0.01 0.073 0.29 3 -0.31 20 23
MAP3K5 0 0.044 0.2 10 -0.19 36 46
PIK3R1 0.023 0.021 -10000 0 -0.59 1 1
apoptosis 0 0.044 0.2 10 -0.19 36 46
mol:LY294002 0 0 -10000 0 -0.001 42 42
EIF4B 0.009 0.067 0.27 4 -0.29 15 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.064 0.22 2 -0.28 12 14
eIF4E/eIF4G1/eIF4A1 0.004 0.051 -10000 0 -0.29 19 19
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.076 -10000 0 -0.31 40 40
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.05 0.21 9 -0.23 1 10
FKBP1A 0.023 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.026 0.056 -10000 0 -0.27 4 4
mol:Amino Acids 0 0 -10000 0 -0.001 42 42
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.018 0.058 0.19 2 -0.29 28 30
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.52 52 52
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.002 0.049 -10000 0 -10000 0 0
TSC1/TSC2 0.025 0.07 0.26 2 -0.32 5 7
tumor necrosis factor receptor activity 0 0 0.001 42 -10000 0 42
RPS6 0.023 0.004 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.023 0.004 -10000 0 -10000 0 0
IRS1 -0.012 0.08 -10000 0 -0.33 50 50
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.029 -10000 0 -0.59 2 2
PDK2 -0.016 0.056 0.2 4 -0.3 22 26
EIF4EBP1 -0.028 0.23 -10000 0 -1 44 44
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PPP2R5D -0.001 0.079 0.32 3 -0.42 21 24
peptide biosynthetic process -0.011 0.016 -10000 0 -10000 0 0
RHEB 0.023 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 13 -10000 0 13
EEF2 -0.011 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.017 0.22 -10000 0 -0.97 44 44
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.073 -10000 0 -0.94 1 1
UGCG 0.016 0.1 -10000 0 -0.65 18 18
AKT1/mTOR/p70S6K/Hsp90/TERT 0.049 0.12 0.3 6 -0.49 16 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.017 0.1 -10000 0 -0.64 18 18
mol:DAG 0.007 0.073 -10000 0 -0.76 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.039 0.13 0.31 5 -0.44 32 37
FRAP1 0.034 0.15 0.34 5 -0.51 33 38
FOXO3 0.038 0.13 0.34 11 -0.52 23 34
AKT1 0.038 0.14 0.34 6 -0.56 24 30
GAB2 0.021 0.01 -10000 0 -10000 0 0
SMPD1 0.01 0.11 -10000 0 -0.62 22 22
SGMS1 0.02 0.06 -10000 0 -0.58 7 7
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 0.003 0.014 -10000 0 -0.37 1 1
CALM1 0.023 0.004 -10000 0 -10000 0 0
cell proliferation 0.053 0.1 0.33 3 -0.45 13 16
EIF3A 0.023 0.004 -10000 0 -10000 0 0
PI3K 0.034 0.021 -10000 0 -0.44 1 1
RPS6KB1 0.012 0.094 -10000 0 -0.84 9 9
mol:sphingomyelin 0.007 0.073 -10000 0 -0.76 7 7
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.028 0.032 0.27 15 -10000 0 15
PIK3R1 0.023 0.022 -10000 0 -0.59 1 1
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.023 0.004 -10000 0 -10000 0 0
MYC 0.069 0.2 0.5 2 -0.95 22 24
MYB 0.034 0.17 -10000 0 -1.1 16 16
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.1 0.3 19 -0.48 11 30
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.089 -10000 0 -0.75 9 9
mol:PI-3-4-5-P3 0.043 0.1 0.3 19 -0.48 10 29
Rac1/GDP 0.017 0.016 -10000 0 -0.34 1 1
T cell proliferation 0.043 0.097 0.3 13 -0.46 8 21
SHC1 0.019 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 0.081 2 -0.077 15 17
PRKCZ 0.042 0.097 0.31 11 -0.49 8 19
NF kappa B1 p50/RelA 0.05 0.14 -10000 0 -0.54 16 16
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.027 0.069 0.31 12 -0.62 3 15
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.087 0.27 51 -0.59 10 61
IL2RB 0.033 0.048 0.27 36 -10000 0 36
TERT 0.052 0.08 0.26 111 -10000 0 111
E2F1 0.054 0.093 -10000 0 -0.37 23 23
SOS1 0.023 0.007 -10000 0 -10000 0 0
RPS6 0.023 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.034 15 -0.042 2 17
PTPN11 0.023 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.067 0.27 37 -0.59 5 42
actin cytoskeleton organization 0.043 0.097 0.3 13 -0.46 8 21
GRB2 0.022 0.012 0.27 1 -10000 0 1
IL2 0.022 0.026 0.27 8 -10000 0 8
PIK3CA 0.023 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.041 0.024 -10000 0 -0.32 1 1
LCK 0.025 0.075 0.27 28 -0.59 9 37
BCL2 0.021 0.19 0.49 1 -0.82 34 35
BARD1 signaling events

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.029 0.04 -10000 0 -0.44 6 6
ATM 0.022 0.007 -10000 0 -10000 0 0
UBE2D3 0.023 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.005 -10000 0 -10000 0 0
FANCD2 0.017 0.017 -10000 0 -10000 0 0
protein ubiquitination 0.067 0.061 0.31 2 -0.31 6 8
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.035 0.022 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.039 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.013 0.091 -10000 0 -0.52 11 11
FANCF 0.023 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.009 0.26 1 -10000 0 1
CCNE1 0.06 0.087 0.26 138 -10000 0 138
CDK2/Cyclin E1 0.059 0.06 -10000 0 -10000 0 0
FANCG 0.023 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.031 0.04 -10000 0 -0.44 6 6
FANCE 0.023 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
FANCA 0.063 0.094 0.26 158 -10000 0 158
DNA repair 0.032 0.085 0.31 3 -0.38 5 8
BRCA1/BARD1/ubiquitin 0.031 0.04 -10000 0 -0.44 6 6
BARD1/DNA-PK 0.048 0.038 -10000 0 -0.35 4 4
FANCL 0.024 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.029 0.04 0.44 6 -10000 0 6
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.066 -10000 0 -0.27 10 10
BRCA1/BACH1/BARD1/TopBP1 0.043 0.038 -10000 0 -0.38 6 6
BRCA1/BARD1/P53 0.051 0.04 -10000 0 -0.35 6 6
BARD1/CSTF1/BRCA1 0.04 0.039 -10000 0 -0.38 6 6
BRCA1/BACH1 0.023 0.009 0.26 1 -10000 0 1
BARD1 0.02 0.051 0.26 1 -0.59 6 7
PCNA 0.024 0.012 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.043 0.037 -10000 0 -0.38 6 6
BRCA1/BARD1/UbcH7 0.042 0.038 -10000 0 -0.38 6 6
BRCA1/BARD1/RAD51/PCNA 0.1 0.082 0.32 2 -0.32 6 8
BARD1/DNA-PK/P53 0.052 0.042 -10000 0 -0.33 4 4
BRCA1/BARD1/Ubiquitin 0.031 0.04 -10000 0 -0.44 6 6
BRCA1/BARD1/CTIP 0.031 0.035 -10000 0 -0.35 6 6
FA complex 0.036 0.04 0.24 3 -0.26 1 4
BARD1/EWS 0.03 0.04 -10000 0 -0.44 6 6
RBBP8 0.009 0.006 -10000 0 -10000 0 0
TP53 0.022 0.007 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.049 0.039 0.34 6 -10000 0 6
BRCA1/BARD1 0.073 0.065 0.34 2 -0.31 6 8
CSTF1 0.022 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.015 0.037 0.18 1 -0.44 6 7
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.12 0.26 338 -10000 0 338
RAD50 0.023 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.031 0.04 -10000 0 -0.44 6 6
EWSR1 0.023 0.006 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.053 0.073 0.42 8 -0.4 11 19
MAP4K1 0.03 0.053 0.26 31 -0.59 2 33
MAP3K8 0.021 0.041 -10000 0 -0.59 4 4
PRKCB 0.019 0.078 0.26 16 -0.59 12 28
DBNL 0.024 0.004 -10000 0 -10000 0 0
CRKL 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.014 0.054 0.22 3 -0.32 11 14
JUN 0.003 0.12 -10000 0 -0.59 31 31
MAP3K7 0.013 0.055 0.24 2 -0.39 4 6
GRAP2 0.016 0.069 0.26 3 -0.59 11 14
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.012 0.065 0.26 1 -0.39 9 10
LAT 0.024 0.039 0.26 10 -0.59 2 12
LCP2 0.024 0.009 0.26 1 -10000 0 1
MAPK8 0.009 0.13 -10000 0 -0.63 31 31
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.06 0.26 3 -0.32 14 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.06 0.072 0.41 8 -0.39 11 19
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 0.1 0.26 2 -0.41 29 31
BAG4 0.019 0.022 -10000 0 -0.59 1 1
BAD 0.005 0.04 0.2 6 -0.19 5 11
NFKBIA 0.023 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.039 0.26 10 -0.59 2 12
BAX 0.005 0.043 0.2 6 -0.17 9 15
EnzymeConsortium:3.1.4.12 0.001 0.026 0.085 4 -0.092 27 31
IKBKB 0.015 0.1 0.28 12 -0.41 20 32
MAP2K2 0.007 0.051 0.22 12 -0.26 1 13
MAP2K1 0.007 0.052 0.22 15 -0.26 1 16
SMPD1 0.001 0.033 0.14 4 -0.15 13 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.28 15 -0.42 23 38
MAP2K4 0.005 0.033 0.18 2 -0.19 1 3
protein ubiquitination 0.002 0.1 0.34 4 -0.4 26 30
EnzymeConsortium:2.7.1.37 0.006 0.054 0.22 14 -0.25 2 16
response to UV 0 0.001 0.002 14 -0.002 3 17
RAF1 0.008 0.052 0.19 29 -0.21 5 34
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.005 0.041 0.13 7 -0.15 20 27
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.008 -10000 0 -10000 0 0
MADD 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.003 0.039 0.17 2 -0.18 7 9
TRADD 0.021 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.009 0.052 0.22 13 -0.25 2 15
MAPK1 0.005 0.059 0.22 13 -0.25 3 16
p50/RELA/I-kappa-B-alpha 0.034 0.008 -10000 0 -10000 0 0
FADD 0.022 0.11 0.28 10 -0.42 23 33
KSR1 0.008 0.05 0.18 28 -0.19 8 36
MAPK8 0.002 0.043 0.25 6 -0.29 3 9
TRAF2 0.024 0.012 0.26 2 -10000 0 2
response to radiation 0 0 0.002 6 -10000 0 6
CHUK -0.004 0.095 -10000 0 -0.42 23 23
TNF R/SODD 0.027 0.022 -10000 0 -0.44 1 1
TNF 0.022 0.074 0.26 19 -0.59 10 29
CYCS 0.008 0.047 0.19 13 -0.19 3 16
IKBKG -0.004 0.098 0.43 1 -0.42 23 24
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.001 0.1 -10000 0 -0.44 28 28
RELA 0.024 0.004 -10000 0 -10000 0 0
RIPK1 0.023 0.004 -10000 0 -10000 0 0
AIFM1 0.007 0.045 0.18 13 -0.19 4 17
TNF/TNF R/SODD 0.035 0.053 -10000 0 -0.37 10 10
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 6 -10000 0 6
CASP8 0.008 0.11 -10000 0 -0.63 25 25
NSMAF 0.015 0.11 0.25 14 -0.4 26 40
response to hydrogen peroxide 0 0.001 0.002 14 -0.002 3 17
BCL2 0.005 0.1 -10000 0 -0.59 26 26
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.022 0.12 -10000 0 -0.42 41 41
KLHL20 0.014 0.067 0.24 9 -0.22 12 21
CYFIP2 0.03 0.046 0.26 26 -0.59 1 27
Rac1/GDP -0.002 0.087 0.26 6 -0.32 18 24
ENAH -0.018 0.11 -10000 0 -0.43 31 31
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.023 0.005 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
CTNNB1 0.023 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.007 0.051 -10000 0 -0.42 1 1
ABI1/Sra1/Nap1 -0.013 0.033 -10000 0 -0.16 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.044 0.071 -10000 0 -0.35 20 20
RAPGEF1 -0.021 0.11 -10000 0 -0.41 28 28
CTNND1 0.023 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.024 0.13 -10000 0 -0.42 48 48
CRK -0.018 0.11 -10000 0 -0.43 32 32
E-cadherin/gamma catenin/alpha catenin 0.03 0.065 -10000 0 -0.38 18 18
alphaE/beta7 Integrin 0.035 0.035 0.2 21 -0.44 2 23
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.039 0.028 -10000 0 -0.35 3 3
DLG1 -0.026 0.12 -10000 0 -0.42 44 44
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.031 -10000 0 -0.29 1 1
MLLT4 0.02 0.036 -10000 0 -0.59 3 3
ARF6/GTP/NME1/Tiam1 0.043 0.025 -10000 0 -10000 0 0
PI3K -0.003 0.045 -10000 0 -0.4 1 1
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.018 0.071 -10000 0 -0.44 18 18
TIAM1 0.025 0.016 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.038 0.06 -10000 0 -0.33 18 18
AKT1 -0.007 0.034 -10000 0 -0.22 1 1
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
CDH1 0.009 0.086 -10000 0 -0.59 18 18
RhoA/GDP -0.001 0.088 0.26 9 -0.32 18 27
actin cytoskeleton organization 0.014 0.054 0.19 15 -0.17 10 25
CDC42/GDP -0.001 0.087 0.26 9 -0.32 18 27
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.006 0.046 -10000 0 -0.27 19 19
ITGB7 0.028 0.047 0.26 21 -0.59 2 23
RAC1 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.042 0.064 -10000 0 -0.35 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin 0.028 0.056 -10000 0 -0.33 18 18
mol:GDP -0.015 0.095 0.27 9 -0.37 19 28
CDC42/GTP/IQGAP1 0.03 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.003 0.09 0.26 5 -0.33 18 23
RAC1/GTP/IQGAP1 0.031 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.034 0.007 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.049 0.19 32 -0.25 3 35
NME1 0.025 0.029 0.26 12 -10000 0 12
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.024 0.12 -10000 0 -0.42 43 43
regulation of cell-cell adhesion 0.002 0.043 -10000 0 -0.29 2 2
WASF2 0.007 0.027 -10000 0 -10000 0 0
Rap1/GTP 0.01 0.061 0.24 1 -0.38 2 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.071 -10000 0 -0.33 20 20
CCND1 0.015 0.057 0.22 30 -0.32 3 33
VAV2 -0.022 0.15 -10000 0 -0.54 37 37
RAP1/GDP 0.004 0.073 0.26 3 -0.36 3 6
adherens junction assembly -0.024 0.12 -10000 0 -0.41 43 43
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.023 0.004 -10000 0 -10000 0 0
PIP5K1C 0.023 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.038 0.067 -10000 0 -0.32 20 20
E-cadherin/beta catenin -0.001 0.064 -10000 0 -0.35 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.026 0.12 -10000 0 -0.42 45 45
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.093 0.27 28 -0.35 21 49
E-cadherin/beta catenin/alpha catenin 0.032 0.065 -10000 0 -0.38 18 18
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.025 0.13 -10000 0 -0.43 48 48
Retinoic acid receptors-mediated 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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.017 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.059 -10000 0 -0.4 9 9
KAT2B 0.024 0.003 -10000 0 -10000 0 0
MAPK14 0.024 0.003 -10000 0 -10000 0 0
AKT1 0.007 0.065 0.2 3 -0.36 13 16
RAR alpha/9cRA/Cyclin H 0.047 0.074 -10000 0 -0.35 16 16
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.022 0.066 -10000 0 -0.44 10 10
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.024 0.058 -10000 0 -0.28 21 21
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.007 0.11 -10000 0 -0.52 21 21
NCOA2 0.009 0.081 -10000 0 -0.59 16 16
NCOA3 0.022 0.006 -10000 0 -10000 0 0
NCOA1 0.023 0.021 -10000 0 -0.59 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARG 0.024 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.032 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.022 0.036 -10000 0 -0.59 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.007 0.1 -10000 0 -0.48 20 20
RARA 0.013 0.055 0.19 17 -0.28 20 37
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.013 0.065 -10000 0 -0.39 11 11
PRKCA 0.011 0.087 0.27 1 -0.59 18 19
RXRs/RARs/NRIP1/9cRA/HDAC1 0.009 0.12 0.45 1 -0.53 21 22
RXRG -0.054 0.16 0.24 12 -0.36 175 187
RXRA 0.022 0.064 0.35 1 -0.28 21 22
RXRB 0.015 0.062 0.24 10 -0.35 18 28
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.032 0.077 0.26 48 -0.59 7 55
CRBP1/9-cic-RA 0.023 0.055 0.18 48 -0.44 7 55
RARB 0.019 0.061 -10000 0 -0.59 9 9
PRKCG 0.03 0.043 0.27 29 -10000 0 29
MNAT1 0.023 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.01 0.1 -10000 0 -0.51 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.007 0.098 0.26 1 -0.44 24 25
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.079 0.25 8 -0.39 12 20
RXRs/RARs/NRIP1/9cRA/HDAC3 0.009 0.12 0.45 1 -0.54 21 22
positive regulation of DNA binding 0.032 0.064 -10000 0 -0.33 17 17
NRIP1 0.01 0.12 0.53 1 -0.81 7 8
RXRs/RARs 0.009 0.12 0.28 1 -0.5 25 26
RXRs/RXRs/DNA/9cRA -0.015 0.09 -10000 0 -0.48 21 21
PRKACA 0.024 0.003 -10000 0 -10000 0 0
CDK7 0.023 0.005 -10000 0 -10000 0 0
TFIIH 0.046 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.052 0.055 -10000 0 -0.32 3 3
CCNH 0.023 0.004 -10000 0 -10000 0 0
CREBBP 0.022 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.044 0.014 -10000 0 -10000 0 0
PLK2 and PLK4 events

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.023 0.005 -10000 0 -9999 0 0
PLK4 0.033 0.048 0.26 36 -9999 0 36
regulation of centriole replication 0.016 0.028 0.26 2 -9999 0 2
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.023 0.004 -10000 0 -10000 0 0
ITGB7 0.028 0.047 0.26 21 -0.59 2 23
ITGA4 0.026 0.026 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.04 0.042 0.23 27 -0.44 2 29
alpha4/beta1 Integrin 0.036 0.018 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.046 -10000 0 -0.59 5 5
positive regulation of NF-kappaB transcription factor activity -0.007 0.12 -10000 0 -0.34 88 88
MAP2K4 0.016 0.045 -10000 0 -0.41 2 2
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.019 0.01 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.022 -10000 0 -0.59 1 1
SMPD1 0.008 0.027 -10000 0 -0.35 4 4
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.015 0.14 0.26 1 -0.59 51 52
TRAIL/TRAILR2 0.025 0.037 -10000 0 -0.42 5 5
TRAIL/TRAILR3 0.026 0.043 -10000 0 -0.45 5 5
TRAIL/TRAILR1 0.024 0.042 -10000 0 -0.42 6 6
TRAIL/TRAILR4 -0.007 0.12 -10000 0 -0.34 88 88
TRAIL/TRAILR1/DAP3/GTP 0.028 0.036 -10000 0 -0.33 4 4
IKK complex 0.01 0.04 -10000 0 -0.43 1 1
RIPK1 0.023 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.035 0.26 1 -0.43 5 6
MAP3K1 0.018 0.061 -10000 0 -0.49 6 6
TRAILR4 (trimer) -0.015 0.14 0.26 1 -0.59 51 52
TRADD 0.021 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.022 -10000 0 -0.59 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.043 -10000 0 -0.42 5 5
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.008 0.034 0.26 1 -0.44 5 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.041 0.044 -10000 0 -0.31 4 4
mol:ceramide 0.008 0.026 -10000 0 -0.35 4 4
FADD 0.02 0.009 -10000 0 -10000 0 0
MAPK8 0.012 0.06 0.26 1 -0.43 5 6
TRAF2 0.024 0.012 0.26 2 -10000 0 2
TRAILR3 (trimer) 0.021 0.024 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.038 -10000 0 -0.36 4 4
DAP3 0.02 0.009 -10000 0 -10000 0 0
CASP10 0.036 0.082 0.28 50 -0.34 1 51
JNK cascade -0.007 0.12 -10000 0 -0.34 88 88
TRAIL (trimer) 0.02 0.046 -10000 0 -0.59 5 5
TNFRSF10C 0.021 0.024 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.036 -10000 0 -0.31 2 2
TRAIL/TRAILR2/FADD 0.031 0.036 -10000 0 -0.36 4 4
cell death 0.008 0.026 -10000 0 -0.35 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.042 -10000 0 -0.42 5 5
TRAILR2 (trimer) 0.019 0.01 -10000 0 -10000 0 0
CASP8 0.013 0.043 -10000 0 -0.54 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.041 0.043 -10000 0 -0.31 4 4
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.015 -10000 0 -0.22 2 2
TRAF2/ASK1 0.03 0.018 -10000 0 -0.27 2 2
ATM 0.022 0.007 -10000 0 -10000 0 0
MAP2K3 -0.017 0.11 0.25 2 -0.34 53 55
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.011 0.096 0.3 1 -0.35 29 30
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.045 0.068 0.26 79 -10000 0 79
TXN 0.006 0.005 0.12 2 -10000 0 2
CALM1 0.023 0.004 -10000 0 -10000 0 0
GADD45A 0.023 0.004 -10000 0 -10000 0 0
GADD45B 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.023 0.005 -10000 0 -10000 0 0
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.021 -10000 0 -0.27 3 3
TAK1/TAB family -0.001 0.019 0.18 1 -0.15 6 7
RAC1/OSM/MEKK3 0.041 0.016 -10000 0 -10000 0 0
TRAF2 0.024 0.012 0.26 2 -10000 0 2
RAC1/OSM/MEKK3/MKK3 0.001 0.09 -10000 0 -0.3 29 29
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.01 0.17 0.26 36 -0.59 63 99
CCM2 0.024 0.009 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.008 0.11 0.18 35 -0.37 64 99
MAPK11 0.021 0.03 -10000 0 -0.59 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.02 0.11 -10000 0 -0.34 64 64
OSM/MEKK3 0.032 0.013 0.2 1 -10000 0 1
TAOK1 0.002 0.054 -10000 0 -0.36 20 20
TAOK2 0.01 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.021 -10000 0 -0.59 1 1
MAP3K10 0.023 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.02 -10000 0 -0.36 1 1
GADD45/MTK1/MTK1 0.062 0.043 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.024 0.041 0.26 12 -0.59 2 14
GNAI2 0.023 0.004 -10000 0 -10000 0 0
mol:S1P 0.012 0.02 0.23 1 -0.3 2 3
GNAO1 0.017 0.098 0.26 30 -0.59 18 48
mol:Sphinganine-1-P 0.011 0.026 -10000 0 -0.44 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.049 0.036 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.006 0.024 -10000 0 -0.25 5 5
S1PR5 0.026 0.042 0.26 14 -0.59 2 16
S1PR4 0.027 0.066 0.26 28 -0.59 6 34
GNAI1 -0.006 0.13 -10000 0 -0.59 43 43
S1P/S1P5/G12 0.044 0.041 0.25 1 -0.27 4 5
S1P/S1P3/Gq 0.025 0.063 -10000 0 -0.3 25 25
S1P/S1P4/Gi 0 0.1 0.26 1 -0.35 40 41
GNAQ 0.022 0.029 -10000 0 -0.59 2 2
GNAZ 0.017 0.058 -10000 0 -0.59 8 8
GNA14 0.023 0.068 0.26 20 -0.59 8 28
GNA15 0.024 0.028 0.26 5 -0.59 1 6
GNA12 0.023 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.029 -10000 0 -0.59 2 2
ABCC1 0.022 0.006 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.03 0.01 -10000 0 -10000 0 0
PRKCZ 0.022 0.021 -10000 0 -0.59 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.05 -10000 0 -0.38 6 6
IRAK/TOLLIP 0.024 0.014 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.024 0.099 0.38 2 -0.44 34 36
IL1A 0.027 0.031 0.26 15 -10000 0 15
IL1B 0.005 0.052 0.26 1 -0.45 11 12
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.04 -10000 0 -0.31 1 1
IL1R2 0.007 0.12 0.26 23 -0.59 34 57
IL1R1 0.016 0.068 -10000 0 -0.59 11 11
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.06 0.26 3 -0.3 13 16
TOLLIP 0.023 0.005 -10000 0 -10000 0 0
TICAM2 0.023 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.032 0.07 0.34 6 -0.37 1 7
JUN -0.011 0.067 0.29 4 -0.29 26 30
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.043 0.066 -10000 0 -0.34 21 21
IL1 alpha/IL1R1/IL1RAP/MYD88 0.055 0.051 -10000 0 -0.35 11 11
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.051 -10000 0 -0.33 11 11
IL1 beta fragment/IL1R1/IL1RAP 0.025 0.064 -10000 0 -0.37 21 21
NFKB1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.006 0.067 0.33 3 -0.3 20 23
IRAK1 -0.001 0.019 0.21 2 -10000 0 2
IL1RN/IL1R1 0.035 0.066 -10000 0 -0.44 13 13
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
PI3K 0.032 0.019 -10000 0 -0.44 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.013 0.051 -10000 0 -0.3 14 14
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.025 0.064 -10000 0 -0.37 21 21
IL1 beta/IL1R2 0.012 0.095 -10000 0 -0.39 44 44
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.06 -10000 0 -0.32 21 21
IRAK3 0.005 0.1 0.26 1 -0.59 27 28
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.044 0.065 -10000 0 -0.34 21 21
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.039 -10000 0 -0.28 11 11
IL1 alpha/IL1R1/IL1RAP 0.044 0.052 -10000 0 -0.38 11 11
RELA 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
MYD88 0.023 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.043 0.036 -10000 0 -10000 0 0
IL1RAP 0.023 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.017 0.052 -10000 0 -0.31 17 17
CASP1 0.021 0.022 -10000 0 -0.59 1 1
IL1RN/IL1R2 0.027 0.1 0.38 4 -0.44 36 40
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.036 0.064 -10000 0 -0.35 21 21
TMEM189-UBE2V1 0.019 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.069 -10000 0 -0.34 22 22
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.032 0.055 0.26 35 -0.59 2 37
TRAF6/TAK1/TAB1/TAB2 0.038 0.017 -10000 0 -10000 0 0
MAP2K6 -0.002 0.07 0.39 4 -0.31 17 21
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.03 0.065 -9999 0 -0.38 18 18
E-cadherin/beta catenin 0.019 0.07 -9999 0 -0.44 18 18
CTNNB1 0.023 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.009 0.086 -9999 0 -0.59 18 18
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.069 0.052 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.055 0.047 0.36 3 -10000 0 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.042 -10000 0 -10000 0 0
CaM/Ca2+ 0.067 0.047 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.043 0.044 0.29 2 -10000 0 2
AKT1 0.013 0.058 0.3 8 -0.29 1 9
MAP2K1 0.007 0.044 0.28 3 -10000 0 3
MAP3K11 0.022 0.042 0.28 3 -10000 0 3
IFNGR1 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.015 0.1 -10000 0 -0.32 44 44
Rap1/GTP 0.014 0.016 -10000 0 -10000 0 0
CRKL/C3G 0.033 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.076 0.055 -10000 0 -10000 0 0
CEBPB 0.027 0.096 0.36 2 -0.48 8 10
STAT3 0.023 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.072 0.099 -10000 0 -0.72 8 8
STAT1 0.026 0.049 0.3 4 -10000 0 4
CALM1 0.023 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.056 0.085 0.26 127 -10000 0 127
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.046 0.29 4 -10000 0 4
CEBPB/PTGES2/Cbp/p300 0.026 0.062 0.25 3 -0.36 2 5
mol:Ca2+ 0.065 0.05 -10000 0 -10000 0 0
MAPK3 0.02 0.083 -10000 0 -0.56 12 12
STAT1 (dimer) 0.027 0.059 -10000 0 -10000 0 0
MAPK1 -0.008 0.17 -10000 0 -0.67 50 50
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.021 0.036 -10000 0 -0.59 3 3
DAPK1 0.025 0.07 0.37 2 -0.34 2 4
SMAD7 0.016 0.034 0.18 3 -10000 0 3
CBL/CRKL/C3G 0.045 0.039 0.29 2 -10000 0 2
PI3K 0.059 0.045 -10000 0 -0.31 1 1
IFNG 0.057 0.085 0.26 127 -10000 0 127
apoptosis 0.022 0.076 0.33 2 -0.41 11 13
CAMK2G 0.024 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.041 0.26 27 -10000 0 27
CAMK2B -0.01 0.17 0.26 36 -0.59 63 99
FRAP1 0.01 0.054 0.29 8 -0.28 1 9
PRKCD 0.013 0.06 0.3 9 -0.29 1 10
RAP1B 0.023 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -10000 0 0
PTPN2 0.023 0.005 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.021 0.058 0.3 9 -0.33 1 10
STAT1 (dimer)/PIASy 0.039 0.047 0.29 3 -10000 0 3
SOCS1 0.013 0.12 -10000 0 -1 10 10
mol:GDP 0.042 0.036 0.28 2 -10000 0 2
CASP1 0.016 0.039 0.23 5 -0.26 2 7
PTGES2 0.024 0.009 0.26 1 -10000 0 1
IRF9 0.027 0.041 0.22 8 -10000 0 8
mol:PI-3-4-5-P3 0.044 0.035 -10000 0 -0.3 1 1
RAP1/GDP 0.034 0.022 -10000 0 -10000 0 0
CBL 0.013 0.044 0.3 2 -10000 0 2
MAP3K1 0.021 0.041 0.28 3 -10000 0 3
PIAS1 0.023 0.004 -10000 0 -10000 0 0
PIAS4 0.023 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.042 -10000 0 -10000 0 0
PTPN11 0.026 0.044 0.29 3 -10000 0 3
CREBBP 0.023 0.006 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.013 0.04 0.35 2 -0.28 1 3
DAPP1 0.015 0.1 0.27 7 -0.37 26 33
Src family/SYK family/BLNK-LAT/BTK-ITK 0.014 0.14 0.29 12 -0.5 31 43
mol:DAG 0.018 0.079 0.24 29 -0.25 9 38
HRAS 0.024 0.013 0.26 2 -10000 0 2
RAP1A 0.024 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.056 0.26 1 -0.37 5 6
PLCG2 0.02 0.023 0.26 1 -0.59 1 2
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.009 0.26 1 -10000 0 1
mol:GTP -0.01 0.042 0.32 6 -0.29 1 7
ARF1/GTP -0.004 0.033 0.29 4 -0.29 1 5
RHOA 0.023 0.005 -10000 0 -10000 0 0
YES1 0.022 0.021 -10000 0 -0.59 1 1
RAP1A/GTP -0.011 0.035 0.2 2 -0.29 1 3
ADAP1 -0.012 0.04 0.36 2 -0.3 2 4
ARAP3 -0.01 0.042 0.32 6 -0.29 1 7
INPPL1 0.022 0.006 -10000 0 -10000 0 0
PREX1 0.027 0.035 0.26 18 -10000 0 18
ARHGEF6 0.018 0.058 -10000 0 -0.59 8 8
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.024 0.005 -10000 0 -10000 0 0
FYN 0.022 0.021 -10000 0 -0.59 1 1
ARF6 0.023 0.004 -10000 0 -10000 0 0
FGR 0.023 0.01 0.26 1 -10000 0 1
mol:Ca2+ 0.012 0.05 0.26 7 -10000 0 7
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.016 0.26 4 -10000 0 4
ZAP70 0.021 0.1 0.26 38 -0.59 19 57
mol:IP3 0.012 0.062 0.2 30 -0.19 5 35
LYN 0.021 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.055 0.32 2 -0.35 5 7
RhoA/GDP 0.032 0.042 -10000 0 -0.3 1 1
PDK1/Src/Hsp90 0.042 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.018 0.067 0.39 5 -0.33 4 9
SRC 0.023 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.009 0.23 1 -10000 0 1
RAC1 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.03 -10000 0 -0.57 2 2
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.04 0.29 5 -0.28 1 6
RhoA/GTP -0.011 0.042 0.36 4 -0.28 1 5
Src family/SYK family/BLNK-LAT 0.023 0.094 0.26 12 -0.41 14 26
BLK 0.048 0.088 0.26 114 -0.59 2 116
PDPK1 0.022 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.042 0.36 4 -0.28 1 5
HCK 0.027 0.028 0.26 12 -10000 0 12
CYTH3 -0.012 0.038 0.36 2 -0.28 1 3
CYTH2 -0.012 0.04 0.33 3 -0.28 1 4
KRAS 0.023 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.049 0.31 1 -0.4 8 9
SGK1 0.006 0.074 -10000 0 -0.34 31 31
INPP5D 0.023 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.058 0.34 2 -0.34 7 9
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.021 0.05 0.39 5 -0.3 1 6
mol:PI-3-4-5-P3 -0.011 0.036 0.27 4 -0.29 1 5
ARAP3/RAP1A/GTP -0.012 0.035 0.21 2 -0.29 1 3
VAV1 0.024 0.024 0.26 2 -0.59 1 3
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.035 0.03 -10000 0 -0.29 1 1
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.056 0.26 1 -0.36 5 6
LAT 0.024 0.039 0.26 10 -0.59 2 12
Rac1/GTP 0.017 0.046 -10000 0 -0.36 5 5
ITK -0.017 0.065 0.36 4 -0.33 22 26
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.017 0.096 0.27 27 -0.34 11 38
LCK 0.025 0.075 0.26 28 -0.59 9 37
BTK -0.011 0.042 0.36 4 -0.28 1 5
PDGFR-beta signaling pathway

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.072 0.3 4 -0.36 10 14
PDGFB-D/PDGFRB/SLAP 0.028 0.028 -10000 0 -0.32 2 2
PDGFB-D/PDGFRB/APS/CBL 0.048 0.039 -10000 0 -0.37 2 2
AKT1 0.026 0.09 0.34 30 -10000 0 30
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.03 0.083 0.32 5 -0.4 11 16
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR 0.001 0.098 -10000 0 -0.44 33 33
mol:Ca2+ 0.023 0.086 0.32 2 -0.41 16 18
MYC 0.055 0.17 0.39 18 -0.79 21 39
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.034 0.042 -10000 0 -0.31 2 2
LRP1/PDGFRB/PDGFB 0.041 0.053 -10000 0 -0.45 9 9
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.022 0.087 0.32 2 -0.42 16 18
PTEN 0.022 0.029 -10000 0 -0.59 2 2
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.022 -10000 0 -0.59 1 1
PDGFB-D/PDGFRB/SHP2 0.034 0.023 -10000 0 -0.44 2 2
PDGFB-D/PDGFRB/GRB10 0.034 0.023 -10000 0 -0.44 2 2
cell cycle arrest 0.028 0.028 -10000 0 -0.32 2 2
HRAS 0.024 0.012 0.26 2 -10000 0 2
HIF1A 0.022 0.085 0.32 30 -10000 0 30
GAB1 0.025 0.091 0.32 3 -0.42 13 16
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.084 0.32 8 -0.36 10 18
PDGFB-D/PDGFRB 0.042 0.03 -10000 0 -0.38 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.023 -10000 0 -0.44 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.021 0.063 0.28 3 -0.37 6 9
positive regulation of MAPKKK cascade 0.034 0.023 -10000 0 -0.44 2 2
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
mol:IP3 0.023 0.088 0.33 2 -0.42 16 18
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.03 -10000 0 -0.44 3 3
SHB 0.024 0.009 0.26 1 -10000 0 1
BLK -0.03 0.17 0.3 1 -0.41 120 121
PTPN2 0.023 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.023 -10000 0 -0.43 2 2
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.027 0.1 0.32 4 -0.44 16 20
CBL 0.022 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.023 -10000 0 -0.44 2 2
LCK 0.006 0.1 -10000 0 -0.53 21 21
PDGFRB 0.023 0.03 -10000 0 -0.6 2 2
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.015 0.065 -10000 0 -0.57 6 6
ABL1 0.019 0.091 0.29 5 -0.39 18 23
PDGFB-D/PDGFRB/CBL 0.02 0.1 0.32 1 -0.45 20 21
PTPN1 0.024 0.021 0.26 6 -10000 0 6
SNX15 0.024 0.004 -10000 0 -10000 0 0
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.035 0.26 19 -10000 0 19
cell proliferation 0.056 0.16 0.37 23 -0.69 21 44
SLA 0.02 0.024 0.26 7 -10000 0 7
actin cytoskeleton reorganization 0.033 0.05 0.33 2 -0.31 1 3
SRC 0.013 0.056 0.28 1 -0.49 6 7
PI3K -0.012 0.023 -10000 0 -0.3 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.033 -10000 0 -0.38 3 3
SH2B2 0.033 0.046 0.26 34 -10000 0 34
PLCgamma1/SPHK1 0.03 0.085 0.32 5 -0.41 11 16
LYN 0.01 0.063 -10000 0 -0.52 8 8
LRP1 0.018 0.061 -10000 0 -0.59 9 9
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.029 -10000 0 -0.59 2 2
STAT5A 0.02 0.046 -10000 0 -0.59 5 5
NCK1-2/p130 Cas 0.054 0.038 -10000 0 -0.31 2 2
SPHK1 0.025 0.041 0.26 12 -0.59 2 14
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.023 0.088 0.33 2 -0.42 16 18
PLCG1 0.022 0.089 0.33 2 -0.43 16 18
NHERF/PDGFRB 0.048 0.043 -10000 0 -0.38 2 2
YES1 0.001 0.11 -10000 0 -0.52 29 29
cell migration 0.048 0.043 -10000 0 -0.38 2 2
SHC/Grb2/SOS1 0.048 0.041 -10000 0 -0.31 2 2
SLC9A3R2 0.022 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.035 0.054 0.26 46 -10000 0 46
NHERF1-2/PDGFRB/PTEN 0.056 0.049 -10000 0 -0.35 4 4
FYN -0.001 0.097 -10000 0 -0.42 30 30
DOK1 0.019 0.047 -10000 0 -0.34 2 2
HRAS/GTP 0.018 0.008 0.18 2 -10000 0 2
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.022 0.12 0.33 3 -0.53 22 25
PRKCD 0.021 0.05 0.34 1 -0.34 2 3
FER 0.018 0.055 -10000 0 -0.35 6 6
MAPKKK cascade 0.038 0.097 0.36 31 -0.31 2 33
RASA1 0.02 0.049 -10000 0 -0.34 2 2
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.034 0.041 -10000 0 -0.32 2 2
PDGFB-D/PDGFRB/SHB 0.034 0.025 -10000 0 -0.44 2 2
chemotaxis 0.02 0.089 0.28 5 -0.38 18 23
STAT1-3-5/STAT1-3-5 0.048 0.047 -10000 0 -0.35 7 7
Bovine Papilomavirus E5/PDGFRB 0.017 0.022 -10000 0 -0.44 2 2
PTPRJ 0.024 0.003 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.051 0.083 -10000 0 -0.48 1 1
CRKL 0.023 0.048 0.29 6 -10000 0 6
mol:DAG 0.037 0.053 0.33 1 -10000 0 1
HRAS 0.033 0.078 0.3 15 -10000 0 15
MAPK8 0.043 0.07 0.25 29 -0.37 2 31
RAP1A 0.023 0.047 0.26 8 -10000 0 8
GAB1 0.024 0.047 0.26 8 -10000 0 8
MAPK14 0.044 0.067 0.25 29 -10000 0 29
EPO 0.063 0.089 0.26 147 -10000 0 147
PLCG1 0.037 0.053 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.013 0.26 1 -10000 0 1
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.063 0.065 -10000 0 -0.37 5 5
GAB1/SHC/GRB2/SOS1 0.041 0.042 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.061 0.061 0.23 5 -10000 0 5
IRS2 0.011 0.073 0.29 4 -0.32 21 25
STAT1 0.044 0.066 0.33 3 -10000 0 3
STAT5B 0.039 0.06 -10000 0 -0.36 1 1
cell proliferation 0.025 0.076 0.24 31 -0.35 2 33
GAB1/SHIP/PIK3R1/SHP2/SHC 0.033 0.034 -10000 0 -0.28 1 1
TEC 0.023 0.049 0.28 6 -0.31 1 7
SOCS3 0.019 0.046 -10000 0 -0.59 5 5
STAT1 (dimer) 0.044 0.066 0.33 3 -10000 0 3
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
EPO/EPOR (dimer)/JAK2 0.08 0.065 0.34 3 -10000 0 3
EPO/EPOR 0.061 0.061 0.23 5 -10000 0 5
LYN 0.02 0.011 -10000 0 -10000 0 0
TEC/VAV2 0.038 0.048 0.28 3 -0.3 1 4
elevation of cytosolic calcium ion concentration 0.026 0.013 0.26 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.062 0.056 -10000 0 -10000 0 0
mol:IP3 0.037 0.053 0.33 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.073 0.29 2 -0.3 20 22
SH2B3 0.026 0.009 -10000 0 -10000 0 0
NFKB1 0.044 0.067 0.25 29 -10000 0 29
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.045 -10000 0 -0.2 8 8
PTPN6 0.022 0.039 0.3 2 -10000 0 2
TEC/VAV2/GRB2 0.046 0.049 0.27 4 -0.3 1 5
EPOR 0.026 0.013 0.26 1 -10000 0 1
INPP5D 0.023 0.004 -10000 0 -10000 0 0
mol:GDP 0.04 0.042 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.023 0.26 1 -0.59 1 2
CRKL/CBL/C3G 0.046 0.049 0.28 4 -10000 0 4
VAV2 0.024 0.048 0.28 7 -10000 0 7
CBL 0.022 0.047 0.28 6 -10000 0 6
SHC/Grb2/SOS1 0.034 0.038 -10000 0 -10000 0 0
STAT5A 0.037 0.065 -10000 0 -0.35 5 5
GRB2 0.023 0.01 0.26 1 -10000 0 1
STAT5 (dimer) 0.05 0.082 0.34 1 -0.42 3 4
LYN/PLCgamma2 0.026 0.023 -10000 0 -0.44 1 1
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.025 0.049 0.27 9 -10000 0 9
BCL2 0.031 0.17 -10000 0 -0.85 28 28
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.018 0.025 0.22 5 -0.32 1 6
CRKL 0.023 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DOCK1 0.023 0.004 -10000 0 -10000 0 0
ITGA4 0.026 0.026 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.065 0.05 0.36 8 -0.35 2 10
EPO 0.062 0.09 0.26 147 -10000 0 147
alpha4/beta7 Integrin 0.04 0.042 0.23 27 -0.44 2 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.018 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.06 0.062 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.069 -10000 0 -0.51 10 10
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.019 -10000 0 -0.44 1 1
ARF6 0.023 0.004 -10000 0 -10000 0 0
JAK2 0.034 0.033 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
MADCAM1 0.031 0.046 0.26 33 -10000 0 33
cell adhesion 0.063 0.049 0.35 8 -0.35 2 10
CRKL/CBL 0.031 0.012 -10000 0 -10000 0 0
ITGB1 0.023 0.004 -10000 0 -10000 0 0
SRC -0.007 0.043 -10000 0 -0.35 6 6
ITGB7 0.028 0.047 0.26 21 -0.59 2 23
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.042 -10000 0 -0.38 6 6
p130Cas/Crk/Dock1 0.027 0.04 0.35 1 -0.3 5 6
VCAM1 0.021 0.054 0.26 6 -0.59 6 12
RHOA 0.023 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.056 0.024 -10000 0 -10000 0 0
BCAR1 -0.007 0.044 0.38 2 -0.32 6 8
EPOR 0.024 0.009 0.26 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
GIT1 0.022 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.071 -10000 0 -0.53 10 10
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.023 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.086 0.31 5 -0.41 11 16
NFATC2 -0.002 0.068 0.21 1 -0.25 29 30
NFATC3 0.013 0.017 -10000 0 -0.41 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.093 0.28 2 -0.37 25 27
Exportin 1/Ran/NUP214 0.046 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.086 -10000 0 -0.45 8 8
BCL2/BAX 0.02 0.08 -10000 0 -0.42 28 28
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.013 -10000 0 -10000 0 0
BAX 0.024 0.014 0.26 3 -10000 0 3
MAPK14 0.022 0.007 -10000 0 -10000 0 0
BAD 0.023 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.019 0.083 -10000 0 -0.42 12 12
Calcineurin A alpha-beta B1/BCL2 0.005 0.1 -10000 0 -0.59 26 26
FKBP8 0.023 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.082 0.42 12 -10000 0 12
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.059 0.26 55 -10000 0 55
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.02 0.071 0.26 14 -0.59 10 24
MAP3K8 0.019 0.042 -10000 0 -0.59 4 4
NFAT4/CK1 alpha 0.017 0.026 -10000 0 -0.26 1 1
MEF2D/NFAT1/Cbp/p300 0.011 0.1 -10000 0 -0.3 58 58
CABIN1 0.012 0.093 0.35 1 -0.37 24 25
CALM1 0.02 0.013 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.005 -10000 0 -10000 0 0
CAMK4 0.032 0.046 0.26 33 -10000 0 33
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.042 0.041 -10000 0 -0.44 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.037 -10000 0 -0.59 3 3
MAPK9 0.023 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.023 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.098 0.31 1 -0.44 11 12
PRKCH 0.023 0.021 -10000 0 -0.59 1 1
CABIN1/Cbp/p300 0.026 0.022 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.009 -10000 0 -10000 0 0
apoptosis 0.011 0.033 -10000 0 -0.34 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.04 -10000 0 -0.32 3 3
PRKCB 0.019 0.078 0.26 16 -0.59 12 28
PRKCE 0.023 0.021 -10000 0 -0.59 1 1
JNK2/NFAT4 0.007 0.059 -10000 0 -0.38 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.023 0.009 0.26 1 -10000 0 1
NUP214 0.023 0.004 -10000 0 -10000 0 0
PRKCZ 0.019 0.024 -10000 0 -0.59 1 1
PRKCA 0.01 0.086 0.26 1 -0.59 18 19
PRKCG 0.029 0.043 0.26 29 -10000 0 29
PRKCQ 0.005 0.11 0.26 10 -0.59 30 40
FKBP38/BCL2 0.019 0.08 -10000 0 -0.44 26 26
EP300 0.019 0.016 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.086 0.33 1 -0.42 8 9
CaM/Ca2+/FKBP38 0.027 0.018 -10000 0 -10000 0 0
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSNK1A1 0.008 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.033 -10000 0 -10000 0 0
NFATc/ERK1 0.029 0.084 0.33 1 -0.42 8 9
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.038 0.092 -10000 0 -0.42 13 13
NR4A1 -0.01 0.18 -10000 0 -0.53 75 75
GSK3B 0.02 0.012 -10000 0 -10000 0 0
positive T cell selection 0.013 0.017 -10000 0 -0.41 1 1
NFAT1/CK1 alpha 0.002 0.052 -10000 0 -0.27 6 6
RCH1/ KPNB1 0.041 0.042 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.036 0.059 0.26 49 -0.59 1 50
MEF2D 0.017 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.018 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.029 0.083 0.33 1 -0.42 8 9
CREBBP 0.018 0.015 -10000 0 -10000 0 0
BCL2 0.005 0.1 -10000 0 -0.59 26 26
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.022 -10000 0 -0.59 1 1
Caspase 8 (4 units) 0.04 0.059 -10000 0 -0.43 3 3
NEF 0.005 0.019 -10000 0 -0.18 3 3
NFKBIA 0.024 0.012 -10000 0 -10000 0 0
BIRC3 0.019 0.053 0.28 10 -0.42 6 16
CYCS 0.034 0.07 0.26 8 -0.34 6 14
RIPK1 0.023 0.004 -10000 0 -10000 0 0
CD247 0.018 0.091 0.3 15 -0.55 17 32
MAP2K7 0.042 0.13 0.32 1 -0.73 15 16
protein ubiquitination 0.013 0.084 0.3 4 -0.38 11 15
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.022 0.029 -10000 0 -0.59 2 2
BID 0.038 0.071 0.22 4 -0.34 7 11
NF-kappa-B/RelA/I kappa B alpha 0.05 0.032 -10000 0 -0.31 2 2
TRADD 0.021 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.021 -10000 0 -0.59 1 1
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.02 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.032 -10000 0 -0.32 2 2
MAPK8 0.04 0.12 0.42 3 -0.66 15 18
APAF1 0.024 0.002 -10000 0 -10000 0 0
TRAF1 0.025 0.016 0.26 4 -10000 0 4
TRAF2 0.024 0.012 0.26 2 -10000 0 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.026 0.058 0.23 6 -0.33 9 15
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.095 -10000 0 -0.43 18 18
CHUK 0.013 0.088 0.31 4 -0.4 11 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.054 0.037 -10000 0 -0.39 2 2
TCRz/NEF 0.018 0.08 0.32 7 -0.46 17 24
TNF 0.022 0.074 0.26 19 -0.59 10 29
FASLG 0.015 0.1 0.3 34 -0.53 17 51
NFKB1 0.025 0.011 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.035 0.053 -10000 0 -0.37 10 10
CASP6 0.053 0.1 -10000 0 -0.52 17 17
CASP7 0.041 0.1 0.36 5 -0.5 8 13
RELA 0.025 0.01 -10000 0 -10000 0 0
CASP2 0.023 0.004 -10000 0 -10000 0 0
CASP3 0.037 0.1 0.34 5 -0.5 8 13
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.022 -10000 0 -0.44 1 1
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.005 -10000 0 -10000 0 0
MAP3K14 0.015 0.091 0.3 1 -0.4 18 19
APAF-1/Caspase 9 0.034 0.06 0.26 5 -0.39 5 10
BCL2 0.032 0.13 0.44 5 -0.57 19 24
Canonical NF-kappaB 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
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.11 0.28 13 -0.33 17 30
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.029 0.032 0.38 1 -10000 0 1
NFKBIA 0.009 0.019 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.017 0.26 3 -10000 0 3
IKBKG 0.019 0.028 -10000 0 -10000 0 0
IKK complex/A20 0.02 0.13 -10000 0 -0.4 38 38
NEMO/A20/RIP2 0.02 0.017 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.014 0.12 -10000 0 -0.4 42 42
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.032 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.11 -10000 0 -0.41 26 26
BCL10/MALT1/TRAF6 0.045 0.014 -10000 0 -10000 0 0
NOD2 0.028 0.04 0.26 24 -10000 0 24
NFKB1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.004 -10000 0 -10000 0 0
MALT1 0.023 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.011 -10000 0 -10000 0 0
ATM 0.022 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.032 0.056 -10000 0 -0.44 10 10
TRAF6 0.023 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.086 0.26 1 -0.59 18 19
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.023 0.004 -10000 0 -10000 0 0
TNF 0.022 0.074 0.26 19 -0.59 10 29
NF kappa B1 p50/RelA 0.051 0.014 -10000 0 -10000 0 0
BCL10 0.023 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.019 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.015 0.12 -10000 0 -0.41 37 37
CYLD 0.021 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.43 39 39
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.039 -10000 0 -0.34 6 6
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.01 -10000 0 -0.29 1 1
GATA1/HDAC4 0.034 0.024 -10000 0 -0.44 1 1
GATA1/HDAC5 0.035 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 0.025 0.074 -10000 0 -0.44 21 21
HDAC5/BCL6/BCoR 0.043 0.031 -10000 0 -0.38 4 4
HDAC9 0.022 0.057 0.26 11 -0.59 6 17
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.039 -10000 0 -0.38 7 7
HDAC4/ANKRA2 0.033 0.018 -10000 0 -0.44 1 1
HDAC5/YWHAB 0.033 0.01 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
GATA2 0.012 0.097 0.26 11 -0.59 21 32
HDAC4/RFXANK 0.034 0.018 -10000 0 -0.44 1 1
BCOR 0.023 0.021 -10000 0 -0.59 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.022 0.006 -10000 0 -10000 0 0
HDAC5 0.023 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.03 0.04 -10000 0 -0.44 6 6
Histones 0.016 0.05 -10000 0 -0.32 8 8
ADRBK1 0.022 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.021 -10000 0 -0.59 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.033 0.009 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.019 -10000 0 -0.44 1 1
HDAC7 0.024 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.032 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.034 0.008 -10000 0 -10000 0 0
CAMK4 0.032 0.046 0.26 33 -10000 0 33
Tubulin/HDAC6 0.047 0.013 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
GATA1 0.025 0.026 0.26 10 -10000 0 10
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.019 0.054 -10000 0 -0.59 7 7
SUMO1/HDAC4 0.034 0.04 -10000 0 -0.24 4 4
SRF 0.023 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.032 0.018 -10000 0 -0.44 1 1
Tubulin 0.035 0.011 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.031 0.019 -10000 0 -0.44 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.032 0.032 -10000 0 -0.44 4 4
HDAC4/HDAC3/SMRT (N-CoR2) 0.046 0.018 -10000 0 -0.38 1 1
HDAC4/SRF 0.05 0.034 -10000 0 -0.38 1 1
HDAC4/ER alpha -0.011 0.18 -10000 0 -0.43 124 124
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.049 -10000 0 -0.32 8 8
cell motility 0.046 0.013 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.022 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.035 0.006 -10000 0 -10000 0 0
BCL6 0.021 0.036 -10000 0 -0.59 3 3
HDAC4/CaMK II delta B 0.023 0.021 -10000 0 -0.59 1 1
Hsp90/HDAC6 0.034 0.007 -10000 0 -10000 0 0
ESR1 -0.029 0.23 0.26 112 -0.59 120 232
HDAC6/HDAC11 0.035 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.038 -10000 0 -0.24 3 3
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.021 -10000 0 -0.59 1 1
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.061 0.03 -10000 0 -0.32 2 2
GNG2 0.019 0.05 -10000 0 -0.59 6 6
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.024 0.012 0.26 2 -10000 0 2
HDAC11 0.024 0.009 0.26 1 -10000 0 1
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.023 0.005 -10000 0 -10000 0 0
RFXANK 0.024 0.003 -10000 0 -10000 0 0
nuclear import -0.026 0.017 0.34 1 -10000 0 1
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.41 58 58
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
AKT1 0.023 0.004 -10000 0 -10000 0 0
AKT2 0.023 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.15 0.4 1 -0.42 69 70
YWHAZ 0.018 0.01 -10000 0 -10000 0 0
CALM1 0.023 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.009 0.007 -10000 0 -0.19 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.02 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.022 0.019 0.26 5 -10000 0 5
PRKCI 0.023 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.009 0.016 0.24 4 -10000 0 4
PRKCZ 0.022 0.021 -10000 0 -0.59 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.02 0.064 0.26 1 -0.34 8 9
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.13 0.17 0.41 1 -0.46 74 75
STX4 0.022 0.006 -10000 0 -10000 0 0
GSK3B 0.017 0.005 -10000 0 -10000 0 0
SFN 0.02 0.071 0.26 14 -0.59 10 24
LNPEP 0.021 0.036 -10000 0 -0.59 3 3
YWHAE 0.022 0.007 -10000 0 -10000 0 0
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.025 0.019 -10000 0 -0.49 1 1
VEGFR1 homodimer/NRP1 0.009 0.017 -10000 0 -0.5 1 1
mol:DAG 0.012 0.031 -10000 0 -0.4 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.023 0.021 -10000 0 -0.46 1 1
CaM/Ca2+ 0.024 0.03 -10000 0 -0.38 2 2
HIF1A 0.027 0.012 -10000 0 -0.32 1 1
GAB1 0.023 0.004 -10000 0 -10000 0 0
AKT1 0.011 0.04 -10000 0 -0.44 1 1
PLCG1 0.012 0.031 -10000 0 -0.4 2 2
NOS3 0.015 0.056 -10000 0 -0.5 3 3
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:NO 0.018 0.065 0.3 1 -0.45 6 7
FLT1 0.013 0.02 -10000 0 -0.58 1 1
PGF 0.023 0.022 0.26 1 -0.59 1 2
VEGFR1 homodimer/NRP2/VEGFR121 0.037 0.028 -10000 0 -0.58 1 1
CALM1 0.023 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.031 0.067 -10000 0 -0.43 7 7
endothelial cell proliferation 0.012 0.085 0.35 7 -0.62 4 11
mol:Ca2+ 0.011 0.031 -10000 0 -0.4 2 2
MAPK3 -0.014 0.052 -10000 0 -0.34 16 16
MAPK1 -0.014 0.052 -10000 0 -0.34 16 16
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
PLGF homodimer 0.023 0.022 0.26 1 -0.59 1 2
PRKACA 0.024 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.097 0.24 -10000 0 -0.59 177 177
VEGFA homodimer 0.025 0.018 0.26 5 -10000 0 5
VEGFR1 homodimer/VEGFA homodimer 0.026 0.023 -10000 0 -0.5 1 1
platelet activating factor biosynthetic process -0.015 0.05 -10000 0 -0.66 1 1
PI3K 0.046 0.032 -10000 0 -0.37 3 3
PRKCA -0.013 0.055 0.25 1 -0.35 17 18
PRKCB -0.009 0.051 -10000 0 -0.36 11 11
VEGFR1 homodimer/PLGF homodimer 0.025 0.024 -10000 0 -0.44 2 2
VEGFA 0.025 0.018 0.26 5 -10000 0 5
VEGFB 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 0.012 0.031 -10000 0 -0.4 2 2
RASA1 0.012 0.03 -10000 0 -0.45 1 1
NRP2 0.024 0.009 0.26 1 -10000 0 1
VEGFR1 homodimer 0.013 0.02 -10000 0 -0.57 1 1
VEGFB homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.031 0.14 -10000 0 -0.47 20 20
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.031 -10000 0 -0.36 3 3
mol:L-citrulline 0.018 0.065 0.3 1 -0.45 6 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.046 0.028 -10000 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.037 0.024 -10000 0 -0.47 1 1
CD2AP 0.023 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.054 0.035 -10000 0 -0.35 3 3
PDPK1 -0.002 0.046 -10000 0 -0.42 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.038 0.024 -10000 0 -0.47 1 1
mol:NADP 0.018 0.065 0.3 1 -0.45 6 7
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.028 -10000 0 -0.42 1 1
VEGFR1 homodimer/NRP2 0.025 0.024 -10000 0 -0.62 1 1
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.049 0.065 -10000 0 -0.39 9 9
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.029 0.064 -10000 0 -0.38 8 8
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.022 0.02 0.26 5 -10000 0 5
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.023 0.004 -10000 0 -10000 0 0
Histones 0.051 0.044 -10000 0 -0.43 1 1
YY1/LSF 0.024 0.049 -10000 0 -0.3 5 5
SMG5 0.02 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.02 0.037 -10000 0 -0.32 8 8
I kappa B alpha/HDAC1 0.028 0.042 -10000 0 -0.45 2 2
SAP18 0.022 0.006 -10000 0 -10000 0 0
RELA 0.019 0.04 -10000 0 -0.3 8 8
HDAC1/Smad7 0.045 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.029 0.039 -10000 0 -0.45 1 1
NuRD/MBD3 Complex 0.025 0.051 -10000 0 -0.31 7 7
NF kappa B1 p50/RelA 0.025 0.065 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.012 0.097 0.26 11 -0.59 21 32
GATA1 0.025 0.026 0.26 10 -10000 0 10
Mad/Max 0.034 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.016 0.081 -10000 0 -0.37 18 18
RBBP7 0.026 0.021 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.004 -10000 0 -10000 0 0
MAX 0.023 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.023 0.004 -10000 0 -10000 0 0
NFKBIA 0.017 0.033 -10000 0 -0.49 2 2
KAT2B 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.029 -10000 0 -0.36 1 1
SIN3 complex 0.055 0.023 -10000 0 -10000 0 0
SMURF1 0.023 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.017 0.26 4 -10000 0 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.021 0.048 -10000 0 -0.38 4 4
YY1/HDAC2 0.024 0.045 -10000 0 -0.3 4 4
YY1/HDAC1 0.024 0.047 -10000 0 -0.29 5 5
NuRD/MBD2 Complex (MeCP1) 0.024 0.054 -10000 0 -0.28 10 10
PPARG -0.06 0.16 -10000 0 -0.36 184 184
HDAC8/hEST1B 0.041 0.018 -10000 0 -10000 0 0
UBE2I 0.022 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.029 0.039 -10000 0 -0.45 1 1
MBD3L2 0.017 0.012 0.26 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.044 0.013 -10000 0 -10000 0 0
CREBBP 0.022 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.022 0.068 -10000 0 -0.36 14 14
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.017 0.03 -10000 0 -0.5 1 1
HDAC2 0.022 0.006 -10000 0 -10000 0 0
YY1 0.015 0.006 -10000 0 -10000 0 0
HDAC8 0.024 0.001 -10000 0 -10000 0 0
SMAD7 0.023 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.024 0.008 0.26 1 -10000 0 1
STAT3 0.016 0.006 -10000 0 -10000 0 0
NFKB1 0.023 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.036 0.047 -10000 0 -0.27 5 5
YY1/SAP30/HDAC1 0.036 0.047 -10000 0 -0.26 5 5
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.033 -10000 0 -0.49 2 2
histone deacetylation 0.024 0.054 -10000 0 -0.28 10 10
STAT3 (dimer non-phopshorylated)/HDAC3 0.018 0.038 -10000 0 -0.43 1 1
nuclear export -0.04 0.018 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GATAD2B 0.02 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.023 0.068 -10000 0 -0.36 18 18
GATA1/HDAC1 0.035 0.018 -10000 0 -10000 0 0
GATA1/HDAC3 0.03 0.043 -10000 0 -0.47 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.032 0.056 -10000 0 -0.44 10 10
SIN3/HDAC complex/Mad/Max 0.015 0.056 -10000 0 -0.28 18 18
NuRD Complex 0.024 0.066 -10000 0 -0.36 10 10
positive regulation of chromatin silencing 0.048 0.042 -10000 0 -0.42 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.023 0.004 -10000 0 -10000 0 0
SIN3A 0.023 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.034 0.038 -10000 0 -0.24 3 3
HDAC complex 0.057 0.022 -10000 0 -10000 0 0
GATA1/Fog1 0.032 0.024 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.044 0.015 -10000 0 -10000 0 0
TNF 0.022 0.074 0.26 19 -0.59 10 29
negative regulation of cell growth 0.015 0.055 -10000 0 -0.28 18 18
NuRD/MBD2/PRMT5 Complex 0.024 0.054 -10000 0 -0.28 10 10
Ran/GTP/Exportin 1 0.034 0.038 -10000 0 -0.24 3 3
NF kappa B/RelA/I kappa B alpha 0.017 0.055 -10000 0 -0.38 9 9
SIN3/HDAC complex/NCoR1 0.007 0.066 -10000 0 -0.32 23 23
TFCP2 0.024 0.002 -10000 0 -10000 0 0
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.023 0.009 0.26 1 -10000 0 1
MBD2 0.023 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.066 -10000 0 -0.44 17 17
AKT1 0.034 0.075 0.35 3 -0.53 3 6
PTK2B 0.008 0.063 0.34 1 -0.36 15 16
VEGFR2 homodimer/Frs2 0.027 0.033 -10000 0 -0.62 2 2
CAV1 -0.097 0.24 -10000 0 -0.59 177 177
CALM1 0.023 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.041 0.036 -10000 0 -0.58 2 2
endothelial cell proliferation 0.045 0.11 0.36 22 -0.61 4 26
mol:Ca2+ 0.016 0.035 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.053 0.036 -10000 0 -0.56 2 2
RP11-342D11.1 0.007 0.032 -10000 0 -0.53 2 2
CDH5 0.019 0.036 -10000 0 -0.59 3 3
VEGFA homodimer 0.048 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.009 0.093 -10000 0 -0.59 21 21
HRAS/GDP 0.032 0.031 -10000 0 -0.57 1 1
SH2D2A 0.039 0.071 0.26 73 -0.59 1 74
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.082 -10000 0 -0.49 8 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.047 0.056 -10000 0 -0.44 3 3
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.05 0.041 -10000 0 -0.63 1 1
GRB10 0.017 0.035 -10000 0 -0.54 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
PAK1 0.022 0.018 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.053 0.049 -10000 0 -0.45 5 5
HRAS 0.024 0.012 0.26 2 -10000 0 2
VEGF/Rho/ROCK1/Integrin Complex 0.013 0.059 -10000 0 -0.48 4 4
HIF1A 0.023 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.051 0.035 -10000 0 -0.55 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.029 -10000 0 -0.59 2 2
Nck/Pak 0.032 0.016 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.039 0.043 -10000 0 -0.72 2 2
mol:GDP 0.04 0.036 -10000 0 -0.61 1 1
mol:NADP 0.025 0.081 0.56 1 -0.45 9 10
eNOS/Hsp90 0.036 0.078 0.54 1 -0.43 8 9
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
mol:IP3 0.016 0.036 -10000 0 -0.54 2 2
HIF1A/ARNT 0.028 0.014 -10000 0 -10000 0 0
SHB 0.024 0.009 0.26 1 -10000 0 1
VEGFA 0.026 0.019 0.27 5 -10000 0 5
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.026 0.084 0.35 1 -0.53 5 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.066 -10000 0 -0.37 18 18
PTPN6 0.023 0.013 0.26 2 -10000 0 2
EPAS1 0.028 0.018 -10000 0 -0.34 2 2
mol:L-citrulline 0.025 0.081 0.56 1 -0.45 9 10
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.05 0.039 -10000 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer 0.043 0.034 -10000 0 -0.58 2 2
VEGFR2/3 heterodimer 0.027 0.043 -10000 0 -0.64 3 3
VEGFB 0.023 0.005 -10000 0 -10000 0 0
MAPK11 0.007 0.049 -10000 0 -0.58 2 2
VEGFR2 homodimer 0.015 0.035 -10000 0 -0.7 2 2
FLT1 0.022 0.006 -10000 0 -10000 0 0
NEDD4 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.008 0.064 0.32 1 -0.66 2 3
MAPK1 0.01 0.064 -10000 0 -0.65 2 2
VEGFA145/NRP2 0.036 0.017 -10000 0 -0.19 1 1
VEGFR1/2 heterodimer 0.026 0.036 -10000 0 -0.68 2 2
KDR 0.015 0.035 -10000 0 -0.7 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.043 0.036 -10000 0 -0.59 2 2
SRC 0.023 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.017 0.073 0.34 4 -0.54 3 7
PI3K 0.029 0.047 -10000 0 -0.64 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.042 0.034 -10000 0 -0.58 2 2
FES 0.015 0.04 -10000 0 -0.42 5 5
GAB1 0.017 0.044 -10000 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.041 0.035 -10000 0 -0.58 2 2
CTNNB1 0.023 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.019 0.13 -10000 0 -0.45 17 17
VEGFR2 homodimer/VEGFA homodimer/Yes 0.04 0.037 -10000 0 -0.5 3 3
PI3K/GAB1 0.043 0.062 0.31 1 -0.53 2 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.055 0.04 -10000 0 -0.46 2 2
PRKACA 0.024 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.042 -10000 0 -0.6 3 3
HSP90AA1 0.023 0.004 -10000 0 -10000 0 0
CDC42 0.017 0.036 -10000 0 -0.55 2 2
actin cytoskeleton reorganization 0.047 0.055 -10000 0 -0.44 3 3
PTK2 0.01 0.062 -10000 0 -0.63 4 4
EDG1 0.007 0.032 -10000 0 -0.53 2 2
mol:DAG 0.016 0.036 -10000 0 -0.54 2 2
CaM/Ca2+ 0.027 0.034 -10000 0 -0.5 2 2
MAP2K3 -0.004 0.041 -10000 0 -0.42 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.041 0.035 -10000 0 -0.56 2 2
PLCG1 0.016 0.036 -10000 0 -0.55 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.051 0.037 -10000 0 -0.56 2 2
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
YES1 0.022 0.021 -10000 0 -0.59 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.042 0.034 -10000 0 -0.58 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.041 0.036 -10000 0 -0.58 2 2
cell migration 0.029 0.08 0.35 3 -0.6 3 6
mol:PI-3-4-5-P3 0.028 0.045 -10000 0 -0.58 2 2
FYN 0.022 0.021 -10000 0 -0.59 1 1
VEGFB/NRP1 0.021 0.033 -10000 0 -0.5 2 2
mol:NO 0.025 0.081 0.56 1 -0.45 9 10
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.025 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.032 -10000 0 -0.56 2 2
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.012 0.085 0.26 4 -0.59 17 21
NOS3 0.025 0.089 0.57 1 -0.53 8 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.066 -10000 0 -0.36 22 22
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.007 0.062 0.35 1 -0.35 17 18
PRKCB -0.004 0.055 -10000 0 -0.38 9 9
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.025 0.034 -10000 0 -0.53 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.04 0.038 -10000 0 -0.64 2 2
VEGFA165/NRP2 0.036 0.017 -10000 0 -0.19 1 1
MAPKKK cascade 0.052 0.07 0.33 10 -0.58 1 11
NRP2 0.024 0.009 0.26 1 -10000 0 1
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.027 0.086 0.42 2 -0.58 4 6
MAP3K13 0.015 0.038 -10000 0 -0.44 4 4
PDPK1 0.017 0.042 -10000 0 -0.61 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.039 0.21 1 -0.3 2 3
SMAD3 0.021 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.037 0.063 -10000 0 -0.44 9 9
SMAD4/Ubc9/PIASy 0.042 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.06 -10000 0 -0.28 2 2
PPM1A 0.023 0.004 -10000 0 -10000 0 0
CALM1 0.023 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.28 6 6
MAP3K1 0.023 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.03 0.042 -10000 0 -0.44 7 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.023 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.019 0.054 -10000 0 -0.59 7 7
UBE2I 0.022 0.006 -10000 0 -10000 0 0
NUP153 0.023 0.004 -10000 0 -10000 0 0
KPNA2 0.036 0.059 0.26 55 -10000 0 55
PIAS4 0.023 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.043 0.037 -10000 0 -10000 0 0
CLOCK 0.022 0.041 -10000 0 -0.59 4 4
TIMELESS/CRY2 0.031 0.023 -10000 0 -10000 0 0
DEC1/BMAL1 0.032 0.013 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.014 -10000 0 -10000 0 0
ARNTL 0.025 0.004 -10000 0 -10000 0 0
TIMELESS 0.018 0.022 -10000 0 -10000 0 0
NPAS2 0.023 0.042 0.27 1 -0.59 4 5
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.007 -10000 0 -0.096 5 5
CHEK1 0.028 0.041 0.26 25 -10000 0 25
mol:HEME 0.007 0.007 0.096 5 -10000 0 5
PER1 0.011 0.079 -10000 0 -0.59 15 15
BMAL/CLOCK/NPAS2 0.05 0.043 -10000 0 -0.38 8 8
BMAL1/CLOCK 0.02 0.055 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.043 0.037 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.037 -10000 0 -10000 0 0
mol:NADPH 0.007 0.007 0.096 5 -10000 0 5
PER1/TIMELESS 0.024 0.049 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.017 0.26 4 -10000 0 4
Arf6 downstream 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
PLAUR 0.04 0.072 0.38 1 -10000 0 1
regulation of axonogenesis -0.011 0.026 0.23 4 -10000 0 4
myoblast fusion -0.025 0.047 -10000 0 -10000 0 0
mol:GTP 0.022 0.032 -10000 0 -0.15 7 7
regulation of calcium-dependent cell-cell adhesion -0.053 0.045 -10000 0 -0.32 2 2
ARF1/GTP 0.029 0.028 -10000 0 -10000 0 0
mol:GM1 0.012 0.025 -10000 0 -10000 0 0
mol:Choline 0.009 0.035 -10000 0 -0.36 5 5
lamellipodium assembly 0.017 0.061 -10000 0 -0.37 7 7
MAPK3 0.031 0.047 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.054 0.045 0.33 2 -10000 0 2
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.048 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.048 -10000 0 -0.26 2 2
ARF6 0.031 0.017 -10000 0 -10000 0 0
RAB11A 0.023 0.004 -10000 0 -10000 0 0
TIAM1 0.026 0.017 0.26 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.031 0.046 0.2 10 -10000 0 10
actin filament bundle formation -0.031 0.051 0.25 4 -10000 0 4
KALRN 0.01 0.055 -10000 0 -0.32 16 16
RAB11FIP3/RAB11A 0.032 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.052 -10000 0 -0.25 4 4
NME1 0.027 0.029 0.27 12 -10000 0 12
Rac1/GDP 0.032 0.052 -10000 0 -0.26 3 3
substrate adhesion-dependent cell spreading 0.022 0.032 -10000 0 -0.15 7 7
cortical actin cytoskeleton organization 0.017 0.061 -10000 0 -0.37 7 7
RAC1 0.024 0.004 -10000 0 -10000 0 0
liver development 0.022 0.032 -10000 0 -0.15 7 7
ARF6/GTP 0.022 0.032 -10000 0 -0.15 7 7
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.048 0.2 2 -0.21 4 6
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.041 -10000 0 -0.41 5 5
RAB11FIP3 0.022 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.061 -10000 0 -0.37 7 7
ruffle organization 0.011 0.026 -10000 0 -0.23 4 4
regulation of epithelial cell migration 0.022 0.032 -10000 0 -0.15 7 7
PLD2 0.02 0.025 -10000 0 -10000 0 0
PIP5K1A 0.011 0.026 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.009 0.035 -10000 0 -0.36 5 5
Rac1/GTP 0.017 0.061 -10000 0 -0.37 7 7
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.004 -10000 0 -10000 0 0
ITGA4 0.026 0.026 0.26 10 -10000 0 10
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.042 0.23 27 -0.44 2 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.019 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.042 0.037 0.34 4 -0.35 2 6
lamellipodium assembly 0 0.079 -10000 0 -0.41 21 21
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.019 -10000 0 -0.44 1 1
ARF6 0.023 0.004 -10000 0 -10000 0 0
TLN1 0.023 0.004 -10000 0 -10000 0 0
PXN 0.01 0.002 -10000 0 -10000 0 0
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
ARF6/GTP 0.046 0.021 -10000 0 -10000 0 0
cell adhesion 0.049 0.02 -10000 0 -10000 0 0
CRKL/CBL 0.031 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.039 0.018 -10000 0 -10000 0 0
ITGB1 0.023 0.004 -10000 0 -10000 0 0
ITGB7 0.028 0.047 0.26 21 -0.59 2 23
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.039 -10000 0 -0.33 6 6
p130Cas/Crk/Dock1 0.04 0.019 -10000 0 -10000 0 0
VCAM1 0.021 0.054 0.26 6 -0.59 6 12
alpha4/beta1 Integrin/Paxillin/Talin 0.05 0.021 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.023 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.046 0.022 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.022 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.05 0.021 -10000 0 -10000 0 0
Rac1/GTP -0.001 0.086 -10000 0 -0.46 21 21
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.034 0.009 -10000 0 -10000 0 0
FBXW11 0.023 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.027 -10000 0 -0.38 3 3
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.043 -10000 0 -0.27 1 1
NFKBIA 0.014 0.036 -10000 0 -0.24 9 9
MAPK14 0.024 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.01 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.02 0.046 -10000 0 -0.59 5 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.01 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.015 0.011 0.25 1 -10000 0 1
PIK3R1 0.022 0.021 -10000 0 -0.59 1 1
NFKB1 0.009 0.012 0.26 2 -10000 0 2
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.025 0.045 -10000 0 -0.25 7 7
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.045 -10000 0 -0.31 1 1
SRC 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.019 -10000 0 -0.44 1 1
NF kappa B1 p50/RelA 0.025 0.045 -10000 0 -0.26 7 7
IKBKB 0.02 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.004 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.025 0.047 -10000 0 -0.24 12 12
cell death 0.023 0.044 -10000 0 -0.3 1 1
NF kappa B1 p105/c-Rel 0.019 0.027 -10000 0 -0.38 3 3
LCK 0.025 0.075 0.26 28 -0.59 9 37
BCL3 0.024 0.009 0.26 1 -10000 0 1
Arf1 pathway

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
coatomer protein complex 0.011 0.032 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.048 -10000 0 -0.19 3 3
AP2 0.034 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.01 -10000 0 -10000 0 0
CLTB 0.024 0.012 0.26 2 -10000 0 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.013 0.009 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.023 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.005 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.017 -10000 0 -10000 0 0
ARF1/GTP 0.023 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.011 0.2 2 -10000 0 2
mol:Choline 0.007 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.017 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.022 0.19 2 -10000 0 2
AP2M1 0.023 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.017 -10000 0 -10000 0 0
ARFIP2 0.014 0.018 -10000 0 -10000 0 0
COPA 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.024 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.013 0.008 -10000 0 -10000 0 0
GGA3 0.022 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0.042 -10000 0 -0.23 22 22
AP2A1 0.023 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.025 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.011 0.051 -10000 0 -0.26 26 26
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.028 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.024 -10000 0 -10000 0 0
PLD2 0.007 0.017 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.005 -10000 0 -10000 0 0
PIP5K1A 0.008 0.017 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.021 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.017 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.005 -10000 0 -10000 0 0
GOSR2 0.009 0.026 -10000 0 -0.31 5 5
USO1 0.009 0.022 -10000 0 -0.32 3 3
GBF1 0.009 0.021 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.027 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.044 0.015 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.011 -10000 0 -0.28 1 1
MDM2/SUMO1 0.032 0.04 -10000 0 -0.24 3 3
HDAC4 0.023 0.021 -10000 0 -0.59 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.018 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.011 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.04 -10000 0 -0.24 4 4
SUMO1/HDAC1 0.034 0.038 -10000 0 -0.24 3 3
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.055 0.019 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.022 0.036 -10000 0 -0.24 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.005 -10000 0 -10000 0 0
UBE2I 0.022 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.038 0.25 1 -0.24 3 4
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.023 0.005 -10000 0 -10000 0 0
PIAS1 0.023 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.023 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.066 0.024 -10000 0 -9999 0 0
NFKB1 0.023 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.035 0.015 -10000 0 -9999 0 0
RELB 0.025 0.022 0.26 7 -9999 0 7
NFKB2 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.033 0.014 -10000 0 -9999 0 0
regulation of B cell activation 0.032 0.014 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 899 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.LL.A441 TCGA.LL.A440 TCGA.JL.A3YX TCGA.JL.A3YW
109_MAP3K5 0.097 0.024 0.0011 0.024
47_PPARGC1A 0.024 0.024 0.024 0.024
105_BMP4 0.024 0.024 0.024 0.024
105_BMP6 0.024 0.024 0.024 0.024
105_BMP7 0.024 0.024 0.024 0.024
105_BMP2 0.024 0.024 0.024 0.024
131_RELN/VLDLR 0.062 0.062 0.062 -0.35
30_TGFB1/TGF beta receptor Type II 0.018 0.024 0.018 0.024
84_STAT5B 0.012 0.025 -0.063 -0.087
84_STAT5A 0.012 0.025 -0.063 -0.087
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/3351778/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BRCA-TP/3471814/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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle