PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C11G0JWG
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C11G0JWG
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 62 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 333
Signaling events mediated by Stem cell factor receptor (c-Kit) 264
Signaling mediated by p38-alpha and p38-beta 261
Class IB PI3K non-lipid kinase events 259
Reelin signaling pathway 220
Aurora B signaling 196
EGFR-dependent Endothelin signaling events 187
FOXA2 and FOXA3 transcription factor networks 183
PLK1 signaling events 168
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 157
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 1037 . 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 ( 1037 ).

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 0.3211 333 16993 51 -0.061 0.73 1000 -1000 -0.037 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2546 264 20630 78 -0.57 0.18 1000 -1000 -0.043 -1000
Signaling mediated by p38-alpha and p38-beta 0.2517 261 11486 44 -0.32 0.024 1000 -1000 -0.016 -1000
Class IB PI3K non-lipid kinase events 0.2498 259 777 3 -0.13 -1000 1000 -1000 -0.012 -1000
Reelin signaling pathway 0.2122 220 12366 56 -0.32 0.054 1000 -1000 -0.03 -1000
Aurora B signaling 0.1890 196 13167 67 -0.22 0.27 1000 -1000 -0.032 -1000
EGFR-dependent Endothelin signaling events 0.1803 187 3930 21 -0.21 0.034 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 0.1765 183 8438 46 -1.1 0.034 1000 -1000 -0.033 -1000
PLK1 signaling events 0.1620 168 14364 85 -0.065 0.24 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1514 157 10680 68 -0.36 0.17 1000 -1000 -0.043 -1000
HIF-1-alpha transcription factor network 0.1504 156 11923 76 -0.49 0.035 1000 -1000 -0.046 -1000
EPHB forward signaling 0.1456 151 12868 85 -0.21 0.14 1000 -1000 -0.058 -1000
Glucocorticoid receptor regulatory network 0.1437 149 17065 114 -0.74 0.28 1000 -1000 -0.045 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1408 146 12895 88 -0.31 0.12 1000 -1000 -0.061 -1000
p75(NTR)-mediated signaling 0.1369 142 17854 125 -0.23 0.099 1000 -1000 -0.055 -1000
Endothelins 0.1321 137 13171 96 -0.34 0.17 1000 -1000 -0.034 -1000
Ephrin B reverse signaling 0.1167 121 5819 48 -0.21 0.096 1000 -1000 -0.027 -1000
IL4-mediated signaling events 0.1070 111 10178 91 -0.67 0.26 1000 -1000 -0.066 -1000
Wnt signaling 0.1070 111 777 7 -0.096 0.019 1000 -1000 -0.014 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1041 108 5878 54 -0.32 0.055 1000 -1000 -0.041 -1000
Glypican 2 network 0.1022 106 424 4 0.033 0.057 1000 -1000 0.018 -1000
IGF1 pathway 0.1022 106 6062 57 -0.11 0.044 1000 -1000 -0.035 -1000
Arf6 signaling events 0.0974 101 6306 62 -0.21 0.05 1000 -1000 -0.036 -1000
Noncanonical Wnt signaling pathway 0.0955 99 2593 26 -0.096 0.024 1000 -1000 -0.037 -1000
Nongenotropic Androgen signaling 0.0906 94 4896 52 -0.24 0.13 1000 -1000 -0.021 -1000
IL23-mediated signaling events 0.0906 94 5670 60 -0.3 0.085 1000 -1000 -0.049 -1000
ErbB2/ErbB3 signaling events 0.0887 92 6025 65 -0.27 0.034 1000 -1000 -0.048 -1000
BMP receptor signaling 0.0887 92 7531 81 -0.38 0.1 1000 -1000 -0.042 -1000
Signaling events regulated by Ret tyrosine kinase 0.0887 92 7611 82 -0.071 0.1 1000 -1000 -0.055 -1000
Plasma membrane estrogen receptor signaling 0.0887 92 7933 86 -0.12 0.11 1000 -1000 -0.051 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0868 90 10901 120 -0.37 0.17 1000 -1000 -0.039 -1000
Calcium signaling in the CD4+ TCR pathway 0.0849 88 2729 31 -0.19 0.025 1000 -1000 -0.038 -1000
Signaling events mediated by PTP1B 0.0839 87 6687 76 -0.45 0.081 1000 -1000 -0.023 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0829 86 7369 85 -0.24 0.024 1000 -1000 -0.037 -1000
Visual signal transduction: Rods 0.0820 85 4467 52 -0.33 0.056 1000 -1000 -0.022 -1000
Syndecan-1-mediated signaling events 0.0791 82 2794 34 -0.071 0.18 1000 -1000 -0.03 -1000
S1P1 pathway 0.0781 81 2947 36 -0.33 0.024 1000 -1000 -0.027 -1000
Glypican 1 network 0.0771 80 3866 48 -0.2 0.045 1000 -1000 -0.019 -1000
Aurora C signaling 0.0762 79 557 7 0 0.15 1000 -1000 -0.017 -1000
ErbB4 signaling events 0.0752 78 5386 69 -0.28 0.062 1000 -1000 -0.026 -1000
TCR signaling in naïve CD8+ T cells 0.0743 77 7210 93 -0.091 0.087 1000 -1000 -0.044 -1000
Integrins in angiogenesis 0.0723 75 6383 84 -0.2 0.12 1000 -1000 -0.04 -1000
amb2 Integrin signaling 0.0714 74 6092 82 -0.34 0.12 1000 -1000 -0.024 -1000
Effects of Botulinum toxin 0.0704 73 1913 26 -0.004 0.1 1000 -1000 -0.006 -1000
Ephrin A reverse signaling 0.0675 70 492 7 -0.033 0.023 1000 -1000 -0.004 -1000
LPA receptor mediated events 0.0665 69 7087 102 -0.19 0.12 1000 -1000 -0.054 -1000
IL6-mediated signaling events 0.0646 67 5037 75 -0.18 0.053 1000 -1000 -0.032 -1000
Signaling events mediated by the Hedgehog family 0.0627 65 3414 52 -0.12 0.029 1000 -1000 -0.029 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0598 62 3244 52 -0.11 0.07 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 0.0598 62 2134 34 -0.12 0.035 1000 -1000 -0.03 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0588 61 2081 34 -0.023 0.06 1000 -1000 -0.021 -1000
E-cadherin signaling in keratinocytes 0.0579 60 2582 43 -0.19 0.031 1000 -1000 -0.019 -1000
Visual signal transduction: Cones 0.0559 58 2210 38 -0.026 0.16 1000 -1000 -0.01 -1000
Fc-epsilon receptor I signaling in mast cells 0.0540 56 5468 97 -0.14 0.034 1000 -1000 -0.045 -1000
Syndecan-3-mediated signaling events 0.0540 56 1975 35 -0.23 0.055 1000 -1000 -0.016 -1000
PDGFR-alpha signaling pathway 0.0530 55 2455 44 -0.3 0.036 1000 -1000 -0.03 -1000
IL12-mediated signaling events 0.0521 54 4749 87 -0.31 0.073 1000 -1000 -0.061 -1000
Canonical Wnt signaling pathway 0.0521 54 2796 51 -0.28 0.13 1000 -1000 -0.035 -1000
Syndecan-2-mediated signaling events 0.0511 53 3696 69 -0.12 0.12 1000 -1000 -0.029 -1000
Presenilin action in Notch and Wnt signaling 0.0501 52 3172 61 -0.28 0.13 1000 -1000 -0.039 -1000
Nectin adhesion pathway 0.0501 52 3301 63 -0.056 0.045 1000 -1000 -0.036 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0501 52 1725 33 -0.38 0.06 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 0.0473 49 2322 47 -0.43 0.04 1000 -1000 -0.027 -1000
Rapid glucocorticoid signaling 0.0463 48 964 20 -0.11 0.027 1000 -1000 -0.004 -1000
Signaling events mediated by HDAC Class III 0.0453 47 1913 40 -0.33 0.045 1000 -1000 -0.025 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0434 45 3363 74 -0.19 0.049 1000 -1000 -0.054 -1000
LPA4-mediated signaling events 0.0405 42 510 12 -0.12 0.006 1000 -1000 -0.02 -1000
TCGA08_rtk_signaling 0.0405 42 1109 26 -0.19 0.037 1000 -1000 -0.009 -1000
Aurora A signaling 0.0395 41 2509 60 -0.081 0.18 1000 -1000 -0.02 -1000
Syndecan-4-mediated signaling events 0.0386 40 2716 67 -0.2 0.12 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 0.0386 40 2836 70 -0.17 0.11 1000 -1000 -0.043 -1000
Insulin Pathway 0.0366 38 2862 74 -0.12 0.06 1000 -1000 -0.047 -1000
Ras signaling in the CD4+ TCR pathway 0.0366 38 655 17 -0.054 0.026 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 0.0357 37 2882 76 -0.16 0.065 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 0.0357 37 300 8 -0.018 0.061 1000 -1000 -0.003 -1000
Regulation of p38-alpha and p38-beta 0.0347 36 1975 54 -0.24 0.053 1000 -1000 -0.042 -1000
Regulation of Telomerase 0.0347 36 3678 102 -0.2 0.14 1000 -1000 -0.029 -1000
IL27-mediated signaling events 0.0338 35 1796 51 -0.19 0.075 1000 -1000 -0.052 -1000
Regulation of nuclear SMAD2/3 signaling 0.0318 33 4521 136 -0.21 0.08 1000 -1000 -0.032 -1000
Thromboxane A2 receptor signaling 0.0318 33 3566 105 -0.19 0.035 1000 -1000 -0.04 -1000
IL2 signaling events mediated by STAT5 0.0318 33 734 22 0.005 0.11 1000 -1000 -0.033 -1000
BCR signaling pathway 0.0318 33 3302 99 -0.078 0.055 1000 -1000 -0.046 -1000
Osteopontin-mediated events 0.0309 32 1251 38 -0.14 0.088 1000 -1000 -0.034 -1000
TCGA08_p53 0.0270 28 198 7 -0.011 0.02 1000 -1000 -0.01 -1000
Arf6 trafficking events 0.0260 27 1924 71 -0.27 0.042 1000 -1000 -0.025 -1000
Signaling mediated by p38-gamma and p38-delta 0.0231 24 372 15 -0.027 0.024 1000 -1000 -0.024 -1000
Caspase cascade in apoptosis 0.0222 23 1765 74 -0.027 0.057 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 0.0212 22 1557 68 -0.16 0.043 1000 -1000 -0.022 -1000
Ceramide signaling pathway 0.0212 22 1743 76 -0.1 0.063 1000 -1000 -0.032 -1000
Hedgehog signaling events mediated by Gli proteins 0.0193 20 1308 65 -0.087 0.056 1000 -1000 -0.036 -1000
FoxO family signaling 0.0193 20 1313 64 -0.017 0.23 1000 -1000 -0.031 -1000
IL2 signaling events mediated by PI3K 0.0193 20 1214 58 -0.001 0.064 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 0.0183 19 769 39 -0.081 0.027 1000 -1000 -0.017 -1000
mTOR signaling pathway 0.0183 19 1024 53 -0.024 0.028 1000 -1000 -0.034 -1000
S1P4 pathway 0.0183 19 480 25 -0.01 0.044 1000 -1000 -0.024 -1000
BARD1 signaling events 0.0174 18 1070 57 -0.047 0.11 1000 -1000 -0.029 -1000
E-cadherin signaling in the nascent adherens junction 0.0174 18 1413 76 -0.025 0.051 1000 -1000 -0.045 -1000
JNK signaling in the CD4+ TCR pathway 0.0164 17 301 17 0.003 0.063 1000 -1000 -0.031 -1000
ceramide signaling pathway 0.0154 16 800 49 -0.002 0.036 1000 -1000 -0.032 -1000
HIF-2-alpha transcription factor network 0.0154 16 722 43 -0.15 0.16 1000 -1000 -0.047 -1000
S1P3 pathway 0.0154 16 713 42 -0.011 0.042 1000 -1000 -0.023 -1000
Retinoic acid receptors-mediated signaling 0.0145 15 870 58 -0.052 0.052 1000 -1000 -0.041 -1000
PLK2 and PLK4 events 0.0135 14 42 3 0.016 0.033 1000 -1000 -0.008 -1000
TRAIL signaling pathway 0.0135 14 684 48 -0.017 0.043 1000 -1000 -0.026 -1000
S1P5 pathway 0.0135 14 249 17 -0.003 0.033 1000 -1000 -0.015 -1000
IL1-mediated signaling events 0.0125 13 820 62 -0.009 0.063 1000 -1000 -0.035 -1000
PDGFR-beta signaling pathway 0.0125 13 1274 97 -0.028 0.056 1000 -1000 -0.049 -1000
p38 MAPK signaling pathway 0.0125 13 590 44 -0.019 0.066 1000 -1000 -0.017 -1000
E-cadherin signaling events 0.0116 12 63 5 0.009 0.031 1000 -1000 0.014 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0106 11 319 28 -0.003 0.051 1000 -1000 -0.016 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0106 11 500 45 0.004 0.055 1000 -1000 -0.036 -1000
Class I PI3K signaling events 0.0106 11 875 73 -0.019 0.05 1000 -1000 -0.031 -1000
EPO signaling pathway 0.0096 10 589 55 0.015 0.081 1000 -1000 -0.026 -1000
IFN-gamma pathway 0.0096 10 724 68 -0.007 0.077 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0096 10 387 37 -0.008 0.067 1000 -1000 -0.025 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0096 10 875 83 -0.019 0.047 1000 -1000 -0.03 -1000
Canonical NF-kappaB pathway 0.0087 9 353 39 0 0.051 1000 -1000 -0.023 -1000
a4b1 and a4b7 Integrin signaling 0.0087 9 45 5 0.024 0.041 1000 -1000 0.012 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0087 9 1169 125 -0.099 0.054 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class II 0.0077 8 662 75 -0.036 0.063 1000 -1000 -0.029 -1000
Insulin-mediated glucose transport 0.0077 8 262 32 -0.12 0.039 1000 -1000 -0.023 -1000
VEGFR1 specific signals 0.0077 8 479 56 -0.099 0.053 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class I 0.0048 5 615 104 -0.059 0.057 1000 -1000 -0.029 -1000
Atypical NF-kappaB pathway 0.0048 5 160 31 0 0.029 1000 -1000 -0.008 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0039 4 112 23 -0.003 0.043 1000 -1000 -0.02 -1000
Circadian rhythm pathway 0.0039 4 96 22 -0.007 0.049 1000 -1000 -0.022 -1000
Arf6 downstream pathway 0.0039 4 212 43 -0.054 0.055 1000 -1000 -0.024 -1000
Paxillin-dependent events mediated by a4b1 0.0039 4 153 36 -0.048 0.052 1000 -1000 -0.033 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0010 1 28 27 -0.008 0.056 1000 -1000 -0.034 -1000
Arf1 pathway 0.0010 1 97 54 -0.001 0.045 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 0 0.068 1000 -1000 0 -1000
Total NA 8160 480994 7203 -20 -990 131000 -131000 -3.9 -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 0.6 0.39 0.99 398 -1 3 401
PLK1 0.37 0.25 0.6 462 -0.89 1 463
BIRC5 0.39 0.25 0.64 355 -0.9 3 358
HSPA1B 0.6 0.39 1 387 -1 3 390
MAP2K1 0.17 0.12 0.31 333 -10000 0 333
BRCA2 0.61 0.41 1 395 -0.98 4 399
FOXM1 0.71 0.5 1.2 450 -1.1 5 455
XRCC1 0.6 0.4 1 395 -1 3 398
FOXM1B/p19 0.13 0.27 0.82 58 -1 5 63
Cyclin D1/CDK4 0.53 0.38 0.9 392 -0.98 3 395
CDC2 0.66 0.44 1.1 445 -0.94 5 450
TGFA 0.53 0.39 0.89 417 -0.94 8 425
SKP2 0.61 0.4 1 400 -1 3 403
CCNE1 0.092 0.097 0.3 169 -10000 0 169
CKS1B 0.65 0.42 1 435 -0.98 3 438
RB1 0.3 0.31 0.66 359 -0.62 7 366
FOXM1C/SP1 0.55 0.36 0.91 367 -1 7 374
AURKB 0.31 0.3 0.63 316 -0.8 19 335
CENPF 0.7 0.46 1.1 468 -0.98 3 471
CDK4 0.084 0.055 0.24 23 -10000 0 23
MYC 0.36 0.38 0.85 262 -0.96 6 268
CHEK2 0.16 0.12 0.31 330 -10000 0 330
ONECUT1 0.55 0.39 0.94 404 -1.1 3 407
CDKN2A -0.061 0.12 0.22 17 -0.23 203 220
LAMA4 0.6 0.41 1 397 -1.1 6 403
FOXM1B/HNF6 0.56 0.4 0.97 370 -1.3 3 373
FOS 0.3 0.65 1 309 -1 63 372
SP1 0.024 0.021 -10000 0 -0.21 4 4
CDC25B 0.61 0.4 1 376 -1 3 379
response to radiation 0.12 0.086 0.24 259 -10000 0 259
CENPB 0.61 0.4 1 402 -1 3 405
CENPA 0.66 0.44 1.1 454 -1 3 457
NEK2 0.73 0.46 1.1 502 -0.96 3 505
HIST1H2BA 0.6 0.39 0.99 390 -1 3 393
CCNA2 0.14 0.13 0.3 387 -10000 0 387
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.64 0.43 1.1 374 -1.2 3 377
CCNB2 0.67 0.44 1.1 462 -1 3 465
CCNB1 0.67 0.46 1.1 415 -1.1 3 418
ETV5 0.61 0.4 1 393 -1 3 396
ESR1 0.47 0.55 1 357 -1 16 373
CCND1 0.55 0.42 0.96 415 -1 3 418
GSK3A 0.14 0.091 0.28 195 -10000 0 195
Cyclin A-E1/CDK1-2 0.24 0.16 0.4 432 -10000 0 432
CDK2 0.058 0.029 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.15 0.11 0.28 361 -10000 0 361
FOXM1B/Cbp/p300 0.25 0.3 0.73 67 -0.94 5 72
GAS1 0.55 0.48 0.99 386 -1.1 33 419
MMP2 0.6 0.41 0.99 395 -1.2 10 405
RB1/FOXM1C 0.48 0.39 0.88 388 -1 3 391
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.32 4 -0.38 442 446
CRKL -0.17 0.21 0.26 1 -0.4 455 456
HRAS -0.13 0.18 -10000 0 -0.36 281 281
mol:PIP3 -0.14 0.2 0.28 2 -0.37 345 347
SPRED1 0.024 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 462 462
FOXO3 -0.14 0.2 0.53 1 -0.36 406 407
AKT1 -0.16 0.21 0.37 1 -0.39 425 426
BAD -0.15 0.2 0.35 1 -0.36 398 399
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 467 467
GSK3B -0.14 0.2 0.53 1 -0.37 391 392
RAF1 -0.097 0.16 0.25 4 -0.35 63 67
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 461 461
STAT1 -0.44 0.52 -10000 0 -1 472 472
HRAS/SPRED1 -0.094 0.16 -10000 0 -0.35 65 65
cell proliferation -0.18 0.22 -10000 0 -0.42 463 463
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.033 -10000 0 -0.58 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 469 469
HRAS/SPRED2 -0.094 0.16 -10000 0 -0.34 68 68
LYN/TEC/p62DOK -0.14 0.22 -10000 0 -0.4 385 385
MAPK3 -0.066 0.12 0.33 5 -0.28 24 29
STAP1 -0.18 0.22 -10000 0 -0.42 465 465
GRAP2 0.016 0.069 0.26 3 -0.58 13 16
JAK2 -0.37 0.45 -10000 0 -0.84 471 471
STAT1 (dimer) -0.43 0.51 -10000 0 -0.97 472 472
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 384 384
actin filament polymerization -0.18 0.22 0.33 1 -0.41 462 463
LYN 0.021 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 471 471
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 411 411
PI3K -0.15 0.22 -10000 0 -0.4 441 441
PTEN 0.023 0.02 -10000 0 -0.58 1 1
SCF/KIT/EPO/EPOR -0.51 0.63 -10000 0 -1.2 465 465
MAPK8 -0.18 0.22 -10000 0 -0.42 463 463
STAT3 (dimer) -0.18 0.22 0.27 1 -0.41 461 462
positive regulation of transcription -0.053 0.11 0.24 13 -0.24 20 33
mol:GDP -0.13 0.19 -10000 0 -0.37 302 302
PIK3C2B -0.17 0.21 -10000 0 -0.42 363 363
CBL/CRKL -0.16 0.2 0.26 1 -0.38 445 446
FER -0.18 0.22 -10000 0 -0.42 464 464
SH2B3 -0.18 0.22 -10000 0 -0.42 464 464
PDPK1 -0.12 0.19 0.35 8 -0.35 310 318
SNAI2 -0.17 0.21 0.28 4 -0.42 415 419
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 473 473
KITLG -0.004 0.059 0.26 10 -0.6 5 15
cell motility -0.32 0.39 -10000 0 -0.73 473 473
PTPN6 0.032 0.018 0.27 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -1 15 15
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 470 470
SOCS1 0.025 0.032 0.26 12 -0.58 1 13
cell migration 0.18 0.22 0.41 468 -10000 0 468
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.042 0.093 0.25 163 -10000 0 163
VAV1 0.023 0.034 0.26 2 -0.58 3 5
GRB10 -0.18 0.22 -10000 0 -0.42 461 461
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 468 468
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.076 0.13 0.3 7 -0.31 24 31
CBL 0.022 0.008 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 466 466
MAP2K2 -0.076 0.14 0.33 6 -0.31 23 29
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 342 342
STAT5A -0.27 0.33 -10000 0 -0.62 470 470
GRB2 0.023 0.01 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 416 420
SHC/GRAP2 0.024 0.05 -10000 0 -0.31 17 17
PTPRO -0.18 0.22 -10000 0 -0.42 468 468
SH2B2 -0.18 0.22 -10000 0 -0.42 462 462
DOK1 0.025 0.015 0.26 4 -10000 0 4
MATK -0.19 0.22 -10000 0 -0.42 468 468
CREBBP -0.027 0.072 -10000 0 -10000 0 0
BCL2 -0.16 0.32 -10000 0 -1.3 58 58
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 -0.32 0.51 0.43 4 -1 338 342
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.088 0.18 -10000 0 -0.34 336 336
ATF2/c-Jun -0.082 0.16 -10000 0 -0.42 96 96
MAPK11 -0.083 0.18 -10000 0 -0.35 305 305
MITF -0.12 0.22 0.28 1 -0.41 334 335
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 340 340
KRT8 -0.11 0.21 -10000 0 -0.4 318 318
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.53 337 337
CEBPB -0.1 0.2 0.29 1 -0.4 314 315
SLC9A1 -0.12 0.21 -10000 0 -0.41 333 333
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.21 -10000 0 -0.39 328 328
p38alpha-beta/MNK1 -0.11 0.25 -10000 0 -0.45 308 308
JUN -0.082 0.16 -10000 0 -0.41 96 96
PPARGC1A -0.2 0.33 0.26 2 -0.56 400 402
USF1 -0.1 0.19 0.32 3 -0.38 315 318
RAB5/GDP/GDI1 -0.082 0.16 -10000 0 -0.3 326 326
NOS2 -0.11 0.22 -10000 0 -0.56 90 90
DDIT3 -0.11 0.21 -10000 0 -0.4 335 335
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.095 0.17 0.28 3 -0.33 319 322
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 308 308
CREB1 -0.12 0.22 -10000 0 -0.43 339 339
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.41 306 306
RPS6KA4 -0.11 0.21 -10000 0 -0.4 333 333
PLA2G4A -0.13 0.22 -10000 0 -0.43 334 334
GDI1 -0.11 0.21 -10000 0 -0.4 339 339
TP53 -0.15 0.27 0.28 1 -0.53 318 319
RPS6KA5 -0.12 0.22 -10000 0 -0.41 342 342
ESR1 -0.16 0.24 0.29 1 -0.43 387 388
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 335 335
MEF2A -0.11 0.21 0.29 1 -0.4 334 335
EIF4EBP1 -0.12 0.22 0.28 1 -0.44 324 325
KRT19 -0.11 0.21 0.32 1 -0.41 315 316
ELK4 -0.1 0.19 0.31 3 -0.38 319 322
ATF6 -0.1 0.19 0.32 3 -0.38 320 323
ATF1 -0.12 0.22 -10000 0 -0.43 341 341
p38alpha-beta/MAPKAPK2 -0.096 0.22 -10000 0 -0.41 293 293
p38alpha-beta/MAPKAPK3 -0.11 0.25 -10000 0 -0.46 306 306
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 0.26 0.57 259 -10000 0 259
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.57 259 259
PDE3B -0.13 0.26 -10000 0 -0.58 259 259
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 0.038 0.028 -10000 0 -10000 0 0
VLDLR 0.008 0.093 -10000 0 -0.58 25 25
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.58 2 2
ITGA3 0.022 0.021 0.26 1 -0.58 1 2
RELN/VLDLR/Fyn -0.2 0.21 -10000 0 -0.38 576 576
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.045 -10000 0 -0.32 7 7
AKT1 -0.15 0.14 -10000 0 -0.27 520 520
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.055 0.26 57 -10000 0 57
RELN/LRP8/DAB1 -0.16 0.19 0.32 4 -0.33 581 585
LRPAP1/LRP8 0.049 0.048 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.15 0.19 0.32 4 -0.31 565 569
DAB1/alpha3/beta1 Integrin -0.14 0.18 -10000 0 -0.32 417 417
long-term memory -0.18 0.22 0.34 5 -0.36 558 563
DAB1/LIS1 -0.15 0.19 0.3 4 -0.31 571 575
DAB1/CRLK/C3G -0.15 0.18 -10000 0 -0.3 558 558
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.15 0.19 0.3 4 -0.31 576 580
ARHGEF2 0.021 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.034 0.18 0.26 12 -0.58 101 113
CDK5R1 0.028 0.035 0.26 22 -10000 0 22
RELN -0.32 0.3 0.26 2 -0.58 592 594
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
RELN/LRP8/Fyn -0.18 0.2 -10000 0 -0.36 569 569
GRIN2A/RELN/LRP8/DAB1/Fyn -0.17 0.22 0.33 4 -0.36 532 536
MAPK8 0.02 0.05 -10000 0 -0.58 7 7
RELN/VLDLR/DAB1 -0.18 0.2 0.32 2 -0.34 580 582
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.18 0.22 1 -0.33 582 583
RELN/LRP8 -0.19 0.2 -10000 0 -0.36 585 585
GRIN2B/RELN/LRP8/DAB1/Fyn -0.17 0.2 0.36 3 -0.33 586 589
PI3K 0.029 0.043 -10000 0 -0.4 9 9
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.032 0.021 -10000 0 -0.43 1 1
RAP1A -0.16 0.15 0.34 3 -0.3 394 397
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.031 0.26 5 -0.58 2 7
CRLK/C3G 0.034 0.01 -10000 0 -10000 0 0
GRIN2B -0.02 0.15 0.26 1 -0.58 69 70
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.088 0.12 -10000 0 -0.35 71 71
neuron adhesion -0.15 0.15 0.32 4 -0.48 21 25
LRP8 0.047 0.071 0.26 101 -10000 0 101
GSK3B -0.14 0.14 -10000 0 -0.37 73 73
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.32 2 -0.32 566 568
MAP3K11 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.16 -10000 0 -0.28 565 565
CDK5 0.025 0.015 0.26 4 -10000 0 4
MAPT -0.023 0.2 0.87 19 -0.52 101 120
neuron migration -0.18 0.18 0.27 2 -0.35 474 476
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.088 0.12 -10000 0 -0.36 70 70
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 584 584
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 0.1 0.1 0.24 302 -0.26 2 304
STMN1 0.081 0.08 0.27 67 -10000 0 67
Aurora B/RasGAP/Survivin 0.2 0.14 0.33 486 -10000 0 486
Chromosomal passenger complex/Cul3 protein complex 0.006 0.14 0.21 60 -0.3 43 103
BIRC5 0.18 0.12 0.27 677 -10000 0 677
DES -0.15 0.32 -10000 0 -0.58 260 260
Aurora C/Aurora B/INCENP 0.11 0.079 0.33 6 -0.3 1 7
Aurora B/TACC1 0.074 0.1 0.18 214 -0.34 23 237
Aurora B/PP2A 0.11 0.083 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.032 0.027 0.14 9 -10000 0 9
mitotic metaphase/anaphase transition -0.006 0.006 -10000 0 -10000 0 0
NDC80 0.14 0.12 0.27 463 -10000 0 463
Cul3 protein complex -0.12 0.2 -10000 0 -0.37 401 401
KIF2C 0.15 0.11 0.24 565 -10000 0 565
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.26 747 -10000 0 747
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.083 0.2 263 -10000 0 263
SEPT1 0.03 0.041 0.26 31 -10000 0 31
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.024 0.26 10 -10000 0 10
NSUN2/NPM1/Nucleolin 0.076 0.19 0.31 31 -0.45 94 125
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.072 0.062 0.24 33 -10000 0 33
AURKB 0.15 0.12 0.26 535 -10000 0 535
AURKC 0.026 0.031 0.26 11 -0.58 1 12
CDCA8 0.11 0.11 0.27 336 -10000 0 336
cytokinesis 0.15 0.15 0.3 391 -0.34 5 396
Aurora B/Septin1 0.18 0.17 0.35 434 -0.33 4 438
AURKA 0.12 0.12 0.26 411 -10000 0 411
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.29 -10000 0 -0.58 409 409
BUB1 0.18 0.11 0.26 690 -10000 0 690
hSgo1/Aurora B/Survivin 0.27 0.18 0.42 604 -10000 0 604
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.19 0.14 0.36 329 -10000 0 329
SGOL1 0.17 0.12 0.26 624 -10000 0 624
CENPA 0.17 0.14 0.3 495 -0.23 2 497
NCAPG 0.13 0.12 0.26 476 -10000 0 476
Aurora B/HC8 Proteasome 0.11 0.083 -10000 0 -10000 0 0
NCAPD2 0.024 0.009 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.083 0.2 107 -10000 0 107
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.12 0.12 0.26 395 -10000 0 395
NPM1 0.068 0.13 0.26 5 -0.38 34 39
RASA1 0.024 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 0.11 0.083 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.21 0.16 0.37 423 -10000 0 423
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 0.075 0.12 0.27 22 -0.31 28 50
MYLK 0.023 0.14 0.24 8 -0.31 119 127
KIF23 0.1 0.11 0.27 307 -10000 0 307
VIM 0.08 0.085 0.38 30 -0.42 2 32
RACGAP1 0.042 0.05 0.27 45 -10000 0 45
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.063 0.14 -10000 0 -0.46 35 35
Chromosomal passenger complex 0.18 0.13 0.28 550 -10000 0 550
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 488 -10000 0 488
TACC1 0.006 0.089 -10000 0 -0.58 23 23
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
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 0.026 0.021 0.26 8 -10000 0 8
EGFR -0.19 0.29 -10000 0 -0.58 363 363
EGF/EGFR -0.16 0.22 -10000 0 -0.37 486 486
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.36 370 370
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.019 -10000 0 -0.58 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.083 0.23 0.26 2 -0.58 182 184
EGF/EGFR dimer/SHC -0.15 0.22 -10000 0 -0.41 395 395
mol:GDP -0.12 0.2 -10000 0 -0.35 370 370
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.019 0.15 0.26 1 -0.58 72 73
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.33 369 369
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.11 0.19 -10000 0 -0.34 369 369
FRAP1 -0.14 0.16 0.16 3 -0.34 370 373
EGF/EGFR dimer -0.21 0.26 -10000 0 -0.46 493 493
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 -0.42 75 75
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.24 0.27 -10000 0 -0.7 147 147
PCK1 -0.93 0.63 -10000 0 -1.4 628 628
HNF4A -0.23 0.28 -10000 0 -0.78 84 84
KCNJ11 -0.28 0.3 -10000 0 -0.74 176 176
AKT1 -0.17 0.16 -10000 0 -0.39 121 121
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.45 0.48 -10000 0 -1 364 364
NKX2-1 -0.035 0.16 0.54 1 -10000 0 1
ACADM -0.25 0.27 -10000 0 -0.7 154 154
TAT -1.1 0.62 -10000 0 -1.4 735 735
CEBPB 0.024 0.009 -10000 0 -10000 0 0
CEBPA 0.02 0.057 -10000 0 -0.58 9 9
TTR -0.41 0.29 -10000 0 -0.74 310 310
PKLR -0.22 0.27 0.54 4 -0.68 139 143
APOA1 -0.28 0.31 -10000 0 -0.84 107 107
CPT1C -0.25 0.27 0.58 1 -0.72 129 130
ALAS1 -0.15 0.16 -10000 0 -0.72 7 7
TFRC -0.42 0.26 -10000 0 -0.67 405 405
FOXF1 0.017 0.047 0.26 6 -0.58 4 10
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.031 0.26 7 -10000 0 7
CPT1A -0.24 0.27 -10000 0 -0.7 138 138
HMGCS1 -0.25 0.26 -10000 0 -0.7 141 141
NR3C1 -0.12 0.12 -10000 0 -0.29 176 176
CPT1B -0.25 0.27 -10000 0 -0.67 181 181
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.023 -10000 0 -10000 0 0
GCK -0.28 0.32 -10000 0 -0.82 176 176
CREB1 -0.076 0.093 -10000 0 -0.22 145 145
IGFBP1 -0.42 0.54 -10000 0 -1.4 232 232
PDX1 -0.12 0.15 0.5 1 -0.54 6 7
UCP2 -0.24 0.27 0.54 1 -0.7 143 144
ALDOB -0.28 0.28 -10000 0 -0.72 187 187
AFP -0.58 0.51 0.36 1 -0.98 536 537
BDH1 -0.25 0.26 -10000 0 -0.68 165 165
HADH -0.28 0.28 -10000 0 -0.73 171 171
F2 -0.28 0.3 -10000 0 -0.86 93 93
HNF1A 0.034 0.031 0.26 7 -10000 0 7
G6PC -0.18 0.12 -10000 0 -0.61 5 5
SLC2A2 -0.16 0.17 -10000 0 -0.62 4 4
INS 0.019 0.078 0.23 21 -10000 0 21
FOXA1 -0.22 0.23 0.28 17 -0.4 507 524
FOXA3 -0.37 0.21 0.32 3 -0.47 735 738
FOXA2 -0.32 0.33 -10000 0 -0.8 207 207
ABCC8 -0.32 0.39 0.57 1 -0.9 230 231
ALB -0.79 0.54 -10000 0 -1.2 670 670
PLK1 signaling events

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.065 0.049 0.1 9 -0.1 620 629
BUB1B 0.083 0.067 0.15 401 -10000 0 401
PLK1 0.05 0.039 0.095 272 -10000 0 272
PLK1S1 0.026 0.035 0.13 11 -0.16 20 31
KIF2A 0.042 0.039 0.18 15 -10000 0 15
regulation of mitotic centrosome separation 0.05 0.039 0.095 272 -10000 0 272
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.24 0.14 0.32 715 -10000 0 715
WEE1 0.044 0.061 0.23 2 -0.27 25 27
cytokinesis 0.12 0.088 0.21 266 -0.37 2 268
PP2A-alpha B56 0.12 0.12 -10000 0 -0.44 25 25
AURKA 0.065 0.053 0.12 423 -0.14 4 427
PICH/PLK1 0.1 0.09 0.22 303 -10000 0 303
CENPE 0.062 0.055 0.16 82 -10000 0 82
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.042 0.038 0.18 15 -10000 0 15
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.081 0.054 0.12 540 -0.14 1 541
PAK1 0.022 0.021 0.26 7 -10000 0 7
SPC24 0.17 0.12 0.26 622 -10000 0 622
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.073 0.07 0.14 453 -0.18 24 477
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 49 -10000 0 49
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.054 145 -10000 0 145
G2 phase of mitotic cell cycle 0.001 0.003 0.015 12 -10000 0 12
STAG2 0.024 0.019 -10000 0 -0.58 1 1
GRASP65/GM130/RAB1/GTP 0.01 0.081 -10000 0 -0.5 24 24
spindle elongation 0.05 0.039 0.095 272 -10000 0 272
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.11 0.13 -10000 0 -0.47 33 33
TPT1 0.013 0.057 0.12 2 -0.17 76 78
CDC25C 0.11 0.07 0.16 458 -0.21 14 472
CDC25B 0.03 0.033 0.26 18 -10000 0 18
SGOL1 0.065 0.049 0.1 620 -0.1 9 629
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.069 0.066 0.32 11 -10000 0 11
CDC14B -0.009 0.074 -10000 0 -0.43 30 30
CDC20 0.15 0.12 0.26 541 -10000 0 541
PLK1/PBIP1 0.038 0.047 0.14 139 -10000 0 139
mitosis -0.005 0.006 0.027 4 -10000 0 4
FBXO5 0.03 0.036 0.16 17 -0.12 1 18
CDC2 0.003 0.004 0.011 187 -10000 0 187
NDC80 0.16 0.12 0.26 593 -10000 0 593
metaphase plate congression 0.029 0.054 0.14 2 -0.19 43 45
ERCC6L 0.091 0.086 0.24 164 -10000 0 164
NLP/gamma Tubulin 0.024 0.024 0.076 31 -0.083 13 44
microtubule cytoskeleton organization 0.013 0.057 0.12 2 -0.17 76 78
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 10 -10000 0 10
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 10 -10000 0 10
PLK1/PRC1-2 0.2 0.12 0.28 660 -10000 0 660
GRASP65/GM130/RAB1/GTP/PLK1 0.07 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 0.042 0.035 0.085 273 -10000 0 273
mitotic prometaphase 0.002 0.005 0.022 49 -10000 0 49
proteasomal ubiquitin-dependent protein catabolic process 0.054 0.052 -10000 0 -0.33 2 2
microtubule-based process 0.17 0.09 0.22 740 -10000 0 740
Golgi organization 0.05 0.039 0.095 272 -10000 0 272
Cohesin/SA2 0.055 0.032 0.16 3 -0.31 1 4
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.2 0.1 0.26 747 -10000 0 747
APC/C/CDC20 0.14 0.1 0.23 536 -10000 0 536
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.032 0.048 0.14 139 -10000 0 139
PRC1 0.081 0.1 0.26 250 -10000 0 250
ECT2 0.05 0.057 0.26 41 -10000 0 41
C13orf34 0.041 0.033 0.092 158 -10000 0 158
NUDC 0.029 0.054 0.15 1 -0.2 43 44
regulation of attachment of spindle microtubules to kinetochore 0.083 0.067 0.15 401 -10000 0 401
spindle assembly 0.036 0.03 0.089 99 -10000 0 99
spindle stabilization 0.026 0.035 0.13 11 -0.16 20 31
APC/C/HCDH1 0.01 0.066 -10000 0 -0.37 30 30
MKLP2/PLK1 0.17 0.091 0.22 740 -10000 0 740
CCNB1 0.071 0.094 0.26 199 -10000 0 199
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.028 0.085 0.23 1 -0.37 36 37
TUBG1 0.023 0.04 0.13 3 -0.16 34 37
G2/M transition of mitotic cell cycle 0.042 0.044 0.2 12 -10000 0 12
MLF1IP 0.025 0.048 0.14 127 -10000 0 127
INCENP 0.024 0.005 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.1 0.13 0.31 264 -0.22 2 266
NFATC2 -0.03 0.23 0.52 6 -0.61 87 93
NFATC3 -0.046 0.13 -10000 0 -0.28 202 202
CD40LG -0.31 0.51 0.66 6 -0.98 317 323
ITCH -0.004 0.085 -10000 0 -0.26 98 98
CBLB -0.004 0.085 -10000 0 -0.26 100 100
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.099 0.38 0.61 47 -1 83 130
JUNB 0.025 0.011 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.1 -10000 0 -0.31 105 105
T cell anergy -0.029 0.14 0.32 1 -0.42 104 105
TLE4 -0.028 0.19 -10000 0 -0.65 51 51
Jun/NFAT1-c-4/p21SNFT -0.19 0.45 0.7 5 -0.86 261 266
AP-1/NFAT1-c-4 -0.33 0.62 0.76 13 -1.1 317 330
IKZF1 -0.019 0.16 0.48 7 -0.52 50 57
T-helper 2 cell differentiation -0.089 0.27 0.48 1 -0.82 78 79
AP-1/NFAT1 -0.1 0.26 0.46 11 -0.47 269 280
CALM1 0.009 0.065 -10000 0 -0.18 102 102
EGR2 -0.28 0.58 0.65 3 -1.3 210 213
EGR3 -0.36 0.64 0.6 4 -1.3 319 323
NFAT1/FOXP3 0.047 0.23 0.47 97 -0.49 60 157
EGR1 -0.16 0.28 -10000 0 -0.57 316 316
JUN 0.015 0.055 0.2 2 -0.58 6 8
EGR4 0.04 0.06 0.26 70 -10000 0 70
mol:Ca2+ -0.012 0.056 -10000 0 -0.18 101 101
GBP3 -0.023 0.17 0.4 2 -0.58 49 51
FOSL1 0.025 0.054 0.26 20 -0.58 5 25
NFAT1-c-4/MAF/IRF4 -0.21 0.47 0.6 7 -0.87 289 296
DGKA -0.02 0.16 0.57 1 -0.51 50 51
CREM 0.023 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.28 0.5 0.62 3 -0.94 311 314
CTLA4 0.035 0.21 0.44 111 -0.56 36 147
NFAT1-c-4 (dimer)/EGR1 -0.3 0.53 0.63 3 -1 320 323
NFAT1-c-4 (dimer)/EGR4 -0.2 0.46 0.6 5 -0.86 291 296
FOS -0.15 0.27 0.2 2 -0.58 291 293
IFNG -0.058 0.28 0.47 19 -0.71 95 114
T cell activation -0.16 0.3 0.68 3 -0.7 140 143
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 0.35 0.66 305 -0.63 2 307
TNF -0.27 0.46 0.54 3 -0.9 312 315
FASLG -0.35 0.65 0.71 4 -1.2 321 325
TBX21 0.021 0.12 0.36 15 -0.58 36 51
BATF3 0.021 0.014 0.26 2 -10000 0 2
PRKCQ 0.004 0.12 0.29 8 -0.58 40 48
PTPN1 -0.019 0.16 0.48 1 -0.52 46 47
NFAT1-c-4/ICER1 -0.21 0.45 0.56 3 -0.86 292 295
GATA3 0.01 0.11 0.26 27 -0.58 33 60
T-helper 1 cell differentiation -0.056 0.27 0.46 20 -0.69 95 115
IL2RA -0.099 0.37 0.6 42 -0.8 122 164
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.019 0.16 -10000 0 -0.51 48 48
E2F1 0.098 0.11 0.26 305 -10000 0 305
PPARG -0.11 0.25 -10000 0 -0.58 228 228
SLC3A2 -0.02 0.16 -10000 0 -0.5 51 51
IRF4 -0.02 0.16 0.26 11 -0.58 79 90
PTGS2 -0.35 0.55 0.61 5 -1 339 344
CSF2 -0.3 0.5 0.66 8 -0.95 316 324
JunB/Fra1/NFAT1-c-4 -0.19 0.44 0.59 3 -0.83 289 292
IL4 -0.093 0.28 -10000 0 -0.88 75 75
IL5 -0.3 0.49 0.62 5 -0.95 316 321
IL2 -0.16 0.3 0.68 3 -0.72 132 135
IL3 -0.052 0.13 -10000 0 -0.83 18 18
RNF128 -0.045 0.21 0.27 5 -0.66 105 110
NFATC1 -0.17 0.35 0.63 2 -0.66 306 308
CDK4 0.13 0.25 0.6 99 -0.59 2 101
PTPRK -0.022 0.17 0.46 2 -0.59 45 47
IL8 -0.3 0.5 0.58 9 -0.96 314 323
POU2F1 0.021 0.012 0.26 1 -10000 0 1
HIF-1-alpha transcription factor network

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.25 0.37 0.66 1 -0.79 212 213
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.34 0.65 2 -0.74 156 158
SMAD4 0.024 0.006 -10000 0 -10000 0 0
ID2 -0.25 0.37 -10000 0 -0.79 210 210
AP1 -0.1 0.21 -10000 0 -0.42 298 298
ABCG2 -0.27 0.39 -10000 0 -0.8 237 237
HIF1A -0.049 0.084 -10000 0 -0.24 17 17
TFF3 -0.26 0.41 0.67 5 -0.8 254 259
GATA2 0.008 0.1 0.26 13 -0.58 26 39
AKT1 -0.056 0.094 -10000 0 -0.26 33 33
response to hypoxia -0.063 0.084 -10000 0 -0.21 104 104
MCL1 -0.24 0.35 -10000 0 -0.79 200 200
NDRG1 -0.23 0.36 -10000 0 -0.79 186 186
SERPINE1 -0.24 0.38 0.66 5 -0.79 211 216
FECH -0.25 0.37 -10000 0 -0.78 212 212
FURIN -0.25 0.37 -10000 0 -0.78 212 212
NCOA2 0 0.12 -10000 0 -0.57 41 41
EP300 -0.061 0.13 0.31 1 -0.33 110 111
HMOX1 -0.25 0.37 -10000 0 -0.79 212 212
BHLHE40 -0.25 0.37 -10000 0 -0.79 208 208
BHLHE41 -0.25 0.38 -10000 0 -0.8 212 212
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.021 0.11 -10000 0 -0.31 1 1
ENG -0.017 0.11 0.38 3 -10000 0 3
JUN 0.018 0.048 -10000 0 -0.58 6 6
RORA -0.25 0.37 -10000 0 -0.79 213 213
ABCB1 -0.26 0.45 -10000 0 -1.1 206 206
TFRC -0.25 0.37 -10000 0 -0.78 214 214
CXCR4 -0.25 0.37 -10000 0 -0.79 212 212
TF -0.41 0.45 -10000 0 -0.86 405 405
CITED2 -0.25 0.37 -10000 0 -0.79 210 210
HIF1A/ARNT -0.28 0.42 0.76 2 -0.92 181 183
LDHA -0.039 0.12 -10000 0 -0.74 23 23
ETS1 -0.25 0.37 -10000 0 -0.79 213 213
PGK1 -0.25 0.37 -10000 0 -0.79 212 212
NOS2 -0.24 0.37 -10000 0 -0.79 206 206
ITGB2 -0.24 0.37 0.67 1 -0.79 209 210
ALDOA -0.24 0.36 -10000 0 -0.79 207 207
Cbp/p300/CITED2 -0.25 0.39 -10000 0 -0.88 180 180
FOS -0.15 0.27 -10000 0 -0.58 285 285
HK2 -0.25 0.37 -10000 0 -0.79 212 212
SP1 0.001 0.058 -10000 0 -0.2 3 3
GCK -0.12 0.34 0.52 1 -1.4 60 61
HK1 -0.25 0.37 -10000 0 -0.79 212 212
NPM1 -0.25 0.37 -10000 0 -0.78 213 213
EGLN1 -0.24 0.36 -10000 0 -0.78 205 205
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.25 0.37 -10000 0 -0.79 209 209
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.37 -10000 0 -1 130 130
IGFBP1 -0.31 0.42 -10000 0 -0.86 281 281
VEGFA -0.16 0.29 -10000 0 -0.65 143 143
HIF1A/JAB1 -0.009 0.067 -10000 0 -0.27 1 1
CP -0.31 0.45 0.66 2 -0.89 294 296
CXCL12 -0.27 0.4 -10000 0 -0.83 228 228
COPS5 0.024 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.012 -10000 0 -10000 0 0
BNIP3 -0.25 0.37 0.74 1 -0.79 212 213
EGLN3 -0.24 0.38 0.74 1 -0.78 212 213
CA9 -0.21 0.39 0.67 6 -0.78 209 215
TERT -0.24 0.37 0.67 4 -0.78 205 209
ENO1 -0.25 0.37 -10000 0 -0.79 212 212
PFKL -0.25 0.37 -10000 0 -0.79 212 212
NCOA1 0.025 0.019 -10000 0 -0.58 1 1
ADM -0.27 0.4 0.66 1 -0.83 233 234
ARNT -0.035 0.07 -10000 0 -10000 0 0
HNF4A 0.019 0.04 0.26 15 -0.18 1 16
ADFP -0.26 0.36 -10000 0 -0.78 219 219
SLC2A1 -0.16 0.29 0.63 2 -0.67 126 128
LEP -0.49 0.41 -10000 0 -0.84 455 455
HIF1A/ARNT/Cbp/p300 -0.21 0.34 -10000 0 -0.77 158 158
EPO -0.11 0.26 0.66 3 -0.74 48 51
CREBBP -0.051 0.12 0.31 1 -0.35 71 72
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 0.69 1 -0.77 137 138
PFKFB3 -0.25 0.37 -10000 0 -0.8 201 201
NT5E -0.25 0.37 -10000 0 -0.79 215 215
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.005 0.12 -10000 0 -0.36 96 96
cell-cell adhesion 0.13 0.15 0.31 393 -10000 0 393
Ephrin B/EPHB2/RasGAP 0.032 0.11 -10000 0 -0.32 74 74
ITSN1 0.024 0.019 -10000 0 -0.58 1 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.12 0.19 -10000 0 -0.36 404 404
HRAS/GDP -0.12 0.18 -10000 0 -0.42 169 169
Ephrin B/EPHB1/GRB7 -0.11 0.21 -10000 0 -0.36 386 386
Endophilin/SYNJ1 -0.026 0.083 0.23 2 -0.3 73 75
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.11 0.22 -10000 0 -0.36 398 398
endothelial cell migration 0.041 0.037 -10000 0 -0.32 7 7
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PAK1 -0.03 0.098 0.35 2 -0.33 76 78
HRAS 0.026 0.021 0.26 8 -10000 0 8
RRAS -0.026 0.084 0.21 4 -0.3 73 77
DNM1 0.02 0.05 0.26 1 -0.58 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.14 0.18 0.35 2 -0.34 418 420
lamellipodium assembly -0.13 0.15 -10000 0 -0.31 393 393
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.094 0.16 -10000 0 -0.32 314 314
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
EPHB2 0.028 0.032 0.26 19 -10000 0 19
EPHB3 0.026 0.021 0.26 8 -10000 0 8
EPHB1 -0.21 0.29 0.26 1 -0.58 404 405
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.12 0.17 -10000 0 -0.42 161 161
Ephrin B/EPHB2 0.022 0.1 -10000 0 -0.32 74 74
Ephrin B/EPHB3 0.021 0.098 -10000 0 -0.32 70 70
JNK cascade -0.13 0.16 0.36 8 -0.32 401 409
Ephrin B/EPHB1 -0.12 0.21 -10000 0 -0.36 418 418
RAP1/GDP -0.097 0.16 -10000 0 -0.39 141 141
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.022 0.16 -10000 0 -0.58 75 75
EFNB1 0.024 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.1 0.19 -10000 0 -0.33 403 403
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.2 -10000 0 -0.33 405 405
Rap1/GTP -0.11 0.17 -10000 0 -0.32 344 344
axon guidance -0.005 0.12 -10000 0 -0.36 96 96
MAPK3 -0.089 0.14 -10000 0 -0.39 106 106
MAPK1 -0.094 0.14 -10000 0 -0.39 107 107
Rac1/GDP -0.11 0.16 -10000 0 -0.4 153 153
actin cytoskeleton reorganization -0.12 0.13 -10000 0 -0.35 127 127
CDC42/GDP -0.11 0.16 -10000 0 -0.4 155 155
PI3K 0.046 0.038 -10000 0 -0.32 7 7
EFNA5 -0.033 0.18 0.26 1 -0.58 96 97
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.004 0.087 -10000 0 -0.27 76 76
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.17 -10000 0 -0.31 368 368
PTK2 0.14 0.27 0.68 198 -10000 0 198
MAP4K4 -0.13 0.16 0.36 8 -0.32 401 409
SRC 0.024 0.005 -10000 0 -10000 0 0
KALRN 0.014 0.077 -10000 0 -0.58 17 17
Intersectin/N-WASP 0.035 0.016 -10000 0 -0.43 1 1
neuron projection morphogenesis -0.11 0.14 0.28 8 -0.42 77 85
MAP2K1 -0.091 0.15 0.2 1 -0.31 296 297
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.096 0.2 -10000 0 -0.34 401 401
cell migration -0.11 0.18 0.29 5 -0.35 283 288
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.084 0.23 2 -0.3 73 75
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.32 556 558
HRAS/GTP -0.1 0.19 -10000 0 -0.32 410 410
Ephrin B1/EPHB1-2 -0.1 0.19 -10000 0 -0.33 402 402
cell adhesion mediated by integrin 0.009 0.086 0.29 71 -0.21 18 89
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:GTP -0.11 0.2 -10000 0 -0.34 415 415
RAC1-CDC42/GTP -0.14 0.15 -10000 0 -0.31 387 387
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.099 0.16 -10000 0 -0.39 146 146
ruffle organization -0.13 0.16 0.36 5 -0.5 66 71
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.087 0.22 2 -0.31 74 76
Ephrin B/EPHB2/KALRN 0.027 0.12 -10000 0 -0.35 84 84
ROCK1 0.017 0.031 0.21 5 -0.34 1 6
RAS family/GDP -0.11 0.12 -10000 0 -0.34 121 121
Rac1/GTP -0.12 0.18 -10000 0 -0.33 393 393
Ephrin B/EPHB1/Src/Paxillin -0.12 0.18 -10000 0 -0.33 403 403
Glucocorticoid receptor regulatory network

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
PCK2 0.091 0.1 0.39 8 -10000 0 8
SMARCC2 0.024 0.013 -10000 0 -0.19 1 1
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.12 0.21 0.4 5 -0.67 74 79
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.033 0.27 19 -10000 0 19
FKBP4 0.025 0.017 0.26 5 -10000 0 5
FKBP5 0.017 0.072 0.26 5 -0.58 14 19
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.32 94 -0.32 5 99
PRL -0.062 0.12 0.57 2 -0.43 8 10
cortisol/GR alpha (dimer)/TIF2 0.18 0.28 0.52 329 -0.45 17 346
RELA -0.036 0.1 0.28 1 -0.26 30 31
FGG 0.21 0.24 0.46 382 -0.45 2 384
GR beta/TIF2 0.081 0.16 0.31 153 -0.41 36 189
IFNG -0.31 0.36 0.42 10 -0.66 437 447
apoptosis -0.27 0.31 0.85 1 -0.64 309 310
CREB1 0.061 0.054 -10000 0 -10000 0 0
histone acetylation 0.027 0.13 0.38 50 -0.43 14 64
BGLAP -0.082 0.14 -10000 0 -0.5 18 18
GR/PKAc 0.13 0.13 0.34 97 -0.32 2 99
NF kappa B1 p50/RelA -0.061 0.18 0.45 3 -0.35 137 140
SMARCD1 0.025 0.012 -10000 0 -10000 0 0
MDM2 0.099 0.11 0.22 334 -10000 0 334
GATA3 0.014 0.12 0.26 27 -0.57 33 60
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.025 0.1 0.47 1 -0.55 4 5
GSK3B 0 0.024 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.8 1 -0.59 183 184
CSN2 0.16 0.19 0.37 345 -0.41 2 347
BRG1/BAF155/BAF170/BAF60A 0.06 0.041 -10000 0 -0.47 5 5
NFATC1 0.023 0.027 -10000 0 -0.58 2 2
POU2F1 0.023 0.016 0.26 1 -10000 0 1
CDKN1A 0.016 0.087 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.007 -10000 0 -10000 0 0
SFN 0.022 0.067 0.26 18 -0.58 10 28
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.35 53 -0.32 3 56
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.39 0.62 2 -0.82 375 377
JUN -0.26 0.29 0.4 9 -0.54 430 439
IL4 -0.12 0.15 -10000 0 -0.5 29 29
CDK5R1 0.022 0.037 0.25 22 -10000 0 22
PRKACA 0.024 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.48 479 479
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.12 0.33 75 -0.32 3 78
cortisol/GR alpha (monomer) 0.28 0.32 0.59 445 -0.52 2 447
NCOA2 -0.004 0.12 -10000 0 -0.58 41 41
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.6 296 296
AP-1/NFAT1-c-4 -0.43 0.45 0.48 7 -0.8 548 555
AFP -0.55 0.65 0.5 1 -1.4 350 351
SUV420H1 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.4 174 -10000 0 174
TP53 0.031 0.028 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.65 0.69 0.44 3 -1.3 485 488
KRT14 -0.71 0.67 -10000 0 -1.3 537 537
TBP 0.028 0.011 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.3 385 -10000 0 385
HDAC1 0.022 0.011 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.44 0.45 0.48 7 -0.8 548 555
MAPK14 0.003 0.022 -10000 0 -10000 0 0
MAPK10 -0.085 0.21 -10000 0 -0.58 149 149
MAPK11 -0.002 0.039 -10000 0 -0.59 3 3
KRT5 -0.74 0.71 0.43 3 -1.4 545 548
interleukin-1 receptor activity -0.001 0.005 -10000 0 -10000 0 0
NCOA1 0.025 0.019 -10000 0 -0.57 1 1
STAT1 0.033 0.033 0.27 19 -10000 0 19
CGA -0.055 0.17 0.39 1 -0.46 31 32
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.36 377 -10000 0 377
MAPK3 0.001 0.022 -10000 0 -10000 0 0
MAPK1 0.003 0.022 -10000 0 -10000 0 0
ICAM1 -0.18 0.24 0.56 2 -0.55 216 218
NFKB1 -0.037 0.1 0.28 1 -0.26 30 31
MAPK8 -0.2 0.22 0.43 3 -0.43 362 365
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.28 0.32 0.86 1 -0.67 312 313
BAX 0.018 0.065 -10000 0 -10000 0 0
POMC -0.16 0.29 -10000 0 -0.9 71 71
EP300 0.15 0.14 0.3 413 -10000 0 413
cortisol/GR alpha (dimer)/p53 0.22 0.26 0.52 359 -0.53 1 360
proteasomal ubiquitin-dependent protein catabolic process 0.078 0.11 0.26 167 -10000 0 167
SGK1 0.19 0.2 0.54 8 -1.1 5 13
IL13 -0.25 0.28 0.49 5 -0.55 349 354
IL6 -0.43 0.52 0.62 1 -1.1 383 384
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.55 1 -0.6 98 99
IL2 -0.33 0.36 0.47 2 -0.71 399 401
CDK5 0.018 0.02 0.26 4 -10000 0 4
PRKACB 0.032 0.059 0.26 45 -0.58 3 48
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.48 4 -0.6 231 235
CDK5R1/CDK5 0.018 0.037 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.017 0.15 0.39 3 -0.39 31 34
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.26 0.5 403 -0.5 1 404
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.16 0.36 247 -10000 0 247
NF kappa B1 p50/RelA/Cbp 0.063 0.19 0.42 56 -0.43 13 69
JUN (dimer) -0.26 0.29 0.42 8 -0.54 431 439
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.21 -10000 0 -0.53 130 130
NR3C1 0.17 0.2 0.39 354 -0.41 2 356
NR4A1 -0.024 0.17 -10000 0 -0.56 94 94
TIF2/SUV420H1 0.01 0.091 -10000 0 -0.43 41 41
MAPKKK cascade -0.27 0.31 0.85 1 -0.64 309 310
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.52 415 -0.45 2 417
PBX1 0.023 0.015 0.26 1 -10000 0 1
POU1F1 0.022 0.015 0.26 2 -10000 0 2
SELE -0.19 0.31 0.56 2 -0.72 174 176
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.36 243 -10000 0 243
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.26 0.5 403 -0.5 1 404
mol:cortisol 0.16 0.19 0.34 458 -0.23 5 463
MMP1 0.034 0.31 0.42 3 -0.92 80 83
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.15 0.38 -10000 0 -0.86 214 214
NCK1/PAK1/Dok-R -0.091 0.16 -10000 0 -0.41 214 214
NCK1/Dok-R -0.18 0.45 -10000 0 -1 213 213
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.041 0.097 0.24 190 -10000 0 190
RELA 0.024 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.044 0.11 0.27 186 -10000 0 186
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.16 0.43 -10000 0 -0.98 213 213
FN1 0.12 0.12 0.26 403 -10000 0 403
PLD2 -0.2 0.46 -10000 0 -1.1 213 213
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.013 0.18 0.26 139 -0.58 73 212
ELK1 -0.17 0.41 -10000 0 -0.96 214 214
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PAK1 0.023 0.021 0.26 7 -10000 0 7
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.48 -10000 0 -1 213 213
CDKN1A -0.1 0.26 -10000 0 -0.62 155 155
ITGA5 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.18 0.45 -10000 0 -1 213 213
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.1 0.28 -10000 0 -0.64 214 214
PLG -0.2 0.46 -10000 0 -1.1 213 213
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.36 -10000 0 -0.83 214 214
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
ANGPT2 -0.14 0.28 -10000 0 -0.72 135 135
BMX -0.31 0.5 -10000 0 -1.2 215 215
ANGPT1 -0.22 0.49 -10000 0 -1.2 190 190
tube development -0.12 0.28 -10000 0 -0.67 184 184
ANGPT4 -0.15 0.27 -10000 0 -0.58 288 288
response to hypoxia -0.013 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.2 0.5 -10000 0 -1.1 213 213
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 383 383
STAT5A (dimer) -0.14 0.33 -10000 0 -0.78 178 178
mol:L-citrulline -0.1 0.28 -10000 0 -0.64 214 214
AGTR1 -0.093 0.26 0.26 61 -0.57 223 284
MAPK14 -0.2 0.46 -10000 0 -1.1 216 216
Tie2/SHP2 -0.092 0.31 -10000 0 -1.1 80 80
TEK -0.1 0.34 -10000 0 -1.2 80 80
RPS6KB1 -0.13 0.37 -10000 0 -0.82 213 213
Angiotensin II/AT1 -0.068 0.19 0.18 61 -0.42 226 287
Tie2/Ang1/GRB2 -0.2 0.48 -10000 0 -1.1 213 213
MAPK3 -0.18 0.42 -10000 0 -0.98 213 213
MAPK1 -0.18 0.42 -10000 0 -0.99 213 213
Tie2/Ang1/GRB7 -0.2 0.48 -10000 0 -1.1 213 213
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.2 0.46 -10000 0 -1.1 213 213
PI3K -0.18 0.43 -10000 0 -0.99 214 214
FES -0.2 0.46 -10000 0 -1.1 216 216
Crk/Dok-R -0.18 0.45 -10000 0 -1 213 213
Tie2/Ang1/ABIN2 -0.2 0.48 -10000 0 -1.1 213 213
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.13 0.34 -10000 0 -0.77 214 214
STAT5A 0.02 0.046 -10000 0 -0.58 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.12 0.37 0.47 1 -0.8 213 214
Tie2/Ang2 -0.17 0.39 -10000 0 -0.93 182 182
Tie2/Ang1 -0.21 0.51 -10000 0 -1.2 214 214
FOXO1 -0.13 0.34 0.47 1 -0.78 214 215
ELF1 0.013 0.036 -10000 0 -10000 0 0
ELF2 -0.19 0.46 -10000 0 -1.1 213 213
mol:Choline -0.19 0.44 -10000 0 -1 213 213
cell migration -0.036 0.1 -10000 0 -0.23 214 214
FYN -0.14 0.32 -10000 0 -0.77 183 183
DOK2 0.02 0.032 0.26 4 -0.58 2 6
negative regulation of cell cycle -0.094 0.24 -10000 0 -0.56 155 155
ETS1 -0.02 0.11 -10000 0 -0.27 153 153
PXN -0.091 0.31 0.45 1 -0.67 213 214
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.12 0.32 -10000 0 -0.73 214 214
RAC1 0.024 0.003 -10000 0 -10000 0 0
TNF -0.023 0.13 0.26 19 -0.28 179 198
MAPKKK cascade -0.19 0.44 -10000 0 -1 213 213
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.2 0.47 -10000 0 -1.1 211 211
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.091 0.25 0.38 1 -0.57 214 215
mol:Phosphatidic acid -0.19 0.44 -10000 0 -1 213 213
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.1 0.28 -10000 0 -0.64 214 214
Rac1/GTP -0.13 0.34 -10000 0 -0.78 214 214
MMP2 -0.2 0.46 -10000 0 -1.1 214 214
p75(NTR)-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
Sortilin/TRAF6 0.034 0.017 -10000 0 -0.43 1 1
Necdin/E2F1 0.061 0.11 -10000 0 -0.4 32 32
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.049 0.18 -10000 0 -0.33 279 279
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.24 0.34 1 -0.41 358 359
NT-4/5 (dimer)/p75(NTR) -0.23 0.29 -10000 0 -0.5 498 498
IKBKB 0.021 0.009 -10000 0 -10000 0 0
AKT1 -0.085 0.16 0.36 1 -0.33 266 267
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.016 0.16 0.26 23 -0.58 77 100
MGDIs/NGR/p75(NTR)/LINGO1 -0.042 0.2 0.34 6 -0.35 272 278
FURIN 0.024 0.009 0.26 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.094 0.21 -10000 0 -0.4 314 314
LINGO1 0.078 0.099 0.26 232 -10000 0 232
Sortilin/TRAF6/NRIF 0.023 0.024 -10000 0 -0.56 1 1
proBDNF (dimer) -0.016 0.16 0.26 23 -0.57 77 100
NTRK1 0.024 0.049 0.26 22 -0.58 3 25
RTN4R 0.032 0.046 0.26 39 -10000 0 39
neuron apoptosis -0.083 0.2 0.34 8 -0.4 188 196
IRAK1 0.025 0.015 0.26 4 -10000 0 4
SHC1 -0.084 0.16 -10000 0 -0.37 216 216
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.057 0.18 -10000 0 -0.34 275 275
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.068 0.19 -10000 0 -0.36 285 285
Mammalian IAPs/DIABLO 0.057 0.033 -10000 0 -0.34 2 2
proNGF (dimer) 0.017 0.075 0.26 7 -0.57 15 22
MAGED1 0.025 0.011 0.26 2 -10000 0 2
APP 0.024 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.57 355 355
ZNF274 0.024 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.067 0.16 -10000 0 -0.32 266 266
NGF 0.017 0.075 0.26 7 -0.58 15 22
cell cycle arrest -0.075 0.15 0.23 43 -0.3 275 318
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.054 0.12 -10000 0 -0.27 203 203
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.19 0.26 -10000 0 -0.45 471 471
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.071 0.19 -10000 0 -0.37 279 279
PSENEN 0.024 0.008 0.26 1 -10000 0 1
mol:ceramide -0.08 0.16 -10000 0 -0.34 276 276
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.045 0.11 -10000 0 -0.24 196 196
p75(NTR)/beta APP -0.094 0.2 -10000 0 -0.42 278 278
BEX1 -0.018 0.23 0.26 161 -0.58 135 296
mol:GDP -0.11 0.16 -10000 0 -0.37 281 281
NGF (dimer) 0.001 0.14 0.34 1 -0.34 126 127
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.026 0.19 0.34 5 -0.32 258 263
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
RAC1/GTP -0.063 0.16 -10000 0 -0.32 279 279
MYD88 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.071 0.19 -10000 0 -0.37 279 279
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.077 0.074 -10000 0 -10000 0 0
NT3 (dimer) -0.061 0.21 0.26 12 -0.57 148 160
TP53 -0.094 0.17 0.36 4 -0.33 301 305
PRDM4 -0.08 0.17 -10000 0 -0.34 275 275
BDNF (dimer) 0.021 0.2 0.34 18 -0.36 184 202
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.019 -10000 0 -0.58 1 1
activation of caspase activity -0.052 0.17 -10000 0 -0.32 279 279
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.057 0.18 -10000 0 -0.34 272 272
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.13 0.2 0.33 3 -0.42 279 282
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.081 0.16 -10000 0 -0.34 276 276
APH1B 0.023 0.019 -10000 0 -0.58 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.073 0.19 -10000 0 -0.37 279 279
PSEN1 0.024 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.15 0.25 -10000 0 -0.46 373 373
MAPK8 -0.099 0.18 0.3 8 -0.37 257 265
MAPK9 -0.098 0.18 0.28 8 -0.37 260 268
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.061 0.21 0.26 12 -0.58 148 160
NTF4 -0.19 0.28 -10000 0 -0.58 355 355
NDN 0.004 0.1 -10000 0 -0.58 32 32
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.045 0.17 -10000 0 -0.31 277 277
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.023 -10000 0 -0.34 1 1
RhoA-B-C/GTP -0.071 0.19 -10000 0 -0.37 279 279
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.065 0.2 -10000 0 -0.35 302 302
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.076 0.2 -10000 0 -0.37 304 304
PRKACB 0.032 0.059 0.26 45 -0.58 3 48
proBDNF (dimer)/p75 ECD 0.003 0.13 -10000 0 -0.41 81 81
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 12 -0.58 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.089 0.17 0.28 14 -0.34 270 284
BAD -0.12 0.19 0.38 8 -0.39 272 280
RIPK2 0.02 0.016 0.26 3 -10000 0 3
NGFR -0.14 0.27 -10000 0 -0.58 278 278
CYCS -0.088 0.15 0.36 2 -0.32 267 269
ADAM17 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.048 0.16 -10000 0 -0.34 202 202
BCL2L11 -0.12 0.19 0.42 6 -0.39 271 277
BDNF (dimer)/p75(NTR) -0.12 0.24 -10000 0 -0.44 337 337
PI3K -0.06 0.18 -10000 0 -0.35 269 269
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.058 0.18 -10000 0 -0.34 275 275
NDNL2 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.099 0.21 -10000 0 -0.42 297 297
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.057 0.18 -10000 0 -0.34 275 275
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.58 1 1
PLG 0.018 0.018 0.26 5 -10000 0 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.19 -10000 0 -0.38 315 315
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
NGFRAP1 0.023 0.027 -10000 0 -0.58 2 2
CASP3 -0.11 0.18 0.38 7 -0.36 283 290
E2F1 0.094 0.11 0.26 305 -10000 0 305
CASP9 0.023 0.006 -10000 0 -10000 0 0
IKK complex -0.004 0.11 -10000 0 -0.39 21 21
NGF (dimer)/TRKA 0.026 0.065 0.2 25 -0.4 18 43
MMP7 -0.039 0.2 0.26 29 -0.58 115 144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.047 0.17 -10000 0 -0.33 268 268
MMP3 0.099 0.13 0.26 362 -0.58 11 373
APAF-1/Caspase 9 -0.088 0.11 -10000 0 -0.28 220 220
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 -0.075 0.14 -10000 0 -0.42 98 98
PTK2B 0.02 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.054 0.19 -10000 0 -0.84 40 40
EDN1 -0.076 0.17 -10000 0 -0.55 93 93
EDN3 -0.23 0.29 0.26 2 -0.58 422 424
EDN2 0.074 0.11 0.26 231 -0.58 5 236
HRAS/GDP -0.094 0.2 -10000 0 -0.5 133 133
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.14 -10000 0 -0.42 92 92
ADCY4 -0.13 0.2 0.28 2 -0.43 263 265
ADCY5 -0.21 0.25 0.23 1 -0.45 451 452
ADCY6 -0.12 0.19 0.28 2 -0.41 255 257
ADCY7 -0.12 0.19 0.27 3 -0.4 256 259
ADCY1 -0.12 0.2 0.25 2 -0.41 266 268
ADCY2 -0.14 0.22 0.27 10 -0.45 275 285
ADCY3 -0.12 0.19 0.25 2 -0.41 255 257
ADCY8 -0.1 0.17 0.27 2 -0.41 197 199
ADCY9 -0.12 0.18 0.27 1 -0.4 243 244
arachidonic acid secretion -0.16 0.27 0.32 1 -0.51 319 320
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.36 144 144
GNAO1 0.018 0.092 0.26 32 -0.58 19 51
HRAS 0.025 0.021 0.26 8 -10000 0 8
ETA receptor/Endothelin-1/G12/GTP -0.061 0.14 -10000 0 -0.4 92 92
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 0.28 1 -0.42 260 261
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.066 0.16 0.38 10 -0.44 92 102
EDNRB -0.027 0.17 -10000 0 -0.57 91 91
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.08 0.16 -10000 0 -0.5 101 101
CYSLTR1 -0.082 0.16 -10000 0 -0.49 97 97
SLC9A1 -0.047 0.095 -10000 0 -0.29 91 91
mol:GDP -0.1 0.21 0.39 1 -0.52 146 147
SLC9A3 -0.11 0.28 -10000 0 -0.64 183 183
RAF1 -0.14 0.24 0.33 1 -0.48 244 245
JUN -0.051 0.18 -10000 0 -0.76 42 42
JAK2 -0.073 0.14 -10000 0 -0.42 99 99
mol:IP3 -0.074 0.17 -10000 0 -0.48 103 103
ETA receptor/Endothelin-1 -0.086 0.16 0.33 7 -0.49 101 108
PLCB1 -0.017 0.15 -10000 0 -0.58 66 66
PLCB2 0.014 0.027 0.26 1 -0.58 1 2
ETA receptor/Endothelin-3 -0.19 0.22 -10000 0 -0.44 431 431
FOS -0.29 0.44 -10000 0 -0.94 313 313
Gai/GDP -0.097 0.29 -10000 0 -0.74 155 155
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 -10000 0 -0.55 130 130
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.44 119 119
GNAQ 0.014 0.032 -10000 0 -0.58 2 2
GNAZ 0.018 0.056 -10000 0 -0.58 9 9
GNAL -0.11 0.25 -10000 0 -0.58 221 221
Gs family/GDP -0.15 0.24 -10000 0 -0.51 244 244
ETA receptor/Endothelin-1/Gq/GTP -0.048 0.12 -10000 0 -0.42 59 59
MAPK14 -0.066 0.16 -10000 0 -0.43 117 117
TRPC6 -0.058 0.21 -10000 0 -0.94 38 38
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 46 46
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.066 0.17 -10000 0 -0.43 135 135
ETB receptor/Endothelin-2 0.023 0.16 0.24 16 -0.4 96 112
ETB receptor/Endothelin-3 -0.19 0.25 -10000 0 -0.44 483 483
ETB receptor/Endothelin-1 -0.079 0.18 -10000 0 -0.47 159 159
MAPK3 -0.25 0.38 -10000 0 -0.79 318 318
MAPK1 -0.25 0.39 -10000 0 -0.81 320 320
Rac1/GDP -0.095 0.2 -10000 0 -0.49 136 136
cAMP biosynthetic process -0.16 0.22 0.31 4 -0.46 281 285
MAPK8 -0.061 0.21 -10000 0 -0.76 57 57
SRC 0.024 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.067 0.17 -10000 0 -0.36 191 191
p130Cas/CRK/Src/PYK2 -0.098 0.22 0.49 1 -0.59 113 114
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.094 0.19 -10000 0 -0.49 138 138
COL1A2 -0.091 0.2 0.38 9 -0.49 145 154
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.021 0.096 0.26 13 -0.35 10 23
mol:DAG -0.075 0.17 -10000 0 -0.48 104 104
MAP2K2 -0.19 0.3 0.34 2 -0.59 324 326
MAP2K1 -0.19 0.29 0.32 2 -0.59 322 324
EDNRA -0.036 0.064 -10000 0 -0.28 21 21
positive regulation of muscle contraction -0.065 0.12 -10000 0 -0.38 89 89
Gq family/GDP -0.059 0.19 -10000 0 -0.51 89 89
HRAS/GTP -0.1 0.2 0.34 1 -0.49 153 154
PRKCH -0.077 0.16 -10000 0 -0.47 102 102
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.073 0.18 0.3 2 -0.5 103 105
PRKCB -0.075 0.18 -10000 0 -0.47 111 111
PRKCE -0.08 0.16 -10000 0 -0.47 106 106
PRKCD -0.076 0.16 -10000 0 -0.46 104 104
PRKCG -0.078 0.17 0.27 1 -0.48 98 99
regulation of vascular smooth muscle contraction -0.34 0.51 -10000 0 -1.1 310 310
PRKCQ -0.086 0.18 -10000 0 -0.49 127 127
PLA2G4A -0.18 0.3 0.33 1 -0.56 319 320
GNA14 0.014 0.07 0.26 19 -0.58 10 29
GNA15 0.022 0.028 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.028 -10000 0 -0.58 2 2
Rac1/GTP -0.061 0.14 -10000 0 -0.4 96 96
MMP1 0.17 0.13 0.39 82 -10000 0 82
Ephrin B reverse signaling

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
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.26 19 -10000 0 19
EFNB1 0.002 0.038 -10000 0 -0.43 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.084 0.18 -10000 0 -0.3 392 392
Ephrin B2/EPHB1-2 -0.1 0.18 0.21 1 -0.33 403 404
neuron projection morphogenesis -0.09 0.16 -10000 0 -0.29 392 392
Ephrin B1/EPHB1-2/Tiam1 -0.095 0.18 -10000 0 -0.32 398 398
DNM1 0.02 0.05 0.27 1 -0.58 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.023 0.12 -10000 0 -0.55 46 46
YES1 -0.026 0.17 -10000 0 -0.77 51 51
Ephrin B1/EPHB1-2/NCK2 -0.096 0.18 -10000 0 -0.32 401 401
PI3K 0.005 0.13 -10000 0 -0.52 55 55
mol:GDP -0.095 0.18 -10000 0 -0.32 398 398
ITGA2B 0.033 0.061 0.26 50 -0.58 3 53
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.027 0.17 -10000 0 -0.76 50 50
MAP3K7 -0.025 0.13 -10000 0 -0.57 49 49
FGR -0.023 0.17 -10000 0 -0.76 50 50
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.01 0.14 -10000 0 -0.52 53 53
LYN -0.023 0.17 -10000 0 -0.75 50 50
Ephrin B1/EPHB1-2/Src Family Kinases -0.029 0.16 -10000 0 -0.71 51 51
Ephrin B1/EPHB1-2 -0.025 0.14 -10000 0 -0.63 46 46
SRC -0.022 0.17 -10000 0 -0.75 51 51
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
EPHB1 -0.21 0.29 0.27 1 -0.58 404 405
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.027 0.092 -10000 0 -0.42 35 35
BLK -0.022 0.18 -10000 0 -0.78 48 48
HCK -0.022 0.17 -10000 0 -0.75 51 51
regulation of stress fiber formation 0.096 0.18 0.32 401 -10000 0 401
MAPK8 -0.026 0.12 -10000 0 -0.54 48 48
Ephrin B1/EPHB1-2/RGS3 -0.095 0.18 -10000 0 -0.32 399 399
endothelial cell migration -0.019 0.11 -10000 0 -0.51 43 43
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.008 0.11 -10000 0 -0.69 26 26
regulation of focal adhesion formation 0.096 0.18 0.32 401 -10000 0 401
chemotaxis 0.095 0.18 0.32 399 -10000 0 399
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.086 0.17 -10000 0 -0.3 392 392
angiogenesis -0.025 0.14 -10000 0 -0.62 48 48
LCK -0.023 0.17 -10000 0 -0.77 50 50
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.61 0.86 5 -1.2 177 182
STAT6 (cleaved dimer) -0.3 0.58 -10000 0 -1.2 225 225
IGHG1 -0.028 0.26 0.53 49 -0.53 10 59
IGHG3 -0.24 0.57 0.7 8 -1.1 217 225
AKT1 -0.086 0.35 0.58 22 -0.79 71 93
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.048 0.3 0.55 24 -0.86 36 60
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.088 0.36 0.6 24 -0.87 60 84
THY1 -0.24 0.61 0.86 6 -1.2 178 184
MYB 0.012 0.082 0.26 1 -0.58 19 20
HMGA1 0.034 0.048 0.26 44 -10000 0 44
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.41 0.65 53 -0.77 142 195
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.08 0.35 0.6 24 -0.9 47 71
SP1 0.034 0.024 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.014 0.046 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.26 0.6 0.71 7 -1.2 205 212
SOCS1 -0.14 0.4 0.65 16 -0.77 144 160
SOCS3 -0.094 0.35 0.61 15 -0.82 70 85
FCER2 -0.39 0.74 0.81 24 -1.3 324 348
PARP14 0.017 0.032 0.25 3 -10000 0 3
CCL17 -0.22 0.62 0.88 36 -1.2 182 218
GRB2 0.023 0.01 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.042 0.29 0.54 32 -0.77 32 64
T cell proliferation -0.26 0.61 0.76 6 -1.2 194 200
IL4R/JAK1 -0.25 0.6 0.76 2 -1.2 186 188
EGR2 -0.37 0.75 0.88 12 -1.5 259 271
JAK2 0.011 0.076 0.23 5 -10000 0 5
JAK3 0.022 0.037 0.28 14 -10000 0 14
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
JAK1 0.017 0.041 -10000 0 -10000 0 0
COL1A2 -0.024 0.27 0.6 5 -1.1 16 21
CCL26 -0.24 0.61 0.94 6 -1.2 176 182
IL4R -0.24 0.66 0.92 22 -1.3 182 204
PTPN6 0.014 0.036 0.22 2 -10000 0 2
IL13RA2 -0.24 0.61 0.86 7 -1.2 178 185
IL13RA1 0.011 0.077 0.26 1 -10000 0 1
IRF4 -0.13 0.49 0.6 11 -1.4 111 122
ARG1 -0.006 0.22 0.58 7 -1.2 1 8
CBL -0.11 0.38 0.6 34 -0.74 135 169
GTF3A 0.055 0.049 0.26 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.024 0.11 0.29 37 -10000 0 37
IRF4/BCL6 -0.12 0.45 0.56 1 -1.3 110 111
CD40LG -0.01 0.14 0.31 12 -0.59 46 58
MAPK14 -0.11 0.38 0.61 31 -0.75 126 157
mitosis -0.079 0.33 0.57 25 -0.74 71 96
STAT6 -0.27 0.76 0.97 42 -1.5 193 235
SPI1 0.027 0.02 0.26 6 -10000 0 6
RPS6KB1 -0.062 0.32 0.56 29 -0.72 63 92
STAT6 (dimer) -0.27 0.76 0.98 41 -1.5 193 234
STAT6 (dimer)/PARP14 -0.3 0.66 0.75 11 -1.3 223 234
mast cell activation 0 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.094 0.36 0.59 30 -0.8 80 110
FRAP1 -0.087 0.35 0.58 22 -0.79 71 93
LTA -0.22 0.62 0.88 31 -1.2 174 205
FES 0.022 0.033 -10000 0 -0.58 3 3
T-helper 1 cell differentiation 0.26 0.72 1.4 199 -0.97 42 241
CCL11 -0.18 0.59 0.78 21 -1.2 162 183
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.074 0.34 0.58 30 -0.82 57 87
IL2RG 0.025 0.074 0.27 45 -0.57 7 52
IL10 -0.21 0.61 0.86 13 -1.2 160 173
IRS1 0.001 0.12 -10000 0 -0.58 40 40
IRS2 0.004 0.1 -10000 0 -0.58 32 32
IL4 -0.011 0.27 0.65 17 -1.1 20 37
IL5 -0.24 0.61 0.87 6 -1.2 177 183
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.52 0.81 45 -0.93 171 216
COL1A1 -0.002 0.36 0.63 60 -0.97 50 110
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.26 0.61 -10000 0 -1.3 167 167
IL2R gamma/JAK3 0.037 0.07 0.37 17 -0.42 6 23
TFF3 -0.3 0.71 0.89 21 -1.4 228 249
ALOX15 -0.3 0.7 0.89 10 -1.4 227 237
MYBL1 0.039 0.065 0.26 81 -10000 0 81
T-helper 2 cell differentiation -0.19 0.53 0.73 24 -1 192 216
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.025 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.084 0.35 0.58 24 -0.82 62 86
mol:PI-3-4-5-P3 -0.086 0.35 0.58 23 -0.79 71 94
PI3K -0.095 0.36 0.6 19 -0.86 70 89
DOK2 0.02 0.032 0.26 4 -0.58 2 6
ETS1 0.004 0.052 -10000 0 -0.54 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.033 0.27 0.51 37 -0.73 25 62
ITGB3 -0.26 0.63 0.86 5 -1.3 189 194
PIGR -0.67 0.8 0.85 14 -1.3 542 556
IGHE -0.016 0.087 0.18 25 -0.22 34 59
MAPKKK cascade -0.031 0.27 0.51 38 -0.71 25 63
BCL6 0.023 0.044 -10000 0 -0.57 5 5
OPRM1 -0.24 0.61 0.91 7 -1.2 175 182
RETNLB -0.24 0.61 0.85 5 -1.3 171 176
SELP -0.36 0.77 0.81 23 -1.5 275 298
AICDA -0.23 0.58 0.79 10 -1.2 181 191
Wnt signaling

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.096 0.21 -10000 0 -0.39 270 270
FZD6 0.014 0.054 -10000 0 -0.58 8 8
WNT6 -0.082 0.25 0.26 43 -0.58 196 239
WNT4 0.018 0.087 0.26 21 -0.58 18 39
FZD3 0.017 0.047 -10000 0 -0.58 6 6
WNT5A 0.019 0.069 0.26 9 -0.58 12 21
WNT11 -0.083 0.23 0.26 11 -0.58 183 194
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.008 0.093 -10000 0 -0.58 25 25
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.19 0.2 -10000 0 -0.36 585 585
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.18 0.17 -10000 0 -0.33 582 582
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.035 0.055 0.26 57 -10000 0 57
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.023 0.069 0.26 23 -0.58 10 33
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.049 0.048 -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 0.035 0.26 22 -10000 0 22
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.084 0.26 146 -10000 0 146
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.21 0.34 2 -0.37 580 582
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.14 0.15 0.35 3 -0.33 53 56
MAP1B 0 0.042 -10000 0 -0.32 17 17
RAC1 0.011 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.16 0.16 -10000 0 -0.3 460 460
RELN -0.32 0.3 0.26 2 -0.58 592 594
PAFAH/LIS1 0.023 0.047 0.32 2 -0.36 9 11
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.12 0.13 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.41 146 146
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.15 0.15 0.33 3 -0.35 64 67
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.051 0.074 0.26 114 -10000 0 114
PAFAH1B2 0.02 0.038 -10000 0 -0.58 4 4
MAP1B/LIS1/Dynein heavy chain 0.014 0.042 -10000 0 -0.31 3 3
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.15 0.35 3 -0.33 38 41
LRP8 0.047 0.071 0.26 101 -10000 0 101
NDEL1/Katanin 60 -0.14 0.15 0.35 3 -0.33 57 60
P39/CDK5 -0.16 0.16 0.34 5 -0.3 430 435
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.18 0.15 0.2 1 -0.31 577 578
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.17 0.19 0.33 1 -0.32 574 575
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 584 584
CDC42 0.01 0.005 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.033 0.045 0.26 38 -10000 0 38
GPC2 0.048 0.082 0.26 113 -0.58 3 116
GPC2/Midkine 0.057 0.069 0.22 132 -0.43 3 135
neuron projection morphogenesis 0.057 0.069 0.22 132 -0.43 3 135
IGF1 pathway

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
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.067 0.16 -10000 0 -0.34 225 225
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.026 0.021 0.26 8 -10000 0 8
IRS1/Crk -0.062 0.16 -10000 0 -0.34 229 229
IGF-1R heterotetramer/IGF1/PTP1B -0.044 0.17 -10000 0 -0.37 199 199
AKT1 -0.067 0.14 0.25 2 -0.32 186 188
BAD -0.065 0.13 0.23 3 -0.46 43 46
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.069 0.16 -10000 0 -0.34 229 229
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.059 0.17 -10000 0 -0.35 229 229
RAF1 -0.048 0.14 -10000 0 -0.49 43 43
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.033 0.16 -10000 0 -0.33 211 211
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.062 0.18 -10000 0 -0.36 242 242
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.064 0.13 0.25 2 -0.33 163 165
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.029 0.12 0.32 7 -0.41 39 46
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.13 -10000 0 -0.32 150 150
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.31 148 148
IGF-1R heterotetramer -0.012 0.1 0.23 2 -0.63 20 22
IGF-1R heterotetramer/IGF1/IRS/Nck -0.046 0.17 -10000 0 -0.35 226 226
Crk/p130 Cas/Paxillin -0.037 0.16 -10000 0 -0.32 214 214
IGF1R -0.012 0.1 0.23 2 -0.63 20 22
IGF1 -0.11 0.26 -10000 0 -0.6 217 217
IRS2/Crk -0.068 0.17 -10000 0 -0.35 238 238
PI3K -0.036 0.17 -10000 0 -0.34 221 221
apoptosis 0.044 0.11 0.38 35 -0.28 4 39
HRAS/GDP 0.019 0.015 -10000 0 -10000 0 0
PRKCD -0.079 0.18 -10000 0 -0.4 216 216
RAF1/14-3-3 E -0.024 0.13 0.3 1 -0.42 42 43
BAD/14-3-3 -0.046 0.11 0.29 4 -0.41 35 39
PRKCZ -0.068 0.14 0.25 2 -0.32 189 191
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.12 -10000 0 -0.41 37 37
PTPN1 0.024 0.019 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.19 -10000 0 -0.42 224 224
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.023 0.15 -10000 0 -0.33 164 164
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.055 0.16 -10000 0 -0.34 226 226
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.34 229 229
IRS1 -0.072 0.17 -10000 0 -0.36 236 236
IRS2 -0.077 0.17 -10000 0 -0.37 238 238
IGF-1R heterotetramer/IGF1 -0.078 0.21 -10000 0 -0.46 231 231
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDPK1 -0.069 0.14 0.28 1 -0.33 193 194
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.09 0.2 -10000 0 -0.43 221 221
SHC1 0.02 0.009 -10000 0 -10000 0 0
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 0.027 0.03 -10000 0 -0.4 3 3
ARNO/beta Arrestin1-2 -0.064 0.16 -10000 0 -0.57 38 38
EGFR -0.19 0.29 -10000 0 -0.58 363 363
EPHA2 0.02 0.042 -10000 0 -0.58 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.26 -10000 0 -0.46 493 493
ARRB2 -0.043 0.13 -10000 0 -0.36 141 141
mol:GTP 0.011 0.049 0.15 19 -0.2 21 40
ARRB1 0.021 0.027 -10000 0 -0.58 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR 0.001 0.12 0.26 4 -0.58 39 43
EGF -0.083 0.23 0.26 2 -0.58 182 184
somatostatin receptor activity 0 0 0.001 1 -0.001 259 260
ARAP2 0.021 0.038 -10000 0 -0.58 4 4
mol:GDP -0.12 0.16 -10000 0 -0.33 275 275
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 125 125
ITGA2B 0.033 0.061 0.26 50 -0.58 3 53
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.039 -10000 0 -0.34 5 5
ADAP1 0.025 0.028 0.26 8 -0.58 1 9
KIF13B 0.019 0.028 -10000 0 -0.58 2 2
HGF/MET -0.065 0.2 -10000 0 -0.45 206 206
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.13 -10000 0 -0.29 282 282
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.17 0.23 -10000 0 -0.4 484 484
ADRB2 -0.1 0.24 -10000 0 -0.58 215 215
receptor agonist activity 0 0 0 1 0 251 252
actin filament binding 0 0 0 1 -0.001 263 264
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 154 155
ARF6/GDP -0.037 0.15 0.25 2 -0.44 86 88
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.4 211 211
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.081 -10000 0 -0.33 35 35
ACAP1 0.028 0.066 0.26 39 -0.58 6 45
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.057 0.17 -10000 0 -0.49 141 141
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.58 60 60
CYTH3 0.004 0.014 -10000 0 -0.42 1 1
CYTH2 0.007 0.097 -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 6 0 255 261
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.012 0.14 -10000 0 -0.58 62 62
GNAQ/ARNO 0.019 0.093 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 156 156
MET -0.072 0.22 -10000 0 -0.58 162 162
GNA14 0.022 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.026 0.26 6 -0.58 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 219 220
GNA11 0.022 0.027 -10000 0 -0.58 2 2
LHCGR -0.069 0.2 -10000 0 -0.58 141 141
AGTR1 -0.094 0.26 0.26 61 -0.58 223 284
desensitization of G-protein coupled receptor protein signaling pathway -0.057 0.17 -10000 0 -0.49 141 141
IPCEF1/ARNO -0.13 0.19 -10000 0 -0.6 61 61
alphaIIb/beta3 Integrin 0.026 0.092 -10000 0 -0.42 35 35
Noncanonical Wnt signaling 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
NFATC2 -0.023 0.16 -10000 0 -0.58 78 78
GNB1/GNG2 -0.074 0.21 -10000 0 -0.47 147 147
mol:DAG -0.076 0.18 0.24 1 -0.44 135 136
PLCG1 -0.079 0.19 0.24 1 -0.46 135 136
YES1 -0.095 0.19 -10000 0 -0.49 136 136
FZD3 0.017 0.047 -10000 0 -0.58 6 6
FZD6 0.014 0.054 -10000 0 -0.58 8 8
G protein -0.062 0.2 0.3 2 -0.47 127 129
MAP3K7 -0.071 0.15 0.23 2 -0.41 105 107
mol:Ca2+ -0.074 0.18 0.23 1 -0.43 135 136
mol:IP3 -0.076 0.18 0.24 1 -0.44 135 136
NLK -0.01 0.13 -10000 0 -0.84 24 24
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.072 0.17 0.25 2 -0.44 110 112
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.096 0.21 -10000 0 -0.39 270 270
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
GNAS -0.089 0.19 -10000 0 -0.49 131 131
GO:0007205 -0.08 0.18 0.23 1 -0.44 134 135
WNT6 -0.082 0.25 0.26 43 -0.58 196 239
WNT4 0.018 0.087 0.26 21 -0.58 18 39
NFAT1/CK1 alpha -0.088 0.2 0.33 2 -0.49 132 134
GNG2 0.018 0.059 -10000 0 -0.58 10 10
WNT5A 0.019 0.069 0.26 9 -0.58 12 21
WNT11 -0.083 0.23 0.26 11 -0.58 183 194
CDC42 -0.083 0.19 -10000 0 -0.47 129 129
Nongenotropic Androgen signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.13 -10000 0 -0.34 135 135
regulation of S phase of mitotic cell cycle -0.022 0.1 -10000 0 -0.3 120 120
GNAO1 0.018 0.092 0.26 32 -0.58 19 51
HRAS 0.025 0.021 0.26 8 -10000 0 8
SHBG/T-DHT 0.015 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 -0.067 0.11 -10000 0 -0.33 113 113
T-DHT/AR -0.039 0.15 0.17 1 -0.42 127 128
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 300 300
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 46 46
mol:GDP -0.06 0.16 -10000 0 -0.47 130 130
cell proliferation -0.13 0.21 0.27 1 -0.44 279 280
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.24 0.38 -10000 0 -0.81 303 303
mol:Ca2+ -0.012 0.027 -10000 0 -0.072 129 129
MAPK3 -0.098 0.16 0.26 4 -0.41 114 118
MAPK1 -0.077 0.14 -10000 0 -0.38 99 99
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
mol:IP3 -0.001 0.002 -10000 0 -0.004 299 299
cAMP biosynthetic process 0.004 0.02 -10000 0 -10000 0 0
GNG2 0.018 0.059 -10000 0 -0.58 10 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 299 299
HRAS/GTP -0.026 0.12 -10000 0 -0.32 124 124
actin cytoskeleton reorganization 0.03 0.033 -10000 0 -0.3 8 8
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 299 299
PI3K 0.027 0.037 -10000 0 -0.34 9 9
apoptosis 0.13 0.21 0.43 303 -10000 0 303
T-DHT/AR/PELP1 -0.023 0.13 -10000 0 -0.37 126 126
HRAS/GDP -0.049 0.16 -10000 0 -0.46 127 127
CREB1 -0.14 0.23 -10000 0 -0.47 303 303
RAC1-CDC42/GTP 0.038 0.035 -10000 0 -0.31 8 8
AR -0.051 0.2 0.25 1 -0.58 126 127
GNB1 0.024 0.005 -10000 0 -10000 0 0
RAF1 -0.059 0.11 -10000 0 -0.32 119 119
RAC1-CDC42/GDP -0.025 0.16 -10000 0 -0.44 127 127
T-DHT/AR/PELP1/Src -0.02 0.12 -10000 0 -0.34 125 125
MAP2K2 -0.068 0.11 -10000 0 -0.33 113 113
T-DHT/AR/PELP1/Src/PI3K -0.022 0.11 -10000 0 -0.3 120 120
GNAZ 0.018 0.056 -10000 0 -0.58 9 9
SHBG 0.022 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.047 0.16 -10000 0 -0.46 89 89
mol:T-DHT -0.001 0.001 0.002 1 -0.004 92 93
RAC1 0.024 0.003 -10000 0 -10000 0 0
GNRH1 0.001 0.027 -10000 0 -0.42 4 4
Gi family/GTP -0.032 0.096 -10000 0 -0.28 86 86
CDC42 0.023 0.005 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.026 0.49 0.8 50 -1.1 76 126
IL23A -0.037 0.49 0.86 33 -1.1 68 101
NF kappa B1 p50/RelA/I kappa B alpha -0.066 0.45 0.76 9 -1.1 80 89
positive regulation of T cell mediated cytotoxicity -0.028 0.55 0.89 61 -1.2 86 147
ITGA3 -0.022 0.48 0.81 41 -1.1 71 112
IL17F -0.01 0.36 0.6 69 -0.69 77 146
IL12B 0.085 0.15 0.36 194 -10000 0 194
STAT1 (dimer) -0.043 0.51 0.76 46 -1.1 80 126
CD4 -0.02 0.49 0.82 48 -1 74 122
IL23 -0.023 0.49 0.82 50 -1.1 67 117
IL23R 0.048 0.2 0.62 16 -0.94 16 32
IL1B -0.039 0.51 0.84 39 -1.2 73 112
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.013 0.49 0.85 62 -1 68 130
TYK2 0.026 0.059 0.24 1 -10000 0 1
STAT4 0.001 0.12 0.26 1 -0.58 40 41
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.007 0.11 0.27 5 -0.57 35 40
IL12RB1 0.035 0.094 0.37 43 -0.6 2 45
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.09 0.32 43 -0.44 2 45
IL23R/JAK2 0.061 0.22 0.56 26 -0.86 15 41
positive regulation of chronic inflammatory response -0.028 0.55 0.89 61 -1.2 86 147
natural killer cell activation -0.004 0.015 -10000 0 -0.051 37 37
JAK2 0.038 0.083 0.26 40 -10000 0 40
PIK3R1 0.019 0.056 -10000 0 -0.57 9 9
NFKB1 0.026 0.009 -10000 0 -10000 0 0
RELA 0.026 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.016 0.48 0.81 53 -1 67 120
ALOX12B -0.022 0.48 0.83 45 -1 71 116
CXCL1 -0.19 0.7 0.85 46 -1.2 270 316
T cell proliferation -0.028 0.55 0.89 61 -1.2 86 147
NFKBIA 0.026 0.009 -10000 0 -10000 0 0
IL17A 0.019 0.32 0.56 87 -0.55 61 148
PI3K -0.062 0.47 0.69 23 -1.1 80 103
IFNG 0.026 0.07 0.18 133 -0.12 14 147
STAT3 (dimer) -0.064 0.45 0.72 13 -1 79 92
IL18R1 0.018 0.075 -10000 0 -0.57 16 16
IL23/IL23R/JAK2/TYK2/SOCS3 0.033 0.35 0.65 83 -0.7 37 120
IL18/IL18R 0.041 0.1 0.29 11 -0.37 49 60
macrophage activation 0 0.03 0.057 101 -0.044 55 156
TNF -0.037 0.51 0.84 42 -1.1 75 117
STAT3/STAT4 -0.061 0.49 0.68 28 -1.1 91 119
STAT4 (dimer) -0.056 0.52 0.74 44 -1.1 93 137
IL18 0.03 0.038 0.26 24 -10000 0 24
IL19 0.018 0.49 0.84 59 -1 68 127
STAT5A (dimer) -0.047 0.5 0.75 40 -1.1 88 128
STAT1 0.029 0.032 0.26 19 -10000 0 19
SOCS3 0.02 0.042 -10000 0 -0.58 5 5
CXCL9 0.003 0.52 0.85 77 -1.1 76 153
MPO -0.053 0.55 0.81 48 -1.2 111 159
positive regulation of humoral immune response -0.028 0.55 0.89 61 -1.2 86 147
IL23/IL23R/JAK2/TYK2 -0.036 0.57 0.9 59 -1.2 82 141
IL6 -0.3 0.74 0.8 37 -1.2 374 411
STAT5A 0.02 0.046 -10000 0 -0.58 6 6
IL2 0.022 0.039 0.3 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.015 -10000 0 -0.051 37 37
CD3E -0.032 0.51 0.85 52 -1.1 80 132
keratinocyte proliferation -0.028 0.55 0.89 61 -1.2 86 147
NOS2 -0.021 0.49 0.82 42 -1.1 70 112
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.008 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.021 0.14 0.31 1 -0.29 53 54
NFATC4 -0.064 0.12 0.26 8 -0.26 73 81
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.069 0.15 -10000 0 -0.31 238 238
JUN -0.009 0.098 0.23 30 -0.45 3 33
HRAS 0.026 0.021 0.26 8 -10000 0 8
DOCK7 -0.08 0.14 0.28 2 -0.3 234 236
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.053 0.15 -10000 0 -0.33 192 192
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.007 -10000 0 -10000 0 0
MAPK10 -0.071 0.11 0.22 7 -0.28 127 134
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.073 0.16 -10000 0 -0.33 238 238
RAF1 -0.017 0.15 0.33 16 -0.3 45 61
ErbB2/ErbB3/neuregulin 2 -0.15 0.18 -10000 0 -0.35 423 423
STAT3 -0.003 0.16 -10000 0 -0.86 35 35
cell migration -0.056 0.1 0.23 14 -0.26 81 95
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.041 0.25 0.43 14 -0.51 93 107
FOS -0.097 0.28 0.33 47 -0.49 305 352
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.069 0.15 -10000 0 -0.31 238 238
MAPK3 -0.013 0.2 0.4 15 -0.52 25 40
MAPK1 -0.024 0.22 0.41 14 -0.58 39 53
JAK2 -0.079 0.14 0.26 1 -0.3 233 234
NF2 -0.002 0.059 -10000 0 -0.68 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.053 0.13 0.23 3 -0.29 196 199
NRG1 -0.14 0.27 0.26 4 -0.58 276 280
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.081 0.15 0.25 2 -0.3 240 242
MAPK9 -0.043 0.083 0.2 10 -0.24 1 11
ERBB2 0.001 0.069 0.24 79 -10000 0 79
ERBB3 0.022 0.033 -10000 0 -0.58 3 3
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
apoptosis 0.02 0.025 -10000 0 -0.17 4 4
STAT3 (dimer) -0.002 0.16 -10000 0 -0.84 35 35
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.004 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.071 0.094 -10000 0 -0.23 181 181
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.016 -10000 0 -10000 0 0
CHRNA1 0.02 0.18 0.36 62 -0.41 18 80
myelination -0.059 0.12 0.3 16 -0.38 1 17
PPP3CB -0.075 0.13 0.27 2 -0.28 234 236
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.26 182 182
NRG2 -0.27 0.3 -10000 0 -0.58 496 496
mol:GDP -0.053 0.13 0.23 3 -0.29 196 199
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.015 0.14 0.33 17 -0.3 44 61
SRC 0.024 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 -0.3 237 239
MAP2K1 -0.051 0.23 0.44 5 -0.53 73 78
heart morphogenesis -0.069 0.15 -10000 0 -0.31 238 238
RAS family/GDP -0.021 0.14 0.29 1 -0.29 48 49
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA -0.002 0.069 -10000 0 -0.68 10 10
CHRNE 0.004 0.028 0.12 5 -0.21 3 8
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.069 0.15 -10000 0 -0.31 238 238
CDC42 0.023 0.005 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.059 0.16 0.33 5 -0.35 107 112
SMAD6-7/SMURF1 0.046 0.015 -10000 0 -10000 0 0
NOG 0.011 0.098 0.26 17 -0.58 25 42
SMAD9 -0.089 0.26 -10000 0 -0.6 174 174
SMAD4 0.023 0.006 -10000 0 -10000 0 0
SMAD5 -0.022 0.14 -10000 0 -0.44 65 65
BMP7/USAG1 -0.2 0.25 -10000 0 -0.45 464 464
SMAD5/SKI -0.016 0.15 0.26 3 -0.43 69 72
SMAD1 0.013 0.062 -10000 0 -0.42 7 7
BMP2 -0.077 0.22 0.26 1 -0.58 171 172
SMAD1/SMAD1/SMAD4 0.018 0.069 -10000 0 -0.4 9 9
BMPR1A 0.023 0.019 -10000 0 -0.58 1 1
BMPR1B 0.1 0.15 0.26 402 -0.58 22 424
BMPR1A-1B/BAMBI 0.084 0.12 0.34 9 -0.34 51 60
AHSG 0.021 0.026 0.26 12 -10000 0 12
CER1 0.019 0.014 0.26 3 -10000 0 3
BMP2-4/CER1 -0.049 0.18 -10000 0 -0.4 206 206
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.039 0.16 -10000 0 -0.41 103 103
BMP2-4 (homodimer) -0.069 0.2 -10000 0 -0.45 213 213
RGMB 0.023 0.019 -10000 0 -0.58 1 1
BMP6/BMPR2/BMPR1A-1B 0.07 0.14 -10000 0 -0.32 90 90
RGMA -0.053 0.2 -10000 0 -0.58 130 130
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.036 0.16 0.24 1 -0.42 116 117
BMP2-4/USAG1 -0.23 0.27 -10000 0 -0.45 551 551
SMAD6/SMURF1/SMAD5 -0.017 0.15 0.27 1 -0.44 68 69
SOSTDC1 -0.26 0.3 0.26 3 -0.58 484 487
BMP7/BMPR2/BMPR1A-1B 0.067 0.14 0.3 4 -0.32 87 91
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.016 0.15 0.26 2 -0.57 68 70
HFE2 0.018 0.022 0.26 7 -10000 0 7
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.047 0.2 -10000 0 -0.41 212 212
SMAD5/SMAD5/SMAD4 -0.017 0.15 0.27 1 -0.44 65 66
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.023 0.15 -10000 0 -0.38 106 106
BMP7 (homodimer) -0.013 0.16 0.26 27 -0.57 71 98
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.001 0.12 -10000 0 -0.43 68 68
SMAD1/SKI 0.02 0.077 -10000 0 -0.44 10 10
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.049 0.18 0.34 1 -0.4 208 209
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.036 0.099 0.26 90 -0.58 14 104
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.086 0.11 -10000 0 -0.42 23 23
CHRDL1 -0.38 0.28 -10000 0 -0.58 691 691
ENDOFIN/SMAD1 0.02 0.078 -10000 0 -0.45 10 10
SMAD6-7/SMURF1/SMAD1 0.036 0.081 -10000 0 -0.44 9 9
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.015 0.11 0.26 38 -0.58 30 68
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.27 -10000 0 -0.46 695 695
BMP2-4/GREM1 -0.04 0.2 -10000 0 -0.4 216 216
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.081 0.25 -10000 0 -0.58 182 182
SMAD1/SMAD6 0.019 0.079 -10000 0 -0.46 10 10
TAK1/SMAD6 0.034 0.01 -10000 0 -10000 0 0
BMP7 -0.013 0.16 0.26 27 -0.58 71 98
BMP6 -0.016 0.15 0.26 2 -0.58 68 70
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.035 0.17 -10000 0 -0.42 118 118
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.018 0.075 -10000 0 -0.46 9 9
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.006 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.046 0.2 0.24 1 -0.48 125 126
CHRD 0.025 0.098 0.26 52 -0.58 19 71
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.051 0.18 -10000 0 -0.48 116 116
BMP4 -0.012 0.14 0.26 1 -0.58 61 62
FST 0.002 0.12 0.26 4 -0.58 38 42
BMP2-4/NOG -0.051 0.19 -10000 0 -0.41 203 203
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.071 0.14 0.33 1 -0.31 86 87
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 -0.002 0.084 -10000 0 -0.55 14 14
Crk/p130 Cas/Paxillin -0.056 0.12 -10000 0 -0.35 121 121
JUN -0.015 0.12 0.23 2 -0.41 27 29
HRAS 0.026 0.021 0.26 8 -10000 0 8
RET51/GFRalpha1/GDNF/GRB10 0.043 0.2 0.35 52 -0.34 168 220
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.043 0.2 0.35 51 -0.34 166 217
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 -0.011 0.15 0.32 4 -0.34 170 174
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.17 0.28 37 -0.31 169 206
GRB7 0.02 0.021 -10000 0 -0.58 1 1
RET51/GFRalpha1/GDNF 0.042 0.2 0.35 51 -0.34 167 218
MAPKKK cascade 0 0.15 0.28 9 -0.33 124 133
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.024 0.18 0.32 3 -0.38 181 184
lamellipodium assembly -0.033 0.13 -10000 0 -0.32 134 134
RET51/GFRalpha1/GDNF/SHC 0.037 0.18 0.35 42 -0.34 130 172
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.14 0.32 4 -0.34 126 130
RET9/GFRalpha1/GDNF/Shank3 -0.013 0.15 0.32 4 -0.34 169 173
MAPK3 -0.032 0.13 0.28 3 -0.3 159 162
DOK1 0.025 0.015 0.26 4 -10000 0 4
DOK6 0.017 0.07 0.26 6 -0.58 13 19
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.031 0.13 -10000 0 -0.31 130 130
DOK5 0.011 0.089 0.26 5 -0.58 22 27
GFRA1 -0.071 0.24 0.26 53 -0.58 181 234
MAPK8 -0.009 0.13 0.22 4 -0.29 133 137
HRAS/GTP 0.029 0.18 0.29 52 -0.34 160 212
tube development -0.006 0.15 0.34 9 -0.32 161 170
MAPK1 -0.031 0.13 0.26 6 -0.3 158 164
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.11 0.25 1 -0.27 156 157
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.038 0.19 0.34 48 -0.34 172 220
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.028 0.19 0.34 38 -0.34 169 207
RET51/GFRalpha1/GDNF/Dok5 0.026 0.2 0.35 47 -0.36 176 223
PRKCA 0.01 0.086 0.26 1 -0.58 21 22
HRAS/GDP 0.019 0.015 0.18 8 -10000 0 8
CREB1 -0.013 0.13 0.23 9 -0.32 96 105
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.019 0.1 0.25 1 -0.27 114 115
RET51/GFRalpha1/GDNF/Grb7 0.042 0.19 0.33 65 -0.35 137 202
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.14 0.26 360 -0.58 13 373
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.014 0.12 0.25 1 -0.4 27 28
RET9/GFRalpha1/GDNF/FRS2 -0.012 0.15 0.32 4 -0.34 169 173
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.02 0.1 0.25 1 -0.27 115 116
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.006 0.14 0.24 14 -0.29 131 145
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.003 0.14 0.25 4 -0.3 133 137
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.011 0.14 0.25 16 -0.31 98 114
PI3K -0.028 0.21 0.3 7 -0.48 135 142
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.14 0.32 3 -0.32 161 164
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.002 0.12 0.24 7 -0.27 126 133
RET51/GFRalpha1/GDNF/FRS2 0.04 0.2 0.34 54 -0.34 168 222
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.58 40 40
IRS2 0.004 0.1 -10000 0 -0.58 32 32
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.011 0.14 0.25 16 -0.3 98 114
RET51/GFRalpha1/GDNF/PKC alpha 0.025 0.2 0.35 42 -0.35 175 217
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.033 0.054 0.26 54 -10000 0 54
RAC1 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.028 0.22 0.34 49 -0.39 180 229
Rac1/GTP -0.022 0.17 0.24 4 -0.38 134 138
RET9/GFRalpha1/GDNF -0.026 0.16 0.32 4 -0.35 183 187
GFRalpha1/GDNF -0.033 0.19 0.37 4 -0.41 185 189
Plasma membrane estrogen 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
GNB1/GNG2 0.001 0.15 -10000 0 -0.32 163 163
ER alpha/Gai/GDP/Gbeta gamma -0.083 0.22 -10000 0 -0.47 199 199
AKT1 -0.12 0.33 -10000 0 -0.78 195 195
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.34 -10000 0 -0.78 195 195
mol:Ca2+ -0.023 0.11 0.27 2 -0.46 26 28
IGF1R 0.012 0.082 0.26 2 -0.58 19 21
E2/ER alpha (dimer)/Striatin -0.017 0.16 -10000 0 -0.37 159 159
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.11 0.31 0.74 195 -10000 0 195
RhoA/GTP -0.016 0.1 -10000 0 -0.29 115 115
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.066 0.21 0.32 4 -0.47 182 186
regulation of stress fiber formation 0.024 0.11 0.28 21 -0.31 8 29
E2/ERA-ERB (dimer) -0.019 0.16 -10000 0 -0.36 162 162
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.01 0.13 -10000 0 -0.33 133 133
pseudopodium formation -0.024 0.11 0.31 8 -0.28 21 29
E2/ER alpha (dimer)/PELP1 -0.014 0.15 -10000 0 -0.36 144 144
GRB2 0.023 0.01 0.26 1 -10000 0 1
GNG2 0.018 0.059 -10000 0 -0.58 10 10
GNAO1 0.018 0.092 0.26 32 -0.58 19 51
HRAS 0.026 0.021 0.26 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.086 0.23 -10000 0 -0.51 206 206
E2/ER beta (dimer) 0.009 0.06 -10000 0 -0.41 20 20
mol:GDP -0.038 0.17 0.26 11 -0.4 158 169
mol:NADP -0.086 0.23 -10000 0 -0.51 206 206
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
mol:IP3 -0.026 0.11 0.27 2 -0.48 25 27
IGF-1R heterotetramer 0.012 0.082 0.26 2 -0.57 19 21
PLCB1 -0.024 0.11 0.28 2 -0.48 28 30
PLCB2 -0.005 0.084 -10000 0 -0.51 16 16
IGF1 -0.1 0.25 -10000 0 -0.58 217 217
mol:L-citrulline -0.086 0.23 -10000 0 -0.51 206 206
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.075 0.25 -10000 0 -0.63 149 149
JNK cascade 0.009 0.06 -10000 0 -0.41 20 20
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.012 0.081 -10000 0 -0.58 19 19
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
ESR1 -0.036 0.23 0.26 111 -0.58 144 255
Gq family/GDP/Gbeta gamma -0.009 0.16 -10000 0 -0.75 35 35
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.018 0.14 -10000 0 -0.59 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.058 0.2 0.31 5 -0.47 151 156
GNAZ 0.018 0.056 -10000 0 -0.58 9 9
E2/ER alpha (dimer) -0.029 0.17 0.18 111 -0.41 150 261
STRN 0.014 0.079 -10000 0 -0.58 18 18
GNAL -0.11 0.25 -10000 0 -0.58 221 221
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.003 0.055 -10000 0 -0.36 22 22
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 46 46
HBEGF -0.053 0.21 0.34 21 -0.5 108 129
cAMP biosynthetic process -0.087 0.18 -10000 0 -0.33 328 328
SRC -0.077 0.21 0.3 7 -0.44 198 205
PI3K 0.029 0.043 -10000 0 -0.4 9 9
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.019 0.16 -10000 0 -0.39 129 129
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.44 204 204
Gs family/GTP -0.084 0.19 -10000 0 -0.33 328 328
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.019 -10000 0 -10000 0 0
vasodilation -0.081 0.22 -10000 0 -0.48 206 206
mol:DAG -0.026 0.11 0.27 2 -0.48 25 27
Gs family/GDP/Gbeta gamma -0.09 0.18 -10000 0 -0.36 257 257
MSN -0.026 0.11 0.32 8 -0.3 21 29
Gq family/GTP -0.001 0.089 -10000 0 -0.54 15 15
mol:PI-3-4-5-P3 -0.11 0.32 -10000 0 -0.75 195 195
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.081 0.22 0.48 206 -10000 0 206
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.022 0.17 0.26 10 -0.38 155 165
NOS3 -0.092 0.25 -10000 0 -0.55 198 198
GNA11 0.023 0.027 -10000 0 -0.58 2 2
MAPKKK cascade -0.083 0.25 0.31 2 -0.57 189 191
E2/ER alpha (dimer)/PELP1/Src -0.069 0.22 0.31 8 -0.48 187 195
ruffle organization -0.024 0.11 0.31 8 -0.28 21 29
ROCK2 -0.025 0.12 0.34 8 -0.28 119 127
GNA14 0.023 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.026 0.26 6 -0.58 1 7
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.045 0.21 0.35 26 -0.49 107 133
MMP2 -0.068 0.2 0.27 12 -0.42 195 207
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.07 0.11 -10000 0 -0.29 92 92
NT3 (dimer)/TRKC -0.18 0.27 -10000 0 -0.47 424 424
NT3 (dimer)/TRKB -0.3 0.31 -10000 0 -0.53 590 590
SHC/Grb2/SOS1/GAB1/PI3K 0.016 0.032 -10000 0 -0.26 6 6
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.016 0.16 0.26 23 -0.58 77 100
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.024 0.049 0.26 22 -0.58 3 25
NTRK2 -0.29 0.3 -10000 0 -0.58 528 528
NTRK3 -0.17 0.28 0.26 5 -0.58 332 337
NT-4/5 (dimer)/TRKB -0.37 0.34 -10000 0 -0.58 663 663
neuron apoptosis 0.17 0.22 0.47 287 -10000 0 287
SHC 2-3/Grb2 -0.19 0.24 -10000 0 -0.52 287 287
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.19 0.25 -10000 0 -0.54 279 279
SHC3 -0.18 0.24 -10000 0 -0.52 273 273
STAT3 (dimer) 0.033 0.043 0.22 35 -0.36 4 39
NT3 (dimer)/TRKA -0.11 0.22 -10000 0 -0.42 290 290
RIN/GDP -0.047 0.12 0.28 5 -0.26 73 78
GIPC1 0.024 0.011 0.26 2 -10000 0 2
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.081 0.15 -10000 0 -0.33 255 255
RIN/GTP 0.014 0.006 0.18 1 -10000 0 1
CCND1 0.024 0.094 0.43 36 -0.83 4 40
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) -0.18 0.28 -10000 0 -0.57 355 355
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 0.034 0.083 0.34 2 -0.36 31 33
TRKA/NEDD4-2 0.031 0.038 0.2 22 -0.36 4 26
ELMO1 0.024 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.008 -10000 0 -10000 0 0
NGF 0.017 0.075 0.26 7 -0.58 15 22
HRAS 0.026 0.021 0.26 8 -10000 0 8
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.021 0.02 -10000 0 -0.58 1 1
RIT2 0.018 0.009 0.26 1 -10000 0 1
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
DNM1 0.02 0.05 0.26 1 -0.58 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.074 0.16 -10000 0 -0.32 283 283
mol:GDP -0.076 0.16 0.35 5 -0.38 95 100
NGF (dimer) 0.017 0.075 0.26 7 -0.57 15 22
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.046 0.11 0.38 2 -0.26 67 69
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
BDNF (dimer)/TRKB -0.19 0.23 -10000 0 -0.4 550 550
KIDINS220/CRKL/C3G 0.034 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.015 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.048 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.061 0.21 0.26 12 -0.57 148 160
RAP1/GDP -0.042 0.094 -10000 0 -0.23 67 67
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.016 0.16 0.26 23 -0.57 77 100
ubiquitin-dependent protein catabolic process 0.036 0.06 -10000 0 -0.33 19 19
Schwann cell development -0.049 0.038 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.051 -10000 0 -0.27 11 11
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.28 0.29 -10000 0 -0.47 626 626
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.08 0.13 -10000 0 -0.43 60 60
STAT3 0.033 0.043 0.22 35 -0.36 4 39
axon guidance -0.27 0.27 -10000 0 -0.45 626 626
MAPK3 0.024 0.086 0.23 5 -0.36 25 30
MAPK1 0.026 0.089 0.23 6 -0.36 26 32
CDC42/GDP -0.045 0.12 0.28 6 -0.26 72 78
NTF3 -0.061 0.21 0.26 12 -0.58 148 160
NTF4 -0.19 0.28 -10000 0 -0.58 355 355
NGF (dimer)/TRKA/FAIM 0.037 0.06 -10000 0 -0.37 16 16
PI3K 0.029 0.043 -10000 0 -0.4 9 9
FRS3 0.024 0.005 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.024 0.004 -10000 0 -10000 0 0
RASGRF1 -0.079 0.16 0.25 3 -0.33 277 280
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.42 404 405
RGS19 0.023 0.01 0.26 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.016 0.096 0.34 2 -0.44 9 11
Rac1/GDP -0.046 0.12 0.31 4 -0.26 72 76
NGF (dimer)/TRKA/GRIT 0.024 0.057 0.18 25 -0.34 18 43
neuron projection morphogenesis -0.073 0.22 -10000 0 -0.74 50 50
NGF (dimer)/TRKA/NEDD4-2 0.036 0.061 -10000 0 -0.33 19 19
MAP2K1 0.029 0.085 0.36 16 -10000 0 16
NGFR -0.14 0.27 -10000 0 -0.58 278 278
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.05 -10000 0 -0.29 19 19
RAS family/GTP/PI3K 0.018 0.027 -10000 0 -0.26 6 6
FRS2 family/SHP2/GRB2/SOS1 0.064 0.027 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.58 1 1
MAPKKK cascade -0.04 0.14 -10000 0 -0.65 38 38
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.037 -10000 0 -0.43 3 3
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.17 0.22 -10000 0 -0.36 545 545
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.061 -10000 0 -0.32 16 16
MATK 0.02 0.087 0.26 27 -0.58 17 44
NEDD4L 0.023 0.019 -10000 0 -0.58 1 1
RAS family/GDP -0.057 0.071 -10000 0 -0.21 69 69
NGF (dimer)/TRKA -0.089 0.17 -10000 0 -0.34 289 289
Rac1/GTP -0.086 0.12 -10000 0 -0.28 210 210
FRS2 family/SHP2/CRK family 0.06 0.029 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.004 0.04 0.2 4 -0.37 2 6
NFATC2 -0.024 0.11 0.2 4 -0.38 78 82
NFATC3 0.006 0.035 0.2 4 -10000 0 4
CD40LG -0.14 0.29 0.49 15 -0.57 226 241
PTGS2 -0.19 0.34 0.49 12 -0.64 308 320
JUNB 0.025 0.011 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.027 0.16 2 -10000 0 2
CaM/Ca2+ 0.008 0.027 0.16 2 -10000 0 2
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.013 0.051 -10000 0 -0.58 6 6
mol:Ca2+ -0.003 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.025 0.054 0.26 20 -0.58 5 25
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.003 0.15 0.47 11 -0.4 52 63
FOS -0.15 0.27 -10000 0 -0.58 286 286
IFNG -0.11 0.28 0.47 40 -0.53 221 261
AP-1/NFAT1-c-4 -0.13 0.34 0.54 37 -0.61 245 282
FASLG -0.12 0.27 0.51 22 -0.54 188 210
NFAT1-c-4/ICER1 -0.016 0.12 0.3 7 -0.35 69 76
IL2RA -0.12 0.28 0.48 29 -0.54 221 250
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.27 0.49 18 -0.53 223 241
JunB/Fra1/NFAT1-c-4 -0.006 0.13 0.34 11 -0.34 74 85
IL4 -0.13 0.27 0.49 12 -0.54 220 232
IL2 -0.015 0.16 -10000 0 -0.94 27 27
IL3 -0.018 0.12 -10000 0 -0.72 23 23
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.014 0.26 2 -10000 0 2
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.038 -10000 0 -0.58 4 4
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.4 259 260
PTP1B/AKT1 -0.066 0.13 0.22 1 -0.35 122 123
FYN 0.022 0.027 -10000 0 -0.58 2 2
p210 bcr-abl/PTP1B -0.081 0.14 0.22 2 -0.36 142 144
EGFR -0.2 0.29 -10000 0 -0.59 363 363
EGF/EGFR -0.2 0.24 -10000 0 -0.42 494 494
CSF1 0.022 0.038 -10000 0 -0.58 4 4
AKT1 0.024 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.047 0.16 0.23 17 -0.37 127 144
Insulin Receptor/Insulin -0.043 0.12 -10000 0 -0.39 48 48
HCK 0.027 0.026 0.26 12 -10000 0 12
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.078 0.14 0.28 3 -0.37 123 126
EGF -0.1 0.23 0.26 2 -0.58 182 184
YES1 0.023 0.02 -10000 0 -0.58 1 1
CAV1 -0.16 0.21 0.27 2 -0.43 304 306
TXN 0.017 0.018 0.26 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.072 0.15 -10000 0 -0.38 138 138
cell migration 0.081 0.14 0.36 142 -0.22 2 144
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.023 0.046 0.26 6 -0.58 5 11
ITGA2B 0.031 0.061 0.26 50 -0.58 3 53
CSF1R 0.024 0.008 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.032 0.04 0.32 1 -0.38 5 6
FGR 0.024 0.009 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.068 0.14 0.22 1 -0.36 125 126
Crk/p130 Cas -0.061 0.14 -10000 0 -0.38 98 98
DOK1 -0.067 0.13 0.23 2 -0.4 81 83
JAK2 -0.048 0.12 -10000 0 -0.44 59 59
Jak2/Leptin Receptor/Leptin -0.27 0.16 -10000 0 -0.38 502 502
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
PTPN1 -0.082 0.14 0.22 2 -0.37 142 144
LYN 0.021 0.009 -10000 0 -10000 0 0
CDH2 0.064 0.095 0.26 180 -0.58 2 182
SRC -0.017 0.099 -10000 0 -0.62 20 20
ITGB3 0.004 0.11 0.26 4 -0.58 32 36
CAT1/PTP1B -0.093 0.19 0.32 4 -0.47 143 147
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.037 0.12 -10000 0 -0.42 40 40
mol:H2O2 -0.004 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.24 0.14 -10000 0 -0.36 421 421
negative regulation of transcription -0.047 0.12 -10000 0 -0.43 59 59
FCGR2A 0.02 0.009 -10000 0 -10000 0 0
FER 0.011 0.061 -10000 0 -0.59 10 10
alphaIIb/beta3 Integrin 0.023 0.092 -10000 0 -0.42 35 35
BLK 0.05 0.087 0.26 135 -0.58 2 137
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.006 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.58 251 251
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 -0.043 0.18 0.31 6 -0.44 102 108
PRL 0.008 0.033 0.26 10 -10000 0 10
SOCS3 0.009 0.16 -10000 0 -1.2 16 16
SPRY2 -0.037 0.17 -10000 0 -0.58 93 93
Insulin Receptor/Insulin/IRS1 0.025 0.081 -10000 0 -0.38 39 39
CSF1/CSF1R -0.064 0.14 -10000 0 -0.37 119 119
Ras protein signal transduction 0.05 0.15 0.64 56 -10000 0 56
IRS1 0.001 0.12 -10000 0 -0.58 40 40
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.45 0.24 -10000 0 -0.58 799 799
STAT5B -0.069 0.14 0.2 3 -0.36 135 138
STAT5A -0.07 0.14 0.2 3 -0.36 139 142
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.072 0.14 0.22 1 -0.37 127 128
CSN2 0.025 0.058 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.009 0.074 -10000 0 -0.59 8 8
YBX1 0.027 0.016 -10000 0 -10000 0 0
LCK 0.026 0.077 0.26 36 -0.58 11 47
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.032 0.26 10 -0.58 1 11
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.039 0.17 -10000 0 -0.41 170 170
CRKL -0.047 0.15 0.31 2 -0.41 82 84
mol:PIP3 0.002 0.061 0.57 1 -0.89 4 5
AKT1 0.01 0.075 0.37 3 -0.79 4 7
PTK2B 0.02 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.14 0.34 1 -0.41 70 71
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.042 0.18 -10000 0 -0.39 197 197
MAP3K5 -0.039 0.15 0.36 1 -0.45 59 60
HGF/MET/CIN85/CBL/ENDOPHILINS -0.029 0.17 -10000 0 -0.36 203 203
AP1 -0.11 0.19 -10000 0 -0.4 290 290
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.24 0.38 -10000 0 -0.77 332 332
STAT3 (dimer) -0.045 0.15 -10000 0 -0.35 160 160
GAB1/CRKL/SHP2/PI3K -0.018 0.15 -10000 0 -0.45 50 50
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.036 0.14 0.34 1 -0.42 62 63
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.023 0.02 -10000 0 -0.58 1 1
ELK1 -0.029 0.096 0.26 39 -0.21 121 160
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.093 -10000 0 -0.32 39 39
PAK1 0.024 0.088 0.38 6 -0.75 4 10
HGF/MET/RANBP10 -0.044 0.18 -10000 0 -0.39 204 204
HRAS -0.1 0.26 -10000 0 -0.64 178 178
DOCK1 -0.045 0.14 0.52 1 -0.41 68 69
GAB1 -0.049 0.16 -10000 0 -0.43 88 88
CRK -0.048 0.15 0.36 1 -0.42 80 81
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.25 -10000 0 -0.57 216 216
JUN 0.02 0.046 -10000 0 -0.58 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.051 0.12 -10000 0 -0.29 207 207
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
cell morphogenesis -0.047 0.16 0.37 6 -0.45 79 85
GRB2/SHC -0.016 0.11 -10000 0 -0.29 113 113
FOS -0.14 0.27 -10000 0 -0.58 285 285
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.029 0.096 0.26 39 -0.21 122 161
HGF/MET/MUC20 -0.054 0.17 -10000 0 -0.39 206 206
cell migration -0.016 0.11 -10000 0 -0.28 113 113
GRB2 0.023 0.01 0.26 1 -10000 0 1
CBL 0.022 0.008 -10000 0 -10000 0 0
MET/RANBP10 -0.041 0.17 -10000 0 -0.42 162 162
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.046 0.14 -10000 0 -0.33 168 168
MET/MUC20 -0.054 0.16 -10000 0 -0.41 170 170
RAP1B -0.039 0.14 0.32 4 -0.39 66 70
RAP1A -0.044 0.14 0.41 2 -0.39 67 69
HGF/MET/RANBP9 -0.042 0.18 -10000 0 -0.39 199 199
RAF1 -0.097 0.24 -10000 0 -0.6 178 178
STAT3 -0.046 0.15 -10000 0 -0.35 160 160
cell proliferation -0.041 0.19 0.28 33 -0.43 145 178
RPS6KB1 -0.015 0.064 -10000 0 -0.22 40 40
MAPK3 -0.041 0.095 0.62 8 -10000 0 8
MAPK1 -0.012 0.17 0.68 49 -10000 0 49
RANBP9 0.024 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.14 0.44 1 -0.48 33 34
SRC -0.051 0.13 0.2 1 -0.32 162 163
PI3K -0.026 0.13 -10000 0 -0.29 165 165
MET/Glomulin -0.046 0.15 -10000 0 -0.38 164 164
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.089 0.23 0.47 1 -0.56 176 177
MET -0.071 0.22 -10000 0 -0.58 162 162
MAP4K1 -0.042 0.15 0.38 1 -0.43 79 80
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.089 0.23 0.47 1 -0.56 177 178
BAD 0.008 0.072 0.36 2 -0.75 4 6
MAP2K4 -0.036 0.13 0.34 1 -0.42 53 54
SHP2/GRB2/SOS1/GAB1 -0.039 0.17 -10000 0 -0.4 160 160
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.047 0.11 -10000 0 -0.27 188 188
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.58 60 60
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.021 0.13 -10000 0 -0.27 193 193
PDPK1 0.013 0.079 0.43 1 -0.83 4 5
HGF/MET/SHIP -0.042 0.18 -10000 0 -0.39 205 205
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.18 14 -10000 0 14
Metarhodopsin II/Arrestin 0.037 0.038 0.32 2 -10000 0 2
PDE6G/GNAT1/GTP 0.036 0.035 -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 0.024 0.028 0.26 14 -10000 0 14
GRK1 0.019 0.016 0.26 4 -10000 0 4
CNG Channel -0.05 0.16 -10000 0 -0.31 273 273
mol:Na + -0.05 0.16 -10000 0 -0.3 277 277
mol:ADP 0.019 0.016 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.015 0.12 0.34 1 -0.36 84 85
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.044 0.17 0.28 5 -0.31 276 281
CNGB1 0.031 0.053 0.26 51 -10000 0 51
RDH5 -0.33 0.3 -10000 0 -0.58 595 595
SAG 0.032 0.052 0.26 50 -10000 0 50
mol:Ca2+ -0.083 0.14 0.35 17 -0.3 228 245
Na + (4 Units) -0.053 0.15 -10000 0 -0.29 271 271
RGS9 -0.026 0.17 0.26 11 -0.58 86 97
GNB1/GNGT1 0.055 0.06 -10000 0 -10000 0 0
GNAT1/GDP 0.024 0.11 0.31 5 -0.32 84 89
GUCY2D 0.023 0.047 0.26 14 -0.58 4 18
GNGT1 0.056 0.088 0.26 160 -10000 0 160
GUCY2F 0.019 0.011 0.26 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.02 0.051 0.21 3 -0.32 15 18
mol:11-cis-retinal -0.33 0.3 -10000 0 -0.57 595 595
mol:cGMP 0.042 0.047 -10000 0 -0.33 8 8
GNB1 0.024 0.005 -10000 0 -10000 0 0
Rhodopsin -0.23 0.23 -10000 0 -0.42 599 599
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.14 0.27 0.26 4 -0.58 282 286
Metarhodopsin II 0.026 0.02 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.052 -10000 0 -0.34 8 8
RGS9BP 0.037 0.054 0.26 57 -10000 0 57
Metarhodopsin II/Transducin 0.025 0.032 0.17 8 -0.17 1 9
GCAP Family/Ca ++ 0.044 0.038 -10000 0 -0.34 4 4
PDE6A/B 0.029 0.066 -10000 0 -0.43 17 17
mol:Pi 0.015 0.12 0.34 1 -0.36 84 85
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.059 0.054 0.32 2 -10000 0 2
PDE6B 0.014 0.078 0.26 3 -0.58 17 20
PDE6A 0.028 0.032 0.26 19 -10000 0 19
PDE6G 0.033 0.048 0.26 43 -10000 0 43
RHO 0.025 0.028 0.26 14 -10000 0 14
PDE6 0.035 0.12 0.3 7 -0.31 94 101
GUCA1A 0.032 0.047 0.26 41 -10000 0 41
GC2/GCAP Family 0.055 0.04 -10000 0 -0.34 4 4
GUCA1C 0.017 0.008 0.26 1 -10000 0 1
GUCA1B 0.021 0.038 -10000 0 -0.58 4 4
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.008 0.26 1 -10000 0 1
CCL5 0.029 0.059 0.26 37 -0.58 4 41
SDCBP 0.021 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.063 0.12 0.22 98 -0.32 22 120
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 0.05 0.12 0.26 5 -0.38 16 21
Syndecan-1/Syntenin 0.052 0.12 0.28 10 -0.4 12 22
MAPK3 0.048 0.11 0.26 11 -0.36 13 24
HGF/MET -0.064 0.2 -10000 0 -0.45 206 206
TGFB1/TGF beta receptor Type II 0.024 0.008 0.26 1 -10000 0 1
BSG 0.024 0.009 0.26 1 -10000 0 1
keratinocyte migration 0.05 0.12 0.26 5 -0.37 16 21
Syndecan-1/RANTES 0.059 0.14 0.3 43 -0.41 17 60
Syndecan-1/CD147 0.064 0.13 0.3 10 -0.36 15 25
Syndecan-1/Syntenin/PIP2 0.048 0.11 0.26 10 -0.39 12 22
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.046 0.11 0.25 9 -0.38 12 21
MMP7 -0.039 0.2 0.26 29 -0.58 115 144
HGF -0.011 0.14 -10000 0 -0.58 60 60
Syndecan-1/CASK 0.043 0.12 0.2 55 -0.31 28 83
Syndecan-1/HGF/MET -0.003 0.2 0.29 6 -0.46 104 110
regulation of cell adhesion 0.042 0.11 0.26 8 -0.39 8 16
HPSE 0.027 0.036 0.26 17 -0.58 1 18
positive regulation of cell migration 0.063 0.12 0.22 98 -0.32 22 120
SDC1 0.067 0.12 0.24 59 -0.26 49 108
Syndecan-1/Collagen 0.063 0.12 0.22 98 -0.32 22 120
PPIB 0.025 0.013 0.26 3 -10000 0 3
MET -0.071 0.22 -10000 0 -0.58 162 162
PRKACA 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 424 -0.58 1 425
MAPK1 0.049 0.12 0.26 11 -0.36 12 23
homophilic cell adhesion 0.063 0.12 0.22 98 -0.37 15 113
MMP1 0.18 0.11 0.26 703 -10000 0 703
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.043 0.2 4 -0.39 5 9
PDGFRB 0.018 0.039 -10000 0 -0.58 4 4
SPHK1 -0.018 0.099 -10000 0 -0.75 14 14
mol:S1P -0.022 0.096 0.39 1 -0.66 14 15
S1P1/S1P/Gi -0.13 0.23 0.32 2 -0.43 329 331
GNAO1 0.006 0.094 0.25 32 -0.58 19 51
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.34 4 -0.4 297 301
PLCG1 -0.12 0.22 0.36 2 -0.42 306 308
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.039 -10000 0 -0.58 4 4
GNAI2 0.009 0.023 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.017 0.13 -10000 0 -0.59 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.03 0.2 1 -0.34 5 6
S1P1/S1P -0.034 0.098 0.25 3 -0.47 18 21
negative regulation of cAMP metabolic process -0.13 0.22 0.31 2 -0.42 329 331
MAPK3 -0.18 0.3 0.3 13 -0.58 336 349
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
KDR 0.011 0.042 -10000 0 -0.59 4 4
PLCB2 -0.025 0.098 0.29 7 -0.41 19 26
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.082 -10000 0 -0.39 18 18
receptor internalization -0.035 0.089 0.18 1 -0.43 18 19
PTGS2 -0.33 0.5 0.4 1 -1 347 348
Rac1/GTP -0.032 0.082 -10000 0 -0.4 18 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.026 0.26 6 -10000 0 6
negative regulation of T cell proliferation -0.13 0.22 0.31 2 -0.42 329 331
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.06 -10000 0 -0.58 9 9
MAPK1 -0.2 0.32 0.32 3 -0.62 353 356
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.31 4 -0.46 18 22
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.37 309 309
fibroblast growth factor receptor signaling pathway -0.1 0.19 -10000 0 -0.37 309 309
LAMA1 -0.038 0.18 0.26 2 -0.58 105 107
PRNP 0.015 0.07 -10000 0 -0.58 14 14
GPC1/SLIT2 -0.013 0.14 -10000 0 -0.42 108 108
SMAD2 -0.001 0.068 0.25 1 -0.34 38 39
GPC1/PrPc/Cu2+ 0.026 0.049 0.18 4 -0.36 15 19
GPC1/Laminin alpha1 -0.015 0.14 -10000 0 -0.41 115 115
TDGF1 0.017 0.06 0.26 1 -0.58 10 11
CRIPTO/GPC1 0.03 0.05 -10000 0 -0.43 11 11
APP/GPC1 0.035 0.02 -10000 0 -0.43 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.041 -10000 0 -0.37 11 11
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.032 0.082 -10000 0 -0.37 39 39
SERPINC1 0.03 0.049 0.26 43 -10000 0 43
FYN 0.004 0.044 -10000 0 -0.36 13 13
FGR 0.005 0.041 -10000 0 -0.37 11 11
positive regulation of MAPKKK cascade 0.009 0.083 0.26 4 -0.36 27 31
SLIT2 -0.037 0.18 -10000 0 -0.58 102 102
GPC1/NRG -0.11 0.2 -10000 0 -0.37 352 352
NRG1 -0.14 0.26 0.26 4 -0.58 276 280
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.025 -10000 0 -0.37 1 1
LYN 0.005 0.036 -10000 0 -0.37 8 8
mol:Spermine 0.006 0.016 -10000 0 -0.42 1 1
cell growth -0.1 0.19 -10000 0 -0.37 309 309
BMP signaling pathway -0.024 0.025 0.57 1 -0.26 5 6
SRC 0.005 0.041 -10000 0 -0.37 11 11
TGFBR1 0.024 0.008 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.28 0.26 26 -0.58 292 318
GPC1 0.025 0.025 0.26 5 -0.58 1 6
TGFBR1 (dimer) 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 6 -10000 0 6
BLK 0.019 0.066 -10000 0 -0.38 13 13
HCK 0.006 0.043 -10000 0 -0.37 11 11
FGF2 -0.2 0.29 -10000 0 -0.58 383 383
FGFR1 0.016 0.05 -10000 0 -0.58 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.002 0.11 -10000 0 -0.58 38 38
cell death 0.034 0.02 -10000 0 -0.43 1 1
ATIII/GPC1 0.036 0.04 0.2 43 -0.43 1 44
PLA2G2A/GPC1 -0.1 0.21 0.2 26 -0.4 324 350
LCK 0.005 0.062 -10000 0 -0.37 22 22
neuron differentiation -0.11 0.2 -10000 0 -0.37 352 352
PrPc/Cu2+ 0.011 0.052 -10000 0 -0.42 14 14
APP 0.024 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.002 0.11 -10000 0 -0.57 38 38
Aurora C signaling

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
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.079 0.32 7 -0.3 1 8
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.02 -10000 0 -0.3 2 2
AURKB 0.15 0.12 0.26 535 -10000 0 535
AURKC 0.026 0.031 0.26 11 -0.58 1 12
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.016 0.081 0.28 1 -0.33 2 3
epithelial cell differentiation 0.033 0.078 0.4 1 -0.34 4 5
ITCH 0.032 0.019 -10000 0 -10000 0 0
WWP1 0.023 0.098 0.47 8 -10000 0 8
FYN 0.022 0.027 -10000 0 -0.58 2 2
EGFR -0.19 0.29 -10000 0 -0.58 363 363
PRL 0.022 0.024 0.26 10 -10000 0 10
neuron projection morphogenesis -0.043 0.15 0.36 11 -0.36 33 44
PTPRZ1 -0.28 0.3 0.26 6 -0.58 523 529
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.054 0.14 -10000 0 -0.37 45 45
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.089 0.16 -10000 0 -0.34 238 238
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.006 0.074 0.38 8 -0.3 6 14
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.11 -10000 0 -0.36 42 42
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.081 0.15 -10000 0 -0.33 228 228
GRIN2B -0.099 0.16 -10000 0 -0.33 257 257
ErbB4/ErbB2/betacellulin 0.013 0.097 -10000 0 -0.32 29 29
STAT1 0.029 0.032 0.26 19 -10000 0 19
HBEGF 0.023 0.027 -10000 0 -0.58 2 2
PRLR 0.022 0.046 0.26 6 -0.58 5 11
E4ICDs/ETO2 0.006 0.089 0.35 1 -0.41 11 12
axon guidance 0.056 0.11 0.32 40 -0.35 2 42
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.032 0.037 -10000 0 -0.38 5 5
CBFA2T3 0.013 0.074 0.26 4 -0.58 15 19
ErbB4/ErbB2/HBEGF 0.03 0.071 -10000 0 -0.31 2 2
MAPK3 -0.049 0.14 0.34 4 -0.37 38 42
STAT1 (dimer) 0.019 0.081 0.28 1 -10000 0 1
MAPK1 -0.048 0.14 0.36 5 -0.36 39 44
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.073 0.15 0.27 1 -0.33 207 208
NRG1 -0.11 0.2 -10000 0 -0.43 272 272
NRG3 -0.003 0.14 0.26 21 -0.58 52 73
NRG2 -0.27 0.3 -10000 0 -0.58 496 496
NRG4 0.027 0.029 0.26 15 -10000 0 15
heart development 0.056 0.11 0.32 40 -0.35 2 42
neural crest cell migration -0.072 0.15 0.27 1 -0.32 207 208
ERBB2 0.035 0.069 0.27 81 -10000 0 81
WWOX/E4ICDs 0.011 0.076 0.28 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.097 0.17 -10000 0 -0.32 259 259
apoptosis 0.014 0.13 0.45 48 -0.26 4 52
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.16 0.18 -10000 0 -0.35 394 394
ErbB4/ErbB2/epiregulin 0.005 0.13 0.36 12 -0.32 78 90
ErbB4/ErbB4/betacellulin/betacellulin -0.004 0.11 0.28 1 -0.35 42 43
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.041 0.086 0.4 1 -0.37 6 7
MDM2 0.009 0.081 0.29 9 -10000 0 9
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.084 0.15 -10000 0 -0.32 262 262
STAT5A 0.05 0.11 0.36 13 -0.39 2 15
ErbB4/EGFR/neuregulin 1 beta -0.19 0.23 -10000 0 -0.43 417 417
DLG4 0.022 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.011 0.071 -10000 0 -10000 0 0
STAT5A (dimer) 0.061 0.1 0.46 1 -0.39 2 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.062 0.11 0.35 8 -0.36 2 10
LRIG1 0.022 0.027 -10000 0 -0.58 2 2
EREG -0.027 0.2 0.26 75 -0.58 115 190
BTC -0.008 0.14 0.26 2 -0.58 54 56
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.047 0.11 0.32 40 -0.35 2 42
ERBB4 -0.006 0.075 0.38 8 -0.3 6 14
STAT5B 0.022 0.027 -10000 0 -0.58 2 2
YAP1 -0.013 0.11 -10000 0 -0.45 45 45
GRB2 0.023 0.01 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.033 0.07 0.32 1 -10000 0 1
glial cell differentiation -0.01 0.07 -10000 0 -10000 0 0
WWOX 0.022 0.014 0.26 2 -10000 0 2
cell proliferation -0.039 0.17 0.35 14 -0.45 44 58
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.046 0.18 0.3 131 -0.47 53 184
FYN 0.023 0.2 0.33 63 -0.53 67 130
LAT/GRAP2/SLP76 0.028 0.18 0.34 50 -0.5 57 107
IKBKB 0.021 0.009 -10000 0 -10000 0 0
AKT1 0.025 0.16 0.31 81 -0.37 78 159
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.017 0.06 0.16 69 -0.14 26 95
MAP3K8 0.02 0.046 -10000 0 -0.58 6 6
mol:Ca2+ -0.022 0.032 -10000 0 -0.092 158 158
integrin-mediated signaling pathway 0.026 0.023 -10000 0 -0.3 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.013 0.2 0.36 51 -0.52 80 131
TRPV6 -0.091 0.27 1.2 15 -0.58 186 201
CD28 0.024 0.048 0.27 9 -0.58 5 14
SHC1 0.031 0.21 0.32 148 -0.46 98 246
receptor internalization -0.01 0.22 0.36 37 -0.48 136 173
PRF1 -0.01 0.24 0.54 9 -0.99 41 50
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 0.29 76 -0.31 74 150
LAT 0.016 0.2 0.33 68 -0.48 94 162
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.023 0.098 0.27 45 -0.58 19 64
CD3E 0.022 0.09 0.27 35 -0.59 16 51
CD3G 0.013 0.11 0.27 37 -0.58 30 67
RASGRP2 0 0.051 0.14 15 -0.17 66 81
RASGRP1 0.027 0.16 0.35 46 -0.41 58 104
HLA-A 0.026 0.022 0.27 7 -10000 0 7
RASSF5 0.019 0.034 0.26 1 -0.58 3 4
RAP1A/GTP/RAPL 0.026 0.023 -10000 0 -0.3 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.082 0.18 162 -0.13 26 188
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.055 -10000 0 -0.21 41 41
PRKCA 0.014 0.1 0.22 53 -0.27 49 102
GRAP2 0.016 0.069 0.26 3 -0.58 13 16
mol:IP3 0.013 0.14 0.26 124 -0.38 52 176
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.004 0.18 0.32 35 -0.66 50 85
ORAI1 0.038 0.17 0.64 4 -0.98 14 18
CSK 0.01 0.2 0.37 37 -0.49 90 127
B7 family/CD28 0.063 0.21 0.4 56 -0.59 53 109
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.003 0.23 0.39 38 -0.52 110 148
PTPN6 0.009 0.2 0.34 46 -0.52 79 125
VAV1 0.006 0.2 0.37 40 -0.57 69 109
Monovalent TCR/CD3 -0.002 0.14 0.27 36 -0.52 52 88
CBL 0.022 0.008 -10000 0 -10000 0 0
LCK 0.02 0.2 0.33 63 -0.57 66 129
PAG1 0.024 0.21 0.33 66 -0.49 88 154
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.003 0.22 0.38 38 -0.52 102 140
CD80 0.087 0.1 0.26 272 -10000 0 272
CD86 0.026 0.019 0.27 6 -10000 0 6
PDK1/CARD11/BCL10/MALT1 -0.006 0.072 0.2 3 -0.26 40 43
HRAS 0.026 0.021 0.26 8 -10000 0 8
GO:0035030 0.022 0.16 0.32 46 -0.48 55 101
CD8A 0.028 0.063 0.27 28 -0.59 6 34
CD8B 0.014 0.11 0.27 30 -0.58 31 61
PTPRC 0.022 0.043 0.26 12 -0.58 3 15
PDK1/PKC theta 0.026 0.19 0.38 74 -0.47 70 144
CSK/PAG1 0.027 0.2 0.32 71 -0.57 60 131
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.02 0.21 7 -10000 0 7
GRAP2/SLP76 0.022 0.2 0.39 36 -0.57 63 99
STIM1 0.025 0.097 1.3 4 -10000 0 4
RAS family/GTP 0.046 0.094 0.22 96 -0.18 36 132
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.014 0.24 0.37 37 -0.51 136 173
mol:DAG -0.017 0.098 0.12 34 -0.34 56 90
RAP1A/GDP 0.022 0.037 0.1 77 -10000 0 77
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.016 0.08 0.27 16 -0.58 15 31
cytotoxic T cell degranulation -0.007 0.23 0.53 9 -0.92 41 50
RAP1A/GTP -0.001 0.017 -10000 0 -0.065 61 61
mol:PI-3-4-5-P3 0.019 0.18 0.34 55 -0.43 79 134
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.022 0.17 0.29 114 -0.49 53 167
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.025 0.1 0.26 51 -0.58 20 71
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.007 0.16 0.34 20 -0.51 53 73
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.031 0.11 0.38 21 -0.49 32 53
CARD11 0.027 0.042 0.26 19 -0.58 2 21
PRKCB 0.015 0.1 0.26 48 -0.27 44 92
PRKCE 0.02 0.097 0.22 59 -0.26 43 102
PRKCQ 0.014 0.2 0.36 54 -0.52 77 131
LCP2 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.024 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.028 0.14 0.3 83 -0.32 76 159
IKK complex 0.037 0.083 0.21 115 -0.12 18 133
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.027 0.11 0.25 80 -0.26 54 134
PDPK1 0.03 0.16 0.35 77 -0.35 71 148
TCR/CD3/MHC I/CD8/Fyn -0.024 0.24 0.39 35 -0.58 111 146
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.033 0.2 6 -0.37 5 11
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.38 378 378
PTK2 -0.057 0.15 0.32 2 -0.5 49 51
IGF1R 0.012 0.082 0.26 2 -0.58 19 21
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.067 0.26 6 -0.58 12 18
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.045 0.12 -10000 0 -0.54 33 33
VEGFA 0.025 0.019 0.26 6 -10000 0 6
ILK -0.043 0.12 -10000 0 -0.5 31 31
ROCK1 0.023 0.019 -10000 0 -0.58 1 1
AKT1 -0.044 0.11 -10000 0 -0.5 27 27
PTK2B -0.013 0.071 0.36 2 -0.34 32 34
alphaV/beta3 Integrin/JAM-A -0.077 0.18 0.3 1 -0.34 277 278
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.032 0.075 -10000 0 -0.37 32 32
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.2 -10000 0 -0.39 229 229
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.012 0.068 -10000 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 0.043 0.084 -10000 0 -0.36 32 32
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.41 445 445
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 0.069 0.1 0.34 3 -0.36 32 35
RPS6KB1 -0.16 0.23 0.42 3 -0.44 298 301
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.56 355 355
GPR124 0.016 0.05 -10000 0 -0.58 7 7
MAPK1 -0.2 0.3 -10000 0 -0.57 365 365
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
alphaV/beta3 Integrin/Tumstatin -0.037 0.17 -10000 0 -0.38 197 197
cell adhesion 0.023 0.084 0.26 1 -0.37 41 42
ANGPTL3 0.021 0.016 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.03 -10000 0 -0.37 3 3
IGF-1R heterotetramer 0.012 0.082 0.26 2 -0.57 19 21
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.002 0.11 -10000 0 -0.58 38 38
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
IGF1 -0.1 0.25 -10000 0 -0.58 217 217
RAC1 0.024 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.081 -10000 0 -0.39 31 31
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.019 -10000 0 -0.58 1 1
alphaV/beta3 Integrin/CD47 0.034 0.074 -10000 0 -0.37 32 32
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.014 0.13 -10000 0 -0.46 67 67
CSF1 0.022 0.038 -10000 0 -0.58 4 4
PIK3C2A -0.041 0.12 -10000 0 -0.5 28 28
PI4 Kinase/Pyk2 -0.077 0.15 -10000 0 -0.32 171 171
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.044 0.081 -10000 0 -0.37 32 32
FAK1/Vinculin -0.038 0.14 0.34 4 -0.41 41 45
alphaV beta3/Integrin/ppsTEM5 0.025 0.081 -10000 0 -0.4 31 31
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.032 0.078 0.26 61 -0.58 8 69
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.58 383 383
F11R -0.12 0.2 -10000 0 -0.43 290 290
alphaV/beta3 Integrin/Lactadherin 0.029 0.09 0.34 1 -0.39 41 42
alphaV/beta3 Integrin/TGFBR2 0.02 0.12 -10000 0 -0.47 51 51
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.035 -10000 0 -0.33 4 4
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.067 -10000 0 -0.34 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 403 -10000 0 403
alphaV/beta3 Integrin/Pyk2 0.026 0.074 -10000 0 -0.34 32 32
SDC1 0.039 0.062 0.26 69 -0.58 1 70
VAV3 -0.011 0.041 -10000 0 -0.32 11 11
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.58 40 40
FAK1/Paxillin -0.038 0.14 0.34 4 -0.41 42 46
cell migration -0.038 0.12 0.3 7 -0.38 37 44
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.066 0.17 -10000 0 -0.33 242 242
SPP1 0.086 0.1 0.26 267 -10000 0 267
KDR 0.022 0.038 -10000 0 -0.58 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.082 0.23 0.26 4 -0.58 180 184
angiogenesis -0.19 0.3 0.3 1 -0.58 328 329
Rac1/GTP 0.021 0.038 -10000 0 -0.3 10 10
EDIL3 -0.006 0.14 0.26 15 -0.58 56 71
cell proliferation 0.02 0.12 -10000 0 -0.47 51 51
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.006 0.071 0.34 1 -0.35 9 10
alphaM/beta2 Integrin/GPIbA 0.01 0.076 0.34 4 -0.41 6 10
alphaM/beta2 Integrin/proMMP-9 0.074 0.11 0.35 15 -0.42 1 16
PLAUR 0.041 0.06 0.26 72 -10000 0 72
HMGB1 -0.004 0.041 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.009 0.063 0.34 1 -10000 0 1
AGER -0.007 0.05 -10000 0 -0.48 3 3
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.026 0.14 0.32 4 -0.36 13 17
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 424 -0.58 1 425
CYR61 -0.005 0.13 -10000 0 -0.58 49 49
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.002 0.11 -10000 0 -0.35 39 39
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.094 0.23 -10000 0 -0.57 195 195
MYH2 -0.014 0.14 0.26 12 -0.46 39 51
MST1R 0.022 0.055 0.26 9 -0.58 7 16
leukocyte activation during inflammatory response -0.19 0.17 0.3 1 -0.33 583 584
APOB -0.34 0.29 -10000 0 -0.58 615 615
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.046 -10000 0 -0.58 6 6
JAM3 0.019 0.042 -10000 0 -0.58 5 5
GP1BA 0.024 0.059 0.26 25 -0.58 6 31
alphaM/beta2 Integrin/CTGF 0.004 0.076 0.34 1 -0.37 13 14
alphaM/beta2 Integrin -0.012 0.12 0.21 6 -0.39 43 49
JAM3 homodimer 0.019 0.042 -10000 0 -0.57 5 5
ICAM2 0.019 0.042 -10000 0 -0.58 5 5
ICAM1 0.028 0.029 0.26 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.12 0.23 7 -0.39 44 51
cell adhesion 0.01 0.076 0.34 4 -0.41 6 10
NFKB1 -0.1 0.2 0.42 4 -0.38 318 322
THY1 0.024 0.021 0.26 7 -10000 0 7
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.21 0.19 0.18 1 -0.36 623 624
alphaM/beta2 Integrin/LRP/tPA 0.007 0.091 0.34 1 -0.36 30 31
IL6 -0.26 0.39 0.35 3 -0.76 371 374
ITGB2 -0.002 0.052 0.26 14 -10000 0 14
elevation of cytosolic calcium ion concentration 0.03 0.084 0.34 18 -10000 0 18
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 0.34 1 -0.38 42 43
JAM2 -0.005 0.13 -10000 0 -0.58 49 49
alphaM/beta2 Integrin/ICAM1 0.023 0.087 0.33 4 -0.33 17 21
alphaM/beta2 Integrin/uPA/Plg 0.019 0.07 0.34 1 -10000 0 1
RhoA/GTP -0.019 0.16 0.24 14 -0.4 67 81
positive regulation of phagocytosis -0.003 0.1 0.31 5 -0.34 24 29
Ron/MSP 0.029 0.064 0.37 1 -0.41 18 19
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.086 0.35 18 -10000 0 18
alphaM/beta2 Integrin/uPAR 0.019 0.078 0.3 8 -10000 0 8
PLAU 0.03 0.038 0.26 27 -10000 0 27
PLAT 0.006 0.093 -10000 0 -0.58 25 25
actin filament polymerization -0.013 0.14 0.28 8 -0.45 37 45
MST1 0.02 0.056 0.26 5 -0.58 8 13
alphaM/beta2 Integrin/lipoprotein(a) -0.19 0.17 0.32 1 -0.33 580 581
TNF -0.1 0.2 0.39 3 -0.75 18 21
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.013 0.068 0.34 1 -10000 0 1
fibrinolysis 0.017 0.069 0.33 1 -10000 0 1
HCK 0.027 0.026 0.26 12 -10000 0 12
dendritic cell antigen processing and presentation -0.011 0.12 0.23 7 -0.39 44 51
VTN 0.032 0.078 0.26 61 -0.58 8 69
alphaM/beta2 Integrin/CYR61 -0.009 0.11 0.34 1 -0.38 52 53
LPA 0.018 0.018 0.26 5 -10000 0 5
LRP1 0.018 0.059 -10000 0 -0.58 10 10
cell migration 0.043 0.084 0.29 13 -0.36 8 21
FN1 0.12 0.12 0.26 403 -10000 0 403
alphaM/beta2 Integrin/Thy1 0.009 0.063 0.34 1 -10000 0 1
MPO -0.012 0.14 0.26 2 -0.58 59 61
KNG1 0.022 0.031 0.26 17 -10000 0 17
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.013 0.15 0.27 17 -0.46 40 57
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.018 0.26 5 -10000 0 5
CTGF 0.017 0.066 0.26 3 -0.58 12 15
alphaM/beta2 Integrin/Hck 0.011 0.067 0.36 5 -10000 0 5
ITGAM -0.003 0.044 0.25 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.045 0.16 0.34 1 -0.36 183 184
HP -0.069 0.23 0.26 33 -0.58 166 199
leukocyte adhesion -0.039 0.14 0.29 4 -0.38 53 57
SELP -0.094 0.24 -10000 0 -0.58 195 195
Effects of Botulinum toxin

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
STX1A 0.01 0.024 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.029 0.11 -10000 0 -0.42 46 46
STXBP1 0.021 0.042 -10000 0 -0.58 5 5
ACh/CHRNA1 0.073 0.091 0.2 330 -0.16 7 337
RAB3GAP2/RIMS1/UNC13B 0.034 0.091 -10000 0 -0.37 34 34
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.021 0.15 0.26 106 -0.58 45 151
mol:ACh -0.004 0.037 0.09 11 -0.14 44 55
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.019 0.085 0.23 1 -0.28 44 45
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.073 0.091 0.2 330 -0.16 7 337
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.26 343 -10000 0 343
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.034 0.11 0.2 194 -0.36 42 236
SNAP25 -0.001 0.061 -10000 0 -0.3 35 35
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.049 0.15 0.26 202 -0.58 37 239
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.033 -10000 0 -0.36 5 5
STX1A/SNAP25 fragment 1/VAMP2 0.019 0.085 0.23 1 -0.28 44 45
Ephrin A reverse signaling

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
MAPKKK cascade -0.008 0.12 -10000 0 -0.36 96 96
EFNA5 -0.033 0.18 0.26 1 -0.58 96 97
FYN -0.025 0.1 0.18 7 -0.34 96 103
neuron projection morphogenesis -0.008 0.12 -10000 0 -0.36 96 96
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.007 0.12 -10000 0 -0.37 96 96
EPHA5 0.023 0.016 0.26 4 -10000 0 4
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.034 0.073 -10000 0 -0.34 34 34
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.12 -10000 0 -0.39 21 21
AP1 -0.094 0.19 -10000 0 -0.33 367 367
mol:PIP3 -0.13 0.18 -10000 0 -0.34 397 397
AKT1 0.007 0.076 0.32 2 -0.4 11 13
PTK2B -0.028 0.1 -10000 0 -0.34 54 54
RHOA 0.003 0.061 0.26 2 -0.31 25 27
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.11 0.23 3 -0.28 105 108
MAGI3 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
apoptosis -0.026 0.12 -10000 0 -0.32 134 134
HRAS/GDP 0.019 0.015 0.18 8 -10000 0 8
positive regulation of microtubule depolymerization -0.052 0.12 0.26 3 -0.32 131 134
NF kappa B1 p50/RelA -0.012 0.12 -10000 0 -0.33 93 93
endothelial cell migration 0.002 0.079 -10000 0 -0.43 29 29
ADCY4 -0.021 0.12 -10000 0 -0.51 38 38
ADCY5 -0.076 0.15 -10000 0 -0.49 75 75
ADCY6 -0.013 0.097 -10000 0 -0.46 31 31
ADCY7 -0.012 0.098 -10000 0 -0.48 31 31
ADCY1 -0.015 0.11 -10000 0 -0.48 35 35
ADCY2 -0.025 0.12 -10000 0 -0.5 44 44
ADCY3 -0.013 0.097 -10000 0 -0.46 31 31
ADCY8 -0.011 0.09 -10000 0 -0.45 28 28
ADCY9 -0.013 0.097 -10000 0 -0.46 31 31
GSK3B -0.027 0.098 0.25 5 -0.34 46 51
arachidonic acid secretion -0.017 0.1 -10000 0 -0.42 44 44
GNG2 0.018 0.059 -10000 0 -0.58 10 10
TRIP6 0.018 0.016 -10000 0 -0.41 1 1
GNAO1 0.002 0.083 -10000 0 -0.37 43 43
HRAS 0.026 0.021 0.26 8 -10000 0 8
NFKBIA -0.021 0.13 0.27 2 -0.34 110 112
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.026 0.12 -10000 0 -0.81 22 22
JUN 0.02 0.046 -10000 0 -0.58 6 6
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.011 0.14 -10000 0 -0.95 22 22
PIK3R1 0.018 0.056 -10000 0 -0.57 9 9
mol:IP3 -0.014 0.11 0.23 3 -0.29 105 108
PLCB3 0.025 0.045 0.2 3 -10000 0 3
FOS -0.14 0.27 -10000 0 -0.58 285 285
positive regulation of mitosis -0.017 0.1 -10000 0 -0.42 44 44
LPA/LPA1-2-3 0.001 0.14 -10000 0 -0.34 133 133
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 -0.017 0.1 -10000 0 -0.36 42 42
GNAZ 0.003 0.069 -10000 0 -0.35 36 36
EGFR/PI3K-beta/Gab1 -0.13 0.2 -10000 0 -0.35 397 397
positive regulation of dendritic cell cytokine production 0 0.14 -10000 0 -0.33 133 133
LPA/LPA2/MAGI-3 0.033 0.016 -10000 0 -10000 0 0
ARHGEF1 0.018 0.069 -10000 0 -0.32 18 18
GNAI2 0.006 0.059 -10000 0 -0.35 25 25
GNAI3 0.007 0.059 -10000 0 -0.34 28 28
GNAI1 -0.01 0.1 -10000 0 -0.38 68 68
LPA/LPA3 -0.026 0.14 0.18 36 -0.41 117 153
LPA/LPA2 0.019 0.014 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.07 -10000 0 -0.39 29 29
HB-EGF/EGFR -0.078 0.2 0.27 2 -0.35 336 338
HBEGF 0.067 0.075 0.27 23 -0.43 3 26
mol:DAG -0.014 0.11 0.23 3 -0.29 105 108
cAMP biosynthetic process -0.031 0.11 0.4 1 -0.43 52 53
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.26 24 -0.33 90 114
GNAQ -0.02 0.11 0.18 4 -0.31 115 119
LPAR2 0.025 0.011 0.26 2 -10000 0 2
LPAR3 -0.035 0.2 0.26 36 -0.58 113 149
LPAR1 0.013 0.086 -10000 0 -0.58 20 20
IL8 -0.13 0.23 0.36 29 -0.41 341 370
PTK2 -0.022 0.1 0.24 1 -0.32 93 94
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.32 134 134
EGFR -0.19 0.29 -10000 0 -0.58 363 363
PLCG1 -0.023 0.12 0.2 4 -0.33 115 119
PLD2 -0.027 0.12 0.24 1 -0.32 131 132
G12/G13 0.036 0.06 -10000 0 -0.32 22 22
PI3K-beta 0.002 0.074 -10000 0 -0.43 13 13
cell migration 0.001 0.064 -10000 0 -0.25 22 22
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
PXN -0.017 0.1 -10000 0 -0.37 42 42
HRAS/GTP -0.017 0.1 -10000 0 -0.43 44 44
RAC1 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 424 -0.58 1 425
PRKCE 0.024 0.003 -10000 0 -10000 0 0
PRKCD -0.015 0.1 0.24 1 -0.28 91 92
Gi(beta/gamma) -0.011 0.1 -10000 0 -0.45 39 39
mol:LPA 0.001 0.016 -10000 0 -0.17 7 7
TRIP6/p130 Cas/FAK1/Paxillin -0.014 0.12 -10000 0 -0.41 28 28
MAPKKK cascade -0.017 0.1 -10000 0 -0.42 44 44
contractile ring contraction involved in cytokinesis 0.002 0.063 0.26 2 -0.31 25 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.021 0.11 0.21 1 -0.32 121 122
GNA15 -0.019 0.11 0.18 5 -0.31 114 119
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.054 0.13 0.26 3 -0.32 131 134
GNA11 -0.02 0.11 0.18 4 -0.31 115 119
Rac1/GTP 0.027 0.13 -10000 0 -0.86 22 22
MMP2 0.002 0.079 -10000 0 -0.44 29 29
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.028 0.23 0.64 2 -0.68 22 24
CRP -0.007 0.24 0.59 15 -0.69 22 37
cell cycle arrest -0.04 0.25 0.58 9 -0.7 41 50
TIMP1 -0.021 0.22 0.52 10 -0.62 25 35
IL6ST -0.034 0.18 -10000 0 -0.57 106 106
Rac1/GDP -0.069 0.2 0.38 2 -0.5 87 89
AP1 -0.073 0.21 0.38 1 -0.54 72 73
GAB2 0.022 0.02 -10000 0 -0.58 1 1
TNFSF11 -0.017 0.24 0.61 11 -0.68 23 34
HSP90B1 0.023 0.11 -10000 0 -0.81 10 10
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.095 0.18 -10000 0 -0.51 92 92
AKT1 0.023 0.066 -10000 0 -0.66 4 4
FOXO1 0.023 0.067 0.43 1 -0.66 3 4
MAP2K6 -0.095 0.19 0.27 2 -0.42 166 168
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.053 0.2 0.4 10 -0.51 70 80
MITF -0.09 0.2 0.32 3 -0.42 164 167
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.004 -10000 0 -10000 0 0
A2M -0.003 0.18 -10000 0 -1.2 24 24
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.018 0.13 -10000 0 -0.53 33 33
STAT3 -0.046 0.26 0.58 9 -0.77 40 49
STAT1 0.012 0.095 -10000 0 -0.83 10 10
CEBPD -0.014 0.24 0.59 8 -0.72 23 31
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.043 -10000 0 -0.4 9 9
JUN 0.02 0.046 -10000 0 -0.58 6 6
PIAS3/MITF -0.072 0.18 0.33 2 -0.49 86 88
MAPK11 -0.095 0.18 -10000 0 -0.52 93 93
STAT3 (dimer)/FOXO1 -0.026 0.22 0.52 12 -0.6 33 45
GRB2/SOS1/GAB family -0.06 0.18 -10000 0 -0.49 71 71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.19 -10000 0 -0.42 169 169
GRB2 0.023 0.01 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.17 0.46 0.57 19 -0.93 242 261
PIK3R1 0.019 0.056 -10000 0 -0.58 9 9
JAK1 0.026 0.009 -10000 0 -10000 0 0
MYC -0.003 0.27 0.58 13 -0.99 30 43
FGG -0.026 0.24 0.61 11 -0.67 25 36
macrophage differentiation -0.04 0.25 0.58 9 -0.7 41 50
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.093 0.21 -10000 0 -0.36 342 342
JUNB -0.031 0.22 0.62 2 -0.65 25 27
FOS -0.14 0.27 -10000 0 -0.58 285 285
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.092 0.2 0.3 10 -0.43 170 180
STAT1/PIAS1 -0.061 0.2 0.36 9 -0.46 103 112
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.07 -10000 0 -0.55 7 7
STAT3 (dimer) -0.044 0.26 0.58 9 -0.76 40 49
PRKCD -0.037 0.21 0.46 14 -0.55 49 63
IL6R 0.001 0.11 -10000 0 -0.57 36 36
SOCS3 -0.092 0.19 -10000 0 -0.6 66 66
gp130 (dimer)/JAK1/JAK1/LMO4 0.014 0.13 -10000 0 -0.36 106 106
Rac1/GTP -0.064 0.2 0.35 9 -0.5 86 95
HCK 0.027 0.026 0.26 12 -10000 0 12
MAPKKK cascade -0.003 0.14 -10000 0 -0.63 29 29
bone resorption -0.015 0.23 0.6 11 -0.64 24 35
IRF1 -0.031 0.23 0.54 9 -0.66 28 37
mol:GDP -0.084 0.2 0.3 10 -0.5 98 108
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.086 0.2 0.3 10 -0.5 99 109
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.2 -10000 0 -0.6 89 89
PTPN11 0.011 0.079 -10000 0 -0.85 7 7
IL6/IL6RA -0.12 0.22 -10000 0 -0.43 314 314
gp130 (dimer)/TYK2/TYK2/LMO4 0.009 0.13 -10000 0 -0.36 106 106
gp130 (dimer)/JAK2/JAK2/LMO4 0.009 0.13 -10000 0 -0.36 100 100
IL6 -0.18 0.29 0.28 1 -0.57 360 361
PIAS3 0.02 0.009 -10000 0 -10000 0 0
PTPRE 0.008 0.031 -10000 0 -0.58 1 1
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.11 0.19 0.23 1 -0.34 298 299
LMO4 0.028 0.037 0.28 2 -0.57 3 5
STAT3 (dimer)/PIAS3 -0.049 0.24 0.55 9 -0.72 41 50
MCL1 0.053 0.097 0.49 1 -0.58 4 5
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.041 0.22 0.44 4 -0.63 108 112
IHH 0.016 0.082 0.27 30 -0.23 15 45
SHH Np/Cholesterol/GAS1 0.001 0.075 -10000 0 -0.34 44 44
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.001 0.074 0.33 44 -10000 0 44
SMO/beta Arrestin2 -0.019 0.21 -10000 0 -0.63 88 88
SMO -0.042 0.21 0.32 1 -0.66 91 92
AKT1 -0.003 0.13 -10000 0 -0.61 20 20
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.019 0.16 -10000 0 -0.58 73 73
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.041 0.21 0.32 1 -0.64 91 92
STIL 0.008 0.17 0.3 27 -0.48 81 108
DHH N/PTCH2 -0.012 0.14 -10000 0 -0.44 99 99
DHH N/PTCH1 -0.027 0.2 -10000 0 -0.55 114 114
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.008 0.099 0.26 2 -0.58 28 30
PTHLH -0.061 0.3 0.52 2 -0.84 113 115
determination of left/right symmetry -0.041 0.21 0.32 1 -0.64 91 92
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
skeletal system development -0.06 0.29 0.52 2 -0.82 113 115
IHH N/Hhip 0.028 0.056 0.26 1 -0.47 1 2
DHH N/Hhip 0.023 0.078 -10000 0 -0.42 29 29
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.041 0.21 0.32 1 -0.64 91 92
pancreas development 0.024 0.028 0.26 8 -0.57 1 9
HHAT 0.02 0.021 -10000 0 -0.58 1 1
PI3K 0.029 0.043 -10000 0 -0.4 9 9
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.007 0.13 -10000 0 -0.58 52 52
somite specification -0.041 0.21 0.32 1 -0.64 91 92
SHH Np/Cholesterol/PTCH1 -0.024 0.16 0.3 1 -0.5 87 88
SHH Np/Cholesterol/PTCH2 -0.006 0.087 -10000 0 -0.34 61 61
SHH Np/Cholesterol/Megalin -0.059 0.15 0.28 3 -0.34 211 214
SHH 0 0.038 0.34 7 -0.43 1 8
catabolic process -0.032 0.21 0.32 2 -0.57 115 117
SMO/Vitamin D3 -0.008 0.2 0.37 14 -0.57 85 99
SHH Np/Cholesterol/Hhip 0.016 0.03 0.28 5 -0.34 2 7
LRP2 -0.12 0.27 0.26 25 -0.58 257 282
receptor-mediated endocytosis -0.079 0.22 0.31 10 -0.63 96 106
SHH Np/Cholesterol/BOC -0.005 0.086 -10000 0 -0.34 59 59
SHH Np/Cholesterol/CDO 0.013 0.042 -10000 0 -0.34 12 12
mesenchymal cell differentiation -0.016 0.03 0.34 2 -0.28 5 7
mol:Vitamin D3 0.003 0.18 0.35 19 -0.51 83 102
IHH N/PTCH2 -0.009 0.14 -10000 0 -0.47 79 79
CDON 0.015 0.065 -10000 0 -0.58 12 12
IHH N/PTCH1 -0.023 0.21 0.36 4 -0.58 115 119
Megalin/LRPAP1 -0.079 0.2 -10000 0 -0.42 260 260
PTCH2 -0.021 0.16 -10000 0 -0.58 77 77
SHH Np/Cholesterol 0.01 0.014 -10000 0 -0.34 1 1
PTCH1 -0.032 0.21 0.32 2 -0.58 115 117
HHIP 0.024 0.029 0.26 8 -0.58 1 9
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 0.034 0.1 0.4 28 -10000 0 28
VDR 0.024 0.003 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.027 0.12 0.25 4 -0.26 199 203
RXRs/LXRs/DNA/Oxysterols -0.007 0.12 -10000 0 -0.44 16 16
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.004 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0.001 0.083 -10000 0 -0.3 58 58
RXRs/NUR77 -0.049 0.18 -10000 0 -0.35 246 246
RXRs/PPAR -0.1 0.17 -10000 0 -0.32 343 343
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.048 0.042 -10000 0 -0.32 10 10
RARA 0.022 0.007 -10000 0 -10000 0 0
NCOA1 0.024 0.019 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.037 0.04 -10000 0 -0.32 10 10
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.07 0.18 0.61 93 -10000 0 93
RARs/THRs/DNA/SMRT 0.002 0.08 -10000 0 -0.3 56 56
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.031 0.15 -10000 0 -0.32 207 207
NR1H4 0.021 0.025 0.26 11 -10000 0 11
RXRs/LXRs/DNA -0.009 0.16 -10000 0 -0.31 189 189
NR1H2 0.027 0.012 -10000 0 -10000 0 0
NR1H3 0.028 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.024 0.15 -10000 0 -0.31 206 206
NR4A1 -0.022 0.16 -10000 0 -0.58 78 78
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.033 0.1 0.18 2 -0.24 182 184
RXRG -0.1 0.24 0.26 2 -0.57 210 212
RXR alpha/CCPG 0.036 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.013 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB -0.005 0.13 -10000 0 -0.58 50 50
PPARG -0.11 0.25 -10000 0 -0.58 228 228
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.012 0.15 -10000 0 -1 11 11
mol:Oxysterols 0.004 0.009 -10000 0 -10000 0 0
cholesterol transport -0.007 0.12 -10000 0 -0.43 16 16
PPARA 0.021 0.038 -10000 0 -0.58 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.017 0.065 -10000 0 -0.58 12 12
RXRs/NUR77/BCL2 -0.068 0.15 -10000 0 -0.3 263 263
SREBF1 -0.007 0.11 0.45 1 -0.52 4 5
RXRs/RXRs/DNA/9cRA -0.031 0.15 -10000 0 -0.32 207 207
ABCA1 -0.011 0.13 -10000 0 -0.8 8 8
RARs/THRs 0.041 0.096 -10000 0 -0.34 54 54
RXRs/FXR -0.027 0.16 -10000 0 -0.33 207 207
BCL2 0.007 0.096 -10000 0 -0.58 27 27
Signaling events mediated by PRL

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
CCNE1 0.063 0.088 0.26 169 -10000 0 169
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.018 0.056 -10000 0 -0.58 9 9
CDKN1A -0.031 0.095 -10000 0 -0.44 29 29
PRL-3/alpha Tubulin 0.029 0.018 -10000 0 -10000 0 0
mol:Ca2+ 0 0.077 0.24 43 -0.43 12 55
AGT 0.031 0.092 0.26 76 -0.58 12 88
CCNA2 -0.065 0.14 0.25 16 -0.31 129 145
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.12 0.2 0.18 2 -0.42 316 318
CDK2/Cyclin E1 0.015 0.11 0.27 3 -0.41 26 29
MAPK3 0.01 0.02 0.26 5 -10000 0 5
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.02 0.26 5 -10000 0 5
PTP4A1 -0.094 0.15 -10000 0 -0.33 289 289
PTP4A3 0.02 0.018 0.26 4 -10000 0 4
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.018 0.26 4 -10000 0 4
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 -0.018 0.075 -10000 0 -0.43 14 14
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.074 0.15 -10000 0 -0.31 271 271
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.013 -10000 0 -10000 0 0
RHOC -0.02 0.083 -10000 0 -0.44 20 20
RHOA -0.023 0.092 -10000 0 -0.48 25 25
cell motility -0.027 0.1 0.24 1 -0.37 39 40
PRL-1/alpha Tubulin -0.075 0.15 -10000 0 -0.31 278 278
PRL-3/alpha1 Integrin 0.025 0.041 -10000 0 -0.35 9 9
ROCK1 -0.025 0.1 0.25 1 -0.37 35 36
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.094 0.15 -10000 0 -0.32 289 289
ATF5 0.025 0.013 0.26 3 -10000 0 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.015 0.14 0.42 80 -0.23 11 91
KIRREL -0.023 0.16 -10000 0 -0.58 80 80
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.015 0.14 0.23 11 -0.42 80 91
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.034 0.12 0.29 4 -0.33 77 81
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.008 0.088 0.24 1 -0.27 75 76
FYN 0.015 0.13 0.27 106 -0.31 76 182
mol:Ca2+ 0.032 0.11 0.28 3 -0.32 72 75
mol:DAG 0.033 0.11 0.29 3 -0.32 72 75
NPHS2 0.014 0.032 0.27 5 -10000 0 5
mol:IP3 0.033 0.11 0.29 3 -0.32 72 75
regulation of endocytosis 0.024 0.1 0.24 6 -0.3 76 82
Nephrin/NEPH1/podocin/Cholesterol 0.024 0.11 0.25 9 -0.32 77 86
establishment of cell polarity 0.015 0.14 0.23 11 -0.42 80 91
Nephrin/NEPH1/podocin/NCK1-2 0.044 0.11 0.3 2 -0.3 75 77
Nephrin/NEPH1/beta Arrestin2 0.027 0.11 0.25 6 -0.3 76 82
NPHS1 0.06 0.092 0.26 161 -10000 0 161
Nephrin/NEPH1/podocin 0.026 0.11 0.31 4 -0.31 76 80
TJP1 0.023 0.02 -10000 0 -0.58 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 0.034 0.12 0.29 3 -0.33 72 75
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.032 0.12 0.3 5 -0.32 74 79
GRB2 0.023 0.01 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.013 0.13 0.28 101 -0.31 82 183
cytoskeleton organization 0.004 0.11 0.27 17 -0.32 72 89
Nephrin/NEPH1 0.017 0.1 0.19 7 -0.3 78 85
Nephrin/NEPH1/ZO-1 0.026 0.12 -10000 0 -0.35 78 78
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 0.001 0.063 -10000 0 -0.32 8 8
adherens junction organization -0.015 0.095 0.22 1 -0.34 52 53
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.086 0.15 0.34 3 -0.29 319 322
FMN1 -0.014 0.09 -10000 0 -0.31 58 58
mol:IP3 -0.001 0.053 -10000 0 -0.27 10 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.009 0.09 -10000 0 -0.32 50 50
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.002 0.063 -10000 0 -0.28 10 10
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.13 -10000 0 -0.5 45 45
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.078 -10000 0 -0.31 44 44
VASP -0.011 0.083 -10000 0 -0.3 48 48
ZYX -0.011 0.084 -10000 0 -0.31 49 49
JUB -0.01 0.085 -10000 0 -0.31 50 50
EGFR(dimer) -0.11 0.18 -10000 0 -0.33 354 354
E-cadherin/beta catenin-gamma catenin 0.031 0.062 -10000 0 -0.35 21 21
mol:PI-3-4-5-P3 0.015 0.073 -10000 0 -0.27 16 16
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.016 0.075 -10000 0 -0.28 16 16
FYN -0.004 0.065 0.23 1 -0.31 10 11
mol:Ca2+ -0.001 0.052 -10000 0 -0.27 10 10
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.019 0.056 -10000 0 -0.58 9 9
mol:DAG -0.001 0.053 -10000 0 -0.27 10 10
CDH1 0.009 0.085 -10000 0 -0.58 21 21
RhoA/GDP -0.085 0.15 0.36 2 -0.34 107 109
establishment of polarity of embryonic epithelium -0.011 0.082 -10000 0 -0.3 48 48
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.58 363 363
CASR -0.003 0.054 0.23 2 -0.26 8 10
RhoA/GTP 0.013 0.057 -10000 0 -0.26 7 7
AKT2 0.001 0.063 -10000 0 -0.28 8 8
actin cable formation -0.018 0.091 0.25 2 -0.31 61 63
apoptosis -0.004 0.073 0.28 22 -0.24 8 30
CTNNA1 0.024 0.006 -10000 0 -10000 0 0
mol:GDP -0.098 0.15 -10000 0 -0.3 322 322
PIP5K1A -0.01 0.079 -10000 0 -0.31 44 44
PLCG1 -0.001 0.053 -10000 0 -0.28 10 10
Rac1/GTP -0.094 0.17 -10000 0 -0.31 353 353
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.032 0.044 -10000 0 -0.32 13 13
RGS9BP 0.037 0.054 0.26 57 -10000 0 57
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.016 0.26 4 -10000 0 4
mol:Na + 0.037 0.045 -10000 0 -10000 0 0
mol:ADP -0.006 0.025 0.25 5 -10000 0 5
GNAT2 0.024 0.014 0.26 3 -10000 0 3
RGS9-1/Gbeta5/R9AP 0.015 0.12 0.34 1 -0.36 84 85
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.015 -10000 0 -10000 0 0
GRK7 0.023 0.017 0.26 5 -10000 0 5
CNGB3 0.022 0.038 0.26 24 -10000 0 24
Cone Metarhodopsin II/X-Arrestin 0.015 0.015 0.18 8 -10000 0 8
mol:Ca2+ 0.12 0.11 0.26 227 -10000 0 227
Cone PDE6 0.03 0.11 0.31 3 -0.32 80 83
Cone Metarhodopsin II 0.025 0.016 -10000 0 -10000 0 0
Na + (4 Units) 0.12 0.093 0.31 65 -10000 0 65
GNAT2/GDP 0.024 0.11 0.29 2 -0.31 83 85
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.034 0.25 1 -10000 0 1
Cone Transducin 0.035 0.047 -10000 0 -0.34 13 13
SLC24A2 0.16 0.12 0.26 603 -10000 0 603
GNB3/GNGT2 0.026 0.054 -10000 0 -0.4 15 15
GNB3 0.017 0.066 0.26 2 -0.58 12 14
GNAT2/GTP 0.018 0.009 0.18 3 -10000 0 3
CNGA3 0.045 0.068 0.26 94 -10000 0 94
ARR3 0.021 0.021 0.26 8 -10000 0 8
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.038 0.045 -10000 0 -10000 0 0
mol:Pi 0.015 0.12 0.34 1 -0.36 84 85
Cone CNG Channel 0.05 0.044 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.16 0.12 0.26 603 -10000 0 603
RGS9 -0.026 0.17 0.26 11 -0.58 86 97
PDE6C 0.02 0.009 0.26 1 -10000 0 1
GNGT2 0.021 0.027 -10000 0 -0.58 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.018 0.26 5 -10000 0 5
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.022 0.027 -10000 0 -0.58 2 2
LAT2 -0.018 0.1 -10000 0 -0.36 51 51
AP1 -0.057 0.18 -10000 0 -0.44 113 113
mol:PIP3 0.009 0.16 0.35 43 -0.43 48 91
IKBKB 0.034 0.13 0.28 115 -0.26 26 141
AKT1 0.012 0.17 0.32 141 -0.34 55 196
IKBKG 0.016 0.11 0.27 51 -0.27 28 79
MS4A2 -0.021 0.15 0.26 4 -0.56 75 79
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.012 0.12 0.31 21 -0.39 27 48
mol:Ca2+ 0.014 0.14 0.3 53 -0.32 47 100
LYN 0.022 0.013 -10000 0 -10000 0 0
CBLB -0.017 0.1 -10000 0 -0.34 54 54
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0.001 0.12 -10000 0 -0.34 115 115
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.003 0.17 0.33 123 -0.33 129 252
PTPN13 -0.014 0.15 -10000 0 -0.57 39 39
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.013 0.13 0.32 35 -0.34 30 65
SYK 0.025 0.011 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.026 0.13 -10000 0 -0.37 86 86
LAT -0.018 0.1 -10000 0 -0.35 53 53
PAK2 0.013 0.13 0.29 30 -0.44 26 56
NFATC2 -0.047 0.16 -10000 0 -0.61 67 67
HRAS 0.009 0.13 0.27 19 -0.46 29 48
GAB2 0.021 0.02 -10000 0 -0.58 1 1
PLA2G1B 0.002 0.1 -10000 0 -0.84 12 12
Fc epsilon R1 -0.022 0.16 -10000 0 -0.4 138 138
Antigen/IgE/Fc epsilon R1 -0.018 0.14 -10000 0 -0.37 136 136
mol:GDP -0.013 0.11 0.25 1 -0.47 28 29
JUN 0.02 0.046 -10000 0 -0.58 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
FOS -0.14 0.27 -10000 0 -0.58 285 285
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.015 0.11 -10000 0 -0.29 98 98
CHUK 0.016 0.11 0.25 69 -0.27 29 98
KLRG1 -0.017 0.094 -10000 0 -0.27 93 93
VAV1 -0.019 0.1 -10000 0 -0.37 49 49
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.016 0.097 -10000 0 -0.36 48 48
negative regulation of mast cell degranulation -0.006 0.096 -10000 0 -0.37 27 27
BTK -0.012 0.11 -10000 0 -0.47 28 28
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.03 0.13 -10000 0 -0.34 132 132
GAB2/PI3K/SHP2 -0.048 0.1 -10000 0 -0.32 101 101
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.023 0.1 -10000 0 -0.29 109 109
RAF1 0.001 0.11 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0 0.15 -10000 0 -0.35 136 136
FCER1G 0.019 0.017 0.26 1 -10000 0 1
FCER1A -0.045 0.19 -10000 0 -0.58 108 108
Antigen/IgE/Fc epsilon R1/Fyn -0.009 0.14 -10000 0 -0.35 130 130
MAPK3 0.002 0.1 -10000 0 -0.86 12 12
MAPK1 -0.003 0.1 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.18 -10000 0 -0.59 63 63
DUSP1 -0.045 0.19 -10000 0 -0.58 117 117
NF-kappa-B/RelA 0.008 0.058 0.14 5 -0.18 13 18
actin cytoskeleton reorganization -0.006 0.15 -10000 0 -0.59 32 32
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.11 -10000 0 -0.45 27 27
FER -0.02 0.11 -10000 0 -0.37 54 54
RELA 0.024 0.005 -10000 0 -10000 0 0
ITK -0.012 0.093 -10000 0 -0.4 47 47
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.006 0.13 0.28 9 -0.48 27 36
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.017 0.1 0.22 1 -0.35 53 54
PTK2 -0.008 0.15 -10000 0 -0.62 32 32
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.023 0.13 -10000 0 -0.44 51 51
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.006 0.16 0.33 39 -0.42 53 92
MAP2K2 -0.002 0.1 -10000 0 -0.85 12 12
MAP2K1 -0.001 0.1 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.007 0.093 -10000 0 -0.35 30 30
MAP2K4 -0.073 0.29 -10000 0 -0.83 128 128
Fc epsilon R1/FcgammaRIIB -0.008 0.15 -10000 0 -0.38 136 136
mol:Choline -0.003 0.17 0.33 123 -0.33 129 252
SHC/Grb2/SOS1 0.013 0.11 -10000 0 -0.4 28 28
FYN 0.022 0.027 -10000 0 -0.58 2 2
DOK1 0.025 0.015 0.26 4 -10000 0 4
PXN -0.008 0.14 -10000 0 -0.56 32 32
HCLS1 -0.018 0.1 -10000 0 -0.35 52 52
PRKCB 0.014 0.14 0.31 50 -0.32 52 102
FCGR2B 0.018 0.039 0.26 1 -0.58 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.006 0.098 -10000 0 -0.38 27 27
LCP2 0.024 0.009 0.26 1 -10000 0 1
PLA2G4A -0.043 0.14 -10000 0 -0.36 121 121
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.003 0.17 0.33 123 -0.33 129 252
IKK complex 0.032 0.11 0.28 89 -0.21 14 103
WIPF1 0.024 0.003 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.075 0.16 -10000 0 -0.3 271 271
Syndecan-3/Neurocan 0.027 0.075 0.28 18 -0.37 20 38
POMC 0.02 0.091 0.26 30 -0.58 19 49
EGFR -0.19 0.29 -10000 0 -0.58 363 363
Syndecan-3/EGFR -0.089 0.16 -10000 0 -0.32 284 284
AGRP 0.021 0.025 0.26 10 -10000 0 10
NCSTN 0.02 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.008 0.26 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.019 -10000 0 -0.58 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.057 0.26 62 -10000 0 62
long-term memory 0.034 0.063 -10000 0 -0.35 16 16
Syndecan-3/IL8 0.021 0.083 0.28 9 -0.34 35 44
PSEN1 0.024 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.58 2 2
limb bud formation 0.001 0.057 -10000 0 -0.39 21 21
MC4R 0.023 0.028 0.26 13 -10000 0 13
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.23 0.3 0.26 2 -0.58 434 436
FGFR/FGF/Syndecan-3 0.001 0.057 -10000 0 -0.39 21 21
neuron projection morphogenesis -0.075 0.16 0.34 5 -0.33 91 96
Syndecan-3/AgRP 0.015 0.061 0.27 1 -0.37 21 22
Syndecan-3/AgRP/MC4R 0.038 0.07 0.33 1 -0.36 20 21
Fyn/Cortactin 0.028 0.022 -10000 0 -0.31 2 2
SDC3 0.001 0.058 -10000 0 -0.39 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.021 0.082 0.28 9 -0.34 35 44
IL8 0.026 0.1 0.26 59 -0.58 19 78
Syndecan-3/Fyn/Cortactin 0.035 0.065 -10000 0 -0.36 16 16
Syndecan-3/CASK 0 0.056 -10000 0 -0.37 21 21
alpha-MSH/MC4R 0.03 0.072 0.37 2 -0.42 19 21
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.03 0.14 -10000 0 -0.6 57 57
PDGF/PDGFRA/CRKL -0.009 0.11 -10000 0 -0.41 60 60
positive regulation of JUN kinase activity 0.025 0.082 -10000 0 -0.34 42 42
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.012 0.11 -10000 0 -0.43 58 58
AP1 -0.3 0.44 -10000 0 -0.96 301 301
mol:IP3 -0.034 0.11 -10000 0 -0.46 54 54
PLCG1 -0.034 0.11 -10000 0 -0.46 54 54
PDGF/PDGFRA/alphaV Integrin -0.009 0.11 -10000 0 -0.43 57 57
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.034 0.11 -10000 0 -0.46 54 54
CAV3 0.02 0.012 0.26 2 -10000 0 2
CAV1 -0.099 0.24 -10000 0 -0.58 209 209
SHC/Grb2/SOS1 0.027 0.083 -10000 0 -0.34 42 42
PDGF/PDGFRA/Shf -0.009 0.11 -10000 0 -0.43 58 58
FOS -0.29 0.43 0.32 1 -0.95 301 302
JUN -0.038 0.045 -10000 0 -0.45 6 6
oligodendrocyte development -0.009 0.11 -10000 0 -0.43 57 57
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
mol:DAG -0.034 0.11 -10000 0 -0.46 54 54
PDGF/PDGFRA -0.03 0.14 -10000 0 -0.6 57 57
actin cytoskeleton reorganization -0.009 0.11 -10000 0 -0.43 57 57
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.015 0.1 -10000 0 -0.38 62 62
PDGF/PDGFRA/Crk/C3G 0.017 0.095 -10000 0 -0.37 57 57
JAK1 -0.025 0.1 0.23 1 -0.42 59 60
ELK1/SRF -0.034 0.088 0.32 1 -0.36 55 56
SHB 0.024 0.008 0.26 1 -10000 0 1
SHF 0.023 0.021 0.26 1 -0.58 1 2
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.045 0.11 0.22 1 -0.47 57 58
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.025 0.082 -10000 0 -0.34 42 42
PDGF/PDGFRA/SHB -0.009 0.11 -10000 0 -0.43 57 57
PDGF/PDGFRA/Caveolin-1 -0.097 0.22 -10000 0 -0.48 238 238
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.051 0.1 -10000 0 -0.43 56 56
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.01 0.11 -10000 0 -0.43 57 57
JAK-STAT cascade -0.025 0.1 0.23 1 -0.42 59 60
cell proliferation -0.009 0.11 -10000 0 -0.43 58 58
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.04 0.15 0.35 70 -0.35 52 122
TBX21 0.013 0.35 0.76 22 -1.3 47 69
B2M 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.024 0.037 -10000 0 -10000 0 0
IL12RB1 0.032 0.074 0.32 41 -0.6 2 43
GADD45B 0.037 0.26 0.64 25 -0.86 35 60
IL12RB2 0.027 0.15 0.27 117 -0.58 42 159
GADD45G 0.054 0.27 0.67 28 -0.89 29 57
natural killer cell activation 0.007 0.025 0.16 1 -10000 0 1
RELB 0.026 0.024 0.26 10 -10000 0 10
RELA 0.024 0.005 -10000 0 -10000 0 0
IL18 0.034 0.041 0.28 24 -10000 0 24
IL2RA 0.027 0.086 0.26 51 -0.58 13 64
IFNG 0.055 0.082 0.26 142 -10000 0 142
STAT3 (dimer) 0.035 0.25 0.55 46 -0.67 52 98
HLA-DRB5 0.024 0.08 0.25 74 -0.58 5 79
FASLG 0.051 0.31 0.72 37 -0.99 41 78
NF kappa B2 p52/RelB 0.02 0.25 0.68 5 -0.77 53 58
CD4 0.01 0.024 -10000 0 -10000 0 0
SOCS1 0.025 0.032 0.26 12 -0.58 1 13
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D 0.009 0.1 0.26 44 -0.59 19 63
CD3E 0.009 0.092 0.27 35 -0.58 16 51
CD3G 0 0.12 0.27 37 -0.59 30 67
IL12Rbeta2/JAK2 0.036 0.12 0.28 38 -0.42 46 84
CCL3 0.033 0.28 0.69 26 -0.93 36 62
CCL4 0.035 0.28 0.71 22 -0.96 30 52
HLA-A 0.027 0.022 0.26 7 -10000 0 7
IL18/IL18R 0.065 0.12 0.37 19 -0.38 49 68
NOS2 0.033 0.28 0.69 24 -0.95 36 60
IL12/IL12R/TYK2/JAK2/SPHK2 0.038 0.15 0.34 67 -0.34 60 127
IL1R1 0.019 0.31 0.69 23 -1.1 42 65
IL4 -0.011 0.037 -10000 0 -10000 0 0
JAK2 0.023 0.036 0.2 1 -10000 0 1
EntrezGene:6957 -0.004 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.024 0.23 0.39 33 -0.64 76 109
RAB7A 0.051 0.24 0.63 23 -0.75 28 51
lysosomal transport 0.052 0.23 0.6 28 -0.71 28 56
FOS -0.31 0.62 0.6 15 -1.2 327 342
STAT4 (dimer) 0.062 0.28 0.59 43 -0.85 46 89
STAT5A (dimer) 0.047 0.28 0.6 54 -0.77 53 107
GZMA 0.025 0.3 0.69 33 -1.1 32 65
GZMB 0.025 0.32 0.68 36 -1.1 44 80
HLX 0.021 0.014 0.26 2 -10000 0 2
LCK 0.027 0.3 0.65 42 -0.86 55 97
TCR/CD3/MHC II/CD4 -0.047 0.18 0.28 25 -0.47 98 123
IL2/IL2R 0.065 0.099 0.41 38 -0.37 19 57
MAPK14 0.047 0.28 0.64 31 -0.86 38 69
CCR5 0.037 0.27 0.68 32 -0.89 33 65
IL1B 0.017 0.082 0.3 3 -0.59 14 17
STAT6 0.041 0.12 0.39 40 -0.53 6 46
STAT4 0.001 0.12 0.26 1 -0.58 40 41
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.032 0.26 19 -10000 0 19
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.008 0.26 1 -10000 0 1
IL12B 0.073 0.11 0.28 212 -10000 0 212
CD8A 0.029 0.064 0.28 28 -0.58 6 34
CD8B 0.014 0.11 0.28 30 -0.58 31 61
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.04 0.15 0.35 52 -0.35 70 122
IL2RB 0.031 0.052 0.26 37 -0.58 2 39
proteasomal ubiquitin-dependent protein catabolic process 0.066 0.27 0.57 48 -0.76 46 94
IL2RG 0.031 0.07 0.26 45 -0.58 7 52
IL12 0.048 0.16 0.3 88 -0.43 59 147
STAT5A 0.02 0.046 -10000 0 -0.58 6 6
CD247 0.006 0.082 0.26 16 -0.58 15 31
IL2 0.022 0.022 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 -0.006 0.15 0.3 17 -0.59 58 75
IL12/IL12R/TYK2/JAK2 0.035 0.31 0.69 44 -0.88 52 96
MAP2K3 0.041 0.28 0.64 30 -0.85 44 74
RIPK2 0.02 0.016 0.26 3 -10000 0 3
MAP2K6 0.046 0.27 0.63 32 -0.82 41 73
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.034 0.26 1 -0.58 1 2
IL18RAP 0.011 0.11 0.28 5 -0.58 35 40
IL12Rbeta1/TYK2 0.041 0.07 0.29 34 -0.46 2 36
EOMES -0.02 0.18 -10000 0 -0.97 29 29
STAT1 (dimer) 0.067 0.27 0.62 63 -0.74 37 100
T cell proliferation 0.05 0.22 0.51 30 -0.64 41 71
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.077 -10000 0 -0.58 16 16
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 -0.73 38 43
ATF2 0.045 0.26 0.61 29 -0.8 36 65
Canonical Wnt signaling pathway

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.021 0.24 2 -10000 0 2
AES 0.022 0.019 0.21 2 -10000 0 2
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.006 -10000 0 -10000 0 0
DKK2 0.011 0.09 0.26 2 -0.58 23 25
TLE1 0.019 0.05 -10000 0 -0.58 6 6
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.3 37 -0.37 4 41
WIF1 -0.28 0.3 0.26 12 -0.57 518 530
beta catenin/RanBP3 0.021 0.09 0.42 36 -0.39 1 37
KREMEN2 0.13 0.12 0.26 448 -10000 0 448
DKK1 0.026 0.16 0.26 137 -0.58 51 188
beta catenin/beta TrCP1 0.11 0.095 0.32 19 -0.38 2 21
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.014 0.26 0.6 80 -1.3 22 102
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 0.078 -10000 0 -0.56 12 12
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.13 0.3 9 -0.6 22 31
Axin1/APC/GSK3 0.047 0.054 0.24 1 -0.31 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.063 0.34 1 -0.4 4 5
HNF1A 0.025 0.028 0.26 9 -10000 0 9
CTBP1 0.022 0.02 0.24 3 -10000 0 3
MYC 0.11 0.34 0.58 244 -1.3 23 267
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.098 0.34 1 -0.34 17 18
NKD1 0.021 0.054 0.26 14 -0.58 6 20
TCF4 0.017 0.056 0.23 2 -0.57 8 10
TCF3 0.022 0.022 0.27 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.057 0.024 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.005 0.13 0.46 35 -0.51 14 49
LEF1 0.051 0.082 0.26 126 -0.54 1 127
DVL1 0.056 0.053 -10000 0 -0.46 1 1
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.15 0.3 11 -0.59 30 41
DKK1/LRP6/Kremen 2 0.1 0.14 0.34 76 -0.34 44 120
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.25 2 -10000 0 2
NLK 0.023 0.014 0.25 2 -10000 0 2
CCND1 0.089 0.26 0.61 170 -1.2 6 176
WNT1 0.024 0.012 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.056 0.3 5 -0.33 4 9
APC 0.016 0.057 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.22 478 -10000 0 478
CREBBP 0.021 0.018 0.27 1 -10000 0 1
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.096 0.1 0.21 403 -0.35 2 405
EPHB2 0.028 0.032 0.26 19 -10000 0 19
Syndecan-2/TACI 0.022 0.06 0.2 53 -0.36 12 65
LAMA1 -0.038 0.18 0.26 2 -0.58 105 107
Syndecan-2/alpha2 ITGB1 -0.038 0.15 -10000 0 -0.33 187 187
HRAS 0.026 0.021 0.26 8 -10000 0 8
Syndecan-2/CASK 0.005 0.017 -10000 0 -0.36 2 2
ITGA5 0.024 0.003 -10000 0 -10000 0 0
BAX 0.002 0.031 0.45 1 -10000 0 1
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.018 -10000 0 -0.33 2 2
LAMA3 -0.12 0.25 -10000 0 -0.58 236 236
EZR 0.024 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.046 0.19 -10000 0 -0.58 119 119
Syndecan-2/MMP2 0.015 0.038 -10000 0 -0.37 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.07 -10000 0 -0.4 26 26
dendrite morphogenesis 0.022 0.034 0.21 19 -0.36 2 21
Syndecan-2/GM-CSF 0.021 0.035 0.21 23 -0.36 2 25
determination of left/right symmetry 0.007 0.02 -10000 0 -0.42 2 2
Syndecan-2/PKC delta 0.019 0.022 0.31 1 -0.36 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.033 0.074 0.19 166 -0.33 2 168
MAPK1 0.037 0.077 0.19 189 -0.32 2 191
Syndecan-2/RACK1 0.03 0.027 0.25 3 -0.31 2 5
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.02 -10000 0 -0.42 2 2
ITGA2 0.009 0.093 -10000 0 -0.58 25 25
MAPK8 0.005 0.033 0.27 5 -0.36 5 10
Syndecan-2/alpha2/beta1 Integrin 0.002 0.12 -10000 0 -0.36 81 81
Syndecan-2/Kininogen 0.019 0.033 0.22 17 -0.36 2 19
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.069 0.31 7 -0.3 2 9
Syndecan-2/CASK/Protein 4.1 0.017 0.019 -10000 0 -0.33 2 2
extracellular matrix organization 0.02 0.023 0.35 1 -0.36 2 3
actin cytoskeleton reorganization 0.095 0.1 0.21 403 -0.35 2 405
Syndecan-2/Caveolin-2/Ras -0.006 0.11 0.26 3 -0.34 91 94
Syndecan-2/Laminin alpha3 -0.058 0.15 -10000 0 -0.36 177 177
Syndecan-2/RasGAP 0.038 0.031 0.26 2 -0.3 2 4
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.022 0.034 0.22 19 -0.36 2 21
GO:0007205 0.002 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.025 -10000 0 -0.3 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
TNFRSF13B 0.027 0.085 0.26 53 -0.58 12 65
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.07 -10000 0 -0.4 26 26
Syndecan-2/Synbindin 0.018 0.02 -10000 0 -0.35 2 2
TGFB1 0.024 0.008 0.26 1 -10000 0 1
CASP3 0.043 0.071 0.19 183 -0.33 2 185
FN1 0.12 0.12 0.26 403 -10000 0 403
Syndecan-2/IL8 0.024 0.071 0.21 59 -0.32 21 80
SDC2 0.007 0.02 -10000 0 -0.42 2 2
KNG1 0.022 0.031 0.26 17 -10000 0 17
Syndecan-2/Neurofibromin 0.018 0.021 -10000 0 -0.36 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.025 0.036 0.26 23 -10000 0 23
Syndecan-2/TGFB1 0.02 0.023 0.35 1 -0.36 2 3
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.018 -10000 0 -0.33 2 2
Syndecan-2/Ezrin 0.029 0.026 0.29 1 -0.33 2 3
PRKACA 0.045 0.073 0.19 194 -0.32 2 196
angiogenesis 0.024 0.071 0.21 59 -0.32 21 80
MMP2 0.018 0.046 -10000 0 -0.58 6 6
IL8 0.026 0.1 0.26 59 -0.58 19 78
calcineurin-NFAT signaling pathway 0.022 0.06 0.2 53 -0.36 12 65
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.083 -10000 0 -0.41 28 28
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.026 0.17 -10000 0 -0.58 86 86
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.046 -10000 0 -0.58 6 6
AP1 -0.074 0.15 -10000 0 -0.31 272 272
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.022 0.033 -10000 0 -0.58 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.1 -10000 0 -0.64 17 17
NICD/RBPSUH 0.02 0.08 -10000 0 -0.4 29 29
WIF1 -0.28 0.3 0.26 12 -0.58 518 530
NOTCH1 0.009 0.073 -10000 0 -0.42 27 27
PSENEN 0.024 0.008 0.26 1 -10000 0 1
KREMEN2 0.13 0.12 0.26 448 -10000 0 448
DKK1 0.026 0.16 0.26 137 -0.58 51 188
beta catenin/beta TrCP1 0.008 0.067 -10000 0 -0.36 5 5
APH1B 0.023 0.019 -10000 0 -0.58 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.061 -10000 0 -0.45 9 9
CtBP/CBP/TCF1/TLE1/AES 0.012 0.039 -10000 0 -0.29 6 6
PSEN1 0.024 0.004 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.58 285 285
JUN 0.02 0.046 -10000 0 -0.58 6 6
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 -0.001 0.067 -10000 0 -0.38 5 5
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.098 0.34 1 -0.34 17 18
HNF1A 0.025 0.02 0.26 7 -10000 0 7
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.014 0.21 -10000 0 -1.3 26 26
NKD1 0.021 0.054 0.26 14 -0.58 6 20
FZD1 0.024 0.003 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.005 0.12 -10000 0 -0.44 29 29
apoptosis -0.074 0.15 -10000 0 -0.31 272 272
Delta 1/NOTCHprecursor 0.019 0.082 -10000 0 -0.4 28 28
DLL1 0.021 0.038 -10000 0 -0.58 4 4
PPARD 0.014 0.095 -10000 0 -0.83 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
APC 0.004 0.084 0.25 1 -0.45 24 25
DVL1 -0.03 0.078 -10000 0 -0.37 32 32
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.1 0.14 0.34 76 -0.34 44 120
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 0.019 0.1 -10000 0 -1.1 7 7
WNT1 0.023 0.012 0.26 2 -10000 0 2
Axin1/APC/beta catenin 0.012 0.099 0.32 5 -0.43 18 23
DKK2 0.011 0.09 0.26 2 -0.58 23 25
NOTCH1 precursor/DVL1 -0.021 0.11 -10000 0 -0.59 23 23
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.003 0.12 -10000 0 -0.44 29 29
PPP2R5D -0.004 0.059 0.29 5 -0.39 11 16
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.2 -10000 0 -0.34 501 501
RBPJ 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.038 -10000 0 -0.58 4 4
alphaV beta3 Integrin 0.02 0.082 -10000 0 -0.43 32 32
PTK2 -0.041 0.16 -10000 0 -0.48 86 86
positive regulation of JNK cascade -0.021 0.12 -10000 0 -0.32 120 120
CDC42/GDP -0.017 0.17 0.43 1 -0.43 120 121
Rac1/GDP -0.018 0.17 -10000 0 -0.42 121 121
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.022 0.15 -10000 0 -0.39 118 118
nectin-3/I-afadin -0.014 0.14 -10000 0 -0.43 105 105
RAPGEF1 -0.035 0.17 0.46 1 -0.47 109 110
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.049 0.18 -10000 0 -0.52 115 115
PDGFB-D/PDGFRB 0.022 0.038 -10000 0 -0.57 4 4
TLN1 -0.023 0.07 -10000 0 -0.39 13 13
Rap1/GTP -0.024 0.12 -10000 0 -0.34 102 102
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.028 -10000 0 -0.34 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.014 0.14 -10000 0 -0.43 105 105
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.038 0.2 0.45 1 -0.52 126 127
MLLT4 0.021 0.034 0.26 1 -0.58 3 4
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.019 0.13 -10000 0 -0.35 106 106
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.031 -10000 0 -0.3 6 6
positive regulation of lamellipodium assembly -0.019 0.13 -10000 0 -0.34 123 123
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.037 0.18 -10000 0 -0.58 104 104
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
CDH1 0.009 0.085 -10000 0 -0.58 21 21
CLDN1 0.008 0.12 0.26 23 -0.58 36 59
JAM-A/CLDN1 0.004 0.13 -10000 0 -0.36 101 101
SRC -0.056 0.2 -10000 0 -0.56 124 124
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.031 -10000 0 -0.3 6 6
FARP2 -0.038 0.2 0.46 1 -0.52 125 126
RAC1 0.024 0.003 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.002 0.13 -10000 0 -0.37 104 104
nectin-1/I-afadin 0.029 0.031 -10000 0 -0.3 6 6
nectin-2/I-afadin 0.032 0.03 -10000 0 -0.3 6 6
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0 0.13 -10000 0 -0.37 105 105
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.021 0.12 -10000 0 -0.32 120 120
alphaV/beta3 Integrin/Talin -0.006 0.1 0.26 1 -0.41 38 39
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.03 -10000 0 -0.3 6 6
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.03 -10000 0 -0.3 6 6
PIP5K1C -0.019 0.077 -10000 0 -0.23 103 103
VAV2 -0.037 0.21 0.44 1 -0.54 120 121
RAP1/GDP -0.014 0.16 -10000 0 -0.4 114 114
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.002 0.13 -10000 0 -0.37 104 104
nectin-3(dimer)/I-afadin/I-afadin -0.014 0.14 -10000 0 -0.43 105 105
Rac1/GTP -0.021 0.16 -10000 0 -0.41 121 121
PTPRM -0.016 0.087 -10000 0 -0.25 107 107
E-cadherin/beta catenin/alpha catenin 0.045 0.068 -10000 0 -0.32 23 23
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.38 0.28 -10000 0 -0.58 687 687
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 19 -10000 0 19
TCEB1 0.021 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.048 -10000 0 -0.28 8 8
HIF1A 0.004 0.029 -10000 0 -0.27 10 10
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.037 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.06 0.087 0.26 163 -10000 0 163
ARNT/IPAS -0.25 0.21 -10000 0 -0.38 693 693
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.045 -10000 0 -0.28 13 13
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.028 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.049 -10000 0 -0.32 4 4
PHD1-3/OS9 0.056 0.049 -10000 0 -0.34 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.042 0.053 -10000 0 -0.3 3 3
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.048 -10000 0 -0.28 13 13
EGLN3 0.04 0.064 0.26 73 -0.58 1 74
EGLN2 0.025 0.017 0.26 5 -10000 0 5
EGLN1 0.02 0.021 -10000 0 -0.58 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.066 -10000 0 -0.51 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.053 0.073 0.28 6 -0.27 11 17
FAS signaling pathway (CD95)

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
SPTAN1 -0.002 0.043 0.21 29 -10000 0 29
RFC1 -0.003 0.039 0.22 24 -10000 0 24
PRKDC 0.017 0.079 0.23 106 -10000 0 106
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.1 -10000 0 -0.63 21 21
FASLG/FAS/FADD/FAF1 -0.005 0.058 0.22 11 -0.3 11 22
MAP2K4 -0.084 0.18 0.39 2 -0.4 119 121
mol:ceramide -0.023 0.099 -10000 0 -0.38 25 25
GSN -0.007 0.056 0.21 28 -0.36 11 39
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.076 0.28 1 -0.36 15 16
FAS 0.004 0.037 -10000 0 -0.59 2 2
BID -0.018 0.021 -10000 0 -10000 0 0
MAP3K1 -0.048 0.12 0.31 2 -0.4 40 42
MAP3K7 0.011 0.019 -10000 0 -10000 0 0
RB1 -0.002 0.039 0.22 25 -10000 0 25
CFLAR 0.027 0.007 -10000 0 -10000 0 0
HGF/MET -0.051 0.2 -10000 0 -0.41 215 215
ARHGDIB -0.001 0.047 0.22 36 -10000 0 36
FADD 0.006 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.063 0.36 11 -0.21 28 39
NFKB1 -0.045 0.12 -10000 0 -0.57 19 19
MAPK8 -0.15 0.26 0.56 2 -0.47 371 373
DFFA -0.003 0.04 0.21 25 -10000 0 25
DNA fragmentation during apoptosis -0.008 0.049 0.21 25 -10000 0 25
FAS/FADD/MET -0.037 0.14 -10000 0 -0.38 135 135
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.036 0.26 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.049 0.23 34 -10000 0 34
DFFB -0.003 0.04 0.21 25 -10000 0 25
CHUK -0.04 0.11 -10000 0 -0.56 16 16
FASLG 0.007 0.088 0.26 40 -0.59 13 53
FAS/FADD 0.009 0.037 -10000 0 -0.33 2 2
HGF -0.011 0.14 -10000 0 -0.58 60 60
LMNA -0.003 0.054 0.19 44 -10000 0 44
CASP6 -0.003 0.039 0.21 25 -10000 0 25
CASP10 0.004 0.042 -10000 0 -0.59 3 3
CASP3 0.001 0.045 0.26 27 -10000 0 27
PTPN13 0.009 0.095 -10000 0 -0.58 26 26
CASP8 -0.021 0.025 -10000 0 -0.18 2 2
IL6 -0.43 0.62 -10000 0 -1.2 378 378
MET -0.071 0.22 -10000 0 -0.58 162 162
ICAD/CAD -0.006 0.032 0.2 10 -10000 0 10
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.1 -10000 0 -0.38 25 25
activation of caspase activity by cytochrome c -0.018 0.021 -10000 0 -10000 0 0
PAK2 -0.002 0.048 0.22 36 -0.19 6 42
BCL2 0.008 0.096 -10000 0 -0.57 27 27
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.043 0.15 -10000 0 -0.32 223 223
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.14 8 -10000 0 8
GNB1/GNG2 0.027 0.04 -10000 0 -0.36 10 10
GNB1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.062 0.14 -10000 0 -0.32 237 237
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 0.082 237 -10000 0 237
GNAL -0.11 0.25 -10000 0 -0.58 221 221
GNG2 0.018 0.059 -10000 0 -0.58 10 10
CRH 0.017 0.023 0.26 8 -10000 0 8
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.03 -10000 0 -0.36 7 7
MAPK11 0.005 0.02 -10000 0 -0.36 3 3
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.58 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.071 0.43 1 -0.26 47 48
CDKN1A -0.009 0.034 -10000 0 -0.77 2 2
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
BAX 0.025 0.017 0.26 5 -10000 0 5
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.02 0.038 -10000 0 -0.58 4 4
FOXO4 0.012 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.33 0.3 0.26 24 -0.58 610 634
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.024 -10000 0 -0.43 1 1
PPARGC1A -0.091 0.24 0.26 10 -0.58 198 208
FHL2 0.021 0.046 -10000 0 -0.58 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.033 0.011 -10000 0 -10000 0 0
HIST2H4A 0.021 0.071 0.26 47 -0.43 1 48
SIRT1/FOXO3a 0.016 0.026 -10000 0 -0.19 3 3
SIRT1 0.022 0.009 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.023 -10000 0 -0.37 1 1
SIRT1/Histone H1b 0.028 0.044 -10000 0 -0.21 6 6
apoptosis -0.045 0.017 -10000 0 -10000 0 0
SIRT1/PGC1A -0.048 0.16 -10000 0 -0.36 198 198
p53/SIRT1 0.027 0.02 0.41 2 -10000 0 2
SIRT1/FOXO4 0.022 0.037 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.037 0.041 -10000 0 -0.34 9 9
HIST1H1E 0.021 0.031 0.21 7 -10000 0 7
SIRT1/p300 0.033 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.024 0.37 1 -0.21 9 10
TP53 0.02 0.011 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0.045 0.017 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.26 0.22 -10000 0 -0.39 704 704
ACSS2 -0.007 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.024 0.21 9 -0.37 1 10
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.011 0.046 -10000 0 -0.26 22 22
epithelial cell differentiation 0.035 0.057 -10000 0 -0.32 21 21
CYFIP2 0.028 0.049 0.26 25 -0.58 3 28
ENAH -0.004 0.06 0.29 10 -10000 0 10
EGFR -0.19 0.29 -10000 0 -0.58 363 363
EPHA2 0.02 0.042 -10000 0 -0.58 5 5
MYO6 -0.013 0.054 0.36 1 -0.31 22 23
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.035 -10000 0 -0.37 3 3
AQP5 -0.19 0.26 0.33 1 -0.5 404 405
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.052 0.36 1 -0.3 21 22
regulation of calcium-dependent cell-cell adhesion -0.024 0.078 0.36 1 -0.3 62 63
EGF -0.083 0.23 0.26 2 -0.58 182 184
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.017 0.12 0.29 1 -0.46 52 53
cortical microtubule organization 0.035 0.057 -10000 0 -0.32 21 21
GO:0000145 -0.013 0.05 0.35 1 -0.29 21 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.039 0.059 -10000 0 -0.32 21 21
MLLT4 0.021 0.034 0.26 1 -0.58 3 4
ARF6/GDP -0.021 0.04 -10000 0 -0.28 20 20
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.039 -10000 0 -0.34 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.002 0.052 -10000 0 -0.29 21 21
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.013 0.052 0.36 1 -0.3 21 22
ARF6/GTP 0.049 0.041 -10000 0 -0.31 5 5
CDH1 0.009 0.085 -10000 0 -0.58 21 21
EGFR/EGFR/EGF/EGF -0.14 0.2 -10000 0 -0.34 491 491
RhoA/GDP 0.036 0.056 -10000 0 -0.3 21 21
actin cytoskeleton organization -0.014 0.051 0.34 1 -0.3 22 23
IGF-1R heterotetramer 0.012 0.082 0.26 2 -0.57 19 21
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.012 0.082 0.26 2 -0.58 19 21
IGF1 -0.1 0.25 -10000 0 -0.58 217 217
DIAPH1 0.026 0.1 -10000 0 -0.57 11 11
Wnt receptor signaling pathway -0.035 0.057 0.32 21 -10000 0 21
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.04 -10000 0 -0.28 20 20
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.015 0.052 0.35 1 -0.3 22 23
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.016 0.055 -10000 0 -0.3 28 28
Ephrin A1/EPHA2 0.024 0.055 -10000 0 -0.3 21 21
SEC6/SEC8 -0.022 0.045 -10000 0 -0.3 23 23
MGAT3 -0.025 0.079 0.36 1 -0.31 62 63
HGF/MET -0.04 0.16 -10000 0 -0.33 216 216
HGF -0.011 0.14 -10000 0 -0.58 60 60
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.011 0.046 -10000 0 -0.26 22 22
actin cable formation 0.04 0.095 0.32 31 -0.28 2 33
KIAA1543 -0.013 0.054 0.35 1 -0.32 21 22
KIFC3 -0.013 0.051 0.36 1 -0.31 21 22
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.013 0.052 -10000 0 -0.31 21 21
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.035 0.057 -10000 0 -0.32 21 21
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.012 0.05 0.36 1 -0.31 19 20
PIP5K1C -0.013 0.053 0.36 1 -0.31 21 22
LIMA1 0.024 0.019 -10000 0 -0.58 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.015 0.088 0.3 23 -10000 0 23
adherens junction assembly -0.023 0.1 0.3 3 -0.64 15 18
IGF-1R heterotetramer/IGF1 -0.044 0.15 -10000 0 -0.32 225 225
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.03 -10000 0 -0.3 6 6
MET -0.071 0.22 -10000 0 -0.58 162 162
PLEKHA7 -0.013 0.057 0.36 1 -0.33 21 22
mol:GTP 0.043 0.038 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.009 0.068 0.37 6 -0.52 1 7
cortical actin cytoskeleton stabilization 0.011 0.046 -10000 0 -0.26 22 22
regulation of cell-cell adhesion -0.014 0.051 0.34 1 -0.3 22 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.046 -10000 0 -0.26 22 22
LPA4-mediated signaling events

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.019 0.064 -10000 0 -0.36 34 34
ADCY5 -0.12 0.17 -10000 0 -0.37 314 314
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.008 0.062 -10000 0 -0.37 25 25
ADCY2 -0.028 0.099 0.24 7 -0.37 75 82
ADCY3 -0.007 0.003 -10000 0 -10000 0 0
ADCY8 -0.004 0.023 0.23 6 -10000 0 6
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.086 0.23 16 -0.25 33 49
TCGA08_rtk_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
PDGFRA -0.01 0.14 -10000 0 -0.58 57 57
HRAS 0.026 0.021 0.26 8 -10000 0 8
EGFR -0.19 0.29 -10000 0 -0.58 363 363
AKT -0.012 0.12 0.3 7 -0.28 89 96
FOXO3 0.022 0.02 -10000 0 -0.58 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.038 -10000 0 -0.58 4 4
AKT3 0.014 0.06 -10000 0 -0.58 10 10
FOXO4 0.025 0.001 -10000 0 -10000 0 0
MET -0.071 0.22 -10000 0 -0.58 162 162
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.016 0.074 0.26 4 -0.58 15 19
PIK3R3 0.024 0.008 0.26 1 -10000 0 1
PIK3R2 0.024 0.004 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.059 0.14 0.21 4 -0.34 147 151
ERBB2 0.021 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.007 0.088 0.32 46 -0.26 1 47
PI3K -0.048 0.14 0.28 11 -0.32 157 168
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.037 0.057 0.26 10 -0.16 2 12
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.023 0.02 -10000 0 -0.58 1 1
Aurora A signaling

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
Aurora A/GADD45A 0.044 0.042 -10000 0 -10000 0 0
BIRC5 0.18 0.11 0.26 677 -10000 0 677
NFKBIA 0.026 0.043 0.28 7 -10000 0 7
CPEB1 -0.081 0.23 0.26 1 -0.58 178 179
AKT1 0.026 0.042 0.28 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.033 0.037 0.21 1 -0.21 1 2
NDEL1/TACC3 0.066 0.068 0.26 16 -10000 0 16
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.002 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.041 0.045 0.28 3 -10000 0 3
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.093 0.068 0.27 26 -10000 0 26
TP53 0.023 0.051 -10000 0 -0.22 12 12
DLG7 0.022 0.031 0.18 1 -10000 0 1
AURKAIP1 0.026 0.025 0.26 11 -10000 0 11
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.07 0.071 0.28 16 -10000 0 16
G2/M transition of mitotic cell cycle 0.033 0.036 0.21 1 -0.21 1 2
AURKA 0.038 0.047 0.24 1 -10000 0 1
AURKB 0.088 0.076 0.17 420 -10000 0 420
CDC25B 0.032 0.038 0.22 3 -10000 0 3
G2/M transition checkpoint 0.019 0.029 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.13 -10000 0 -0.3 177 177
Aurora A/CPEB -0.026 0.13 -10000 0 -0.3 177 177
Aurora A/TACC1/TRAP/chTOG 0.044 0.071 -10000 0 -0.31 21 21
BRCA1 0.023 0.021 0.26 1 -0.58 1 2
centrosome duplication 0.041 0.044 0.27 3 -10000 0 3
regulation of centrosome cycle 0.064 0.066 0.25 16 -10000 0 16
spindle assembly 0.042 0.07 -10000 0 -0.3 21 21
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.088 0.28 29 -10000 0 29
CENPA 0.098 0.082 0.19 433 -0.21 3 436
Aurora A/PP2A 0.044 0.043 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.031 0.04 0.24 1 -10000 0 1
negative regulation of DNA binding 0.019 0.063 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.029 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.049 0.24 1 -10000 0 1
TACC1 0.006 0.089 -10000 0 -0.58 23 23
TACC3 0.058 0.084 0.26 150 -10000 0 150
Aurora A/Antizyme1 0.055 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.044 0.043 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.002 0.027 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.04 0.024 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.093 0.068 0.27 26 -10000 0 26
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.096 0.073 0.24 37 -10000 0 37
PAK1 0.023 0.021 0.26 7 -10000 0 7
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.085 0.1 0.29 9 -0.57 6 15
Syndecan-4/Syndesmos 0.095 0.11 0.38 5 -0.7 6 11
positive regulation of JNK cascade 0.083 0.14 0.36 8 -0.64 8 16
Syndecan-4/ADAM12 0.11 0.12 0.35 35 -0.72 6 41
CCL5 0.029 0.059 0.26 37 -0.58 4 41
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.003 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
PLG -0.008 0.032 0.26 5 -10000 0 5
ADAM12 0.037 0.062 0.26 61 -0.58 2 63
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.014 0.26 3 -10000 0 3
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 0.064 0.15 0.39 3 -0.74 8 11
Syndecan-4/CXCL12/CXCR4 0.088 0.14 0.38 7 -0.69 8 15
Syndecan-4/Laminin alpha3 0.034 0.15 0.39 4 -0.75 7 11
MDK 0.033 0.045 0.26 38 -10000 0 38
Syndecan-4/FZD7 0.095 0.12 0.38 5 -0.69 7 12
Syndecan-4/Midkine 0.1 0.11 0.37 13 -0.7 6 19
FZD7 0.014 0.079 -10000 0 -0.58 18 18
Syndecan-4/FGFR1/FGF -0.01 0.16 0.35 1 -0.54 18 19
THBS1 0.021 0.038 -10000 0 -0.58 4 4
integrin-mediated signaling pathway 0.093 0.12 0.36 9 -0.69 7 16
positive regulation of MAPKKK cascade 0.083 0.14 0.36 8 -0.64 8 16
Syndecan-4/TACI 0.098 0.12 0.36 16 -0.72 6 22
CXCR4 0.03 0.036 0.26 24 -10000 0 24
cell adhesion 0.061 0.085 0.24 90 -0.25 20 110
Syndecan-4/Dynamin 0.099 0.11 0.39 3 -0.73 6 9
Syndecan-4/TSP1 0.098 0.11 0.38 5 -0.72 6 11
Syndecan-4/GIPC 0.099 0.11 0.39 3 -0.73 6 9
Syndecan-4/RANTES 0.1 0.11 0.37 7 -0.72 6 13
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.038 0.18 0.26 2 -0.58 105 107
LAMA3 -0.12 0.25 -10000 0 -0.58 236 236
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.024 0.23 0.7 92 -0.54 21 113
Syndecan-4/alpha-Actinin 0.099 0.1 0.39 4 -0.72 6 10
TFPI -0.002 0.12 -10000 0 -0.58 45 45
F2 0.024 0.032 0.27 9 -10000 0 9
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.002 0.18 0.37 3 -0.56 32 35
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.012 0.092 0.26 8 -0.58 23 31
Syndecan-4/CXCL12 0.076 0.14 0.39 4 -0.72 8 12
FGF6 0.015 0.026 -10000 0 -0.58 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.02 0.16 -10000 0 -0.58 74 74
TNFRSF13B 0.027 0.085 0.26 53 -0.58 12 65
FGF2 -0.2 0.29 -10000 0 -0.58 383 383
FGFR1 0.016 0.05 -10000 0 -0.58 7 7
Syndecan-4/PI-4-5-P2 0.075 0.1 0.32 4 -0.72 6 10
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.26 400 -10000 0 400
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.012 0.026 -10000 0 -10000 0 0
vasculogenesis 0.097 0.1 0.37 6 -0.69 6 12
SDC4 0.088 0.1 0.36 7 -0.78 5 12
Syndecan-4/Tenascin C 0.094 0.12 0.36 9 -0.73 7 16
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.086 0.1 0.37 4 -0.7 6 10
MMP9 0.12 0.12 0.26 424 -0.57 1 425
Rac1/GTP 0.062 0.086 0.25 85 -0.26 20 105
cytoskeleton organization 0.093 0.1 0.37 6 -0.67 6 12
GIPC1 0.024 0.011 0.26 2 -10000 0 2
Syndecan-4/TFPI 0.087 0.13 0.39 4 -0.72 7 11
Regulation of Androgen receptor activity

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
HDAC1 0.007 0.011 -10000 0 -10000 0 0
SMARCC1 0.006 0.028 -10000 0 -0.59 1 1
REL 0.017 0.069 -10000 0 -0.58 13 13
HDAC7 -0.036 0.11 0.37 3 -0.37 51 54
JUN 0.019 0.046 -10000 0 -0.58 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.019 -10000 0 -0.58 1 1
KAT5 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.007 0.061 -10000 0 -0.44 18 18
FOXO1 0.02 0.038 -10000 0 -0.58 4 4
T-DHT/AR -0.023 0.12 0.33 1 -0.37 64 65
MAP2K6 0.004 0.082 0.25 1 -0.58 18 19
BRM/BAF57 0.024 0.028 -10000 0 -10000 0 0
MAP2K4 0.014 0.021 -10000 0 -10000 0 0
SMARCA2 0.017 0.019 -10000 0 -10000 0 0
PDE9A -0.062 0.26 -10000 0 -1.1 58 58
NCOA2 -0.005 0.12 -10000 0 -0.57 41 41
CEBPA 0.019 0.056 -10000 0 -0.57 9 9
EHMT2 0.02 0.012 -10000 0 -10000 0 0
cell proliferation 0 0.15 0.37 24 -0.45 23 47
NR0B1 0.028 0.043 0.26 34 -10000 0 34
EGR1 -0.17 0.28 -10000 0 -0.58 316 316
RXRs/9cRA -0.045 0.15 -10000 0 -0.34 207 207
AR/RACK1/Src -0.016 0.11 0.31 7 -0.36 30 37
AR/GR -0.025 0.12 0.25 2 -0.3 123 125
GNB2L1 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.015 7 7
MAPK8 -0.002 0.042 -10000 0 -0.43 7 7
T-DHT/AR/TIF2/CARM1 -0.015 0.12 0.34 2 -0.37 49 51
SRC -0.019 0.066 0.19 28 -0.34 22 50
NR3C1 0.019 0.056 -10000 0 -0.58 9 9
KLK3 -0.16 0.41 -10000 0 -1.1 140 140
APPBP2 0.016 0.019 -10000 0 -10000 0 0
TRIM24 0.018 0.02 0.26 1 -10000 0 1
T-DHT/AR/TIP60 -0.014 0.095 0.35 3 -0.39 24 27
TMPRSS2 -0.13 0.37 -10000 0 -1.1 132 132
RXRG -0.1 0.24 0.26 2 -0.58 210 212
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.023 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.022 0.011 -10000 0 -10000 0 0
NR2C2 0.018 0.056 -10000 0 -0.58 9 9
KLK2 -0.051 0.2 0.32 7 -0.66 82 89
AR -0.038 0.11 -10000 0 -0.3 128 128
SENP1 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.016 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 134 -0.023 36 170
GATA2 0.012 0.099 0.26 14 -0.58 26 40
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.26 422 -10000 0 422
T-DHT/AR/RACK1/Src -0.011 0.1 0.34 10 -0.38 25 35
positive regulation of transcription 0.012 0.099 0.26 14 -0.57 26 40
DNAJA1 0.017 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.011 -10000 0 -10000 0 0
NCOA1 0.021 0.031 -10000 0 -0.61 1 1
SPDEF -0.015 0.16 0.26 29 -0.58 69 98
T-DHT/AR/TIF2 -0.004 0.099 0.32 6 -0.38 24 30
T-DHT/AR/Hsp90 -0.015 0.094 0.33 3 -0.39 24 27
GSK3B 0.021 0.011 -10000 0 -10000 0 0
NR2C1 0.025 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.06 0.23 1 -0.36 23 24
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.026 0.017 -10000 0 -10000 0 0
POU2F1 0.009 0.051 -10000 0 -0.2 2 2
T-DHT/AR/DAX-1 -0.014 0.098 0.32 5 -0.39 25 30
CREBBP 0.022 0.007 -10000 0 -10000 0 0
SMARCE1 0.017 0.019 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.048 0.17 -10000 0 -0.32 254 254
TC10/GTP -0.038 0.14 -10000 0 -0.29 239 239
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.08 -10000 0 -0.34 39 39
HRAS 0.026 0.021 0.26 8 -10000 0 8
APS homodimer 0.034 0.048 0.26 44 -10000 0 44
GRB14 0.013 0.18 0.26 139 -0.58 73 212
FOXO3 -0.02 0.16 -10000 0 -0.59 69 69
AKT1 -0.018 0.11 0.33 7 -0.29 83 90
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.056 0.047 0.43 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 -0.58 246 246
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.024 -10000 0 -10000 0 0
CAV1 -0.084 0.15 -10000 0 -0.35 223 223
CBL/APS/CAP/Crk-II/C3G -0.027 0.16 -10000 0 -0.31 242 242
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.079 -10000 0 -0.34 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.074 -10000 0 -0.3 44 44
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.066 -10000 0 -0.41 8 8
RPS6KB1 -0.018 0.097 0.33 6 -0.48 1 7
PARD6A 0.023 0.02 0.26 6 -10000 0 6
CBL 0.022 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.039 -10000 0 -0.55 4 4
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.008 0.094 -10000 0 -0.29 19 19
HRAS/GTP -0.02 0.045 -10000 0 -0.28 23 23
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.072 -10000 0 -0.33 26 26
PRKCI 0.014 0.057 -10000 0 -0.46 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.004 0.1 -10000 0 -0.3 105 105
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.036 -10000 0 -0.46 4 4
PI3K 0.038 0.078 -10000 0 -0.31 44 44
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.015 0.18 8 -10000 0 8
AKT2 -0.018 0.11 0.31 7 -0.29 86 93
PRKCZ 0.005 0.084 -10000 0 -0.49 14 14
SH2B2 0.034 0.048 0.26 44 -10000 0 44
SHC/SHIP 0.012 0.059 -10000 0 -0.31 28 28
F2RL2 0.046 0.12 0.26 143 -0.58 18 161
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.034 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.037 0.17 -10000 0 -0.33 245 245
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.049 0.028 -10000 0 -10000 0 0
INPP5D -0.019 0.063 -10000 0 -0.32 39 39
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.019 0.14 -10000 0 -0.68 44 44
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.58 40 40
p62DOK/RasGAP 0.042 0.036 -10000 0 -0.47 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.063 -10000 0 -0.32 39 39
GRB2 0.023 0.01 0.26 1 -10000 0 1
EIF4EBP1 -0.021 0.091 0.31 3 -0.48 1 4
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 0.023 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.008 0.055 -10000 0 -0.28 28 28
Insulin Receptor/Insulin/IRS1 0.029 0.076 -10000 0 -0.34 40 40
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.06 0.073 -10000 0 -0.32 18 18
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.054 0.2 0.32 1 -0.52 61 62
MAP3K8 0.01 0.049 -10000 0 -0.58 6 6
FOS -0.019 0.14 0.32 2 -0.46 43 45
PRKCA -0.002 0.087 0.24 1 -0.58 21 22
PTPN7 0.021 0.059 0.26 38 -10000 0 38
HRAS 0.024 0.022 0.26 8 -10000 0 8
PRKCB 0.006 0.08 0.25 18 -0.58 14 32
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.036 -10000 0 -10000 0 0
MAPK3 0.008 0.091 -10000 0 -0.8 5 5
MAP2K1 -0.011 0.12 -10000 0 -0.51 40 40
ELK1 0.007 0.029 -10000 0 -10000 0 0
BRAF -0.012 0.099 -10000 0 -0.49 36 36
mol:GTP -0.002 0.003 -10000 0 -0.006 301 301
MAPK1 -0.007 0.12 -10000 0 -0.55 24 24
RAF1 -0.011 0.098 -10000 0 -0.48 36 36
KRAS 0.023 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.042 -10000 0 -0.57 1 1
SVIL 0.009 0.051 -10000 0 -0.58 4 4
ZNF318 0.041 0.056 0.21 8 -10000 0 8
JMJD2C -0.001 0.042 0.11 27 -0.13 75 102
T-DHT/AR/Ubc9 -0.031 0.14 -10000 0 -0.38 127 127
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 0.013 0.031 -10000 0 -10000 0 0
AKT1 0.028 0.019 -10000 0 -10000 0 0
PTK2B 0.011 0.027 -10000 0 -10000 0 0
MED1 0.026 0.021 -10000 0 -10000 0 0
MAK 0.036 0.089 0.29 10 -0.56 12 22
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.008 0.055 -10000 0 -0.58 5 5
GSN 0.004 0.074 -10000 0 -0.58 12 12
NCOA2 -0.008 0.12 -10000 0 -0.58 41 41
NCOA6 0.012 0.034 -10000 0 -10000 0 0
DNA-PK 0.052 0.055 0.24 1 -10000 0 1
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.011 0.028 -10000 0 -10000 0 0
cell proliferation 0.005 0.12 0.36 2 -0.59 25 27
XRCC5 0.027 0.016 -10000 0 -10000 0 0
UBE3A 0.007 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.039 0.16 -10000 0 -0.38 147 147
FHL2 0.004 0.12 -10000 0 -0.71 12 12
RANBP9 0.012 0.034 -10000 0 -10000 0 0
JMJD1A -0.01 0.055 0.12 36 -0.14 133 169
CDK6 0.021 0.051 0.26 2 -0.58 7 9
TGFB1I1 0.009 0.048 -10000 0 -0.58 3 3
T-DHT/AR/CyclinD1 -0.04 0.14 0.19 1 -0.37 139 140
XRCC6 0.026 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.035 0.17 0.31 1 -0.38 149 150
CTDSP1 0.017 0.02 -10000 0 -10000 0 0
CTDSP2 0.035 0.038 -10000 0 -10000 0 0
BRCA1 0.011 0.04 -10000 0 -0.57 1 1
TCF4 0.027 0.061 -10000 0 -0.57 8 8
CDKN2A 0.065 0.091 0.27 163 -10000 0 163
SRF 0.033 0.023 -10000 0 -0.15 2 2
NKX3-1 -0.057 0.2 0.37 2 -0.69 55 57
KLK3 -0.16 0.48 -10000 0 -1.4 134 134
TMF1 0.018 0.017 -10000 0 -10000 0 0
HNRNPA1 0.029 0.021 -10000 0 -10000 0 0
AOF2 -0.008 0.024 -10000 0 -0.069 134 134
APPL1 0.02 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.024 0.15 -10000 0 -0.36 141 141
AR -0.064 0.2 0.21 1 -0.59 126 127
UBA3 0.016 0.02 -10000 0 -10000 0 0
PATZ1 0.028 0.021 -10000 0 -10000 0 0
PAWR 0.017 0.025 -10000 0 -0.58 1 1
PRKDC 0.024 0.017 -10000 0 -10000 0 0
PA2G4 0.032 0.028 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.02 0.13 -10000 0 -0.34 120 120
RPS6KA3 0.006 0.062 -10000 0 -0.58 7 7
T-DHT/AR/ARA70 -0.035 0.14 -10000 0 -0.36 139 139
LATS2 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.017 0.14 0.19 7 -0.33 137 144
Cyclin D3/CDK11 p58 0.019 0.006 -10000 0 -10000 0 0
VAV3 0.013 0.066 0.26 16 -0.58 7 23
KLK2 -0.076 0.28 0.34 3 -0.98 80 83
CASP8 0.027 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.038 0.15 -10000 0 -0.37 136 136
TMPRSS2 -0.13 0.34 -10000 0 -0.99 132 132
CCND1 0.011 0.044 0.26 1 -0.58 4 5
PIAS1 0.008 0.046 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.031 0.067 2 -0.072 167 169
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.001 0.066 -10000 0 -0.21 5 5
T-DHT/AR/CDK6 -0.031 0.15 -10000 0 -0.36 145 145
CMTM2 0.023 0.013 0.26 1 -10000 0 1
SNURF 0.012 0.081 -10000 0 -0.58 19 19
ZMIZ1 0.01 0.042 -10000 0 -0.15 2 2
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.021 -10000 0 -10000 0 0
FKBP4 0.013 0.038 0.26 4 -10000 0 4
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.025 0.27 2 -0.55 1 3
CDKN2C 0.014 0.029 -10000 0 -0.56 1 1
CDKN2A 0.061 0.087 0.26 163 -10000 0 163
CCND2 -0.016 0.037 0.2 2 -0.2 16 18
RB1 0.016 0.048 0.25 16 -0.24 8 24
CDK4 -0.017 0.038 0.21 2 -0.23 11 13
CDK6 -0.018 0.041 0.22 2 -0.2 21 23
G1/S progression -0.01 0.059 0.19 40 -0.26 15 55
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 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.012 0.08 0.26 1 -0.58 18 19
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.093 0.12 -10000 0 -0.24 397 397
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 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 0.027 -10000 0 -0.58 2 2
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.04 0.097 -10000 0 -0.34 72 72
PRKG1 -0.014 0.15 -10000 0 -0.58 64 64
DUSP8 0.022 0.033 -10000 0 -0.58 3 3
PGK/cGMP/p38 alpha -0.019 0.13 -10000 0 -0.34 98 98
apoptosis -0.038 0.093 -10000 0 -0.33 69 69
RAL/GTP 0.032 0.006 -10000 0 -10000 0 0
LYN 0.021 0.009 -10000 0 -10000 0 0
DUSP1 -0.045 0.19 -10000 0 -0.58 117 117
PAK1 0.023 0.021 0.26 7 -10000 0 7
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.053 0.024 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.008 0.26 1 -10000 0 1
RAC1-CDC42/GTP 0.031 0.008 -10000 0 -10000 0 0
MAPK11 -0.009 0.13 0.28 6 -0.37 62 68
BLK 0.05 0.087 0.26 135 -0.58 2 137
HCK 0.027 0.026 0.26 12 -10000 0 12
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.014 0.26 2 -10000 0 2
TRAF6/MEKK3 0.028 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.13 0.28 5 -0.38 65 70
positive regulation of innate immune response -0.011 0.15 0.33 5 -0.45 60 65
LCK 0.026 0.077 0.26 36 -0.58 11 47
p38alpha-beta/MKP7 -0.002 0.14 0.33 5 -0.44 53 58
p38alpha-beta/MKP5 -0.003 0.14 0.37 3 -0.45 49 52
PGK/cGMP -0.01 0.11 -10000 0 -0.42 64 64
PAK2 0.024 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.033 0.17 0.34 4 -0.44 88 92
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.24 0.3 -10000 0 -0.58 457 457
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 0.13 0.45 11 -0.52 2 13
RAD9A 0.023 0.006 -10000 0 -10000 0 0
AP1 -0.094 0.21 -10000 0 -0.42 297 297
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 -0.004 0.09 -10000 0 -0.36 13 13
ER alpha/Oestrogen -0.027 0.17 0.18 111 -0.41 150 261
NFX1/SIN3/HDAC complex 0.023 0.059 0.24 1 -0.33 15 16
EGF -0.081 0.23 0.26 2 -0.57 182 184
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.054 0.12 0.41 4 -0.45 4 8
SAP18 0.024 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.022 -10000 0 -10000 0 0
WT1 0.14 0.12 0.26 500 -10000 0 500
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.005 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.05 0.1 -10000 0 -0.46 2 2
Mad/Max 0.041 0.014 -10000 0 -10000 0 0
TERT 0.058 0.13 0.46 11 -0.53 2 13
CCND1 0.08 0.16 0.48 36 -1 4 40
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.02 0.26 7 -10000 0 7
RBBP4 0.024 0.019 -10000 0 -0.57 1 1
TERF2 0.021 0.014 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.039 0.051 -10000 0 -0.4 4 4
CDKN1B 0.029 0.051 0.23 1 -0.68 3 4
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.016 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.022 0.046 -10000 0 -0.57 6 6
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 285 285
IFN-gamma/IRF1 0.065 0.065 0.24 32 -0.32 3 35
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.046 0.069 0.26 96 -10000 0 96
Telomerase 0.028 0.08 -10000 0 -0.65 5 5
IRF1 0.029 0.019 0.27 3 -0.19 3 6
ESR1 -0.035 0.23 0.26 111 -0.57 144 255
KU/TER 0.034 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.056 0.24 1 -0.33 9 10
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.057 0.24 1 -0.34 9 10
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.012 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.013 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.009 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.059 0.13 0.46 2 -0.57 6 8
NR2F2 0.012 0.038 -10000 0 -0.58 3 3
MAPK3 0.006 0.02 -10000 0 -10000 0 0
MAPK1 0.006 0.02 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.022 0.011 0.25 1 -10000 0 1
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.016 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.57 363 363
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.2 0.26 -10000 0 -0.46 493 493
MYC 0.008 0.085 -10000 0 -0.57 21 21
IL2 0.029 0.025 0.26 8 -10000 0 8
KU 0.034 0.009 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.022 0.011 0.25 1 -10000 0 1
TRF2/BLM 0.044 0.047 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.068 0.12 0.43 7 -0.5 2 9
SP1/HDAC2 0.046 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.047 0.099 -10000 0 -0.46 2 2
Smad3/Myc 0.006 0.056 -10000 0 -0.37 20 20
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.059 0.084 0.26 142 -0.19 3 145
Telomerase/PinX1 0.039 0.096 -10000 0 -0.45 2 2
Telomerase/AKT1/mTOR/p70S6K 0.026 0.1 0.31 3 -0.58 14 17
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.044 0.094 -10000 0 -0.42 1 1
response to DNA damage stimulus -0.002 0.028 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.034 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.05 0.1 -10000 0 -0.46 2 2
E2F1 0.099 0.11 0.27 305 -10000 0 305
ZNFX1 0.024 0.006 -10000 0 -10000 0 0
PIF1 0.068 0.092 0.26 192 -10000 0 192
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.011 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.025 0.011 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 -0.013 0.12 0.46 7 -0.52 3 10
IL27/IL27R/JAK1 0.038 0.16 0.69 5 -0.58 10 15
TBX21 -0.001 0.17 0.45 18 -0.51 44 62
IL12B 0.075 0.099 0.27 212 -10000 0 212
IL12A -0.015 0.1 0.14 17 -0.42 58 75
IL6ST -0.038 0.18 0.2 1 -0.57 106 107
IL27RA/JAK1 0.022 0.07 0.65 1 -1.2 2 3
IL27 0.047 0.075 0.27 99 -10000 0 99
TYK2 0.03 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.098 0.16 0.75 2 -0.52 11 13
T-helper 2 cell differentiation -0.013 0.12 0.46 7 -0.52 3 10
T cell proliferation during immune response -0.013 0.12 0.46 7 -0.52 3 10
MAPKKK cascade 0.013 0.12 0.52 3 -0.46 7 10
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.034 0.26 19 -10000 0 19
IL12RB1 0.034 0.055 0.27 40 -0.58 2 42
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.008 0.19 0.45 36 -0.53 51 87
IL27/IL27R/JAK2/TYK2 0.013 0.12 0.52 3 -0.47 7 10
positive regulation of T cell mediated cytotoxicity 0.013 0.12 0.52 3 -0.46 7 10
STAT1 (dimer) 0.035 0.2 0.65 22 -0.66 16 38
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.025 0.12 0.45 3 -0.45 7 10
T cell proliferation -0.093 0.19 0.36 3 -0.46 81 84
IL12/IL12R/TYK2/JAK2 0.058 0.18 0.46 3 -0.73 26 29
IL17A -0.098 0.16 0.75 2 -0.52 11 13
mast cell activation -0.013 0.12 0.46 7 -0.52 3 10
IFNG 0.021 0.046 0.12 122 -0.097 9 131
T cell differentiation 0 0.006 0.025 3 -0.02 5 8
STAT3 (dimer) 0.023 0.11 0.45 3 -0.45 7 10
STAT5A (dimer) 0.021 0.12 0.45 3 -0.45 13 16
STAT4 (dimer) 0.012 0.14 0.45 3 -0.45 22 25
STAT4 0.001 0.12 0.26 1 -0.58 40 41
T cell activation -0.005 0.011 0.12 2 -0.11 6 8
IL27R/JAK2/TYK2 0.019 0.13 -10000 0 -1.1 2 2
GATA3 -0.024 0.27 0.62 35 -1.3 33 68
IL18 0.009 0.02 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production 0.023 0.11 0.44 3 -0.44 7 10
IL27/EBI3 0.051 0.072 0.25 51 -0.39 6 57
IL27RA 0.01 0.072 0.74 1 -1.3 2 3
IL6 -0.19 0.29 0.26 1 -0.58 360 361
STAT5A 0.02 0.046 -10000 0 -0.58 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.015 0.039 0.45 2 -0.52 1 3
IL1B 0.001 0.051 0.14 3 -0.42 14 17
EBI3 0.024 0.055 0.26 11 -0.58 6 17
TNF 0.005 0.047 0.14 24 -0.42 10 34
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.017 0.17 0.3 3 -0.4 141 144
AKT1 0.025 0.01 -10000 0 -10000 0 0
GSC -0.031 0.27 -10000 0 -1.3 40 40
NKX2-5 0.056 0.084 0.26 148 -10000 0 148
muscle cell differentiation -0.028 0.063 0.35 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.065 0.067 -10000 0 -0.44 1 1
SMAD4 0.012 0.045 -10000 0 -10000 0 0
CBFB 0.022 0.008 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.11 0.2 0.27 1 -0.36 378 379
SMAD3/SMAD4/VDR 0.054 0.059 -10000 0 -0.34 1 1
MYC 0.005 0.085 -10000 0 -0.58 21 21
CDKN2B -0.045 0.18 -10000 0 -0.97 18 18
AP1 -0.051 0.16 -10000 0 -0.31 258 258
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.009 0.088 -10000 0 -0.36 31 31
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.013 0.058 -10000 0 -0.34 11 11
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.045 0.081 0.26 114 -10000 0 114
SMAD3/SMAD4/GR 0.024 0.071 -10000 0 -0.39 9 9
GATA3 0.013 0.11 0.26 27 -0.57 33 60
SKI/SIN3/HDAC complex/NCoR1 0.005 0.078 -10000 0 -0.35 34 34
MEF2C/TIF2 0.027 0.089 0.31 3 -0.32 14 17
endothelial cell migration -0.03 0.085 0.58 3 -10000 0 3
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.02 0.26 7 -10000 0 7
RBBP4 0.023 0.019 -10000 0 -0.58 1 1
RUNX2 0.027 0.027 0.26 13 -10000 0 13
RUNX3 0.022 0.04 0.26 3 -0.58 4 7
RUNX1 0.023 0.019 -10000 0 -0.58 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.015 0.058 -10000 0 -0.58 9 9
VDR 0.024 0.003 -10000 0 -10000 0 0
CDKN1A 0.015 0.08 -10000 0 -1.1 3 3
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.055 0.079 -10000 0 -0.26 24 24
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.03 0.086 -10000 0 -0.59 3 3
SMAD3/SMAD4/ATF2 0.033 0.059 -10000 0 -0.4 2 2
SMAD3/SMAD4/ATF3 -0.014 0.14 -10000 0 -0.4 108 108
SAP30 0.024 0.016 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.041 0.031 -10000 0 -10000 0 0
JUN -0.06 0.15 0.29 1 -0.3 256 257
SMAD3/SMAD4/IRF7 0.051 0.08 0.33 20 -10000 0 20
TFE3 0.029 0.009 -10000 0 -0.2 1 1
COL1A2 0.046 0.09 0.4 2 -0.6 6 8
mesenchymal cell differentiation -0.034 0.059 -10000 0 -0.34 1 1
DLX1 0.05 0.12 0.26 156 -0.58 17 173
TCF3 0.024 0.009 0.26 1 -10000 0 1
FOS -0.14 0.27 -10000 0 -0.58 286 286
SMAD3/SMAD4/Max 0.028 0.058 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.044 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.013 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.033 0.055 -10000 0 -10000 0 0
IRF7 0.047 0.07 0.27 89 -10000 0 89
ESR1 -0.041 0.23 0.26 111 -0.58 144 255
HNF4A 0.023 0.03 0.26 16 -10000 0 16
MEF2C 0.054 0.091 0.4 11 -0.44 2 13
SMAD2-3/SMAD4 0.034 0.065 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.37 1 1
IGHV3OR16-13 0.006 0.04 -10000 0 -0.34 12 12
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.024 0.26 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.005 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.042 0.061 -10000 0 -0.46 1 1
MSG1/HSC70 -0.15 0.23 -10000 0 -0.42 400 400
SMAD2 0.022 0.03 -10000 0 -10000 0 0
SMAD3 0.014 0.04 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.04 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.059 0.25 10 -0.51 3 13
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 -0.004 0.12 -10000 0 -0.58 41 41
NCOA1 0.024 0.019 -10000 0 -0.58 1 1
MYOD/E2A 0.032 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.064 -10000 0 -0.41 1 1
IFNB1 0.021 0.071 0.33 22 -10000 0 22
SMAD3/SMAD4/MEF2C 0.071 0.086 0.35 1 -0.42 2 3
CITED1 -0.21 0.3 0.26 15 -0.58 400 415
SMAD2-3/SMAD4/ARC105 0.041 0.066 -10000 0 -10000 0 0
RBL1 0.023 0.021 0.26 1 -0.58 1 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.066 -10000 0 -0.48 9 9
RUNX1-3/PEBPB2 0.04 0.038 -10000 0 -0.45 4 4
SMAD7 -0.032 0.14 -10000 0 -0.45 18 18
MYC/MIZ-1 0.015 0.066 -10000 0 -0.43 21 21
SMAD3/SMAD4 0.033 0.073 0.3 22 -0.34 3 25
IL10 0.006 0.081 0.34 2 -0.37 28 30
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.021 0.01 -10000 0 -10000 0 0
CDK2 0.025 0.008 -10000 0 -10000 0 0
IL5 0.003 0.083 0.37 1 -0.36 32 33
CDK4 0.025 0.008 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.044 0.18 0.26 1 -0.58 109 110
SMAD3/SMAD4/SP1 0.046 0.064 -10000 0 -0.49 1 1
FOXG1 0.017 0.068 0.26 68 -10000 0 68
FOXO3 0.011 0.018 -10000 0 -0.43 1 1
FOXO1 0.009 0.029 -10000 0 -0.43 4 4
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.053 0.09 0.4 11 -0.44 2 13
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.05 0.098 0.3 3 -0.4 16 19
MYOD1 0.021 0.028 0.26 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.033 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.029 0.1 0.35 1 -0.4 34 35
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.024 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.069 -10000 0 -0.44 3 3
SMAD3/SMAD4/SP1-3 0.061 0.064 -10000 0 -0.44 1 1
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.031 0.014 -10000 0 -0.2 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.08 0.094 0.34 21 -0.39 1 22
ITGB5 0.016 0.043 -10000 0 -0.4 1 1
TGIF/SIN3/HDAC complex/CtBP 0.012 0.063 -10000 0 -0.3 24 24
SMAD3/SMAD4/AR -0.017 0.15 -10000 0 -0.4 123 123
AR -0.05 0.2 0.26 1 -0.58 126 127
negative regulation of cell growth 0 0.083 -10000 0 -0.38 8 8
SMAD3/SMAD4/MYOD 0.032 0.058 -10000 0 -10000 0 0
E2F5 0.022 0.022 0.26 7 -10000 0 7
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.068 0.074 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.055 -10000 0 -0.37 11 11
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.035 0.17 -10000 0 -0.31 258 258
SMAD3/SMAD4/RUNX2 0.035 0.059 0.34 1 -10000 0 1
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.023 0.027 -10000 0 -0.58 2 2
Thromboxane A2 receptor signaling

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.027 0.028 0.26 14 -10000 0 14
GNB1/GNG2 -0.016 0.048 -10000 0 -0.19 61 61
AKT1 0.023 0.092 0.36 10 -0.3 19 29
EGF -0.083 0.23 0.26 2 -0.58 182 184
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.058 0.25 2 -0.33 3 5
mol:Ca2+ 0.022 0.11 0.39 12 -0.31 63 75
LYN 0.012 0.054 0.25 2 -0.4 1 3
RhoA/GTP 0.009 0.045 0.14 3 -0.14 8 11
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.019 0.12 0.45 9 -0.35 60 69
GNG2 0.018 0.059 -10000 0 -0.58 10 10
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.59 35 35
G beta5/gamma2 -0.012 0.067 -10000 0 -0.26 61 61
PRKCH 0.018 0.12 0.43 9 -0.36 60 69
DNM1 0.02 0.05 0.26 1 -0.58 7 8
TXA2/TP beta/beta Arrestin3 0.008 0.032 -10000 0 -0.4 2 2
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.008 0.1 0.26 7 -0.58 29 36
G12 family/GTP 0 0.09 -10000 0 -0.31 57 57
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.021 0.038 -10000 0 -0.58 4 4
RhoA/GTP/ROCK1 0.031 0.015 -10000 0 -0.36 1 1
mol:GDP -0.012 0.099 0.36 31 -0.34 7 38
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 -0.014 0.15 -10000 0 -0.58 64 64
mol:IP3 0.019 0.14 0.45 9 -0.38 66 75
cell morphogenesis 0.031 0.015 -10000 0 -0.36 1 1
PLCB2 0.011 0.17 0.55 6 -0.52 69 75
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.025 0.07 0.25 6 -0.32 3 9
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.059 0.26 3 -0.35 2 5
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.027 0.026 0.26 12 -10000 0 12
PRKCB1 0.018 0.13 0.44 9 -0.38 62 71
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.014 0.17 0.56 6 -0.53 62 68
LCK 0.016 0.073 0.25 2 -0.39 11 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.33 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.007 0.1 -10000 0 -0.42 47 47
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.31 1 1
MAPK14 0.018 0.089 0.33 15 -0.23 53 68
TGM2/GTP 0.015 0.15 0.5 8 -0.44 55 63
MAPK11 0.017 0.09 0.34 15 -0.24 49 64
ARHGEF1 0.011 0.066 0.27 9 -0.19 31 40
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.02 0.13 0.46 9 -0.39 60 69
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.022 0.1 0.4 11 -0.28 56 67
cAMP biosynthetic process 0.016 0.13 0.43 9 -0.36 61 70
Gq family/GTP/EBP50 0.015 0.043 0.22 4 -0.22 15 19
actin cytoskeleton reorganization 0.031 0.015 -10000 0 -0.36 1 1
SRC 0.013 0.057 0.25 2 -0.35 2 4
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.047 0.1 0.26 2 -0.29 64 66
VCAM1 0.02 0.11 0.4 10 -0.32 58 68
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.59 35 35
platelet activation 0.023 0.12 0.42 13 -0.31 56 69
PGI2/IP 0.02 0.017 0.18 12 -10000 0 12
PRKACA 0.009 0.053 -10000 0 -0.28 29 29
Gq family/GDP/G beta5/gamma2 0 0.1 -10000 0 -0.5 28 28
TXA2/TP beta/beta Arrestin2 -0.006 0.067 -10000 0 -0.44 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.047 -10000 0 -0.27 27 27
mol:DAG 0.018 0.14 0.48 8 -0.43 63 71
EGFR -0.19 0.29 -10000 0 -0.58 363 363
TXA2/TP alpha 0.015 0.16 0.52 7 -0.5 63 70
Gq family/GTP 0.002 0.049 0.25 1 -0.24 25 26
YES1 0.014 0.059 0.25 2 -0.32 3 5
GNAI2/GTP 0.014 0.051 -10000 0 -0.32 5 5
PGD2/DP 0.006 0.076 0.18 7 -0.4 32 39
SLC9A3R1 0.035 0.053 0.26 52 -10000 0 52
FYN 0.012 0.058 0.26 1 -0.37 4 5
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.025 0.026 0.26 6 -0.58 1 7
PGK/cGMP 0.007 0.097 -10000 0 -0.36 64 64
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.035 0.069 -10000 0 -0.4 11 11
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.021 0.13 0.43 10 -0.39 55 65
PRKCB 0.021 0.13 0.42 10 -0.37 60 70
PRKCE 0.018 0.12 0.44 9 -0.36 58 67
PRKCD 0.017 0.13 0.45 8 -0.39 59 67
PRKCG 0.019 0.13 0.47 8 -0.39 59 67
muscle contraction 0.015 0.16 0.53 7 -0.5 62 69
PRKCZ 0.018 0.12 0.43 9 -0.35 59 68
ARR3 0.021 0.021 0.26 8 -10000 0 8
TXA2/TP beta 0.025 0.058 -10000 0 -0.29 16 16
PRKCQ 0.015 0.14 0.42 12 -0.4 62 74
MAPKKK cascade 0.014 0.15 0.52 6 -0.47 64 70
SELE 0.016 0.12 0.38 12 -0.4 56 68
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.069 -10000 0 -0.42 11 11
ROCK1 0.023 0.019 -10000 0 -0.58 1 1
GNA14 0.023 0.068 0.26 19 -0.58 10 29
chemotaxis 0.013 0.18 0.59 6 -0.61 59 65
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.027 -10000 0 -0.58 2 2
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.02 -10000 0 -0.58 1 1
ELF1 0.03 0.052 -10000 0 -0.36 10 10
CCNA2 0.11 0.12 0.26 387 -10000 0 387
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.028 0.26 14 -10000 0 14
PIK3R1 0.019 0.056 -10000 0 -0.58 9 9
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.045 0.1 0.31 17 -0.52 12 29
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.024 0.046 -10000 0 -0.39 12 12
IL2RA 0.02 0.11 0.29 59 -0.76 13 72
IL2RB 0.031 0.052 0.26 37 -0.58 2 39
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.07 0.26 45 -0.58 7 52
G1/S transition of mitotic cell cycle 0.044 0.14 0.33 5 -0.83 16 21
PTPN11 0.025 0.003 -10000 0 -10000 0 0
CCND2 0.005 0.09 0.35 2 -0.8 12 14
LCK 0.026 0.077 0.26 36 -0.58 11 47
GRB2 0.024 0.01 0.26 1 -10000 0 1
IL2 0.023 0.022 0.26 8 -10000 0 8
CDK6 0.02 0.051 0.26 2 -0.58 7 9
CCND3 0.046 0.1 0.44 4 -0.58 5 9
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.022 0.13 0.33 10 -0.39 39 49
IKBKB 0.023 0.089 0.3 9 -0.31 13 22
AKT1 0.039 0.11 0.28 64 -0.24 19 83
IKBKG 0.027 0.074 0.35 4 -0.31 5 9
CALM1 0.001 0.097 0.26 1 -0.42 21 22
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.022 0.16 0.38 10 -0.52 44 54
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.1 -10000 0 -0.36 44 44
DOK1 0.025 0.015 0.26 4 -10000 0 4
AP-1 -0.022 0.099 0.28 4 -0.25 51 55
LYN 0.021 0.009 -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 0.003 0.16 0.37 18 -0.45 91 109
CD22 -0.013 0.14 0.28 20 -0.46 59 79
CAMK2G 0.002 0.096 0.3 1 -0.42 18 19
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.001 0.088 -10000 0 -0.33 53 53
GO:0007205 0.001 0.1 -10000 0 -0.36 45 45
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0.001 0.1 0.26 1 -0.44 20 21
NFATC1 0.03 0.13 0.3 25 -0.44 35 60
B-cell antigen/BCR complex 0.003 0.16 0.37 18 -0.45 91 109
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.023 0.049 0.17 10 -0.13 28 38
HRAS 0.011 0.11 0.26 13 -0.36 37 50
NFKBIA 0.023 0.048 0.17 10 -0.12 17 27
NF-kappa-B/RelA/I kappa B beta 0.027 0.043 0.18 9 -10000 0 9
RasGAP/Csk 0.03 0.12 0.33 19 -0.36 66 85
mol:GDP 0.003 0.1 -10000 0 -0.35 39 39
PTEN 0.023 0.02 -10000 0 -0.58 1 1
CD79B 0.011 0.1 0.26 18 -0.58 26 44
NF-kappa-B/RelA/I kappa B alpha 0.027 0.042 0.17 10 -10000 0 10
GRB2 0.023 0.01 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.022 0.16 0.35 11 -0.5 49 60
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
mol:IP3 0.002 0.1 -10000 0 -0.37 44 44
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.078 0.16 -10000 0 -0.44 80 80
CHUK 0.024 0.082 0.32 5 -0.32 16 21
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.018 0.096 -10000 0 -0.41 18 18
PTPN6 -0.015 0.13 0.26 19 -0.57 32 51
RELA 0.024 0.005 -10000 0 -10000 0 0
BCL2A1 0.024 0.036 0.19 6 -10000 0 6
VAV2 0.013 0.14 0.3 7 -0.58 30 37
ubiquitin-dependent protein catabolic process 0.025 0.048 0.17 10 -0.12 24 34
BTK 0.015 0.063 -10000 0 -0.97 4 4
CD19 0.004 0.14 0.27 33 -0.44 60 93
MAP4K1 0.032 0.053 0.26 40 -0.58 2 42
CD72 0.03 0.043 0.26 28 -0.58 1 29
PAG1 0.021 0.014 0.26 2 -10000 0 2
MAPK14 0.024 0.14 0.36 12 -0.45 41 53
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0.003 0.11 -10000 0 -0.39 42 42
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.14 0.27 3 -0.42 73 76
RAF1 0.01 0.1 0.28 6 -0.42 18 24
RasGAP/p62DOK/SHIP 0.03 0.12 0.3 18 -0.36 66 84
CD79A -0.005 0.17 0.26 71 -0.58 77 148
re-entry into mitotic cell cycle -0.022 0.098 0.28 4 -0.25 48 52
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.017 0.098 0.28 20 -0.37 14 34
MAPK1 0.01 0.091 0.3 3 -0.36 17 20
CD72/SHP1 0.028 0.15 0.37 23 -0.55 31 54
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.022 0.15 0.36 14 -0.45 44 58
actin cytoskeleton organization 0.03 0.14 0.32 20 -0.51 28 48
NF-kappa-B/RelA 0.055 0.082 0.3 10 -0.21 1 11
Calcineurin 0.018 0.092 -10000 0 -0.4 16 16
PI3K -0.014 0.097 -10000 0 -0.45 27 27
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.005 0.11 -10000 0 -0.4 49 49
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.011 0.2 0.4 15 -0.69 53 68
DAPP1 -0.019 0.21 -10000 0 -0.77 54 54
cytokine secretion 0.03 0.13 0.28 30 -0.41 35 65
mol:DAG 0.002 0.1 -10000 0 -0.37 44 44
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
MAP2K1 0.01 0.098 0.28 7 -0.4 17 24
B-cell antigen/BCR complex/FcgammaRIIB 0.014 0.13 0.34 18 -0.42 66 84
mol:PI-3-4-5-P3 0.005 0.091 0.22 15 -0.33 23 38
ETS1 0 0.09 0.28 1 -0.4 19 20
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.033 0.13 0.33 19 -0.36 70 89
B-cell antigen/BCR complex/LYN -0.012 0.14 0.3 5 -0.46 65 70
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.14 0.32 16 -0.55 28 44
B-cell antigen/BCR complex/LYN/SYK 0.013 0.14 0.35 21 -0.45 57 78
CARD11 0.003 0.1 0.28 3 -0.45 21 24
FCGR2B 0.018 0.039 0.26 1 -0.58 4 5
PPP3CA 0.024 0.011 0.26 2 -10000 0 2
BCL10 0.024 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 44 -0.14 4 48
PTPRC 0.021 0.042 0.26 12 -0.58 3 15
PDPK1 0.019 0.082 0.24 35 -0.23 19 54
PPP3CB 0.024 0.003 -10000 0 -10000 0 0
PPP3CC 0.02 0.01 -10000 0 -10000 0 0
POU2F2 0.021 0.034 0.21 6 -10000 0 6
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 0.043 0.075 0.3 2 -0.31 27 29
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.085 0.35 12 -0.34 2 14
alphaV/beta3 Integrin/Osteopontin/Src 0.082 0.073 0.24 2 -10000 0 2
AP1 -0.037 0.18 -10000 0 -0.56 30 30
ILK 0.03 0.077 0.3 1 -0.33 27 28
bone resorption 0.019 0.088 0.27 1 -0.49 11 12
PTK2B 0.02 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.067 0.094 0.31 8 -0.3 24 32
ITGAV 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.023 0.074 -10000 0 -0.42 27 27
alphaV/beta3 Integrin/Osteopontin 0.078 0.1 0.34 4 -0.35 32 36
MAP3K1 0.029 0.08 0.26 14 -0.33 32 46
JUN 0.02 0.046 -10000 0 -0.58 6 6
MAPK3 0.02 0.072 0.28 12 -0.31 24 36
MAPK1 0.021 0.073 0.27 13 -0.31 25 38
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.016 0.085 0.26 16 -0.37 28 44
ITGB3 0.008 0.11 0.27 4 -0.57 32 36
NFKBIA 0.018 0.071 0.31 6 -0.35 4 10
FOS -0.14 0.27 -10000 0 -0.58 285 285
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.022 0.1 0.46 7 -0.55 2 9
NF kappa B1 p50/RelA 0.064 0.079 0.36 6 -10000 0 6
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.082 0.24 1 -0.42 32 33
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.03 0.077 0.26 14 -0.32 32 46
VAV3 0.016 0.077 0.26 16 -0.31 30 46
MAP3K14 0.031 0.078 0.27 11 -0.32 32 43
ROCK2 0.008 0.096 -10000 0 -0.58 27 27
SPP1 0.088 0.1 0.26 267 -10000 0 267
RAC1 0.024 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.072 0.3 3 -0.29 27 30
MMP2 -0.054 0.15 0.35 3 -0.51 30 33
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 0.026 0.048 0.14 163 -10000 0 163
TP53 0.01 0.018 -10000 0 -0.19 2 2
Senescence 0.009 0.022 -10000 0 -0.19 2 2
Apoptosis 0.009 0.022 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.011 0.06 0.29 29 -10000 0 29
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 -0.27 0.3 -10000 0 -0.58 488 488
CLTC 0.025 0.067 0.24 8 -0.43 12 20
calcium ion-dependent exocytosis 0.009 0.025 -10000 0 -0.26 2 2
Dynamin 2/GTP 0.022 0.013 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.016 0.046 -10000 0 -0.34 10 10
CPE 0.005 0.05 -10000 0 -0.36 18 18
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.019 -10000 0 -0.17 5 5
CTNND1 0.007 0.056 0.19 84 -10000 0 84
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.044 0.2 4 -0.32 8 12
TSHR -0.003 0.073 0.14 4 -0.37 39 43
INS -0.002 0.091 -10000 0 -0.48 34 34
BIN1 0.019 0.053 -10000 0 -0.58 8 8
mol:Choline 0.011 0.019 -10000 0 -0.17 5 5
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.016 0.14 14 -10000 0 14
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.013 -10000 0 -10000 0 0
JUP 0.016 0.039 0.23 1 -0.33 7 8
ASAP2/amphiphysin II 0.042 0.035 -10000 0 -0.34 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.056 -10000 0 -0.26 28 28
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.028 0.26 14 -10000 0 14
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 -0.037 0.065 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 0.028 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.013 0.044 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.024 0.063 0.24 13 -0.35 12 25
JIP4/KLC1 0.041 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.019 0.034 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.008 0.057 0.19 87 -10000 0 87
NME1 0.013 0.016 0.14 14 -10000 0 14
clathrin coat assembly 0.027 0.07 0.24 10 -0.42 12 22
IL2RA 0.019 0.055 -10000 0 -0.31 14 14
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.27 404 404
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.029 -10000 0 -0.3 8 8
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.039 0.19 2 -0.33 7 9
SDC1 0.02 0.044 -10000 0 -0.32 9 9
ARF6/GDP 0.021 0.013 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.039 0.068 -10000 0 -0.34 9 9
mol:Phosphatidic acid 0.011 0.019 -10000 0 -0.17 5 5
endocytosis -0.04 0.034 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.039 0.14 0.25 2 -0.31 171 173
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.019 -10000 0 -0.58 1 1
Dynamin 2/GDP 0.026 0.017 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.086 0.16 0.26 3 -0.3 298 301
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.035 0.066 0.32 2 -0.36 5 7
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.011 0.23 2 -10000 0 2
SNTA1 0.024 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.034 0.29 7 -10000 0 7
MAPK12 0.004 0.071 0.21 61 -0.33 22 83
CCND1 0.011 0.048 -10000 0 -0.38 7 7
p38 gamma/SNTA1 0.022 0.07 0.32 2 -0.31 21 23
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.072 0.21 65 -0.33 22 87
MAP2K6 -0.003 0.051 -10000 0 -0.35 22 22
MAPT -0.027 0.12 0.25 15 -0.32 120 135
MAPK13 0.011 0.011 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.023 -10000 0 -0.35 4 4
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 0.008 0.11 0.26 2 -0.41 45 47
ACTA1 0.013 0.11 0.26 7 -0.5 29 36
NUMA1 0.004 0.11 0.26 2 -0.39 47 49
SPTAN1 -0.002 0.11 0.27 7 -0.49 30 37
LIMK1 -0.001 0.11 0.27 5 -0.49 30 35
BIRC3 0.023 0.042 0.26 12 -0.58 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.017 0.26 5 -10000 0 5
CASP10 -0.011 0.092 0.21 11 -0.46 30 41
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.003 0.12 0.26 2 -0.45 42 44
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.002 0.11 0.27 7 -0.48 30 37
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.006 0.12 0.28 4 -0.48 38 42
MADD 0.024 0.004 -10000 0 -10000 0 0
TFAP2A 0.011 0.14 -10000 0 -0.66 32 32
BID 0.004 0.053 0.18 3 -0.27 29 32
MAP3K1 -0.004 0.096 -10000 0 -0.38 52 52
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.002 0.11 0.26 7 -0.49 29 36
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.043 0.25 4 -0.21 5 9
neuron apoptosis 0.003 0.12 -10000 0 -0.69 25 25
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.11 0.26 2 -0.44 41 43
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 -0.001 0.16 -10000 0 -0.91 25 25
TRAF2 0.025 0.015 0.26 4 -10000 0 4
ICAD/CAD -0.004 0.1 0.25 1 -0.49 28 29
CASP7 0.002 0.061 0.26 5 -0.31 9 14
KRT18 0.015 0.078 -10000 0 -0.74 8 8
apoptosis 0.002 0.12 0.3 5 -0.46 44 49
DFFA -0.003 0.11 0.25 3 -0.5 29 32
DFFB -0.003 0.11 0.25 3 -0.5 29 32
PARP1 0.017 0.044 0.21 5 -0.25 4 9
actin filament polymerization 0.001 0.1 0.46 30 -0.3 8 38
TNF 0.024 0.07 0.26 24 -0.58 10 34
CYCS 0.006 0.049 0.22 6 -0.22 23 29
SATB1 -0.009 0.16 -10000 0 -0.78 31 31
SLK -0.002 0.11 0.28 4 -0.5 29 33
p15 BID/BAX 0.013 0.062 0.24 2 -0.24 33 35
CASP2 0.002 0.066 0.23 7 -0.31 16 23
JNK cascade 0.004 0.096 0.38 52 -10000 0 52
CASP3 0 0.11 0.26 4 -0.5 32 36
LMNB2 0 0.13 0.27 5 -0.5 45 50
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.033 -10000 0 -0.34 2 2
negative regulation of DNA binding 0.012 0.13 -10000 0 -0.65 32 32
stress fiber formation -0.002 0.1 0.28 4 -0.49 29 33
GZMB 0.011 0.1 0.28 11 -0.51 29 40
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.019 0.12 0.3 7 -0.54 24 31
APP 0.003 0.12 -10000 0 -0.7 25 25
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM 0.004 0.12 0.29 5 -0.45 46 51
LMNA 0.008 0.082 0.28 3 -0.36 26 29
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.069 -10000 0 -0.31 21 21
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.001 0.11 0.27 4 -0.49 29 33
APAF-1/Caspase 9 -0.003 0.12 -10000 0 -0.61 35 35
nuclear fragmentation during apoptosis 0.004 0.11 0.26 2 -0.39 47 49
CFL2 -0.001 0.11 0.3 8 -0.48 30 38
GAS2 -0.027 0.14 0.27 6 -0.38 95 101
positive regulation of apoptosis 0.014 0.12 0.27 8 -0.49 31 39
PRF1 0.016 0.08 0.26 8 -0.58 17 25
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 0.011 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.02 0.3 1 -10000 0 1
CDKN1B 0.01 0.057 -10000 0 -0.34 15 15
CDKN1A 0.009 0.062 -10000 0 -0.34 19 19
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
FOXO3 0.013 0.056 -10000 0 -0.34 13 13
AKT1 0.006 0.057 -10000 0 -0.33 25 25
BAD 0.024 0.011 0.26 2 -10000 0 2
AKT3 0.007 0.034 -10000 0 -0.35 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.06 -10000 0 -0.34 19 19
AKT1/ASK1 0.031 0.069 -10000 0 -0.32 21 21
BAD/YWHAZ 0.037 0.023 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.03 0.067 0.31 21 -10000 0 21
TSC1 0.011 0.053 -10000 0 -0.34 13 13
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.036 0.072 0.27 1 -0.34 18 19
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.061 -10000 0 -0.32 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.055 0.32 1 -0.33 17 18
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.004 0.016 -10000 0 -0.35 2 2
MAP3K5 0.022 0.033 -10000 0 -0.58 3 3
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.076 0.3 21 -0.25 4 25
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.062 -10000 0 -0.35 17 17
CASP9 0.011 0.046 -10000 0 -0.32 11 11
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.073 0.3 8 -0.32 17 25
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.06 0.25 3 -0.44 6 9
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.052 -10000 0 -0.32 20 20
CHUK 0.009 0.056 -10000 0 -0.33 17 17
BAD/BCL-XL 0.038 0.068 0.29 3 -0.53 3 6
mTORC2 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.032 0.099 0.31 7 -0.39 25 32
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.011 0.065 0.27 2 -0.34 19 21
MAPKKK cascade -0.036 0.07 0.34 18 -0.26 1 19
MDM2/Cbp/p300 0.042 0.074 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.07 0.26 34 -0.59 3 37
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.071 0.32 4 -0.53 3 7
glucose import -0.16 0.16 0.21 2 -0.32 487 489
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.05 0.18 3 -0.29 10 13
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.16 0.16 0.21 2 -0.32 487 489
GSK3A 0.01 0.06 -10000 0 -0.35 17 17
FOXO1 0.011 0.041 -10000 0 -0.29 9 9
GSK3B 0.009 0.06 -10000 0 -0.35 18 18
SFN 0.022 0.067 0.26 18 -0.58 10 28
G1/S transition of mitotic cell cycle 0.014 0.066 0.31 3 -0.43 7 10
p27Kip1/14-3-3 family 0.02 0.05 0.37 1 -0.45 3 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.002 -10000 0 -10000 0 0
MAP4K4 0.003 0.062 -10000 0 -0.42 6 6
BAG4 0.018 0.034 -10000 0 -0.58 3 3
PKC zeta/ceramide -0.001 0.052 -10000 0 -0.26 14 14
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 12 -0.58 3 15
BAX 0.002 0.041 -10000 0 -0.35 10 10
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.065 0.68 9 -10000 0 9
BAD -0.015 0.046 0.19 3 -0.25 12 15
SMPD1 0.014 0.058 0.2 12 -0.25 17 29
RB1 -0.015 0.043 -10000 0 -0.28 9 9
FADD/Caspase 8 0.027 0.089 0.27 12 -0.43 7 19
MAP2K4 -0.016 0.044 -10000 0 -0.3 7 7
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.056 0.22 10 -0.31 6 16
EGF -0.083 0.23 0.26 2 -0.58 182 184
mol:ceramide -0.014 0.048 0.15 1 -0.26 13 14
MADD 0.024 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.008 -10000 0 -10000 0 0
ASAH1 0.021 0.016 0.26 3 -10000 0 3
negative regulation of cell cycle -0.015 0.043 -10000 0 -0.27 9 9
cell proliferation -0.045 0.12 0.28 1 -0.27 193 194
BID -0.021 0.17 -10000 0 -0.66 59 59
MAP3K1 -0.015 0.046 0.19 2 -0.25 14 16
EIF2A -0.014 0.048 0.29 3 -0.25 5 8
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.006 0.054 0.32 2 -0.31 5 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.059 0.32 2 -0.35 4 6
Cathepsin D/ceramide 0.005 0.058 0.17 34 -0.24 12 46
FADD 0.005 0.062 0.23 10 -0.43 5 15
KSR1 -0.009 0.054 0.2 22 -0.26 11 33
MAPK8 -0.013 0.058 -10000 0 -0.28 17 17
PRKRA -0.015 0.047 0.2 4 -0.26 11 15
PDGFA 0.024 0.004 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.26 4 -10000 0 4
IGF1 -0.1 0.25 -10000 0 -0.58 217 217
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.047 0.15 1 -0.26 13 14
CTSD 0.032 0.044 0.26 36 -10000 0 36
regulation of nitric oxide biosynthetic process 0.034 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.047 0.13 0.29 1 -0.29 191 192
PRKCD 0.024 0.009 0.26 1 -10000 0 1
PRKCZ 0.023 0.019 -10000 0 -0.58 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.008 -10000 0 -10000 0 0
RelA/NF kappa B1 0.034 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.019 -10000 0 -0.58 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.049 -10000 0 -0.39 6 6
TNFR1A/BAG4/TNF-alpha 0.036 0.054 -10000 0 -0.36 12 12
mol:Sphingosine-1-phosphate 0.011 0.002 -10000 0 -10000 0 0
MAP2K1 -0.009 0.055 0.32 2 -0.33 4 6
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
CYCS 0.001 0.049 0.18 19 -0.23 11 30
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.03 -10000 0 -0.43 3 3
EIF2AK2 -0.016 0.043 0.19 5 -0.28 6 11
TNF-alpha/TNFR1A/FAN 0.04 0.044 -10000 0 -0.36 6 6
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.082 -10000 0 -0.38 31 31
MAP2K2 -0.01 0.054 0.32 2 -0.31 5 7
SMPD3 -0.002 0.1 0.27 4 -0.29 96 100
TNF 0.024 0.07 0.26 24 -0.58 10 34
PKC zeta/PAR4 0.033 0.022 -10000 0 -0.43 2 2
mol:PHOSPHOCHOLINE 0.042 0.097 0.24 184 -0.21 3 187
NF kappa B1/RelA/I kappa B alpha 0.063 0.03 -10000 0 -0.32 2 2
AIFM1 0 0.049 0.18 20 -0.21 15 35
BCL2 0.007 0.096 -10000 0 -0.58 27 27
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.058 -10000 0 -0.39 17 17
forebrain development -0.043 0.21 0.35 1 -0.53 124 125
GNAO1 0.017 0.092 0.26 32 -0.58 19 51
SMO/beta Arrestin2 0.027 0.045 -10000 0 -0.43 8 8
SMO 0.017 0.054 -10000 0 -0.58 8 8
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.023 0.082 0.28 1 -0.49 11 12
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 0.023 -10000 0 -10000 0 0
GNAI1 -0.004 0.12 -10000 0 -0.58 46 46
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.19 -10000 0 -0.62 65 65
SAP30 0.025 0.016 0.26 4 -10000 0 4
mol:GDP 0.017 0.054 -10000 0 -0.58 8 8
MIM/GLI2A 0.022 0.024 0.28 4 -10000 0 4
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.023 0.009 -10000 0 -10000 0 0
GLI2 0.009 0.066 -10000 0 -0.3 22 22
GLI3 0.012 0.085 0.29 1 -0.47 14 15
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.018 0.059 -10000 0 -0.58 10 10
Gi family/GTP -0.006 0.095 -10000 0 -0.33 54 54
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.016 0.088 -10000 0 -0.46 20 20
GLI2/Su(fu) 0.012 0.081 -10000 0 -0.4 19 19
FOXA2 0.01 0.1 0.42 1 -0.68 14 15
neural tube patterning -0.043 0.21 0.35 1 -0.53 124 125
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.043 -10000 0 -0.37 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.022 0.024 0.28 4 -10000 0 4
embryonic limb morphogenesis -0.043 0.21 0.35 1 -0.53 124 125
SUFU 0.015 0.027 -10000 0 -0.32 2 2
LGALS3 0.017 0.062 -10000 0 -0.58 11 11
catabolic process 0.026 0.1 0.29 1 -0.53 17 18
GLI3A/CBP 0.003 0.09 -10000 0 -0.36 57 57
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.045 0.22 0.35 1 -0.54 124 125
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
IFT172 0.024 0.019 -10000 0 -0.58 1 1
RBBP7 0.026 0.02 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.059 -10000 0 -0.39 12 12
GNAZ 0.017 0.057 -10000 0 -0.58 9 9
RBBP4 0.023 0.019 -10000 0 -0.58 1 1
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.018 0.07 -10000 0 -0.37 14 14
STK36 0.021 0.024 -10000 0 -0.58 1 1
Gi family/GNB1/GNG2/GDP -0.011 0.11 -10000 0 -0.41 41 41
PTCH1 -0.087 0.33 -10000 0 -1.1 84 84
MIM/GLI1 -0.031 0.2 0.36 1 -0.58 76 77
CREBBP 0.003 0.09 -10000 0 -0.36 57 57
Su(fu)/SIN3/HDAC complex 0.007 0.092 -10000 0 -0.42 33 33
FoxO family signaling

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
G6PC 0.012 0.06 -10000 0 -10000 0 0
PLK1 0.25 0.19 0.51 194 -0.57 1 195
CDKN1B 0.16 0.13 0.39 59 -0.43 6 65
FOXO3 0.2 0.16 0.46 176 -0.62 1 177
KAT2B 0.056 0.034 -10000 0 -0.58 1 1
FOXO1/SIRT1 0.011 0.054 -10000 0 -0.3 4 4
CAT 0.19 0.17 0.66 11 -1.1 3 14
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.057 0.029 -10000 0 -10000 0 0
FOXO1 0.017 0.062 -10000 0 -0.33 3 3
MAPK10 -0.017 0.12 0.21 9 -0.3 147 156
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.034 0.085 0.41 2 -0.51 1 3
response to oxidative stress 0.035 0.027 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.17 0.14 0.39 142 -0.52 2 144
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.064 0.082 -10000 0 -0.68 9 9
FOXO1/SKP2 0.027 0.058 -10000 0 -0.31 2 2
mol:GDP 0.035 0.026 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.13 0.13 0.46 3 -0.51 14 17
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.022 0.12 -10000 0 -0.53 32 32
MST1 0.052 0.06 0.27 5 -0.52 8 13
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.01 0.12 -10000 0 -0.46 43 43
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.037 0.21 10 -0.3 7 17
MAPK9 0.031 0.025 0.21 11 -10000 0 11
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
SIRT1 0.011 0.021 -10000 0 -10000 0 0
SOD2 0.15 0.13 0.46 17 -0.42 2 19
RBL2 0.11 0.25 0.5 4 -0.61 74 78
RAL/GDP 0.057 0.022 -10000 0 -10000 0 0
CHUK 0.057 0.028 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.058 0.021 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.059 0.18 -10000 0 -1.2 15 15
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.048 0.033 -10000 0 -10000 0 0
CCNB1 0.21 0.17 0.56 52 -0.57 1 53
FOXO1-3a-4/beta catenin 0.15 0.12 0.4 49 -0.38 5 54
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.057 -10000 0 -0.31 2 2
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
SGK1 0.052 0.049 -10000 0 -0.57 4 4
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.032 0.076 0.44 1 -0.41 1 2
SFN 0.022 0.067 0.26 18 -0.58 10 28
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.063 0.11 0.36 1 -0.42 17 18
CREBBP 0.022 0.008 -10000 0 -10000 0 0
FBXO32 0.23 0.21 0.6 117 -1.2 4 121
BCL6 0.17 0.16 0.51 4 -0.83 9 13
RALB 0.025 0.004 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.022 0.078 -10000 0 -0.67 3 3
UGCG 0.009 0.12 -10000 0 -0.68 28 28
AKT1/mTOR/p70S6K/Hsp90/TERT 0.047 0.12 0.29 13 -0.43 27 40
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.12 -10000 0 -0.67 28 28
mol:DAG 0.005 0.084 -10000 0 -0.76 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.14 0.3 6 -0.42 50 56
FRAP1 0.03 0.15 0.33 6 -0.49 50 56
FOXO3 0.036 0.14 0.33 12 -0.51 32 44
AKT1 0.036 0.15 0.32 11 -0.53 35 46
GAB2 0.021 0.021 -10000 0 -0.58 1 1
SMPD1 0.009 0.11 -10000 0 -0.64 25 25
SGMS1 0.019 0.064 -10000 0 -0.54 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.034 -10000 0 -0.34 9 9
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.046 0.11 0.27 10 -0.46 22 32
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.031 0.044 -10000 0 -0.38 10 10
RPS6KB1 0.011 0.097 -10000 0 -0.84 11 11
mol:sphingomyelin 0.005 0.084 -10000 0 -0.76 11 11
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.028 0.028 0.26 14 -10000 0 14
PIK3R1 0.019 0.057 -10000 0 -0.58 9 9
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.064 0.2 0.41 10 -0.92 27 37
MYB 0.032 0.18 0.49 2 -1.1 20 22
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.036 0.11 0.29 19 -0.48 19 38
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.093 -10000 0 -0.76 11 11
mol:PI-3-4-5-P3 0.04 0.11 0.29 20 -0.46 19 39
Rac1/GDP 0.016 0.034 0.19 1 -0.34 8 9
T cell proliferation 0.04 0.1 0.29 12 -0.47 14 26
SHC1 0.02 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 0.012 0.11 3 -0.076 19 22
PRKCZ 0.039 0.1 0.3 10 -0.49 14 24
NF kappa B1 p50/RelA 0.047 0.14 0.32 6 -0.45 39 45
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.076 0.3 11 -0.52 8 19
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
IL2RA 0.027 0.086 0.26 51 -0.58 13 64
IL2RB 0.031 0.053 0.26 37 -0.58 2 39
TERT 0.053 0.08 0.26 132 -10000 0 132
E2F1 0.053 0.093 0.34 2 -0.36 27 29
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.034 19 -0.051 3 22
PTPN11 0.024 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.07 0.26 45 -0.58 7 52
actin cytoskeleton organization 0.04 0.1 0.29 12 -0.47 14 26
GRB2 0.023 0.011 0.26 1 -10000 0 1
IL2 0.022 0.024 0.26 8 -10000 0 8
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.039 -10000 0 -0.32 8 8
LCK 0.026 0.077 0.26 36 -0.58 11 47
BCL2 0.018 0.2 0.38 4 -0.79 44 48
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.023 0.028 0.26 1 -0.58 2 3
ANTXR2 0.018 0.059 -10000 0 -0.58 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.077 12 12
monocyte activation 0.003 0.086 0.26 2 -0.35 54 56
MAP2K2 0.002 0.084 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.008 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 0.12 1 -0.11 1 2
MAP2K6 -0.009 0.041 -10000 0 -0.3 19 19
CYAA -0.009 0.036 -10000 0 -0.34 11 11
MAP2K4 -0.004 0.008 -10000 0 -0.11 1 1
IL1B -0.008 0.047 0.22 2 -0.29 24 26
Channel 0.026 0.042 -10000 0 -0.36 11 11
NLRP1 -0.007 0.032 -10000 0 -0.32 10 10
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.067 -10000 0 -0.39 28 28
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.077 12 -10000 0 12
MAPK3 -0.004 0.008 0.084 1 -10000 0 1
MAPK1 -0.004 0.009 0.12 2 -0.11 1 3
PGR -0.081 0.14 0.2 2 -0.31 265 267
PA/Cellular Receptors 0.027 0.046 -10000 0 -0.39 11 11
apoptosis -0.002 0.008 -10000 0 -0.077 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.04 -10000 0 -0.34 11 11
macrophage activation -0.005 0.01 0.12 3 -10000 0 3
TNF 0.024 0.07 0.26 24 -0.58 10 34
VCAM1 0.003 0.087 0.26 2 -0.35 54 56
platelet activation -0.001 0.067 -10000 0 -0.39 28 28
MAPKKK cascade -0.002 0.025 0.093 14 -0.14 5 19
IL18 -0.003 0.026 -10000 0 -0.23 9 9
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.077 12 12
LEF -0.002 0.008 -10000 0 -0.077 12 12
CASP1 -0.003 0.027 -10000 0 -0.17 18 18
mol:cAMP -0.001 0.067 -10000 0 -0.39 28 28
necrosis -0.002 0.008 -10000 0 -0.077 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.04 -10000 0 -0.34 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.018 0.065 0.16 1 -0.29 46 47
FRAP1 -0.001 0.083 0.4 1 -0.46 24 25
AKT1 -0.011 0.064 0.19 1 -0.29 34 35
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0.024 0.069 0.23 5 -0.27 13 18
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.036 -10000 0 -0.2 6 6
TSC2 0.023 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.006 0.047 -10000 0 -0.25 12 12
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.004 0.078 -10000 0 -0.31 57 57
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.047 -10000 0 -0.23 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.012 0.076 0.26 7 -0.3 23 30
MAP3K5 -0.001 0.047 0.2 10 -0.2 42 52
PIK3R1 0.019 0.056 -10000 0 -0.58 9 9
apoptosis -0.001 0.047 0.2 10 -0.2 43 53
mol:LY294002 0 0 -10000 0 -0.001 50 50
EIF4B 0.01 0.07 0.3 4 -0.27 21 25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.067 0.22 2 -0.28 13 15
eIF4E/eIF4G1/eIF4A1 0.003 0.05 -10000 0 -0.29 19 19
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.016 0.081 -10000 0 -0.29 59 59
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.054 0.22 15 -0.19 3 18
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.027 0.06 -10000 0 -0.25 11 11
mol:Amino Acids 0 0 -10000 0 -0.001 50 50
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.059 0.17 4 -0.28 39 43
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.006 0.14 -10000 0 -0.52 62 62
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.048 -10000 0 -0.24 12 12
TSC1/TSC2 0.027 0.075 0.25 6 -0.29 13 19
tumor necrosis factor receptor activity 0 0 0.001 50 -10000 0 50
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.012 0.08 -10000 0 -0.33 58 58
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.02 -10000 0 -0.57 1 1
PDK2 -0.018 0.058 0.18 7 -0.28 34 41
EIF4EBP1 -0.024 0.23 -10000 0 -1 47 47
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D 0.001 0.079 0.42 2 -0.41 23 25
peptide biosynthetic process -0.011 0.017 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 19 -0.003 2 21
EEF2 -0.011 0.017 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.014 0.21 -10000 0 -0.97 47 47
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.092 0.26 32 -0.58 19 51
CDC42/GTP -0.002 0.095 -10000 0 -0.31 43 43
PLCG1 -0.01 0.086 -10000 0 -0.32 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
cell migration -0.003 0.093 -10000 0 -0.3 43 43
S1PR5 0.027 0.042 0.26 19 -0.58 2 21
S1PR4 0.029 0.065 0.26 38 -0.58 6 44
MAPK3 -0.007 0.081 0.27 1 -0.31 37 38
MAPK1 -0.006 0.082 -10000 0 -0.32 40 40
S1P/S1P5/Gi -0.002 0.085 -10000 0 -0.32 40 40
GNAI1 -0.003 0.12 -10000 0 -0.58 46 46
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.027 -10000 0 -0.36 2 2
RHOA 0.006 0.058 0.24 1 -0.31 6 7
S1P/S1P4/Gi -0.002 0.091 -10000 0 -0.33 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.056 -10000 0 -0.58 9 9
S1P/S1P4/G12/G13 0.044 0.043 -10000 0 -0.33 6 6
GNA12 0.024 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
BARD1 signaling events

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
BARD1/CSTF1 0.027 0.054 -10000 0 -0.4 15 15
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.016 -10000 0 -10000 0 0
protein ubiquitination 0.065 0.069 0.31 2 -0.3 15 17
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.022 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.014 0.087 -10000 0 -0.47 14 14
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.021 0.26 1 -0.58 1 2
CCNE1 0.063 0.088 0.26 169 -10000 0 169
CDK2/Cyclin E1 0.061 0.061 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.028 0.057 -10000 0 -0.41 16 16
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
FANCA 0.06 0.089 0.26 166 -10000 0 166
DNA repair 0.029 0.086 0.29 5 -0.37 7 12
BRCA1/BARD1/ubiquitin 0.028 0.057 -10000 0 -0.41 16 16
BARD1/DNA-PK 0.046 0.051 -10000 0 -0.34 13 13
FANCL 0.024 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.027 0.054 0.39 15 -10000 0 15
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.071 -10000 0 -0.27 21 21
BRCA1/BACH1/BARD1/TopBP1 0.04 0.052 -10000 0 -0.37 15 15
BRCA1/BARD1/P53 0.049 0.052 -10000 0 -0.34 15 15
BARD1/CSTF1/BRCA1 0.038 0.051 -10000 0 -0.37 13 13
BRCA1/BACH1 0.023 0.021 0.26 1 -0.57 1 2
BARD1 0.015 0.073 0.26 1 -0.58 15 16
PCNA 0.024 0.011 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.04 0.051 -10000 0 -0.37 14 14
BRCA1/BARD1/UbcH7 0.039 0.052 -10000 0 -0.37 14 14
BRCA1/BARD1/RAD51/PCNA 0.093 0.087 0.32 2 -0.32 14 16
BARD1/DNA-PK/P53 0.05 0.053 -10000 0 -0.32 13 13
BRCA1/BARD1/Ubiquitin 0.028 0.057 -10000 0 -0.41 16 16
BRCA1/BARD1/CTIP 0.029 0.048 -10000 0 -0.34 15 15
FA complex 0.035 0.038 0.24 3 -0.26 1 4
BARD1/EWS 0.027 0.056 -10000 0 -0.43 15 15
RBBP8 0.01 0.006 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.052 0.33 15 -10000 0 15
BRCA1/BARD1 0.072 0.073 0.33 2 -0.3 15 17
CSTF1 0.023 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.054 0.18 1 -0.42 15 16
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.11 0.26 360 -10000 0 360
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.028 0.057 -10000 0 -0.41 16 16
EWSR1 0.023 0.006 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.021 0.12 -10000 0 -0.41 47 47
KLHL20 0.015 0.066 0.23 11 -0.22 17 28
CYFIP2 0.028 0.049 0.26 25 -0.58 3 28
Rac1/GDP 0 0.087 0.26 8 -0.31 21 29
ENAH -0.017 0.11 -10000 0 -0.4 44 44
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.05 -10000 0 -0.25 20 20
ABI1/Sra1/Nap1 -0.013 0.033 -10000 0 -0.15 20 20
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.07 -10000 0 -0.34 23 23
RAPGEF1 -0.019 0.11 0.26 2 -0.38 38 40
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.023 0.13 -10000 0 -0.41 56 56
CRK -0.017 0.1 -10000 0 -0.4 45 45
E-cadherin/gamma catenin/alpha catenin 0.031 0.064 -10000 0 -0.37 21 21
alphaE/beta7 Integrin 0.036 0.035 -10000 0 -0.43 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.028 -10000 0 -0.34 3 3
DLG1 -0.025 0.12 -10000 0 -0.41 53 53
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.032 -10000 0 -0.19 20 20
MLLT4 0.021 0.034 0.26 1 -0.58 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.004 0.047 -10000 0 -0.24 20 20
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.019 0.07 -10000 0 -0.34 32 32
TIAM1 0.025 0.015 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.04 0.059 -10000 0 -0.32 21 21
AKT1 -0.007 0.036 -10000 0 -0.21 1 1
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
CDH1 0.009 0.085 -10000 0 -0.58 21 21
RhoA/GDP 0 0.087 0.26 8 -0.31 20 28
actin cytoskeleton organization 0.014 0.054 0.19 20 -0.16 13 33
CDC42/GDP 0 0.086 0.26 8 -0.31 22 30
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.046 -10000 0 -0.24 33 33
ITGB7 0.029 0.046 0.26 27 -0.58 2 29
RAC1 0.024 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.043 0.063 -10000 0 -0.34 21 21
E-cadherin/Ca2+/beta catenin/alpha catenin 0.029 0.055 -10000 0 -0.32 21 21
mol:GDP -0.014 0.093 0.27 8 -0.36 22 30
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.004 0.089 0.26 5 -0.32 20 25
RAC1/GTP/IQGAP1 0.032 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.049 0.18 42 -0.24 4 46
NME1 0.026 0.03 0.26 15 -10000 0 15
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.12 -10000 0 -0.42 49 49
regulation of cell-cell adhesion 0.003 0.042 -10000 0 -0.22 20 20
WASF2 0.007 0.027 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.06 0.24 2 -0.28 20 22
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.07 -10000 0 -0.32 23 23
CCND1 0.014 0.056 0.2 39 -0.3 4 43
VAV2 -0.02 0.15 -10000 0 -0.54 41 41
RAP1/GDP 0.006 0.072 0.26 3 -0.29 20 23
adherens junction assembly -0.022 0.12 -10000 0 -0.4 49 49
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.024 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.04 0.066 -10000 0 -0.31 23 23
E-cadherin/beta catenin -0.001 0.064 -10000 0 -0.35 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.024 0.12 -10000 0 -0.4 54 54
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.091 0.26 30 -0.34 25 55
E-cadherin/beta catenin/alpha catenin 0.032 0.064 -10000 0 -0.37 21 21
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.024 0.13 -10000 0 -0.42 56 56
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.055 0.073 0.38 13 -0.39 12 25
MAP4K1 0.032 0.053 0.26 40 -0.58 2 42
MAP3K8 0.02 0.046 -10000 0 -0.58 6 6
PRKCB 0.019 0.077 0.26 18 -0.58 14 32
DBNL 0.024 0.003 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.014 0.055 0.26 1 -0.31 15 16
JUN 0.003 0.13 -10000 0 -0.6 37 37
MAP3K7 0.015 0.053 0.23 2 -0.29 14 16
GRAP2 0.016 0.069 0.26 3 -0.58 13 16
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.013 0.065 0.25 1 -0.38 11 12
LAT 0.025 0.039 0.26 14 -0.58 2 16
LCP2 0.024 0.009 0.26 1 -10000 0 1
MAPK8 0.008 0.13 -10000 0 -0.63 37 37
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.059 0.25 3 -0.31 17 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.063 0.072 0.38 13 -0.37 12 25
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.002 0.1 0.26 2 -0.43 29 31
BAG4 0.018 0.034 -10000 0 -0.58 3 3
BAD 0.005 0.039 0.2 4 -0.19 6 10
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 12 -0.58 3 15
BAX 0.005 0.042 0.22 6 -0.18 7 13
EnzymeConsortium:3.1.4.12 0.002 0.026 0.085 4 -0.096 25 29
IKBKB 0.016 0.1 0.31 5 -0.43 20 25
MAP2K2 0.008 0.052 0.21 13 -0.24 2 15
MAP2K1 0.009 0.053 0.22 15 -0.24 2 17
SMPD1 0.002 0.032 0.14 3 -0.16 13 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.28 19 -0.44 23 42
MAP2K4 0.006 0.035 0.19 4 -0.21 4 8
protein ubiquitination 0.003 0.1 0.34 4 -0.42 26 30
EnzymeConsortium:2.7.1.37 0.008 0.055 0.22 14 -0.24 3 17
response to UV 0 0.001 0.002 18 -0.002 3 21
RAF1 0.009 0.052 0.19 39 -0.22 5 44
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.006 0.041 0.13 5 -0.15 21 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.009 -10000 0 -10000 0 0
MADD 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.04 0.19 3 -0.2 7 10
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.01 0.052 0.22 13 -0.23 2 15
MAPK1 0.007 0.059 0.21 13 -0.25 5 18
p50/RELA/I-kappa-B-alpha 0.034 0.01 -10000 0 -10000 0 0
FADD 0.022 0.11 0.28 11 -0.46 20 31
KSR1 0.009 0.05 0.18 33 -0.21 6 39
MAPK8 0.002 0.048 0.24 8 -0.3 7 15
TRAF2 0.025 0.015 0.26 4 -10000 0 4
response to radiation 0 0 0.002 8 -10000 0 8
CHUK -0.002 0.095 -10000 0 -0.43 24 24
TNF R/SODD 0.027 0.03 -10000 0 -0.43 3 3
TNF 0.024 0.07 0.26 24 -0.58 10 34
CYCS 0.008 0.046 0.18 14 -0.2 4 18
IKBKG -0.002 0.098 0.43 1 -0.43 24 25
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.001 0.1 -10000 0 -0.46 27 27
RELA 0.024 0.005 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.007 0.045 0.16 16 -0.19 6 22
TNF/TNF R/SODD 0.036 0.054 -10000 0 -0.36 12 12
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 8 -10000 0 8
CASP8 0.002 0.13 -10000 0 -0.62 41 41
NSMAF 0.016 0.11 0.26 10 -0.42 26 36
response to hydrogen peroxide 0 0.001 0.002 18 -0.002 3 21
BCL2 0.007 0.096 -10000 0 -0.58 27 27
HIF-2-alpha transcription factor network

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
MMP14 0.025 0.087 0.4 2 -0.55 15 17
oxygen homeostasis 0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 19 -10000 0 19
TCEB1 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.088 0.087 0.39 5 -0.44 1 6
EPO 0.15 0.17 0.53 57 -0.55 2 59
FIH (dimer) 0.032 0.02 -10000 0 -10000 0 0
APEX1 0.033 0.024 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.54 20 -0.57 3 23
FLT1 -0.016 0.16 -10000 0 -0.65 40 40
ADORA2A 0.16 0.17 0.51 50 -0.59 2 52
germ cell development 0.14 0.16 0.55 21 -0.52 4 25
SLC11A2 0.14 0.15 0.52 15 -0.57 3 18
BHLHE40 0.13 0.16 0.53 12 -0.61 3 15
HIF1AN 0.032 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.13 0.41 44 -0.36 2 46
ETS1 0.026 0.035 -10000 0 -0.58 3 3
CITED2 0.016 0.089 -10000 0 -0.69 6 6
KDR -0.014 0.17 -10000 0 -0.78 25 25
PGK1 0.14 0.16 0.52 14 -0.56 3 17
SIRT1 0.026 0.004 -10000 0 -10000 0 0
response to hypoxia 0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.65 7 -0.65 3 10
EPAS1 0.07 0.088 0.29 38 -0.36 5 43
SP1 0.029 0.012 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.53 14 -0.58 32 46
EFNA1 0.11 0.14 0.5 6 -0.55 2 8
FXN 0.15 0.16 0.51 16 -0.55 3 19
POU5F1 0.14 0.16 0.55 20 -0.54 4 24
neuron apoptosis -0.15 0.18 0.63 3 -0.6 12 15
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.048 0.068 0.27 73 -0.59 1 74
EGLN2 0.034 0.026 0.26 5 -10000 0 5
EGLN1 0.027 0.028 -10000 0 -0.59 1 1
VHL/Elongin B/Elongin C 0.041 0.028 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.029 0.024 -10000 0 -10000 0 0
SLC2A1 0.15 0.16 0.54 15 -0.59 2 17
TWIST1 0.14 0.19 0.47 34 -0.56 31 65
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.42 7 -0.37 1 8
VEGFA 0.13 0.16 0.55 13 -0.57 3 16
CREBBP 0.023 0.007 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.022 0.038 -10000 0 -0.58 4 4
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.011 0.092 -10000 0 -0.29 80 80
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.096 -10000 0 -0.49 30 30
AKT3 -0.011 0.17 -10000 0 -1 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.038 -10000 0 -0.57 4 4
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.008 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 46 46
mol:GDP 0 0 -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
mol:Ca2+ -0.001 0.096 -10000 0 -0.35 48 48
MAPK3 -0.008 0.089 0.27 2 -0.34 42 44
MAPK1 -0.005 0.088 0.27 1 -0.34 42 43
JAK2 -0.008 0.1 -10000 0 -0.39 36 36
CXCR4 -0.008 0.093 -10000 0 -0.39 31 31
FLT1 0.023 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.01 0.091 0.21 1 -0.34 45 46
S1P/S1P3/Gi -0.001 0.096 -10000 0 -0.35 48 48
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP 0 0.099 -10000 0 -0.39 28 28
VEGFA 0.025 0.02 0.25 6 -10000 0 6
S1P/S1P2/Gi -0.002 0.089 -10000 0 -0.33 43 43
VEGFR1 homodimer/VEGFA homodimer 0.035 0.022 -10000 0 -0.19 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.041 -10000 0 -0.29 15 15
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
G12/G13 0.033 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.026 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.027 -10000 0 -0.58 2 2
Rac1/GTP -0.001 0.099 -10000 0 -0.37 32 32
Retinoic acid receptors-mediated signaling

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.022 -10000 0 -0.37 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.062 -10000 0 -0.4 11 11
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.066 0.2 5 -0.36 15 20
RAR alpha/9cRA/Cyclin H 0.046 0.074 -10000 0 -0.34 18 18
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.066 -10000 0 -0.43 11 11
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.023 0.065 -10000 0 -0.43 11 11
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.008 0.11 -10000 0 -0.57 18 18
NCOA2 -0.004 0.12 -10000 0 -0.58 41 41
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.024 0.019 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARG 0.025 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.007 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.05 -10000 0 -0.58 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.007 0.1 -10000 0 -0.52 19 19
RARA 0.013 0.056 0.2 12 -0.27 26 38
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.079 -10000 0 -0.38 21 21
PRKCA 0.011 0.086 0.26 1 -0.57 21 22
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.12 0.45 1 -0.58 18 19
RXRG -0.052 0.16 0.25 12 -0.36 194 206
RXRA 0.022 0.064 0.35 1 -0.27 25 26
RXRB 0.016 0.062 0.24 11 -0.34 21 32
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.034 0.076 0.26 63 -0.58 7 70
CRBP1/9-cic-RA 0.025 0.054 0.18 63 -0.42 7 70
RARB 0.018 0.065 -10000 0 -0.58 12 12
PRKCG 0.031 0.044 0.26 36 -10000 0 36
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.01 0.1 -10000 0 -0.54 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.008 0.1 -10000 0 -0.49 19 19
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.08 0.26 8 -0.38 14 22
RXRs/RARs/NRIP1/9cRA/HDAC3 0.01 0.12 0.45 1 -0.59 18 19
positive regulation of DNA binding 0.032 0.065 -10000 0 -0.32 18 18
NRIP1 0.01 0.12 0.54 1 -0.76 9 10
RXRs/RARs 0.008 0.12 -10000 0 -0.53 24 24
RXRs/RXRs/DNA/9cRA -0.015 0.092 -10000 0 -0.51 22 22
PRKACA 0.024 0.003 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.052 0.057 -10000 0 -0.35 2 2
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.015 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.024 0.009 0.26 1 -9999 0 1
PLK4 0.033 0.045 0.26 39 -9999 0 39
regulation of centriole replication 0.016 0.027 0.26 2 -9999 0 2
TRAIL signaling pathway

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
TNFSF10 0.02 0.05 -10000 0 -0.58 7 7
positive regulation of NF-kappaB transcription factor activity -0.007 0.12 -10000 0 -0.34 104 104
MAP2K4 0.016 0.047 0.22 1 -0.38 4 5
IKBKB 0.021 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.01 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.034 -10000 0 -0.58 3 3
SMPD1 0.008 0.03 -10000 0 -0.35 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.017 0.14 0.26 1 -0.58 63 64
TRAIL/TRAILR2 0.026 0.04 -10000 0 -0.38 8 8
TRAIL/TRAILR3 0.027 0.044 -10000 0 -0.38 9 9
TRAIL/TRAILR1 0.024 0.048 -10000 0 -0.35 14 14
TRAIL/TRAILR4 -0.007 0.12 -10000 0 -0.34 104 104
TRAIL/TRAILR1/DAP3/GTP 0.029 0.039 -10000 0 -0.33 7 7
IKK complex 0.011 0.04 -10000 0 -0.42 1 1
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.037 0.26 1 -0.42 7 8
MAP3K1 0.017 0.062 -10000 0 -0.46 8 8
TRAILR4 (trimer) -0.017 0.14 0.26 1 -0.57 63 64
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.034 -10000 0 -0.57 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.045 -10000 0 -0.38 8 8
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.007 0.037 0.26 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.047 -10000 0 -0.31 7 7
mol:ceramide 0.008 0.03 -10000 0 -0.35 6 6
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.012 0.063 0.26 1 -0.44 7 8
TRAF2 0.025 0.015 0.26 4 -10000 0 4
TRAILR3 (trimer) 0.022 0.022 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.031 0.042 -10000 0 -0.36 7 7
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.035 0.084 0.28 60 -0.34 3 63
JNK cascade -0.007 0.12 -10000 0 -0.34 104 104
TRAIL (trimer) 0.02 0.05 -10000 0 -0.57 7 7
TNFRSF10C 0.022 0.022 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.04 -10000 0 -0.31 5 5
TRAIL/TRAILR2/FADD 0.032 0.037 -10000 0 -0.35 5 5
cell death 0.008 0.03 -10000 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.042 -10000 0 -0.41 6 6
TRAILR2 (trimer) 0.02 0.01 -10000 0 -10000 0 0
CASP8 0.012 0.051 -10000 0 -0.56 6 6
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.043 0.044 -10000 0 -0.3 5 5
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.001 0.087 0.35 20 -10000 0 20
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.027 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.092 0.26 32 -0.58 19 51
RhoA/GTP -0.001 0.089 -10000 0 -0.36 20 20
negative regulation of cAMP metabolic process -0.001 0.085 -10000 0 -0.32 40 40
GNAZ 0.018 0.056 -10000 0 -0.58 9 9
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.027 0.042 0.26 19 -0.58 2 21
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.002 0.085 -10000 0 -0.32 40 40
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 46 46
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.03 0.01 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.58 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 0.051 -10000 0 -0.37 7 7
IRAK/TOLLIP 0.024 0.014 -10000 0 -10000 0 0
IKBKB 0.021 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.026 0.096 0.37 3 -0.43 37 40
IL1A 0.028 0.032 0.26 19 -10000 0 19
IL1B 0.004 0.056 0.26 1 -0.44 15 16
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.039 -10000 0 -0.3 1 1
IL1R2 0.009 0.12 0.26 29 -0.58 37 66
IL1R1 0.014 0.079 -10000 0 -0.58 18 18
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.064 0.26 2 -0.31 19 21
TOLLIP 0.024 0.005 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.032 0.069 0.29 19 -0.37 1 20
JUN -0.009 0.068 0.3 6 -0.28 29 35
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.039 0.08 -10000 0 -0.33 39 39
IL1 alpha/IL1R1/IL1RAP/MYD88 0.055 0.058 -10000 0 -0.34 18 18
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.058 -10000 0 -0.32 18 18
IL1 beta fragment/IL1R1/IL1RAP 0.023 0.072 -10000 0 -0.36 31 31
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 0.069 0.33 5 -0.29 24 29
IRAK1 -0.001 0.019 0.21 2 -10000 0 2
IL1RN/IL1R1 0.033 0.072 -10000 0 -0.43 20 20
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.043 -10000 0 -0.4 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.058 -10000 0 -0.3 21 21
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.023 0.072 -10000 0 -0.36 31 31
IL1 beta/IL1R2 0.013 0.095 -10000 0 -0.38 50 50
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.027 0.072 -10000 0 -0.32 31 31
IRAK3 0.004 0.11 0.26 1 -0.58 34 35
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.043 0.073 -10000 0 -0.33 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.045 -10000 0 -0.28 18 18
IL1 alpha/IL1R1/IL1RAP 0.043 0.059 -10000 0 -0.37 18 18
RELA 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.036 -10000 0 -10000 0 0
IL1RAP 0.024 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.016 0.059 -10000 0 -0.6 2 2
CASP1 0.021 0.02 -10000 0 -0.58 1 1
IL1RN/IL1R2 0.029 0.1 0.37 5 -0.43 39 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.035 0.072 -10000 0 -0.34 31 31
TMEM189-UBE2V1 0.019 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.017 0.074 -10000 0 -0.36 25 25
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.032 0.052 0.26 37 -0.58 2 39
TRAF6/TAK1/TAB1/TAB2 0.039 0.017 -10000 0 -10000 0 0
MAP2K6 0 0.069 0.37 6 -0.3 17 23
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.025 0.075 0.3 4 -0.37 14 18
PDGFB-D/PDGFRB/SLAP 0.028 0.033 -10000 0 -0.37 4 4
PDGFB-D/PDGFRB/APS/CBL 0.048 0.043 -10000 0 -0.36 4 4
AKT1 0.025 0.095 0.35 37 -10000 0 37
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.086 0.32 6 -0.4 16 22
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.45 38 38
mol:Ca2+ 0.023 0.089 0.29 7 -0.43 18 25
MYC 0.053 0.17 0.38 26 -0.78 25 51
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.31 3 3
LRP1/PDGFRB/PDGFB 0.041 0.054 -10000 0 -0.42 12 12
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.022 0.09 0.3 6 -0.43 18 24
PTEN 0.023 0.02 -10000 0 -0.58 1 1
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PDGFB-D/PDGFRB/SHP2 0.034 0.03 -10000 0 -0.43 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.03 -10000 0 -0.43 4 4
cell cycle arrest 0.028 0.033 -10000 0 -0.37 4 4
HRAS 0.026 0.021 0.26 8 -10000 0 8
HIF1A 0.02 0.089 0.33 36 -10000 0 36
GAB1 0.025 0.095 0.31 5 -0.42 17 22
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.087 0.32 10 -0.37 14 24
PDGFB-D/PDGFRB 0.042 0.032 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.027 -10000 0 -0.37 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.022 0.067 0.28 3 -0.37 10 13
positive regulation of MAPKKK cascade 0.034 0.03 -10000 0 -0.42 4 4
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
mol:IP3 0.023 0.091 0.3 6 -0.44 18 24
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 0.035 -10000 0 -0.43 5 5
SHB 0.024 0.008 0.26 1 -10000 0 1
BLK -0.028 0.17 0.3 5 -0.4 138 143
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.03 -10000 0 -0.42 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.026 0.1 0.31 7 -0.44 21 28
CBL 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.03 -10000 0 -0.43 4 4
LCK 0.004 0.11 -10000 0 -0.5 35 35
PDGFRB 0.022 0.039 -10000 0 -0.58 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.015 0.061 -10000 0 -0.53 6 6
ABL1 0.019 0.095 0.3 7 -0.38 25 32
PDGFB-D/PDGFRB/CBL 0.02 0.11 0.3 3 -0.45 28 31
PTPN1 0.024 0.02 0.26 6 -10000 0 6
SNX15 0.024 0.005 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.032 0.26 19 -10000 0 19
cell proliferation 0.054 0.16 0.36 30 -0.68 25 55
SLA 0.021 0.022 0.26 7 -10000 0 7
actin cytoskeleton reorganization 0.034 0.051 0.33 2 -0.31 2 4
SRC 0.012 0.06 -10000 0 -0.5 8 8
PI3K -0.013 0.031 -10000 0 -0.29 8 8
PDGFB-D/PDGFRB/GRB7/SHC 0.034 0.035 -10000 0 -0.37 4 4
SH2B2 0.034 0.048 0.26 44 -10000 0 44
PLCgamma1/SPHK1 0.032 0.088 0.32 6 -0.41 16 22
LYN 0.009 0.063 -10000 0 -0.47 11 11
LRP1 0.018 0.059 -10000 0 -0.58 10 10
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.027 -10000 0 -0.58 2 2
STAT5A 0.02 0.046 -10000 0 -0.58 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.3 3 3
SPHK1 0.027 0.042 0.26 19 -0.58 2 21
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.023 0.091 0.3 6 -0.44 18 24
PLCG1 0.022 0.092 0.3 6 -0.45 18 24
NHERF/PDGFRB 0.048 0.045 -10000 0 -0.36 4 4
YES1 -0.001 0.11 -10000 0 -0.51 38 38
cell migration 0.047 0.045 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.049 0.042 -10000 0 -0.31 3 3
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
SLC9A3R1 0.035 0.053 0.26 52 -10000 0 52
NHERF1-2/PDGFRB/PTEN 0.056 0.049 0.3 2 -0.34 4 6
FYN -0.003 0.1 -10000 0 -0.42 43 43
DOK1 0.021 0.049 0.33 1 -0.34 3 4
HRAS/GTP 0.019 0.015 0.18 8 -10000 0 8
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.022 0.12 0.33 4 -0.52 28 32
PRKCD 0.021 0.051 0.34 1 -0.34 3 4
FER 0.017 0.06 -10000 0 -0.34 12 12
MAPKKK cascade 0.037 0.097 0.36 34 -0.3 3 37
RASA1 0.02 0.05 -10000 0 -0.34 3 3
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.035 0.043 0.3 1 -0.31 3 4
PDGFB-D/PDGFRB/SHB 0.034 0.031 -10000 0 -0.43 4 4
chemotaxis 0.02 0.093 0.29 7 -0.37 25 32
STAT1-3-5/STAT1-3-5 0.048 0.049 -10000 0 -0.37 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.028 -10000 0 -0.43 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.02 -10000 0 -0.31 3 3
TRAF2/ASK1 0.03 0.025 -10000 0 -0.36 3 3
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.019 0.11 0.25 2 -0.34 64 66
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.098 0.26 1 -0.35 37 38
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.052 0.077 0.26 122 -10000 0 122
TXN 0.007 0.006 0.12 3 -10000 0 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.58 1 1
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.028 -10000 0 -0.42 3 3
TAK1/TAB family 0 0.02 0.18 2 -0.14 6 8
RAC1/OSM/MEKK3 0.042 0.016 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.26 4 -10000 0 4
RAC1/OSM/MEKK3/MKK3 -0.001 0.093 -10000 0 -0.31 33 33
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.007 0.16 0.26 42 -0.58 69 111
CCM2 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.011 0.1 -10000 0 -0.36 70 70
MAPK11 0.021 0.033 -10000 0 -0.58 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.022 0.1 -10000 0 -0.34 71 71
OSM/MEKK3 0.032 0.013 -10000 0 -10000 0 0
TAOK1 -0.006 0.077 -10000 0 -0.36 44 44
TAOK2 0.011 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.033 -10000 0 -0.58 3 3
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.026 -10000 0 -0.35 3 3
GADD45/MTK1/MTK1 0.066 0.047 -10000 0 -10000 0 0
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.031 0.064 -9999 0 -0.37 21 21
E-cadherin/beta catenin 0.02 0.069 -9999 0 -0.43 21 21
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.009 0.085 -9999 0 -0.58 21 21
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.026 0.042 0.26 19 -0.58 2 21
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.02 0.22 1 -0.3 2 3
GNAO1 0.018 0.092 0.26 32 -0.58 19 51
mol:Sphinganine-1-P 0.012 0.026 -10000 0 -0.43 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.035 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.02 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 -0.24 5 5
S1PR5 0.027 0.042 0.26 19 -0.58 2 21
S1PR4 0.029 0.065 0.26 38 -0.58 6 44
GNAI1 -0.003 0.12 -10000 0 -0.58 46 46
S1P/S1P5/G12 0.046 0.042 0.25 4 -0.26 4 8
S1P/S1P3/Gq 0.026 0.064 -10000 0 -0.32 20 20
S1P/S1P4/Gi 0.003 0.096 0.26 1 -0.34 41 42
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
GNAZ 0.018 0.056 -10000 0 -0.58 9 9
GNA14 0.023 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.026 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.027 -10000 0 -0.58 2 2
ABCC1 0.023 0.006 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.034 -10000 0 -0.58 3 3
Caspase 8 (4 units) 0.039 0.061 -10000 0 -0.51 2 2
NEF 0.004 0.023 -10000 0 -0.18 9 9
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.02 0.056 -10000 0 -0.51 5 5
CYCS 0.036 0.077 0.25 26 -0.3 11 37
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.017 0.089 0.3 16 -0.62 15 31
MAP2K7 0.041 0.13 0.37 2 -0.7 17 19
protein ubiquitination 0.014 0.084 0.28 8 -0.36 12 20
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.023 0.027 -10000 0 -0.58 2 2
BID 0.036 0.073 0.24 2 -0.3 14 16
NF-kappa-B/RelA/I kappa B alpha 0.05 0.034 -10000 0 -0.31 3 3
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.033 -10000 0 -0.58 3 3
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.05 0.034 -10000 0 -0.31 3 3
MAPK8 0.037 0.12 0.42 4 -0.65 17 21
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.015 0.26 4 -10000 0 4
TRAF2 0.025 0.015 0.26 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.06 0.23 4 -0.31 15 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.094 -10000 0 -0.41 20 20
CHUK 0.013 0.087 0.31 4 -0.4 12 16
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.04 -10000 0 -0.35 4 4
TCRz/NEF 0.016 0.082 0.32 9 -0.43 24 33
TNF 0.024 0.07 0.26 24 -0.58 10 34
FASLG 0.011 0.11 0.29 40 -0.57 24 64
NFKB1 0.025 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.054 -10000 0 -0.36 12 12
CASP6 0.052 0.1 0.38 1 -0.5 20 21
CASP7 0.041 0.1 0.36 9 -0.44 13 22
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.36 6 -0.46 11 17
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.03 -10000 0 -0.43 3 3
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.006 -10000 0 -10000 0 0
MAP3K14 0.016 0.089 0.3 1 -0.42 14 15
APAF-1/Caspase 9 0.033 0.061 0.25 5 -0.37 5 10
BCL2 0.03 0.13 0.44 5 -0.54 23 28
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 0.039 0.31 3 -0.29 1 4
DAPP1 0.016 0.1 0.27 7 -0.35 36 43
Src family/SYK family/BLNK-LAT/BTK-ITK 0.017 0.14 0.29 13 -0.48 39 52
mol:DAG 0.021 0.081 0.24 35 -0.24 14 49
HRAS 0.026 0.022 0.26 8 -10000 0 8
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.062 0.27 1 -0.34 9 10
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.008 0.26 1 -10000 0 1
mol:GTP -0.011 0.037 0.32 4 -0.28 1 5
ARF1/GTP -0.004 0.032 0.27 6 -0.28 1 7
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
RAP1A/GTP -0.011 0.034 0.2 1 -0.28 1 2
ADAP1 -0.011 0.04 0.33 3 -0.29 2 5
ARAP3 -0.01 0.037 0.31 4 -0.28 1 5
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.033 0.26 20 -10000 0 20
ARHGEF6 0.016 0.07 -10000 0 -0.58 14 14
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.58 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
mol:Ca2+ 0.016 0.056 0.23 21 -10000 0 21
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 4 -10000 0 4
ZAP70 0.024 0.099 0.26 51 -0.58 20 71
mol:IP3 0.017 0.069 0.2 57 -0.18 8 65
LYN 0.021 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.06 0.36 2 -0.33 10 12
RhoA/GDP 0.03 0.042 0.25 1 -10000 0 1
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.019 0.072 0.32 12 -0.34 3 15
SRC 0.024 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.012 0.23 2 -10000 0 2
RAC1 0.024 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.021 -10000 0 -0.55 1 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.038 0.3 4 -0.27 1 5
RhoA/GTP -0.012 0.037 0.34 3 -0.27 1 4
Src family/SYK family/BLNK-LAT 0.025 0.097 0.26 17 -0.37 25 42
BLK 0.05 0.087 0.26 135 -0.58 2 137
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.037 0.33 3 -0.27 1 4
HCK 0.027 0.026 0.26 12 -10000 0 12
CYTH3 -0.012 0.038 0.36 2 -0.28 2 4
CYTH2 -0.011 0.038 0.33 3 -0.27 1 4
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.009 0.052 0.31 1 -0.49 6 7
SGK1 0.006 0.075 -10000 0 -0.35 32 32
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.016 0.064 0.38 2 -0.34 11 13
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.044 0.32 5 -10000 0 5
mol:PI-3-4-5-P3 -0.011 0.034 0.28 3 -0.28 1 4
ARAP3/RAP1A/GTP -0.011 0.034 0.2 1 -0.28 1 2
VAV1 0.023 0.034 0.26 2 -0.58 3 5
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.04 0.038 -10000 0 -0.28 1 1
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.061 0.27 1 -0.34 9 10
LAT 0.025 0.039 0.26 14 -0.58 2 16
Rac1/GTP 0.015 0.054 -10000 0 -0.35 11 11
ITK -0.019 0.064 0.33 3 -0.31 30 33
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.021 0.1 0.28 33 -0.33 16 49
LCK 0.026 0.077 0.26 36 -0.58 11 47
BTK -0.011 0.038 0.33 3 -0.27 1 4
EPO 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
BCL2L1 0.051 0.082 -10000 0 -0.48 1 1
CRKL 0.026 0.048 0.31 6 -10000 0 6
mol:DAG 0.038 0.052 -10000 0 -10000 0 0
HRAS 0.034 0.078 0.31 18 -10000 0 18
MAPK8 0.041 0.071 0.24 32 -0.35 5 37
RAP1A 0.027 0.048 0.31 7 -10000 0 7
GAB1 0.026 0.047 0.32 5 -10000 0 5
MAPK14 0.043 0.066 0.24 34 -10000 0 34
EPO 0.062 0.087 0.26 163 -10000 0 163
PLCG1 0.038 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 0.064 0.062 -10000 0 -0.35 5 5
GAB1/SHC/GRB2/SOS1 0.042 0.042 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.061 0.06 0.22 6 -10000 0 6
IRS2 0.015 0.072 0.29 7 -0.3 32 39
STAT1 0.045 0.065 0.33 3 -10000 0 3
STAT5B 0.04 0.06 0.33 1 -0.35 1 2
cell proliferation 0.023 0.076 0.24 36 -0.33 5 41
GAB1/SHIP/PIK3R1/SHP2/SHC 0.033 0.042 -10000 0 -0.29 6 6
TEC 0.025 0.048 0.29 5 -0.28 2 7
SOCS3 0.02 0.042 -10000 0 -0.58 5 5
STAT1 (dimer) 0.044 0.065 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
EPO/EPOR (dimer)/JAK2 0.081 0.064 0.34 3 -10000 0 3
EPO/EPOR 0.061 0.06 0.22 6 -10000 0 6
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.047 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 0.055 -10000 0 -10000 0 0
mol:IP3 0.038 0.052 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.031 0.077 0.29 2 -0.3 30 32
SH2B3 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.043 0.066 0.25 34 -10000 0 34
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.044 0.17 6 -0.21 8 14
PTPN6 0.023 0.04 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.047 0.049 0.28 3 -0.29 1 4
EPOR 0.026 0.013 0.26 1 -10000 0 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.042 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
CRKL/CBL/C3G 0.046 0.048 0.28 4 -10000 0 4
VAV2 0.027 0.049 0.3 8 -10000 0 8
CBL 0.025 0.048 0.31 6 -10000 0 6
SHC/Grb2/SOS1 0.036 0.038 -10000 0 -10000 0 0
STAT5A 0.038 0.065 0.33 1 -0.34 6 7
GRB2 0.023 0.01 0.26 1 -10000 0 1
STAT5 (dimer) 0.051 0.081 0.34 1 -0.34 13 14
LYN/PLCgamma2 0.027 0.027 -10000 0 -0.43 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.028 0.05 0.3 9 -10000 0 9
BCL2 0.031 0.17 -10000 0 -0.83 34 34
IFN-gamma 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
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 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.056 0.047 0.33 5 -10000 0 5
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.042 -10000 0 -0.22 1 1
CaM/Ca2+ 0.067 0.047 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.043 0.043 0.28 2 -10000 0 2
AKT1 0.012 0.063 0.29 10 -0.28 6 16
MAP2K1 0.008 0.045 0.29 4 -0.3 1 5
MAP3K11 0.023 0.043 0.29 4 -10000 0 4
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.017 0.098 -10000 0 -0.4 10 10
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.034 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.077 0.055 -10000 0 -10000 0 0
CEBPB 0.028 0.096 0.32 2 -0.49 7 9
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.075 0.096 -10000 0 -0.67 10 10
STAT1 0.026 0.048 0.29 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.056 0.082 0.26 142 -10000 0 142
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.046 0.29 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.027 0.062 0.31 3 -0.33 4 7
mol:Ca2+ 0.066 0.049 -10000 0 -10000 0 0
MAPK3 0.022 0.08 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.059 -10000 0 -0.3 1 1
MAPK1 -0.006 0.16 -10000 0 -0.67 54 54
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
JAK1 0.026 0.007 -10000 0 -10000 0 0
CAMK2D 0.022 0.033 -10000 0 -0.58 3 3
DAPK1 0.027 0.069 0.3 2 -0.34 2 4
SMAD7 0.017 0.036 0.18 5 -10000 0 5
CBL/CRKL/C3G 0.045 0.039 0.29 4 -10000 0 4
PI3K 0.057 0.053 -10000 0 -0.29 8 8
IFNG 0.056 0.083 0.26 142 -10000 0 142
apoptosis 0.024 0.073 0.28 1 -0.4 10 11
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.04 0.26 30 -10000 0 30
CAMK2B -0.007 0.16 0.26 42 -0.58 69 111
FRAP1 0.009 0.058 0.28 10 -0.27 6 16
PRKCD 0.012 0.065 0.3 12 -0.28 6 18
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -0.22 1 1
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 0.022 0.057 0.29 10 -0.32 1 11
STAT1 (dimer)/PIASy 0.039 0.047 0.28 5 -10000 0 5
SOCS1 0.016 0.11 -10000 0 -1 10 10
mol:GDP 0.042 0.036 0.27 4 -10000 0 4
CASP1 0.016 0.039 0.19 9 -0.24 3 12
PTGES2 0.024 0.008 0.26 1 -10000 0 1
IRF9 0.028 0.042 0.24 8 -10000 0 8
mol:PI-3-4-5-P3 0.042 0.044 -10000 0 -0.28 8 8
RAP1/GDP 0.036 0.023 -10000 0 -10000 0 0
CBL 0.022 0.041 0.29 4 -10000 0 4
MAP3K1 0.022 0.043 0.29 4 -0.31 1 5
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.042 -10000 0 -0.22 1 1
PTPN11 0.026 0.045 0.31 3 -10000 0 3
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

Figure 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 0.019 0.024 0.21 5 -0.31 1 6
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.023 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.067 0.049 0.35 10 -0.34 2 12
EPO 0.061 0.087 0.26 163 -10000 0 163
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.43 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.017 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.06 0.06 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.075 -10000 0 -0.44 19 19
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.043 -10000 0 -0.4 9 9
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.034 0.031 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
MADCAM1 0.031 0.045 0.26 37 -10000 0 37
cell adhesion 0.065 0.048 0.34 10 -0.34 2 12
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.013 0.043 -10000 0 -0.34 9 9
ITGB7 0.029 0.046 0.26 27 -0.58 2 29
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.047 -10000 0 -0.37 10 10
p130Cas/Crk/Dock1 0.026 0.042 0.35 1 -0.29 8 9
VCAM1 0.019 0.062 0.26 6 -0.58 10 16
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.024 -10000 0 -10000 0 0
BCAR1 -0.008 0.044 0.38 2 -0.31 9 11
EPOR 0.024 0.008 0.26 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.011 0.078 -10000 0 -0.46 19 19
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 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.085 0.31 5 -0.44 9 14
NFATC2 -0.004 0.071 0.21 1 -0.26 35 36
NFATC3 0.014 0.016 -10000 0 -0.41 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.093 0.26 3 -0.37 29 32
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.033 0.086 0.26 6 -0.39 12 18
BCL2/BAX 0.021 0.076 -10000 0 -0.37 34 34
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.013 -10000 0 -10000 0 0
BAX 0.025 0.017 0.26 5 -10000 0 5
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.011 0.26 2 -10000 0 2
CABIN1/MEF2D 0.019 0.082 -10000 0 -0.37 16 16
Calcineurin A alpha-beta B1/BCL2 0.007 0.096 -10000 0 -0.57 27 27
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.081 0.37 16 -10000 0 16
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.037 0.058 0.26 63 -10000 0 63
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.022 0.067 0.26 18 -0.58 10 28
MAP3K8 0.019 0.046 -10000 0 -0.58 6 6
NFAT4/CK1 alpha 0.019 0.028 -10000 0 -0.28 2 2
MEF2D/NFAT1/Cbp/p300 0.013 0.1 -10000 0 -0.3 50 50
CABIN1 0.012 0.092 0.26 3 -0.37 28 31
CALM1 0.021 0.012 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.58 1 1
CAMK4 0.032 0.048 0.26 37 -0.58 1 38
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.042 0.039 -10000 0 -0.43 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.05 -10000 0 -0.58 7 7
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.022 0.097 0.32 1 -0.45 11 12
PRKCH 0.023 0.019 -10000 0 -0.58 1 1
CABIN1/Cbp/p300 0.028 0.022 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.008 -10000 0 -10000 0 0
apoptosis 0.012 0.032 -10000 0 -0.33 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.04 -10000 0 -0.31 4 4
PRKCB 0.019 0.077 0.26 18 -0.58 14 32
PRKCE 0.024 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.008 0.059 -10000 0 -0.38 1 1
BAD/BCL-XL 0.034 0.01 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.021 -10000 0 -0.58 1 1
PRKCA 0.01 0.086 0.26 1 -0.58 21 22
PRKCG 0.03 0.044 0.26 36 -10000 0 36
PRKCQ 0.002 0.12 0.26 8 -0.58 40 48
FKBP38/BCL2 0.02 0.076 -10000 0 -0.38 34 34
EP300 0.02 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.087 0.34 1 -0.44 7 8
CaM/Ca2+/FKBP38 0.028 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.033 0.035 0.18 35 -0.36 1 36
NFATc/ERK1 0.03 0.083 0.34 1 -0.42 9 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.039 0.093 0.25 5 -0.4 19 24
NR4A1 -0.006 0.16 -10000 0 -0.52 76 76
GSK3B 0.023 0.008 -10000 0 -10000 0 0
positive T cell selection 0.014 0.016 -10000 0 -0.4 1 1
NFAT1/CK1 alpha 0 0.056 -10000 0 -0.27 11 11
RCH1/ KPNB1 0.041 0.041 -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 0.035 0.055 0.26 50 -0.58 1 51
MEF2D 0.018 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.082 0.34 1 -0.42 9 10
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.007 0.096 -10000 0 -0.58 27 27
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.11 0.28 16 -0.32 24 40
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.034 0.37 1 -0.43 1 2
NFKBIA 0.012 0.025 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.021 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.016 0.26 3 -10000 0 3
IKBKG 0.019 0.03 -10000 0 -10000 0 0
IKK complex/A20 0.021 0.12 -10000 0 -0.4 39 39
NEMO/A20/RIP2 0.02 0.016 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.014 0.12 0.28 1 -0.4 46 47
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 0.012 0.11 -10000 0 -0.38 39 39
BCL10/MALT1/TRAF6 0.045 0.015 -10000 0 -10000 0 0
NOD2 0.027 0.043 0.26 26 -0.58 1 27
NFKB1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
MALT1 0.023 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.034 0.053 -10000 0 -0.42 10 10
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.086 0.26 1 -0.58 21 22
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.07 0.26 24 -0.58 10 34
NF kappa B1 p50/RelA 0.051 0.016 -10000 0 -10000 0 0
BCL10 0.024 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.025 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.015 0.12 -10000 0 -0.4 41 41
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.42 46 46
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.029 0.046 0.26 27 -0.58 2 29
ITGA4 0.027 0.023 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.43 2 6
alpha4/beta1 Integrin 0.037 0.017 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.02 0.082 -10000 0 -0.43 32 32
AKT1 0.032 0.086 0.37 3 -0.54 7 10
PTK2B 0.003 0.086 0.35 1 -0.74 6 7
VEGFR2 homodimer/Frs2 0.025 0.06 -10000 0 -0.64 7 7
CAV1 -0.099 0.24 -10000 0 -0.58 209 209
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.039 0.059 -10000 0 -0.6 7 7
endothelial cell proliferation 0.044 0.11 0.36 20 -0.57 8 28
mol:Ca2+ 0.014 0.054 -10000 0 -0.5 8 8
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.051 0.06 -10000 0 -0.54 8 8
RP11-342D11.1 0.004 0.053 -10000 0 -0.52 8 8
CDH5 0.018 0.05 -10000 0 -0.58 7 7
VEGFA homodimer 0.049 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.011 0.088 0.26 1 -0.58 22 23
HRAS/GDP 0.03 0.049 -10000 0 -0.58 4 4
SH2D2A 0.04 0.074 0.26 90 -0.58 2 92
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.087 -10000 0 -0.53 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.046 0.074 -10000 0 -0.5 9 9
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.059 -10000 0 -0.65 4 4
GRB10 0.015 0.055 -10000 0 -0.65 5 5
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
PAK1 0.023 0.021 0.26 7 -10000 0 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.074 -10000 0 -0.51 12 12
HRAS 0.026 0.021 0.26 8 -10000 0 8
VEGF/Rho/ROCK1/Integrin Complex 0.008 0.075 -10000 0 -0.5 10 10
HIF1A 0.024 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 0.049 0.059 -10000 0 -0.53 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.033 -10000 0 -0.58 3 3
Nck/Pak 0.033 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.036 0.064 -10000 0 -0.56 9 9
mol:GDP 0.039 0.054 -10000 0 -0.63 4 4
mol:NADP 0.025 0.084 0.56 1 -0.47 11 12
eNOS/Hsp90 0.037 0.08 0.55 1 -0.46 9 10
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
mol:IP3 0.014 0.054 -10000 0 -0.5 8 8
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.026 0.019 0.26 6 -10000 0 6
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.022 0.1 0.35 1 -0.66 9 10
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.039 0.096 -10000 0 -0.41 34 34
PTPN6 0.024 0.012 0.26 2 -10000 0 2
EPAS1 0.025 0.055 -10000 0 -0.56 8 8
mol:L-citrulline 0.025 0.084 0.56 1 -0.47 11 12
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.048 0.06 -10000 0 -0.57 7 7
VEGFR2 homodimer/VEGFA homodimer 0.041 0.06 -10000 0 -0.56 8 8
VEGFR2/3 heterodimer 0.024 0.068 -10000 0 -0.65 9 9
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.005 0.068 -10000 0 -0.61 7 7
VEGFR2 homodimer 0.012 0.065 -10000 0 -0.68 8 8
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.007 0.073 0.27 1 -0.62 5 6
MAPK1 0.01 0.075 0.26 5 -0.58 6 11
VEGFA145/NRP2 0.035 0.025 0.2 6 -0.32 3 9
VEGFR1/2 heterodimer 0.023 0.062 -10000 0 -0.62 8 8
KDR 0.012 0.066 -10000 0 -0.68 8 8
VEGFA165/NRP1/VEGFR2 homodimer 0.041 0.062 -10000 0 -0.56 8 8
SRC 0.024 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.015 0.081 0.33 3 -0.56 7 10
PI3K 0.026 0.068 -10000 0 -0.66 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.039 0.059 -10000 0 -0.56 8 8
FES 0.013 0.059 -10000 0 -0.47 11 11
GAB1 0.015 0.062 -10000 0 -0.67 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.058 -10000 0 -0.54 8 8
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.018 0.13 -10000 0 -0.48 21 21
VEGFR2 homodimer/VEGFA homodimer/Yes 0.038 0.061 -10000 0 -0.54 9 9
PI3K/GAB1 0.039 0.079 0.31 1 -0.58 6 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.054 0.061 -10000 0 -0.62 5 5
PRKACA 0.024 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.036 0.066 -10000 0 -0.61 9 9
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.014 0.057 -10000 0 -0.53 8 8
actin cytoskeleton reorganization 0.045 0.073 -10000 0 -0.5 9 9
PTK2 0.006 0.088 -10000 0 -0.76 8 8
EDG1 0.004 0.053 -10000 0 -0.52 8 8
mol:DAG 0.014 0.054 -10000 0 -0.5 8 8
CaM/Ca2+ 0.026 0.052 -10000 0 -0.47 8 8
MAP2K3 -0.005 0.06 -10000 0 -0.64 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.039 0.058 -10000 0 -0.54 8 8
PLCG1 0.014 0.055 -10000 0 -0.51 8 8
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.049 0.058 -10000 0 -0.52 8 8
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.04 0.059 -10000 0 -0.56 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.06 -10000 0 -0.56 8 8
cell migration 0.024 0.093 0.33 1 -0.62 8 9
mol:PI-3-4-5-P3 0.026 0.063 -10000 0 -0.6 6 6
FYN 0.022 0.027 -10000 0 -0.58 2 2
VEGFB/NRP1 0.019 0.053 -10000 0 -0.49 8 8
mol:NO 0.025 0.084 0.56 1 -0.47 11 12
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.044 -10000 0 -0.58 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.056 -10000 0 -0.54 8 8
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
NOS3 0.025 0.091 0.57 1 -0.53 11 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.079 -10000 0 -0.39 29 29
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.008 0.073 0.35 1 -0.41 19 20
PRKCB -0.005 0.066 -10000 0 -0.42 15 15
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.022 0.055 -10000 0 -0.52 8 8
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.061 -10000 0 -0.58 8 8
VEGFA165/NRP2 0.035 0.025 0.2 6 -0.32 3 9
MAPKKK cascade 0.05 0.079 0.33 11 -0.59 4 15
NRP2 0.023 0.028 0.26 1 -0.58 2 3
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.019 -10000 0 -0.58 1 1
FAK1/Paxillin 0.022 0.1 0.42 2 -0.7 8 10
MAP3K13 0.013 0.059 -10000 0 -0.47 11 11
PDPK1 0.015 0.056 0.27 1 -0.52 5 6
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.044 -10000 0 -0.34 9 9
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.009 -10000 0 -0.28 1 1
GATA1/HDAC4 0.036 0.025 -10000 0 -0.43 1 1
GATA1/HDAC5 0.036 0.021 -10000 0 -10000 0 0
GATA2/HDAC5 0.025 0.076 -10000 0 -0.43 26 26
HDAC5/BCL6/BCoR 0.043 0.037 -10000 0 -0.37 7 7
HDAC9 0.022 0.058 0.26 10 -0.58 8 18
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.041 -10000 0 -0.37 9 9
HDAC4/ANKRA2 0.034 0.017 -10000 0 -0.43 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 0.099 0.26 14 -0.58 26 40
HDAC4/RFXANK 0.035 0.018 -10000 0 -0.43 1 1
BCOR 0.023 0.027 -10000 0 -0.58 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.01 0.26 1 -10000 0 1
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.03 0.047 -10000 0 -0.4 11 11
Histones 0.017 0.047 -10000 0 -0.31 8 8
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.58 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.009 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.018 -10000 0 -0.43 1 1
HDAC7 0.024 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.035 0.011 -10000 0 -10000 0 0
CAMK4 0.032 0.048 0.26 37 -0.58 1 38
Tubulin/HDAC6 0.047 0.019 -10000 0 -0.37 1 1
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
GATA1 0.026 0.03 0.26 16 -10000 0 16
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.019 0.056 -10000 0 -0.58 9 9
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.23 5 5
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.017 -10000 0 -0.43 1 1
Tubulin 0.035 0.018 -10000 0 -0.43 1 1
HDAC4/14-3-3 E 0.032 0.018 -10000 0 -0.43 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.032 0.039 -10000 0 -0.43 7 7
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.018 -10000 0 -0.37 1 1
HDAC4/SRF 0.05 0.035 -10000 0 -0.37 2 2
HDAC4/ER alpha -0.016 0.18 -10000 0 -0.42 148 148
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.017 0.047 -10000 0 -0.31 8 8
cell motility 0.047 0.018 -10000 0 -0.37 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.036 0.006 -10000 0 -10000 0 0
BCL6 0.021 0.042 -10000 0 -0.58 5 5
HDAC4/CaMK II delta B 0.023 0.019 -10000 0 -0.57 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.036 0.23 0.26 111 -0.58 144 255
HDAC6/HDAC11 0.036 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.019 -10000 0 -0.58 1 1
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.063 0.03 -10000 0 -0.31 2 2
GNG2 0.018 0.059 -10000 0 -0.58 10 10
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.023 0.022 0.26 2 -0.58 1 3
HDAC11 0.025 0.011 0.26 2 -10000 0 2
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.025 0.011 0.26 2 -10000 0 2
nuclear import -0.027 0.016 0.33 1 -10000 0 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.099 0.15 -10000 0 -0.42 62 62
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.004 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.11 0.15 0.4 1 -0.43 66 67
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.008 0.028 -10000 0 -0.43 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.021 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.024 0.023 0.26 9 -10000 0 9
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.01 0.017 0.24 5 -10000 0 5
PRKCZ 0.023 0.019 -10000 0 -0.58 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.064 -10000 0 -0.33 12 12
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.12 0.16 0.41 1 -0.49 66 67
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.022 0.067 0.26 18 -0.58 10 28
LNPEP 0.02 0.05 -10000 0 -0.58 7 7
YWHAE 0.022 0.007 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.026 0.018 -10000 0 -0.47 1 1
VEGFR1 homodimer/NRP1 0.01 0.016 -10000 0 -0.49 1 1
mol:DAG 0.012 0.031 -10000 0 -0.39 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.02 -10000 0 -0.45 1 1
CaM/Ca2+ 0.026 0.029 -10000 0 -0.37 2 2
HIF1A 0.028 0.012 -10000 0 -0.31 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.01 0.048 -10000 0 -0.34 9 9
PLCG1 0.012 0.031 -10000 0 -0.39 2 2
NOS3 0.016 0.054 -10000 0 -0.5 3 3
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:NO 0.02 0.063 0.3 1 -0.45 6 7
FLT1 0.013 0.019 -10000 0 -0.56 1 1
PGF 0.024 0.022 0.26 2 -0.58 1 3
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.03 -10000 0 -0.39 3 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.032 0.065 -10000 0 -0.43 7 7
endothelial cell proliferation 0.012 0.082 0.3 13 -0.51 6 19
mol:Ca2+ 0.012 0.031 -10000 0 -0.39 2 2
MAPK3 -0.013 0.05 0.23 1 -0.32 19 20
MAPK1 -0.012 0.049 0.23 1 -0.33 17 18
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
PLGF homodimer 0.024 0.022 0.26 2 -0.57 1 3
PRKACA 0.024 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.099 0.24 -10000 0 -0.58 209 209
VEGFA homodimer 0.025 0.019 0.26 6 -10000 0 6
VEGFR1 homodimer/VEGFA homodimer 0.026 0.022 -10000 0 -0.49 1 1
platelet activating factor biosynthetic process -0.014 0.047 -10000 0 -0.32 17 17
PI3K 0.044 0.044 -10000 0 -0.33 10 10
PRKCA -0.011 0.053 0.24 1 -0.34 19 20
PRKCB -0.009 0.049 -10000 0 -0.34 14 14
VEGFR1 homodimer/PLGF homodimer 0.026 0.023 -10000 0 -0.43 2 2
VEGFA 0.025 0.019 0.26 6 -10000 0 6
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.012 0.031 -10000 0 -0.39 2 2
RASA1 0.013 0.029 -10000 0 -0.44 1 1
NRP2 0.023 0.028 0.26 1 -0.58 2 3
VEGFR1 homodimer 0.013 0.019 -10000 0 -0.56 1 1
VEGFB homodimer 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.029 0.14 -10000 0 -0.45 23 23
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.043 -10000 0 -0.33 10 10
mol:L-citrulline 0.02 0.063 0.3 1 -0.45 6 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.028 -10000 0 -0.42 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.038 0.023 -10000 0 -0.45 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.053 0.047 -10000 0 -0.32 10 10
PDPK1 -0.004 0.05 -10000 0 -0.31 9 9
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.023 -10000 0 -0.45 1 1
mol:NADP 0.02 0.063 0.3 1 -0.45 6 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.028 -10000 0 -0.41 1 1
VEGFR1 homodimer/NRP2 0.025 0.028 -10000 0 -0.44 3 3
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.049 0.064 -10000 0 -0.38 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 0.03 0.064 -10000 0 -0.38 8 8
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.02 0.26 6 -10000 0 6
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.053 0.042 -10000 0 -0.41 1 1
YY1/LSF 0.024 0.05 -10000 0 -0.3 7 7
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.034 -10000 0 -0.32 8 8
I kappa B alpha/HDAC1 0.03 0.04 -10000 0 -0.44 2 2
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.019 0.04 -10000 0 -0.32 8 8
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.031 0.037 -10000 0 -0.44 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.29 11 11
NF kappa B1 p50/RelA 0.025 0.066 0.38 1 -0.39 5 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.012 0.099 0.26 14 -0.58 26 40
GATA1 0.026 0.03 0.26 16 -10000 0 16
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.079 -10000 0 -0.36 19 19
RBBP7 0.026 0.02 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.019 -10000 0 -0.58 1 1
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.031 -10000 0 -0.48 2 2
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.03 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.022 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.016 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 0.022 0.047 -10000 0 -0.38 4 4
YY1/HDAC2 0.024 0.046 -10000 0 -0.29 5 5
YY1/HDAC1 0.024 0.048 -10000 0 -0.29 6 6
NuRD/MBD2 Complex (MeCP1) 0.024 0.054 -10000 0 -0.27 13 13
PPARG -0.059 0.16 -10000 0 -0.35 209 209
HDAC8/hEST1B 0.041 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.037 -10000 0 -0.44 1 1
MBD3L2 0.018 0.011 0.26 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.067 -10000 0 -0.34 15 15
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.018 0.028 -10000 0 -0.49 1 1
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.011 -10000 0 -0.29 1 1
HDAC8 0.025 0.001 -10000 0 -10000 0 0
SMAD7 0.024 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.008 0.26 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.036 0.049 -10000 0 -0.27 6 6
YY1/SAP30/HDAC1 0.036 0.048 -10000 0 -0.27 3 3
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.031 -10000 0 -0.48 2 2
histone deacetylation 0.024 0.054 -10000 0 -0.27 13 13
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.037 -10000 0 -0.42 1 1
nuclear export -0.041 0.019 -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 0.024 0.068 -10000 0 -0.34 23 23
GATA1/HDAC1 0.036 0.02 -10000 0 -10000 0 0
GATA1/HDAC3 0.032 0.042 -10000 0 -0.46 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.053 -10000 0 -0.42 10 10
SIN3/HDAC complex/Mad/Max 0.016 0.054 -10000 0 -0.28 18 18
NuRD Complex 0.025 0.066 -10000 0 -0.38 9 9
positive regulation of chromatin silencing 0.051 0.04 -10000 0 -0.4 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.23 4 4
HDAC complex 0.057 0.023 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.025 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.015 -10000 0 -10000 0 0
TNF 0.024 0.07 0.26 24 -0.58 10 34
negative regulation of cell growth 0.016 0.053 -10000 0 -0.28 18 18
NuRD/MBD2/PRMT5 Complex 0.024 0.054 -10000 0 -0.27 13 13
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NF kappa B/RelA/I kappa B alpha 0.018 0.055 -10000 0 -0.38 9 9
SIN3/HDAC complex/NCoR1 0.007 0.067 -10000 0 -0.32 28 28
TFCP2 0.024 0.019 -10000 0 -0.58 1 1
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.009 0.26 1 -10000 0 1
MBD2 0.024 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.034 0.01 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.038 -10000 0 -0.37 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.044 -10000 0 -0.34 2 2
NFKBIA 0.014 0.038 -10000 0 -0.25 11 11
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.017 0.067 -10000 0 -0.58 13 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.013 0.25 2 -10000 0 2
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
NFKB1 0.01 0.012 0.26 2 -10000 0 2
RELA 0.024 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.023 0.047 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.047 -10000 0 -0.34 3 3
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.043 -10000 0 -0.4 9 9
NF kappa B1 p50/RelA 0.023 0.047 -10000 0 -0.26 10 10
IKBKB 0.021 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.056 -10000 0 -0.26 22 22
cell death 0.023 0.045 -10000 0 -0.32 3 3
NF kappa B1 p105/c-Rel 0.018 0.038 -10000 0 -0.37 8 8
LCK 0.026 0.077 0.26 36 -0.58 11 47
BCL3 0.024 0.008 0.26 1 -10000 0 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.006 -10000 0 -10000 0 0
SMAD2 -0.003 0.038 0.21 1 -0.3 2 3
SMAD3 0.022 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4 0.037 0.065 -10000 0 -0.45 11 11
SMAD4/Ubc9/PIASy 0.043 0.019 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.059 -10000 0 -0.28 1 1
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.044 -10000 0 -0.28 6 6
MAP3K1 0.023 0.019 -10000 0 -0.58 1 1
TRAP-1/SMAD4 0.028 0.053 -10000 0 -0.41 14 14
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.017 0.067 -10000 0 -0.58 13 13
UBE2I 0.023 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.005 -10000 0 -10000 0 0
KPNA2 0.037 0.058 0.26 63 -10000 0 63
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.042 0.037 -10000 0 -10000 0 0
CLOCK 0.019 0.062 -10000 0 -0.57 11 11
TIMELESS/CRY2 0.031 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.012 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.018 -10000 0 -10000 0 0
ARNTL 0.026 0.004 -10000 0 -10000 0 0
TIMELESS 0.018 0.025 -10000 0 -10000 0 0
NPAS2 0.023 0.043 0.26 1 -0.57 5 6
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.007 -10000 0 -0.092 6 6
CHEK1 0.028 0.038 0.26 25 -10000 0 25
mol:HEME 0.007 0.007 0.092 6 -10000 0 6
PER1 0.013 0.072 -10000 0 -0.58 15 15
BMAL/CLOCK/NPAS2 0.049 0.054 -10000 0 -0.36 16 16
BMAL1/CLOCK 0.018 0.064 -10000 0 -0.49 1 1
S phase of mitotic cell cycle 0.042 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 0.092 6 -10000 0 6
PER1/TIMELESS 0.024 0.047 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.016 0.26 4 -10000 0 4
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.039 0.068 0.36 3 -10000 0 3
regulation of axonogenesis -0.01 0.026 0.23 6 -10000 0 6
myoblast fusion -0.026 0.046 -10000 0 -0.22 1 1
mol:GTP 0.022 0.031 -10000 0 -0.15 11 11
regulation of calcium-dependent cell-cell adhesion -0.054 0.043 -10000 0 -10000 0 0
ARF1/GTP 0.03 0.029 -10000 0 -10000 0 0
mol:GM1 0.012 0.024 -10000 0 -10000 0 0
mol:Choline 0.008 0.038 -10000 0 -0.35 8 8
lamellipodium assembly 0.018 0.058 -10000 0 -0.37 7 7
MAPK3 0.031 0.045 0.2 9 -10000 0 9
ARF6/GTP/NME1/Tiam1 0.055 0.044 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.046 0.22 1 -10000 0 1
ARF1/GDP 0.025 0.048 -10000 0 -0.24 4 4
ARF6 0.032 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.016 0.26 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.031 0.044 0.2 9 -10000 0 9
actin filament bundle formation -0.032 0.05 0.24 5 -10000 0 5
KALRN 0.01 0.054 -10000 0 -0.31 18 18
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.05 -10000 0 -0.25 5 5
NME1 0.028 0.03 0.26 15 -10000 0 15
Rac1/GDP 0.033 0.051 -10000 0 -0.25 5 5
substrate adhesion-dependent cell spreading 0.022 0.031 -10000 0 -0.15 11 11
cortical actin cytoskeleton organization 0.018 0.058 -10000 0 -0.37 7 7
RAC1 0.024 0.003 -10000 0 -10000 0 0
liver development 0.022 0.031 -10000 0 -0.15 11 11
ARF6/GTP 0.022 0.031 -10000 0 -0.15 11 11
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.046 0.2 3 -0.21 5 8
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.029 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.045 -10000 0 -0.4 8 8
RAB11FIP3 0.023 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.018 0.058 -10000 0 -0.37 7 7
ruffle organization 0.01 0.026 -10000 0 -0.23 6 6
regulation of epithelial cell migration 0.022 0.031 -10000 0 -0.15 11 11
PLD2 0.02 0.024 -10000 0 -10000 0 0
PIP5K1A 0.01 0.026 -10000 0 -0.23 6 6
mol:Phosphatidic acid 0.008 0.038 -10000 0 -0.35 8 8
Rac1/GTP 0.018 0.058 -10000 0 -0.37 7 7
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.023 0.26 10 -10000 0 10
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.43 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.018 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.044 0.036 0.33 4 -0.34 2 6
lamellipodium assembly -0.002 0.085 -10000 0 -0.41 29 29
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.043 -10000 0 -0.4 9 9
ARF6 0.024 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.004 -10000 0 -10000 0 0
PXN 0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.056 -10000 0 -0.58 9 9
ARF6/GTP 0.047 0.021 -10000 0 -10000 0 0
cell adhesion 0.05 0.019 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.017 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.029 0.046 0.26 27 -0.58 2 29
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.043 -10000 0 -0.32 10 10
p130Cas/Crk/Dock1 0.041 0.019 -10000 0 -10000 0 0
VCAM1 0.019 0.062 0.26 6 -0.58 10 16
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.02 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.022 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.048 0.021 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.02 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.093 -10000 0 -0.46 29 29
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.011 -10000 0 -0.27 1 1
MDM2/SUMO1 0.033 0.04 -10000 0 -0.23 4 4
HDAC4 0.023 0.019 -10000 0 -0.58 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.009 0.018 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.23 5 5
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.23 4 4
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.056 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.036 -10000 0 -0.24 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.038 0.25 1 -0.24 4 5
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.032 0.18 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.048 -10000 0 -0.17 8 8
AP2 0.034 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.01 -10000 0 -10000 0 0
CLTB 0.025 0.017 0.26 5 -10000 0 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.01 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.006 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.011 0.2 2 -10000 0 2
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.022 0.19 2 -0.15 1 3
AP2M1 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 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 0.003 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.024 -10000 0 -0.2 3 3
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.043 -10000 0 -0.24 21 21
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.009 0.024 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.012 0.051 -10000 0 -0.26 29 29
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.024 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 0.14 2 -10000 0 2
PIP5K1A 0.007 0.016 -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 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.006 0.14 2 -10000 0 2
GOSR2 0.009 0.027 -10000 0 -0.31 6 6
USO1 0.009 0.023 -10000 0 -0.32 4 4
GBF1 0.01 0.02 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.015 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.068 0.025 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.017 -10000 0 -9999 0 0
RELB 0.026 0.024 0.26 10 -9999 0 10
NFKB2 0.024 0.008 0.26 1 -9999 0 1
NF kappa B2 p52/RelB 0.034 0.016 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.016 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1019 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.V7.A7HQ TCGA.S3.A6ZH TCGA.S3.A6ZG TCGA.S3.A6ZF
109_MAP3K5 -0.16 -0.34 0.025 0.059
47_PPARGC1A 0.025 -0.58 0.025 -0.58
105_BMP4 0.025 0.025 0.025 0.025
105_BMP6 0.025 0.025 0.025 0.025
105_BMP7 0.025 0.025 0.025 0.025
105_BMP2 -0.58 -0.58 -0.58 0.025
131_RELN/VLDLR -0.34 -0.34 -0.34 -0.34
30_TGFB1/TGF beta receptor Type II 0.024 0.02 0.024 0.024
84_STAT5B -0.34 -0.53 -0.061 -0.06
84_STAT5A -0.34 -0.53 -0.061 -0.06
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/8100368/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/8266076/Gistic2_Analysis_8266108/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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