Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 76 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 340
PLK2 and PLK4 events 211
Circadian rhythm pathway 155
TCGA08_retinoblastoma 146
PLK1 signaling events 136
S1P3 pathway 129
Osteopontin-mediated events 113
Signaling events regulated by Ret tyrosine kinase 110
Effects of Botulinum toxin 107
Nongenotropic Androgen signaling 95
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • 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.

Pathway.Name 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 340 17384 51 -0.023 1.9 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 211 635 3 0.015 0.067 1000 -1000 -0.016 -1000
Circadian rhythm pathway 155 3414 22 -0.095 0.27 1000 -1000 -0.014 -1000
TCGA08_retinoblastoma 146 1170 8 -0.077 0.071 1000 -1000 -0.003 -1000
PLK1 signaling events 136 11627 85 -0.12 0.24 1000 -1000 -0.023 -1000
S1P3 pathway 129 5446 42 -0.54 0.041 1000 -1000 -0.018 -1000
Osteopontin-mediated events 113 4319 38 -0.039 0.19 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 110 9076 82 -0.19 0.029 1000 -1000 -0.057 -1000
Effects of Botulinum toxin 107 2801 26 -0.12 0.054 1000 -1000 -0.024 -1000
Nongenotropic Androgen signaling 95 4986 52 -0.16 0.086 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 90 2353 26 -0.031 0.045 1000 -1000 -0.017 -1000
IGF1 pathway 90 5180 57 -0.088 0.053 1000 -1000 -0.05 -1000
Aurora B signaling 89 6001 67 -0.063 0.18 1000 -1000 -0.03 -1000
Endothelins 88 8520 96 -0.11 0.09 1000 -1000 -0.042 -1000
Retinoic acid receptors-mediated signaling 84 4877 58 -0.39 0.05 1000 -1000 -0.02 -1000
mTOR signaling pathway 83 4424 53 -0.16 0.029 1000 -1000 -0.035 -1000
Syndecan-1-mediated signaling events 80 2742 34 -0.046 0.033 1000 -1000 -0.031 -1000
IL2 signaling events mediated by STAT5 79 1756 22 -0.35 0.029 1000 -1000 -0.039 -1000
Ras signaling in the CD4+ TCR pathway 74 1267 17 0 0.03 1000 -1000 -0.015 -1000
Thromboxane A2 receptor signaling 72 7565 105 -0.16 0.044 1000 -1000 -0.044 -1000
Aurora A signaling 71 4303 60 -0.002 0.17 1000 -1000 -0.026 -1000
Ephrin B reverse signaling 69 3349 48 -0.18 0.06 1000 -1000 -0.041 -1000
TCGA08_p53 69 488 7 -0.007 0.029 1000 -1000 -0.015 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 67 5562 83 -0.13 0.065 1000 -1000 -0.03 -1000
FoxO family signaling 67 4334 64 -0.022 0.36 1000 -1000 -0.03 -1000
Canonical Wnt signaling pathway 67 3443 51 -0.33 0.14 1000 -1000 -0.031 -1000
Insulin Pathway 65 4828 74 -0.1 0.059 1000 -1000 -0.054 -1000
Reelin signaling pathway 62 3483 56 -0.072 0.074 1000 -1000 -0.031 -1000
BARD1 signaling events 61 3487 57 -0.046 0.2 1000 -1000 -0.043 -1000
IL2 signaling events mediated by PI3K 61 3542 58 -0.17 0.029 1000 -1000 -0.029 -1000
LPA receptor mediated events 61 6281 102 -0.057 0.032 1000 -1000 -0.06 -1000
TRAIL signaling pathway 58 2815 48 -0.033 0.032 1000 -1000 -0.033 -1000
Integrins in angiogenesis 58 4913 84 -0.082 0.055 1000 -1000 -0.054 -1000
Insulin-mediated glucose transport 57 1851 32 -0.086 0.037 1000 -1000 -0.028 -1000
Plasma membrane estrogen receptor signaling 57 4913 86 -0.13 0.13 1000 -1000 -0.053 -1000
Signaling events mediated by the Hedgehog family 55 2871 52 -0.044 0.05 1000 -1000 -0.038 -1000
IL4-mediated signaling events 55 5078 91 -0.56 0.3 1000 -1000 -0.079 -1000
PDGFR-alpha signaling pathway 55 2451 44 -0.093 0.038 1000 -1000 -0.026 -1000
Nectin adhesion pathway 55 3475 63 -0.12 0.048 1000 -1000 -0.036 -1000
HIF-2-alpha transcription factor network 55 2366 43 -0.055 0.19 1000 -1000 -0.046 -1000
Class I PI3K signaling events 55 4055 73 -0.032 0.085 1000 -1000 -0.027 -1000
Regulation of Telomerase 55 5681 102 -0.26 0.065 1000 -1000 -0.041 -1000
IL1-mediated signaling events 53 3336 62 -0.069 0.058 1000 -1000 -0.055 -1000
Wnt signaling 53 371 7 0.007 0.029 1000 -1000 -0.009 -1000
Signaling mediated by p38-gamma and p38-delta 51 772 15 -0.083 0.028 1000 -1000 -0.029 -1000
Coregulation of Androgen receptor activity 48 3662 76 -0.34 0.043 1000 -1000 -0.031 -1000
amb2 Integrin signaling 48 3961 82 -0.056 0.076 1000 -1000 -0.035 -1000
IL23-mediated signaling events 47 2826 60 -0.01 0.23 1000 -1000 -0.028 -1000
Signaling events mediated by PRL 46 1596 34 -0.063 0.051 1000 -1000 -0.034 -1000
Presenilin action in Notch and Wnt signaling 44 2693 61 -0.3 0.065 1000 -1000 -0.036 -1000
RXR and RAR heterodimerization with other nuclear receptor 44 2309 52 -0.15 0.098 1000 -1000 -0.024 -1000
p75(NTR)-mediated signaling 43 5401 125 -0.071 0.075 1000 -1000 -0.061 -1000
FAS signaling pathway (CD95) 40 1897 47 -0.036 0.046 1000 -1000 -0.028 -1000
Paxillin-dependent events mediated by a4b1 40 1475 36 -0.076 0.063 1000 -1000 -0.04 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 39 904 23 -0.014 0.092 1000 -1000 -0.015 -1000
Glucocorticoid receptor regulatory network 38 4409 114 -0.3 0.16 1000 -1000 -0.06 -1000
BMP receptor signaling 37 3052 81 -0.053 0.054 1000 -1000 -0.046 -1000
E-cadherin signaling in keratinocytes 37 1598 43 -0.048 0.044 1000 -1000 -0.028 -1000
Canonical NF-kappaB pathway 36 1432 39 -0.055 0.05 1000 -1000 -0.025 -1000
Regulation of nuclear SMAD2/3 signaling 35 4883 136 -0.1 0.14 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 35 1615 45 -0.085 0.067 1000 -1000 -0.043 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 35 1169 33 -0.012 0.076 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 34 1284 37 -0.019 0.067 1000 -1000 -0.033 -1000
PDGFR-beta signaling pathway 34 3391 97 -0.072 0.061 1000 -1000 -0.058 -1000
Noncanonical Wnt signaling pathway 33 862 26 -0.025 0.043 1000 -1000 -0.033 -1000
Arf6 signaling events 33 2094 62 -0.014 0.068 1000 -1000 -0.014 -1000
Regulation of p38-alpha and p38-beta 33 1816 54 -0.054 0.063 1000 -1000 -0.039 -1000
Caspase cascade in apoptosis 32 2391 74 -0.058 0.042 1000 -1000 -0.031 -1000
Syndecan-3-mediated signaling events 32 1124 35 -0.013 0.043 1000 -1000 -0.029 -1000
E-cadherin signaling in the nascent adherens junction 32 2445 76 -0.089 0.057 1000 -1000 -0.056 -1000
Neurotrophic factor-mediated Trk receptor signaling 32 3903 120 -0.15 0.076 1000 -1000 -0.05 -1000
IL12-mediated signaling events 31 2725 87 -0.36 0.049 1000 -1000 -0.062 -1000
Signaling events mediated by PTP1B 31 2407 76 -0.076 0.037 1000 -1000 -0.034 -1000
HIF-1-alpha transcription factor network 30 2282 76 -0.042 0.34 1000 -1000 -0.085 -1000
EPHB forward signaling 30 2628 85 -0.069 0.13 1000 -1000 -0.061 -1000
E-cadherin signaling events 30 150 5 0.026 0.044 1000 -1000 0.027 -1000
ErbB4 signaling events 28 1970 69 -0.032 0.18 1000 -1000 -0.043 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 28 2398 85 -0.068 0.068 1000 -1000 -0.036 -1000
Glypican 1 network 28 1379 48 -0.043 0.054 1000 -1000 -0.027 -1000
BCR signaling pathway 28 2801 99 -0.07 0.068 1000 -1000 -0.061 -1000
ErbB2/ErbB3 signaling events 27 1769 65 -0.035 0.092 1000 -1000 -0.054 -1000
Syndecan-2-mediated signaling events 27 1895 69 -0.04 0.054 1000 -1000 -0.027 -1000
ceramide signaling pathway 27 1349 49 -0.052 0.041 1000 -1000 -0.031 -1000
IL6-mediated signaling events 27 2040 75 -0.27 0.046 1000 -1000 -0.027 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 26 1451 54 -0.058 0.039 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 26 1034 39 -0.13 0.03 1000 -1000 -0.022 -1000
TCR signaling in naïve CD8+ T cells 26 2488 93 -0.091 0.075 1000 -1000 -0.039 -1000
EGFR-dependent Endothelin signaling events 26 548 21 -0.053 0.059 1000 -1000 -0.047 -1000
Aurora C signaling 25 178 7 -0.001 0.039 1000 -1000 -0.016 -1000
Fc-epsilon receptor I signaling in mast cells 25 2442 97 -0.065 0.062 1000 -1000 -0.062 -1000
Syndecan-4-mediated signaling events 25 1698 67 -0.027 0.076 1000 -1000 -0.033 -1000
Ceramide signaling pathway 24 1836 76 -0.038 0.065 1000 -1000 -0.028 -1000
Regulation of Androgen receptor activity 24 1712 70 -0.39 0.046 1000 -1000 -0.041 -1000
Atypical NF-kappaB pathway 23 742 31 -0.038 0.029 1000 -1000 -0.034 -1000
IL27-mediated signaling events 23 1213 51 -0.03 0.075 1000 -1000 -0.044 -1000
IFN-gamma pathway 22 1528 68 -0.063 0.068 1000 -1000 -0.051 -1000
Class I PI3K signaling events mediated by Akt 22 1523 68 -0.1 0.054 1000 -1000 -0.041 -1000
Stabilization and expansion of the E-cadherin adherens junction 22 1700 74 -0.13 0.073 1000 -1000 -0.065 -1000
FOXA2 and FOXA3 transcription factor networks 21 976 46 -0.03 0.25 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class I 21 2230 104 -0.047 0.066 1000 -1000 -0.036 -1000
Calcium signaling in the CD4+ TCR pathway 21 669 31 -0.07 0.029 1000 -1000 -0.046 -1000
Sphingosine 1-phosphate (S1P) pathway 20 561 28 -0.031 0.041 1000 -1000 -0.021 -1000
JNK signaling in the CD4+ TCR pathway 20 348 17 -0.026 0.059 1000 -1000 -0.026 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 20 1637 78 -0.18 0.039 1000 -1000 -0.031 -1000
Arf1 pathway 20 1104 54 -0.029 0.035 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class II 19 1480 75 -0.033 0.058 1000 -1000 -0.035 -1000
Hedgehog signaling events mediated by Gli proteins 19 1267 65 -0.036 0.055 1000 -1000 -0.034 -1000
EPO signaling pathway 19 1074 55 -0.076 0.036 1000 -1000 -0.042 -1000
Signaling mediated by p38-alpha and p38-beta 19 876 44 -0.038 0.046 1000 -1000 -0.033 -1000
Nephrin/Neph1 signaling in the kidney podocyte 18 626 34 -0.04 0.082 1000 -1000 -0.029 -1000
S1P5 pathway 18 307 17 -0.02 0.029 1000 -1000 -0.01 -1000
Signaling events mediated by VEGFR1 and VEGFR2 18 2270 125 -0.074 0.068 1000 -1000 -0.067 -1000
VEGFR1 specific signals 18 1032 56 -0.053 0.053 1000 -1000 -0.04 -1000
p38 MAPK signaling pathway 18 832 44 -0.021 0.055 1000 -1000 -0.017 -1000
Arf6 downstream pathway 17 771 43 -0.047 0.057 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class III 17 719 40 -0.053 0.058 1000 -1000 -0.036 -1000
Class IB PI3K non-lipid kinase events 17 51 3 -0.029 0.029 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 15 196 13 0 0.074 1000 -1000 0 -1000
Visual signal transduction: Cones 14 535 38 -0.018 0.059 1000 -1000 -0.02 -1000
a4b1 and a4b7 Integrin signaling 14 72 5 0.028 0.04 1000 -1000 0.027 -1000
Sumoylation by RanBP2 regulates transcriptional repression 14 395 27 -0.039 0.064 1000 -1000 -0.039 -1000
S1P4 pathway 14 360 25 -0.028 0.041 1000 -1000 -0.023 -1000
Ephrin A reverse signaling 13 92 7 -0.025 0.035 1000 -1000 -0.017 -1000
S1P1 pathway 12 436 36 -0.021 0.029 1000 -1000 -0.041 -1000
Angiopoietin receptor Tie2-mediated signaling 12 1079 88 -0.046 0.041 1000 -1000 -0.066 -1000
Arf6 trafficking events 11 825 71 -0.034 0.051 1000 -1000 -0.031 -1000
Visual signal transduction: Rods 11 603 52 -0.067 0.069 1000 -1000 -0.056 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 9 672 68 -0.057 0.046 1000 -1000 -0.066 -1000
Rapid glucocorticoid signaling 7 147 20 -0.016 0.038 1000 -1000 -0.015 -1000
Glypican 2 network 6 27 4 0.029 0.042 1000 -1000 0.027 -1000
LPA4-mediated signaling events 5 61 12 -0.026 0 1000 -1000 -0.015 -1000
Total 6078 327999 7203 -11 12 131000 -131000 -4.5 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 1.2 0.39 1.3 474 -10000 0 474
PLK1 0.32 0.38 0.96 111 -10000 0 111
BIRC5 0.35 0.41 1 119 -10000 0 119
HSPA1B 1.2 0.38 1.4 478 -10000 0 478
MAP2K1 0.48 0.17 0.52 498 -10000 0 498
BRCA2 1.4 0.52 1.5 477 -10000 0 477
FOXM1 1.9 0.91 2.3 462 -10000 0 462
XRCC1 1.2 0.42 1.4 476 -10000 0 476
FOXM1B/p19 0.27 0.47 1.1 123 -10000 0 123
Cyclin D1/CDK4 0.67 0.51 1.1 325 -10000 0 325
CDC2 1.5 0.49 1.7 482 -10000 0 482
TGFA 0.74 0.51 1.1 349 -10000 0 349
SKP2 1.4 0.55 1.5 480 -10000 0 480
CCNE1 0.009 0.033 0.13 33 -10000 0 33
CKS1B 1.5 0.57 1.7 482 -10000 0 482
RB1 0.037 0.18 0.79 25 -0.74 2 27
FOXM1C/SP1 0.9 0.44 1.1 417 -10000 0 417
AURKB 0.34 0.41 1 119 -0.74 1 120
CENPF 1.7 0.54 1.8 496 -10000 0 496
CDK4 0.13 0.072 0.18 343 -10000 0 343
MYC 0.6 0.54 1.1 288 -10000 0 288
CHEK2 0.41 0.18 0.48 467 -10000 0 467
ONECUT1 0.76 0.55 1.2 342 -10000 0 342
CDKN2A -0.023 0.11 -10000 0 -0.34 52 52
LAMA4 1.1 0.51 1.4 441 -1.1 3 444
FOXM1B/HNF6 0.77 0.56 1.2 337 -10000 0 337
FOS 1.1 0.55 1.4 425 -10000 0 425
SP1 -0.018 0.093 -10000 0 -0.1 206 206
CDC25B 1.2 0.44 1.4 480 -10000 0 480
response to radiation 0.25 0.074 0.27 497 -10000 0 497
CENPB 1.2 0.44 1.4 477 -10000 0 477
CENPA 1.2 0.4 1.4 477 -10000 0 477
NEK2 1.6 0.56 1.8 484 -10000 0 484
HIST1H2BA 1.2 0.42 1.4 477 -10000 0 477
CCNA2 0.009 0.031 0.12 30 -10000 0 30
EP300 0.027 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 1.4 0.58 1.7 455 -10000 0 455
CCNB2 1.7 0.53 1.8 496 -10000 0 496
CCNB1 1.8 0.65 2 479 -10000 0 479
ETV5 1.4 0.57 1.6 484 -10000 0 484
ESR1 1 0.56 1.3 415 -1 2 417
CCND1 0.78 0.55 1.2 348 -10000 0 348
GSK3A 0.27 0.1 0.31 471 -10000 0 471
Cyclin A-E1/CDK1-2 0.033 0.1 0.37 42 -10000 0 42
CDK2 0.076 0.071 0.14 284 -10000 0 284
G2/M transition of mitotic cell cycle 0.44 0.14 0.47 508 -10000 0 508
FOXM1B/Cbp/p300 0.089 0.26 0.92 25 -10000 0 25
GAS1 1 0.55 1.3 414 -1 1 415
MMP2 1.1 0.56 1.4 430 -1.1 4 434
RB1/FOXM1C 0.57 0.56 1.1 271 -10000 0 271
CREBBP 0.028 0.008 -10000 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.022 0.013 -10000 0 0 137 137
PLK4 0.015 0.015 -10000 0 0 269 269
regulation of centriole replication 0.067 0.11 0.19 229 -9999 0 229
Circadian rhythm pathway

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
chromatin modification 0.003 0.033 0.42 3 -10000 0 3
CLOCK 0.051 0.034 0.088 227 -0.042 13 240
TIMELESS/CRY2 0.21 0.22 0.45 242 -0.35 3 245
DEC1/BMAL1 0.058 0.028 -10000 0 -10000 0 0
ATR 0.022 0.013 -10000 0 0 139 139
NR1D1 0.13 0.24 0.43 22 -0.81 13 35
ARNTL 0.051 0.034 0.089 231 -0.042 13 244
TIMELESS 0.27 0.32 0.63 241 -0.37 3 244
NPAS2 0.051 0.034 0.088 229 -0.042 13 242
CRY2 0.029 0.003 -10000 0 0 6 6
mol:CO -0.095 0.11 0.13 3 -0.22 245 248
CHEK1 0.002 0.007 -10000 0 0 527 527
mol:HEME 0.095 0.11 0.22 245 -0.13 3 248
PER1 0.028 0.007 -10000 0 0 38 38
BMAL/CLOCK/NPAS2 0.14 0.13 0.3 226 -0.17 3 229
BMAL1/CLOCK 0.13 0.2 0.36 216 -0.59 8 224
S phase of mitotic cell cycle 0.003 0.033 0.42 3 -10000 0 3
TIMELESS/CHEK1/ATR 0.003 0.034 0.42 3 -10000 0 3
mol:NADPH 0.095 0.11 0.22 245 -0.13 3 248
PER1/TIMELESS 0.2 0.22 0.45 229 -0.35 3 232
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.029 0.005 -10000 0 0 16 16
TCGA08_retinoblastoma

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
CDKN2B -0.042 0.033 -10000 0 -0.064 328 328
CDKN2C -0.019 0.049 -10000 0 -0.064 276 276
CDKN2A 0.013 0.023 -10000 0 -0.063 7 7
CCND2 -0.022 0.039 -10000 0 -0.12 40 40
RB1 0.071 0.089 0.17 221 -0.2 7 228
CDK4 -0.015 0.038 -10000 0 -0.14 40 40
CDK6 -0.017 0.037 -10000 0 -0.13 39 39
G1/S progression -0.077 0.092 0.2 7 -0.18 205 212
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.12 0.045 0.14 1 -0.14 479 480
BUB1B 0.16 0.069 0.19 460 -0.14 1 461
PLK1 0.069 0.029 0.082 395 -10000 0 395
PLK1S1 0.034 0.017 0.053 177 -10000 0 177
KIF2A 0.048 0.032 0.14 13 -10000 0 13
regulation of mitotic centrosome separation 0.069 0.029 0.082 394 -10000 0 394
GOLGA2 0.029 0.005 -10000 0 0 16 16
Hec1/SPC24 0.005 0.019 -10000 0 -10000 0 0
WEE1 0.08 0.066 0.17 10 -0.26 12 22
cytokinesis 0.23 0.087 0.26 462 -0.16 1 463
PP2A-alpha B56 0.13 0.081 -10000 0 -0.49 6 6
AURKA 0.081 0.036 0.12 118 -10000 0 118
PICH/PLK1 0.11 0.083 0.17 332 -10000 0 332
CENPE 0.063 0.061 0.22 58 -10000 0 58
RhoA/GTP 0.022 0.007 -10000 0 -0.15 1 1
positive regulation of microtubule depolymerization 0.05 0.03 0.14 13 -10000 0 13
PPP2CA 0.029 0.004 -10000 0 0 13 13
FZR1 0.027 0.008 -10000 0 0 46 46
TPX2 0.11 0.031 0.12 455 -10000 0 455
PAK1 0.029 0.009 -10000 0 -0.03 1 1
SPC24 0.02 0.014 -10000 0 0 175 175
FBXW11 0.029 0.005 -10000 0 0 18 18
CLSPN 0.049 0.038 0.14 35 -0.2 5 40
GORASP1 0.029 0.003 -10000 0 0 5 5
metaphase 0.002 0.005 0.012 80 -0.01 1 81
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.034 0.017 0.053 177 -10000 0 177
G2 phase of mitotic cell cycle 0.005 0.003 0.018 21 -10000 0 21
STAG2 0.029 0.006 -10000 0 0 22 22
GRASP65/GM130/RAB1/GTP 0.026 0.033 -10000 0 -0.42 2 2
spindle elongation 0.069 0.029 0.082 394 -10000 0 394
ODF2 0.035 0.007 -10000 0 -0.03 2 2
BUB1 0.01 0.058 -10000 0 -0.61 3 3
TPT1 0.031 0.042 0.1 1 -0.15 24 25
CDC25C 0.084 0.061 0.14 237 -0.21 6 243
CDC25B 0.03 0.02 -10000 0 -0.029 45 45
SGOL1 0.12 0.045 0.14 479 -0.15 1 480
RHOA 0.029 0.003 -10000 0 0 6 6
CCNB1/CDK1 0.008 0.025 -10000 0 -0.14 1 1
CDC14B -0.014 0.003 0.001 20 -10000 0 20
CDC20 0.007 0.012 -10000 0 0 431 431
PLK1/PBIP1 0.04 0.026 0.074 120 -10000 0 120
mitosis 0 0.001 -10000 0 -10000 0 0
FBXO5 0.13 0.079 0.17 382 -0.12 6 388
CDC2 0.007 0.004 0.01 354 -10000 0 354
NDC80 0.003 0.009 -10000 0 0 503 503
metaphase plate congression 0.045 0.043 -10000 0 -0.2 12 12
ERCC6L 0.093 0.079 0.16 324 -0.15 1 325
NLP/gamma Tubulin 0.029 0.026 0.074 28 -0.082 9 37
microtubule cytoskeleton organization 0.031 0.042 0.1 1 -0.15 24 25
G2/M transition DNA damage checkpoint 0.001 0.002 0.016 3 -10000 0 3
PPP1R12A 0.031 0.006 -10000 0 -0.031 2 2
interphase 0.001 0.002 0.016 3 -10000 0 3
PLK1/PRC1-2 0.007 0.023 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.091 0.03 0.14 10 -10000 0 10
RAB1A 0.029 0.004 -10000 0 0 11 11
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.071 0.026 0.08 445 -10000 0 445
mitotic prometaphase 0.003 0.004 0.023 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.065 0.054 -10000 0 -0.29 3 3
microtubule-based process 0.009 0.023 0.099 6 -10000 0 6
Golgi organization 0.069 0.029 0.082 394 -10000 0 394
Cohesin/SA2 0.068 0.026 0.1 111 -10000 0 111
PPP1CB/MYPT1 0.045 0.014 -10000 0 -0.17 1 1
KIF20A 0.005 0.011 -10000 0 0 469 469
APC/C/CDC20 0.013 0.028 0.097 10 -10000 0 10
PPP2R1A 0.029 0.006 -10000 0 0 22 22
chromosome segregation 0.04 0.026 0.073 120 -10000 0 120
PRC1 0.007 0.013 -10000 0 0 424 424
ECT2 0.24 0.069 0.25 520 -10000 0 520
C13orf34 0.062 0.025 0.072 406 -10000 0 406
NUDC 0.045 0.044 0.13 1 -0.2 12 13
regulation of attachment of spindle microtubules to kinetochore 0.16 0.069 0.19 460 -0.14 1 461
spindle assembly 0.048 0.026 0.081 139 -10000 0 139
spindle stabilization 0.034 0.017 0.053 177 -10000 0 177
APC/C/HCDH1 -0.015 0.019 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.023 0.099 6 -10000 0 6
CCNB1 0.005 0.012 -10000 0 -0.026 1 1
PPP1CB 0.03 0.009 -10000 0 -0.028 7 7
BTRC 0.029 0.005 -10000 0 0 17 17
ROCK2 0.056 0.032 0.16 4 -0.22 3 7
TUBG1 0.03 0.046 0.12 5 -0.16 24 29
G2/M transition of mitotic cell cycle 0.12 0.08 0.17 370 -0.14 1 371
MLF1IP -0.013 0.014 0.14 3 -10000 0 3
INCENP 0.034 0.006 -10000 0 -0.031 2 2
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.029 0.005 -10000 0 0 15 15
mol:S1P -0.016 0.016 0.072 4 -0.033 95 99
S1P1/S1P/Gi -0.053 0.092 0.26 4 -0.23 49 53
GNAO1 -0.019 0.046 0.12 4 -0.063 284 288
S1P/S1P3/G12/G13 -0.015 0.047 0.16 4 -0.066 6 10
AKT1 -0.043 0.11 0.28 2 -0.5 21 23
AKT3 -0.54 0.5 0.67 3 -0.98 316 319
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.005 -10000 0 0 15 15
GNAI2 -0.022 0.047 0.12 4 -0.063 314 318
GNAI3 -0.017 0.04 0.1 2 -0.057 265 267
GNAI1 -0.018 0.044 0.1 4 -0.058 296 300
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.018 0.019 0.087 4 -0.038 108 112
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.15 0.43 4 -0.27 267 271
MAPK3 -0.14 0.14 0.38 4 -0.27 260 264
MAPK1 -0.14 0.14 0.38 4 -0.27 255 259
JAK2 -0.14 0.15 0.37 4 -0.28 236 240
CXCR4 -0.14 0.14 0.36 3 -0.27 256 259
FLT1 -0.025 0.052 0.16 4 -0.072 295 299
RhoA/GDP 0.022 0.007 -10000 0 -0.15 1 1
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
SRC -0.13 0.14 0.38 4 -0.27 237 241
S1P/S1P3/Gi -0.13 0.15 0.44 4 -0.27 267 271
RAC1 0.028 0.006 -10000 0 0 28 28
RhoA/GTP -0.12 0.15 0.36 4 -0.26 265 269
VEGFA -0.022 0.05 0.16 4 -0.07 272 276
S1P/S1P2/Gi -0.074 0.1 0.31 4 -0.25 49 53
VEGFR1 homodimer/VEGFA homodimer -0.029 0.075 0.34 4 -0.11 53 57
RHOA 0.029 0.003 -10000 0 0 6 6
S1P/S1P3/Gq -0.028 0.06 -10000 0 -0.2 48 48
GNAQ 0.028 0.006 -10000 0 0 28 28
GNAZ -0.017 0.043 0.1 4 -0.058 284 288
G12/G13 0.041 0.012 -10000 0 -10000 0 0
GNA14 0.029 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 47 47
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 14 14
GNA11 0.025 0.011 -10000 0 0 84 84
Rac1/GTP -0.12 0.15 0.36 4 -0.26 267 271
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.1 0.2 0.37 174 -0.32 1 175
NF kappa B1 p50/RelA/I kappa B alpha 0.11 0.24 0.44 169 -0.33 5 174
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.058 0.16 59 -0.19 7 66
AP1 0.087 0.28 0.49 149 -0.37 6 155
ILK 0.075 0.17 0.34 122 -0.3 2 124
bone resorption -0.009 0.15 0.25 79 -0.34 3 82
PTK2B 0.024 0.011 -10000 0 0 99 99
PYK2/p130Cas 0.064 0.14 0.27 93 -0.27 3 96
ITGAV 0.009 0.061 0.1 165 -10000 0 165
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.039 0.1 -10000 0 -0.16 217 217
alphaV/beta3 Integrin/Osteopontin 0.023 0.1 0.26 59 -0.16 61 120
MAP3K1 0.075 0.17 0.34 118 -0.3 2 120
JUN 0.027 0.027 0.098 29 -0.035 57 86
MAPK3 0.13 0.25 0.48 176 -0.32 1 177
MAPK1 0.14 0.25 0.48 174 -0.32 1 175
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 47 47
MAPK8 0.074 0.18 0.36 121 -0.3 2 123
ITGB3 0.013 0.06 0.1 163 -10000 0 163
NFKBIA 0.13 0.25 0.48 175 -0.33 2 177
FOS 0.024 0.026 0.095 24 -0.035 45 69
CD44 0.017 0.015 -10000 0 0 239 239
CHUK 0.028 0.007 -10000 0 0 36 36
PLAU 0.19 0.37 0.72 170 -0.58 3 173
NF kappa B1 p50/RelA 0.12 0.27 0.5 165 -10000 0 165
BCAR1 0.027 0.009 -10000 0 0 59 59
RELA 0.029 0.003 -10000 0 0 6 6
alphaV beta3 Integrin 0.042 0.11 0.17 154 -0.18 65 219
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.069 0.16 0.31 120 -0.29 2 122
VAV3 0.069 0.16 0.29 141 -0.28 2 143
MAP3K14 0.12 0.22 0.4 176 -0.29 2 178
ROCK2 0.029 0.005 -10000 0 0 18 18
SPP1 -0.004 0.039 0.091 65 -10000 0 65
RAC1 0.028 0.006 -10000 0 0 28 28
Rac1/GTP 0.056 0.15 0.26 135 -0.27 2 137
MMP2 0.018 0.19 0.34 86 -0.35 35 121
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.001 0.048 -10000 0 -0.4 5 5
Crk/p130 Cas/Paxillin -0.17 0.097 -10000 0 -0.26 220 220
JUN -0.07 0.091 0.18 3 -0.26 23 26
HRAS 0.028 0.006 -10000 0 0 28 28
RET51/GFRalpha1/GDNF/GRB10 -0.017 0.1 -10000 0 -0.14 221 221
RAP1A 0.029 0.003 -10000 0 0 7 7
FRS2 0.028 0.007 -10000 0 0 30 30
RAP1A/GDP 0.022 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.017 0.1 -10000 0 -0.14 222 222
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.004 -10000 0 0 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 0 37 37
RET9/GFRalpha1/GDNF/Enigma -0.024 0.089 -10000 0 -0.13 224 224
RHOA 0.029 0.003 -10000 0 0 6 6
RAP1A/GTP -0.018 0.098 -10000 0 -0.13 219 219
GRB7 0.027 0.008 -10000 0 0 42 42
RET51/GFRalpha1/GDNF -0.011 0.097 -10000 0 -0.14 186 186
MAPKKK cascade -0.09 0.077 0.11 1 -0.24 2 3
BCAR1 0.027 0.009 -10000 0 0 59 59
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.097 -10000 0 -0.16 403 403
lamellipodium assembly -0.15 0.096 -10000 0 -0.24 233 233
RET51/GFRalpha1/GDNF/SHC -0.016 0.1 -10000 0 -0.14 217 217
PIK3CA 0.021 0.014 -10000 0 0 171 171
RET9/GFRalpha1/GDNF/SHC -0.023 0.088 -10000 0 -0.13 220 220
RET9/GFRalpha1/GDNF/Shank3 -0.031 0.084 -10000 0 -0.13 223 223
MAPK3 -0.071 0.079 0.29 4 -0.22 9 13
DOK1 0.029 0.004 -10000 0 0 10 10
DOK6 0.027 0.008 -10000 0 0 49 49
PXN 0.029 0.005 -10000 0 0 14 14
neurite development -0.077 0.086 0.25 6 -0.29 20 26
DOK5 0.017 0.015 -10000 0 0 245 245
GFRA1 0.016 0.015 -10000 0 0 257 257
MAPK8 -0.071 0.088 0.18 1 -0.26 23 24
HRAS/GTP -0.035 0.12 -10000 0 -0.18 200 200
tube development -0.035 0.082 0.21 4 -0.13 218 222
MAPK1 -0.067 0.075 0.3 3 -10000 0 3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.057 0.089 -10000 0 -0.17 205 205
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
SRC 0.028 0.007 -10000 0 0 31 31
PDLIM7 0.029 0.005 -10000 0 0 17 17
RET51/GFRalpha1/GDNF/Dok6 -0.015 0.11 -10000 0 -0.14 212 212
SHC1 0.029 0.006 -10000 0 0 20 20
RET51/GFRalpha1/GDNF/Dok4 -0.018 0.1 -10000 0 -0.14 221 221
RET51/GFRalpha1/GDNF/Dok5 0.01 0.1 -10000 0 -0.15 134 134
PRKCA 0.029 0.006 -10000 0 0 23 23
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
CREB1 -0.062 0.11 0.22 1 -0.38 7 8
PIK3R1 0.021 0.013 -10000 0 0 161 161
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.093 -10000 0 -0.18 216 216
RET51/GFRalpha1/GDNF/Grb7 -0.018 0.1 -10000 0 -0.14 219 219
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.029 0.004 -10000 0 0 11 11
DOK4 0.028 0.008 -10000 0 0 39 39
JNK cascade -0.069 0.091 0.18 5 -0.25 23 28
RET9/GFRalpha1/GDNF/FRS2 -0.023 0.087 -10000 0 -0.13 215 215
SHANK3 0.023 0.013 -10000 0 0 132 132
RASA1 0.027 0.008 -10000 0 0 50 50
NCK1 0.026 0.009 -10000 0 0 63 63
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.088 -10000 0 -0.17 200 200
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.054 0.091 0.2 1 -0.27 7 8
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.1 0.2 1 -0.18 204 205
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.092 -10000 0 -0.3 5 5
PI3K -0.19 0.14 0.33 1 -0.34 229 230
SOS1 0.028 0.007 -10000 0 0 34 34
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.024 0.092 -10000 0 -0.13 218 218
GRB10 0.029 0.004 -10000 0 0 12 12
activation of MAPKK activity -0.049 0.089 0.18 1 -0.28 4 5
RET51/GFRalpha1/GDNF/FRS2 -0.015 0.1 -10000 0 -0.14 212 212
GAB1 0.028 0.006 -10000 0 0 25 25
IRS1 0.011 0.014 -10000 0 0 349 349
IRS2 0.028 0.006 -10000 0 0 25 25
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.059 0.095 -10000 0 -0.27 16 16
RET51/GFRalpha1/GDNF/PKC alpha -0.016 0.1 -10000 0 -0.14 220 220
GRB2 0.029 0.006 -10000 0 0 20 20
PRKACA 0.025 0.01 -10000 0 0 80 80
GDNF 0.028 0.007 -10000 0 0 36 36
RAC1 0.028 0.006 -10000 0 0 28 28
RET51/GFRalpha1/GDNF/IRS1 -0.11 0.11 -10000 0 -0.17 394 394
Rac1/GTP -0.17 0.12 -10000 0 -0.28 225 225
RET9/GFRalpha1/GDNF -0.034 0.083 -10000 0 -0.13 225 225
GFRalpha1/GDNF -0.044 0.099 -10000 0 -0.16 225 225
Effects of Botulinum toxin

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
STX1A -0.017 0.002 0 8 -10000 0 8
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.042 0.01 -10000 0 -10000 0 0
STXBP1 0.026 0.01 -10000 0 0 76 76
ACh/CHRNA1 -0.042 0.044 -10000 0 -0.073 365 365
RAB3GAP2/RIMS1/UNC13B 0.054 0.018 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.029 0.006 -10000 0 0 20 20
mol:ACh -0.055 0.038 0.09 1 -0.081 361 362
RAB3GAP2 0.028 0.006 -10000 0 0 27 27
STX1A/SNAP25/VAMP2 -0.099 0.096 -10000 0 -0.17 342 342
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.042 0.044 -10000 0 -0.073 365 365
UNC13B 0.029 0.005 -10000 0 0 14 14
CHRNA1 0.028 0.007 -10000 0 0 37 37
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.042 0.044 -10000 0 -0.073 364 364
SNAP25 0.001 0 -10000 0 -10000 0 0
VAMP2 -0.12 0.082 -10000 0 -0.18 388 388
SYT1 0.028 0.007 -10000 0 0 34 34
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.036 0.033 -10000 0 -0.13 57 57
STX1A/SNAP25 fragment 1/VAMP2 -0.099 0.096 -10000 0 -0.17 342 342
Nongenotropic Androgen 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
PTK2 -0.012 0.008 0 163 -10000 0 163
GNB1/GNG2 -0.052 0.09 -10000 0 -0.13 314 314
regulation of S phase of mitotic cell cycle -0.08 0.11 0.14 1 -0.2 224 225
GNAO1 0.027 0.009 -10000 0 -0.002 50 50
HRAS 0.022 0.021 -10000 0 -0.023 89 89
SHBG/T-DHT 0.019 0.004 -10000 0 -10000 0 0
PELP1 0.022 0.021 -10000 0 -0.033 64 64
AKT1 -0.016 0.004 0 28 -10000 0 28
MAP2K1 -0.082 0.098 0.24 15 -0.24 36 51
T-DHT/AR -0.077 0.082 -10000 0 -0.15 319 319
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.003 0.011 26 -0.008 7 33
GNAI2 0.029 0.007 -10000 0 -0.015 12 12
GNAI3 0.024 0.012 -10000 0 0 99 99
GNAI1 0.028 0.007 -10000 0 -0.002 29 29
mol:GDP -0.16 0.14 -10000 0 -0.29 270 270
cell proliferation -0.12 0.18 0.39 23 -0.47 63 86
PIK3CA 0.021 0.014 -10000 0 0 171 171
FOS -0.1 0.26 0.56 26 -0.71 66 92
mol:Ca2+ -0.012 0.023 0.055 16 -0.059 31 47
MAPK3 -0.11 0.14 0.32 24 -0.37 60 84
MAPK1 -0.063 0.15 0.31 26 -0.48 35 61
PIK3R1 0.021 0.013 -10000 0 0 161 161
mol:IP3 0 0.004 0.016 26 -10000 0 26
cAMP biosynthetic process -0.001 0.025 0.27 3 -10000 0 3
GNG2 0.029 0.004 -10000 0 0 12 12
potassium channel inhibitor activity 0 0.004 0.016 26 -10000 0 26
HRAS/GTP -0.049 0.093 0.22 12 -0.13 280 292
actin cytoskeleton reorganization 0.003 0.056 -10000 0 -0.12 75 75
SRC 0.022 0.02 -10000 0 -0.033 59 59
voltage-gated calcium channel activity 0 0.004 0.016 26 -10000 0 26
PI3K 0.002 0.056 -10000 0 -0.13 75 75
apoptosis 0.086 0.18 0.45 68 -0.45 24 92
T-DHT/AR/PELP1 -0.062 0.083 -10000 0 -0.13 315 315
HRAS/GDP -0.15 0.15 0.13 3 -0.3 235 238
CREB1 -0.11 0.15 0.24 1 -0.46 78 79
RAC1-CDC42/GTP 0.009 0.061 -10000 0 -0.12 75 75
AR 0.01 0.017 -10000 0 -0.034 23 23
GNB1 0.028 0.006 -10000 0 0 24 24
RAF1 -0.075 0.09 0.22 14 -0.21 24 38
RAC1-CDC42/GDP -0.15 0.15 -10000 0 -0.31 226 226
T-DHT/AR/PELP1/Src -0.05 0.089 -10000 0 -0.13 281 281
MAP2K2 -0.092 0.1 0.25 11 -0.26 38 49
T-DHT/AR/PELP1/Src/PI3K -0.08 0.11 0.14 1 -0.2 224 225
GNAZ 0.027 0.009 -10000 0 -0.001 49 49
SHBG 0.028 0.006 -10000 0 0 26 26
Gi family/GNB1/GNG2/GDP -0.041 0.1 -10000 0 -0.36 25 25
mol:T-DHT 0 0.001 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 28 28
GNRH1 -0.014 0.007 0 104 -10000 0 104
Gi family/GTP -0.045 0.066 0.17 1 -0.2 35 36
CDC42 0.029 0.004 -10000 0 0 11 11
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.025 0.011 -10000 0 0 96 96
HRAS 0.028 0.006 -10000 0 0 28 28
EGFR 0.027 0.009 -10000 0 0 55 55
AKT -0.031 0.12 0.22 29 -0.24 50 79
FOXO3 0.028 0.007 -10000 0 0 38 38
AKT1 0.028 0.006 -10000 0 0 28 28
FOXO1 0.028 0.008 -10000 0 0 39 39
AKT3 0.012 0.015 -10000 0 0 333 333
FOXO4 0.029 0.003 -10000 0 0 7 7
MET 0.025 0.011 -10000 0 0 87 87
PIK3CA 0.021 0.014 -10000 0 0 171 171
PIK3CB 0.025 0.011 -10000 0 0 82 82
NRAS 0.014 0.015 -10000 0 0 300 300
PIK3CG 0.028 0.007 -10000 0 0 37 37
PIK3R3 0.019 0.014 -10000 0 0 207 207
PIK3R2 0.027 0.008 -10000 0 0 49 49
NF1 0.026 0.009 -10000 0 0 62 62
RAS 0.045 0.075 0.17 79 -0.25 4 83
ERBB2 0.027 0.008 -10000 0 0 43 43
proliferation/survival/translation 0.016 0.12 0.29 40 -0.22 12 52
PI3K 0.04 0.096 0.2 79 -0.21 21 100
PIK3R1 0.021 0.013 -10000 0 0 161 161
KRAS 0.024 0.011 -10000 0 0 99 99
FOXO 0.025 0.082 0.22 35 -10000 0 35
AKT2 0.027 0.009 -10000 0 0 51 51
PTEN 0.028 0.007 -10000 0 0 31 31
IGF1 pathway

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
NCK2 0.029 0.004 -10000 0 0 11 11
PTK2 0.021 0.014 -10000 0 0 163 163
CRKL -0.079 0.075 0.13 6 -0.2 126 132
GRB2/SOS1/SHC 0.053 0.02 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 28 28
IRS1/Crk -0.079 0.073 0.099 3 -0.2 126 129
IGF-1R heterotetramer/IGF1/PTP1B 0.011 0.099 -10000 0 -0.17 121 121
AKT1 -0.051 0.11 0.15 47 -0.23 75 122
BAD -0.059 0.1 0.16 22 -0.23 74 96
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.078 0.074 0.12 5 -0.2 124 129
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.082 0.073 0.17 3 -0.22 103 106
RAF1 -0.036 0.11 0.27 3 -0.47 3 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.048 0.1 0.18 2 -0.2 124 126
YWHAZ 0.026 0.01 -10000 0 0 79 79
IGF-1R heterotetramer/IGF1/IRS1 -0.06 0.094 0.16 2 -0.21 134 136
PIK3CA 0.021 0.014 -10000 0 0 171 171
RPS6KB1 -0.053 0.11 0.15 44 -0.23 73 117
GNB2L1 0.029 0.005 -10000 0 0 15 15
positive regulation of MAPKKK cascade -0.03 0.1 0.26 9 -0.35 3 12
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 161 161
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.088 0.067 -10000 0 -0.2 116 116
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.036 0.11 -10000 0 -0.15 115 115
IGF-1R heterotetramer 0.006 0.037 0.046 226 -0.089 8 234
IGF-1R heterotetramer/IGF1/IRS/Nck -0.055 0.098 0.17 3 -0.2 134 137
Crk/p130 Cas/Paxillin -0.06 0.1 0.22 2 -0.2 133 135
IGF1R 0.006 0.037 0.046 226 -0.089 8 234
IGF1 -0.007 0.052 0.046 242 -0.089 93 335
IRS2/Crk -0.081 0.071 0.16 2 -0.22 99 101
PI3K -0.052 0.1 -10000 0 -0.19 153 153
apoptosis 0.047 0.1 0.25 22 -0.2 15 37
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
PRKCD -0.08 0.11 -10000 0 -0.28 112 112
RAF1/14-3-3 E -0.031 0.11 0.25 4 -0.41 3 7
BAD/14-3-3 -0.05 0.11 0.21 14 -0.26 22 36
PRKCZ -0.053 0.11 0.15 45 -0.23 74 119
Crk/p130 Cas/Paxillin/FAK1 -0.056 0.095 0.14 13 -0.24 48 61
PTPN1 0.027 0.008 -10000 0 0 49 49
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.074 0.12 -10000 0 -0.28 124 124
BCAR1 0.027 0.009 -10000 0 0 59 59
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.027 0.1 0.18 1 -0.15 121 122
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.007 -10000 0 0 34 34
IRS1/NCK2 -0.081 0.075 0.12 9 -0.2 130 139
GRB10 0.029 0.004 -10000 0 0 12 12
PTPN11 -0.08 0.074 0.13 6 -0.2 129 135
IRS1 -0.056 0.089 0.12 9 -0.21 128 137
IRS2 -0.078 0.074 0.13 6 -0.2 125 131
IGF-1R heterotetramer/IGF1 -0.003 0.12 0.15 3 -0.21 128 131
GRB2 0.029 0.006 -10000 0 0 20 20
PDPK1 -0.047 0.12 0.19 28 -0.23 77 105
YWHAE 0.028 0.008 -10000 0 0 41 41
PRKD1 -0.076 0.11 0.18 6 -0.28 109 115
SHC1 0.029 0.006 -10000 0 0 20 20
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.034 0.073 0.2 82 -0.32 1 83
STMN1 0.033 0.093 0.2 126 -10000 0 126
Aurora B/RasGAP/Survivin 0.047 0.039 -10000 0 -0.11 1 1
Chromosomal passenger complex/Cul3 protein complex 0.008 0.097 0.21 47 -0.19 18 65
BIRC5 0.038 0.022 0.062 64 -10000 0 64
DES -0.052 0.14 -10000 0 -0.49 30 30
Aurora C/Aurora B/INCENP 0.054 0.035 -10000 0 -10000 0 0
Aurora B/TACC1 -0.063 0.072 -10000 0 -0.13 311 311
Aurora B/PP2A 0.037 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.005 0.014 0.12 3 -0.11 3 6
mitotic metaphase/anaphase transition -0.005 0.005 0.02 1 -10000 0 1
NDC80 0.13 0.1 0.21 356 -10000 0 356
Cul3 protein complex -0.011 0.094 -10000 0 -0.14 178 178
KIF2C 0.11 0.096 0.2 296 -10000 0 296
PEBP1 0.043 0.009 -10000 0 -0.032 1 1
KIF20A 0.002 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.035 0.026 -10000 0 -0.15 2 2
SEPT1 0.029 0.004 -10000 0 0 12 12
SMC2 0.017 0.015 -10000 0 0 246 246
SMC4 0.001 0.006 -10000 0 0 534 534
NSUN2/NPM1/Nucleolin 0 0.046 -10000 0 -0.47 4 4
PSMA3 0.029 0.005 -10000 0 0 17 17
G2/M transition of mitotic cell cycle 0 0.003 0.018 2 -10000 0 2
H3F3B 0.009 0.018 0.14 1 -0.2 3 4
AURKB 0.028 0.019 -10000 0 -10000 0 0
AURKC 0.028 0.006 -10000 0 0 28 28
CDCA8 0.042 0.021 0.064 85 -10000 0 85
cytokinesis 0.004 0.034 0.24 10 -10000 0 10
Aurora B/Septin1 0.14 0.13 0.26 252 -10000 0 252
AURKA 0.002 0.007 -10000 0 -10000 0 0
INCENP 0.052 0.013 0.068 142 -10000 0 142
KLHL13 0.019 0.014 -10000 0 0 194 194
BUB1 0.002 0.008 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.009 0.024 -10000 0 -10000 0 0
EVI5 0.04 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.002 0.013 -10000 0 -10000 0 0
SGOL1 0.004 0.01 -10000 0 0 485 485
CENPA 0.017 0.048 0.17 29 -10000 0 29
NCAPG 0.002 0.007 -10000 0 0 523 523
Aurora B/HC8 Proteasome 0.036 0.024 -10000 0 -0.16 1 1
NCAPD2 0.014 0.015 -10000 0 0 297 297
Aurora B/PP1-gamma 0.037 0.023 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 6 6
NCAPH 0.011 0.014 -10000 0 0 347 347
NPM1 -0.002 0.038 -10000 0 -0.56 2 2
RASA1 0.027 0.008 -10000 0 0 50 50
KLHL9 0.028 0.007 -10000 0 0 37 37
mitotic prometaphase 0.013 0.006 0.021 154 -10000 0 154
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.024 -10000 0 -0.16 1 1
PPP1CC 0.029 0.006 -10000 0 0 23 23
Centraspindlin 0.002 0.013 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.007 -10000 0 -0.15 1 1
NSUN2 0 0.012 -10000 0 -0.29 1 1
MYLK -0.005 0.054 0.14 1 -0.2 38 39
KIF23 0.001 0.005 -10000 0 -10000 0 0
VIM 0.011 0.068 0.18 71 -10000 0 71
RACGAP1 0.005 0.013 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0.012 -10000 0 -0.29 1 1
Chromosomal passenger complex 0.18 0.12 0.24 390 -10000 0 390
Chromosomal passenger complex/EVI5 0.064 0.057 -10000 0 -10000 0 0
TACC1 0.005 0.011 -10000 0 0 458 458
PPP2R5D 0.028 0.006 -10000 0 0 25 25
CUL3 0.029 0.004 -10000 0 0 10 10
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.044 0.21 0.39 135 -0.32 3 138
PTK2B 0.024 0.013 -10000 0 -0.03 5 5
mol:Ca2+ 0.036 0.2 0.57 11 -0.68 7 18
EDN1 0.026 0.15 0.26 132 -0.22 4 136
EDN3 0.027 0.009 -10000 0 0 58 58
EDN2 0.027 0.008 -10000 0 0 48 48
HRAS/GDP 0.017 0.21 0.42 33 -0.44 31 64
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.024 0.16 0.27 80 -0.37 28 108
ADCY4 0.088 0.19 0.3 216 -0.28 3 219
ADCY5 0.086 0.19 0.3 214 -0.28 3 217
ADCY6 0.089 0.2 0.3 217 -0.28 3 220
ADCY7 0.086 0.19 0.3 210 -0.28 3 213
ADCY1 0.09 0.19 0.32 182 -0.28 3 185
ADCY2 0.085 0.19 0.3 205 -0.29 2 207
ADCY3 0.089 0.19 0.3 215 -0.28 3 218
ADCY8 0.001 0.13 0.3 60 -0.27 20 80
ADCY9 0.084 0.2 0.3 208 -0.27 9 217
arachidonic acid secretion -0.1 0.27 0.59 20 -0.57 77 97
ETB receptor/Endothelin-1/Gq/GTP 0.042 0.14 0.25 91 -0.3 29 120
GNAO1 0.027 0.008 -10000 0 0 46 46
HRAS 0.023 0.02 0.053 4 -0.02 88 92
ETA receptor/Endothelin-1/G12/GTP 0.04 0.17 0.39 69 -0.24 11 80
ETA receptor/Endothelin-1/Gs/GTP 0.041 0.16 0.37 73 -0.21 17 90
mol:GTP 0.003 0.015 0.058 32 -10000 0 32
COL3A1 0.042 0.25 0.55 95 -0.42 4 99
EDNRB 0.051 0.11 0.22 174 -0.12 3 177
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.013 0.24 0.39 124 -0.38 78 202
CYSLTR1 0.038 0.22 0.41 122 -0.32 4 126
SLC9A1 0.028 0.14 0.26 124 -0.29 6 130
mol:GDP 0.014 0.21 0.43 31 -0.44 36 67
SLC9A3 0.072 0.2 0.43 12 -0.58 16 28
RAF1 0.003 0.24 0.55 28 -0.44 58 86
JUN 0.031 0.21 0.69 11 -0.75 9 20
JAK2 0.038 0.21 0.39 126 -0.32 4 130
mol:IP3 0.021 0.17 0.31 82 -0.39 28 110
ETA receptor/Endothelin-1 -0.054 0.097 0.33 5 -0.37 4 9
PLCB1 0.022 0.022 0.065 8 -0.034 61 69
PLCB2 0.021 0.026 0.076 18 -0.035 78 96
ETA receptor/Endothelin-3 0.016 0.11 0.21 121 -0.19 2 123
FOS -0.057 0.35 0.73 24 -0.83 67 91
Gai/GDP -0.001 0.2 -10000 0 -0.69 38 38
CRK 0.028 0.01 -10000 0 -0.03 6 6
mol:Ca ++ 0.078 0.25 0.4 156 -0.4 24 180
BCAR1 0.023 0.017 -10000 0 -0.029 37 37
PRKCB1 0.039 0.18 0.29 88 -0.37 30 118
GNAQ 0.02 0.031 0.11 13 -0.039 38 51
GNAZ 0.027 0.008 -10000 0 0 47 47
GNAL 0.029 0.006 -10000 0 0 20 20
Gs family/GDP 0.014 0.2 0.4 31 -0.41 35 66
ETA receptor/Endothelin-1/Gq/GTP 0.015 0.17 0.3 81 -0.37 31 112
MAPK14 0.025 0.13 0.29 25 -0.31 24 49
TRPC6 0.035 0.2 0.57 11 -0.71 7 18
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.024 0.011 -10000 0 0 98 98
GNAI1 0.028 0.006 -10000 0 0 27 27
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.034 0.14 0.29 34 -0.32 28 62
ETB receptor/Endothelin-2 0.071 0.068 0.17 157 -0.084 5 162
ETB receptor/Endothelin-3 0.071 0.068 0.17 156 -0.083 4 160
ETB receptor/Endothelin-1 0.032 0.15 0.36 81 -0.22 3 84
MAPK3 -0.051 0.34 0.69 24 -0.77 69 93
MAPK1 -0.053 0.34 0.69 24 -0.76 70 94
Rac1/GDP 0.015 0.2 0.42 29 -0.42 35 64
cAMP biosynthetic process 0.051 0.18 0.28 134 -0.29 22 156
MAPK8 0.029 0.22 0.58 11 -0.72 13 24
SRC 0.028 0.01 -10000 0 -0.03 7 7
ETB receptor/Endothelin-1/Gi/GTP 0.054 0.11 0.21 154 -0.24 9 163
p130Cas/CRK/Src/PYK2 0.007 0.22 0.49 22 -0.53 25 47
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.015 0.2 0.42 29 -0.43 34 63
COL1A2 0.08 0.28 0.66 91 -0.5 5 96
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.013 0.11 0.2 117 -0.22 1 118
mol:DAG 0.021 0.17 0.31 82 -0.39 28 110
MAP2K2 -0.031 0.27 0.63 24 -0.56 71 95
MAP2K1 -0.02 0.28 0.64 24 -0.57 65 89
EDNRA 0.023 0.15 0.27 134 -0.22 12 146
positive regulation of muscle contraction 0.028 0.17 0.32 129 -0.28 3 132
Gq family/GDP -0.027 0.17 0.42 15 -0.41 31 46
HRAS/GTP 0.021 0.21 0.44 33 -0.43 36 69
PRKCH 0.032 0.18 0.35 34 -0.39 28 62
RAC1 0.028 0.006 -10000 0 0 28 28
PRKCA 0.035 0.17 0.29 84 -0.37 26 110
PRKCB 0.039 0.18 0.29 89 -0.37 30 119
PRKCE 0.035 0.18 0.35 39 -0.37 29 68
PRKCD 0.031 0.18 0.36 34 -0.38 31 65
PRKCG 0.035 0.18 0.38 31 -0.37 28 59
regulation of vascular smooth muscle contraction -0.083 0.4 0.72 24 -1 68 92
PRKCQ 0.035 0.18 0.35 42 -0.39 28 70
PLA2G4A -0.11 0.29 0.6 20 -0.63 78 98
GNA14 0.02 0.031 0.11 13 -0.041 18 31
GNA15 0.022 0.026 0.095 13 -0.034 67 80
GNA12 0.028 0.007 -10000 0 0 34 34
GNA11 0.021 0.025 0.096 11 -0.034 58 69
Rac1/GTP 0.04 0.17 0.39 68 -0.24 9 77
MMP1 0.032 0.11 0.4 34 -10000 0 34
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.008 -10000 0 0 50 50
HDAC3 0.029 0.003 -10000 0 0 7 7
VDR 0.029 0.004 -10000 0 0 8 8
Cbp/p300/PCAF 0.032 0.026 -10000 0 -0.13 10 10
EP300 0.027 0.009 -10000 0 0 51 51
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.032 0.081 0.17 1 -0.27 33 34
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.005 -10000 0 0 19 19
AKT1 0.008 0.09 0.21 13 -0.23 12 25
RAR alpha/9cRA/Cyclin H -0.076 0.13 -10000 0 -0.24 199 199
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.034 0.076 -10000 0 -0.24 42 42
CDC2 -0.005 0.007 -10000 0 -0.018 16 16
response to UV -0.009 0.012 -10000 0 -0.025 208 208
RAR alpha/Jnk1 -0.025 0.07 -10000 0 -0.22 25 25
NCOR2 0.029 0.005 -10000 0 0 17 17
VDR/VDR/Vit D3 0.022 0.003 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.2 0.26 -10000 0 -0.51 215 215
NCOA2 0.027 0.008 -10000 0 0 46 46
NCOA3 0.027 0.009 -10000 0 0 59 59
NCOA1 0.029 0.005 -10000 0 0 14 14
VDR/VDR/DNA 0.029 0.004 -10000 0 0 8 8
RARG 0.003 0.033 -10000 0 -0.037 222 222
RAR gamma1/9cRA 0.01 0.033 -10000 0 -10000 0 0
MAPK3 0.001 0.036 -10000 0 -0.041 224 224
MAPK1 0.027 0.008 -10000 0 0 42 42
MAPK8 -0.002 0.04 -10000 0 -0.053 206 206
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.17 -10000 0 -0.33 211 211
RARA -0.029 0.053 -10000 0 -0.22 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.032 0.073 -10000 0 -0.24 39 39
PRKCA -0.012 0.053 -10000 0 -0.083 200 200
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.22 0.29 -10000 0 -0.57 218 218
RXRG -0.027 0.061 -10000 0 -0.24 5 5
RXRA -0.079 0.092 -10000 0 -0.27 28 28
RXRB -0.026 0.052 -10000 0 -0.22 3 3
VDR/Vit D3/DNA 0.022 0.003 -10000 0 -10000 0 0
RBP1 0.019 0.014 -10000 0 0 196 196
CRBP1/9-cic-RA -0.028 0.076 -10000 0 -0.15 158 158
RARB -0.003 0.04 -10000 0 -0.055 206 206
PRKCG -0.012 0.053 -10000 0 -0.08 205 205
MNAT1 0.029 0.005 -10000 0 0 14 14
RAR alpha/RXRs -0.11 0.19 0.26 1 -0.37 155 156
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.095 0.15 -10000 0 -0.3 132 132
proteasomal ubiquitin-dependent protein catabolic process -0.043 0.09 -10000 0 -0.29 34 34
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.22 0.29 -10000 0 -0.58 216 216
positive regulation of DNA binding -0.076 0.12 -10000 0 -0.22 199 199
NRIP1 -0.39 0.51 -10000 0 -1 213 213
RXRs/RARs -0.15 0.21 -10000 0 -0.4 215 215
RXRs/RXRs/DNA/9cRA -0.13 0.16 -10000 0 -0.33 212 212
PRKACA 0.025 0.01 -10000 0 0 80 80
CDK7 0.026 0.01 -10000 0 0 74 74
TFIIH 0.05 0.023 -10000 0 -10000 0 0
RAR alpha/9cRA -0.008 0.083 -10000 0 -0.24 18 18
CCNH 0.027 0.008 -10000 0 0 47 47
CREBBP 0.028 0.008 -10000 0 0 40 40
RAR gamma2/9cRA 0.006 0.056 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.005 -10000 0 0 15 15
mol:PIP3 -0.12 0.11 0.14 15 -0.25 226 241
FRAP1 -0.003 0.066 -10000 0 -0.42 8 8
AKT1 -0.1 0.12 0.16 19 -0.22 207 226
INSR 0.025 0.011 -10000 0 0 85 85
Insulin Receptor/Insulin 0.022 0.047 -10000 0 -0.13 43 43
mol:GTP -0.091 0.11 0.18 7 -0.25 55 62
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.049 0.05 -10000 0 -0.19 13 13
TSC2 0.029 0.006 -10000 0 0 22 22
RHEB/GDP -0.085 0.09 0.11 18 -0.19 173 191
TSC1 0.029 0.006 -10000 0 0 21 21
Insulin Receptor/IRS1 -0.15 0.14 -10000 0 -0.27 335 335
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.047 0.06 0.14 1 -0.22 13 14
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.029 0.004 -10000 0 0 10 10
RPS6KB1 -0.036 0.086 0.21 4 -0.3 14 18
MAP3K5 -0.006 0.047 0.19 6 -0.2 25 31
PIK3R1 0.021 0.014 -10000 0 -0.03 2 2
apoptosis -0.006 0.047 0.19 6 -0.2 26 32
mol:LY294002 -0.001 0.001 0.001 1 -0.001 344 345
EIF4B -0.039 0.081 0.21 6 -0.27 14 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.025 0.089 0.2 4 -0.26 13 17
eIF4E/eIF4G1/eIF4A1 -0.028 0.044 -10000 0 -0.25 7 7
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.12 0.13 -10000 0 -0.25 245 245
mTOR/RHEB/GTP/Raptor/GBL -0.029 0.056 0.16 5 -0.17 7 12
FKBP1A 0.021 0.02 -10000 0 -0.029 71 71
RHEB/GTP -0.08 0.097 0.15 20 -0.24 37 57
mol:Amino Acids -0.001 0.001 0.001 1 -0.001 344 345
FKBP12/Rapamycin 0.016 0.014 -10000 0 -10000 0 0
PDPK1 -0.12 0.11 0.13 28 -0.24 212 240
EIF4E 0.028 0.008 -10000 0 0 39 39
ASK1/PP5C 0.003 0.14 -10000 0 -0.54 30 30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.005 0.071 -10000 0 -0.25 40 40
TSC1/TSC2 -0.096 0.12 0.18 15 -0.27 54 69
tumor necrosis factor receptor activity 0.001 0.001 0.001 344 -0.001 1 345
RPS6 0.028 0.007 -10000 0 0 32 32
PPP5C 0.028 0.006 -10000 0 0 25 25
EIF4G1 0.025 0.011 -10000 0 0 94 94
IRS1 -0.16 0.13 -10000 0 -0.27 346 346
INS 0.028 0.006 -10000 0 0 24 24
PTEN 0.014 0.026 -10000 0 -0.03 140 140
PDK2 -0.12 0.11 0.14 15 -0.24 214 229
EIF4EBP1 -0.05 0.27 -10000 0 -1 40 40
PIK3CA 0.013 0.021 -10000 0 -0.029 68 68
PPP2R5D -0.005 0.068 0.23 6 -0.36 8 14
peptide biosynthetic process -0.035 0.039 0.18 9 -0.22 1 10
RHEB 0.027 0.009 -10000 0 0 53 53
EIF4A1 0.028 0.006 -10000 0 0 26 26
mol:Rapamycin 0 0.001 0.003 19 -0.002 3 22
EEF2 -0.035 0.039 0.18 9 -0.22 1 10
eIF4E/4E-BP1 -0.035 0.26 -10000 0 -0.96 40 40
Syndecan-1-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
TGFB1 0.024 0.012 -10000 0 0 112 112
CCL5 0.025 0.011 -10000 0 0 83 83
SDCBP 0.028 0.007 -10000 0 0 36 36
FGFR/FGF2/Syndecan-1 -0.016 0.14 0.23 43 -0.32 52 95
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 -0.014 0.14 0.23 33 -0.32 50 83
Syndecan-1/Syntenin -0.009 0.14 0.25 37 -0.32 50 87
MAPK3 -0.036 0.14 0.2 40 -0.3 58 98
HGF/MET 0.033 0.033 -10000 0 -0.16 12 12
TGFB1/TGF beta receptor Type II 0.024 0.012 -10000 0 0 112 112
BSG 0.027 0.009 -10000 0 0 52 52
keratinocyte migration -0.013 0.14 0.23 33 -0.31 50 83
Syndecan-1/RANTES -0.015 0.16 0.24 42 -0.32 67 109
Syndecan-1/CD147 -0.006 0.15 0.24 36 -0.31 56 92
Syndecan-1/Syntenin/PIP2 -0.011 0.14 0.22 36 -0.3 50 86
LAMA5 0.026 0.01 -10000 0 0 67 67
positive regulation of cell-cell adhesion -0.011 0.14 0.22 36 -0.3 50 86
MMP7 0.017 0.015 -10000 0 0 236 236
HGF 0.029 0.005 -10000 0 0 17 17
Syndecan-1/CASK -0.036 0.12 0.19 27 -0.3 57 84
Syndecan-1/HGF/MET -0.007 0.15 0.25 34 -0.31 53 87
regulation of cell adhesion -0.046 0.13 0.24 11 -0.31 55 66
HPSE 0.027 0.008 -10000 0 0 43 43
positive regulation of cell migration -0.016 0.14 0.23 43 -0.32 52 95
SDC1 -0.012 0.13 0.22 41 -0.33 42 83
Syndecan-1/Collagen -0.016 0.14 0.23 43 -0.32 52 95
PPIB 0.029 0.005 -10000 0 0 14 14
MET 0.025 0.011 -10000 0 0 87 87
PRKACA 0.025 0.01 -10000 0 0 80 80
MMP9 0.023 0.013 -10000 0 0 129 129
MAPK1 -0.034 0.14 0.2 39 -0.31 55 94
homophilic cell adhesion -0.016 0.14 0.24 42 -0.32 55 97
MMP1 0.022 0.013 -10000 0 0 142 142
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.009 -10000 0 -10000 0 0
ELF1 0.027 0.017 -10000 0 -10000 0 0
CCNA2 0.003 0.009 -10000 0 0 493 493
PIK3CA 0.021 0.014 -10000 0 -10000 0 0
JAK3 0.027 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.013 -10000 0 -10000 0 0
JAK1 0.029 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.016 0.1 -10000 0 -0.47 9 9
SHC1 0.029 0.006 -10000 0 -10000 0 0
SP1 -0.21 0.14 -10000 0 -0.29 415 415
IL2RA -0.024 0.047 0.41 6 -10000 0 6
IL2RB 0.027 0.009 -10000 0 -10000 0 0
SOS1 0.028 0.007 -10000 0 -10000 0 0
IL2RG 0.026 0.01 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.31 0.29 0.32 29 -0.48 387 416
PTPN11 0.029 0.004 -10000 0 -10000 0 0
CCND2 -0.35 0.24 0.41 3 -0.52 378 381
LCK 0.028 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.006 -10000 0 -10000 0 0
IL2 0.028 0.007 -10000 0 -10000 0 0
CDK6 0.028 0.007 -10000 0 0 32 32
CCND3 -0.013 0.1 -10000 0 -0.49 4 4
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.003 0.12 -10000 0 -0.33 33 33
MAP3K8 0.023 0.023 0.061 26 -0.037 62 88
FOS 0.025 0.13 0.46 26 -0.38 12 38
PRKCA 0.024 0.028 0.1 25 -0.042 60 85
PTPN7 0.022 0.039 0.16 25 -0.049 59 84
HRAS 0.022 0.021 0.051 1 -0.023 89 90
PRKCB 0.001 0.016 0.07 26 -10000 0 26
NRAS 0.012 0.017 -10000 0 -0.002 320 320
RAS family/GTP 0.023 0.044 0.18 23 -10000 0 23
MAPK3 0.026 0.12 0.32 26 -0.43 21 47
MAP2K1 0.03 0.078 0.27 27 -0.28 8 35
ELK1 0.022 0.028 0.072 25 -0.052 61 86
BRAF 0.021 0.049 0.22 14 -0.24 4 18
mol:GTP 0 0.003 0.012 26 -0.006 45 71
MAPK1 0.019 0.12 0.32 26 -0.4 30 56
RAF1 0.022 0.054 0.22 14 -0.32 4 18
KRAS 0.019 0.02 -10000 0 -0.011 149 149
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.011 0.021 0.1 8 -0.03 13 21
GNB1/GNG2 -0.067 0.065 -10000 0 -0.18 97 97
AKT1 -0.017 0.23 0.47 78 -0.37 9 87
EGF 0.027 0.008 -10000 0 0 43 43
mol:TXA2 0 0.002 0.035 1 -10000 0 1
FGR -0.024 0.067 0.22 9 -10000 0 9
mol:Ca2+ -0.065 0.29 0.56 78 -0.36 62 140
LYN -0.026 0.065 0.22 9 -10000 0 9
RhoA/GTP -0.041 0.11 0.25 59 -0.19 1 60
mol:PGI2 0 0.002 0.029 1 -10000 0 1
SYK -0.059 0.3 0.57 79 -0.38 61 140
GNG2 0.029 0.004 -10000 0 0 12 12
ARRB2 0.028 0.006 -10000 0 0 26 26
TP alpha/Gq family/GDP/G beta5/gamma2 -0.066 0.17 -10000 0 -0.43 79 79
G beta5/gamma2 -0.08 0.086 0.17 1 -0.25 92 93
PRKCH -0.068 0.31 0.58 78 -0.42 64 142
DNM1 0.029 0.005 -10000 0 0 17 17
TXA2/TP beta/beta Arrestin3 0.03 0.035 -10000 0 -0.51 1 1
mol:GTP 0.001 0.011 0.066 9 -10000 0 9
PTGDR 0.029 0.005 0.06 1 0 12 13
G12 family/GTP -0.14 0.13 -10000 0 -0.31 115 115
ADRBK1 0.03 0.003 -10000 0 0 7 7
ADRBK2 0.026 0.01 -10000 0 0 77 77
RhoA/GTP/ROCK1 0.039 0.013 0.16 1 -0.13 1 2
mol:GDP 0.044 0.24 0.46 47 -0.42 76 123
mol:NADP -0.001 0.029 0.069 1 -0.029 279 280
RAB11A 0.029 0.005 -10000 0 0 14 14
PRKG1 -0.001 0.03 0.069 1 -0.029 289 290
mol:IP3 -0.096 0.33 0.59 78 -0.44 81 159
cell morphogenesis 0.038 0.013 0.16 1 -0.13 1 2
PLCB2 -0.16 0.38 0.62 71 -0.6 95 166
mol:cGMP 0 0.002 0.036 1 -10000 0 1
BLK -0.02 0.062 0.22 9 -10000 0 9
mol:PDG2 0 0.002 0.029 1 -10000 0 1
HCK -0.024 0.064 0.23 7 -10000 0 7
RHOA 0.029 0.003 -10000 0 0 6 6
PTGIR 0.029 0.007 0.06 1 0 27 28
PRKCB1 -0.084 0.32 0.59 78 -0.44 67 145
GNAQ 0.028 0.006 -10000 0 0 28 28
mol:L-citrulline -0.001 0.029 0.069 1 -0.029 279 280
TXA2/TXA2-R family -0.11 0.38 0.64 78 -0.57 82 160
LCK -0.023 0.066 0.22 10 -10000 0 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.016 0.057 0.18 7 -10000 0 7
TXA2-R family/G12 family/GDP/G beta/gamma -0.015 0.12 -10000 0 -0.43 39 39
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.054 0.16 5 -10000 0 5
MAPK14 -0.028 0.24 0.48 79 -10000 0 79
TGM2/GTP -0.14 0.35 0.62 70 -0.52 80 150
MAPK11 -0.03 0.24 0.48 79 -10000 0 79
ARHGEF1 -0.031 0.2 0.4 76 -0.21 6 82
GNAI2 0.029 0.003 -10000 0 0 6 6
JNK cascade -0.064 0.33 0.61 79 -0.42 64 143
RAB11/GDP 0.013 0.034 -10000 0 -0.051 76 76
ICAM1 -0.028 0.29 0.58 80 -0.37 5 85
cAMP biosynthetic process -0.1 0.31 0.55 78 -0.41 81 159
Gq family/GTP/EBP50 -0.052 0.1 0.24 1 -0.2 150 151
actin cytoskeleton reorganization 0.038 0.013 0.16 1 -0.13 1 2
SRC -0.024 0.065 0.23 7 -10000 0 7
GNB5 0.028 0.007 -10000 0 0 33 33
GNB1 0.028 0.006 -10000 0 0 24 24
EGF/EGFR -0.033 0.082 0.23 11 -0.26 13 24
VCAM1 -0.037 0.3 0.6 79 -0.36 72 151
TP beta/Gq family/GDP/G beta5/gamma2 -0.066 0.17 -10000 0 -0.43 79 79
platelet activation -0.06 0.28 0.54 78 -0.34 13 91
PGI2/IP 0.021 0.012 0.09 1 -0.15 2 3
PRKACA -0.002 0.024 0.17 1 -0.15 2 3
Gq family/GDP/G beta5/gamma2 -0.051 0.14 -10000 0 -0.44 49 49
TXA2/TP beta/beta Arrestin2 0.018 0.057 -10000 0 -0.34 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.024 0.22 1 -0.15 3 4
mol:DAG -0.1 0.34 0.61 78 -0.48 83 161
EGFR 0.027 0.009 -10000 0 0 55 55
TXA2/TP alpha -0.16 0.38 0.61 78 -0.57 90 168
Gq family/GTP -0.033 0.078 -10000 0 -0.19 90 90
YES1 -0.024 0.065 0.22 9 -10000 0 9
GNAI2/GTP -0.02 0.063 0.15 18 -0.18 5 23
PGD2/DP 0.022 0.005 0.09 1 -10000 0 1
SLC9A3R1 0.022 0.013 -10000 0 0 141 141
FYN -0.028 0.069 0.22 10 -0.2 1 11
mol:NO -0.001 0.029 0.069 1 -0.029 279 280
GNA15 0.027 0.008 -10000 0 0 47 47
PGK/cGMP 0.037 0.013 0.15 1 -10000 0 1
RhoA/GDP 0.013 0.034 -10000 0 -0.051 76 76
TP alpha/TGM2/GDP/G beta/gamma -0.075 0.066 -10000 0 -0.23 5 5
NOS3 -0.001 0.029 0.069 1 -0.029 279 280
RAC1 0.028 0.006 -10000 0 0 28 28
PRKCA -0.069 0.31 0.58 78 -0.42 61 139
PRKCB -0.069 0.31 0.58 78 -0.41 63 141
PRKCE -0.059 0.31 0.58 79 -0.42 56 135
PRKCD -0.069 0.32 0.59 78 -0.43 64 142
PRKCG -0.087 0.32 0.59 78 -0.45 66 144
muscle contraction -0.11 0.36 0.62 78 -0.52 92 170
PRKCZ -0.057 0.3 0.57 79 -0.38 60 139
ARR3 0.029 0.003 -10000 0 0 5 5
TXA2/TP beta -0.009 0.07 0.21 12 -0.19 2 14
PRKCQ -0.06 0.31 0.58 78 -0.42 56 134
MAPKKK cascade -0.11 0.36 0.61 78 -0.51 93 171
SELE -0.03 0.28 0.55 79 -10000 0 79
TP beta/GNAI2/GDP/G beta/gamma -0.013 0.065 0.22 5 -10000 0 5
ROCK1 0.029 0.005 -10000 0 0 15 15
GNA14 0.029 0.005 -10000 0 0 19 19
chemotaxis -0.11 0.4 0.67 79 -0.62 75 154
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 14 14
GNA11 0.025 0.011 -10000 0 0 84 84
Rac1/GTP 0.021 0.01 0.16 1 -10000 0 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.073 0.052 0.19 2 -10000 0 2
BIRC5 0.023 0.012 -10000 0 0 122 122
NFKBIA 0.065 0.049 0.2 4 -10000 0 4
CPEB1 0.029 0.005 -10000 0 0 19 19
AKT1 0.065 0.052 0.29 3 -10000 0 3
NDEL1 0.028 0.007 -10000 0 0 32 32
Aurora A/BRCA1 0.066 0.046 0.17 1 -10000 0 1
NDEL1/TACC3 0.045 0.053 -10000 0 -10000 0 0
GADD45A 0.027 0.009 -10000 0 0 53 53
GSK3B 0.024 0.016 0.084 3 -10000 0 3
PAK1/Aurora A 0.075 0.051 0.18 2 -10000 0 2
MDM2 0.028 0.006 -10000 0 0 26 26
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.17 0.066 0.2 488 -10000 0 488
TP53 0.053 0.056 -10000 0 -0.31 4 4
DLG7 0.076 0.052 0.11 386 -10000 0 386
AURKAIP1 0.028 0.006 -10000 0 0 27 27
ARHGEF7 0.028 0.006 -10000 0 0 25 25
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.058 0.063 0.18 30 -10000 0 30
G2/M transition of mitotic cell cycle 0.065 0.045 0.16 1 -10000 0 1
AURKA 0.093 0.064 0.14 386 -10000 0 386
AURKB 0.025 0.025 -10000 0 -0.16 2 2
CDC25B 0.07 0.049 0.18 3 -10000 0 3
G2/M transition checkpoint 0 0.002 -10000 0 -10000 0 0
mRNA polyadenylation 0.07 0.044 0.16 1 -10000 0 1
Aurora A/CPEB 0.07 0.044 0.17 1 -10000 0 1
Aurora A/TACC1/TRAP/chTOG -0.002 0.054 -10000 0 -10000 0 0
BRCA1 0.026 0.009 -10000 0 0 61 61
centrosome duplication 0.075 0.051 0.18 2 -10000 0 2
regulation of centrosome cycle 0.044 0.052 -10000 0 -10000 0 0
spindle assembly -0.002 0.053 -10000 0 -10000 0 0
TDRD7 0.028 0.006 -10000 0 0 27 27
Aurora A/RasGAP/Survivin 0.076 0.064 0.18 33 -10000 0 33
CENPA 0.039 0.035 -10000 0 -10000 0 0
Aurora A/PP2A 0.079 0.05 0.18 3 -10000 0 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.043 0.049 0.18 8 -0.26 2 10
negative regulation of DNA binding 0.053 0.056 -10000 0 -0.31 4 4
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.04 0.013 -10000 0 -10000 0 0
RASA1 0.027 0.008 -10000 0 0 50 50
Ajuba/Aurora A 0 0.002 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.015 0.073 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process 0.093 0.064 0.14 386 -10000 0 386
TACC1 0.005 0.011 -10000 0 0 458 458
TACC3 0.016 0.015 -10000 0 0 261 261
Aurora A/Antizyme1 0.066 0.063 0.18 17 -10000 0 17
Aurora A/RasGAP 0.075 0.051 -10000 0 -10000 0 0
OAZ1 0.019 0.014 -10000 0 0 196 196
RAN 0.029 0.004 -10000 0 0 12 12
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.021 0.017 0.084 3 -10000 0 3
GIT1 0.028 0.007 -10000 0 0 31 31
GIT1/beta-PIX/PAK1 0.051 0.022 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.17 0.066 0.19 488 -10000 0 488
PPP2R5D 0.028 0.006 -10000 0 0 25 25
Aurora A/TPX2 0.15 0.11 0.23 365 -10000 0 365
PAK1 0.027 0.008 -10000 0 0 47 47
CKAP5 0.02 0.014 -10000 0 0 179 179
Ephrin B reverse signaling

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
EFNB2 0.027 0.009 -10000 0 0 58 58
EPHB2 0 0.032 -10000 0 -10000 0 0
EFNB1 -0.027 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.06 0.042 0.19 1 -0.14 2 3
Ephrin B2/EPHB1-2 0.045 0.039 -10000 0 -0.12 18 18
neuron projection morphogenesis -0.023 0.052 0.075 9 -10000 0 9
Ephrin B1/EPHB1-2/Tiam1 0.003 0.068 0.17 6 -10000 0 6
DNM1 0.001 0.031 -10000 0 -10000 0 0
cell-cell signaling 0.001 0.005 0.018 2 -10000 0 2
MAP2K4 -0.12 0.21 0.22 3 -0.49 138 141
YES1 -0.16 0.32 -10000 0 -0.7 139 139
Ephrin B1/EPHB1-2/NCK2 0.003 0.067 0.18 5 -10000 0 5
PI3K -0.11 0.22 -10000 0 -0.47 140 140
mol:GDP 0.001 0.066 0.17 6 -10000 0 6
ITGA2B 0.029 0.006 -10000 0 0 23 23
endothelial cell proliferation 0.03 0.034 -10000 0 -0.13 20 20
FYN -0.18 0.32 -10000 0 -0.72 139 139
MAP3K7 -0.12 0.22 0.23 5 -0.51 135 140
FGR -0.16 0.31 -10000 0 -0.69 140 140
TIAM1 0.029 0.006 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 161 161
RGS3 0.029 0.005 -10000 0 0 16 16
cell adhesion -0.13 0.21 0.2 5 -0.47 140 145
LYN -0.16 0.32 -10000 0 -0.7 139 139
Ephrin B1/EPHB1-2/Src Family Kinases -0.15 0.29 -10000 0 -0.64 140 140
Ephrin B1/EPHB1-2 -0.12 0.24 -10000 0 -0.54 135 135
SRC -0.16 0.31 -10000 0 -0.69 139 139
ITGB3 0.024 0.011 -10000 0 0 98 98
EPHB1 -0.003 0.031 -10000 0 -10000 0 0
EPHB4 0.029 0.005 -10000 0 0 19 19
RAC1 0.028 0.006 -10000 0 0 28 28
Ephrin B2/EPHB4 0.031 0.034 -10000 0 -0.13 20 20
alphaIIb/beta3 Integrin 0.016 0.067 -10000 0 -0.16 67 67
BLK -0.17 0.31 -10000 0 -0.7 140 140
HCK -0.16 0.31 -10000 0 -0.7 138 138
regulation of stress fiber formation 0 0.065 -10000 0 -0.16 6 6
MAPK8 -0.13 0.2 0.2 1 -0.47 139 140
Ephrin B1/EPHB1-2/RGS3 0.004 0.067 0.17 6 -10000 0 6
endothelial cell migration -0.1 0.18 0.25 5 -0.42 135 140
NCK2 0.029 0.004 -10000 0 0 11 11
PTPN13 0.023 0.016 -10000 0 0 183 183
regulation of focal adhesion formation 0 0.065 -10000 0 -0.16 6 6
chemotaxis -0.002 0.066 -10000 0 -0.16 7 7
PIK3CA 0.021 0.014 -10000 0 0 171 171
Rac1/GTP -0.008 0.066 0.14 7 -10000 0 7
angiogenesis -0.12 0.24 -10000 0 -0.54 138 138
LCK -0.16 0.31 -10000 0 -0.69 140 140
TCGA08_p53

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
CDKN2A -0.007 0.008 0 340 -10000 0 340
TP53 0.025 0.076 -10000 0 -0.22 36 36
Senescence 0.023 0.08 -10000 0 -0.22 40 40
Apoptosis 0.023 0.08 -10000 0 -0.22 40 40
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.042 0.3 10 -10000 0 10
MDM4 0.029 0.006 -10000 0 0 22 22
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.008 -10000 0 0 48 48
NFATC1 0.057 0.094 0.26 9 -0.33 13 22
NFATC2 -0.015 0.059 0.25 4 -0.22 7 11
NFATC3 -0.001 0.026 -10000 0 -0.31 2 2
YWHAE 0.028 0.008 -10000 0 0 41 41
Calcineurin A alpha-beta B1/CABIN1 -0.008 0.062 0.25 1 -0.25 18 19
Exportin 1/Ran/NUP214 0.05 0.022 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 0.029 4 -10000 0 4
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.003 0.077 0.21 1 -0.25 19 20
BCL2/BAX 0.012 0.07 -10000 0 -0.16 74 74
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.032 0.12 4 -0.15 9 13
CaM/Ca2+ 0 0.032 0.12 4 -0.15 9 13
BAX 0.029 0.006 -10000 0 0 22 22
MAPK14 0.005 0.03 0.059 4 -0.029 234 238
BAD 0.03 0.003 -10000 0 0 4 4
CABIN1/MEF2D 0.005 0.066 0.23 1 -0.25 18 19
Calcineurin A alpha-beta B1/BCL2 0.023 0.012 -10000 0 0 122 122
FKBP8 0.025 0.011 -10000 0 0 88 88
activation-induced cell death of T cells -0.005 0.065 0.25 18 -0.23 1 19
KPNB1 0.029 0.006 -10000 0 0 21 21
KPNA2 0.003 0.009 -10000 0 0 494 494
XPO1 0.007 0.027 -10000 0 -0.023 243 243
SFN 0.028 0.007 -10000 0 0 38 38
MAP3K8 0.005 0.03 0.061 4 -0.032 216 220
NFAT4/CK1 alpha -0.046 0.031 0.15 4 -0.19 8 12
MEF2D/NFAT1/Cbp/p300 -0.057 0.12 -10000 0 -0.26 44 44
CABIN1 -0.008 0.063 0.25 1 -0.25 18 19
CALM1 0.004 0.031 0.063 4 -0.034 214 218
RAN 0.007 0.028 -10000 0 -0.028 220 220
MAP3K1 0.027 0.009 -10000 0 0 52 52
CAMK4 0.028 0.008 -10000 0 0 39 39
mol:Ca2+ -0.003 0.007 0.067 4 -10000 0 4
MAPK3 0.029 0.006 -10000 0 0 22 22
YWHAH 0.027 0.008 -10000 0 0 43 43
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.016 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 0 44 44
MAPK8 0.005 0.031 0.066 4 -0.033 220 224
MAPK9 0.029 0.005 -10000 0 0 18 18
YWHAG 0.029 0.004 -10000 0 0 12 12
FKBP1A 0.028 0.007 -10000 0 0 37 37
NFAT1-c-4/YWHAQ 0.04 0.11 0.26 6 -0.35 14 20
PRKCH 0.029 0.005 -10000 0 0 15 15
CABIN1/Cbp/p300 0.001 0.05 -10000 0 -0.17 10 10
CASP3 0.005 0.028 0.059 4 -0.031 195 199
PIM1 0.028 0.006 -10000 0 0 28 28
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.018 0.065 4 -0.02 8 12
apoptosis 0.01 0.035 0.19 1 -0.15 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.058 -10000 0 -0.23 16 16
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.029 0.005 -10000 0 0 18 18
JNK2/NFAT4 -0.001 0.071 -10000 0 -0.19 64 64
BAD/BCL-XL 0.04 0.013 -10000 0 -10000 0 0
PRKCD 0.029 0.005 -10000 0 0 15 15
NUP214 0.007 0.028 -10000 0 -0.027 227 227
PRKCZ 0.004 0.03 0.066 4 -0.033 219 223
PRKCA 0.029 0.006 -10000 0 0 23 23
PRKCG 0.029 0.006 -10000 0 0 21 21
PRKCQ 0.027 0.008 -10000 0 0 48 48
FKBP38/BCL2 -0.002 0.081 -10000 0 -0.17 102 102
EP300 0.001 0.033 0.071 4 -0.039 208 212
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.028 0.008 -10000 0 0 39 39
NFATc/JNK1 0.063 0.097 0.27 6 -0.33 13 19
CaM/Ca2+/FKBP38 -0.002 0.052 0.13 4 -0.14 43 47
FKBP12/FK506 0.021 0.005 -10000 0 -10000 0 0
CSNK1A1 -0.031 0.02 0.1 4 -0.14 8 12
CaM/Ca2+/CAMK IV 0.007 0.04 0.13 4 -0.14 8 12
NFATc/ERK1 0.065 0.098 0.26 8 -0.32 13 21
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.018 0.074 0.21 1 -0.25 19 20
NR4A1 -0.13 0.13 0.17 3 -0.29 209 212
GSK3B 0.005 0.03 0.066 4 -0.033 215 219
positive T cell selection -0.001 0.026 -10000 0 -0.31 2 2
NFAT1/CK1 alpha -0.024 0.05 0.19 5 -0.18 13 18
RCH1/ KPNB1 0.005 0.014 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 0 15 15
PRKACA 0.004 0.028 0.058 3 -0.031 195 198
AKAP5 0.029 0.005 -10000 0 0 14 14
MEF2D 0.002 0.034 0.071 4 -0.039 221 225
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.01 -10000 0 0 79 79
NFATc/p38 alpha 0.062 0.096 0.26 4 -0.34 11 15
CREBBP 0.002 0.033 0.071 4 -0.039 211 215
BCL2 0.023 0.012 -10000 0 0 122 122
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.025 0.082 -10000 0 -10000 0 0
PLK1 0.27 0.4 0.9 75 -0.88 12 87
CDKN1B 0.19 0.3 0.62 88 -0.45 2 90
FOXO3 0.23 0.41 0.75 99 -0.79 23 122
KAT2B 0.061 0.067 0.11 298 -0.076 5 303
FOXO1/SIRT1 0.009 0.086 0.27 5 -0.28 3 8
CAT 0.24 0.38 0.8 49 -0.88 17 66
CTNNB1 0.026 0.014 -10000 0 -0.024 38 38
AKT1 0.074 0.089 0.19 96 -10000 0 96
FOXO1 0.037 0.094 0.52 1 -0.3 2 3
MAPK10 0.013 0.062 0.18 35 -10000 0 35
mol:GTP 0 0.007 0.025 31 -0.021 2 33
FOXO4 0.011 0.16 0.44 31 -0.49 5 36
response to oxidative stress 0.06 0.069 0.16 93 -0.084 1 94
FOXO3A/SIRT1 0.22 0.37 0.64 108 -0.7 30 138
XPO1 0.018 0.023 -10000 0 -0.031 88 88
EP300 0.016 0.027 0.081 1 -10000 0 1
BCL2L11 0.085 0.14 0.77 1 -1 4 5
FOXO1/SKP2 0.022 0.078 0.39 1 -0.28 3 4
mol:GDP 0.06 0.069 0.16 93 -0.083 1 94
RAN 0.018 0.026 -10000 0 -0.033 111 111
GADD45A 0.2 0.3 0.74 68 -0.67 3 71
YWHAQ 0.029 0.005 -10000 0 0 15 15
FOXO1/14-3-3 family 0.002 0.14 -10000 0 -0.53 23 23
MST1 0.082 0.083 0.18 118 -0.1 6 124
CSNK1D 0.028 0.006 -10000 0 0 25 25
CSNK1E 0.027 0.008 -10000 0 0 46 46
FOXO4/14-3-3 family 0.004 0.12 0.23 1 -0.51 18 19
YWHAB 0.027 0.008 -10000 0 0 44 44
MAPK8 0.014 0.064 0.18 36 -10000 0 36
MAPK9 0.014 0.063 0.18 31 -10000 0 31
YWHAG 0.029 0.004 -10000 0 0 12 12
YWHAE 0.028 0.008 -10000 0 0 41 41
YWHAZ 0.026 0.01 -10000 0 0 79 79
SIRT1 -0.01 0.054 0.15 32 -0.11 3 35
SOD2 0.039 0.45 0.62 58 -0.74 105 163
RBL2 0.16 0.37 0.67 40 -0.83 27 67
RAL/GDP 0.066 0.069 0.18 60 -10000 0 60
CHUK 0.081 0.082 0.18 122 -0.11 4 126
Ran/GTP 0.015 0.024 -10000 0 -10000 0 0
CSNK1G2 0.027 0.008 -10000 0 0 46 46
RAL/GTP 0.064 0.076 0.26 30 -10000 0 30
CSNK1G1 0.029 0.005 -10000 0 0 14 14
FASLG 0.092 0.093 -10000 0 -10000 0 0
SKP2 0.021 0.013 -10000 0 0 156 156
USP7 0.018 0.025 -10000 0 -0.033 101 101
IKBKB 0.079 0.081 0.18 115 -0.1 1 116
CCNB1 0.36 0.43 0.71 294 -0.94 9 303
FOXO1-3a-4/beta catenin 0.12 0.29 0.6 64 -10000 0 64
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.077 0.39 1 -0.28 3 4
CSNK1A1 0.029 0.004 -10000 0 0 13 13
SGK1 0.061 0.067 0.11 298 -0.076 5 303
CSNK1G3 0.029 0.006 -10000 0 0 21 21
Ran/GTP/Exportin 1 0.029 0.036 0.14 1 -10000 0 1
ZFAND5 0.01 0.14 0.46 9 -0.64 2 11
SFN 0.028 0.007 -10000 0 0 38 38
CDK2 -0.01 0.025 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.082 0.15 0.31 47 -0.52 12 59
CREBBP -0.022 0.028 -10000 0 -0.08 1 1
FBXO32 0.095 0.61 0.79 124 -0.8 143 267
BCL6 0.18 0.34 0.67 33 -0.89 21 54
RALB 0.017 0.027 -10000 0 -0.035 111 111
RALA 0.017 0.027 -10000 0 -0.035 109 109
YWHAH 0.027 0.008 -10000 0 0 43 43
Canonical Wnt signaling pathway

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
HDAC1 0.056 0.055 0.13 152 -0.057 1 153
AES 0.042 0.044 0.11 126 -10000 0 126
FBXW11 0.029 0.005 -10000 0 0 18 18
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.037 0.017 -10000 0 -10000 0 0
SMAD4 0.028 0.007 -10000 0 0 33 33
DKK2 0.028 0.008 -10000 0 0 40 40
TLE1 0.053 0.044 0.11 135 -0.062 1 136
MACF1 0.027 0.009 -10000 0 -0.029 2 2
CTNNB1 0.026 0.076 0.28 14 -0.41 1 15
WIF1 0.026 0.015 -10000 0 -0.03 31 31
beta catenin/RanBP3 0.14 0.2 0.41 168 -0.35 1 169
KREMEN2 0.029 0.006 -10000 0 -0.001 24 24
DKK1 0.029 0.006 -10000 0 0 25 25
beta catenin/beta TrCP1 0.048 0.077 0.28 14 -0.39 1 15
FZD1 0.018 0.024 -10000 0 -0.03 94 94
AXIN2 -0.079 0.17 0.63 5 -0.74 17 22
AXIN1 0.028 0.01 -10000 0 -0.029 8 8
RAN 0.03 0.006 -10000 0 -0.031 2 2
Axin1/APC/GSK3/beta catenin 0.021 0.1 -10000 0 -0.47 19 19
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.042 0.18 0.29 7 -0.53 42 49
Axin1/APC/GSK3 0.014 0.062 0.21 12 -0.38 2 14
Axin1/APC/GSK3/beta catenin/Macf1 0.003 0.079 0.28 8 -0.37 7 15
HNF1A 0.056 0.047 0.12 148 -0.062 2 150
CTBP1 0.052 0.048 0.12 136 -0.062 2 138
MYC 0.006 0.48 0.59 126 -1.1 59 185
RANBP3 0.029 0.008 -10000 0 -0.03 1 1
DKK2/LRP6/Kremen 2 0.049 0.025 -10000 0 -10000 0 0
NKD1 0.022 0.018 -10000 0 -0.03 52 52
TCF4 0.053 0.049 0.12 152 -0.063 2 154
TCF3 0.051 0.047 0.12 130 -0.063 1 131
WNT1/LRP6/FZD1/Axin1 0.064 0.038 -10000 0 -10000 0 0
Ran/GTP 0.024 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.11 0.28 0.54 115 -0.56 12 127
LEF1 0.05 0.051 0.12 142 -0.063 2 144
DVL1 0.02 0.061 0.2 3 -0.35 5 8
CSNK2A1 0.028 0.008 -10000 0 0 39 39
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.13 0.2 -10000 0 -0.5 87 87
DKK1/LRP6/Kremen 2 0.048 0.025 -10000 0 -10000 0 0
LRP6 0.017 0.022 -10000 0 -0.03 82 82
CSNK1A1 0.058 0.054 0.12 165 -0.066 2 167
NLK 0.006 0.032 -10000 0 -0.04 177 177
CCND1 -0.33 0.56 0.65 14 -1.2 155 169
WNT1 0.019 0.023 -10000 0 -0.03 103 103
GSK3A 0.018 0.023 -10000 0 -0.03 97 97
GSK3B 0.017 0.024 -10000 0 -0.03 107 107
FRAT1 0.016 0.024 -10000 0 -0.03 117 117
PPP2R5D 0.03 0.051 -10000 0 -0.31 7 7
APC -0.019 0.084 0.2 54 -10000 0 54
WNT1/LRP6/FZD1 0.017 0.043 0.18 5 -0.2 3 8
CREBBP 0.051 0.046 0.12 127 -0.062 2 129
Insulin Pathway

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
CBL/APS/CAP -0.072 0.093 -10000 0 -0.15 302 302
TC10/GTP -0.05 0.023 -10000 0 -0.13 31 31
Insulin Receptor/Insulin/IRS1/Shp2 -0.067 0.11 -10000 0 -0.15 325 325
HRAS 0.028 0.006 -10000 0 0 28 28
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.028 0.007 -10000 0 0 33 33
FOXO3 -0.034 0.14 -10000 0 -0.6 33 33
AKT1 -0.06 0.11 0.25 10 -0.29 5 15
INSR -0.02 0.027 0.067 14 -10000 0 14
Insulin Receptor/Insulin 0.037 0.065 0.2 25 -0.14 39 64
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.029 0.004 -10000 0 0 12 12
SORBS1 0.027 0.009 -10000 0 0 52 52
CRK 0.028 0.007 -10000 0 0 37 37
PTPN1 -0.037 0.045 -10000 0 -10000 0 0
CAV1 -0.096 0.076 0.17 5 -0.22 81 86
CBL/APS/CAP/Crk-II/C3G 0.048 0.055 -10000 0 -0.13 34 34
Insulin Receptor/Insulin/IRS1/NCK2 -0.066 0.11 -10000 0 -0.15 325 325
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.058 0.095 -10000 0 -0.16 238 238
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.1 0.15 -10000 0 -0.45 68 68
RPS6KB1 -0.067 0.099 0.23 9 -0.28 5 14
PARD6A 0.026 0.009 -10000 0 0 61 61
CBL 0.029 0.005 -10000 0 0 15 15
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.023 0.044 -10000 0 -0.7 2 2
PIK3R1 0.021 0.013 -10000 0 0 161 161
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.079 0.095 0.18 7 -0.24 45 52
HRAS/GTP -0.097 0.057 -10000 0 -0.21 32 32
Insulin Receptor -0.02 0.027 0.067 14 -10000 0 14
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.061 0.11 -10000 0 -0.15 284 284
PRKCI 0.002 0.08 -10000 0 -0.36 19 19
Insulin Receptor/Insulin/GRB14/PDK1 -0.083 0.076 0.056 7 -0.22 55 62
SHC1 0.029 0.006 -10000 0 0 20 20
negative regulation of MAPKKK cascade 0.043 0.048 -10000 0 -0.61 2 2
PI3K -0.056 0.1 -10000 0 -0.16 227 227
NCK2 0.029 0.004 -10000 0 0 11 11
RHOQ 0.029 0.005 -10000 0 0 18 18
mol:H2O2 -0.006 0.006 0.019 3 -10000 0 3
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
AKT2 -0.061 0.11 0.24 8 -0.29 5 13
PRKCZ -0.016 0.1 -10000 0 -0.37 33 33
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.087 0.06 0.15 4 -0.2 35 39
F2RL2 0.027 0.009 -10000 0 0 54 54
TRIP10 0.028 0.007 -10000 0 0 36 36
Insulin Receptor/Insulin/Shc 0.037 0.054 -10000 0 -0.12 42 42
TC10/GTP/CIP4/Exocyst 0.037 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.059 0.071 -10000 0 -0.14 35 35
RAPGEF1 0.029 0.005 -10000 0 0 18 18
RASA1 0.027 0.008 -10000 0 0 50 50
NCK1 0.026 0.009 -10000 0 0 63 63
CBL/APS/CAP/Crk-II 0.038 0.049 -10000 0 -0.13 35 35
TC10/GDP 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.049 0.065 -10000 0 -0.14 38 38
INPP5D -0.088 0.055 -10000 0 -0.13 287 287
SOS1 0.028 0.007 -10000 0 0 34 34
SGK1 -0.01 0.008 -10000 0 -0.025 48 48
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.004 -10000 0 0 9 9
IRS1 0.011 0.014 -10000 0 0 349 349
p62DOK/RasGAP 0.044 0.049 -10000 0 -0.62 2 2
INS -0.022 0.029 0.068 18 -10000 0 18
mol:PI-3-4-P2 -0.087 0.054 -10000 0 -0.13 287 287
GRB2 0.029 0.006 -10000 0 0 20 20
EIF4EBP1 -0.069 0.092 0.19 6 -0.28 5 11
PTPRA -0.026 0.023 0.067 2 -10000 0 2
PIK3CA 0.021 0.014 -10000 0 0 171 171
TC10/GTP/CIP4 0.037 0.012 -10000 0 -10000 0 0
PDPK1 0.029 0.005 -10000 0 0 17 17
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.098 0.1 -10000 0 -0.3 52 52
Insulin Receptor/Insulin/IRS1 -0.066 0.096 -10000 0 -0.14 327 327
Insulin Receptor/Insulin/IRS3 0.027 0.06 -10000 0 -0.17 43 43
Par3/Par6 0.046 0.044 -10000 0 -0.13 1 1
Reelin signaling pathway

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
CDK5R1/CDK5 0.035 0.018 -10000 0 -10000 0 0
VLDLR 0.027 0.009 -10000 0 0 60 60
CRKL 0.028 0.007 -10000 0 0 31 31
LRPAP1 0.028 0.007 -10000 0 0 37 37
FYN 0.024 0.011 -10000 0 0 99 99
ITGA3 0.026 0.01 -10000 0 0 67 67
RELN/VLDLR/Fyn -0.006 0.093 -10000 0 -0.16 146 146
MAPK8IP1/MKK7/MAP3K11/JNK1 0.074 0.039 -10000 0 -0.14 1 1
AKT1 -0.044 0.09 -10000 0 -0.21 83 83
MAP2K7 0.028 0.007 -10000 0 0 37 37
RAPGEF1 0.029 0.005 -10000 0 0 18 18
DAB1 0.029 0.005 -10000 0 0 14 14
RELN/LRP8/DAB1 0.021 0.069 -10000 0 -0.13 90 90
LRPAP1/LRP8 0.039 0.018 -10000 0 -0.16 2 2
RELN/LRP8/DAB1/Fyn 0.012 0.092 -10000 0 -0.14 140 140
DAB1/alpha3/beta1 Integrin 0.004 0.093 -10000 0 -0.15 123 123
long-term memory 0.012 0.1 -10000 0 -0.15 129 129
DAB1/LIS1 0.031 0.09 -10000 0 -0.15 90 90
DAB1/CRLK/C3G 0.015 0.086 -10000 0 -0.15 92 92
PIK3CA 0.021 0.014 -10000 0 0 171 171
DAB1/NCK2 0.032 0.092 -10000 0 -0.15 93 93
ARHGEF2 0.028 0.006 -10000 0 0 27 27
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.027 0.008 -10000 0 0 48 48
CDK5R1 0.028 0.007 -10000 0 0 38 38
RELN 0.023 0.013 -10000 0 0 131 131
PIK3R1 0.021 0.013 -10000 0 0 161 161
RELN/LRP8/Fyn -0.002 0.091 -10000 0 -0.15 140 140
GRIN2A/RELN/LRP8/DAB1/Fyn 0.018 0.1 -10000 0 -0.15 140 140
MAPK8 0.029 0.004 -10000 0 0 11 11
RELN/VLDLR/DAB1 0.014 0.071 -10000 0 -0.13 98 98
ITGB1 0.029 0.006 -10000 0 0 22 22
MAP1B -0.042 0.072 0.14 37 -0.24 11 48
RELN/LRP8 0.019 0.075 -10000 0 -0.15 88 88
GRIN2B/RELN/LRP8/DAB1/Fyn 0.017 0.1 -10000 0 -0.15 129 129
PI3K 0 0.067 -10000 0 -0.16 75 75
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.024 0.058 -10000 0 -0.16 47 47
RAP1A -0.059 0.087 0.35 8 -10000 0 8
PAFAH1B1 0.028 0.007 -10000 0 0 33 33
MAPK8IP1 0.029 0.003 -10000 0 0 7 7
CRLK/C3G 0.041 0.012 -10000 0 -10000 0 0
GRIN2B 0.027 0.009 -10000 0 0 58 58
NCK2 0.029 0.004 -10000 0 0 11 11
neuron differentiation -0.034 0.087 -10000 0 -0.27 31 31
neuron adhesion -0.072 0.096 0.34 10 -10000 0 10
LRP8 0.029 0.006 -10000 0 0 20 20
GSK3B -0.048 0.093 0.16 7 -0.29 27 34
RELN/VLDLR/DAB1/Fyn 0.007 0.093 -10000 0 -0.14 144 144
MAP3K11 0.029 0.003 -10000 0 0 6 6
RELN/VLDLR/DAB1/P13K -0.034 0.099 -10000 0 -0.2 125 125
CDK5 0.025 0.011 -10000 0 0 84 84
MAPT -0.012 0.016 -10000 0 -10000 0 0
neuron migration -0.058 0.11 0.24 7 -0.28 55 62
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.034 0.087 -10000 0 -0.27 31 31
RELN/VLDLR 0.028 0.085 -10000 0 -0.14 93 93
BARD1 signaling events

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
BARD1/CSTF1 0.033 0.019 -10000 0 -10000 0 0
ATM 0.028 0.007 -10000 0 0 31 31
UBE2D3 0.027 0.008 -10000 0 0 42 42
PRKDC 0.025 0.011 -10000 0 0 97 97
ATR 0.022 0.013 -10000 0 0 139 139
UBE2L3 0.028 0.007 -10000 0 0 31 31
FANCD2 0.052 0.064 0.14 161 -10000 0 161
protein ubiquitination 0.054 0.065 -10000 0 -10000 0 0
XRCC5 0.028 0.007 -10000 0 0 38 38
XRCC6 0.027 0.008 -10000 0 0 50 50
M/R/N Complex 0.043 0.027 -10000 0 -10000 0 0
MRE11A 0.025 0.01 -10000 0 0 81 81
DNA-PK 0.043 0.028 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.031 0.075 0.21 8 -0.52 4 12
FANCF 0.029 0.005 -10000 0 0 16 16
BRCA1 0.026 0.009 -10000 0 0 61 61
CCNE1 0.003 0.009 -10000 0 0 506 506
CDK2/Cyclin E1 0.003 0.01 -10000 0 -10000 0 0
FANCG 0.029 0.005 -10000 0 0 15 15
BRCA1/BACH1/BARD1 0.034 0.019 -10000 0 -10000 0 0
FANCE 0.029 0.005 -10000 0 0 19 19
FANCC 0.029 0.006 -10000 0 0 23 23
NBN 0.025 0.011 -10000 0 0 83 83
FANCA 0.025 0.011 -10000 0 0 85 85
DNA repair 0.2 0.2 0.37 262 -0.36 2 264
BRCA1/BARD1/ubiquitin 0.034 0.019 -10000 0 -10000 0 0
BARD1/DNA-PK 0.07 0.049 -10000 0 -10000 0 0
FANCL 0.027 0.008 -10000 0 0 44 44
mRNA polyadenylation -0.033 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.016 0.07 0.18 35 -0.32 4 39
BRCA1/BACH1/BARD1/TopBP1 0.018 0.028 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.048 0.074 -10000 0 -0.14 45 45
BARD1/CSTF1/BRCA1 0.041 0.028 -10000 0 -10000 0 0
BRCA1/BACH1 0.026 0.009 -10000 0 0 61 61
BARD1 0.025 0.011 -10000 0 0 90 90
PCNA 0.022 0.013 -10000 0 0 145 145
BRCA1/BARD1/UbcH5C 0.044 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.045 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.061 0.059 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.053 0.08 -10000 0 -0.14 50 50
BRCA1/BARD1/Ubiquitin 0.034 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP -0.022 0.049 0.16 30 -10000 0 30
FA complex 0.029 0.052 0.21 10 -0.21 6 16
BARD1/EWS 0.034 0.018 -10000 0 -10000 0 0
RBBP8 -0.009 0.067 0.19 54 -10000 0 54
TP53 0.024 0.011 -10000 0 0 102 102
TOPBP1 0.01 0.014 -10000 0 0 362 362
G1/S transition of mitotic cell cycle -0.046 0.072 0.14 45 -10000 0 45
BRCA1/BARD1 0.059 0.071 -10000 0 -10000 0 0
CSTF1 0.027 0.009 -10000 0 0 56 56
BARD1/EWS-Fli1 0.018 0.008 -10000 0 -10000 0 0
CDK2 0.018 0.015 -10000 0 0 227 227
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.013 0.015 -10000 0 0 309 309
RAD50 0.029 0.005 -10000 0 0 15 15
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.034 0.019 -10000 0 -10000 0 0
EWSR1 0.027 0.008 -10000 0 0 43 43
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.026 0.095 -10000 0 -0.47 4 4
UGCG -0.018 0.12 -10000 0 -0.7 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT -0.079 0.18 -10000 0 -0.49 49 49
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.017 0.12 -10000 0 -0.69 16 16
mol:DAG -0.005 0.13 -10000 0 -0.84 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.12 0.23 -10000 0 -0.51 107 107
FRAP1 -0.14 0.27 -10000 0 -0.59 108 108
FOXO3 -0.11 0.23 -10000 0 -0.61 65 65
AKT1 -0.11 0.25 0.34 1 -0.62 77 78
GAB2 0.01 0.028 -10000 0 -0.035 139 139
SMPD1 -0.024 0.14 -10000 0 -0.7 21 21
SGMS1 -0.012 0.1 -10000 0 -0.65 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 -0.022 0.065 0.15 41 -0.14 74 115
CALM1 0.028 0.006 -10000 0 0 26 26
cell proliferation -0.017 0.15 -10000 0 -0.53 19 19
EIF3A 0.029 0.004 -10000 0 0 10 10
PI3K -0.01 0.067 -10000 0 -0.17 75 75
RPS6KB1 -0.017 0.12 -10000 0 -0.93 8 8
mol:sphingomyelin -0.005 0.13 -10000 0 -0.84 12 12
natural killer cell activation -0.002 0.004 -10000 0 -0.018 7 7
JAK3 0.01 0.029 0.16 1 -0.037 120 121
PIK3R1 0.008 0.026 0.17 1 -0.037 94 95
JAK1 0.012 0.03 0.17 1 -0.036 135 136
NFKB1 0.027 0.008 -10000 0 0 47 47
MYC -0.079 0.3 0.44 1 -0.85 62 63
MYB -0.062 0.26 0.54 1 -1 36 37
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.063 0.15 0.36 1 -0.46 35 36
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.003 0.13 -10000 0 -0.87 8 8
mol:PI-3-4-5-P3 -0.062 0.14 0.35 1 -0.45 34 35
Rac1/GDP -0.025 0.066 0.14 49 -0.14 21 70
T cell proliferation -0.064 0.14 0.33 1 -0.43 33 34
SHC1 0.011 0.029 -10000 0 -0.035 151 151
RAC1 0.019 0.022 -10000 0 -0.03 86 86
positive regulation of cyclin-dependent protein kinase activity -0.004 0.019 0.24 1 -10000 0 1
PRKCZ -0.066 0.14 0.33 1 -0.44 34 35
NF kappa B1 p50/RelA -0.11 0.24 -10000 0 -0.53 101 101
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.027 0.1 0.67 1 -0.36 17 18
HSP90AA1 0.029 0.006 -10000 0 0 21 21
RELA 0.029 0.003 -10000 0 0 6 6
IL2RA 0.011 0.028 -10000 0 -0.035 144 144
IL2RB 0.01 0.029 0.17 1 -0.036 142 143
TERT 0.027 0.009 -10000 0 0 60 60
E2F1 -0.014 0.11 0.47 1 -0.41 36 37
SOS1 0.011 0.028 -10000 0 -0.035 144 144
RPS6 0.028 0.007 -10000 0 0 32 32
mol:cAMP 0.002 0.008 0.036 2 -0.084 1 3
PTPN11 0.011 0.03 -10000 0 -0.036 155 155
IL2RG 0.01 0.029 0.16 1 -0.038 115 116
actin cytoskeleton organization -0.064 0.14 0.33 1 -0.43 33 34
GRB2 0.011 0.029 -10000 0 -0.036 151 151
IL2 0.01 0.03 0.16 1 -0.038 128 129
PIK3CA 0.008 0.025 -10000 0 -0.036 85 85
Rac1/GTP -0.006 0.058 -10000 0 -0.12 72 72
LCK 0.01 0.03 0.17 1 -0.037 133 134
BCL2 -0.17 0.3 -10000 0 -0.75 103 103
LPA receptor mediated events

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
GNB1/GNG2 0.013 0.062 -10000 0 -0.15 60 60
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.094 0.22 5 -0.26 28 33
AP1 -0.018 0.085 0.21 48 -0.13 97 145
mol:PIP3 -0.056 0.061 0.028 8 -0.15 141 149
AKT1 -0.027 0.1 0.26 10 -0.32 4 14
PTK2B -0.048 0.11 0.19 31 -0.2 143 174
RHOA -0.006 0.059 0.18 2 -0.32 4 6
PIK3CB 0.021 0.018 -10000 0 -0.035 3 3
mol:Ca2+ -0.039 0.06 0.16 6 -0.18 28 34
MAGI3 0.024 0.017 -10000 0 -0.029 48 48
RELA 0.03 0.003 -10000 0 0 6 6
apoptosis -0.004 0.075 0.25 30 -0.15 53 83
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.055 0.1 0.16 36 -0.22 100 136
NF kappa B1 p50/RelA -0.05 0.11 0.22 54 -0.19 72 126
endothelial cell migration -0.045 0.098 -10000 0 -0.32 62 62
ADCY4 -0.01 0.095 0.24 32 -0.21 53 85
ADCY5 -0.008 0.093 0.24 32 -0.2 51 83
ADCY6 -0.008 0.093 0.24 32 -0.2 51 83
ADCY7 -0.007 0.093 0.24 31 -0.2 51 82
ADCY1 -0.008 0.093 0.24 32 -0.2 50 82
ADCY2 -0.007 0.092 0.24 32 -0.2 47 79
ADCY3 -0.009 0.094 0.24 32 -0.2 53 85
ADCY8 -0.05 0.097 0.24 8 -0.25 53 61
ADCY9 -0.018 0.1 0.24 32 -0.23 54 86
GSK3B -0.05 0.11 0.17 43 -0.22 102 145
arachidonic acid secretion -0.021 0.092 0.22 31 -0.2 57 88
GNG2 0.021 0.021 -10000 0 -0.033 13 13
TRIP6 0.01 0.031 -10000 0 -0.27 3 3
GNAO1 -0.012 0.089 0.3 31 -0.16 61 92
HRAS 0.028 0.006 -10000 0 0 28 28
NFKBIA -0.047 0.084 0.21 4 -0.26 32 36
GAB1 0.028 0.006 -10000 0 0 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.027 0.14 -10000 0 -0.81 14 14
JUN 0.028 0.007 -10000 0 0 34 34
LPA/LPA2/NHERF2 -0.008 0.053 -10000 0 -0.1 122 122
TIAM1 0.013 0.15 -10000 0 -0.94 14 14
PIK3R1 0.013 0.021 -10000 0 -0.033 11 11
mol:IP3 -0.032 0.058 0.16 6 -0.18 26 32
PLCB3 -0.028 0.056 0.13 35 -0.13 62 97
FOS 0.024 0.012 -10000 0 0 105 105
positive regulation of mitosis -0.021 0.092 0.22 31 -0.2 57 88
LPA/LPA1-2-3 -0.013 0.044 0.044 45 -0.13 62 107
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.027 0.009 -10000 0 0 59 59
stress fiber formation -0.018 0.097 0.23 31 -0.27 27 58
GNAZ -0.01 0.086 0.3 30 -0.16 53 83
EGFR/PI3K-beta/Gab1 -0.056 0.064 0.044 24 -0.15 141 165
positive regulation of dendritic cell cytokine production -0.013 0.044 0.042 45 -0.13 62 107
LPA/LPA2/MAGI-3 0.009 0.028 -10000 0 -0.068 57 57
ARHGEF1 -0.027 0.08 0.24 37 -10000 0 37
GNAI2 -0.013 0.089 0.3 31 -0.16 61 92
GNAI3 -0.011 0.084 0.3 28 -0.16 55 83
GNAI1 -0.011 0.088 0.3 31 -0.16 56 87
LPA/LPA3 -0.008 0.022 0.019 3 -0.07 62 65
LPA/LPA2 -0.008 0.022 0.019 3 -0.069 62 65
LPA/LPA1 -0.022 0.056 -10000 0 -0.18 62 62
HB-EGF/EGFR -0.006 0.079 0.17 79 -0.14 29 108
HBEGF 0.006 0.084 0.2 87 -10000 0 87
mol:DAG -0.032 0.058 0.16 6 -0.18 26 32
cAMP biosynthetic process -0.022 0.094 0.22 32 -0.22 40 72
NFKB1 0.027 0.008 -10000 0 0 47 47
SRC 0.028 0.007 -10000 0 0 31 31
GNB1 0.02 0.021 -10000 0 -0.032 11 11
LYN -0.04 0.083 0.22 7 -0.25 27 34
GNAQ 0.005 0.039 0.13 31 -0.064 60 91
LPAR2 0 0.002 -10000 0 -10000 0 0
LPAR3 0 0.002 -10000 0 -10000 0 0
LPAR1 -0.015 0.034 -10000 0 -0.11 62 62
IL8 0.032 0.24 0.56 67 -0.34 52 119
PTK2 0.005 0.066 0.26 22 -0.13 45 67
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
CASP3 -0.004 0.076 0.25 30 -0.15 53 83
EGFR 0.028 0.01 0.055 4 0 55 59
PLCG1 -0.003 0.044 0.13 27 -0.1 41 68
PLD2 0.008 0.076 0.26 30 -0.13 57 87
G12/G13 0.013 0.062 -10000 0 -0.15 61 61
PI3K-beta -0.056 0.064 -10000 0 -0.24 25 25
cell migration 0 0.059 0.21 1 -0.25 14 15
SLC9A3R2 0.025 0.011 -10000 0 0 92 92
PXN -0.018 0.098 0.23 31 -0.27 27 58
HRAS/GTP -0.022 0.093 0.22 31 -0.2 58 89
RAC1 0.028 0.006 -10000 0 0 28 28
MMP9 0.023 0.013 -10000 0 0 129 129
PRKCE 0.023 0.019 -10000 0 -0.03 57 57
PRKCD -0.045 0.062 0.17 7 -0.19 26 33
Gi(beta/gamma) -0.011 0.092 0.24 29 -0.2 41 70
mol:LPA -0.015 0.034 -10000 0 -0.11 62 62
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.083 0.24 20 -0.23 17 37
MAPKKK cascade -0.021 0.092 0.22 31 -0.2 57 88
contractile ring contraction involved in cytokinesis -0.005 0.06 -10000 0 -0.31 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.005 0.039 0.13 31 -0.064 59 90
GNA15 0.005 0.037 0.13 30 -0.064 53 83
GNA12 0.026 0.012 -10000 0 -0.03 15 15
GNA13 0.027 0.011 -10000 0 -0.03 16 16
MAPT -0.057 0.1 0.16 36 -0.22 100 136
GNA11 0.003 0.041 0.13 28 -0.079 52 80
Rac1/GTP 0.027 0.14 -10000 0 -0.86 14 14
MMP2 -0.046 0.099 -10000 0 -0.32 62 62
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.014 -10000 0 0 186 186
positive regulation of NF-kappaB transcription factor activity 0.015 0.047 -10000 0 -0.16 29 29
MAP2K4 -0.02 0.077 -10000 0 -0.3 15 15
IKBKB 0.028 0.008 -10000 0 0 39 39
TNFRSF10B 0.024 0.012 -10000 0 0 106 106
TNFRSF10A 0.024 0.012 -10000 0 0 108 108
SMPD1 -0.012 0.039 0.099 29 -0.12 29 58
IKBKG 0.028 0.006 -10000 0 0 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.024 0.012 -10000 0 0 107 107
TRAIL/TRAILR2 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR3 -0.028 0.088 -10000 0 -0.17 139 139
TRAIL/TRAILR1 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR4 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR1/DAP3/GTP 0.019 0.048 -10000 0 -0.13 29 29
IKK complex -0.002 0.067 -10000 0 -0.27 18 18
RIPK1 0.028 0.008 -10000 0 0 40 40
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.005 -10000 0 -10000 0 0
MAPK3 -0.01 0.054 0.19 34 -10000 0 34
MAP3K1 -0.02 0.083 0.18 1 -0.33 19 20
TRAILR4 (trimer) 0.024 0.012 -10000 0 0 107 107
TRADD 0.026 0.01 -10000 0 0 65 65
TRAILR1 (trimer) 0.024 0.012 -10000 0 0 108 108
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.018 0.073 -10000 0 -0.26 18 18
CFLAR 0.029 0.004 -10000 0 0 10 10
MAPK1 -0.009 0.054 0.19 34 -10000 0 34
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.071 -10000 0 -0.14 30 30
mol:ceramide -0.012 0.039 0.099 29 -0.12 29 58
FADD 0.029 0.005 -10000 0 0 19 19
MAPK8 -0.033 0.089 0.2 2 -0.3 24 26
TRAF2 0.028 0.006 -10000 0 0 24 24
TRAILR3 (trimer) 0.015 0.015 -10000 0 0 280 280
CHUK 0.028 0.007 -10000 0 0 36 36
TRAIL/TRAILR1/FADD 0.025 0.048 -10000 0 -0.14 26 26
DAP3 0.028 0.006 -10000 0 0 26 26
CASP10 0.011 0.081 0.14 122 -0.19 23 145
JNK cascade 0.015 0.047 -10000 0 -0.16 29 29
TRAIL (trimer) 0.02 0.014 -10000 0 0 186 186
TNFRSF10C 0.015 0.015 -10000 0 0 280 280
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.058 -10000 0 -0.13 26 26
TRAIL/TRAILR2/FADD 0.025 0.048 -10000 0 -0.14 26 26
cell death -0.012 0.039 0.099 29 -0.12 29 58
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.018 0.073 -10000 0 -0.26 18 18
TRAILR2 (trimer) 0.024 0.012 -10000 0 0 106 106
CASP8 -0.005 0.06 -10000 0 -0.5 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.032 0.071 -10000 0 -0.14 30 30
Integrins in angiogenesis

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 0.038 0.016 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.024 0.072 -10000 0 -0.15 72 72
PTK2 -0.02 0.13 0.29 15 -0.35 23 38
IGF1R 0.022 0.013 -10000 0 0 140 140
PI4KB 0.028 0.007 -10000 0 0 34 34
MFGE8 0.027 0.008 -10000 0 0 47 47
SRC 0.028 0.007 -10000 0 0 31 31
CDKN1B -0.005 0.058 -10000 0 -0.29 16 16
VEGFA 0.026 0.01 -10000 0 0 70 70
ILK -0.005 0.057 -10000 0 -0.28 16 16
ROCK1 0.029 0.005 -10000 0 0 15 15
AKT1 -0.023 0.053 -10000 0 -0.27 16 16
PTK2B -0.021 0.085 0.32 10 -0.23 2 12
alphaV/beta3 Integrin/JAM-A 0.025 0.073 -10000 0 -0.15 68 68
CBL 0.029 0.005 -10000 0 0 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.029 0.068 -10000 0 -0.15 65 65
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.082 0.12 -10000 0 -0.17 348 348
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.006 0.079 0.18 5 -0.32 11 16
alphaV/beta3 Integrin/Syndecan-1 0.029 0.067 -10000 0 -0.15 63 63
PI4KA 0.028 0.007 -10000 0 0 33 33
IGF-1R heterotetramer/IGF1/IRS1 -0.069 0.12 -10000 0 -0.19 229 229
PI4 Kinase 0.039 0.014 -10000 0 -10000 0 0
PIK3CA 0.021 0.014 -10000 0 0 171 171
alphaV/beta3 Integrin/Osteopontin 0.009 0.064 -10000 0 -0.15 62 62
RPS6KB1 -0.069 0.12 0.28 12 -0.32 15 27
TLN1 0.029 0.005 -10000 0 0 16 16
MAPK3 -0.076 0.16 0.22 1 -0.4 90 91
GPR124 0.026 0.01 -10000 0 0 74 74
MAPK1 -0.072 0.16 0.22 1 -0.4 90 91
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 161 161
alphaV/beta3 Integrin/Tumstatin 0.028 0.068 -10000 0 -0.15 67 67
cell adhesion 0.013 0.083 -10000 0 -0.18 71 71
ANGPTL3 0.029 0.004 -10000 0 0 13 13
VEGFR2 homodimer/VEGFA homodimer/Src 0.049 0.024 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 140 140
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
TGFBR2 0.029 0.005 -10000 0 0 14 14
ITGB3 0.024 0.011 -10000 0 0 98 98
IGF1 0.028 0.007 -10000 0 0 33 33
RAC1 0.028 0.006 -10000 0 0 28 28
regulation of cell-matrix adhesion 0.021 0.07 -10000 0 -0.15 73 73
apoptosis 0.028 0.007 -10000 0 0 33 33
CD47 0.027 0.008 -10000 0 0 48 48
alphaV/beta3 Integrin/CD47 0.027 0.066 -10000 0 -0.15 61 61
VCL 0.029 0.005 -10000 0 0 15 15
alphaV/beta3 Integrin/Del1 0.019 0.066 -10000 0 -0.15 64 64
CSF1 0.028 0.006 -10000 0 0 27 27
PIK3C2A -0.003 0.053 -10000 0 -0.27 13 13
PI4 Kinase/Pyk2 -0.064 0.061 0.1 27 -0.24 4 31
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.075 -10000 0 -0.14 59 59
FAK1/Vinculin -0.01 0.12 0.27 17 -0.3 21 38
alphaV beta3/Integrin/ppsTEM5 0.022 0.071 -10000 0 -0.15 73 73
RHOA 0.029 0.003 -10000 0 0 6 6
VTN 0.028 0.007 -10000 0 0 33 33
BCAR1 0.027 0.009 -10000 0 0 59 59
FGF2 0.027 0.008 -10000 0 0 44 44
F11R -0.03 0.014 0.2 1 -10000 0 1
alphaV/beta3 Integrin/Lactadherin 0.021 0.076 -10000 0 -0.16 79 79
alphaV/beta3 Integrin/TGFBR2 0.027 0.071 -10000 0 -0.15 69 69
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.056 -10000 0 -0.14 22 22
HSP90AA1 0.029 0.006 -10000 0 0 21 21
alphaV/beta3 Integrin/Talin 0.027 0.063 -10000 0 -0.13 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.014 -10000 0 0 214 214
alphaV/beta3 Integrin/Pyk2 -0.04 0.068 0.17 37 -0.23 2 39
SDC1 0.029 0.005 -10000 0 0 17 17
VAV3 -0.037 0.057 0.17 21 -0.23 1 22
PTPN11 0.029 0.004 -10000 0 0 9 9
IRS1 0.011 0.014 -10000 0 0 349 349
FAK1/Paxillin -0.01 0.12 0.27 17 -0.3 21 38
cell migration -0.019 0.11 0.25 18 -0.28 21 39
ITGAV 0.028 0.007 -10000 0 0 33 33
PI3K 0.002 0.094 -10000 0 -0.16 103 103
SPP1 0.018 0.015 -10000 0 0 228 228
KDR 0.029 0.006 -10000 0 0 21 21
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.007 -10000 0 0 33 33
COL4A3 0.029 0.004 -10000 0 0 9 9
angiogenesis -0.077 0.17 0.31 2 -0.42 92 94
Rac1/GTP -0.041 0.057 0.17 20 -0.22 1 21
EDIL3 0.023 0.012 -10000 0 0 125 125
cell proliferation 0.027 0.071 -10000 0 -0.15 69 69
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.08 0.12 -10000 0 -0.36 49 49
CaM/Ca2+ 0.019 0.022 -10000 0 -0.15 9 9
AKT1 0.028 0.006 -10000 0 0 28 28
AKT2 0.027 0.009 -10000 0 0 51 51
STXBP4 0.029 0.005 -10000 0 0 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.045 0.12 0.22 1 -0.36 46 47
YWHAZ 0.026 0.01 -10000 0 0 79 79
CALM1 0.028 0.006 -10000 0 0 26 26
YWHAQ 0.029 0.005 -10000 0 0 15 15
TBC1D4 -0.03 0.013 0.2 1 -10000 0 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.008 -10000 0 0 43 43
YWHAB 0.027 0.008 -10000 0 0 44 44
SNARE/Synip -0.086 0.09 -10000 0 -0.14 383 383
YWHAG 0.029 0.004 -10000 0 0 12 12
ASIP 0.027 0.008 -10000 0 0 42 42
PRKCI 0.014 0.015 -10000 0 0 288 288
AS160/CaM/Ca2+ 0.019 0.022 -10000 0 -0.15 9 9
RHOQ 0.029 0.005 -10000 0 0 18 18
GYS1 -0.014 0.012 0.24 1 -10000 0 1
PRKCZ 0.029 0.006 -10000 0 0 23 23
TRIP10 0.028 0.007 -10000 0 0 36 36
TC10/GTP/CIP4/Exocyst 0.037 0.012 -10000 0 -10000 0 0
AS160/14-3-3 -0.008 0.07 0.16 4 -0.31 16 20
VAMP2 0.007 0.013 -10000 0 0 417 417
SLC2A4 -0.05 0.13 -10000 0 -0.4 47 47
STX4 0.029 0.004 -10000 0 0 11 11
GSK3B 0.009 0.004 -10000 0 -10000 0 0
SFN 0.028 0.007 -10000 0 0 38 38
LNPEP 0.027 0.009 -10000 0 0 54 54
YWHAE 0.028 0.008 -10000 0 0 41 41
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.034 0.071 -10000 0 -0.13 72 72
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.14 -10000 0 -0.32 75 75
AKT1 -0.13 0.27 -10000 0 -0.67 103 103
PIK3CA 0.021 0.014 -10000 0 0 171 171
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.28 -10000 0 -0.68 103 103
mol:Ca2+ -0.043 0.077 0.16 11 -0.32 20 31
IGF1R 0.022 0.013 -10000 0 0 140 140
E2/ER alpha (dimer)/Striatin 0.015 0.057 -10000 0 -0.13 70 70
SHC1 0.029 0.006 -10000 0 0 20 20
apoptosis 0.13 0.26 0.64 103 -10000 0 103
RhoA/GTP -0.025 0.035 -10000 0 -0.14 22 22
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.022 0.15 0.24 2 -0.32 76 78
regulation of stress fiber formation -0.032 0.1 0.2 2 -0.24 62 64
E2/ERA-ERB (dimer) 0.014 0.058 -10000 0 -0.13 73 73
KRAS 0.024 0.011 -10000 0 0 99 99
G13/GTP 0.013 0.053 -10000 0 -0.12 73 73
pseudopodium formation 0.032 0.1 0.24 62 -0.2 2 64
E2/ER alpha (dimer)/PELP1 0.014 0.058 -10000 0 -0.13 73 73
GRB2 0.029 0.006 -10000 0 0 20 20
GNG2 0.029 0.004 -10000 0 0 12 12
GNAO1 0.027 0.008 -10000 0 0 46 46
HRAS 0.028 0.006 -10000 0 0 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.067 0.17 -10000 0 -0.39 103 103
E2/ER beta (dimer) 0.021 0.003 -10000 0 -10000 0 0
mol:GDP -0.035 0.069 -10000 0 -0.25 36 36
mol:NADP -0.067 0.17 -10000 0 -0.39 103 103
PIK3R1 0.021 0.013 -10000 0 0 161 161
mol:IP3 -0.046 0.074 -10000 0 -0.34 18 18
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 140 140
PLCB1 -0.034 0.072 0.14 6 -0.31 22 28
PLCB2 -0.038 0.071 -10000 0 -0.31 24 24
IGF1 0.028 0.007 -10000 0 0 33 33
mol:L-citrulline -0.067 0.17 -10000 0 -0.39 103 103
RHOA 0.029 0.003 -10000 0 0 6 6
Gai/GDP -0.007 0.17 -10000 0 -0.59 35 35
JNK cascade 0.021 0.003 -10000 0 -10000 0 0
BCAR1 0.027 0.009 -10000 0 0 59 59
ESR2 0.029 0.005 -10000 0 0 14 14
GNAQ 0.028 0.006 -10000 0 0 28 28
ESR1 0.024 0.012 -10000 0 0 109 109
Gq family/GDP/Gbeta gamma -0.072 0.22 -10000 0 -0.66 60 60
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.003 0.11 -10000 0 -0.73 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.021 0.15 0.24 2 -0.32 74 76
GNAZ 0.027 0.008 -10000 0 0 47 47
E2/ER alpha (dimer) -0.002 0.057 -10000 0 -0.15 73 73
STRN 0.029 0.005 -10000 0 0 14 14
GNAL 0.029 0.006 -10000 0 0 20 20
PELP1 0.028 0.006 -10000 0 0 26 26
MAPK11 -0.02 0.012 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.024 0.011 -10000 0 0 98 98
GNAI1 0.028 0.006 -10000 0 0 27 27
HBEGF -0.02 0.15 0.29 14 -0.4 31 45
cAMP biosynthetic process 0.01 0.05 -10000 0 -0.11 72 72
SRC -0.039 0.14 -10000 0 -0.43 28 28
PI3K 0 0.067 -10000 0 -0.16 75 75
GNB1 0.028 0.006 -10000 0 0 24 24
G13/GDP/Gbeta gamma 0.017 0.091 -10000 0 -0.24 35 35
SOS1 0.028 0.007 -10000 0 0 34 34
IGF-1R heterotetramer/IGF1 -0.07 0.11 -10000 0 -0.29 79 79
Gs family/GTP 0.017 0.054 -10000 0 -0.12 72 72
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.029 -10000 0 -10000 0 0
vasodilation -0.064 0.16 -10000 0 -0.37 103 103
mol:DAG -0.046 0.074 -10000 0 -0.34 18 18
Gs family/GDP/Gbeta gamma -0.029 0.081 -10000 0 -0.24 35 35
MSN 0.03 0.1 0.24 60 -0.21 2 62
Gq family/GTP -0.016 0.082 -10000 0 -0.32 25 25
mol:PI-3-4-5-P3 -0.11 0.27 -10000 0 -0.66 103 103
NRAS 0.014 0.015 -10000 0 0 300 300
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.064 0.16 0.37 103 -10000 0 103
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
RhoA/GDP -0.018 0.087 -10000 0 -0.25 35 35
NOS3 -0.071 0.18 -10000 0 -0.4 103 103
GNA11 0.025 0.011 -10000 0 0 84 84
MAPKKK cascade -0.065 0.2 -10000 0 -0.47 102 102
E2/ER alpha (dimer)/PELP1/Src -0.025 0.15 0.26 2 -0.33 77 79
ruffle organization 0.032 0.1 0.24 62 -0.2 2 64
ROCK2 0.048 0.11 0.26 61 -10000 0 61
GNA14 0.029 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 47 47
GNA13 0.029 0.005 -10000 0 0 14 14
MMP9 -0.014 0.15 0.29 28 -0.41 28 56
MMP2 -0.044 0.14 0.26 6 -0.4 35 41
Signaling events mediated by the Hedgehog family

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
TGFB2 0.031 0.21 0.5 81 -0.44 16 97
IHH -0.005 0.078 0.16 89 -10000 0 89
SHH Np/Cholesterol/GAS1 -0.044 0.037 0.14 1 -0.13 76 77
LRPAP1 0.028 0.007 -10000 0 0 37 37
dorsoventral neural tube patterning 0.044 0.037 0.13 76 -0.14 1 77
SMO/beta Arrestin2 0.025 0.13 0.3 84 -0.39 8 92
SMO 0.028 0.13 0.31 84 -0.4 8 92
AKT1 -0.025 0.15 0.27 13 -0.44 19 32
ARRB2 0.028 0.006 -10000 0 0 26 26
BOC 0.025 0.01 -10000 0 0 80 80
ADRBK1 0.029 0.003 -10000 0 0 7 7
heart looping 0.028 0.13 0.31 84 -0.39 8 92
STIL 0.002 0.065 0.27 20 -10000 0 20
DHH N/PTCH2 0.042 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.006 0.13 0.32 79 -0.25 23 102
PIK3CA 0.021 0.014 -10000 0 0 171 171
DHH 0.029 0.003 -10000 0 0 5 5
PTHLH 0.032 0.19 0.5 71 -0.42 21 92
determination of left/right symmetry 0.028 0.13 0.31 84 -0.39 8 92
PIK3R1 0.021 0.013 -10000 0 0 161 161
skeletal system development 0.032 0.19 0.5 71 -0.41 21 92
IHH N/Hhip 0.049 0.042 0.18 3 -10000 0 3
DHH N/Hhip 0.042 0.01 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.028 0.13 0.31 84 -0.39 8 92
pancreas development 0.028 0.006 -10000 0 0 27 27
HHAT 0.029 0.005 -10000 0 0 18 18
PI3K 0 0.067 -10000 0 -0.16 75 75
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.025 0.011 -10000 0 0 95 95
somite specification 0.028 0.13 0.31 84 -0.39 8 92
SHH Np/Cholesterol/PTCH1 -0.002 0.12 0.27 75 -0.23 20 95
SHH Np/Cholesterol/PTCH2 -0.032 0.016 0.14 1 -0.13 5 6
SHH Np/Cholesterol/Megalin -0.025 0.018 -10000 0 -0.13 4 4
SHH -0.03 0.014 0.2 1 -10000 0 1
catabolic process 0.023 0.16 0.38 84 -0.27 23 107
SMO/Vitamin D3 0.004 0.12 0.26 76 -0.36 8 84
SHH Np/Cholesterol/Hhip -0.031 0.017 0.14 1 -0.13 5 6
LRP2 0.022 0.013 -10000 0 0 141 141
receptor-mediated endocytosis 0.025 0.12 0.28 75 -0.4 7 82
SHH Np/Cholesterol/BOC -0.04 0.032 0.14 1 -0.13 55 56
SHH Np/Cholesterol/CDO -0.032 0.018 0.14 1 -0.13 7 8
mesenchymal cell differentiation 0.031 0.016 0.13 5 -0.14 1 6
mol:Vitamin D3 0.005 0.12 0.24 102 -0.27 7 109
IHH N/PTCH2 0.05 0.041 0.18 4 -0.088 7 11
CDON 0.028 0.007 -10000 0 0 33 33
IHH N/PTCH1 -0.034 0.052 -10000 0 -0.27 23 23
Megalin/LRPAP1 0.03 0.023 -10000 0 -0.16 2 2
PTCH2 0.029 0.006 -10000 0 0 22 22
SHH Np/Cholesterol -0.022 0.013 0.16 1 -0.12 5 6
PTCH1 0.023 0.16 0.38 84 -0.27 23 107
HHIP 0.028 0.006 -10000 0 0 27 27
IL4-mediated signaling events

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
BCL2L1 0.025 0.58 1.1 16 -1.2 42 58
STAT6 (cleaved dimer) -0.092 0.5 0.65 3 -1.2 62 65
IGHG1 0.09 0.31 0.68 40 -0.98 2 42
IGHG3 -0.006 0.53 0.81 6 -1.1 50 56
AKT1 -0.039 0.37 -10000 0 -0.98 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.016 0.33 0.58 7 -0.96 28 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.08 0.39 0.64 3 -1 39 42
THY1 0.077 0.65 1.2 49 -1.2 42 91
MYB 0.026 0.009 -10000 0 0 62 62
HMGA1 0.029 0.006 -10000 0 0 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.051 0.42 0.77 32 -0.94 24 56
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.021 0.4 0.64 11 -1.1 27 38
SP1 0.11 0.13 0.3 177 -0.14 6 183
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.018 0.059 -10000 0 -0.15 5 5
STAT6 (dimer)/ETS1 -0.049 0.54 0.72 6 -1.2 53 59
SOCS1 -0.001 0.4 0.62 17 -0.78 46 63
SOCS3 0.029 0.35 0.87 1 -0.88 17 18
FCER2 0.043 0.48 0.95 10 -1 21 31
PARP14 0.022 0.013 -10000 0 -10000 0 0
CCL17 0.005 0.57 0.97 6 -1.2 46 52
GRB2 0.029 0.006 -10000 0 0 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.044 0.31 0.59 13 -0.68 25 38
T cell proliferation -0.056 0.58 -10000 0 -1.3 63 63
IL4R/JAK1 -0.069 0.61 0.79 2 -1.4 65 67
EGR2 0.012 0.58 1.1 8 -1.2 46 54
JAK2 0.043 0.11 0.25 48 -10000 0 48
JAK3 0.002 0.034 0.11 2 -10000 0 2
PIK3R1 0.021 0.013 -10000 0 0 161 161
JAK1 0.023 0.059 0.14 17 -10000 0 17
COL1A2 0.16 0.39 0.73 101 -1.1 8 109
CCL26 0.007 0.57 0.97 7 -1.2 45 52
IL4R -0.018 0.7 1.1 37 -1.4 65 102
PTPN6 -0.012 0.05 -10000 0 -0.1 13 13
IL13RA2 0.016 0.58 1.1 11 -1.2 45 56
IL13RA1 0.045 0.11 0.25 47 -10000 0 47
IRF4 0.066 0.21 0.73 1 -0.78 3 4
ARG1 0.079 0.26 0.68 11 -0.69 4 15
CBL 0.029 0.38 0.68 13 -0.88 25 38
GTF3A 0.16 0.14 0.31 276 -0.11 1 277
PIK3CA 0.021 0.014 -10000 0 0 171 171
IL13RA1/JAK2 0.074 0.16 0.35 57 -10000 0 57
IRF4/BCL6 0.046 0.18 0.54 1 -0.64 6 7
CD40LG 0.03 0.018 0.33 2 -10000 0 2
MAPK14 0.031 0.38 0.7 8 -0.9 23 31
mitosis -0.032 0.35 -10000 0 -0.9 29 29
STAT6 0.033 0.71 1.4 40 -1.4 49 89
SPI1 0.029 0.011 0.27 1 -10000 0 1
RPS6KB1 -0.036 0.34 0.63 2 -0.88 28 30
STAT6 (dimer) 0.032 0.7 1.4 40 -1.4 49 89
STAT6 (dimer)/PARP14 -0.055 0.54 -10000 0 -1.2 50 50
mast cell activation -0.01 0.028 -10000 0 -0.068 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.006 0.39 0.66 5 -1.1 28 33
FRAP1 -0.039 0.37 -10000 0 -0.98 29 29
LTA 0.009 0.57 0.98 8 -1.2 43 51
FES 0.029 0.006 -10000 0 0 22 22
T-helper 1 cell differentiation -0.044 0.7 1.3 47 -1.4 40 87
CCL11 0.002 0.55 0.98 21 -1.2 46 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.02 0.38 0.64 6 -1.1 25 31
IL2RG 0 0.034 0.12 2 -10000 0 2
IL10 0.007 0.57 0.97 6 -1.2 45 51
IRS1 0.011 0.014 -10000 0 0 349 349
IRS2 0.028 0.006 -10000 0 0 25 25
IL4 0.11 0.31 0.79 37 -1.1 6 43
IL5 0.007 0.57 0.97 6 -1.2 44 50
IL4/IL4R/JAK1/IL13RA1/JAK2 0.052 0.58 1.1 39 -1.2 33 72
COL1A1 0.3 0.51 0.94 142 -1.1 11 153
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.088 0.61 -10000 0 -1.4 65 65
IL2R gamma/JAK3 0.028 0.046 0.18 2 -0.15 23 25
TFF3 -0.56 0.62 0.97 5 -1.3 154 159
ALOX15 0.007 0.57 1.1 7 -1.2 50 57
MYBL1 0.024 0.012 -10000 0 0 104 104
T-helper 2 cell differentiation -0.024 0.54 0.85 13 -1.2 51 64
SHC1 0.029 0.006 -10000 0 0 20 20
CEBPB 0.027 0.013 0.27 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.02 0.39 0.64 8 -1.1 29 37
mol:PI-3-4-5-P3 -0.038 0.37 -10000 0 -0.98 29 29
PI3K -0.047 0.39 -10000 0 -1.1 29 29
DOK2 0.024 0.012 -10000 0 0 105 105
ETS1 -0.023 0.064 -10000 0 -0.14 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.045 0.3 0.58 13 -0.65 25 38
ITGB3 -0.064 0.68 1.1 9 -1.4 80 89
PIGR -0.017 0.62 1.2 13 -1.3 54 67
IGHE -0.051 0.12 0.22 12 -0.31 49 61
MAPKKK cascade 0.046 0.3 0.58 13 -0.64 24 37
BCL6 0.025 0.011 -10000 0 -10000 0 0
OPRM1 0.007 0.57 0.97 6 -1.2 45 51
RETNLB 0.013 0.57 1 7 -1.2 44 51
SELP -0.017 0.6 1 7 -1.2 50 57
AICDA 0.004 0.53 1 4 -1.1 45 49
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.016 0.037 0.11 22 -10000 0 22
PDGF/PDGFRA/CRKL 0.01 0.07 -10000 0 -0.16 65 65
positive regulation of JUN kinase activity 0.036 0.076 -10000 0 -0.14 61 61
CRKL 0.028 0.007 -10000 0 0 31 31
PDGF/PDGFRA/Caveolin-3 0.01 0.071 -10000 0 -0.16 65 65
AP1 -0.093 0.25 0.6 18 -0.69 61 79
mol:IP3 -0.022 0.06 0.18 30 -0.22 7 37
PLCG1 -0.022 0.06 0.18 30 -0.22 7 37
PDGF/PDGFRA/alphaV Integrin 0.008 0.071 -10000 0 -0.16 66 66
RAPGEF1 0.029 0.005 -10000 0 0 18 18
CRK 0.028 0.007 -10000 0 0 37 37
mol:Ca2+ -0.022 0.06 0.18 30 -0.22 7 37
CAV3 0.029 0.004 -10000 0 0 10 10
CAV1 0.024 0.012 -10000 0 0 109 109
SHC/Grb2/SOS1 0.038 0.077 -10000 0 -0.14 61 61
PDGF/PDGFRA/Shf 0.009 0.07 -10000 0 -0.12 105 105
FOS -0.085 0.26 0.65 24 -0.7 59 83
JUN -0.026 0.058 0.18 32 -0.22 1 33
oligodendrocyte development 0.008 0.071 -10000 0 -0.16 66 66
GRB2 0.029 0.006 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 161 161
mol:DAG -0.022 0.06 0.18 30 -0.22 7 37
PDGF/PDGFRA -0.016 0.037 0.11 22 -10000 0 22
actin cytoskeleton reorganization 0.01 0.071 -10000 0 -0.16 65 65
SRF -0.026 0.021 -10000 0 -10000 0 0
SHC1 0.029 0.006 -10000 0 0 20 20
PI3K -0.011 0.084 -10000 0 -0.16 107 107
PDGF/PDGFRA/Crk/C3G 0.02 0.071 -10000 0 -0.14 64 64
JAK1 -0.026 0.041 0.15 14 -0.18 9 23
ELK1/SRF -0.049 0.062 0.14 25 -0.21 5 30
SHB 0.029 0.004 -10000 0 0 8 8
SHF 0.028 0.007 -10000 0 0 33 33
CSNK2A1 0.024 0.036 -10000 0 -0.087 27 27
GO:0007205 -0.034 0.081 0.19 31 -0.21 56 87
SOS1 0.028 0.007 -10000 0 0 34 34
Ras protein signal transduction 0.036 0.076 -10000 0 -0.14 61 61
PDGF/PDGFRA/SHB 0.01 0.071 -10000 0 -0.16 65 65
PDGF/PDGFRA/Caveolin-1 -0.015 0.099 -10000 0 -0.19 125 125
ITGAV 0.028 0.007 -10000 0 0 33 33
ELK1 -0.039 0.085 0.22 30 -0.19 53 83
PIK3CA 0.021 0.014 -10000 0 0 171 171
PDGF/PDGFRA/Crk 0.008 0.07 -10000 0 -0.16 65 65
JAK-STAT cascade -0.026 0.041 0.15 14 -0.18 9 23
cell proliferation 0.009 0.07 -10000 0 -0.16 65 65
Nectin adhesion pathway

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
PDGFRB 0.029 0.005 -10000 0 0 15 15
alphaV beta3 Integrin 0.014 0.068 -10000 0 -0.17 67 67
PTK2 -0.037 0.11 -10000 0 -0.32 51 51
positive regulation of JNK cascade -0.016 0.11 -10000 0 -0.3 53 53
CDC42/GDP -0.018 0.15 -10000 0 -0.4 56 56
Rac1/GDP -0.02 0.15 -10000 0 -0.4 56 56
RAP1B 0.029 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CTNNB1 0.029 0.003 -10000 0 0 7 7
CDC42/GTP -0.017 0.14 -10000 0 -0.37 50 50
nectin-3/I-afadin 0.026 0.043 -10000 0 -0.16 23 23
RAPGEF1 -0.039 0.14 0.26 3 -0.4 55 58
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.039 0.15 0.28 1 -0.45 56 57
PDGFB-D/PDGFRB 0.029 0.005 -10000 0 0 15 15
TLN1 -0.094 0.12 -10000 0 -0.25 186 186
Rap1/GTP -0.029 0.11 -10000 0 -0.31 56 56
IQGAP1 0.028 0.006 -10000 0 0 25 25
Rap1/GTP/I-afadin 0.041 0.042 -10000 0 -0.13 21 21
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.026 0.043 -10000 0 -0.16 23 23
PVR 0.028 0.007 -10000 0 0 32 32
Necl-5(dimer) 0.028 0.007 -10000 0 0 32 32
mol:GDP -0.038 0.17 -10000 0 -0.48 56 56
MLLT4 0.026 0.01 -10000 0 0 70 70
PIK3CA 0.021 0.014 -10000 0 0 171 171
PI3K 0.027 0.091 -10000 0 -0.15 77 77
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.031 0.041 -10000 0 -0.16 21 21
positive regulation of lamellipodium assembly -0.016 0.12 -10000 0 -0.32 55 55
PVRL1 0.029 0.005 -10000 0 0 18 18
PVRL3 0.025 0.011 -10000 0 0 93 93
PVRL2 0.028 0.007 -10000 0 0 32 32
PIK3R1 0.021 0.013 -10000 0 0 161 161
CDH1 0.026 0.01 -10000 0 0 73 73
CLDN1 0.017 0.015 -10000 0 0 233 233
JAM-A/CLDN1 0.006 0.094 -10000 0 -0.14 137 137
SRC -0.039 0.16 -10000 0 -0.48 56 56
ITGB3 0.024 0.011 -10000 0 0 98 98
nectin-1(dimer)/I-afadin/I-afadin 0.031 0.041 -10000 0 -0.16 21 21
FARP2 -0.034 0.18 -10000 0 -0.49 50 50
RAC1 0.028 0.006 -10000 0 0 28 28
CTNNA1 0.029 0.004 -10000 0 0 11 11
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.045 -10000 0 -0.14 22 22
nectin-1/I-afadin 0.031 0.041 -10000 0 -0.16 21 21
nectin-2/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
RAC1/GTP/IQGAP1/filamentous actin 0.036 0.015 -10000 0 -0.13 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.037 0.046 -10000 0 -0.14 23 23
CDC42/GTP/IQGAP1/filamentous actin 0.037 0.014 -10000 0 -0.13 2 2
F11R 0.029 0.004 -10000 0 0 13 13
positive regulation of filopodium formation -0.016 0.11 -10000 0 -0.3 53 53
alphaV/beta3 Integrin/Talin -0.12 0.12 0.2 5 -0.26 196 201
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
nectin-2(dimer)/I-afadin/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
PIP5K1C -0.092 0.12 -10000 0 -0.26 186 186
VAV2 -0.034 0.18 -10000 0 -0.5 51 51
RAP1/GDP -0.014 0.14 -10000 0 -0.37 58 58
ITGAV 0.028 0.007 -10000 0 0 33 33
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.046 -10000 0 -0.14 23 23
nectin-3(dimer)/I-afadin/I-afadin 0.026 0.043 -10000 0 -0.16 23 23
Rac1/GTP -0.019 0.14 -10000 0 -0.38 55 55
PTPRM -0.1 0.13 0.099 24 -0.27 210 234
E-cadherin/beta catenin/alpha catenin 0.048 0.071 -10000 0 -0.15 25 25
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.029 0.004 -10000 0 0 11 11
HIF-2-alpha transcription factor 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
MMP14 0.002 0.099 0.65 5 -0.72 6 11
oxygen homeostasis 0.044 0.072 0.18 92 -10000 0 92
TCEB2 0.029 0.005 -10000 0 0 17 17
TCEB1 0.028 0.007 -10000 0 0 37 37
VHL/Elongin B/Elongin C/HIF2A 0.11 0.25 0.54 90 -0.34 2 92
EPO 0.14 0.34 0.82 67 -10000 0 67
FIH (dimer) 0.045 0.093 0.21 90 -10000 0 90
APEX1 0.026 0.073 0.17 67 -10000 0 67
SERPINE1 0.095 0.33 0.85 50 -10000 0 50
FLT1 -0.021 0.13 -10000 0 -0.65 21 21
ADORA2A 0.19 0.38 0.86 92 -10000 0 92
germ cell development 0.17 0.38 0.87 83 -10000 0 83
SLC11A2 0.15 0.37 0.86 74 -10000 0 74
BHLHE40 0.15 0.36 0.85 74 -10000 0 74
HIF1AN 0.045 0.093 0.21 90 -10000 0 90
HIF2A/ARNT/SIRT1 0.041 0.2 0.45 30 -0.4 1 31
ETS1 0.02 0.026 0.26 2 -10000 0 2
CITED2 -0.045 0.19 -10000 0 -0.75 36 36
KDR -0.013 0.1 -10000 0 -0.64 12 12
PGK1 0.016 0.26 0.87 25 -10000 0 25
SIRT1 0.019 0.022 -10000 0 -0.03 92 92
response to hypoxia -0.001 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.057 0.27 0.64 23 -10000 0 23
EPAS1 0.15 0.34 0.81 86 -10000 0 86
SP1 0.038 0.051 0.3 18 -0.16 2 20
ABCG2 0.15 0.38 0.86 79 -0.58 3 82
EFNA1 0.14 0.36 0.85 74 -10000 0 74
FXN 0.19 0.38 0.85 90 -10000 0 90
POU5F1 0.16 0.38 0.86 81 -10000 0 81
neuron apoptosis -0.055 0.27 -10000 0 -0.63 22 22
EP300 0.027 0.009 -10000 0 0 51 51
EGLN3 0.042 0.092 0.22 83 -10000 0 83
EGLN2 0.044 0.093 0.22 86 -10000 0 86
EGLN1 0.044 0.091 0.21 85 -10000 0 85
VHL/Elongin B/Elongin C 0.054 0.019 -10000 0 -10000 0 0
VHL 0.029 0.004 -10000 0 0 9 9
ARNT 0.026 0.073 0.17 66 -10000 0 66
SLC2A1 0.18 0.38 0.89 80 -10000 0 80
TWIST1 0.18 0.38 0.86 88 -10000 0 88
ELK1 0.021 0.035 -10000 0 -0.14 24 24
HIF2A/ARNT/Cbp/p300 0.09 0.27 0.65 54 -0.4 1 55
VEGFA 0.13 0.35 0.85 66 -10000 0 66
CREBBP 0.028 0.008 -10000 0 0 40 40
Class I PI3K 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
ARF5/GTP 0.06 0.1 0.21 85 -10000 0 85
DAPP1 -0.029 0.098 0.2 8 -0.26 42 50
Src family/SYK family/BLNK-LAT/BTK-ITK -0.005 0.12 0.22 2 -0.42 19 21
mol:DAG 0.023 0.089 0.19 60 -0.2 9 69
HRAS 0.014 0.035 0.049 111 -10000 0 111
RAP1A 0.014 0.036 0.05 100 -10000 0 100
ARF5/GDP 0.053 0.066 0.19 3 -0.25 8 11
PLCG2 0.026 0.01 -10000 0 0 65 65
PLCG1 0.028 0.007 -10000 0 0 31 31
ARF5 0.028 0.006 -10000 0 0 25 25
mol:GTP 0.059 0.097 0.21 92 -10000 0 92
ARF1/GTP 0.056 0.089 0.25 54 -10000 0 54
RHOA 0.029 0.003 -10000 0 0 6 6
YES1 0.028 0.008 -10000 0 0 40 40
RAP1A/GTP 0.072 0.11 0.16 309 -10000 0 309
ADAP1 0.054 0.092 0.2 89 -10000 0 89
ARAP3 0.058 0.096 0.21 92 -10000 0 92
INPPL1 0.029 0.006 -10000 0 0 20 20
PREX1 0.027 0.008 -10000 0 0 47 47
ARHGEF6 0.029 0.005 -10000 0 0 18 18
ARHGEF7 0.028 0.006 -10000 0 0 25 25
ARF1 0.027 0.009 -10000 0 0 55 55
NRAS -0.008 0.022 0.041 39 -10000 0 39
FYN 0.024 0.011 -10000 0 0 99 99
ARF6 0.029 0.004 -10000 0 0 11 11
FGR 0.029 0.005 -10000 0 0 15 15
mol:Ca2+ 0.009 0.053 0.14 36 -10000 0 36
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.029 0.006 -10000 0 0 20 20
ZAP70 0.029 0.004 -10000 0 0 11 11
mol:IP3 0.006 0.065 0.17 32 -0.16 3 35
LYN 0.027 0.009 -10000 0 0 52 52
ARF1/GDP 0.049 0.066 0.19 3 -0.25 8 11
RhoA/GDP 0.085 0.1 0.21 132 -10000 0 132
PDK1/Src/Hsp90 0.054 0.019 -10000 0 -10000 0 0
BLNK 0.028 0.007 -10000 0 0 31 31
actin cytoskeleton reorganization 0.07 0.096 0.23 72 -0.26 2 74
SRC 0.028 0.007 -10000 0 0 31 31
PLEKHA2 -0.023 0.009 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 28 28
PTEN -0.01 0.035 -10000 0 -0.039 321 321
HSP90AA1 0.029 0.006 -10000 0 0 21 21
ARF6/GTP 0.063 0.1 0.21 91 -10000 0 91
RhoA/GTP 0.063 0.1 0.22 93 -10000 0 93
Src family/SYK family/BLNK-LAT -0.032 0.09 -10000 0 -0.3 27 27
BLK 0.024 0.011 -10000 0 0 102 102
PDPK1 0.029 0.005 -10000 0 0 17 17
CYTH1 0.054 0.092 0.2 89 -10000 0 89
HCK 0.027 0.008 -10000 0 0 47 47
CYTH3 0.054 0.092 0.2 89 -10000 0 89
CYTH2 0.054 0.092 0.2 89 -10000 0 89
KRAS 0.006 0.033 0.049 31 -10000 0 31
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.034 0.058 0.17 48 -0.19 1 49
SGK1 0.046 0.064 0.18 49 -0.18 6 55
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.042 0.064 0.18 6 -0.26 8 14
SOS1 0.028 0.007 -10000 0 0 34 34
SYK 0.028 0.006 -10000 0 0 24 24
ARF6/GDP 0.069 0.098 0.21 109 -10000 0 109
mol:PI-3-4-5-P3 0.061 0.098 0.21 88 -10000 0 88
ARAP3/RAP1A/GTP 0.072 0.11 0.16 309 -10000 0 309
VAV1 0.028 0.008 -10000 0 0 41 41
mol:PI-3-4-P2 -0.016 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.014 0.035 0.2 9 -10000 0 9
PLEKHA1 -0.023 0.023 0.18 7 -10000 0 7
Rac1/GDP 0.053 0.065 0.2 2 -0.25 8 10
LAT 0.029 0.004 -10000 0 0 8 8
Rac1/GTP 0.016 0.055 0.19 1 -0.28 8 9
ITK 0.047 0.093 0.21 69 -10000 0 69
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.02 0.11 0.22 54 -0.27 10 64
LCK 0.028 0.006 -10000 0 0 26 26
BTK 0.048 0.094 0.21 73 -10000 0 73
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.2 0.62 1 -0.57 25 26
RAD9A 0.029 0.004 -10000 0 0 8 8
AP1 -0.003 0.069 -10000 0 -0.17 61 61
IFNAR2 0.01 0.032 0.098 1 -0.043 145 146
AKT1 -0.02 0.05 -10000 0 -0.17 20 20
ER alpha/Oestrogen -0.012 0.057 0.07 1 -0.15 73 74
NFX1/SIN3/HDAC complex -0.012 0.075 0.2 3 -0.34 14 17
EGF 0.012 0.028 -10000 0 -0.037 128 128
SMG5 0.029 0.006 -10000 0 0 23 23
SMG6 0.028 0.007 -10000 0 0 29 29
SP3/HDAC2 0.016 0.043 0.16 1 -10000 0 1
TERT/c-Abl -0.1 0.2 0.55 1 -0.52 36 37
SAP18 0.013 0.026 -10000 0 -0.031 139 139
MRN complex 0.043 0.027 -10000 0 -10000 0 0
WT1 0.01 0.03 0.11 1 -0.043 125 126
WRN 0.023 0.012 -10000 0 0 121 121
SP1 0.008 0.036 0.14 1 -0.051 146 147
SP3 0.012 0.029 0.066 1 -0.038 143 144
TERF2IP 0.026 0.009 -10000 0 0 62 62
Telomerase/Nucleolin -0.11 0.19 -10000 0 -0.46 60 60
Mad/Max 0.018 0.04 -10000 0 -10000 0 0
TERT -0.12 0.2 -10000 0 -0.58 26 26
CCND1 -0.26 0.43 0.8 1 -0.96 147 148
MAX 0.011 0.03 -10000 0 -0.038 145 145
RBBP7 0.013 0.027 -10000 0 -0.032 143 143
RBBP4 0.013 0.026 -10000 0 -0.031 130 130
TERF2 -0.031 0.019 0.077 8 -10000 0 8
PTGES3 0.024 0.011 -10000 0 0 100 100
SIN3A 0.013 0.027 -10000 0 -0.031 142 142
Telomerase/911 -0.008 0.085 0.22 1 -0.32 6 7
CDKN1B -0.028 0.062 0.2 28 -0.37 2 30
RAD1 0.027 0.008 -10000 0 0 46 46
XRCC5 0.028 0.007 -10000 0 0 38 38
XRCC6 0.027 0.008 -10000 0 0 50 50
SAP30 0.012 0.026 -10000 0 -0.032 135 135
TRF2/PARP2 -0.03 0.022 0.068 11 -10000 0 11
UBE3A 0.012 0.028 0.061 1 -0.037 131 132
JUN 0.011 0.029 -10000 0 -0.037 137 137
E6 -0.002 0.004 0.031 1 -10000 0 1
HPV-16 E6/E6AP 0.008 0.023 0.095 1 -10000 0 1
FOS 0.01 0.027 -10000 0 -0.038 120 120
IFN-gamma/IRF1 0.014 0.049 -10000 0 -0.19 9 9
PARP2 0.026 0.01 -10000 0 0 73 73
BLM 0.018 0.014 -10000 0 0 212 212
Telomerase -0.013 0.084 -10000 0 -0.32 16 16
IRF1 -0.031 0.025 0.17 6 -0.14 2 8
ESR1 0.01 0.026 -10000 0 -0.034 122 122
KU/TER 0.038 0.016 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.021 -10000 0 -0.081 8 8
ubiquitin-dependent protein catabolic process -0.013 0.077 0.2 3 -0.32 16 19
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.014 0.077 0.21 2 -0.32 17 19
HDAC1 0.013 0.026 -10000 0 -0.031 130 130
HDAC2 0.008 0.034 0.12 1 -0.05 136 137
ATM 0.02 0.026 0.24 2 -10000 0 2
SMAD3 -0.025 0.015 -10000 0 -0.2 1 1
ABL1 0.029 0.006 -10000 0 0 21 21
MXD1 0.012 0.029 -10000 0 -0.038 142 142
MRE11A 0.025 0.01 -10000 0 0 81 81
HUS1 0.029 0.005 -10000 0 0 16 16
RPS6KB1 0.029 0.006 -10000 0 0 23 23
TERT/NF kappa B1/14-3-3 -0.1 0.21 -10000 0 -0.55 34 34
NR2F2 0.032 0.012 -10000 0 -0.09 1 1
MAPK3 -0.035 0.016 -10000 0 -0.18 2 2
MAPK1 -0.033 0.014 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.025 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 47 47
HNRNPC 0.028 0.006 -10000 0 0 28 28
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.02 0.025 0.24 2 -10000 0 2
NBN 0.025 0.011 -10000 0 0 83 83
EGFR 0.013 0.027 -10000 0 -0.038 117 117
mol:Oestrogen -0.002 0.003 0.021 1 -10000 0 1
EGF/EGFR 0.007 0.062 -10000 0 -0.17 43 43
MYC 0.008 0.023 0.08 1 -0.037 80 81
IL2 0.008 0.035 0.12 1 -0.052 135 136
KU 0.038 0.016 -10000 0 -10000 0 0
RAD50 0.029 0.005 -10000 0 0 15 15
HSP90AA1 0.029 0.006 -10000 0 0 21 21
TGFB1 0.025 0.013 -10000 0 -10000 0 0
TRF2/BLM -0.021 0.022 0.084 3 -10000 0 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.1 0.21 0.55 1 -0.54 31 32
SP1/HDAC2 0.014 0.048 0.24 1 -10000 0 1
PINX1 0.024 0.012 -10000 0 0 111 111
Telomerase/EST1A -0.11 0.19 -10000 0 -0.46 59 59
Smad3/Myc -0.042 0.057 -10000 0 -0.16 86 86
911 complex 0.053 0.02 -10000 0 -10000 0 0
IFNG -0.03 0.028 0.18 7 -0.16 3 10
Telomerase/PinX1 -0.11 0.19 -10000 0 -0.47 54 54
Telomerase/AKT1/mTOR/p70S6K -0.064 0.14 -10000 0 -0.4 48 48
SIN3B 0.012 0.026 -10000 0 -0.032 130 130
YWHAE 0.028 0.008 -10000 0 0 41 41
Telomerase/EST1B -0.11 0.19 -10000 0 -0.47 56 56
response to DNA damage stimulus 0.008 0.021 0.085 14 -0.1 8 22
MRN complex/TRF2/Rap1 0.065 0.049 -10000 0 -10000 0 0
TRF2/WRN -0.028 0.022 0.084 4 -10000 0 4
Telomerase/hnRNP C1/C2 -0.11 0.19 -10000 0 -0.47 55 55
E2F1 0.009 0.031 -10000 0 -0.043 138 138
ZNFX1 0.013 0.026 -10000 0 -0.031 133 133
PIF1 0.029 0.005 -10000 0 0 14 14
NCL 0.029 0.004 -10000 0 0 8 8
DKC1 0.024 0.012 -10000 0 0 107 107
telomeric DNA binding 0 0 -10000 0 -10000 0 0
IL1-mediated signaling 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
UBC13/UEV1A 0.021 0.008 -10000 0 -0.15 1 1
PRKCZ 0.029 0.006 -10000 0 0 23 23
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.01 -10000 0 0 67 67
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.01 0.046 -10000 0 -0.24 3 3
IRAK/TOLLIP -0.031 0.017 0.17 2 -0.13 1 3
IKBKB 0.028 0.008 -10000 0 0 39 39
IKBKG 0.028 0.006 -10000 0 0 25 25
IL1 alpha/IL1R2 0.039 0.024 -10000 0 -0.16 6 6
IL1A 0.029 0.006 -10000 0 0 22 22
IL1B -0.009 0.064 0.19 49 -10000 0 49
IRAK/TRAF6/p62/Atypical PKCs 0.058 0.052 -10000 0 -0.14 1 1
IL1R2 0.028 0.007 -10000 0 0 32 32
IL1R1 0.018 0.015 -10000 0 0 228 228
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.053 0.11 0.18 8 -0.29 37 45
TOLLIP 0.028 0.006 -10000 0 0 25 25
TICAM2 0.028 0.007 -10000 0 0 30 30
MAP3K3 0.029 0.005 -10000 0 0 14 14
TAK1/TAB1/TAB2 0.019 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.009 0.065 0.23 1 -0.29 6 7
JUN -0.024 0.061 0.17 16 -10000 0 16
MAP3K7 0.028 0.007 -10000 0 0 30 30
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.014 0.11 0.29 2 -0.17 136 138
IL1 alpha/IL1R1/IL1RAP/MYD88 0.012 0.095 -10000 0 -0.14 133 133
PIK3R1 0.021 0.013 -10000 0 0 161 161
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.019 0.096 -10000 0 -0.14 118 118
IL1 beta fragment/IL1R1/IL1RAP -0.045 0.078 0.16 28 -0.23 20 48
NFKB1 0.027 0.008 -10000 0 0 47 47
MAPK8 -0.035 0.033 0.14 14 -10000 0 14
IRAK1 -0.025 0.008 -10000 0 -0.13 1 1
IL1RN/IL1R1 -0.037 0.098 -10000 0 -0.16 210 210
IRAK4 0.027 0.009 -10000 0 0 55 55
PRKCI 0.014 0.015 -10000 0 0 288 288
TRAF6 0.029 0.004 -10000 0 0 12 12
PI3K 0 0.067 -10000 0 -0.16 75 75
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.026 0.1 0.19 14 -0.25 27 41
CHUK 0.028 0.007 -10000 0 0 36 36
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.045 0.078 0.16 28 -0.23 20 48
IL1 beta/IL1R2 -0.031 0.069 0.19 37 -10000 0 37
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.035 0.017 0.14 3 -10000 0 3
NF kappa B1 p50/RelA -0.053 0.092 0.12 19 -0.24 40 59
IRAK3 0.028 0.008 -10000 0 0 40 40
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.005 0.1 0.29 2 -0.16 122 124
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.02 0.091 0.2 7 -0.25 8 15
IL1 alpha/IL1R1/IL1RAP -0.01 0.08 -10000 0 -0.14 133 133
RELA 0.029 0.003 -10000 0 0 6 6
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.029 0.006 -10000 0 0 20 20
MYD88 0.029 0.003 -10000 0 0 5 5
IRAK/TRAF6/MEKK3 -0.039 0.019 0.17 3 -10000 0 3
IL1RAP 0.02 0.014 -10000 0 0 180 180
UBE2N 0.029 0.004 -10000 0 0 13 13
IRAK/TRAF6 -0.052 0.075 0.086 24 -0.23 16 40
CASP1 0.025 0.011 -10000 0 0 88 88
IL1RN/IL1R2 0.038 0.025 -10000 0 -0.16 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0 0.1 0.29 3 -0.15 137 140
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.069 0.14 -10000 0 -0.28 116 116
PIK3CA 0.021 0.014 -10000 0 0 171 171
IL1RN 0.028 0.007 -10000 0 0 31 31
TRAF6/TAK1/TAB1/TAB2 0.038 0.018 -10000 0 -0.12 1 1
MAP2K6 -0.028 0.034 0.16 14 -10000 0 14
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0.007 0.064 0.2 3 -0.21 13 16
FZD6 0.024 0.012 -10000 0 0 105 105
WNT6 0.029 0.004 -10000 0 0 8 8
WNT4 0.029 0.004 -10000 0 0 11 11
FZD3 0.022 0.013 -10000 0 0 140 140
WNT5A 0.029 0.005 -10000 0 0 17 17
WNT11 0.026 0.01 -10000 0 0 74 74
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.034 0.018 0.17 2 -10000 0 2
SNTA1 0.028 0.008 -10000 0 0 40 40
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.015 0.088 0.17 135 -10000 0 135
MAPK12 -0.002 0.059 0.16 57 -0.18 11 68
CCND1 -0.083 0.16 -10000 0 -0.36 135 135
p38 gamma/SNTA1 0.002 0.082 0.17 75 -0.19 14 89
MAP2K3 0.027 0.008 -10000 0 0 44 44
PKN1 0.025 0.01 -10000 0 0 80 80
G2/M transition checkpoint -0.002 0.059 0.16 57 -0.18 11 68
MAP2K6 0.007 0.073 0.19 66 -0.19 12 78
MAPT -0.008 0.059 0.19 6 -0.29 11 17
MAPK13 -0.029 0.017 0.2 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.001 0.034 -10000 0 -0.21 14 14
Coregulation of Androgen receptor activity

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
NRIP1 0.018 0.014 -10000 0 -10000 0 0
SVIL 0.028 0.007 -10000 0 -10000 0 0
ZNF318 0.029 0.006 -10000 0 -10000 0 0
JMJD2C -0.001 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.1 0.077 -10000 0 -0.16 318 318
CARM1 0.027 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.005 -10000 0 -10000 0 0
PELP1 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
AKT1 0.028 0.007 -10000 0 -10000 0 0
PTK2B 0.024 0.011 -10000 0 -10000 0 0
MED1 0.028 0.007 -10000 0 -10000 0 0
MAK 0.022 0.013 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.029 0.004 -10000 0 -10000 0 0
GSN 0.025 0.011 -10000 0 -10000 0 0
NCOA2 0.027 0.008 -10000 0 -10000 0 0
NCOA6 0.028 0.007 -10000 0 -10000 0 0
DNA-PK 0.043 0.028 -10000 0 -10000 0 0
NCOA4 0.029 0.003 -10000 0 -10000 0 0
PIAS3 0.029 0.005 -10000 0 -10000 0 0
cell proliferation -0.14 0.23 -10000 0 -0.59 117 117
XRCC5 0.028 0.008 -10000 0 -10000 0 0
UBE3A 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.1 0.077 -10000 0 -0.16 320 320
FHL2 -0.061 0.072 0.53 2 -0.4 11 13
RANBP9 0.028 0.008 -10000 0 -10000 0 0
JMJD1A -0.052 0.057 -10000 0 -0.12 129 129
CDK6 0.028 0.007 -10000 0 0 32 32
TGFB1I1 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.13 0.092 -10000 0 -0.18 366 366
XRCC6 0.027 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.094 -10000 0 -0.24 111 111
CTDSP1 0.029 0.004 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.009 -10000 0 -10000 0 0
TCF4 0.028 0.008 -10000 0 -10000 0 0
CDKN2A 0.012 0.015 -10000 0 -10000 0 0
SRF 0.03 0.018 0.3 2 -10000 0 2
NKX3-1 -0.17 0.14 -10000 0 -0.44 73 73
KLK3 -0.025 0.065 -10000 0 -10000 0 0
TMF1 0.029 0.004 -10000 0 -10000 0 0
HNRNPA1 0.029 0.004 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 -0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.1 0.078 -10000 0 -0.16 316 316
AR -0.027 0.042 -10000 0 -0.29 5 5
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.027 0.008 -10000 0 -10000 0 0
PAWR 0.029 0.004 -10000 0 -10000 0 0
PRKDC 0.025 0.011 -10000 0 -10000 0 0
PA2G4 0.029 0.006 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 0 22 22
T-DHT/AR/Cyclin D3/CDK11 p58 -0.088 0.071 -10000 0 -0.14 307 307
RPS6KA3 0.028 0.006 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.1 0.077 -10000 0 -0.16 320 320
LATS2 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.091 0.07 -10000 0 -0.14 317 317
Cyclin D3/CDK11 p58 0.021 0.005 -10000 0 -10000 0 0
VAV3 0.026 0.01 -10000 0 -10000 0 0
KLK2 -0.073 0.054 -10000 0 -0.39 8 8
CASP8 0.029 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.084 0.082 -10000 0 -0.15 269 269
TMPRSS2 -0.34 0.32 -10000 0 -0.7 241 241
CCND1 0.021 0.014 -10000 0 -10000 0 0
PIAS1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.021 -10000 0 -0.072 5 5
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.1 0.079 -10000 0 -0.16 307 307
CMTM2 0.027 0.009 -10000 0 -10000 0 0
SNURF 0.028 0.007 -10000 0 0 37 37
ZMIZ1 -0.048 0.025 -10000 0 -10000 0 0
CCND3 0.028 0.006 -10000 0 0 27 27
TGIF1 0.028 0.006 -10000 0 -10000 0 0
FKBP4 0.026 0.01 -10000 0 -10000 0 0
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.024 0.07 0.18 8 -0.15 62 70
alphaM/beta2 Integrin/GPIbA 0.051 0.037 0.18 11 -0.15 3 14
alphaM/beta2 Integrin/proMMP-9 0.041 0.037 0.18 7 -0.15 2 9
PLAUR 0.027 0.008 -10000 0 0 43 43
HMGB1 -0.026 0.02 0.1 11 -10000 0 11
alphaM/beta2 Integrin/Talin 0.052 0.037 0.18 11 -0.15 4 15
AGER -0.027 0.02 0.1 11 -10000 0 11
RAP1A 0.029 0.003 -10000 0 0 7 7
SELPLG 0.029 0.005 -10000 0 0 19 19
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.065 0.063 0.36 10 -0.2 8 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.023 0.013 -10000 0 0 129 129
CYR61 0.028 0.008 -10000 0 0 41 41
TLN1 0.029 0.005 -10000 0 0 16 16
Rap1/GTP -0.019 0.12 0.19 17 -0.28 41 58
RHOA 0.029 0.003 -10000 0 0 6 6
P-selectin oligomer 0.028 0.007 -10000 0 0 34 34
MYH2 -0.037 0.13 0.2 30 -0.34 32 62
MST1R 0.029 0.004 -10000 0 0 12 12
leukocyte activation during inflammatory response 0.049 0.042 -10000 0 -0.13 3 3
APOB 0.029 0.005 -10000 0 0 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.023 0.013 -10000 0 0 135 135
JAM3 0.028 0.008 -10000 0 0 39 39
GP1BA 0.028 0.006 -10000 0 0 25 25
alphaM/beta2 Integrin/CTGF 0.01 0.088 0.18 10 -0.15 117 127
alphaM/beta2 Integrin -0.026 0.11 0.18 39 -0.3 34 73
JAM3 homodimer 0.028 0.008 -10000 0 0 39 39
ICAM2 0.029 0.005 -10000 0 0 18 18
ICAM1 0.023 0.012 -10000 0 0 122 122
phagocytosis triggered by activation of immune response cell surface activating receptor -0.026 0.12 0.18 41 -0.29 37 78
cell adhesion 0.05 0.036 0.17 11 -0.15 3 14
NFKB1 -0.043 0.087 0.43 11 -0.33 8 19
THY1 0.02 0.014 -10000 0 0 185 185
RhoA/GDP 0.022 0.007 -10000 0 -0.15 1 1
Lipoprotein(a) 0.036 0.012 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.021 0.092 -10000 0 -0.15 110 110
IL6 -0.056 0.078 0.42 1 -0.53 9 10
ITGB2 -0.026 0.02 0.1 11 -10000 0 11
elevation of cytosolic calcium ion concentration 0.073 0.053 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/JAM2/JAM3 0.005 0.099 -10000 0 -0.14 155 155
JAM2 0.019 0.014 -10000 0 0 194 194
alphaM/beta2 Integrin/ICAM1 0.074 0.057 0.25 4 -0.14 6 10
alphaM/beta2 Integrin/uPA/Plg 0.07 0.063 -10000 0 -0.15 11 11
RhoA/GTP -0.041 0.14 0.2 45 -0.34 40 85
positive regulation of phagocytosis -0.023 0.1 0.21 8 -0.32 16 24
Ron/MSP 0.043 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.076 0.054 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/uPAR 0.049 0.034 0.18 5 -0.15 2 7
PLAU 0.02 0.014 -10000 0 0 186 186
PLAT 0.022 0.013 -10000 0 0 151 151
actin filament polymerization -0.038 0.13 0.22 21 -0.33 33 54
MST1 0.029 0.003 -10000 0 0 7 7
alphaM/beta2 Integrin/lipoprotein(a) 0.055 0.045 -10000 0 -0.13 3 3
TNF -0.05 0.078 0.41 10 -10000 0 10
RAP1B 0.029 0.006 -10000 0 0 22 22
alphaM/beta2 Integrin/uPA 0.033 0.037 0.18 2 -0.15 3 5
fibrinolysis 0.067 0.062 -10000 0 -0.15 11 11
HCK 0.027 0.008 -10000 0 0 47 47
dendritic cell antigen processing and presentation -0.026 0.12 0.18 41 -0.29 37 78
VTN 0.028 0.007 -10000 0 0 33 33
alphaM/beta2 Integrin/CYR61 0.045 0.047 0.18 8 -0.15 18 26
LPA 0.027 0.008 -10000 0 0 45 45
LRP1 0.029 0.006 -10000 0 0 21 21
cell migration -0.01 0.09 0.17 96 -10000 0 96
FN1 0.018 0.014 -10000 0 0 214 214
alphaM/beta2 Integrin/Thy1 0.034 0.037 0.18 4 -0.15 2 6
MPO 0.029 0.005 -10000 0 0 15 15
KNG1 0.025 0.011 -10000 0 0 88 88
RAP1/GDP 0.038 0.009 -10000 0 -10000 0 0
ROCK1 -0.041 0.14 0.19 49 -0.33 39 88
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.027 0.009 -10000 0 0 57 57
CTGF 0.022 0.013 -10000 0 0 149 149
alphaM/beta2 Integrin/Hck 0.05 0.035 0.18 10 -0.15 2 12
ITGAM -0.027 0.02 0.1 11 -10000 0 11
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.057 0.062 -10000 0 -0.16 31 31
HP 0.01 0.014 -10000 0 0 367 367
leukocyte adhesion -0.029 0.11 0.3 4 -0.29 1 5
SELP 0.028 0.007 -10000 0 0 34 34
IL23-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
CCL2 0.18 0.51 1.2 52 -1.2 17 69
IL23A 0.18 0.42 1.1 41 -10000 0 41
NF kappa B1 p50/RelA/I kappa B alpha 0.12 0.33 0.74 40 -0.81 8 48
positive regulation of T cell mediated cytotoxicity 0.21 0.52 1.3 61 -0.96 2 63
ITGA3 0.11 0.49 1.1 29 -1.1 35 64
IL17F 0.12 0.32 0.76 47 -0.66 1 48
IL12B 0.07 0.14 0.36 75 -10000 0 75
STAT1 (dimer) 0.004 0.25 0.91 11 -0.82 7 18
CD4 0.2 0.44 1.1 45 -1.1 2 47
IL23 0.15 0.38 0.95 40 -10000 0 40
IL23R 0.14 0.27 0.94 29 -0.79 4 33
IL1B 0.19 0.44 1.2 42 -0.89 1 43
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.17 0.42 1 43 -0.94 1 44
TYK2 0.038 0.097 0.24 74 -10000 0 74
STAT4 0.029 0.005 -10000 0 0 17 17
STAT3 0.013 0.025 -10000 0 -0.032 11 11
IL18RAP 0.008 0.036 0.092 25 -10000 0 25
IL12RB1 0.038 0.097 0.24 74 -10000 0 74
PIK3CA 0.012 0.021 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.072 0.093 0.26 74 -10000 0 74
IL23R/JAK2 0.16 0.26 0.72 60 -0.77 3 63
positive regulation of chronic inflammatory response 0.21 0.52 1.3 61 -0.96 2 63
natural killer cell activation -0.01 0.022 -10000 0 -0.062 57 57
JAK2 0.068 0.14 0.36 75 -10000 0 75
PIK3R1 0.011 0.023 -10000 0 -0.032 10 10
NFKB1 0.025 0.026 0.097 1 -10000 0 1
RELA 0.024 0.029 0.097 1 -10000 0 1
positive regulation of dendritic cell antigen processing and presentation 0.15 0.38 0.94 40 -10000 0 40
ALOX12B 0.17 0.41 1 41 -0.94 1 42
CXCL1 0.18 0.46 1.1 47 -1.2 8 55
T cell proliferation 0.21 0.52 1.3 61 -0.96 2 63
NFKBIA 0.024 0.028 0.097 1 -10000 0 1
IL17A 0.11 0.29 0.69 53 -10000 0 53
PI3K 0.042 0.3 0.8 27 -0.85 6 33
IFNG 0.04 0.093 0.31 43 -10000 0 43
STAT3 (dimer) 0.046 0.3 0.79 26 -0.84 7 33
IL18R1 0.008 0.036 0.092 25 -0.057 4 29
IL23/IL23R/JAK2/TYK2/SOCS3 0.16 0.35 0.88 61 -0.7 5 66
IL18/IL18R 0.033 0.077 0.32 24 -10000 0 24
macrophage activation 0.003 0.021 0.062 28 -10000 0 28
TNF 0.18 0.42 1.1 42 -0.89 1 43
STAT3/STAT4 0.13 0.35 0.81 30 -0.83 8 38
STAT4 (dimer) 0.16 0.38 0.92 39 -0.84 8 47
IL18 0.009 0.03 0.088 16 -10000 0 16
IL19 0.17 0.42 1.1 42 -0.94 1 43
STAT5A (dimer) 0.16 0.39 0.92 43 -0.84 8 51
STAT1 0.013 0.015 -10000 0 0 316 316
SOCS3 0.029 0.006 -10000 0 0 21 21
CXCL9 0.23 0.5 1.3 56 -0.94 1 57
MPO 0.17 0.41 1 41 -0.94 1 42
positive regulation of humoral immune response 0.21 0.52 1.3 61 -0.96 2 63
IL23/IL23R/JAK2/TYK2 0.21 0.52 1.3 61 -0.99 2 63
IL6 0.16 0.43 1.1 33 -1.1 9 42
STAT5A 0.028 0.007 -10000 0 0 35 35
IL2 0.006 0.062 0.23 25 -0.097 6 31
positive regulation of tyrosine phosphorylation of STAT protein -0.01 0.022 -10000 0 -0.062 57 57
CD3E 0.17 0.43 1.1 44 -1 3 47
keratinocyte proliferation 0.21 0.52 1.3 61 -0.96 2 63
NOS2 0.18 0.42 0.99 61 -0.87 2 63
Signaling events mediated by PRL

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
CCNE1 0.003 0.009 -10000 0 0 506 506
mol:Halofuginone -0.003 0.012 -10000 0 -0.16 3 3
ITGA1 0.023 0.013 -10000 0 0 128 128
CDKN1A -0.021 0.089 -10000 0 -0.4 24 24
PRL-3/alpha Tubulin 0.029 0.029 -10000 0 -0.16 7 7
mol:Ca2+ -0.019 0.036 0.26 7 -10000 0 7
AGT 0.027 0.009 -10000 0 0 58 58
CCNA2 0.051 0.088 0.3 2 -0.62 3 5
TUBA1B 0.029 0.003 -10000 0 0 5 5
EGR1 -0.014 0.028 -10000 0 -0.36 3 3
CDK2/Cyclin E1 -0.007 0.043 -10000 0 -0.3 4 4
MAPK3 -0.022 0.02 0.19 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.023 0.022 -10000 0 -10000 0 0
MAPK1 -0.021 0.021 0.19 2 -10000 0 2
PTP4A1 -0.063 0.067 -10000 0 -0.65 3 3
PTP4A3 0.021 0.014 -10000 0 0 162 162
PTP4A2 0.028 0.006 -10000 0 0 26 26
ITGB1 -0.021 0.024 0.19 4 -10000 0 4
SRC 0.028 0.007 -10000 0 0 31 31
RAC1 -0.017 0.08 -10000 0 -0.4 19 19
Rab GGTase beta/Rab GGTase alpha 0.023 0.022 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.06 0.082 0.34 2 -0.62 3 5
RABGGTA 0.029 0.006 -10000 0 0 23 23
BCAR1 -0.019 0.036 0.26 7 -10000 0 7
RHOC -0.011 0.064 -10000 0 -0.44 9 9
RHOA -0.013 0.072 -10000 0 -0.43 13 13
cell motility -0.008 0.076 0.29 2 -0.42 10 12
PRL-1/alpha Tubulin -0.06 0.083 0.34 2 -0.62 3 5
PRL-3/alpha1 Integrin 0.022 0.029 -10000 0 -0.16 6 6
ROCK1 -0.012 0.073 0.27 1 -0.42 10 11
RABGGTB 0.016 0.015 -10000 0 0 257 257
CDK2 0.018 0.015 -10000 0 0 227 227
mitosis -0.063 0.066 -10000 0 -0.64 3 3
ATF5 0.029 0.005 -10000 0 0 19 19
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.01 0.13 -10000 0 -0.45 38 38
HDAC1 0.038 0.022 0.097 16 -0.071 1 17
AES 0.027 0.016 0.069 11 -0.038 1 12
FBXW11 0.029 0.005 -10000 0 0 18 18
DTX1 0.029 0.004 -10000 0 0 9 9
LRP6/FZD1 0.037 0.016 -10000 0 -10000 0 0
TLE1 0.03 0.013 0.066 10 -0.029 13 23
AP1 -0.008 0.072 0.2 7 -0.2 54 61
NCSTN 0.021 0.02 -10000 0 -0.023 88 88
ADAM10 0.029 0.006 -10000 0 -0.029 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.13 0.22 -10000 0 -0.59 66 66
NICD/RBPSUH 0.003 0.13 -10000 0 -0.45 38 38
WIF1 0.02 0.021 -10000 0 -0.029 79 79
NOTCH1 -0.011 0.13 -10000 0 -0.47 39 39
PSENEN 0.02 0.019 -10000 0 -0.012 129 129
KREMEN2 0.029 0.006 -10000 0 0 23 23
DKK1 0.028 0.006 -10000 0 0 25 25
beta catenin/beta TrCP1 -0.003 0.066 -10000 0 -0.33 1 1
APH1B 0.018 0.021 -10000 0 -0.015 144 144
APH1A 0.021 0.02 -10000 0 -0.02 98 98
AXIN1 -0.012 0.1 -10000 0 -0.44 21 21
CtBP/CBP/TCF1/TLE1/AES 0.013 0.1 0.25 22 -0.28 12 34
PSEN1 0.02 0.021 -10000 0 -0.03 80 80
FOS 0.024 0.012 -10000 0 0 105 105
JUN 0.028 0.007 -10000 0 0 34 34
MAP3K7 0.033 0.012 -10000 0 -0.046 1 1
CTNNB1 -0.012 0.059 -10000 0 -0.33 1 1
MAPK3 0.029 0.006 -10000 0 0 22 22
DKK2/LRP6/Kremen 2 0.048 0.024 -10000 0 -10000 0 0
HNF1A 0.034 0.01 0.069 14 -0.038 1 15
CTBP1 0.031 0.012 0.068 13 -10000 0 13
MYC -0.16 0.36 -10000 0 -1.2 59 59
NKD1 0.029 0.008 -10000 0 -10000 0 0
FZD1 0.02 0.021 -10000 0 -0.029 81 81
NOTCH1 precursor/Deltex homolog 1 0.004 0.13 -10000 0 -0.45 39 39
apoptosis -0.007 0.072 0.2 7 -0.2 54 61
Delta 1/NOTCHprecursor 0.002 0.13 -10000 0 -0.45 38 38
DLL1 0.027 0.008 -10000 0 0 49 49
PPARD -0.02 0.1 -10000 0 -1 5 5
Gamma Secretase 0.042 0.077 -10000 0 -0.14 65 65
APC -0.017 0.11 -10000 0 -0.44 28 28
DVL1 -0.005 0.057 -10000 0 -0.25 22 22
CSNK2A1 0.009 0.028 -10000 0 -0.032 170 170
MAP3K7IP1 0.005 0.008 0.022 28 -10000 0 28
DKK1/LRP6/Kremen 2 0.048 0.024 -10000 0 -10000 0 0
LRP6 0.019 0.02 -10000 0 -0.029 63 63
CSNK1A1 0.009 0.029 -10000 0 -0.032 183 183
NLK 0.018 0.019 -10000 0 -10000 0 0
CCND1 -0.3 0.51 -10000 0 -1.1 147 147
WNT1 0.02 0.021 -10000 0 -0.029 84 84
Axin1/APC/beta catenin -0.024 0.1 -10000 0 -0.42 17 17
DKK2 0.028 0.008 -10000 0 0 40 40
NOTCH1 precursor/DVL1 -0.01 0.13 -10000 0 -0.46 36 36
GSK3B 0.03 0.006 -10000 0 -0.03 1 1
FRAT1 0.031 0.007 -10000 0 -0.036 1 1
NOTCH/Deltex homolog 1 0.012 0.13 -10000 0 -0.45 39 39
PPP2R5D 0.011 0.047 -10000 0 -0.36 6 6
MAPK1 0.027 0.008 -10000 0 0 42 42
WNT1/LRP6/FZD1 0.065 0.034 -10000 0 -10000 0 0
RBPJ 0.029 0.005 -10000 0 0 19 19
CREBBP 0.012 0.024 -10000 0 -0.026 135 135
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 -0.15 0.34 0.67 1 -0.96 83 84
VDR 0.029 0.004 -10000 0 0 8 8
FAM120B 0.027 0.008 -10000 0 0 48 48
RXRs/LXRs/DNA/9cRA 0.015 0.12 0.41 35 -0.33 1 36
RXRs/LXRs/DNA/Oxysterols 0.021 0.14 0.5 35 -0.42 2 37
MED1 0.028 0.007 -10000 0 0 36 36
mol:9cRA 0.009 0.027 0.1 39 -10000 0 39
RARs/THRs/DNA/Src-1 -0.028 0.091 -10000 0 -0.23 26 26
RXRs/NUR77 0.007 0.12 0.3 22 -0.21 6 28
RXRs/PPAR 0.003 0.076 0.25 4 -0.24 11 15
NCOR2 0.029 0.005 -10000 0 0 17 17
VDR/VDR/Vit D3 0.022 0.003 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.065 0.03 -10000 0 -10000 0 0
RARA 0.028 0.007 -10000 0 0 34 34
NCOA1 0.029 0.005 -10000 0 0 14 14
VDR/VDR/DNA 0.029 0.004 -10000 0 0 8 8
RARs/RARs/DNA/9cRA 0.05 0.029 -10000 0 -10000 0 0
RARG 0.029 0.005 -10000 0 0 18 18
RPS6KB1 -0.074 0.17 0.52 11 -0.42 84 95
RARs/THRs/DNA/SMRT -0.031 0.094 -10000 0 -0.24 30 30
THRA 0.021 0.013 -10000 0 0 160 160
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.022 0.003 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.097 0.12 0.32 103 -10000 0 103
NR1H4 0.029 0.005 -10000 0 0 14 14
RXRs/LXRs/DNA 0.098 0.11 0.44 35 -0.24 2 37
NR1H2 0.032 0.029 0.13 37 -0.074 2 39
NR1H3 0.036 0.029 0.14 39 -0.073 4 43
RXRs/VDR/DNA/Vit D3 0.084 0.076 0.28 41 -10000 0 41
NR4A1 0.017 0.015 -10000 0 0 234 234
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.017 0.068 0.19 37 -0.23 6 43
RXRG -0.006 0.046 0.13 41 -10000 0 41
RXR alpha/CCPG 0.041 0.039 -10000 0 -0.16 12 12
RXRA -0.006 0.047 0.13 43 -10000 0 43
RXRB 0.029 0.038 0.14 38 -10000 0 38
THRB 0.028 0.007 -10000 0 0 31 31
PPARG 0.029 0.004 -10000 0 0 13 13
PPARD 0.029 0.005 -10000 0 0 17 17
TNF 0.014 0.13 0.45 35 -10000 0 35
mol:Oxysterols 0.006 0.025 0.097 39 -10000 0 39
cholesterol transport 0.021 0.14 0.5 35 -0.42 2 37
PPARA 0.025 0.011 -10000 0 0 97 97
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.029 0.006 -10000 0 0 20 20
RXRs/NUR77/BCL2 -0.077 0.11 0.16 1 -0.2 206 207
SREBF1 0.01 0.14 0.44 33 -0.77 4 37
RXRs/RXRs/DNA/9cRA 0.096 0.12 0.4 43 -10000 0 43
ABCA1 0.025 0.16 0.62 35 -0.43 1 36
RARs/THRs 0.034 0.097 -10000 0 -0.14 114 114
RXRs/FXR 0.091 0.081 0.3 40 -10000 0 40
BCL2 0.023 0.012 -10000 0 0 122 122
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.042 0.009 -10000 0 -10000 0 0
Necdin/E2F1 -0.059 0.099 -10000 0 -0.16 263 263
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.061 0.033 -10000 0 -0.13 3 3
NGF (dimer)/p75(NTR)/BEX1 -0.019 0.08 -10000 0 -0.13 180 180
NT-4/5 (dimer)/p75(NTR) 0.021 0.004 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 0 39 39
AKT1 0.006 0.1 0.17 134 -10000 0 134
IKBKG 0.028 0.006 -10000 0 0 25 25
BDNF 0.029 0.005 -10000 0 0 14 14
MGDIs/NGR/p75(NTR)/LINGO1 0.054 0.018 -10000 0 -10000 0 0
FURIN 0.028 0.007 -10000 0 0 29 29
proBDNF (dimer)/p75(NTR)/Sortilin 0.057 0.015 -10000 0 -10000 0 0
LINGO1 0.028 0.006 -10000 0 0 24 24
Sortilin/TRAF6/NRIF -0.071 0.042 -10000 0 -0.23 1 1
proBDNF (dimer) 0.029 0.005 -10000 0 0 14 14
NTRK1 0.029 0.005 -10000 0 0 14 14
RTN4R 0.028 0.007 -10000 0 0 32 32
neuron apoptosis -0.036 0.13 0.3 3 -0.43 32 35
IRAK1 0.028 0.007 -10000 0 0 31 31
SHC1 -0.025 0.011 0.17 1 -10000 0 1
ARHGDIA 0.025 0.011 -10000 0 0 96 96
RhoA/GTP 0.022 0.007 -10000 0 -0.15 1 1
Gamma Secretase 0.043 0.078 -10000 0 -0.14 65 65
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.036 -10000 0 -0.13 17 17
MAGEH1 0.028 0.006 -10000 0 0 27 27
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.041 0.09 -10000 0 -0.13 274 274
Mammalian IAPs/DIABLO 0.012 0.051 -10000 0 -0.13 46 46
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.029 0.006 -10000 0 0 21 21
APP 0.028 0.007 -10000 0 0 29 29
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.028 0.007 -10000 0 0 35 35
RhoA/GDP/RHOGDI 0.014 0.053 0.17 2 -0.12 72 74
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.001 0.055 0.23 10 -10000 0 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.029 0.05 -10000 0 -0.21 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.038 0.009 -10000 0 -10000 0 0
NCSTN 0.029 0.005 -10000 0 0 18 18
mol:GTP 0.037 0.01 -10000 0 -10000 0 0
PSENEN 0.026 0.01 -10000 0 0 75 75
mol:ceramide -0.027 0.035 0.18 14 -10000 0 14
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.036 0.066 0.18 45 -0.23 5 50
p75(NTR)/beta APP 0.038 0.025 -10000 0 -0.16 7 7
BEX1 0.019 0.014 -10000 0 0 210 210
mol:GDP -0.013 0.002 -10000 0 -10000 0 0
NGF (dimer) -0.019 0.087 -10000 0 -0.13 200 200
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.039 0.076 -10000 0 -0.14 72 72
PIK3R1 0.021 0.013 -10000 0 0 161 161
RAC1/GTP 0.031 0.013 -10000 0 -10000 0 0
MYD88 0.029 0.003 -10000 0 0 5 5
CHUK 0.028 0.007 -10000 0 0 36 36
NGF (dimer)/p75(NTR)/PKA 0.038 0.01 -10000 0 -10000 0 0
RHOB 0.029 0.006 -10000 0 0 23 23
RHOA 0.029 0.003 -10000 0 0 6 6
MAGE-G1/E2F1 0.038 0.017 -10000 0 -0.16 1 1
NT3 (dimer) 0.024 0.012 -10000 0 0 116 116
TP53 -0.057 0.058 0.31 3 -10000 0 3
PRDM4 -0.03 0.032 0.18 12 -10000 0 12
BDNF (dimer) -0.006 0.1 -10000 0 -0.14 192 192
PIK3CA 0.021 0.014 -10000 0 0 171 171
SORT1 0.029 0.004 -10000 0 0 11 11
activation of caspase activity 0.054 0.031 -10000 0 -0.13 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.053 0.018 -10000 0 -10000 0 0
RHOC 0.029 0.003 -10000 0 0 7 7
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.045 0.063 0.24 7 -0.24 7 14
DIABLO 0.019 0.014 -10000 0 0 192 192
SMPD2 -0.028 0.035 0.18 14 -10000 0 14
APH1B 0.026 0.01 -10000 0 0 70 70
APH1A 0.028 0.007 -10000 0 0 30 30
proNGF (dimer)/p75(NTR)/Sortilin 0.038 0.009 -10000 0 -10000 0 0
PSEN1 0.029 0.005 -10000 0 0 14 14
APAF-1/Pro-Caspase 9 0.041 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.034 0.019 -10000 0 -10000 0 0
MAPK8 -0.04 0.059 0.24 7 -0.24 7 14
MAPK9 -0.041 0.057 0.23 6 -0.24 5 11
APAF1 0.028 0.006 -10000 0 0 27 27
NTF3 0.024 0.012 -10000 0 0 116 116
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.013 0.015 -10000 0 0 316 316
RAC1/GDP 0.021 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.057 0.034 -10000 0 -0.13 8 8
p75 CTF/Sortilin/TRAF6/NRIF 0.075 0.041 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.037 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.075 0.039 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.071 0.026 -10000 0 -10000 0 0
PRKACB 0.029 0.006 -10000 0 0 21 21
proBDNF (dimer)/p75 ECD 0.035 0.018 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.012 -10000 0 0 122 122
BIRC2 0.021 0.013 -10000 0 0 159 159
neuron projection morphogenesis -0.036 0.063 0.18 13 -0.21 9 22
BAD -0.046 0.062 0.22 6 -0.28 6 12
RIPK2 0.019 0.014 -10000 0 0 200 200
NGFR 0.029 0.005 -10000 0 0 18 18
CYCS -0.031 0.049 0.18 27 -10000 0 27
ADAM17 0.024 0.012 -10000 0 0 106 106
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.034 0.03 -10000 0 -10000 0 0
BCL2L11 -0.046 0.063 0.22 6 -0.28 7 13
BDNF (dimer)/p75(NTR) 0.042 0.01 -10000 0 -10000 0 0
PI3K 0.008 0.062 -10000 0 -0.13 75 75
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.026 -10000 0 -0.13 1 1
NDNL2 0.028 0.008 -10000 0 0 39 39
YWHAE 0.028 0.008 -10000 0 0 41 41
PRKCI 0.014 0.015 -10000 0 0 288 288
NGF (dimer)/p75(NTR) 0.021 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.051 0.023 -10000 0 -0.13 3 3
TRAF6 0.029 0.004 -10000 0 0 12 12
RAC1 0.028 0.006 -10000 0 0 28 28
PRKCZ 0.029 0.006 -10000 0 0 23 23
PLG 0.027 0.009 -10000 0 0 57 57
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.019 0.024 0.14 7 -10000 0 7
SQSTM1 0.029 0.006 -10000 0 0 20 20
NGFRAP1 0.03 0.002 -10000 0 0 3 3
CASP3 -0.047 0.068 0.22 6 -0.3 13 19
E2F1 0.028 0.008 -10000 0 0 41 41
CASP9 0.029 0.004 -10000 0 0 13 13
IKK complex 0.064 0.063 0.18 2 -0.24 3 5
NGF (dimer)/TRKA 0.021 0.003 -10000 0 -10000 0 0
MMP7 0.017 0.015 -10000 0 0 236 236
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.061 0.03 -10000 0 -10000 0 0
MMP3 0.028 0.007 -10000 0 0 36 36
APAF-1/Caspase 9 -0.042 0.048 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.004 0.067 0.26 4 -0.2 27 31
RFC1 -0.002 0.068 0.23 8 -0.2 25 33
PRKDC 0.024 0.1 0.22 80 -0.2 26 106
RIPK1 0.026 0.016 -10000 0 -0.081 9 9
CASP7 0.008 0.069 -10000 0 -0.54 7 7
FASLG/FAS/FADD/FAF1 0.022 0.072 0.2 2 -0.18 12 14
MAP2K4 0.001 0.094 0.34 12 -0.31 14 26
mol:ceramide 0.009 0.065 0.31 9 -0.26 3 12
GSN -0.013 0.068 0.22 4 -0.2 24 28
FASLG/FAS/FADD/FAF1/Caspase 8 0.005 0.072 0.19 14 -0.28 2 16
FAS 0.027 0.013 0.078 9 -0.047 7 16
BID -0.036 0.015 0.18 1 -10000 0 1
MAP3K1 0.018 0.082 0.28 11 -0.32 8 19
MAP3K7 0.027 0.011 -10000 0 -0.037 9 9
RB1 0.002 0.071 0.22 18 -0.2 23 41
CFLAR 0.028 0.015 -10000 0 -0.081 9 9
HGF/MET 0.007 0.081 -10000 0 -0.15 105 105
ARHGDIB 0.007 0.085 0.22 36 -0.2 23 59
FADD 0.028 0.012 0.078 10 -0.047 8 18
actin filament polymerization 0.015 0.072 0.22 29 -0.22 4 33
NFKB1 -0.022 0.18 0.39 9 -0.6 43 52
MAPK8 -0.008 0.11 0.39 13 -0.42 13 26
DFFA -0.005 0.069 0.3 4 -0.2 30 34
DNA fragmentation during apoptosis -0.004 0.067 0.22 6 -0.2 29 35
FAS/FADD/MET 0.038 0.051 -10000 0 -0.16 24 24
CFLAR/RIP1 0.038 0.024 -10000 0 -0.12 9 9
FAIM3 0.028 0.01 -10000 0 -0.018 21 21
FAF1 0.029 0.015 0.098 10 -0.053 8 18
PARP1 0.011 0.088 0.22 44 -0.2 27 71
DFFB -0.004 0.067 0.22 6 -0.2 28 34
CHUK -0.029 0.17 0.32 9 -0.56 44 53
FASLG 0.029 0.015 0.098 10 -0.053 9 19
FAS/FADD 0.034 0.04 0.13 1 -0.16 17 18
HGF 0.029 0.005 -10000 0 0 17 17
LMNA 0.038 0.1 0.27 46 -0.2 10 56
CASP6 0.046 0.1 0.21 126 -0.2 10 136
CASP10 0.029 0.013 0.078 10 -0.048 9 19
CASP3 0.005 0.076 0.15 69 -0.22 31 100
PTPN13 0.021 0.014 -10000 0 0 171 171
CASP8 -0.033 0.009 -10000 0 -10000 0 0
IL6 -0.035 0.22 0.67 9 -0.72 31 40
MET 0.025 0.011 -10000 0 0 87 87
ICAD/CAD -0.013 0.065 0.27 6 -0.2 28 34
FASLG/FAS/FADD/FAF1/Caspase 10 0.009 0.065 0.32 9 -0.26 3 12
activation of caspase activity by cytochrome c -0.036 0.015 0.18 1 -10000 0 1
PAK2 0.025 0.1 0.25 66 -0.2 22 88
BCL2 0.022 0.014 -10000 0 -0.002 130 130
Paxillin-dependent events mediated by a4b1

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
CRKL 0.028 0.007 -10000 0 0 31 31
Rac1/GDP 0.021 0.028 -10000 0 -0.034 62 62
DOCK1 0.029 0.005 -10000 0 0 19 19
ITGA4 0.028 0.008 -10000 0 0 40 40
RAC1 0.028 0.006 -10000 0 0 28 28
alpha4/beta7 Integrin 0.04 0.015 -10000 0 -0.16 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 0 37 37
alpha4/beta1 Integrin 0.046 0.026 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.038 0.022 -10000 0 -10000 0 0
lamellipodium assembly -0.068 0.15 -10000 0 -0.34 103 103
PIK3CA 0.021 0.014 -10000 0 0 171 171
PI3K 0 0.067 -10000 0 -0.16 75 75
ARF6 0.029 0.004 -10000 0 0 11 11
TLN1 0.029 0.005 -10000 0 0 16 16
PXN -0.028 0.013 -10000 0 -10000 0 0
PIK3R1 0.021 0.013 -10000 0 0 161 161
ARF6/GTP -0.025 0.07 0.13 90 -10000 0 90
cell adhesion 0.061 0.049 -10000 0 -0.16 5 5
CRKL/CBL 0.041 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.037 0.022 -10000 0 -10000 0 0
ITGB1 0.029 0.006 -10000 0 0 22 22
ITGB7 0.029 0.004 -10000 0 0 9 9
ARF6/GDP 0.022 0.028 -10000 0 -0.034 65 65
alpha4/beta1 Integrin/Paxillin/VCAM1 0.048 0.079 -10000 0 -0.14 58 58
p130Cas/Crk/Dock1 0.05 0.025 -10000 0 -0.15 2 2
VCAM1 0.021 0.013 -10000 0 0 161 161
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.05 -10000 0 -0.16 5 5
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.05 -10000 0 -0.14 5 5
BCAR1 0.027 0.009 -10000 0 0 59 59
mol:GDP -0.06 0.049 0.14 5 -10000 0 5
CBL 0.029 0.005 -10000 0 0 15 15
PRKACA 0.025 0.01 -10000 0 0 80 80
GIT1 0.028 0.007 -10000 0 0 31 31
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.05 -10000 0 -0.16 5 5
Rac1/GTP -0.076 0.16 -10000 0 -0.37 103 103
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.028 0.007 -10000 0 0 33 33
SMAD2 -0.001 0.046 0.18 1 -0.23 2 3
SMAD3 -0.014 0.048 -10000 0 -0.23 7 7
SMAD3/SMAD4 0.061 0.089 -10000 0 -0.5 10 10
SMAD4/Ubc9/PIASy 0.051 0.022 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.092 0.059 -10000 0 -0.23 1 1
PPM1A 0.029 0.004 -10000 0 0 13 13
CALM1 0.028 0.006 -10000 0 0 26 26
SMAD2/SMAD4 0.013 0.045 -10000 0 -0.22 2 2
MAP3K1 0.027 0.009 -10000 0 0 52 52
TRAP-1/SMAD4 0.041 0.011 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 0 22 22
MAPK1 0.027 0.008 -10000 0 0 42 42
NUP214 0.029 0.005 -10000 0 0 18 18
CTDSP1 0.029 0.004 -10000 0 0 13 13
CTDSP2 0.029 0.005 -10000 0 0 18 18
CTDSPL 0.029 0.003 -10000 0 0 5 5
KPNB1 0.029 0.006 -10000 0 0 21 21
TGFBRAP1 0.029 0.004 -10000 0 0 10 10
UBE2I 0.029 0.006 -10000 0 0 22 22
NUP153 0.027 0.008 -10000 0 0 45 45
KPNA2 0.003 0.009 -10000 0 0 494 494
PIAS4 0.027 0.008 -10000 0 0 47 47
Glucocorticoid receptor regulatory network

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
PCK2 -0.06 0.078 -10000 0 -0.46 6 6
SMARCC2 0.029 0.006 -10000 0 0 22 22
SMARCC1 0.029 0.004 -10000 0 0 8 8
TBX21 0.04 0.08 0.32 5 -10000 0 5
SUMO2 0.006 0.032 -10000 0 -0.038 185 185
STAT1 (dimer) 0.018 0.052 0.31 13 -0.18 7 20
FKBP4 0.026 0.01 -10000 0 0 71 71
FKBP5 0.027 0.009 -10000 0 0 59 59
GR alpha/HSP90/FKBP51/HSP90 -0.038 0.095 -10000 0 -0.24 16 16
PRL 0.043 0.064 0.71 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.092 0.16 -10000 0 -0.43 26 26
RELA 0.008 0.095 0.18 116 -0.18 14 130
FGG -0.13 0.12 -10000 0 -0.42 29 29
GR beta/TIF2 -0.077 0.063 -10000 0 -0.28 3 3
IFNG 0.11 0.17 0.57 37 -10000 0 37
apoptosis -0.18 0.21 0.48 2 -0.61 33 35
CREB1 0.03 0.004 -10000 0 -10000 0 0
histone acetylation 0.042 0.066 -10000 0 -10000 0 0
BGLAP 0.056 0.068 0.66 1 -10000 0 1
GR/PKAc -0.016 0.091 -10000 0 -0.21 2 2
NF kappa B1 p50/RelA 0.08 0.13 0.32 103 -0.3 14 117
SMARCD1 0.029 0.003 -10000 0 0 5 5
MDM2 -0.036 0.041 -10000 0 -0.22 1 1
GATA3 -0.024 0.015 -10000 0 -10000 0 0
AKT1 0.029 0.007 -10000 0 -10000 0 0
CSF2 0.012 0.043 -10000 0 -10000 0 0
GSK3B 0.006 0.032 -10000 0 -0.037 183 183
NR1I3 -0.16 0.19 -10000 0 -0.64 11 11
CSN2 -0.12 0.11 -10000 0 -0.39 26 26
BRG1/BAF155/BAF170/BAF60A 0.064 0.032 -10000 0 -0.14 2 2
NFATC1 0.027 0.009 -10000 0 -10000 0 0
POU2F1 0.029 0.008 0.2 1 -10000 0 1
CDKN1A -0.06 0.22 -10000 0 -1.2 16 16
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 0.039 2 -10000 0 2
SFN 0.028 0.007 -10000 0 0 38 38
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.024 0.1 -10000 0 -0.23 12 12
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.3 0.34 0.59 2 -0.72 208 210
JUN 0.089 0.17 0.5 42 -10000 0 42
IL4 0.052 0.058 -10000 0 -10000 0 0
CDK5R1 0.006 0.03 -10000 0 -0.035 189 189
PRKACA 0.025 0.01 -10000 0 0 80 80
cortisol/GR alpha (monomer)/AP-1 -0.073 0.076 -10000 0 -0.27 14 14
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.028 0.1 -10000 0 -0.23 12 12
cortisol/GR alpha (monomer) -0.15 0.14 -10000 0 -0.49 24 24
NCOA2 0.027 0.008 -10000 0 0 46 46
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.036 0.095 0.18 115 -0.3 1 116
AP-1/NFAT1-c-4 0.098 0.21 0.61 33 -10000 0 33
AFP 0.059 0.12 0.47 4 -10000 0 4
SUV420H1 0.029 0.004 -10000 0 0 8 8
IRF1 -0.001 0.15 0.53 11 -0.72 9 20
TP53 -0.038 0.081 -10000 0 -0.5 16 16
PPP5C 0.028 0.006 -10000 0 0 25 25
KRT17 0.097 0.19 0.68 26 -10000 0 26
KRT14 0.066 0.12 0.66 14 -10000 0 14
TBP 0.028 0.011 0.19 1 -10000 0 1
CREBBP 0.023 0.038 -10000 0 -0.22 13 13
HDAC1 0.028 0.009 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
AP-1 0.098 0.21 0.6 34 -10000 0 34
MAPK14 0.006 0.032 -10000 0 -0.038 183 183
MAPK10 0.005 0.032 -10000 0 -0.038 176 176
MAPK11 0.004 0.029 -10000 0 -0.038 147 147
KRT5 0.16 0.26 0.65 103 -10000 0 103
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.023 0.018 -10000 0 -10000 0 0
STAT1 0.018 0.052 0.31 13 -0.18 7 20
CGA 0.055 0.06 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.066 0.1 -10000 0 -0.44 14 14
MAPK3 0.005 0.032 -10000 0 -0.038 182 182
MAPK1 0.005 0.032 -10000 0 -0.038 180 180
ICAM1 0.1 0.23 0.63 65 -0.72 7 72
NFKB1 0.009 0.094 0.18 111 -0.18 14 125
MAPK8 0.077 0.14 0.4 39 -10000 0 39
MAPK9 0.005 0.032 -10000 0 -0.038 187 187
cortisol/GR alpha (dimer) -0.19 0.22 0.49 2 -0.61 42 44
BAX -0.04 0.11 -10000 0 -10000 0 0
POMC 0.004 0.12 0.64 1 -10000 0 1
EP300 0.022 0.037 -10000 0 -0.22 12 12
cortisol/GR alpha (dimer)/p53 -0.13 0.16 -10000 0 -0.46 30 30
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.052 0.22 13 -0.19 1 14
SGK1 -0.033 0.088 -10000 0 -0.28 39 39
IL13 0.078 0.13 0.49 10 -10000 0 10
IL6 0.064 0.18 0.52 24 -0.83 9 33
PRKACG 0.029 0.005 -10000 0 0 19 19
IL5 0.066 0.12 0.49 2 -10000 0 2
IL2 0.085 0.17 0.48 29 -10000 0 29
CDK5 0.007 0.028 -10000 0 -0.034 158 158
PRKACB 0.029 0.006 -10000 0 0 21 21
HSP90AA1 0.029 0.006 -10000 0 0 21 21
IL8 0.1 0.2 0.62 59 -10000 0 59
CDK5R1/CDK5 0.011 0.038 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.091 0.12 0.41 22 -0.24 12 34
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.066 0.16 -10000 0 -0.41 24 24
SMARCA4 0.027 0.009 -10000 0 0 60 60
chromatin remodeling -0.072 0.083 -10000 0 -0.32 7 7
NF kappa B1 p50/RelA/Cbp 0.077 0.13 0.42 18 -0.26 17 35
JUN (dimer) 0.089 0.17 0.5 42 -10000 0 42
YWHAH 0.027 0.008 -10000 0 0 43 43
VIPR1 0.041 0.083 0.4 4 -10000 0 4
NR3C1 -0.1 0.085 -10000 0 -0.38 3 3
NR4A1 0.017 0.014 -10000 0 -10000 0 0
TIF2/SUV420H1 0.04 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.18 0.21 0.48 2 -0.61 33 35
cortisol/GR alpha (dimer)/Src-1 -0.097 0.16 -10000 0 -0.43 26 26
PBX1 0.029 0.009 0.2 1 -10000 0 1
POU1F1 0.029 0.008 0.2 1 -10000 0 1
SELE 0.076 0.12 0.41 22 -10000 0 22
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.073 0.084 -10000 0 -0.33 7 7
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.066 0.16 -10000 0 -0.41 24 24
mol:cortisol -0.078 0.076 -10000 0 -0.26 9 9
MMP1 0.14 0.25 0.63 110 -0.51 5 115
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.037 0.091 -10000 0 -0.15 73 73
SMAD6-7/SMURF1 0.054 0.019 -10000 0 -10000 0 0
NOG 0.029 0.005 -10000 0 0 19 19
SMAD9 -0.019 0.14 -10000 0 -0.48 41 41
SMAD4 0.028 0.007 -10000 0 0 33 33
SMAD5 -0.026 0.084 0.2 2 -0.34 20 22
BMP7/USAG1 0.014 0.052 -10000 0 -0.17 36 36
SMAD5/SKI -0.014 0.093 0.21 2 -0.34 19 21
SMAD1 -0.022 0.089 -10000 0 -0.42 16 16
BMP2 0.028 0.007 -10000 0 0 34 34
SMAD1/SMAD1/SMAD4 -0.053 0.079 -10000 0 -0.37 16 16
BMPR1A 0.029 0.006 -10000 0 0 22 22
BMPR1B 0.025 0.011 -10000 0 0 91 91
BMPR1A-1B/BAMBI 0.031 0.06 -10000 0 -0.14 49 49
AHSG 0.025 0.011 -10000 0 0 89 89
CER1 0.028 0.008 -10000 0 0 40 40
BMP2-4/CER1 0.051 0.022 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.1 -10000 0 -0.32 37 37
BMP2-4 (homodimer) 0.04 0.013 -10000 0 -10000 0 0
RGMB 0.028 0.007 -10000 0 0 37 37
BMP6/BMPR2/BMPR1A-1B 0.043 0.067 -10000 0 -0.14 46 46
RGMA 0.028 0.007 -10000 0 0 34 34
SMURF1 0.029 0.006 -10000 0 0 20 20
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.02 0.073 -10000 0 -0.26 23 23
BMP2-4/USAG1 0.041 0.03 -10000 0 -0.15 2 2
SMAD6/SMURF1/SMAD5 -0.014 0.093 0.2 1 -0.34 20 21
SOSTDC1 0.022 0.013 -10000 0 0 139 139
BMP7/BMPR2/BMPR1A-1B 0.031 0.084 -10000 0 -0.15 76 76
SKI 0.029 0.006 -10000 0 0 23 23
BMP6 (homodimer) 0.027 0.008 -10000 0 0 46 46
HFE2 0.029 0.005 -10000 0 0 15 15
ZFYVE16 0.026 0.009 -10000 0 0 61 61
MAP3K7 0.028 0.007 -10000 0 0 30 30
BMP2-4/CHRD 0.046 0.026 -10000 0 -10000 0 0
SMAD5/SMAD5/SMAD4 -0.014 0.093 0.21 2 -0.34 21 23
MAPK1 0.027 0.008 -10000 0 0 42 42
TAK1/TAB family -0.003 0.082 -10000 0 -0.26 21 21
BMP7 (homodimer) 0.023 0.013 -10000 0 0 134 134
NUP214 0.029 0.005 -10000 0 0 18 18
BMP6/FETUA 0.034 0.018 -10000 0 -10000 0 0
SMAD1/SKI -0.008 0.09 -10000 0 -0.4 16 16
SMAD6 0.029 0.005 -10000 0 0 16 16
CTDSP2 0.029 0.005 -10000 0 0 18 18
BMP2-4/FETUA 0.046 0.026 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.026 0.009 -10000 0 0 61 61
BMPR2 (homodimer) 0.029 0.004 -10000 0 0 8 8
GADD34/PP1CA 0.036 0.056 -10000 0 -0.14 43 43
BMPR1A-1B (homodimer) 0.02 0.061 -10000 0 -0.16 53 53
CHRDL1 0.016 0.015 -10000 0 0 262 262
ENDOFIN/SMAD1 -0.008 0.091 -10000 0 -0.41 15 15
SMAD6-7/SMURF1/SMAD1 0.013 0.1 -10000 0 -0.39 16 16
SMAD6/SMURF1 0.029 0.006 -10000 0 0 20 20
BAMBI 0.026 0.009 -10000 0 0 63 63
SMURF2 0.029 0.005 -10000 0 0 15 15
BMP2-4/CHRDL1 -0.032 0.098 -10000 0 -0.14 235 235
BMP2-4/GREM1 0.049 0.024 -10000 0 -10000 0 0
SMAD7 0.028 0.006 -10000 0 0 28 28
SMAD8A/SMAD8A/SMAD4 -0.011 0.14 -10000 0 -0.46 45 45
SMAD1/SMAD6 -0.008 0.091 -10000 0 -0.4 16 16
TAK1/SMAD6 0.041 0.012 -10000 0 -10000 0 0
BMP7 0.023 0.013 -10000 0 0 134 134
BMP6 0.027 0.008 -10000 0 0 46 46
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.02 0.079 0.16 1 -0.3 22 23
PPM1A 0.029 0.004 -10000 0 0 13 13
SMAD1/SMURF2 -0.008 0.092 -10000 0 -0.41 16 16
SMAD7/SMURF1 0.041 0.012 -10000 0 -10000 0 0
CTDSPL 0.029 0.003 -10000 0 0 5 5
PPP1CA 0.029 0.004 -10000 0 0 8 8
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.029 0.004 -10000 0 0 13 13
PPP1R15A 0.026 0.01 -10000 0 0 69 69
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.018 0.087 0.16 1 -0.28 31 32
CHRD 0.025 0.011 -10000 0 0 93 93
BMPR2 0.029 0.004 -10000 0 0 8 8
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.02 0.077 0.18 1 -0.27 23 24
BMP4 0.029 0.006 -10000 0 0 22 22
FST 0.025 0.011 -10000 0 0 91 91
BMP2-4/NOG 0.053 0.022 -10000 0 -0.15 1 1
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.037 0.088 -10000 0 -0.15 74 74
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.027 0.094 0.18 1 -0.27 24 25
adherens junction organization -0.03 0.098 -10000 0 -0.3 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.028 0.1 0.22 5 -0.24 15 20
FMN1 -0.031 0.092 -10000 0 -0.28 42 42
mol:IP3 -0.03 0.071 0.12 45 -0.21 20 65
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.022 0.098 0.15 1 -0.28 45 46
CTNNB1 0.024 0.02 -10000 0 -0.031 61 61
AKT1 -0.035 0.076 0.19 2 -0.22 30 32
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.02 0.1 -10000 0 -0.31 31 31
CTNND1 -0.007 0.031 0.045 4 -10000 0 4
mol:PI-4-5-P2 -0.028 0.091 0.19 7 -0.27 44 51
VASP -0.032 0.092 -10000 0 -0.28 44 44
ZYX -0.039 0.096 -10000 0 -0.29 49 49
JUB -0.023 0.093 0.14 1 -0.27 45 46
EGFR(dimer) -0.013 0.11 -10000 0 -0.28 48 48
E-cadherin/beta catenin-gamma catenin 0.044 0.041 -10000 0 -0.14 19 19
mol:PI-3-4-5-P3 -0.018 0.08 0.2 1 -0.22 34 35
PIK3CA 0.006 0.025 -10000 0 -0.036 72 72
PI3K -0.018 0.081 0.21 1 -0.23 34 35
FYN -0.048 0.12 0.17 3 -0.29 71 74
mol:Ca2+ -0.03 0.07 0.12 45 -0.21 20 65
JUP 0.022 0.021 -10000 0 -0.031 61 61
PIK3R1 0.021 0.017 -10000 0 -0.037 1 1
mol:DAG -0.03 0.071 0.12 45 -0.21 20 65
CDH1 0.02 0.021 -10000 0 -0.031 62 62
RhoA/GDP -0.027 0.1 0.22 5 -0.25 12 17
establishment of polarity of embryonic epithelium -0.031 0.09 -10000 0 -0.27 44 44
SRC 0.028 0.007 -10000 0 0 31 31
RAC1 0.028 0.006 -10000 0 0 28 28
RHOA 0.029 0.003 -10000 0 0 6 6
EGFR 0.027 0.009 -10000 0 0 55 55
CASR -0.023 0.082 0.18 2 -0.21 17 19
RhoA/GTP -0.021 0.086 0.18 2 -0.23 11 13
AKT2 -0.036 0.078 0.19 2 -0.23 32 34
actin cable formation -0.038 0.09 0.22 2 -0.32 28 30
apoptosis 0.021 0.096 0.25 31 -0.2 5 36
CTNNA1 -0.007 0.031 -10000 0 -10000 0 0
mol:GDP -0.03 0.09 0.18 2 -0.23 23 25
PIP5K1A -0.029 0.092 0.17 6 -0.27 44 50
PLCG1 -0.031 0.072 0.12 45 -0.21 20 65
Rac1/GTP -0.012 0.11 -10000 0 -0.27 48 48
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 -0.031 0.01 -10000 0 -0.089 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.12 0.23 13 -0.34 19 32
ERC1 0.026 0.01 -10000 0 0 67 67
RIP2/NOD2 0.026 0.022 -10000 0 -10000 0 0
NFKBIA -0.055 0.043 -10000 0 -0.32 12 12
BIRC2 0.021 0.013 -10000 0 0 159 159
IKBKB 0.028 0.008 -10000 0 0 39 39
RIPK2 0.019 0.014 -10000 0 0 200 200
IKBKG 0.026 0.11 -10000 0 -0.42 19 19
IKK complex/A20 0.045 0.13 -10000 0 -0.39 29 29
NEMO/A20/RIP2 0.019 0.014 -10000 0 0 200 200
XPO1 0.027 0.009 -10000 0 0 51 51
NEMO/ATM 0.035 0.13 0.24 6 -0.39 33 39
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 0 12 12
Exportin 1/RanGTP 0.036 0.013 -10000 0 -10000 0 0
IKK complex/ELKS 0.034 0.12 -10000 0 -0.37 29 29
BCL10/MALT1/TRAF6 0.05 0.022 -10000 0 -10000 0 0
NOD2 0.028 0.008 -10000 0 0 41 41
NFKB1 -0.029 0.012 -10000 0 -0.089 10 10
RELA -0.032 0.009 -10000 0 -0.089 10 10
MALT1 0.026 0.01 -10000 0 0 75 75
cIAP1/UbcH5C 0.029 0.021 -10000 0 -10000 0 0
ATM 0.028 0.007 -10000 0 0 31 31
TNF/TNFR1A 0.032 0.037 -10000 0 -0.16 16 16
TRAF6 0.029 0.004 -10000 0 0 12 12
PRKCA 0.029 0.006 -10000 0 0 23 23
CHUK 0.028 0.007 -10000 0 0 36 36
UBE2D3 0.027 0.008 -10000 0 0 42 42
TNF 0.029 0.005 -10000 0 0 15 15
NF kappa B1 p50/RelA 0.043 0.052 -10000 0 -0.2 17 17
BCL10 0.029 0.004 -10000 0 0 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.054 0.043 -10000 0 -0.32 12 12
beta TrCP1/SCF ubiquitin ligase complex -0.031 0.01 -10000 0 -0.089 10 10
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
IKK complex 0.044 0.13 -10000 0 -0.4 29 29
CYLD 0.028 0.008 -10000 0 0 40 40
IKK complex/PKC alpha 0.05 0.13 -10000 0 -0.4 27 27
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.033 0.019 0.079 60 -10000 0 60
HSPA8 0.02 0.024 -10000 0 -0.042 68 68
SMAD3/SMAD4/ER alpha -0.051 0.088 0.25 11 -0.27 3 14
AKT1 0.026 0.013 -10000 0 -0.038 16 16
GSC 0 0.059 -10000 0 -0.44 3 3
NKX2-5 -0.031 0.01 0.039 1 -0.082 1 2
muscle cell differentiation -0.027 0.11 0.3 26 -0.3 4 30
SMAD2-3/SMAD4/SP1 0.052 0.14 0.37 10 -10000 0 10
SMAD4 -0.007 0.079 0.2 18 -10000 0 18
CBFB 0.026 0.009 -10000 0 0 61 61
SAP18 0.021 0.021 -10000 0 -0.032 67 67
Cbp/p300/MSG1 0.058 0.044 0.16 1 -0.14 9 10
SMAD3/SMAD4/VDR 0.063 0.1 0.31 9 -10000 0 9
MYC 0.017 0.015 -10000 0 -10000 0 0
CDKN2B -0.057 0.12 -10000 0 -0.51 16 16
AP1 -0.025 0.088 0.26 2 -0.25 1 3
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.021 0.11 0.21 8 -0.39 24 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.022 0.073 -10000 0 -0.3 19 19
SP3 -0.023 0.038 0.17 20 -10000 0 20
CREB1 0.029 0.004 -10000 0 0 8 8
FOXH1 -0.023 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.031 0.099 0.25 14 -0.25 3 17
GATA3 -0.033 0.009 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.012 0.09 0.24 1 -0.36 22 23
MEF2C/TIF2 -0.006 0.11 0.26 11 -0.29 12 23
endothelial cell migration -0.1 0.21 0.72 1 -0.66 68 69
MAX 0.008 0.056 -10000 0 -0.14 68 68
RBBP7 0.021 0.02 -10000 0 -0.032 65 65
RBBP4 0.02 0.021 -10000 0 -0.032 66 66
RUNX2 0.028 0.007 -10000 0 0 29 29
RUNX3 0.029 0.004 -10000 0 0 13 13
RUNX1 0.029 0.004 -10000 0 0 10 10
CTBP1 0.027 0.008 -10000 0 0 45 45
NR3C1 0.008 0.056 -10000 0 -0.14 68 68
VDR 0.029 0.004 -10000 0 0 8 8
CDKN1A 0.005 0.22 0.44 1 -0.98 20 21
KAT2B 0.002 0.005 0.018 11 -10000 0 11
SMAD2/SMAD2/SMAD4/FOXH1 0.017 0.064 -10000 0 -10000 0 0
DCP1A 0.029 0.004 -10000 0 0 11 11
SKI 0.021 0.02 -10000 0 -0.032 66 66
SERPINE1 0.099 0.21 0.66 68 -0.73 1 69
SMAD3/SMAD4/ATF2 -0.011 0.09 0.24 26 -10000 0 26
SMAD3/SMAD4/ATF3 -0.013 0.089 0.25 17 -0.26 1 18
SAP30 0.02 0.021 -10000 0 -0.032 67 67
Cbp/p300/PIAS3 0.063 0.054 0.19 64 -0.15 7 71
JUN -0.023 0.089 0.27 6 -0.24 1 7
SMAD3/SMAD4/IRF7 -0.014 0.094 0.24 30 -10000 0 30
TFE3 0 0.068 0.14 101 -10000 0 101
COL1A2 0.14 0.25 0.52 156 -0.59 7 163
mesenchymal cell differentiation 0.011 0.089 -10000 0 -0.23 29 29
DLX1 0.029 0.005 -10000 0 0 14 14
TCF3 0.027 0.009 -10000 0 0 51 51
FOS -0.008 0.041 0.16 7 -10000 0 7
SMAD3/SMAD4/Max -0.03 0.098 0.25 14 -0.25 3 17
Cbp/p300/SNIP1 0.05 0.038 -10000 0 -0.14 10 10
ZBTB17 0.029 0.005 -10000 0 -10000 0 0
LAMC1 -0.014 0.081 0.28 8 -10000 0 8
TGIF2/HDAC complex/SMAD3/SMAD4 -0.011 0.089 0.24 30 -10000 0 30
IRF7 -0.03 0.007 -10000 0 -10000 0 0
ESR1 -0.031 0.028 0.11 5 -0.082 11 16
HNF4A 0.028 0.007 -10000 0 0 38 38
MEF2C 0.005 0.11 0.26 14 -0.29 12 26
SMAD2-3/SMAD4 -0.014 0.092 0.26 12 -10000 0 12
Cbp/p300/Src-1 0.056 0.044 -10000 0 -0.14 12 12
IGHV3OR16-13 -0.007 0.033 -10000 0 -0.42 3 3
TGIF2/HDAC complex 0.028 0.007 -10000 0 0 36 36
CREBBP 0.032 0.014 0.071 4 -10000 0 4
SKIL 0.01 0.014 -10000 0 0 361 361
HDAC1 0.02 0.021 -10000 0 -0.032 65 65
HDAC2 0.02 0.021 -10000 0 -0.032 66 66
SNIP1 0.02 0.022 -10000 0 -0.038 63 63
GCN5L2 0.005 0.013 0.038 68 -10000 0 68
SMAD3/SMAD4/TFE3 0.002 0.1 0.27 22 -10000 0 22
MSG1/HSC70 0.03 0.03 -10000 0 -10000 0 0
SMAD2 -0.031 0.01 -10000 0 -10000 0 0
SMAD3 -0.007 0.078 0.2 18 -10000 0 18
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.076 0.23 15 -0.23 4 19
SMAD2/SMAD2/SMAD4 -0.006 0.06 0.18 2 -0.19 22 24
NCOR1 0.02 0.021 -10000 0 -0.032 65 65
NCOA2 0.027 0.008 -10000 0 0 46 46
NCOA1 0.029 0.005 -10000 0 0 14 14
MYOD/E2A 0.04 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.092 0.13 0.37 16 -10000 0 16
IFNB1 -0.023 0.082 0.22 20 -10000 0 20
SMAD3/SMAD4/MEF2C 0.008 0.13 0.33 12 -0.31 12 24
CITED1 0.025 0.015 -10000 0 -0.029 33 33
SMAD2-3/SMAD4/ARC105 0.038 0.096 0.32 1 -10000 0 1
RBL1 0.026 0.01 -10000 0 0 67 67
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.019 0.076 -10000 0 -0.34 11 11
RUNX1-3/PEBPB2 0.053 0.02 -10000 0 -10000 0 0
SMAD7 0.016 0.16 0.44 22 -0.39 4 26
MYC/MIZ-1 0.012 0.056 -10000 0 -0.16 46 46
SMAD3/SMAD4 0.053 0.13 0.35 56 -0.44 3 59
IL10 -0.016 0.092 0.27 6 -10000 0 6
PIASy/HDAC complex 0.016 0.031 -10000 0 -0.067 64 64
PIAS3 0.031 0.008 -10000 0 -10000 0 0
CDK2 0.02 0.018 -10000 0 -10000 0 0
IL5 -0.015 0.094 0.28 8 -10000 0 8
CDK4 0.033 0.014 0.073 30 -10000 0 30
PIAS4 0.016 0.031 -10000 0 -0.067 64 64
ATF3 0.029 0.006 -10000 0 0 23 23
SMAD3/SMAD4/SP1 0.018 0.13 0.35 7 -10000 0 7
FOXG1 0.029 0.007 -10000 0 -10000 0 0
FOXO3 -0.031 0.011 -10000 0 -10000 0 0
FOXO1 -0.031 0.013 -10000 0 -0.18 1 1
FOXO4 -0.032 0.008 -10000 0 -10000 0 0
heart looping 0.005 0.11 0.26 14 -0.29 12 26
CEBPB 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.012 0.091 0.24 29 -10000 0 29
MYOD1 0.029 0.004 -10000 0 0 9 9
SMAD3/SMAD4/HNF4 -0.011 0.089 0.24 29 -10000 0 29
SMAD3/SMAD4/GATA3 -0.012 0.096 0.26 20 -10000 0 20
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.014 -10000 0 0 361 361
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.094 0.3 5 -10000 0 5
SMAD3/SMAD4/SP1-3 0.065 0.13 0.34 16 -0.27 3 19
MED15 0.028 0.007 -10000 0 0 31 31
SP1 0.022 0.088 0.14 187 -0.17 3 190
SIN3B 0.019 0.021 -10000 0 -0.032 65 65
SIN3A 0.021 0.021 -10000 0 -0.032 68 68
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.033 0.073 -10000 0 -0.2 11 11
ITGB5 0.004 0.12 0.3 23 -10000 0 23
TGIF/SIN3/HDAC complex/CtBP -0.006 0.082 0.24 1 -0.33 19 20
SMAD3/SMAD4/AR -0.086 0.098 0.25 8 -0.26 8 16
AR 0.012 0.015 -10000 0 0 328 328
negative regulation of cell growth 0.007 0.092 0.25 13 -0.3 15 28
SMAD3/SMAD4/MYOD -0.012 0.091 0.24 25 -10000 0 25
E2F5 0.025 0.011 -10000 0 0 84 84
E2F4 0.027 0.009 -10000 0 0 60 60
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.046 0.072 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.017 0.063 -10000 0 -0.28 8 8
TFDP1 0.028 0.007 -10000 0 0 38 38
SMAD3/SMAD4/AP1 -0.003 0.096 0.26 1 -0.25 1 2
SMAD3/SMAD4/RUNX2 -0.011 0.09 0.24 29 -10000 0 29
TGIF2 0.028 0.007 -10000 0 0 36 36
TGIF1 0.028 0.006 -10000 0 0 26 26
ATF2 0.029 0.005 -10000 0 0 16 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.009 -10000 0 0 62 62
Caspase 8 (4 units) 0.026 0.06 -10000 0 -0.19 9 9
NEF -0.004 0.001 -10000 0 -10000 0 0
NFKBIA -0.031 0.039 0.17 15 -0.089 60 75
BIRC3 -0.082 0.1 0.16 8 -0.31 79 87
CYCS -0.024 0.043 0.24 1 -0.25 2 3
RIPK1 0.028 0.008 -10000 0 0 40 40
CD247 -0.031 0.004 -10000 0 -10000 0 0
MAP2K7 -0.023 0.15 -10000 0 -0.61 27 27
protein ubiquitination -0.034 0.096 0.21 7 -0.3 33 40
CRADD 0.029 0.004 -10000 0 0 13 13
DAXX 0.029 0.005 -10000 0 0 17 17
FAS 0.027 0.008 -10000 0 0 43 43
BID -0.02 0.039 0.15 5 -0.25 2 7
NF-kappa-B/RelA/I kappa B alpha 0.011 0.097 -10000 0 -0.21 84 84
TRADD 0.026 0.01 -10000 0 0 65 65
MAP3K5 0.028 0.007 -10000 0 0 32 32
CFLAR 0.029 0.004 -10000 0 0 10 10
FADD 0.029 0.005 -10000 0 0 19 19
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.011 0.098 -10000 0 -0.21 84 84
MAPK8 -0.029 0.14 -10000 0 -0.57 27 27
APAF1 0.028 0.006 -10000 0 0 27 27
TRAF1 0.029 0.005 -10000 0 0 16 16
TRAF2 0.028 0.006 -10000 0 0 24 24
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.009 0.037 0.17 5 -0.25 1 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.035 0.11 0.2 12 -0.36 33 45
CHUK -0.037 0.1 0.21 7 -0.32 33 40
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.067 0.053 -10000 0 -0.14 15 15
TCRz/NEF 0.023 0.006 -10000 0 -10000 0 0
TNF 0.029 0.005 -10000 0 0 15 15
FASLG -0.029 0.005 -10000 0 -10000 0 0
NFKB1 -0.03 0.039 0.17 15 -0.089 60 75
TNFR1A/BAG4/TNF-alpha 0.042 0.04 -10000 0 -0.14 15 15
CASP6 0.005 0.16 -10000 0 -0.52 39 39
CASP7 -0.075 0.16 0.38 15 -0.41 79 94
RELA -0.033 0.04 0.17 16 -0.089 61 77
CASP2 0.027 0.008 -10000 0 0 44 44
CASP3 -0.085 0.17 0.38 15 -0.42 86 101
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
TNFR1A/BAG4 0.03 0.036 -10000 0 -0.16 15 15
CASP8 0.029 0.004 -10000 0 0 8 8
CASP9 0.029 0.004 -10000 0 0 13 13
MAP3K14 -0.038 0.1 0.23 2 -0.34 33 35
APAF-1/Caspase 9 -0.082 0.086 0.16 1 -0.27 60 61
BCL2 -0.044 0.13 -10000 0 -0.52 28 28
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.028 0.006 -10000 0 0 26 26
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.029 0.005 -10000 0 0 17 17
TCEB1 0.028 0.007 -10000 0 0 37 37
HIF1A/p53 -0.012 0.065 0.17 5 -0.31 16 21
HIF1A -0.007 0.056 -10000 0 -0.33 13 13
COPS5 0.026 0.01 -10000 0 0 78 78
VHL/Elongin B/Elongin C/RBX1/CUL2 0.076 0.054 -10000 0 -10000 0 0
FIH (dimer) 0.029 0.006 -10000 0 0 20 20
CDKN2A 0.012 0.014 -10000 0 0 340 340
ARNT/IPAS 0.039 0.014 -10000 0 -10000 0 0
HIF1AN 0.029 0.006 -10000 0 0 20 20
GNB2L1 0.029 0.005 -10000 0 0 15 15
HIF1A/ARNT -0.011 0.065 0.24 1 -0.33 13 14
CUL2 0.024 0.012 -10000 0 0 113 113
OS9 0.029 0.005 -10000 0 0 17 17
RACK1/Elongin B/Elongin C 0.054 0.019 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.01 0.066 0.17 7 -0.31 15 22
PHD1-3/OS9 0.062 0.047 -10000 0 -0.14 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.033 0.072 0.25 1 -0.31 14 15
VHL 0.029 0.004 -10000 0 0 9 9
HSP90AA1 0.029 0.006 -10000 0 0 21 21
HIF1A/JAB1 -0.01 0.064 0.24 1 -0.32 13 14
EGLN3 0.026 0.01 -10000 0 0 70 70
EGLN2 0.028 0.008 -10000 0 0 39 39
EGLN1 0.028 0.007 -10000 0 0 33 33
TP53 0.024 0.011 -10000 0 0 102 102
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.034 0.078 -10000 0 -0.6 6 6
ARNT 0.028 0.007 -10000 0 0 36 36
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.009 -10000 0 0 51 51
HIF1A/p19ARF -0.007 0.05 0.24 1 -0.32 8 9
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.009 0.036 0.16 20 -0.17 1 21
CRKL 0.028 0.007 -10000 0 0 31 31
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
DOCK1 0.029 0.005 -10000 0 0 19 19
ITGA4 0.028 0.008 -10000 0 0 40 40
alpha4/beta7 Integrin/MAdCAM1 0.066 0.041 -10000 0 -0.14 1 1
EPO 0.029 0.005 -10000 0 0 19 19
alpha4/beta7 Integrin 0.04 0.015 -10000 0 -0.16 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 0 37 37
alpha4/beta1 Integrin 0.039 0.014 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.038 0.015 -10000 0 -10000 0 0
lamellipodium assembly -0.009 0.11 -10000 0 -0.46 12 12
PIK3CA 0.021 0.014 -10000 0 0 171 171
PI3K 0 0.067 -10000 0 -0.16 75 75
ARF6 0.029 0.004 -10000 0 0 11 11
JAK2 -0.008 0.032 0.11 26 -0.24 1 27
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 161 161
MADCAM1 0.027 0.009 -10000 0 0 52 52
cell adhesion 0.063 0.04 -10000 0 -0.14 1 1
CRKL/CBL 0.041 0.012 -10000 0 -10000 0 0
ITGB1 0.029 0.006 -10000 0 0 22 22
SRC -0.007 0.1 0.17 117 -10000 0 117
ITGB7 0.029 0.004 -10000 0 0 9 9
RAC1 0.028 0.006 -10000 0 0 28 28
alpha4/beta1 Integrin/VCAM1 0.021 0.067 -10000 0 -0.14 68 68
p130Cas/Crk/Dock1 -0.019 0.11 0.23 28 -10000 0 28
VCAM1 0.021 0.013 -10000 0 0 161 161
RHOA 0.029 0.003 -10000 0 0 6 6
alpha4/beta1 Integrin/Paxillin/GIT1 0.067 0.04 -10000 0 -0.14 6 6
BCAR1 -0.011 0.093 0.23 28 -10000 0 28
EPOR 0.027 0.009 -10000 0 0 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.029 0.005 -10000 0 0 15 15
GIT1 0.028 0.007 -10000 0 0 31 31
Rac1/GTP -0.01 0.12 -10000 0 -0.48 12 12
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.003 0.086 0.24 9 -0.33 10 19
PDGFB-D/PDGFRB/SLAP 0.023 0.032 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/APS/CBL 0.035 0.021 -10000 0 -0.13 5 5
AKT1 -0.039 0.11 0.26 23 -0.25 5 28
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.088 0.27 6 -0.35 11 17
PIK3CA 0.021 0.014 -10000 0 0 171 171
FGR -0.002 0.081 0.32 1 -0.38 12 13
mol:Ca2+ 0 0.082 0.26 4 -0.38 11 15
MYC -0.027 0.24 0.4 5 -0.68 59 64
SHC1 0.029 0.006 -10000 0 0 20 20
HRAS/GDP -0.036 0.055 0.16 40 -10000 0 40
LRP1/PDGFRB/PDGFB 0.048 0.037 -10000 0 -0.15 13 13
GRB10 0.029 0.004 -10000 0 0 12 12
PTPN11 0.029 0.004 -10000 0 0 9 9
GO:0007205 -0.001 0.083 0.26 4 -0.38 11 15
PTEN 0.028 0.007 -10000 0 0 31 31
GRB2 0.029 0.006 -10000 0 0 20 20
GRB7 0.027 0.008 -10000 0 0 42 42
PDGFB-D/PDGFRB/SHP2 0.034 0.031 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/GRB10 0.034 0.031 -10000 0 -0.16 5 5
cell cycle arrest 0.023 0.032 -10000 0 -0.16 5 5
HRAS 0.028 0.006 -10000 0 0 28 28
HIF1A -0.044 0.1 0.24 23 -0.22 10 33
GAB1 -0.009 0.097 0.3 3 -0.34 18 21
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.009 0.1 0.29 11 -0.32 15 26
PDGFB-D/PDGFRB 0.04 0.044 -10000 0 -0.15 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.032 0.031 -10000 0 -0.16 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.025 0.098 0.26 6 -0.3 22 28
positive regulation of MAPKKK cascade 0.034 0.031 -10000 0 -0.16 5 5
PIK3R1 0.021 0.013 -10000 0 0 161 161
mol:IP3 -0.001 0.084 0.26 4 -0.39 11 15
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.02 0.022 -10000 0 -0.047 2 2
PDGFB-D/PDGFRB/GRB7 0.031 0.035 -10000 0 -0.16 8 8
SHB 0.029 0.004 -10000 0 0 8 8
BLK -0.06 0.16 0.32 1 -0.39 93 94
PTPN2 0.014 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.031 -10000 0 -0.16 5 5
BCAR1 0.027 0.009 -10000 0 0 59 59
VAV2 -0.021 0.12 0.3 4 -0.36 34 38
CBL 0.029 0.005 -10000 0 0 15 15
PDGFB-D/PDGFRB/DEP1 0.034 0.031 -10000 0 -0.16 5 5
LCK -0.001 0.074 0.32 1 -0.37 9 10
PDGFRB 0.014 0.028 -10000 0 -10000 0 0
ACP1 0.027 0.009 -10000 0 0 58 58
HCK 0.002 0.052 0.32 1 -10000 0 1
ABL1 -0.01 0.087 0.27 4 -0.29 16 20
PDGFB-D/PDGFRB/CBL -0.008 0.1 0.33 1 -0.39 17 18
PTPN1 0.012 0.027 -10000 0 -10000 0 0
SNX15 0.029 0.003 -10000 0 0 5 5
STAT3 0.028 0.007 -10000 0 0 38 38
STAT1 0.013 0.015 -10000 0 0 316 316
cell proliferation -0.019 0.22 0.38 6 -0.6 59 65
SLA 0.021 0.014 -10000 0 0 170 170
actin cytoskeleton reorganization -0.022 0.1 0.33 15 -10000 0 15
SRC 0.001 0.064 0.32 1 -0.88 1 2
PI3K -0.072 0.067 -10000 0 -0.22 37 37
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.032 -10000 0 -0.15 8 8
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.007 0.09 0.27 6 -0.36 11 17
LYN -0.006 0.09 0.31 1 -0.45 13 14
LRP1 0.029 0.006 -10000 0 0 21 21
SOS1 0.028 0.007 -10000 0 0 34 34
STAT5B 0.028 0.007 -10000 0 0 34 34
STAT5A 0.028 0.007 -10000 0 0 35 35
NCK1-2/p130 Cas 0.054 0.069 -10000 0 -0.15 6 6
SPHK1 0.02 0.023 -10000 0 -10000 0 0
EDG1 -0.001 0.003 0.019 1 -10000 0 1
mol:DAG -0.001 0.084 0.26 4 -0.39 11 15
PLCG1 -0.001 0.085 0.26 4 -0.4 11 15
NHERF/PDGFRB -0.013 0.1 -10000 0 -0.16 171 171
YES1 -0.001 0.083 0.31 1 -0.52 7 8
cell migration -0.013 0.1 -10000 0 -0.16 171 171
SHC/Grb2/SOS1 0.061 0.061 -10000 0 -0.15 4 4
SLC9A3R2 0.025 0.011 -10000 0 0 92 92
SLC9A3R1 0.022 0.013 -10000 0 0 141 141
NHERF1-2/PDGFRB/PTEN -0.005 0.11 -10000 0 -0.16 171 171
FYN -0.063 0.17 -10000 0 -0.42 88 88
DOK1 -0.028 0.06 0.16 49 -10000 0 49
HRAS/GTP 0.021 0.005 -10000 0 -10000 0 0
PDGFB 0.027 0.008 -10000 0 0 47 47
RAC1 -0.058 0.2 0.3 3 -0.52 63 66
PRKCD -0.029 0.06 0.16 48 -10000 0 48
FER -0.028 0.059 0.16 46 -10000 0 46
MAPKKK cascade -0.026 0.081 0.33 9 -10000 0 9
RASA1 -0.028 0.057 0.16 42 -10000 0 42
NCK1 0.026 0.009 -10000 0 0 63 63
NCK2 0.029 0.004 -10000 0 0 11 11
p62DOK/Csk -0.031 0.064 0.16 50 -10000 0 50
PDGFB-D/PDGFRB/SHB 0.034 0.031 -10000 0 -0.16 5 5
chemotaxis -0.01 0.085 0.26 4 -0.28 16 20
STAT1-3-5/STAT1-3-5 0.061 0.066 -10000 0 -0.16 6 6
Bovine Papilomavirus E5/PDGFRB 0.013 0.023 -10000 0 -0.15 5 5
PTPRJ 0.029 0.004 -10000 0 0 8 8
Noncanonical Wnt signaling pathway

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
NFATC2 0.026 0.01 -10000 0 0 76 76
GNB1/GNG2 0.043 0.081 0.2 4 -0.22 9 13
mol:DAG -0.009 0.075 0.17 25 -0.22 9 34
PLCG1 -0.01 0.077 0.17 25 -0.22 9 34
YES1 -0.008 0.065 0.2 15 -0.22 9 24
FZD3 0.022 0.013 -10000 0 0 140 140
FZD6 0.024 0.012 -10000 0 0 105 105
G protein 0.016 0.1 0.21 64 -0.26 2 66
MAP3K7 -0.025 0.067 0.23 6 -0.24 2 8
mol:Ca2+ -0.009 0.074 0.17 25 -0.21 9 34
mol:IP3 -0.009 0.075 0.17 25 -0.22 9 34
NLK -0.02 0.16 -10000 0 -0.79 24 24
GNB1 0.028 0.006 -10000 0 0 24 24
CAMK2A -0.017 0.072 0.2 11 -0.24 2 13
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.007 0.064 0.2 3 -0.21 13 16
CSNK1A1 0.029 0.004 -10000 0 0 13 13
GNAS -0.012 0.058 0.18 4 -0.22 10 14
GO:0007205 -0.006 0.072 0.2 13 -0.22 7 20
WNT6 0.029 0.004 -10000 0 0 8 8
WNT4 0.029 0.004 -10000 0 0 11 11
NFAT1/CK1 alpha -0.007 0.092 0.24 21 -0.27 2 23
GNG2 0.029 0.004 -10000 0 0 12 12
WNT5A 0.029 0.005 -10000 0 0 17 17
WNT11 0.026 0.01 -10000 0 0 74 74
CDC42 -0.005 0.068 0.19 22 -0.23 3 25
Arf6 signaling events

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
CENTA1/KIF3B 0.01 0.03 -10000 0 -0.12 26 26
ARNO/beta Arrestin1-2 0.026 0.029 -10000 0 -0.1 6 6
EGFR 0.027 0.009 -10000 0 0 55 55
EPHA2 0.029 0.005 -10000 0 0 16 16
USP6 0.028 0.006 -10000 0 0 26 26
IQSEC1 0.029 0.004 -10000 0 0 8 8
EGFR/EGFR/EGF/EGF 0.024 0.056 -10000 0 -0.16 43 43
ARRB2 0.007 0.002 -10000 0 -10000 0 0
mol:GTP 0.001 0.02 0.11 4 -0.069 16 20
ARRB1 0.028 0.007 -10000 0 0 36 36
FBXO8 0.027 0.008 -10000 0 0 43 43
TSHR 0.028 0.007 -10000 0 0 32 32
EGF 0.027 0.008 -10000 0 0 43 43
somatostatin receptor activity 0 0 0 5 -0.001 29 34
ARAP2 0 0 0 7 0 25 32
mol:GDP -0.008 0.071 0.14 2 -0.24 25 27
mol:PI-3-4-5-P3 0 0 0 6 -0.001 28 34
ITGA2B 0.028 0.006 -10000 0 0 23 23
ARF6 0.029 0.004 -10000 0 0 11 11
Ephrin A1/EPHA2/NCK1/GIT1 0.068 0.041 -10000 0 -10000 0 0
ADAP1 0 0 0 2 0 16 18
KIF13B 0.024 0.012 -10000 0 0 112 112
HGF/MET 0.033 0.033 -10000 0 -0.16 12 12
PXN 0.029 0.005 -10000 0 0 14 14
ARF6/GTP -0.014 0.077 0.16 5 -0.25 29 34
EGFR/EGFR/EGF/EGF/ARFGEP100 0.039 0.055 -10000 0 -0.15 41 41
ADRB2 0.029 0.004 -10000 0 0 11 11
receptor agonist activity 0 0 0 8 0 25 33
actin filament binding 0 0 0 5 0 29 34
SRC 0.028 0.007 -10000 0 0 31 31
ITGB3 0.025 0.011 -10000 0 0 98 98
GNAQ 0.028 0.006 -10000 0 0 28 28
EFA6/PI-4-5-P2 0 0 0.001 15 -0.001 18 33
ARF6/GDP -0.003 0.072 0.16 9 -0.28 21 30
ARF6/GDP/GULP/ACAP1 -0.004 0.089 -10000 0 -0.25 30 30
alphaIIb/beta3 Integrin/paxillin/GIT1 0.042 0.076 -10000 0 -0.14 71 71
ACAP1 0 0 0 4 -10000 0 4
ACAP2 0 0 0 5 0 26 31
LHCGR/beta Arrestin2 0.021 0.019 -10000 0 -10000 0 0
EFNA1 0.027 0.008 -10000 0 0 45 45
HGF 0.029 0.005 -10000 0 0 17 17
CYTH3 0 0 0.001 9 -0.001 26 35
CYTH2 0 0.001 0.002 2 -0.004 29 31
NCK1 0.026 0.009 -10000 0 0 63 63
fibronectin binding 0 0 0 7 0 22 29
endosomal lumen acidification 0 0 0 7 0 16 23
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.025 0.011 -10000 0 0 92 92
GNAQ/ARNO 0.019 0.006 -10000 0 -0.003 35 35
mol:Phosphatidic acid 0 0 0 5 0 26 31
PIP3-E 0 0 0 6 0 24 30
MET 0.025 0.011 -10000 0 0 87 87
GNA14 0.029 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 47 47
GIT1 0.028 0.007 -10000 0 0 31 31
mol:PI-4-5-P2 0 0 0.001 11 -0.001 24 35
GNA11 0.025 0.011 -10000 0 0 84 84
LHCGR 0.029 0.005 -10000 0 0 19 19
AGTR1 0.027 0.009 -10000 0 0 51 51
desensitization of G-protein coupled receptor protein signaling pathway 0.021 0.019 -10000 0 -10000 0 0
IPCEF1/ARNO 0.021 0.037 -10000 0 -0.1 43 43
alphaIIb/beta3 Integrin 0.016 0.067 -10000 0 -0.16 67 67
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.037 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.028 0.008 -10000 0 0 40 40
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.011 -10000 0 0 90 90
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.009 -10000 0 0 52 52
RAC1-CDC42/GTP/PAK family -0.032 0.066 -10000 0 -0.15 115 115
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.028 0.008 -10000 0 0 40 40
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 0 14 14
FYN 0.024 0.011 -10000 0 0 99 99
MAP3K12 0.029 0.003 -10000 0 0 6 6
FGR 0.029 0.005 -10000 0 0 15 15
p38 alpha/TAB1 -0.049 0.095 -10000 0 -0.31 44 44
PRKG1 0.029 0.004 -10000 0 0 8 8
DUSP8 0.028 0.006 -10000 0 0 26 26
PGK/cGMP/p38 alpha -0.027 0.11 0.17 3 -0.34 37 40
apoptosis -0.047 0.09 -10000 0 -0.3 45 45
RAL/GTP 0.039 0.008 -10000 0 -10000 0 0
LYN 0.027 0.009 -10000 0 0 52 52
DUSP1 0.023 0.012 -10000 0 0 125 125
PAK1 0.027 0.008 -10000 0 0 47 47
SRC 0.028 0.007 -10000 0 0 31 31
RAC1/OSM/MEKK3/MKK3 0.063 0.036 -10000 0 -10000 0 0
TRAF6 0.029 0.004 -10000 0 0 12 12
RAC1 0.028 0.006 -10000 0 0 28 28
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 0.029 0.004 -10000 0 0 13 13
RAC1-CDC42/GTP 0.038 0.01 -10000 0 -10000 0 0
MAPK11 -0.05 0.12 0.19 5 -0.32 48 53
BLK 0.024 0.011 -10000 0 0 102 102
HCK 0.027 0.008 -10000 0 0 47 47
MAP2K3 0.027 0.008 -10000 0 0 44 44
DUSP16 0.027 0.009 -10000 0 0 58 58
DUSP10 0.028 0.007 -10000 0 0 36 36
TRAF6/MEKK3 0.036 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.033 0.12 0.18 4 -0.37 37 41
positive regulation of innate immune response -0.051 0.13 0.22 4 -0.41 38 42
LCK 0.028 0.006 -10000 0 0 26 26
p38alpha-beta/MKP7 -0.045 0.13 0.2 2 -0.4 36 38
p38alpha-beta/MKP5 -0.044 0.13 0.23 3 -0.4 38 41
PGK/cGMP 0.022 0.003 -10000 0 -10000 0 0
PAK2 0.025 0.011 -10000 0 0 92 92
p38alpha-beta/MKP1 -0.054 0.14 0.23 3 -0.39 47 50
CDC42 0.029 0.004 -10000 0 0 11 11
RALB 0.029 0.004 -10000 0 0 10 10
RALA 0.029 0.005 -10000 0 0 14 14
PAK3 0.021 0.014 -10000 0 0 169 169
Caspase cascade in apoptosis

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
TOP1 0.009 0.11 0.28 5 -0.37 22 27
ACTA1 -0.005 0.082 0.22 13 -0.24 10 23
NUMA1 0.011 0.11 0.28 5 -0.36 25 30
SPTAN1 -0.007 0.079 0.24 8 -0.24 8 16
LIMK1 -0.004 0.081 0.24 11 -0.24 8 19
BIRC3 0.023 0.012 -10000 0 0 122 122
BIRC2 0.021 0.015 -10000 0 -0.03 7 7
BAX 0.029 0.006 -10000 0 0 22 22
CASP10 -0.028 0.052 0.18 29 -0.15 9 38
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 5 -0.001 46 51
PTK2 -0.002 0.11 0.28 5 -0.35 33 38
DIABLO 0.018 0.016 -10000 0 -0.002 203 203
apoptotic nuclear changes -0.007 0.078 0.24 8 -0.24 8 16
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.004 -10000 0 0 13 13
GSN -0.016 0.084 0.24 9 -0.24 14 23
MADD 0.029 0.004 -10000 0 0 8 8
TFAP2A 0.023 0.14 -10000 0 -0.89 10 10
BID -0.014 0.043 0.11 27 -0.14 28 55
MAP3K1 -0.021 0.12 -10000 0 -0.39 50 50
TRADD 0.026 0.01 -10000 0 0 65 65
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.042 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.005 0.1 0.24 48 -0.24 10 58
CASP9 0.028 0.009 -10000 0 -0.029 11 11
DNA repair -0.025 0.062 0.25 3 -0.18 19 22
neuron apoptosis -0.009 0.16 -10000 0 -0.72 23 23
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.099 0.26 7 -0.33 21 28
APAF1 0.026 0.013 -10000 0 -0.014 52 52
CASP6 -0.022 0.24 -10000 0 -0.89 38 38
TRAF2 0.028 0.006 -10000 0 0 24 24
ICAD/CAD -0.013 0.078 0.24 10 -0.25 7 17
CASP7 0.028 0.097 0.2 65 -0.25 24 89
KRT18 0.015 0.069 -10000 0 -0.66 3 3
apoptosis -0.015 0.14 0.3 13 -0.42 35 48
DFFA -0.005 0.078 0.25 8 -0.25 7 15
DFFB -0.004 0.079 0.23 10 -0.25 7 17
PARP1 0.025 0.062 0.18 19 -0.25 3 22
actin filament polymerization 0.012 0.079 0.24 7 -0.28 8 15
TNF 0.029 0.005 -10000 0 0 15 15
CYCS -0.009 0.054 0.16 7 -0.22 16 23
SATB1 -0.058 0.23 -10000 0 -0.87 38 38
SLK -0.005 0.081 0.29 8 -0.25 7 15
p15 BID/BAX -0.021 0.049 0.19 2 -0.2 5 7
CASP2 -0.028 0.087 0.18 16 -0.27 37 53
JNK cascade 0.021 0.12 0.39 50 -10000 0 50
CASP3 0.004 0.084 0.23 13 -0.24 9 22
LMNB2 -0.03 0.19 0.23 16 -0.47 63 79
RIPK1 0.028 0.008 -10000 0 0 40 40
CASP4 0.028 0.007 -10000 0 0 36 36
Mammalian IAPs/DIABLO 0.012 0.051 -10000 0 -0.13 46 46
negative regulation of DNA binding 0.024 0.14 -10000 0 -0.87 10 10
stress fiber formation -0.005 0.08 0.29 8 -0.24 7 15
GZMB -0.021 0.048 0.2 25 -10000 0 25
CASP1 -0.02 0.085 -10000 0 -0.26 55 55
LMNB1 0.012 0.14 0.23 22 -0.4 39 61
APP -0.009 0.16 -10000 0 -0.74 23 23
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
response to stress 0 0 0.001 15 -0.001 9 24
CASP8 -0.017 0.002 0 8 -10000 0 8
VIM -0.006 0.14 0.26 20 -0.42 38 58
LMNA -0.004 0.13 0.24 14 -0.39 38 52
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.023 0.088 -10000 0 -0.27 41 41
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.007 0.078 0.26 6 -0.24 8 14
APAF-1/Caspase 9 -0.032 0.17 -10000 0 -0.54 15 15
nuclear fragmentation during apoptosis 0.011 0.11 0.28 5 -0.35 25 30
CFL2 -0.013 0.08 0.27 9 -0.24 7 16
GAS2 -0.003 0.085 0.28 14 -0.25 7 21
positive regulation of apoptosis -0.003 0.15 0.23 22 -0.44 43 65
PRF1 0.027 0.011 -10000 0 -0.01 37 37
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.029 0.006 -10000 0 0 21 21
Syndecan-3/Src/Cortactin 0.028 0.096 -10000 0 -0.42 16 16
Syndecan-3/Neurocan 0.008 0.087 -10000 0 -0.46 17 17
POMC 0.029 0.004 -10000 0 0 12 12
EGFR 0.027 0.009 -10000 0 0 55 55
Syndecan-3/EGFR 0.007 0.091 -10000 0 -0.48 17 17
AGRP 0.027 0.009 -10000 0 0 57 57
NCSTN 0.029 0.005 -10000 0 0 18 18
PSENEN 0.026 0.01 -10000 0 0 75 75
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.01 -10000 0 0 70 70
APH1A 0.028 0.007 -10000 0 0 30 30
NCAN 0.027 0.008 -10000 0 0 50 50
long-term memory 0.007 0.098 -10000 0 -0.45 17 17
Syndecan-3/IL8 0.006 0.088 -10000 0 -0.46 17 17
PSEN1 0.029 0.005 -10000 0 0 14 14
Src/Cortactin 0.04 0.013 -10000 0 -10000 0 0
FYN 0.024 0.011 -10000 0 0 99 99
limb bud formation -0.013 0.083 -10000 0 -0.47 17 17
MC4R 0 0 -10000 0 -10000 0 0
SRC 0.028 0.007 -10000 0 0 31 31
PTN 0.023 0.012 -10000 0 0 127 127
FGFR/FGF/Syndecan-3 -0.013 0.084 -10000 0 -0.48 17 17
neuron projection morphogenesis -0.005 0.11 0.26 6 -0.43 14 20
Syndecan-3/AgRP 0.009 0.088 -10000 0 -0.46 17 17
Syndecan-3/AgRP/MC4R 0.008 0.085 -10000 0 -0.44 17 17
Fyn/Cortactin 0.016 0.066 -10000 0 -0.16 65 65
SDC3 -0.013 0.084 -10000 0 -0.48 17 17
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.006 0.086 -10000 0 -0.45 17 17
IL8 0.025 0.011 -10000 0 0 95 95
Syndecan-3/Fyn/Cortactin 0.007 0.1 -10000 0 -0.46 17 17
Syndecan-3/CASK -0.013 0.08 -10000 0 -0.46 17 17
alpha-MSH/MC4R 0.022 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.043 0.078 -10000 0 -0.14 65 65
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.047 0.1 -10000 0 -0.32 64 64
KLHL20 -0.059 0.078 0.48 1 -0.27 18 19
CYFIP2 0.028 0.006 -10000 0 0 24 24
Rac1/GDP -0.046 0.079 0.25 4 -0.26 16 20
ENAH -0.048 0.1 -10000 0 -0.32 66 66
AP1M1 0.026 0.01 -10000 0 0 67 67
RAP1B 0.029 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CTNNB1 0.029 0.003 -10000 0 0 7 7
CDC42/GTP -0.059 0.05 0.12 6 -0.23 2 8
ABI1/Sra1/Nap1 -0.053 0.045 -10000 0 -0.17 34 34
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.048 -10000 0 -0.14 9 9
RAPGEF1 -0.048 0.1 0.25 3 -0.31 56 59
CTNND1 0.029 0.003 -10000 0 0 5 5
regulation of calcium-dependent cell-cell adhesion -0.024 0.12 -10000 0 -0.32 69 69
CRK -0.047 0.1 -10000 0 -0.32 61 61
E-cadherin/gamma catenin/alpha catenin 0.043 0.044 -10000 0 -0.16 20 20
alphaE/beta7 Integrin 0.041 0.014 -10000 0 -0.16 1 1
IQGAP1 0.028 0.006 -10000 0 0 25 25
NCKAP1 0.029 0.005 -10000 0 0 17 17
Rap1/GTP/I-afadin 0.04 0.042 -10000 0 -0.13 21 21
DLG1 -0.034 0.1 0.19 1 -0.32 54 55
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.044 0.042 -10000 0 -0.15 13 13
MLLT4 0.026 0.01 -10000 0 0 70 70
ARF6/GTP/NME1/Tiam1 0.048 0.024 -10000 0 -0.13 1 1
PI3K -0.054 0.054 -10000 0 -0.21 7 7
ARF6 0.029 0.004 -10000 0 0 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.03 0.042 -10000 0 -0.18 19 19
TIAM1 0.028 0.006 -10000 0 -0.001 21 21
E-cadherin(dimer)/Ca2+ 0.052 0.043 -10000 0 -0.13 9 9
AKT1 -0.013 0.069 0.14 52 -0.14 1 53
PIK3R1 0.021 0.013 -10000 0 0 161 161
CDH1 0.026 0.01 -10000 0 0 74 74
RhoA/GDP -0.046 0.078 0.24 4 -0.26 15 19
actin cytoskeleton organization -0.043 0.058 0.41 1 -0.21 10 11
CDC42/GDP -0.045 0.079 0.24 5 -0.26 15 20
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.015 0.059 -10000 0 -0.19 37 37
ITGB7 0.029 0.004 -10000 0 0 9 9
RAC1 0.028 0.007 -10000 0 -0.001 29 29
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.057 0.047 -10000 0 -0.14 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin 0.039 0.033 -10000 0 -0.12 9 9
mol:GDP -0.044 0.084 0.25 4 -0.28 21 25
CDC42/GTP/IQGAP1 0.037 0.014 -10000 0 -0.13 2 2
JUP 0.027 0.008 -10000 0 0 43 43
p120 catenin/RhoA/GDP -0.049 0.081 0.24 4 -0.26 16 20
RAC1/GTP/IQGAP1 0.036 0.015 -10000 0 -0.13 2 2
PIP5K1C/AP1M1 0.037 0.017 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 6 6
CDC42 0.029 0.004 -10000 0 0 11 11
CTNNA1 0.029 0.004 -10000 0 0 11 11
positive regulation of S phase of mitotic cell cycle -0.045 0.057 0.12 1 -0.13 140 141
NME1 0.027 0.008 -10000 0 0 43 43
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.049 0.11 -10000 0 -0.32 68 68
regulation of cell-cell adhesion -0.054 0.041 0.083 20 -0.21 2 22
WASF2 -0.031 0.035 0.09 4 -0.1 35 39
Rap1/GTP -0.055 0.058 0.25 2 -0.25 2 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.064 -10000 0 -0.15 20 20
CCND1 -0.055 0.069 0.13 1 -0.16 141 142
VAV2 -0.041 0.16 -10000 0 -0.65 24 24
RAP1/GDP -0.046 0.066 0.25 3 -0.24 4 7
adherens junction assembly -0.048 0.1 -10000 0 -0.32 68 68
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.029 0.005 -10000 0 0 15 15
PIP5K1C 0.027 0.008 -10000 0 0 44 44
regulation of heterotypic cell-cell adhesion -0.06 0.03 0.17 4 -0.23 2 6
E-cadherin/beta catenin -0.012 0.05 -10000 0 -0.18 41 41
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.046 0.1 -10000 0 -0.33 62 62
PIK3CA 0.021 0.014 -10000 0 0 171 171
Rac1/GTP -0.089 0.11 0.57 1 -0.39 36 37
E-cadherin/beta catenin/alpha catenin 0.048 0.032 -10000 0 -0.15 9 9
ITGAE 0.028 0.007 -10000 0 0 31 31
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.025 0.12 -10000 0 -0.33 69 69
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.028 0.007 -10000 0 0 31 31
RAS family/GTP/Tiam1 0.035 0.05 -10000 0 -0.24 2 2
NT3 (dimer)/TRKC 0.034 0.019 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.045 0.026 -10000 0 -10000 0 0
SHC/Grb2/SOS1/GAB1/PI3K -0.013 0.082 0.2 5 -0.24 9 14
RAPGEF1 0.029 0.005 -10000 0 0 18 18
BDNF 0.029 0.005 -10000 0 0 14 14
PIK3CA 0.021 0.014 -10000 0 0 171 171
DYNLT1 0.025 0.011 -10000 0 0 82 82
NTRK1 0.029 0.005 -10000 0 0 14 14
NTRK2 0.029 0.006 -10000 0 0 20 20
NTRK3 0.029 0.006 -10000 0 0 21 21
NT-4/5 (dimer)/TRKB 0.038 0.01 -10000 0 -10000 0 0
neuron apoptosis 0.019 0.11 0.29 44 -10000 0 44
SHC 2-3/Grb2 -0.021 0.12 -10000 0 -0.31 44 44
SHC1 0.029 0.006 -10000 0 0 20 20
SHC2 -0.041 0.15 -10000 0 -0.39 74 74
SHC3 0 0.093 -10000 0 -0.41 18 18
STAT3 (dimer) -0.052 0.14 -10000 0 -0.28 141 141
NT3 (dimer)/TRKA 0.045 0.026 -10000 0 -10000 0 0
RIN/GDP 0.042 0.079 0.21 26 -0.26 11 37
GIPC1 0.025 0.01 -10000 0 0 80 80
KRAS 0.024 0.011 -10000 0 0 99 99
DNAJA3 -0.013 0.057 0.18 2 -0.18 9 11
RIN/GTP 0.021 0.005 -10000 0 -10000 0 0
CCND1 -0.15 0.21 -10000 0 -0.52 140 140
MAGED1 0.029 0.006 -10000 0 0 21 21
PTPN11 0.029 0.004 -10000 0 0 9 9
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.053 0.02 -10000 0 -10000 0 0
GRB2 0.029 0.006 -10000 0 0 20 20
NGF (dimer)/TRKA/MATK 0.036 0.012 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.039 0.016 -10000 0 -0.16 1 1
ELMO1 0.028 0.007 -10000 0 0 30 30
RhoG/GTP/ELMO1/DOCK1 0.037 0.013 -10000 0 -0.13 1 1
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 28 28
DOCK1 0.029 0.005 -10000 0 0 19 19
GAB2 0.026 0.009 -10000 0 0 62 62
RIT2 0.028 0.006 -10000 0 0 28 28
RIT1 0.026 0.009 -10000 0 0 64 64
FRS2 0.028 0.007 -10000 0 0 30 30
DNM1 0.029 0.005 -10000 0 0 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.028 0.007 -10000 0 0 37 37
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.009 0.065 0.22 1 -0.18 11 12
mol:GDP 0.041 0.1 0.26 23 -0.39 12 35
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.021 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.036 0.074 0.21 18 -0.25 11 29
TIAM1 0.029 0.006 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 161 161
BDNF (dimer)/TRKB 0.054 0.019 -10000 0 -10000 0 0
KIDINS220/CRKL/C3G 0.041 0.012 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.02 -10000 0 -0.16 3 3
FRS2 family/SHP2 0.054 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.068 0.035 -10000 0 -0.14 2 2
RIT1/GTP 0.019 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.024 0.012 -10000 0 0 116 116
RAP1/GDP 0.032 0.064 0.16 18 -0.23 11 29
KIDINS220/CRKL 0.028 0.007 -10000 0 0 31 31
BDNF (dimer) 0.029 0.005 -10000 0 0 14 14
ubiquitin-dependent protein catabolic process 0.035 0.014 -10000 0 -0.13 1 1
Schwann cell development -0.01 0.013 -10000 0 -0.054 3 3
EHD4 0.028 0.008 -10000 0 0 40 40
FRS2 family/GRB2/SOS1 0.067 0.033 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.003 0.06 -10000 0 -0.26 16 16
RAP1B 0.029 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CDC42/GTP -0.028 0.076 0.14 92 -10000 0 92
ABL1 0.029 0.006 -10000 0 0 21 21
SH2B family/GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
Rap1/GTP 0.002 0.074 -10000 0 -0.27 22 22
STAT3 -0.051 0.14 -10000 0 -0.28 141 141
axon guidance -0.04 0.051 0.1 53 -10000 0 53
MAPK3 -0.028 0.033 0.18 14 -10000 0 14
MAPK1 -0.028 0.032 0.18 12 -10000 0 12
CDC42/GDP 0.044 0.08 0.21 29 -0.26 11 40
NTF3 0.024 0.012 -10000 0 0 116 116
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.036 0.015 -10000 0 -0.13 2 2
PI3K 0 0.067 -10000 0 -0.16 75 75
FRS3 0.028 0.006 -10000 0 0 26 26
FAIM 0.028 0.008 -10000 0 0 39 39
GAB1 0.028 0.006 -10000 0 0 25 25
RASGRF1 -0.014 0.057 0.18 2 -0.17 9 11
SOS1 0.028 0.007 -10000 0 0 34 34
MCF2L -0.013 0.061 0.16 57 -10000 0 57
RGS19 0.026 0.009 -10000 0 0 61 61
CDC42 0.029 0.004 -10000 0 0 11 11
RAS family/GTP 0.044 0.079 0.27 6 -0.35 7 13
Rac1/GDP 0.042 0.08 0.21 27 -0.26 11 38
NGF (dimer)/TRKA/GRIT 0.02 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.24 -10000 0 -0.86 38 38
NGF (dimer)/TRKA/NEDD4-2 0.036 0.014 -10000 0 -0.13 1 1
MAP2K1 -0.029 0.068 0.35 2 -10000 0 2
NGFR 0.029 0.005 -10000 0 0 18 18
NGF (dimer)/TRKA/GIPC/GAIP -0.008 0.052 -10000 0 -0.18 38 38
RAS family/GTP/PI3K 0.013 0.067 -10000 0 -0.18 32 32
FRS2 family/SHP2/GRB2/SOS1 0.076 0.038 -10000 0 -10000 0 0
NRAS 0.014 0.015 -10000 0 0 300 300
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
PRKCI 0.014 0.015 -10000 0 0 288 288
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 28 28
PRKCZ 0.029 0.006 -10000 0 0 23 23
MAPKKK cascade 0.014 0.041 -10000 0 -0.36 2 2
RASA1 0.027 0.008 -10000 0 0 50 50
TRKA/c-Abl 0.041 0.018 -10000 0 -0.16 3 3
SQSTM1 0.029 0.006 -10000 0 0 20 20
BDNF (dimer)/TRKB/GIPC 0.045 0.059 -10000 0 -0.14 32 32
NGF (dimer)/TRKA/p62/Atypical PKCs 0.065 0.05 -10000 0 -10000 0 0
MATK 0.027 0.008 -10000 0 0 45 45
NEDD4L 0.027 0.008 -10000 0 0 47 47
RAS family/GDP -0.012 0.033 -10000 0 -0.19 12 12
NGF (dimer)/TRKA -0.007 0.054 0.15 1 -0.18 11 12
Rac1/GTP -0.012 0.043 -10000 0 -0.19 6 6
FRS2 family/SHP2/CRK family 0.069 0.044 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.016 0.11 0.37 12 -0.3 10 22
TBX21 -0.11 0.27 0.78 9 -0.76 4 13
B2M 0.028 0.007 -10000 0 -10000 0 0
TYK2 -0.012 0.051 0.18 9 -10000 0 9
IL12RB1 -0.013 0.051 0.18 9 -10000 0 9
GADD45B -0.08 0.26 0.75 10 -0.73 13 23
IL12RB2 -0.015 0.055 0.19 12 -10000 0 12
GADD45G -0.074 0.26 0.72 7 -0.87 15 22
natural killer cell activation -0.006 0.034 0.15 13 -10000 0 13
RELB 0.028 0.006 -10000 0 0 27 27
RELA 0.029 0.003 -10000 0 0 6 6
IL18 0.001 0.03 0.11 2 -10000 0 2
IL2RA 0.027 0.008 -10000 0 0 45 45
IFNG 0.027 0.008 -10000 0 0 46 46
STAT3 (dimer) -0.1 0.25 0.63 11 -0.65 27 38
HLA-DRB5 0.017 0.026 0.083 16 -0.046 50 66
FASLG -0.1 0.27 0.79 9 -0.76 4 13
NF kappa B2 p52/RelB -0.098 0.26 0.59 6 -0.6 29 35
CD4 0.02 0.027 0.083 20 -0.047 55 75
SOCS1 0.028 0.007 -10000 0 0 31 31
EntrezGene:6955 0 0.015 0.06 25 -0.053 3 28
CD3D 0.021 0.027 0.092 18 -0.053 47 65
CD3E 0.022 0.027 0.084 17 -0.046 60 77
CD3G 0.021 0.028 0.092 19 -0.05 54 73
IL12Rbeta2/JAK2 0.005 0.078 0.29 9 -0.18 1 10
CCL3 -0.1 0.29 0.86 17 -0.76 4 21
CCL4 -0.1 0.27 0.78 10 -0.61 22 32
HLA-A 0.029 0.005 -10000 0 -10000 0 0
IL18/IL18R 0.015 0.068 0.43 4 -10000 0 4
NOS2 -0.08 0.25 0.75 11 -0.6 8 19
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.11 0.36 14 -0.3 5 19
IL1R1 -0.36 0.53 0.76 5 -1 207 212
IL4 0.027 0.051 -10000 0 -0.19 11 11
JAK2 -0.013 0.052 0.18 9 -10000 0 9
EntrezGene:6957 0 0.013 0.052 22 -0.05 2 24
TCR/CD3/MHC I/CD8 -0.012 0.082 -10000 0 -0.46 4 4
RAB7A -0.063 0.24 0.71 5 -0.7 3 8
lysosomal transport -0.059 0.23 0.71 5 -0.66 3 8
FOS -0.14 0.43 0.74 21 -1.1 72 93
STAT4 (dimer) -0.058 0.26 0.71 11 -0.68 8 19
STAT5A (dimer) -0.1 0.25 0.6 5 -0.6 26 31
GZMA -0.11 0.28 0.85 8 -0.82 5 13
GZMB -0.099 0.28 0.84 13 -0.86 2 15
HLX 0.029 0.006 -10000 0 0 22 22
LCK -0.11 0.27 0.72 9 -0.63 24 33
TCR/CD3/MHC II/CD4 -0.023 0.15 0.34 23 -0.34 63 86
IL2/IL2R 0.049 0.062 -10000 0 -0.14 28 28
MAPK14 -0.074 0.26 0.73 9 -0.78 10 19
CCR5 -0.057 0.23 0.72 7 -0.66 3 10
IL1B -0.017 0.049 0.19 7 -10000 0 7
STAT6 -0.025 0.14 0.49 8 -0.7 8 16
STAT4 0.029 0.005 -10000 0 0 17 17
STAT3 0.028 0.007 -10000 0 0 38 38
STAT1 0.013 0.015 -10000 0 0 316 316
NFKB1 0.027 0.008 -10000 0 0 47 47
NFKB2 0.029 0.005 -10000 0 0 15 15
IL12B -0.015 0.055 0.19 11 -10000 0 11
CD8A 0.029 0.003 -10000 0 -10000 0 0
CD8B 0.029 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.016 0.11 0.29 10 -0.37 12 22
IL2RB 0.027 0.009 -10000 0 0 52 52
proteasomal ubiquitin-dependent protein catabolic process -0.052 0.25 0.71 11 -0.64 7 18
IL2RG 0.026 0.01 -10000 0 0 65 65
IL12 0.007 0.076 0.29 10 -0.17 1 11
STAT5A 0.028 0.007 -10000 0 0 35 35
CD247 0.023 0.027 0.085 19 -0.047 62 81
IL2 0.028 0.007 -10000 0 0 34 34
SPHK2 0.029 0.006 -10000 0 0 21 21
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.013 0.051 0.18 10 -10000 0 10
IL12/IL12R/TYK2/JAK2 -0.12 0.28 0.87 8 -0.68 19 27
MAP2K3 -0.085 0.27 0.73 9 -0.77 17 26
RIPK2 0.019 0.014 -10000 0 0 200 200
MAP2K6 -0.069 0.25 0.73 9 -0.75 11 20
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.02 0.027 0.094 22 -0.056 34 56
IL18RAP 0.002 0.035 0.11 4 -10000 0 4
IL12Rbeta1/TYK2 0.005 0.066 0.23 8 -10000 0 8
EOMES 0.008 0.074 -10000 0 -0.52 2 2
STAT1 (dimer) -0.051 0.22 0.64 11 -0.63 7 18
T cell proliferation -0.039 0.22 0.64 11 -0.54 7 18
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.002 0.035 0.11 4 -10000 0 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.086 0.17 -10000 0 -0.55 10 10
ATF2 -0.074 0.25 0.71 7 -0.74 9 16
Signaling events mediated by PTP1B

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
PDGFRB 0.029 0.005 -10000 0 0 15 15
Jak2/Leptin Receptor 0.01 0.11 -10000 0 -0.38 26 26
PTP1B/AKT1 0.001 0.088 -10000 0 -0.34 6 6
FYN 0.024 0.011 -10000 0 0 99 99
p210 bcr-abl/PTP1B -0.007 0.089 -10000 0 -0.35 6 6
EGFR 0.018 0.025 -10000 0 -0.046 1 1
EGF/EGFR 0.006 0.099 -10000 0 -0.3 15 15
CSF1 0.028 0.006 -10000 0 0 27 27
AKT1 0.014 0.027 -10000 0 -10000 0 0
INSR 0.017 0.022 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.005 0.091 -10000 0 -0.33 10 10
Insulin Receptor/Insulin 0.004 0.098 -10000 0 -0.33 6 6
HCK 0.027 0.008 -10000 0 0 47 47
CRK 0.028 0.007 -10000 0 0 37 37
TYK2 0 0.1 0.27 16 -0.35 6 22
EGF 0.017 0.026 -10000 0 -10000 0 0
YES1 0.028 0.008 -10000 0 0 40 40
CAV1 -0.031 0.1 0.22 1 -0.34 23 24
TXN 0.015 0.025 -10000 0 -0.059 1 1
PTP1B/IRS1/GRB2 -0.059 0.1 -10000 0 -0.31 23 23
cell migration 0.007 0.089 0.35 6 -10000 0 6
STAT3 0.019 0.022 -10000 0 -10000 0 0
PRLR 0.023 0.017 0.15 1 -10000 0 1
ITGA2B 0.011 0.027 -10000 0 -0.045 1 1
CSF1R 0.029 0.005 -10000 0 0 16 16
Prolactin Receptor/Prolactin 0.037 0.019 0.29 1 -10000 0 1
FGR 0.029 0.005 -10000 0 0 15 15
PTP1B/p130 Cas 0.001 0.092 -10000 0 -0.35 6 6
Crk/p130 Cas 0.006 0.1 -10000 0 -0.34 6 6
DOK1 -0.016 0.087 0.28 1 -0.35 8 9
JAK2 -0.003 0.11 -10000 0 -0.38 30 30
Jak2/Leptin Receptor/Leptin -0.002 0.12 0.28 2 -0.35 11 13
PIK3R1 0.021 0.013 -10000 0 0 161 161
PTPN1 -0.008 0.09 -10000 0 -0.36 6 6
LYN 0.027 0.009 -10000 0 0 52 52
CDH2 0.02 0.014 -10000 0 0 188 188
SRC 0.009 0.095 -10000 0 -0.47 16 16
ITGB3 0.014 0.024 -10000 0 -0.045 1 1
CAT1/PTP1B -0.02 0.12 0.27 8 -0.42 13 21
CAPN1 0.013 0.027 -10000 0 -0.05 1 1
CSK 0.029 0.006 -10000 0 0 22 22
PI3K -0.012 0.096 -10000 0 -0.34 6 6
mol:H2O2 0 0.003 0.02 1 -0.037 1 2
STAT3 (dimer) -0.002 0.11 0.32 2 -0.32 12 14
negative regulation of transcription -0.002 0.11 -10000 0 -0.37 30 30
FCGR2A 0.028 0.006 -10000 0 0 27 27
FER 0.015 0.026 -10000 0 -0.059 1 1
alphaIIb/beta3 Integrin 0.015 0.068 -10000 0 -0.17 67 67
BLK 0.024 0.011 -10000 0 0 102 102
Insulin Receptor/Insulin/Shc 0.036 0.058 -10000 0 -0.15 42 42
RHOA 0.013 0.027 -10000 0 -0.05 1 1
LEPR 0.029 0.007 -10000 0 -0.043 2 2
BCAR1 0.027 0.009 -10000 0 0 59 59
p210 bcr-abl/Grb2 0.029 0.006 -10000 0 0 20 20
mol:NADPH -0.001 0.002 -10000 0 -0.031 1 1
TRPV6 -0.031 0.13 0.22 5 -0.37 33 38
PRL 0.024 0.017 0.15 1 -10000 0 1
SOCS3 0 0.15 0.66 2 -1.1 9 11
SPRY2 -0.001 0.026 -10000 0 -0.065 1 1
Insulin Receptor/Insulin/IRS1 -0.076 0.1 -10000 0 -0.16 336 336
CSF1/CSF1R 0.005 0.1 -10000 0 -0.34 7 7
Ras protein signal transduction -0.009 0.087 0.55 12 -10000 0 12
IRS1 0.011 0.014 -10000 0 0 349 349
INS 0.015 0.026 -10000 0 -10000 0 0
LEP 0.016 0.024 -10000 0 -10000 0 0
STAT5B -0.009 0.11 -10000 0 -0.39 21 21
STAT5A -0.009 0.11 -10000 0 -0.37 22 22
GRB2 0.029 0.006 -10000 0 0 20 20
PDGFB-D/PDGFRB 0 0.095 -10000 0 -0.36 6 6
CSN2 0.007 0.077 0.63 1 -10000 0 1
PIK3CA 0.021 0.014 -10000 0 0 171 171
LAT 0.012 0.087 -10000 0 -0.47 14 14
YBX1 0.002 0.033 -10000 0 -10000 0 0
LCK 0.028 0.006 -10000 0 0 26 26
SHC1 0.029 0.006 -10000 0 0 20 20
NOX4 0.008 0.023 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 0.33 0.46 0.91 3 -0.92 3 6
HDAC7 -0.004 0.005 -10000 0 -0.078 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.025 0.29 0.7 50 -0.72 3 53
SMAD4 -0.022 0.02 -10000 0 -10000 0 0
ID2 0.33 0.46 0.89 15 -0.92 3 18
AP1 0.02 0.072 0.24 11 -0.16 60 71
ABCG2 0.28 0.46 0.88 19 -0.92 3 22
HIF1A 0.12 0.15 0.34 61 -10000 0 61
TFF3 0.029 0.37 0.9 11 -1 3 14
GATA2 0.032 0.029 0.21 12 -0.067 1 13
AKT1 0.15 0.18 0.41 96 -10000 0 96
response to hypoxia 0.082 0.16 0.34 119 -10000 0 119
MCL1 0.31 0.45 0.89 12 -0.92 3 15
NDRG1 0.2 0.42 0.89 8 -1 2 10
SERPINE1 0.24 0.44 0.89 12 -0.92 3 15
FECH 0.32 0.46 0.9 6 -0.92 3 9
FURIN 0.32 0.46 0.9 7 -0.92 3 10
NCOA2 0.027 0.008 -10000 0 -10000 0 0
EP300 0.23 0.3 0.69 109 -0.4 2 111
HMOX1 0.3 0.45 0.91 2 -0.92 3 5
BHLHE40 0.1 0.39 0.8 80 -0.91 3 83
BHLHE41 0.1 0.39 0.8 80 -0.91 3 83
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.19 0.41 88 -10000 0 88
ENG 0.12 0.18 0.47 2 -10000 0 2
JUN 0.03 0.017 0.14 11 -0.047 1 12
RORA 0.33 0.46 0.89 13 -0.92 3 16
ABCB1 -0.009 0.065 0.65 1 -10000 0 1
TFRC 0.13 0.39 0.89 5 -0.92 3 8
CXCR4 0.33 0.46 -10000 0 -0.92 3 3
TF 0.32 0.45 0.9 6 -0.92 3 9
CITED2 0.31 0.46 0.9 8 -0.97 3 11
HIF1A/ARNT -0.042 0.26 0.84 12 -1 3 15
LDHA 0.018 0.14 0.64 22 -0.71 3 25
ETS1 0.31 0.45 0.89 13 -0.92 3 16
PGK1 0.14 0.39 0.9 3 -0.92 3 6
NOS2 0.1 0.39 0.8 80 -0.91 3 83
ITGB2 0.32 0.46 0.89 15 -0.92 3 18
ALDOA 0.33 0.46 0.9 10 -0.92 3 13
Cbp/p300/CITED2 0.24 0.45 0.89 79 -0.98 3 82
FOS 0.027 0.021 0.14 13 -10000 0 13
HK2 0.34 0.46 0.9 8 -0.92 3 11
SP1 -0.03 0.023 0.23 4 -10000 0 4
GCK 0.29 0.34 0.87 72 -10000 0 72
HK1 0.33 0.46 0.91 3 -0.92 3 6
NPM1 0.33 0.46 0.89 13 -0.92 3 16
EGLN1 0.32 0.45 0.9 7 -0.92 3 10
CREB1 0.084 0.1 0.27 126 -10000 0 126
PGM1 0.28 0.44 0.9 6 -0.92 3 9
SMAD3 -0.022 0.02 -10000 0 -10000 0 0
EDN1 0.19 0.26 0.84 28 -1.1 1 29
IGFBP1 0.33 0.46 0.9 10 -0.92 3 13
VEGFA 0.25 0.4 0.84 79 -0.67 1 80
HIF1A/JAB1 0.075 0.11 0.27 11 -10000 0 11
CP 0.062 0.35 0.92 4 -1 3 7
CXCL12 0.28 0.46 0.9 7 -0.94 3 10
COPS5 0.024 0.013 -10000 0 -0.03 11 11
SMAD3/SMAD4 0.038 0.017 -10000 0 -0.11 3 3
BNIP3 0.3 0.45 0.89 10 -0.92 3 13
EGLN3 0.28 0.45 0.9 4 -0.95 3 7
CA9 0.26 0.44 0.9 5 -0.92 3 8
TERT 0.28 0.45 0.9 5 -0.92 3 8
ENO1 0.33 0.46 0.89 13 -0.92 3 16
PFKL 0.32 0.46 0.89 18 -0.92 3 21
NCOA1 0.026 0.014 -10000 0 -0.03 30 30
ADM 0.26 0.44 0.92 3 -0.92 3 6
ARNT 0.12 0.15 0.34 71 -10000 0 71
HNF4A 0.027 0.007 -10000 0 -10000 0 0
ADFP 0.1 0.39 0.8 80 -0.91 3 83
SLC2A1 0.25 0.4 0.82 77 -0.67 1 78
LEP 0.32 0.45 0.89 14 -0.92 3 17
HIF1A/ARNT/Cbp/p300 0.018 0.29 0.72 49 -0.72 4 53
EPO 0.26 0.36 0.79 52 -0.71 2 54
CREBBP 0.24 0.29 0.71 103 -10000 0 103
HIF1A/ARNT/Cbp/p300/HDAC7 -0.001 0.26 0.68 35 -0.7 4 39
PFKFB3 0.3 0.46 0.9 4 -0.97 3 7
NT5E 0.24 0.44 0.89 11 -1 3 14
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.035 0.017 -10000 0 -0.13 3 3
cell-cell adhesion 0.063 0.031 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.06 0.065 -10000 0 -0.14 26 26
ITSN1 0.029 0.004 -10000 0 0 9 9
PIK3CA 0.021 0.014 -10000 0 0 171 171
SHC1 0.029 0.006 -10000 0 0 20 20
Ephrin B1/EPHB3 0.032 0.018 -10000 0 -0.13 1 1
Ephrin B1/EPHB1 0.037 0.013 -10000 0 -0.13 1 1
HRAS/GDP -0.069 0.069 0.12 4 -0.22 32 36
Ephrin B/EPHB1/GRB7 0.062 0.061 -10000 0 -0.14 23 23
Endophilin/SYNJ1 -0.038 0.055 0.18 17 -10000 0 17
KRAS 0.024 0.011 -10000 0 0 99 99
Ephrin B/EPHB1/Src 0.063 0.06 -10000 0 -0.14 21 21
endothelial cell migration 0.007 0.067 -10000 0 -0.14 80 80
GRB2 0.029 0.006 -10000 0 0 20 20
GRB7 0.027 0.008 -10000 0 0 42 42
PAK1 -0.039 0.065 0.3 3 -10000 0 3
HRAS 0.028 0.006 -10000 0 0 28 28
RRAS -0.036 0.057 0.18 17 -0.22 3 20
DNM1 0.029 0.005 -10000 0 0 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.029 0.064 0.16 36 -10000 0 36
lamellipodium assembly -0.063 0.031 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.004 0.05 -10000 0 -0.23 6 6
PIK3R1 0.021 0.013 -10000 0 0 161 161
EPHB2 0.029 0.006 -10000 0 0 21 21
EPHB3 0.024 0.012 -10000 0 0 105 105
EPHB1 0.028 0.007 -10000 0 0 35 35
EPHB4 0.029 0.005 -10000 0 0 19 19
mol:GDP -0.045 0.078 0.22 5 -0.24 19 24
Ephrin B/EPHB2 0.054 0.05 -10000 0 -0.13 23 23
Ephrin B/EPHB3 0.044 0.051 -10000 0 -0.13 21 21
JNK cascade -0.014 0.097 0.33 26 -10000 0 26
Ephrin B/EPHB1 0.053 0.05 -10000 0 -0.13 21 21
RAP1/GDP -0.058 0.089 0.23 7 -0.27 9 16
EFNB2 0.027 0.009 -10000 0 0 58 58
EFNB3 0.028 0.007 -10000 0 0 31 31
EFNB1 0.029 0.004 -10000 0 0 8 8
Ephrin B2/EPHB1-2 0.042 0.039 -10000 0 -0.13 18 18
RAP1B 0.029 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CDC42/GTP -0.049 0.064 0.14 31 -10000 0 31
Rap1/GTP -0.068 0.039 0.067 12 -10000 0 12
axon guidance 0.035 0.017 -10000 0 -0.13 3 3
MAPK3 -0.026 0.05 0.16 1 -0.24 5 6
MAPK1 -0.02 0.047 0.16 6 -0.22 1 7
Rac1/GDP -0.054 0.086 0.24 6 -0.26 11 17
actin cytoskeleton reorganization -0.035 0.049 -10000 0 -0.19 3 3
CDC42/GDP -0.056 0.087 0.23 7 -0.27 9 16
PI3K 0.022 0.078 -10000 0 -0.14 80 80
EFNA5 0.027 0.008 -10000 0 0 42 42
Ephrin B2/EPHB4 0.03 0.034 -10000 0 -0.13 20 20
Ephrin B/EPHB2/Intersectin/N-WASP 0.002 0.055 -10000 0 -0.25 7 7
CDC42 0.029 0.004 -10000 0 0 11 11
RAS family/GTP -0.028 0.041 0.057 7 -10000 0 7
PTK2 0.13 0.26 0.56 149 -10000 0 149
MAP4K4 -0.014 0.098 0.33 26 -10000 0 26
SRC 0.028 0.007 -10000 0 0 31 31
KALRN 0.029 0.006 -10000 0 0 23 23
Intersectin/N-WASP 0.042 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.044 0.085 0.25 21 -10000 0 21
MAP2K1 -0.017 0.048 0.16 5 -0.22 4 9
WASL 0.029 0.006 -10000 0 0 22 22
Ephrin B1/EPHB1-2/NCK1 0.074 0.033 -10000 0 -0.14 1 1
cell migration -0.022 0.073 0.26 4 -0.27 6 10
NRAS 0.014 0.015 -10000 0 0 300 300
SYNJ1 -0.039 0.056 0.18 17 -10000 0 17
PXN 0.029 0.005 -10000 0 0 14 14
TF -0.044 0.053 0.16 17 -10000 0 17
HRAS/GTP -0.051 0.053 0.12 41 -10000 0 41
Ephrin B1/EPHB1-2 0.05 0.021 -10000 0 -0.13 1 1
cell adhesion mediated by integrin 0.019 0.061 0.16 2 -0.21 15 17
RAC1 0.028 0.006 -10000 0 0 28 28
mol:GTP -0.043 0.059 0.14 45 -10000 0 45
RAC1-CDC42/GTP -0.062 0.04 -10000 0 -10000 0 0
RASA1 0.027 0.008 -10000 0 0 50 50
RAC1-CDC42/GDP -0.06 0.088 0.23 7 -0.27 9 16
ruffle organization -0.049 0.078 0.27 10 -10000 0 10
NCK1 0.026 0.009 -10000 0 0 63 63
receptor internalization -0.046 0.053 0.16 18 -0.22 1 19
Ephrin B/EPHB2/KALRN 0.065 0.06 -10000 0 -0.14 23 23
ROCK1 0.006 0.082 0.17 107 -10000 0 107
RAS family/GDP -0.038 0.05 -10000 0 -0.2 9 9
Rac1/GTP -0.065 0.032 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0 0.053 -10000 0 -0.21 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.044 0.044 -9999 0 -0.16 19 19
E-cadherin/beta catenin 0.036 0.028 -9999 0 -0.16 8 8
CTNNB1 0.029 0.003 -9999 0 0 7 7
JUP 0.027 0.008 -9999 0 0 43 43
CDH1 0.026 0.01 -9999 0 0 73 73
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.006 0.079 0.38 3 -0.63 1 4
epithelial cell differentiation -0.021 0.067 0.24 1 -0.63 1 2
ITCH -0.007 0.04 0.086 18 -0.12 1 19
WWP1 -0.005 0.092 0.74 3 -1.1 1 4
FYN 0.024 0.011 -10000 0 0 99 99
EGFR 0.027 0.009 -10000 0 0 55 55
PRL 0.028 0.008 -10000 0 0 39 39
neuron projection morphogenesis -0.032 0.082 0.3 7 -0.51 1 8
PTPRZ1 0.028 0.006 -10000 0 0 27 27
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.026 0.084 0.32 2 -0.54 1 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.02 0.051 0.36 2 -0.57 1 3
ADAM17 -0.005 0.038 0.085 18 -0.12 1 19
ErbB4/ErbB4 -0.007 0.08 0.76 2 -0.68 1 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.093 0.41 1 -0.4 4 5
NCOR1 0.027 0.008 -10000 0 0 42 42
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.024 0.076 0.29 1 -0.56 1 2
GRIN2B -0.029 0.073 0.26 3 -0.54 1 4
ErbB4/ErbB2/betacellulin -0.009 0.074 0.36 3 -0.56 1 4
STAT1 0.013 0.015 -10000 0 0 316 316
HBEGF 0.029 0.004 -10000 0 0 11 11
PRLR 0.027 0.008 -10000 0 0 50 50
E4ICDs/ETO2 0.003 0.075 0.36 2 -0.63 1 3
axon guidance -0.001 0.061 0.42 2 -0.69 1 3
NEDD4 -0.01 0.04 0.087 15 -0.12 1 16
Prolactin receptor/Prolactin receptor/Prolactin 0.038 0.016 -10000 0 -10000 0 0
CBFA2T3 0.026 0.009 -10000 0 0 64 64
ErbB4/ErbB2/HBEGF -0.008 0.076 0.36 3 -0.56 1 4
MAPK3 -0.023 0.088 0.29 10 -0.52 1 11
STAT1 (dimer) -0.001 0.05 -10000 0 -0.47 1 1
MAPK1 -0.021 0.084 0.3 9 -0.52 1 10
JAK2 0.027 0.008 -10000 0 0 46 46
ErbB4/ErbB2/neuregulin 1 beta -0.026 0.05 0.31 2 -0.56 1 3
NRG1 0.005 0.074 0.18 78 -10000 0 78
NRG3 0.007 0.013 -10000 0 0 422 422
NRG2 0.029 0.003 -10000 0 0 7 7
NRG4 0.027 0.008 -10000 0 0 46 46
heart development -0.001 0.061 0.42 2 -0.69 1 3
neural crest cell migration -0.026 0.05 0.31 2 -0.55 1 3
ERBB2 0.008 0.078 0.18 89 -10000 0 89
WWOX/E4ICDs 0.004 0.074 0.36 2 -0.63 1 3
SHC1 0.029 0.006 -10000 0 0 20 20
ErbB4/EGFR/neuregulin 4 0.003 0.089 0.35 3 -0.61 1 4
apoptosis 0.18 0.17 0.38 93 -0.43 1 94
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.006 0.079 0.38 3 -0.63 1 4
ErbB4/ErbB2/epiregulin -0.008 0.074 0.36 3 -0.56 1 4
ErbB4/ErbB4/betacellulin/betacellulin 0.005 0.077 0.38 3 -0.63 1 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.03 0.089 0.38 1 -0.58 1 2
MDM2 -0.013 0.078 0.39 5 -0.63 1 6
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.008 0.064 0.32 2 -0.51 1 3
STAT5A -0.007 0.062 0.38 3 -0.68 1 4
ErbB4/EGFR/neuregulin 1 beta -0.019 0.074 0.32 2 -0.56 1 3
DLG4 0.029 0.006 -10000 0 0 23 23
GRB2/SHC 0.041 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.002 0.069 0.26 1 -0.6 1 2
STAT5A (dimer) 0.013 0.079 0.35 1 -0.69 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.014 0.072 0.38 3 -0.68 1 4
LRIG1 0.028 0.007 -10000 0 0 32 32
EREG 0.028 0.008 -10000 0 0 40 40
BTC 0.027 0.008 -10000 0 0 47 47
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.06 0.42 2 -0.7 1 3
ERBB4 -0.007 0.08 0.76 2 -0.69 1 3
STAT5B 0.028 0.007 -10000 0 0 34 34
YAP1 0.014 0.05 -10000 0 -0.48 4 4
GRB2 0.029 0.006 -10000 0 0 20 20
ErbB4/ErbB2/neuregulin 4 -0.009 0.078 0.36 3 -0.56 1 4
glial cell differentiation -0.002 0.068 0.59 1 -0.26 1 2
WWOX 0.026 0.01 -10000 0 0 67 67
cell proliferation -0.01 0.078 0.32 3 -0.57 1 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.033 -10000 0 -0.16 11 11
CRKL -0.007 0.11 0.23 1 -0.45 23 24
mol:PIP3 0.013 0.075 -10000 0 -0.83 4 4
AKT1 -0.004 0.071 -10000 0 -0.7 4 4
PTK2B 0.024 0.011 -10000 0 0 99 99
RAPGEF1 -0.015 0.1 -10000 0 -0.43 22 22
RANBP10 0.027 0.009 -10000 0 0 60 60
PIK3CA 0.021 0.014 -10000 0 0 171 171
HGF/MET/SHIP2 0.046 0.036 -10000 0 -0.14 11 11
MAP3K5 -0.008 0.11 0.25 1 -0.45 22 23
HGF/MET/CIN85/CBL/ENDOPHILINS 0.068 0.048 -10000 0 -0.14 12 12
AP1 -0.021 0.071 0.14 34 -0.16 46 80
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.029 0.006 -10000 0 0 20 20
apoptosis -0.068 0.27 -10000 0 -0.71 82 82
STAT3 (dimer) -0.001 0.078 0.17 11 -0.25 19 30
GAB1/CRKL/SHP2/PI3K -0.009 0.11 -10000 0 -0.44 21 21
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.009 0.11 0.28 3 -0.44 21 24
PTPN11 0.029 0.004 -10000 0 0 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.028 0.007 -10000 0 0 31 31
PTEN 0.028 0.007 -10000 0 0 31 31
ELK1 0.033 0.15 0.42 48 -0.26 1 49
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.006 0.05 0.14 6 -0.19 10 16
PAK1 0.002 0.087 0.38 1 -0.68 4 5
HGF/MET/RANBP10 0.042 0.038 -10000 0 -0.14 12 12
HRAS 0.004 0.1 -10000 0 -0.47 22 22
DOCK1 -0.013 0.11 0.34 2 -0.44 22 24
GAB1 0.002 0.11 -10000 0 -0.46 23 23
CRK -0.003 0.11 0.28 3 -0.45 22 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.095 -10000 0 -0.43 17 17
JUN 0.028 0.007 -10000 0 0 34 34
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0 0.033 -10000 0 -0.18 14 14
PIK3R1 0.021 0.013 -10000 0 0 161 161
cell morphogenesis 0.001 0.13 0.29 17 -0.37 16 33
GRB2/SHC 0.041 0.052 0.2 3 -0.18 13 16
FOS 0.024 0.012 -10000 0 0 105 105
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.033 0.15 0.41 48 -0.26 1 49
HGF/MET/MUC20 0.03 0.028 -10000 0 -0.13 12 12
cell migration 0.04 0.051 0.19 3 -0.18 13 16
GRB2 0.029 0.006 -10000 0 0 20 20
CBL 0.029 0.005 -10000 0 0 15 15
MET/RANBP10 0.03 0.034 -10000 0 -0.16 12 12
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.005 0.06 0.2 1 -0.26 8 9
MET/MUC20 0.015 0.025 -10000 0 -0.15 12 12
RAP1B -0.018 0.1 0.25 1 -0.43 20 21
RAP1A -0.023 0.098 0.33 1 -0.42 21 22
HGF/MET/RANBP9 0.044 0.036 -10000 0 -0.14 11 11
RAF1 -0.002 0.1 -10000 0 -0.46 21 21
STAT3 -0.002 0.077 0.17 11 -0.26 19 30
cell proliferation -0.007 0.095 0.28 8 -0.34 14 22
RPS6KB1 0.019 0.047 -10000 0 -0.24 8 8
MAPK3 0.025 0.16 0.65 27 -10000 0 27
MAPK1 0.041 0.19 0.67 39 -10000 0 39
RANBP9 0.028 0.008 -10000 0 0 39 39
MAPK8 -0.01 0.1 0.25 1 -0.42 19 20
SRC -0.021 0.054 0.18 1 -0.26 8 9
PI3K 0.008 0.066 0.21 1 -0.18 17 18
MET/Glomulin 0.028 0.034 0.12 1 -0.11 1 2
SOS1 0.028 0.007 -10000 0 0 34 34
MAP2K1 -0.01 0.095 -10000 0 -0.43 21 21
MET 0.025 0.011 -10000 0 0 87 87
MAP4K1 -0.001 0.12 0.27 1 -0.47 22 23
PTK2 0.021 0.014 -10000 0 0 163 163
MAP2K2 -0.021 0.098 0.27 1 -0.45 20 21
BAD -0.013 0.069 -10000 0 -0.68 4 4
MAP2K4 -0.014 0.1 0.23 1 -0.41 22 23
SHP2/GRB2/SOS1/GAB1 0.015 0.11 -10000 0 -0.38 26 26
INPPL1 0.029 0.006 -10000 0 0 20 20
PXN 0.029 0.005 -10000 0 0 14 14
SH3KBP1 0.029 0.005 -10000 0 0 17 17
HGS -0.009 0.042 0.18 1 -0.18 14 15
PLCgamma1/PKC 0.021 0.005 -10000 0 -10000 0 0
HGF 0.029 0.005 -10000 0 0 17 17
RASA1 0.027 0.008 -10000 0 0 50 50
NCK1 0.026 0.009 -10000 0 0 63 63
PTPRJ 0.029 0.004 -10000 0 0 8 8
NCK/PLCgamma1 0.039 0.05 0.2 3 -0.18 14 17
PDPK1 0.001 0.067 -10000 0 -0.73 4 4
HGF/MET/SHIP 0.03 0.028 -10000 0 -0.13 12 12
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.04 0.048 -10000 0 -0.15 26 26
fibroblast growth factor receptor signaling pathway 0.04 0.047 -10000 0 -0.15 26 26
LAMA1 0.024 0.012 -10000 0 0 110 110
PRNP 0.027 0.008 -10000 0 0 42 42
GPC1/SLIT2 0.022 0.058 -10000 0 -0.16 48 48
SMAD2 -0.043 0.026 0.17 6 -10000 0 6
GPC1/PrPc/Cu2+ 0.034 0.024 -10000 0 -0.13 9 9
GPC1/Laminin alpha1 0.034 0.018 -10000 0 -10000 0 0
TDGF1 0.029 0.003 -10000 0 0 6 6
CRIPTO/GPC1 0.042 0.009 -10000 0 -10000 0 0
APP/GPC1 0.038 0.025 -10000 0 -0.16 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.035 0.013 -10000 0 -10000 0 0
FLT1 0.028 0.006 -10000 0 0 28 28
GPC1/TGFB/TGFBR1/TGFBR2 0.054 0.027 -10000 0 -0.14 7 7
SERPINC1 0.029 0.004 -10000 0 0 12 12
FYN -0.032 0.016 -10000 0 -10000 0 0
FGR -0.037 0.01 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.028 0.076 0.24 8 -0.27 12 20
SLIT2 0.025 0.011 -10000 0 0 90 90
GPC1/NRG 0.037 0.017 -10000 0 -10000 0 0
NRG1 0.026 0.01 -10000 0 0 79 79
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.024 -10000 0 -10000 0 0
LYN -0.035 0.014 -10000 0 -10000 0 0
mol:Spermine -0.016 0.003 -10000 0 -10000 0 0
cell growth 0.04 0.047 -10000 0 -0.15 26 26
BMP signaling pathway -0.029 0.006 0 20 -10000 0 20
SRC -0.036 0.012 -10000 0 -10000 0 0
TGFBR1 0.029 0.005 -10000 0 0 16 16
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.016 0.015 -10000 0 0 248 248
GPC1 0.029 0.006 -10000 0 0 20 20
TGFBR1 (dimer) 0.029 0.005 -10000 0 0 16 16
VEGFA 0.026 0.01 -10000 0 0 70 70
BLK -0.031 0.016 -10000 0 -10000 0 0
HCK -0.035 0.013 -10000 0 -10000 0 0
FGF2 0.027 0.008 -10000 0 0 44 44
FGFR1 0.026 0.01 -10000 0 0 75 75
VEGFR1 homodimer 0.028 0.006 -10000 0 0 28 28
TGFBR2 0.029 0.005 -10000 0 0 14 14
cell death 0.038 0.025 -10000 0 -0.16 7 7
ATIII/GPC1 0.042 0.01 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.042 0.1 -10000 0 -0.16 227 227
LCK -0.037 0.011 -10000 0 -10000 0 0
neuron differentiation 0.036 0.017 -10000 0 -10000 0 0
PrPc/Cu2+ 0.018 0.022 -10000 0 -0.15 9 9
APP 0.028 0.007 -10000 0 0 29 29
TGFBR2 (dimer) 0.029 0.005 -10000 0 0 14 14
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 -0.031 0.11 0.24 3 -0.37 28 31
IKBKB 0.006 0.08 0.28 6 -0.32 6 12
AKT1 -0.001 0.099 0.27 33 -0.23 4 37
IKBKG 0.004 0.065 0.28 2 -0.26 7 9
CALM1 -0.01 0.065 -10000 0 -0.29 8 8
PIK3CA 0.021 0.014 -10000 0 0 171 171
MAP3K1 -0.027 0.14 0.36 1 -0.47 33 34
MAP3K7 0.028 0.007 -10000 0 0 30 30
mol:Ca2+ -0.004 0.07 0.2 1 -0.28 12 13
DOK1 0.029 0.004 -10000 0 0 10 10
AP-1 -0.022 0.074 0.25 3 -0.23 16 19
LYN 0.027 0.009 -10000 0 0 52 52
BLNK 0.028 0.007 -10000 0 0 31 31
SHC1 0.029 0.006 -10000 0 0 20 20
BCR complex 0.04 0.013 -10000 0 -10000 0 0
CD22 -0.037 0.082 0.23 2 -0.31 22 24
CAMK2G -0.019 0.069 -10000 0 -0.28 10 10
CSNK2A1 0.028 0.008 -10000 0 0 39 39
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.063 0.037 -10000 0 -0.23 2 2
GO:0007205 -0.005 0.071 0.2 1 -0.29 12 13
SYK 0.028 0.006 -10000 0 0 24 24
ELK1 -0.009 0.078 0.28 5 -0.28 12 17
NFATC1 -0.029 0.091 0.23 5 -0.37 15 20
B-cell antigen/BCR complex 0.04 0.013 -10000 0 -10000 0 0
PAG1/CSK 0.039 0.014 -10000 0 -10000 0 0
NFKBIB 0.009 0.048 0.16 2 -0.13 19 21
HRAS -0.017 0.071 0.2 1 -0.28 15 16
NFKBIA 0.01 0.047 0.16 2 -0.12 45 47
NF-kappa-B/RelA/I kappa B beta 0.013 0.043 0.13 6 -0.1 44 50
RasGAP/Csk 0.068 0.053 -10000 0 -0.14 4 4
mol:GDP -0.005 0.07 0.19 1 -0.28 12 13
PTEN 0.028 0.007 -10000 0 0 31 31
CD79B 0.029 0.005 -10000 0 0 14 14
NF-kappa-B/RelA/I kappa B alpha 0.013 0.042 0.13 6 -0.099 44 50
GRB2 0.029 0.006 -10000 0 0 20 20
PI3K/BCAP/CD19 -0.07 0.15 0.3 1 -0.43 29 30
PIK3R1 0.021 0.013 -10000 0 0 161 161
mol:IP3 -0.004 0.071 0.2 1 -0.29 12 13
CSK 0.029 0.006 -10000 0 0 22 22
FOS -0.016 0.085 0.25 6 -0.28 16 22
CHUK 0.001 0.082 0.23 5 -0.28 23 28
IBTK 0.028 0.007 -10000 0 0 30 30
CARD11/BCL10/MALT1/TAK1 0.01 0.083 -10000 0 -0.28 8 8
PTPN6 -0.036 0.085 0.21 4 -0.3 22 26
RELA 0.029 0.003 -10000 0 0 6 6
BCL2A1 0.007 0.031 0.099 6 -0.085 11 17
VAV2 -0.018 0.096 0.25 2 -0.36 21 23
ubiquitin-dependent protein catabolic process 0.009 0.048 0.14 3 -0.12 49 52
BTK 0.018 0.045 -10000 0 -0.98 1 1
CD19 -0.014 0.079 0.23 2 -0.31 17 19
MAP4K1 0.026 0.01 -10000 0 0 68 68
CD72 0.029 0.005 -10000 0 0 14 14
PAG1 0.027 0.008 -10000 0 0 45 45
MAPK14 -0.027 0.13 0.3 4 -0.42 29 33
SH3BP5 0.029 0.004 -10000 0 0 12 12
PIK3AP1 -0.008 0.071 0.28 2 -0.29 11 13
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.001 0.089 -10000 0 -0.36 20 20
RAF1 -0.024 0.068 0.24 2 -0.28 15 17
RasGAP/p62DOK/SHIP 0.057 0.046 -10000 0 -0.14 6 6
CD79A 0.028 0.007 -10000 0 0 36 36
re-entry into mitotic cell cycle -0.022 0.073 0.23 4 -0.22 17 21
RASA1 0.027 0.008 -10000 0 0 50 50
MAPK3 -0.039 0.063 0.25 3 -0.27 10 13
MAPK1 -0.033 0.066 0.25 4 -0.27 10 14
CD72/SHP1 -0.022 0.11 0.26 22 -0.32 16 38
NFKB1 0.027 0.008 -10000 0 0 47 47
MAPK8 -0.029 0.12 0.29 2 -0.43 27 29
actin cytoskeleton organization -0.022 0.093 0.25 6 -0.34 18 24
NF-kappa-B/RelA 0.022 0.088 0.26 3 -0.22 31 34
Calcineurin 0.008 0.083 -10000 0 -0.27 10 10
PI3K -0.053 0.081 -10000 0 -0.3 16 16
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.065 0.22 1 -0.3 9 10
SOS1 0.028 0.007 -10000 0 0 34 34
Bam32/HPK1 -0.02 0.21 -10000 0 -0.68 44 44
DAPP1 -0.038 0.23 -10000 0 -0.77 43 43
cytokine secretion -0.027 0.086 0.22 5 -0.35 15 20
mol:DAG -0.004 0.071 0.2 1 -0.29 12 13
PLCG2 0.026 0.01 -10000 0 0 65 65
MAP2K1 -0.03 0.066 0.25 2 -0.27 14 16
B-cell antigen/BCR complex/FcgammaRIIB 0.05 0.024 -10000 0 -0.14 1 1
mol:PI-3-4-5-P3 -0.011 0.11 0.25 34 -0.26 7 41
ETS1 -0.02 0.072 0.23 2 -0.27 10 12
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.061 0.062 -10000 0 -0.15 24 24
B-cell antigen/BCR complex/LYN 0.006 0.083 0.21 1 -0.31 19 20
MALT1 0.026 0.01 -10000 0 0 75 75
TRAF6 0.029 0.004 -10000 0 0 12 12
RAC1 -0.023 0.093 0.24 4 -0.36 17 21
B-cell antigen/BCR complex/LYN/SYK -0.003 0.12 0.3 7 -0.3 13 20
CARD11 -0.013 0.07 0.19 2 -0.28 12 14
FCGR2B 0.027 0.008 -10000 0 0 47 47
PPP3CA 0.027 0.008 -10000 0 0 45 45
BCL10 0.029 0.004 -10000 0 0 10 10
IKK complex 0.011 0.045 0.15 21 -0.12 4 25
PTPRC 0.024 0.011 -10000 0 0 102 102
PDPK1 -0.007 0.094 0.23 40 -0.21 4 44
PPP3CB 0.029 0.005 -10000 0 0 15 15
PPP3CC 0.024 0.011 -10000 0 0 102 102
POU2F2 0.007 0.031 0.15 4 -0.082 12 16
ErbB2/ErbB3 signaling events

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
USP8 -0.021 0.026 0.18 8 -10000 0 8
RAS family/GTP 0.029 0.11 0.4 27 -0.26 1 28
NFATC4 -0.023 0.089 0.24 31 -10000 0 31
ERBB2IP 0.012 0.028 -10000 0 -0.048 7 7
HSP90 (dimer) 0.029 0.006 -10000 0 0 21 21
mammary gland morphogenesis -0.02 0.1 0.32 23 -10000 0 23
JUN 0.033 0.14 0.44 44 -10000 0 44
HRAS 0.023 0.02 0.065 4 -0.031 59 63
DOCK7 -0.022 0.09 0.26 21 -10000 0 21
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.015 0.079 0.19 30 -10000 0 30
AKT1 -0.015 0.009 0.013 37 -10000 0 37
BAD -0.025 0.007 -10000 0 -10000 0 0
MAPK10 -0.016 0.076 0.2 30 -10000 0 30
mol:GTP 0.001 0.004 0.018 19 -10000 0 19
ErbB2/ErbB3/neuregulin 1 beta -0.02 0.11 0.34 23 -10000 0 23
RAF1 0.092 0.17 0.43 66 -10000 0 66
ErbB2/ErbB3/neuregulin 2 -0.019 0.065 0.16 35 -10000 0 35
STAT3 -0.028 0.23 -10000 0 -0.87 38 38
cell migration -0.013 0.078 0.24 20 -10000 0 20
mol:PI-3-4-5-P3 -0.001 0.002 0.013 2 -10000 0 2
cell proliferation 0.067 0.25 0.7 45 -0.61 5 50
FOS 0.045 0.27 0.67 53 -0.43 27 80
NRAS 0.012 0.017 -10000 0 -0.031 21 21
mol:Ca2+ -0.02 0.1 0.32 23 -10000 0 23
MAPK3 0.071 0.23 0.66 42 -0.54 4 46
MAPK1 0.066 0.23 0.64 44 -0.64 5 49
JAK2 -0.023 0.09 0.26 21 -10000 0 21
NF2 -0.001 0.064 -10000 0 -0.64 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.062 0.19 12 -0.19 26 38
NRG1 -0.006 0.03 0.076 6 -10000 0 6
GRB2/SOS1 0.041 0.014 -10000 0 -10000 0 0
MAPK8 -0.018 0.1 0.34 12 -0.24 16 28
MAPK9 -0.015 0.077 0.2 32 -10000 0 32
ERBB2 -0.027 0.02 0.26 1 -10000 0 1
ERBB3 -0.007 0.03 0.076 6 -10000 0 6
SHC1 0.024 0.019 0.064 6 -0.03 56 62
RAC1 0.028 0.006 -10000 0 0 28 28
apoptosis 0.017 0.01 -10000 0 -10000 0 0
STAT3 (dimer) -0.026 0.22 -10000 0 -0.85 38 38
RNF41 -0.027 0.026 0.15 9 -10000 0 9
FRAP1 -0.012 0.005 0.003 45 -10000 0 45
RAC1-CDC42/GTP -0.035 0.058 0.17 2 -0.16 1 3
ErbB2/ErbB2/HSP90 (dimer) -0.031 0.025 0.2 1 -0.15 2 3
CHRNA1 0.077 0.22 0.66 45 -0.43 1 46
myelination -0.016 0.098 0.25 40 -10000 0 40
PPP3CB -0.023 0.088 0.25 22 -10000 0 22
KRAS 0.02 0.02 0.063 3 -0.031 47 50
RAC1-CDC42/GDP 0.019 0.082 0.21 3 -0.2 7 10
NRG2 0.029 0.003 -10000 0 0 7 7
mol:GDP 0 0.062 0.19 12 -0.19 26 38
SOS1 0.023 0.019 0.061 2 -0.03 53 55
MAP2K2 0.062 0.17 0.47 48 -10000 0 48
SRC 0.028 0.007 -10000 0 0 31 31
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.026 0.088 0.25 20 -10000 0 20
MAP2K1 0.084 0.22 0.64 43 -0.61 6 49
heart morphogenesis -0.02 0.1 0.32 23 -10000 0 23
RAS family/GDP 0.05 0.091 0.33 17 -0.24 2 19
GRB2 0.024 0.019 0.06 3 -0.03 56 59
PRKACA 0.005 0.065 -10000 0 -0.67 5 5
CHRNE 0.012 0.057 0.27 15 -10000 0 15
HSP90AA1 0.029 0.006 -10000 0 0 21 21
activation of caspase activity 0.015 0.009 -10000 0 -0.013 37 37
nervous system development -0.02 0.1 0.32 23 -10000 0 23
CDC42 0.029 0.004 -10000 0 0 11 11
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.02 0.03 0.16 2 -0.24 1 3
EPHB2 0.029 0.006 -10000 0 0 21 21
Syndecan-2/TACI -0.025 0.024 0.16 3 -10000 0 3
LAMA1 0.024 0.012 -10000 0 0 110 110
Syndecan-2/alpha2 ITGB1 0.036 0.073 -10000 0 -0.14 57 57
HRAS 0.028 0.006 -10000 0 0 28 28
Syndecan-2/CASK -0.015 0.017 -10000 0 -0.12 13 13
ITGA5 0.029 0.006 -10000 0 0 20 20
BAX -0.027 0.027 -10000 0 -10000 0 0
EPB41 0.028 0.007 -10000 0 0 37 37
positive regulation of cell-cell adhesion -0.023 0.018 -10000 0 -10000 0 0
LAMA3 0.026 0.01 -10000 0 0 74 74
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.027 0.008 -10000 0 0 45 45
Syndecan-2/MMP2 -0.033 0.044 0.16 4 -0.24 6 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.037 -10000 0 -0.16 17 17
dendrite morphogenesis -0.025 0.025 0.16 4 -10000 0 4
Syndecan-2/GM-CSF -0.025 0.024 0.16 4 -10000 0 4
determination of left/right symmetry -0.015 0.006 -10000 0 -10000 0 0
Syndecan-2/PKC delta -0.026 0.025 0.16 4 -10000 0 4
GNB2L1 0.029 0.005 -10000 0 0 15 15
MAPK3 -0.014 0.069 0.18 58 -0.22 3 61
MAPK1 -0.012 0.067 0.18 57 -10000 0 57
Syndecan-2/RACK1 0.027 0.031 0.15 3 -0.12 13 16
NF1 0.026 0.009 -10000 0 0 62 62
FGFR/FGF/Syndecan-2 -0.015 0.006 -10000 0 -10000 0 0
ITGA2 0.027 0.009 -10000 0 0 60 60
MAPK8 -0.022 0.024 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.054 0.062 -10000 0 -0.14 26 26
Syndecan-2/Kininogen -0.022 0.025 0.16 3 -10000 0 3
ITGB1 0.029 0.006 -10000 0 0 22 22
SRC -0.019 0.067 0.17 55 -10000 0 55
Syndecan-2/CASK/Protein 4.1 -0.022 0.017 -10000 0 -10000 0 0
extracellular matrix organization -0.038 0.047 0.16 4 -0.23 5 9
actin cytoskeleton reorganization -0.02 0.03 0.16 2 -0.23 1 3
Syndecan-2/Caveolin-2/Ras 0.026 0.041 0.16 4 -0.14 26 30
Syndecan-2/Laminin alpha3 -0.031 0.037 0.16 4 -0.24 1 5
Syndecan-2/RasGAP 0.033 0.041 -10000 0 -0.13 15 15
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
PRKCD 0.029 0.005 -10000 0 0 15 15
Syndecan-2 dimer -0.025 0.025 0.16 4 -10000 0 4
GO:0007205 -0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.04 0.031 0.15 5 -10000 0 5
RHOA 0.029 0.003 -10000 0 0 6 6
SDCBP 0.028 0.007 -10000 0 0 36 36
TNFRSF13B 0.028 0.007 -10000 0 0 38 38
RASA1 0.027 0.008 -10000 0 0 50 50
alpha2/beta1 Integrin 0.033 0.037 -10000 0 -0.16 17 17
Syndecan-2/Synbindin -0.024 0.024 0.16 3 -10000 0 3
TGFB1 0.024 0.012 -10000 0 0 112 112
CASP3 -0.013 0.065 0.18 53 -10000 0 53
FN1 0.018 0.014 -10000 0 0 214 214
Syndecan-2/IL8 -0.021 0.026 0.16 4 -10000 0 4
SDC2 -0.015 0.006 -10000 0 -10000 0 0
KNG1 0.025 0.011 -10000 0 0 88 88
Syndecan-2/Neurofibromin -0.025 0.026 0.16 2 -10000 0 2
TRAPPC4 0.027 0.008 -10000 0 0 50 50
CSF2 0.029 0.005 -10000 0 0 18 18
Syndecan-2/TGFB1 -0.039 0.047 0.16 4 -0.24 5 9
Syndecan-2/Syntenin/PI-4-5-P2 -0.023 0.018 -10000 0 -10000 0 0
Syndecan-2/Ezrin -0.024 0.017 -10000 0 -10000 0 0
PRKACA -0.013 0.061 0.18 45 -10000 0 45
angiogenesis -0.021 0.025 0.16 4 -10000 0 4
MMP2 0.023 0.013 -10000 0 0 135 135
IL8 0.025 0.011 -10000 0 0 95 95
calcineurin-NFAT signaling pathway -0.025 0.024 0.16 3 -10000 0 3
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.05 0.13 0.25 2 -0.39 43 45
BAG4 0.026 0.009 -10000 0 0 62 62
BAD -0.029 0.044 0.18 1 -0.16 25 26
NFKBIA 0.028 0.006 -10000 0 0 27 27
BIRC3 0.023 0.013 -10000 0 0 124 124
BAX -0.027 0.046 0.18 4 -0.16 24 28
EnzymeConsortium:3.1.4.12 -0.012 0.03 0.068 1 -0.093 35 36
IKBKB -0.049 0.13 0.26 5 -0.42 33 38
MAP2K2 -0.047 0.051 0.17 3 -0.2 13 16
MAP2K1 -0.04 0.046 0.14 5 -0.19 9 14
SMPD1 -0.017 0.037 -10000 0 -0.13 30 30
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.045 0.13 0.22 5 -0.4 37 42
MAP2K4 -0.034 0.041 -10000 0 -0.17 17 17
protein ubiquitination -0.052 0.12 0.27 2 -0.41 35 37
EnzymeConsortium:2.7.1.37 -0.051 0.049 0.16 1 -0.2 10 11
response to UV 0 0 -10000 0 -0.002 4 4
RAF1 -0.035 0.046 0.15 6 -0.18 14 20
CRADD 0.027 0.01 -10000 0 -0.029 13 13
mol:ceramide -0.021 0.045 0.088 1 -0.15 34 35
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.027 -10000 0 -0.13 13 13
MADD 0.027 0.01 -10000 0 -0.029 15 15
MAP3K1 -0.028 0.043 -10000 0 -0.16 25 25
TRADD 0.025 0.012 -10000 0 -0.029 10 10
RELA/p50 0.029 0.003 -10000 0 0 6 6
MAPK3 -0.046 0.052 0.17 1 -0.21 14 15
MAPK1 -0.048 0.057 0.17 1 -0.23 20 21
p50/RELA/I-kappa-B-alpha 0.038 0.032 -10000 0 -0.16 13 13
FADD -0.048 0.13 0.23 5 -0.39 43 48
KSR1 -0.028 0.046 0.15 4 -0.16 23 27
MAPK8 -0.042 0.04 0.21 1 -0.19 7 8
TRAF2 0.028 0.007 -10000 0 -0.002 26 26
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.052 0.12 0.23 2 -0.41 34 36
TNF R/SODD 0.03 0.036 -10000 0 -0.16 15 15
TNF 0.027 0.01 -10000 0 -0.029 15 15
CYCS -0.015 0.054 0.14 6 -0.17 11 17
IKBKG -0.052 0.12 0.23 7 -0.4 33 40
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.041 0.13 -10000 0 -0.4 43 43
RELA 0.029 0.003 -10000 0 0 6 6
RIPK1 0.028 0.008 -10000 0 0 40 40
AIFM1 -0.012 0.055 0.15 7 -0.17 9 16
TNF/TNF R/SODD 0.041 0.04 -10000 0 -0.14 15 15
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.016 0.063 -10000 0 -0.62 4 4
NSMAF -0.043 0.13 0.23 8 -0.4 38 46
response to hydrogen peroxide 0 0 -10000 0 -0.002 4 4
BCL2 0.023 0.012 -10000 0 0 122 122
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.2 0.31 0.78 1 -0.84 63 64
CRP -0.2 0.3 -10000 0 -0.84 65 65
cell cycle arrest -0.24 0.37 -10000 0 -1 72 72
TIMP1 -0.2 0.31 -10000 0 -0.81 73 73
IL6ST 0.003 0.036 -10000 0 -0.09 2 2
Rac1/GDP -0.066 0.11 -10000 0 -0.39 9 9
AP1 -0.001 0.14 0.42 6 -0.51 18 24
GAB2 0.025 0.016 0.1 1 -0.031 24 25
TNFSF11 -0.21 0.3 -10000 0 -0.84 66 66
HSP90B1 -0.027 0.14 -10000 0 -0.81 13 13
GAB1 0.027 0.014 0.094 1 -0.031 22 23
MAPK14 -0.025 0.082 0.36 1 -0.5 2 3
AKT1 -0.015 0.09 0.59 1 -0.42 5 6
FOXO1 -0.023 0.086 0.54 1 -0.47 3 4
MAP2K6 -0.026 0.087 -10000 0 -0.34 4 4
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.1 0.15 0.52 1 -0.5 11 12
MITF -0.055 0.091 0.38 1 -0.37 7 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.009 -10000 0 0 61 61
A2M -0.059 0.28 0.66 3 -1.2 31 34
CEBPB 0.027 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.003 0.1 -10000 0 -0.41 18 18
STAT3 -0.26 0.41 -10000 0 -1.1 73 73
STAT1 0.046 0.072 -10000 0 -0.88 1 1
CEBPD -0.25 0.38 -10000 0 -0.98 91 91
PIK3CA 0.019 0.015 -10000 0 -0.029 11 11
PI3K 0 0.067 -10000 0 -0.16 75 75
JUN 0.025 0.014 -10000 0 -0.03 24 24
PIAS3/MITF -0.055 0.094 0.36 1 -0.35 7 8
MAPK11 -0.019 0.077 0.36 1 -0.44 3 4
STAT3 (dimer)/FOXO1 -0.2 0.28 -10000 0 -0.76 64 64
GRB2/SOS1/GAB family 0.017 0.1 0.28 1 -0.28 5 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.068 0.24 1 -0.26 8 9
GRB2 0.027 0.014 0.094 1 -0.031 22 23
JAK2 0.027 0.008 -10000 0 0 46 46
LBP -0.14 0.24 0.68 1 -0.7 25 26
PIK3R1 0.02 0.015 0.094 1 -0.029 9 10
JAK1 0.005 0.035 0.13 1 -0.076 4 5
MYC -0.18 0.38 0.75 1 -0.93 82 83
FGG -0.21 0.3 -10000 0 -0.85 64 64
macrophage differentiation -0.24 0.37 -10000 0 -1 72 72
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.092 -10000 0 -0.19 8 8
JUNB -0.27 0.41 -10000 0 -0.94 139 139
FOS 0.022 0.016 -10000 0 -0.03 25 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.04 0.1 -10000 0 -0.38 8 8
STAT1/PIAS1 -0.033 0.13 0.4 2 -0.38 9 11
GRB2/SOS1/GAB family/SHP2/PI3K -0.003 0.088 0.49 1 -0.4 8 9
STAT3 (dimer) -0.26 0.4 -10000 0 -1.1 73 73
PRKCD -0.14 0.2 0.6 1 -0.57 41 42
IL6R 0.005 0.035 0.13 1 -0.069 2 3
SOCS3 -0.011 0.095 0.46 1 -0.85 2 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.069 -10000 0 -0.17 8 8
Rac1/GTP -0.078 0.12 -10000 0 -0.42 10 10
HCK 0.027 0.01 -10000 0 -0.035 4 4
MAPKKK cascade -0.003 0.12 0.45 1 -0.54 18 19
bone resorption -0.2 0.28 -10000 0 -0.79 65 65
IRF1 -0.21 0.32 0.74 2 -0.87 65 67
mol:GDP -0.056 0.098 -10000 0 -0.38 9 9
SOS1 0.026 0.015 -10000 0 -0.031 23 23
VAV1 -0.058 0.097 -10000 0 -0.38 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.007 0.063 -10000 0 -0.45 3 3
PTPN11 0.003 0.09 -10000 0 -0.82 6 6
IL6/IL6RA 0.007 0.053 0.24 1 -0.18 9 10
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.06 -10000 0 -0.15 11 11
gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.061 -10000 0 -0.15 11 11
IL6 0.004 0.037 0.16 1 -0.09 2 3
PIAS3 0.029 0.005 -10000 0 0 16 16
PTPRE 0.033 0.026 0.12 1 -0.15 1 2
PIAS1 0.029 0.005 -10000 0 0 15 15
RAC1 0.007 0.029 -10000 0 -0.035 59 59
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.021 0.071 -10000 0 -0.29 9 9
LMO4 0.004 0.038 0.16 1 -0.09 2 3
STAT3 (dimer)/PIAS3 -0.24 0.36 -10000 0 -0.99 74 74
MCL1 -0.012 0.099 0.71 1 -0.59 1 2
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.029 0.006 -10000 0 0 20 20
VLDLR 0.027 0.009 -10000 0 0 60 60
LRPAP1 0.028 0.007 -10000 0 0 37 37
NUDC 0.029 0.005 -10000 0 0 18 18
RELN/LRP8 0.019 0.075 -10000 0 -0.15 88 88
CaM/Ca2+ 0.019 0.022 -10000 0 -0.15 9 9
KATNA1 0.028 0.007 -10000 0 0 33 33
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.04 0.073 0.16 49 -0.23 1 50
IQGAP1/CaM 0.037 0.03 -10000 0 -0.16 11 11
DAB1 0.029 0.005 -10000 0 0 14 14
IQGAP1 0.028 0.006 -10000 0 0 25 25
PLA2G7 0.025 0.011 -10000 0 0 83 83
CALM1 0.028 0.006 -10000 0 0 26 26
DYNLT1 0.025 0.011 -10000 0 0 82 82
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.039 0.018 -10000 0 -0.16 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.003 -10000 0 0 7 7
CDK5R1 0.028 0.007 -10000 0 0 38 38
LIS1/Poliovirus Protein 3A -0.023 0.009 -10000 0 -10000 0 0
CDK5R2 0.029 0.004 -10000 0 0 8 8
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.015 0.078 -10000 0 -0.15 98 98
YWHAE 0.028 0.008 -10000 0 0 41 41
NDEL1/14-3-3 E -0.034 0.1 0.29 16 -0.25 1 17
MAP1B -0.012 0.052 0.13 1 -0.19 43 44
RAC1 -0.013 0.04 -10000 0 -0.26 14 14
p35/CDK5 -0.036 0.086 0.21 22 -0.22 1 23
RELN 0.023 0.013 -10000 0 0 131 131
PAFAH/LIS1 -0.031 0.016 -10000 0 -10000 0 0
LIS1/CLIP170 -0.036 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.058 0.086 0.18 9 -0.25 2 11
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.024 0.091 0.19 2 -0.25 28 30
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.029 0.087 0.27 13 -0.21 1 14
LIS1/IQGAP1 -0.036 0.014 -10000 0 -0.15 2 2
RHOA -0.008 0.019 -10000 0 -0.29 2 2
PAFAH1B1 -0.03 0.011 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.008 -10000 0 0 47 47
PAFAH1B2 0.029 0.005 -10000 0 0 19 19
MAP1B/LIS1/Dynein heavy chain -0.041 0.042 -10000 0 -0.22 4 4
NDEL1/Katanin 60/Dynein heavy chain -0.039 0.1 0.27 17 -0.25 1 18
LRP8 0.029 0.006 -10000 0 0 20 20
NDEL1/Katanin 60 -0.035 0.099 0.28 16 -0.25 1 17
P39/CDK5 -0.037 0.087 0.2 24 -0.22 1 25
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.035 0.013 -10000 0 -10000 0 0
CDK5 -0.035 0.077 0.18 17 -0.23 1 18
PPP2R5D 0.028 0.006 -10000 0 0 25 25
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.03 0.009 -10000 0 -10000 0 0
CSNK2A1 0.028 0.008 -10000 0 0 39 39
RELN/VLDLR/DAB1/LIS1 0.021 0.079 -10000 0 -0.14 85 85
RELN/VLDLR 0.028 0.085 -10000 0 -0.14 93 93
CDC42 -0.009 0.02 -10000 0 -0.26 3 3
Cellular roles of Anthrax toxin

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
ANTXR1 0.028 0.006 -10000 0 0 26 26
ANTXR2 0.028 0.008 -10000 0 0 41 41
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.007 -10000 0 -0.036 24 24
monocyte activation -0.021 0.14 0.19 1 -0.35 76 77
MAP2K2 -0.13 0.27 -10000 0 -0.63 123 123
MAP2K1 -0.016 0.01 0.15 1 -0.062 2 3
MAP2K7 -0.015 0.007 -10000 0 -0.062 2 2
MAP2K6 0.005 0.056 0.15 70 -0.062 2 72
CYAA -0.025 0.02 -10000 0 -0.12 24 24
MAP2K4 -0.015 0.008 -10000 0 -10000 0 0
IL1B -0.01 0.052 0.15 43 -0.12 2 45
Channel 0.028 0.035 -10000 0 -0.12 24 24
NLRP1 -0.016 0.009 0.12 1 -0.062 2 3
CALM1 0.028 0.006 -10000 0 0 26 26
negative regulation of phagocytosis -0.009 0.079 -10000 0 -0.44 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.007 0.036 24 -10000 0 24
MAPK3 -0.016 0.007 -10000 0 -0.062 2 2
MAPK1 -0.015 0.007 -10000 0 -0.062 2 2
PGR -0.006 0.027 -10000 0 -0.13 23 23
PA/Cellular Receptors 0.03 0.038 -10000 0 -0.14 24 24
apoptosis -0.007 0.007 -10000 0 -0.036 24 24
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.035 -10000 0 -0.12 24 24
macrophage activation -0.025 0.015 -10000 0 -0.11 11 11
TNF 0.029 0.005 -10000 0 0 15 15
VCAM1 -0.022 0.14 -10000 0 -0.36 76 76
platelet activation -0.009 0.079 -10000 0 -0.44 18 18
MAPKKK cascade 0.016 0.035 0.095 4 -0.11 10 14
IL18 0.008 0.07 0.14 104 -0.12 2 106
negative regulation of macrophage activation -0.007 0.007 -10000 0 -0.036 24 24
LEF -0.007 0.007 -10000 0 -0.036 24 24
CASP1 -0.014 0.023 0.044 5 -0.087 44 49
mol:cAMP -0.009 0.08 -10000 0 -0.44 18 18
necrosis -0.007 0.007 -10000 0 -0.036 24 24
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.033 -10000 0 -0.12 24 24
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.012 0.11 0.32 13 -0.33 18 31
FYN -0.022 0.13 0.32 13 -0.37 27 40
LAT/GRAP2/SLP76 -0.019 0.1 0.29 9 -0.33 20 29
IKBKB 0.028 0.008 -10000 0 0 39 39
AKT1 -0.022 0.1 0.29 9 -0.3 29 38
B2M 0.022 0.021 0.11 1 -0.05 10 11
IKBKG -0.019 0.041 0.12 11 -0.12 8 19
MAP3K8 0.029 0.005 -10000 0 0 16 16
mol:Ca2+ -0.026 0.013 0.08 1 -0.058 3 4
integrin-mediated signaling pathway 0.038 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.027 0.13 0.32 9 -0.39 30 39
TRPV6 0.075 0.33 1.3 37 -10000 0 37
CD28 0.02 0.022 -10000 0 -10000 0 0
SHC1 -0.013 0.11 0.29 13 -0.36 20 33
receptor internalization -0.012 0.099 0.3 6 -0.37 21 27
PRF1 -0.026 0.19 0.8 1 -0.92 20 21
KRAS 0.024 0.011 -10000 0 0 99 99
GRB2 0.029 0.006 -10000 0 0 20 20
COT/AKT1 -0.018 0.091 0.26 10 -0.25 28 38
LAT -0.017 0.1 0.31 9 -0.37 19 28
EntrezGene:6955 -0.001 0.004 0.07 1 -0.021 10 11
CD3D 0.023 0.017 0.11 1 -0.05 6 7
CD3E 0.018 0.024 -10000 0 -0.05 9 9
CD3G 0.018 0.023 -10000 0 -0.05 11 11
RASGRP2 -0.003 0.016 -10000 0 -0.14 2 2
RASGRP1 -0.052 0.13 0.29 6 -0.31 72 78
HLA-A 0.018 0.025 0.11 1 -0.05 9 10
RASSF5 0.029 0.004 -10000 0 0 11 11
RAP1A/GTP/RAPL 0.039 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.05 0.18 8 -0.12 11 19
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.036 0.045 -10000 0 -0.16 28 28
PRKCA -0.025 0.066 0.21 12 -0.21 12 24
GRAP2 0.027 0.008 -10000 0 0 48 48
mol:IP3 -0.031 0.078 -10000 0 -0.27 20 20
EntrezGene:6957 0 0.005 0.077 1 -0.021 12 13
TCR/CD3/MHC I/CD8 -0.014 0.09 0.32 4 -0.34 23 27
ORAI1 -0.091 0.28 -10000 0 -1.1 37 37
CSK -0.014 0.1 0.36 6 -0.38 17 23
B7 family/CD28 0.014 0.11 0.39 3 -0.39 18 21
CHUK 0.028 0.007 -10000 0 0 36 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.015 0.11 0.3 5 -0.39 20 25
PTPN6 -0.01 0.11 0.32 9 -0.36 20 29
VAV1 -0.014 0.11 0.33 7 -0.37 19 26
Monovalent TCR/CD3 -0.005 0.063 0.39 1 -0.18 51 52
CBL 0.029 0.005 -10000 0 0 15 15
LCK -0.01 0.12 0.32 10 -0.37 22 32
PAG1 -0.01 0.11 0.29 12 -0.39 16 28
RAP1A 0.029 0.003 -10000 0 0 7 7
TCR/CD3/MHC I/CD8/LCK -0.015 0.11 0.28 8 -0.38 22 30
CD80 0.019 0.023 -10000 0 -10000 0 0
CD86 0.018 0.023 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.03 0.06 -10000 0 -0.2 25 25
HRAS 0.028 0.006 -10000 0 0 28 28
GO:0035030 -0.029 0.091 0.28 5 -0.33 20 25
CD8A 0.022 0.022 0.11 1 -0.049 8 9
CD8B 0.019 0.025 0.11 1 -0.051 9 10
PTPRC 0.018 0.02 -10000 0 -0.03 45 45
PDK1/PKC theta -0.031 0.11 0.31 11 -0.36 24 35
CSK/PAG1 -0.016 0.11 0.32 9 -0.39 15 24
SOS1 0.028 0.007 -10000 0 0 34 34
peptide-MHC class I 0.036 0.03 0.18 1 -0.17 6 7
GRAP2/SLP76 0.012 0.12 0.33 7 -0.36 21 28
STIM1 -0.036 0.069 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.071 0.19 29 -0.18 7 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.013 0.1 0.3 6 -0.38 22 28
mol:DAG -0.039 0.059 -10000 0 -0.23 23 23
RAP1A/GDP 0.002 0.026 0.086 8 -0.062 4 12
PLCG1 0.028 0.007 -10000 0 0 31 31
CD247 0.019 0.023 0.1 1 -0.049 12 13
cytotoxic T cell degranulation -0.024 0.18 0.79 1 -0.87 20 21
RAP1A/GTP -0.004 0.008 -10000 0 -0.057 2 2
mol:PI-3-4-5-P3 -0.022 0.11 0.31 9 -0.34 28 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.032 0.099 0.23 2 -0.34 17 19
NRAS 0.014 0.015 -10000 0 0 300 300
ZAP70 0.029 0.007 -10000 0 -0.029 6 6
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.028 0.099 0.27 9 -0.33 19 28
MALT1 0.026 0.01 -10000 0 0 75 75
TRAF6 0.029 0.004 -10000 0 0 12 12
CD8 heterodimer 0.039 0.022 0.18 1 -10000 0 1
CARD11 0.028 0.007 -10000 0 0 36 36
PRKCB -0.034 0.04 -10000 0 -0.17 23 23
PRKCE -0.026 0.065 0.21 11 -0.21 11 22
PRKCQ -0.027 0.12 0.31 9 -0.39 24 33
LCP2 0.028 0.007 -10000 0 0 35 35
BCL10 0.029 0.004 -10000 0 0 10 10
regulation of survival gene product expression -0.018 0.091 0.26 11 -0.26 28 39
IKK complex -0.003 0.043 0.16 18 -0.12 1 19
RAS family/GDP -0.004 0.009 -10000 0 -0.038 10 10
MAP3K14 -0.021 0.072 0.21 11 -0.21 26 37
PDPK1 -0.024 0.097 0.28 10 -0.29 28 38
TCR/CD3/MHC I/CD8/Fyn -0.016 0.12 0.48 1 -0.42 23 24
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.006 -10000 0 0 28 28
EGFR 0.027 0.009 -10000 0 0 55 55
EGF/EGFR 0.032 0.053 -10000 0 -0.12 41 41
EGF/EGFR dimer/SHC/GRB2/SOS1 0.059 0.068 -10000 0 -0.14 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.028 0.006 -10000 0 0 28 28
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.027 0.008 -10000 0 0 43 43
EGF/EGFR dimer/SHC 0.038 0.055 -10000 0 -0.14 41 41
mol:GDP 0.052 0.065 -10000 0 -0.14 36 36
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.027 0.008 -10000 0 0 49 49
GRB2/SOS1 0.04 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.053 0.038 0.092 17 -10000 0 17
SHC1 0.029 0.006 -10000 0 0 20 20
HRAS/GDP 0.047 0.066 -10000 0 -0.14 36 36
FRAP1 -0.046 0.039 0.1 20 -10000 0 20
EGF/EGFR dimer 0.024 0.055 -10000 0 -0.16 43 43
SOS1 0.028 0.007 -10000 0 0 34 34
GRB2 0.029 0.006 -10000 0 0 20 20
ETA receptor/Endothelin-1 0.038 0.017 -10000 0 -0.16 1 1
Aurora C signaling

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
INCENP 0.029 0.003 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.039 0.03 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.001 0.043 -9999 0 -0.37 7 7
AURKB 0.022 0.013 -9999 0 0 137 137
AURKC 0.028 0.006 -9999 0 0 28 28
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.008 -10000 0 0 46 46
LAT2 -0.009 0.075 0.15 3 -0.27 23 26
AP1 0.027 0.1 0.24 1 -0.36 14 15
mol:PIP3 -0.017 0.092 0.27 7 -0.31 18 25
IKBKB -0.01 0.071 0.21 18 -0.19 15 33
AKT1 -0.008 0.13 0.26 46 -0.28 2 48
IKBKG -0.012 0.066 0.2 15 -0.19 11 26
MS4A2 -0.01 0.031 0.062 6 -10000 0 6
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.024 -10000 0 -0.032 4 4
MAP3K1 0.014 0.11 0.24 40 -0.3 15 55
mol:Ca2+ -0.012 0.077 0.22 12 -0.25 17 29
LYN -0.01 0.03 0.065 2 -10000 0 2
CBLB -0.007 0.074 0.15 5 -0.26 23 28
SHC1 0.029 0.006 -10000 0 0 20 20
RasGAP/p62DOK 0.013 0.074 -10000 0 -0.13 107 107
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.03 0.089 0.31 13 -0.2 3 16
PTPN13 -0.021 0.11 -10000 0 -0.46 12 12
PTPN11 -0.008 0.034 0.067 5 -10000 0 5
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.012 0.11 0.29 14 -0.32 4 18
SYK -0.008 0.032 0.065 2 -10000 0 2
GRB2 0.025 0.016 -10000 0 -0.03 39 39
LAT/PLCgamma1/GRB2/SLP76/GADs -0.025 0.075 0.16 1 -0.29 21 22
LAT -0.007 0.073 0.14 4 -0.26 23 27
PAK2 0.022 0.12 0.24 62 -0.33 15 77
NFATC2 -0.02 0.072 -10000 0 -0.39 20 20
HRAS 0.003 0.095 0.23 8 -0.33 18 26
GAB2 0.026 0.009 -10000 0 0 62 62
PLA2G1B -0.004 0.066 -10000 0 -0.91 2 2
Fc epsilon R1 0.039 0.046 -10000 0 -0.12 28 28
Antigen/IgE/Fc epsilon R1 0.037 0.041 -10000 0 -0.11 23 23
mol:GDP 0.011 0.092 0.2 4 -0.35 17 21
JUN 0.028 0.007 -10000 0 0 34 34
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.032 1 1
FOS 0.024 0.012 -10000 0 0 105 105
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.004 0.077 -10000 0 -0.27 24 24
CHUK -0.012 0.065 0.18 14 -0.19 16 30
KLRG1 -0.011 0.062 -10000 0 -0.25 17 17
VAV1 -0.006 0.074 0.14 6 -0.27 21 27
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.007 0.075 0.14 4 -0.26 24 28
negative regulation of mast cell degranulation -0.02 0.051 -10000 0 -0.25 14 14
BTK 0.014 0.088 0.21 2 -0.36 14 16
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0 0.068 0.19 24 -0.18 17 41
GAB2/PI3K/SHP2 -0.059 0.063 -10000 0 -0.22 19 19
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.059 0.12 2 -0.2 22 24
RAF1 0.02 0.063 -10000 0 -0.96 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.058 0.049 -10000 0 -0.12 23 23
FCER1G -0.016 0.025 0.065 1 -10000 0 1
FCER1A -0.009 0.031 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/Fyn 0.036 0.079 -10000 0 -0.14 77 77
MAPK3 -0.003 0.067 -10000 0 -0.89 2 2
MAPK1 -0.006 0.071 -10000 0 -0.95 2 2
NFKB1 0.027 0.008 -10000 0 0 47 47
MAPK8 -0.004 0.16 -10000 0 -0.54 27 27
DUSP1 0.023 0.012 -10000 0 0 125 125
NF-kappa-B/RelA -0.012 0.054 0.14 14 -0.15 9 23
actin cytoskeleton reorganization -0.005 0.1 -10000 0 -0.5 7 7
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.03 0.09 0.19 1 -0.36 16 17
FER -0.006 0.073 0.14 4 -0.27 22 26
RELA 0.029 0.003 -10000 0 0 6 6
ITK 0.002 0.043 0.13 6 -0.23 12 18
SOS1 0.028 0.007 -10000 0 0 34 34
PLCG1 0.007 0.095 0.28 7 -0.33 15 22
cytokine secretion -0.012 0.034 0.072 9 -0.1 15 24
SPHK1 -0.007 0.073 0.14 5 -0.26 22 27
PTK2 -0.006 0.1 -10000 0 -0.52 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.002 0.083 -10000 0 -0.3 22 22
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.02 0.096 0.25 7 -0.3 23 30
MAP2K2 -0.009 0.067 -10000 0 -0.91 2 2
MAP2K1 0.006 0.061 -10000 0 -0.91 2 2
MAP2K7 0.028 0.007 -10000 0 0 37 37
KLRG1/SHP2 -0.005 0.072 0.18 37 -0.25 13 50
MAP2K4 -0.065 0.3 -10000 0 -0.87 65 65
Fc epsilon R1/FcgammaRIIB 0.062 0.053 -10000 0 -0.13 23 23
mol:Choline -0.03 0.088 0.3 13 -0.2 3 16
SHC/Grb2/SOS1 0.051 0.084 -10000 0 -0.26 18 18
FYN 0.024 0.011 -10000 0 0 99 99
DOK1 0.029 0.004 -10000 0 0 10 10
PXN -0.014 0.099 -10000 0 -0.49 7 7
HCLS1 -0.006 0.076 0.15 9 -0.27 22 31
PRKCB -0.014 0.076 0.21 10 -0.24 21 31
FCGR2B 0.027 0.008 -10000 0 0 47 47
IGHE 0 0.006 0.023 9 -10000 0 9
KLRG1/SHIP -0.02 0.052 -10000 0 -0.26 14 14
LCP2 0.025 0.014 -10000 0 -0.03 27 27
PLA2G4A -0.045 0.089 0.14 7 -0.29 29 36
RASA1 0.027 0.008 -10000 0 0 50 50
mol:Phosphatidic acid -0.03 0.088 0.3 13 -0.2 3 16
IKK complex -0.009 0.067 0.21 17 -0.17 2 19
WIPF1 0.029 0.005 -10000 0 0 14 14
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.076 0.11 0.24 51 -0.39 11 62
Syndecan-4/Syndesmos 0.073 0.1 0.31 5 -0.44 1 6
positive regulation of JNK cascade 0.062 0.12 0.3 5 -0.42 1 6
Syndecan-4/ADAM12 0.039 0.086 0.29 2 -0.45 1 3
CCL5 0.025 0.011 -10000 0 0 83 83
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
DNM2 0.027 0.009 -10000 0 0 56 56
ITGA5 0.029 0.006 -10000 0 0 20 20
SDCBP 0.028 0.007 -10000 0 0 36 36
PLG -0.008 0.039 -10000 0 -0.09 20 20
ADAM12 0.022 0.013 -10000 0 0 141 141
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.006 -10000 0 0 25 25
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.019 0.034 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.062 0.097 0.32 3 -0.45 1 4
Syndecan-4/CXCL12/CXCR4 0.066 0.12 0.31 5 -0.44 1 6
Syndecan-4/Laminin alpha3 0.065 0.099 0.31 5 -0.44 1 6
MDK 0.029 0.003 -10000 0 0 7 7
Syndecan-4/FZD7 0.071 0.1 0.32 4 -0.45 1 5
Syndecan-4/Midkine 0.074 0.1 0.31 5 -0.44 1 6
FZD7 0.028 0.006 -10000 0 0 27 27
Syndecan-4/FGFR1/FGF 0.067 0.1 0.32 3 -0.43 1 4
THBS1 0.025 0.011 -10000 0 0 96 96
integrin-mediated signaling pathway 0.041 0.083 0.28 2 -0.43 1 3
positive regulation of MAPKKK cascade 0.062 0.12 0.3 5 -0.42 1 6
Syndecan-4/TACI 0.074 0.099 0.31 5 -0.44 1 6
CXCR4 0.029 0.005 -10000 0 0 17 17
cell adhesion 0.021 0.065 0.15 19 -0.19 12 31
Syndecan-4/Dynamin 0.07 0.099 0.31 5 -0.45 1 6
Syndecan-4/TSP1 0.064 0.1 0.31 5 -0.45 1 6
Syndecan-4/GIPC 0.065 0.098 0.31 5 -0.45 1 6
Syndecan-4/RANTES 0.067 0.1 0.31 5 -0.44 1 6
ITGB1 0.029 0.006 -10000 0 0 22 22
LAMA1 0.024 0.012 -10000 0 0 110 110
LAMA3 0.026 0.01 -10000 0 0 74 74
RAC1 0.028 0.006 -10000 0 0 28 28
PRKCA -0.027 0.09 0.6 9 -10000 0 9
Syndecan-4/alpha-Actinin 0.074 0.1 0.31 5 -0.44 1 6
TFPI 0.027 0.009 -10000 0 0 52 52
F2 0.019 0.032 0.079 1 -0.05 1 2
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.038 0.095 0.33 7 -0.44 1 8
ACTN1 0.029 0.006 -10000 0 0 21 21
TNC 0.021 0.014 -10000 0 0 168 168
Syndecan-4/CXCL12 0.066 0.11 0.31 5 -0.45 1 6
FGF6 0.027 0.009 -10000 0 0 60 60
RHOA 0.029 0.003 -10000 0 0 6 6
CXCL12 0.025 0.011 -10000 0 0 91 91
TNFRSF13B 0.028 0.007 -10000 0 0 38 38
FGF2 0.027 0.008 -10000 0 0 44 44
FGFR1 0.026 0.01 -10000 0 0 75 75
Syndecan-4/PI-4-5-P2 0.041 0.088 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.026 -10000 0 -0.071 7 7
cell migration -0.014 0.014 -10000 0 -10000 0 0
PRKCD -0.007 0.04 -10000 0 -0.081 23 23
vasculogenesis 0.063 0.1 0.31 5 -0.43 1 6
SDC4 0.05 0.093 0.34 2 -0.46 1 3
Syndecan-4/Tenascin C 0.042 0.084 0.29 2 -0.44 1 3
Syndecan-4/PI-4-5-P2/PKC alpha -0.018 0.025 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.07 0.099 0.31 5 -0.45 1 6
MMP9 0.007 0.027 -10000 0 -0.053 2 2
Rac1/GTP 0.013 0.062 0.15 19 -0.19 12 31
cytoskeleton organization 0.072 0.099 0.31 5 -0.43 1 6
GIPC1 0.025 0.01 -10000 0 0 80 80
Syndecan-4/TFPI 0.067 0.1 0.33 3 -0.45 1 4
Ceramide signaling pathway

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.03 0.011 -10000 0 -10000 0 0
MAP4K4 -0.036 0.087 0.19 1 -0.3 33 34
BAG4 0.026 0.009 -10000 0 0 62 62
PKC zeta/ceramide 0.029 0.031 -10000 0 -0.18 9 9
NFKBIA 0.028 0.006 -10000 0 0 27 27
BIRC3 0.023 0.012 -10000 0 0 122 122
BAX 0.007 0.059 -10000 0 -0.33 16 16
RIPK1 0.028 0.008 -10000 0 0 40 40
AKT1 -0.009 0.11 0.68 15 -10000 0 15
BAD 0.001 0.03 0.22 2 -0.18 10 12
SMPD1 -0.01 0.065 0.18 6 -0.2 29 35
RB1 0.006 0.043 0.18 20 -0.18 10 30
FADD/Caspase 8 -0.035 0.098 0.22 7 -0.32 35 42
MAP2K4 -0.009 0.027 -10000 0 -0.18 10 10
NSMAF 0.028 0.007 -10000 0 0 35 35
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.006 0.037 0.19 10 -0.18 10 20
EGF 0.027 0.008 -10000 0 0 43 43
mol:ceramide 0.012 0.03 0.13 1 -0.18 10 11
MADD 0.029 0.004 -10000 0 0 8 8
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.026 0.014 -10000 0 -10000 0 0
ASAH1 0.025 0.011 -10000 0 0 94 94
negative regulation of cell cycle 0.006 0.043 0.18 20 -0.18 10 30
cell proliferation -0.033 0.054 0.18 6 -0.22 9 15
BID -0.038 0.18 -10000 0 -0.66 38 38
MAP3K1 0 0.027 -10000 0 -0.18 10 10
EIF2A 0.065 0.1 0.25 56 -0.19 2 58
TRADD 0.026 0.01 -10000 0 0 65 65
CRADD 0.029 0.004 -10000 0 0 13 13
MAPK3 -0.022 0.047 0.19 4 -0.22 9 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.025 0.05 0.19 4 -0.22 8 12
Cathepsin D/ceramide 0.029 0.032 -10000 0 -0.18 10 10
FADD -0.036 0.088 0.19 4 -0.29 34 38
KSR1 0.002 0.035 0.22 5 -0.18 10 15
MAPK8 0 0.041 -10000 0 -0.18 1 1
PRKRA 0.006 0.045 0.21 16 -0.18 10 26
PDGFA 0.027 0.008 -10000 0 0 48 48
TRAF2 0.028 0.006 -10000 0 0 24 24
IGF1 0.028 0.007 -10000 0 0 33 33
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.012 0.029 0.13 1 -0.18 10 11
CTSD 0.028 0.007 -10000 0 0 30 30
regulation of nitric oxide biosynthetic process 0.038 0.026 -10000 0 -0.16 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.035 0.057 0.2 6 -0.23 9 15
PRKCD 0.029 0.005 -10000 0 0 15 15
PRKCZ 0.029 0.006 -10000 0 0 23 23
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.026 0.014 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.026 -10000 0 -0.16 7 7
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.029 0.004 -10000 0 0 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.021 0.092 -10000 0 -0.3 33 33
TNFR1A/BAG4/TNF-alpha 0.042 0.04 -10000 0 -0.14 15 15
mol:Sphingosine-1-phosphate -0.03 0.011 -10000 0 -10000 0 0
MAP2K1 -0.014 0.038 0.17 12 -0.19 10 22
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 0 6 6
CYCS 0.024 0.058 0.16 10 -0.17 10 20
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
NFKB1 0.027 0.008 -10000 0 0 47 47
TNFR1A/BAG4 0.03 0.036 -10000 0 -0.16 15 15
EIF2AK2 0.06 0.089 0.22 42 -0.18 5 47
TNF-alpha/TNFR1A/FAN 0.044 0.038 -10000 0 -0.15 14 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.018 0.11 -10000 0 -0.4 34 34
MAP2K2 -0.026 0.046 0.18 7 -0.21 8 15
SMPD3 -0.027 0.11 0.18 4 -0.32 58 62
TNF 0.029 0.005 -10000 0 0 15 15
PKC zeta/PAR4 0.042 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.011 0.037 0.13 4 -0.14 12 16
NF kappa B1/RelA/I kappa B alpha 0.065 0.058 -10000 0 -0.15 17 17
AIFM1 0.029 0.062 0.2 15 -0.17 8 23
BCL2 0.023 0.012 -10000 0 0 122 122
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.055 0.19 35 -10000 0 35
SMARCC1 -0.013 0.034 0.62 1 -10000 0 1
REL 0.029 0.004 -10000 0 -10000 0 0
HDAC7 -0.13 0.11 0.29 2 -0.31 32 34
JUN 0.028 0.007 -10000 0 -10000 0 0
EP300 0.027 0.009 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.015 0.079 0.18 74 -10000 0 74
FOXO1 0.028 0.008 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.12 0.32 2 -0.33 20 22
MAP2K6 -0.03 0.018 -10000 0 -10000 0 0
BRM/BAF57 -0.003 0.081 -10000 0 -0.16 111 111
MAP2K4 -0.027 0.024 -10000 0 -10000 0 0
SMARCA2 0.021 0.013 -10000 0 -10000 0 0
PDE9A -0.15 0.28 -10000 0 -0.9 59 59
NCOA2 0.027 0.008 -10000 0 -10000 0 0
CEBPA 0.027 0.009 -10000 0 -10000 0 0
EHMT2 0.029 0.005 -10000 0 -10000 0 0
cell proliferation -0.14 0.14 -10000 0 -0.37 42 42
NR0B1 0.028 0.008 -10000 0 0 39 39
EGR1 0.018 0.014 -10000 0 -10000 0 0
RXRs/9cRA 0.046 0.034 -10000 0 -0.13 13 13
AR/RACK1/Src -0.076 0.096 0.3 3 -0.29 2 5
AR/GR -0.12 0.1 0.18 2 -0.21 265 267
GNB2L1 0.029 0.005 -10000 0 -10000 0 0
PKN1 0.025 0.01 -10000 0 -10000 0 0
RCHY1 0.027 0.008 -10000 0 0 48 48
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.041 0.027 0.18 4 -0.19 1 5
T-DHT/AR/TIF2/CARM1 -0.073 0.091 0.3 2 -0.29 2 4
SRC -0.052 0.065 0.24 1 -10000 0 1
NR3C1 0.029 0.005 -10000 0 0 15 15
KLK3 -0.049 0.079 -10000 0 -10000 0 0
APPBP2 -0.029 0.024 -10000 0 -10000 0 0
TRIM24 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.08 0.068 0.14 1 -0.2 19 20
TMPRSS2 -0.39 0.45 -10000 0 -0.89 245 245
RXRG 0.028 0.006 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.028 0.007 -10000 0 -10000 0 0
RXRB 0.029 0.005 -10000 0 -10000 0 0
CARM1 0.027 0.009 -10000 0 -10000 0 0
NR2C2 0.029 0.004 -10000 0 -10000 0 0
KLK2 -0.062 0.08 0.32 1 -0.34 3 4
AR -0.11 0.11 0.17 1 -0.22 252 253
SENP1 0.028 0.007 -10000 0 -10000 0 0
HSP90AA1 0.029 0.006 -10000 0 0 21 21
MDM2 0.028 0.006 -10000 0 -10000 0 0
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.028 0.006 -10000 0 0 28 28
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.028 0.006 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.076 0.1 0.28 7 -0.3 2 9
positive regulation of transcription 0.028 0.006 -10000 0 0 28 28
DNAJA1 -0.028 0.025 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.056 0.3 3 -0.22 18 21
NCOA1 0.031 0.018 0.23 1 -10000 0 1
SPDEF 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.058 0.084 0.29 2 -0.27 32 34
T-DHT/AR/Hsp90 -0.079 0.089 0.26 5 -0.26 4 9
GSK3B -0.001 0.032 -10000 0 -0.041 1 1
NR2C1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.045 0.07 0.27 1 -0.2 1 2
SIRT1 0.029 0.004 -10000 0 -10000 0 0
ZMIZ2 0.029 0.004 -10000 0 -10000 0 0
POU2F1 -0.044 0.08 -10000 0 -0.13 252 252
T-DHT/AR/DAX-1 -0.076 0.089 0.26 6 -0.24 3 9
CREBBP 0.028 0.008 -10000 0 -10000 0 0
SMARCE1 0.028 0.007 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.04 0.021 -10000 0 -0.2 3 3
FBXW11 0.029 0.005 -10000 0 0 18 18
NF kappa B1 p50/c-Rel -0.037 0.016 0.16 1 -0.14 4 5
NF kappa B1 p50/RelA/I kappa B alpha -0.029 0.053 0.23 1 -0.23 10 11
NFKBIA -0.005 0.039 -10000 0 -0.15 13 13
MAPK14 0.029 0.005 -10000 0 0 19 19
NF kappa B1 p105/p50 -0.037 0.017 0.16 1 -0.14 5 6
ARRB2 0.007 0.002 -10000 0 -10000 0 0
REL 0.029 0.004 -10000 0 0 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.036 0.019 0.16 1 -0.14 7 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.038 0.017 0.16 1 -0.14 6 7
PIK3CA 0.021 0.014 -10000 0 0 171 171
NF kappa B1 p50 dimer -0.032 0.016 -10000 0 -0.16 5 5
PIK3R1 0.021 0.013 -10000 0 0 161 161
NFKB1 -0.029 0.015 0.19 1 -10000 0 1
RELA 0.029 0.003 -10000 0 0 6 6
positive regulation of anti-apoptosis -0.007 0.042 -10000 0 -0.21 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.032 0.055 -10000 0 -0.25 9 9
SRC 0.028 0.007 -10000 0 0 31 31
PI3K 0 0.067 -10000 0 -0.16 75 75
NF kappa B1 p50/RelA -0.007 0.042 -10000 0 -0.21 5 5
IKBKB 0.028 0.008 -10000 0 0 39 39
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -10000 0 0 18 18
SYK 0.028 0.006 -10000 0 0 24 24
I kappa B alpha/PIK3R1 0.006 0.053 -10000 0 -0.22 15 15
cell death -0.031 0.053 -10000 0 -0.24 9 9
NF kappa B1 p105/c-Rel -0.037 0.016 0.16 1 -0.14 4 5
LCK 0.028 0.006 -10000 0 0 26 26
BCL3 0.028 0.007 -10000 0 0 35 35
IL27-mediated signaling events

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
TGFB1 0.023 0.012 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.002 0.14 0.72 4 -0.4 25 29
IL27/IL27R/JAK1 0.058 0.13 0.56 6 -0.94 3 9
TBX21 0.046 0.14 0.43 31 -0.56 3 34
IL12B 0.032 0.014 0.092 26 -10000 0 26
IL12A -0.012 0.016 0.046 23 -10000 0 23
IL6ST -0.01 0.035 0.096 29 -10000 0 29
IL27RA/JAK1 0.012 0.11 0.38 2 -1 3 5
IL27 -0.011 0.036 0.095 30 -10000 0 30
TYK2 -0.011 0.042 0.15 26 -10000 0 26
T-helper cell lineage commitment -0.03 0.093 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.002 0.14 0.72 4 -0.4 25 29
T cell proliferation during immune response -0.002 0.14 0.72 4 -0.4 25 29
MAPKKK cascade 0.002 0.14 0.4 25 -0.72 4 29
STAT3 0.028 0.007 -10000 0 0 38 38
STAT2 0.026 0.01 -10000 0 0 76 76
STAT1 0.006 0.019 0.079 1 -10000 0 1
IL12RB1 0.029 0.011 0.06 26 -10000 0 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.041 0.14 0.45 25 -0.56 3 28
IL27/IL27R/JAK2/TYK2 0.002 0.14 0.4 25 -0.74 4 29
positive regulation of T cell mediated cytotoxicity 0.002 0.14 0.4 25 -0.72 4 29
STAT1 (dimer) 0.075 0.13 0.55 2 -0.78 3 5
JAK2 -0.008 0.039 0.12 24 -10000 0 24
JAK1 -0.006 0.029 0.078 2 -10000 0 2
STAT2 (dimer) 0.01 0.13 0.42 4 -0.64 4 8
T cell proliferation -0.013 0.13 0.36 25 -0.71 4 29
IL12/IL12R/TYK2/JAK2 0.018 0.19 0.48 22 -0.72 25 47
IL17A -0.029 0.092 -10000 0 -10000 0 0
mast cell activation -0.002 0.14 0.72 4 -0.4 25 29
IFNG 0.016 0.065 0.28 27 -0.12 1 28
T cell differentiation -0.001 0.006 0.028 19 -0.022 3 22
STAT3 (dimer) 0.015 0.14 0.38 7 -0.57 7 14
STAT5A (dimer) 0.016 0.14 0.39 8 -0.59 6 14
STAT4 (dimer) 0.017 0.14 0.41 6 -0.57 6 12
STAT4 0.029 0.005 -10000 0 0 17 17
T cell activation -0.001 0.012 0.11 1 -0.25 1 2
IL27R/JAK2/TYK2 0.048 0.12 0.42 24 -0.95 3 27
GATA3 0.009 0.13 0.61 20 -10000 0 20
IL18 -0.012 0.013 0.003 138 -10000 0 138
positive regulation of mast cell cytokine production 0.015 0.14 0.38 7 -0.55 7 14
IL27/EBI3 0.046 0.031 0.17 23 -10000 0 23
IL27RA 0.019 0.12 0.46 3 -1.1 3 6
IL6 0.027 0.009 -10000 0 -10000 0 0
STAT5A 0.028 0.007 -10000 0 0 35 35
monocyte differentiation 0.001 0.004 0.018 26 -10000 0 26
IL2 -0.009 0.045 0.45 3 -10000 0 3
IL1B -0.014 0.008 0.005 76 -10000 0 76
EBI3 -0.012 0.035 0.096 27 -10000 0 27
TNF -0.015 0.007 0.009 40 -10000 0 40
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.057 0.065 0.36 9 -0.17 2 11
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.028 0.007 -10000 0 0 31 31
STAT1 (dimer)/Cbp/p300 0.009 0.088 0.22 1 -10000 0 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.046 0.2 9 -0.16 8 17
antigen processing and presentation of peptide antigen via MHC class I -0.027 0.067 0.13 3 -0.23 27 30
CaM/Ca2+ 0.053 0.069 0.33 9 -0.17 2 11
RAP1A 0.029 0.003 -10000 0 0 7 7
STAT1 (dimer)/SHP2 -0.015 0.05 0.22 3 -10000 0 3
AKT1 0 0.11 0.29 30 -0.23 6 36
MAP2K1 -0.033 0.076 0.31 14 -10000 0 14
MAP3K11 -0.026 0.083 0.33 16 -10000 0 16
IFNGR1 -0.018 0.031 0.079 15 -10000 0 15
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.009 0.095 0.21 1 -0.29 44 45
Rap1/GTP -0.063 0.042 -10000 0 -0.19 1 1
CRKL/C3G 0.041 0.012 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.068 0.062 0.27 8 -0.15 8 16
CEBPB -0.036 0.15 0.4 7 -0.59 20 27
STAT3 0.028 0.007 -10000 0 0 38 38
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.021 0.19 -10000 0 -0.86 21 21
STAT1 -0.018 0.047 0.38 2 -10000 0 2
CALM1 0.028 0.007 -10000 0 -0.001 27 27
IFN-gamma (dimer) -0.023 0.025 0.07 7 -10000 0 7
PIK3CA 0.021 0.014 -10000 0 0 171 171
STAT1 (dimer)/PIAS1 -0.02 0.051 0.37 2 -10000 0 2
CEBPB/PTGES2/Cbp/p300 -0.053 0.094 -10000 0 -0.4 18 18
mol:Ca2+ 0.052 0.061 0.34 8 -0.17 2 10
MAPK3 -0.039 0.16 0.45 3 -0.68 25 28
STAT1 (dimer) -0.029 0.1 0.5 3 -0.36 11 14
MAPK1 -0.053 0.19 0.44 4 -0.71 36 40
JAK2 -0.019 0.03 0.077 14 -10000 0 14
PIK3R1 0.021 0.014 -10000 0 0 163 163
JAK1 -0.02 0.031 0.08 14 -10000 0 14
CAMK2D 0.027 0.009 -10000 0 -0.002 49 49
DAPK1 -0.023 0.1 0.42 5 -0.41 14 19
SMAD7 0.025 0.11 0.39 28 -10000 0 28
CBL/CRKL/C3G -0.036 0.088 0.33 14 -10000 0 14
PI3K 0.019 0.083 0.27 4 -0.23 7 11
IFNG -0.023 0.025 0.07 7 -10000 0 7
apoptosis 0.003 0.097 0.47 4 -0.41 2 6
CAMK2G 0.029 0.006 -10000 0 -0.002 17 17
STAT3 (dimer) 0.028 0.007 -10000 0 0 38 38
CAMK2A 0.029 0.006 -10000 0 -0.008 14 14
CAMK2B 0.029 0.005 -10000 0 -0.002 13 13
FRAP1 -0.004 0.1 0.26 32 -0.22 6 38
PRKCD 0 0.12 0.3 30 -0.23 5 35
RAP1B 0.029 0.006 -10000 0 0 22 22
negative regulation of cell growth -0.027 0.067 0.13 3 -0.23 27 30
PTPN2 0.028 0.008 -10000 0 -0.004 27 27
EP300 0.026 0.016 0.072 13 -0.035 19 32
IRF1 0 0.094 0.2 19 -0.32 11 30
STAT1 (dimer)/PIASy -0.017 0.053 0.23 6 -10000 0 6
SOCS1 -0.032 0.22 -10000 0 -1.1 22 22
mol:GDP -0.036 0.083 0.31 14 -10000 0 14
CASP1 0.001 0.081 0.28 5 -0.22 12 17
PTGES2 0.029 0.005 -10000 0 0 17 17
IRF9 -0.022 0.063 0.29 12 -0.19 4 16
mol:PI-3-4-5-P3 -0.034 0.065 0.17 2 -0.22 7 9
RAP1/GDP -0.057 0.06 0.18 6 -10000 0 6
CBL -0.026 0.081 0.34 15 -10000 0 15
MAP3K1 -0.024 0.08 0.33 15 -10000 0 15
PIAS1 0.029 0.005 -10000 0 0 15 15
PIAS4 0.027 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.027 0.067 0.13 3 -0.23 27 30
PTPN11 -0.018 0.084 0.35 15 -0.19 1 16
CREBBP 0.026 0.015 0.072 14 -0.035 18 32
RAPGEF1 0.029 0.005 -10000 0 0 18 18
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.027 0.014 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.032 0.022 -10000 0 -10000 0 0
CDKN1B 0.02 0.077 0.25 13 -0.32 9 22
CDKN1A 0.009 0.066 0.21 13 -0.31 10 23
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.011 -10000 0 0 97 97
FOXO3 0.007 0.057 -10000 0 -0.3 9 9
AKT1 0.014 0.059 -10000 0 -0.34 10 10
BAD 0.03 0.003 -10000 0 0 4 4
AKT3 -0.1 0.11 -10000 0 -0.21 280 280
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.061 0.18 4 -0.31 11 15
AKT1/ASK1 0.033 0.064 0.21 2 -0.3 13 15
BAD/YWHAZ 0.044 0.027 -10000 0 -10000 0 0
RICTOR 0.028 0.008 -10000 0 0 39 39
RAF1 0.029 0.003 -10000 0 0 7 7
JNK cascade -0.032 0.063 0.29 13 -0.2 2 15
TSC1 0.007 0.052 -10000 0 -0.3 8 8
YWHAZ 0.026 0.01 -10000 0 0 79 79
AKT1/RAF1 0.037 0.067 0.22 2 -0.31 13 15
EP300 0.027 0.009 -10000 0 0 51 51
mol:GDP 0.014 0.058 -10000 0 -0.33 10 10
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.005 0.058 -10000 0 -0.31 11 11
YWHAQ 0.029 0.005 -10000 0 0 15 15
TBC1D4 -0.014 0.01 0.19 1 -10000 0 1
MAP3K5 0.028 0.007 -10000 0 0 32 32
MAPKAP1 0.029 0.005 -10000 0 0 18 18
negative regulation of cell cycle -0.018 0.065 0.3 7 -0.17 4 11
YWHAH 0.027 0.008 -10000 0 0 43 43
AKT1S1 0.006 0.059 0.18 1 -0.31 11 12
CASP9 0.007 0.058 0.18 1 -0.31 10 11
YWHAB 0.027 0.008 -10000 0 0 44 44
p27Kip1/KPNA1 0.021 0.089 0.26 19 -0.32 9 28
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.054 0.019 -10000 0 -10000 0 0
YWHAE 0.028 0.008 -10000 0 0 41 41
SRC 0.028 0.007 -10000 0 0 31 31
AKT2/p21CIP1 0.002 0.061 0.2 11 -0.31 9 20
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.033 -10000 0 -0.28 3 3
CHUK 0.011 0.065 0.24 8 -0.31 10 18
BAD/BCL-XL -0.006 0.062 -10000 0 -0.33 9 9
mTORC2 0.034 0.013 -10000 0 -10000 0 0
AKT2 0.006 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.016 0.084 0.22 4 -0.38 9 13
PDPK1 0.029 0.005 -10000 0 0 17 17
MDM2 0.011 0.07 0.26 4 -0.31 12 16
MAPKKK cascade -0.036 0.066 0.3 13 -0.22 2 15
MDM2/Cbp/p300 0.04 0.076 0.32 5 -0.31 13 18
TSC1/TSC2 -0.004 0.062 0.25 4 -0.32 11 15
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.073 0.31 5 -0.3 13 18
glucose import -0.02 0.035 0.19 11 -10000 0 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.012 0.046 0.2 4 -0.2 8 12
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.018 0.031 0.19 11 -10000 0 11
GSK3A 0.009 0.06 0.28 4 -0.3 9 13
FOXO1 0.006 0.052 -10000 0 -0.3 8 8
GSK3B 0.009 0.065 0.2 11 -0.32 11 22
SFN 0.028 0.007 -10000 0 0 38 38
G1/S transition of mitotic cell cycle 0.006 0.076 0.28 14 -0.32 9 23
p27Kip1/14-3-3 family 0.019 0.043 0.23 1 -0.39 1 2
PRKACA 0.025 0.01 -10000 0 0 80 80
KPNA1 0.029 0.005 -10000 0 0 18 18
HSP90AA1 0.029 0.006 -10000 0 0 21 21
YWHAG 0.029 0.004 -10000 0 0 12 12
RHEB 0.027 0.009 -10000 0 0 53 53
CREBBP 0.028 0.008 -10000 0 0 40 40
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.011 0.058 -10000 0 -0.2 28 28
epithelial cell differentiation 0.048 0.041 -10000 0 -0.13 9 9
CYFIP2 0.028 0.006 -10000 0 0 24 24
ENAH -0.05 0.062 0.21 7 -10000 0 7
EGFR 0.027 0.009 -10000 0 0 55 55
EPHA2 0.029 0.005 -10000 0 0 16 16
MYO6 -0.047 0.026 0.16 4 -0.22 1 5
CTNNB1 0.029 0.003 -10000 0 0 7 7
ABI1/Sra1/Nap1 0.052 0.03 -10000 0 -0.15 9 9
AQP5 -0.012 0.05 -10000 0 -0.32 4 4
CTNND1 0.029 0.003 -10000 0 0 5 5
mol:PI-4-5-P2 -0.045 0.027 0.16 4 -10000 0 4
regulation of calcium-dependent cell-cell adhesion -0.044 0.027 0.16 4 -10000 0 4
EGF 0.027 0.008 -10000 0 0 43 43
NCKAP1 0.029 0.005 -10000 0 0 17 17
AQP3 -0.13 0.17 -10000 0 -0.39 150 150
cortical microtubule organization 0.048 0.041 -10000 0 -0.13 9 9
GO:0000145 -0.043 0.025 0.14 4 -10000 0 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.053 0.044 -10000 0 -0.13 9 9
MLLT4 0.026 0.01 -10000 0 0 70 70
ARF6/GDP -0.065 0.034 -10000 0 -10000 0 0
ARF6 0.029 0.004 -10000 0 0 11 11
Ephrin A1/EPHA2/NCK1/GIT1 0.068 0.041 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.051 0.065 -10000 0 -0.23 52 52
PVRL2 0.028 0.007 -10000 0 0 32 32
ZYX -0.042 0.026 0.15 1 -0.22 1 2
ARF6/GTP 0.073 0.044 -10000 0 -10000 0 0
CDH1 0.026 0.01 -10000 0 0 73 73
EGFR/EGFR/EGF/EGF -0.062 0.032 0.095 7 -0.22 2 9
RhoA/GDP 0.048 0.045 -10000 0 -0.13 10 10
actin cytoskeleton organization -0.05 0.027 0.14 3 -0.22 1 4
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 140 140
GIT1 0.028 0.007 -10000 0 0 31 31
IGF1R 0.022 0.013 -10000 0 0 140 140
IGF1 0.028 0.007 -10000 0 0 33 33
DIAPH1 0.028 0.13 -10000 0 -0.54 25 25
Wnt receptor signaling pathway -0.048 0.041 0.13 9 -10000 0 9
RHOA 0.029 0.003 -10000 0 0 6 6
RhoA/GTP -0.065 0.034 -10000 0 -10000 0 0
CTNNA1 0.029 0.004 -10000 0 0 11 11
VCL -0.051 0.028 0.14 3 -0.23 1 4
EFNA1 0.027 0.008 -10000 0 0 45 45
LPP -0.048 0.033 0.14 4 -0.3 1 5
Ephrin A1/EPHA2 -0.05 0.034 0.096 21 -10000 0 21
SEC6/SEC8 -0.064 0.033 -10000 0 -0.23 1 1
MGAT3 -0.045 0.027 0.16 4 -10000 0 4
HGF/MET -0.044 0.048 0.096 49 -10000 0 49
HGF 0.029 0.005 -10000 0 0 17 17
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.011 0.058 -10000 0 -0.2 28 28
actin cable formation -0.031 0.086 0.28 12 -0.28 7 19
KIAA1543 -0.046 0.022 0.14 4 -10000 0 4
KIFC3 -0.047 0.024 0.16 2 -10000 0 2
NCK1 0.026 0.009 -10000 0 0 63 63
EXOC3 0.027 0.009 -10000 0 0 59 59
ACTN1 -0.048 0.026 0.16 4 -0.22 1 5
NCK1/GIT1 0.037 0.016 -10000 0 -10000 0 0
mol:GDP 0.048 0.041 -10000 0 -0.13 9 9
EXOC4 0.028 0.007 -10000 0 0 33 33
STX4 -0.048 0.024 0.16 4 -10000 0 4
PIP5K1C -0.046 0.027 0.16 4 -10000 0 4
LIMA1 0.029 0.006 -10000 0 0 20 20
ABI1 0.029 0.005 -10000 0 0 15 15
ROCK1 -0.046 0.076 0.24 12 -10000 0 12
adherens junction assembly -0.065 0.1 0.22 1 -0.57 15 16
IGF-1R heterotetramer/IGF1 -0.074 0.042 0.096 3 -0.22 3 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.03 0.042 -10000 0 -0.16 22 22
MET 0.025 0.011 -10000 0 0 87 87
PLEKHA7 -0.049 0.024 0.16 4 -10000 0 4
mol:GTP 0.066 0.04 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.045 0.089 0.28 15 -10000 0 15
cortical actin cytoskeleton stabilization -0.011 0.058 -10000 0 -0.2 28 28
regulation of cell-cell adhesion -0.05 0.027 0.14 3 -0.22 1 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.058 -10000 0 -0.2 28 28
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.12 0.25 0.65 8 -0.77 1 9
PCK1 0.17 0.24 0.63 63 -10000 0 63
HNF4A 0.15 0.3 0.79 29 -0.77 1 30
KCNJ11 0.12 0.27 -10000 0 -0.82 1 1
AKT1 0.096 0.19 0.41 34 -0.4 1 35
response to starvation 0 0.01 0.17 2 -10000 0 2
DLK1 0.14 0.29 0.83 18 -0.82 1 19
NKX2-1 0.11 0.18 0.7 3 -10000 0 3
ACADM 0.12 0.25 0.64 7 -0.77 1 8
TAT 0.11 0.19 0.55 9 -10000 0 9
CEBPB 0.027 0.013 0.19 2 -10000 0 2
CEBPA 0.027 0.013 0.18 2 -10000 0 2
TTR 0.14 0.18 0.72 10 -10000 0 10
PKLR 0.13 0.26 0.69 17 -0.77 1 18
APOA1 0.2 0.37 0.94 50 -1 1 51
CPT1C 0.12 0.26 0.75 14 -0.77 1 15
ALAS1 0.088 0.19 0.86 3 -0.63 1 4
TFRC 0.25 0.36 0.76 141 -10000 0 141
FOXF1 0.027 0.01 -10000 0 -10000 0 0
NF1 0.028 0.02 0.24 4 -10000 0 4
HNF1A (dimer) -0.03 0.01 -10000 0 -0.25 1 1
CPT1A 0.12 0.25 0.66 8 -0.85 2 10
HMGCS1 0.14 0.29 0.71 41 -0.77 1 42
NR3C1 -0.006 0.028 -10000 0 -10000 0 0
CPT1B 0.1 0.24 0.63 6 -0.77 1 7
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.012 -10000 0 -0.25 1 1
GCK 0.12 0.25 0.65 6 -0.77 1 7
CREB1 0.064 0.079 0.23 98 -10000 0 98
IGFBP1 0.099 0.16 0.52 4 -10000 0 4
PDX1 0.093 0.18 -10000 0 -0.98 1 1
UCP2 0.038 0.37 0.65 14 -0.78 49 63
ALDOB 0.13 0.27 -10000 0 -0.82 1 1
AFP 0.041 0.064 0.37 3 -10000 0 3
BDH1 0.15 0.28 0.74 32 -0.79 1 33
HADH 0.11 0.28 -10000 0 -0.95 4 4
F2 0.17 0.31 0.81 20 -0.96 1 21
HNF1A -0.03 0.01 -10000 0 -0.25 1 1
G6PC 0.051 0.084 -10000 0 -10000 0 0
SLC2A2 0.12 0.2 0.6 5 -10000 0 5
INS 0.028 0.023 -10000 0 -0.24 4 4
FOXA1 0.017 0.035 0.35 2 -10000 0 2
FOXA3 0.098 0.16 0.29 211 -10000 0 211
FOXA2 0.19 0.36 0.88 27 -0.92 1 28
ABCC8 0.12 0.27 -10000 0 -0.82 1 1
ALB 0.042 0.066 0.52 2 -10000 0 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.028 0.085 -10000 0 -0.24 28 28
Ran/GTP/Exportin 1/HDAC1 -0.032 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.09 0.2 1 -0.31 27 28
SUMO1 0.029 0.004 -10000 0 0 8 8
ZFPM1 0.026 0.009 -10000 0 0 64 64
NPC/RanGAP1/SUMO1/Ubc9 -0.006 0.035 -10000 0 -0.25 4 4
FKBP3 0.029 0.006 -10000 0 0 23 23
Histones 0.055 0.062 -10000 0 -0.22 13 13
YY1/LSF 0 0.064 -10000 0 -0.22 21 21
SMG5 0.029 0.006 -10000 0 0 23 23
RAN 0.029 0.004 -10000 0 0 12 12
I kappa B alpha/HDAC3 -0.022 0.042 -10000 0 -0.2 22 22
I kappa B alpha/HDAC1 0.017 0.065 -10000 0 -0.23 26 26
SAP18 0.028 0.007 -10000 0 0 31 31
RELA -0.005 0.075 0.25 1 -0.37 8 9
HDAC1/Smad7 0.051 0.022 -10000 0 -10000 0 0
RANGAP1 0.027 0.008 -10000 0 0 48 48
HDAC3/TR2 0.027 0.052 -10000 0 -0.22 14 14
NuRD/MBD3 Complex 0.003 0.066 0.18 6 -0.25 16 22
NF kappa B1 p50/RelA 0.003 0.092 0.22 1 -0.32 22 23
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.028 0.006 -10000 0 0 28 28
GATA1 0.028 0.007 -10000 0 0 31 31
Mad/Max 0.042 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.009 0.086 0.24 1 -0.34 18 19
RBBP7 0.029 0.005 -10000 0 0 19 19
NPC 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.028 0.008 -10000 0 0 39 39
MAX 0.029 0.005 -10000 0 0 16 16
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.029 0.005 -10000 0 0 18 18
NFKBIA 0.001 0.051 -10000 0 -0.31 12 12
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.001 0.068 0.18 4 -0.26 18 22
SIN3 complex 0.054 0.042 -10000 0 -10000 0 0
SMURF1 0.029 0.006 -10000 0 0 20 20
CHD3 0.028 0.007 -10000 0 0 36 36
SAP30 0.027 0.008 -10000 0 0 46 46
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.008 -10000 0 0 42 42
YY1/HDAC3 -0.011 0.063 -10000 0 -0.28 16 16
YY1/HDAC2 0.002 0.063 -10000 0 -0.23 22 22
YY1/HDAC1 0.001 0.062 -10000 0 -0.22 20 20
NuRD/MBD2 Complex (MeCP1) 0.005 0.066 0.18 5 -0.24 20 25
PPARG -0.001 0.078 0.28 1 -0.26 21 22
HDAC8/hEST1B 0.048 0.025 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 0 22 22
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -10000 0 0 18 18
TNFRSF1A 0.026 0.01 -10000 0 0 78 78
HDAC3/SMRT (N-CoR2) 0.026 0.052 -10000 0 -0.22 14 14
MBD3L2 0.028 0.007 -10000 0 0 37 37
ubiquitin-dependent protein catabolic process 0.05 0.022 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 0 40 40
NuRD/MBD3/MBD3L2 Complex -0.002 0.087 0.25 1 -0.32 21 22
HDAC1 0.027 0.008 -10000 0 0 50 50
HDAC3 0.005 0.032 -10000 0 -0.32 3 3
HDAC2 0.028 0.007 -10000 0 0 38 38
YY1 0 0.025 -10000 0 -0.19 9 9
HDAC8 0.028 0.006 -10000 0 0 26 26
SMAD7 0.028 0.006 -10000 0 0 28 28
NCOR2 0.029 0.005 -10000 0 0 17 17
MXD1 0.029 0.004 -10000 0 0 12 12
STAT3 0.003 0.04 -10000 0 -0.23 15 15
NFKB1 0.027 0.008 -10000 0 0 47 47
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.004 -10000 0 0 10 10
YY1/LSF/HDAC1 0.013 0.067 -10000 0 -0.22 20 20
YY1/SAP30/HDAC1 0.013 0.066 -10000 0 -0.22 20 20
EP300 0.027 0.009 -10000 0 0 51 51
STAT3 (dimer non-phopshorylated) 0.003 0.04 -10000 0 -0.23 15 15
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.051 -10000 0 -0.31 12 12
histone deacetylation 0.006 0.066 0.18 5 -0.24 20 25
STAT3 (dimer non-phopshorylated)/HDAC3 -0.001 0.068 -10000 0 -0.3 12 12
nuclear export -0.047 0.024 -10000 0 -10000 0 0
PRKACA 0.025 0.01 -10000 0 0 80 80
GATAD2B 0.029 0.006 -10000 0 0 21 21
GATAD2A 0.027 0.008 -10000 0 0 44 44
GATA2/HDAC3 0.025 0.052 -10000 0 -0.22 14 14
GATA1/HDAC1 0.038 0.015 -10000 0 -10000 0 0
GATA1/HDAC3 0.025 0.051 -10000 0 -0.22 14 14
CHD4 0.027 0.009 -10000 0 0 59 59
TNF-alpha/TNFR1A 0.032 0.037 -10000 0 -0.16 16 16
SIN3/HDAC complex/Mad/Max -0.001 0.075 0.24 2 -0.31 14 16
NuRD Complex -0.005 0.085 0.19 5 -0.33 18 23
positive regulation of chromatin silencing 0.052 0.06 -10000 0 -0.22 13 13
SIN3B 0.026 0.009 -10000 0 0 62 62
MTA2 0.029 0.003 -10000 0 0 6 6
SIN3A 0.029 0.005 -10000 0 0 19 19
XPO1 0.027 0.009 -10000 0 0 51 51
SUMO1/HDAC1 0.022 0.052 -10000 0 -0.22 11 11
HDAC complex 0.066 0.039 -10000 0 -0.14 2 2
GATA1/Fog1 0.037 0.016 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.05 0.023 -10000 0 -10000 0 0
TNF 0.029 0.005 -10000 0 0 15 15
negative regulation of cell growth -0.001 0.075 0.24 2 -0.31 14 16
NuRD/MBD2/PRMT5 Complex 0.005 0.066 0.18 5 -0.24 20 25
Ran/GTP/Exportin 1 0.022 0.052 -10000 0 -0.22 12 12
NF kappa B/RelA/I kappa B alpha -0.017 0.075 -10000 0 -0.29 29 29
SIN3/HDAC complex/NCoR1 -0.009 0.084 0.17 4 -0.34 22 26
TFCP2 0.027 0.008 -10000 0 0 42 42
NR2C1 0.029 0.005 -10000 0 0 14 14
MBD3 0.027 0.009 -10000 0 0 52 52
MBD2 0.028 0.007 -10000 0 0 35 35
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.022 0.049 0.23 8 -10000 0 8
NFATC2 -0.019 0.05 0.23 8 -10000 0 8
NFATC3 -0.021 0.051 0.22 9 -10000 0 9
CD40LG -0.048 0.16 0.51 22 -10000 0 22
PTGS2 -0.059 0.15 0.51 20 -10000 0 20
JUNB 0.02 0.014 -10000 0 0 189 189
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.031 0.088 35 -0.16 6 41
CaM/Ca2+ -0.017 0.031 0.088 35 -0.16 6 41
CALM1 -0.024 0.027 0.093 10 -10000 0 10
JUN -0.023 0.028 0.093 10 -10000 0 10
mol:Ca2+ -0.003 0.007 0.037 13 -0.027 1 14
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.01 0.09 2 -10000 0 2
FOSL1 0.029 0.003 -10000 0 0 5 5
CREM 0.028 0.008 -10000 0 -0.03 6 6
Jun/NFAT1-c-4/p21SNFT -0.045 0.11 0.35 27 -10000 0 27
FOS -0.021 0.025 0.099 4 -10000 0 4
IFNG -0.068 0.12 0.46 9 -10000 0 9
AP-1/NFAT1-c-4 -0.07 0.13 0.5 17 -10000 0 17
FASLG -0.052 0.16 0.5 28 -10000 0 28
NFAT1-c-4/ICER1 -0.037 0.1 0.3 30 -10000 0 30
IL2RA -0.052 0.15 0.49 17 -10000 0 17
FKBP12/FK506 0.021 0.005 -10000 0 -10000 0 0
CSF2 -0.049 0.16 0.51 22 -10000 0 22
JunB/Fra1/NFAT1-c-4 -0.059 0.098 0.3 19 -10000 0 19
IL4 -0.05 0.16 0.49 30 -10000 0 30
IL2 -0.036 0.21 -10000 0 -0.93 30 30
IL3 0.001 0.11 -10000 0 -0.65 14 14
FKBP1A 0.028 0.007 -10000 0 0 37 37
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.029 0.004 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.029 0.006 -10000 0 0 21 21
SPHK1 0.029 0.005 -10000 0 0 19 19
GNAI2 0.029 0.003 -10000 0 0 6 6
mol:S1P 0.004 0.009 0.13 3 -10000 0 3
GNAO1 0.027 0.008 -10000 0 0 46 46
mol:Sphinganine-1-P -0.031 0.013 0.19 1 -10000 0 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.039 0.17 1 -0.26 3 4
GNAI3 0.024 0.011 -10000 0 0 98 98
G12/G13 0.041 0.012 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.003 0.03 -10000 0 -0.28 3 3
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.028 0.006 -10000 0 0 27 27
S1P/S1P5/G12 0.018 0.036 0.16 1 -0.26 3 4
S1P/S1P3/Gq -0.008 0.082 -10000 0 -0.32 25 25
S1P/S1P4/Gi 0.009 0.062 0.18 2 -0.24 12 14
GNAQ 0.028 0.006 -10000 0 0 28 28
GNAZ 0.027 0.008 -10000 0 0 47 47
GNA14 0.029 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 47 47
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 14 14
GNA11 0.025 0.011 -10000 0 0 84 84
ABCC1 0.029 0.005 -10000 0 0 17 17
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.052 0.048 -10000 0 -0.14 12 12
MAP4K1 0.026 0.01 -10000 0 0 68 68
MAP3K8 0.029 0.005 -10000 0 0 16 16
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.029 0.004 -10000 0 0 11 11
CRKL 0.028 0.007 -10000 0 0 31 31
MAP3K1 -0.016 0.05 -10000 0 -0.26 10 10
JUN -0.001 0.064 0.24 1 -0.57 4 5
MAP3K7 -0.014 0.046 0.15 3 -0.21 10 13
GRAP2 0.027 0.008 -10000 0 0 48 48
CRK 0.028 0.007 -10000 0 0 37 37
MAP2K4 -0.026 0.084 0.26 1 -0.35 21 22
LAT 0.029 0.004 -10000 0 0 8 8
LCP2 0.028 0.007 -10000 0 0 35 35
MAPK8 0.004 0.056 -10000 0 -0.59 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.061 -10000 0 -0.27 16 16
LAT/GRAP2/SLP76/HPK1/HIP-55 0.059 0.055 -10000 0 -0.14 12 12
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.008 0.12 0.38 18 -0.32 1 19
CRKL -0.019 0.12 0.39 13 -0.33 1 14
HRAS -0.019 0.12 0.39 10 -0.38 4 14
mol:PIP3 0.008 0.13 0.4 16 -0.43 2 18
SPRED1 0.028 0.008 -10000 0 0 41 41
SPRED2 0.029 0.004 -10000 0 0 10 10
GAB1 -0.01 0.12 0.42 15 -0.41 2 17
FOXO3 -0.013 0.13 0.41 13 -0.42 10 23
AKT1 -0.006 0.14 0.4 16 -0.45 10 26
BAD -0.013 0.13 0.38 15 -0.42 10 25
megakaryocyte differentiation -0.006 0.13 0.45 15 -0.41 2 17
GSK3B -0.008 0.14 0.39 17 -0.43 9 26
RAF1 -0.02 0.11 0.34 14 -0.32 4 18
SHC1 0.029 0.006 -10000 0 0 20 20
STAT3 -0.011 0.12 0.42 13 -0.41 2 15
STAT1 -0.012 0.23 0.65 10 -0.75 8 18
HRAS/SPRED1 -0.012 0.11 0.34 12 -0.32 4 16
cell proliferation -0.009 0.12 0.44 15 -0.41 2 17
PIK3CA 0.017 0.018 -10000 0 -0.029 35 35
TEC 0.027 0.009 -10000 0 0 56 56
RPS6KB1 0.001 0.14 0.43 16 -0.47 2 18
HRAS/SPRED2 -0.011 0.11 0.35 12 -0.32 4 16
LYN/TEC/p62DOK 0.013 0.13 0.4 10 -0.38 3 13
MAPK3 -0.028 0.092 0.32 8 -0.31 4 12
STAP1 -0.008 0.12 0.42 15 -0.41 2 17
GRAP2 0.027 0.008 -10000 0 0 48 48
JAK2 -0.021 0.22 0.57 15 -0.72 9 24
STAT1 (dimer) -0.01 0.23 0.64 11 -0.73 8 19
mol:Gleevec 0.001 0.009 -10000 0 -0.036 17 17
GRB2/SOCS1/VAV1 0.015 0.14 0.41 13 -0.41 2 15
actin filament polymerization -0.001 0.12 0.43 15 -0.4 2 17
LYN 0.027 0.009 -10000 0 0 52 52
STAP1/STAT5A (dimer) -0.031 0.18 0.47 14 -0.51 16 30
PIK3R1 0.021 0.015 -10000 0 -0.029 7 7
CBL/CRKL/GRB2 -0.015 0.13 0.37 14 -0.32 1 15
PI3K -0.017 0.12 0.42 9 -0.38 4 13
PTEN 0.026 0.014 -10000 0 -0.031 23 23
SCF/KIT/EPO/EPOR 0.007 0.23 0.63 9 -0.68 4 13
MAPK8 -0.009 0.13 0.45 15 -0.41 2 17
STAT3 (dimer) -0.011 0.12 0.42 13 -0.41 2 15
positive regulation of transcription -0.021 0.08 0.3 8 -0.26 3 11
mol:GDP -0.017 0.12 0.38 8 -0.35 4 12
PIK3C2B -0.01 0.13 0.45 15 -0.41 2 17
CBL/CRKL -0.016 0.12 0.38 16 -0.32 1 17
FER -0.01 0.12 0.42 14 -0.41 2 16
SH2B3 -0.009 0.12 0.42 15 -0.34 1 16
PDPK1 0 0.12 0.39 17 -0.39 2 19
SNAI2 -0.01 0.12 0.42 14 -0.41 2 16
positive regulation of cell proliferation -0.017 0.2 0.55 14 -0.57 13 27
KITLG 0.021 0.04 0.14 10 -10000 0 10
cell motility -0.017 0.2 0.55 14 -0.57 13 27
PTPN6 0 0.036 -10000 0 -0.076 15 15
EPOR -0.029 0.2 1 1 -0.75 16 17
STAT5A (dimer) -0.021 0.18 0.5 15 -0.53 15 30
SOCS1 0.028 0.007 -10000 0 0 31 31
cell migration 0.011 0.12 0.41 2 -0.43 13 15
SOS1 0.028 0.007 -10000 0 0 34 34
EPO 0.021 0.032 0.091 9 -0.044 18 27
VAV1 0.028 0.008 -10000 0 0 41 41
GRB10 -0.009 0.12 0.42 15 -0.41 2 17
PTPN11 0.001 0.034 -10000 0 -0.07 11 11
SCF/KIT 0.002 0.13 0.47 15 -0.42 2 17
GO:0007205 0 0.012 -10000 0 -0.046 18 18
MAP2K1 -0.021 0.094 0.32 13 -0.27 2 15
CBL 0.029 0.005 -10000 0 0 15 15
KIT -0.011 0.21 0.69 17 -0.7 13 30
MAP2K2 -0.027 0.091 0.33 9 -0.3 2 11
SHC/Grb2/SOS1 0.019 0.13 0.42 11 -0.41 2 13
STAT5A -0.02 0.19 0.5 15 -0.54 15 30
GRB2 0.029 0.006 -10000 0 0 20 20
response to radiation -0.007 0.13 0.42 15 -0.41 2 17
SHC/GRAP2 0.039 0.014 -10000 0 -10000 0 0
PTPRO -0.007 0.12 0.45 15 -0.41 2 17
SH2B2 0 0.12 0.43 15 -0.4 2 17
DOK1 0.029 0.004 -10000 0 0 10 10
MATK -0.01 0.12 0.43 13 -0.41 2 15
CREBBP 0.001 0.084 0.36 16 -10000 0 16
BCL2 -0.18 0.45 0.95 1 -1.1 103 104
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.005 0.043 0.13 53 -0.15 1 54
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.001 0.055 0.12 1 -0.2 30 31
AP2 0.026 0.045 -10000 0 -0.16 25 25
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.032 0.023 -10000 0 -10000 0 0
CLTB 0.029 0.005 -10000 0 0 14 14
coatomer protein complex/ARF1/GTP/ER cargo protein -0.001 0.041 -10000 0 -0.18 23 23
CD4 0.026 0.01 -10000 0 0 72 72
CLTA 0.029 0.004 -10000 0 0 12 12
mol:GTP -0.004 0.004 0.012 4 -0.022 25 29
ARFGAP1 -0.015 0.005 0 61 -10000 0 61
mol:PI-4-5-P2 -0.004 0.024 0.093 7 -0.15 1 8
ARF1/GTP -0.025 0.03 -10000 0 -0.15 26 26
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.015 0.031 -10000 0 -0.16 21 21
mol:Choline -0.005 0.024 0.093 7 -0.15 1 8
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.019 0.024 0.048 1 -10000 0 1
DDEF1 -0.003 0.023 0.093 7 -0.16 1 8
ARF1/GDP -0.002 0.013 -10000 0 -0.099 4 4
AP2M1 0.025 0.011 -10000 0 0 96 96
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.024 0.025 -10000 0 -0.12 24 24
Rac/GTP 0.019 0.012 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.035 -10000 0 -0.12 24 24
ARFIP2 -0.029 0.011 0.027 11 -10000 0 11
COPA 0.029 0.005 -10000 0 0 19 19
RAC1 0.028 0.006 -10000 0 0 28 28
ARF1/GTP/coatomer protein complex -0.001 0.04 -10000 0 -0.16 28 28
ARF1/GTP/ARHGAP10 0.012 0.031 -10000 0 -0.13 25 25
GGA3 0.029 0.005 -10000 0 0 19 19
ARF1/GTP/Membrin 0.006 0.053 -10000 0 -0.16 41 41
AP2A1 0.027 0.008 -10000 0 0 49 49
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.01 0.035 -10000 0 -0.18 6 6
ARF1/GDP/Membrin 0.012 0.058 -10000 0 -0.26 17 17
Arfaptin 2/Rac/GDP 0.034 0.02 -10000 0 -10000 0 0
CYTH2 -0.004 0.004 0.012 4 -0.022 25 29
ARF1/GTP/GGA3 0.029 0.039 -10000 0 -0.14 25 25
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.021 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.005 0.044 -10000 0 -0.22 7 7
PLD2 -0.005 0.024 0.093 7 -0.15 1 8
ARF-GAP1/v-SNARE -0.015 0.005 0 61 -10000 0 61
PIP5K1A -0.004 0.024 0.094 7 -0.15 1 8
ARF1/GTP/Membrin/GBF1/p115 0.004 0.037 -10000 0 -0.13 32 32
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.005 0.024 0.093 7 -0.15 1 8
KDEL Receptor/Ligand/ARF-GAP1 -0.015 0.005 0 61 -10000 0 61
GOSR2 0.001 0.054 -10000 0 -0.35 12 12
USO1 0.001 0.053 -10000 0 -0.35 12 12
GBF1 0.001 0.052 -10000 0 -0.34 12 12
ARF1/GTP/Arfaptin 2 0.027 0.041 -10000 0 -0.14 25 25
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.035 0.044 -10000 0 -0.15 20 20
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.065 0.038 -10000 0 -0.14 5 5
HDAC3 0.029 0.003 -10000 0 0 7 7
Ran/GTP/Exportin 1/HDAC4 -0.033 0.012 -10000 0 -10000 0 0
GATA1/HDAC4 0.04 0.013 -10000 0 -10000 0 0
GATA1/HDAC5 0.038 0.022 -10000 0 -0.16 4 4
GATA2/HDAC5 0.037 0.028 -10000 0 -0.16 9 9
HDAC5/BCL6/BCoR 0.042 0.04 -10000 0 -0.15 15 15
HDAC9 0.027 0.009 -10000 0 0 51 51
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.03 -10000 0 -0.15 8 8
HDAC4/ANKRA2 0.039 0.015 -10000 0 -10000 0 0
HDAC5/YWHAB 0.037 0.022 -10000 0 -0.16 4 4
NPC/RanGAP1/SUMO1/Ubc9 -0.006 0.035 -10000 0 -0.25 4 4
GATA2 0.028 0.006 -10000 0 0 28 28
HDAC4/RFXANK 0.038 0.015 -10000 0 -10000 0 0
BCOR 0.029 0.005 -10000 0 0 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.013 -10000 0 0 132 132
HDAC5 0.028 0.007 -10000 0 0 29 29
GNB1/GNG2 0.041 0.014 -10000 0 -0.16 1 1
Histones -0.02 0.07 -10000 0 -0.23 31 31
ADRBK1 0.029 0.003 -10000 0 0 7 7
HDAC4 0.029 0.006 -10000 0 0 20 20
XPO1 0.027 0.009 -10000 0 0 51 51
HDAC5/ANKRA2 0.037 0.023 -10000 0 -0.16 4 4
HDAC4/Ubc9 0.041 0.011 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.023 -10000 0 -0.16 5 5
TUBA1B 0.029 0.003 -10000 0 0 5 5
HDAC6 0.028 0.007 -10000 0 0 31 31
HDAC5/RFXANK 0.037 0.023 -10000 0 -0.16 4 4
CAMK4 0.028 0.008 -10000 0 0 39 39
Tubulin/HDAC6 0.052 0.021 -10000 0 -10000 0 0
SUMO1 0.029 0.004 -10000 0 0 8 8
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 0 44 44
GATA1 0.028 0.007 -10000 0 0 31 31
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.028 0.008 -10000 0 0 41 41
NR3C1 0.029 0.005 -10000 0 0 15 15
SUMO1/HDAC4 0.023 0.055 -10000 0 -0.22 13 13
SRF 0.028 0.007 -10000 0 0 29 29
HDAC4/YWHAB 0.039 0.014 -10000 0 -10000 0 0
Tubulin 0.04 0.012 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.039 0.016 -10000 0 -0.16 1 1
GNB1 0.028 0.006 -10000 0 0 24 24
RANGAP1 0.027 0.008 -10000 0 0 48 48
BCL6/BCoR 0.032 0.033 -10000 0 -0.16 12 12
HDAC4/HDAC3/SMRT (N-CoR2) 0.054 0.029 -10000 0 -0.15 9 9
HDAC4/SRF 0.051 0.024 -10000 0 -0.15 2 2
HDAC4/ER alpha 0.013 0.069 -10000 0 -0.16 72 72
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.02 0.07 -10000 0 -0.23 31 31
cell motility 0.051 0.021 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 0 22 22
HDAC7/HDAC3 0.022 0.002 -10000 0 -10000 0 0
BCL6 0.024 0.011 -10000 0 0 98 98
HDAC4/CaMK II delta B 0.029 0.006 -10000 0 0 20 20
Hsp90/HDAC6 0.04 0.013 -10000 0 -10000 0 0
ESR1 0.024 0.012 -10000 0 0 109 109
HDAC6/HDAC11 0.041 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.052 -10000 0 -0.22 12 12
NPC 0.017 0.002 -10000 0 -10000 0 0
MEF2C 0.026 0.01 -10000 0 0 66 66
RAN 0.029 0.004 -10000 0 0 12 12
HDAC4/MEF2C 0.058 0.065 -10000 0 -0.14 29 29
GNG2 0.029 0.004 -10000 0 0 12 12
NCOR2 0.029 0.005 -10000 0 0 17 17
TUBB2A 0.027 0.008 -10000 0 0 43 43
HDAC11 0.029 0.003 -10000 0 0 7 7
HSP90AA1 0.029 0.006 -10000 0 0 21 21
RANBP2 0.029 0.004 -10000 0 0 10 10
ANKRA2 0.027 0.009 -10000 0 0 56 56
RFXANK 0.027 0.009 -10000 0 0 53 53
nuclear import -0.016 0.039 0.19 5 -10000 0 5
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.009 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.052 0.023 -10000 0 -0.15 1 1
forebrain development -0.005 0.086 -10000 0 -0.52 4 4
GNAO1 0.023 0.018 -10000 0 -0.035 40 40
SMO/beta Arrestin2 0.033 0.025 -10000 0 -10000 0 0
SMO 0.023 0.019 -10000 0 -0.038 45 45
ARRB2 0.024 0.017 -10000 0 -0.034 39 39
GLI3/SPOP 0.018 0.09 0.23 6 -0.34 14 20
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.029 0.005 -10000 0 0 19 19
GNAI2 0.024 0.017 -10000 0 -0.035 42 42
SIN3/HDAC complex 0.055 0.043 -10000 0 -10000 0 0
GNAI1 0.023 0.017 -10000 0 -0.034 41 41
XPO1 0.021 0.02 -10000 0 -0.044 36 36
GLI1/Su(fu) -0.002 0.09 -10000 0 -0.56 5 5
SAP30 0.027 0.008 -10000 0 -10000 0 0
mol:GDP 0.023 0.019 -10000 0 -0.038 45 45
MIM/GLI2A 0.013 0.036 -10000 0 -0.13 29 29
IFT88 0.027 0.008 -10000 0 0 44 44
GNAI3 0.021 0.017 -10000 0 -0.034 29 29
GLI2 -0.009 0.077 0.22 1 -0.35 14 15
GLI3 0.004 0.087 0.23 6 -0.35 14 20
CSNK1D 0.028 0.006 -10000 0 0 25 25
CSNK1E 0.027 0.008 -10000 0 0 46 46
SAP18 0.028 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.008 -10000 0 0 44 44
GNG2 0.029 0.004 -10000 0 0 12 12
Gi family/GTP 0.009 0.052 -10000 0 -0.21 9 9
SIN3B 0.027 0.009 -10000 0 -10000 0 0
SIN3A 0.029 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) -0.001 0.097 0.22 3 -0.38 17 20
GLI2/Su(fu) -0.009 0.089 0.2 1 -0.39 18 19
FOXA2 -0.036 0.21 -10000 0 -0.78 38 38
neural tube patterning -0.005 0.086 -10000 0 -0.52 4 4
SPOP 0.029 0.005 -10000 0 0 16 16
Su(fu)/PIAS1 0.019 0.044 -10000 0 -0.19 16 16
GNB1 0.028 0.006 -10000 0 0 24 24
CSNK1G2 0.027 0.008 -10000 0 0 46 46
CSNK1G3 0.029 0.006 -10000 0 0 21 21
MTSS1 0.013 0.036 -10000 0 -0.13 29 29
embryonic limb morphogenesis -0.005 0.086 -10000 0 -0.52 4 4
SUFU 0.006 0.016 -10000 0 -10000 0 0
LGALS3 0.027 0.009 -10000 0 0 56 56
catabolic process 0.006 0.11 0.25 1 -0.43 18 19
GLI3A/CBP -0.03 0.013 -10000 0 -10000 0 0
KIF3A 0.029 0.005 -10000 0 0 17 17
GLI1 -0.005 0.087 -10000 0 -0.53 4 4
RAB23 0.029 0.006 -10000 0 0 20 20
CSNK1A1 0.029 0.004 -10000 0 0 13 13
IFT172 0.029 0.005 -10000 0 0 17 17
RBBP7 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.016 0.045 -10000 0 -0.19 15 15
GNAZ 0.023 0.018 -10000 0 -0.034 38 38
RBBP4 0.028 0.008 -10000 0 -10000 0 0
CSNK1G1 0.029 0.005 -10000 0 0 14 14
PIAS1 0.029 0.005 -10000 0 0 15 15
PRKACA 0.025 0.01 -10000 0 0 80 80
GLI2/SPOP 0.006 0.086 0.21 1 -0.37 15 16
STK36 0.022 0.021 -10000 0 -0.042 50 50
Gi family/GNB1/GNG2/GDP 0.003 0.064 -10000 0 -0.3 7 7
PTCH1 -0.018 0.13 -10000 0 -0.91 9 9
MIM/GLI1 -0.008 0.11 -10000 0 -0.62 4 4
CREBBP -0.03 0.014 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.001 0.099 0.19 6 -0.4 20 26
EPO 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
BCL2L1 -0.007 0.13 0.59 1 -0.45 2 3
CRKL -0.026 0.092 0.27 13 -10000 0 13
mol:DAG -0.034 0.075 0.36 2 -0.28 7 9
HRAS -0.033 0.1 0.27 23 -10000 0 23
MAPK8 -0.018 0.078 0.18 35 -10000 0 35
RAP1A -0.025 0.095 0.27 15 -10000 0 15
GAB1 -0.024 0.095 0.27 15 -10000 0 15
MAPK14 -0.018 0.078 0.17 36 -10000 0 36
EPO -0.02 0.034 0.077 6 -10000 0 6
PLCG1 -0.034 0.077 0.36 2 -0.29 7 9
EPOR/TRPC2/IP3 Receptors -0.023 0.029 0.076 2 -10000 0 2
RAPGEF1 0.029 0.005 -10000 0 0 18 18
EPO/EPOR (dimer)/SOCS3 0.036 0.049 0.2 1 -0.16 2 3
GAB1/SHC/GRB2/SOS1 -0.037 0.099 0.26 13 -10000 0 13
EPO/EPOR (dimer) 0.024 0.042 0.16 1 -10000 0 1
IRS2 -0.024 0.094 0.27 15 -10000 0 15
STAT1 -0.024 0.076 0.49 2 -0.34 3 5
STAT5B -0.045 0.095 0.44 2 -0.32 6 8
cell proliferation -0.024 0.082 0.19 32 -10000 0 32
GAB1/SHIP/PIK3R1/SHP2/SHC -0.065 0.078 0.17 1 -0.23 16 17
TEC -0.021 0.092 0.27 14 -10000 0 14
SOCS3 0.029 0.006 -10000 0 0 21 21
STAT1 (dimer) -0.024 0.076 0.48 2 -0.34 3 5
JAK2 -0.019 0.033 0.071 9 -10000 0 9
PIK3R1 0.021 0.013 -10000 0 0 161 161
EPO/EPOR (dimer)/JAK2 0.035 0.092 0.48 2 -0.21 5 7
EPO/EPOR 0.024 0.042 0.16 1 -10000 0 1
LYN 0.016 0.028 0.09 2 -0.047 83 85
TEC/VAV2 -0.029 0.091 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration -0.023 0.029 0.076 2 -10000 0 2
SHC1 0.029 0.006 -10000 0 0 20 20
EPO/EPOR (dimer)/LYN 0.028 0.06 0.31 2 -0.16 8 10
mol:IP3 -0.034 0.075 0.36 2 -0.28 7 9
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.048 0.09 0.26 8 -0.24 9 17
SH2B3 -0.018 0.035 0.068 14 -10000 0 14
NFKB1 -0.018 0.077 0.18 33 -0.24 2 35
EPO/EPOR (dimer)/JAK2/SOCS3 0.008 0.03 0.2 1 -0.19 4 5
PTPN6 -0.033 0.076 0.28 6 -10000 0 6
TEC/VAV2/GRB2 -0.03 0.1 0.27 12 -10000 0 12
EPOR -0.023 0.029 0.077 2 -10000 0 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.038 0.099 0.26 13 -10000 0 13
SOS1 0.028 0.007 -10000 0 0 34 34
PLCG2 0.026 0.01 -10000 0 0 65 65
CRKL/CBL/C3G -0.039 0.095 0.26 11 -10000 0 11
VAV2 -0.026 0.093 0.27 14 -10000 0 14
CBL -0.024 0.095 0.27 15 -10000 0 15
SHC/Grb2/SOS1 -0.052 0.065 0.27 2 -10000 0 2
STAT5A -0.045 0.097 0.44 2 -0.33 9 11
GRB2 0.029 0.006 -10000 0 0 20 20
STAT5 (dimer) -0.076 0.14 0.57 2 -0.4 44 46
LYN/PLCgamma2 0.021 0.042 -10000 0 -0.16 12 12
PTPN11 0.029 0.004 -10000 0 0 9 9
BTK -0.024 0.095 0.27 15 -10000 0 15
BCL2 -0.07 0.26 0.5 1 -0.64 84 85
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0 0.094 0.53 8 -0.85 3 11
MKNK1 0.029 0.005 -10000 0 0 15 15
MAPK14 -0.01 0.059 0.2 24 -0.3 3 27
ATF2/c-Jun -0.038 0.055 0.14 7 -0.25 7 14
MAPK11 -0.018 0.051 0.2 18 -0.3 3 21
MITF -0.001 0.047 0.22 17 -0.34 3 20
MAPKAPK5 -0.001 0.047 0.22 17 -0.34 3 20
KRT8 -0.001 0.049 0.25 8 -0.3 4 12
MAPKAPK3 0.029 0.003 -10000 0 0 5 5
MAPKAPK2 0.029 0.004 -10000 0 0 11 11
p38alpha-beta/CK2 -0.022 0.065 0.27 17 -0.42 3 20
CEBPB 0 0.045 0.22 17 -0.25 3 20
SLC9A1 -0.002 0.047 0.22 17 -0.34 3 20
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.001 0.072 0.36 17 -0.33 3 20
p38alpha-beta/MNK1 0.045 0.054 0.25 17 -0.35 3 20
JUN -0.037 0.055 -10000 0 -0.25 7 7
PPARGC1A 0 0.049 0.22 17 -0.34 3 20
USF1 0 0.05 0.23 17 -0.34 3 20
RAB5/GDP/GDI1 -0.005 0.071 -10000 0 -0.2 10 10
NOS2 0 0.047 0.22 17 -0.33 3 20
DDIT3 0.011 0.065 0.23 19 -0.34 3 22
RAB5A 0.029 0.004 -10000 0 0 8 8
HSPB1 -0.011 0.044 0.26 4 -0.29 3 7
p38alpha-beta/HBP1 0.043 0.054 0.25 17 -0.35 3 20
CREB1 -0.027 0.098 0.24 9 -0.21 99 108
RAB5/GDP 0.022 0.003 -10000 0 -10000 0 0
EIF4E -0.035 0.053 0.18 15 -0.32 3 18
RPS6KA4 -0.001 0.047 0.22 17 -0.34 3 20
PLA2G4A -0.018 0.046 0.18 6 -0.38 3 9
GDI1 -0.002 0.05 0.23 17 -0.29 5 22
TP53 -0.022 0.06 0.26 8 -0.46 3 11
RPS6KA5 -0.001 0.047 0.22 17 -0.34 3 20
ESR1 -0.025 0.079 0.22 14 -0.22 60 74
HBP1 0.028 0.007 -10000 0 0 37 37
MEF2C -0.006 0.057 0.22 15 -0.26 13 28
MEF2A -0.002 0.046 0.25 7 -0.34 3 10
EIF4EBP1 -0.023 0.093 0.24 9 -0.36 3 12
KRT19 -0.008 0.061 0.25 8 -0.23 20 28
ELK4 -0.001 0.047 0.22 16 -0.34 3 19
ATF6 -0.001 0.049 0.23 17 -0.34 3 20
ATF1 -0.028 0.099 0.24 9 -0.35 3 12
p38alpha-beta/MAPKAPK2 0.045 0.052 0.25 15 -0.35 3 18
p38alpha-beta/MAPKAPK3 0.046 0.054 0.25 17 -0.35 3 20
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.04 0.021 0.2 1 -10000 0 1
KIRREL -0.022 0.03 0.049 67 -10000 0 67
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.041 0.022 -10000 0 -0.2 1 1
PLCG1 0.028 0.007 -10000 0 0 31 31
ARRB2 0.028 0.006 -10000 0 0 26 26
WASL 0.029 0.006 -10000 0 0 22 22
Nephrin/NEPH1/podocin/CD2AP 0.067 0.038 0.2 1 -10000 0 1
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.034 0.16 1 -0.19 1 2
FYN -0.004 0.064 0.14 76 -0.21 1 77
mol:Ca2+ 0.061 0.038 -10000 0 -0.17 1 1
mol:DAG 0.063 0.039 -10000 0 -0.17 1 1
NPHS2 -0.02 0.033 0.051 80 -10000 0 80
mol:IP3 0.063 0.039 -10000 0 -0.17 1 1
regulation of endocytosis 0.032 0.053 -10000 0 -0.21 1 1
Nephrin/NEPH1/podocin/Cholesterol 0.052 0.031 0.16 3 -0.16 1 4
establishment of cell polarity 0.04 0.021 -10000 0 -0.2 1 1
Nephrin/NEPH1/podocin/NCK1-2 0.082 0.047 -10000 0 -0.16 1 1
Nephrin/NEPH1/beta Arrestin2 0.034 0.054 -10000 0 -0.21 1 1
NPHS1 -0.024 0.027 0.053 38 -10000 0 38
Nephrin/NEPH1/podocin 0.03 0.049 0.19 3 -0.22 1 4
TJP1 0.028 0.008 -10000 0 0 39 39
NCK1 0.026 0.009 -10000 0 0 63 63
NCK2 0.029 0.004 -10000 0 0 11 11
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.067 0.039 -10000 0 -0.17 1 1
CD2AP 0.028 0.007 -10000 0 0 31 31
Nephrin/NEPH1/podocin/GRB2 0.067 0.039 0.2 1 -0.17 1 2
GRB2 0.029 0.006 -10000 0 0 20 20
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.072 0.15 82 -0.15 1 83
cytoskeleton organization -0.017 0.048 0.2 12 -0.2 1 13
Nephrin/NEPH1 0.034 0.018 -10000 0 -0.13 1 1
Nephrin/NEPH1/ZO-1 0.049 0.03 -10000 0 -0.16 1 1
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.02 0.057 0.19 9 -0.16 1 10
GNAI2 0.029 0.003 -10000 0 0 6 6
S1P/S1P5/G12 0.019 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.027 0.008 -10000 0 0 46 46
RhoA/GTP 0.021 0.058 0.17 1 -0.19 9 10
negative regulation of cAMP metabolic process 0.012 0.052 0.18 1 -0.2 10 11
GNAZ 0.027 0.008 -10000 0 0 47 47
GNAI3 0.024 0.011 -10000 0 0 98 98
GNA12 0.028 0.007 -10000 0 0 34 34
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.012 0.052 0.18 1 -0.2 10 11
RhoA/GDP 0.022 0.007 -10000 0 -0.15 1 1
RHOA 0.029 0.003 -10000 0 0 6 6
GNAI1 0.028 0.006 -10000 0 0 27 27
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.068 -10000 0 -0.17 67 67
AKT1 -0.049 0.11 -10000 0 -0.39 7 7
PTK2B -0.044 0.099 0.3 12 -0.31 2 14
VEGFR2 homodimer/Frs2 -0.06 0.048 -10000 0 -10000 0 0
CAV1 0.024 0.012 -10000 0 0 109 109
CALM1 0.028 0.006 -10000 0 0 26 26
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.059 0.05 0.28 1 -10000 0 1
endothelial cell proliferation -0.029 0.1 0.34 3 -0.38 4 7
mol:Ca2+ -0.047 0.081 0.32 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.011 0.09 0.28 1 -0.23 1 2
RP11-342D11.1 -0.047 0.069 0.33 2 -10000 0 2
CDH5 0.027 0.009 -10000 0 0 60 60
VEGFA homodimer 0.068 0.036 -10000 0 -0.14 1 1
SHC1 0.029 0.006 -10000 0 0 20 20
SHC2 0.025 0.01 -10000 0 0 81 81
HRAS/GDP -0.068 0.065 -10000 0 -10000 0 0
SH2D2A 0.029 0.005 -10000 0 0 14 14
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.022 0.086 -10000 0 -0.45 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.061 0.05 0.28 1 -10000 0 1
VEGFR1 homodimer 0.028 0.006 -10000 0 0 28 28
SHC/GRB2/SOS1 0.022 0.096 -10000 0 -10000 0 0
GRB10 -0.049 0.081 0.32 4 -10000 0 4
PTPN11 0.029 0.004 -10000 0 0 9 9
GRB2 0.029 0.006 -10000 0 0 20 20
PAK1 0.027 0.008 -10000 0 0 47 47
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.014 0.097 0.28 1 -0.23 1 2
HRAS 0.028 0.006 -10000 0 0 28 28
VEGF/Rho/ROCK1/Integrin Complex -0.026 0.093 0.29 1 -0.35 13 14
HIF1A 0.029 0.005 -10000 0 0 17 17
FRS2 0.028 0.007 -10000 0 0 30 30
oxygen and reactive oxygen species metabolic process -0.054 0.07 0.27 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.029 0.005 -10000 0 0 16 16
Nck/Pak 0.036 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.07 0.06 0.28 1 -0.24 1 2
mol:GDP -0.061 0.071 0.22 1 -10000 0 1
mol:NADP -0.019 0.086 0.3 1 -0.47 3 4
eNOS/Hsp90 -0.021 0.087 0.29 2 -0.45 3 5
PIK3R1 0.021 0.013 -10000 0 0 161 161
mol:IP3 -0.047 0.081 0.32 4 -10000 0 4
HIF1A/ARNT 0.04 0.015 -10000 0 -0.16 1 1
SHB 0.029 0.004 -10000 0 0 8 8
VEGFA -0.026 0.01 -10000 0 -10000 0 0
VEGFC 0.024 0.012 -10000 0 0 112 112
FAK1/Vinculin -0.038 0.12 0.34 5 -0.39 9 14
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 0 6 6
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0 0.1 0.28 1 -0.24 28 29
PTPN6 0.027 0.009 -10000 0 0 59 59
EPAS1 -0.025 0.015 -10000 0 -10000 0 0
mol:L-citrulline -0.019 0.086 0.3 1 -0.47 3 4
ITGAV 0.028 0.007 -10000 0 0 33 33
PIK3CA 0.021 0.014 -10000 0 0 171 171
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.015 0.088 0.28 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer -0.062 0.052 0.2 3 -10000 0 3
VEGFR2/3 heterodimer -0.063 0.048 -10000 0 -10000 0 0
VEGFB 0.028 0.006 -10000 0 0 24 24
MAPK11 -0.045 0.089 0.35 4 -0.33 1 5
VEGFR2 homodimer -0.061 0.064 0.4 2 -10000 0 2
FLT1 0.028 0.006 -10000 0 0 28 28
NEDD4 -0.029 0.006 -10000 0 -10000 0 0
MAPK3 -0.042 0.088 0.33 8 -10000 0 8
MAPK1 -0.039 0.089 0.33 9 -10000 0 9
VEGFA145/NRP2 0.036 0.017 -10000 0 -10000 0 0
VEGFR1/2 heterodimer -0.062 0.049 -10000 0 -10000 0 0
KDR -0.061 0.064 0.41 2 -10000 0 2
VEGFA165/NRP1/VEGFR2 homodimer -0.049 0.072 0.26 1 -10000 0 1
SRC 0.028 0.007 -10000 0 0 31 31
platelet activating factor biosynthetic process -0.041 0.091 0.33 9 -10000 0 9
PI3K -0.046 0.087 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.056 0.051 0.28 1 -10000 0 1
FES -0.049 0.082 0.33 4 -10000 0 4
GAB1 -0.048 0.093 0.3 2 -0.34 4 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.058 0.049 0.28 1 -10000 0 1
CTNNB1 0.029 0.003 -10000 0 0 7 7
SOS1 0.028 0.007 -10000 0 0 34 34
ARNT 0.028 0.007 -10000 0 0 36 36
eNOS/Caveolin-1 -0.025 0.091 -10000 0 -0.47 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.057 0.049 0.28 1 -10000 0 1
PI3K/GAB1 -0.058 0.14 0.29 1 -0.37 22 23
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.024 0.09 0.28 1 -10000 0 1
PRKACA 0.025 0.01 -10000 0 0 80 80
VEGFR2/3 heterodimer/VEGFC homodimer -0.073 0.058 0.28 1 -0.24 16 17
HSP90AA1 0.029 0.006 -10000 0 0 21 21
CDC42 -0.05 0.084 0.33 4 -10000 0 4
actin cytoskeleton reorganization -0.06 0.049 0.27 1 -10000 0 1
PTK2 -0.046 0.11 0.36 3 -0.4 9 12
EDG1 -0.047 0.069 0.33 2 -10000 0 2
mol:DAG -0.047 0.081 0.32 4 -10000 0 4
CaM/Ca2+ -0.051 0.08 0.3 3 -10000 0 3
MAP2K3 -0.043 0.078 0.34 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.061 0.062 0.23 4 -10000 0 4
PLCG1 -0.048 0.082 0.33 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.015 0.087 0.28 1 -10000 0 1
IQGAP1 0.028 0.006 -10000 0 0 25 25
YES1 0.028 0.008 -10000 0 0 40 40
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.061 0.05 0.28 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.054 0.049 0.28 1 -10000 0 1
cell migration -0.046 0.12 0.31 5 -0.37 10 15
mol:PI-3-4-5-P3 -0.044 0.083 0.23 2 -10000 0 2
FYN 0.024 0.011 -10000 0 0 99 99
VEGFB/NRP1 -0.05 0.081 0.3 4 -10000 0 4
mol:NO -0.019 0.086 0.3 1 -0.47 3 4
PXN 0.029 0.005 -10000 0 0 14 14
HRAS/GTP -0.074 0.05 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.065 0.053 0.26 1 -10000 0 1
VHL 0.029 0.004 -10000 0 0 9 9
ITGB3 0.024 0.011 -10000 0 0 98 98
NOS3 -0.022 0.092 0.31 1 -0.54 3 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.064 0.055 0.28 1 -10000 0 1
RAC1 0.028 0.006 -10000 0 0 28 28
PRKCA -0.049 0.084 0.32 6 -10000 0 6
PRKCB -0.043 0.079 0.31 7 -10000 0 7
VCL 0.029 0.005 -10000 0 0 15 15
VEGFA165/NRP1 -0.053 0.058 0.27 1 -10000 0 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.061 0.05 0.28 1 -10000 0 1
VEGFA165/NRP2 0.036 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.069 0.076 0.3 3 -10000 0 3
NRP2 0.028 0.007 -10000 0 0 35 35
VEGFC homodimer 0.024 0.012 -10000 0 0 112 112
NCK1 0.026 0.009 -10000 0 0 63 63
ROCK1 0.029 0.005 -10000 0 0 15 15
FAK1/Paxillin -0.039 0.13 0.34 5 -0.38 10 15
MAP3K13 -0.041 0.079 0.33 4 -10000 0 4
PDPK1 -0.046 0.08 0.23 1 -10000 0 1
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.042 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.024 0.008 -10000 0 -10000 0 0
mol:DAG -0.041 0.021 0.17 3 -10000 0 3
VEGFR1 homodimer/NRP1/VEGFR 121 -0.03 0.013 -10000 0 -10000 0 0
CaM/Ca2+ -0.049 0.025 0.17 3 -10000 0 3
HIF1A 0.032 0.006 -10000 0 -10000 0 0
GAB1 0.028 0.006 -10000 0 0 25 25
AKT1 -0.029 0.088 0.24 2 -10000 0 2
PLCG1 -0.041 0.021 0.17 3 -10000 0 3
NOS3 -0.016 0.059 0.44 1 -0.3 2 3
CBL 0.029 0.005 -10000 0 0 15 15
mol:NO -0.011 0.065 0.4 2 -0.29 2 4
FLT1 -0.03 0.008 -10000 0 -10000 0 0
PGF 0.029 0.005 -10000 0 0 18 18
VEGFR1 homodimer/NRP2/VEGFR121 -0.037 0.019 -10000 0 -10000 0 0
CALM1 0.028 0.006 -10000 0 0 26 26
PIK3CA 0.021 0.014 -10000 0 0 171 171
eNOS/Hsp90 -0.009 0.074 0.32 1 -0.29 3 4
endothelial cell proliferation -0.022 0.046 0.33 1 -0.31 1 2
mol:Ca2+ -0.041 0.021 0.17 3 -10000 0 3
MAPK3 -0.053 0.035 0.32 1 -10000 0 1
MAPK1 -0.048 0.036 0.32 1 -10000 0 1
PIK3R1 0.021 0.013 -10000 0 0 161 161
PLGF homodimer 0.029 0.005 -10000 0 0 18 18
PRKACA 0.025 0.01 -10000 0 0 80 80
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.024 0.012 -10000 0 0 109 109
VEGFA homodimer 0.026 0.01 -10000 0 0 70 70
VEGFR1 homodimer/VEGFA homodimer -0.034 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.053 0.048 0.3 1 -0.23 1 2
PI3K 0.017 0.074 -10000 0 -10000 0 0
PRKCA -0.045 0.028 -10000 0 -10000 0 0
PRKCB -0.037 0.019 0.16 3 -10000 0 3
VEGFR1 homodimer/PLGF homodimer -0.038 0.01 -10000 0 -10000 0 0
VEGFA 0.026 0.01 -10000 0 0 70 70
VEGFB 0.028 0.006 -10000 0 0 24 24
mol:IP3 -0.041 0.021 0.17 3 -10000 0 3
RASA1 -0.043 0.03 0.17 4 -10000 0 4
NRP2 0.028 0.007 -10000 0 0 35 35
VEGFR1 homodimer -0.03 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.028 0.006 -10000 0 0 24 24
NCK1 0.026 0.009 -10000 0 0 63 63
eNOS/Caveolin-1 -0.012 0.08 0.4 2 -0.31 7 9
PTPN11 0.029 0.004 -10000 0 0 9 9
mol:PI-3-4-5-P3 0.016 0.073 -10000 0 -10000 0 0
mol:L-citrulline -0.011 0.065 0.4 2 -0.29 2 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.053 0.038 -10000 0 -0.14 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.035 0.02 -10000 0 -10000 0 0
CD2AP 0.028 0.007 -10000 0 0 31 31
PI3K/GAB1 0.02 0.081 -10000 0 -10000 0 0
PDPK1 -0.019 0.089 0.32 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.039 0.017 -10000 0 -10000 0 0
mol:NADP -0.011 0.065 0.4 2 -0.29 2 4
HSP90AA1 0.029 0.006 -10000 0 0 21 21
ubiquitin-dependent protein catabolic process 0.051 0.037 -10000 0 -0.14 2 2
VEGFR1 homodimer/NRP2 -0.036 0.012 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.018 0.014 -10000 0 -0.1 7 7
TRAF2/ASK1 0.037 0.013 -10000 0 -0.13 1 1
ATM 0.028 0.007 -10000 0 0 31 31
MAP2K3 -0.021 0.1 -10000 0 -0.31 40 40
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.015 0.089 0.18 1 -0.35 20 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.029 0.006 -10000 0 0 23 23
TXN -0.003 0.036 -10000 0 -0.21 17 17
CALM1 0.028 0.006 -10000 0 0 26 26
GADD45A 0.027 0.009 -10000 0 0 53 53
GADD45B 0.027 0.008 -10000 0 0 50 50
MAP3K1 0.027 0.009 -10000 0 0 52 52
MAP3K6 0.029 0.005 -10000 0 0 17 17
MAP3K7 0.028 0.007 -10000 0 0 30 30
MAP3K4 0.027 0.008 -10000 0 0 48 48
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.04 0.015 -10000 0 -0.16 1 1
TAK1/TAB family 0.016 0.028 -10000 0 -0.14 2 2
RAC1/OSM/MEKK3 0.051 0.021 -10000 0 -10000 0 0
TRAF2 0.028 0.006 -10000 0 0 24 24
RAC1/OSM/MEKK3/MKK3 0.003 0.097 -10000 0 -0.27 39 39
TRAF6 0.003 0.001 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 28 28
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.029 0.004 -10000 0 0 12 12
CCM2 0.029 0.004 -10000 0 0 13 13
CaM/Ca2+/CAMKIIB 0.036 0.022 -10000 0 -0.13 8 8
MAPK11 0.023 0.013 -10000 0 0 132 132
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.047 0.032 -10000 0 -0.13 9 9
OSM/MEKK3 0.042 0.009 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 -10000 0 0
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.005 -10000 0 0 19 19
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.028 0.007 -10000 0 0 32 32
MAP3K10 0.027 0.009 -10000 0 0 53 53
MAP3K3 0.029 0.005 -10000 0 0 14 14
TRX/ASK1 0.016 0.039 -10000 0 -0.17 23 23
GADD45/MTK1/MTK1 0.055 0.048 -10000 0 -0.13 7 7
Arf6 downstream pathway

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
PLAUR 0.001 0.093 0.6 12 -10000 0 12
regulation of axonogenesis 0.002 0.05 0.27 6 -0.21 12 18
myoblast fusion -0.021 0.061 0.33 1 -0.35 13 14
mol:GTP 0.027 0.038 0.23 12 -0.18 7 19
regulation of calcium-dependent cell-cell adhesion -0.047 0.053 0.15 1 -0.31 13 14
ARF1/GTP 0.032 0.048 0.21 10 -0.14 29 39
mol:GM1 0.01 0.034 0.2 13 -0.13 7 20
mol:Choline -0.011 0.042 0.16 25 -10000 0 25
lamellipodium assembly 0.005 0.069 0.35 12 -0.38 6 18
MAPK3 -0.005 0.064 0.39 13 -10000 0 13
ARF6/GTP/NME1/Tiam1 0.048 0.054 0.31 13 -0.15 1 14
ARF1 0.027 0.009 -10000 0 0 55 55
ARF6/GDP 0.021 0.061 0.36 13 -0.33 1 14
ARF1/GDP 0.019 0.058 0.31 11 -0.23 7 18
ARF6 0.043 0.022 0.17 13 -10000 0 13
RAB11A 0.029 0.005 -10000 0 0 14 14
TIAM1 0.021 0.023 -10000 0 -0.043 18 18
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.004 0.064 0.39 13 -10000 0 13
actin filament bundle formation -0.025 0.059 0.23 7 -0.3 12 19
KALRN 0.002 0.022 0.15 2 -0.28 1 3
RAB11FIP3/RAB11A 0.041 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.06 0.3 12 -0.23 7 19
NME1 0.022 0.021 -10000 0 -0.042 14 14
Rac1/GDP 0.025 0.059 0.3 12 -0.23 7 19
substrate adhesion-dependent cell spreading 0.027 0.038 0.23 12 -0.18 7 19
cortical actin cytoskeleton organization 0.005 0.069 0.35 12 -0.38 6 18
RAC1 0.028 0.006 -10000 0 0 28 28
liver development 0.027 0.038 0.23 12 -0.18 7 19
ARF6/GTP 0.027 0.038 0.23 12 -0.18 7 19
RhoA/GTP 0.042 0.035 0.21 12 -0.14 8 20
mol:GDP 0.007 0.065 0.4 12 -0.22 6 18
ARF6/GTP/RAB11FIP3/RAB11A 0.057 0.036 0.21 13 -0.13 7 20
RHOA 0.029 0.003 -10000 0 0 6 6
PLD1 -0.007 0.034 0.21 10 -0.15 6 16
RAB11FIP3 0.028 0.006 -10000 0 0 28 28
tube morphogenesis 0.005 0.069 0.35 12 -0.38 6 18
ruffle organization -0.002 0.05 0.21 12 -0.27 6 18
regulation of epithelial cell migration 0.027 0.038 0.23 12 -0.18 7 19
PLD2 -0.007 0.038 0.21 13 -0.14 6 19
PIP5K1A -0.002 0.05 0.21 12 -0.28 6 18
mol:Phosphatidic acid -0.011 0.042 0.16 25 -10000 0 25
Rac1/GTP 0.005 0.069 0.35 12 -0.38 6 18
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.009 -10000 0 0 51 51
HDAC4 0.029 0.006 -10000 0 0 20 20
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.015 0.024 -10000 0 -0.12 16 16
CDKN1A -0.015 0.084 0.37 2 -0.49 13 15
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.029 0.006 -10000 0 0 22 22
FOXO3 0.004 0.013 0.26 1 -10000 0 1
FOXO1 0.028 0.008 -10000 0 0 39 39
FOXO4 0 0.026 -10000 0 -0.19 10 10
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.008 -10000 0 0 50 50
TAT 0.026 0.009 -10000 0 0 61 61
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.002 -10000 0 -10000 0 0
PPARGC1A 0.028 0.006 -10000 0 0 26 26
FHL2 0.029 0.004 -10000 0 0 12 12
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.042 0.022 0.15 13 -10000 0 13
HIST2H4A -0.015 0.024 0.12 16 -10000 0 16
SIRT1/FOXO3a 0.031 0.039 0.22 3 -10000 0 3
SIRT1 -0.025 0.035 0.18 16 -10000 0 16
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.058 0.024 0.16 13 -10000 0 13
SIRT1/Histone H1b 0.007 0.068 -10000 0 -0.22 21 21
apoptosis -0.053 0.029 -10000 0 -0.16 13 13
SIRT1/PGC1A 0.04 0.019 0.14 14 -10000 0 14
p53/SIRT1 0.023 0.088 0.34 13 -0.17 73 86
SIRT1/FOXO4 0.005 0.065 -10000 0 -0.21 20 20
FOXO1/FHL2/SIRT1 0.051 0.031 0.15 11 -0.13 3 14
HIST1H1E 0.002 0.03 0.13 8 -0.19 10 18
SIRT1/p300 0.042 0.024 0.15 13 -0.16 1 14
muscle cell differentiation 0.023 0.025 -10000 0 -0.12 15 15
TP53 -0.02 0.034 0.19 13 -10000 0 13
KU70/SIRT1/BAX 0.054 0.03 0.16 13 -10000 0 13
CREBBP 0.028 0.008 -10000 0 0 40 40
MEF2D 0.029 0.005 -10000 0 0 14 14
HIV-1 Tat/SIRT1 0.041 0.022 0.15 10 -10000 0 10
ACSS2 -0.029 0.027 0.12 15 -10000 0 15
SIRT1/PCAF/MYOD -0.024 0.025 0.12 15 -10000 0 15
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.029 0.005 0 17 -9999 0 17
PI3K Class IB/PDE3B 0.029 0.005 -9999 0 0 17 17
PDE3B 0.029 0.005 -9999 0 0 17 17
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.04 0.013 -9999 0 -10000 0 0
FBXW11 0.029 0.005 -9999 0 0 18 18
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -9999 0 0 18 18
CHUK 0.028 0.007 -9999 0 0 36 36
NF kappa B2 p100/RelB 0.074 0.045 -9999 0 -0.14 2 2
NFKB1 0.027 0.008 -9999 0 0 47 47
MAP3K14 0.029 0.006 -9999 0 0 21 21
NF kappa B1 p50/RelB 0.037 0.028 -9999 0 -0.16 8 8
RELB 0.028 0.006 -9999 0 0 27 27
NFKB2 0.029 0.005 -9999 0 0 15 15
NF kappa B2 p52/RelB 0.037 0.014 -9999 0 -0.13 2 2
regulation of B cell activation 0.037 0.014 -9999 0 -0.13 2 2
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.045 0.021 -10000 0 -10000 0 0
RGS9BP 0.027 0.009 -10000 0 0 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.036 0.012 -10000 0 -10000 0 0
mol:ADP -0.016 0.004 -10000 0 -10000 0 0
GNAT2 0.029 0.003 -10000 0 0 5 5
RGS9-1/Gbeta5/R9AP 0.048 0.03 -10000 0 -0.15 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.036 0.012 -10000 0 -10000 0 0
GRK7 0.028 0.008 -10000 0 0 39 39
CNGB3 0.027 0.008 -10000 0 0 48 48
Cone Metarhodopsin II/X-Arrestin 0.022 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.054 0.18 40 -10000 0 40
Cone PDE6 0.059 0.05 -10000 0 -0.14 5 5
Cone Metarhodopsin II 0.018 0.005 -10000 0 -10000 0 0
Na + (4 Units) 0.047 0.024 -10000 0 -10000 0 0
GNAT2/GDP 0.054 0.037 -10000 0 -0.13 6 6
GNB5 0.028 0.007 -10000 0 0 33 33
mol:GMP (4 units) -0.015 0.06 0.18 49 -10000 0 49
Cone Transducin 0.049 0.022 -10000 0 -10000 0 0
SLC24A2 0.028 0.007 -10000 0 0 31 31
GNB3/GNGT2 0.038 0.015 -10000 0 -10000 0 0
GNB3 0.027 0.009 -10000 0 0 59 59
GNAT2/GTP 0.022 0.002 -10000 0 -10000 0 0
CNGA3 0.029 0.004 -10000 0 0 9 9
ARR3 0.029 0.003 -10000 0 0 5 5
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.036 0.012 -10000 0 -10000 0 0
mol:Pi 0.048 0.03 -10000 0 -0.14 6 6
Cone CNG Channel 0.056 0.036 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.028 0.007 -10000 0 0 31 31
RGS9 0.029 0.005 -10000 0 0 15 15
PDE6C 0.029 0.005 -10000 0 0 18 18
GNGT2 0.029 0.005 -10000 0 0 18 18
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.027 0.009 -10000 0 0 55 55
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.029 0.006 -9999 0 0 22 22
ITGB7 0.029 0.004 -9999 0 0 9 9
ITGA4 0.028 0.008 -9999 0 0 40 40
alpha4/beta7 Integrin 0.04 0.015 -9999 0 -0.16 1 1
alpha4/beta1 Integrin 0.039 0.014 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.027 0.008 -10000 0 0 50 50
Ran/GTP/Exportin 1/HDAC4 -0.039 0.02 -10000 0 -0.15 2 2
MDM2/SUMO1 0.023 0.054 -10000 0 -0.22 13 13
HDAC4 0.029 0.006 -10000 0 0 20 20
Ran/GTP/Exportin 1/HDAC1 -0.037 0.021 -10000 0 -0.14 3 3
SUMO1 0.029 0.004 -10000 0 0 8 8
NPC/RanGAP1/SUMO1 0.002 0.02 -10000 0 -0.2 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.009 0.049 0.15 32 -0.26 3 35
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 0 12 12
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.004 -10000 0 0 10 10
SUMO1/HDAC4 0.023 0.055 -10000 0 -0.22 13 13
SUMO1/HDAC1 0.022 0.052 -10000 0 -0.22 11 11
RANGAP1 0.027 0.008 -10000 0 0 48 48
MDM2/SUMO1/SUMO1 0.064 0.035 -10000 0 -0.14 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.006 0.035 -10000 0 -0.25 4 4
Ran/GTP 0.009 0.049 -10000 0 -0.21 13 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.028 0.006 -10000 0 0 26 26
UBE2I 0.029 0.006 -10000 0 0 22 22
Ran/GTP/Exportin 1 -0.014 0.063 0.16 39 -0.22 12 51
NPC 0.017 0.002 -10000 0 -10000 0 0
PIAS2 0.028 0.007 -10000 0 0 33 33
PIAS1 0.029 0.005 -10000 0 0 15 15
EntrezGene:9972 0 0 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.027 0.008 -10000 0 0 46 46
CDC42/GTP 0.02 0.058 0.17 1 -0.19 10 11
PLCG1 -0.01 0.053 0.16 1 -0.2 10 11
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 0 6 6
GNAI3 0.024 0.011 -10000 0 0 98 98
G12/G13 0.041 0.012 -10000 0 -10000 0 0
cell migration 0.02 0.057 0.16 1 -0.19 10 11
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.01 0.051 0.16 1 -0.2 8 9
MAPK1 -0.006 0.046 0.16 1 -0.21 4 5
S1P/S1P5/Gi 0.012 0.052 0.18 1 -0.2 10 11
GNAI1 0.028 0.006 -10000 0 0 27 27
CDC42/GDP 0.022 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.019 0.005 -10000 0 -10000 0 0
RHOA -0.028 0.029 0.2 8 -10000 0 8
S1P/S1P4/Gi 0.012 0.052 0.18 1 -0.2 10 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.008 -10000 0 0 47 47
S1P/S1P4/G12/G13 0.034 0.014 -10000 0 -10000 0 0
GNA12 0.028 0.007 -10000 0 0 34 34
GNA13 0.029 0.005 -10000 0 0 14 14
CDC42 0.029 0.004 -10000 0 0 11 11
Ephrin A reverse 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
MAPKKK cascade 0.034 0.018 -10000 0 -0.13 3 3
EFNA5 0.027 0.008 -10000 0 0 42 42
FYN -0.025 0.032 0.17 11 -0.22 1 12
neuron projection morphogenesis 0.034 0.018 -10000 0 -0.13 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.035 0.018 -10000 0 -0.13 3 3
EPHA5 0.028 0.007 -10000 0 0 29 29
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.038 0.019 0.12 1 -10000 0 1
PDGFRB 0.024 0.02 0.072 1 -10000 0 1
SPHK1 0.004 0.083 -10000 0 -0.67 8 8
mol:S1P 0.001 0.079 0.26 1 -0.58 8 9
S1P1/S1P/Gi 0.001 0.099 0.48 12 -0.33 7 19
GNAO1 0.02 0.023 0.088 11 -0.045 3 14
PDGFB-D/PDGFRB/PLCgamma1 0.005 0.11 0.44 13 -0.35 4 17
PLCG1 -0.004 0.097 0.45 12 -0.32 6 18
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.019 0.072 1 -10000 0 1
GNAI2 0.021 0.024 0.088 11 -0.045 3 14
GNAI3 0.022 0.019 0.079 10 -0.043 3 13
GNAI1 0.026 0.017 0.078 11 -0.043 3 14
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.01 0.049 0.14 50 -10000 0 50
S1P1/S1P -0.01 0.071 0.29 11 -0.39 8 19
negative regulation of cAMP metabolic process 0.01 0.1 0.48 12 -0.32 7 19
MAPK3 -0.002 0.11 0.56 11 -0.47 4 15
calcium-dependent phospholipase C activity 0 0.005 0.031 11 -10000 0 11
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.007 -10000 0 -0.15 1 1
KDR 0.029 0.009 0.063 3 -0.037 4 7
PLCB2 0.001 0.084 0.28 16 -0.36 8 24
RAC1 0.028 0.006 -10000 0 0 28 28
RhoA/GTP -0.02 0.048 -10000 0 -0.35 8 8
receptor internalization -0.01 0.065 0.27 10 -0.37 8 18
PTGS2 0.002 0.13 0.66 11 -0.89 3 14
Rac1/GTP -0.021 0.048 -10000 0 -0.35 8 8
RHOA 0.029 0.003 -10000 0 0 6 6
VEGFA 0.026 0.012 0.063 2 -0.037 4 6
negative regulation of T cell proliferation 0.01 0.1 0.48 12 -0.32 7 19
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.017 0.076 10 -0.043 3 13
MAPK1 0.001 0.1 0.55 10 -0.48 4 14
S1P1/S1P/PDGFB-D/PDGFRB 0.003 0.09 0.32 17 -0.34 8 25
ABCC1 0.023 0.02 -10000 0 -0.041 2 2
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.038 0.12 0.81 3 -10000 0 3
NCK1/PAK1/Dok-R -0.044 0.056 -10000 0 -0.32 2 2
NCK1/Dok-R 0.015 0.071 0.71 1 -10000 0 1
PIK3CA 0.02 0.015 -10000 0 -0.029 10 10
mol:beta2-estradiol 0 0.021 -10000 0 -0.18 7 7
RELA 0.029 0.003 -10000 0 0 6 6
SHC1 0.027 0.014 0.075 1 -10000 0 1
Rac/GDP 0.021 0.005 -10000 0 -10000 0 0
F2 0.013 0.044 -10000 0 -0.23 11 11
TNIP2 0.028 0.007 -10000 0 0 38 38
NF kappa B/RelA 0.036 0.076 0.69 1 -10000 0 1
FN1 0.018 0.014 -10000 0 0 214 214
PLD2 -0.011 0.059 0.82 1 -10000 0 1
PTPN11 0.029 0.004 -10000 0 0 9 9
GRB14 0.028 0.007 -10000 0 0 33 33
ELK1 -0.017 0.065 0.72 1 -10000 0 1
GRB7 0.027 0.008 -10000 0 0 42 42
PAK1 0.027 0.008 -10000 0 0 47 47
Tie2/Ang1/alpha5/beta1 Integrin 0.038 0.071 -10000 0 -10000 0 0
CDKN1A -0.041 0.16 0.72 5 -0.72 16 21
ITGA5 0.029 0.006 -10000 0 0 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.017 0.072 0.71 1 -10000 0 1
CRK 0.028 0.007 -10000 0 0 37 37
mol:NO -0.031 0.12 0.6 6 -10000 0 6
PLG -0.012 0.058 0.82 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.025 0.1 0.72 3 -10000 0 3
GRB2 0.029 0.006 -10000 0 0 20 20
PIK3R1 0.019 0.017 0.076 1 -10000 0 1
ANGPT2 -0.026 0.14 0.74 6 -0.69 2 8
BMX -0.012 0.061 0.82 1 -10000 0 1
ANGPT1 0.001 0.063 0.53 6 -10000 0 6
tube development -0.043 0.12 0.69 6 -10000 0 6
ANGPT4 0.023 0.019 0.081 6 -0.031 20 26
response to hypoxia -0.002 0.009 0.084 3 -10000 0 3
Tie2/Ang1/GRB14 -0.004 0.068 0.75 1 -10000 0 1
alpha5/beta1 Integrin 0.041 0.011 -10000 0 -10000 0 0
FGF2 0.026 0.014 -10000 0 -0.079 5 5
STAT5A (dimer) -0.041 0.15 0.73 5 -0.67 4 9
mol:L-citrulline -0.031 0.12 0.6 6 -10000 0 6
AGTR1 0.026 0.016 0.11 5 -0.033 16 21
MAPK14 0 0.092 0.8 2 -0.76 1 3
Tie2/SHP2 0.005 0.09 -10000 0 -10000 0 0
TEK -0.001 0.09 0.88 1 -10000 0 1
RPS6KB1 -0.04 0.12 0.76 3 -0.55 1 4
Angiotensin II/AT1 0.02 0.02 0.2 5 -10000 0 5
Tie2/Ang1/GRB2 -0.002 0.068 0.75 1 -10000 0 1
MAPK3 -0.02 0.061 0.73 1 -10000 0 1
MAPK1 -0.014 0.063 0.73 1 -10000 0 1
Tie2/Ang1/GRB7 -0.003 0.057 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 47 47
MAPK8 -0.011 0.063 0.82 1 -10000 0 1
PI3K -0.035 0.12 0.9 2 -10000 0 2
FES -0.004 0.11 0.8 2 -0.71 3 5
Crk/Dok-R 0.018 0.072 0.71 1 -10000 0 1
Tie2/Ang1/ABIN2 -0.002 0.067 0.75 1 -10000 0 1
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.035 0.12 0.67 5 -10000 0 5
STAT5A 0.026 0.012 -10000 0 -0.033 15 15
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0 0.14 0.76 3 -10000 0 3
Tie2/Ang2 -0.036 0.14 0.75 5 -10000 0 5
Tie2/Ang1 0.002 0.064 0.96 1 -10000 0 1
FOXO1 -0.037 0.12 0.66 6 -10000 0 6
ELF1 -0.01 0.033 0.26 1 -10000 0 1
ELF2 -0.002 0.061 0.92 1 -10000 0 1
mol:Choline -0.009 0.062 0.82 1 -10000 0 1
cell migration -0.025 0.036 -10000 0 -0.18 1 1
FYN -0.046 0.13 0.7 6 -10000 0 6
DOK2 0.024 0.012 -10000 0 0 105 105
negative regulation of cell cycle -0.037 0.15 0.71 5 -0.64 16 21
ETS1 -0.009 0.034 0.2 5 -10000 0 5
PXN 0 0.14 0.72 3 -10000 0 3
ITGB1 0.029 0.006 -10000 0 0 22 22
NOS3 -0.035 0.12 0.69 4 -10000 0 4
RAC1 0.028 0.006 -10000 0 0 28 28
TNF -0.007 0.038 0.22 7 -10000 0 7
MAPKKK cascade -0.009 0.062 0.82 1 -10000 0 1
RASA1 0.027 0.008 -10000 0 0 50 50
Tie2/Ang1/Shc 0.005 0.072 0.8 1 -10000 0 1
NCK1 0.026 0.009 -10000 0 0 63 63
vasculogenesis -0.028 0.11 0.59 6 -10000 0 6
mol:Phosphatidic acid -0.009 0.062 0.82 1 -10000 0 1
mol:Angiotensin II 0.001 0.009 0.085 6 -10000 0 6
mol:NADP -0.031 0.12 0.6 6 -10000 0 6
Rac1/GTP -0.033 0.11 0.65 1 -0.52 1 2
MMP2 -0.007 0.073 0.82 1 -10000 0 1
Arf6 trafficking events

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
SLC2A4 0.028 0.006 -10000 0 0 26 26
CLTC 0.011 0.068 -10000 0 -0.4 9 9
calcium ion-dependent exocytosis 0 0.033 0.16 1 -0.21 8 9
Dynamin 2/GTP -0.024 0.037 0.14 23 -10000 0 23
EXOC4 0.028 0.007 -10000 0 0 33 33
CD59 0 0.044 0.19 1 -0.37 6 7
CPE -0.023 0.01 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 0 7 7
membrane fusion -0.002 0.028 -10000 0 -0.18 7 7
CTNND1 -0.028 0.046 0.15 30 -10000 0 30
DNM2 0.027 0.009 -10000 0 0 56 56
mol:PI-4-5-P2 0.001 0.051 0.21 1 -0.24 11 12
TSHR -0.025 0.007 -10000 0 -10000 0 0
INS -0.004 0.1 -10000 0 -0.48 23 23
BIN1 0.029 0.004 -10000 0 0 13 13
mol:Choline -0.002 0.028 -10000 0 -0.18 7 7
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.024 0.008 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.029 0.004 -10000 0 0 11 11
mol:Ca2+ -0.024 0.036 0.14 23 -10000 0 23
JUP -0.003 0.049 -10000 0 -0.4 6 6
ASAP2/amphiphysin II 0.036 0.014 -10000 0 -0.12 2 2
ARF6/GTP 0.022 0.003 -10000 0 -10000 0 0
CDH1 -0.006 0.055 -10000 0 -0.46 6 6
clathrin-independent pinocytosis 0.021 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.029 0.006 -10000 0 0 23 23
positive regulation of endocytosis 0.021 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.008 -10000 0 0 50 50
substrate adhesion-dependent cell spreading 0.007 0.054 0.19 1 -0.26 10 11
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.005 -10000 0 0 17 17
regulation of calcium-dependent cell-cell adhesion -0.026 0.064 0.33 7 -0.21 1 8
positive regulation of phagocytosis -0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.038 0.009 -10000 0 -10000 0 0
ACAP1 0.001 0.026 -10000 0 -0.18 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.001 0.047 -10000 0 -0.35 7 7
clathrin heavy chain/ACAP1 -0.002 0.062 0.21 4 -0.34 9 13
JIP4/KLC1 0.051 0.021 -10000 0 -10000 0 0
EXOC1 0.028 0.006 -10000 0 0 25 25
exocyst 0.007 0.054 0.19 1 -0.26 10 11
RALA/GTP 0.021 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.008 -10000 0 -10000 0 0
receptor recycling 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 -0.028 0.046 0.15 30 -10000 0 30
NME1 -0.024 0.008 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.072 -10000 0 -0.38 12 12
IL2RA 0.003 0.052 -10000 0 -0.38 7 7
VAMP3 -0.025 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.027 0.065 -10000 0 -0.33 9 9
EXOC6 0.028 0.007 -10000 0 0 37 37
PLD1 0.002 0.01 -10000 0 -0.12 1 1
PLD2 0.003 0.01 -10000 0 -10000 0 0
EXOC5 0.029 0.004 -10000 0 0 13 13
PIP5K1C -0.004 0.04 -10000 0 -0.26 6 6
SDC1 0 0.046 -10000 0 -0.35 7 7
ARF6/GDP -0.017 0.039 0.16 26 -10000 0 26
EXOC7 0.029 0.005 -10000 0 0 16 16
E-cadherin/beta catenin 0.028 0.067 0.22 1 -0.34 7 8
mol:Phosphatidic acid -0.002 0.028 -10000 0 -0.18 7 7
endocytosis -0.034 0.013 0.12 2 -10000 0 2
SCAMP2 0.029 0.006 -10000 0 0 20 20
ADRB2 0.001 0.07 0.22 4 -0.39 10 14
EXOC3 0.027 0.009 -10000 0 0 59 59
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.028 0.018 0.17 2 -10000 0 2
KLC1 0.029 0.006 -10000 0 0 23 23
AVPR2 0.007 0.077 0.22 12 -0.4 10 22
RALA 0.029 0.005 -10000 0 0 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.065 0.19 1 -0.34 7 8
Visual signal transduction: Rods

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
mol:K + 0.029 0.005 -10000 0 0 16 16
GNAT1/GTP 0.022 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.038 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.038 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.029 0.004 -10000 0 0 8 8
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.041 0.043 -10000 0 -0.14 7 7
mol:Na + -0.061 0.029 0.12 6 -10000 0 6
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.048 0.03 -10000 0 -0.15 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.05 0.05 -10000 0 -10000 0 0
CNGB1 0.028 0.008 -10000 0 0 41 41
RDH5 0.028 0.007 -10000 0 0 31 31
SAG 0.029 0.004 -10000 0 0 11 11
mol:Ca2+ -0.048 0.086 0.31 21 -10000 0 21
Na + (4 Units) -0.067 0.026 0.077 2 -10000 0 2
RGS9 0.029 0.005 -10000 0 0 15 15
GNB1/GNGT1 0.041 0.014 -10000 0 -0.16 1 1
GNAT1/GDP 0.054 0.038 -10000 0 -0.13 6 6
GUCY2D 0.028 0.006 -10000 0 0 28 28
GNGT1 0.029 0.006 -10000 0 0 22 22
GUCY2F 0.03 0.002 -10000 0 0 2 2
GNB5 0.028 0.007 -10000 0 0 33 33
mol:GMP (4 units) -0.038 0.016 0.14 1 -10000 0 1
mol:11-cis-retinal 0.028 0.007 -10000 0 0 31 31
mol:cGMP 0.048 0.028 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 0 24 24
Rhodopsin 0.04 0.013 -10000 0 -10000 0 0
SLC24A1 0.029 0.005 -10000 0 0 16 16
CNGA1 0.028 0.006 -10000 0 0 27 27
Metarhodopsin II 0.018 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.065 0.032 -10000 0 -10000 0 0
RGS9BP 0.027 0.009 -10000 0 0 57 57
Metarhodopsin II/Transducin 0.006 0.026 -10000 0 -0.18 2 2
GCAP Family/Ca ++ 0.052 0.017 -10000 0 -10000 0 0
PDE6A/B 0.04 0.013 -10000 0 -10000 0 0
mol:Pi 0.048 0.03 -10000 0 -0.14 6 6
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.051 0.021 -10000 0 -0.13 1 1
PDE6B 0.027 0.008 -10000 0 0 46 46
PDE6A 0.029 0.004 -10000 0 0 13 13
PDE6G 0.029 0.006 -10000 0 0 21 21
RHO 0.029 0.005 -10000 0 0 19 19
PDE6 0.062 0.052 -10000 0 -0.14 6 6
GUCA1A 0.028 0.006 -10000 0 0 26 26
GC2/GCAP Family 0.069 0.024 -10000 0 -10000 0 0
GUCA1C 0.028 0.006 -10000 0 0 26 26
GUCA1B 0.028 0.006 -10000 0 0 25 25
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.027 0.035 0.22 10 -10000 0 10
NFATC2 -0.024 0.18 0.43 11 -0.52 5 16
NFATC3 -0.003 0.074 0.36 3 -0.25 2 5
CD40LG -0.005 0.22 0.68 14 -0.74 1 15
ITCH -0.032 0.047 0.3 9 -10000 0 9
CBLB -0.032 0.049 0.3 10 -10000 0 10
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.009 0.18 0.64 13 -0.56 1 14
JUNB 0.02 0.014 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.035 0.019 -10000 0 -0.17 9 9
T cell anergy -0.01 0.081 0.48 11 -10000 0 11
TLE4 -0.046 0.16 0.32 1 -0.53 38 39
Jun/NFAT1-c-4/p21SNFT -0.012 0.16 0.56 4 -0.7 1 5
AP-1/NFAT1-c-4 -0.027 0.21 0.59 9 -0.81 1 10
IKZF1 -0.025 0.12 0.32 1 -0.38 4 5
T-helper 2 cell differentiation 0.002 0.15 -10000 0 -0.63 3 3
AP-1/NFAT1 -0.019 0.15 0.35 17 -0.36 8 25
CALM1 -0.032 0.039 0.2 15 -10000 0 15
EGR2 0.002 0.15 0.98 3 -0.73 1 4
EGR3 -0.007 0.15 0.83 3 -0.68 2 5
NFAT1/FOXP3 -0.013 0.14 0.38 14 -0.39 4 18
EGR1 0.003 0.024 0.15 1 -10000 0 1
JUN -0.013 0.052 0.12 53 -10000 0 53
EGR4 0.007 0.029 0.15 1 -10000 0 1
mol:Ca2+ -0.011 0.003 -10000 0 -10000 0 0
GBP3 -0.03 0.17 0.43 22 -0.54 25 47
FOSL1 0.029 0.003 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 0.046 0.15 0.57 2 -0.7 1 3
DGKA -0.022 0.12 0.41 8 -0.38 3 11
CREM 0.029 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.005 0.16 0.52 2 -0.72 1 3
CTLA4 -0.026 0.11 0.47 8 -0.33 4 12
NFAT1-c-4 (dimer)/EGR1 -0.053 0.16 0.59 2 -0.8 1 3
NFAT1-c-4 (dimer)/EGR4 -0.01 0.16 0.52 5 -0.72 1 6
FOS -0.012 0.048 0.12 49 -10000 0 49
IFNG 0.004 0.18 0.58 25 -0.64 7 32
T cell activation 0 0.16 0.65 5 -10000 0 5
MAF 0.026 0.009 -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 -0.005 0.13 1 1 -0.82 3 4
TNF -0.057 0.15 0.6 4 -0.76 1 5
FASLG -0.004 0.17 0.85 2 -0.83 1 3
TBX21 0.04 0.054 0.28 26 -10000 0 26
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.027 0.008 -10000 0 -10000 0 0
PTPN1 -0.027 0.12 0.32 1 -0.38 4 5
NFAT1-c-4/ICER1 -0.005 0.16 0.5 5 -0.72 1 6
GATA3 0.028 0.007 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.014 0.18 0.57 27 -0.64 7 34
IL2RA -0.017 0.16 0.63 6 -0.54 4 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.019 0.12 0.42 9 -0.38 4 13
E2F1 0.028 0.015 0.18 4 -10000 0 4
PPARG 0.029 0.004 -10000 0 -10000 0 0
SLC3A2 -0.025 0.12 0.42 2 -0.4 3 5
IRF4 0.027 0.008 -10000 0 -10000 0 0
PTGS2 -0.018 0.2 0.58 13 -0.74 1 14
CSF2 -0.007 0.22 0.69 13 -0.74 1 14
JunB/Fra1/NFAT1-c-4 0.014 0.16 0.57 2 -0.65 2 4
IL4 0.001 0.15 -10000 0 -0.66 3 3
IL5 -0.007 0.22 0.64 18 -0.74 1 19
IL2 0 0.16 0.65 5 -10000 0 5
IL3 -0.008 0.083 -10000 0 -0.52 12 12
RNF128 -0.034 0.048 0.32 9 -10000 0 9
NFATC1 0.006 0.13 0.83 3 -1 1 4
CDK4 0.004 0.14 0.8 3 -0.79 2 5
PTPRK -0.027 0.13 0.4 4 -0.47 8 12
IL8 -0.052 0.15 0.6 1 -0.74 1 2
POU2F1 0.029 0.004 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.046 0.022 -9999 0 -0.12 1 1
MAPK9 0.003 0.009 -9999 0 -0.21 1 1
adrenocorticotropin secretion -0.016 0.005 0 44 -10000 0 44
GNB1/GNG2 0.038 0.012 -9999 0 -0.13 1 1
GNB1 0.028 0.006 -9999 0 0 24 24
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.003 0.001 -9999 0 -10000 0 0
Gs family/GTP 0.018 0.004 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.004 0.001 -9999 0 -10000 0 0
GNAL 0.029 0.006 -9999 0 0 20 20
GNG2 0.029 0.004 -9999 0 0 12 12
CRH 0.027 0.008 -9999 0 0 44 44
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.003 0 -9999 0 -10000 0 0
MAPK11 0.003 0.002 -9999 0 -10000 0 0
Glypican 2 network

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
MDK 0.029 0.003 -9999 0 0 7 7
GPC2 0.029 0.006 -9999 0 0 20 20
GPC2/Midkine 0.042 0.009 -9999 0 -9999 0 0
neuron projection morphogenesis 0.042 0.009 -9999 0 -9999 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.024 0.011 0.18 1 -10000 0 1
ADCY5 -0.024 0.014 0.18 2 -10000 0 2
ADCY6 -0.026 0.005 -10000 0 -10000 0 0
ADCY7 -0.024 0.008 -10000 0 -10000 0 0
ADCY1 -0.025 0.006 -10000 0 -10000 0 0
ADCY2 -0.024 0.009 -10000 0 -10000 0 0
ADCY3 -0.025 0.01 0.18 1 -10000 0 1
ADCY8 -0.008 0.02 0.18 4 -10000 0 4
PRKCE -0.016 0.003 0 18 -10000 0 18
ADCY9 -0.023 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0 0.089 0.21 34 -0.24 1 35
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 557 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.61.2614 TCGA.61.2613 TCGA.61.2612 TCGA.61.2113
109_MAP3K5 0.061 -0.0013 0.011 -0.025
47_PPARGC1A 0.03 0.03 0.03 0.03
105_BMP4 0.03 0.03 0.03 0.03
105_BMP6 0.03 0.03 0.03 0.03
105_BMP7 0 0.03 0.03 0.03
105_BMP2 0 0.03 0.03 0.03
131_RELN/VLDLR 0.076 0.076 0.076 0.076
30_TGFB1/TGF beta receptor Type II 0.03 0.03 0 0.03
84_STAT5B 0.038 -0.025 -0.025 0.068
84_STAT5A 0.038 -0.025 -0.025 0.068
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV-TP/2170683/2.GDAC_MergeDataFiles.Finished/OV-TP.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/OV-TP/2283658/1.Gistic2_Analysis.Finished/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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