PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1NK3DD9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1NK3DD9
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 56 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 334
Class IB PI3K non-lipid kinase events 287
Signaling events mediated by Stem cell factor receptor (c-Kit) 285
Signaling mediated by p38-alpha and p38-beta 275
Reelin signaling pathway 236
EGFR-dependent Endothelin signaling events 200
Aurora B signaling 193
FOXA2 and FOXA3 transcription factor networks 166
PLK1 signaling events 166
Angiopoietin receptor Tie2-mediated signaling 164
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 1093 . 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 ( 1093 ).

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 0.3056 334 17073 51 -0.053 0.69 1000 -1000 -0.048 -1000
Class IB PI3K non-lipid kinase events 0.2626 287 861 3 -0.13 -1000 1000 -1000 -0.019 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2608 285 22300 78 -0.57 0.18 1000 -1000 -0.057 -1000
Signaling mediated by p38-alpha and p38-beta 0.2516 275 12131 44 -0.32 0.024 1000 -1000 -0.019 -1000
Reelin signaling pathway 0.2159 236 13266 56 -0.32 0.054 1000 -1000 -0.03 -1000
EGFR-dependent Endothelin signaling events 0.1830 200 4205 21 -0.21 0.034 1000 -1000 -0.033 -1000
Aurora B signaling 0.1766 193 12988 67 -0.21 0.27 1000 -1000 -0.04 -1000
FOXA2 and FOXA3 transcription factor networks 0.1519 166 7649 46 -1.1 0.034 1000 -1000 -0.057 -1000
PLK1 signaling events 0.1519 166 14140 85 -0.063 0.23 1000 -1000 -0.032 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1500 164 14439 88 -0.32 0.11 1000 -1000 -0.058 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1482 162 11024 68 -0.34 0.15 1000 -1000 -0.046 -1000
HIF-1-alpha transcription factor network 0.1455 159 12102 76 -0.48 0.035 1000 -1000 -0.057 -1000
Glucocorticoid receptor regulatory network 0.1400 153 17489 114 -0.72 0.28 1000 -1000 -0.043 -1000
EPHB forward signaling 0.1391 152 12921 85 -0.2 0.14 1000 -1000 -0.058 -1000
Endothelins 0.1354 148 14252 96 -0.34 0.17 1000 -1000 -0.03 -1000
p75(NTR)-mediated signaling 0.1308 143 17891 125 -0.22 0.096 1000 -1000 -0.06 -1000
IL4-mediated signaling events 0.1199 131 11973 91 -0.66 0.25 1000 -1000 -0.051 -1000
Ephrin B reverse signaling 0.1125 123 5923 48 -0.2 0.089 1000 -1000 -0.024 -1000
Wnt signaling 0.1089 119 836 7 -0.097 0.017 1000 -1000 -0.009 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1052 115 6256 54 -0.32 0.054 1000 -1000 -0.04 -1000
IGF1 pathway 0.1043 114 6547 57 -0.11 0.044 1000 -1000 -0.033 -1000
Noncanonical Wnt signaling pathway 0.1006 110 2882 26 -0.097 0.024 1000 -1000 -0.03 -1000
Arf6 signaling events 0.1006 110 6827 62 -0.21 0.05 1000 -1000 -0.019 -1000
Plasma membrane estrogen receptor signaling 0.0961 105 9047 86 -0.12 0.11 1000 -1000 -0.045 -1000
IL23-mediated signaling events 0.0942 103 6207 60 -0.3 0.084 1000 -1000 -0.046 -1000
Nongenotropic Androgen signaling 0.0933 102 5320 52 -0.25 0.13 1000 -1000 -0.026 -1000
ErbB2/ErbB3 signaling events 0.0897 98 6381 65 -0.26 0.034 1000 -1000 -0.059 -1000
BMP receptor signaling 0.0897 98 7966 81 -0.38 0.1 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 0.0878 96 7935 82 -0.07 0.097 1000 -1000 -0.053 -1000
Calcium signaling in the CD4+ TCR pathway 0.0860 94 2933 31 -0.19 0.027 1000 -1000 -0.042 -1000
Signaling events mediated by PTP1B 0.0851 93 7141 76 -0.44 0.082 1000 -1000 -0.036 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0851 93 11277 120 -0.35 0.17 1000 -1000 -0.044 -1000
S1P1 pathway 0.0796 87 3150 36 -0.33 0.024 1000 -1000 -0.026 -1000
Visual signal transduction: Rods 0.0796 87 4562 52 -0.33 0.055 1000 -1000 -0.029 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0787 86 7388 85 -0.24 0.024 1000 -1000 -0.033 -1000
Aurora C signaling 0.0769 84 588 7 0 0.14 1000 -1000 -0.015 -1000
TCR signaling in naïve CD8+ T cells 0.0741 81 7620 93 -0.089 0.084 1000 -1000 -0.035 -1000
Effects of Botulinum toxin 0.0732 80 2093 26 -0.003 0.1 1000 -1000 -0.003 -1000
ErbB4 signaling events 0.0723 79 5468 69 -0.27 0.06 1000 -1000 -0.028 -1000
Glypican 1 network 0.0723 79 3801 48 -0.2 0.045 1000 -1000 -0.02 -1000
IL6-mediated signaling events 0.0704 77 5834 75 -0.18 0.053 1000 -1000 -0.032 -1000
amb2 Integrin signaling 0.0695 76 6263 82 -0.33 0.12 1000 -1000 -0.025 -1000
LPA receptor mediated events 0.0659 72 7394 102 -0.19 0.12 1000 -1000 -0.054 -1000
Signaling events mediated by the Hedgehog family 0.0650 71 3700 52 -0.12 0.028 1000 -1000 -0.027 -1000
Integrins in angiogenesis 0.0650 71 6022 84 -0.2 0.11 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 0.0640 70 2395 34 -0.073 0.18 1000 -1000 -0.037 -1000
Ephrin A reverse signaling 0.0622 68 481 7 -0.028 0.023 1000 -1000 -0.004 -1000
IL12-mediated signaling events 0.0613 67 5914 87 -0.32 0.072 1000 -1000 -0.06 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0576 63 2156 34 -0.024 0.058 1000 -1000 -0.024 -1000
PDGFR-alpha signaling pathway 0.0567 62 2758 44 -0.3 0.036 1000 -1000 -0.032 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0558 61 3212 52 -0.12 0.071 1000 -1000 -0.029 -1000
Canonical Wnt signaling pathway 0.0540 59 3017 51 -0.28 0.12 1000 -1000 -0.041 -1000
Visual signal transduction: Cones 0.0531 58 2226 38 -0.024 0.16 1000 -1000 -0.013 -1000
Fc-epsilon receptor I signaling in mast cells 0.0531 58 5659 97 -0.14 0.033 1000 -1000 -0.051 -1000
Syndecan-2-mediated signaling events 0.0522 57 3997 69 -0.12 0.11 1000 -1000 -0.031 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0512 56 1877 33 -0.38 0.059 1000 -1000 -0.036 -1000
Presenilin action in Notch and Wnt signaling 0.0494 54 3342 61 -0.27 0.12 1000 -1000 -0.039 -1000
Nectin adhesion pathway 0.0494 54 3450 63 -0.056 0.047 1000 -1000 -0.04 -1000
TCGA08_rtk_signaling 0.0494 54 1410 26 -0.19 0.037 1000 -1000 -0.009 -1000
Glypican 2 network 0.0467 51 207 4 0.033 0.058 1000 -1000 0.016 -1000
Rapid glucocorticoid signaling 0.0467 51 1030 20 -0.11 0.026 1000 -1000 -0.004 -1000
E-cadherin signaling in keratinocytes 0.0467 51 2235 43 -0.19 0.033 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 0.0467 51 875 17 -0.056 0.025 1000 -1000 -0.012 -1000
FAS signaling pathway (CD95) 0.0457 50 2359 47 -0.43 0.039 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 0.0448 49 1744 35 -0.23 0.054 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class III 0.0430 47 1892 40 -0.32 0.045 1000 -1000 -0.022 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0421 46 3438 74 -0.19 0.049 1000 -1000 -0.062 -1000
LPA4-mediated signaling events 0.0412 45 540 12 -0.11 0.006 1000 -1000 -0.023 -1000
Aurora A signaling 0.0393 43 2627 60 -0.079 0.18 1000 -1000 -0.013 -1000
Signaling events mediated by PRL 0.0393 43 1474 34 -0.12 0.035 1000 -1000 -0.034 -1000
Coregulation of Androgen receptor activity 0.0384 42 3204 76 -0.14 0.063 1000 -1000 -0.016 -1000
Regulation of Androgen receptor activity 0.0384 42 2958 70 -0.16 0.11 1000 -1000 -0.043 -1000
Syndecan-4-mediated signaling events 0.0375 41 2777 67 -0.2 0.12 1000 -1000 -0.04 -1000
Thromboxane A2 receptor signaling 0.0348 38 4041 105 -0.19 0.036 1000 -1000 -0.035 -1000
Regulation of p38-alpha and p38-beta 0.0348 38 2091 54 -0.24 0.052 1000 -1000 -0.042 -1000
TCGA08_retinoblastoma 0.0348 38 310 8 -0.018 0.06 1000 -1000 -0.002 -1000
Regulation of Telomerase 0.0348 38 3932 102 -0.2 0.14 1000 -1000 -0.034 -1000
Insulin Pathway 0.0348 38 2848 74 -0.12 0.06 1000 -1000 -0.047 -1000
IL27-mediated signaling events 0.0339 37 1919 51 -0.18 0.075 1000 -1000 -0.038 -1000
BCR signaling pathway 0.0339 37 3679 99 -0.077 0.056 1000 -1000 -0.045 -1000
Regulation of nuclear SMAD2/3 signaling 0.0311 34 4637 136 -0.19 0.077 1000 -1000 -0.027 -1000
Osteopontin-mediated events 0.0302 33 1275 38 -0.14 0.086 1000 -1000 -0.031 -1000
IL2 signaling events mediated by STAT5 0.0293 32 719 22 0.006 0.11 1000 -1000 -0.028 -1000
TCGA08_p53 0.0265 29 207 7 -0.011 0.02 1000 -1000 -0.004 -1000
HIF-2-alpha transcription factor network 0.0247 27 1179 43 -0.15 0.16 1000 -1000 -0.038 -1000
Class I PI3K signaling events mediated by Akt 0.0229 25 1702 68 -0.16 0.043 1000 -1000 -0.024 -1000
Caspase cascade in apoptosis 0.0220 24 1786 74 -0.025 0.057 1000 -1000 -0.028 -1000
Ceramide signaling pathway 0.0220 24 1851 76 -0.1 0.063 1000 -1000 -0.03 -1000
S1P5 pathway 0.0220 24 414 17 -0.007 0.033 1000 -1000 -0.004 -1000
S1P4 pathway 0.0220 24 622 25 -0.012 0.044 1000 -1000 -0.014 -1000
IL2 signaling events mediated by PI3K 0.0201 22 1311 58 -0.001 0.065 1000 -1000 -0.047 -1000
Hedgehog signaling events mediated by Gli proteins 0.0192 21 1375 65 -0.087 0.056 1000 -1000 -0.045 -1000
BARD1 signaling events 0.0183 20 1165 57 -0.046 0.1 1000 -1000 -0.031 -1000
Cellular roles of Anthrax toxin 0.0183 20 818 39 -0.079 0.027 1000 -1000 -0.018 -1000
mTOR signaling pathway 0.0183 20 1073 53 -0.022 0.028 1000 -1000 -0.034 -1000
JNK signaling in the CD4+ TCR pathway 0.0174 19 325 17 0.002 0.064 1000 -1000 -0.025 -1000
S1P3 pathway 0.0165 18 788 42 -0.014 0.042 1000 -1000 -0.027 -1000
FoxO family signaling 0.0156 17 1093 64 -0.016 0.23 1000 -1000 -0.032 -1000
Retinoic acid receptors-mediated signaling 0.0156 17 1039 58 -0.051 0.051 1000 -1000 -0.025 -1000
ceramide signaling pathway 0.0146 16 801 49 -0.001 0.036 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 0.0146 16 251 15 -0.026 0.024 1000 -1000 -0.025 -1000
Arf6 trafficking events 0.0146 16 1162 71 -0.27 0.042 1000 -1000 -0.019 -1000
IL1-mediated signaling events 0.0137 15 948 62 -0.015 0.061 1000 -1000 -0.025 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0128 14 393 28 -0.007 0.051 1000 -1000 -0.015 -1000
PLK2 and PLK4 events 0.0128 14 44 3 0.016 0.033 1000 -1000 -0.005 -1000
E-cadherin signaling in the nascent adherens junction 0.0128 14 1068 76 -0.023 0.054 1000 -1000 -0.049 -1000
PDGFR-beta signaling pathway 0.0128 14 1403 97 -0.024 0.056 1000 -1000 -0.05 -1000
p38 MAPK signaling pathway 0.0119 13 610 44 -0.018 0.067 1000 -1000 -0.018 -1000
TRAIL signaling pathway 0.0110 12 582 48 -0.015 0.043 1000 -1000 -0.026 -1000
Class I PI3K signaling events 0.0110 12 927 73 -0.018 0.051 1000 -1000 -0.029 -1000
IFN-gamma pathway 0.0101 11 783 68 -0.006 0.076 1000 -1000 -0.042 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0101 11 419 37 -0.009 0.067 1000 -1000 -0.023 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0101 11 517 45 0.003 0.054 1000 -1000 -0.036 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0091 10 877 83 -0.019 0.047 1000 -1000 -0.028 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0091 10 1260 125 -0.1 0.053 1000 -1000 -0.031 -1000
E-cadherin signaling events 0.0091 10 54 5 0.012 0.033 1000 -1000 0.007 -1000
Signaling events mediated by HDAC Class II 0.0082 9 702 75 -0.035 0.062 1000 -1000 -0.03 -1000
a4b1 and a4b7 Integrin signaling 0.0082 9 48 5 0.024 0.041 1000 -1000 0.013 -1000
EPO signaling pathway 0.0082 9 528 55 0.014 0.08 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 0.0082 9 297 32 -0.12 0.039 1000 -1000 -0.021 -1000
Canonical NF-kappaB pathway 0.0073 8 349 39 0 0.051 1000 -1000 -0.031 -1000
VEGFR1 specific signals 0.0073 8 473 56 -0.1 0.052 1000 -1000 -0.038 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0046 5 119 23 -0.004 0.043 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 0.0046 5 612 104 -0.06 0.057 1000 -1000 -0.028 -1000
Atypical NF-kappaB pathway 0.0046 5 179 31 0 0.028 1000 -1000 -0.013 -1000
Circadian rhythm pathway 0.0037 4 97 22 -0.007 0.049 1000 -1000 -0.013 -1000
Paxillin-dependent events mediated by a4b1 0.0037 4 177 36 -0.047 0.051 1000 -1000 -0.034 -1000
Arf6 downstream pathway 0.0027 3 153 43 -0.055 0.056 1000 -1000 -0.023 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0009 1 27 27 -0.008 0.056 1000 -1000 -0.035 -1000
Arf1 pathway 0.0009 1 97 54 -0.001 0.045 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 0 0.067 1000 -1000 0 -1000
Total NA 8463 501486 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 0.57 0.39 0.97 399 -1 3 402
PLK1 0.35 0.24 0.62 336 -0.9 1 337
BIRC5 0.37 0.24 0.66 263 -0.89 3 266
HSPA1B 0.57 0.38 0.97 398 -1 3 401
MAP2K1 0.16 0.11 0.3 320 -10000 0 320
BRCA2 0.58 0.4 0.98 409 -0.99 4 413
FOXM1 0.66 0.48 1.1 457 -1.3 3 460
XRCC1 0.57 0.39 0.97 399 -1 3 402
FOXM1B/p19 0.12 0.26 0.78 66 -0.99 5 71
Cyclin D1/CDK4 0.5 0.37 0.88 402 -0.99 3 405
CDC2 0.62 0.43 1 456 -1.1 3 459
TGFA 0.5 0.39 0.87 430 -0.92 8 438
SKP2 0.58 0.39 0.98 401 -1 3 404
CCNE1 0.09 0.095 0.29 179 -10000 0 179
CKS1B 0.57 0.39 0.93 457 -1 3 460
RB1 0.29 0.3 0.66 341 -0.62 6 347
FOXM1C/SP1 0.52 0.36 0.89 375 -1.1 5 380
AURKB 0.29 0.3 0.63 258 -0.83 18 276
CENPF 0.66 0.45 1.1 484 -0.99 3 487
CDK4 0.08 0.053 0.23 25 -10000 0 25
MYC 0.34 0.36 0.82 270 -0.96 6 276
CHEK2 0.16 0.11 0.3 305 -10000 0 305
ONECUT1 0.53 0.39 0.9 431 -1.1 3 434
CDKN2A -0.053 0.11 0.22 27 -0.22 217 244
LAMA4 0.57 0.4 0.97 406 -1.1 6 412
FOXM1B/HNF6 0.53 0.4 0.94 395 -1.3 3 398
FOS 0.27 0.64 0.99 313 -0.99 76 389
SP1 0.024 0.021 -10000 0 -0.2 5 5
CDC25B 0.58 0.39 0.97 405 -1 3 408
response to radiation 0.11 0.084 0.23 260 -10000 0 260
CENPB 0.57 0.39 0.97 402 -1 3 405
CENPA 0.63 0.43 1 469 -1 3 472
NEK2 0.69 0.44 1.1 512 -0.97 3 515
HIST1H2BA 0.57 0.39 0.97 391 -1 3 394
CCNA2 0.14 0.13 0.3 401 -10000 0 401
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.6 0.42 1 399 -1.2 3 402
CCNB2 0.63 0.43 1 475 -1 3 478
CCNB1 0.63 0.45 1.1 435 -1.1 3 438
ETV5 0.58 0.4 0.99 396 -1 3 399
ESR1 0.44 0.55 1 367 -0.99 19 386
CCND1 0.52 0.41 0.93 426 -1 3 429
GSK3A 0.13 0.089 0.27 190 -10000 0 190
Cyclin A-E1/CDK1-2 0.23 0.16 0.41 406 -10000 0 406
CDK2 0.056 0.028 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.14 0.11 0.26 366 -10000 0 366
FOXM1B/Cbp/p300 0.26 0.29 0.72 84 -1.1 3 87
GAS1 0.52 0.49 0.96 394 -1.1 38 432
MMP2 0.57 0.41 0.97 398 -1.2 10 408
RB1/FOXM1C 0.46 0.38 0.86 399 -1 3 402
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.13 0.26 0.56 287 -10000 0 287
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.56 287 287
PDE3B -0.13 0.26 -10000 0 -0.57 287 287
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.16 0.2 0.34 3 -0.38 469 472
CRKL -0.17 0.21 0.26 1 -0.4 482 483
HRAS -0.12 0.18 -10000 0 -0.35 321 321
mol:PIP3 -0.14 0.2 0.29 1 -0.38 355 356
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 -0.42 489 489
FOXO3 -0.14 0.2 0.53 1 -0.36 402 403
AKT1 -0.16 0.21 0.37 1 -0.38 450 451
BAD -0.15 0.2 0.34 2 -0.36 440 442
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 489 489
GSK3B -0.14 0.2 0.53 1 -0.36 420 421
RAF1 -0.097 0.16 0.25 4 -0.3 244 248
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 486 486
STAT1 -0.44 0.52 -10000 0 -1 495 495
HRAS/SPRED1 -0.094 0.16 -10000 0 -0.34 76 76
cell proliferation -0.18 0.22 -10000 0 -0.42 489 489
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.031 -10000 0 -0.57 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 493 493
HRAS/SPRED2 -0.094 0.16 -10000 0 -0.3 306 306
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.4 411 411
MAPK3 -0.066 0.12 0.3 7 -0.27 35 42
STAP1 -0.18 0.22 -10000 0 -0.42 490 490
GRAP2 0.017 0.063 0.26 3 -0.57 12 15
JAK2 -0.37 0.44 -10000 0 -0.84 495 495
STAT1 (dimer) -0.43 0.51 -10000 0 -0.97 495 495
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 418 418
actin filament polymerization -0.18 0.22 0.33 1 -0.41 489 490
LYN 0.021 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.59 497 497
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 434 434
PI3K -0.15 0.22 -10000 0 -0.4 463 463
PTEN 0.023 0.019 -10000 0 -0.57 1 1
SCF/KIT/EPO/EPOR -0.51 0.63 -10000 0 -1.2 492 492
MAPK8 -0.19 0.22 -10000 0 -0.42 489 489
STAT3 (dimer) -0.18 0.22 0.27 1 -0.41 486 487
positive regulation of transcription -0.052 0.1 0.24 13 -0.23 24 37
mol:GDP -0.13 0.19 -10000 0 -0.37 337 337
PIK3C2B -0.17 0.21 -10000 0 -0.42 380 380
CBL/CRKL -0.16 0.2 -10000 0 -0.38 471 471
FER -0.18 0.22 -10000 0 -0.42 490 490
SH2B3 -0.18 0.22 -10000 0 -0.42 491 491
PDPK1 -0.12 0.19 0.34 9 -0.35 329 338
SNAI2 -0.18 0.21 0.28 4 -0.42 437 441
positive regulation of cell proliferation -0.32 0.38 -10000 0 -0.73 495 495
KITLG -0.004 0.058 0.25 10 -0.59 5 15
cell motility -0.32 0.38 -10000 0 -0.73 495 495
PTPN6 0.032 0.017 0.27 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -1 15 15
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 497 497
SOCS1 0.025 0.033 0.26 14 -0.57 1 15
cell migration 0.18 0.22 0.42 493 -10000 0 493
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.041 0.091 0.24 169 -10000 0 169
VAV1 0.023 0.033 0.26 2 -0.57 3 5
GRB10 -0.18 0.22 -10000 0 -0.42 488 488
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 495 495
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.13 0.3 7 -0.28 45 52
CBL 0.022 0.007 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 493 493
MAP2K2 -0.075 0.13 0.28 12 -0.28 49 61
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 359 359
STAT5A -0.27 0.33 -10000 0 -0.62 497 497
GRB2 0.023 0.009 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 436 440
SHC/GRAP2 0.024 0.046 -10000 0 -0.29 17 17
PTPRO -0.18 0.22 -10000 0 -0.42 489 489
SH2B2 -0.18 0.22 -10000 0 -0.42 489 489
DOK1 0.025 0.014 0.26 4 -10000 0 4
MATK -0.19 0.22 -10000 0 -0.42 495 495
CREBBP -0.027 0.072 -10000 0 -0.18 19 19
BCL2 -0.16 0.32 -10000 0 -1.3 60 60
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.32 0.5 0.42 4 -1 357 361
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.088 0.18 -10000 0 -0.34 351 351
ATF2/c-Jun -0.081 0.16 -10000 0 -0.41 99 99
MAPK11 -0.082 0.18 -10000 0 -0.35 322 322
MITF -0.12 0.22 0.28 1 -0.41 353 354
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 359 359
KRT8 -0.11 0.21 -10000 0 -0.4 335 335
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.52 356 356
CEBPB -0.1 0.2 0.28 1 -0.4 332 333
SLC9A1 -0.11 0.21 -10000 0 -0.41 352 352
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.39 348 348
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.45 325 325
JUN -0.081 0.16 -10000 0 -0.41 99 99
PPARGC1A -0.2 0.33 0.26 1 -0.56 420 421
USF1 -0.1 0.19 0.31 3 -0.38 335 338
RAB5/GDP/GDI1 -0.081 0.16 -10000 0 -0.3 351 351
NOS2 -0.11 0.22 -10000 0 -0.55 93 93
DDIT3 -0.11 0.2 -10000 0 -0.4 353 353
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.094 0.17 0.28 4 -0.32 356 360
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 323 323
CREB1 -0.12 0.22 -10000 0 -0.43 356 356
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.4 320 320
RPS6KA4 -0.11 0.21 -10000 0 -0.4 351 351
PLA2G4A -0.13 0.22 -10000 0 -0.42 353 353
GDI1 -0.11 0.21 -10000 0 -0.4 358 358
TP53 -0.15 0.27 0.28 1 -0.52 337 338
RPS6KA5 -0.12 0.22 -10000 0 -0.41 360 360
ESR1 -0.15 0.24 0.28 1 -0.42 409 410
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 354 354
MEF2A -0.11 0.21 0.28 1 -0.4 353 354
EIF4EBP1 -0.12 0.22 0.28 1 -0.43 341 342
KRT19 -0.11 0.21 0.31 1 -0.41 327 328
ELK4 -0.1 0.19 0.3 3 -0.38 336 339
ATF6 -0.1 0.19 0.31 3 -0.38 339 342
ATF1 -0.12 0.22 -10000 0 -0.43 360 360
p38alpha-beta/MAPKAPK2 -0.095 0.22 -10000 0 -0.41 308 308
p38alpha-beta/MAPKAPK3 -0.1 0.25 -10000 0 -0.45 325 325
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.027 -10000 0 -10000 0 0
VLDLR 0.007 0.096 -10000 0 -0.57 29 29
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.021 0.026 -10000 0 -0.57 2 2
ITGA3 0.022 0.021 0.26 1 -0.57 1 2
RELN/VLDLR/Fyn -0.19 0.21 -10000 0 -0.37 604 604
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.044 -10000 0 -0.32 7 7
AKT1 -0.15 0.14 -10000 0 -0.27 550 550
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.26 61 -10000 0 61
RELN/LRP8/DAB1 -0.16 0.19 0.32 4 -0.32 608 612
LRPAP1/LRP8 0.048 0.047 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.14 0.18 0.31 4 -0.3 592 596
DAB1/alpha3/beta1 Integrin -0.14 0.17 -10000 0 -0.3 528 528
long-term memory -0.18 0.22 0.32 6 -0.35 584 590
DAB1/LIS1 -0.14 0.19 0.3 4 -0.3 603 607
DAB1/CRLK/C3G -0.14 0.18 -10000 0 -0.3 595 595
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.14 0.19 0.3 4 -0.3 604 608
ARHGEF2 0.02 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.033 0.18 0.26 13 -0.57 107 120
CDK5R1 0.028 0.034 0.26 23 -10000 0 23
RELN -0.32 0.29 0.26 2 -0.57 619 621
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RELN/LRP8/Fyn -0.18 0.2 -10000 0 -0.35 596 596
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 0.33 4 -0.35 559 563
MAPK8 0.02 0.051 -10000 0 -0.57 8 8
RELN/VLDLR/DAB1 -0.17 0.19 0.32 2 -0.34 608 610
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.18 0.22 2 -0.32 609 611
RELN/LRP8 -0.18 0.2 -10000 0 -0.35 612 612
GRIN2B/RELN/LRP8/DAB1/Fyn -0.16 0.2 0.36 3 -0.32 614 617
PI3K 0.028 0.049 -10000 0 -0.38 14 14
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.021 -10000 0 -0.25 3 3
RAP1A -0.16 0.15 0.31 5 -0.3 468 473
PAFAH1B1 0.022 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.029 0.26 4 -0.57 2 6
CRLK/C3G 0.033 0.01 -10000 0 -10000 0 0
GRIN2B -0.018 0.14 0.26 1 -0.57 70 71
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.086 0.12 -10000 0 -0.35 78 78
neuron adhesion -0.14 0.15 0.34 6 -0.47 24 30
LRP8 0.046 0.068 0.26 103 -10000 0 103
GSK3B -0.14 0.14 -10000 0 -0.3 188 188
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.31 2 -0.32 594 596
MAP3K11 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.15 0.16 -10000 0 -0.28 591 591
CDK5 0.025 0.015 0.26 4 -10000 0 4
MAPT -0.021 0.2 0.88 21 -0.51 106 127
neuron migration -0.18 0.18 0.27 2 -0.34 505 507
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.087 0.12 -10000 0 -0.35 78 78
RELN/VLDLR -0.17 0.2 -10000 0 -0.33 612 612
EGFR-dependent Endothelin signaling events

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.022 0.26 9 -10000 0 9
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EGF/EGFR -0.16 0.22 -10000 0 -0.36 518 518
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.35 395 395
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.027 0.26 1 -0.57 2 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.082 0.23 0.26 2 -0.57 194 196
EGF/EGFR dimer/SHC -0.15 0.22 -10000 0 -0.4 422 422
mol:GDP -0.12 0.19 -10000 0 -0.35 395 395
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.017 0.15 0.26 1 -0.57 74 75
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.32 394 394
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.11 0.18 -10000 0 -0.33 394 394
FRAP1 -0.14 0.16 0.16 3 -0.33 395 398
EGF/EGFR dimer -0.21 0.25 -10000 0 -0.45 537 537
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
ETA receptor/Endothelin-1 0.002 0.12 -10000 0 -0.41 78 78
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.1 0.099 0.23 313 -0.26 2 315
STMN1 0.078 0.078 0.26 68 -10000 0 68
Aurora B/RasGAP/Survivin 0.19 0.14 0.33 504 -10000 0 504
Chromosomal passenger complex/Cul3 protein complex 0.006 0.14 0.19 189 -0.24 133 322
BIRC5 0.18 0.11 0.26 711 -10000 0 711
DES -0.16 0.32 -10000 0 -0.59 250 250
Aurora C/Aurora B/INCENP 0.11 0.078 0.32 9 -0.3 1 10
Aurora B/TACC1 0.072 0.098 -10000 0 -0.33 25 25
Aurora B/PP2A 0.11 0.082 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.032 0.026 0.14 8 -10000 0 8
mitotic metaphase/anaphase transition -0.006 0.005 -10000 0 -10000 0 0
NDC80 0.14 0.12 0.26 484 -10000 0 484
Cul3 protein complex -0.11 0.2 -10000 0 -0.36 415 415
KIF2C 0.15 0.1 0.23 597 -10000 0 597
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.25 790 -10000 0 790
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.082 -10000 0 -10000 0 0
SEPT1 0.03 0.042 0.26 35 -10000 0 35
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.021 0.26 9 -10000 0 9
NSUN2/NPM1/Nucleolin 0.074 0.19 0.32 26 -0.45 90 116
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.006 -10000 0 -10000 0 0
H3F3B 0.07 0.06 0.23 33 -10000 0 33
AURKB 0.14 0.12 0.25 560 -10000 0 560
AURKC 0.026 0.032 0.26 14 -0.57 1 15
CDCA8 0.11 0.11 0.26 355 -10000 0 355
cytokinesis 0.14 0.14 0.32 310 -0.33 6 316
Aurora B/Septin1 0.18 0.17 0.36 382 -0.33 3 385
AURKA 0.11 0.11 0.25 428 -10000 0 428
INCENP 0.03 0.008 -10000 0 -10000 0 0
KLHL13 -0.21 0.29 -10000 0 -0.57 424 424
BUB1 0.17 0.11 0.25 709 -10000 0 709
hSgo1/Aurora B/Survivin 0.27 0.18 0.41 630 -10000 0 630
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.14 0.36 331 -10000 0 331
SGOL1 0.16 0.11 0.26 656 -10000 0 656
CENPA 0.17 0.14 0.3 497 -0.23 2 499
NCAPG 0.13 0.12 0.26 505 -10000 0 505
Aurora B/HC8 Proteasome 0.11 0.082 -10000 0 -10000 0 0
NCAPD2 0.024 0.009 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.11 0.081 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.11 0.11 0.26 408 -10000 0 408
NPM1 0.067 0.12 0.25 5 -0.36 35 40
RASA1 0.024 0.004 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.081 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.2 0.15 0.37 391 -10000 0 391
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 0.073 0.12 0.27 15 -0.77 2 17
MYLK 0.02 0.14 0.23 8 -0.31 128 136
KIF23 0.098 0.11 0.26 319 -10000 0 319
VIM 0.078 0.084 0.37 32 -0.41 2 34
RACGAP1 0.04 0.046 0.27 41 -10000 0 41
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.062 0.14 -10000 0 -0.47 34 34
Chromosomal passenger complex 0.17 0.12 0.28 547 -10000 0 547
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 490 -10000 0 490
TACC1 0.006 0.089 -10000 0 -0.57 25 25
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.24 0.27 0.52 1 -0.72 125 126
PCK1 -0.92 0.63 -10000 0 -1.4 655 655
HNF4A -0.23 0.28 0.66 2 -0.8 73 75
KCNJ11 -0.28 0.29 -10000 0 -0.76 163 163
AKT1 -0.16 0.16 0.37 1 -0.4 109 110
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.44 0.47 -10000 0 -1.1 348 348
NKX2-1 -0.044 0.16 0.39 21 -0.38 35 56
ACADM -0.25 0.27 0.52 1 -0.76 106 107
TAT -1.1 0.63 -10000 0 -1.4 765 765
CEBPB 0.024 0.01 -10000 0 -10000 0 0
CEBPA 0.02 0.058 -10000 0 -0.57 10 10
TTR -0.4 0.29 0.57 1 -0.79 253 254
PKLR -0.22 0.27 0.62 3 -0.76 85 88
APOA1 -0.28 0.31 0.79 1 -0.87 92 93
CPT1C -0.24 0.27 0.55 2 -0.74 111 113
ALAS1 -0.15 0.16 -10000 0 -0.69 8 8
TFRC -0.42 0.26 -10000 0 -0.73 282 282
FOXF1 0.02 0.041 0.26 6 -0.57 4 10
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.032 0.27 8 -10000 0 8
CPT1A -0.23 0.27 0.53 2 -0.73 116 118
HMGCS1 -0.24 0.27 0.62 2 -0.74 116 118
NR3C1 -0.12 0.12 -10000 0 -0.26 269 269
CPT1B -0.24 0.27 0.52 1 -0.76 106 107
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.023 -10000 0 -10000 0 0
GCK -0.27 0.32 0.52 1 -0.89 134 135
CREB1 -0.076 0.093 -10000 0 -0.26 46 46
IGFBP1 -0.41 0.54 -10000 0 -1.4 238 238
PDX1 -0.12 0.15 -10000 0 -0.57 4 4
UCP2 -0.24 0.27 0.52 2 -0.74 106 108
ALDOB -0.28 0.28 0.68 1 -0.77 137 138
AFP -0.56 0.5 -10000 0 -1.1 472 472
BDH1 -0.24 0.26 -10000 0 -0.77 92 92
HADH -0.27 0.28 -10000 0 -0.8 107 107
F2 -0.28 0.3 0.79 1 -0.88 79 80
HNF1A 0.034 0.032 0.27 8 -10000 0 8
G6PC -0.18 0.12 -10000 0 -0.55 10 10
SLC2A2 -0.16 0.17 0.62 1 -0.78 2 3
INS 0.018 0.077 0.24 5 -10000 0 5
FOXA1 -0.22 0.23 0.34 4 -0.43 429 433
FOXA3 -0.36 0.21 0.3 6 -0.46 795 801
FOXA2 -0.32 0.32 0.77 1 -0.81 191 192
ABCC8 -0.32 0.38 -10000 0 -1 178 178
ALB -0.76 0.54 0.35 1 -1.1 715 716
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 -0.063 0.048 0.1 8 -0.1 577 585
BUB1B 0.082 0.066 0.15 419 -10000 0 419
PLK1 0.049 0.038 0.11 151 -10000 0 151
PLK1S1 0.025 0.034 0.13 10 -0.17 19 29
KIF2A 0.041 0.039 0.25 8 -10000 0 8
regulation of mitotic centrosome separation 0.048 0.038 0.11 151 -10000 0 151
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.23 0.14 0.32 692 -10000 0 692
WEE1 0.043 0.06 0.23 2 -0.27 25 27
cytokinesis 0.12 0.086 0.21 269 -0.37 2 271
PP2A-alpha B56 0.11 0.12 -10000 0 -0.46 22 22
AURKA 0.063 0.052 0.12 444 -0.14 4 448
PICH/PLK1 0.096 0.087 0.21 312 -10000 0 312
CENPE 0.061 0.054 0.16 87 -10000 0 87
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.041 0.038 0.25 8 -10000 0 8
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.078 0.054 0.12 569 -0.14 2 571
PAK1 0.022 0.019 0.25 6 -10000 0 6
SPC24 0.17 0.11 0.26 664 -10000 0 664
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.071 0.069 0.14 435 -0.19 22 457
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 55 -10000 0 55
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.022 0.019 0.054 137 -10000 0 137
G2 phase of mitotic cell cycle 0.001 0.003 0.015 12 -10000 0 12
STAG2 0.024 0.018 -10000 0 -0.57 1 1
GRASP65/GM130/RAB1/GTP 0.011 0.08 -10000 0 -0.5 25 25
spindle elongation 0.048 0.038 0.11 151 -10000 0 151
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.1 0.13 -10000 0 -0.48 33 33
TPT1 0.013 0.056 0.12 2 -0.17 77 79
CDC25C 0.11 0.067 0.16 482 -0.2 14 496
CDC25B 0.029 0.031 0.26 18 -10000 0 18
SGOL1 0.063 0.048 0.1 577 -0.1 8 585
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.068 0.064 0.31 11 -10000 0 11
CDC14B -0.01 0.075 -10000 0 -0.42 34 34
CDC20 0.14 0.12 0.26 565 -10000 0 565
PLK1/PBIP1 0.036 0.046 0.14 139 -10000 0 139
mitosis -0.004 0.005 0.027 4 -10000 0 4
FBXO5 0.03 0.035 0.16 15 -0.12 1 16
CDC2 0.003 0.004 0.011 192 -10000 0 192
NDC80 0.16 0.12 0.26 619 -10000 0 619
metaphase plate congression 0.028 0.054 0.14 2 -0.19 49 51
ERCC6L 0.087 0.083 0.24 169 -10000 0 169
NLP/gamma Tubulin 0.023 0.024 0.078 24 -0.085 10 34
microtubule cytoskeleton organization 0.013 0.056 0.12 2 -0.17 78 80
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 13 -10000 0 13
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 13 -10000 0 13
PLK1/PRC1-2 0.2 0.12 0.27 759 -10000 0 759
GRASP65/GM130/RAB1/GTP/PLK1 0.069 0.03 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.041 0.035 0.098 157 -10000 0 157
mitotic prometaphase 0.002 0.005 0.022 51 -10000 0 51
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.051 -10000 0 -0.31 3 3
microtubule-based process 0.17 0.089 0.22 784 -10000 0 784
Golgi organization 0.048 0.038 0.11 151 -10000 0 151
Cohesin/SA2 0.053 0.031 0.16 3 -0.3 1 4
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.26 790 -10000 0 790
APC/C/CDC20 0.14 0.099 0.23 560 -10000 0 560
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.03 0.046 0.14 139 -10000 0 139
PRC1 0.079 0.099 0.26 257 -10000 0 257
ECT2 0.049 0.057 0.23 59 -10000 0 59
C13orf34 0.04 0.033 0.094 143 -10000 0 143
NUDC 0.028 0.054 0.14 2 -0.19 49 51
regulation of attachment of spindle microtubules to kinetochore 0.082 0.066 0.15 422 -10000 0 422
spindle assembly 0.035 0.029 0.092 81 -10000 0 81
spindle stabilization 0.025 0.034 0.13 10 -0.17 19 29
APC/C/HCDH1 0.009 0.067 -10000 0 -0.35 36 36
MKLP2/PLK1 0.17 0.089 0.22 784 -10000 0 784
CCNB1 0.069 0.091 0.26 205 -10000 0 205
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.026 0.086 0.23 1 -0.38 39 40
TUBG1 0.023 0.038 0.13 3 -0.16 33 36
G2/M transition of mitotic cell cycle 0.041 0.043 0.19 12 -10000 0 12
MLF1IP 0.023 0.045 0.14 147 -10000 0 147
INCENP 0.024 0.005 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.16 0.39 -10000 0 -0.86 241 241
NCK1/PAK1/Dok-R -0.096 0.17 -10000 0 -0.41 241 241
NCK1/Dok-R -0.19 0.46 -10000 0 -1 241 241
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.044 0.099 0.24 212 -10000 0 212
RELA 0.023 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 0.048 0.11 0.27 210 -10000 0 210
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.17 0.44 -10000 0 -0.97 240 240
FN1 0.11 0.11 0.26 421 -10000 0 421
PLD2 -0.22 0.47 -10000 0 -1.1 240 240
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.011 0.18 0.26 142 -0.57 80 222
ELK1 -0.19 0.42 -10000 0 -0.96 241 241
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 0.023 0.019 0.26 6 -10000 0 6
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.49 -10000 0 -1 241 241
CDKN1A -0.11 0.26 -10000 0 -0.62 175 175
ITGA5 0.024 0.007 0.26 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.19 0.46 -10000 0 -1 240 240
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.11 0.29 0.38 2 -0.64 241 243
PLG -0.22 0.47 -10000 0 -1.1 241 241
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.16 0.36 -10000 0 -0.82 241 241
GRB2 0.023 0.009 0.26 1 -10000 0 1
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
ANGPT2 -0.15 0.28 -10000 0 -0.72 151 151
BMX -0.32 0.51 -10000 0 -1.2 242 242
ANGPT1 -0.23 0.5 -10000 0 -1.2 212 212
tube development -0.13 0.29 -10000 0 -0.66 219 219
ANGPT4 -0.15 0.26 -10000 0 -0.57 305 305
response to hypoxia -0.014 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.22 0.51 -10000 0 -1.1 240 240
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
STAT5A (dimer) -0.15 0.34 -10000 0 -0.78 203 203
mol:L-citrulline -0.11 0.29 0.38 2 -0.64 241 243
AGTR1 -0.097 0.26 0.26 59 -0.57 244 303
MAPK14 -0.21 0.47 -10000 0 -1.1 243 243
Tie2/SHP2 -0.1 0.32 -10000 0 -1.1 90 90
TEK -0.11 0.35 -10000 0 -1.2 90 90
RPS6KB1 -0.14 0.38 -10000 0 -0.82 241 241
Angiotensin II/AT1 -0.071 0.19 0.18 59 -0.41 247 306
Tie2/Ang1/GRB2 -0.21 0.49 -10000 0 -1.1 241 241
MAPK3 -0.19 0.43 -10000 0 -0.98 240 240
MAPK1 -0.2 0.43 -10000 0 -0.99 240 240
Tie2/Ang1/GRB7 -0.22 0.49 -10000 0 -1.1 241 241
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.22 0.48 -10000 0 -1.1 241 241
PI3K -0.19 0.44 -10000 0 -0.99 241 241
FES -0.21 0.47 -10000 0 -1.1 243 243
Crk/Dok-R -0.19 0.46 -10000 0 -1 241 241
Tie2/Ang1/ABIN2 -0.21 0.5 -10000 0 -1.1 241 241
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.14 0.34 -10000 0 -0.77 241 241
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.38 0.47 1 -0.8 240 241
Tie2/Ang2 -0.18 0.4 -10000 0 -0.93 207 207
Tie2/Ang1 -0.23 0.52 -10000 0 -1.2 241 241
FOXO1 -0.14 0.35 0.47 1 -0.78 241 242
ELF1 0.011 0.037 -10000 0 -10000 0 0
ELF2 -0.21 0.47 -10000 0 -1.1 240 240
mol:Choline -0.2 0.45 -10000 0 -1 240 240
cell migration -0.039 0.1 -10000 0 -0.23 241 241
FYN -0.15 0.33 -10000 0 -0.77 208 208
DOK2 0.02 0.031 0.26 4 -0.57 2 6
negative regulation of cell cycle -0.1 0.24 -10000 0 -0.56 175 175
ETS1 -0.023 0.11 -10000 0 -0.27 173 173
PXN -0.1 0.32 0.42 2 -0.67 240 242
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.13 0.33 -10000 0 -0.73 241 241
RAC1 0.024 0.003 -10000 0 -10000 0 0
TNF -0.026 0.13 0.26 21 -0.27 201 222
MAPKKK cascade -0.2 0.45 -10000 0 -1 240 240
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.21 0.48 -10000 0 -1.1 241 241
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.099 0.26 0.37 2 -0.57 241 243
mol:Phosphatidic acid -0.2 0.45 -10000 0 -1 240 240
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.11 0.29 0.38 2 -0.64 241 243
Rac1/GTP -0.14 0.35 -10000 0 -0.77 241 241
MMP2 -0.22 0.48 -10000 0 -1.1 241 241
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.099 0.13 0.3 282 -0.22 2 284
NFATC2 -0.025 0.23 0.47 9 -0.58 106 115
NFATC3 -0.04 0.12 -10000 0 -0.28 172 172
CD40LG -0.29 0.5 0.65 6 -0.97 321 327
ITCH -0.002 0.082 -10000 0 -0.26 98 98
CBLB -0.002 0.083 -10000 0 -0.26 99 99
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.093 0.39 0.59 53 -0.98 94 147
JUNB 0.024 0.011 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.1 -10000 0 -0.3 105 105
T cell anergy -0.026 0.14 0.33 1 -0.41 104 105
TLE4 -0.026 0.19 0.36 1 -0.55 87 88
Jun/NFAT1-c-4/p21SNFT -0.17 0.43 0.67 6 -0.84 258 264
AP-1/NFAT1-c-4 -0.31 0.61 0.74 15 -1.1 316 331
IKZF1 -0.017 0.16 0.47 7 -0.46 80 87
T-helper 2 cell differentiation -0.084 0.28 0.48 1 -0.81 90 91
AP-1/NFAT1 -0.098 0.26 0.44 13 -0.46 288 301
CALM1 0.011 0.063 -10000 0 -10000 0 0
EGR2 -0.25 0.55 0.69 2 -1.4 165 167
EGR3 -0.33 0.62 0.67 2 -1.3 298 300
NFAT1/FOXP3 0.05 0.22 0.46 107 -0.44 89 196
EGR1 -0.16 0.27 -10000 0 -0.56 336 336
JUN 0.015 0.054 -10000 0 -0.57 6 6
EGR4 0.04 0.06 0.26 75 -10000 0 75
mol:Ca2+ -0.01 0.054 -10000 0 -0.18 96 96
GBP3 -0.021 0.17 0.39 2 -0.55 58 60
FOSL1 0.027 0.048 0.26 26 -0.57 3 29
NFAT1-c-4/MAF/IRF4 -0.19 0.45 0.59 7 -0.86 286 293
DGKA -0.017 0.16 0.56 1 -0.45 81 82
CREM 0.023 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.26 0.48 0.6 3 -0.93 306 309
CTLA4 0.038 0.21 0.43 124 -0.48 53 177
NFAT1-c-4 (dimer)/EGR1 -0.28 0.51 0.61 4 -1 319 323
NFAT1-c-4 (dimer)/EGR4 -0.18 0.45 0.59 6 -0.84 289 295
FOS -0.15 0.27 -10000 0 -0.57 310 310
IFNG -0.054 0.27 0.47 18 -0.7 101 119
T cell activation -0.15 0.29 0.62 4 -0.66 190 194
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 0.15 0.33 0.64 300 -0.61 2 302
TNF -0.25 0.44 0.54 4 -0.89 311 315
FASLG -0.32 0.63 0.79 2 -1.2 309 311
TBX21 0.021 0.12 0.35 15 -0.57 36 51
BATF3 0.021 0.015 0.26 3 -10000 0 3
PRKCQ 0.006 0.11 0.28 8 -0.57 39 47
PTPN1 -0.017 0.16 0.39 3 -0.48 63 66
NFAT1-c-4/ICER1 -0.19 0.44 0.54 4 -0.84 289 293
GATA3 0.01 0.11 0.26 28 -0.57 35 63
T-helper 1 cell differentiation -0.052 0.27 0.46 20 -0.68 102 122
IL2RA -0.094 0.37 0.59 47 -0.82 127 174
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.16 0.36 1 -0.48 64 65
E2F1 0.096 0.11 0.26 320 -10000 0 320
PPARG -0.11 0.25 -10000 0 -0.57 252 252
SLC3A2 -0.018 0.16 0.36 1 -0.48 65 66
IRF4 -0.019 0.16 0.26 13 -0.57 83 96
PTGS2 -0.34 0.54 0.63 4 -1 348 352
CSF2 -0.28 0.48 0.64 9 -0.95 315 324
JunB/Fra1/NFAT1-c-4 -0.17 0.43 0.6 4 -0.81 284 288
IL4 -0.089 0.29 0.48 1 -0.86 90 91
IL5 -0.28 0.48 0.58 7 -0.94 320 327
IL2 -0.15 0.3 0.62 4 -0.67 186 190
IL3 -0.05 0.13 -10000 0 -0.82 18 18
RNF128 -0.041 0.2 0.27 5 -0.65 105 110
NFATC1 -0.15 0.34 0.61 2 -0.65 300 302
CDK4 0.12 0.24 0.61 97 -0.57 2 99
PTPRK -0.02 0.17 0.42 3 -0.52 68 71
IL8 -0.28 0.49 0.58 9 -0.96 313 322
POU2F1 0.021 0.012 0.26 1 -10000 0 1
HIF-1-alpha transcription factor network

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
PKM2 -0.26 0.36 -10000 0 -0.78 224 224
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.34 0.66 3 -0.78 133 136
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.24 0.37 -10000 0 -0.79 219 219
AP1 -0.1 0.21 -10000 0 -0.42 310 310
ABCG2 -0.26 0.39 -10000 0 -0.81 239 239
HIF1A -0.048 0.084 -10000 0 -0.29 5 5
TFF3 -0.25 0.41 0.66 5 -0.8 254 259
GATA2 0.009 0.095 0.25 13 -0.57 26 39
AKT1 -0.055 0.094 0.24 1 -0.24 55 56
response to hypoxia -0.062 0.084 0.21 1 -0.22 92 93
MCL1 -0.24 0.35 -10000 0 -0.79 208 208
NDRG1 -0.22 0.36 -10000 0 -0.8 186 186
SERPINE1 -0.24 0.38 0.65 4 -0.79 220 224
FECH -0.24 0.37 -10000 0 -0.79 219 219
FURIN -0.24 0.37 -10000 0 -0.8 210 210
NCOA2 -0.002 0.12 -10000 0 -0.56 48 48
EP300 -0.06 0.13 0.34 2 -0.33 115 117
HMOX1 -0.24 0.37 0.65 1 -0.79 219 220
BHLHE40 -0.24 0.37 -10000 0 -0.79 219 219
BHLHE41 -0.25 0.38 -10000 0 -0.81 220 220
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.019 0.11 -10000 0 -0.3 1 1
ENG -0.016 0.11 0.38 3 -10000 0 3
JUN 0.018 0.046 -10000 0 -0.57 6 6
RORA -0.25 0.37 -10000 0 -0.79 221 221
ABCB1 -0.26 0.45 -10000 0 -1.1 220 220
TFRC -0.24 0.37 -10000 0 -0.79 217 217
CXCR4 -0.24 0.37 0.65 1 -0.79 219 220
TF -0.4 0.45 -10000 0 -0.87 408 408
CITED2 -0.24 0.37 -10000 0 -0.79 217 217
HIF1A/ARNT -0.27 0.42 0.75 2 -0.95 172 174
LDHA -0.037 0.12 -10000 0 -0.76 20 20
ETS1 -0.25 0.37 -10000 0 -0.79 220 220
PGK1 -0.24 0.37 -10000 0 -0.79 220 220
NOS2 -0.24 0.37 -10000 0 -0.79 214 214
ITGB2 -0.24 0.37 0.65 1 -0.79 218 219
ALDOA -0.24 0.37 -10000 0 -0.79 211 211
Cbp/p300/CITED2 -0.25 0.39 -10000 0 -0.9 170 170
FOS -0.15 0.27 -10000 0 -0.57 306 306
HK2 -0.24 0.37 -10000 0 -0.79 220 220
SP1 0.001 0.057 -10000 0 -0.2 3 3
GCK -0.12 0.33 0.57 1 -1.4 59 60
HK1 -0.24 0.37 -10000 0 -0.79 218 218
NPM1 -0.24 0.37 -10000 0 -0.79 221 221
EGLN1 -0.24 0.36 -10000 0 -0.78 208 208
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.25 0.37 -10000 0 -0.79 219 219
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.36 -10000 0 -1 132 132
IGFBP1 -0.31 0.42 -10000 0 -0.87 279 279
VEGFA -0.16 0.29 0.56 1 -0.69 114 115
HIF1A/JAB1 -0.009 0.067 -10000 0 -0.27 1 1
CP -0.3 0.45 0.64 2 -0.89 301 303
CXCL12 -0.26 0.4 -10000 0 -0.83 238 238
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.011 -10000 0 -0.17 1 1
BNIP3 -0.24 0.37 0.72 1 -0.82 195 196
EGLN3 -0.24 0.38 0.68 2 -0.79 219 221
CA9 -0.21 0.39 0.66 6 -0.78 211 217
TERT -0.23 0.37 0.66 4 -0.78 214 218
ENO1 -0.25 0.37 -10000 0 -0.79 221 221
PFKL -0.24 0.37 -10000 0 -0.8 203 203
NCOA1 0.024 0.019 -10000 0 -0.57 1 1
ADM -0.26 0.4 -10000 0 -0.84 236 236
ARNT -0.035 0.07 -10000 0 -10000 0 0
HNF4A 0.019 0.041 0.26 19 -10000 0 19
ADFP -0.26 0.36 -10000 0 -0.78 224 224
SLC2A1 -0.16 0.29 0.62 3 -0.68 118 121
LEP -0.48 0.41 -10000 0 -0.86 444 444
HIF1A/ARNT/Cbp/p300 -0.2 0.34 0.66 1 -0.79 145 146
EPO -0.11 0.26 0.64 4 -0.75 49 53
CREBBP -0.05 0.12 0.34 2 -0.33 82 84
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 0.72 1 -0.79 125 126
PFKFB3 -0.24 0.37 -10000 0 -0.8 213 213
NT5E -0.25 0.37 -10000 0 -0.8 223 223
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 0.09 0.1 0.42 5 -10000 0 5
SMARCC2 0.024 0.013 -10000 0 -0.19 1 1
SMARCC1 0.024 0.012 -10000 0 -0.15 2 2
TBX21 -0.12 0.21 0.39 6 -0.6 94 100
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.032 0.26 19 -10000 0 19
FKBP4 0.025 0.017 0.26 5 -10000 0 5
FKBP5 0.015 0.078 0.26 5 -0.57 18 23
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.31 126 -0.35 7 133
PRL -0.062 0.12 0.52 3 -0.49 1 4
cortisol/GR alpha (dimer)/TIF2 0.18 0.28 0.52 335 -0.48 17 352
RELA -0.037 0.1 0.28 1 -0.26 34 35
FGG 0.21 0.24 0.48 360 -0.49 3 363
GR beta/TIF2 0.078 0.16 0.31 158 -0.4 42 200
IFNG -0.3 0.36 0.41 9 -0.67 441 450
apoptosis -0.26 0.3 0.85 1 -0.66 283 284
CREB1 0.06 0.053 -10000 0 -10000 0 0
histone acetylation 0.025 0.13 0.36 54 -0.37 23 77
BGLAP -0.08 0.14 0.41 1 -0.5 19 20
GR/PKAc 0.13 0.13 0.36 78 -0.33 3 81
NF kappa B1 p50/RelA -0.062 0.18 0.42 4 -0.35 159 163
SMARCD1 0.024 0.012 -10000 0 -10000 0 0
MDM2 0.098 0.11 0.23 319 -10000 0 319
GATA3 0.014 0.11 0.26 28 -0.56 35 63
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.024 0.1 0.47 1 -0.5 7 8
GSK3B 0.001 0.023 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.79 1 -0.62 148 149
CSN2 0.16 0.19 0.38 335 -0.43 4 339
BRG1/BAF155/BAF170/BAF60A 0.06 0.041 -10000 0 -0.44 6 6
NFATC1 0.023 0.026 -10000 0 -0.57 2 2
POU2F1 0.023 0.015 0.26 1 -10000 0 1
CDKN1A 0.016 0.086 -10000 0 -1.3 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.007 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.32 90 -0.32 6 96
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.39 0.62 2 -0.84 374 376
JUN -0.25 0.29 0.44 6 -0.55 413 419
IL4 -0.11 0.15 -10000 0 -0.47 42 42
CDK5R1 0.022 0.036 0.25 23 -10000 0 23
PRKACA 0.024 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.48 494 494
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.13 0.33 75 -0.34 5 80
cortisol/GR alpha (monomer) 0.28 0.32 0.6 442 -0.53 4 446
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.59 315 315
AP-1/NFAT1-c-4 -0.42 0.45 0.47 7 -0.8 562 569
AFP -0.53 0.64 -10000 0 -1.4 352 352
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.43 114 -10000 0 114
TP53 0.031 0.027 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.64 0.68 0.42 4 -1.3 500 504
KRT14 -0.69 0.66 -10000 0 -1.3 556 556
TBP 0.028 0.013 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.29 477 -10000 0 477
HDAC1 0.022 0.011 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.43 0.45 0.47 7 -0.8 562 569
MAPK14 0.004 0.022 -10000 0 -10000 0 0
MAPK10 -0.083 0.2 -10000 0 -0.57 158 158
MAPK11 -0.001 0.038 -10000 0 -0.58 3 3
KRT5 -0.72 0.7 0.42 4 -1.4 567 571
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.019 -10000 0 -0.56 1 1
STAT1 0.033 0.032 0.26 19 -10000 0 19
CGA -0.053 0.17 0.42 2 -0.47 25 27
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.36 399 -10000 0 399
MAPK3 0.001 0.022 -10000 0 -10000 0 0
MAPK1 0.003 0.022 -10000 0 -10000 0 0
ICAM1 -0.18 0.24 0.6 3 -0.56 220 223
NFKB1 -0.038 0.1 0.28 1 -0.25 45 46
MAPK8 -0.19 0.22 0.41 4 -0.43 375 379
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.27 0.32 0.86 1 -0.7 283 284
BAX 0.017 0.064 -10000 0 -10000 0 0
POMC -0.16 0.3 -10000 0 -0.96 73 73
EP300 0.14 0.14 0.29 464 -10000 0 464
cortisol/GR alpha (dimer)/p53 0.21 0.26 0.53 350 -0.5 3 353
proteasomal ubiquitin-dependent protein catabolic process 0.077 0.11 0.27 157 -10000 0 157
SGK1 0.19 0.2 0.45 38 -1.1 6 44
IL13 -0.25 0.28 0.51 5 -0.59 292 297
IL6 -0.43 0.52 0.49 2 -1.1 404 406
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.49 4 -0.53 202 206
IL2 -0.33 0.35 0.45 3 -0.69 441 444
CDK5 0.018 0.019 0.25 4 -10000 0 4
PRKACB 0.032 0.06 0.26 47 -0.57 4 51
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.52 4 -0.63 203 207
CDK5R1/CDK5 0.019 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.018 0.15 0.38 3 -0.38 40 43
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 417 -0.46 3 420
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.16 0.35 267 -0.63 1 268
NF kappa B1 p50/RelA/Cbp 0.061 0.19 0.4 71 -0.4 19 90
JUN (dimer) -0.25 0.29 0.44 6 -0.55 412 418
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.2 -10000 0 -0.65 85 85
NR3C1 0.17 0.2 0.39 365 -0.43 4 369
NR4A1 -0.03 0.18 -10000 0 -0.55 112 112
TIF2/SUV420H1 0.008 0.094 -10000 0 -0.42 48 48
MAPKKK cascade -0.26 0.3 0.85 1 -0.66 283 284
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.52 428 -0.5 3 431
PBX1 0.023 0.015 0.26 1 -10000 0 1
POU1F1 0.021 0.015 0.26 2 -10000 0 2
SELE -0.19 0.31 0.55 3 -0.75 163 166
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.36 263 -0.64 1 264
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 417 -0.46 3 420
mol:cortisol 0.16 0.19 0.35 442 -0.28 3 445
MMP1 0.031 0.31 0.42 2 -0.92 84 86
EPHB forward 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
Ephrin A5/EPHB2 -0.002 0.11 -10000 0 -0.36 95 95
cell-cell adhesion 0.13 0.15 0.31 391 -10000 0 391
Ephrin B/EPHB2/RasGAP 0.031 0.11 -10000 0 -0.31 82 82
ITSN1 0.023 0.026 -10000 0 -0.57 2 2
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.12 0.19 -10000 0 -0.36 412 412
HRAS/GDP -0.11 0.18 -10000 0 -0.41 181 181
Ephrin B/EPHB1/GRB7 -0.1 0.2 -10000 0 -0.35 398 398
Endophilin/SYNJ1 -0.027 0.083 0.22 2 -0.29 80 82
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.21 -10000 0 -0.36 411 411
endothelial cell migration 0.04 0.042 -10000 0 -0.32 11 11
GRB2 0.023 0.009 0.26 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 -0.031 0.099 0.35 2 -0.33 83 85
HRAS 0.026 0.022 0.26 9 -10000 0 9
RRAS -0.027 0.084 0.23 2 -0.3 80 82
DNM1 0.02 0.048 0.26 1 -0.57 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.14 0.18 0.35 2 -0.34 429 431
lamellipodium assembly -0.13 0.15 -10000 0 -0.31 391 391
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.089 0.16 -10000 0 -0.32 319 319
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
EPHB2 0.027 0.031 0.26 19 -10000 0 19
EPHB3 0.025 0.02 0.26 8 -10000 0 8
EPHB1 -0.2 0.29 0.26 1 -0.57 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.11 0.17 -10000 0 -0.42 173 173
Ephrin B/EPHB2 0.021 0.1 -10000 0 -0.31 82 82
Ephrin B/EPHB3 0.02 0.097 -10000 0 -0.31 77 77
JNK cascade -0.12 0.15 0.36 9 -0.31 408 417
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.35 430 430
RAP1/GDP -0.093 0.16 -10000 0 -0.38 153 153
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.023 0.16 -10000 0 -0.57 82 82
EFNB1 0.024 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.098 0.18 -10000 0 -0.32 411 411
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.19 -10000 0 -0.41 162 162
Rap1/GTP -0.11 0.17 -10000 0 -0.32 325 325
axon guidance -0.002 0.11 -10000 0 -0.36 95 95
MAPK3 -0.084 0.14 -10000 0 -0.39 107 107
MAPK1 -0.089 0.14 -10000 0 -0.39 110 110
Rac1/GDP -0.1 0.16 -10000 0 -0.39 165 165
actin cytoskeleton reorganization -0.11 0.12 -10000 0 -0.34 135 135
CDC42/GDP -0.1 0.16 -10000 0 -0.39 167 167
PI3K 0.045 0.044 -10000 0 -0.32 11 11
EFNA5 -0.028 0.17 0.26 1 -0.57 95 96
Ephrin B2/EPHB4 0.03 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.089 -10000 0 -0.27 85 85
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.16 -10000 0 -0.31 332 332
PTK2 0.14 0.26 0.67 204 -10000 0 204
MAP4K4 -0.12 0.15 0.36 9 -0.31 408 417
SRC 0.023 0.005 -10000 0 -10000 0 0
KALRN 0.014 0.078 -10000 0 -0.57 19 19
Intersectin/N-WASP 0.034 0.021 -10000 0 -0.42 2 2
neuron projection morphogenesis -0.1 0.14 0.29 9 -0.42 81 90
MAP2K1 -0.086 0.15 -10000 0 -0.3 299 299
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.088 0.19 -10000 0 -0.33 409 409
cell migration -0.1 0.18 0.29 6 -0.35 289 295
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.084 0.23 2 -0.3 80 82
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.32 577 579
HRAS/GTP -0.099 0.19 -10000 0 -0.32 414 414
Ephrin B1/EPHB1-2 -0.096 0.18 -10000 0 -0.33 410 410
cell adhesion mediated by integrin 0.011 0.086 0.28 79 -0.21 20 99
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.33 425 425
RAC1-CDC42/GTP -0.13 0.15 -10000 0 -0.32 337 337
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.095 0.16 -10000 0 -0.38 157 157
ruffle organization -0.12 0.16 0.36 5 -0.49 71 76
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.086 0.22 2 -0.3 82 84
Ephrin B/EPHB2/KALRN 0.026 0.12 -10000 0 -0.34 92 92
ROCK1 0.017 0.031 0.19 30 -0.33 1 31
RAS family/GDP -0.1 0.12 -10000 0 -0.34 131 131
Rac1/GTP -0.12 0.17 -10000 0 -0.32 391 391
Ephrin B/EPHB1/Src/Paxillin -0.12 0.18 -10000 0 -0.32 416 416
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.073 0.14 -10000 0 -0.42 104 104
PTK2B 0.02 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.2 -10000 0 -0.81 47 47
EDN1 -0.073 0.16 -10000 0 -0.53 98 98
EDN3 -0.22 0.29 0.26 3 -0.57 442 445
EDN2 0.074 0.11 0.26 245 -0.57 5 250
HRAS/GDP -0.094 0.2 -10000 0 -0.48 154 154
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.14 -10000 0 -0.4 112 112
ADCY4 -0.13 0.2 0.28 2 -0.42 279 281
ADCY5 -0.21 0.24 -10000 0 -0.44 470 470
ADCY6 -0.12 0.19 0.28 2 -0.4 270 272
ADCY7 -0.12 0.18 0.28 2 -0.4 269 271
ADCY1 -0.12 0.2 0.25 2 -0.4 284 286
ADCY2 -0.14 0.22 0.29 6 -0.44 292 298
ADCY3 -0.12 0.18 0.26 1 -0.4 270 271
ADCY8 -0.1 0.17 0.27 2 -0.4 207 209
ADCY9 -0.11 0.18 0.26 1 -0.4 256 257
arachidonic acid secretion -0.16 0.28 0.32 1 -0.51 345 346
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.36 157 157
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.025 0.022 0.26 9 -10000 0 9
ETA receptor/Endothelin-1/G12/GTP -0.059 0.14 -10000 0 -0.39 104 104
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.42 275 275
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.064 0.16 0.37 10 -0.44 98 108
EDNRB -0.029 0.17 -10000 0 -0.56 100 100
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.078 0.16 -10000 0 -0.5 106 106
CYSLTR1 -0.081 0.16 -10000 0 -0.49 102 102
SLC9A1 -0.045 0.093 -10000 0 -0.28 109 109
mol:GDP -0.1 0.21 0.33 2 -0.49 168 170
SLC9A3 -0.11 0.28 -10000 0 -0.63 199 199
RAF1 -0.14 0.24 0.33 1 -0.47 282 283
JUN -0.05 0.18 -10000 0 -0.77 44 44
JAK2 -0.072 0.14 -10000 0 -0.42 104 104
mol:IP3 -0.075 0.17 -10000 0 -0.45 126 126
ETA receptor/Endothelin-1 -0.083 0.16 0.32 7 -0.49 106 113
PLCB1 -0.019 0.15 -10000 0 -0.57 74 74
PLCB2 0.014 0.026 0.26 1 -0.57 1 2
ETA receptor/Endothelin-3 -0.19 0.21 0.24 1 -0.43 449 450
FOS -0.29 0.44 -10000 0 -0.94 334 334
Gai/GDP -0.1 0.29 -10000 0 -0.74 166 166
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.21 0.27 2 -0.54 146 148
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.42 138 138
GNAQ 0.013 0.036 -10000 0 -0.57 3 3
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNAL -0.11 0.24 -10000 0 -0.57 235 235
Gs family/GDP -0.15 0.24 -10000 0 -0.5 265 265
ETA receptor/Endothelin-1/Gq/GTP -0.047 0.12 -10000 0 -0.39 77 77
MAPK14 -0.066 0.16 -10000 0 -0.41 142 142
TRPC6 -0.057 0.21 -10000 0 -0.91 44 44
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.17 -10000 0 -0.42 149 149
ETB receptor/Endothelin-2 0.022 0.15 0.24 17 -0.4 102 119
ETB receptor/Endothelin-3 -0.19 0.24 0.24 1 -0.44 502 503
ETB receptor/Endothelin-1 -0.078 0.18 -10000 0 -0.47 168 168
MAPK3 -0.25 0.38 -10000 0 -0.79 340 340
MAPK1 -0.26 0.4 -10000 0 -0.81 341 341
Rac1/GDP -0.094 0.19 -10000 0 -0.48 152 152
cAMP biosynthetic process -0.16 0.22 0.4 2 -0.48 248 250
MAPK8 -0.059 0.21 -10000 0 -0.75 64 64
SRC 0.023 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.068 0.17 -10000 0 -0.36 208 208
p130Cas/CRK/Src/PYK2 -0.097 0.22 0.49 1 -0.57 126 127
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.093 0.19 -10000 0 -0.48 151 151
COL1A2 -0.089 0.2 0.37 9 -0.48 156 165
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.021 0.097 0.25 14 -0.38 11 25
mol:DAG -0.075 0.17 -10000 0 -0.45 126 126
MAP2K2 -0.19 0.3 0.34 2 -0.6 341 343
MAP2K1 -0.19 0.3 0.32 2 -0.59 344 346
EDNRA -0.035 0.07 0.28 1 -0.3 25 26
positive regulation of muscle contraction -0.063 0.12 -10000 0 -0.38 97 97
Gq family/GDP -0.059 0.19 -10000 0 -0.49 105 105
HRAS/GTP -0.1 0.2 0.34 1 -0.47 170 171
PRKCH -0.077 0.16 -10000 0 -0.44 122 122
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.073 0.18 0.28 3 -0.46 133 136
PRKCB -0.074 0.18 0.24 1 -0.46 126 127
PRKCE -0.08 0.16 -10000 0 -0.44 131 131
PRKCD -0.076 0.16 -10000 0 -0.44 120 120
PRKCG -0.078 0.17 0.27 1 -0.44 130 131
regulation of vascular smooth muscle contraction -0.34 0.51 -10000 0 -1.1 331 331
PRKCQ -0.084 0.18 -10000 0 -0.48 136 136
PLA2G4A -0.18 0.31 0.33 1 -0.56 345 346
GNA14 0.014 0.067 0.25 19 -0.57 10 29
GNA15 0.022 0.027 0.25 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.037 -10000 0 -0.57 4 4
Rac1/GTP -0.059 0.14 0.29 1 -0.39 104 105
MMP1 0.17 0.13 0.4 74 -10000 0 74
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.034 0.016 -10000 0 -0.42 1 1
Necdin/E2F1 0.061 0.11 -10000 0 -0.39 34 34
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.045 0.17 -10000 0 -0.32 290 290
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.24 0.34 1 -0.4 372 373
NT-4/5 (dimer)/p75(NTR) -0.22 0.29 -10000 0 -0.49 513 513
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.082 0.16 0.36 1 -0.32 275 276
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.012 0.16 0.26 24 -0.57 75 99
MGDIs/NGR/p75(NTR)/LINGO1 -0.037 0.2 0.34 7 -0.34 281 288
FURIN 0.024 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.087 0.2 -10000 0 -0.39 318 318
LINGO1 0.077 0.097 0.26 247 -10000 0 247
Sortilin/TRAF6/NRIF 0.024 0.024 -10000 0 -0.55 1 1
proBDNF (dimer) -0.012 0.16 0.26 24 -0.56 75 99
NTRK1 0.024 0.051 0.26 25 -0.57 4 29
RTN4R 0.032 0.044 0.26 40 -10000 0 40
neuron apoptosis -0.078 0.19 0.34 6 -0.51 72 78
IRAK1 0.025 0.014 0.26 4 -10000 0 4
SHC1 -0.079 0.15 -10000 0 -0.36 224 224
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.053 0.18 -10000 0 -0.34 286 286
MAGEH1 0.024 0.018 -10000 0 -0.57 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.063 0.19 -10000 0 -0.36 294 294
Mammalian IAPs/DIABLO 0.057 0.032 -10000 0 -0.33 2 2
proNGF (dimer) 0.017 0.074 0.26 8 -0.56 16 24
MAGED1 0.025 0.01 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 -0.56 363 363
ZNF274 0.024 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.064 0.15 -10000 0 -0.32 277 277
NGF 0.017 0.074 0.26 8 -0.57 16 24
cell cycle arrest -0.072 0.15 0.23 47 -0.29 286 333
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.052 0.12 -10000 0 -0.27 209 209
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.18 0.26 -10000 0 -0.45 465 465
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.067 0.19 -10000 0 -0.36 290 290
PSENEN 0.024 0.011 0.26 2 -10000 0 2
mol:ceramide -0.076 0.16 -10000 0 -0.33 285 285
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.043 0.11 -10000 0 -0.36 30 30
p75(NTR)/beta APP -0.089 0.2 -10000 0 -0.41 287 287
BEX1 -0.016 0.23 0.26 172 -0.57 139 311
mol:GDP -0.1 0.16 -10000 0 -0.36 292 292
NGF (dimer) 0.002 0.14 0.34 1 -0.34 133 134
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.021 0.18 0.34 6 -0.32 267 273
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RAC1/GTP -0.059 0.16 -10000 0 -0.31 288 288
MYD88 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.067 0.19 -10000 0 -0.36 290 290
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 0.073 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.56 157 169
TP53 -0.089 0.16 0.35 3 -0.33 304 307
PRDM4 -0.076 0.16 -10000 0 -0.34 286 286
BDNF (dimer) 0.023 0.2 0.33 21 -0.35 192 213
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.018 -10000 0 -0.57 1 1
activation of caspase activity -0.048 0.17 -10000 0 -0.32 290 290
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.18 -10000 0 -0.34 283 283
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 0.29 5 -0.41 290 295
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.076 0.16 -10000 0 -0.33 285 285
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.069 0.18 -10000 0 -0.36 290 290
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.15 0.25 -10000 0 -0.45 398 398
MAPK8 -0.094 0.18 0.3 8 -0.36 262 270
MAPK9 -0.093 0.17 0.28 8 -0.36 262 270
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.061 0.21 0.26 12 -0.57 157 169
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NDN 0.005 0.1 -10000 0 -0.57 34 34
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.041 0.16 -10000 0 -0.3 287 287
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.022 -10000 0 -0.33 1 1
RhoA-B-C/GTP -0.067 0.19 -10000 0 -0.36 290 290
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.059 0.19 -10000 0 -0.34 311 311
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.07 0.2 -10000 0 -0.36 313 313
PRKACB 0.032 0.06 0.26 47 -0.57 4 51
proBDNF (dimer)/p75 ECD 0.007 0.12 -10000 0 -0.42 75 75
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.086 0.17 0.28 14 -0.34 281 295
BAD -0.11 0.18 0.34 8 -0.38 272 280
RIPK2 0.02 0.016 0.26 3 -10000 0 3
NGFR -0.14 0.26 -10000 0 -0.57 287 287
CYCS -0.084 0.15 0.36 2 -0.32 276 278
ADAM17 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.044 0.16 -10000 0 -0.34 209 209
BCL2L11 -0.11 0.18 0.34 8 -0.38 272 280
BDNF (dimer)/p75(NTR) -0.11 0.23 -10000 0 -0.44 326 326
PI3K -0.057 0.18 -10000 0 -0.34 278 278
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.053 0.18 -10000 0 -0.34 285 285
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) -0.094 0.2 -10000 0 -0.41 307 307
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.053 0.18 -10000 0 -0.34 286 286
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
PLG 0.018 0.021 0.26 8 -10000 0 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.1 0.18 -10000 0 -0.37 324 324
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
NGFRAP1 0.023 0.031 -10000 0 -0.57 3 3
CASP3 -0.1 0.17 0.33 7 -0.36 280 287
E2F1 0.093 0.11 0.26 320 -10000 0 320
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.002 0.11 -10000 0 -0.4 19 19
NGF (dimer)/TRKA 0.026 0.066 -10000 0 -0.4 20 20
MMP7 -0.037 0.19 0.26 33 -0.57 121 154
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.043 0.17 -10000 0 -0.32 279 279
MMP3 0.096 0.14 0.26 380 -0.57 14 394
APAF-1/Caspase 9 -0.085 0.11 -10000 0 -0.44 10 10
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.23 0.61 0.77 17 -1.2 207 224
STAT6 (cleaved dimer) -0.3 0.58 -10000 0 -1.2 251 251
IGHG1 -0.025 0.26 0.51 62 -0.52 11 73
IGHG3 -0.23 0.57 0.66 21 -1.1 241 262
AKT1 -0.082 0.34 0.55 30 -0.74 90 120
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.044 0.29 0.51 33 -0.69 62 95
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.083 0.36 0.57 32 -0.8 76 108
THY1 -0.23 0.61 0.78 17 -1.2 198 215
MYB 0.011 0.086 0.26 1 -0.57 23 24
HMGA1 0.034 0.048 0.26 48 -10000 0 48
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.41 0.62 63 -0.71 191 254
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.075 0.35 0.57 32 -0.8 64 96
SP1 0.034 0.025 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.014 0.046 -10000 0 -0.54 1 1
STAT6 (dimer)/ETS1 -0.26 0.6 0.67 14 -1.2 242 256
SOCS1 -0.13 0.4 0.6 28 -0.74 197 225
SOCS3 -0.089 0.35 0.61 12 -0.81 70 82
FCER2 -0.37 0.73 0.79 27 -1.3 344 371
PARP14 0.017 0.031 0.24 3 -10000 0 3
CCL17 -0.22 0.62 0.85 41 -1.2 193 234
GRB2 0.023 0.009 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.039 0.29 0.52 36 -0.69 42 78
T cell proliferation -0.25 0.61 0.72 12 -1.2 229 241
IL4R/JAK1 -0.24 0.6 0.7 6 -1.2 227 233
EGR2 -0.34 0.74 0.85 14 -1.4 258 272
JAK2 0.012 0.076 0.26 1 -10000 0 1
JAK3 0.022 0.035 0.27 14 -10000 0 14
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
JAK1 0.017 0.041 -10000 0 -10000 0 0
COL1A2 -0.022 0.27 0.56 11 -1.1 18 29
CCL26 -0.23 0.61 0.89 7 -1.2 192 199
IL4R -0.24 0.66 0.86 33 -1.3 221 254
PTPN6 0.014 0.035 0.21 2 -10000 0 2
IL13RA2 -0.23 0.61 0.79 16 -1.2 194 210
IL13RA1 0.012 0.077 0.26 1 -10000 0 1
IRF4 -0.13 0.49 0.57 12 -1.4 119 131
ARG1 -0.004 0.22 0.57 6 -0.64 6 12
CBL -0.11 0.38 0.56 47 -0.68 178 225
GTF3A 0.055 0.048 0.26 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.025 0.11 0.3 22 -10000 0 22
IRF4/BCL6 -0.11 0.44 0.51 2 -1.3 118 120
CD40LG -0.011 0.13 0.31 12 -0.57 51 63
MAPK14 -0.1 0.38 0.58 39 -0.7 166 205
mitosis -0.075 0.33 0.54 34 -0.69 90 124
STAT6 -0.27 0.76 0.93 52 -1.4 236 288
SPI1 0.027 0.019 0.26 6 -10000 0 6
RPS6KB1 -0.058 0.32 0.53 43 -0.68 78 121
STAT6 (dimer) -0.26 0.76 0.93 51 -1.4 236 287
STAT6 (dimer)/PARP14 -0.29 0.66 0.73 14 -1.3 254 268
mast cell activation 0 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.088 0.35 0.56 38 -0.72 111 149
FRAP1 -0.082 0.34 0.55 30 -0.74 90 120
LTA -0.22 0.62 0.85 39 -1.2 194 233
FES 0.022 0.031 -10000 0 -0.57 3 3
T-helper 1 cell differentiation 0.25 0.72 1.3 236 -0.93 51 287
CCL11 -0.17 0.59 0.76 23 -1.2 191 214
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.069 0.34 0.55 39 -0.73 80 119
IL2RG 0.025 0.071 0.26 46 -0.56 7 53
IL10 -0.2 0.6 0.8 25 -1.2 197 222
IRS1 0.001 0.11 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
IL4 -0.008 0.26 0.62 20 -1.1 20 40
IL5 -0.23 0.61 0.77 21 -1.2 222 243
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.52 0.79 53 -0.91 197 250
COL1A1 0.002 0.36 0.69 32 -1 46 78
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.61 -10000 0 -1.3 193 193
IL2R gamma/JAK3 0.037 0.068 0.31 26 -0.38 7 33
TFF3 -0.28 0.7 0.84 27 -1.3 260 287
ALOX15 -0.3 0.7 0.8 23 -1.3 266 289
MYBL1 0.038 0.063 0.26 81 -10000 0 81
T-helper 2 cell differentiation -0.19 0.52 0.7 30 -0.96 230 260
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.079 0.34 0.55 34 -0.74 83 117
mol:PI-3-4-5-P3 -0.082 0.34 0.55 30 -0.74 90 120
PI3K -0.09 0.36 0.57 24 -0.8 90 114
DOK2 0.02 0.031 0.26 4 -0.57 2 6
ETS1 0.003 0.054 -10000 0 -0.53 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.029 0.27 0.48 50 -0.63 38 88
ITGB3 -0.25 0.63 0.82 6 -1.3 204 210
PIGR -0.66 0.8 0.84 14 -1.3 586 600
IGHE -0.015 0.086 0.18 26 -0.22 29 55
MAPKKK cascade -0.028 0.27 0.48 51 -0.61 38 89
BCL6 0.022 0.046 -10000 0 -0.56 6 6
OPRM1 -0.23 0.61 0.87 8 -1.2 195 203
RETNLB -0.24 0.61 0.77 17 -1.2 217 234
SELP -0.35 0.77 0.79 28 -1.4 300 328
AICDA -0.23 0.58 0.77 12 -1.2 193 205
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.031 0.26 19 -10000 0 19
EFNB1 0.002 0.036 -10000 0 -0.42 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.077 0.17 -10000 0 -0.3 400 400
Ephrin B2/EPHB1-2 -0.097 0.18 -10000 0 -0.32 411 411
neuron projection morphogenesis -0.083 0.16 -10000 0 -0.28 400 400
Ephrin B1/EPHB1-2/Tiam1 -0.088 0.18 -10000 0 -0.31 407 407
DNM1 0.02 0.048 0.27 1 -0.57 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.021 0.12 -10000 0 -0.56 45 45
YES1 -0.023 0.17 -10000 0 -0.77 50 50
Ephrin B1/EPHB1-2/NCK2 -0.089 0.18 -10000 0 -0.31 410 410
PI3K 0.006 0.13 -10000 0 -0.5 59 59
mol:GDP -0.088 0.18 -10000 0 -0.31 407 407
ITGA2B 0.033 0.06 0.26 54 -0.57 3 57
endothelial cell proliferation 0.029 0.011 -10000 0 -10000 0 0
FYN -0.024 0.16 -10000 0 -0.76 49 49
MAP3K7 -0.023 0.12 -10000 0 -0.57 48 48
FGR -0.02 0.16 -10000 0 -0.76 49 49
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.008 0.13 -10000 0 -0.52 54 54
LYN -0.021 0.16 -10000 0 -0.75 49 49
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.15 -10000 0 -0.71 50 50
Ephrin B1/EPHB1-2 -0.022 0.13 -10000 0 -0.63 45 45
SRC -0.019 0.16 -10000 0 -0.75 50 50
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
EPHB1 -0.2 0.29 0.26 1 -0.57 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.027 0.089 -10000 0 -0.41 36 36
BLK -0.019 0.17 -10000 0 -0.78 47 47
HCK -0.019 0.16 -10000 0 -0.75 50 50
regulation of stress fiber formation 0.089 0.18 0.31 410 -10000 0 410
MAPK8 -0.024 0.12 -10000 0 -0.54 47 47
Ephrin B1/EPHB1-2/RGS3 -0.088 0.18 -10000 0 -0.31 409 409
endothelial cell migration -0.017 0.11 -10000 0 -0.51 42 42
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.68 26 26
regulation of focal adhesion formation 0.089 0.18 0.31 410 -10000 0 410
chemotaxis 0.088 0.18 0.31 409 -10000 0 409
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.08 0.17 -10000 0 -0.29 400 400
angiogenesis -0.023 0.13 -10000 0 -0.62 47 47
LCK -0.02 0.17 -10000 0 -0.77 49 49
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 -0.097 0.21 0.22 1 -0.39 297 298
FZD6 0.014 0.054 -10000 0 -0.57 9 9
WNT6 -0.076 0.24 0.26 47 -0.57 200 247
WNT4 0.017 0.086 0.26 20 -0.57 20 40
FZD3 0.015 0.054 -10000 0 -0.57 9 9
WNT5A 0.017 0.073 0.26 9 -0.57 15 24
WNT11 -0.085 0.23 0.26 10 -0.57 199 209
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 0.007 0.096 -10000 0 -0.57 29 29
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.18 0.2 -10000 0 -0.35 612 612
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.18 0.17 -10000 0 -0.32 609 609
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.26 61 -10000 0 61
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.023 0.066 0.26 23 -0.57 10 33
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.048 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.028 0.034 0.26 23 -10000 0 23
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.054 0.083 0.26 155 -10000 0 155
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.19 0.21 0.34 2 -0.37 608 610
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.15 0.33 4 -0.32 59 63
MAP1B -0.001 0.045 -10000 0 -0.31 21 21
RAC1 0.011 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.15 0.15 -10000 0 -0.3 498 498
RELN -0.32 0.29 0.26 2 -0.57 619 621
PAFAH/LIS1 0.023 0.045 0.32 2 -0.36 9 11
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.13 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.36 224 224
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.14 0.15 0.31 4 -0.34 66 70
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 0.26 123 -10000 0 123
PAFAH1B2 0.019 0.044 -10000 0 -0.57 6 6
MAP1B/LIS1/Dynein heavy chain 0.014 0.043 -10000 0 -0.35 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.12 0.15 0.34 3 -0.33 39 42
LRP8 0.046 0.068 0.26 103 -10000 0 103
NDEL1/Katanin 60 -0.13 0.15 0.35 3 -0.33 62 65
P39/CDK5 -0.15 0.16 0.34 6 -0.3 452 458
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 -0.3 601 602
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.16 0.19 0.33 1 -0.32 602 603
RELN/VLDLR -0.17 0.2 -10000 0 -0.33 612 612
CDC42 0.01 0.005 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.067 0.15 -10000 0 -0.34 240 240
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.026 0.022 0.26 9 -10000 0 9
IRS1/Crk -0.061 0.16 -10000 0 -0.34 246 246
IGF-1R heterotetramer/IGF1/PTP1B -0.044 0.17 -10000 0 -0.36 213 213
AKT1 -0.067 0.14 0.25 2 -0.32 199 201
BAD -0.065 0.13 0.24 2 -0.31 182 184
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.16 -10000 0 -0.34 244 244
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.16 -10000 0 -0.34 246 246
RAF1 -0.047 0.13 0.28 2 -0.47 48 50
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.032 0.16 -10000 0 -0.33 214 214
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.062 0.17 -10000 0 -0.36 246 246
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.32 165 167
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.029 0.12 0.3 10 -0.4 43 53
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.13 -10000 0 -0.31 161 161
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.3 160 160
IGF-1R heterotetramer -0.011 0.098 0.25 1 -0.62 20 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.045 0.17 -10000 0 -0.34 243 243
Crk/p130 Cas/Paxillin -0.037 0.16 -10000 0 -0.32 227 227
IGF1R -0.011 0.098 0.25 1 -0.62 20 21
IGF1 -0.11 0.25 -10000 0 -0.59 233 233
IRS2/Crk -0.067 0.17 -10000 0 -0.35 245 245
PI3K -0.036 0.17 -10000 0 -0.34 224 224
apoptosis 0.044 0.11 0.37 40 -0.27 5 45
HRAS/GDP 0.019 0.015 -10000 0 -10000 0 0
PRKCD -0.078 0.17 -10000 0 -0.39 230 230
RAF1/14-3-3 E -0.024 0.13 0.3 1 -0.41 47 48
BAD/14-3-3 -0.046 0.11 0.28 5 -0.4 40 45
PRKCZ -0.067 0.14 0.25 2 -0.32 199 201
Crk/p130 Cas/Paxillin/FAK1 -0.028 0.12 -10000 0 -0.41 38 38
PTPN1 0.024 0.018 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.18 -10000 0 -0.41 240 240
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.14 -10000 0 -0.32 176 176
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.054 0.16 -10000 0 -0.34 243 243
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.34 246 246
IRS1 -0.071 0.17 -10000 0 -0.36 246 246
IRS2 -0.076 0.17 -10000 0 -0.36 245 245
IGF-1R heterotetramer/IGF1 -0.078 0.21 -10000 0 -0.46 232 232
GRB2 0.023 0.009 0.26 1 -10000 0 1
PDPK1 -0.069 0.14 0.28 1 -0.33 205 206
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.19 -10000 0 -0.42 238 238
SHC1 0.02 0.009 -10000 0 -10000 0 0
Noncanonical Wnt signaling 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
NFATC2 -0.026 0.16 -10000 0 -0.57 88 88
GNB1/GNG2 -0.076 0.21 -10000 0 -0.48 159 159
mol:DAG -0.077 0.18 0.24 1 -0.44 151 152
PLCG1 -0.08 0.19 0.24 1 -0.46 151 152
YES1 -0.095 0.19 0.2 1 -0.49 147 148
FZD3 0.015 0.054 -10000 0 -0.57 9 9
FZD6 0.014 0.054 -10000 0 -0.57 9 9
G protein -0.063 0.2 0.3 2 -0.47 144 146
MAP3K7 -0.071 0.15 0.23 2 -0.4 128 130
mol:Ca2+ -0.074 0.18 0.23 1 -0.43 151 152
mol:IP3 -0.077 0.18 0.24 1 -0.44 151 152
NLK -0.009 0.13 -10000 0 -0.84 24 24
GNB1 0.023 0.005 -10000 0 -10000 0 0
CAMK2A -0.072 0.17 0.23 4 -0.41 145 149
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.097 0.21 0.22 1 -0.39 297 298
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
GNAS -0.09 0.19 -10000 0 -0.49 142 142
GO:0007205 -0.081 0.18 0.22 2 -0.43 152 154
WNT6 -0.076 0.24 0.26 47 -0.57 200 247
WNT4 0.017 0.086 0.26 20 -0.57 20 40
NFAT1/CK1 alpha -0.09 0.2 0.32 2 -0.49 144 146
GNG2 0.017 0.065 -10000 0 -0.57 13 13
WNT5A 0.017 0.073 0.26 9 -0.57 15 24
WNT11 -0.085 0.23 0.26 10 -0.57 199 209
CDC42 -0.083 0.19 -10000 0 -0.47 139 139
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 0.029 -10000 0 -0.39 3 3
ARNO/beta Arrestin1-2 -0.063 0.16 -10000 0 -0.55 45 45
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EPHA2 0.02 0.04 -10000 0 -0.57 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.25 -10000 0 -0.45 537 537
ARRB2 -0.042 0.13 -10000 0 -0.36 146 146
mol:GTP 0.012 0.049 0.16 18 -0.21 17 35
ARRB1 0.021 0.026 -10000 0 -0.57 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR 0.001 0.12 0.26 4 -0.57 42 46
EGF -0.083 0.23 0.26 2 -0.57 194 196
somatostatin receptor activity 0 0 0.001 1 -0.001 277 278
ARAP2 0.021 0.04 -10000 0 -0.57 5 5
mol:GDP -0.12 0.16 -10000 0 -0.33 296 296
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 183 183
ITGA2B 0.033 0.06 0.26 54 -0.57 3 57
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
ADAP1 0.025 0.029 0.26 10 -0.57 1 11
KIF13B 0.019 0.027 -10000 0 -0.57 2 2
HGF/MET -0.066 0.2 -10000 0 -0.44 225 225
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 0.19 1 -0.28 306 307
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.17 0.23 -10000 0 -0.4 514 514
ADRB2 -0.1 0.24 -10000 0 -0.57 229 229
receptor agonist activity 0 0 0 1 0 271 272
actin filament binding 0 0 0 1 -0.001 280 281
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 172 173
ARF6/GDP -0.037 0.15 0.25 2 -0.43 92 94
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.4 226 226
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.079 -10000 0 -0.32 36 36
ACAP1 0.029 0.066 0.26 47 -0.57 6 53
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.055 0.17 -10000 0 -0.48 146 146
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 0.14 0.26 2 -0.57 65 67
CYTH3 0.004 0.018 -10000 0 -0.42 2 2
CYTH2 0.006 0.099 -10000 0 -1 10 10
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 220 221
endosomal lumen acidification 0 0 0.001 6 0 263 269
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.014 0.14 -10000 0 -0.57 69 69
GNAQ/ARNO 0.018 0.095 -10000 0 -0.95 10 10
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 188 188
MET -0.073 0.22 -10000 0 -0.57 177 177
GNA14 0.022 0.065 0.26 19 -0.57 10 29
GNA15 0.024 0.025 0.26 6 -0.57 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 233 234
GNA11 0.021 0.036 -10000 0 -0.57 4 4
LHCGR -0.069 0.2 -10000 0 -0.57 146 146
AGTR1 -0.098 0.26 0.26 59 -0.57 244 303
desensitization of G-protein coupled receptor protein signaling pathway -0.055 0.17 -10000 0 -0.48 146 146
IPCEF1/ARNO -0.13 0.19 -10000 0 -0.58 71 71
alphaIIb/beta3 Integrin 0.027 0.089 -10000 0 -0.41 36 36
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0 0.15 -10000 0 -0.32 176 176
ER alpha/Gai/GDP/Gbeta gamma -0.085 0.22 -10000 0 -0.46 221 221
AKT1 -0.12 0.33 -10000 0 -0.77 205 205
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.33 -10000 0 -0.78 204 204
mol:Ca2+ -0.026 0.1 0.26 2 -0.45 29 31
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
E2/ER alpha (dimer)/Striatin -0.016 0.16 -10000 0 -0.36 168 168
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.11 0.31 0.73 205 -10000 0 205
RhoA/GTP -0.015 0.1 -10000 0 -0.28 123 123
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.067 0.21 0.31 4 -0.46 200 204
regulation of stress fiber formation 0.024 0.1 0.24 137 -0.24 21 158
E2/ERA-ERB (dimer) -0.019 0.16 -10000 0 -0.36 169 169
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.009 0.13 -10000 0 -0.32 139 139
pseudopodium formation -0.024 0.1 0.24 21 -0.24 137 158
E2/ER alpha (dimer)/PELP1 -0.013 0.15 -10000 0 -0.35 153 153
GRB2 0.023 0.009 0.26 1 -10000 0 1
GNG2 0.017 0.065 -10000 0 -0.57 13 13
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.026 0.022 0.26 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.088 0.23 -10000 0 -0.5 222 222
E2/ER beta (dimer) 0.008 0.063 -10000 0 -0.4 24 24
mol:GDP -0.039 0.16 0.25 13 -0.39 169 182
mol:NADP -0.088 0.23 -10000 0 -0.5 222 222
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 -0.027 0.11 0.27 2 -0.47 28 30
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
PLCB1 -0.025 0.11 0.28 2 -0.45 33 35
PLCB2 -0.005 0.082 -10000 0 -0.49 17 17
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
mol:L-citrulline -0.088 0.23 -10000 0 -0.5 222 222
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.64 159 159
JNK cascade 0.008 0.063 -10000 0 -0.4 24 24
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.011 0.085 -10000 0 -0.57 23 23
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
ESR1 -0.035 0.23 0.26 116 -0.57 151 267
Gq family/GDP/Gbeta gamma -0.01 0.16 -10000 0 -0.74 39 39
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.017 0.13 -10000 0 -0.57 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.059 0.2 0.31 5 -0.46 169 174
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
E2/ER alpha (dimer) -0.028 0.16 0.18 116 -0.41 157 273
STRN 0.013 0.08 -10000 0 -0.57 20 20
GNAL -0.11 0.24 -10000 0 -0.57 235 235
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.057 -10000 0 -0.36 26 26
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
HBEGF -0.056 0.21 0.33 22 -0.49 123 145
cAMP biosynthetic process -0.086 0.18 -10000 0 -0.32 348 348
SRC -0.079 0.21 0.29 7 -0.44 213 220
PI3K 0.028 0.049 -10000 0 -0.38 14 14
GNB1 0.023 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.16 -10000 0 -0.38 142 142
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.43 223 223
Gs family/GTP -0.083 0.18 -10000 0 -0.33 348 348
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.019 -10000 0 -10000 0 0
vasodilation -0.083 0.22 0.24 1 -0.48 222 223
mol:DAG -0.027 0.11 0.27 2 -0.47 28 30
Gs family/GDP/Gbeta gamma -0.09 0.18 -10000 0 -0.36 263 263
MSN -0.026 0.11 0.24 21 -0.26 137 158
Gq family/GTP -0.001 0.087 -10000 0 -0.51 16 16
mol:PI-3-4-5-P3 -0.11 0.32 -10000 0 -0.75 204 204
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.083 0.22 0.48 222 -0.24 1 223
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.16 0.26 10 -0.38 166 176
NOS3 -0.094 0.25 -10000 0 -0.53 222 222
GNA11 0.022 0.036 -10000 0 -0.57 4 4
MAPKKK cascade -0.084 0.25 0.31 2 -0.56 208 210
E2/ER alpha (dimer)/PELP1/Src -0.071 0.22 0.31 8 -0.47 206 214
ruffle organization -0.024 0.1 0.24 21 -0.24 137 158
ROCK2 -0.025 0.12 0.34 8 -0.28 137 145
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.048 0.2 0.35 24 -0.48 117 141
MMP2 -0.069 0.2 0.27 12 -0.42 210 222
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.02 0.48 0.8 45 -1.1 74 119
IL23A -0.031 0.48 0.85 31 -1.1 71 102
NF kappa B1 p50/RelA/I kappa B alpha -0.059 0.44 0.76 8 -0.91 129 137
positive regulation of T cell mediated cytotoxicity -0.023 0.54 0.87 61 -1 131 192
ITGA3 -0.016 0.47 0.81 35 -1.1 70 105
IL17F -0.007 0.36 0.59 72 -0.68 75 147
IL12B 0.084 0.15 0.36 207 -10000 0 207
STAT1 (dimer) -0.037 0.5 0.75 45 -0.96 134 179
CD4 -0.015 0.48 0.84 37 -1 70 107
IL23 -0.016 0.48 0.82 48 -1.1 69 117
IL23R 0.047 0.2 0.54 28 -0.89 18 46
IL1B -0.033 0.5 0.84 35 -1.1 75 110
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.018 0.48 0.84 57 -1 69 126
TYK2 0.026 0.058 0.21 6 -10000 0 6
STAT4 0.001 0.12 0.26 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.008 0.11 0.27 5 -0.56 35 40
IL12RB1 0.034 0.091 0.37 42 -0.58 2 44
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.088 0.3 45 -0.43 2 47
IL23R/JAK2 0.06 0.22 0.53 36 -0.84 16 52
positive regulation of chronic inflammatory response -0.023 0.54 0.87 61 -1 131 192
natural killer cell activation -0.004 0.015 -10000 0 -0.051 35 35
JAK2 0.038 0.081 0.26 28 -10000 0 28
PIK3R1 0.017 0.064 -10000 0 -0.56 13 13
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 -0.01 0.47 0.81 51 -1 70 121
ALOX12B -0.017 0.47 0.83 39 -1 68 107
CXCL1 -0.18 0.69 0.83 45 -1.2 276 321
T cell proliferation -0.023 0.54 0.87 61 -1 131 192
NFKBIA 0.026 0.009 -10000 0 -10000 0 0
IL17A 0.02 0.31 0.56 81 -0.55 59 140
PI3K -0.055 0.46 0.68 25 -0.93 130 155
IFNG 0.025 0.067 0.17 139 -0.11 17 156
STAT3 (dimer) -0.056 0.44 0.71 14 -1 81 95
IL18R1 0.016 0.078 -10000 0 -0.56 19 19
IL23/IL23R/JAK2/TYK2/SOCS3 0.036 0.34 0.64 85 -0.64 50 135
IL18/IL18R 0.041 0.1 0.28 11 -0.36 52 63
macrophage activation 0 0.029 0.056 102 -0.044 53 155
TNF -0.03 0.49 0.85 35 -1.1 74 109
STAT3/STAT4 -0.054 0.48 0.68 24 -0.96 133 157
STAT4 (dimer) -0.049 0.51 0.74 39 -0.98 148 187
IL18 0.03 0.038 0.26 26 -10000 0 26
IL19 0.022 0.48 0.84 53 -1 66 119
STAT5A (dimer) -0.04 0.49 0.74 39 -0.97 132 171
STAT1 0.028 0.031 0.26 19 -10000 0 19
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
CXCL9 0.008 0.5 0.87 61 -1.1 71 132
MPO -0.045 0.54 0.82 41 -1.2 109 150
positive regulation of humoral immune response -0.023 0.54 0.87 61 -1 131 192
IL23/IL23R/JAK2/TYK2 -0.03 0.55 0.88 60 -1.1 114 174
IL6 -0.3 0.74 0.8 34 -1.2 395 429
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
IL2 0.021 0.037 0.3 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.015 -10000 0 -0.051 35 35
CD3E -0.027 0.5 0.85 46 -1.1 79 125
keratinocyte proliferation -0.023 0.54 0.87 61 -1 131 192
NOS2 -0.016 0.48 0.8 44 -1.1 73 117
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.01 0.13 -10000 0 -0.33 152 152
regulation of S phase of mitotic cell cycle -0.024 0.11 -10000 0 -0.29 135 135
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.025 0.022 0.25 9 -10000 0 9
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 -0.069 0.11 -10000 0 -0.32 125 125
T-DHT/AR -0.042 0.15 0.17 1 -0.42 142 143
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 321 321
GNAI2 0.023 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
mol:GDP -0.063 0.16 -10000 0 -0.47 144 144
cell proliferation -0.14 0.21 0.27 3 -0.44 290 293
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.25 0.38 -10000 0 -0.81 325 325
mol:Ca2+ -0.013 0.028 -10000 0 -0.073 148 148
MAPK3 -0.1 0.16 0.26 4 -0.42 118 122
MAPK1 -0.08 0.14 -10000 0 -0.39 108 108
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 -0.001 0.002 -10000 0 -0.004 317 317
cAMP biosynthetic process 0.004 0.021 -10000 0 -10000 0 0
GNG2 0.017 0.065 -10000 0 -0.57 13 13
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 317 317
HRAS/GTP -0.028 0.12 -10000 0 -0.32 139 139
actin cytoskeleton reorganization 0.029 0.037 -10000 0 -0.3 12 12
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 317 317
PI3K 0.026 0.042 -10000 0 -0.34 13 13
apoptosis 0.13 0.21 0.44 315 -10000 0 315
T-DHT/AR/PELP1 -0.025 0.13 -10000 0 -0.36 141 141
HRAS/GDP -0.052 0.16 -10000 0 -0.45 141 141
CREB1 -0.14 0.23 -10000 0 -0.47 313 313
RAC1-CDC42/GTP 0.037 0.04 -10000 0 -0.3 12 12
AR -0.054 0.2 0.25 1 -0.57 141 142
GNB1 0.023 0.005 -10000 0 -10000 0 0
RAF1 -0.061 0.11 -10000 0 -0.32 134 134
RAC1-CDC42/GDP -0.028 0.16 -10000 0 -0.44 141 141
T-DHT/AR/PELP1/Src -0.022 0.13 -10000 0 -0.34 140 140
MAP2K2 -0.07 0.11 -10000 0 -0.32 127 127
T-DHT/AR/PELP1/Src/PI3K -0.025 0.11 -10000 0 -0.3 135 135
GNAZ 0.017 0.057 -10000 0 -0.57 10 10
SHBG 0.022 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.052 0.16 -10000 0 -0.47 99 99
mol:T-DHT -0.001 0.001 0.002 1 -0.004 86 87
RAC1 0.024 0.003 -10000 0 -10000 0 0
GNRH1 0.001 0.029 -10000 0 -0.42 5 5
Gi family/GTP -0.036 0.1 -10000 0 -0.28 103 103
CDC42 0.023 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.008 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.14 0.31 2 -0.3 62 64
NFATC4 -0.063 0.12 0.27 9 -0.26 84 93
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 -0.3 252 252
JUN -0.009 0.096 0.23 25 -0.45 3 28
HRAS 0.026 0.022 0.26 9 -10000 0 9
DOCK7 -0.079 0.14 0.28 2 -0.3 251 253
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.052 0.15 -10000 0 -0.33 207 207
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.006 -10000 0 -10000 0 0
MAPK10 -0.07 0.11 0.2 10 -0.27 138 148
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.073 0.16 -10000 0 -0.33 252 252
RAF1 -0.019 0.14 0.32 15 -0.3 59 74
ErbB2/ErbB3/neuregulin 2 -0.14 0.18 -10000 0 -0.34 437 437
STAT3 -0.001 0.16 -10000 0 -0.86 34 34
cell migration -0.055 0.1 0.24 15 -0.25 86 101
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.044 0.24 0.44 9 -0.53 80 89
FOS -0.1 0.28 0.37 12 -0.49 326 338
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.069 0.15 -10000 0 -0.3 252 252
MAPK3 -0.015 0.2 0.39 13 -0.53 22 35
MAPK1 -0.027 0.21 0.4 11 -0.6 39 50
JAK2 -0.077 0.14 0.26 1 -0.3 247 248
NF2 -0.002 0.057 -10000 0 -0.68 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.053 0.13 0.22 4 -0.28 234 238
NRG1 -0.14 0.26 0.25 4 -0.57 292 296
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.08 0.15 0.25 2 -0.3 255 257
MAPK9 -0.042 0.083 0.2 11 -0.26 3 14
ERBB2 0.001 0.071 0.24 85 -0.44 1 86
ERBB3 0.021 0.041 -10000 0 -0.57 5 5
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
apoptosis 0.019 0.025 -10000 0 -0.16 7 7
STAT3 (dimer) 0 0.15 -10000 0 -0.84 34 34
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.004 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.07 0.093 -10000 0 -0.23 227 227
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.02 -10000 0 -0.38 1 1
CHRNA1 0.017 0.18 0.36 42 -0.45 12 54
myelination -0.058 0.12 0.3 17 -0.26 32 49
PPP3CB -0.074 0.13 0.27 2 -0.28 248 250
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.26 197 197
NRG2 -0.26 0.29 -10000 0 -0.57 509 509
mol:GDP -0.053 0.13 0.22 4 -0.28 234 238
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.017 0.14 0.32 16 -0.31 50 66
SRC 0.023 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.079 0.14 0.28 2 -0.3 251 253
MAP2K1 -0.053 0.22 0.44 3 -0.61 41 44
heart morphogenesis -0.069 0.15 -10000 0 -0.3 252 252
RAS family/GDP -0.021 0.14 0.33 2 -0.29 61 63
GRB2 0.023 0.009 0.25 1 -10000 0 1
PRKACA -0.002 0.067 -10000 0 -0.68 10 10
CHRNE 0.004 0.027 0.12 4 -0.21 3 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.069 0.15 -10000 0 -0.3 252 252
CDC42 0.023 0.005 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.058 0.16 0.31 7 -0.35 114 121
SMAD6-7/SMURF1 0.046 0.015 -10000 0 -10000 0 0
NOG 0.012 0.095 0.26 19 -0.57 25 44
SMAD9 -0.088 0.25 -10000 0 -0.59 189 189
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.021 0.14 -10000 0 -0.44 68 68
BMP7/USAG1 -0.19 0.25 -10000 0 -0.42 532 532
SMAD5/SKI -0.015 0.15 0.27 1 -0.44 67 68
SMAD1 0.013 0.062 -10000 0 -0.43 7 7
BMP2 -0.074 0.22 0.26 2 -0.57 179 181
SMAD1/SMAD1/SMAD4 0.018 0.069 -10000 0 -0.42 7 7
BMPR1A 0.023 0.026 -10000 0 -0.57 2 2
BMPR1B 0.1 0.15 0.26 425 -0.57 23 448
BMPR1A-1B/BAMBI 0.083 0.12 0.34 9 -0.33 53 62
AHSG 0.021 0.029 0.26 16 -10000 0 16
CER1 0.018 0.013 0.26 3 -10000 0 3
BMP2-4/CER1 -0.046 0.18 -10000 0 -0.39 214 214
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.038 0.16 -10000 0 -0.4 117 117
BMP2-4 (homodimer) -0.066 0.2 -10000 0 -0.45 219 219
RGMB 0.023 0.019 -10000 0 -0.57 1 1
BMP6/BMPR2/BMPR1A-1B 0.07 0.14 -10000 0 -0.31 96 96
RGMA -0.053 0.2 -10000 0 -0.57 139 139
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.036 0.16 -10000 0 -0.41 123 123
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.44 577 577
SMAD6/SMURF1/SMAD5 -0.016 0.15 0.27 1 -0.44 68 69
SOSTDC1 -0.25 0.3 0.26 3 -0.57 507 510
BMP7/BMPR2/BMPR1A-1B 0.068 0.14 0.3 4 -0.32 90 94
SKI 0.023 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.016 0.15 0.26 2 -0.56 72 74
HFE2 0.018 0.023 0.26 9 -10000 0 9
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.043 0.2 -10000 0 -0.4 220 220
SMAD5/SMAD5/SMAD4 -0.016 0.15 0.27 1 -0.44 71 72
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.022 0.15 -10000 0 -0.37 112 112
BMP7 (homodimer) -0.011 0.16 0.26 30 -0.56 73 103
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.001 0.12 -10000 0 -0.41 75 75
SMAD1/SKI 0.02 0.076 -10000 0 -0.43 11 11
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.045 0.18 0.34 1 -0.39 216 217
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.036 0.095 0.26 94 -0.57 14 108
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.085 0.11 -10000 0 -0.41 25 25
CHRDL1 -0.38 0.28 -10000 0 -0.57 729 729
ENDOFIN/SMAD1 0.019 0.078 -10000 0 -0.45 11 11
SMAD6-7/SMURF1/SMAD1 0.036 0.081 -10000 0 -0.44 9 9
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.016 0.11 0.26 39 -0.57 30 69
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.26 -10000 0 -0.45 729 729
BMP2-4/GREM1 -0.037 0.2 -10000 0 -0.4 224 224
SMAD7 0.023 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.081 0.25 -10000 0 -0.57 193 193
SMAD1/SMAD6 0.019 0.078 -10000 0 -0.45 11 11
TAK1/SMAD6 0.033 0.01 -10000 0 -10000 0 0
BMP7 -0.011 0.16 0.26 30 -0.57 73 103
BMP6 -0.016 0.15 0.26 2 -0.57 72 74
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.034 0.17 -10000 0 -0.42 122 122
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.075 -10000 0 -0.45 10 10
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.007 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.047 0.2 0.23 1 -0.48 133 134
CHRD 0.026 0.095 0.26 58 -0.57 19 77
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.05 0.18 -10000 0 -0.48 123 123
BMP4 -0.01 0.14 0.26 1 -0.57 62 63
FST -0.001 0.12 0.26 3 -0.57 45 48
BMP2-4/NOG -0.047 0.19 0.34 1 -0.4 209 210
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.072 0.14 0.3 4 -0.3 90 94
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 0.082 -10000 0 -0.55 14 14
Crk/p130 Cas/Paxillin -0.056 0.12 -10000 0 -0.34 135 135
JUN -0.015 0.12 0.25 1 -0.41 26 27
HRAS 0.026 0.022 0.26 9 -10000 0 9
RET51/GFRalpha1/GDNF/GRB10 0.041 0.19 0.34 53 -0.34 177 230
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.042 0.19 0.34 52 -0.34 176 228
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 5 -0.33 180 185
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.02 0.16 0.28 37 -0.3 179 216
GRB7 0.019 0.032 -10000 0 -0.57 3 3
RET51/GFRalpha1/GDNF 0.04 0.19 0.34 52 -0.34 176 228
MAPKKK cascade 0 0.15 0.28 11 -0.32 130 141
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.024 0.18 0.32 4 -0.38 192 196
lamellipodium assembly -0.033 0.13 -10000 0 -0.31 143 143
RET51/GFRalpha1/GDNF/SHC 0.035 0.18 0.34 42 -0.34 139 181
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.14 0.32 5 -0.33 135 140
RET9/GFRalpha1/GDNF/Shank3 -0.013 0.15 0.32 5 -0.33 180 185
MAPK3 -0.031 0.13 0.25 6 -0.3 155 161
DOK1 0.025 0.014 0.26 4 -10000 0 4
DOK6 0.017 0.07 0.26 7 -0.57 14 21
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.031 0.12 -10000 0 -0.32 82 82
DOK5 0.011 0.087 0.26 5 -0.57 23 28
GFRA1 -0.07 0.24 0.26 53 -0.57 192 245
MAPK8 -0.009 0.13 0.21 4 -0.45 25 29
HRAS/GTP 0.028 0.18 0.29 53 -0.34 169 222
tube development -0.006 0.14 0.34 11 -0.31 171 182
MAPK1 -0.031 0.13 0.28 4 -0.3 141 145
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.11 0.25 1 -0.26 171 172
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.037 0.19 0.33 49 -0.33 182 231
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.027 0.18 0.34 38 -0.34 179 217
RET51/GFRalpha1/GDNF/Dok5 0.025 0.2 0.34 48 -0.35 187 235
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
HRAS/GDP 0.019 0.015 0.18 9 -10000 0 9
CREB1 -0.014 0.13 0.22 14 -0.31 104 118
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.02 0.1 0.25 1 -0.26 127 128
RET51/GFRalpha1/GDNF/Grb7 0.04 0.18 0.33 66 -0.34 146 212
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.097 0.13 0.26 374 -0.57 13 387
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.014 0.12 0.24 1 -0.4 26 27
RET9/GFRalpha1/GDNF/FRS2 -0.012 0.15 0.32 5 -0.33 181 186
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.02 0.1 0.25 1 -0.26 127 128
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.005 0.14 0.24 16 -0.28 140 156
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.002 0.14 0.25 4 -0.29 142 146
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.01 0.13 0.25 16 -0.3 105 121
PI3K -0.029 0.2 0.28 11 -0.47 144 155
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.14 0.31 4 -0.31 171 175
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.005 0.12 0.23 9 -0.26 134 143
RET51/GFRalpha1/GDNF/FRS2 0.038 0.19 0.34 56 -0.34 178 234
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.01 0.13 0.25 16 -0.3 105 121
RET51/GFRalpha1/GDNF/PKC alpha 0.024 0.19 0.35 42 -0.34 185 227
GRB2 0.023 0.009 0.26 1 -10000 0 1
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.052 0.26 54 -10000 0 54
RAC1 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.027 0.22 0.34 50 -0.38 191 241
Rac1/GTP -0.022 0.16 0.23 4 -0.37 143 147
RET9/GFRalpha1/GDNF -0.026 0.16 0.18 70 -0.34 197 267
GFRalpha1/GDNF -0.033 0.18 0.36 5 -0.4 197 202
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.003 0.039 0.22 2 -0.37 2 4
NFATC2 -0.026 0.11 0.19 4 -0.37 88 92
NFATC3 0.006 0.034 0.22 2 -10000 0 2
CD40LG -0.14 0.29 0.47 17 -0.55 260 277
PTGS2 -0.19 0.33 0.48 13 -0.64 328 341
JUNB 0.024 0.01 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.027 0.15 2 -10000 0 2
CaM/Ca2+ 0.008 0.027 0.15 2 -10000 0 2
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.013 0.049 -10000 0 -0.57 6 6
mol:Ca2+ -0.003 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.027 0.048 0.26 26 -0.57 3 29
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.005 0.15 0.46 12 -0.4 55 67
FOS -0.15 0.27 -10000 0 -0.57 306 306
IFNG -0.11 0.28 0.46 42 -0.53 228 270
AP-1/NFAT1-c-4 -0.13 0.34 0.52 40 -0.6 261 301
FASLG -0.12 0.26 0.5 24 -0.54 198 222
NFAT1-c-4/ICER1 -0.018 0.12 0.29 9 -0.34 78 87
IL2RA -0.12 0.28 0.47 32 -0.54 236 268
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.27 0.47 20 -0.53 239 259
JunB/Fra1/NFAT1-c-4 -0.007 0.13 0.34 12 -0.34 77 89
IL4 -0.13 0.26 0.46 14 -0.53 239 253
IL2 -0.014 0.15 -10000 0 -0.94 27 27
IL3 -0.017 0.11 -10000 0 -0.72 23 23
FKBP1A 0.024 0.004 -10000 0 -10000 0 0
BATF3 0.021 0.015 0.26 3 -10000 0 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.4 244 245
PTP1B/AKT1 -0.067 0.13 0.22 1 -0.33 147 148
FYN 0.021 0.026 -10000 0 -0.57 2 2
p210 bcr-abl/PTP1B -0.082 0.14 0.22 2 -0.35 162 164
EGFR -0.2 0.28 -10000 0 -0.58 390 390
EGF/EGFR -0.2 0.24 -10000 0 -0.41 531 531
CSF1 0.021 0.044 -10000 0 -0.57 6 6
AKT1 0.023 0.005 -10000 0 -10000 0 0
INSR 0.023 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.048 0.16 0.24 14 -0.36 142 156
Insulin Receptor/Insulin -0.043 0.12 -10000 0 -0.37 54 54
HCK 0.027 0.026 0.26 13 -10000 0 13
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.078 0.13 0.28 3 -0.35 146 149
EGF -0.099 0.22 0.25 2 -0.58 194 196
YES1 0.023 0.019 -10000 0 -0.57 1 1
CAV1 -0.16 0.21 0.27 2 -0.42 332 334
TXN 0.017 0.017 0.25 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.073 0.15 -10000 0 -0.37 151 151
cell migration 0.082 0.14 0.35 162 -0.22 2 164
STAT3 0.022 0.004 -10000 0 -10000 0 0
PRLR 0.022 0.052 0.25 7 -0.57 7 14
ITGA2B 0.031 0.06 0.25 54 -0.57 3 57
CSF1R 0.024 0.008 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.031 0.043 0.31 1 -0.39 7 8
FGR 0.024 0.009 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.069 0.14 0.22 1 -0.35 141 142
Crk/p130 Cas -0.062 0.14 -10000 0 -0.36 118 118
DOK1 -0.067 0.13 0.23 2 -0.34 131 133
JAK2 -0.048 0.12 -10000 0 -0.45 56 56
Jak2/Leptin Receptor/Leptin -0.26 0.16 -10000 0 -0.39 441 441
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
PTPN1 -0.083 0.14 0.22 2 -0.35 162 164
LYN 0.021 0.008 -10000 0 -10000 0 0
CDH2 0.063 0.092 0.26 187 -0.57 2 189
SRC -0.018 0.098 -10000 0 -0.62 21 21
ITGB3 0.005 0.1 0.25 4 -0.57 33 37
CAT1/PTP1B -0.092 0.19 0.32 4 -0.45 165 169
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.038 0.12 -10000 0 -0.42 46 46
mol:H2O2 -0.004 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.24 0.14 -10000 0 -0.36 406 406
negative regulation of transcription -0.047 0.12 -10000 0 -0.44 56 56
FCGR2A 0.02 0.012 0.26 1 -10000 0 1
FER 0.011 0.058 -10000 0 -0.58 10 10
alphaIIb/beta3 Integrin 0.023 0.09 -10000 0 -0.42 36 36
BLK 0.051 0.087 0.26 151 -0.57 2 153
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.006 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.57 266 266
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.009 0.26 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.041 0.17 0.32 5 -0.44 109 114
PRL 0.007 0.032 0.26 10 -10000 0 10
SOCS3 0.01 0.16 -10000 0 -1.2 16 16
SPRY2 -0.041 0.18 -10000 0 -0.57 106 106
Insulin Receptor/Insulin/IRS1 0.026 0.08 -10000 0 -0.37 41 41
CSF1/CSF1R -0.065 0.14 -10000 0 -0.36 137 137
Ras protein signal transduction 0.051 0.15 0.64 60 -10000 0 60
IRS1 0.001 0.11 -10000 0 -0.57 42 42
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.44 0.24 -10000 0 -0.57 841 841
STAT5B -0.069 0.14 0.2 3 -0.35 145 148
STAT5A -0.07 0.14 0.2 3 -0.35 147 150
GRB2 0.023 0.009 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.073 0.14 0.22 1 -0.35 150 151
CSN2 0.025 0.057 0.4 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.01 0.072 -10000 0 -0.55 9 9
YBX1 0.027 0.015 0.22 1 -10000 0 1
LCK 0.026 0.075 0.26 40 -0.57 11 51
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.019 0.036 0.25 10 -0.57 2 12
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.069 0.11 -10000 0 -0.28 94 94
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.46 448 448
NT3 (dimer)/TRKB -0.29 0.3 -10000 0 -0.52 615 615
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.033 -10000 0 -0.26 8 8
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.012 0.16 0.26 24 -0.57 75 99
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.024 0.051 0.26 25 -0.57 4 29
NTRK2 -0.28 0.3 -10000 0 -0.57 552 552
NTRK3 -0.17 0.28 0.26 5 -0.57 347 352
NT-4/5 (dimer)/TRKB -0.35 0.33 -10000 0 -0.56 691 691
neuron apoptosis 0.17 0.22 0.47 288 -10000 0 288
SHC 2-3/Grb2 -0.18 0.24 -10000 0 -0.52 288 288
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.18 0.25 -10000 0 -0.54 288 288
SHC3 -0.17 0.23 -10000 0 -0.52 281 281
STAT3 (dimer) 0.033 0.043 -10000 0 -0.36 4 4
NT3 (dimer)/TRKA -0.1 0.21 -10000 0 -0.41 303 303
RIN/GDP -0.045 0.12 0.3 4 -0.26 84 88
GIPC1 0.024 0.008 0.26 1 -10000 0 1
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.078 0.15 -10000 0 -0.33 265 265
RIN/GTP 0.014 0.008 0.18 2 -10000 0 2
CCND1 0.025 0.094 0.43 39 -0.82 4 43
MAGED1 0.025 0.01 0.26 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 -0.56 363 363
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.035 0.082 0.34 3 -0.35 34 37
TRKA/NEDD4-2 0.031 0.04 -10000 0 -0.37 5 5
ELMO1 0.024 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.008 -10000 0 -10000 0 0
NGF 0.017 0.074 0.26 8 -0.57 16 24
HRAS 0.026 0.022 0.26 9 -10000 0 9
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.021 0.019 -10000 0 -0.57 1 1
RIT2 0.018 0.011 0.26 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
DNM1 0.02 0.048 0.26 1 -0.57 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.071 0.16 -10000 0 -0.32 281 281
mol:GDP -0.074 0.16 0.35 5 -0.36 121 126
NGF (dimer) 0.017 0.074 0.26 8 -0.56 16 24
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.044 0.1 0.38 2 -0.25 80 82
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
BDNF (dimer)/TRKB -0.18 0.23 -10000 0 -0.39 572 572
KIDINS220/CRKL/C3G 0.033 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.048 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.56 157 169
RAP1/GDP -0.041 0.093 -10000 0 -0.22 76 76
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.012 0.16 0.26 24 -0.56 75 99
ubiquitin-dependent protein catabolic process 0.036 0.061 -10000 0 -0.36 18 18
Schwann cell development -0.048 0.038 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.048 -10000 0 -0.27 8 8
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.28 -10000 0 -0.46 647 647
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 -0.077 0.13 -10000 0 -0.43 64 64
STAT3 0.033 0.043 -10000 0 -0.36 4 4
axon guidance -0.26 0.26 -10000 0 -0.44 647 647
MAPK3 0.024 0.085 0.24 3 -0.35 27 30
MAPK1 0.027 0.088 0.24 4 -0.35 28 32
CDC42/GDP -0.043 0.12 0.29 5 -0.25 85 90
NTF3 -0.061 0.21 0.26 12 -0.57 157 169
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NGF (dimer)/TRKA/FAIM 0.037 0.061 -10000 0 -0.36 18 18
PI3K 0.028 0.049 -10000 0 -0.38 14 14
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 -0.077 0.16 0.25 3 -0.33 272 275
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.41 425 426
RGS19 0.023 0.01 0.26 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.094 0.33 3 -0.43 10 13
Rac1/GDP -0.044 0.12 0.31 4 -0.25 91 95
NGF (dimer)/TRKA/GRIT 0.024 0.057 -10000 0 -0.34 20 20
neuron projection morphogenesis -0.068 0.21 -10000 0 -0.74 50 50
NGF (dimer)/TRKA/NEDD4-2 0.036 0.061 -10000 0 -0.36 18 18
MAP2K1 0.029 0.085 0.36 17 -10000 0 17
NGFR -0.14 0.26 -10000 0 -0.57 287 287
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.05 -10000 0 -0.29 21 21
RAS family/GTP/PI3K 0.017 0.03 -10000 0 -0.26 9 9
FRS2 family/SHP2/GRB2/SOS1 0.063 0.026 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAPKKK cascade -0.039 0.14 -10000 0 -0.65 41 41
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.039 -10000 0 -0.42 4 4
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.36 566 566
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.062 -10000 0 -0.31 18 18
MATK 0.02 0.086 0.26 30 -0.57 18 48
NEDD4L 0.023 0.019 -10000 0 -0.57 1 1
RAS family/GDP -0.055 0.07 -10000 0 -0.2 70 70
NGF (dimer)/TRKA -0.085 0.16 -10000 0 -0.34 298 298
Rac1/GTP -0.083 0.12 -10000 0 -0.27 254 254
FRS2 family/SHP2/CRK family 0.06 0.029 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.044 -10000 0 -0.39 6 6
PDGFRB 0.018 0.037 -10000 0 -0.57 4 4
SPHK1 -0.018 0.097 -10000 0 -0.75 14 14
mol:S1P -0.021 0.095 0.39 1 -0.66 14 15
S1P1/S1P/Gi -0.13 0.23 0.31 2 -0.43 362 364
GNAO1 0.006 0.092 0.24 32 -0.57 20 52
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.34 3 -0.4 316 319
PLCG1 -0.13 0.22 0.35 2 -0.42 325 327
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.037 -10000 0 -0.57 4 4
GNAI2 0.009 0.023 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.021 0.13 -10000 0 -0.58 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.031 0.2 1 -0.37 5 6
S1P1/S1P -0.034 0.097 0.34 1 -0.46 18 19
negative regulation of cAMP metabolic process -0.13 0.23 0.31 2 -0.42 362 364
MAPK3 -0.18 0.3 0.3 12 -0.58 357 369
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 0.044 -10000 0 -0.57 5 5
PLCB2 -0.025 0.097 0.29 7 -0.41 19 26
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.081 -10000 0 -0.39 18 18
receptor internalization -0.035 0.088 -10000 0 -0.43 18 18
PTGS2 -0.33 0.5 0.38 2 -1 367 369
Rac1/GTP -0.032 0.081 -10000 0 -0.39 18 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.25 7 -10000 0 7
negative regulation of T cell proliferation -0.13 0.23 0.31 2 -0.42 362 364
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.06 -10000 0 -0.57 10 10
MAPK1 -0.2 0.33 0.34 2 -0.62 372 374
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.31 4 -0.48 17 21
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
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 0.036 0.037 0.32 2 -10000 0 2
PDE6G/GNAT1/GTP 0.035 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.027 0.26 14 -10000 0 14
GRK1 0.019 0.016 0.26 4 -10000 0 4
CNG Channel -0.048 0.16 -10000 0 -0.3 284 284
mol:Na + -0.047 0.16 -10000 0 -0.3 274 274
mol:ADP 0.019 0.016 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 86 87
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.041 0.16 0.28 5 -0.3 272 277
CNGB1 0.03 0.051 0.26 52 -10000 0 52
RDH5 -0.33 0.29 -10000 0 -0.57 641 641
SAG 0.032 0.052 0.26 54 -10000 0 54
mol:Ca2+ -0.08 0.14 0.36 18 -0.49 5 23
Na + (4 Units) -0.051 0.14 -10000 0 -0.29 250 250
RGS9 -0.024 0.16 0.26 11 -0.57 88 99
GNB1/GNGT1 0.054 0.059 0.2 159 -10000 0 159
GNAT1/GDP 0.025 0.11 0.3 5 -0.31 86 91
GUCY2D 0.024 0.044 0.26 19 -0.57 3 22
GNGT1 0.055 0.086 0.26 169 -10000 0 169
GUCY2F 0.018 0.011 0.26 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.02 0.049 0.2 3 -0.31 16 19
mol:11-cis-retinal -0.33 0.29 -10000 0 -0.56 641 641
mol:cGMP 0.042 0.044 -10000 0 -0.32 7 7
GNB1 0.023 0.005 -10000 0 -10000 0 0
Rhodopsin -0.24 0.22 -10000 0 -0.42 634 634
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.14 0.26 0.26 4 -0.57 294 298
Metarhodopsin II 0.026 0.019 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.05 -10000 0 -0.34 7 7
RGS9BP 0.036 0.052 0.26 57 -10000 0 57
Metarhodopsin II/Transducin 0.024 0.031 0.17 8 -0.17 1 9
GCAP Family/Ca ++ 0.044 0.037 -10000 0 -0.33 4 4
PDE6A/B 0.029 0.064 -10000 0 -0.38 21 21
mol:Pi 0.016 0.12 0.33 1 -0.36 86 87
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.058 0.053 0.32 2 -10000 0 2
PDE6B 0.014 0.077 0.26 3 -0.57 18 21
PDE6A 0.028 0.032 0.26 20 -10000 0 20
PDE6G 0.032 0.045 0.26 42 -10000 0 42
RHO 0.024 0.028 0.26 15 -10000 0 15
PDE6 0.035 0.12 0.3 8 -0.31 97 105
GUCA1A 0.031 0.045 0.26 42 -10000 0 42
GC2/GCAP Family 0.054 0.039 -10000 0 -0.34 4 4
GUCA1C 0.017 0.008 0.26 1 -10000 0 1
GUCA1B 0.022 0.036 -10000 0 -0.57 4 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.041 0.17 -10000 0 -0.42 172 172
CRKL -0.047 0.15 0.31 2 -0.4 87 89
mol:PIP3 0.002 0.059 0.56 1 -0.89 4 5
AKT1 0.01 0.074 0.37 3 -0.79 4 7
PTK2B 0.02 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.14 0.33 2 -0.4 73 75
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 -0.38 214 214
MAP3K5 -0.04 0.15 0.36 1 -0.44 61 62
HGF/MET/CIN85/CBL/ENDOPHILINS -0.03 0.17 -10000 0 -0.35 222 222
AP1 -0.11 0.19 -10000 0 -0.39 307 307
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 -0.77 356 356
STAT3 (dimer) -0.047 0.15 -10000 0 -0.45 82 82
GAB1/CRKL/SHP2/PI3K -0.02 0.15 -10000 0 -0.44 58 58
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.036 0.14 0.34 1 -0.42 64 65
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
ELK1 -0.03 0.096 0.29 25 -0.22 36 61
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.092 -10000 0 -0.32 41 41
PAK1 0.024 0.087 0.36 7 -0.75 4 11
HGF/MET/RANBP10 -0.045 0.18 -10000 0 -0.38 223 223
HRAS -0.11 0.26 -10000 0 -0.64 193 193
DOCK1 -0.046 0.14 0.52 1 -0.41 71 72
GAB1 -0.05 0.15 -10000 0 -0.42 95 95
CRK -0.049 0.15 0.36 1 -0.41 85 86
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.25 -10000 0 -0.57 231 231
JUN 0.02 0.044 -10000 0 -0.57 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.052 0.12 -10000 0 -0.28 226 226
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
cell morphogenesis -0.049 0.16 0.37 6 -0.45 88 94
GRB2/SHC -0.016 0.11 -10000 0 -0.28 123 123
FOS -0.14 0.27 -10000 0 -0.57 306 306
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.03 0.095 0.29 25 -0.22 39 64
HGF/MET/MUC20 -0.055 0.17 -10000 0 -0.38 225 225
cell migration -0.016 0.11 -10000 0 -0.28 123 123
GRB2 0.023 0.009 0.26 1 -10000 0 1
CBL 0.022 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.042 0.17 -10000 0 -0.41 180 180
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.048 0.14 -10000 0 -0.33 186 186
MET/MUC20 -0.055 0.16 -10000 0 -0.4 186 186
RAP1B -0.039 0.14 0.33 4 -0.43 48 52
RAP1A -0.045 0.13 0.32 3 -0.38 70 73
HGF/MET/RANBP9 -0.043 0.18 -10000 0 -0.38 218 218
RAF1 -0.099 0.24 -10000 0 -0.6 192 192
STAT3 -0.048 0.15 -10000 0 -0.45 82 82
cell proliferation -0.042 0.19 0.32 12 -0.42 159 171
RPS6KB1 -0.015 0.063 -10000 0 -0.26 22 22
MAPK3 -0.042 0.093 0.62 8 -10000 0 8
MAPK1 -0.011 0.17 0.68 54 -10000 0 54
RANBP9 0.023 0.005 -10000 0 -10000 0 0
MAPK8 -0.029 0.14 0.43 1 -0.47 41 42
SRC -0.052 0.13 0.2 1 -0.4 75 76
PI3K -0.028 0.13 -10000 0 -0.29 180 180
MET/Glomulin -0.047 0.14 -10000 0 -0.37 179 179
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.091 0.23 0.47 1 -0.55 192 193
MET -0.073 0.22 -10000 0 -0.57 177 177
MAP4K1 -0.042 0.15 0.38 1 -0.46 67 68
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.09 0.23 0.47 1 -0.55 192 193
BAD 0.008 0.071 0.34 4 -0.75 4 8
MAP2K4 -0.037 0.13 0.34 1 -0.42 52 53
SHP2/GRB2/SOS1/GAB1 -0.041 0.17 -10000 0 -0.4 174 174
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 -0.048 0.11 -10000 0 -0.27 206 206
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 0.26 2 -0.57 65 67
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.022 0.13 -10000 0 -0.26 210 210
PDPK1 0.012 0.077 0.42 1 -0.83 4 5
HGF/MET/SHIP -0.043 0.18 -10000 0 -0.38 224 224
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.078 0.31 10 -0.3 1 11
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.019 -10000 0 -0.3 2 2
AURKB 0.14 0.12 0.26 560 -10000 0 560
AURKC 0.026 0.032 0.26 14 -0.57 1 15
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.043 0.17 0.3 134 -0.45 57 191
FYN 0.02 0.19 0.32 63 -0.52 71 134
LAT/GRAP2/SLP76 0.026 0.17 0.34 47 -0.5 57 104
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.022 0.15 0.3 83 -0.36 85 168
B2M 0.024 0.008 -10000 0 -10000 0 0
IKBKG 0.016 0.058 0.16 74 -0.14 28 102
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
mol:Ca2+ -0.022 0.032 -10000 0 -0.089 170 170
integrin-mediated signaling pathway 0.026 0.022 -10000 0 -0.29 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.2 0.35 50 -0.52 82 132
TRPV6 -0.089 0.26 1.2 15 -0.57 195 210
CD28 0.024 0.05 0.26 10 -0.57 6 16
SHC1 0.029 0.21 0.31 158 -0.45 103 261
receptor internalization -0.012 0.22 0.35 36 -0.47 144 180
PRF1 -0.011 0.24 0.55 7 -0.97 43 50
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
COT/AKT1 0.031 0.13 0.29 76 -0.3 79 155
LAT 0.012 0.2 0.32 72 -0.46 102 174
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.023 0.095 0.26 49 -0.57 19 68
CD3E 0.023 0.086 0.27 37 -0.58 16 53
CD3G 0.012 0.11 0.26 38 -0.57 33 71
RASGRP2 0 0.05 0.14 15 -0.17 70 85
RASGRP1 0.024 0.15 0.32 54 -0.4 61 115
HLA-A 0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.019 0.033 0.26 1 -0.57 3 4
RAP1A/GTP/RAPL 0.026 0.022 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.079 0.17 169 -0.13 28 197
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.055 -10000 0 -0.21 42 42
PRKCA 0.014 0.098 0.22 55 -0.26 57 112
GRAP2 0.017 0.063 0.25 3 -0.57 12 15
mol:IP3 0.014 0.14 0.26 129 -0.38 52 181
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.17 0.3 36 -0.66 48 84
ORAI1 0.037 0.17 0.64 4 -0.96 15 19
CSK 0.007 0.2 0.35 40 -0.46 107 147
B7 family/CD28 0.062 0.21 0.39 60 -0.59 53 113
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0 0.22 0.37 38 -0.5 116 154
PTPN6 0.003 0.19 0.33 45 -0.46 101 146
VAV1 0.003 0.2 0.35 42 -0.47 104 146
Monovalent TCR/CD3 -0.001 0.14 0.26 39 -0.5 56 95
CBL 0.022 0.007 -10000 0 -10000 0 0
LCK 0.017 0.2 0.32 64 -0.57 65 129
PAG1 0.02 0.2 0.31 75 -0.45 104 179
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0 0.22 0.36 37 -0.49 114 151
CD80 0.084 0.1 0.26 279 -10000 0 279
CD86 0.026 0.018 0.26 6 -10000 0 6
PDK1/CARD11/BCL10/MALT1 -0.005 0.071 0.19 4 -0.25 44 48
HRAS 0.026 0.022 0.26 9 -10000 0 9
GO:0035030 0.021 0.16 0.32 44 -0.48 54 98
CD8A 0.029 0.058 0.27 29 -0.58 5 34
CD8B 0.014 0.11 0.27 30 -0.57 32 62
PTPRC 0.021 0.041 0.26 12 -0.57 3 15
PDK1/PKC theta 0.024 0.18 0.37 80 -0.45 75 155
CSK/PAG1 0.021 0.19 0.31 70 -0.53 67 137
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.01 -10000 0 -10000 0 0
GRAP2/SLP76 0.019 0.2 0.38 35 -0.48 90 125
STIM1 0.025 0.095 1.3 4 -10000 0 4
RAS family/GTP 0.044 0.091 0.22 90 -0.18 39 129
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.23 0.35 36 -0.5 144 180
mol:DAG -0.016 0.096 0.12 32 -0.32 64 96
RAP1A/GDP 0.021 0.038 0.098 94 -0.065 9 103
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.016 0.077 0.26 16 -0.57 15 31
cytotoxic T cell degranulation -0.008 0.22 0.54 7 -0.9 43 50
RAP1A/GTP -0.001 0.017 -10000 0 -0.063 68 68
mol:PI-3-4-5-P3 0.017 0.17 0.33 55 -0.43 82 137
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.022 0.17 0.29 119 -0.48 54 173
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.027 0.098 0.26 61 -0.57 20 81
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.006 0.16 0.36 16 -0.5 55 71
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.032 0.11 0.38 21 -0.48 32 53
CARD11 0.027 0.041 0.26 21 -0.57 2 23
PRKCB 0.014 0.1 0.25 52 -0.27 45 97
PRKCE 0.019 0.095 0.22 62 -0.26 45 107
PRKCQ 0.012 0.2 0.35 55 -0.5 82 137
LCP2 0.024 0.008 0.25 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.14 0.29 86 -0.31 83 169
IKK complex 0.035 0.08 0.21 121 -0.12 27 148
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.025 0.11 0.25 77 -0.26 49 126
PDPK1 0.027 0.15 0.33 81 -0.35 75 156
TCR/CD3/MHC I/CD8/Fyn -0.028 0.24 0.39 29 -0.57 116 145
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.01 0.024 0.13 40 -10000 0 40
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.031 0.11 -10000 0 -0.41 46 46
STXBP1 0.02 0.048 -10000 0 -0.57 7 7
ACh/CHRNA1 0.072 0.09 0.19 351 -0.16 8 359
RAB3GAP2/RIMS1/UNC13B 0.035 0.087 -10000 0 -0.36 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.14 0.26 117 -0.57 45 162
mol:ACh -0.003 0.036 0.089 12 -0.14 43 55
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.021 0.082 0.23 1 -0.27 43 44
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.072 0.09 0.19 351 -0.15 8 359
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.26 362 -10000 0 362
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.032 0.11 0.2 196 -0.36 43 239
SNAP25 0 0.058 0.094 59 -0.3 34 93
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.046 0.15 0.26 204 -0.57 39 243
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.036 -10000 0 -0.36 7 7
STX1A/SNAP25 fragment 1/VAMP2 0.021 0.082 0.23 1 -0.27 43 44
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.081 0.28 1 -0.33 2 3
epithelial cell differentiation 0.032 0.08 0.39 1 -0.43 3 4
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.022 0.097 0.46 8 -10000 0 8
FYN 0.021 0.026 -10000 0 -0.57 2 2
EGFR -0.19 0.28 -10000 0 -0.57 390 390
PRL 0.022 0.023 0.26 10 -10000 0 10
neuron projection morphogenesis -0.041 0.14 0.37 13 -0.36 34 47
PTPRZ1 -0.27 0.3 0.26 6 -0.57 541 547
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.14 -10000 0 -0.38 42 42
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.087 0.15 -10000 0 -0.34 243 243
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.007 0.074 0.38 8 -0.3 6 14
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.002 0.11 -10000 0 -0.36 41 41
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.079 0.15 -10000 0 -0.32 232 232
GRIN2B -0.097 0.16 -10000 0 -0.32 261 261
ErbB4/ErbB2/betacellulin 0.013 0.097 -10000 0 -0.32 32 32
STAT1 0.028 0.031 0.26 19 -10000 0 19
HBEGF 0.023 0.026 -10000 0 -0.57 2 2
PRLR 0.021 0.051 0.26 7 -0.57 7 14
E4ICDs/ETO2 0.006 0.087 0.35 1 -0.4 11 12
axon guidance 0.054 0.11 0.4 8 -0.37 2 10
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.031 0.04 -10000 0 -0.39 7 7
CBFA2T3 0.014 0.071 0.26 4 -0.57 15 19
ErbB4/ErbB2/HBEGF 0.03 0.072 -10000 0 -0.34 3 3
MAPK3 -0.047 0.14 0.34 4 -0.36 41 45
STAT1 (dimer) 0.019 0.081 -10000 0 -10000 0 0
MAPK1 -0.047 0.14 0.36 5 -0.36 41 46
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.071 0.15 0.27 1 -0.32 220 221
NRG1 -0.1 0.19 -10000 0 -0.42 288 288
NRG3 0.001 0.13 0.26 24 -0.57 50 74
NRG2 -0.26 0.29 -10000 0 -0.57 509 509
NRG4 0.026 0.028 0.26 15 -10000 0 15
heart development 0.054 0.11 0.4 8 -0.37 2 10
neural crest cell migration -0.07 0.15 0.27 1 -0.32 222 223
ERBB2 0.035 0.071 0.27 87 -0.41 1 88
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 0.16 -10000 0 -0.32 278 278
apoptosis 0.012 0.12 0.46 47 -0.26 2 49
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.15 0.17 -10000 0 -0.34 389 389
ErbB4/ErbB2/epiregulin 0.007 0.13 0.35 12 -0.31 76 88
ErbB4/ErbB4/betacellulin/betacellulin -0.004 0.11 0.28 1 -0.35 45 46
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.04 0.087 0.39 1 -0.4 6 7
MDM2 0.008 0.079 0.29 8 -10000 0 8
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.083 0.14 -10000 0 -0.32 244 244
STAT5A 0.049 0.11 0.36 12 -0.37 3 15
ErbB4/EGFR/neuregulin 1 beta -0.18 0.23 -10000 0 -0.43 426 426
DLG4 0.022 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.01 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.059 0.1 0.45 1 -0.46 3 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.11 0.35 6 -0.35 3 9
LRIG1 0.022 0.031 -10000 0 -0.57 3 3
EREG -0.024 0.2 0.26 77 -0.57 116 193
BTC -0.007 0.13 0.26 2 -0.57 57 59
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.044 0.11 0.4 7 -0.37 2 9
ERBB4 -0.007 0.074 0.38 8 -0.3 6 14
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
YAP1 -0.013 0.11 0.22 3 -0.39 74 77
GRB2 0.023 0.009 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.033 0.071 0.32 1 -0.41 1 2
glial cell differentiation -0.01 0.07 -10000 0 -10000 0 0
WWOX 0.021 0.013 0.26 2 -10000 0 2
cell proliferation -0.038 0.17 0.34 14 -0.45 47 61
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.36 330 330
fibroblast growth factor receptor signaling pathway -0.1 0.18 -10000 0 -0.36 330 330
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
PRNP 0.015 0.072 -10000 0 -0.57 16 16
GPC1/SLIT2 -0.015 0.14 -10000 0 -0.42 117 117
SMAD2 -0.001 0.068 0.24 1 -0.33 42 43
GPC1/PrPc/Cu2+ 0.026 0.05 -10000 0 -0.36 17 17
GPC1/Laminin alpha1 -0.011 0.14 -10000 0 -0.42 106 106
TDGF1 0.019 0.048 0.26 1 -0.57 7 8
CRIPTO/GPC1 0.031 0.042 -10000 0 -0.42 8 8
APP/GPC1 0.035 0.02 -10000 0 -0.42 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.006 0.034 -10000 0 -0.36 8 8
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.031 0.082 -10000 0 -0.36 43 43
SERPINC1 0.031 0.05 0.26 50 -10000 0 50
FYN 0.005 0.037 -10000 0 -0.36 10 10
FGR 0.006 0.034 -10000 0 -0.36 8 8
positive regulation of MAPKKK cascade 0.011 0.079 0.28 3 -0.36 23 26
SLIT2 -0.04 0.18 -10000 0 -0.57 116 116
GPC1/NRG -0.11 0.2 -10000 0 -0.42 293 293
NRG1 -0.14 0.26 0.26 4 -0.57 292 296
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.025 -10000 0 -0.36 1 1
LYN 0.006 0.031 -10000 0 -0.36 6 6
mol:Spermine 0.006 0.016 -10000 0 -0.42 1 1
cell growth -0.1 0.18 -10000 0 -0.36 330 330
BMP signaling pathway -0.025 0.025 0.56 1 -0.26 6 7
SRC 0.006 0.034 -10000 0 -0.36 8 8
TGFBR1 0.024 0.008 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.27 0.26 26 -0.57 310 336
GPC1 0.025 0.025 0.26 6 -0.57 1 7
TGFBR1 (dimer) 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 7 -10000 0 7
BLK 0.021 0.062 -10000 0 -0.37 10 10
HCK 0.008 0.037 -10000 0 -0.36 8 8
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 42 42
cell death 0.035 0.02 -10000 0 -0.42 1 1
ATIII/GPC1 0.037 0.04 -10000 0 -0.42 1 1
PLA2G2A/GPC1 -0.098 0.21 -10000 0 -0.42 310 310
LCK 0.007 0.056 -10000 0 -0.36 19 19
neuron differentiation -0.11 0.2 -10000 0 -0.42 293 293
PrPc/Cu2+ 0.011 0.053 -10000 0 -0.42 16 16
APP 0.024 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.001 0.11 -10000 0 -0.56 42 42
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.028 0.22 0.63 2 -0.64 29 31
CRP -0.006 0.24 0.59 15 -0.68 23 38
cell cycle arrest -0.039 0.25 0.55 12 -0.67 48 60
TIMP1 -0.021 0.21 0.61 2 -0.63 21 23
IL6ST -0.037 0.19 -10000 0 -0.56 120 120
Rac1/GDP -0.069 0.2 0.38 2 -0.46 108 110
AP1 -0.073 0.21 0.37 1 -0.55 63 64
GAB2 0.022 0.02 -10000 0 -0.57 1 1
TNFSF11 -0.018 0.24 0.6 12 -0.65 28 40
HSP90B1 0.022 0.11 -10000 0 -0.74 13 13
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.095 0.18 -10000 0 -0.52 92 92
AKT1 0.022 0.066 -10000 0 -0.66 4 4
FOXO1 0.023 0.068 0.43 1 -0.54 5 6
MAP2K6 -0.096 0.18 0.27 2 -0.46 130 132
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.053 0.2 0.38 13 -0.48 85 98
MITF -0.09 0.19 0.26 11 -0.41 177 188
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 25 25
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.018 0.13 -10000 0 -0.52 33 33
STAT3 -0.045 0.26 0.56 11 -0.73 48 59
STAT1 0.012 0.093 -10000 0 -0.83 10 10
CEBPD -0.014 0.23 0.57 9 -0.66 32 41
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.05 -10000 0 -0.38 14 14
JUN 0.02 0.044 -10000 0 -0.57 6 6
PIAS3/MITF -0.072 0.18 0.32 2 -0.46 97 99
MAPK11 -0.094 0.18 -10000 0 -0.53 91 91
STAT3 (dimer)/FOXO1 -0.026 0.22 0.51 13 -0.56 46 59
GRB2/SOS1/GAB family -0.061 0.18 -10000 0 -0.48 77 77
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.19 0.24 1 -0.34 313 314
GRB2 0.023 0.009 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.17 0.46 0.61 13 -0.92 259 272
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.026 0.008 -10000 0 -10000 0 0
MYC -0.004 0.27 0.54 26 -0.91 37 63
FGG -0.026 0.23 0.6 12 -0.64 31 43
macrophage differentiation -0.039 0.25 0.55 12 -0.67 48 60
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.092 0.21 -10000 0 -0.35 355 355
JUNB -0.03 0.22 0.6 2 -0.62 30 32
FOS -0.14 0.27 -10000 0 -0.57 306 306
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.092 0.2 0.29 11 -0.42 181 192
STAT1/PIAS1 -0.061 0.2 0.35 11 -0.39 169 180
GRB2/SOS1/GAB family/SHP2/PI3K 0.023 0.07 -10000 0 -0.52 8 8
STAT3 (dimer) -0.044 0.26 0.56 11 -0.72 47 58
PRKCD -0.037 0.2 0.44 17 -0.51 61 78
IL6R 0.001 0.11 -10000 0 -0.56 38 38
SOCS3 -0.092 0.19 -10000 0 -0.65 50 50
gp130 (dimer)/JAK1/JAK1/LMO4 0.012 0.13 -10000 0 -0.35 120 120
Rac1/GTP -0.064 0.2 0.34 10 -0.47 102 112
HCK 0.026 0.026 0.26 13 -10000 0 13
MAPKKK cascade -0.002 0.14 -10000 0 -0.62 30 30
bone resorption -0.015 0.23 0.59 12 -0.61 28 40
IRF1 -0.031 0.22 0.52 11 -0.63 33 44
mol:GDP -0.084 0.19 0.28 12 -0.4 176 188
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.085 0.2 0.28 12 -0.41 176 188
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.2 -10000 0 -0.58 97 97
PTPN11 0.011 0.081 -10000 0 -0.84 8 8
IL6/IL6RA -0.12 0.22 -10000 0 -0.39 377 377
gp130 (dimer)/TYK2/TYK2/LMO4 0.007 0.13 -10000 0 -0.35 120 120
gp130 (dimer)/JAK2/JAK2/LMO4 0.007 0.13 -10000 0 -0.35 114 114
IL6 -0.18 0.28 0.27 1 -0.56 380 381
PIAS3 0.02 0.009 -10000 0 -10000 0 0
PTPRE 0.008 0.035 -10000 0 -0.57 2 2
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.11 0.19 0.22 2 -0.33 332 334
LMO4 0.028 0.036 0.28 2 -0.56 3 5
STAT3 (dimer)/PIAS3 -0.049 0.24 0.53 10 -0.68 48 58
MCL1 0.053 0.098 0.49 1 -0.55 5 6
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.006 0.07 0.34 1 -0.33 10 11
alphaM/beta2 Integrin/GPIbA 0.01 0.075 0.33 4 -0.4 6 10
alphaM/beta2 Integrin/proMMP-9 0.074 0.11 0.34 17 -0.41 1 18
PLAUR 0.042 0.062 0.26 83 -10000 0 83
HMGB1 -0.003 0.04 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.009 0.063 0.34 1 -10000 0 1
AGER -0.006 0.05 0.26 1 -0.47 3 4
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.025 0.14 0.32 4 -0.36 14 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
CYR61 -0.004 0.12 -10000 0 -0.57 51 51
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.37 33 33
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.092 0.23 -10000 0 -0.56 205 205
MYH2 -0.013 0.14 0.29 8 -0.47 36 44
MST1R 0.022 0.053 0.26 10 -0.57 7 17
leukocyte activation during inflammatory response -0.18 0.17 0.29 1 -0.33 587 588
APOB -0.33 0.29 -10000 0 -0.57 647 647
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.048 0.26 1 -0.57 7 8
JAM3 0.019 0.041 -10000 0 -0.57 5 5
GP1BA 0.024 0.057 0.26 26 -0.57 6 32
alphaM/beta2 Integrin/CTGF 0.004 0.077 0.34 1 -0.4 13 14
alphaM/beta2 Integrin -0.012 0.12 0.2 7 -0.4 41 48
JAM3 homodimer 0.019 0.041 -10000 0 -0.56 5 5
ICAM2 0.019 0.041 -10000 0 -0.57 5 5
ICAM1 0.027 0.027 0.26 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.12 0.22 6 -0.39 43 49
cell adhesion 0.01 0.075 0.33 4 -0.4 6 10
NFKB1 -0.098 0.2 0.41 5 -0.37 335 340
THY1 0.024 0.021 0.26 8 -10000 0 8
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.21 0.19 -10000 0 -0.36 646 646
alphaM/beta2 Integrin/LRP/tPA 0.008 0.09 0.34 1 -0.38 27 28
IL6 -0.26 0.39 0.36 4 -0.76 391 395
ITGB2 -0.002 0.052 0.26 16 -10000 0 16
elevation of cytosolic calcium ion concentration 0.031 0.085 0.33 20 -10000 0 20
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 0.34 1 -0.38 47 48
JAM2 -0.007 0.13 -10000 0 -0.57 55 55
alphaM/beta2 Integrin/ICAM1 0.024 0.086 0.33 4 -0.33 17 21
alphaM/beta2 Integrin/uPA/Plg 0.019 0.07 0.33 1 -10000 0 1
RhoA/GTP -0.018 0.15 0.24 15 -0.47 44 59
positive regulation of phagocytosis -0.001 0.1 0.3 5 -0.36 19 24
Ron/MSP 0.03 0.061 0.36 1 -0.4 18 19
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.087 0.34 20 -10000 0 20
alphaM/beta2 Integrin/uPAR 0.02 0.079 0.38 4 -10000 0 4
PLAU 0.03 0.036 0.26 26 -10000 0 26
PLAT 0.006 0.091 0.26 1 -0.57 26 27
actin filament polymerization -0.011 0.14 0.29 8 -0.45 35 43
MST1 0.021 0.055 0.26 8 -0.57 8 16
alphaM/beta2 Integrin/lipoprotein(a) -0.18 0.17 0.32 1 -0.33 587 588
TNF -0.098 0.2 0.39 3 -0.76 17 20
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 0.32 1 -10000 0 1
HCK 0.027 0.026 0.26 13 -10000 0 13
dendritic cell antigen processing and presentation -0.011 0.12 0.22 6 -0.39 43 49
VTN 0.033 0.077 0.26 68 -0.57 8 76
alphaM/beta2 Integrin/CYR61 -0.008 0.1 0.34 1 -0.4 48 49
LPA 0.018 0.017 0.26 5 -10000 0 5
LRP1 0.018 0.062 -10000 0 -0.57 12 12
cell migration 0.043 0.083 0.28 15 -0.36 8 23
FN1 0.11 0.11 0.26 421 -10000 0 421
alphaM/beta2 Integrin/Thy1 0.01 0.063 0.34 1 -10000 0 1
MPO -0.01 0.13 0.26 2 -0.57 58 60
KNG1 0.023 0.032 0.26 20 -10000 0 20
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.012 0.15 0.28 14 -0.47 38 52
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.021 0.26 8 -10000 0 8
CTGF 0.016 0.068 0.26 3 -0.57 14 17
alphaM/beta2 Integrin/Hck 0.011 0.067 0.35 5 -10000 0 5
ITGAM -0.003 0.043 0.25 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.043 0.16 0.34 1 -0.36 185 186
HP -0.07 0.22 0.26 34 -0.57 178 212
leukocyte adhesion -0.039 0.14 0.28 4 -0.43 39 43
SELP -0.092 0.23 -10000 0 -0.57 205 205
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.033 0.077 -10000 0 -0.34 40 40
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.12 -10000 0 -0.41 17 17
AP1 -0.093 0.19 -10000 0 -0.33 388 388
mol:PIP3 -0.13 0.18 -10000 0 -0.34 416 416
AKT1 0.006 0.08 0.3 4 -0.42 13 17
PTK2B -0.027 0.1 -10000 0 -0.34 55 55
RHOA 0.003 0.061 0.26 2 -0.3 27 29
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.11 0.28 3 -0.28 95 98
MAGI3 0.023 0.018 -10000 0 -0.56 1 1
RELA 0.023 0.005 -10000 0 -10000 0 0
apoptosis -0.025 0.12 -10000 0 -0.32 143 143
HRAS/GDP 0.019 0.015 0.18 9 -10000 0 9
positive regulation of microtubule depolymerization -0.05 0.12 0.26 3 -0.32 121 124
NF kappa B1 p50/RelA -0.011 0.12 -10000 0 -0.33 96 96
endothelial cell migration 0.002 0.081 0.26 1 -0.42 33 34
ADCY4 -0.023 0.12 -10000 0 -0.49 45 45
ADCY5 -0.076 0.15 -10000 0 -0.48 84 84
ADCY6 -0.015 0.099 -10000 0 -0.46 35 35
ADCY7 -0.014 0.098 -10000 0 -0.47 34 34
ADCY1 -0.017 0.11 -10000 0 -0.48 39 39
ADCY2 -0.029 0.13 -10000 0 -0.5 51 51
ADCY3 -0.015 0.099 -10000 0 -0.46 35 35
ADCY8 -0.012 0.091 -10000 0 -0.45 30 30
ADCY9 -0.015 0.098 -10000 0 -0.46 35 35
GSK3B -0.026 0.099 0.24 6 -0.34 49 55
arachidonic acid secretion -0.019 0.11 -10000 0 -0.37 68 68
GNG2 0.017 0.065 -10000 0 -0.57 13 13
TRIP6 0.018 0.015 -10000 0 -0.4 1 1
GNAO1 0.002 0.083 -10000 0 -0.36 47 47
HRAS 0.026 0.022 0.26 9 -10000 0 9
NFKBIA -0.02 0.13 0.28 3 -0.34 101 104
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.027 0.12 -10000 0 -0.81 22 22
JUN 0.02 0.044 -10000 0 -0.57 6 6
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.012 0.14 -10000 0 -0.95 22 22
PIK3R1 0.016 0.065 -10000 0 -0.56 13 13
mol:IP3 -0.013 0.11 0.28 3 -0.29 95 98
PLCB3 0.025 0.045 0.2 3 -10000 0 3
FOS -0.14 0.27 -10000 0 -0.57 306 306
positive regulation of mitosis -0.019 0.11 -10000 0 -0.37 68 68
LPA/LPA1-2-3 0.002 0.14 -10000 0 -0.33 142 142
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
stress fiber formation -0.016 0.1 -10000 0 -0.38 42 42
GNAZ 0.003 0.07 -10000 0 -0.34 40 40
EGFR/PI3K-beta/Gab1 -0.13 0.2 -10000 0 -0.35 416 416
positive regulation of dendritic cell cytokine production 0 0.13 -10000 0 -0.33 142 142
LPA/LPA2/MAGI-3 0.033 0.02 -10000 0 -0.35 1 1
ARHGEF1 0.018 0.07 -10000 0 -0.3 25 25
GNAI2 0.006 0.06 -10000 0 -0.33 32 32
GNAI3 0.006 0.06 -10000 0 -0.33 32 32
GNAI1 -0.013 0.11 -10000 0 -0.37 83 83
LPA/LPA3 -0.025 0.14 0.18 39 -0.41 123 162
LPA/LPA2 0.019 0.015 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.071 -10000 0 -0.38 33 33
HB-EGF/EGFR -0.079 0.2 0.27 2 -0.34 362 364
HBEGF 0.066 0.073 0.27 24 -0.42 3 27
mol:DAG -0.013 0.11 0.28 3 -0.29 95 98
cAMP biosynthetic process -0.033 0.11 0.32 2 -0.42 57 59
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.27 24 -0.34 83 107
GNAQ -0.02 0.11 0.21 1 -0.31 122 123
LPAR2 0.025 0.011 0.26 2 -10000 0 2
LPAR3 -0.034 0.19 0.26 39 -0.57 119 158
LPAR1 0.012 0.088 -10000 0 -0.49 29 29
IL8 -0.13 0.23 0.35 30 -0.43 291 321
PTK2 -0.022 0.1 0.24 1 -0.32 99 100
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.32 143 143
EGFR -0.19 0.28 -10000 0 -0.57 390 390
PLCG1 -0.022 0.11 0.2 4 -0.32 120 124
PLD2 -0.027 0.12 0.24 1 -0.31 136 137
G12/G13 0.036 0.061 -10000 0 -0.31 26 26
PI3K-beta 0 0.079 -10000 0 -0.45 15 15
cell migration 0.002 0.063 -10000 0 -0.25 22 22
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
PXN -0.017 0.1 -10000 0 -0.38 42 42
HRAS/GTP -0.02 0.11 -10000 0 -0.38 68 68
RAC1 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
PRKCE 0.024 0.003 -10000 0 -10000 0 0
PRKCD -0.014 0.1 0.3 2 -0.41 10 12
Gi(beta/gamma) -0.014 0.11 -10000 0 -0.44 47 47
mol:LPA 0.001 0.016 -10000 0 -0.18 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.013 0.12 -10000 0 -0.44 25 25
MAPKKK cascade -0.019 0.11 -10000 0 -0.37 68 68
contractile ring contraction involved in cytokinesis 0.002 0.063 0.26 2 -0.3 27 29
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.02 0.11 0.21 1 -0.31 127 128
GNA15 -0.018 0.1 0.2 2 -0.31 120 122
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.051 0.12 0.26 3 -0.33 122 125
GNA11 -0.02 0.1 0.21 1 -0.31 123 124
Rac1/GTP 0.028 0.13 -10000 0 -0.86 22 22
MMP2 0.002 0.081 0.26 1 -0.43 33 34
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.04 0.22 0.41 5 -0.63 113 118
IHH 0.016 0.082 0.26 31 -0.22 37 68
SHH Np/Cholesterol/GAS1 0 0.075 -10000 0 -0.33 49 49
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0 0.075 0.33 49 -10000 0 49
SMO/beta Arrestin2 -0.019 0.21 -10000 0 -0.62 97 97
SMO -0.042 0.21 0.32 1 -0.65 97 98
AKT1 -0.004 0.13 -10000 0 -0.59 25 25
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.018 0.15 -10000 0 -0.57 76 76
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.041 0.21 0.32 1 -0.64 97 98
STIL 0.006 0.17 0.3 31 -0.48 87 118
DHH N/PTCH2 -0.008 0.14 -10000 0 -0.44 97 97
DHH N/PTCH1 -0.027 0.2 -10000 0 -0.51 144 144
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.008 0.096 0.26 2 -0.57 29 31
PTHLH -0.061 0.3 0.43 10 -0.83 120 130
determination of left/right symmetry -0.041 0.21 0.32 1 -0.64 97 98
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
skeletal system development -0.059 0.29 0.42 14 -0.82 120 134
IHH N/Hhip 0.027 0.056 0.24 2 -0.46 2 4
DHH N/Hhip 0.022 0.077 -10000 0 -0.41 31 31
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.041 0.21 0.32 1 -0.64 97 98
pancreas development 0.023 0.03 0.26 5 -0.56 2 7
HHAT 0.02 0.02 -10000 0 -0.57 1 1
PI3K 0.028 0.049 -10000 0 -0.38 14 14
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.57 61 61
somite specification -0.041 0.21 0.32 1 -0.64 97 98
SHH Np/Cholesterol/PTCH1 -0.024 0.16 0.26 4 -0.48 97 101
SHH Np/Cholesterol/PTCH2 -0.004 0.082 -10000 0 -0.33 59 59
SHH Np/Cholesterol/Megalin -0.06 0.15 0.28 3 -0.33 228 231
SHH 0 0.037 0.34 7 -0.42 1 8
catabolic process -0.033 0.21 0.31 2 -0.57 123 125
SMO/Vitamin D3 -0.009 0.2 0.36 15 -0.57 88 103
SHH Np/Cholesterol/Hhip 0.015 0.028 0.25 3 -0.33 3 6
LRP2 -0.12 0.26 0.26 26 -0.57 277 303
receptor-mediated endocytosis -0.079 0.22 0.3 11 -0.62 101 112
SHH Np/Cholesterol/BOC -0.004 0.083 -10000 0 -0.33 61 61
SHH Np/Cholesterol/CDO 0.013 0.04 -10000 0 -0.33 12 12
mesenchymal cell differentiation -0.015 0.028 0.33 3 -0.24 3 6
mol:Vitamin D3 0.002 0.18 0.34 21 -0.49 93 114
IHH N/PTCH2 -0.006 0.14 -10000 0 -0.47 76 76
CDON 0.015 0.065 -10000 0 -0.57 13 13
IHH N/PTCH1 -0.024 0.21 0.35 4 -0.57 123 127
Megalin/LRPAP1 -0.079 0.2 -10000 0 -0.42 277 277
PTCH2 -0.018 0.15 -10000 0 -0.57 76 76
SHH Np/Cholesterol 0.01 0.013 -10000 0 -0.33 1 1
PTCH1 -0.033 0.21 0.31 2 -0.57 123 125
HHIP 0.023 0.03 0.26 5 -0.57 2 7
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.035 -10000 0 -0.42 5 5
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.38 407 407
PTK2 -0.056 0.15 0.32 2 -0.51 44 46
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.067 0.26 6 -0.57 13 19
SRC 0.023 0.005 -10000 0 -10000 0 0
CDKN1B -0.044 0.12 -10000 0 -0.53 35 35
VEGFA 0.025 0.019 0.26 7 -10000 0 7
ILK -0.042 0.12 -10000 0 -0.49 32 32
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
AKT1 -0.043 0.1 -10000 0 -0.49 28 28
PTK2B -0.013 0.069 0.36 2 -0.33 32 34
alphaV/beta3 Integrin/JAM-A -0.076 0.17 0.3 1 -0.34 270 271
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.032 0.072 -10000 0 -0.36 33 33
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.19 -10000 0 -0.38 246 246
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.013 0.068 -10000 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 0.043 0.081 -10000 0 -0.36 33 33
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.58 197 197
PI4 Kinase 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.068 0.099 0.34 3 -0.35 33 36
RPS6KB1 -0.16 0.22 0.42 3 -0.55 177 180
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.58 334 334
GPR124 0.016 0.048 -10000 0 -0.57 7 7
MAPK1 -0.2 0.29 -10000 0 -0.58 356 356
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
alphaV/beta3 Integrin/Tumstatin -0.031 0.16 -10000 0 -0.37 197 197
cell adhesion 0.023 0.082 0.25 1 -0.36 42 43
ANGPTL3 0.021 0.015 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.032 -10000 0 -0.36 4 4
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 42 42
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
RAC1 0.024 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.025 0.077 -10000 0 -0.39 29 29
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.018 -10000 0 -0.57 1 1
alphaV/beta3 Integrin/CD47 0.034 0.072 -10000 0 -0.36 33 33
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.014 0.13 -10000 0 -0.45 72 72
CSF1 0.021 0.044 -10000 0 -0.57 6 6
PIK3C2A -0.04 0.11 -10000 0 -0.49 28 28
PI4 Kinase/Pyk2 -0.076 0.15 -10000 0 -0.51 24 24
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.078 -10000 0 -0.36 33 33
FAK1/Vinculin -0.037 0.13 0.34 4 -0.41 40 44
alphaV beta3/Integrin/ppsTEM5 0.026 0.077 -10000 0 -0.4 29 29
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.033 0.077 0.26 68 -0.57 8 76
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
F11R -0.12 0.19 -10000 0 -0.42 312 312
alphaV/beta3 Integrin/Lactadherin 0.03 0.087 0.34 1 -0.38 42 43
alphaV/beta3 Integrin/TGFBR2 0.02 0.12 -10000 0 -0.45 55 55
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.038 -10000 0 -0.33 6 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.065 -10000 0 -0.33 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.11 0.26 421 -10000 0 421
alphaV/beta3 Integrin/Pyk2 0.027 0.072 -10000 0 -0.33 33 33
SDC1 0.038 0.059 0.26 68 -0.57 1 69
VAV3 -0.011 0.041 -10000 0 -0.31 13 13
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
FAK1/Paxillin -0.037 0.13 0.34 4 -0.41 40 44
cell migration -0.036 0.12 0.3 6 -0.38 36 42
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.066 0.17 -10000 0 -0.32 245 245
SPP1 0.084 0.1 0.26 279 -10000 0 279
KDR 0.021 0.04 -10000 0 -0.57 5 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.074 0.22 0.26 4 -0.57 179 183
angiogenesis -0.19 0.3 -10000 0 -0.58 333 333
Rac1/GTP 0.021 0.038 -10000 0 -0.29 11 11
EDIL3 -0.007 0.14 0.26 15 -0.57 62 77
cell proliferation 0.02 0.12 -10000 0 -0.45 55 55
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CCL5 0.029 0.056 0.26 38 -0.57 4 42
SDCBP 0.021 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.063 0.12 0.27 24 -0.41 9 33
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.049 0.12 0.27 2 -0.37 17 19
Syndecan-1/Syntenin 0.051 0.12 0.29 7 -0.38 14 21
MAPK3 0.047 0.11 0.27 8 -0.42 7 15
HGF/MET -0.066 0.2 -10000 0 -0.44 225 225
TGFB1/TGF beta receptor Type II 0.025 0.013 0.26 3 -10000 0 3
BSG 0.024 0.009 0.26 1 -10000 0 1
keratinocyte migration 0.049 0.12 0.27 2 -0.36 17 19
Syndecan-1/RANTES 0.058 0.13 0.31 35 -0.4 18 53
Syndecan-1/CD147 0.063 0.12 0.33 5 -0.4 10 15
Syndecan-1/Syntenin/PIP2 0.047 0.11 0.27 7 -0.37 14 21
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.046 0.11 0.26 6 -0.36 14 20
MMP7 -0.037 0.19 0.26 33 -0.57 121 154
HGF -0.011 0.14 0.26 2 -0.57 65 67
Syndecan-1/CASK 0.042 0.12 0.26 7 -0.37 17 24
Syndecan-1/HGF/MET -0.004 0.2 0.32 4 -0.46 105 109
regulation of cell adhesion 0.041 0.11 0.29 4 -0.4 7 11
HPSE 0.027 0.035 0.26 18 -0.57 1 19
positive regulation of cell migration 0.063 0.12 0.27 24 -0.41 9 33
SDC1 0.065 0.12 0.28 20 -0.41 9 29
Syndecan-1/Collagen 0.063 0.12 0.27 24 -0.41 9 33
PPIB 0.024 0.013 0.26 3 -10000 0 3
MET -0.073 0.22 -10000 0 -0.57 177 177
PRKACA 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
MAPK1 0.048 0.11 0.27 8 -0.41 7 15
homophilic cell adhesion 0.061 0.12 0.27 24 -0.38 14 38
MMP1 0.18 0.11 0.26 739 -10000 0 739
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.005 0.11 -10000 0 -0.36 95 95
EFNA5 -0.028 0.17 0.26 1 -0.57 95 96
FYN -0.022 0.098 -10000 0 -0.33 95 95
neuron projection morphogenesis -0.005 0.11 -10000 0 -0.36 95 95
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.004 0.11 -10000 0 -0.36 95 95
EPHA5 0.023 0.017 0.26 5 -10000 0 5
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.042 0.14 0.36 56 -0.36 42 98
TBX21 0.014 0.34 0.76 21 -1.2 49 70
B2M 0.025 0.012 -10000 0 -10000 0 0
TYK2 0.024 0.036 0.19 1 -10000 0 1
IL12RB1 0.031 0.072 0.32 41 -0.6 2 43
GADD45B 0.037 0.26 0.64 22 -0.89 32 54
IL12RB2 0.028 0.15 0.27 118 -0.57 42 160
GADD45G 0.055 0.26 0.67 25 -0.9 29 54
natural killer cell activation 0.007 0.025 0.081 53 -0.043 21 74
RELB 0.026 0.022 0.26 10 -10000 0 10
RELA 0.023 0.005 -10000 0 -10000 0 0
IL18 0.034 0.04 0.27 26 -10000 0 26
IL2RA 0.027 0.088 0.26 58 -0.57 15 73
IFNG 0.054 0.08 0.26 146 -10000 0 146
STAT3 (dimer) 0.035 0.24 0.56 39 -0.71 45 84
HLA-DRB5 -0.006 0.011 -10000 0 -0.025 249 249
FASLG 0.049 0.31 0.75 29 -1.1 37 66
NF kappa B2 p52/RelB 0.022 0.25 0.67 5 -0.8 48 53
CD4 0.009 0.024 -10000 0 -10000 0 0
SOCS1 0.025 0.033 0.26 14 -0.57 1 15
EntrezGene:6955 -0.006 0.016 0.023 57 -0.028 273 330
CD3D 0.009 0.098 0.26 49 -0.58 19 68
CD3E 0.009 0.089 0.26 37 -0.57 16 53
CD3G -0.001 0.12 0.26 38 -0.57 33 71
IL12Rbeta2/JAK2 0.037 0.12 0.3 28 -0.43 42 70
CCL3 0.033 0.28 0.69 21 -0.96 34 55
CCL4 0.035 0.27 0.69 21 -0.94 32 53
HLA-A 0.002 0.008 0.023 73 -0.048 12 85
IL18/IL18R 0.065 0.12 0.38 15 -0.37 52 67
NOS2 0.032 0.28 0.68 23 -0.95 37 60
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.14 0.36 56 -0.36 47 103
IL1R1 0.017 0.31 0.68 22 -1.1 47 69
IL4 -0.011 0.037 -10000 0 -10000 0 0
JAK2 0.023 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.005 0.014 0.023 58 -0.026 248 306
TCR/CD3/MHC I/CD8 -0.024 0.22 0.37 33 -0.77 57 90
RAB7A 0.052 0.24 0.64 18 -0.81 23 41
lysosomal transport 0.053 0.23 0.64 19 -0.76 23 42
FOS -0.32 0.62 0.6 12 -1.2 349 361
STAT4 (dimer) 0.063 0.28 0.6 35 -0.85 47 82
STAT5A (dimer) 0.047 0.28 0.61 48 -0.77 53 101
GZMA 0.025 0.29 0.7 27 -1.1 34 61
GZMB 0.023 0.32 0.73 23 -1.1 43 66
HLX 0.021 0.015 0.26 3 -10000 0 3
LCK 0.028 0.29 0.66 36 -0.88 52 88
TCR/CD3/MHC II/CD4 -0.054 0.17 0.24 27 -0.32 215 242
IL2/IL2R 0.065 0.098 0.41 39 -0.36 21 60
MAPK14 0.048 0.27 0.64 28 -0.89 35 63
CCR5 0.037 0.27 0.7 25 -0.92 31 56
IL1B 0.017 0.078 0.29 3 -0.58 14 17
STAT6 0.039 0.12 0.41 31 -0.6 7 38
STAT4 0.001 0.12 0.26 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 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 0.072 0.11 0.28 227 -10000 0 227
CD8A 0.029 0.059 0.28 29 -0.57 5 34
CD8B 0.014 0.11 0.27 30 -0.57 32 62
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.042 0.14 0.36 42 -0.36 56 98
IL2RB 0.03 0.05 0.26 38 -0.57 2 40
proteasomal ubiquitin-dependent protein catabolic process 0.066 0.26 0.58 41 -0.76 47 88
IL2RG 0.03 0.067 0.26 46 -0.57 7 53
IL12 0.049 0.15 0.29 94 -0.42 57 151
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
CD247 0.006 0.079 0.26 16 -0.57 15 31
IL2 0.022 0.021 0.26 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.004 0.14 0.29 18 -0.58 57 75
IL12/IL12R/TYK2/JAK2 0.033 0.3 0.71 35 -0.88 53 88
MAP2K3 0.042 0.28 0.63 28 -0.86 43 71
RIPK2 0.02 0.016 0.26 3 -10000 0 3
MAP2K6 0.046 0.27 0.63 28 -0.84 41 69
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.013 -10000 0 -0.028 275 275
IL18RAP 0.012 0.11 0.28 5 -0.57 35 40
IL12Rbeta1/TYK2 0.04 0.068 0.29 34 -0.46 2 36
EOMES -0.021 0.18 -10000 0 -1 30 30
STAT1 (dimer) 0.067 0.26 0.62 60 -0.74 37 97
T cell proliferation 0.05 0.22 0.51 26 -0.64 43 69
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.08 -10000 0 -0.57 19 19
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.012 0.19 0.42 2 -0.72 39 41
ATF2 0.045 0.25 0.6 27 -0.82 35 62
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.014 0.14 0.42 85 -0.24 2 87
KIRREL -0.024 0.16 -10000 0 -0.57 87 87
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.014 0.14 0.24 2 -0.42 85 87
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.034 0.12 0.29 3 -0.32 84 87
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 -0.28 70 71
FYN 0.013 0.13 0.27 110 -0.3 83 193
mol:Ca2+ 0.031 0.11 0.28 3 -0.32 79 82
mol:DAG 0.032 0.11 0.28 3 -0.32 79 82
NPHS2 0.014 0.032 0.26 5 -10000 0 5
mol:IP3 0.032 0.11 0.28 3 -0.32 79 82
regulation of endocytosis 0.023 0.1 0.24 4 -0.29 83 87
Nephrin/NEPH1/podocin/Cholesterol 0.023 0.11 0.25 9 -0.32 84 93
establishment of cell polarity 0.014 0.14 0.24 2 -0.42 85 87
Nephrin/NEPH1/podocin/NCK1-2 0.043 0.11 0.32 1 -0.3 82 83
Nephrin/NEPH1/beta Arrestin2 0.026 0.11 0.25 4 -0.29 83 87
NPHS1 0.058 0.09 0.26 166 -10000 0 166
Nephrin/NEPH1/podocin 0.024 0.11 0.3 4 -0.31 83 87
TJP1 0.023 0.019 -10000 0 -0.57 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.033 0.12 0.29 3 -0.32 79 82
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.031 0.12 0.32 2 -0.32 81 83
GRB2 0.023 0.009 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.012 0.13 0.29 97 -0.31 89 186
cytoskeleton organization 0.003 0.11 0.29 12 -0.33 66 78
Nephrin/NEPH1 0.016 0.1 0.2 2 -0.3 85 87
Nephrin/NEPH1/ZO-1 0.025 0.12 -10000 0 -0.34 85 85
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.033 0.15 -10000 0 -0.59 66 66
PDGF/PDGFRA/CRKL -0.011 0.11 -10000 0 -0.41 69 69
positive regulation of JUN kinase activity 0.024 0.083 -10000 0 -0.33 47 47
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.014 0.11 -10000 0 -0.42 67 67
AP1 -0.3 0.44 -10000 0 -0.96 323 323
mol:IP3 -0.036 0.11 -10000 0 -0.45 63 63
PLCG1 -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA/alphaV Integrin -0.011 0.11 -10000 0 -0.43 66 66
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.11 -10000 0 -0.45 63 63
CAV3 0.02 0.011 0.26 2 -10000 0 2
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
SHC/Grb2/SOS1 0.026 0.084 -10000 0 -0.33 47 47
PDGF/PDGFRA/Shf -0.011 0.11 -10000 0 -0.42 68 68
FOS -0.3 0.43 0.32 1 -0.94 323 324
JUN -0.038 0.044 -10000 0 -0.44 6 6
oligodendrocyte development -0.011 0.11 -10000 0 -0.42 66 66
GRB2 0.023 0.009 0.26 1 -10000 0 1
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:DAG -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA -0.033 0.15 -10000 0 -0.59 66 66
actin cytoskeleton reorganization -0.011 0.11 -10000 0 -0.42 67 67
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.012 0.11 -10000 0 -0.38 72 72
PDGF/PDGFRA/Crk/C3G 0.015 0.098 -10000 0 -0.36 66 66
JAK1 -0.027 0.1 0.23 1 -0.42 67 68
ELK1/SRF -0.035 0.091 0.32 1 -0.35 64 65
SHB 0.024 0.008 0.26 1 -10000 0 1
SHF 0.024 0.021 0.26 2 -0.57 1 3
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.047 0.11 0.22 1 -0.46 66 67
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.083 -10000 0 -0.33 47 47
PDGF/PDGFRA/SHB -0.011 0.11 -10000 0 -0.42 67 67
PDGF/PDGFRA/Caveolin-1 -0.099 0.22 -10000 0 -0.48 256 256
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.053 0.11 0.24 1 -0.43 65 66
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.012 0.11 -10000 0 -0.41 69 69
JAK-STAT cascade -0.027 0.1 0.23 1 -0.42 67 68
cell proliferation -0.011 0.11 -10000 0 -0.42 68 68
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.034 0.1 0.99 2 -10000 0 2
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.025 0.12 -10000 0 -0.35 14 14
RXRs/LXRs/DNA/Oxysterols -0.006 0.12 -10000 0 -0.42 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 62 62
RXRs/NUR77 -0.05 0.18 -10000 0 -0.35 266 266
RXRs/PPAR -0.1 0.17 -10000 0 -0.32 350 350
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 0.043 -10000 0 -0.31 12 12
RARA 0.023 0.012 0.26 2 -10000 0 2
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.037 0.041 -10000 0 -0.3 12 12
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.071 0.18 0.61 99 -10000 0 99
RARs/THRs/DNA/SMRT 0.002 0.079 -10000 0 -0.29 60 60
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.028 0.15 -10000 0 -0.32 216 216
NR1H4 0.021 0.026 0.26 13 -10000 0 13
RXRs/LXRs/DNA -0.007 0.15 -10000 0 -0.3 197 197
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 -0.022 0.15 -10000 0 -0.3 215 215
NR4A1 -0.028 0.17 -10000 0 -0.57 95 95
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.031 0.1 -10000 0 -0.23 190 190
RXRG -0.098 0.24 0.26 2 -0.56 219 221
RXR alpha/CCPG 0.035 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.012 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB -0.006 0.13 -10000 0 -0.57 55 55
PPARG -0.12 0.25 -10000 0 -0.57 252 252
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.01 0.14 -10000 0 -1 10 10
mol:Oxysterols 0.004 0.009 -10000 0 -0.12 1 1
cholesterol transport -0.005 0.12 -10000 0 -0.42 16 16
PPARA 0.02 0.044 -10000 0 -0.57 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.016 0.067 -10000 0 -0.57 14 14
RXRs/NUR77/BCL2 -0.069 0.15 -10000 0 -0.3 282 282
SREBF1 -0.006 0.11 0.44 1 -0.5 3 4
RXRs/RXRs/DNA/9cRA -0.028 0.15 -10000 0 -0.32 216 216
ABCA1 -0.01 0.13 -10000 0 -0.84 8 8
RARs/THRs 0.04 0.096 -10000 0 -0.33 60 60
RXRs/FXR -0.024 0.16 -10000 0 -0.33 216 216
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.021 0.22 3 -10000 0 3
AES 0.022 0.019 0.21 2 -10000 0 2
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.009 0.095 0.26 2 -0.57 28 30
TLE1 0.019 0.048 0.22 1 -0.57 6 7
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.3 47 -0.37 4 51
WIF1 -0.28 0.3 0.26 13 -0.56 544 557
beta catenin/RanBP3 0.02 0.089 0.41 40 -0.4 1 41
KREMEN2 0.12 0.12 0.26 473 -10000 0 473
DKK1 0.026 0.16 0.26 146 -0.57 54 200
beta catenin/beta TrCP1 0.11 0.094 0.3 36 -0.38 2 38
FZD1 0.024 0.004 -10000 0 -10000 0 0
AXIN2 0.016 0.26 0.6 83 -1.3 22 105
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 0.046 0.076 -10000 0 -0.56 12 12
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.13 0.29 10 -0.57 24 34
Axin1/APC/GSK3 0.046 0.053 0.24 2 -0.31 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.063 0.31 2 -0.4 4 6
HNF1A 0.025 0.028 0.25 11 -10000 0 11
CTBP1 0.021 0.02 0.25 2 -10000 0 2
MYC 0.11 0.33 0.57 261 -1.3 24 285
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.099 0.34 1 -0.33 22 23
NKD1 0.022 0.053 0.26 16 -0.57 6 22
TCF4 0.016 0.062 0.23 2 -0.56 11 13
TCF3 0.022 0.022 0.27 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.057 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.005 0.12 0.45 36 -0.5 15 51
LEF1 0.052 0.082 0.25 140 -0.53 1 141
DVL1 0.055 0.053 0.22 1 -0.36 2 3
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.14 0.29 13 -0.59 30 43
DKK1/LRP6/Kremen 2 0.099 0.14 0.34 80 -0.34 47 127
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.24 2 -10000 0 2
NLK 0.023 0.014 0.25 2 -10000 0 2
CCND1 0.091 0.26 0.61 179 -1.2 6 185
WNT1 0.024 0.011 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.055 0.29 5 -0.3 9 14
APC 0.016 0.056 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.22 518 -0.24 1 519
CREBBP 0.021 0.018 0.27 1 -10000 0 1
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 0.033 0.043 -10000 0 -0.31 13 13
RGS9BP 0.036 0.052 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 0.015 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 86 87
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.015 -10000 0 -10000 0 0
GRK7 0.023 0.019 0.26 7 -10000 0 7
CNGB3 0.022 0.037 0.26 25 -10000 0 25
Cone Metarhodopsin II/X-Arrestin 0.015 0.014 0.18 8 -10000 0 8
mol:Ca2+ 0.12 0.1 0.29 177 -10000 0 177
Cone PDE6 0.031 0.11 0.31 3 -0.31 82 85
Cone Metarhodopsin II 0.025 0.017 -10000 0 -10000 0 0
Na + (4 Units) 0.11 0.092 0.31 69 -10000 0 69
GNAT2/GDP 0.025 0.1 0.28 3 -0.31 85 88
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.032 0.22 2 -10000 0 2
Cone Transducin 0.036 0.046 -10000 0 -0.33 13 13
SLC24A2 0.16 0.12 0.26 621 -10000 0 621
GNB3/GNGT2 0.026 0.053 -10000 0 -0.4 14 14
GNB3 0.018 0.064 0.26 5 -0.57 12 17
GNAT2/GTP 0.018 0.01 0.18 4 -10000 0 4
CNGA3 0.045 0.068 0.26 101 -10000 0 101
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 0.016 0.12 0.33 1 -0.36 86 87
Cone CNG Channel 0.049 0.043 0.28 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.16 0.12 0.26 621 -10000 0 621
RGS9 -0.024 0.16 0.26 11 -0.57 88 99
PDE6C 0.019 0.008 0.26 1 -10000 0 1
GNGT2 0.021 0.026 -10000 0 -0.57 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.26 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 0.026 -10000 0 -0.57 2 2
LAT2 -0.02 0.1 -10000 0 -0.36 56 56
AP1 -0.059 0.18 -10000 0 -0.44 120 120
mol:PIP3 0.009 0.17 0.35 46 -0.42 55 101
IKBKB 0.033 0.13 0.28 119 -0.26 29 148
AKT1 0.012 0.17 0.32 146 -0.44 21 167
IKBKG 0.016 0.11 0.25 74 -0.28 31 105
MS4A2 -0.022 0.15 0.25 5 -0.55 82 87
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.12 0.3 25 -0.39 32 57
mol:Ca2+ 0.014 0.14 0.3 57 -0.32 53 110
LYN 0.022 0.012 -10000 0 -10000 0 0
CBLB -0.019 0.1 -10000 0 -0.36 55 55
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0.001 0.12 -10000 0 -0.33 124 124
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.004 0.17 0.33 126 -0.33 137 263
PTPN13 -0.015 0.15 -10000 0 -0.55 44 44
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.012 0.13 0.32 39 -0.34 31 70
SYK 0.025 0.01 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.027 0.13 -10000 0 -0.42 58 58
LAT -0.019 0.1 -10000 0 -0.36 57 57
PAK2 0.012 0.13 0.29 31 -0.43 31 62
NFATC2 -0.049 0.16 -10000 0 -0.55 86 86
HRAS 0.008 0.13 0.27 21 -0.45 35 56
GAB2 0.021 0.019 -10000 0 -0.57 1 1
PLA2G1B 0.002 0.098 -10000 0 -0.84 12 12
Fc epsilon R1 -0.022 0.16 -10000 0 -0.4 144 144
Antigen/IgE/Fc epsilon R1 -0.018 0.14 -10000 0 -0.36 144 144
mol:GDP -0.014 0.12 0.25 1 -0.47 33 34
JUN 0.02 0.044 -10000 0 -0.57 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
FOS -0.14 0.27 -10000 0 -0.57 306 306
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.37 60 60
CHUK 0.015 0.11 0.25 74 -0.27 33 107
KLRG1 -0.018 0.097 -10000 0 -0.32 57 57
VAV1 -0.02 0.1 -10000 0 -0.37 57 57
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.1 -10000 0 -0.36 55 55
negative regulation of mast cell degranulation -0.006 0.098 -10000 0 -0.37 32 32
BTK -0.013 0.11 -10000 0 -0.48 32 32
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.03 0.13 -10000 0 -0.33 144 144
GAB2/PI3K/SHP2 -0.048 0.1 -10000 0 -0.34 84 84
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 -10000 0 -0.45 34 34
RAF1 0.002 0.1 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0 0.15 -10000 0 -0.35 146 146
FCER1G 0.019 0.017 0.25 1 -10000 0 1
FCER1A -0.044 0.18 -10000 0 -0.57 115 115
Antigen/IgE/Fc epsilon R1/Fyn -0.009 0.14 -10000 0 -0.34 140 140
MAPK3 0.003 0.099 -10000 0 -0.86 12 12
MAPK1 -0.002 0.1 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.18 -10000 0 -0.59 68 68
DUSP1 -0.045 0.19 -10000 0 -0.57 126 126
NF-kappa-B/RelA 0.007 0.058 0.14 5 -0.18 17 22
actin cytoskeleton reorganization -0.007 0.15 -10000 0 -0.57 37 37
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.12 -10000 0 -0.45 32 32
FER -0.021 0.11 -10000 0 -0.37 61 61
RELA 0.023 0.005 -10000 0 -10000 0 0
ITK -0.012 0.091 -10000 0 -0.4 48 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.004 0.13 0.28 9 -0.48 32 41
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.018 0.1 0.21 2 -0.36 57 59
PTK2 -0.009 0.15 -10000 0 -0.6 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.024 0.14 -10000 0 -0.44 58 58
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.006 0.16 0.33 42 -0.42 58 100
MAP2K2 -0.001 0.098 -10000 0 -0.85 12 12
MAP2K1 0 0.099 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.095 -10000 0 -0.36 32 32
MAP2K4 -0.072 0.29 -10000 0 -0.83 134 134
Fc epsilon R1/FcgammaRIIB -0.008 0.15 -10000 0 -0.37 146 146
mol:Choline -0.004 0.17 0.33 126 -0.32 137 263
SHC/Grb2/SOS1 0.011 0.11 -10000 0 -0.42 29 29
FYN 0.021 0.026 -10000 0 -0.57 2 2
DOK1 0.025 0.014 0.26 4 -10000 0 4
PXN -0.009 0.14 -10000 0 -0.55 36 36
HCLS1 -0.019 0.1 -10000 0 -0.36 56 56
PRKCB 0.013 0.14 0.28 72 -0.37 37 109
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.007 0.1 -10000 0 -0.38 32 32
LCP2 0.024 0.008 0.26 1 -10000 0 1
PLA2G4A -0.045 0.14 -10000 0 -0.37 129 129
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.17 0.33 126 -0.32 137 263
IKK complex 0.032 0.11 0.27 98 -0.21 18 116
WIPF1 0.024 0.003 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin 0.094 0.1 0.21 421 -0.34 2 423
EPHB2 0.027 0.031 0.26 19 -10000 0 19
Syndecan-2/TACI 0.024 0.06 0.2 63 -0.36 12 75
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
Syndecan-2/alpha2 ITGB1 -0.038 0.15 -10000 0 -0.32 201 201
HRAS 0.026 0.022 0.26 9 -10000 0 9
Syndecan-2/CASK 0.005 0.016 -10000 0 -0.35 2 2
ITGA5 0.024 0.007 0.26 1 -10000 0 1
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 -0.32 2 2
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
EZR 0.023 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.052 0.2 -10000 0 -0.57 138 138
Syndecan-2/MMP2 0.015 0.038 0.18 1 -0.36 9 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.071 -10000 0 -0.39 29 29
dendrite morphogenesis 0.022 0.033 0.21 19 -0.35 2 21
Syndecan-2/GM-CSF 0.022 0.036 0.21 26 -0.36 2 28
determination of left/right symmetry 0.007 0.019 -10000 0 -0.41 2 2
Syndecan-2/PKC delta 0.019 0.021 0.31 1 -0.35 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.073 0.19 172 -0.32 2 174
MAPK1 0.037 0.076 0.19 196 -0.32 2 198
Syndecan-2/RACK1 0.03 0.026 0.26 2 -0.31 2 4
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.019 -10000 0 -0.41 2 2
ITGA2 0.008 0.094 -10000 0 -0.57 28 28
MAPK8 0.005 0.033 0.27 5 -0.35 6 11
Syndecan-2/alpha2/beta1 Integrin 0.004 0.12 -10000 0 -0.35 84 84
Syndecan-2/Kininogen 0.02 0.033 0.21 19 -0.36 2 21
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.069 0.27 12 -0.29 2 14
Syndecan-2/CASK/Protein 4.1 0.017 0.018 -10000 0 -0.32 2 2
extracellular matrix organization 0.02 0.023 0.24 3 -0.35 2 5
actin cytoskeleton reorganization 0.093 0.1 0.21 421 -0.34 2 423
Syndecan-2/Caveolin-2/Ras -0.009 0.11 0.27 2 -0.33 104 106
Syndecan-2/Laminin alpha3 -0.057 0.14 -10000 0 -0.3 254 254
Syndecan-2/RasGAP 0.038 0.03 0.26 2 -0.3 2 4
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.022 0.033 0.21 19 -0.35 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 0.024 -10000 0 -0.29 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.028 0.084 0.26 63 -0.57 12 75
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.071 -10000 0 -0.39 29 29
Syndecan-2/Synbindin 0.018 0.02 -10000 0 -0.34 2 2
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CASP3 0.042 0.071 0.19 190 -0.32 2 192
FN1 0.11 0.11 0.26 421 -10000 0 421
Syndecan-2/IL8 0.023 0.07 0.21 60 -0.32 23 83
SDC2 0.007 0.019 -10000 0 -0.41 2 2
KNG1 0.023 0.032 0.26 20 -10000 0 20
Syndecan-2/Neurofibromin 0.018 0.02 -10000 0 -0.35 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.026 0.037 0.26 26 -10000 0 26
Syndecan-2/TGFB1 0.02 0.023 0.24 3 -0.35 2 5
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.018 -10000 0 -0.32 2 2
Syndecan-2/Ezrin 0.029 0.025 0.29 1 -0.32 2 3
PRKACA 0.044 0.072 0.19 203 -0.32 2 205
angiogenesis 0.023 0.07 0.21 60 -0.32 23 83
MMP2 0.018 0.048 0.26 1 -0.57 7 8
IL8 0.025 0.099 0.26 60 -0.57 21 81
calcineurin-NFAT signaling pathway 0.024 0.06 0.2 63 -0.35 12 75
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.38 0.28 -10000 0 -0.57 728 728
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.029 0.049 -10000 0 -0.27 16 16
HIF1A 0.004 0.029 -10000 0 -0.26 12 12
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.037 0.28 1 -10000 0 1
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.059 0.085 0.26 170 -10000 0 170
ARNT/IPAS -0.25 0.2 -10000 0 -0.38 728 728
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.02 0.046 -10000 0 -0.28 15 15
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.05 -10000 0 -0.28 15 15
PHD1-3/OS9 0.056 0.048 -10000 0 -0.33 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.042 0.054 0.31 1 -0.3 5 6
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.049 -10000 0 -0.28 14 14
EGLN3 0.04 0.063 0.26 77 -0.57 1 78
EGLN2 0.025 0.016 0.26 5 -10000 0 5
EGLN1 0.02 0.02 -10000 0 -0.57 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.065 -10000 0 -0.51 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.052 0.073 0.24 38 -0.27 14 52
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.084 -10000 0 -0.46 14 14
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.028 0.17 -10000 0 -0.57 95 95
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.044 -10000 0 -0.57 6 6
AP1 -0.074 0.15 -10000 0 -0.31 293 293
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.021 0.036 -10000 0 -0.57 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.1 -10000 0 -0.63 19 19
NICD/RBPSUH 0.02 0.081 -10000 0 -0.41 28 28
WIF1 -0.27 0.3 0.26 13 -0.57 544 557
NOTCH1 0.008 0.075 -10000 0 -0.43 29 29
PSENEN 0.024 0.011 0.26 2 -10000 0 2
KREMEN2 0.12 0.12 0.26 473 -10000 0 473
DKK1 0.026 0.16 0.26 146 -0.57 54 200
beta catenin/beta TrCP1 0.009 0.067 -10000 0 -0.36 5 5
APH1B 0.023 0.018 -10000 0 -0.57 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 0.038 -10000 0 -0.28 7 7
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 306 306
JUN 0.02 0.044 -10000 0 -0.57 6 6
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 0 0.066 0.25 1 -0.37 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.099 0.34 1 -0.33 22 23
HNF1A 0.025 0.02 0.25 8 -10000 0 8
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.013 0.21 -10000 0 -1.3 27 27
NKD1 0.022 0.053 0.26 16 -0.57 6 22
FZD1 0.024 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.006 0.12 -10000 0 -0.45 28 28
apoptosis -0.074 0.15 -10000 0 -0.31 293 293
Delta 1/NOTCHprecursor 0.018 0.083 -10000 0 -0.42 23 23
DLL1 0.02 0.041 -10000 0 -0.57 5 5
PPARD 0.015 0.092 -10000 0 -0.82 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.31 1 1
APC 0.004 0.082 -10000 0 -0.49 20 20
DVL1 -0.029 0.077 -10000 0 -0.36 35 35
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.099 0.14 0.34 80 -0.34 47 127
LRP6 0.023 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.009 -10000 0 -10000 0 0
CCND1 0.02 0.1 -10000 0 -1.1 7 7
WNT1 0.023 0.011 0.26 2 -10000 0 2
Axin1/APC/beta catenin 0.013 0.098 0.32 5 -0.46 14 19
DKK2 0.009 0.095 0.26 2 -0.57 28 30
NOTCH1 precursor/DVL1 -0.02 0.11 -10000 0 -0.59 24 24
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.003 0.12 -10000 0 -0.46 28 28
PPP2R5D -0.004 0.057 0.29 5 -0.36 16 21
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.19 -10000 0 -0.33 526 526
RBPJ 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
alphaV beta3 Integrin 0.021 0.079 -10000 0 -0.42 33 33
PTK2 -0.04 0.16 -10000 0 -0.48 92 92
positive regulation of JNK cascade -0.021 0.12 -10000 0 -0.32 120 120
CDC42/GDP -0.018 0.17 0.42 1 -0.43 127 128
Rac1/GDP -0.018 0.17 -10000 0 -0.43 126 126
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 -0.4 118 118
nectin-3/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
RAPGEF1 -0.036 0.17 0.46 1 -0.47 113 114
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.05 0.18 -10000 0 -0.54 113 113
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.56 4 4
TLN1 -0.024 0.071 -10000 0 -0.4 14 14
Rap1/GTP -0.024 0.12 -10000 0 -0.34 109 109
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
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 0.44 1 -0.52 128 129
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.018 0.13 -10000 0 -0.34 116 116
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.029 -10000 0 -0.3 6 6
positive regulation of lamellipodium assembly -0.02 0.13 -10000 0 -0.34 128 128
PVRL1 0.022 0.007 -10000 0 -10000 0 0
PVRL3 -0.039 0.18 -10000 0 -0.57 114 114
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
CLDN1 0.007 0.12 0.26 23 -0.57 40 63
JAM-A/CLDN1 0.003 0.13 -10000 0 -0.35 112 112
SRC -0.056 0.21 -10000 0 -0.58 119 119
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.029 -10000 0 -0.3 6 6
FARP2 -0.038 0.2 0.43 1 -0.54 110 111
RAC1 0.024 0.003 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.001 0.13 -10000 0 -0.37 114 114
nectin-1/I-afadin 0.029 0.029 -10000 0 -0.3 6 6
nectin-2/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.001 0.13 -10000 0 -0.36 115 115
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 2 -0.41 40 42
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
PIP5K1C -0.019 0.079 -10000 0 -0.23 112 112
VAV2 -0.038 0.21 0.43 1 -0.54 128 129
RAP1/GDP -0.014 0.16 0.39 1 -0.4 116 117
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.13 -10000 0 -0.37 114 114
nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
Rac1/GTP -0.021 0.16 -10000 0 -0.41 128 128
PTPRM -0.017 0.088 -10000 0 -0.25 116 116
E-cadherin/beta catenin/alpha catenin 0.047 0.062 -10000 0 -0.32 20 20
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.012 0.14 -10000 0 -0.57 66 66
HRAS 0.026 0.022 0.26 9 -10000 0 9
EGFR -0.19 0.28 -10000 0 -0.57 390 390
AKT -0.014 0.12 0.28 7 -0.28 101 108
FOXO3 0.022 0.019 -10000 0 -0.57 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.019 0.041 -10000 0 -0.57 5 5
AKT3 0.014 0.06 -10000 0 -0.57 11 11
FOXO4 0.024 0.001 -10000 0 -10000 0 0
MET -0.073 0.22 -10000 0 -0.57 177 177
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.016 0.073 0.26 4 -0.57 16 20
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 -0.061 0.14 0.21 4 -0.24 354 358
ERBB2 0.02 0.02 -10000 0 -0.57 1 1
proliferation/survival/translation -0.006 0.089 0.32 50 -0.26 1 51
PI3K -0.05 0.14 0.24 14 -0.32 171 185
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.037 0.057 0.24 11 -0.16 2 13
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
Glypican 2 network

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
MDK 0.033 0.044 0.26 40 -10000 0 40
GPC2 0.049 0.081 0.26 126 -0.57 3 129
GPC2/Midkine 0.058 0.069 0.36 16 -0.42 3 19
neuron projection morphogenesis 0.057 0.069 0.36 16 -0.42 3 19
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.042 0.15 -10000 0 -0.32 238 238
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.13 9 -10000 0 9
GNB1/GNG2 0.026 0.043 -10000 0 -0.36 13 13
GNB1 0.023 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.061 0.14 -10000 0 -0.31 251 251
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.02 0.034 0.081 251 -10000 0 251
GNAL -0.11 0.24 -10000 0 -0.57 235 235
GNG2 0.017 0.065 -10000 0 -0.57 13 13
CRH 0.017 0.023 0.26 9 -10000 0 9
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.031 -10000 0 -0.35 8 8
MAPK11 0.005 0.019 -10000 0 -0.35 3 3
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.001 0.064 0.22 2 -0.32 12 14
adherens junction organization -0.013 0.091 0.22 1 -0.34 50 51
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.085 0.15 0.3 5 -0.33 117 122
FMN1 -0.011 0.085 -10000 0 -0.3 54 54
mol:IP3 -0.001 0.053 -10000 0 -0.28 13 13
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.087 -10000 0 -0.32 48 48
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.002 0.063 -10000 0 -0.28 13 13
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.012 0.13 -10000 0 -0.54 35 35
CTNND1 0.024 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.075 -10000 0 -0.3 42 42
VASP -0.009 0.08 -10000 0 -0.3 46 46
ZYX -0.009 0.081 -10000 0 -0.31 44 44
JUB -0.008 0.082 -10000 0 -0.3 48 48
EGFR(dimer) -0.1 0.18 -10000 0 -0.32 375 375
E-cadherin/beta catenin-gamma catenin 0.033 0.055 -10000 0 -0.35 18 18
mol:PI-3-4-5-P3 0.016 0.073 -10000 0 -0.28 19 19
PIK3CA 0.023 0.007 -10000 0 -10000 0 0
PI3K 0.016 0.075 -10000 0 -0.28 19 19
FYN -0.003 0.067 0.22 2 -0.32 11 13
mol:Ca2+ -0.001 0.053 -10000 0 -0.27 13 13
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
mol:DAG -0.001 0.053 -10000 0 -0.28 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
RhoA/GDP -0.084 0.15 0.32 3 -0.34 110 113
establishment of polarity of embryonic epithelium -0.009 0.079 -10000 0 -0.3 46 46
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.57 390 390
CASR -0.003 0.055 0.23 2 -0.27 11 13
RhoA/GTP 0.013 0.057 -10000 0 -0.26 10 10
AKT2 0.001 0.063 -10000 0 -0.29 11 11
actin cable formation -0.016 0.086 0.25 2 -0.32 43 45
apoptosis -0.005 0.073 0.28 25 -0.23 10 35
CTNNA1 0.024 0.006 -10000 0 -10000 0 0
mol:GDP -0.097 0.15 -10000 0 -0.3 345 345
PIP5K1A -0.008 0.077 -10000 0 -0.31 42 42
PLCG1 -0.001 0.054 -10000 0 -0.28 13 13
Rac1/GTP -0.092 0.17 -10000 0 -0.38 141 141
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.056 0.2 0.29 1 -0.39 192 193
MAP3K8 0.009 0.051 -10000 0 -0.57 7 7
FOS -0.02 0.14 0.29 2 -0.44 52 54
PRKCA -0.002 0.086 0.24 1 -0.57 22 23
PTPN7 0.021 0.06 0.24 61 -10000 0 61
HRAS 0.024 0.022 0.25 9 -10000 0 9
PRKCB 0.006 0.079 0.25 19 -0.57 15 34
NRAS 0.023 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.036 -10000 0 -10000 0 0
MAPK3 0.008 0.09 -10000 0 -0.66 7 7
MAP2K1 -0.012 0.12 -10000 0 -0.5 45 45
ELK1 0.006 0.029 -10000 0 -10000 0 0
BRAF -0.012 0.099 -10000 0 -0.48 39 39
mol:GTP -0.002 0.003 -10000 0 -0.006 323 323
MAPK1 -0.009 0.12 -10000 0 -0.47 41 41
RAF1 -0.011 0.097 -10000 0 -0.48 39 39
KRAS 0.022 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.003 0.04 0.22 27 -10000 0 27
RFC1 -0.003 0.036 0.22 23 -0.19 4 27
PRKDC 0.016 0.078 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 22 22
FASLG/FAS/FADD/FAF1 -0.005 0.059 0.22 11 -0.29 14 25
MAP2K4 -0.084 0.18 0.39 2 -0.42 113 115
mol:ceramide -0.024 0.1 -10000 0 -0.39 27 27
GSN -0.006 0.053 0.22 26 -0.35 11 37
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.078 0.28 1 -0.37 17 18
FAS 0.003 0.044 -10000 0 -0.58 4 4
BID -0.018 0.021 -10000 0 -10000 0 0
MAP3K1 -0.047 0.12 0.39 1 -0.43 35 36
MAP3K7 0.011 0.019 -10000 0 -10000 0 0
RB1 -0.003 0.036 0.22 22 -10000 0 22
CFLAR 0.027 0.018 -10000 0 -0.54 1 1
HGF/MET -0.052 0.19 -10000 0 -0.4 233 233
ARHGDIB -0.001 0.043 0.22 34 -10000 0 34
FADD 0.006 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.059 0.35 11 -0.21 30 41
NFKB1 -0.044 0.12 -10000 0 -0.58 18 18
MAPK8 -0.15 0.26 0.56 2 -0.47 389 391
DFFA -0.004 0.036 0.22 22 -10000 0 22
DNA fragmentation during apoptosis -0.006 0.045 0.21 26 -10000 0 26
FAS/FADD/MET -0.038 0.14 -10000 0 -0.38 143 143
CFLAR/RIP1 0.039 0.018 -10000 0 -0.38 1 1
FAIM3 0.026 0.035 0.26 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.046 0.22 36 -10000 0 36
DFFB -0.004 0.037 0.22 22 -10000 0 22
CHUK -0.039 0.11 -10000 0 -0.56 15 15
FASLG 0.006 0.089 0.25 42 -0.58 15 57
FAS/FADD 0.009 0.039 -10000 0 -0.32 4 4
HGF -0.011 0.14 0.26 2 -0.57 65 67
LMNA -0.003 0.053 -10000 0 -10000 0 0
CASP6 -0.003 0.036 0.22 22 -10000 0 22
CASP10 0.004 0.04 -10000 0 -0.58 3 3
CASP3 0 0.042 0.26 24 -10000 0 24
PTPN13 0.01 0.091 -10000 0 -0.57 26 26
CASP8 -0.021 0.024 -10000 0 -10000 0 0
IL6 -0.43 0.62 -10000 0 -1.2 399 399
MET -0.073 0.22 -10000 0 -0.57 177 177
ICAD/CAD -0.006 0.032 0.2 13 -10000 0 13
FASLG/FAS/FADD/FAF1/Caspase 10 -0.024 0.1 -10000 0 -0.39 27 27
activation of caspase activity by cytochrome c -0.018 0.02 -10000 0 -10000 0 0
PAK2 -0.003 0.047 0.22 35 -0.19 6 41
BCL2 0.008 0.094 -10000 0 -0.56 28 28
Syndecan-3-mediated signaling events

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
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.071 0.16 -10000 0 -0.48 25 25
Syndecan-3/Neurocan 0.027 0.073 0.27 18 -0.37 20 38
POMC 0.019 0.093 0.26 30 -0.57 22 52
EGFR -0.19 0.28 -10000 0 -0.57 390 390
Syndecan-3/EGFR -0.088 0.16 -10000 0 -0.31 305 305
AGRP 0.021 0.024 0.26 10 -10000 0 10
NCSTN 0.02 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.011 0.26 2 -10000 0 2
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.055 0.26 64 -10000 0 64
long-term memory 0.035 0.062 -10000 0 -0.35 16 16
Syndecan-3/IL8 0.02 0.081 0.28 9 -0.34 36 45
PSEN1 0.024 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.021 0.026 -10000 0 -0.57 2 2
limb bud formation 0.002 0.055 -10000 0 -0.39 21 21
MC4R 0.023 0.026 0.26 13 -10000 0 13
SRC 0.023 0.005 -10000 0 -10000 0 0
PTN -0.23 0.29 0.26 2 -0.57 455 457
FGFR/FGF/Syndecan-3 0.002 0.056 -10000 0 -0.39 21 21
neuron projection morphogenesis -0.071 0.15 0.33 5 -0.47 23 28
Syndecan-3/AgRP 0.015 0.06 0.26 1 -0.37 21 22
Syndecan-3/AgRP/MC4R 0.038 0.068 0.33 1 -0.36 20 21
Fyn/Cortactin 0.028 0.021 -10000 0 -0.3 2 2
SDC3 0.002 0.056 -10000 0 -0.39 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.02 0.08 0.28 9 -0.33 36 45
IL8 0.025 0.099 0.26 60 -0.57 21 81
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 16 16
Syndecan-3/CASK 0 0.054 -10000 0 -0.37 21 21
alpha-MSH/MC4R 0.029 0.072 0.36 2 -0.41 22 24
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.02 0.07 0.42 1 -0.26 52 53
CDKN1A -0.009 0.033 -10000 0 -0.77 2 2
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
BAX 0.025 0.014 0.26 4 -10000 0 4
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.019 0.041 -10000 0 -0.57 5 5
FOXO4 0.012 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.32 0.3 0.26 26 -0.57 635 661
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.023 -10000 0 -0.42 1 1
PPARGC1A -0.09 0.24 0.26 10 -0.57 211 221
FHL2 0.022 0.041 0.26 1 -0.57 5 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.02 0.07 0.26 52 -0.42 1 53
SIRT1/FOXO3a 0.015 0.026 -10000 0 -0.19 4 4
SIRT1 0.022 0.009 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.023 -10000 0 -0.36 1 1
SIRT1/Histone H1b 0.028 0.043 -10000 0 -0.21 6 6
apoptosis -0.044 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A -0.047 0.16 -10000 0 -0.36 209 209
p53/SIRT1 0.027 0.019 0.41 2 -10000 0 2
SIRT1/FOXO4 0.022 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.037 0.041 -10000 0 -0.33 10 10
HIST1H1E 0.021 0.03 0.2 6 -10000 0 6
SIRT1/p300 0.032 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.023 0.36 1 -10000 0 1
TP53 0.02 0.011 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0.045 0.016 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.25 0.21 -10000 0 -0.42 635 635
ACSS2 -0.007 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.023 -10000 0 -0.36 1 1
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.012 0.041 -10000 0 -0.26 19 19
epithelial cell differentiation 0.037 0.052 -10000 0 -0.31 18 18
CYFIP2 0.028 0.048 0.26 26 -0.57 3 29
ENAH -0.003 0.059 0.3 11 -10000 0 11
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EPHA2 0.02 0.04 -10000 0 -0.57 5 5
MYO6 -0.011 0.05 0.36 1 -0.3 19 20
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.034 -10000 0 -0.36 3 3
AQP5 -0.18 0.26 0.31 2 -0.5 419 421
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.049 0.36 1 -0.3 18 19
regulation of calcium-dependent cell-cell adhesion -0.022 0.074 0.36 1 -0.29 62 63
EGF -0.082 0.23 0.26 2 -0.57 194 196
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.015 0.12 0.29 1 -0.47 55 56
cortical microtubule organization 0.037 0.052 -10000 0 -0.31 18 18
GO:0000145 -0.011 0.046 0.35 1 -0.28 18 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.041 0.053 -10000 0 -0.31 18 18
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
ARF6/GDP -0.02 0.037 -10000 0 -0.27 18 18
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0 0.048 -10000 0 -0.28 18 18
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.011 0.049 0.36 1 -0.3 18 19
ARF6/GTP 0.049 0.04 -10000 0 -0.31 5 5
CDH1 0.012 0.076 -10000 0 -0.57 18 18
EGFR/EGFR/EGF/EGF -0.14 0.2 -10000 0 -0.33 519 519
RhoA/GDP 0.038 0.051 -10000 0 -0.3 18 18
actin cytoskeleton organization -0.012 0.047 0.34 1 -0.29 19 20
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
DIAPH1 0.026 0.1 -10000 0 -0.55 15 15
Wnt receptor signaling pathway -0.037 0.052 0.31 18 -10000 0 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.037 -10000 0 -0.28 15 15
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.013 0.048 0.35 1 -0.3 19 20
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.014 0.052 -10000 0 -0.29 25 25
Ephrin A1/EPHA2 0.026 0.051 -10000 0 -0.29 20 20
SEC6/SEC8 -0.021 0.04 -10000 0 -0.3 19 19
MGAT3 -0.022 0.075 0.36 1 -0.3 62 63
HGF/MET -0.039 0.15 -10000 0 -0.32 232 232
HGF -0.011 0.14 0.26 2 -0.57 65 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.012 0.042 -10000 0 -0.26 19 19
actin cable formation 0.042 0.094 0.32 34 -0.29 1 35
KIAA1543 -0.012 0.053 0.35 1 -0.33 18 19
KIFC3 -0.012 0.047 0.36 1 -0.3 18 19
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.011 0.048 -10000 0 -0.3 18 18
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.037 0.052 -10000 0 -0.31 18 18
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.011 0.047 0.36 1 -0.3 17 18
PIP5K1C -0.011 0.05 0.36 1 -0.3 18 19
LIMA1 0.024 0.018 -10000 0 -0.57 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.017 0.088 0.31 26 -10000 0 26
adherens junction assembly -0.021 0.1 0.3 3 -0.63 16 19
IGF-1R heterotetramer/IGF1 -0.041 0.15 -10000 0 -0.31 234 234
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
MET -0.073 0.22 -10000 0 -0.57 177 177
PLEKHA7 -0.012 0.056 0.36 1 -0.35 18 19
mol:GTP 0.043 0.037 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.007 0.066 0.37 7 -0.51 1 8
cortical actin cytoskeleton stabilization 0.012 0.041 -10000 0 -0.26 19 19
regulation of cell-cell adhesion -0.012 0.047 0.34 1 -0.29 19 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.012 0.042 -10000 0 -0.26 19 19
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.018 0.063 -10000 0 -0.36 36 36
ADCY5 -0.11 0.16 -10000 0 -0.36 328 328
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.009 0.062 -10000 0 -0.36 28 28
ADCY2 -0.03 0.1 0.24 8 -0.36 85 93
ADCY3 -0.007 0.003 -10000 0 -10000 0 0
ADCY8 -0.004 0.023 0.23 6 -10000 0 6
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.085 0.23 16 -0.25 33 49
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 0.041 -10000 0 -10000 0 0
BIRC5 0.18 0.11 0.26 711 -10000 0 711
NFKBIA 0.024 0.04 0.28 8 -10000 0 8
CPEB1 -0.079 0.22 0.26 1 -0.57 187 188
AKT1 0.023 0.04 0.29 7 -10000 0 7
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.033 0.036 0.21 1 -10000 0 1
NDEL1/TACC3 0.066 0.067 0.26 17 -10000 0 17
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.001 0.026 -10000 0 -10000 0 0
PAK1/Aurora A 0.04 0.043 0.27 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.09 0.067 0.27 26 -10000 0 26
TP53 0.022 0.051 0.19 1 -0.22 13 14
DLG7 0.022 0.03 0.18 1 -10000 0 1
AURKAIP1 0.026 0.024 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 0.069 0.071 0.28 17 -10000 0 17
G2/M transition of mitotic cell cycle 0.031 0.034 0.2 1 -10000 0 1
AURKA 0.037 0.045 0.24 1 -10000 0 1
AURKB 0.086 0.074 0.17 434 -10000 0 434
CDC25B 0.031 0.039 0.22 3 -10000 0 3
G2/M transition checkpoint 0.019 0.028 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.13 -10000 0 -0.29 185 185
Aurora A/CPEB -0.025 0.13 -10000 0 -0.3 185 185
Aurora A/TACC1/TRAP/chTOG 0.044 0.07 -10000 0 -0.3 22 22
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
centrosome duplication 0.04 0.043 0.27 2 -10000 0 2
regulation of centrosome cycle 0.064 0.066 0.26 17 -10000 0 17
spindle assembly 0.042 0.069 -10000 0 -0.3 22 22
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.087 0.28 29 -10000 0 29
CENPA 0.095 0.081 0.18 445 -0.21 3 448
Aurora A/PP2A 0.043 0.042 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.03 0.039 0.24 1 -10000 0 1
negative regulation of DNA binding 0.018 0.063 -10000 0 -0.22 13 13
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.028 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.045 0.24 1 -10000 0 1
TACC1 0.006 0.089 -10000 0 -0.57 25 25
TACC3 0.058 0.083 0.26 162 -10000 0 162
Aurora A/Antizyme1 0.054 0.043 -10000 0 -10000 0 0
Aurora A/RasGAP 0.043 0.042 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.001 0.027 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.024 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.089 0.067 0.27 26 -10000 0 26
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.094 0.072 0.24 39 -10000 0 39
PAK1 0.023 0.019 0.26 6 -10000 0 6
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.062 0.087 0.26 179 -10000 0 179
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.018 0.057 -10000 0 -0.57 10 10
CDKN1A -0.031 0.093 -10000 0 -0.44 29 29
PRL-3/alpha Tubulin 0.03 0.019 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.075 0.24 44 -0.42 13 57
AGT 0.029 0.089 0.26 73 -0.57 13 86
CCNA2 -0.065 0.14 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.12 0.2 -10000 0 -0.41 336 336
CDK2/Cyclin E1 0.016 0.11 -10000 0 -0.49 16 16
MAPK3 0.01 0.018 0.26 4 -10000 0 4
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.018 0.26 4 -10000 0 4
PTP4A1 -0.093 0.14 -10000 0 -0.32 299 299
PTP4A3 0.021 0.02 0.26 6 -10000 0 6
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.017 0.26 3 -10000 0 3
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 -0.016 0.071 -10000 0 -0.43 12 12
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.072 0.15 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.015 -10000 0 -10000 0 0
RHOC -0.019 0.079 -10000 0 -0.42 19 19
RHOA -0.021 0.089 -10000 0 -0.47 24 24
cell motility -0.026 0.1 0.25 1 -0.37 40 41
PRL-1/alpha Tubulin -0.073 0.15 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.041 -10000 0 -0.33 10 10
ROCK1 -0.024 0.098 0.25 1 -0.36 36 37
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.093 0.14 -10000 0 -0.32 299 299
ATF5 0.025 0.013 0.26 3 -10000 0 3
Coregulation 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
NRIP1 0.012 0.04 -10000 0 -0.57 1 1
SVIL 0.01 0.052 -10000 0 -0.57 5 5
ZNF318 0.039 0.054 0.19 90 -10000 0 90
JMJD2C -0.001 0.042 0.11 32 -0.13 78 110
T-DHT/AR/Ubc9 -0.034 0.14 -10000 0 -0.37 139 139
CARM1 0.019 0.015 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.011 -10000 0 -10000 0 0
CTNNB1 0.014 0.029 -10000 0 -10000 0 0
AKT1 0.027 0.018 -10000 0 -10000 0 0
PTK2B 0.012 0.026 -10000 0 -10000 0 0
MED1 0.025 0.02 -10000 0 -10000 0 0
MAK 0.034 0.083 0.25 14 -0.54 11 25
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.01 0.052 -10000 0 -0.57 5 5
GSN 0.006 0.071 -10000 0 -0.57 12 12
NCOA2 -0.01 0.12 -10000 0 -0.57 48 48
NCOA6 0.013 0.033 -10000 0 -10000 0 0
DNA-PK 0.05 0.053 0.23 2 -10000 0 2
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.027 -10000 0 -10000 0 0
cell proliferation 0.004 0.11 0.35 1 -0.57 24 25
XRCC5 0.026 0.015 -10000 0 -10000 0 0
UBE3A 0.009 0.044 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.042 0.15 -10000 0 -0.39 151 151
FHL2 0.002 0.1 -10000 0 -0.86 7 7
RANBP9 0.013 0.033 -10000 0 -10000 0 0
JMJD1A -0.015 0.047 0.12 1 -0.14 131 132
CDK6 0.02 0.058 0.26 2 -0.57 10 12
TGFB1I1 0.01 0.046 -10000 0 -0.57 3 3
T-DHT/AR/CyclinD1 -0.042 0.14 -10000 0 -0.38 140 140
XRCC6 0.025 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.041 0.16 -10000 0 -0.38 150 150
CTDSP1 0.018 0.019 -10000 0 -10000 0 0
CTDSP2 0.034 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.039 -10000 0 -0.57 1 1
TCF4 0.024 0.066 -10000 0 -0.56 11 11
CDKN2A 0.063 0.088 0.26 170 -10000 0 170
SRF 0.032 0.023 -10000 0 -10000 0 0
NKX3-1 -0.047 0.096 -10000 0 -0.21 248 248
KLK3 -0.14 0.46 -10000 0 -1.4 126 126
TMF1 0.018 0.016 -10000 0 -10000 0 0
HNRNPA1 0.028 0.02 -10000 0 -10000 0 0
AOF2 -0.007 0.023 -10000 0 -0.069 126 126
APPL1 0.019 0.032 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.028 0.14 -10000 0 -0.36 150 150
AR -0.067 0.2 -10000 0 -0.58 141 141
UBA3 0.017 0.019 -10000 0 -10000 0 0
PATZ1 0.027 0.021 -10000 0 -10000 0 0
PAWR 0.018 0.024 -10000 0 -0.57 1 1
PRKDC 0.023 0.016 -10000 0 -10000 0 0
PA2G4 0.031 0.027 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.024 0.13 -10000 0 -0.34 130 130
RPS6KA3 0.008 0.062 -10000 0 -0.57 8 8
T-DHT/AR/ARA70 -0.037 0.14 -10000 0 -0.37 139 139
LATS2 0.027 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.022 0.14 -10000 0 -0.34 140 140
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.014 0.063 0.25 19 -0.57 7 26
KLK2 -0.076 0.27 0.32 2 -0.99 81 83
CASP8 0.026 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.042 0.15 -10000 0 -0.37 149 149
TMPRSS2 -0.13 0.33 -10000 0 -0.98 136 136
CCND1 0.012 0.042 0.26 1 -0.57 4 5
PIAS1 0.01 0.044 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.028 -10000 0 -0.07 168 168
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.003 0.063 -10000 0 -0.21 4 4
T-DHT/AR/CDK6 -0.035 0.14 -10000 0 -0.36 159 159
CMTM2 0.023 0.012 0.25 1 -10000 0 1
SNURF 0.012 0.082 -10000 0 -0.57 21 21
ZMIZ1 0.01 0.039 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.021 -10000 0 -10000 0 0
FKBP4 0.014 0.036 0.26 4 -10000 0 4
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.008 0.01 -10000 0 -10000 0 0
SMARCC1 0.006 0.027 -10000 0 -0.5 2 2
REL 0.017 0.068 -10000 0 -0.57 14 14
HDAC7 -0.036 0.11 0.37 3 -0.41 36 39
JUN 0.019 0.044 -10000 0 -0.57 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.018 -10000 0 -0.57 1 1
KAT5 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.008 0.065 -10000 0 -0.43 23 23
FOXO1 0.019 0.041 -10000 0 -0.57 5 5
T-DHT/AR -0.023 0.12 0.33 1 -0.39 59 60
MAP2K6 0.002 0.088 0.24 1 -0.57 23 24
BRM/BAF57 0.026 0.027 -10000 0 -10000 0 0
MAP2K4 0.014 0.02 -10000 0 -10000 0 0
SMARCA2 0.018 0.018 -10000 0 -10000 0 0
PDE9A -0.061 0.26 -10000 0 -1 63 63
NCOA2 -0.008 0.12 -10000 0 -0.57 48 48
CEBPA 0.019 0.057 -10000 0 -0.57 10 10
EHMT2 0.021 0.012 -10000 0 -10000 0 0
cell proliferation 0.001 0.15 0.38 24 -0.45 25 49
NR0B1 0.027 0.042 0.26 35 -10000 0 35
EGR1 -0.16 0.27 -10000 0 -0.57 336 336
RXRs/9cRA -0.042 0.15 -10000 0 -0.33 216 216
AR/RACK1/Src -0.016 0.11 0.32 6 -0.36 36 42
AR/GR -0.028 0.12 0.29 1 -0.3 128 129
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 -0.013 14 14
MAPK8 -0.002 0.042 -10000 0 -0.43 8 8
T-DHT/AR/TIF2/CARM1 -0.017 0.12 0.32 1 -0.42 35 36
SRC -0.019 0.068 0.19 29 -0.34 27 56
NR3C1 0.018 0.06 -10000 0 -0.57 11 11
KLK3 -0.14 0.39 0.38 1 -1.1 134 135
APPBP2 0.016 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.015 0.097 0.42 1 -0.39 29 30
TMPRSS2 -0.12 0.36 -10000 0 -1.1 135 135
RXRG -0.1 0.24 0.26 2 -0.57 219 221
mol:9cRA -0.001 0.002 -10000 0 -0.011 5 5
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 0.057 -10000 0 -0.57 10 10
KLK2 -0.051 0.2 0.32 5 -0.66 85 90
AR -0.04 0.11 -10000 0 -0.3 138 138
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.016 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 126 -0.023 42 168
GATA2 0.013 0.095 0.26 13 -0.57 26 39
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.25 446 -10000 0 446
T-DHT/AR/RACK1/Src -0.013 0.1 0.34 9 -0.38 30 39
positive regulation of transcription 0.013 0.094 0.26 13 -0.56 26 39
DNAJA1 0.017 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.022 0.029 -10000 0 -0.6 1 1
SPDEF -0.01 0.15 0.26 33 -0.57 68 101
T-DHT/AR/TIF2 -0.005 0.1 0.32 6 -0.37 31 37
T-DHT/AR/Hsp90 -0.016 0.097 0.37 2 -0.38 30 32
GSK3B 0.021 0.01 -10000 0 -10000 0 0
NR2C1 0.025 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.062 0.23 1 -0.35 28 29
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.025 0.016 -10000 0 -10000 0 0
POU2F1 0.009 0.05 -10000 0 -0.2 2 2
T-DHT/AR/DAX-1 -0.015 0.1 0.33 3 -0.39 31 34
CREBBP 0.022 0.007 -10000 0 -10000 0 0
SMARCE1 0.018 0.018 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.083 0.1 0.3 6 -0.57 6 12
Syndecan-4/Syndesmos 0.094 0.1 0.39 4 -0.7 6 10
positive regulation of JNK cascade 0.083 0.13 0.36 6 -0.64 8 14
Syndecan-4/ADAM12 0.1 0.12 0.41 8 -0.72 6 14
CCL5 0.029 0.056 0.26 38 -0.57 4 42
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.007 0.26 1 -10000 0 1
SDCBP 0.021 0.008 -10000 0 -10000 0 0
PLG -0.008 0.034 0.25 8 -10000 0 8
ADAM12 0.036 0.061 0.26 64 -0.57 2 66
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.066 0.15 0.41 2 -0.74 8 10
Syndecan-4/CXCL12/CXCR4 0.087 0.14 0.38 6 -0.69 8 14
Syndecan-4/Laminin alpha3 0.033 0.15 0.39 3 -0.74 7 10
MDK 0.033 0.044 0.26 40 -10000 0 40
Syndecan-4/FZD7 0.094 0.12 0.38 6 -0.69 7 13
Syndecan-4/Midkine 0.1 0.11 0.38 8 -0.69 6 14
FZD7 0.013 0.082 -10000 0 -0.57 21 21
Syndecan-4/FGFR1/FGF -0.01 0.16 -10000 0 -0.56 16 16
THBS1 0.021 0.04 -10000 0 -0.57 5 5
integrin-mediated signaling pathway 0.092 0.12 0.37 6 -0.69 7 13
positive regulation of MAPKKK cascade 0.083 0.13 0.36 6 -0.64 8 14
Syndecan-4/TACI 0.098 0.12 0.38 8 -0.72 6 14
CXCR4 0.029 0.034 0.26 24 -10000 0 24
cell adhesion 0.06 0.083 0.25 84 -0.25 21 105
Syndecan-4/Dynamin 0.098 0.1 0.41 2 -0.73 6 8
Syndecan-4/TSP1 0.097 0.11 0.39 4 -0.72 6 10
Syndecan-4/GIPC 0.098 0.1 0.4 2 -0.73 6 8
Syndecan-4/RANTES 0.099 0.11 0.37 5 -0.72 6 11
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.024 0.22 0.7 96 -0.53 22 118
Syndecan-4/alpha-Actinin 0.098 0.1 0.4 3 -0.72 6 9
TFPI -0.005 0.13 0.26 1 -0.57 54 55
F2 0.025 0.034 0.26 13 -10000 0 13
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
positive regulation of cell adhesion 0 0.17 0.37 3 -0.55 31 34
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.092 0.26 11 -0.57 25 36
Syndecan-4/CXCL12 0.076 0.14 0.38 5 -0.72 8 13
FGF6 0.015 0.025 -10000 0 -0.57 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.019 0.15 -10000 0 -0.57 78 78
TNFRSF13B 0.028 0.084 0.26 63 -0.57 12 75
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
Syndecan-4/PI-4-5-P2 0.075 0.1 0.34 2 -0.72 6 8
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.25 416 -10000 0 416
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.012 0.025 -10000 0 -10000 0 0
vasculogenesis 0.095 0.1 0.37 6 -0.68 6 12
SDC4 0.087 0.1 0.4 3 -0.78 5 8
Syndecan-4/Tenascin C 0.093 0.12 0.39 4 -0.72 7 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.085 0.1 0.37 3 -0.7 6 9
MMP9 0.12 0.12 0.26 453 -0.56 1 454
Rac1/GTP 0.061 0.084 0.25 83 -0.25 21 104
cytoskeleton organization 0.092 0.1 0.37 6 -0.67 6 12
GIPC1 0.024 0.008 0.26 1 -10000 0 1
Syndecan-4/TFPI 0.085 0.13 0.4 3 -0.72 7 10
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.027 0.027 0.26 14 -10000 0 14
GNB1/GNG2 -0.016 0.048 -10000 0 -0.19 66 66
AKT1 0.023 0.092 0.36 10 -0.28 26 36
EGF -0.082 0.23 0.26 2 -0.57 194 196
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.06 0.25 2 -0.31 6 8
mol:Ca2+ 0.021 0.11 0.42 10 -0.3 73 83
LYN 0.013 0.056 0.25 2 -0.35 3 5
RhoA/GTP 0.009 0.045 0.13 3 -0.14 25 28
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.019 0.12 0.44 10 -0.35 63 73
GNG2 0.017 0.065 -10000 0 -0.57 13 13
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.57 40 40
G beta5/gamma2 -0.012 0.067 -10000 0 -0.26 65 65
PRKCH 0.017 0.12 0.45 8 -0.36 63 71
DNM1 0.02 0.048 0.26 1 -0.57 7 8
TXA2/TP beta/beta Arrestin3 0.008 0.031 -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 -0.57 32 39
G12 family/GTP 0 0.09 -10000 0 -0.3 64 64
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.02 0.041 -10000 0 -0.57 5 5
RhoA/GTP/ROCK1 0.031 0.014 -10000 0 -0.36 1 1
mol:GDP -0.011 0.099 0.37 33 -0.33 8 41
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 -0.014 0.14 -10000 0 -0.57 69 69
mol:IP3 0.019 0.14 0.46 9 -0.38 74 83
cell morphogenesis 0.031 0.014 -10000 0 -0.36 1 1
PLCB2 0.01 0.17 0.52 7 -0.52 74 81
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.026 0.072 0.26 6 -0.31 6 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.061 0.25 3 -0.32 5 8
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.026 0.021 0.26 9 -10000 0 9
PRKCB1 0.018 0.13 0.46 8 -0.38 66 74
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.014 0.17 0.54 7 -0.53 65 72
LCK 0.016 0.074 0.25 2 -0.36 14 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.25 27 27
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.1 -10000 0 -0.43 49 49
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.24 21 21
MAPK14 0.018 0.089 0.32 17 -0.23 60 77
TGM2/GTP 0.014 0.15 0.51 8 -0.43 69 77
MAPK11 0.017 0.089 0.35 13 -0.24 52 65
ARHGEF1 0.011 0.066 0.27 10 -0.18 54 64
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.02 0.13 0.47 9 -0.39 65 74
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.022 0.1 0.4 11 -0.28 62 73
cAMP biosynthetic process 0.016 0.13 0.45 8 -0.36 71 79
Gq family/GTP/EBP50 0.015 0.043 0.22 5 -0.27 6 11
actin cytoskeleton reorganization 0.031 0.014 -10000 0 -0.36 1 1
SRC 0.013 0.058 0.25 2 -0.32 5 7
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.047 0.1 0.26 2 -0.29 76 78
VCAM1 0.02 0.11 0.39 11 -0.31 63 74
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.57 40 40
platelet activation 0.023 0.12 0.43 12 -0.31 62 74
PGI2/IP 0.019 0.015 0.18 9 -10000 0 9
PRKACA 0.008 0.053 -10000 0 -0.28 33 33
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.48 36 36
TXA2/TP beta/beta Arrestin2 -0.006 0.066 -10000 0 -0.44 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.047 -10000 0 -0.26 30 30
mol:DAG 0.017 0.14 0.51 7 -0.42 70 77
EGFR -0.19 0.28 -10000 0 -0.57 390 390
TXA2/TP alpha 0.014 0.16 0.52 7 -0.49 73 80
Gq family/GTP 0.001 0.049 0.25 1 -0.22 45 46
YES1 0.014 0.061 0.25 2 -0.3 6 8
GNAI2/GTP 0.013 0.052 -10000 0 -0.26 22 22
PGD2/DP 0.005 0.076 0.18 7 -0.4 35 42
SLC9A3R1 0.036 0.054 0.26 60 -10000 0 60
FYN 0.012 0.059 0.26 1 -0.34 7 8
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.025 0.025 0.26 6 -0.57 1 7
PGK/cGMP 0.007 0.096 -10000 0 -0.36 69 69
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.034 0.072 -10000 0 -0.32 29 29
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 -0.38 60 70
PRKCB 0.02 0.13 0.44 9 -0.37 63 72
PRKCE 0.018 0.12 0.47 8 -0.36 61 69
PRKCD 0.017 0.13 0.46 8 -0.39 63 71
PRKCG 0.019 0.13 0.47 8 -0.39 63 71
muscle contraction 0.014 0.16 0.51 8 -0.49 68 76
PRKCZ 0.017 0.12 0.44 9 -0.35 63 72
ARR3 0.021 0.021 0.26 8 -10000 0 8
TXA2/TP beta 0.024 0.06 -10000 0 -0.27 32 32
PRKCQ 0.015 0.14 0.42 12 -0.39 65 77
MAPKKK cascade 0.014 0.15 0.5 7 -0.46 72 79
SELE 0.016 0.12 0.41 10 -0.39 62 72
TP beta/GNAI2/GDP/G beta/gamma 0.034 0.071 -10000 0 -0.32 29 29
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
GNA14 0.023 0.065 0.26 19 -0.57 10 29
chemotaxis 0.012 0.18 0.57 7 -0.61 63 70
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.086 0.26 1 -0.57 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.091 0.12 -10000 0 -0.24 418 418
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
FYN 0.021 0.026 -10000 0 -0.57 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 -0.039 0.098 -10000 0 -0.34 73 73
PRKG1 -0.014 0.14 -10000 0 -0.57 69 69
DUSP8 0.022 0.031 -10000 0 -0.57 3 3
PGK/cGMP/p38 alpha -0.018 0.13 -10000 0 -0.35 97 97
apoptosis -0.038 0.093 -10000 0 -0.33 71 71
RAL/GTP 0.032 0.006 -10000 0 -10000 0 0
LYN 0.021 0.008 -10000 0 -10000 0 0
DUSP1 -0.045 0.19 -10000 0 -0.57 126 126
PAK1 0.023 0.019 0.26 6 -10000 0 6
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 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 0.29 5 -0.38 65 70
BLK 0.051 0.087 0.26 151 -0.57 2 153
HCK 0.027 0.026 0.26 13 -10000 0 13
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.014 0.26 2 -10000 0 2
TRAF6/MEKK3 0.028 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.004 0.13 0.3 4 -0.38 70 74
positive regulation of innate immune response -0.01 0.15 0.33 5 -0.45 64 69
LCK 0.026 0.075 0.26 40 -0.57 11 51
p38alpha-beta/MKP7 -0.002 0.14 0.34 4 -0.43 60 64
p38alpha-beta/MKP5 -0.003 0.14 0.37 3 -0.44 54 57
PGK/cGMP -0.01 0.11 -10000 0 -0.42 69 69
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.032 0.17 0.34 4 -0.44 94 98
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.24 0.29 -10000 0 -0.57 479 479
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.025 0.26 2 -0.54 1 3
CDKN2C 0.014 0.028 -10000 0 -0.55 1 1
CDKN2A 0.06 0.085 0.26 170 -10000 0 170
CCND2 -0.016 0.036 0.2 2 -0.21 14 16
RB1 0.015 0.047 0.26 15 -0.23 8 23
CDK4 -0.017 0.037 0.21 2 -0.22 12 14
CDK6 -0.018 0.04 0.22 2 -0.2 24 26
G1/S progression -0.01 0.059 0.19 42 -0.27 15 57
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 0.47 9 -0.52 2 11
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.094 0.21 -10000 0 -0.42 305 305
IFNAR2 0.028 0.02 -10000 0 -0.57 1 1
AKT1 -0.003 0.088 -10000 0 -0.23 101 101
ER alpha/Oestrogen -0.025 0.16 0.18 116 -0.4 157 273
NFX1/SIN3/HDAC complex 0.023 0.059 0.24 1 -0.33 16 17
EGF -0.081 0.23 0.26 2 -0.56 194 196
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 0.055 0.12 0.42 4 -0.49 2 6
SAP18 0.023 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.022 -10000 0 -10000 0 0
WT1 0.14 0.12 0.26 534 -10000 0 534
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 0.051 0.1 -10000 0 -0.5 1 1
Mad/Max 0.041 0.014 -10000 0 -10000 0 0
TERT 0.058 0.13 0.49 7 -0.59 1 8
CCND1 0.081 0.16 0.54 20 -1 4 24
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.019 0.26 7 -10000 0 7
RBBP4 0.024 0.019 -10000 0 -0.56 1 1
TERF2 0.021 0.013 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.039 0.05 -10000 0 -0.38 5 5
CDKN1B 0.029 0.049 -10000 0 -0.67 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.015 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.022 0.044 -10000 0 -0.56 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 -0.56 306 306
IFN-gamma/IRF1 0.064 0.063 0.26 11 -0.32 3 14
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.044 0.067 0.26 97 -10000 0 97
Telomerase 0.03 0.08 0.27 2 -0.6 6 8
IRF1 0.029 0.018 0.26 3 -0.18 3 6
ESR1 -0.034 0.23 0.26 116 -0.56 151 267
KU/TER 0.034 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.056 0.23 1 -0.33 10 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.057 0.23 1 -0.34 10 11
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.012 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.014 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.008 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.06 0.13 0.46 2 -0.59 5 7
NR2F2 0.012 0.037 -10000 0 -0.57 3 3
MAPK3 0.006 0.019 -10000 0 -10000 0 0
MAPK1 0.006 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.022 0.014 0.25 3 -10000 0 3
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.016 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.56 390 390
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.2 0.25 -10000 0 -0.44 534 534
MYC 0.008 0.084 -10000 0 -0.57 22 22
IL2 0.029 0.024 0.26 8 -10000 0 8
KU 0.034 0.009 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.023 0.014 0.25 3 -10000 0 3
TRF2/BLM 0.043 0.045 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.068 0.12 0.45 5 -0.55 1 6
SP1/HDAC2 0.046 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.049 0.1 -10000 0 -0.49 1 1
Smad3/Myc 0.007 0.054 -10000 0 -0.36 20 20
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.058 0.081 0.26 146 -0.19 3 149
Telomerase/PinX1 0.041 0.097 -10000 0 -0.49 1 1
Telomerase/AKT1/mTOR/p70S6K 0.027 0.1 0.29 6 -0.57 14 20
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.045 0.095 -10000 0 -10000 0 0
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.051 0.1 -10000 0 -0.5 1 1
E2F1 0.097 0.11 0.26 320 -10000 0 320
ZNFX1 0.024 0.006 -10000 0 -10000 0 0
PIF1 0.069 0.092 0.26 211 -10000 0 211
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.01 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.049 0.16 -10000 0 -0.32 252 252
TC10/GTP -0.039 0.14 -10000 0 -0.29 259 259
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.078 -10000 0 -0.34 41 41
HRAS 0.026 0.022 0.26 9 -10000 0 9
APS homodimer 0.034 0.046 0.26 45 -10000 0 45
GRB14 0.011 0.18 0.26 142 -0.57 80 222
FOXO3 -0.022 0.16 -10000 0 -0.6 74 74
AKT1 -0.02 0.11 0.3 10 -0.45 2 12
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.055 0.046 0.42 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 -0.57 267 267
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.024 -10000 0 -10000 0 0
CAV1 -0.083 0.15 -10000 0 -0.35 238 238
CBL/APS/CAP/Crk-II/C3G -0.028 0.16 -10000 0 -0.31 262 262
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.078 -10000 0 -0.34 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.075 -10000 0 -0.3 49 49
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.014 0.064 -10000 0 -0.43 6 6
RPS6KB1 -0.019 0.096 0.29 9 -0.48 1 10
PARD6A 0.023 0.019 0.26 6 -10000 0 6
CBL 0.022 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.038 -10000 0 -0.55 4 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.007 0.094 -10000 0 -0.36 1 1
HRAS/GTP -0.02 0.044 -10000 0 -0.28 21 21
Insulin Receptor 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.069 -10000 0 -0.32 26 26
PRKCI 0.013 0.059 -10000 0 -0.45 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.005 0.1 -10000 0 -0.29 108 108
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.035 -10000 0 -0.46 4 4
PI3K 0.037 0.079 -10000 0 -0.3 49 49
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 9 -10000 0 9
AKT2 -0.019 0.11 0.31 7 -0.45 2 9
PRKCZ 0.004 0.086 -10000 0 -0.48 17 17
SH2B2 0.034 0.046 0.26 45 -10000 0 45
SHC/SHIP 0.012 0.057 -10000 0 -0.3 28 28
F2RL2 0.046 0.12 0.26 155 -0.57 20 175
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.036 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.033 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.038 0.17 -10000 0 -0.32 266 266
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 0.062 -10000 0 -0.31 41 41
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.02 0.14 -10000 0 -0.69 47 47
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
p62DOK/RasGAP 0.042 0.035 -10000 0 -0.47 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.31 41 41
GRB2 0.023 0.009 0.26 1 -10000 0 1
EIF4EBP1 -0.021 0.089 0.26 6 -0.48 1 7
PTPRA 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.052 -10000 0 -0.27 26 26
Insulin Receptor/Insulin/IRS1 0.029 0.074 -10000 0 -0.34 41 41
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.06 0.073 -10000 0 -0.31 20 20
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.014 0.26 3 -10000 0 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.012 0.12 0.48 8 -0.5 4 12
IL27/IL27R/JAK1 0.037 0.16 0.73 6 -0.62 11 17
TBX21 -0.001 0.17 0.49 16 -0.5 46 62
IL12B 0.075 0.098 0.26 227 -10000 0 227
IL12A -0.013 0.097 0.14 18 -0.42 57 75
IL6ST -0.041 0.19 0.2 1 -0.56 120 121
IL27RA/JAK1 0.022 0.079 0.51 2 -1.2 3 5
IL27 0.048 0.076 0.27 112 -10000 0 112
TYK2 0.03 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.097 0.16 1.1 1 -0.79 2 3
T-helper 2 cell differentiation -0.012 0.12 0.48 8 -0.5 4 12
T cell proliferation during immune response -0.012 0.12 0.48 8 -0.5 4 12
MAPKKK cascade 0.012 0.12 0.5 4 -0.48 8 12
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.033 0.26 19 -10000 0 19
IL12RB1 0.033 0.053 0.26 41 -0.57 2 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.009 0.18 0.47 33 -0.52 51 84
IL27/IL27R/JAK2/TYK2 0.012 0.12 0.51 4 -0.48 8 12
positive regulation of T cell mediated cytotoxicity 0.012 0.12 0.5 4 -0.48 8 12
STAT1 (dimer) 0.035 0.21 0.67 23 -0.67 18 41
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.024 0.12 0.44 4 -0.46 8 12
T cell proliferation -0.091 0.18 0.37 4 -0.47 75 79
IL12/IL12R/TYK2/JAK2 0.059 0.18 0.44 5 -0.72 28 33
IL17A -0.097 0.16 1.1 1 -0.79 2 3
mast cell activation -0.012 0.12 0.48 8 -0.5 4 12
IFNG 0.021 0.045 0.12 120 -0.097 9 129
T cell differentiation 0 0.006 0.017 9 -0.02 7 16
STAT3 (dimer) 0.023 0.12 0.44 4 -0.46 8 12
STAT5A (dimer) 0.021 0.12 0.44 4 -0.46 13 17
STAT4 (dimer) 0.011 0.14 0.44 4 -0.44 25 29
STAT4 0.001 0.12 0.26 1 -0.57 43 44
T cell activation -0.005 0.011 0.12 3 -0.1 6 9
IL27R/JAK2/TYK2 0.016 0.14 -10000 0 -1.1 3 3
GATA3 -0.023 0.27 0.61 39 -1.3 35 74
IL18 0.009 0.02 0.13 26 -10000 0 26
positive regulation of mast cell cytokine production 0.022 0.11 0.43 4 -0.45 8 12
IL27/EBI3 0.053 0.072 0.25 53 -0.38 6 59
IL27RA 0.01 0.081 0.74 1 -1.3 3 4
IL6 -0.18 0.28 0.26 1 -0.57 380 381
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.041 0.45 3 -0.52 1 4
IL1B 0.001 0.048 0.13 3 -0.42 14 17
EBI3 0.025 0.054 0.26 14 -0.57 6 20
TNF 0.006 0.043 0.14 25 -0.42 9 34
BCR signaling pathway

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
JUN 0.024 0.13 0.3 15 -0.39 38 53
IKBKB 0.024 0.089 0.32 7 -0.31 15 22
AKT1 0.04 0.11 0.26 96 -0.24 21 117
IKBKG 0.028 0.073 0.35 4 -0.31 5 9
CALM1 0.002 0.096 0.25 1 -0.42 21 22
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.025 0.16 0.35 14 -0.52 46 60
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.1 -10000 0 -0.35 47 47
DOK1 0.025 0.014 0.26 4 -10000 0 4
AP-1 -0.021 0.098 0.25 8 -0.25 48 56
LYN 0.021 0.008 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
BCR complex 0.005 0.16 0.36 21 -0.44 95 116
CD22 -0.01 0.13 0.27 23 -0.44 64 87
CAMK2G 0.003 0.094 0.26 7 -0.41 18 25
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.086 -10000 0 -0.33 55 55
GO:0007205 0.002 0.1 -10000 0 -0.36 47 47
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0.002 0.1 0.26 1 -0.42 21 22
NFATC1 0.031 0.13 0.28 44 -0.43 37 81
B-cell antigen/BCR complex 0.005 0.16 0.36 21 -0.44 95 116
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.023 0.048 0.17 10 -0.13 28 38
HRAS 0.012 0.11 0.27 15 -0.35 39 54
NFKBIA 0.024 0.047 0.17 10 -0.12 23 33
NF-kappa-B/RelA/I kappa B beta 0.027 0.042 0.17 10 -10000 0 10
RasGAP/Csk 0.033 0.12 0.33 21 -0.36 69 90
mol:GDP 0.004 0.098 -10000 0 -0.33 47 47
PTEN 0.022 0.019 -10000 0 -0.57 1 1
CD79B 0.012 0.098 0.26 21 -0.57 27 48
NF-kappa-B/RelA/I kappa B alpha 0.028 0.042 0.17 10 -10000 0 10
GRB2 0.023 0.009 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.024 0.16 0.35 11 -0.49 53 64
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.003 0.1 -10000 0 -0.36 46 46
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.077 0.16 -10000 0 -0.43 82 82
CHUK 0.024 0.082 0.29 7 -0.3 19 26
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.018 0.095 -10000 0 -0.4 18 18
PTPN6 -0.012 0.12 0.25 22 -0.56 32 54
RELA 0.024 0.005 -10000 0 -10000 0 0
BCL2A1 0.025 0.035 0.19 6 -10000 0 6
VAV2 0.014 0.14 0.28 11 -0.58 31 42
ubiquitin-dependent protein catabolic process 0.025 0.047 0.17 10 -0.12 36 46
BTK 0.015 0.061 -10000 0 -0.97 4 4
CD19 0.006 0.14 0.27 35 -0.43 63 98
MAP4K1 0.033 0.054 0.26 48 -0.57 2 50
CD72 0.03 0.042 0.26 30 -0.57 1 31
PAG1 0.02 0.014 0.26 2 -10000 0 2
MAPK14 0.027 0.14 0.35 16 -0.44 44 60
SH3BP5 0.023 0.018 -10000 0 -0.57 1 1
PIK3AP1 0.004 0.11 0.23 1 -0.38 47 48
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.13 0.26 3 -0.42 75 78
RAF1 0.011 0.1 0.26 16 -0.41 19 35
RasGAP/p62DOK/SHIP 0.032 0.12 0.3 21 -0.35 69 90
CD79A -0.002 0.17 0.26 85 -0.57 81 166
re-entry into mitotic cell cycle -0.021 0.097 0.26 6 -0.25 47 53
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.097 0.27 27 -0.36 14 41
MAPK1 0.011 0.09 0.26 11 -0.36 17 28
CD72/SHP1 0.03 0.14 0.35 29 -0.54 31 60
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.025 0.14 0.33 19 -0.44 46 65
actin cytoskeleton organization 0.032 0.14 0.31 29 -0.5 30 59
NF-kappa-B/RelA 0.056 0.081 0.3 10 -0.21 1 11
Calcineurin 0.019 0.091 -10000 0 -0.39 16 16
PI3K -0.013 0.095 -10000 0 -0.44 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.006 0.11 -10000 0 -0.39 51 51
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.014 0.2 0.43 6 -0.7 51 57
DAPP1 -0.015 0.2 -10000 0 -0.79 51 51
cytokine secretion 0.032 0.13 0.26 53 -0.4 37 90
mol:DAG 0.003 0.1 -10000 0 -0.36 46 46
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
MAP2K1 0.011 0.097 0.27 11 -0.4 17 28
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.13 0.34 21 -0.41 70 91
mol:PI-3-4-5-P3 0.005 0.089 0.22 17 -0.32 25 42
ETS1 0.001 0.089 0.27 3 -0.39 19 22
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.13 0.33 22 -0.36 75 97
B-cell antigen/BCR complex/LYN -0.01 0.14 0.25 20 -0.45 67 87
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.14 0.31 25 -0.54 30 55
B-cell antigen/BCR complex/LYN/SYK 0.015 0.14 0.35 24 -0.44 58 82
CARD11 0.004 0.1 0.28 6 -0.44 21 27
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
PPP3CA 0.024 0.011 0.26 2 -10000 0 2
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 49 -0.14 4 53
PTPRC 0.021 0.041 0.26 12 -0.57 3 15
PDPK1 0.02 0.082 0.21 56 -0.23 20 76
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.009 -10000 0 -10000 0 0
POU2F2 0.021 0.033 0.21 6 -10000 0 6
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.016 0.16 0.3 3 -0.39 149 152
AKT1 0.025 0.01 -10000 0 -10000 0 0
GSC -0.03 0.27 -10000 0 -1.3 41 41
NKX2-5 0.001 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.026 0.065 0.32 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.068 0.065 -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 -0.099 0.19 0.26 1 -0.36 379 380
SMAD3/SMAD4/VDR 0.055 0.058 -10000 0 -0.34 1 1
MYC 0.005 0.084 -10000 0 -0.57 22 22
CDKN2B -0.042 0.17 -10000 0 -0.79 28 28
AP1 -0.05 0.16 -10000 0 -0.3 267 267
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.01 0.086 -10000 0 -0.36 32 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.013 0.057 -10000 0 -0.34 12 12
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.046 0.081 0.26 127 -10000 0 127
SMAD3/SMAD4/GR 0.024 0.072 -10000 0 -0.37 12 12
GATA3 0.013 0.11 0.26 28 -0.55 36 64
SKI/SIN3/HDAC complex/NCoR1 0.005 0.077 -10000 0 -0.35 34 34
MEF2C/TIF2 0.023 0.087 0.32 3 -0.31 21 24
endothelial cell migration -0.029 0.094 0.57 13 -10000 0 13
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.019 0.26 7 -10000 0 7
RBBP4 0.023 0.018 -10000 0 -0.57 1 1
RUNX2 0.027 0.028 0.26 15 -10000 0 15
RUNX3 0.022 0.043 0.26 5 -0.57 5 10
RUNX1 0.023 0.019 -10000 0 -0.57 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.014 0.061 -10000 0 -0.57 11 11
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.016 0.078 -10000 0 -1.1 3 3
KAT2B 0.024 0.019 -10000 0 -0.57 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.078 0.3 1 -0.26 22 23
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.094 -10000 0 -0.58 13 13
SMAD3/SMAD4/ATF2 0.033 0.061 -10000 0 -0.41 3 3
SMAD3/SMAD4/ATF3 -0.011 0.14 -10000 0 -0.39 113 113
SAP30 0.024 0.015 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.04 0.031 -10000 0 -10000 0 0
JUN -0.059 0.15 0.29 1 -0.3 265 266
SMAD3/SMAD4/IRF7 0.052 0.081 0.32 25 -10000 0 25
TFE3 0.028 0.009 -10000 0 -10000 0 0
COL1A2 0.045 0.094 0.39 4 -0.6 8 12
mesenchymal cell differentiation -0.035 0.058 -10000 0 -10000 0 0
DLX1 0.055 0.1 0.26 168 -0.57 9 177
TCF3 0.024 0.009 0.26 1 -10000 0 1
FOS -0.14 0.27 -10000 0 -0.57 307 307
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 0.034 0.055 -10000 0 -0.2 1 1
IRF7 0.048 0.072 0.27 102 -10000 0 102
ESR1 -0.04 0.23 0.25 116 -0.57 151 267
HNF4A 0.023 0.032 0.26 20 -10000 0 20
MEF2C 0.047 0.087 0.4 8 -0.44 3 11
SMAD2-3/SMAD4 0.034 0.065 -10000 0 -0.22 1 1
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.36 1 1
IGHV3OR16-13 0.006 0.039 -10000 0 -0.34 12 12
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.023 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.023 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 0.006 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.043 0.061 -10000 0 -0.45 1 1
MSG1/HSC70 -0.13 0.22 -10000 0 -0.42 400 400
SMAD2 0.022 0.03 -10000 0 -10000 0 0
SMAD3 0.015 0.04 -10000 0 -0.18 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.042 -10000 0 -0.32 3 3
SMAD2/SMAD2/SMAD4 0.026 0.058 0.25 9 -0.51 3 12
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
MYOD/E2A 0.032 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.064 -10000 0 -0.41 1 1
IFNB1 0.022 0.071 0.31 38 -10000 0 38
SMAD3/SMAD4/MEF2C 0.065 0.084 -10000 0 -0.42 3 3
CITED1 -0.19 0.29 0.26 15 -0.57 400 415
SMAD2-3/SMAD4/ARC105 0.042 0.066 -10000 0 -10000 0 0
RBL1 0.023 0.027 0.26 1 -0.57 2 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.017 0.065 -10000 0 -0.43 12 12
RUNX1-3/PEBPB2 0.04 0.039 -10000 0 -0.42 5 5
SMAD7 -0.032 0.14 -10000 0 -0.48 10 10
MYC/MIZ-1 0.015 0.065 -10000 0 -0.42 22 22
SMAD3/SMAD4 0.033 0.073 0.3 24 -0.37 3 27
IL10 0.007 0.08 0.3 5 -0.36 30 35
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 0.004 0.083 0.29 5 -0.35 35 40
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.041 0.18 0.26 1 -0.57 112 113
SMAD3/SMAD4/SP1 0.047 0.064 -10000 0 -0.37 2 2
FOXG1 0.017 0.068 0.26 74 -10000 0 74
FOXO3 0.011 0.017 -10000 0 -0.42 1 1
FOXO1 0.009 0.031 -10000 0 -0.42 5 5
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.047 0.086 0.4 8 -0.43 3 11
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.054 0.089 0.29 5 -0.39 9 14
MYOD1 0.021 0.027 0.26 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.033 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.029 0.099 0.35 1 -0.38 37 38
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.023 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.069 -10000 0 -0.4 4 4
SMAD3/SMAD4/SP1-3 0.062 0.063 -10000 0 -0.44 1 1
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.03 0.015 -10000 0 -0.2 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.056 0.074 0.28 1 -0.25 13 14
ITGB5 0.016 0.042 -10000 0 -0.4 1 1
TGIF/SIN3/HDAC complex/CtBP 0.013 0.062 -10000 0 -0.3 24 24
SMAD3/SMAD4/AR -0.019 0.15 -10000 0 -0.38 137 137
AR -0.053 0.2 0.26 1 -0.57 141 142
negative regulation of cell growth 0 0.083 -10000 0 -0.31 30 30
SMAD3/SMAD4/MYOD 0.032 0.057 -10000 0 -0.21 1 1
E2F5 0.022 0.021 0.26 7 -10000 0 7
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.073 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.054 -10000 0 -0.37 11 11
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.035 0.17 -10000 0 -0.3 266 266
SMAD3/SMAD4/RUNX2 0.035 0.058 -10000 0 -10000 0 0
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.022 0.031 -10000 0 -0.57 3 3
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.043 0.072 0.32 1 -0.3 27 28
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.082 0.36 9 -0.34 1 10
alphaV/beta3 Integrin/Osteopontin/Src 0.081 0.071 0.23 3 -10000 0 3
AP1 -0.036 0.18 -10000 0 -0.54 32 32
ILK 0.03 0.074 0.29 1 -0.32 27 28
bone resorption 0.019 0.088 -10000 0 -0.5 12 12
PTK2B 0.02 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.068 0.092 0.3 8 -0.3 21 29
ITGAV 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.022 0.075 -10000 0 -0.41 31 31
alphaV/beta3 Integrin/Osteopontin 0.077 0.1 0.36 3 -0.34 33 36
MAP3K1 0.029 0.077 0.26 14 -0.32 33 47
JUN 0.021 0.044 -10000 0 -0.57 6 6
MAPK3 0.02 0.069 0.27 10 -0.3 24 34
MAPK1 0.021 0.07 0.27 11 -0.3 22 33
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.016 0.082 0.26 15 -0.37 28 43
ITGB3 0.009 0.1 0.26 4 -0.56 33 37
NFKBIA 0.018 0.068 0.32 4 -0.34 4 8
FOS -0.14 0.27 -10000 0 -0.57 306 306
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.022 0.098 0.45 6 -0.55 2 8
NF kappa B1 p50/RelA 0.063 0.076 0.37 5 -10000 0 5
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.026 0.08 -10000 0 -0.41 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.03 0.075 0.25 14 -0.32 33 47
VAV3 0.017 0.075 0.26 16 -0.3 31 47
MAP3K14 0.031 0.075 0.26 9 -0.32 28 37
ROCK2 0.007 0.099 -10000 0 -0.57 31 31
SPP1 0.086 0.1 0.26 279 -10000 0 279
RAC1 0.024 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.069 0.3 3 -0.28 29 32
MMP2 -0.054 0.14 0.34 2 -0.51 31 33
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.02 -10000 0 -0.57 1 1
ELF1 0.03 0.054 -10000 0 -0.36 12 12
CCNA2 0.11 0.11 0.26 401 -10000 0 401
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.027 0.027 0.26 14 -10000 0 14
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.046 0.1 0.3 18 -0.49 13 31
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.024 0.045 -10000 0 -0.38 12 12
IL2RA 0.02 0.12 0.43 11 -0.76 15 26
IL2RB 0.031 0.05 0.26 38 -0.57 2 40
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.067 0.26 46 -0.57 7 53
G1/S transition of mitotic cell cycle 0.042 0.14 0.35 3 -0.8 17 20
PTPN11 0.025 0.003 -10000 0 -10000 0 0
CCND2 0.006 0.087 0.43 1 -0.8 12 13
LCK 0.027 0.075 0.26 40 -0.57 11 51
GRB2 0.023 0.009 0.26 1 -10000 0 1
IL2 0.022 0.021 0.26 8 -10000 0 8
CDK6 0.019 0.058 0.26 2 -0.57 10 12
CCND3 0.047 0.1 0.42 6 -0.57 5 11
TCGA08_p53

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.025 0.046 0.13 170 -10000 0 170
TP53 0.009 0.018 -10000 0 -0.19 2 2
Senescence 0.008 0.022 -10000 0 -0.19 2 2
Apoptosis 0.008 0.022 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.011 0.06 0.29 31 -10000 0 31
MDM4 0.02 0.009 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.088 -10000 0 -0.63 9 9
oxygen homeostasis 0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.087 0.088 0.36 9 -0.43 1 10
EPO 0.15 0.17 0.51 76 -0.49 4 80
FIH (dimer) 0.032 0.02 -10000 0 -10000 0 0
APEX1 0.033 0.025 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.48 47 -0.52 6 53
FLT1 -0.018 0.17 -10000 0 -0.71 34 34
ADORA2A 0.16 0.17 0.47 88 -0.5 5 93
germ cell development 0.14 0.16 0.48 46 -0.5 5 51
SLC11A2 0.14 0.16 0.47 38 -0.54 4 42
BHLHE40 0.13 0.16 0.47 36 -0.55 5 41
HIF1AN 0.032 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.13 0.41 48 -0.38 3 51
ETS1 0.026 0.039 -10000 0 -0.58 4 4
CITED2 0.015 0.09 -10000 0 -0.66 7 7
KDR -0.018 0.18 -10000 0 -0.7 40 40
PGK1 0.14 0.16 0.47 43 -0.52 5 48
SIRT1 0.025 0.004 -10000 0 -10000 0 0
response to hypoxia 0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.58 20 -0.55 8 28
EPAS1 0.068 0.088 0.29 48 -0.37 6 54
SP1 0.029 0.012 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.48 35 -0.55 42 77
EFNA1 0.11 0.14 0.49 10 -0.53 3 13
FXN 0.15 0.16 0.46 52 -0.52 4 56
POU5F1 0.14 0.16 0.49 44 -0.52 5 49
neuron apoptosis -0.15 0.18 0.53 8 -0.58 20 28
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.047 0.067 0.27 77 -0.58 1 78
EGLN2 0.033 0.026 0.27 5 -10000 0 5
EGLN1 0.027 0.028 -10000 0 -0.58 1 1
VHL/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.028 0.024 -10000 0 -10000 0 0
SLC2A1 0.14 0.16 0.46 58 -0.49 6 64
TWIST1 0.13 0.19 0.46 50 -0.55 39 89
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.41 10 -0.38 3 13
VEGFA 0.13 0.16 0.48 36 -0.54 4 40
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.02 0.3 1 -10000 0 1
CDKN1B 0.011 0.056 -10000 0 -0.34 15 15
CDKN1A 0.01 0.061 -10000 0 -0.34 19 19
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -0.34 13 13
AKT1 0.006 0.056 -10000 0 -0.33 25 25
BAD 0.024 0.009 0.26 1 -10000 0 1
AKT3 0.006 0.035 -10000 0 -0.35 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.009 0.059 0.21 1 -0.34 19 20
AKT1/ASK1 0.031 0.067 -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 0.065 0.31 21 -10000 0 21
TSC1 0.011 0.051 -10000 0 -0.34 13 13
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.036 0.07 0.27 1 -0.34 18 19
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.01 0.059 -10000 0 -0.32 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.054 0.32 1 -0.33 17 18
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.004 0.015 -10000 0 -0.34 2 2
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAPKAP1 0.024 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.075 0.29 23 -0.21 12 35
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.06 -10000 0 -0.35 17 17
CASP9 0.011 0.045 -10000 0 -0.32 11 11
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.072 0.32 5 -0.34 14 19
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 0.023 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.058 0.25 2 -0.37 10 12
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.051 -10000 0 -0.32 21 21
CHUK 0.01 0.055 -10000 0 -0.33 17 17
BAD/BCL-XL 0.038 0.066 0.28 3 -0.34 13 16
mTORC2 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.032 0.097 0.29 10 -0.39 24 34
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.012 0.064 0.27 2 -0.34 19 21
MAPKKK cascade -0.036 0.069 0.34 18 -0.25 3 21
MDM2/Cbp/p300 0.042 0.072 0.31 7 -0.34 14 21
TSC1/TSC2 0.014 0.068 0.26 37 -0.36 13 50
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.069 0.29 8 -0.32 14 22
glucose import -0.16 0.15 0.21 2 -0.31 521 523
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.048 0.18 3 -0.41 4 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 -10000 0 -0.31 521 521
GSK3A 0.01 0.059 -10000 0 -0.35 17 17
FOXO1 0.012 0.04 -10000 0 -0.28 9 9
GSK3B 0.01 0.059 -10000 0 -0.35 18 18
SFN 0.021 0.07 0.26 21 -0.57 12 33
G1/S transition of mitotic cell cycle 0.014 0.065 0.27 7 -0.35 16 23
p27Kip1/14-3-3 family 0.021 0.049 0.31 2 -0.39 4 6
PRKACA 0.024 0.004 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Caspase cascade in apoptosis

Figure 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 44 46
ACTA1 0.012 0.11 0.26 6 -0.48 31 37
NUMA1 0.004 0.11 0.26 2 -0.39 48 50
SPTAN1 -0.002 0.11 0.27 7 -0.48 32 39
LIMK1 -0.001 0.11 0.26 6 -0.48 32 38
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.014 0.26 4 -10000 0 4
CASP10 -0.011 0.09 0.2 11 -0.44 33 44
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.003 0.12 0.26 2 -0.44 45 47
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.002 0.1 0.27 7 -0.47 32 39
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.006 0.12 0.28 4 -0.47 40 44
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.013 0.13 -10000 0 -0.64 33 33
BID 0.003 0.053 0.18 3 -0.26 32 35
MAP3K1 -0.003 0.093 -10000 0 -0.4 47 47
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 0.001 0.11 0.26 7 -0.48 31 38
CASP9 0.023 0.005 -10000 0 -10000 0 0
DNA repair -0.016 0.043 0.25 4 -0.21 4 8
neuron apoptosis 0.004 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 0.15 -10000 0 -0.91 25 25
TRAF2 0.025 0.015 0.26 4 -10000 0 4
ICAD/CAD -0.004 0.1 0.24 2 -0.48 30 32
CASP7 0.002 0.06 0.28 2 -0.39 4 6
KRT18 0.015 0.079 -10000 0 -0.72 9 9
apoptosis 0.002 0.12 0.3 5 -0.45 45 50
DFFA -0.003 0.1 0.25 3 -0.48 32 35
DFFB -0.003 0.1 0.25 3 -0.48 32 35
PARP1 0.016 0.043 0.21 4 -0.25 4 8
actin filament polymerization 0.001 0.1 0.45 33 -0.29 9 42
TNF 0.024 0.065 0.26 25 -0.57 9 34
CYCS 0.005 0.048 0.2 8 -0.22 23 31
SATB1 -0.008 0.15 -10000 0 -0.78 31 31
SLK -0.002 0.1 0.28 4 -0.49 31 35
p15 BID/BAX 0.013 0.062 0.24 2 -0.24 36 38
CASP2 0.003 0.063 0.29 2 -0.38 6 8
JNK cascade 0.003 0.093 0.39 47 -10000 0 47
CASP3 0 0.11 0.26 4 -0.5 33 37
LMNB2 0.001 0.13 0.33 2 -0.52 41 43
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.032 -10000 0 -0.33 2 2
negative regulation of DNA binding 0.014 0.13 -10000 0 -0.63 33 33
stress fiber formation -0.002 0.1 0.28 4 -0.48 31 35
GZMB 0.011 0.1 0.27 11 -0.49 32 43
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.02 0.12 0.3 7 -0.51 28 35
APP 0.004 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 -0.44 49 54
LMNA 0.008 0.08 0.32 2 -0.37 23 25
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.066 -10000 0 -0.3 20 20
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.001 0.1 0.27 4 -0.48 32 36
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.61 38 38
nuclear fragmentation during apoptosis 0.004 0.1 0.26 2 -0.38 48 50
CFL2 -0.001 0.11 0.3 8 -0.46 34 42
GAS2 -0.025 0.14 0.27 6 -0.38 95 101
positive regulation of apoptosis 0.014 0.11 0.27 8 -0.49 31 39
PRF1 0.016 0.077 0.26 8 -0.57 17 25
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0.004 0.059 -10000 0 -0.38 5 5
BAG4 0.018 0.032 -10000 0 -0.57 3 3
PKC zeta/ceramide -0.001 0.052 -10000 0 -0.25 16 16
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BAX 0.001 0.041 -10000 0 -0.35 11 11
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.068 0.7 10 -10000 0 10
BAD -0.015 0.046 0.19 4 -0.24 15 19
SMPD1 0.014 0.056 0.23 7 -0.24 17 24
RB1 -0.015 0.044 -10000 0 -0.26 11 11
FADD/Caspase 8 0.026 0.085 0.28 5 -0.36 9 14
MAP2K4 -0.016 0.044 0.2 1 -0.3 8 9
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.056 0.19 33 -0.3 7 40
EGF -0.082 0.23 0.26 2 -0.57 194 196
mol:ceramide -0.014 0.048 0.14 1 -0.25 15 16
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.009 -10000 0 -10000 0 0
ASAH1 0.021 0.015 0.26 3 -10000 0 3
negative regulation of cell cycle -0.016 0.044 -10000 0 -0.26 11 11
cell proliferation -0.044 0.12 0.27 1 -0.27 204 205
BID -0.02 0.17 -10000 0 -0.66 60 60
MAP3K1 -0.015 0.047 0.2 3 -0.24 16 19
EIF2A -0.014 0.049 0.29 3 -0.25 6 9
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.006 0.054 0.25 4 -0.3 6 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.059 0.26 4 -0.31 6 10
Cathepsin D/ceramide 0.004 0.057 0.17 31 -0.24 14 45
FADD 0.006 0.059 0.26 3 -0.39 4 7
KSR1 -0.009 0.055 0.2 24 -0.25 13 37
MAPK8 -0.014 0.058 -10000 0 -0.28 19 19
PRKRA -0.015 0.047 0.2 4 -0.27 11 15
PDGFA 0.024 0.008 0.26 1 -10000 0 1
TRAF2 0.025 0.015 0.26 4 -10000 0 4
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.047 0.14 1 -0.25 15 16
CTSD 0.031 0.041 0.26 34 -10000 0 34
regulation of nitric oxide biosynthetic process 0.034 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.047 0.13 0.29 1 -0.29 203 204
PRKCD 0.024 0.009 0.26 1 -10000 0 1
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.034 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.018 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.044 -10000 0 -0.35 5 5
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 11 11
mol:Sphingosine-1-phosphate 0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.009 0.055 0.24 5 -0.3 6 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
CYCS 0 0.049 0.18 19 -0.22 13 32
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.42 3 3
EIF2AK2 -0.016 0.043 0.19 3 -0.28 7 10
TNF-alpha/TNFR1A/FAN 0.04 0.044 -10000 0 -0.36 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.078 -10000 0 -0.37 31 31
MAP2K2 -0.01 0.055 0.23 6 -0.29 7 13
SMPD3 -0.002 0.098 0.26 4 -0.29 95 99
TNF 0.024 0.065 0.26 25 -0.57 9 34
PKC zeta/PAR4 0.033 0.021 -10000 0 -0.42 2 2
mol:PHOSPHOCHOLINE 0.042 0.097 0.24 195 -0.24 2 197
NF kappa B1/RelA/I kappa B alpha 0.063 0.03 -10000 0 -0.31 2 2
AIFM1 -0.001 0.049 0.18 20 -0.22 12 32
BCL2 0.008 0.094 -10000 0 -0.57 28 28
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.09 0.29 47 -10000 0 47
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 -10000 0 -0.28 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
RhoA/GTP -0.003 0.091 -10000 0 -0.29 47 47
negative regulation of cAMP metabolic process -0.004 0.088 -10000 0 -0.27 88 88
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.27 88 88
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
CDC42/GTP -0.005 0.096 -10000 0 -0.3 52 52
PLCG1 -0.012 0.087 -10000 0 -0.31 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
cell migration -0.005 0.094 -10000 0 -0.3 52 52
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
S1PR4 0.029 0.062 0.26 38 -0.57 6 44
MAPK3 -0.008 0.082 0.26 1 -0.31 41 42
MAPK1 -0.008 0.084 -10000 0 -0.32 45 45
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.27 88 88
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 -10000 0 -0.28 3 3
RHOA 0.006 0.058 0.24 1 -0.31 6 7
S1P/S1P4/Gi -0.004 0.094 -10000 0 -0.28 92 92
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
S1P/S1P4/G12/G13 0.044 0.041 -10000 0 -0.33 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.022 0.077 -10000 0 -0.51 7 7
UGCG 0.009 0.12 -10000 0 -0.67 30 30
AKT1/mTOR/p70S6K/Hsp90/TERT 0.048 0.12 0.3 10 -0.42 26 36
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.12 -10000 0 -0.66 30 30
mol:DAG 0.004 0.085 -10000 0 -0.76 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.13 0.3 6 -0.41 54 60
FRAP1 0.031 0.15 0.33 6 -0.46 58 64
FOXO3 0.036 0.14 0.33 12 -0.49 34 46
AKT1 0.037 0.14 0.31 12 -0.51 38 50
GAB2 0.021 0.02 -10000 0 -0.57 1 1
SMPD1 0.01 0.11 -10000 0 -0.64 25 25
SGMS1 0.018 0.065 -10000 0 -0.54 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.039 -10000 0 -0.33 14 14
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.046 0.11 0.32 4 -0.48 22 26
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.05 -10000 0 -0.39 14 14
RPS6KB1 0.012 0.091 -10000 0 -0.84 10 10
mol:sphingomyelin 0.004 0.085 -10000 0 -0.76 12 12
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.027 0.027 0.26 14 -10000 0 14
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.065 0.2 0.39 14 -0.86 31 45
MYB 0.028 0.19 0.48 2 -1.1 24 26
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.036 0.11 0.29 18 -0.43 23 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.088 -10000 0 -0.75 10 10
mol:PI-3-4-5-P3 0.04 0.11 0.29 17 -0.42 23 40
Rac1/GDP 0.014 0.039 -10000 0 -0.33 12 12
T cell proliferation 0.04 0.1 0.29 12 -0.49 12 24
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.013 0.1 3 -0.076 23 26
PRKCZ 0.04 0.1 0.3 10 -0.51 12 22
NF kappa B1 p50/RelA 0.047 0.14 0.32 6 -0.42 51 57
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.075 0.29 11 -0.52 8 19
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
IL2RA 0.027 0.088 0.26 58 -0.57 15 73
IL2RB 0.031 0.051 0.26 38 -0.57 2 40
TERT 0.054 0.08 0.26 147 -10000 0 147
E2F1 0.051 0.094 0.34 2 -0.36 30 32
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.033 23 -0.05 3 26
PTPN11 0.023 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.26 46 -0.57 7 53
actin cytoskeleton organization 0.04 0.1 0.29 12 -0.49 12 24
GRB2 0.023 0.011 0.26 1 -10000 0 1
IL2 0.021 0.023 0.26 8 -10000 0 8
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.043 -10000 0 -0.31 12 12
LCK 0.027 0.075 0.26 40 -0.57 11 51
BCL2 0.018 0.19 0.42 2 -0.79 44 46
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.062 -10000 0 -0.39 20 20
forebrain development -0.042 0.2 0.35 1 -0.52 128 129
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
SMO/beta Arrestin2 0.027 0.045 -10000 0 -0.42 9 9
SMO 0.017 0.055 -10000 0 -0.57 9 9
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.024 0.081 0.32 2 -0.49 11 13
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 0.022 -10000 0 -10000 0 0
GNAI1 -0.008 0.13 -10000 0 -0.57 57 57
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.19 -10000 0 -0.61 68 68
SAP30 0.024 0.015 0.26 4 -10000 0 4
mol:GDP 0.017 0.055 -10000 0 -0.57 9 9
MIM/GLI2A 0.021 0.02 0.26 2 -10000 0 2
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.022 0.009 -10000 0 -10000 0 0
GLI2 0.01 0.066 -10000 0 -0.3 23 23
GLI3 0.013 0.084 0.34 2 -0.44 16 18
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 0.017 0.065 -10000 0 -0.57 13 13
Gi family/GTP -0.009 0.098 -10000 0 -0.33 62 62
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.017 0.086 -10000 0 -0.46 19 19
GLI2/Su(fu) 0.013 0.081 -10000 0 -0.39 20 20
FOXA2 0.008 0.1 -10000 0 -0.73 12 12
neural tube patterning -0.042 0.2 0.35 1 -0.52 128 129
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.043 -10000 0 -0.37 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.021 0.02 0.26 2 -10000 0 2
embryonic limb morphogenesis -0.042 0.2 0.35 1 -0.52 128 129
SUFU 0.015 0.027 -10000 0 -0.4 1 1
LGALS3 0.016 0.067 -10000 0 -0.57 14 14
catabolic process 0.026 0.1 0.32 2 -0.5 20 22
GLI3A/CBP 0.003 0.089 -10000 0 -0.36 59 59
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.044 0.21 0.35 1 -0.54 126 127
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
IFT172 0.024 0.018 -10000 0 -0.57 1 1
RBBP7 0.026 0.019 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.061 -10000 0 -0.38 15 15
GNAZ 0.016 0.057 -10000 0 -0.57 10 10
RBBP4 0.023 0.019 -10000 0 -0.57 1 1
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.018 0.07 -10000 0 -0.33 20 20
STK36 0.021 0.023 -10000 0 -0.57 1 1
Gi family/GNB1/GNG2/GDP -0.015 0.11 -10000 0 -0.4 51 51
PTCH1 -0.087 0.32 -10000 0 -1.1 89 89
MIM/GLI1 -0.03 0.19 -10000 0 -0.63 63 63
CREBBP 0.003 0.089 -10000 0 -0.36 59 59
Su(fu)/SIN3/HDAC complex 0.007 0.09 -10000 0 -0.41 35 35
BARD1 signaling events

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
BARD1/CSTF1 0.026 0.057 -10000 0 -0.39 18 18
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.015 -10000 0 -10000 0 0
protein ubiquitination 0.065 0.071 0.3 2 -0.3 18 20
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.022 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.015 0.086 -10000 0 -0.47 14 14
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
CCNE1 0.062 0.087 0.26 179 -10000 0 179
CDK2/Cyclin E1 0.06 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.06 -10000 0 -0.41 19 19
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
FANCA 0.059 0.088 0.26 178 -10000 0 178
DNA repair 0.027 0.085 0.3 4 -0.37 7 11
BRCA1/BARD1/ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BARD1/DNA-PK 0.045 0.052 -10000 0 -0.33 15 15
FANCL 0.024 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.056 0.39 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.07 -10000 0 -0.27 22 22
BRCA1/BACH1/BARD1/TopBP1 0.039 0.055 -10000 0 -0.36 18 18
BRCA1/BARD1/P53 0.048 0.054 -10000 0 -0.33 18 18
BARD1/CSTF1/BRCA1 0.037 0.053 -10000 0 -0.36 16 16
BRCA1/BACH1 0.023 0.02 0.26 1 -0.56 1 2
BARD1 0.014 0.076 0.26 1 -0.57 18 19
PCNA 0.024 0.011 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.04 0.053 -10000 0 -0.36 17 17
BRCA1/BARD1/UbcH7 0.038 0.054 -10000 0 -0.36 17 17
BRCA1/BARD1/RAD51/PCNA 0.091 0.088 0.31 2 -0.31 17 19
BARD1/DNA-PK/P53 0.05 0.054 -10000 0 -0.31 15 15
BRCA1/BARD1/Ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BRCA1/BARD1/CTIP 0.028 0.05 -10000 0 -0.33 18 18
FA complex 0.035 0.037 0.25 2 -0.26 1 3
BARD1/EWS 0.026 0.059 -10000 0 -0.42 18 18
RBBP8 0.01 0.005 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.053 0.33 18 -10000 0 18
BRCA1/BARD1 0.071 0.075 0.33 2 -0.3 18 20
CSTF1 0.023 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.056 0.18 1 -0.42 18 19
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.1 0.11 0.26 373 -10000 0 373
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.06 -10000 0 -0.41 19 19
EWSR1 0.023 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure 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
ANTXR1 0.022 0.037 0.26 1 -0.57 4 5
ANTXR2 0.018 0.06 -10000 0 -0.57 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.009 -10000 0 -0.078 14 14
monocyte activation 0.003 0.085 0.25 2 -0.35 55 57
MAP2K2 0.003 0.082 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.008 -10000 0 -0.11 2 2
MAP2K7 -0.004 0.009 0.12 1 -0.11 2 3
MAP2K6 -0.01 0.044 0.085 1 -0.3 24 25
CYAA -0.009 0.039 -10000 0 -0.35 13 13
MAP2K4 -0.004 0.008 -10000 0 -10000 0 0
IL1B -0.008 0.045 0.22 2 -0.28 25 27
Channel 0.025 0.046 -10000 0 -0.37 13 13
NLRP1 -0.007 0.033 -10000 0 -0.32 11 11
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.066 -10000 0 -0.39 29 29
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.009 0.078 14 -10000 0 14
MAPK3 -0.004 0.008 0.085 1 -0.11 1 2
MAPK1 -0.004 0.009 0.12 2 -0.11 2 4
PGR -0.079 0.14 0.2 2 -0.31 280 282
PA/Cellular Receptors 0.027 0.05 -10000 0 -0.4 13 13
apoptosis -0.002 0.009 -10000 0 -0.078 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.044 -10000 0 -0.35 13 13
macrophage activation -0.005 0.01 0.12 3 -10000 0 3
TNF 0.024 0.065 0.26 25 -0.57 9 34
VCAM1 0.003 0.085 0.25 2 -0.35 55 57
platelet activation -0.001 0.066 -10000 0 -0.39 29 29
MAPKKK cascade -0.002 0.026 0.12 3 -0.14 5 8
IL18 -0.003 0.026 -10000 0 -0.22 10 10
negative regulation of macrophage activation -0.002 0.009 -10000 0 -0.078 14 14
LEF -0.002 0.009 -10000 0 -0.079 14 14
CASP1 -0.003 0.027 -10000 0 -0.17 20 20
mol:cAMP -0.001 0.067 -10000 0 -0.39 29 29
necrosis -0.002 0.009 -10000 0 -0.078 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.044 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.065 0.16 1 -0.29 51 52
FRAP1 -0.001 0.082 0.4 1 -0.45 25 26
AKT1 -0.011 0.065 0.18 2 -0.28 38 40
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0.023 0.07 0.23 5 -0.26 15 20
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.21 4 4
TSC2 0.023 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.005 0.048 -10000 0 -0.25 14 14
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.077 -10000 0 -0.31 58 58
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.015 0.046 -10000 0 -0.23 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.012 0.075 0.26 7 -0.31 21 28
MAP3K5 -0.001 0.046 0.2 10 -0.19 46 56
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
apoptosis -0.001 0.046 0.2 10 -0.19 47 57
mol:LY294002 0 0 -10000 0 -0.001 52 52
EIF4B 0.011 0.069 0.3 4 -0.3 13 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.066 0.23 1 -0.28 12 13
eIF4E/eIF4G1/eIF4A1 0.004 0.049 -10000 0 -0.28 22 22
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.081 -10000 0 -0.3 60 60
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.055 0.22 17 -0.19 3 20
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.027 0.061 -10000 0 -0.24 14 14
mol:Amino Acids 0 0 -10000 0 -0.001 52 52
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.06 0.17 5 -0.28 44 49
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.52 65 65
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.048 -10000 0 -0.24 7 7
TSC1/TSC2 0.026 0.075 0.25 6 -0.28 15 21
tumor necrosis factor receptor activity 0 0 0.001 52 -10000 0 52
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.011 0.079 -10000 0 -0.33 60 60
INS 0.016 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.56 1 1
PDK2 -0.018 0.059 0.18 8 -0.28 38 46
EIF4EBP1 -0.022 0.22 -10000 0 -1 46 46
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D 0.001 0.078 0.36 3 -0.42 23 26
peptide biosynthetic process -0.01 0.018 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 26 -0.003 3 29
EEF2 -0.01 0.018 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.011 0.21 -10000 0 -0.97 46 46
JNK signaling in the CD4+ TCR pathway

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.056 0.07 0.38 14 -0.38 11 25
MAP4K1 0.033 0.054 0.26 48 -0.57 2 50
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
PRKCB 0.019 0.076 0.26 19 -0.57 15 34
DBNL 0.024 0.003 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.015 0.054 0.25 1 -0.31 16 17
JUN 0.002 0.13 -10000 0 -0.6 42 42
MAP3K7 0.015 0.052 0.23 2 -0.29 14 16
GRAP2 0.017 0.063 0.26 3 -0.57 12 15
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.013 0.066 0.24 1 -0.38 13 14
LAT 0.025 0.038 0.26 15 -0.57 2 17
LCP2 0.024 0.008 0.26 1 -10000 0 1
MAPK8 0.006 0.14 -10000 0 -0.63 42 42
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.022 0.058 0.25 3 -0.31 17 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.064 0.07 0.37 14 -0.37 11 25
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.014 0.096 -10000 0 -0.29 96 96
GNAO1 0.018 0.09 0.26 32 -0.57 20 52
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.091 -10000 0 -0.47 29 29
AKT3 -0.014 0.17 -10000 0 -1.1 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.56 4 4
GNAI2 0.023 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.1 -10000 0 -0.35 56 56
MAPK3 -0.009 0.091 0.27 2 -0.38 33 35
MAPK1 -0.008 0.092 0.27 1 -0.4 31 32
JAK2 -0.01 0.1 -10000 0 -0.39 41 41
CXCR4 -0.011 0.096 -10000 0 -0.4 32 32
FLT1 0.023 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.011 0.094 -10000 0 -0.4 30 30
S1P/S1P3/Gi -0.004 0.1 -10000 0 -0.35 56 56
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.1 -10000 0 -0.38 33 33
VEGFA 0.025 0.021 0.26 6 -10000 0 6
S1P/S1P2/Gi -0.005 0.093 -10000 0 -0.28 92 92
VEGFR1 homodimer/VEGFA homodimer 0.035 0.022 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.019 0.042 -10000 0 -0.28 18 18
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
GNAZ 0.017 0.057 -10000 0 -0.57 10 10
G12/G13 0.033 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
Rac1/GTP -0.004 0.1 -10000 0 -0.39 33 33
FoxO family signaling

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
G6PC 0.012 0.06 -10000 0 -10000 0 0
PLK1 0.24 0.18 0.57 59 -0.57 1 60
CDKN1B 0.15 0.13 0.4 41 -0.45 5 46
FOXO3 0.2 0.16 0.45 173 -0.55 2 175
KAT2B 0.055 0.033 -10000 0 -0.57 1 1
FOXO1/SIRT1 0.012 0.055 -10000 0 -0.28 7 7
CAT 0.18 0.17 0.61 14 -1 5 19
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.056 0.028 -10000 0 -10000 0 0
FOXO1 0.017 0.062 -10000 0 -0.3 9 9
MAPK10 -0.016 0.12 0.2 12 -0.29 156 168
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.034 0.084 0.38 3 -0.42 2 5
response to oxidative stress 0.034 0.026 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.17 0.13 0.44 39 -0.5 3 42
XPO1 0.024 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.062 0.084 -10000 0 -0.69 10 10
FOXO1/SKP2 0.026 0.058 -10000 0 -0.3 5 5
mol:GDP 0.034 0.026 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.13 0.13 0.45 3 -0.54 10 13
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.022 0.12 -10000 0 -0.5 36 36
MST1 0.052 0.059 0.27 8 -0.51 8 16
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 -0.45 47 47
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.037 0.2 14 -0.3 8 22
MAPK9 0.031 0.024 0.2 15 -10000 0 15
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
SIRT1 0.012 0.02 -10000 0 -10000 0 0
SOD2 0.15 0.13 0.46 16 -0.42 3 19
RBL2 0.1 0.25 0.54 2 -0.62 73 75
RAL/GDP 0.056 0.021 -10000 0 -10000 0 0
CHUK 0.055 0.028 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.057 0.021 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.055 0.18 -10000 0 -1.3 16 16
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.006 -10000 0 -10000 0 0
IKBKB 0.047 0.032 -10000 0 -10000 0 0
CCNB1 0.2 0.17 0.55 53 -0.57 1 54
FOXO1-3a-4/beta catenin 0.15 0.12 0.41 45 -0.39 6 51
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.058 -10000 0 -0.29 5 5
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
SGK1 0.051 0.05 -10000 0 -0.55 5 5
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.032 0.075 0.44 1 -10000 0 1
SFN 0.021 0.07 0.26 21 -0.57 12 33
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.062 0.11 0.28 4 -0.39 21 25
CREBBP 0.022 0.008 -10000 0 -10000 0 0
FBXO32 0.23 0.2 0.62 97 -1.2 3 100
BCL6 0.16 0.16 0.52 3 -0.87 10 13
RALB 0.025 0.003 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.021 -10000 0 -0.36 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.062 -10000 0 -0.35 16 16
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
MAPK14 0.024 0.003 -10000 0 -10000 0 0
AKT1 0.006 0.067 0.2 6 -0.37 17 23
RAR alpha/9cRA/Cyclin H 0.046 0.074 -10000 0 -0.34 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.066 -10000 0 -0.4 14 14
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 0.064 -10000 0 -0.42 12 12
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.009 0.11 -10000 0 -0.52 26 26
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARG 0.025 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.02 0.051 -10000 0 -0.57 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.1 -10000 0 -0.47 25 25
RARA 0.013 0.055 0.18 25 -0.27 28 53
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.079 -10000 0 -0.38 22 22
PRKCA 0.012 0.084 0.26 1 -0.57 22 23
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.12 0.45 1 -0.52 27 28
RXRG -0.051 0.15 0.24 13 -0.35 204 217
RXRA 0.022 0.064 0.2 11 -0.26 28 39
RXRB 0.016 0.061 0.22 17 -0.34 22 39
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.036 0.076 0.26 73 -0.57 7 80
CRBP1/9-cic-RA 0.026 0.053 0.18 73 -0.42 7 80
RARB 0.017 0.067 -10000 0 -0.57 14 14
PRKCG 0.032 0.045 0.26 41 -10000 0 41
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.5 30 30
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.008 0.1 0.25 2 -0.43 30 32
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.079 0.24 12 -0.36 18 30
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.12 0.45 1 -0.52 27 28
positive regulation of DNA binding 0.032 0.064 -10000 0 -0.32 19 19
NRIP1 0.012 0.12 0.54 1 -0.74 10 11
RXRs/RARs 0.01 0.12 0.28 1 -0.5 31 32
RXRs/RXRs/DNA/9cRA -0.013 0.091 -10000 0 -0.48 25 25
PRKACA 0.024 0.004 -10000 0 -10000 0 0
CDK7 0.023 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.051 0.056 -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 0.044 0.015 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.001 0.098 0.26 2 -0.43 26 28
BAG4 0.018 0.032 -10000 0 -0.57 3 3
BAD 0.005 0.038 0.2 4 -0.17 8 12
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BAX 0.005 0.042 0.22 6 -0.18 6 12
EnzymeConsortium:3.1.4.12 0.002 0.026 0.085 4 -0.094 24 28
IKBKB 0.017 0.1 0.34 3 -0.42 19 22
MAP2K2 0.008 0.051 0.21 17 -0.24 2 19
MAP2K1 0.009 0.053 0.23 15 -0.24 2 17
SMPD1 0.002 0.032 0.2 1 -0.16 13 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.11 0.3 12 -0.44 22 34
MAP2K4 0.006 0.034 0.19 4 -0.22 3 7
protein ubiquitination 0.004 0.1 0.34 4 -0.41 24 28
EnzymeConsortium:2.7.1.37 0.008 0.054 0.23 14 -0.25 2 16
response to UV 0 0.001 0.002 21 -0.002 2 23
RAF1 0.009 0.052 0.19 41 -0.22 4 45
CRADD 0.024 0.004 -10000 0 -10000 0 0
mol:ceramide 0.006 0.04 0.14 5 -0.15 20 25
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.009 -10000 0 -10000 0 0
MADD 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.039 0.18 4 -0.19 7 11
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.023 0.005 -10000 0 -10000 0 0
MAPK3 0.01 0.052 0.22 14 -0.22 3 17
MAPK1 0.007 0.059 0.22 14 -0.23 8 22
p50/RELA/I-kappa-B-alpha 0.034 0.01 -10000 0 -10000 0 0
FADD 0.024 0.11 0.28 12 -0.44 20 32
KSR1 0.009 0.05 0.18 36 -0.2 7 43
MAPK8 0.002 0.048 0.24 8 -0.28 8 16
TRAF2 0.025 0.015 0.26 4 -10000 0 4
response to radiation 0 0 0.002 10 -10000 0 10
CHUK -0.001 0.093 -10000 0 -0.41 24 24
TNF R/SODD 0.027 0.029 -10000 0 -0.42 3 3
TNF 0.025 0.065 0.26 25 -0.57 9 34
CYCS 0.008 0.045 0.18 14 -0.18 5 19
IKBKG -0.001 0.095 0.43 1 -0.42 23 24
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.002 0.1 -10000 0 -0.44 27 27
RELA 0.023 0.005 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.007 0.044 0.17 13 -0.2 4 17
TNF/TNF R/SODD 0.036 0.051 -10000 0 -0.36 11 11
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 10 -10000 0 10
CASP8 0.003 0.13 -10000 0 -0.62 42 42
NSMAF 0.017 0.11 0.26 11 -0.41 25 36
response to hydrogen peroxide 0 0.001 0.002 21 -0.002 2 23
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.011 0.23 2 -10000 0 2
SNTA1 0.024 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.034 0.3 8 -10000 0 8
MAPK12 -0.009 0.048 0.21 1 -0.33 22 23
CCND1 0.01 0.047 -10000 0 -0.38 7 7
p38 gamma/SNTA1 0.021 0.07 0.32 2 -0.32 22 24
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint -0.009 0.048 0.21 1 -0.33 22 23
MAP2K6 -0.006 0.051 -10000 0 -0.35 23 23
MAPT -0.026 0.12 0.25 15 -0.32 124 139
MAPK13 0.011 0.011 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.006 0.001 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.27 0.29 -10000 0 -0.57 524 524
CLTC 0.025 0.067 0.28 1 -0.42 13 14
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 0.049 -10000 0 -0.36 19 19
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.019 -10000 0 -10000 0 0
CTNND1 0.008 0.056 0.19 91 -10000 0 91
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.043 0.21 3 -0.33 7 10
TSHR -0.003 0.072 -10000 0 -0.36 42 42
INS -0.001 0.088 -10000 0 -0.48 34 34
BIN1 0.02 0.051 -10000 0 -0.57 8 8
mol:Choline 0.011 0.019 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.017 0.14 17 -10000 0 17
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.013 -10000 0 -10000 0 0
JUP 0.017 0.039 0.23 1 -0.33 7 8
ASAP2/amphiphysin II 0.042 0.033 -10000 0 -0.33 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.01 0.053 -10000 0 -0.37 9 9
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.028 0.26 16 -10000 0 16
substrate adhesion-dependent cell spreading 0.016 0.039 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.064 0.34 7 -10000 0 7
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.015 0.028 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.043 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.024 0.063 0.29 5 -0.35 12 17
JIP4/KLC1 0.041 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.02 0.033 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.008 0.057 0.19 94 -10000 0 94
NME1 0.013 0.017 0.14 17 -10000 0 17
clathrin coat assembly 0.028 0.069 0.28 3 -0.41 13 16
IL2RA 0.019 0.054 -10000 0 -0.32 13 13
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.37 35 35
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.029 -10000 0 -0.29 9 9
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.039 0.19 1 -0.36 6 7
SDC1 0.019 0.043 -10000 0 -0.33 8 8
ARF6/GDP 0.021 0.014 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.04 0.067 -10000 0 -0.35 7 7
mol:Phosphatidic acid 0.011 0.019 -10000 0 -10000 0 0
endocytosis -0.04 0.033 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.037 0.14 0.26 1 -0.39 47 48
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.018 -10000 0 -0.57 1 1
Dynamin 2/GDP 0.026 0.017 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.079 0.15 0.27 2 -0.43 36 38
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.065 0.32 2 -0.36 5 7
IL1-mediated signaling 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
UBC13/UEV1A 0.018 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.05 -10000 0 -0.35 8 8
IRAK/TOLLIP 0.026 0.009 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.025 0.094 0.36 3 -0.42 40 43
IL1A 0.028 0.03 0.26 18 -10000 0 18
IL1B 0.004 0.053 0.26 1 -0.43 15 16
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.027 -10000 0 -0.3 1 1
IL1R2 0.008 0.12 0.26 29 -0.57 40 69
IL1R1 0.012 0.084 -10000 0 -0.57 22 22
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.062 0.26 4 -0.3 20 24
TOLLIP 0.024 0.004 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.056 -10000 0 -0.37 1 1
JUN -0.015 0.056 0.26 2 -0.27 35 37
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.085 -10000 0 -0.34 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88 0.053 0.061 -10000 0 -0.33 23 23
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.061 0.061 -10000 0 -0.31 23 23
IL1 beta fragment/IL1R1/IL1RAP 0.022 0.073 -10000 0 -0.35 36 36
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.011 0.054 0.34 1 -0.28 28 29
IRAK1 0.012 0.008 -10000 0 -10000 0 0
IL1RN/IL1R1 0.031 0.074 -10000 0 -0.42 24 24
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.38 14 14
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.059 -10000 0 -0.29 25 25
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.022 0.073 -10000 0 -0.35 36 36
IL1 beta/IL1R2 0.013 0.093 -10000 0 -0.37 53 53
IRAK/TRAF6/TAK1/TAB1/TAB2 0.032 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.077 -10000 0 -0.32 44 44
IRAK3 0.003 0.11 0.26 1 -0.57 39 40
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.074 -10000 0 -0.32 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.047 -10000 0 -0.27 23 23
IL1 alpha/IL1R1/IL1RAP 0.041 0.063 -10000 0 -0.36 23 23
RELA 0.023 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 0.038 0.021 -10000 0 -10000 0 0
IL1RAP 0.023 0.018 -10000 0 -0.57 1 1
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.018 0.06 -10000 0 -0.29 35 35
CASP1 0.021 0.019 -10000 0 -0.57 1 1
IL1RN/IL1R2 0.028 0.099 0.36 5 -0.42 42 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.034 0.073 -10000 0 -0.33 36 36
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.071 -10000 0 -0.34 34 34
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.049 0.26 37 -0.57 2 39
TRAF6/TAK1/TAB1/TAB2 0.033 0.011 -10000 0 -10000 0 0
MAP2K6 -0.008 0.053 0.25 5 -0.29 22 27
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.026 0.041 0.26 20 -0.57 2 22
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.019 0.22 1 -0.29 2 3
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
mol:Sphinganine-1-P 0.012 0.026 0.26 1 -0.42 2 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.035 -10000 0 -0.23 3 3
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 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.006 0.023 -10000 0 -0.24 5 5
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
S1PR4 0.029 0.062 0.26 38 -0.57 6 44
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
S1P/S1P5/G12 0.046 0.041 0.24 4 -0.24 5 9
S1P/S1P3/Gq 0.026 0.063 -10000 0 -0.29 31 31
S1P/S1P4/Gi 0 0.097 -10000 0 -0.28 81 81
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
ABCC1 0.023 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.024 0.009 0.26 1 -9999 0 1
PLK4 0.033 0.044 0.26 41 -9999 0 41
regulation of centriole replication 0.016 0.026 0.26 2 -9999 0 2
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.019 0.11 -10000 0 -0.43 34 34
KLHL20 0.016 0.064 0.24 8 -0.22 13 21
CYFIP2 0.028 0.048 0.26 26 -0.57 3 29
Rac1/GDP 0.001 0.084 0.26 8 -0.31 17 25
ENAH -0.015 0.1 -10000 0 -0.45 24 24
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 0.01 0.046 -10000 0 -0.32 2 2
ABI1/Sra1/Nap1 -0.012 0.031 -10000 0 -0.16 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.047 0.064 -10000 0 -0.33 20 20
RAPGEF1 -0.018 0.1 0.26 2 -0.39 28 30
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.12 -10000 0 -0.41 50 50
CRK -0.015 0.099 -10000 0 -0.42 30 30
E-cadherin/gamma catenin/alpha catenin 0.033 0.057 -10000 0 -0.36 18 18
alphaE/beta7 Integrin 0.036 0.034 -10000 0 -0.42 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
DLG1 -0.023 0.12 -10000 0 -0.44 32 32
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.031 -10000 0 -0.21 4 4
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.003 0.045 -10000 0 -0.29 3 3
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.021 0.062 -10000 0 -0.42 18 18
TIAM1 0.025 0.015 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.041 0.054 -10000 0 -0.31 18 18
AKT1 -0.007 0.035 0.14 1 -0.21 1 2
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
RhoA/GDP 0.002 0.083 0.26 8 -0.31 16 24
actin cytoskeleton organization 0.015 0.052 0.18 18 -0.16 11 29
CDC42/GDP 0.002 0.082 0.26 9 -0.31 16 25
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.04 -10000 0 -0.26 18 18
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.045 0.057 -10000 0 -0.33 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin 0.03 0.049 -10000 0 -0.31 18 18
mol:GDP -0.012 0.09 0.26 9 -0.36 17 26
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 0.085 0.26 7 -0.32 16 23
RAC1/GTP/IQGAP1 0.032 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.047 0.18 39 -0.24 4 43
NME1 0.026 0.031 0.26 18 -10000 0 18
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.021 0.11 -10000 0 -0.45 31 31
regulation of cell-cell adhesion 0.004 0.039 -10000 0 -0.28 2 2
WASF2 0.008 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.056 0.24 3 -0.37 2 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.054 0.064 -10000 0 -0.32 19 19
CCND1 0.015 0.054 0.2 38 -0.3 4 42
VAV2 -0.018 0.15 -10000 0 -0.55 36 36
RAP1/GDP 0.008 0.069 0.26 4 -0.35 3 7
adherens junction assembly -0.02 0.11 -10000 0 -0.43 31 31
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.024 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.042 0.061 -10000 0 -0.3 19 19
E-cadherin/beta catenin 0.001 0.057 -10000 0 -0.34 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.022 0.12 -10000 0 -0.44 32 32
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.089 0.26 34 -0.34 25 59
E-cadherin/beta catenin/alpha catenin 0.034 0.057 -10000 0 -0.36 18 18
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.12 -10000 0 -0.42 50 50
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 0.073 0.3 4 -0.36 15 19
PDGFB-D/PDGFRB/SLAP 0.028 0.033 0.2 9 -0.36 4 13
PDGFB-D/PDGFRB/APS/CBL 0.048 0.042 -10000 0 -0.35 4 4
AKT1 0.025 0.095 0.34 38 -10000 0 38
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.032 0.084 0.32 6 -0.38 18 24
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.44 40 40
mol:Ca2+ 0.024 0.087 0.29 7 -0.42 18 25
MYC 0.053 0.17 0.36 35 -0.73 29 64
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.3 3 3
LRP1/PDGFRB/PDGFB 0.041 0.054 -10000 0 -0.4 14 14
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.023 0.088 0.29 7 -0.43 18 25
PTEN 0.022 0.019 -10000 0 -0.57 1 1
GRB2 0.023 0.009 0.26 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PDGFB-D/PDGFRB/SHP2 0.034 0.028 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.028 -10000 0 -0.42 4 4
cell cycle arrest 0.028 0.033 0.2 9 -0.36 4 13
HRAS 0.026 0.022 0.26 9 -10000 0 9
HIF1A 0.019 0.089 0.33 37 -10000 0 37
GAB1 0.026 0.093 0.29 8 -0.4 20 28
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.026 0.086 0.32 10 -0.37 14 24
PDGFB-D/PDGFRB 0.042 0.031 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.026 -10000 0 -0.42 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.023 0.065 0.28 3 -0.37 10 13
positive regulation of MAPKKK cascade 0.034 0.028 -10000 0 -0.42 4 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.024 0.089 0.29 7 -0.43 18 25
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.039 -10000 0 -0.42 7 7
SHB 0.024 0.008 0.26 1 -10000 0 1
BLK -0.024 0.16 0.29 5 -0.4 144 149
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.029 -10000 0 -0.41 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.028 0.1 0.3 9 -0.43 23 32
CBL 0.022 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.029 -10000 0 -0.42 4 4
LCK 0.006 0.11 -10000 0 -0.5 36 36
PDGFRB 0.022 0.037 -10000 0 -0.57 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.016 0.06 -10000 0 -0.5 7 7
ABL1 0.021 0.093 0.3 7 -0.37 28 35
PDGFB-D/PDGFRB/CBL 0.021 0.1 0.3 3 -0.44 29 32
PTPN1 0.024 0.019 0.25 6 -10000 0 6
SNX15 0.023 0.005 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 0.26 19 -10000 0 19
cell proliferation 0.054 0.15 0.33 49 -0.64 29 78
SLA 0.021 0.024 0.26 9 -10000 0 9
actin cytoskeleton reorganization 0.034 0.05 0.33 2 -0.3 2 4
SRC 0.012 0.059 -10000 0 -0.49 8 8
PI3K -0.013 0.032 -10000 0 -0.28 10 10
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.038 -10000 0 -0.36 6 6
SH2B2 0.034 0.046 0.26 45 -10000 0 45
PLCgamma1/SPHK1 0.032 0.086 0.32 6 -0.4 18 24
LYN 0.009 0.064 -10000 0 -0.46 12 12
LRP1 0.018 0.062 -10000 0 -0.57 12 12
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.3 3 3
SPHK1 0.027 0.041 0.26 20 -0.57 2 22
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.024 0.089 0.29 7 -0.43 18 25
PLCG1 0.024 0.09 0.3 6 -0.44 18 24
NHERF/PDGFRB 0.049 0.045 -10000 0 -0.36 4 4
YES1 0.001 0.11 -10000 0 -0.51 37 37
cell migration 0.048 0.045 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.049 0.041 -10000 0 -0.3 3 3
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
SLC9A3R1 0.036 0.054 0.26 60 -10000 0 60
NHERF1-2/PDGFRB/PTEN 0.056 0.048 0.29 2 -0.33 4 6
FYN -0.003 0.1 -10000 0 -0.42 45 45
DOK1 0.021 0.049 0.33 1 -0.33 3 4
HRAS/GTP 0.019 0.015 0.18 9 -10000 0 9
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.023 0.12 0.33 4 -0.49 33 37
PRKCD 0.022 0.051 0.33 1 -0.33 3 4
FER 0.018 0.059 -10000 0 -0.34 12 12
MAPKKK cascade 0.037 0.096 0.36 34 -0.3 3 37
RASA1 0.021 0.049 -10000 0 -0.33 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 0.03 -10000 0 -0.42 4 4
chemotaxis 0.021 0.091 0.28 9 -0.36 28 37
STAT1-3-5/STAT1-3-5 0.049 0.047 -10000 0 -0.36 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.027 -10000 0 -0.42 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
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 0.019 -10000 0 -0.3 3 3
TRAF2/ASK1 0.03 0.024 -10000 0 -0.36 3 3
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.018 0.11 0.27 1 -0.35 57 58
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.098 0.26 1 -0.34 43 44
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.054 0.077 0.26 138 -10000 0 138
TXN 0.007 0.006 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.027 -10000 0 -0.41 3 3
TAK1/TAB family 0 0.019 0.18 2 -0.14 6 8
RAC1/OSM/MEKK3 0.042 0.016 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.26 4 -10000 0 4
RAC1/OSM/MEKK3/MKK3 0 0.091 -10000 0 -0.31 31 31
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 -0.005 0.15 0.26 44 -0.57 69 113
CCM2 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.012 0.1 -10000 0 -0.36 69 69
MAPK11 0.021 0.032 -10000 0 -0.57 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.023 0.1 -10000 0 -0.33 71 71
OSM/MEKK3 0.032 0.013 -10000 0 -10000 0 0
TAOK1 -0.008 0.081 -10000 0 -0.36 54 54
TAOK2 0.011 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.025 -10000 0 -0.34 3 3
GADD45/MTK1/MTK1 0.067 0.047 -10000 0 -10000 0 0
TRAIL signaling pathway

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.048 -10000 0 -0.57 7 7
positive regulation of NF-kappaB transcription factor activity -0.005 0.11 -10000 0 -0.4 71 71
MAP2K4 0.016 0.046 -10000 0 -0.38 4 4
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.032 -10000 0 -0.57 3 3
SMPD1 0.008 0.029 -10000 0 -0.34 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.015 0.14 0.26 1 -0.57 64 65
TRAIL/TRAILR2 0.026 0.038 -10000 0 -0.37 8 8
TRAIL/TRAILR3 0.027 0.042 -10000 0 -0.42 7 7
TRAIL/TRAILR1 0.024 0.046 -10000 0 -0.41 10 10
TRAIL/TRAILR4 -0.005 0.11 -10000 0 -0.4 71 71
TRAIL/TRAILR1/DAP3/GTP 0.029 0.038 -10000 0 -0.32 7 7
IKK complex 0.011 0.04 -10000 0 -0.41 1 1
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.035 0.25 1 -0.42 7 8
MAP3K1 0.019 0.059 -10000 0 -0.44 7 7
TRAILR4 (trimer) -0.015 0.14 0.26 1 -0.56 64 65
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.032 -10000 0 -0.56 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.044 -10000 0 -0.36 9 9
CFLAR 0.024 0.018 -10000 0 -0.57 1 1
MAPK1 0.008 0.035 0.25 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.046 -10000 0 -0.3 7 7
mol:ceramide 0.008 0.029 -10000 0 -0.34 6 6
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.013 0.062 0.26 1 -0.44 7 8
TRAF2 0.025 0.015 0.26 4 -10000 0 4
TRAILR3 (trimer) 0.022 0.021 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.031 0.041 -10000 0 -0.35 7 7
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.036 0.084 0.28 61 -0.34 3 64
JNK cascade -0.005 0.11 -10000 0 -0.4 71 71
TRAIL (trimer) 0.02 0.048 -10000 0 -0.56 7 7
TNFRSF10C 0.022 0.021 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.039 -10000 0 -0.31 5 5
TRAIL/TRAILR2/FADD 0.032 0.036 -10000 0 -0.35 5 5
cell death 0.008 0.029 -10000 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.041 -10000 0 -0.41 6 6
TRAILR2 (trimer) 0.02 0.009 -10000 0 -10000 0 0
CASP8 0.012 0.05 -10000 0 -0.56 6 6
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.043 0.043 -10000 0 -0.29 5 5
Class I PI3K signaling events

Figure 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
ARF5/GTP -0.013 0.04 0.3 4 -0.28 1 5
DAPP1 0.017 0.1 0.27 7 -0.35 36 43
Src family/SYK family/BLNK-LAT/BTK-ITK 0.019 0.14 0.28 19 -0.48 39 58
mol:DAG 0.022 0.078 0.23 36 -0.24 13 49
HRAS 0.027 0.022 0.25 9 -10000 0 9
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.059 0.27 1 -0.32 9 10
PLCG2 0.02 0.028 0.26 1 -0.57 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 -0.01 0.037 0.31 5 -0.28 1 6
ARF1/GTP -0.004 0.033 0.26 8 -0.28 1 9
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
RAP1A/GTP -0.011 0.033 0.2 1 -0.27 1 2
ADAP1 -0.011 0.04 0.3 5 -0.28 2 7
ARAP3 -0.01 0.037 0.31 5 -0.28 1 6
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.027 0.033 0.26 21 -10000 0 21
ARHGEF6 0.017 0.067 -10000 0 -0.57 14 14
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.021 0.026 -10000 0 -0.57 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 0.053 0.23 19 -10000 0 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 4 -10000 0 4
ZAP70 0.026 0.098 0.26 61 -0.57 20 81
mol:IP3 0.017 0.066 0.21 44 -0.2 4 48
LYN 0.021 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.057 0.28 2 -0.32 9 11
RhoA/GDP 0.03 0.041 0.25 1 -10000 0 1
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.02 0.068 0.3 13 -0.35 2 15
SRC 0.023 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.011 0.23 2 -10000 0 2
RAC1 0.024 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.02 -10000 0 -0.54 1 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.038 0.3 5 -0.27 1 6
RhoA/GTP -0.012 0.037 0.33 4 -0.27 1 5
Src family/SYK family/BLNK-LAT 0.026 0.096 0.25 18 -0.37 24 42
BLK 0.051 0.087 0.26 151 -0.57 2 153
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.037 0.32 4 -0.26 1 5
HCK 0.027 0.026 0.26 13 -10000 0 13
CYTH3 -0.012 0.039 0.33 3 -0.27 3 6
CYTH2 -0.011 0.039 0.32 4 -0.26 1 5
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.009 0.053 0.31 1 -0.41 11 12
SGK1 0.005 0.076 -10000 0 -0.35 39 39
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.06 0.24 4 -0.31 12 16
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.044 0.31 6 -10000 0 6
mol:PI-3-4-5-P3 -0.011 0.035 0.28 4 -0.27 1 5
ARAP3/RAP1A/GTP -0.011 0.033 0.2 1 -0.28 1 2
VAV1 0.023 0.033 0.26 2 -0.57 3 5
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.04 0.039 -10000 0 -0.28 1 1
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.059 0.27 1 -0.33 8 9
LAT 0.025 0.038 0.26 15 -0.57 2 17
Rac1/GTP 0.016 0.051 -10000 0 -0.32 14 14
ITK -0.018 0.062 0.32 4 -0.31 30 34
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.021 0.095 0.26 32 -0.33 15 47
LCK 0.026 0.075 0.26 40 -0.57 11 51
BTK -0.011 0.039 0.32 4 -0.26 1 5
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.069 0.051 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.055 0.046 0.33 5 -10000 0 5
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.042 -10000 0 -0.22 2 2
CaM/Ca2+ 0.067 0.046 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.042 0.042 0.28 2 -10000 0 2
AKT1 0.01 0.064 0.29 11 -0.28 10 21
MAP2K1 0.007 0.045 0.29 4 -0.29 1 5
MAP3K11 0.023 0.042 0.29 4 -10000 0 4
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.019 0.095 -10000 0 -0.39 11 11
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.033 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.076 0.054 -10000 0 -10000 0 0
CEBPB 0.028 0.094 0.32 2 -0.49 7 9
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.075 0.094 -10000 0 -0.67 10 10
STAT1 0.026 0.047 0.29 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.054 0.08 0.26 146 -10000 0 146
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.045 0.28 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.028 0.061 0.34 2 -0.33 4 6
mol:Ca2+ 0.065 0.048 -10000 0 -10000 0 0
MAPK3 0.022 0.078 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.059 -10000 0 -0.29 1 1
MAPK1 -0.006 0.16 -10000 0 -0.67 58 58
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.031 -10000 0 -0.57 3 3
DAPK1 0.027 0.069 0.29 3 -0.34 2 5
SMAD7 0.017 0.036 0.17 8 -10000 0 8
CBL/CRKL/C3G 0.045 0.038 0.29 4 -10000 0 4
PI3K 0.056 0.056 -10000 0 -0.29 12 12
IFNG 0.054 0.08 0.26 146 -10000 0 146
apoptosis 0.024 0.071 0.28 1 -0.4 10 11
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.005 -10000 0 -10000 0 0
CAMK2A 0.032 0.042 0.26 36 -10000 0 36
CAMK2B -0.004 0.15 0.26 44 -0.57 69 113
FRAP1 0.008 0.06 0.28 11 -0.26 10 21
PRKCD 0.011 0.067 0.3 13 -0.28 10 23
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -0.22 2 2
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.022 0.057 0.28 13 -0.32 1 14
STAT1 (dimer)/PIASy 0.038 0.046 0.27 6 -10000 0 6
SOCS1 0.016 0.11 -10000 0 -1 10 10
mol:GDP 0.041 0.036 0.27 4 -10000 0 4
CASP1 0.016 0.039 0.19 9 -0.24 3 12
PTGES2 0.024 0.008 0.26 1 -10000 0 1
IRF9 0.028 0.041 0.24 8 -10000 0 8
mol:PI-3-4-5-P3 0.041 0.047 -10000 0 -0.28 12 12
RAP1/GDP 0.035 0.022 -10000 0 -10000 0 0
CBL 0.021 0.04 0.29 4 -10000 0 4
MAP3K1 0.022 0.042 0.29 4 -0.3 1 5
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.042 -10000 0 -0.22 2 2
PTPN11 0.025 0.044 0.29 4 -10000 0 4
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 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
PTK2 0.019 0.023 0.21 5 -0.3 1 6
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.067 0.048 0.35 10 -0.33 2 12
EPO 0.059 0.085 0.26 169 -10000 0 169
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.016 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.059 0.059 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.077 -10000 0 -0.42 23 23
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.38 14 14
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.033 0.03 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
MADCAM1 0.031 0.044 0.26 39 -10000 0 39
cell adhesion 0.064 0.047 0.34 10 -0.33 2 12
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.013 0.043 -10000 0 -0.33 10 10
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.044 0.046 -10000 0 -0.36 11 11
p130Cas/Crk/Dock1 0.026 0.041 0.35 1 -0.28 9 10
VCAM1 0.019 0.062 0.26 6 -0.57 11 17
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.023 -10000 0 -10000 0 0
BCAR1 -0.009 0.042 0.38 1 -0.3 10 11
EPOR 0.024 0.008 0.26 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.079 -10000 0 -0.43 23 23
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.032 -10000 0 -0.57 3 3
Caspase 8 (4 units) 0.038 0.062 -10000 0 -0.46 3 3
NEF 0.003 0.024 -10000 0 -0.18 11 11
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.02 0.054 -10000 0 -0.5 5 5
CYCS 0.036 0.077 0.26 26 -0.29 12 38
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.017 0.086 0.29 16 -0.43 26 42
MAP2K7 0.041 0.13 0.37 2 -0.7 17 19
protein ubiquitination 0.015 0.082 0.31 5 -0.37 11 16
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.022 0.036 -10000 0 -0.57 4 4
BID 0.035 0.073 0.23 2 -0.29 16 18
NF-kappa-B/RelA/I kappa B alpha 0.05 0.033 -10000 0 -0.31 3 3
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
CFLAR 0.024 0.018 -10000 0 -0.57 1 1
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.033 -10000 0 -0.31 3 3
MAPK8 0.038 0.12 0.4 5 -0.63 18 23
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.013 0.26 3 -10000 0 3
TRAF2 0.025 0.015 0.26 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.059 0.23 4 -0.3 16 20
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.091 -10000 0 -0.42 18 18
CHUK 0.014 0.085 0.33 3 -0.4 11 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.054 0.041 -10000 0 -0.33 5 5
TCRz/NEF 0.016 0.08 0.31 9 -0.42 26 35
TNF 0.024 0.065 0.26 25 -0.57 9 34
FASLG 0.011 0.11 0.28 42 -0.57 26 68
NFKB1 0.025 0.011 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 11 11
CASP6 0.052 0.1 0.38 1 -0.49 23 24
CASP7 0.04 0.1 0.38 6 -0.46 11 17
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 0.38 5 -0.47 10 15
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.42 3 3
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.005 -10000 0 -10000 0 0
MAP3K14 0.016 0.087 0.29 1 -0.42 13 14
APAF-1/Caspase 9 0.032 0.061 0.25 5 -0.37 5 10
BCL2 0.031 0.12 0.42 6 -0.53 24 30
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.084 0.31 5 -0.43 11 16
NFATC2 -0.006 0.071 0.19 2 -0.26 35 37
NFATC3 0.014 0.016 -10000 0 -0.4 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.094 0.29 2 -0.38 28 30
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.087 0.27 2 -0.44 11 13
BCL2/BAX 0.021 0.074 -10000 0 -0.41 28 28
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.013 -10000 0 -10000 0 0
BAX 0.025 0.014 0.26 4 -10000 0 4
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.009 0.26 1 -10000 0 1
CABIN1/MEF2D 0.019 0.083 -10000 0 -0.4 16 16
Calcineurin A alpha-beta B1/BCL2 0.008 0.094 -10000 0 -0.56 28 28
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.082 0.4 16 -10000 0 16
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 64 -10000 0 64
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
MAP3K8 0.019 0.048 -10000 0 -0.57 7 7
NFAT4/CK1 alpha 0.018 0.028 -10000 0 -0.28 2 2
MEF2D/NFAT1/Cbp/p300 0.008 0.11 -10000 0 -0.3 66 66
CABIN1 0.012 0.093 0.29 2 -0.38 27 29
CALM1 0.02 0.013 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
CAMK4 0.031 0.046 0.26 37 -0.57 1 38
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.041 0.038 -10000 0 -0.42 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.051 -10000 0 -0.57 8 8
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.096 0.28 2 -0.45 12 14
PRKCH 0.023 0.018 -10000 0 -0.57 1 1
CABIN1/Cbp/p300 0.027 0.023 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.009 -10000 0 -10000 0 0
apoptosis 0.011 0.034 -10000 0 -0.35 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.039 -10000 0 -0.28 4 4
PRKCB 0.019 0.076 0.26 19 -0.57 15 34
PRKCE 0.024 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.008 0.059 -10000 0 -0.37 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.021 0.02 -10000 0 -0.57 1 1
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
PRKCG 0.03 0.045 0.26 41 -10000 0 41
PRKCQ 0.004 0.11 0.26 8 -0.57 39 47
FKBP38/BCL2 0.021 0.074 -10000 0 -0.42 28 28
EP300 0.019 0.016 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.086 0.32 1 -0.42 10 11
CaM/Ca2+/FKBP38 0.027 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.034 -10000 0 -0.36 1 1
NFATc/ERK1 0.03 0.082 0.32 1 -0.41 10 11
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.039 0.093 0.28 1 -0.42 18 19
NR4A1 -0.013 0.17 -10000 0 -0.51 94 94
GSK3B 0.022 0.008 -10000 0 -10000 0 0
positive T cell selection 0.014 0.016 -10000 0 -0.4 1 1
NFAT1/CK1 alpha -0.002 0.056 -10000 0 -0.26 12 12
RCH1/ KPNB1 0.041 0.04 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.034 0.053 0.26 52 -0.57 1 53
MEF2D 0.017 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.082 0.32 1 -0.41 10 11
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.021 0.079 -10000 0 -0.42 33 33
AKT1 0.031 0.088 0.37 3 -0.56 8 11
PTK2B 0.003 0.084 0.35 1 -0.69 7 8
VEGFR2 homodimer/Frs2 0.024 0.063 -10000 0 -0.61 9 9
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.038 0.062 -10000 0 -0.57 9 9
endothelial cell proliferation 0.043 0.11 0.35 24 -0.56 9 33
mol:Ca2+ 0.014 0.056 -10000 0 -0.5 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.05 0.062 -10000 0 -0.52 10 10
RP11-342D11.1 0.004 0.055 -10000 0 -0.5 10 10
CDH5 0.018 0.048 -10000 0 -0.57 7 7
VEGFA homodimer 0.05 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.011 0.086 0.26 1 -0.57 23 24
HRAS/GDP 0.03 0.049 -10000 0 -0.57 4 4
SH2D2A 0.04 0.072 0.26 95 -0.57 2 97
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.086 -10000 0 -0.54 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.045 0.074 -10000 0 -0.48 11 11
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.059 -10000 0 -0.64 4 4
GRB10 0.014 0.057 -10000 0 -0.63 6 6
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
PAK1 0.023 0.019 0.26 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.05 0.075 -10000 0 -0.71 7 7
HRAS 0.026 0.022 0.26 9 -10000 0 9
VEGF/Rho/ROCK1/Integrin Complex 0.01 0.073 -10000 0 -0.48 11 11
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.048 0.061 -10000 0 -0.51 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.031 -10000 0 -0.57 3 3
Nck/Pak 0.033 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.036 0.066 -10000 0 -0.54 11 11
mol:GDP 0.039 0.054 -10000 0 -0.62 4 4
mol:NADP 0.025 0.083 0.56 1 -0.47 11 12
eNOS/Hsp90 0.036 0.08 0.54 1 -0.45 10 11
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.014 0.056 -10000 0 -0.51 9 9
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 7 -10000 0 7
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.022 0.1 0.35 1 -0.68 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 0.095 -10000 0 -0.4 37 37
PTPN6 0.024 0.011 0.26 2 -10000 0 2
EPAS1 0.024 0.057 -10000 0 -0.53 10 10
mol:L-citrulline 0.025 0.083 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 0.061 -10000 0 -0.52 9 9
VEGFR2 homodimer/VEGFA homodimer 0.041 0.062 -10000 0 -0.54 10 10
VEGFR2/3 heterodimer 0.023 0.07 -10000 0 -0.62 11 11
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.004 0.069 -10000 0 -0.66 7 7
VEGFR2 homodimer 0.011 0.069 -10000 0 -0.66 10 10
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.006 0.073 0.26 5 -0.56 7 12
MAPK1 0.009 0.075 0.26 3 -0.57 7 10
VEGFA145/NRP2 0.035 0.025 -10000 0 -0.39 2 2
VEGFR1/2 heterodimer 0.023 0.065 -10000 0 -0.6 10 10
KDR 0.011 0.069 -10000 0 -0.66 10 10
VEGFA165/NRP1/VEGFR2 homodimer 0.041 0.064 -10000 0 -0.56 9 9
SRC 0.023 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.014 0.082 0.33 3 -0.52 9 12
PI3K 0.025 0.072 -10000 0 -0.73 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.039 0.062 -10000 0 -0.54 10 10
FES 0.013 0.061 -10000 0 -0.48 12 12
GAB1 0.014 0.062 -10000 0 -0.67 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.061 -10000 0 -0.53 10 10
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 -0.53 18 18
VEGFR2 homodimer/VEGFA homodimer/Yes 0.037 0.063 -10000 0 -0.52 11 11
PI3K/GAB1 0.039 0.082 -10000 0 -0.55 8 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.053 0.063 -10000 0 -0.57 7 7
PRKACA 0.024 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.036 0.068 -10000 0 -0.57 11 11
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.014 0.059 -10000 0 -0.54 9 9
actin cytoskeleton reorganization 0.045 0.074 -10000 0 -0.47 11 11
PTK2 0.005 0.088 -10000 0 -0.74 9 9
EDG1 0.004 0.055 -10000 0 -0.5 10 10
mol:DAG 0.014 0.056 -10000 0 -0.51 9 9
CaM/Ca2+ 0.025 0.054 -10000 0 -0.57 6 6
MAP2K3 -0.006 0.061 -10000 0 -0.62 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.039 0.061 -10000 0 -0.66 6 6
PLCG1 0.014 0.057 -10000 0 -0.52 9 9
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.049 0.061 -10000 0 -0.5 10 10
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.039 0.062 -10000 0 -0.54 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.062 -10000 0 -0.57 9 9
cell migration 0.024 0.093 0.33 1 -0.64 8 9
mol:PI-3-4-5-P3 0.025 0.067 -10000 0 -0.61 7 7
FYN 0.021 0.026 -10000 0 -0.57 2 2
VEGFB/NRP1 0.019 0.055 -10000 0 -0.52 8 8
mol:NO 0.025 0.083 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 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.032 0.059 -10000 0 -0.66 6 6
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
NOS3 0.025 0.09 0.57 1 -0.54 11 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.03 0.081 -10000 0 -0.4 31 31
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.009 0.073 0.35 1 -0.4 21 22
PRKCB -0.006 0.067 -10000 0 -0.44 14 14
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.022 0.057 -10000 0 -0.5 10 10
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.064 -10000 0 -0.55 10 10
VEGFA165/NRP2 0.035 0.025 -10000 0 -0.39 2 2
MAPKKK cascade 0.05 0.079 0.33 11 -0.58 4 15
NRP2 0.023 0.027 0.26 1 -0.57 2 3
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
FAK1/Paxillin 0.022 0.1 0.42 2 -0.65 10 12
MAP3K13 0.012 0.061 -10000 0 -0.45 14 14
PDPK1 0.014 0.06 0.27 1 -0.58 5 6
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.033 0.057 -9999 0 -0.36 18 18
E-cadherin/beta catenin 0.022 0.062 -9999 0 -0.42 18 18
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.012 0.076 -9999 0 -0.57 18 18
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.049 0.045 -10000 0 -0.33 11 11
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.008 -10000 0 -0.28 1 1
GATA1/HDAC4 0.036 0.025 -10000 0 -0.42 1 1
GATA1/HDAC5 0.036 0.022 -10000 0 -10000 0 0
GATA2/HDAC5 0.025 0.072 -10000 0 -0.42 26 26
HDAC5/BCL6/BCoR 0.043 0.037 -10000 0 -0.36 8 8
HDAC9 0.021 0.061 0.26 10 -0.57 10 20
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.043 -10000 0 -0.36 11 11
HDAC4/ANKRA2 0.034 0.016 -10000 0 -0.42 1 1
HDAC5/YWHAB 0.033 0.01 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.26 13 -0.57 26 39
HDAC4/RFXANK 0.035 0.018 -10000 0 -0.42 1 1
BCOR 0.023 0.026 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.012 0.26 2 -10000 0 2
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.05 -10000 0 -0.4 14 14
Histones 0.016 0.049 -10000 0 -0.32 9 9
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.009 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.018 -10000 0 -0.42 1 1
HDAC7 0.024 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.035 0.012 -10000 0 -10000 0 0
CAMK4 0.031 0.046 0.26 37 -0.57 1 38
Tubulin/HDAC6 0.047 0.018 -10000 0 -0.36 1 1
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
GATA1 0.026 0.029 0.26 17 -10000 0 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.018 0.06 -10000 0 -0.57 11 11
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.24 4 4
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.017 -10000 0 -0.42 1 1
Tubulin 0.034 0.017 -10000 0 -0.42 1 1
HDAC4/14-3-3 E 0.032 0.018 -10000 0 -0.42 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.031 0.04 -10000 0 -0.42 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0.046 0.017 -10000 0 -0.36 1 1
HDAC4/SRF 0.05 0.034 -10000 0 -0.36 2 2
HDAC4/ER alpha -0.015 0.17 -10000 0 -0.41 155 155
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.049 -10000 0 -0.32 9 9
cell motility 0.046 0.018 -10000 0 -0.36 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.035 0.006 -10000 0 -10000 0 0
BCL6 0.02 0.044 -10000 0 -0.57 6 6
HDAC4/CaMK II delta B 0.023 0.018 -10000 0 -0.56 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.035 0.23 0.26 116 -0.57 151 267
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 0.026 -10000 0 -0.57 2 2
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.062 0.03 -10000 0 -0.31 2 2
GNG2 0.017 0.065 -10000 0 -0.57 13 13
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.023 0.021 0.26 2 -0.57 1 3
HDAC11 0.024 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 0.013 0.26 3 -10000 0 3
nuclear import -0.027 0.016 0.33 1 -10000 0 1
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 0.03 0.046 0.26 30 -0.57 2 32
ITGA4 0.026 0.022 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
alpha4/beta1 Integrin 0.036 0.016 -10000 0 -10000 0 0
EPO signaling pathway

Figure 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
BCL2L1 0.051 0.081 -10000 0 -0.48 1 1
CRKL 0.025 0.047 0.31 6 -10000 0 6
mol:DAG 0.038 0.051 -10000 0 -10000 0 0
HRAS 0.034 0.078 0.31 18 -10000 0 18
MAPK8 0.04 0.07 0.25 28 -0.34 5 33
RAP1A 0.027 0.048 0.3 8 -10000 0 8
GAB1 0.026 0.046 0.32 5 -10000 0 5
MAPK14 0.042 0.065 0.25 28 -10000 0 28
EPO 0.061 0.085 0.26 169 -10000 0 169
PLCG1 0.038 0.051 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.013 0.26 1 -10000 0 1
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.063 0.061 -10000 0 -0.35 5 5
GAB1/SHC/GRB2/SOS1 0.042 0.041 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.06 0.059 -10000 0 -10000 0 0
IRS2 0.014 0.071 0.31 5 -0.3 26 31
STAT1 0.044 0.064 0.32 3 -10000 0 3
STAT5B 0.04 0.058 -10000 0 -0.34 1 1
cell proliferation 0.022 0.075 0.24 30 -0.32 5 35
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.044 -10000 0 -0.33 1 1
TEC 0.025 0.047 0.29 5 -0.3 1 6
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
STAT1 (dimer) 0.044 0.063 0.32 3 -10000 0 3
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
EPO/EPOR (dimer)/JAK2 0.08 0.062 0.33 3 -10000 0 3
EPO/EPOR 0.06 0.059 -10000 0 -10000 0 0
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.046 0.28 3 -0.29 1 4
elevation of cytosolic calcium ion concentration 0.026 0.013 0.26 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.061 0.054 -10000 0 -10000 0 0
mol:IP3 0.038 0.051 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.03 0.079 0.29 2 -0.3 32 34
SH2B3 0.026 0.009 -10000 0 -10000 0 0
NFKB1 0.042 0.066 0.25 28 -10000 0 28
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.042 -10000 0 -0.27 2 2
PTPN6 0.023 0.039 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.047 0.048 0.28 3 -0.28 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 0.041 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
CRKL/CBL/C3G 0.046 0.047 0.28 4 -10000 0 4
VAV2 0.027 0.048 0.3 8 -10000 0 8
CBL 0.025 0.047 0.31 6 -10000 0 6
SHC/Grb2/SOS1 0.036 0.037 -10000 0 -10000 0 0
STAT5A 0.038 0.063 -10000 0 -0.33 6 6
GRB2 0.023 0.009 0.26 1 -10000 0 1
STAT5 (dimer) 0.051 0.079 0.34 1 -0.43 2 3
LYN/PLCgamma2 0.027 0.026 -10000 0 -0.42 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.027 0.048 0.3 8 -10000 0 8
BCL2 0.031 0.17 -10000 0 -0.83 35 35
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.41 67 67
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.004 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.11 0.15 0.4 1 -0.42 74 75
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 0.026 -10000 0 -0.42 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.02 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.024 0.024 0.26 11 -10000 0 11
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.01 0.016 0.24 5 -10000 0 5
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.063 0.26 1 -0.3 17 18
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.12 0.16 0.41 1 -0.47 74 75
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
LNPEP 0.019 0.051 -10000 0 -0.57 8 8
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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
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 0.033 0.11 0.29 13 -0.32 27 40
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.034 0.36 1 -0.42 1 2
NFKBIA 0.012 0.025 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.016 0.26 3 -10000 0 3
IKBKG 0.019 0.03 -10000 0 -10000 0 0
IKK complex/A20 0.021 0.12 -10000 0 -0.42 30 30
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 -10000 0 -0.4 49 49
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 -0.41 31 31
BCL10/MALT1/TRAF6 0.045 0.014 -10000 0 -10000 0 0
NOD2 0.028 0.043 0.26 30 -0.57 1 31
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 0.049 -10000 0 -0.42 9 9
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.065 0.26 25 -0.57 9 34
NF kappa B1 p50/RelA 0.051 0.016 -10000 0 -10000 0 0
BCL10 0.024 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.025 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.015 0.12 -10000 0 -0.4 45 45
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.42 49 49
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 -0.46 1 1
VEGFR1 homodimer/NRP1 0.01 0.015 -10000 0 -0.48 1 1
mol:DAG 0.013 0.03 -10000 0 -0.38 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.02 -10000 0 -0.44 1 1
CaM/Ca2+ 0.026 0.029 -10000 0 -0.36 2 2
HIF1A 0.028 0.011 -10000 0 -0.31 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.009 0.051 -10000 0 -0.42 1 1
PLCG1 0.013 0.03 -10000 0 -0.38 2 2
NOS3 0.016 0.052 -10000 0 -0.52 2 2
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:NO 0.02 0.061 0.29 2 -0.45 5 7
FLT1 0.013 0.018 -10000 0 -0.55 1 1
PGF 0.024 0.024 0.26 5 -0.57 1 6
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.03 -10000 0 -0.44 2 2
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.032 0.063 -10000 0 -0.43 6 6
endothelial cell proliferation 0.011 0.081 0.33 6 -0.6 4 10
mol:Ca2+ 0.013 0.03 -10000 0 -0.38 2 2
MAPK3 -0.012 0.049 -10000 0 -0.32 19 19
MAPK1 -0.012 0.048 -10000 0 -0.32 17 17
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
PLGF homodimer 0.024 0.024 0.26 5 -0.56 1 6
PRKACA 0.024 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
VEGFA homodimer 0.025 0.019 0.26 7 -10000 0 7
VEGFR1 homodimer/VEGFA homodimer 0.027 0.022 -10000 0 -0.48 1 1
platelet activating factor biosynthetic process -0.013 0.046 -10000 0 -0.63 1 1
PI3K 0.044 0.048 -10000 0 -0.32 14 14
PRKCA -0.011 0.052 0.24 1 -0.33 20 21
PRKCB -0.009 0.048 -10000 0 -0.35 11 11
VEGFR1 homodimer/PLGF homodimer 0.027 0.024 -10000 0 -0.42 2 2
VEGFA 0.025 0.019 0.26 7 -10000 0 7
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.03 -10000 0 -0.38 2 2
RASA1 0.013 0.028 -10000 0 -0.43 1 1
NRP2 0.023 0.027 0.26 1 -0.57 2 3
VEGFR1 homodimer 0.013 0.018 -10000 0 -0.55 1 1
VEGFB homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.029 0.14 -10000 0 -0.44 25 25
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.047 -10000 0 -0.32 14 14
mol:L-citrulline 0.02 0.061 0.29 2 -0.45 5 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.028 -10000 0 -0.41 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 0.052 0.05 -10000 0 -0.31 14 14
PDPK1 -0.004 0.053 -10000 0 -0.4 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.023 -10000 0 -0.45 1 1
mol:NADP 0.02 0.061 0.29 2 -0.45 5 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.027 -10000 0 -0.4 1 1
VEGFR1 homodimer/NRP2 0.025 0.027 -10000 0 -0.44 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.004 0.039 0.21 1 -0.31 3 4
SMAD3 0.022 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.063 -10000 0 -0.44 11 11
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.058 -10000 0 -10000 0 0
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.28 7 7
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
TRAP-1/SMAD4 0.027 0.056 -10000 0 -0.42 16 16
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.015 0.072 -10000 0 -0.57 16 16
UBE2I 0.023 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.005 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 64 -10000 0 64
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.05 0.061 -10000 0 -0.37 8 8
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.061 -10000 0 -0.35 7 7
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.021 0.26 7 -10000 0 7
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 0.041 -10000 0 -0.4 1 1
YY1/LSF 0.024 0.049 -10000 0 -0.3 7 7
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.03 -10000 0 -0.3 7 7
I kappa B alpha/HDAC1 0.03 0.036 -10000 0 -0.42 1 1
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.019 0.036 -10000 0 -0.3 7 7
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.031 0.036 -10000 0 -0.43 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.39 3 3
NF kappa B1 p50/RelA 0.026 0.064 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.26 13 -0.57 26 39
GATA1 0.026 0.029 0.26 17 -10000 0 17
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.079 -10000 0 -0.36 20 20
RBBP7 0.026 0.019 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.018 -10000 0 -0.57 1 1
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.026 -10000 0 -0.47 1 1
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.029 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.022 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.015 0.26 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 0.046 -10000 0 -0.38 3 3
YY1/HDAC2 0.024 0.045 -10000 0 -0.29 5 5
YY1/HDAC1 0.025 0.047 -10000 0 -0.24 13 13
NuRD/MBD2 Complex (MeCP1) 0.024 0.054 -10000 0 -0.27 13 13
PPARG -0.06 0.16 -10000 0 -0.34 225 225
HDAC8/hEST1B 0.041 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.036 -10000 0 -0.43 1 1
MBD3L2 0.017 0.011 0.26 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 0.066 -10000 0 -0.35 14 14
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.019 0.027 -10000 0 -0.48 1 1
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.011 -10000 0 -0.29 1 1
HDAC8 0.024 0.001 -10000 0 -10000 0 0
SMAD7 0.023 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.024 0.007 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 0.048 -10000 0 -0.27 6 6
YY1/SAP30/HDAC1 0.036 0.047 -10000 0 -0.25 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.026 -10000 0 -0.47 1 1
histone deacetylation 0.024 0.053 -10000 0 -0.4 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.035 -10000 0 -0.41 1 1
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -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 0.025 0.065 -10000 0 -0.33 23 23
GATA1/HDAC1 0.036 0.02 -10000 0 -10000 0 0
GATA1/HDAC3 0.032 0.041 -10000 0 -0.45 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.049 -10000 0 -0.42 9 9
SIN3/HDAC complex/Mad/Max 0.016 0.053 -10000 0 -0.29 18 18
NuRD Complex 0.025 0.065 -10000 0 -0.38 9 9
positive regulation of chromatin silencing 0.05 0.039 -10000 0 -0.39 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.005 -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 0.022 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.025 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.044 0.015 -10000 0 -10000 0 0
TNF 0.024 0.065 0.26 25 -0.57 9 34
negative regulation of cell growth 0.016 0.053 -10000 0 -0.29 18 18
NuRD/MBD2/PRMT5 Complex 0.024 0.054 -10000 0 -0.27 13 13
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NF kappa B/RelA/I kappa B alpha 0.018 0.052 -10000 0 -0.35 8 8
SIN3/HDAC complex/NCoR1 0.007 0.066 -10000 0 -0.32 28 28
TFCP2 0.024 0.018 -10000 0 -0.57 1 1
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.009 0.26 1 -10000 0 1
MBD2 0.023 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.034 0.011 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.043 -10000 0 -0.33 2 2
NFKBIA 0.014 0.037 -10000 0 -0.25 11 11
MAPK14 0.024 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.01 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.017 0.067 -10000 0 -0.57 14 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.013 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.012 0.25 2 -10000 0 2
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
NFKB1 0.01 0.011 0.26 2 -10000 0 2
RELA 0.023 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.024 0.046 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.046 -10000 0 -0.33 3 3
SRC 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.38 14 14
NF kappa B1 p50/RelA 0.024 0.046 -10000 0 -0.26 10 10
IKBKB 0.02 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.057 -10000 0 -0.26 26 26
cell death 0.024 0.044 -10000 0 -0.32 3 3
NF kappa B1 p105/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
LCK 0.026 0.075 0.26 40 -0.57 11 51
BCL3 0.024 0.011 0.26 2 -10000 0 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.041 0.035 -10000 0 -10000 0 0
CLOCK 0.02 0.06 -10000 0 -0.56 11 11
TIMELESS/CRY2 0.031 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.014 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.017 -10000 0 -10000 0 0
ARNTL 0.026 0.004 -10000 0 -10000 0 0
TIMELESS 0.018 0.024 -10000 0 -10000 0 0
NPAS2 0.023 0.041 0.26 1 -0.56 5 6
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.006 -10000 0 -0.09 6 6
CHEK1 0.027 0.035 0.26 23 -10000 0 23
mol:HEME 0.007 0.006 0.09 6 -10000 0 6
PER1 0.013 0.072 -10000 0 -0.57 16 16
BMAL/CLOCK/NPAS2 0.049 0.052 -10000 0 -0.36 16 16
BMAL1/CLOCK 0.019 0.062 -10000 0 -0.48 1 1
S phase of mitotic cell cycle 0.041 0.035 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.042 0.036 -10000 0 -10000 0 0
mol:NADPH 0.007 0.006 0.09 6 -10000 0 6
PER1/TIMELESS 0.024 0.046 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.018 0.26 6 -10000 0 6
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.26 10 -10000 0 10
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.017 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.043 0.035 0.33 4 -0.33 2 6
lamellipodium assembly -0.003 0.088 -10000 0 -0.41 34 34
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.38 14 14
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 0.016 0.065 -10000 0 -0.57 13 13
ARF6/GTP 0.047 0.02 -10000 0 -10000 0 0
cell adhesion 0.05 0.019 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.016 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.048 0.043 -10000 0 -0.31 11 11
p130Cas/Crk/Dock1 0.041 0.019 -10000 0 -10000 0 0
VCAM1 0.019 0.062 0.26 6 -0.57 11 17
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.019 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.021 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.047 0.021 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.019 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.097 -10000 0 -0.46 34 34
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.04 0.069 0.35 3 -10000 0 3
regulation of axonogenesis -0.011 0.026 0.24 4 -10000 0 4
myoblast fusion -0.026 0.047 -10000 0 -0.22 1 1
mol:GTP 0.023 0.031 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.055 0.044 -10000 0 -0.3 2 2
ARF1/GTP 0.03 0.028 -10000 0 -10000 0 0
mol:GM1 0.012 0.024 -10000 0 -10000 0 0
mol:Choline 0.008 0.038 -10000 0 -0.34 9 9
lamellipodium assembly 0.018 0.058 -10000 0 -0.36 7 7
MAPK3 0.032 0.045 0.2 5 -10000 0 5
ARF6/GTP/NME1/Tiam1 0.056 0.045 0.31 2 -10000 0 2
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.047 0.22 1 -10000 0 1
ARF1/GDP 0.025 0.047 -10000 0 -0.26 2 2
ARF6 0.032 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.015 0.25 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.032 0.044 0.2 9 -10000 0 9
actin filament bundle formation -0.032 0.05 0.25 4 -10000 0 4
KALRN 0.01 0.054 -10000 0 -0.31 20 20
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.033 0.05 -10000 0 -0.25 4 4
NME1 0.028 0.031 0.26 18 -10000 0 18
Rac1/GDP 0.033 0.051 -10000 0 -0.25 4 4
substrate adhesion-dependent cell spreading 0.023 0.031 -10000 0 -10000 0 0
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 0.023 0.031 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.031 -10000 0 -10000 0 0
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.047 0.21 2 -0.21 5 7
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 -0.39 9 9
RAB11FIP3 0.023 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.018 0.058 -10000 0 -0.36 7 7
ruffle organization 0.011 0.026 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.023 0.031 -10000 0 -10000 0 0
PLD2 0.02 0.024 -10000 0 -10000 0 0
PIP5K1A 0.011 0.026 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.008 0.038 -10000 0 -0.34 9 9
Rac1/GTP 0.018 0.058 -10000 0 -0.37 7 7
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.011 -10000 0 -0.26 1 1
MDM2/SUMO1 0.033 0.039 -10000 0 -0.23 4 4
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.017 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.24 4 4
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 0.17 7 -10000 0 7
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.047 -10000 0 -0.19 4 4
AP2 0.034 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.01 -10000 0 -10000 0 0
CLTB 0.025 0.015 0.26 4 -10000 0 4
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 0.13 2 -10000 0 2
mol:PI-4-5-P2 0.007 0.015 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.012 0.2 3 -10000 0 3
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.02 -10000 0 -0.13 2 2
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 0.023 -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 0.041 -10000 0 -0.24 20 20
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.023 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.013 0.048 -10000 0 -0.26 28 28
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.023 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 0.13 2 -10000 0 2
PIP5K1A 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.006 0.13 2 -10000 0 2
GOSR2 0.008 0.028 -10000 0 -0.31 7 7
USO1 0.009 0.02 -10000 0 -0.32 3 3
GBF1 0.009 0.024 -10000 0 -0.31 5 5
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.015 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.067 0.025 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.016 -10000 0 -9999 0 0
RELB 0.026 0.022 0.26 10 -9999 0 10
NFKB2 0.024 0.008 0.26 1 -9999 0 1
NF kappa B2 p52/RelB 0.033 0.016 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.016 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1075 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z7.A8R6 TCGA.Z7.A8R5 TCGA.XX.A89A TCGA.XX.A899
109_MAP3K5 -0.33 0.025 0.025 0.025
47_PPARGC1A -0.57 0.024 0.024 0.024
105_BMP4 0.024 0.024 0.024 0.024
105_BMP6 0.024 0.024 0.024 0.024
105_BMP7 0.024 0.024 0.024 0.024
105_BMP2 -0.57 0.024 0.024 0.024
131_RELN/VLDLR -0.33 -0.33 0.063 0.063
30_TGFB1/TGF beta receptor Type II -0.033 0.024 0.018 0.019
84_STAT5B -0.16 -0.06 0.12 0.029
84_STAT5A -0.16 -0.06 0.12 0.029
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/22315252/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/22506563/GDAC_Gistic2Report_22529547/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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