PARADIGM pathway analysis of mRNA expression and copy number data
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1WS8R7B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Ovarian Serous Cystadenocarcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1WS8R7B
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 77 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 345
PLK2 and PLK4 events 211
Circadian rhythm pathway 154
S1P3 pathway 145
PLK1 signaling events 138
TCGA08_retinoblastoma 131
Osteopontin-mediated events 114
Signaling events regulated by Ret tyrosine kinase 108
Effects of Botulinum toxin 107
Nongenotropic Androgen signaling 99
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 345 17622 51 -0.039 1.9 1000 -1000 -0.051 -1000
PLK2 and PLK4 events 211 633 3 0.015 0.066 1000 -1000 -0.019 -1000
Circadian rhythm pathway 154 3404 22 -0.095 0.27 1000 -1000 -0.017 -1000
S1P3 pathway 145 6107 42 -0.54 0.04 1000 -1000 -0.023 -1000
PLK1 signaling events 138 11806 85 -0.12 0.24 1000 -1000 -0.032 -1000
TCGA08_retinoblastoma 131 1051 8 -0.076 0.069 1000 -1000 -0.004 -1000
Osteopontin-mediated events 114 4362 38 -0.039 0.19 1000 -1000 -0.037 -1000
Signaling events regulated by Ret tyrosine kinase 108 8911 82 -0.19 0.029 1000 -1000 -0.056 -1000
Effects of Botulinum toxin 107 2794 26 -0.12 0.054 1000 -1000 -0.026 -1000
Nongenotropic Androgen signaling 99 5198 52 -0.16 0.086 1000 -1000 -0.029 -1000
Aurora B signaling 91 6128 67 -0.064 0.18 1000 -1000 -0.035 -1000
mTOR signaling pathway 90 4821 53 -0.16 0.029 1000 -1000 -0.038 -1000
Endothelins 90 8702 96 -0.11 0.089 1000 -1000 -0.048 -1000
TCGA08_rtk_signaling 88 2310 26 -0.031 0.044 1000 -1000 -0.016 -1000
IGF1 pathway 88 5068 57 -0.088 0.052 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 84 2887 34 -0.046 0.033 1000 -1000 -0.034 -1000
FoxO family signaling 81 5184 64 -0.022 0.36 1000 -1000 -0.033 -1000
Retinoic acid receptors-mediated signaling 80 4684 58 -0.39 0.05 1000 -1000 -0.042 -1000
IL2 signaling events mediated by STAT5 79 1747 22 -0.36 0.029 1000 -1000 -0.034 -1000
Insulin Pathway 71 5280 74 -0.1 0.058 1000 -1000 -0.054 -1000
Thromboxane A2 receptor signaling 70 7403 105 -0.16 0.044 1000 -1000 -0.045 -1000
Ephrin B reverse signaling 70 3386 48 -0.17 0.044 1000 -1000 -0.045 -1000
TCGA08_p53 69 487 7 -0.007 0.028 1000 -1000 -0.015 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 66 5500 83 -0.13 0.064 1000 -1000 -0.034 -1000
BARD1 signaling events 61 3516 57 -0.046 0.2 1000 -1000 -0.044 -1000
Reelin signaling pathway 61 3440 56 -0.072 0.073 1000 -1000 -0.028 -1000
IL2 signaling events mediated by PI3K 61 3565 58 -0.17 0.029 1000 -1000 -0.038 -1000
IL4-mediated signaling events 59 5436 91 -0.56 0.3 1000 -1000 -0.082 -1000
Canonical Wnt signaling pathway 59 3038 51 -0.33 0.14 1000 -1000 -0.036 -1000
LPA receptor mediated events 59 6110 102 -0.057 0.033 1000 -1000 -0.049 -1000
IL1-mediated signaling events 58 3616 62 -0.07 0.057 1000 -1000 -0.057 -1000
Integrins in angiogenesis 58 4951 84 -0.083 0.055 1000 -1000 -0.051 -1000
Insulin-mediated glucose transport 57 1842 32 -0.087 0.036 1000 -1000 -0.027 -1000
TRAIL signaling pathway 57 2778 48 -0.029 0.032 1000 -1000 -0.034 -1000
Ras signaling in the CD4+ TCR pathway 57 969 17 0 0.029 1000 -1000 -0.014 -1000
Plasma membrane estrogen receptor signaling 56 4836 86 -0.13 0.13 1000 -1000 -0.051 -1000
Presenilin action in Notch and Wnt signaling 54 3342 61 -0.3 0.064 1000 -1000 -0.035 -1000
PDGFR-alpha signaling pathway 54 2416 44 -0.093 0.037 1000 -1000 -0.035 -1000
Nectin adhesion pathway 54 3413 63 -0.12 0.047 1000 -1000 -0.045 -1000
HIF-2-alpha transcription factor network 54 2360 43 -0.056 0.19 1000 -1000 -0.047 -1000
Signaling events mediated by the Hedgehog family 53 2803 52 -0.045 0.049 1000 -1000 -0.034 -1000
Regulation of Telomerase 53 5482 102 -0.26 0.065 1000 -1000 -0.044 -1000
Wnt signaling 52 369 7 0.007 0.029 1000 -1000 -0.009 -1000
Signaling mediated by p38-gamma and p38-delta 51 774 15 -0.083 0.027 1000 -1000 -0.031 -1000
Coregulation of Androgen receptor activity 48 3651 76 -0.34 0.042 1000 -1000 -0.027 -1000
Aurora A signaling 48 2938 60 -0.003 0.17 1000 -1000 -0.026 -1000
amb2 Integrin signaling 47 3931 82 -0.056 0.075 1000 -1000 -0.042 -1000
RXR and RAR heterodimerization with other nuclear receptor 47 2458 52 -0.15 0.097 1000 -1000 -0.034 -1000
Class I PI3K signaling events 46 3426 73 -0.032 0.084 1000 -1000 -0.033 -1000
Signaling events mediated by PRL 46 1595 34 -0.063 0.051 1000 -1000 -0.034 -1000
p75(NTR)-mediated signaling 43 5388 125 -0.071 0.075 1000 -1000 -0.064 -1000
IL23-mediated signaling events 42 2541 60 -0.01 0.23 1000 -1000 -0.042 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 39 908 23 -0.014 0.091 1000 -1000 -0.024 -1000
FAS signaling pathway (CD95) 39 1833 47 -0.036 0.045 1000 -1000 -0.039 -1000
BMP receptor signaling 37 3033 81 -0.053 0.053 1000 -1000 -0.05 -1000
Glucocorticoid receptor regulatory network 37 4288 114 -0.3 0.16 1000 -1000 -0.057 -1000
Canonical NF-kappaB pathway 36 1419 39 -0.055 0.05 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 36 1336 37 -0.019 0.066 1000 -1000 -0.035 -1000
Paxillin-dependent events mediated by a4b1 36 1307 36 -0.075 0.063 1000 -1000 -0.035 -1000
Regulation of nuclear SMAD2/3 signaling 35 4890 136 -0.099 0.14 1000 -1000 -0.038 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 34 1152 33 -0.012 0.076 1000 -1000 -0.023 -1000
PDGFR-beta signaling pathway 34 3352 97 -0.072 0.06 1000 -1000 -0.06 -1000
Noncanonical Wnt signaling pathway 33 858 26 -0.025 0.043 1000 -1000 -0.034 -1000
Arf6 signaling events 33 2069 62 -0.014 0.067 1000 -1000 -0.013 -1000
Neurotrophic factor-mediated Trk receptor signaling 33 4036 120 -0.16 0.076 1000 -1000 -0.051 -1000
Signaling events mediated by PTP1B 32 2458 76 -0.077 0.037 1000 -1000 -0.034 -1000
Syndecan-3-mediated signaling events 32 1121 35 -0.013 0.043 1000 -1000 -0.034 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 32 1472 45 -0.086 0.066 1000 -1000 -0.049 -1000
E-cadherin signaling in the nascent adherens junction 32 2457 76 -0.089 0.056 1000 -1000 -0.058 -1000
EPHB forward signaling 31 2687 85 -0.069 0.13 1000 -1000 -0.065 -1000
IL12-mediated signaling events 30 2624 87 -0.36 0.049 1000 -1000 -0.07 -1000
HIF-1-alpha transcription factor network 30 2328 76 -0.042 0.34 1000 -1000 -0.073 -1000
Regulation of p38-alpha and p38-beta 30 1649 54 -0.054 0.062 1000 -1000 -0.044 -1000
ErbB2/ErbB3 signaling events 29 1914 65 -0.036 0.092 1000 -1000 -0.064 -1000
Caspase cascade in apoptosis 29 2219 74 -0.055 0.041 1000 -1000 -0.032 -1000
ceramide signaling pathway 29 1440 49 -0.052 0.041 1000 -1000 -0.025 -1000
E-cadherin signaling events 29 147 5 0.026 0.044 1000 -1000 0.026 -1000
ErbB4 signaling events 28 1966 69 -0.032 0.18 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 28 2399 85 -0.069 0.068 1000 -1000 -0.042 -1000
Glypican 1 network 28 1369 48 -0.043 0.053 1000 -1000 -0.031 -1000
Syndecan-2-mediated signaling events 27 1929 69 -0.04 0.04 1000 -1000 -0.035 -1000
BCR signaling pathway 27 2685 99 -0.07 0.068 1000 -1000 -0.064 -1000
E-cadherin signaling in keratinocytes 27 1182 43 -0.048 0.044 1000 -1000 -0.031 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 26 1442 54 -0.058 0.039 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 26 1027 39 -0.13 0.029 1000 -1000 -0.026 -1000
Fc-epsilon receptor I signaling in mast cells 26 2594 97 -0.063 0.061 1000 -1000 -0.063 -1000
IL27-mediated signaling events 26 1375 51 -0.03 0.074 1000 -1000 -0.04 -1000
IL6-mediated signaling events 26 2013 75 -0.27 0.045 1000 -1000 -0.031 -1000
EGFR-dependent Endothelin signaling events 26 564 21 -0.056 0.058 1000 -1000 -0.05 -1000
Aurora C signaling 25 176 7 -0.001 0.039 1000 -1000 -0.012 -1000
FOXA2 and FOXA3 transcription factor networks 25 1173 46 -0.03 0.25 1000 -1000 -0.054 -1000
Syndecan-4-mediated signaling events 25 1715 67 -0.027 0.075 1000 -1000 -0.039 -1000
Regulation of Androgen receptor activity 25 1819 70 -0.39 0.046 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 24 1927 78 -0.18 0.038 1000 -1000 -0.045 -1000
EPO signaling pathway 23 1296 55 -0.076 0.035 1000 -1000 -0.042 -1000
Ceramide signaling pathway 23 1817 76 -0.038 0.066 1000 -1000 -0.025 -1000
Atypical NF-kappaB pathway 23 726 31 -0.038 0.029 1000 -1000 -0.034 -1000
TCR signaling in naïve CD8+ T cells 23 2145 93 -0.091 0.075 1000 -1000 -0.05 -1000
IFN-gamma pathway 22 1554 68 -0.064 0.068 1000 -1000 -0.054 -1000
Stabilization and expansion of the E-cadherin adherens junction 22 1635 74 -0.13 0.071 1000 -1000 -0.063 -1000
Sphingosine 1-phosphate (S1P) pathway 20 560 28 -0.031 0.04 1000 -1000 -0.02 -1000
Class I PI3K signaling events mediated by Akt 20 1401 68 -0.1 0.053 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class I 20 2182 104 -0.046 0.065 1000 -1000 -0.037 -1000
Calcium signaling in the CD4+ TCR pathway 20 648 31 -0.071 0.029 1000 -1000 -0.045 -1000
Arf1 pathway 20 1130 54 -0.029 0.035 1000 -1000 -0.025 -1000
Nephrin/Neph1 signaling in the kidney podocyte 19 665 34 -0.04 0.081 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 19 1459 75 -0.033 0.058 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 19 339 17 -0.027 0.059 1000 -1000 -0.03 -1000
Hedgehog signaling events mediated by Gli proteins 19 1271 65 -0.036 0.054 1000 -1000 -0.033 -1000
Arf6 downstream pathway 18 776 43 -0.047 0.056 1000 -1000 -0.025 -1000
S1P5 pathway 18 312 17 -0.02 0.029 1000 -1000 -0.009 -1000
Signaling mediated by p38-alpha and p38-beta 18 830 44 -0.038 0.046 1000 -1000 -0.039 -1000
Signaling events mediated by VEGFR1 and VEGFR2 18 2306 125 -0.075 0.067 1000 -1000 -0.065 -1000
VEGFR1 specific signals 18 1017 56 -0.053 0.052 1000 -1000 -0.046 -1000
p38 MAPK signaling pathway 18 819 44 -0.021 0.055 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class III 17 709 40 -0.053 0.058 1000 -1000 -0.032 -1000
Class IB PI3K non-lipid kinase events 17 51 3 -0.028 0.028 1000 -1000 -0.026 -1000
Visual signal transduction: Cones 14 532 38 -0.018 0.058 1000 -1000 -0.021 -1000
a4b1 and a4b7 Integrin signaling 14 72 5 0.027 0.04 1000 -1000 0.026 -1000
Sumoylation by RanBP2 regulates transcriptional repression 14 393 27 -0.039 0.063 1000 -1000 -0.04 -1000
S1P4 pathway 14 365 25 -0.029 0.04 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 14 194 13 0 0.073 1000 -1000 0 -1000
Ephrin A reverse signaling 13 92 7 -0.025 0.034 1000 -1000 -0.019 -1000
Angiopoietin receptor Tie2-mediated signaling 12 1074 88 -0.045 0.04 1000 -1000 -0.065 -1000
S1P1 pathway 11 428 36 -0.021 0.029 1000 -1000 -0.039 -1000
Arf6 trafficking events 11 815 71 -0.034 0.051 1000 -1000 -0.032 -1000
Visual signal transduction: Rods 11 596 52 -0.067 0.069 1000 -1000 -0.054 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 8 576 68 -0.057 0.046 1000 -1000 -0.067 -1000
Glypican 2 network 7 28 4 0.028 0.042 1000 -1000 0.026 -1000
Rapid glucocorticoid signaling 7 146 20 -0.016 0.037 1000 -1000 -0.015 -1000
LPA4-mediated signaling events 5 68 12 -0.026 0 1000 -1000 -0.015 -1000
Total 6045 327838 7203 -11 12 131000 -131000 -4.8 -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 0.95 113 -10000 0 113
BIRC5 0.35 0.41 1 124 -10000 0 124
HSPA1B 1.2 0.39 1.3 481 -10000 0 481
MAP2K1 0.48 0.17 0.52 501 -10000 0 501
BRCA2 1.4 0.53 1.5 476 -10000 0 476
FOXM1 1.9 0.91 2.3 463 -10000 0 463
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 1.1 326 -10000 0 326
CDC2 1.5 0.49 1.7 488 -10000 0 488
TGFA 0.74 0.51 1.1 350 -10000 0 350
SKP2 1.4 0.55 1.5 481 -10000 0 481
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 0.8 25 -0.74 2 27
FOXM1C/SP1 0.89 0.44 1.1 418 -10000 0 418
AURKB 0.34 0.4 0.99 120 -0.74 1 121
CENPF 1.7 0.54 1.8 496 -10000 0 496
CDK4 0.13 0.072 0.18 344 -10000 0 344
MYC 0.59 0.54 1.1 286 -10000 0 286
CHEK2 0.41 0.18 0.47 469 -10000 0 469
ONECUT1 0.76 0.55 1.2 347 -10000 0 347
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 1.2 342 -10000 0 342
FOS 1.1 0.55 1.4 425 -10000 0 425
SP1 -0.039 0.086 -10000 0 -0.069 386 386
CDC25B 1.2 0.44 1.4 479 -10000 0 479
response to radiation 0.25 0.074 0.27 501 -10000 0 501
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 0.01 0.032 0.12 37 -10000 0 37
EP300 0.027 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 1.4 0.58 1.7 455 -10000 0 455
CCNB2 1.7 0.53 1.8 498 -10000 0 498
CCNB1 1.8 0.65 2 480 -10000 0 480
ETV5 1.4 0.58 1.6 483 -10000 0 483
ESR1 1 0.56 1.3 415 -1 2 417
CCND1 0.78 0.55 1.2 352 -10000 0 352
GSK3A 0.27 0.1 0.31 473 -10000 0 473
Cyclin A-E1/CDK1-2 0.031 0.1 0.36 44 -10000 0 44
CDK2 0.076 0.07 0.14 284 -10000 0 284
G2/M transition of mitotic cell cycle 0.44 0.15 0.47 510 -10000 0 510
FOXM1B/Cbp/p300 0.084 0.25 0.9 27 -10000 0 27
GAS1 1 0.55 1.3 414 -1 1 415
MMP2 1.1 0.56 1.4 430 -1.1 3 433
RB1/FOXM1C 0.57 0.56 1.1 271 -10000 0 271
CREBBP 0.027 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 0 136 136
PLK4 0.015 0.015 -10000 0 0 268 268
regulation of centriole replication 0.066 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 0.05 0.034 0.088 227 -0.042 13 240
TIMELESS/CRY2 0.19 0.23 0.45 242 -10000 0 242
DEC1/BMAL1 0.058 0.027 -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 0.088 230 -0.041 14 244
TIMELESS 0.27 0.32 0.63 241 -10000 0 241
NPAS2 0.051 0.034 0.088 228 -0.041 14 242
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 0.027 0.007 -10000 0 0 37 37
BMAL/CLOCK/NPAS2 0.14 0.13 0.29 226 -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 0.18 0.23 0.45 229 -10000 0 229
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.029 0.005 -10000 0 0 16 16
S1P3 pathway

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
PDGFRB 0.029 0.005 -10000 0 0 15 15
mol:S1P -0.016 0.016 0.072 4 -0.03 279 283
S1P1/S1P/Gi -0.053 0.092 0.26 4 -0.23 49 53
GNAO1 -0.02 0.046 0.12 4 -0.063 285 289
S1P/S1P3/G12/G13 -0.015 0.047 0.16 4 -0.055 263 267
AKT1 -0.042 0.11 0.27 2 -0.5 20 22
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 0.099 2 -0.058 265 267
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 -0.034 282 286
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 -0.27 269 273
MAPK1 -0.14 0.14 0.38 4 -0.27 262 266
JAK2 -0.14 0.15 0.34 5 -0.28 246 251
CXCR4 -0.14 0.14 0.36 3 -0.27 264 267
FLT1 -0.025 0.052 0.16 4 -0.072 295 299
RhoA/GDP 0.021 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 -0.27 245 249
S1P/S1P3/Gi -0.13 0.15 0.43 4 -0.27 267 271
RAC1 0.028 0.006 -10000 0 0 27 27
RhoA/GTP -0.12 0.15 0.36 4 -0.26 268 272
VEGFA -0.022 0.05 0.16 4 -0.07 272 276
S1P/S1P2/Gi -0.074 0.1 0.31 4 -0.22 89 93
VEGFR1 homodimer/VEGFA homodimer -0.029 0.074 0.34 4 -0.11 14 18
RHOA 0.029 0.003 -10000 0 0 6 6
S1P/S1P3/Gq -0.029 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 0.04 0.012 -10000 0 -10000 0 0
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GNA12 0.028 0.007 -10000 0 0 33 33
GNA13 0.029 0.005 -10000 0 0 14 14
GNA11 0.025 0.01 -10000 0 0 83 83
Rac1/GTP -0.12 0.15 0.36 4 -0.26 270 274
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 0.081 405 -10000 0 405
PLK1S1 0.034 0.017 0.053 178 -10000 0 178
KIF2A 0.048 0.031 0.16 9 -10000 0 9
regulation of mitotic centrosome separation 0.069 0.029 0.082 395 -10000 0 395
GOLGA2 0.029 0.005 -10000 0 0 15 15
Hec1/SPC24 0.005 0.019 -10000 0 -10000 0 0
WEE1 0.08 0.066 0.17 9 -0.26 11 20
cytokinesis 0.22 0.087 0.26 462 -10000 0 462
PP2A-alpha B56 0.13 0.081 -10000 0 -0.54 4 4
AURKA 0.081 0.036 0.12 131 -10000 0 131
PICH/PLK1 0.11 0.083 0.17 332 -10000 0 332
CENPE 0.063 0.061 0.22 56 -10000 0 56
RhoA/GTP 0.021 0.007 -10000 0 -0.15 1 1
positive regulation of microtubule depolymerization 0.05 0.03 0.16 9 -10000 0 9
PPP2CA 0.029 0.004 -10000 0 0 13 13
FZR1 0.027 0.008 -10000 0 0 45 45
TPX2 0.11 0.031 0.12 470 -10000 0 470
PAK1 0.028 0.011 -10000 0 -0.029 7 7
SPC24 0.02 0.014 -10000 0 0 175 175
FBXW11 0.028 0.005 -10000 0 0 18 18
CLSPN 0.049 0.037 0.14 34 -0.22 4 38
GORASP1 0.029 0.003 -10000 0 0 6 6
metaphase 0.002 0.005 0.012 86 -0.01 1 87
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.034 0.017 0.053 178 -10000 0 178
G2 phase of mitotic cell cycle 0.005 0.003 0.018 20 -10000 0 20
STAG2 0.028 0.006 -10000 0 0 21 21
GRASP65/GM130/RAB1/GTP 0.025 0.033 -10000 0 -0.42 2 2
spindle elongation 0.069 0.029 0.082 395 -10000 0 395
ODF2 0.034 0.007 -10000 0 -0.03 2 2
BUB1 0.001 0.05 -10000 0 -0.61 3 3
TPT1 0.03 0.042 0.1 1 -0.15 25 26
CDC25C 0.084 0.061 0.15 215 -0.21 6 221
CDC25B 0.03 0.02 -10000 0 -0.034 20 20
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 19 -10000 0 19
CDC20 0.007 0.012 -10000 0 0 431 431
PLK1/PBIP1 0.04 0.026 0.074 123 -10000 0 123
mitosis 0 0.001 -10000 0 -10000 0 0
FBXO5 0.13 0.078 0.17 382 -0.13 4 386
CDC2 0.007 0.004 0.009 384 -10000 0 384
NDC80 0.003 0.009 -10000 0 0 503 503
metaphase plate congression 0.045 0.043 0.13 1 -0.19 14 15
ERCC6L 0.093 0.078 0.16 324 -0.15 1 325
NLP/gamma Tubulin 0.029 0.025 0.06 102 -0.081 9 111
microtubule cytoskeleton organization 0.03 0.042 0.1 1 -0.15 25 26
G2/M transition DNA damage checkpoint 0.001 0.002 0.014 4 -10000 0 4
PPP1R12A 0.031 0.007 -10000 0 -0.03 3 3
interphase 0.001 0.002 0.014 4 -10000 0 4
PLK1/PRC1-2 0.007 0.023 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.09 0.03 0.14 13 -10000 0 13
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 0.078 484 -10000 0 484
mitotic prometaphase 0.003 0.004 0.022 16 -10000 0 16
proteasomal ubiquitin-dependent protein catabolic process 0.065 0.053 -10000 0 -0.29 3 3
microtubule-based process 0.009 0.023 0.098 6 -10000 0 6
Golgi organization 0.069 0.029 0.082 395 -10000 0 395
Cohesin/SA2 0.068 0.026 0.099 134 -10000 0 134
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 0.096 10 -10000 0 10
PPP2R1A 0.028 0.006 -10000 0 0 21 21
chromosome segregation 0.039 0.026 0.073 123 -10000 0 123
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 0.072 407 -10000 0 407
NUDC 0.045 0.043 0.13 1 -0.19 14 15
regulation of attachment of spindle microtubules to kinetochore 0.16 0.068 0.19 460 -0.14 1 461
spindle assembly 0.048 0.026 0.079 150 -10000 0 150
spindle stabilization 0.034 0.017 0.053 178 -10000 0 178
APC/C/HCDH1 -0.018 0.016 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.023 0.099 6 -10000 0 6
CCNB1 0.005 0.012 -10000 0 -10000 0 0
PPP1CB 0.03 0.009 -10000 0 -0.028 8 8
BTRC 0.028 0.005 -10000 0 0 17 17
ROCK2 0.055 0.032 -10000 0 -0.22 3 3
TUBG1 0.031 0.046 0.12 5 -0.16 25 30
G2/M transition of mitotic cell cycle 0.11 0.08 0.17 371 -10000 0 371
MLF1IP -0.013 0.011 0.11 2 -10000 0 2
INCENP 0.034 0.006 -10000 0 -0.031 2 2
TCGA08_retinoblastoma

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
CDKN2B -0.042 0.033 -10000 0 -0.064 328 328
CDKN2C -0.019 0.048 -10000 0 -0.065 273 273
CDKN2A 0.013 0.023 -10000 0 -0.065 6 6
CCND2 -0.022 0.039 -10000 0 -0.26 2 2
RB1 0.069 0.088 0.17 187 -0.2 7 194
CDK4 -0.015 0.038 -10000 0 -0.14 39 39
CDK6 -0.017 0.037 -10000 0 -0.29 2 2
G1/S progression -0.076 0.092 0.2 7 -0.18 200 207
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 0.37 173 -0.28 2 175
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 0.025 0.058 0.16 60 -0.19 7 67
AP1 0.084 0.28 0.47 157 -0.34 17 174
ILK 0.075 0.17 0.34 123 -0.3 2 125
bone resorption -0.01 0.15 0.25 80 -0.34 3 83
PTK2B 0.024 0.011 -10000 0 0 98 98
PYK2/p130Cas 0.061 0.14 0.27 95 -0.27 3 98
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 0.099 -10000 0 -0.16 217 217
alphaV/beta3 Integrin/Osteopontin 0.023 0.1 0.25 59 -0.16 61 120
MAP3K1 0.075 0.17 0.34 119 -0.3 2 121
JUN 0.026 0.028 0.098 29 -0.034 62 91
MAPK3 0.13 0.25 0.47 177 -0.32 1 178
MAPK1 0.13 0.25 0.48 175 -0.32 1 176
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 0.074 0.18 0.36 122 -0.3 2 124
ITGB3 0.012 0.06 0.1 163 -10000 0 163
NFKBIA 0.13 0.25 0.47 177 -0.33 2 179
FOS 0.023 0.026 0.095 24 -0.035 49 73
CD44 0.017 0.015 -10000 0 0 239 239
CHUK 0.027 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 0.5 166 -0.32 1 167
BCAR1 0.026 0.009 -10000 0 0 56 56
RELA 0.029 0.003 -10000 0 0 6 6
alphaV beta3 Integrin 0.04 0.11 0.17 155 -0.18 65 220
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.069 0.16 0.31 121 -0.29 2 123
VAV3 0.07 0.16 0.3 142 -0.28 2 144
MAP3K14 0.12 0.22 0.4 178 -0.29 2 180
ROCK2 0.028 0.005 -10000 0 0 18 18
SPP1 -0.005 0.038 0.09 65 -10000 0 65
RAC1 0.028 0.006 -10000 0 0 27 27
Rac1/GTP 0.055 0.15 0.26 135 -0.27 2 137
MMP2 0.017 0.19 0.33 89 -0.35 36 125
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 -0.26 224 224
JUN -0.071 0.091 0.18 3 -0.26 22 25
HRAS 0.028 0.006 -10000 0 0 27 27
RET51/GFRalpha1/GDNF/GRB10 -0.018 0.1 -10000 0 -0.14 222 222
RAP1A 0.029 0.003 -10000 0 0 7 7
FRS2 0.028 0.007 -10000 0 0 30 30
RAP1A/GDP 0.021 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.018 0.1 -10000 0 -0.14 223 223
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 0 36 36
RET9/GFRalpha1/GDNF/Enigma -0.025 0.089 -10000 0 -0.13 225 225
RHOA 0.029 0.003 -10000 0 0 6 6
RAP1A/GTP -0.018 0.098 -10000 0 -0.14 220 220
GRB7 0.027 0.008 -10000 0 0 41 41
RET51/GFRalpha1/GDNF -0.012 0.097 -10000 0 -0.14 187 187
MAPKKK cascade -0.09 0.076 0.1 1 -0.24 2 3
BCAR1 0.026 0.009 -10000 0 0 56 56
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.097 -10000 0 -0.16 404 404
lamellipodium assembly -0.15 0.097 -10000 0 -0.24 234 234
RET51/GFRalpha1/GDNF/SHC -0.017 0.1 -10000 0 -0.14 218 218
PIK3CA 0.02 0.014 -10000 0 0 172 172
RET9/GFRalpha1/GDNF/SHC -0.024 0.088 -10000 0 -0.13 221 221
RET9/GFRalpha1/GDNF/Shank3 -0.031 0.084 -10000 0 -0.13 224 224
MAPK3 -0.072 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 0.016 0.015 -10000 0 0 246 246
GFRA1 0.016 0.015 -10000 0 0 257 257
MAPK8 -0.072 0.088 0.18 1 -0.26 22 23
HRAS/GTP -0.036 0.12 -10000 0 -0.18 200 200
tube development -0.035 0.082 0.21 4 -0.13 219 223
MAPK1 -0.067 0.075 0.3 3 -10000 0 3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.057 0.089 -10000 0 -0.17 206 206
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
SRC 0.028 0.007 -10000 0 0 31 31
PDLIM7 0.028 0.005 -10000 0 0 17 17
RET51/GFRalpha1/GDNF/Dok6 -0.016 0.11 -10000 0 -0.14 213 213
SHC1 0.028 0.006 -10000 0 0 21 21
RET51/GFRalpha1/GDNF/Dok4 -0.019 0.1 -10000 0 -0.14 222 222
RET51/GFRalpha1/GDNF/Dok5 0.009 0.1 -10000 0 -0.15 135 135
PRKCA 0.028 0.006 -10000 0 0 23 23
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
CREB1 -0.063 0.11 0.22 1 -0.38 7 8
PIK3R1 0.021 0.013 -10000 0 0 159 159
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.094 -10000 0 -0.18 217 217
RET51/GFRalpha1/GDNF/Grb7 -0.019 0.1 -10000 0 -0.14 220 220
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.029 0.004 -10000 0 0 11 11
DOK4 0.027 0.007 -10000 0 0 37 37
JNK cascade -0.069 0.091 0.18 5 -0.25 22 27
RET9/GFRalpha1/GDNF/FRS2 -0.024 0.087 -10000 0 -0.13 216 216
SHANK3 0.023 0.012 -10000 0 0 130 130
RASA1 0.027 0.008 -10000 0 0 49 49
NCK1 0.026 0.009 -10000 0 0 63 63
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.088 -10000 0 -0.17 199 199
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.055 0.091 0.2 1 -0.28 6 7
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.056 0.1 0.2 1 -0.26 22 23
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.052 0.091 -10000 0 -0.3 5 5
PI3K -0.19 0.14 0.33 1 -0.34 230 231
SOS1 0.028 0.007 -10000 0 0 35 35
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.025 0.091 -10000 0 -0.13 219 219
GRB10 0.029 0.004 -10000 0 0 12 12
activation of MAPKK activity -0.05 0.089 0.18 1 -0.28 4 5
RET51/GFRalpha1/GDNF/FRS2 -0.016 0.1 -10000 0 -0.14 213 213
GAB1 0.028 0.006 -10000 0 0 24 24
IRS1 0.011 0.014 -10000 0 0 349 349
IRS2 0.028 0.006 -10000 0 0 24 24
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.059 0.095 -10000 0 -0.27 16 16
RET51/GFRalpha1/GDNF/PKC alpha -0.017 0.1 -10000 0 -0.14 221 221
GRB2 0.028 0.005 -10000 0 0 20 20
PRKACA 0.025 0.01 -10000 0 0 80 80
GDNF 0.027 0.007 -10000 0 0 36 36
RAC1 0.028 0.006 -10000 0 0 27 27
RET51/GFRalpha1/GDNF/IRS1 -0.11 0.11 -10000 0 -0.17 401 401
Rac1/GTP -0.17 0.12 -10000 0 -0.29 225 225
RET9/GFRalpha1/GDNF -0.034 0.083 -10000 0 -0.13 226 226
GFRalpha1/GDNF -0.044 0.099 -10000 0 -0.16 226 226
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 0.041 0.01 -10000 0 -10000 0 0
STXBP1 0.025 0.01 -10000 0 0 75 75
ACh/CHRNA1 -0.043 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 0.028 0.005 -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 -0.1 0.095 -10000 0 -0.17 339 339
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 0.027 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 -0.073 363 363
SNAP25 0.001 0 -10000 0 -10000 0 0
VAMP2 -0.12 0.082 -10000 0 -0.18 389 389
SYT1 0.028 0.007 -10000 0 0 34 34
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 -0.037 0.033 -10000 0 -0.13 57 57
STX1A/SNAP25 fragment 1/VAMP2 -0.1 0.095 -10000 0 -0.17 339 339
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 0 164 -10000 0 164
GNB1/GNG2 -0.052 0.09 -10000 0 -0.13 314 314
regulation of S phase of mitotic cell cycle -0.08 0.11 0.13 3 -0.2 224 227
GNAO1 0.024 0.015 -10000 0 -0.012 74 74
HRAS 0.021 0.02 -10000 0 -0.034 61 61
SHBG/T-DHT 0.019 0.004 -10000 0 -10000 0 0
PELP1 0.021 0.021 -10000 0 -0.033 64 64
AKT1 -0.016 0.004 0 27 -10000 0 27
MAP2K1 -0.083 0.098 0.24 15 -0.24 36 51
T-DHT/AR -0.078 0.083 -10000 0 -0.15 319 319
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.003 0.01 26 -0.007 17 43
GNAI2 0.025 0.015 -10000 0 -0.025 42 42
GNAI3 0.022 0.015 -10000 0 -0.005 117 117
GNAI1 0.025 0.013 -10000 0 -0.014 51 51
mol:GDP -0.16 0.14 -10000 0 -0.27 307 307
cell proliferation -0.12 0.18 0.39 24 -0.46 64 88
PIK3CA 0.02 0.014 -10000 0 0 172 172
FOS -0.1 0.26 0.56 26 -0.71 66 92
mol:Ca2+ -0.012 0.023 0.054 16 -0.058 32 48
MAPK3 -0.11 0.14 0.32 24 -0.37 60 84
MAPK1 -0.063 0.15 0.31 26 -0.44 41 67
PIK3R1 0.021 0.013 -10000 0 0 159 159
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 -0.13 297 309
actin cytoskeleton reorganization 0.002 0.056 -10000 0 -0.12 76 76
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 0.001 0.057 -10000 0 -0.13 76 76
apoptosis 0.086 0.18 0.44 70 -0.45 24 94
T-DHT/AR/PELP1 -0.063 0.083 -10000 0 -0.13 317 317
HRAS/GDP -0.15 0.15 0.13 3 -0.29 259 262
CREB1 -0.11 0.15 0.24 1 -0.46 78 79
RAC1-CDC42/GTP 0.008 0.061 -10000 0 -0.12 76 76
AR 0.01 0.017 -10000 0 -0.034 23 23
GNB1 0.028 0.006 -10000 0 0 24 24
RAF1 -0.076 0.09 0.22 14 -0.21 31 45
RAC1-CDC42/GDP -0.15 0.15 0.12 1 -0.31 227 228
T-DHT/AR/PELP1/Src -0.051 0.089 -10000 0 -0.13 285 285
MAP2K2 -0.093 0.1 0.25 11 -0.26 38 49
T-DHT/AR/PELP1/Src/PI3K -0.08 0.11 0.13 3 -0.2 224 227
GNAZ 0.024 0.014 -10000 0 -0.01 72 72
SHBG 0.028 0.006 -10000 0 0 25 25
Gi family/GNB1/GNG2/GDP -0.041 0.1 -10000 0 -0.34 30 30
mol:T-DHT 0 0.001 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 27 27
GNRH1 -0.014 0.007 0 103 -10000 0 103
Gi family/GTP -0.046 0.066 0.16 1 -0.2 36 37
CDC42 0.029 0.004 -10000 0 0 11 11
Aurora B 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
Condensin I complex 0.033 0.072 0.2 81 -0.32 1 82
STMN1 0.032 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 0.009 0.097 0.21 47 -0.2 14 61
BIRC5 0.038 0.022 0.06 83 -10000 0 83
DES -0.052 0.14 -10000 0 -0.5 26 26
Aurora C/Aurora B/INCENP 0.054 0.035 -10000 0 -10000 0 0
Aurora B/TACC1 -0.064 0.072 -10000 0 -0.13 311 311
Aurora B/PP2A 0.036 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.004 0.013 0.12 3 -0.11 3 6
mitotic metaphase/anaphase transition -0.005 0.005 -10000 0 -10000 0 0
NDC80 0.13 0.1 0.21 356 -10000 0 356
Cul3 protein complex -0.011 0.094 -10000 0 -0.15 178 178
KIF2C 0.11 0.096 0.2 297 -10000 0 297
PEBP1 0.042 0.009 0.061 7 -10000 0 7
KIF20A 0.002 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.034 0.026 -10000 0 -0.15 2 2
SEPT1 0.029 0.004 -10000 0 0 12 12
SMC2 0.016 0.015 -10000 0 0 246 246
SMC4 0.001 0.006 -10000 0 0 534 534
NSUN2/NPM1/Nucleolin 0.001 0.037 -10000 0 -0.41 3 3
PSMA3 0.028 0.005 -10000 0 0 17 17
G2/M transition of mitotic cell cycle 0 0.003 0.02 1 -10000 0 1
H3F3B 0.009 0.018 0.14 1 -0.2 3 4
AURKB 0.028 0.019 0.063 2 -10000 0 2
AURKC 0.028 0.006 -10000 0 0 27 27
CDCA8 0.041 0.021 0.062 111 -10000 0 111
cytokinesis 0.004 0.034 0.24 10 -10000 0 10
Aurora B/Septin1 0.14 0.12 0.26 261 -10000 0 261
AURKA 0.002 0.007 -10000 0 -10000 0 0
INCENP 0.052 0.013 0.065 189 -10000 0 189
KLHL13 0.019 0.014 -10000 0 0 193 193
BUB1 0.002 0.008 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.008 0.024 -10000 0 -10000 0 0
EVI5 0.04 0.009 0.057 30 -10000 0 30
RhoA/GTP 0.002 0.013 -10000 0 -10000 0 0
SGOL1 0.004 0.01 -10000 0 0 485 485
CENPA 0.017 0.047 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 0.036 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 0.012 -10000 0 -0.29 1 1
RASA1 0.027 0.008 -10000 0 0 49 49
KLHL9 0.027 0.007 -10000 0 0 36 36
mitotic prometaphase 0.013 0.006 0.021 149 -10000 0 149
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.024 -10000 0 -0.16 1 1
PPP1CC 0.028 0.006 -10000 0 0 22 22
Centraspindlin 0.002 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.007 -10000 0 -0.15 1 1
NSUN2 0 0.012 -10000 0 -0.29 1 1
MYLK -0.005 0.055 0.14 1 -0.2 39 40
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 0.24 400 -10000 0 400
Chromosomal passenger complex/EVI5 0.064 0.057 -10000 0 -10000 0 0
TACC1 0.005 0.011 -10000 0 0 457 457
PPP2R5D 0.028 0.006 -10000 0 0 26 26
CUL3 0.029 0.004 -10000 0 0 9 9
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.005 -10000 0 0 14 14
mol:PIP3 -0.12 0.11 0.14 15 -0.24 228 243
FRAP1 -0.003 0.066 -10000 0 -0.42 8 8
AKT1 -0.1 0.12 0.15 23 -0.22 214 237
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 -0.09 0.11 0.16 22 -0.21 177 199
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.049 0.05 -10000 0 -0.2 10 10
TSC2 0.028 0.006 -10000 0 0 23 23
RHEB/GDP -0.085 0.09 0.11 18 -0.19 172 190
TSC1 0.028 0.006 -10000 0 -0.001 21 21
Insulin Receptor/IRS1 -0.15 0.14 -10000 0 -0.27 335 335
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.047 0.059 0.14 1 -0.22 11 12
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 -0.32 11 15
MAP3K5 -0.006 0.047 0.19 6 -0.2 25 31
PIK3R1 0.021 0.014 -10000 0 -0.029 5 5
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 0.08 0.22 4 -0.29 11 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.025 0.089 0.2 4 -0.28 10 14
eIF4E/eIF4G1/eIF4A1 -0.028 0.044 -10000 0 -0.26 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.12 0.13 -10000 0 -0.22 309 309
mTOR/RHEB/GTP/Raptor/GBL -0.029 0.057 0.14 11 -0.17 7 18
FKBP1A 0.019 0.021 -10000 0 -0.029 81 81
RHEB/GTP -0.08 0.097 0.15 20 -0.24 38 58
mol:Amino Acids -0.001 0.001 0.001 1 -0.001 344 345
FKBP12/Rapamycin 0.016 0.015 -10000 0 -10000 0 0
PDPK1 -0.12 0.11 0.13 28 -0.24 213 241
EIF4E 0.027 0.007 -10000 0 0 37 37
ASK1/PP5C 0.002 0.14 -10000 0 -0.54 30 30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.004 0.07 -10000 0 -0.25 39 39
TSC1/TSC2 -0.096 0.12 0.17 22 -0.22 177 199
tumor necrosis factor receptor activity 0.001 0.001 0.001 344 -0.001 1 345
RPS6 0.028 0.007 -10000 0 0 31 31
PPP5C 0.028 0.006 -10000 0 0 25 25
EIF4G1 0.024 0.011 -10000 0 0 95 95
IRS1 -0.16 0.13 -10000 0 -0.27 346 346
INS 0.028 0.006 -10000 0 0 23 23
PTEN 0.012 0.027 -10000 0 -0.03 156 156
PDK2 -0.12 0.11 0.13 28 -0.24 214 242
EIF4EBP1 -0.049 0.27 -10000 0 -1 39 39
PIK3CA 0.012 0.021 -10000 0 -0.029 78 78
PPP2R5D -0.005 0.068 0.24 4 -0.36 8 12
peptide biosynthetic process -0.035 0.039 0.17 9 -0.22 1 10
RHEB 0.026 0.01 -10000 0 -0.002 56 56
EIF4A1 0.028 0.006 -10000 0 0 25 25
mol:Rapamycin 0 0.001 0.003 36 -0.002 3 39
EEF2 -0.035 0.039 0.18 9 -0.22 1 10
eIF4E/4E-BP1 -0.034 0.26 -10000 0 -0.96 39 39
Endothelins

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
AKT1 0.044 0.21 0.39 135 -0.32 3 138
PTK2B 0.023 0.015 -10000 0 -0.029 17 17
mol:Ca2+ 0.036 0.2 0.57 11 -0.68 7 18
EDN1 0.025 0.14 0.26 131 -0.22 4 135
EDN3 0.026 0.009 -10000 0 0 57 57
EDN2 0.027 0.008 -10000 0 0 47 47
HRAS/GDP 0.017 0.21 0.42 33 -0.42 36 69
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.015 0.16 0.27 80 -0.36 28 108
ADCY4 0.088 0.19 0.3 218 -0.28 3 221
ADCY5 0.086 0.19 0.3 210 -0.29 2 212
ADCY6 0.089 0.2 0.3 217 -0.29 2 219
ADCY7 0.086 0.19 0.3 210 -0.29 2 212
ADCY1 0.089 0.19 0.3 216 -0.29 2 218
ADCY2 0.085 0.19 0.3 202 -0.29 2 204
ADCY3 0.089 0.19 0.32 181 -0.29 2 183
ADCY8 0.001 0.13 0.3 60 -0.27 20 80
ADCY9 0.083 0.2 0.3 211 -0.27 9 220
arachidonic acid secretion -0.1 0.27 0.56 23 -0.59 70 93
ETB receptor/Endothelin-1/Gq/GTP 0.042 0.14 0.24 107 -0.3 29 136
GNAO1 0.027 0.008 -10000 0 0 44 44
HRAS 0.022 0.02 0.052 4 -0.021 88 92
ETA receptor/Endothelin-1/G12/GTP 0.028 0.16 0.39 71 -0.23 14 85
ETA receptor/Endothelin-1/Gs/GTP 0.041 0.16 0.36 74 -0.23 9 83
mol:GTP 0.003 0.015 0.056 34 -10000 0 34
COL3A1 0.042 0.25 0.55 95 -0.42 4 99
EDNRB 0.05 0.11 0.22 175 -0.11 4 179
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.012 0.24 0.39 124 -0.38 79 203
CYSLTR1 0.038 0.22 0.41 122 -0.32 4 126
SLC9A1 0.028 0.14 0.26 124 -0.28 7 131
mol:GDP 0.014 0.21 0.42 33 -0.43 36 69
SLC9A3 0.071 0.2 0.43 12 -0.6 15 27
RAF1 0.003 0.24 0.53 30 -0.44 59 89
JUN 0.031 0.21 0.69 11 -0.77 8 19
JAK2 0.038 0.21 0.39 126 -0.32 4 130
mol:IP3 0.02 0.17 0.31 83 -0.37 31 114
ETA receptor/Endothelin-1 -0.054 0.097 0.3 6 -0.37 4 10
PLCB1 0.021 0.023 0.07 3 -0.034 70 73
PLCB2 0.018 0.027 0.076 17 -0.037 57 74
ETA receptor/Endothelin-3 0.015 0.11 0.2 121 -0.22 1 122
FOS -0.058 0.35 0.73 24 -0.83 67 91
Gai/GDP -0.003 0.2 -10000 0 -0.69 36 36
CRK 0.026 0.013 -10000 0 -0.029 18 18
mol:Ca ++ 0.078 0.25 0.4 156 -0.39 24 180
BCAR1 0.022 0.017 -10000 0 -0.029 45 45
PRKCB1 0.038 0.18 0.29 86 -0.36 31 117
GNAQ 0.018 0.032 0.11 13 -0.053 2 15
GNAZ 0.027 0.008 -10000 0 0 47 47
GNAL 0.028 0.005 -10000 0 0 19 19
Gs family/GDP 0.014 0.2 0.39 33 -0.4 35 68
ETA receptor/Endothelin-1/Gq/GTP 0.015 0.17 0.29 81 -0.37 30 111
MAPK14 0.025 0.13 0.28 27 -0.3 24 51
TRPC6 0.035 0.2 0.6 9 -0.72 7 16
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 0.23 88 -0.32 29 117
ETB receptor/Endothelin-2 0.07 0.068 0.17 157 -0.082 6 163
ETB receptor/Endothelin-3 0.07 0.068 0.17 156 -0.081 5 161
ETB receptor/Endothelin-1 0.03 0.15 0.3 109 -0.21 5 114
MAPK3 -0.051 0.34 0.69 24 -0.76 69 93
MAPK1 -0.053 0.33 0.69 24 -0.76 70 94
Rac1/GDP 0.015 0.2 0.41 31 -0.42 35 66
cAMP biosynthetic process 0.051 0.18 0.28 131 -0.32 13 144
MAPK8 0.029 0.21 0.58 11 -0.76 11 22
SRC 0.026 0.012 -10000 0 -0.029 19 19
ETB receptor/Endothelin-1/Gi/GTP 0.051 0.11 0.2 148 -0.23 11 159
p130Cas/CRK/Src/PYK2 0.007 0.21 0.49 22 -0.52 24 46
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.015 0.2 0.4 33 -0.42 36 69
COL1A2 0.078 0.28 0.66 90 -0.5 5 95
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.012 0.11 0.2 117 -0.22 1 118
mol:DAG 0.02 0.17 0.31 83 -0.37 31 114
MAP2K2 -0.031 0.27 0.61 26 -0.56 71 97
MAP2K1 -0.02 0.27 0.6 28 -0.56 68 96
EDNRA 0.023 0.15 0.27 134 -0.22 12 146
positive regulation of muscle contraction 0.027 0.17 0.32 128 -0.29 2 130
Gq family/GDP -0.027 0.16 0.39 19 -0.4 32 51
HRAS/GTP 0.021 0.21 0.43 35 -0.41 40 75
PRKCH 0.032 0.18 0.28 84 -0.38 29 113
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA 0.035 0.17 0.29 84 -0.36 26 110
PRKCB 0.038 0.18 0.29 86 -0.35 34 120
PRKCE 0.034 0.18 0.29 82 -0.36 30 112
PRKCD 0.031 0.18 0.29 84 -0.36 33 117
PRKCG 0.035 0.18 0.36 37 -0.37 28 65
regulation of vascular smooth muscle contraction -0.083 0.4 0.72 24 -1 68 92
PRKCQ 0.034 0.18 0.29 87 -0.37 31 118
PLA2G4A -0.11 0.29 0.58 22 -0.63 77 99
GNA14 0.017 0.032 0.11 13 -0.053 2 15
GNA15 0.02 0.027 0.095 13 -0.041 7 20
GNA12 0.028 0.007 -10000 0 0 33 33
GNA11 0.019 0.026 0.095 11 -0.039 9 20
Rac1/GTP 0.026 0.16 0.38 71 -0.23 12 83
MMP1 0.032 0.1 0.4 34 -10000 0 34
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.024 0.011 -10000 0 0 96 96
HRAS 0.028 0.006 -10000 0 0 27 27
EGFR 0.027 0.009 -10000 0 0 54 54
AKT -0.031 0.12 0.22 28 -0.24 50 78
FOXO3 0.027 0.007 -10000 0 0 38 38
AKT1 0.028 0.006 -10000 0 0 27 27
FOXO1 0.027 0.007 -10000 0 0 39 39
AKT3 0.012 0.014 -10000 0 0 334 334
FOXO4 0.029 0.003 -10000 0 0 7 7
MET 0.025 0.011 -10000 0 0 87 87
PIK3CA 0.02 0.014 -10000 0 0 172 172
PIK3CB 0.025 0.01 -10000 0 0 82 82
NRAS 0.014 0.015 -10000 0 0 300 300
PIK3CG 0.027 0.007 -10000 0 0 37 37
PIK3R3 0.018 0.014 -10000 0 0 206 206
PIK3R2 0.027 0.008 -10000 0 0 49 49
NF1 0.026 0.009 -10000 0 0 61 61
RAS 0.044 0.074 0.18 55 -0.25 4 59
ERBB2 0.027 0.008 -10000 0 0 42 42
proliferation/survival/translation 0.017 0.12 0.29 40 -0.22 12 52
PI3K 0.04 0.096 0.2 71 -0.21 21 92
PIK3R1 0.021 0.013 -10000 0 0 159 159
KRAS 0.024 0.011 -10000 0 0 99 99
FOXO 0.025 0.081 0.22 31 -10000 0 31
AKT2 0.027 0.008 -10000 0 0 51 51
PTEN 0.028 0.007 -10000 0 0 31 31
IGF1 pathway

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
NCK2 0.029 0.004 -10000 0 0 11 11
PTK2 0.021 0.013 -10000 0 0 164 164
CRKL -0.079 0.075 0.13 6 -0.2 128 134
GRB2/SOS1/SHC 0.052 0.02 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 27 27
IRS1/Crk -0.08 0.072 0.098 3 -0.2 129 132
IGF-1R heterotetramer/IGF1/PTP1B 0.01 0.099 -10000 0 -0.17 122 122
AKT1 -0.051 0.11 0.14 76 -0.23 75 151
BAD -0.059 0.11 0.16 26 -0.23 74 100
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.079 0.074 0.12 5 -0.21 123 128
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.083 0.073 0.17 3 -0.22 103 106
RAF1 -0.036 0.11 0.25 5 -0.47 3 8
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.049 0.1 -10000 0 -0.2 124 124
YWHAZ 0.025 0.01 -10000 0 0 79 79
IGF-1R heterotetramer/IGF1/IRS1 -0.061 0.094 0.16 2 -0.21 134 136
PIK3CA 0.02 0.014 -10000 0 0 172 172
RPS6KB1 -0.053 0.11 0.14 60 -0.23 73 133
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 0 159 159
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.088 0.067 0.048 3 -0.21 114 117
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.036 0.1 -10000 0 -0.15 115 115
IGF-1R heterotetramer 0.005 0.037 0.045 227 -0.089 8 235
IGF-1R heterotetramer/IGF1/IRS/Nck -0.056 0.098 0.17 3 -0.2 134 137
Crk/p130 Cas/Paxillin -0.061 0.099 0.22 2 -0.2 135 137
IGF1R 0.005 0.037 0.045 227 -0.089 8 235
IGF1 -0.007 0.052 0.06 25 -0.089 93 118
IRS2/Crk -0.082 0.071 0.16 2 -0.22 99 101
PI3K -0.053 0.1 -10000 0 -0.19 153 153
apoptosis 0.048 0.1 0.25 22 -0.2 14 36
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
PRKCD -0.081 0.11 -10000 0 -0.27 122 122
RAF1/14-3-3 E -0.031 0.11 0.23 7 -0.41 3 10
BAD/14-3-3 -0.05 0.11 0.21 14 -0.26 22 36
PRKCZ -0.053 0.11 0.14 61 -0.23 74 135
Crk/p130 Cas/Paxillin/FAK1 -0.056 0.094 0.14 12 -0.24 48 60
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 -0.28 125 125
BCAR1 0.026 0.009 -10000 0 0 56 56
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.026 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 35 35
IRS1/NCK2 -0.081 0.075 0.12 9 -0.2 129 138
GRB10 0.029 0.004 -10000 0 0 12 12
PTPN11 -0.081 0.074 0.13 6 -0.2 128 134
IRS1 -0.056 0.09 0.12 9 -0.21 128 137
IRS2 -0.079 0.074 0.13 6 -0.21 124 130
IGF-1R heterotetramer/IGF1 -0.004 0.12 0.15 3 -0.21 129 132
GRB2 0.028 0.005 -10000 0 0 20 20
PDPK1 -0.047 0.12 0.17 43 -0.23 77 120
YWHAE 0.027 0.008 -10000 0 0 40 40
PRKD1 -0.077 0.11 0.2 4 -0.28 119 123
SHC1 0.028 0.006 -10000 0 0 21 21
Syndecan-1-mediated signaling events

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
TGFB1 0.023 0.012 -10000 0 0 112 112
CCL5 0.025 0.01 -10000 0 0 82 82
SDCBP 0.027 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 -0.021 0.14 0.22 48 -0.32 49 97
Syndecan-1/Syntenin -0.016 0.14 0.22 56 -0.31 50 106
MAPK3 -0.036 0.14 0.2 45 -0.3 58 103
HGF/MET 0.033 0.033 -10000 0 -0.16 12 12
TGFB1/TGF beta receptor Type II 0.023 0.012 -10000 0 0 112 112
BSG 0.027 0.008 -10000 0 0 51 51
keratinocyte migration -0.02 0.14 0.21 48 -0.31 49 97
Syndecan-1/RANTES -0.022 0.15 0.22 61 -0.31 67 128
Syndecan-1/CD147 -0.006 0.15 0.24 36 -0.31 56 92
Syndecan-1/Syntenin/PIP2 -0.018 0.14 0.2 55 -0.3 50 105
LAMA5 0.026 0.01 -10000 0 0 67 67
positive regulation of cell-cell adhesion -0.018 0.13 0.2 55 -0.3 50 105
MMP7 0.017 0.015 -10000 0 0 236 236
HGF 0.028 0.005 -10000 0 0 17 17
Syndecan-1/CASK -0.036 0.12 0.19 27 -0.3 58 85
Syndecan-1/HGF/MET -0.007 0.15 0.25 34 -0.3 53 87
regulation of cell adhesion -0.046 0.13 0.18 33 -0.3 56 89
HPSE 0.027 0.008 -10000 0 0 42 42
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 0.004 -10000 0 0 13 13
MET 0.025 0.011 -10000 0 0 87 87
PRKACA 0.025 0.01 -10000 0 0 80 80
MMP9 0.023 0.012 -10000 0 0 129 129
MAPK1 -0.035 0.13 0.2 39 -0.3 55 94
homophilic cell adhesion -0.016 0.14 0.22 57 -0.31 56 113
MMP1 0.022 0.013 -10000 0 0 142 142
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.026 0.083 -10000 0 -10000 0 0
PLK1 0.27 0.4 0.82 99 -0.83 15 114
CDKN1B 0.19 0.3 0.62 91 -0.47 1 92
FOXO3 0.23 0.41 0.6 242 -0.79 23 265
KAT2B 0.06 0.067 0.11 306 -0.076 5 311
FOXO1/SIRT1 0.008 0.086 0.27 5 -0.28 3 8
CAT 0.24 0.38 0.78 53 -0.87 18 71
CTNNB1 0.023 0.018 -10000 0 -0.029 54 54
AKT1 0.074 0.089 0.18 109 -10000 0 109
FOXO1 0.037 0.094 0.39 2 -0.29 3 5
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 99 -0.082 2 101
FOXO3A/SIRT1 0.22 0.37 0.64 107 -0.7 30 137
XPO1 0.017 0.023 -10000 0 -0.031 93 93
EP300 0.016 0.027 -10000 0 -10000 0 0
BCL2L11 0.084 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 99 -0.082 2 101
RAN 0.015 0.028 -10000 0 -0.033 132 132
GADD45A 0.19 0.29 0.73 71 -0.67 3 74
YWHAQ 0.029 0.005 -10000 0 0 15 15
FOXO1/14-3-3 family 0.003 0.14 -10000 0 -0.51 24 24
MST1 0.078 0.086 0.14 291 -10000 0 291
CSNK1D 0.028 0.006 -10000 0 0 25 25
CSNK1E 0.027 0.008 -10000 0 0 45 45
FOXO4/14-3-3 family 0.004 0.12 0.22 1 -0.52 17 18
YWHAB 0.027 0.008 -10000 0 0 44 44
MAPK8 0.013 0.064 0.18 37 -10000 0 37
MAPK9 0.013 0.063 0.18 36 -10000 0 36
YWHAG 0.029 0.004 -10000 0 0 12 12
YWHAE 0.027 0.008 -10000 0 0 40 40
YWHAZ 0.025 0.01 -10000 0 0 79 79
SIRT1 -0.01 0.054 0.14 39 -0.098 4 43
SOD2 0.039 0.45 0.61 64 -0.74 105 169
RBL2 0.16 0.37 0.68 39 -0.87 23 62
RAL/GDP 0.066 0.069 0.18 61 -10000 0 61
CHUK 0.077 0.085 0.14 294 -10000 0 294
Ran/GTP 0.015 0.024 -10000 0 -10000 0 0
CSNK1G2 0.027 0.008 -10000 0 0 45 45
RAL/GTP 0.064 0.076 0.25 30 -10000 0 30
CSNK1G1 0.029 0.004 -10000 0 0 13 13
FASLG 0.091 0.093 -10000 0 -10000 0 0
SKP2 0.021 0.013 -10000 0 0 156 156
USP7 0.016 0.026 -10000 0 -0.032 117 117
IKBKB 0.075 0.084 0.14 283 -10000 0 283
CCNB1 0.36 0.43 0.71 287 -0.98 8 295
FOXO1-3a-4/beta catenin 0.12 0.29 0.6 64 -10000 0 64
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.078 0.39 1 -0.28 3 4
CSNK1A1 0.029 0.004 -10000 0 0 13 13
SGK1 0.06 0.067 0.11 306 -0.076 5 311
CSNK1G3 0.028 0.006 -10000 0 0 21 21
Ran/GTP/Exportin 1 0.028 0.036 0.14 1 -10000 0 1
ZFAND5 0.01 0.14 0.46 8 -0.64 2 10
SFN 0.027 0.007 -10000 0 0 38 38
CDK2 -0.01 0.025 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.081 0.15 0.3 51 -0.48 14 65
CREBBP -0.022 0.028 -10000 0 -0.08 1 1
FBXO32 0.094 0.61 0.79 124 -0.8 143 267
BCL6 0.17 0.34 0.67 33 -0.91 20 53
RALB 0.014 0.028 -10000 0 -0.034 142 142
RALA 0.014 0.028 -10000 0 -0.034 138 138
YWHAH 0.027 0.008 -10000 0 0 42 42
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.008 -10000 0 0 50 50
HDAC3 0.029 0.003 -10000 0 0 7 7
VDR 0.029 0.003 -10000 0 0 8 8
Cbp/p300/PCAF 0.032 0.026 -10000 0 -0.13 10 10
EP300 0.027 0.008 -10000 0 0 50 50
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.032 0.081 0.17 1 -0.28 32 33
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.028 0.005 -10000 0 0 19 19
AKT1 0.008 0.089 0.23 9 -0.27 6 15
RAR alpha/9cRA/Cyclin H -0.076 0.13 -10000 0 -0.24 198 198
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.033 0.075 -10000 0 -0.26 32 32
CDC2 -0.005 0.007 -10000 0 -0.017 20 20
response to UV -0.009 0.012 -10000 0 -0.025 206 206
RAR alpha/Jnk1 -0.025 0.069 -10000 0 -0.22 24 24
NCOR2 0.028 0.005 -10000 0 0 17 17
VDR/VDR/Vit D3 0.021 0.003 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.2 0.26 -10000 0 -0.52 212 212
NCOA2 0.027 0.008 -10000 0 0 45 45
NCOA3 0.026 0.009 -10000 0 0 60 60
NCOA1 0.029 0.005 -10000 0 0 14 14
VDR/VDR/DNA 0.029 0.003 -10000 0 0 8 8
RARG 0.003 0.033 -10000 0 -0.04 204 204
RAR gamma1/9cRA 0.01 0.032 -10000 0 -10000 0 0
MAPK3 0.001 0.036 -10000 0 -0.046 202 202
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 -0.33 201 201
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 -0.27 28 28
PRKCA -0.012 0.053 -10000 0 -0.083 200 200
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.22 0.29 -10000 0 -0.58 213 213
RXRG -0.027 0.061 -10000 0 -0.24 5 5
RXRA -0.079 0.092 -10000 0 -0.24 42 42
RXRB -0.027 0.052 -10000 0 -0.22 3 3
VDR/Vit D3/DNA 0.021 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 0.052 -10000 0 -0.081 205 205
MNAT1 0.029 0.005 -10000 0 0 14 14
RAR alpha/RXRs -0.11 0.19 -10000 0 -0.38 137 137
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.096 0.15 -10000 0 -0.38 45 45
proteasomal ubiquitin-dependent protein catabolic process -0.042 0.089 -10000 0 -0.3 33 33
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.22 0.29 -10000 0 -0.58 213 213
positive regulation of DNA binding -0.075 0.12 -10000 0 -0.22 198 198
NRIP1 -0.39 0.51 -10000 0 -1 213 213
RXRs/RARs -0.15 0.21 -10000 0 -0.41 207 207
RXRs/RXRs/DNA/9cRA -0.13 0.16 -10000 0 -0.33 205 205
PRKACA 0.025 0.01 -10000 0 0 80 80
CDK7 0.026 0.01 -10000 0 0 71 71
TFIIH 0.05 0.022 -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 46 46
CREBBP 0.027 0.008 -10000 0 0 41 41
RAR gamma2/9cRA -0.046 0.032 0.093 13 -10000 0 13
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.009 -10000 0 -10000 0 0
ELF1 0.002 0.031 -10000 0 -10000 0 0
CCNA2 0.003 0.009 -10000 0 0 492 492
PIK3CA 0.02 0.014 -10000 0 -10000 0 0
JAK3 0.027 0.008 -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 -0.45 10 10
SHC1 0.028 0.006 -10000 0 -10000 0 0
SP1 -0.21 0.14 -10000 0 -0.29 415 415
IL2RA -0.024 0.046 0.4 6 -10000 0 6
IL2RB 0.027 0.008 -10000 0 -10000 0 0
SOS1 0.027 0.007 -10000 0 -10000 0 0
IL2RG 0.026 0.009 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.31 0.29 0.33 23 -0.48 384 407
PTPN11 0.029 0.003 -10000 0 -10000 0 0
CCND2 -0.36 0.24 0.4 3 -0.52 378 381
LCK 0.028 0.006 -10000 0 -10000 0 0
GRB2 0.028 0.005 -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
Insulin Pathway

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
CBL/APS/CAP -0.073 0.093 -10000 0 -0.14 328 328
TC10/GTP -0.05 0.023 -10000 0 -0.13 31 31
Insulin Receptor/Insulin/IRS1/Shp2 -0.067 0.11 -10000 0 -0.15 322 322
HRAS 0.028 0.006 -10000 0 0 27 27
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 0.23 13 -0.29 5 18
INSR -0.02 0.027 0.056 39 -10000 0 39
Insulin Receptor/Insulin 0.036 0.065 0.2 24 -0.14 39 63
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 0.027 0.007 -10000 0 0 36 36
PTPN1 -0.037 0.046 -10000 0 -10000 0 0
CAV1 -0.097 0.076 0.16 5 -0.22 83 88
CBL/APS/CAP/Crk-II/C3G 0.047 0.055 -10000 0 -0.13 34 34
Insulin Receptor/Insulin/IRS1/NCK2 -0.067 0.11 -10000 0 -0.15 326 326
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.061 0.092 -10000 0 -0.16 241 241
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.1 0.15 -10000 0 -0.45 67 67
RPS6KB1 -0.067 0.099 0.21 13 -0.23 28 41
PARD6A 0.026 0.009 -10000 0 0 59 59
CBL 0.029 0.005 -10000 0 0 14 14
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.044 -10000 0 -0.7 2 2
PIK3R1 0.021 0.013 -10000 0 0 159 159
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.079 0.096 0.15 20 -0.24 45 65
HRAS/GTP -0.097 0.058 0.032 4 -0.15 242 246
Insulin Receptor -0.02 0.027 0.056 39 -10000 0 39
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.062 0.11 -10000 0 -0.15 292 292
PRKCI 0.001 0.08 -10000 0 -0.36 17 17
Insulin Receptor/Insulin/GRB14/PDK1 -0.083 0.077 0.054 8 -0.22 55 63
SHC1 0.028 0.006 -10000 0 0 21 21
negative regulation of MAPKKK cascade 0.043 0.048 -10000 0 -0.61 2 2
PI3K -0.057 0.1 -10000 0 -0.16 239 239
NCK2 0.029 0.004 -10000 0 0 11 11
RHOQ 0.028 0.005 -10000 0 0 18 18
mol:H2O2 -0.006 0.006 0.012 30 -10000 0 30
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
AKT2 -0.06 0.11 0.23 9 -0.29 5 14
PRKCZ -0.017 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 53 53
TRIP10 0.027 0.007 -10000 0 0 36 36
Insulin Receptor/Insulin/Shc 0.036 0.054 -10000 0 -0.12 42 42
TC10/GTP/CIP4/Exocyst 0.036 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.058 0.071 -10000 0 -0.14 35 35
RAPGEF1 0.028 0.005 -10000 0 0 17 17
RASA1 0.027 0.008 -10000 0 0 49 49
NCK1 0.026 0.009 -10000 0 0 63 63
CBL/APS/CAP/Crk-II 0.037 0.049 -10000 0 -0.13 35 35
TC10/GDP 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.048 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 35 35
SGK1 -0.01 0.008 -10000 0 -0.025 48 48
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 0 8 8
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 0.03 0.057 43 -10000 0 43
mol:PI-3-4-P2 -0.087 0.054 -10000 0 -0.13 287 287
GRB2 0.028 0.005 -10000 0 0 20 20
EIF4EBP1 -0.069 0.093 0.18 7 -0.23 27 34
PTPRA -0.026 0.023 0.051 26 -10000 0 26
PIK3CA 0.02 0.014 -10000 0 0 172 172
TC10/GTP/CIP4 0.036 0.012 -10000 0 -10000 0 0
PDPK1 0.028 0.005 -10000 0 0 18 18
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.098 0.1 -10000 0 -0.28 58 58
Insulin Receptor/Insulin/IRS1 -0.066 0.095 -10000 0 -0.14 327 327
Insulin Receptor/Insulin/IRS3 0.026 0.06 -10000 0 -0.17 43 43
Par3/Par6 0.046 0.044 -10000 0 -0.13 1 1
Thromboxane A2 receptor 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
TGM2 0.01 0.02 0.099 8 -0.03 13 21
GNB1/GNG2 -0.067 0.065 -10000 0 -0.19 93 93
AKT1 -0.017 0.23 0.47 77 -0.37 9 86
EGF 0.027 0.008 -10000 0 0 40 40
mol:TXA2 0 0.002 0.035 1 -10000 0 1
FGR -0.024 0.066 0.22 9 -10000 0 9
mol:Ca2+ -0.065 0.29 0.56 78 -0.36 45 123
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 78 -0.38 44 122
GNG2 0.029 0.004 -10000 0 0 12 12
ARRB2 0.028 0.006 -10000 0 0 25 25
TP alpha/Gq family/GDP/G beta5/gamma2 -0.066 0.17 -10000 0 -0.43 80 80
G beta5/gamma2 -0.08 0.086 0.17 1 -0.25 91 92
PRKCH -0.069 0.31 0.58 78 -0.42 60 138
DNM1 0.029 0.005 -10000 0 0 16 16
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 0.023 0.018 0.059 1 -0.024 67 68
G12 family/GTP -0.14 0.13 -10000 0 -0.32 101 101
ADRBK1 0.029 0.003 -10000 0 0 7 7
ADRBK2 0.026 0.01 -10000 0 0 77 77
RhoA/GTP/ROCK1 0.038 0.013 0.16 1 -0.14 1 2
mol:GDP 0.044 0.24 0.46 47 -0.42 76 123
mol:NADP -0.002 0.029 0.068 1 -0.029 288 289
RAB11A 0.029 0.004 -10000 0 0 13 13
PRKG1 -0.003 0.03 0.068 1 -0.029 306 307
mol:IP3 -0.096 0.33 0.59 78 -0.44 79 157
cell morphogenesis 0.038 0.013 0.16 1 -0.13 1 2
PLCB2 -0.16 0.38 0.62 71 -0.62 87 158
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 -0.025 0.064 0.23 7 -10000 0 7
RHOA 0.029 0.003 -10000 0 0 6 6
PTGIR 0.023 0.018 0.059 1 -0.019 78 79
PRKCB1 -0.085 0.32 0.59 78 -0.44 60 138
GNAQ 0.028 0.006 -10000 0 0 28 28
mol:L-citrulline -0.002 0.029 0.068 1 -0.029 288 289
TXA2/TXA2-R family -0.11 0.38 0.64 78 -0.57 79 157
LCK -0.023 0.066 0.22 10 -10000 0 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.016 0.057 0.16 13 -10000 0 13
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.12 -10000 0 -0.44 40 40
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.054 0.16 7 -10000 0 7
MAPK14 -0.028 0.24 0.48 78 -10000 0 78
TGM2/GTP -0.14 0.35 0.62 70 -0.52 75 145
MAPK11 -0.031 0.24 0.48 78 -10000 0 78
ARHGEF1 -0.031 0.2 0.39 76 -10000 0 76
GNAI2 0.029 0.003 -10000 0 0 6 6
JNK cascade -0.065 0.33 0.61 78 -0.42 60 138
RAB11/GDP 0.012 0.034 -10000 0 -0.083 17 17
ICAM1 -0.028 0.28 0.58 79 -0.37 5 84
cAMP biosynthetic process -0.1 0.31 0.54 78 -0.41 77 155
Gq family/GTP/EBP50 -0.053 0.1 0.24 1 -0.21 146 147
actin cytoskeleton reorganization 0.038 0.013 0.16 1 -0.13 1 2
SRC -0.025 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 -0.25 15 26
VCAM1 -0.037 0.3 0.6 78 -0.36 65 143
TP beta/Gq family/GDP/G beta5/gamma2 -0.066 0.17 -10000 0 -0.43 80 80
platelet activation -0.06 0.28 0.54 78 -0.36 1 79
PGI2/IP 0.021 0.012 0.09 1 -0.15 2 3
PRKACA -0.003 0.024 0.17 1 -0.15 2 3
Gq family/GDP/G beta5/gamma2 -0.051 0.14 -10000 0 -0.36 75 75
TXA2/TP beta/beta Arrestin2 0.018 0.054 -10000 0 -0.34 8 8
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 -0.5 67 145
EGFR 0.027 0.009 -10000 0 0 54 54
TXA2/TP alpha -0.16 0.38 0.61 78 -0.57 83 161
Gq family/GTP -0.033 0.077 -10000 0 -0.21 72 72
YES1 -0.024 0.065 0.22 9 -10000 0 9
GNAI2/GTP -0.021 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 -0.029 0.069 0.22 10 -0.2 1 11
mol:NO -0.002 0.029 0.068 1 -0.029 288 289
GNA15 0.027 0.008 -10000 0 0 46 46
PGK/cGMP 0.037 0.012 0.15 1 -10000 0 1
RhoA/GDP 0.013 0.034 -10000 0 -0.074 22 22
TP alpha/TGM2/GDP/G beta/gamma -0.076 0.065 -10000 0 -0.23 5 5
NOS3 -0.002 0.029 0.068 1 -0.029 288 289
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA -0.069 0.31 0.58 78 -0.42 59 137
PRKCB -0.069 0.31 0.58 78 -0.41 60 138
PRKCE -0.059 0.31 0.59 78 -0.42 55 133
PRKCD -0.069 0.32 0.59 78 -0.43 60 138
PRKCG -0.088 0.32 0.59 78 -0.46 58 136
muscle contraction -0.11 0.36 0.62 78 -0.54 78 156
PRKCZ -0.058 0.3 0.57 78 -0.38 41 119
ARR3 0.029 0.003 -10000 0 0 5 5
TXA2/TP beta -0.01 0.07 0.22 11 -0.19 3 14
PRKCQ -0.06 0.31 0.58 78 -0.42 55 133
MAPKKK cascade -0.11 0.36 0.61 78 -0.52 82 160
SELE -0.03 0.28 0.55 78 -10000 0 78
TP beta/GNAI2/GDP/G beta/gamma -0.021 0.063 0.22 5 -10000 0 5
ROCK1 0.029 0.005 -10000 0 0 15 15
GNA14 0.028 0.005 -10000 0 0 19 19
chemotaxis -0.11 0.4 0.67 78 -0.62 74 152
GNA12 0.028 0.007 -10000 0 0 33 33
GNA13 0.029 0.005 -10000 0 0 14 14
GNA11 0.025 0.01 -10000 0 0 83 83
Rac1/GTP 0.021 0.009 0.16 1 -10000 0 1
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 0.026 0.009 -10000 0 0 57 57
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 0.002 0.072 0.18 3 -10000 0 3
Ephrin B2/EPHB1-2 0.044 0.039 -10000 0 -0.12 18 18
neuron projection morphogenesis -0.027 0.05 0.065 74 -10000 0 74
Ephrin B1/EPHB1-2/Tiam1 0.002 0.067 0.17 6 -10000 0 6
DNM1 0 0.031 -10000 0 -10000 0 0
cell-cell signaling 0.001 0.005 0.017 3 -10000 0 3
MAP2K4 -0.12 0.21 0.23 1 -0.49 137 138
YES1 -0.16 0.31 -10000 0 -0.7 138 138
Ephrin B1/EPHB1-2/NCK2 0.002 0.066 0.18 5 -10000 0 5
PI3K -0.11 0.22 -10000 0 -0.47 139 139
mol:GDP -0.001 0.066 0.16 8 -10000 0 8
ITGA2B 0.028 0.006 -10000 0 0 23 23
endothelial cell proliferation 0.03 0.034 -10000 0 -0.13 20 20
FYN -0.17 0.32 -10000 0 -0.72 138 138
MAP3K7 -0.12 0.22 0.23 5 -0.51 134 139
FGR -0.16 0.31 -10000 0 -0.69 139 139
TIAM1 0.028 0.005 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 159 159
RGS3 0.029 0.005 -10000 0 0 16 16
cell adhesion -0.13 0.21 0.2 5 -0.47 139 144
LYN -0.16 0.31 -10000 0 -0.7 138 138
Ephrin B1/EPHB1-2/Src Family Kinases -0.15 0.28 -10000 0 -0.64 139 139
Ephrin B1/EPHB1-2 -0.12 0.24 -10000 0 -0.55 134 134
SRC -0.15 0.31 -10000 0 -0.69 138 138
ITGB3 0.024 0.011 -10000 0 0 98 98
EPHB1 -0.004 0.031 -10000 0 -10000 0 0
EPHB4 0.028 0.005 -10000 0 0 19 19
RAC1 0.028 0.006 -10000 0 0 27 27
Ephrin B2/EPHB4 0.03 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 -0.7 139 139
HCK -0.15 0.31 -10000 0 -0.7 137 137
regulation of stress fiber formation 0.002 0.065 -10000 0 -0.17 5 5
MAPK8 -0.13 0.2 -10000 0 -0.47 135 135
Ephrin B1/EPHB1-2/RGS3 0.003 0.067 0.17 6 -10000 0 6
endothelial cell migration -0.1 0.18 0.34 2 -0.42 134 136
NCK2 0.029 0.004 -10000 0 0 11 11
PTPN13 0.022 0.016 -10000 0 0 183 183
regulation of focal adhesion formation 0.002 0.065 -10000 0 -0.17 5 5
chemotaxis 0 0.066 -10000 0 -0.17 6 6
PIK3CA 0.02 0.014 -10000 0 0 172 172
Rac1/GTP -0.012 0.065 0.14 8 -10000 0 8
angiogenesis -0.12 0.24 -10000 0 -0.54 137 137
LCK -0.16 0.31 -10000 0 -0.69 139 139
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 0 339 -10000 0 339
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 0.028 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 0.056 0.094 0.26 9 -0.33 14 23
NFATC2 -0.015 0.059 0.25 4 -0.23 6 10
NFATC3 -0.001 0.023 -10000 0 -0.31 1 1
YWHAE 0.027 0.008 -10000 0 0 40 40
Calcineurin A alpha-beta B1/CABIN1 -0.008 0.062 0.24 1 -0.26 17 18
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 -0.004 0.077 0.21 1 -0.25 18 19
BCL2/BAX 0.011 0.07 -10000 0 -0.16 74 74
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.032 0.12 4 -0.15 9 13
CaM/Ca2+ -0.001 0.032 0.12 4 -0.15 9 13
BAX 0.028 0.006 -10000 0 0 21 21
MAPK14 0.005 0.03 0.059 4 -0.032 215 219
BAD 0.029 0.002 -10000 0 0 4 4
CABIN1/MEF2D 0.003 0.065 0.23 1 -0.25 17 18
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 -0.003 0.065 0.25 17 -0.23 1 18
KPNB1 0.028 0.006 -10000 0 0 21 21
KPNA2 0.003 0.009 -10000 0 0 494 494
XPO1 0.005 0.027 -10000 0 -0.029 202 202
SFN 0.027 0.007 -10000 0 0 38 38
MAP3K8 0.005 0.03 0.06 4 -0.032 216 220
NFAT4/CK1 alpha -0.047 0.031 0.15 4 -0.19 8 12
MEF2D/NFAT1/Cbp/p300 -0.058 0.12 -10000 0 -0.26 44 44
CABIN1 -0.008 0.062 0.25 1 -0.26 17 18
CALM1 0.004 0.031 0.063 4 -0.034 215 219
RAN 0.006 0.028 -10000 0 -0.028 228 228
MAP3K1 0.027 0.008 -10000 0 0 51 51
CAMK4 0.027 0.007 -10000 0 0 39 39
mol:Ca2+ -0.003 0.007 0.067 4 -10000 0 4
MAPK3 0.028 0.006 -10000 0 0 22 22
YWHAH 0.027 0.008 -10000 0 0 42 42
Calcineurin A alpha-beta B1/AKAP79/PKA 0.035 0.016 -10000 0 -10000 0 0
YWHAB 0.027 0.008 -10000 0 0 44 44
MAPK8 0.004 0.03 0.065 4 -0.033 220 224
MAPK9 0.028 0.005 -10000 0 0 18 18
YWHAG 0.029 0.004 -10000 0 0 12 12
FKBP1A 0.027 0.007 -10000 0 0 39 39
NFAT1-c-4/YWHAQ 0.039 0.11 0.26 6 -0.35 15 21
PRKCH 0.029 0.005 -10000 0 0 15 15
CABIN1/Cbp/p300 0.001 0.05 -10000 0 -0.16 11 11
CASP3 0.005 0.028 0.059 4 -0.032 195 199
PIM1 0.028 0.006 -10000 0 0 28 28
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.018 0.065 4 -10000 0 4
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 0.056 -10000 0 -0.23 15 15
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.028 0.005 -10000 0 0 18 18
JNK2/NFAT4 -0.001 0.069 -10000 0 -0.18 62 62
BAD/BCL-XL 0.04 0.013 -10000 0 -10000 0 0
PRKCD 0.029 0.005 -10000 0 0 15 15
NUP214 0.006 0.028 -10000 0 -0.029 216 216
PRKCZ 0.004 0.03 0.065 4 -0.033 219 223
PRKCA 0.028 0.006 -10000 0 0 23 23
PRKCG 0.028 0.005 -10000 0 0 20 20
PRKCQ 0.027 0.008 -10000 0 0 47 47
FKBP38/BCL2 -0.002 0.081 -10000 0 -0.17 102 102
EP300 0 0.033 0.071 4 -0.039 217 221
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.008 -10000 0 0 40 40
NFATc/JNK1 0.062 0.097 0.27 6 -0.32 14 20
CaM/Ca2+/FKBP38 -0.002 0.052 0.13 4 -0.14 43 47
FKBP12/FK506 0.02 0.006 -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 0.064 0.098 0.26 8 -0.32 14 22
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.017 0.073 0.21 1 -0.25 18 19
NR4A1 -0.13 0.13 0.17 4 -0.29 209 213
GSK3B 0.005 0.03 0.065 4 -0.033 215 219
positive T cell selection -0.001 0.023 -10000 0 -0.3 1 1
NFAT1/CK1 alpha -0.025 0.05 0.21 4 -0.18 12 16
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 0.001 0.034 0.071 4 -0.039 225 229
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.025 0.01 -10000 0 0 79 79
NFATc/p38 alpha 0.062 0.095 0.26 4 -0.32 13 17
CREBBP 0.001 0.033 0.071 4 -0.039 215 219
BCL2 0.023 0.012 -10000 0 0 122 122
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.033 0.019 -10000 0 -10000 0 0
ATM 0.028 0.007 -10000 0 0 30 30
UBE2D3 0.027 0.008 -10000 0 0 40 40
PRKDC 0.024 0.011 -10000 0 0 98 98
ATR 0.022 0.013 -10000 0 0 139 139
UBE2L3 0.028 0.007 -10000 0 0 31 31
FANCD2 0.052 0.063 0.14 189 -10000 0 189
protein ubiquitination 0.053 0.064 -10000 0 -10000 0 0
XRCC5 0.027 0.007 -10000 0 0 37 37
XRCC6 0.027 0.008 -10000 0 0 49 49
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 0.042 0.027 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.03 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 60 60
CCNE1 0.003 0.008 -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 0.033 0.018 -10000 0 -10000 0 0
FANCE 0.028 0.005 -10000 0 0 19 19
FANCC 0.028 0.006 -10000 0 0 22 22
NBN 0.025 0.01 -10000 0 0 82 82
FANCA 0.025 0.011 -10000 0 0 85 85
DNA repair 0.2 0.2 0.36 274 -0.36 2 276
BRCA1/BARD1/ubiquitin 0.033 0.018 -10000 0 -10000 0 0
BARD1/DNA-PK 0.07 0.048 -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 0.027 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.048 0.073 -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 60 60
BARD1 0.025 0.011 -10000 0 0 89 89
PCNA 0.022 0.013 -10000 0 0 147 147
BRCA1/BARD1/UbcH5C 0.044 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.044 0.026 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.061 0.058 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.052 0.08 -10000 0 -0.14 50 50
BRCA1/BARD1/Ubiquitin 0.033 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP -0.022 0.049 0.16 30 -10000 0 30
FA complex 0.028 0.049 0.19 8 -0.21 5 13
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 0 101 101
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 0.058 0.07 -10000 0 -10000 0 0
CSTF1 0.026 0.009 -10000 0 0 57 57
BARD1/EWS-Fli1 0.018 0.008 -10000 0 -10000 0 0
CDK2 0.017 0.014 -10000 0 0 227 227
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.013 0.015 -10000 0 0 308 308
RAD50 0.029 0.005 -10000 0 0 15 15
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.033 0.018 -10000 0 -10000 0 0
EWSR1 0.027 0.008 -10000 0 0 43 43
Reelin 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
CDK5R1/CDK5 0.035 0.018 -10000 0 -10000 0 0
VLDLR 0.026 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 33 33
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 0.073 0.039 -10000 0 -0.14 1 1
AKT1 -0.044 0.09 -10000 0 -0.21 84 84
MAP2K7 0.027 0.007 -10000 0 0 37 37
RAPGEF1 0.028 0.005 -10000 0 0 17 17
DAB1 0.029 0.005 -10000 0 0 14 14
RELN/LRP8/DAB1 0.021 0.068 -10000 0 -0.13 90 90
LRPAP1/LRP8 0.039 0.017 -10000 0 -0.16 2 2
RELN/LRP8/DAB1/Fyn 0.011 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 0.011 0.1 -10000 0 -0.15 129 129
DAB1/LIS1 0.03 0.09 -10000 0 -0.15 90 90
DAB1/CRLK/C3G 0.015 0.086 -10000 0 -0.15 90 90
PIK3CA 0.02 0.014 -10000 0 0 172 172
DAB1/NCK2 0.031 0.092 -10000 0 -0.15 93 93
ARHGEF2 0.028 0.006 -10000 0 0 28 28
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 0.027 0.007 -10000 0 0 37 37
RELN 0.022 0.012 -10000 0 0 131 131
PIK3R1 0.021 0.013 -10000 0 0 159 159
RELN/LRP8/Fyn -0.002 0.091 -10000 0 -0.15 140 140
GRIN2A/RELN/LRP8/DAB1/Fyn 0.017 0.1 -10000 0 -0.15 139 139
MAPK8 0.029 0.004 -10000 0 0 11 11
RELN/VLDLR/DAB1 0.014 0.071 -10000 0 -0.13 98 98
ITGB1 0.028 0.006 -10000 0 0 22 22
MAP1B -0.043 0.068 -10000 0 -0.24 11 11
RELN/LRP8 0.018 0.075 -10000 0 -0.15 88 88
GRIN2B/RELN/LRP8/DAB1/Fyn 0.016 0.1 -10000 0 -0.15 129 129
PI3K -0.001 0.068 -10000 0 -0.16 76 76
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.023 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 32 32
MAPK8IP1 0.029 0.003 -10000 0 0 7 7
CRLK/C3G 0.04 0.012 -10000 0 -10000 0 0
GRIN2B 0.026 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 0.028 0.005 -10000 0 0 20 20
GSK3B -0.048 0.093 0.16 7 -0.28 30 37
RELN/VLDLR/DAB1/Fyn 0.006 0.093 -10000 0 -0.14 144 144
MAP3K11 0.029 0.003 -10000 0 0 6 6
RELN/VLDLR/DAB1/P13K -0.035 0.099 -10000 0 -0.2 126 126
CDK5 0.025 0.011 -10000 0 0 84 84
MAPT -0.013 0.016 -10000 0 -10000 0 0
neuron migration -0.058 0.11 0.24 7 -0.28 53 60
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.034 0.088 -10000 0 -0.27 31 31
RELN/VLDLR 0.027 0.085 -10000 0 -0.14 93 93
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.026 0.095 -10000 0 -0.52 2 2
UGCG -0.018 0.12 -10000 0 -0.7 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT -0.078 0.18 -10000 0 -0.48 50 50
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.017 0.12 -10000 0 -0.69 16 16
mol:DAG -0.003 0.12 -10000 0 -0.85 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.12 0.23 0.3 1 -0.51 106 107
FRAP1 -0.14 0.27 0.33 1 -0.59 111 112
FOXO3 -0.11 0.23 0.32 1 -0.61 65 66
AKT1 -0.11 0.25 0.31 2 -0.62 77 79
GAB2 0.01 0.028 -10000 0 -0.035 139 139
SMPD1 -0.024 0.14 -10000 0 -0.7 21 21
SGMS1 -0.011 0.098 -10000 0 -0.66 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.023 0.065 0.15 41 -0.14 75 116
CALM1 0.028 0.006 -10000 0 0 26 26
cell proliferation -0.017 0.15 0.28 1 -0.53 19 20
EIF3A 0.029 0.004 -10000 0 0 10 10
PI3K -0.011 0.068 -10000 0 -0.17 76 76
RPS6KB1 -0.017 0.12 -10000 0 -0.93 8 8
mol:sphingomyelin -0.003 0.12 -10000 0 -0.85 11 11
natural killer cell activation -0.002 0.004 -10000 0 -0.018 7 7
JAK3 0.01 0.029 0.16 1 -0.037 115 116
PIK3R1 0.008 0.026 0.17 1 -0.038 86 87
JAK1 0.011 0.03 0.17 1 -0.036 124 125
NFKB1 0.027 0.008 -10000 0 0 45 45
MYC -0.079 0.3 0.4 2 -0.85 63 65
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 -0.064 0.15 0.35 1 -0.44 38 39
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 -0.43 38 39
Rac1/GDP -0.025 0.066 0.14 49 -0.13 75 124
T cell proliferation -0.063 0.14 0.29 3 -0.42 36 39
SHC1 0.011 0.029 -10000 0 -0.035 151 151
RAC1 0.017 0.023 -10000 0 -0.029 102 102
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 -0.42 38 39
NF kappa B1 p50/RelA -0.11 0.24 0.32 1 -0.53 102 103
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.027 0.1 0.67 1 -0.36 17 18
HSP90AA1 0.028 0.005 -10000 0 0 20 20
RELA 0.029 0.003 -10000 0 0 6 6
IL2RA 0.01 0.028 -10000 0 -0.035 144 144
IL2RB 0.01 0.029 0.17 1 -0.037 110 111
TERT 0.026 0.009 -10000 0 0 61 61
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 31 31
mol:cAMP 0.002 0.008 -10000 0 -0.084 1 1
PTPN11 0.011 0.03 -10000 0 -0.036 155 155
IL2RG 0.01 0.029 0.16 1 -0.038 112 113
actin cytoskeleton organization -0.063 0.14 0.29 3 -0.42 36 39
GRB2 0.011 0.029 -10000 0 -0.036 151 151
IL2 0.01 0.03 0.16 1 -0.038 120 121
PIK3CA 0.008 0.025 -10000 0 -0.036 85 85
Rac1/GTP -0.007 0.058 -10000 0 -0.12 75 75
LCK 0.01 0.03 0.17 1 -0.038 123 124
BCL2 -0.17 0.3 -10000 0 -0.75 105 105
IL4-mediated signaling events

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
BCL2L1 0.025 0.58 1.1 18 -1.2 45 63
STAT6 (cleaved dimer) -0.1 0.5 0.65 3 -1.2 62 65
IGHG1 0.09 0.31 0.68 42 -0.98 2 44
IGHG3 -0.006 0.53 0.8 9 -1.1 52 61
AKT1 -0.039 0.37 -10000 0 -0.98 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.016 0.33 0.57 8 -0.96 28 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.08 0.39 0.64 3 -1 39 42
THY1 0.077 0.65 1.1 80 -1.2 43 123
MYB 0.026 0.009 -10000 0 0 62 62
HMGA1 0.028 0.006 -10000 0 0 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.051 0.42 0.75 41 -0.94 24 65
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.021 0.4 0.64 13 -1.1 27 40
SP1 0.11 0.13 0.3 177 -0.14 6 183
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.018 0.058 -10000 0 -0.14 7 7
STAT6 (dimer)/ETS1 -0.049 0.54 0.7 12 -1.2 57 69
SOCS1 -0.002 0.4 0.61 19 -0.78 47 66
SOCS3 0.029 0.35 0.87 1 -0.88 17 18
FCER2 0.043 0.48 0.93 12 -1 23 35
PARP14 0.022 0.013 -10000 0 -10000 0 0
CCL17 0.005 0.57 0.94 9 -1.2 48 57
GRB2 0.028 0.005 -10000 0 0 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.043 0.31 0.58 14 -0.68 25 39
T cell proliferation -0.056 0.58 0.78 1 -1.3 66 67
IL4R/JAK1 -0.069 0.61 0.79 3 -1.4 65 68
EGR2 0.012 0.58 1.1 8 -1.2 46 54
JAK2 0.042 0.11 0.24 56 -10000 0 56
JAK3 0.002 0.034 0.11 3 -10000 0 3
PIK3R1 0.021 0.013 -10000 0 0 159 159
JAK1 0.023 0.059 0.16 6 -10000 0 6
COL1A2 0.16 0.39 0.73 101 -1.1 8 109
CCL26 0.007 0.57 0.95 10 -1.2 48 58
IL4R -0.018 0.7 1.1 40 -1.4 65 105
PTPN6 -0.012 0.05 -10000 0 -0.096 38 38
IL13RA2 0.016 0.58 1.1 14 -1.2 48 62
IL13RA1 0.045 0.11 0.24 62 -10000 0 62
IRF4 0.067 0.21 0.73 1 -0.79 3 4
ARG1 0.079 0.26 0.68 11 -0.69 4 15
CBL 0.028 0.38 0.68 14 -0.88 25 39
GTF3A 0.16 0.14 0.31 276 -0.11 1 277
PIK3CA 0.02 0.014 -10000 0 0 172 172
IL13RA1/JAK2 0.073 0.16 0.32 102 -10000 0 102
IRF4/BCL6 0.046 0.18 0.54 1 -0.75 3 4
CD40LG 0.029 0.018 0.33 2 -10000 0 2
MAPK14 0.031 0.38 0.68 14 -0.9 23 37
mitosis -0.032 0.35 0.59 1 -0.9 29 30
STAT6 0.032 0.71 1.3 42 -1.4 49 91
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 1.3 42 -1.4 49 91
STAT6 (dimer)/PARP14 -0.055 0.54 0.78 4 -1.2 51 55
mast cell activation -0.01 0.028 -10000 0 -0.07 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.007 0.39 0.63 11 -1.1 29 40
FRAP1 -0.039 0.37 -10000 0 -0.98 29 29
LTA 0.009 0.57 0.96 11 -1.2 47 58
FES 0.028 0.006 -10000 0 0 22 22
T-helper 1 cell differentiation -0.044 0.7 1.3 49 -1.3 42 91
CCL11 0.002 0.55 0.96 23 -1.1 49 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.019 0.38 0.62 12 -1.1 25 37
IL2RG 0 0.034 0.12 2 -10000 0 2
IL10 0.007 0.57 0.93 11 -1.2 49 60
IRS1 0.011 0.014 -10000 0 0 349 349
IRS2 0.028 0.006 -10000 0 0 24 24
IL4 0.11 0.31 0.78 40 -0.99 7 47
IL5 0.007 0.57 0.94 9 -1.2 49 58
IL4/IL4R/JAK1/IL13RA1/JAK2 0.052 0.58 1.1 42 -1.2 33 75
COL1A1 0.3 0.51 0.92 153 -1 12 165
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 0.94 7 -1.3 156 163
ALOX15 0.007 0.57 1 9 -1.2 50 59
MYBL1 0.024 0.011 -10000 0 0 104 104
T-helper 2 cell differentiation -0.025 0.54 0.81 30 -1.1 58 88
SHC1 0.028 0.006 -10000 0 0 21 21
CEBPB 0.027 0.013 0.27 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.02 0.39 0.62 13 -1.1 28 41
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 0.011 -10000 0 0 104 104
ETS1 -0.023 0.063 -10000 0 -0.14 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.045 0.3 0.57 15 -0.64 26 41
ITGB3 -0.064 0.68 1.1 14 -1.3 81 95
PIGR -0.017 0.62 1.1 18 -1.2 58 76
IGHE -0.051 0.12 0.22 13 -0.31 52 65
MAPKKK cascade 0.046 0.3 0.57 15 -0.63 26 41
BCL6 0.024 0.011 -10000 0 -10000 0 0
OPRM1 0.007 0.57 0.94 9 -1.2 49 58
RETNLB 0.013 0.57 0.98 11 -1.2 48 59
SELP -0.017 0.6 0.95 13 -1.2 54 67
AICDA 0.005 0.53 0.88 11 -1.1 47 58
Canonical Wnt signaling pathway

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
HDAC1 0.055 0.055 0.12 160 -0.057 1 161
AES 0.042 0.044 0.11 126 -10000 0 126
FBXW11 0.028 0.005 -10000 0 0 18 18
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.016 -10000 0 -10000 0 0
SMAD4 0.028 0.007 -10000 0 0 33 33
DKK2 0.027 0.008 -10000 0 -0.001 39 39
TLE1 0.052 0.044 0.11 138 -0.062 1 139
MACF1 0.026 0.01 -10000 0 -0.029 6 6
CTNNB1 0.026 0.076 0.28 14 -0.41 1 15
WIF1 0.025 0.016 -10000 0 -0.03 40 40
beta catenin/RanBP3 0.14 0.2 0.41 170 -0.35 1 171
KREMEN2 0.028 0.007 -10000 0 -0.001 25 25
DKK1 0.028 0.006 -10000 0 0 22 22
beta catenin/beta TrCP1 0.048 0.077 0.28 14 -0.39 1 15
FZD1 0.015 0.025 -10000 0 -10000 0 0
AXIN2 -0.079 0.17 0.63 5 -0.74 17 22
AXIN1 0.027 0.012 -10000 0 -10000 0 0
RAN 0.03 0.006 -10000 0 -0.031 2 2
Axin1/APC/GSK3/beta catenin 0.02 0.1 -10000 0 -0.48 16 16
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.041 0.18 0.28 8 -0.57 35 43
Axin1/APC/GSK3 0.014 0.062 0.21 12 -0.32 3 15
Axin1/APC/GSK3/beta catenin/Macf1 0.002 0.079 0.28 7 -0.37 7 14
HNF1A 0.055 0.046 0.12 146 -0.062 2 148
CTBP1 0.052 0.048 0.12 134 -0.062 2 136
MYC 0.007 0.48 0.59 127 -1.1 59 186
RANBP3 0.029 0.008 -10000 0 -0.03 1 1
DKK2/LRP6/Kremen 2 0.048 0.025 -10000 0 -10000 0 0
NKD1 0.02 0.02 -10000 0 -0.03 72 72
TCF4 0.053 0.049 0.12 159 -0.063 2 161
TCF3 0.051 0.046 0.12 132 -0.063 1 133
WNT1/LRP6/FZD1/Axin1 0.063 0.037 -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 0.54 117 -0.54 14 131
LEF1 0.049 0.051 0.12 149 -0.063 2 151
DVL1 0.018 0.06 0.18 5 -0.33 6 11
CSNK2A1 0.027 0.008 -10000 0 -0.029 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.13 0.2 -10000 0 -0.49 90 90
DKK1/LRP6/Kremen 2 0.048 0.024 -10000 0 -10000 0 0
LRP6 0.015 0.023 -10000 0 -10000 0 0
CSNK1A1 0.057 0.054 0.12 170 -0.066 2 172
NLK 0.006 0.032 -10000 0 -0.04 177 177
CCND1 -0.33 0.56 0.66 13 -1.2 155 168
WNT1 0.016 0.025 -10000 0 -10000 0 0
GSK3A 0.015 0.024 -10000 0 -10000 0 0
GSK3B 0.015 0.025 -10000 0 -0.034 2 2
FRAT1 0.01 0.027 -10000 0 -0.03 171 171
PPP2R5D 0.03 0.051 -10000 0 -0.31 7 7
APC -0.019 0.084 0.19 61 -10000 0 61
WNT1/LRP6/FZD1 0.017 0.043 0.18 5 -0.22 2 7
CREBBP 0.051 0.046 0.12 128 -0.062 2 130
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.012 0.062 -10000 0 -0.15 61 61
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.094 0.22 5 -0.27 24 29
AP1 -0.019 0.085 0.21 48 -0.15 55 103
mol:PIP3 -0.056 0.061 0.032 1 -0.15 143 144
AKT1 -0.027 0.1 0.2 39 -0.3 5 44
PTK2B -0.047 0.11 0.19 31 -0.23 105 136
RHOA -0.007 0.059 0.17 30 -0.32 4 34
PIK3CB 0.02 0.018 -10000 0 -0.037 2 2
mol:Ca2+ -0.038 0.061 0.16 6 -0.18 28 34
MAGI3 0.023 0.018 -10000 0 -0.029 55 55
RELA 0.029 0.003 -10000 0 0 6 6
apoptosis -0.005 0.076 0.25 30 -0.15 54 84
HRAS/GDP 0.021 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.055 0.1 0.16 14 -0.23 88 102
NF kappa B1 p50/RelA -0.05 0.11 0.22 55 -0.22 36 91
endothelial cell migration -0.046 0.099 -10000 0 -0.32 63 63
ADCY4 -0.01 0.095 0.24 32 -0.2 53 85
ADCY5 -0.008 0.093 0.24 32 -0.2 51 83
ADCY6 -0.009 0.093 0.24 32 -0.2 51 83
ADCY7 -0.008 0.093 0.24 31 -0.21 51 82
ADCY1 -0.009 0.093 0.24 32 -0.2 50 82
ADCY2 -0.008 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 42 -0.23 94 136
arachidonic acid secretion -0.022 0.092 0.22 32 -0.2 58 90
GNG2 0.017 0.024 -10000 0 -0.034 8 8
TRIP6 0.01 0.031 -10000 0 -0.27 3 3
GNAO1 -0.012 0.089 0.3 31 -0.16 62 93
HRAS 0.028 0.006 -10000 0 0 27 27
NFKBIA -0.047 0.084 0.21 4 -0.27 29 33
GAB1 0.028 0.006 -10000 0 0 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.026 0.14 -10000 0 -0.81 14 14
JUN 0.028 0.007 -10000 0 0 34 34
LPA/LPA2/NHERF2 -0.009 0.053 -10000 0 -0.1 123 123
TIAM1 0.013 0.15 -10000 0 -0.94 14 14
PIK3R1 0.01 0.023 -10000 0 -0.037 2 2
mol:IP3 -0.032 0.058 0.16 6 -0.18 26 32
PLCB3 -0.028 0.057 0.13 36 -0.13 62 98
FOS 0.024 0.012 -10000 0 0 105 105
positive regulation of mitosis -0.022 0.092 0.22 32 -0.2 58 90
LPA/LPA1-2-3 -0.013 0.044 0.051 20 -0.13 63 83
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.026 0.009 -10000 0 0 56 56
stress fiber formation -0.018 0.098 0.23 31 -0.27 27 58
GNAZ -0.011 0.086 0.3 30 -0.16 53 83
EGFR/PI3K-beta/Gab1 -0.057 0.064 0.043 25 -0.15 143 168
positive regulation of dendritic cell cytokine production -0.013 0.044 0.051 16 -0.13 63 79
LPA/LPA2/MAGI-3 0.008 0.028 -10000 0 -0.068 58 58
ARHGEF1 -0.027 0.08 0.24 37 -10000 0 37
GNAI2 -0.014 0.089 0.3 31 -0.16 62 93
GNAI3 -0.011 0.084 0.3 28 -0.16 55 83
GNAI1 -0.012 0.088 0.3 31 -0.16 57 88
LPA/LPA3 -0.009 0.022 0.022 1 -0.07 63 64
LPA/LPA2 -0.008 0.022 0.022 1 -0.069 63 64
LPA/LPA1 -0.023 0.057 -10000 0 -0.18 63 63
HB-EGF/EGFR -0.007 0.078 0.16 78 -0.15 29 107
HBEGF 0.006 0.084 0.2 86 -10000 0 86
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 41 73
NFKB1 0.027 0.008 -10000 0 0 45 45
SRC 0.028 0.007 -10000 0 0 31 31
GNB1 0.016 0.024 -10000 0 -0.034 1 1
LYN -0.04 0.083 0.21 8 -0.25 27 35
GNAQ 0.005 0.039 0.13 31 -0.064 61 92
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 63 63
IL8 0.033 0.24 0.57 65 -0.35 48 113
PTK2 0.004 0.066 0.26 22 -0.13 46 68
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
CASP3 -0.005 0.076 0.25 30 -0.15 54 84
EGFR 0.028 0.01 0.054 4 0 54 58
PLCG1 -0.003 0.044 0.13 27 -0.13 15 42
PLD2 0.008 0.076 0.26 30 -0.13 58 88
G12/G13 0.012 0.062 -10000 0 -0.15 62 62
PI3K-beta -0.057 0.064 -10000 0 -0.24 27 27
cell migration 0 0.059 0.21 1 -0.25 14 15
SLC9A3R2 0.025 0.011 -10000 0 0 93 93
PXN -0.018 0.099 0.23 31 -0.28 27 58
HRAS/GTP -0.022 0.093 0.22 32 -0.2 58 90
RAC1 0.028 0.006 -10000 0 0 27 27
MMP9 0.023 0.013 -10000 0 0 129 129
PRKCE 0.02 0.021 -10000 0 -0.03 78 78
PRKCD -0.045 0.062 0.17 7 -0.19 24 31
Gi(beta/gamma) -0.012 0.092 0.24 29 -0.19 52 81
mol:LPA -0.015 0.034 -10000 0 -0.11 63 63
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.083 0.24 20 -0.24 16 36
MAPKKK cascade -0.022 0.092 0.22 32 -0.2 58 90
contractile ring contraction involved in cytokinesis -0.006 0.06 0.17 27 -0.31 4 31
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.005 0.039 0.13 31 -0.064 60 91
GNA15 0.005 0.037 0.13 30 -0.064 54 84
GNA12 0.026 0.012 -10000 0 -0.03 15 15
GNA13 0.027 0.011 -10000 0 -0.03 16 16
MAPT -0.056 0.1 0.17 12 -0.23 88 100
GNA11 0.003 0.042 0.13 28 -0.079 53 81
Rac1/GTP 0.027 0.14 -10000 0 -0.86 14 14
MMP2 -0.046 0.1 -10000 0 -0.32 63 63
IL1-mediated signaling 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
UBC13/UEV1A 0.021 0.008 -10000 0 -0.15 1 1
PRKCZ 0.028 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 -0.22 5 5
IRAK/TOLLIP -0.031 0.017 0.17 2 -0.13 1 3
IKBKB 0.027 0.007 -10000 0 0 39 39
IKBKG 0.028 0.006 -10000 0 0 25 25
IL1 alpha/IL1R2 0.038 0.024 -10000 0 -0.16 6 6
IL1A 0.028 0.006 -10000 0 0 22 22
IL1B -0.009 0.064 0.19 49 -10000 0 49
IRAK/TRAF6/p62/Atypical PKCs 0.057 0.052 -10000 0 -0.14 1 1
IL1R2 0.028 0.007 -10000 0 0 32 32
IL1R1 0.017 0.014 -10000 0 0 228 228
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.054 0.11 0.18 8 -0.29 35 43
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 0.004 -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 -0.015 0.11 0.29 2 -0.17 137 139
IL1 alpha/IL1R1/IL1RAP/MYD88 0.011 0.094 -10000 0 -0.14 133 133
PIK3R1 0.021 0.013 -10000 0 0 159 159
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.018 0.096 -10000 0 -0.14 118 118
IL1 beta fragment/IL1R1/IL1RAP -0.045 0.078 0.16 28 -0.16 134 162
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.035 0.033 0.14 14 -10000 0 14
IRAK1 -0.025 0.008 -10000 0 -0.13 1 1
IL1RN/IL1R1 -0.038 0.098 -10000 0 -0.16 210 210
IRAK4 0.026 0.009 -10000 0 0 55 55
PRKCI 0.014 0.015 -10000 0 0 289 289
TRAF6 0.029 0.004 -10000 0 0 12 12
PI3K -0.001 0.068 -10000 0 -0.16 76 76
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.027 0.1 0.19 14 -0.24 28 42
CHUK 0.027 0.007 -10000 0 0 36 36
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.045 0.078 0.16 28 -0.16 134 162
IL1 beta/IL1R2 -0.031 0.069 0.19 37 -0.15 53 90
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.036 0.017 0.14 3 -10000 0 3
NF kappa B1 p50/RelA -0.054 0.092 0.12 19 -0.25 40 59
IRAK3 0.027 0.008 -10000 0 0 40 40
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.004 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 -0.011 0.08 -10000 0 -0.15 133 133
RELA 0.029 0.003 -10000 0 0 6 6
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.005 -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 0.085 24 -0.23 16 40
CASP1 0.025 0.011 -10000 0 0 88 88
IL1RN/IL1R2 0.037 0.024 -10000 0 -0.16 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0 0.1 0.29 3 -0.16 137 140
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.07 0.14 -10000 0 -0.28 114 114
PIK3CA 0.02 0.014 -10000 0 0 172 172
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
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.037 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 0.3 14 -0.34 24 38
IGF1R 0.022 0.013 -10000 0 0 140 140
PI4KB 0.028 0.007 -10000 0 0 35 35
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 71 71
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 0.21 33 -0.23 2 35
alphaV/beta3 Integrin/JAM-A 0.025 0.073 -10000 0 -0.15 68 68
CBL 0.029 0.005 -10000 0 0 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.028 0.067 -10000 0 -0.15 65 65
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.083 0.12 -10000 0 -0.17 350 350
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.006 0.079 0.18 5 -0.28 17 22
alphaV/beta3 Integrin/Syndecan-1 0.028 0.067 -10000 0 -0.15 63 63
PI4KA 0.028 0.007 -10000 0 0 33 33
IGF-1R heterotetramer/IGF1/IRS1 -0.07 0.12 -10000 0 -0.19 230 230
PI4 Kinase 0.039 0.014 -10000 0 -10000 0 0
PIK3CA 0.02 0.014 -10000 0 0 172 172
alphaV/beta3 Integrin/Osteopontin 0.009 0.064 -10000 0 -0.15 62 62
RPS6KB1 -0.07 0.12 0.3 9 -0.32 15 24
TLN1 0.029 0.005 -10000 0 0 16 16
MAPK3 -0.076 0.16 -10000 0 -0.39 95 95
GPR124 0.026 0.01 -10000 0 0 73 73
MAPK1 -0.073 0.16 -10000 0 -0.39 92 92
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
alphaV/beta3 Integrin/Tumstatin 0.028 0.068 -10000 0 -0.15 67 67
cell adhesion 0.009 0.081 -10000 0 -0.18 71 71
ANGPTL3 0.029 0.004 -10000 0 0 13 13
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 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 32 32
RAC1 0.028 0.006 -10000 0 0 27 27
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 49 49
alphaV/beta3 Integrin/CD47 0.026 0.066 -10000 0 -0.15 61 61
VCL 0.029 0.004 -10000 0 0 13 13
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 0.046 0.075 -10000 0 -0.14 59 59
FAK1/Vinculin -0.01 0.12 0.28 15 -0.29 23 38
alphaV beta3/Integrin/ppsTEM5 0.021 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 0.026 0.009 -10000 0 0 56 56
FGF2 0.027 0.008 -10000 0 0 43 43
F11R -0.03 0.014 0.19 1 -10000 0 1
alphaV/beta3 Integrin/Lactadherin 0.021 0.075 -10000 0 -0.16 79 79
alphaV/beta3 Integrin/TGFBR2 0.027 0.071 -10000 0 -0.16 69 69
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.055 -10000 0 -0.14 22 22
HSP90AA1 0.028 0.005 -10000 0 0 20 20
alphaV/beta3 Integrin/Talin 0.026 0.063 -10000 0 -0.13 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.014 -10000 0 0 213 213
alphaV/beta3 Integrin/Pyk2 -0.04 0.068 0.17 38 -0.23 2 40
SDC1 0.028 0.005 -10000 0 0 17 17
VAV3 -0.038 0.057 0.17 21 -0.23 1 22
PTPN11 0.029 0.003 -10000 0 0 8 8
IRS1 0.011 0.014 -10000 0 0 349 349
FAK1/Paxillin -0.011 0.12 0.27 16 -0.29 24 40
cell migration -0.02 0.11 0.26 16 -0.28 23 39
ITGAV 0.028 0.007 -10000 0 0 33 33
PI3K 0.001 0.094 -10000 0 -0.16 106 106
SPP1 0.017 0.014 -10000 0 0 227 227
KDR 0.028 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 0.003 -10000 0 0 8 8
angiogenesis -0.077 0.17 0.31 2 -0.42 93 95
Rac1/GTP -0.042 0.057 0.16 31 -0.22 1 32
EDIL3 0.023 0.012 -10000 0 0 124 124
cell proliferation 0.026 0.071 -10000 0 -0.15 69 69
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.081 0.12 -10000 0 -0.36 48 48
CaM/Ca2+ 0.018 0.022 -10000 0 -0.15 9 9
AKT1 0.028 0.006 -10000 0 0 27 27
AKT2 0.027 0.008 -10000 0 0 51 51
STXBP4 0.028 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 43 44
YWHAZ 0.025 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 0.19 1 -10000 0 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.008 -10000 0 0 42 42
YWHAB 0.027 0.008 -10000 0 0 44 44
SNARE/Synip -0.087 0.09 -10000 0 -0.15 384 384
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 0 289 289
AS160/CaM/Ca2+ 0.018 0.022 -10000 0 -0.15 9 9
RHOQ 0.028 0.005 -10000 0 0 18 18
GYS1 -0.014 0.012 0.24 1 -10000 0 1
PRKCZ 0.028 0.006 -10000 0 0 23 23
TRIP10 0.027 0.007 -10000 0 0 36 36
TC10/GTP/CIP4/Exocyst 0.036 0.012 -10000 0 -10000 0 0
AS160/14-3-3 -0.008 0.07 0.16 4 -0.32 15 19
VAMP2 0.007 0.013 -10000 0 0 417 417
SLC2A4 -0.05 0.13 0.22 1 -0.4 44 45
STX4 0.029 0.004 -10000 0 0 11 11
GSK3B 0.009 0.004 -10000 0 -10000 0 0
SFN 0.027 0.007 -10000 0 0 38 38
LNPEP 0.027 0.009 -10000 0 0 53 53
YWHAE 0.027 0.008 -10000 0 0 40 40
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.019 0.014 -10000 0 0 188 188
positive regulation of NF-kappaB transcription factor activity 0.015 0.046 -10000 0 -0.16 29 29
MAP2K4 -0.02 0.076 -10000 0 -0.3 14 14
IKBKB 0.027 0.007 -10000 0 0 39 39
TNFRSF10B 0.024 0.011 -10000 0 0 105 105
TNFRSF10A 0.024 0.012 -10000 0 0 107 107
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 0 106 106
TRAIL/TRAILR2 0.015 0.047 -10000 0 -0.16 29 29
TRAIL/TRAILR3 -0.028 0.088 -10000 0 -0.18 138 138
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 -0.003 0.067 -10000 0 -0.27 18 18
RIPK1 0.027 0.007 -10000 0 0 38 38
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 0.082 0.18 1 -0.33 18 19
TRAILR4 (trimer) 0.024 0.012 -10000 0 0 106 106
TRADD 0.026 0.009 -10000 0 0 63 63
TRAILR1 (trimer) 0.024 0.012 -10000 0 0 107 107
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.018 0.073 -10000 0 -0.26 17 17
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 0.031 0.071 -10000 0 -0.14 30 30
mol:ceramide -0.012 0.039 0.098 29 -0.12 29 58
FADD 0.028 0.005 -10000 0 0 19 19
MAPK8 -0.029 0.085 0.21 1 -0.3 21 22
TRAF2 0.028 0.006 -10000 0 0 23 23
TRAILR3 (trimer) 0.015 0.015 -10000 0 0 279 279
CHUK 0.027 0.007 -10000 0 0 36 36
TRAIL/TRAILR1/FADD 0.024 0.047 -10000 0 -0.14 26 26
DAP3 0.028 0.006 -10000 0 0 27 27
CASP10 0.011 0.081 0.14 102 -0.19 23 125
JNK cascade 0.015 0.046 -10000 0 -0.16 29 29
TRAIL (trimer) 0.019 0.014 -10000 0 0 188 188
TNFRSF10C 0.015 0.015 -10000 0 0 279 279
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.058 -10000 0 -0.13 26 26
TRAIL/TRAILR2/FADD 0.025 0.047 -10000 0 -0.14 26 26
cell death -0.012 0.039 0.098 29 -0.12 29 58
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.018 0.072 -10000 0 -0.26 17 17
TRAILR2 (trimer) 0.024 0.011 -10000 0 0 105 105
CASP8 -0.006 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 0.07 -10000 0 -0.14 30 30
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.002 0.12 -10000 0 -0.4 17 17
MAP3K8 0.022 0.023 0.06 26 -0.037 62 88
FOS 0.025 0.13 0.46 26 -0.38 12 38
PRKCA 0.022 0.029 0.1 25 -0.041 68 93
PTPN7 0.022 0.039 0.16 25 -0.049 59 84
HRAS 0.022 0.021 -10000 0 -0.023 88 88
PRKCB 0.001 0.016 0.07 26 -10000 0 26
NRAS 0.012 0.017 -10000 0 -0.032 20 20
RAS family/GTP 0.022 0.043 0.18 23 -10000 0 23
MAPK3 0.025 0.12 0.32 26 -0.43 21 47
MAP2K1 0.029 0.078 0.27 26 -0.28 8 34
ELK1 0.021 0.028 0.071 26 -0.052 61 87
BRAF 0.02 0.05 0.22 14 -0.24 4 18
mol:GTP 0 0.003 0.012 26 -0.006 47 73
MAPK1 0.019 0.12 0.32 26 -0.4 30 56
RAF1 0.02 0.055 0.19 24 -0.32 4 28
KRAS 0.019 0.02 -10000 0 -0.011 149 149
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.033 0.071 -10000 0 -0.13 72 72
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.14 -10000 0 -0.37 46 46
AKT1 -0.13 0.27 -10000 0 -0.67 103 103
PIK3CA 0.02 0.014 -10000 0 0 172 172
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.28 -10000 0 -0.68 103 103
mol:Ca2+ -0.043 0.078 -10000 0 -0.32 20 20
IGF1R 0.022 0.013 -10000 0 0 140 140
E2/ER alpha (dimer)/Striatin 0.014 0.057 -10000 0 -0.13 70 70
SHC1 0.028 0.006 -10000 0 0 21 21
apoptosis 0.13 0.26 0.64 103 -10000 0 103
RhoA/GTP -0.025 0.035 -10000 0 -0.14 23 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.022 0.15 0.24 2 -0.32 75 77
regulation of stress fiber formation -0.031 0.1 0.2 2 -0.24 63 65
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 0.031 0.1 0.24 63 -0.2 2 65
E2/ER alpha (dimer)/PELP1 0.013 0.058 -10000 0 -0.13 73 73
GRB2 0.028 0.005 -10000 0 0 20 20
GNG2 0.029 0.004 -10000 0 0 12 12
GNAO1 0.027 0.008 -10000 0 0 44 44
HRAS 0.028 0.006 -10000 0 0 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.068 0.17 -10000 0 -0.4 94 94
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 -0.068 0.17 -10000 0 -0.4 94 94
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.047 0.074 -10000 0 -0.3 25 25
IGF-1R heterotetramer 0.022 0.013 -10000 0 0 140 140
PLCB1 -0.035 0.072 -10000 0 -0.31 22 22
PLCB2 -0.038 0.071 -10000 0 -0.31 24 24
IGF1 0.028 0.007 -10000 0 0 32 32
mol:L-citrulline -0.068 0.17 -10000 0 -0.4 94 94
RHOA 0.029 0.003 -10000 0 0 6 6
Gai/GDP -0.006 0.16 -10000 0 -0.58 38 38
JNK cascade 0.021 0.003 -10000 0 -10000 0 0
BCAR1 0.026 0.009 -10000 0 0 56 56
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 -0.071 0.22 -10000 0 -0.55 82 82
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.004 0.11 -10000 0 -0.73 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.021 0.15 0.24 2 -0.33 73 75
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 15 15
GNAL 0.028 0.005 -10000 0 0 19 19
PELP1 0.028 0.006 -10000 0 0 25 25
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 15 -0.42 27 42
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 -0.001 0.068 -10000 0 -0.16 76 76
GNB1 0.028 0.006 -10000 0 0 24 24
G13/GDP/Gbeta gamma 0.016 0.091 -10000 0 -0.24 35 35
SOS1 0.028 0.007 -10000 0 0 35 35
IGF-1R heterotetramer/IGF1 -0.07 0.11 -10000 0 -0.3 77 77
Gs family/GTP 0.016 0.054 -10000 0 -0.12 72 72
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.028 -10000 0 -10000 0 0
vasodilation -0.065 0.16 -10000 0 -0.38 95 95
mol:DAG -0.047 0.074 -10000 0 -0.3 25 25
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 -0.017 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 0.065 0.16 0.38 95 -10000 0 95
GRB2/SOS1 0.039 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 -0.42 94 94
GNA11 0.025 0.01 -10000 0 0 83 83
MAPKKK cascade -0.065 0.2 -10000 0 -0.48 101 101
E2/ER alpha (dimer)/PELP1/Src -0.025 0.15 0.26 2 -0.33 76 78
ruffle organization 0.031 0.1 0.24 63 -0.2 2 65
ROCK2 0.047 0.11 0.26 61 -10000 0 61
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GNA13 0.029 0.005 -10000 0 0 14 14
MMP9 -0.015 0.15 0.28 29 -0.41 27 56
MMP2 -0.044 0.14 0.28 4 -0.41 32 36
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.01 0.13 -10000 0 -0.45 37 37
HDAC1 0.038 0.022 0.097 16 -0.071 1 17
AES 0.026 0.016 0.068 11 -0.038 1 12
FBXW11 0.028 0.005 -10000 0 0 18 18
DTX1 0.029 0.004 -10000 0 0 9 9
LRP6/FZD1 0.036 0.016 -10000 0 -10000 0 0
TLE1 0.029 0.014 0.066 10 -0.028 16 26
AP1 -0.009 0.073 0.2 7 -0.19 58 65
NCSTN 0.011 0.026 -10000 0 -0.029 161 161
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 -0.68 46 46
NICD/RBPSUH 0.005 0.13 -10000 0 -0.45 36 36
WIF1 0.011 0.027 -10000 0 -0.029 166 166
NOTCH1 -0.01 0.12 -10000 0 -0.47 37 37
PSENEN 0.011 0.025 -10000 0 -0.029 141 141
KREMEN2 0.028 0.006 -10000 0 0 24 24
DKK1 0.028 0.006 -10000 0 0 22 22
beta catenin/beta TrCP1 -0.003 0.066 0.22 1 -0.27 2 3
APH1B 0.009 0.026 -10000 0 -0.029 156 156
APH1A 0.011 0.026 -10000 0 -0.029 159 159
AXIN1 -0.012 0.1 -10000 0 -0.44 20 20
CtBP/CBP/TCF1/TLE1/AES 0.013 0.1 0.25 22 -0.28 12 34
PSEN1 0.011 0.027 -10000 0 -0.029 167 167
FOS 0.024 0.011 -10000 0 0 105 105
JUN 0.028 0.007 -10000 0 0 34 34
MAP3K7 0.033 0.011 -10000 0 -0.046 1 1
CTNNB1 -0.012 0.059 0.22 1 -0.28 2 3
MAPK3 0.028 0.006 -10000 0 0 22 22
DKK2/LRP6/Kremen 2 0.047 0.024 -10000 0 -10000 0 0
HNF1A 0.033 0.01 0.068 14 -0.038 1 15
CTBP1 0.031 0.012 0.068 12 -10000 0 12
MYC -0.16 0.36 -10000 0 -1.2 59 59
NKD1 0.029 0.008 -10000 0 -10000 0 0
FZD1 0.011 0.027 -10000 0 -0.029 165 165
NOTCH1 precursor/Deltex homolog 1 0.005 0.13 -10000 0 -0.45 37 37
apoptosis -0.009 0.073 0.2 7 -0.19 58 65
Delta 1/NOTCHprecursor 0.003 0.13 -10000 0 -0.45 37 37
DLL1 0.027 0.008 -10000 0 0 48 48
PPARD -0.02 0.1 -10000 0 -0.99 5 5
Gamma Secretase 0.041 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 0.008 0.028 -10000 0 -0.032 170 170
MAP3K7IP1 0.005 0.008 0.018 99 -0.017 1 100
DKK1/LRP6/Kremen 2 0.048 0.024 -10000 0 -10000 0 0
LRP6 0.01 0.025 -10000 0 -0.029 148 148
CSNK1A1 0.008 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 0.011 0.027 -10000 0 -0.029 171 171
Axin1/APC/beta catenin -0.024 0.1 -10000 0 -0.42 17 17
DKK2 0.027 0.007 -10000 0 0 38 38
NOTCH1 precursor/DVL1 -0.01 0.13 -10000 0 -0.46 36 36
GSK3B 0.029 0.006 -10000 0 -0.03 1 1
FRAT1 0.031 0.007 -10000 0 -0.036 1 1
NOTCH/Deltex homolog 1 0.013 0.13 -10000 0 -0.46 37 37
PPP2R5D 0.01 0.047 -10000 0 -0.36 6 6
MAPK1 0.027 0.008 -10000 0 0 42 42
WNT1/LRP6/FZD1 0.064 0.033 -10000 0 -10000 0 0
RBPJ 0.028 0.005 -10000 0 0 18 18
CREBBP 0.011 0.024 0.064 1 -0.026 146 147
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 0.1 25 -10000 0 25
PDGF/PDGFRA/CRKL 0.009 0.07 -10000 0 -0.16 65 65
positive regulation of JUN kinase activity 0.034 0.075 -10000 0 -0.14 61 61
CRKL 0.028 0.007 -10000 0 0 31 31
PDGF/PDGFRA/Caveolin-3 0.009 0.071 -10000 0 -0.16 65 65
AP1 -0.093 0.25 0.6 18 -0.7 60 78
mol:IP3 -0.022 0.06 0.18 30 -0.22 7 37
PLCG1 -0.023 0.06 0.18 30 -0.22 7 37
PDGF/PDGFRA/alphaV Integrin 0.008 0.071 -10000 0 -0.16 66 66
RAPGEF1 0.028 0.005 -10000 0 0 17 17
CRK 0.027 0.007 -10000 0 0 36 36
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 0.037 0.077 -10000 0 -0.14 61 61
PDGF/PDGFRA/Shf 0.009 0.07 -10000 0 -0.16 65 65
FOS -0.085 0.26 0.64 25 -0.7 59 84
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 0.028 0.005 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:DAG -0.022 0.06 0.18 30 -0.22 7 37
PDGF/PDGFRA -0.016 0.037 0.1 25 -10000 0 25
actin cytoskeleton reorganization 0.01 0.071 -10000 0 -0.16 65 65
SRF -0.026 0.021 -10000 0 -10000 0 0
SHC1 0.028 0.006 -10000 0 0 21 21
PI3K -0.012 0.084 -10000 0 -0.16 108 108
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 -0.22 4 29
SHB 0.029 0.003 -10000 0 0 8 8
SHF 0.028 0.007 -10000 0 0 32 32
CSNK2A1 0.024 0.036 -10000 0 -0.086 28 28
GO:0007205 -0.035 0.081 0.19 31 -0.21 56 87
SOS1 0.028 0.007 -10000 0 0 35 35
Ras protein signal transduction 0.034 0.075 -10000 0 -0.14 61 61
PDGF/PDGFRA/SHB 0.01 0.071 -10000 0 -0.16 65 65
PDGF/PDGFRA/Caveolin-1 -0.016 0.099 -10000 0 -0.19 125 125
ITGAV 0.028 0.007 -10000 0 0 33 33
ELK1 -0.04 0.085 0.22 30 -0.19 53 83
PIK3CA 0.02 0.014 -10000 0 0 172 172
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 -0.038 0.11 -10000 0 -0.33 51 51
positive regulation of JNK cascade -0.015 0.11 -10000 0 -0.3 49 49
CDC42/GDP -0.017 0.15 -10000 0 -0.4 53 53
Rac1/GDP -0.02 0.15 -10000 0 -0.4 51 51
RAP1B 0.028 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 47 47
nectin-3/I-afadin 0.025 0.043 -10000 0 -0.16 23 23
RAPGEF1 -0.04 0.14 0.26 1 -0.41 54 55
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.042 0.15 0.28 1 -0.45 55 56
PDGFB-D/PDGFRB 0.029 0.005 -10000 0 0 15 15
TLN1 -0.095 0.12 -10000 0 -0.25 187 187
Rap1/GTP -0.03 0.11 -10000 0 -0.31 55 55
IQGAP1 0.028 0.006 -10000 0 0 25 25
Rap1/GTP/I-afadin 0.04 0.042 -10000 0 -0.13 21 21
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.025 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 -0.037 0.17 -10000 0 -0.48 53 53
MLLT4 0.026 0.01 -10000 0 0 70 70
PIK3CA 0.02 0.014 -10000 0 0 172 172
PI3K 0.026 0.091 -10000 0 -0.15 78 78
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 48 48
PVRL1 0.028 0.005 -10000 0 0 17 17
PVRL3 0.024 0.011 -10000 0 0 93 93
PVRL2 0.028 0.007 -10000 0 0 32 32
PIK3R1 0.021 0.013 -10000 0 0 159 159
CDH1 0.026 0.01 -10000 0 0 71 71
CLDN1 0.017 0.014 -10000 0 0 233 233
JAM-A/CLDN1 0.005 0.094 -10000 0 -0.14 136 136
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 -0.033 0.17 -10000 0 -0.49 48 48
RAC1 0.028 0.006 -10000 0 0 27 27
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 0.036 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 -0.015 0.11 -10000 0 -0.3 49 49
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 -0.093 0.12 -10000 0 -0.26 187 187
VAV2 -0.034 0.18 -10000 0 -0.53 41 41
RAP1/GDP -0.014 0.14 -10000 0 -0.38 52 52
ITGAV 0.028 0.007 -10000 0 0 33 33
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.036 0.046 -10000 0 -0.14 23 23
nectin-3(dimer)/I-afadin/I-afadin 0.025 0.043 -10000 0 -0.16 23 23
Rac1/GTP -0.019 0.14 -10000 0 -0.4 48 48
PTPRM -0.1 0.13 0.099 24 -0.27 210 234
E-cadherin/beta catenin/alpha catenin 0.047 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 0.001 0.099 0.65 5 -0.72 6 11
oxygen homeostasis 0.044 0.072 0.18 92 -10000 0 92
TCEB2 0.028 0.005 -10000 0 0 18 18
TCEB1 0.027 0.007 -10000 0 0 36 36
VHL/Elongin B/Elongin C/HIF2A 0.11 0.25 0.54 90 -0.35 1 91
EPO 0.15 0.34 0.82 67 -10000 0 67
FIH (dimer) 0.045 0.093 0.21 91 -10000 0 91
APEX1 0.025 0.072 0.17 67 -10000 0 67
SERPINE1 0.093 0.32 0.88 43 -10000 0 43
FLT1 -0.02 0.13 -10000 0 -0.65 20 20
ADORA2A 0.19 0.38 0.86 90 -10000 0 90
germ cell development 0.16 0.38 0.85 85 -10000 0 85
SLC11A2 0.15 0.37 0.87 71 -10000 0 71
BHLHE40 0.14 0.36 0.86 68 -10000 0 68
HIF1AN 0.045 0.092 0.21 91 -10000 0 91
HIF2A/ARNT/SIRT1 0.041 0.2 0.45 30 -10000 0 30
ETS1 -0.023 0.023 0.26 2 -10000 0 2
CITED2 -0.046 0.19 -10000 0 -0.75 36 36
KDR -0.012 0.098 -10000 0 -0.62 13 13
PGK1 0.015 0.26 0.87 25 -10000 0 25
SIRT1 0.017 0.024 -10000 0 -0.03 110 110
response to hypoxia -0.001 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.058 0.27 0.64 23 -10000 0 23
EPAS1 0.15 0.34 0.81 86 -10000 0 86
SP1 0.037 0.051 0.3 18 -0.16 2 20
ABCG2 0.14 0.38 0.86 75 -0.62 1 76
EFNA1 0.14 0.36 0.88 67 -10000 0 67
FXN 0.19 0.38 0.85 90 -10000 0 90
POU5F1 0.15 0.38 0.86 79 -10000 0 79
neuron apoptosis -0.056 0.27 -10000 0 -0.62 24 24
EP300 0.027 0.008 -10000 0 0 50 50
EGLN3 0.042 0.092 0.22 85 -10000 0 85
EGLN2 0.044 0.093 0.22 86 -10000 0 86
EGLN1 0.043 0.091 0.21 87 -10000 0 87
VHL/Elongin B/Elongin C 0.053 0.019 -10000 0 -10000 0 0
VHL 0.029 0.004 -10000 0 0 9 9
ARNT 0.026 0.073 0.17 65 -10000 0 65
SLC2A1 0.18 0.38 0.89 80 -10000 0 80
TWIST1 0.19 0.38 0.86 89 -10000 0 89
ELK1 0.02 0.035 -10000 0 -0.14 24 24
HIF2A/ARNT/Cbp/p300 0.087 0.26 0.61 60 -10000 0 60
VEGFA 0.12 0.35 0.84 62 -10000 0 62
CREBBP 0.027 0.008 -10000 0 0 41 41
Signaling events mediated by the Hedgehog family

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
TGFB2 0.03 0.21 0.5 81 -0.45 15 96
IHH -0.006 0.078 0.16 88 -10000 0 88
SHH Np/Cholesterol/GAS1 -0.045 0.037 0.14 1 -0.13 76 77
LRPAP1 0.028 0.007 -10000 0 0 33 33
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 9 93
SMO 0.028 0.13 0.31 84 -0.4 9 93
AKT1 -0.024 0.15 0.33 2 -0.45 18 20
ARRB2 0.028 0.006 -10000 0 0 25 25
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 9 93
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 0.31 79 -0.25 23 102
PIK3CA 0.02 0.014 -10000 0 0 172 172
DHH 0.029 0.003 -10000 0 0 5 5
PTHLH 0.031 0.19 0.5 71 -0.43 14 85
determination of left/right symmetry 0.028 0.13 0.31 84 -0.39 9 93
PIK3R1 0.021 0.013 -10000 0 0 159 159
skeletal system development 0.032 0.19 0.49 71 -0.42 14 85
IHH N/Hhip 0.048 0.042 0.18 3 -0.088 8 11
DHH N/Hhip 0.041 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 9 93
pancreas development 0.028 0.006 -10000 0 0 26 26
HHAT 0.028 0.005 -10000 0 0 18 18
PI3K -0.001 0.068 -10000 0 -0.16 76 76
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.024 0.011 -10000 0 0 94 94
somite specification 0.028 0.13 0.31 84 -0.39 9 93
SHH Np/Cholesterol/PTCH1 -0.003 0.12 0.27 75 -0.26 9 84
SHH Np/Cholesterol/PTCH2 -0.032 0.016 0.14 1 -0.13 5 6
SHH Np/Cholesterol/Megalin -0.025 0.019 -10000 0 -0.13 4 4
SHH -0.03 0.014 0.19 1 -10000 0 1
catabolic process 0.023 0.16 0.38 84 -0.32 8 92
SMO/Vitamin D3 0.004 0.12 0.26 76 -0.36 9 85
SHH Np/Cholesterol/Hhip -0.032 0.016 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 8 83
SHH Np/Cholesterol/BOC -0.041 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 0.004 0.12 0.24 102 -0.27 8 110
IHH N/PTCH2 0.049 0.041 0.18 4 -10000 0 4
CDON 0.028 0.007 -10000 0 0 32 32
IHH N/PTCH1 -0.034 0.053 -10000 0 -0.28 24 24
Megalin/LRPAP1 0.03 0.023 -10000 0 -0.16 2 2
PTCH2 0.028 0.006 -10000 0 0 21 21
SHH Np/Cholesterol -0.022 0.013 0.16 1 -0.12 5 6
PTCH1 0.023 0.16 0.38 84 -0.32 8 92
HHIP 0.028 0.006 -10000 0 0 26 26
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 -0.61 18 19
RAD9A 0.029 0.003 -10000 0 0 8 8
AP1 -0.004 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 -0.2 11 11
ER alpha/Oestrogen -0.013 0.057 -10000 0 -0.15 73 73
NFX1/SIN3/HDAC complex -0.013 0.075 0.18 5 -0.34 14 19
EGF 0.012 0.028 -10000 0 -0.037 128 128
SMG5 0.028 0.006 -10000 0 0 24 24
SMG6 0.028 0.006 -10000 0 0 28 28
SP3/HDAC2 0.016 0.043 0.16 1 -10000 0 1
TERT/c-Abl -0.1 0.2 0.55 1 -0.56 23 24
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 0 120 120
SP1 0.008 0.036 0.14 1 -0.052 145 146
SP3 0.011 0.029 0.065 1 -0.038 143 144
TERF2IP 0.026 0.009 -10000 0 0 60 60
Telomerase/Nucleolin -0.11 0.19 -10000 0 -0.5 35 35
Mad/Max 0.018 0.04 -10000 0 -10000 0 0
TERT -0.12 0.2 -10000 0 -0.62 18 18
CCND1 -0.26 0.43 0.8 1 -0.96 147 148
MAX 0.011 0.029 -10000 0 -0.038 145 145
RBBP7 0.013 0.027 -10000 0 -0.032 143 143
RBBP4 0.013 0.026 -10000 0 -0.031 131 131
TERF2 -0.031 0.018 0.076 7 -10000 0 7
PTGES3 0.024 0.011 -10000 0 0 100 100
SIN3A 0.013 0.026 -10000 0 -0.031 143 143
Telomerase/911 -0.009 0.084 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 0.027 0.007 -10000 0 0 37 37
XRCC6 0.027 0.008 -10000 0 0 49 49
SAP30 0.012 0.026 -10000 0 -0.032 135 135
TRF2/PARP2 -0.03 0.022 0.083 6 -10000 0 6
UBE3A 0.012 0.028 -10000 0 -0.037 131 131
JUN 0.011 0.028 -10000 0 -0.037 137 137
E6 -0.002 0.004 0.03 1 -10000 0 1
HPV-16 E6/E6AP 0.008 0.022 0.095 1 -10000 0 1
FOS 0.009 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 71 71
BLM 0.018 0.014 -10000 0 0 212 212
Telomerase -0.013 0.083 -10000 0 -0.35 12 12
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 0.037 0.015 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.02 -10000 0 -0.081 7 7
ubiquitin-dependent protein catabolic process -0.014 0.075 0.18 5 -0.3 18 23
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.014 0.077 0.18 5 -0.3 18 23
HDAC1 0.012 0.026 -10000 0 -0.031 131 131
HDAC2 0.008 0.034 0.12 1 -0.05 136 137
ATM 0.02 0.025 0.24 2 -10000 0 2
SMAD3 -0.025 0.015 -10000 0 -0.2 1 1
ABL1 0.028 0.005 -10000 0 0 20 20
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 0.028 0.006 -10000 0 0 23 23
TERT/NF kappa B1/14-3-3 -0.1 0.21 -10000 0 -0.6 23 23
NR2F2 0.031 0.012 -10000 0 -0.089 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 0.024 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 45 45
HNRNPC 0.028 0.006 -10000 0 0 27 27
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 0.01 -10000 0 0 82 82
EGFR 0.012 0.027 -10000 0 -0.038 118 118
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 0.079 1 -0.037 80 81
IL2 0.008 0.035 0.12 1 -0.052 135 136
KU 0.037 0.015 -10000 0 -10000 0 0
RAD50 0.029 0.005 -10000 0 0 15 15
HSP90AA1 0.028 0.005 -10000 0 0 20 20
TGFB1 0.024 0.012 -10000 0 -10000 0 0
TRF2/BLM -0.022 0.022 0.083 3 -10000 0 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.1 0.21 0.55 1 -0.58 21 22
SP1/HDAC2 0.013 0.048 0.24 1 -10000 0 1
PINX1 0.024 0.012 -10000 0 0 109 109
Telomerase/EST1A -0.11 0.19 -10000 0 -0.51 34 34
Smad3/Myc -0.042 0.057 -10000 0 -0.16 86 86
911 complex 0.053 0.019 -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 -0.51 34 34
Telomerase/AKT1/mTOR/p70S6K -0.064 0.14 -10000 0 -0.42 41 41
SIN3B 0.012 0.026 -10000 0 -0.032 130 130
YWHAE 0.027 0.008 -10000 0 0 40 40
Telomerase/EST1B -0.11 0.19 -10000 0 -0.51 33 33
response to DNA damage stimulus 0.008 0.02 0.084 14 -0.1 7 21
MRN complex/TRF2/Rap1 0.065 0.048 -10000 0 -10000 0 0
TRF2/WRN -0.029 0.021 0.083 4 -10000 0 4
Telomerase/hnRNP C1/C2 -0.11 0.19 -10000 0 -0.51 32 32
E2F1 0.009 0.031 -10000 0 -0.043 138 138
ZNFX1 0.012 0.026 -10000 0 -0.031 134 134
PIF1 0.029 0.004 -10000 0 0 13 13
NCL 0.029 0.003 -10000 0 0 7 7
DKC1 0.024 0.012 -10000 0 0 107 107
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0.007 0.064 0.2 3 -0.21 13 16
FZD6 0.024 0.011 -10000 0 0 105 105
WNT6 0.029 0.003 -10000 0 0 7 7
WNT4 0.029 0.004 -10000 0 0 11 11
FZD3 0.022 0.013 -10000 0 0 139 139
WNT5A 0.028 0.005 -10000 0 0 17 17
WNT11 0.025 0.01 -10000 0 0 74 74
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.035 0.018 0.17 2 -10000 0 2
SNTA1 0.027 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 -0.27 13 19
MAPK13 -0.03 0.017 0.19 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0 0.034 -10000 0 -0.21 14 14
Coregulation of Androgen receptor activity

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
NRIP1 0.018 0.014 -10000 0 -10000 0 0
SVIL 0.028 0.007 -10000 0 -10000 0 0
ZNF318 0.028 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 -0.16 317 317
CARM1 0.026 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.005 -10000 0 0 16 16
PELP1 0.028 0.006 -10000 0 0 25 25
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
AKT1 0.028 0.006 -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 0.027 0.007 -10000 0 -10000 0 0
DNA-PK 0.042 0.027 -10000 0 -10000 0 0
NCOA4 0.029 0.003 -10000 0 0 5 5
PIAS3 0.028 0.005 -10000 0 -10000 0 0
cell proliferation -0.14 0.23 -10000 0 -0.59 116 116
XRCC5 0.027 0.007 -10000 0 -10000 0 0
UBE3A 0.027 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 0.027 0.007 -10000 0 -10000 0 0
JMJD1A -0.052 0.057 -10000 0 -0.14 11 11
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 0.008 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.094 -10000 0 -0.24 110 110
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 0.027 0.007 -10000 0 -10000 0 0
CDKN2A 0.012 0.014 -10000 0 -10000 0 0
SRF 0.029 0.018 0.3 2 -10000 0 2
NKX3-1 -0.17 0.14 -10000 0 -0.44 72 72
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 0.008 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.1 0.078 -10000 0 -0.16 316 316
AR -0.028 0.043 -10000 0 -0.29 6 6
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 0.024 0.011 -10000 0 -10000 0 0
PA2G4 0.028 0.006 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 0 23 23
T-DHT/AR/Cyclin D3/CDK11 p58 -0.089 0.071 -10000 0 -0.14 307 307
RPS6KA3 0.028 0.006 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.1 0.078 -10000 0 -0.16 320 320
LATS2 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.091 0.071 -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 -0.072 0.054 -10000 0 -0.39 8 8
CASP8 0.029 0.003 -10000 0 0 8 8
T-DHT/AR/TIF2/CARM1 -0.085 0.082 -10000 0 -0.15 268 268
TMPRSS2 -0.34 0.32 -10000 0 -0.7 241 241
CCND1 0.021 0.013 -10000 0 -10000 0 0
PIAS1 0.028 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 0.026 0.009 -10000 0 0 57 57
SNURF 0.027 0.007 -10000 0 0 36 36
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
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.073 0.052 0.19 2 -10000 0 2
BIRC5 0.023 0.012 -10000 0 0 122 122
NFKBIA 0.064 0.049 0.2 4 -10000 0 4
CPEB1 0.028 0.005 -10000 0 0 19 19
AKT1 0.065 0.051 0.29 3 -10000 0 3
NDEL1 0.028 0.007 -10000 0 0 31 31
Aurora A/BRCA1 0.065 0.046 0.16 1 -10000 0 1
NDEL1/TACC3 0.046 0.053 0.18 1 -10000 0 1
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 0.19 488 -10000 0 488
TP53 0.053 0.056 0.17 2 -0.31 4 6
DLG7 0.076 0.052 0.12 74 -10000 0 74
AURKAIP1 0.028 0.006 -10000 0 0 27 27
ARHGEF7 0.028 0.006 -10000 0 0 24 24
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.048 0.056 0.18 1 -10000 0 1
G2/M transition of mitotic cell cycle 0.064 0.045 0.16 1 -10000 0 1
AURKA 0.093 0.064 0.14 74 -10000 0 74
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 0.069 0.043 0.16 1 -10000 0 1
Aurora A/CPEB 0.07 0.044 0.16 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 60 60
centrosome duplication 0.074 0.051 0.18 2 -10000 0 2
regulation of centrosome cycle 0.044 0.052 0.17 1 -10000 0 1
spindle assembly -0.003 0.053 -10000 0 -10000 0 0
TDRD7 0.028 0.006 -10000 0 0 26 26
Aurora A/RasGAP/Survivin 0.076 0.063 -10000 0 -10000 0 0
CENPA 0.038 0.034 -10000 0 -10000 0 0
Aurora A/PP2A 0.078 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 9 -0.26 2 11
negative regulation of DNA binding 0.052 0.056 0.17 2 -0.31 4 6
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.04 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.008 -10000 0 0 49 49
Ajuba/Aurora A 0 0.002 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.015 0.073 23 -10000 0 23
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.064 0.14 74 -10000 0 74
TACC1 0.005 0.011 -10000 0 0 457 457
TACC3 0.016 0.015 -10000 0 0 259 259
Aurora A/Antizyme1 0.06 0.059 -10000 0 -10000 0 0
Aurora A/RasGAP 0.074 0.051 -10000 0 -10000 0 0
OAZ1 0.019 0.014 -10000 0 0 195 195
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 0.021 -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 26 26
Aurora A/TPX2 0.005 0.031 0.16 17 -10000 0 17
PAK1 0.027 0.008 -10000 0 0 47 47
CKAP5 0.02 0.014 -10000 0 0 179 179
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 63 71
alphaM/beta2 Integrin/GPIbA 0.051 0.036 0.18 11 -0.15 3 14
alphaM/beta2 Integrin/proMMP-9 0.04 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 0.051 0.036 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 0.028 0.005 -10000 0 0 18 18
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.064 0.063 0.36 10 -0.2 8 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.023 0.012 -10000 0 0 129 129
CYR61 0.027 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 21 -0.29 39 60
RHOA 0.029 0.003 -10000 0 0 6 6
P-selectin oligomer 0.028 0.007 -10000 0 0 34 34
MYH2 -0.038 0.13 0.22 17 -0.34 32 49
MST1R 0.029 0.004 -10000 0 0 12 12
leukocyte activation during inflammatory response 0.048 0.042 0.16 1 -0.13 3 4
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 0.022 0.013 -10000 0 0 134 134
JAM3 0.027 0.007 -10000 0 0 38 38
GP1BA 0.028 0.006 -10000 0 0 24 24
alphaM/beta2 Integrin/CTGF 0.009 0.088 0.18 10 -0.15 117 127
alphaM/beta2 Integrin -0.028 0.11 0.17 41 -0.3 34 75
JAM3 homodimer 0.027 0.007 -10000 0 0 38 38
ICAM2 0.028 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 -0.027 0.12 0.18 39 -0.3 36 75
cell adhesion 0.05 0.036 0.17 11 -0.15 3 14
NFKB1 -0.044 0.087 0.42 11 -0.33 8 19
THY1 0.02 0.014 -10000 0 0 185 185
RhoA/GDP 0.021 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 0.052 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/JAM2/JAM3 0.004 0.099 -10000 0 -0.14 156 156
JAM2 0.019 0.014 -10000 0 0 193 193
alphaM/beta2 Integrin/ICAM1 0.073 0.056 0.25 4 -0.14 6 10
alphaM/beta2 Integrin/uPA/Plg 0.069 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 -0.024 0.1 0.2 9 -0.32 17 26
Ron/MSP 0.043 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.075 0.053 -10000 0 -0.14 2 2
alphaM/beta2 Integrin/uPAR 0.048 0.034 0.18 5 -0.15 2 7
PLAU 0.02 0.014 -10000 0 0 184 184
PLAT 0.021 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) 0.054 0.045 -10000 0 -0.13 3 3
TNF -0.05 0.078 0.41 10 -10000 0 10
RAP1B 0.028 0.006 -10000 0 0 22 22
alphaM/beta2 Integrin/uPA 0.033 0.037 0.18 2 -0.15 3 5
fibrinolysis 0.066 0.061 -10000 0 -0.15 11 11
HCK 0.027 0.008 -10000 0 0 47 47
dendritic cell antigen processing and presentation -0.027 0.12 0.18 39 -0.3 36 75
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 0.028 0.006 -10000 0 0 21 21
cell migration -0.011 0.09 0.17 96 -10000 0 96
FN1 0.018 0.014 -10000 0 0 213 213
alphaM/beta2 Integrin/Thy1 0.034 0.037 0.17 4 -0.15 2 6
MPO 0.029 0.005 -10000 0 0 15 15
KNG1 0.025 0.011 -10000 0 0 89 89
RAP1/GDP 0.038 0.009 -10000 0 -10000 0 0
ROCK1 -0.042 0.14 0.19 38 -0.33 39 77
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.026 0.009 -10000 0 0 57 57
CTGF 0.021 0.013 -10000 0 0 149 149
alphaM/beta2 Integrin/Hck 0.049 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 0.056 0.062 -10000 0 -0.16 31 31
HP 0.01 0.014 -10000 0 0 366 366
leukocyte adhesion -0.029 0.11 0.29 4 -0.29 1 5
SELP 0.028 0.007 -10000 0 0 34 34
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.15 0.34 0.67 1 -0.96 83 84
VDR 0.029 0.003 -10000 0 0 8 8
FAM120B 0.027 0.008 -10000 0 0 47 47
RXRs/LXRs/DNA/9cRA 0.015 0.12 0.4 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 35 35
mol:9cRA 0.009 0.027 0.1 39 -10000 0 39
RARs/THRs/DNA/Src-1 -0.028 0.09 -10000 0 -0.18 134 134
RXRs/NUR77 0.007 0.12 0.3 21 -0.21 6 27
RXRs/PPAR 0.003 0.076 0.24 4 -0.24 11 15
NCOR2 0.028 0.005 -10000 0 0 17 17
VDR/VDR/Vit D3 0.021 0.003 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.064 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 0.003 -10000 0 0 8 8
RARs/RARs/DNA/9cRA 0.05 0.028 -10000 0 -10000 0 0
RARG 0.028 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 0.093 -10000 0 -0.18 141 141
THRA 0.021 0.013 -10000 0 0 160 160
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.021 0.003 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.096 0.12 0.4 43 -10000 0 43
NR1H4 0.029 0.004 -10000 0 0 13 13
RXRs/LXRs/DNA 0.097 0.11 0.44 35 -0.26 1 36
NR1H2 0.026 0.034 0.13 37 -0.079 1 38
NR1H3 0.033 0.032 0.13 39 -0.082 2 41
RXRs/VDR/DNA/Vit D3 0.083 0.075 0.29 38 -10000 0 38
NR4A1 0.017 0.014 -10000 0 0 234 234
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.01 0.069 0.19 38 -0.23 6 44
RXRG -0.006 0.046 0.12 41 -10000 0 41
RXR alpha/CCPG 0.04 0.039 -10000 0 -0.16 12 12
RXRA -0.006 0.047 0.12 43 -10000 0 43
RXRB -0.006 0.048 0.13 42 -10000 0 42
THRB 0.028 0.007 -10000 0 0 31 31
PPARG 0.029 0.004 -10000 0 0 13 13
PPARD 0.028 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 -0.46 1 36
PPARA 0.024 0.011 -10000 0 0 96 96
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.028 0.005 -10000 0 0 20 20
RXRs/NUR77/BCL2 -0.077 0.11 0.16 1 -0.2 207 208
SREBF1 0.01 0.13 0.44 32 -0.77 4 36
RXRs/RXRs/DNA/9cRA 0.096 0.12 0.4 43 -10000 0 43
ABCA1 0.025 0.16 0.62 35 -10000 0 35
RARs/THRs 0.033 0.096 -10000 0 -0.14 114 114
RXRs/FXR 0.091 0.081 0.31 39 -10000 0 39
BCL2 0.023 0.012 -10000 0 0 122 122
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.06 0.1 0.21 85 -10000 0 85
DAPP1 -0.029 0.098 0.2 8 -0.31 23 31
Src family/SYK family/BLNK-LAT/BTK-ITK -0.005 0.12 0.22 2 -0.42 18 20
mol:DAG 0.023 0.089 0.19 61 -0.21 7 68
HRAS 0.013 0.035 0.052 78 -10000 0 78
RAP1A 0.014 0.036 0.049 98 -10000 0 98
ARF5/GDP 0.053 0.065 0.19 5 -0.25 8 13
PLCG2 0.026 0.009 -10000 0 0 63 63
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 0.027 0.008 -10000 0 0 40 40
RAP1A/GTP 0.072 0.11 0.23 89 -10000 0 89
ADAP1 0.054 0.092 0.2 89 -10000 0 89
ARAP3 0.058 0.096 0.21 92 -10000 0 92
INPPL1 0.028 0.006 -10000 0 0 21 21
PREX1 0.027 0.008 -10000 0 0 47 47
ARHGEF6 0.028 0.005 -10000 0 0 17 17
ARHGEF7 0.028 0.006 -10000 0 0 24 24
ARF1 0.026 0.009 -10000 0 0 55 55
NRAS -0.008 0.022 0.045 10 -10000 0 10
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 37 -10000 0 37
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.005 -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 5 -0.25 9 14
RhoA/GDP 0.084 0.1 0.21 133 -10000 0 133
PDK1/Src/Hsp90 0.053 0.019 -10000 0 -10000 0 0
BLNK 0.028 0.007 -10000 0 0 31 31
actin cytoskeleton reorganization 0.07 0.095 0.24 70 -0.26 2 72
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 27 27
PTEN -0.01 0.035 -10000 0 -0.04 321 321
HSP90AA1 0.028 0.005 -10000 0 0 20 20
ARF6/GTP 0.063 0.1 0.23 76 -10000 0 76
RhoA/GTP 0.063 0.1 0.23 76 -10000 0 76
Src family/SYK family/BLNK-LAT -0.032 0.089 -10000 0 -0.3 26 26
BLK 0.024 0.011 -10000 0 0 100 100
PDPK1 0.028 0.005 -10000 0 0 18 18
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 0.051 27 -10000 0 27
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.034 0.059 0.17 49 -0.19 1 50
SGK1 0.046 0.064 0.18 50 -0.18 6 56
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.042 0.063 0.17 9 -0.26 8 17
SOS1 0.028 0.007 -10000 0 0 35 35
SYK 0.028 0.006 -10000 0 0 23 23
ARF6/GDP 0.069 0.098 0.24 72 -10000 0 72
mol:PI-3-4-5-P3 0.061 0.098 0.21 88 -10000 0 88
ARAP3/RAP1A/GTP 0.072 0.11 0.23 89 -10000 0 89
VAV1 0.027 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 0.064 0.19 3 -0.25 8 11
LAT 0.029 0.003 -10000 0 0 8 8
Rac1/GTP 0.016 0.054 0.19 1 -0.28 7 8
ITK 0.048 0.093 0.24 53 -10000 0 53
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.02 0.11 0.22 55 -0.27 9 64
LCK 0.028 0.006 -10000 0 0 26 26
BTK 0.048 0.094 0.24 55 -10000 0 55
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.003 0.008 -10000 0 0 506 506
mol:Halofuginone -0.003 0.012 -10000 0 -0.16 3 3
ITGA1 0.023 0.012 -10000 0 0 127 127
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 0.035 0.26 7 -10000 0 7
AGT 0.026 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 0.022 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 0.013 -10000 0 0 163 163
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 -0.018 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 0.028 0.006 -10000 0 0 21 21
BCAR1 -0.019 0.036 0.26 7 -10000 0 7
RHOC -0.011 0.064 -10000 0 -0.44 9 9
RHOA -0.014 0.072 -10000 0 -0.43 13 13
cell motility -0.009 0.076 0.29 2 -0.4 11 13
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 -0.4 11 12
RABGGTB 0.016 0.015 -10000 0 0 257 257
CDK2 0.017 0.014 -10000 0 0 227 227
mitosis -0.063 0.066 -10000 0 -0.64 3 3
ATF5 0.028 0.005 -10000 0 0 18 18
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.042 0.008 -10000 0 -10000 0 0
Necdin/E2F1 -0.06 0.099 -10000 0 -0.16 264 264
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.06 0.032 -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 0.027 0.007 -10000 0 0 39 39
AKT1 0.006 0.1 0.16 139 -10000 0 139
IKBKG 0.028 0.006 -10000 0 0 25 25
BDNF 0.029 0.004 -10000 0 0 13 13
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 0.056 0.015 -10000 0 -10000 0 0
LINGO1 0.028 0.006 -10000 0 0 23 23
Sortilin/TRAF6/NRIF -0.071 0.042 -10000 0 -0.23 1 1
proBDNF (dimer) 0.029 0.004 -10000 0 0 13 13
NTRK1 0.029 0.005 -10000 0 0 15 15
RTN4R 0.028 0.007 -10000 0 0 32 32
neuron apoptosis -0.035 0.13 0.29 3 -0.51 21 24
IRAK1 0.028 0.007 -10000 0 0 31 31
SHC1 -0.025 0.011 0.17 1 -10000 0 1
ARHGDIA 0.024 0.011 -10000 0 0 96 96
RhoA/GTP 0.021 0.007 -10000 0 -0.15 1 1
Gamma Secretase 0.043 0.077 -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 0.089 -10000 0 -0.13 275 275
Mammalian IAPs/DIABLO 0.012 0.051 -10000 0 -0.13 46 46
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.028 0.006 -10000 0 0 21 21
APP 0.028 0.006 -10000 0 0 27 27
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.028 0.007 -10000 0 0 34 34
RhoA/GDP/RHOGDI 0.013 0.053 0.16 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 0.028 0.005 -10000 0 0 18 18
mol:GTP 0.037 0.01 -10000 0 -10000 0 0
PSENEN 0.025 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 0.065 0.18 45 -0.23 5 50
p75(NTR)/beta APP 0.038 0.025 -10000 0 -0.16 7 7
BEX1 0.018 0.014 -10000 0 0 210 210
mol:GDP -0.013 0.002 -10000 0 -10000 0 0
NGF (dimer) -0.02 0.086 -10000 0 -0.13 200 200
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.038 0.075 -10000 0 -0.14 72 72
PIK3R1 0.021 0.013 -10000 0 0 159 159
RAC1/GTP 0.031 0.013 -10000 0 -10000 0 0
MYD88 0.029 0.003 -10000 0 0 5 5
CHUK 0.027 0.007 -10000 0 0 36 36
NGF (dimer)/p75(NTR)/PKA 0.037 0.01 -10000 0 -10000 0 0
RHOB 0.028 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) 0.023 0.012 -10000 0 0 116 116
TP53 -0.058 0.057 0.31 3 -10000 0 3
PRDM4 -0.03 0.032 0.18 12 -10000 0 12
BDNF (dimer) -0.007 0.1 -10000 0 -0.14 193 193
PIK3CA 0.02 0.014 -10000 0 0 172 172
SORT1 0.029 0.004 -10000 0 0 11 11
activation of caspase activity 0.053 0.03 -10000 0 -0.13 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.052 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 0.062 0.24 7 -0.24 7 14
DIABLO 0.019 0.014 -10000 0 0 191 191
SMPD2 -0.028 0.035 0.18 14 -10000 0 14
APH1B 0.026 0.01 -10000 0 0 69 69
APH1A 0.028 0.007 -10000 0 0 31 31
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) 0.033 0.019 -10000 0 -10000 0 0
MAPK8 -0.04 0.058 0.24 7 -0.24 7 14
MAPK9 -0.042 0.057 0.23 6 -0.24 5 11
APAF1 0.028 0.006 -10000 0 0 27 27
NTF3 0.023 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 0.056 0.033 -10000 0 -0.13 8 8
p75 CTF/Sortilin/TRAF6/NRIF 0.074 0.041 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.036 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.075 0.038 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.07 0.025 -10000 0 -10000 0 0
PRKACB 0.028 0.006 -10000 0 0 21 21
proBDNF (dimer)/p75 ECD 0.034 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 0.064 0.18 12 -0.21 9 21
BAD -0.046 0.062 0.22 7 -0.28 6 13
RIPK2 0.019 0.014 -10000 0 0 199 199
NGFR 0.028 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 0.033 0.029 -10000 0 -10000 0 0
BCL2L11 -0.046 0.062 0.22 6 -0.28 7 13
BDNF (dimer)/p75(NTR) 0.041 0.01 -10000 0 -10000 0 0
PI3K 0.008 0.062 -10000 0 -0.13 76 76
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.048 0.025 -10000 0 -0.13 1 1
NDNL2 0.027 0.007 -10000 0 0 38 38
YWHAE 0.027 0.008 -10000 0 0 40 40
PRKCI 0.014 0.015 -10000 0 0 289 289
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 0.05 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 27 27
PRKCZ 0.028 0.006 -10000 0 0 23 23
PLG 0.026 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 0.028 0.005 -10000 0 0 20 20
NGFRAP1 0.029 0.002 -10000 0 0 3 3
CASP3 -0.047 0.068 0.22 6 -0.3 13 19
E2F1 0.027 0.008 -10000 0 0 41 41
CASP9 0.029 0.004 -10000 0 0 13 13
IKK complex 0.064 0.062 0.18 1 -0.24 3 4
NGF (dimer)/TRKA 0.021 0.004 -10000 0 -10000 0 0
MMP7 0.017 0.015 -10000 0 0 236 236
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.06 0.03 -10000 0 -10000 0 0
MMP3 0.027 0.007 -10000 0 0 36 36
APAF-1/Caspase 9 -0.042 0.048 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 0.18 0.51 1.3 46 -1.2 17 63
IL23A 0.18 0.42 1.1 41 -10000 0 41
NF kappa B1 p50/RelA/I kappa B alpha 0.12 0.33 0.8 9 -0.88 3 12
positive regulation of T cell mediated cytotoxicity 0.21 0.52 1.3 61 -1 1 62
ITGA3 0.11 0.49 1.1 29 -1.1 35 64
IL17F 0.12 0.32 0.76 47 -10000 0 47
IL12B 0.069 0.14 0.36 74 -10000 0 74
STAT1 (dimer) 0.004 0.25 1 6 -0.88 2 8
CD4 0.2 0.43 1.2 35 -1.1 2 37
IL23 0.15 0.38 0.95 40 -10000 0 40
IL23R 0.14 0.27 0.86 39 -0.79 4 43
IL1B 0.19 0.44 1.2 42 -10000 0 42
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.17 0.42 1.1 30 -0.94 1 31
TYK2 0.038 0.096 0.24 74 -10000 0 74
STAT4 0.028 0.005 -10000 0 0 17 17
STAT3 0.005 0.028 -10000 0 -10000 0 0
IL18RAP 0.004 0.037 0.091 25 -10000 0 25
IL12RB1 0.038 0.097 0.24 74 -10000 0 74
PIK3CA 0.005 0.024 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.071 0.093 0.26 73 -10000 0 73
IL23R/JAK2 0.15 0.26 0.72 60 -0.77 3 63
positive regulation of chronic inflammatory response 0.21 0.52 1.3 61 -1 1 62
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 0.005 0.025 -10000 0 -10000 0 0
NFKB1 0.025 0.027 0.096 1 -10000 0 1
RELA 0.023 0.029 0.096 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 1.1 29 -0.94 1 30
CXCL1 0.18 0.46 1.2 35 -1.2 8 43
T cell proliferation 0.21 0.52 1.3 61 -1 1 62
NFKBIA 0.023 0.028 0.096 1 -10000 0 1
IL17A 0.11 0.29 0.74 35 -10000 0 35
PI3K 0.043 0.3 0.84 17 -0.89 4 21
IFNG 0.04 0.093 0.34 36 -10000 0 36
STAT3 (dimer) 0.046 0.3 0.81 19 -0.86 5 24
IL18R1 0.004 0.037 0.091 25 -10000 0 25
IL23/IL23R/JAK2/TYK2/SOCS3 0.16 0.35 0.88 61 -0.7 5 66
IL18/IL18R 0.032 0.077 0.32 24 -10000 0 24
macrophage activation 0.003 0.021 0.06 27 -10000 0 27
TNF 0.18 0.42 1.2 30 -10000 0 30
STAT3/STAT4 0.12 0.34 0.79 22 -0.9 3 25
STAT4 (dimer) 0.16 0.38 0.97 27 -0.94 2 29
IL18 0.008 0.03 0.088 16 -10000 0 16
IL19 0.17 0.42 1.1 30 -0.94 1 31
STAT5A (dimer) 0.16 0.39 0.97 29 -0.94 2 31
STAT1 0.013 0.015 -10000 0 0 316 316
SOCS3 0.028 0.006 -10000 0 0 21 21
CXCL9 0.23 0.5 1.3 55 -0.94 1 56
MPO 0.17 0.41 1.1 29 -0.94 1 30
positive regulation of humoral immune response 0.21 0.52 1.3 61 -1 1 62
IL23/IL23R/JAK2/TYK2 0.21 0.52 1.3 61 -1.1 1 62
IL6 0.16 0.43 1.1 32 -1.2 8 40
STAT5A 0.028 0.007 -10000 0 0 34 34
IL2 0.005 0.061 0.23 25 -0.12 1 26
positive regulation of tyrosine phosphorylation of STAT protein -0.01 0.022 -10000 0 -0.062 57 57
CD3E 0.17 0.43 1.2 33 -1 3 36
keratinocyte proliferation 0.21 0.52 1.3 61 -1 1 62
NOS2 0.18 0.42 1 56 -0.93 1 57
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.028 0.007 -10000 0 0 33 33
SMAD2 -0.001 0.045 0.16 4 -0.23 2 6
SMAD3 -0.014 0.048 -10000 0 -0.23 7 7
SMAD3/SMAD4 0.06 0.089 -10000 0 -0.5 10 10
SMAD4/Ubc9/PIASy 0.051 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.091 0.058 -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 0.16 1 -0.19 5 6
MAP3K1 0.027 0.008 -10000 0 0 51 51
TRAP-1/SMAD4 0.04 0.011 -10000 0 -10000 0 0
MAPK3 0.028 0.006 -10000 0 0 22 22
MAPK1 0.027 0.008 -10000 0 0 42 42
NUP214 0.028 0.005 -10000 0 0 17 17
CTDSP1 0.029 0.004 -10000 0 0 12 12
CTDSP2 0.028 0.005 -10000 0 0 18 18
CTDSPL 0.029 0.003 -10000 0 0 5 5
KPNB1 0.028 0.006 -10000 0 0 21 21
TGFBRAP1 0.029 0.004 -10000 0 0 10 10
UBE2I 0.028 0.006 -10000 0 0 23 23
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 46 46
FAS signaling pathway (CD95)

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
SPTAN1 -0.005 0.066 0.3 2 -0.2 27 29
RFC1 -0.002 0.067 0.24 6 -0.2 25 31
PRKDC 0.024 0.1 0.22 79 -0.2 26 105
RIPK1 0.026 0.016 -10000 0 -0.081 9 9
CASP7 0.009 0.065 -10000 0 -0.54 6 6
FASLG/FAS/FADD/FAF1 0.022 0.071 0.24 1 -0.28 1 2
MAP2K4 0.002 0.093 0.35 11 -0.34 8 19
mol:ceramide 0.009 0.064 0.31 9 -0.26 3 12
GSN -0.013 0.067 0.22 3 -0.2 24 27
FASLG/FAS/FADD/FAF1/Caspase 8 0.004 0.072 0.19 14 -0.28 2 16
FAS 0.027 0.013 0.078 9 -0.048 7 16
BID -0.036 0.015 0.18 1 -10000 0 1
MAP3K1 0.018 0.081 0.29 10 -0.34 6 16
MAP3K7 0.027 0.011 -10000 0 -0.037 9 9
RB1 0.001 0.07 0.22 17 -0.2 23 40
CFLAR 0.027 0.014 -10000 0 -0.081 9 9
HGF/MET 0.006 0.081 -10000 0 -0.15 105 105
ARHGDIB 0.007 0.084 0.22 34 -0.2 23 57
FADD 0.028 0.012 0.077 10 -0.047 8 18
actin filament polymerization 0.015 0.072 0.22 29 -0.22 4 33
NFKB1 -0.02 0.18 0.39 9 -0.6 41 50
MAPK8 -0.008 0.11 0.4 12 -0.43 13 25
DFFA -0.005 0.069 0.32 3 -0.2 30 33
DNA fragmentation during apoptosis -0.004 0.067 0.22 6 -0.2 29 35
FAS/FADD/MET 0.038 0.05 -10000 0 -0.16 24 24
CFLAR/RIP1 0.038 0.023 -10000 0 -0.12 9 9
FAIM3 0.028 0.01 -10000 0 -0.038 10 10
FAF1 0.028 0.014 0.098 10 -0.053 8 18
PARP1 0.011 0.087 0.22 42 -0.2 27 69
DFFB -0.004 0.066 0.22 4 -0.2 28 32
CHUK -0.028 0.16 0.32 9 -0.56 42 51
FASLG 0.028 0.015 0.098 10 -0.053 9 19
FAS/FADD 0.034 0.04 -10000 0 -0.16 17 17
HGF 0.028 0.005 -10000 0 0 17 17
LMNA 0.037 0.1 0.27 47 -0.2 11 58
CASP6 0.045 0.11 0.21 126 -0.2 12 138
CASP10 0.028 0.013 0.077 10 -0.048 9 19
CASP3 0.005 0.076 0.15 71 -0.22 31 102
PTPN13 0.02 0.014 -10000 0 0 170 170
CASP8 -0.033 0.009 -10000 0 -10000 0 0
IL6 -0.033 0.22 0.67 9 -0.87 17 26
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 0.31 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 65 -0.2 22 87
BCL2 0.022 0.014 -10000 0 -0.002 130 130
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.037 0.091 -10000 0 -0.15 73 73
SMAD6-7/SMURF1 0.053 0.018 -10000 0 -10000 0 0
NOG 0.028 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 0.083 0.2 2 -0.34 19 21
BMP7/USAG1 0.014 0.052 -10000 0 -0.17 36 36
SMAD5/SKI -0.014 0.093 0.2 2 -0.34 19 21
SMAD1 -0.023 0.088 -10000 0 -0.42 16 16
BMP2 0.027 0.007 -10000 0 0 37 37
SMAD1/SMAD1/SMAD4 -0.053 0.079 -10000 0 -0.37 16 16
BMPR1A 0.028 0.006 -10000 0 0 21 21
BMPR1B 0.025 0.011 -10000 0 0 90 90
BMPR1A-1B/BAMBI 0.03 0.059 -10000 0 -0.15 49 49
AHSG 0.025 0.011 -10000 0 0 90 90
CER1 0.027 0.007 -10000 0 0 39 39
BMP2-4/CER1 0.05 0.022 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.036 0.1 -10000 0 -0.3 41 41
BMP2-4 (homodimer) 0.039 0.013 -10000 0 -10000 0 0
RGMB 0.027 0.007 -10000 0 0 36 36
BMP6/BMPR2/BMPR1A-1B 0.042 0.066 -10000 0 -0.14 46 46
RGMA 0.028 0.007 -10000 0 0 33 33
SMURF1 0.028 0.005 -10000 0 0 20 20
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.019 0.071 -10000 0 -0.26 22 22
BMP2-4/USAG1 0.04 0.03 -10000 0 -0.15 2 2
SMAD6/SMURF1/SMAD5 -0.014 0.092 0.2 1 -0.34 21 22
SOSTDC1 0.022 0.013 -10000 0 0 138 138
BMP7/BMPR2/BMPR1A-1B 0.031 0.084 -10000 0 -0.15 76 76
SKI 0.028 0.006 -10000 0 0 23 23
BMP6 (homodimer) 0.027 0.008 -10000 0 0 45 45
HFE2 0.029 0.005 -10000 0 0 16 16
ZFYVE16 0.026 0.009 -10000 0 0 60 60
MAP3K7 0.028 0.007 -10000 0 0 30 30
BMP2-4/CHRD 0.045 0.026 -10000 0 -10000 0 0
SMAD5/SMAD5/SMAD4 -0.014 0.093 0.2 2 -0.33 21 23
MAPK1 0.027 0.008 -10000 0 0 42 42
TAK1/TAB family -0.002 0.081 -10000 0 -0.26 21 21
BMP7 (homodimer) 0.022 0.012 -10000 0 0 133 133
NUP214 0.028 0.005 -10000 0 0 17 17
BMP6/FETUA 0.034 0.018 -10000 0 -10000 0 0
SMAD1/SKI -0.009 0.09 -10000 0 -0.4 16 16
SMAD6 0.029 0.005 -10000 0 0 15 15
CTDSP2 0.028 0.005 -10000 0 0 18 18
BMP2-4/FETUA 0.045 0.025 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.026 0.009 -10000 0 0 60 60
BMPR2 (homodimer) 0.029 0.003 -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 0.09 -10000 0 -0.41 15 15
SMAD6-7/SMURF1/SMAD1 0.013 0.099 -10000 0 -0.39 16 16
SMAD6/SMURF1 0.028 0.005 -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 -0.15 233 233
BMP2-4/GREM1 0.048 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 0.09 -10000 0 -0.4 16 16
TAK1/SMAD6 0.04 0.012 -10000 0 -10000 0 0
BMP7 0.022 0.013 -10000 0 0 133 133
BMP6 0.027 0.008 -10000 0 0 45 45
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.019 0.077 0.16 1 -0.29 21 22
PPM1A 0.029 0.004 -10000 0 0 13 13
SMAD1/SMURF2 -0.009 0.091 -10000 0 -0.41 16 16
SMAD7/SMURF1 0.04 0.012 -10000 0 -10000 0 0
CTDSPL 0.029 0.003 -10000 0 0 5 5
PPP1CA 0.029 0.003 -10000 0 0 8 8
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.029 0.004 -10000 0 0 12 12
PPP1R15A 0.026 0.01 -10000 0 0 68 68
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.017 0.085 -10000 0 -0.3 24 24
CHRD 0.024 0.011 -10000 0 0 94 94
BMPR2 0.029 0.003 -10000 0 0 8 8
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.019 0.075 0.18 1 -0.26 22 23
BMP4 0.028 0.006 -10000 0 0 22 22
FST 0.025 0.011 -10000 0 0 91 91
BMP2-4/NOG 0.052 0.022 -10000 0 -0.15 1 1
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.037 0.088 -10000 0 -0.15 74 74
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 -0.43 9 9
SMARCC2 0.028 0.006 -10000 0 0 22 22
SMARCC1 0.029 0.003 -10000 0 0 8 8
TBX21 0.04 0.08 0.32 5 -10000 0 5
SUMO2 0.005 0.032 -10000 0 -0.038 184 184
STAT1 (dimer) 0.017 0.052 0.31 13 -0.18 7 20
FKBP4 0.026 0.01 -10000 0 0 71 71
FKBP5 0.026 0.009 -10000 0 0 59 59
GR alpha/HSP90/FKBP51/HSP90 -0.04 0.094 -10000 0 -0.24 15 15
PRL 0.043 0.063 0.71 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 -0.094 0.15 -10000 0 -0.43 23 23
RELA 0.008 0.095 0.18 112 -0.19 6 118
FGG -0.13 0.12 -10000 0 -0.43 23 23
GR beta/TIF2 -0.078 0.063 -10000 0 -0.28 3 3
IFNG 0.11 0.17 0.54 45 -10000 0 45
apoptosis -0.18 0.21 0.5 1 -0.64 27 28
CREB1 0.027 0.013 -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 0.09 -10000 0 -0.21 2 2
NF kappa B1 p50/RelA 0.079 0.13 0.33 96 -0.3 14 110
SMARCD1 0.029 0.003 -10000 0 0 5 5
MDM2 -0.036 0.041 -10000 0 -0.22 1 1
GATA3 -0.027 0.007 -10000 0 -10000 0 0
AKT1 0.029 0.007 -10000 0 -10000 0 0
CSF2 0.013 0.043 -10000 0 -10000 0 0
GSK3B 0.006 0.032 -10000 0 -0.038 177 177
NR1I3 -0.16 0.18 -10000 0 -0.65 10 10
CSN2 -0.12 0.11 -10000 0 -0.39 26 26
BRG1/BAF155/BAF170/BAF60A 0.063 0.032 -10000 0 -0.14 2 2
NFATC1 0.025 0.012 -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 0.038 2 -10000 0 2
SFN 0.027 0.007 -10000 0 0 38 38
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.024 0.1 -10000 0 -0.24 10 10
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.3 0.34 0.58 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 0.005 0.03 -10000 0 -0.035 192 192
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 -0.029 0.1 -10000 0 -0.24 10 10
cortisol/GR alpha (monomer) -0.15 0.14 -10000 0 -0.49 23 23
NCOA2 0.027 0.008 -10000 0 0 45 45
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.036 0.094 0.18 112 -0.3 1 113
AP-1/NFAT1-c-4 0.098 0.21 0.61 33 -10000 0 33
AFP 0.059 0.12 -10000 0 -10000 0 0
SUV420H1 0.029 0.003 -10000 0 0 8 8
IRF1 -0.002 0.15 0.52 10 -0.72 9 19
TP53 -0.038 0.084 -10000 0 -0.52 16 16
PPP5C 0.028 0.006 -10000 0 0 25 25
KRT17 0.097 0.19 0.62 33 -10000 0 33
KRT14 0.066 0.12 0.66 14 -10000 0 14
TBP 0.025 0.015 0.19 1 -10000 0 1
CREBBP 0.022 0.038 -10000 0 -0.22 13 13
HDAC1 0.027 0.009 -10000 0 -10000 0 0
HDAC2 0.027 0.007 -10000 0 -10000 0 0
AP-1 0.098 0.21 0.61 33 -10000 0 33
MAPK14 0.005 0.032 -10000 0 -0.038 180 180
MAPK10 0.005 0.032 -10000 0 -0.039 169 169
MAPK11 0.004 0.029 -10000 0 -0.038 148 148
KRT5 0.16 0.26 0.65 103 -10000 0 103
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.021 0.02 -10000 0 -10000 0 0
STAT1 0.017 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 -0.065 0.1 -10000 0 -0.39 25 25
MAPK3 0.005 0.032 -10000 0 -0.038 182 182
MAPK1 0.004 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 0.18 112 -0.19 6 118
MAPK8 0.077 0.14 0.42 33 -10000 0 33
MAPK9 0.005 0.032 -10000 0 -0.038 185 185
cortisol/GR alpha (dimer) -0.19 0.22 0.5 1 -0.65 33 34
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 -0.48 22 22
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.052 0.22 13 -0.19 1 14
SGK1 -0.033 0.087 -10000 0 -0.29 37 37
IL13 0.078 0.13 0.5 8 -10000 0 8
IL6 0.064 0.18 0.58 17 -0.83 9 26
PRKACG 0.028 0.005 -10000 0 0 19 19
IL5 0.065 0.12 -10000 0 -10000 0 0
IL2 0.085 0.16 0.52 20 -10000 0 20
CDK5 0.007 0.028 -10000 0 -0.034 162 162
PRKACB 0.028 0.006 -10000 0 0 21 21
HSP90AA1 0.028 0.005 -10000 0 0 20 20
IL8 0.1 0.2 0.64 57 -10000 0 57
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 0.15 -10000 0 -0.41 22 22
SMARCA4 0.026 0.009 -10000 0 0 60 60
chromatin remodeling -0.073 0.083 -10000 0 -0.33 6 6
NF kappa B1 p50/RelA/Cbp 0.078 0.13 0.42 18 -0.27 12 30
JUN (dimer) 0.089 0.17 0.5 42 -10000 0 42
YWHAH 0.027 0.008 -10000 0 0 42 42
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 0.5 1 -0.64 27 28
cortisol/GR alpha (dimer)/Src-1 -0.097 0.16 -10000 0 -0.43 26 26
PBX1 0.028 0.009 0.2 1 -10000 0 1
POU1F1 0.029 0.008 0.2 1 -10000 0 1
SELE 0.076 0.12 0.43 14 -10000 0 14
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.073 0.084 -10000 0 -0.33 6 6
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.066 0.15 -10000 0 -0.41 22 22
mol:cortisol -0.078 0.076 -10000 0 -0.27 5 5
MMP1 0.14 0.25 0.63 110 -0.51 5 115
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 -0.031 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.12 0.24 10 -0.35 18 28
ERC1 0.026 0.01 -10000 0 0 67 67
RIP2/NOD2 0.026 0.021 -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 0.027 0.007 -10000 0 0 39 39
RIPK2 0.019 0.014 -10000 0 0 199 199
IKBKG 0.027 0.1 -10000 0 -0.41 20 20
IKK complex/A20 0.046 0.13 0.24 7 -0.38 30 37
NEMO/A20/RIP2 0.019 0.014 -10000 0 0 199 199
XPO1 0.027 0.008 -10000 0 0 51 51
NEMO/ATM 0.035 0.13 0.23 9 -0.39 33 42
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 0.035 0.012 -10000 0 -10000 0 0
IKK complex/ELKS 0.034 0.12 -10000 0 -0.36 32 32
BCL10/MALT1/TRAF6 0.05 0.022 -10000 0 -10000 0 0
NOD2 0.027 0.008 -10000 0 0 40 40
NFKB1 -0.03 0.012 -10000 0 -10000 0 0
RELA -0.032 0.009 -10000 0 -10000 0 0
MALT1 0.025 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 30 30
TNF/TNFR1A 0.032 0.037 -10000 0 -0.16 16 16
TRAF6 0.029 0.004 -10000 0 0 12 12
PRKCA 0.028 0.006 -10000 0 0 23 23
CHUK 0.027 0.007 -10000 0 0 36 36
UBE2D3 0.027 0.008 -10000 0 0 40 40
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 -10000 0 0
TNFRSF1A 0.025 0.01 -10000 0 0 78 78
IKK complex 0.044 0.13 0.24 8 -0.38 32 40
CYLD 0.027 0.007 -10000 0 0 39 39
IKK complex/PKC alpha 0.05 0.13 0.24 8 -0.38 31 39
Paxillin-independent events mediated by a4b1 and a4b7

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
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 0.028 0.005 -10000 0 0 19 19
ITGA4 0.027 0.008 -10000 0 0 40 40
alpha4/beta7 Integrin/MAdCAM1 0.065 0.04 -10000 0 -0.14 1 1
EPO 0.028 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 0.027 0.007 -10000 0 0 36 36
alpha4/beta1 Integrin 0.039 0.013 -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 0.02 0.014 -10000 0 0 172 172
PI3K -0.001 0.068 -10000 0 -0.16 76 76
ARF6 0.029 0.004 -10000 0 0 11 11
JAK2 -0.009 0.032 -10000 0 -0.24 1 1
PXN 0.029 0.005 -10000 0 0 14 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
MADCAM1 0.027 0.008 -10000 0 0 51 51
cell adhesion 0.063 0.039 -10000 0 -0.14 1 1
CRKL/CBL 0.04 0.011 -10000 0 -10000 0 0
ITGB1 0.028 0.006 -10000 0 0 22 22
SRC -0.008 0.1 0.17 116 -10000 0 116
ITGB7 0.029 0.004 -10000 0 0 9 9
RAC1 0.028 0.006 -10000 0 0 27 27
alpha4/beta1 Integrin/VCAM1 0.021 0.067 -10000 0 -0.15 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 0.066 0.04 -10000 0 -0.14 6 6
BCAR1 -0.012 0.093 0.15 111 -10000 0 111
EPOR 0.026 0.009 -10000 0 0 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.029 0.005 -10000 0 0 14 14
GIT1 0.028 0.007 -10000 0 0 31 31
Rac1/GTP -0.01 0.12 -10000 0 -0.48 12 12
Paxillin-dependent events mediated by a4b1

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
CRKL 0.028 0.007 -10000 0 0 31 31
Rac1/GDP 0.021 0.028 -10000 0 -0.038 1 1
DOCK1 0.028 0.005 -10000 0 0 19 19
ITGA4 0.027 0.008 -10000 0 0 40 40
RAC1 0.028 0.006 -10000 0 0 27 27
alpha4/beta7 Integrin 0.04 0.015 -10000 0 -0.16 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 0 36 36
alpha4/beta1 Integrin 0.046 0.025 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.038 0.022 -10000 0 -10000 0 0
lamellipodium assembly -0.066 0.15 -10000 0 -0.34 98 98
PIK3CA 0.02 0.014 -10000 0 0 172 172
PI3K -0.001 0.068 -10000 0 -0.16 76 76
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 0 159 159
ARF6/GTP -0.025 0.07 0.14 63 -10000 0 63
cell adhesion 0.06 0.048 -10000 0 -0.16 5 5
CRKL/CBL 0.04 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.037 0.022 -10000 0 -10000 0 0
ITGB1 0.028 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 -0.038 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0.047 0.078 -10000 0 -0.14 58 58
p130Cas/Crk/Dock1 0.049 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 0.061 0.05 -10000 0 -0.14 5 5
BCAR1 0.026 0.009 -10000 0 0 56 56
mol:GDP -0.059 0.049 0.14 5 -10000 0 5
CBL 0.029 0.005 -10000 0 0 14 14
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 -0.075 0.16 -10000 0 -0.37 98 98
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 0.032 0.019 0.079 61 -10000 0 61
HSPA8 0.02 0.024 -10000 0 -0.042 68 68
SMAD3/SMAD4/ER alpha -0.051 0.088 0.23 19 -0.29 2 21
AKT1 0.026 0.013 -10000 0 -0.043 1 1
GSC 0.001 0.059 -10000 0 -10000 0 0
NKX2-5 -0.031 0.01 0.039 1 -0.082 1 2
muscle cell differentiation -0.027 0.11 0.36 5 -0.3 2 7
SMAD2-3/SMAD4/SP1 0.026 0.14 0.36 11 -10000 0 11
SMAD4 -0.007 0.079 0.2 19 -10000 0 19
CBFB 0.026 0.009 -10000 0 0 59 59
SAP18 0.02 0.021 -10000 0 -0.032 67 67
Cbp/p300/MSG1 0.057 0.044 -10000 0 -0.14 9 9
SMAD3/SMAD4/VDR 0.063 0.1 0.3 10 -10000 0 10
MYC 0.017 0.015 -10000 0 -10000 0 0
CDKN2B -0.057 0.12 -10000 0 -0.66 4 4
AP1 -0.025 0.088 0.26 2 -10000 0 2
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.021 0.11 0.21 8 -0.38 24 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.022 0.073 -10000 0 -0.35 10 10
SP3 -0.023 0.037 0.17 20 -10000 0 20
CREB1 0.029 0.003 -10000 0 0 8 8
FOXH1 -0.023 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.031 0.1 0.23 25 -0.26 1 26
GATA3 -0.033 0.009 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.012 0.09 0.18 4 -0.36 22 26
MEF2C/TIF2 -0.005 0.11 0.26 11 -0.29 12 23
endothelial cell migration -0.099 0.21 0.62 2 -0.65 68 70
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 42 42
NR3C1 0.008 0.056 -10000 0 -0.14 68 68
VDR 0.029 0.003 -10000 0 0 8 8
CDKN1A 0.006 0.22 -10000 0 -0.98 20 20
KAT2B 0.002 0.005 0.018 14 -10000 0 14
SMAD2/SMAD2/SMAD4/FOXH1 -0.002 0.066 -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 -0.63 2 70
SMAD3/SMAD4/ATF2 -0.012 0.09 0.23 30 -10000 0 30
SMAD3/SMAD4/ATF3 -0.013 0.089 0.23 29 -0.26 1 30
SAP30 0.02 0.021 -10000 0 -0.032 67 67
Cbp/p300/PIAS3 0.062 0.054 0.18 64 -0.15 7 71
JUN -0.023 0.09 0.27 6 -10000 0 6
SMAD3/SMAD4/IRF7 -0.013 0.095 0.24 33 -10000 0 33
TFE3 0 0.067 0.13 101 -10000 0 101
COL1A2 0.14 0.25 0.52 156 -0.6 7 163
mesenchymal cell differentiation 0.011 0.09 -10000 0 -0.23 30 30
DLX1 0.029 0.005 -10000 0 0 15 15
TCF3 0.027 0.008 -10000 0 0 50 50
FOS -0.008 0.041 0.16 7 -10000 0 7
SMAD3/SMAD4/Max -0.03 0.098 0.25 15 -0.26 1 16
Cbp/p300/SNIP1 0.049 0.038 -10000 0 -0.14 10 10
ZBTB17 0.029 0.005 -10000 0 -10000 0 0
LAMC1 -0.014 0.081 0.26 11 -10000 0 11
TGIF2/HDAC complex/SMAD3/SMAD4 -0.011 0.09 0.24 31 -10000 0 31
IRF7 -0.03 0.007 -10000 0 -10000 0 0
ESR1 -0.032 0.026 0.11 5 -0.078 16 21
HNF4A 0.027 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 0.25 20 -10000 0 20
Cbp/p300/Src-1 0.055 0.044 -10000 0 -0.14 12 12
IGHV3OR16-13 -0.007 0.033 -10000 0 -0.42 3 3
TGIF2/HDAC complex 0.027 0.007 -10000 0 0 36 36
CREBBP 0.031 0.014 0.069 8 -10000 0 8
SKIL 0.01 0.014 -10000 0 0 362 362
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 0.001 0.1 0.25 24 -10000 0 24
MSG1/HSC70 0.03 0.03 -10000 0 -10000 0 0
SMAD2 -0.031 0.01 -10000 0 -10000 0 0
SMAD3 -0.006 0.078 0.2 19 -10000 0 19
SMAD3/E2F4-5/DP1/p107/SMAD4 0.011 0.076 0.24 14 -0.25 2 16
SMAD2/SMAD2/SMAD4 -0.006 0.06 0.18 2 -0.2 19 21
NCOR1 0.02 0.02 -10000 0 -0.032 65 65
NCOA2 0.027 0.008 -10000 0 0 45 45
NCOA1 0.029 0.005 -10000 0 0 14 14
MYOD/E2A 0.039 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.09 0.13 0.37 16 -10000 0 16
IFNB1 -0.022 0.082 0.23 12 -10000 0 12
SMAD3/SMAD4/MEF2C 0.009 0.13 0.33 12 -0.31 10 22
CITED1 0.024 0.016 -10000 0 -0.029 41 41
SMAD2-3/SMAD4/ARC105 0.038 0.096 0.3 2 -10000 0 2
RBL1 0.026 0.01 -10000 0 0 67 67
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.019 0.077 -10000 0 -0.46 4 4
RUNX1-3/PEBPB2 0.052 0.02 -10000 0 -10000 0 0
SMAD7 0.016 0.16 0.44 22 -0.42 1 23
MYC/MIZ-1 0.012 0.056 -10000 0 -0.16 46 46
SMAD3/SMAD4 0.054 0.13 0.34 64 -0.44 3 67
IL10 -0.016 0.093 0.26 8 -10000 0 8
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 -0.014 0.094 0.27 10 -10000 0 10
CDK4 0.033 0.014 0.073 29 -10000 0 29
PIAS4 0.016 0.031 -10000 0 -0.067 64 64
ATF3 0.028 0.006 -10000 0 0 23 23
SMAD3/SMAD4/SP1 0.018 0.13 0.33 8 -10000 0 8
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 0.026 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.011 0.091 0.24 31 -10000 0 31
MYOD1 0.029 0.003 -10000 0 0 8 8
SMAD3/SMAD4/HNF4 -0.011 0.089 0.24 31 -10000 0 31
SMAD3/SMAD4/GATA3 -0.012 0.097 0.23 41 -10000 0 41
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.014 -10000 0 0 362 362
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.094 0.3 5 -10000 0 5
SMAD3/SMAD4/SP1-3 0.064 0.13 0.34 16 -10000 0 16
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 0.02 -10000 0 -0.032 68 68
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.032 0.073 -10000 0 -10000 0 0
ITGB5 0.004 0.12 0.3 22 -10000 0 22
TGIF/SIN3/HDAC complex/CtBP -0.007 0.081 0.19 3 -0.29 25 28
SMAD3/SMAD4/AR -0.086 0.099 0.23 13 -0.27 6 19
AR 0.012 0.014 -10000 0 0 328 328
negative regulation of cell growth 0.007 0.092 0.27 8 -0.31 10 18
SMAD3/SMAD4/MYOD -0.012 0.091 0.24 30 -10000 0 30
E2F5 0.025 0.01 -10000 0 0 83 83
E2F4 0.026 0.009 -10000 0 0 58 58
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.041 0.073 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.018 0.063 -10000 0 -0.46 1 1
TFDP1 0.027 0.007 -10000 0 0 37 37
SMAD3/SMAD4/AP1 -0.02 0.094 0.24 8 -10000 0 8
SMAD3/SMAD4/RUNX2 -0.011 0.09 0.24 30 -10000 0 30
TGIF2 0.027 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
Hypoxic and oxygen homeostasis regulation of HIF-1-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
HIF3A 0.028 0.006 -10000 0 0 26 26
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.028 0.005 -10000 0 0 18 18
TCEB1 0.027 0.007 -10000 0 0 36 36
HIF1A/p53 -0.012 0.065 0.24 1 -0.31 16 17
HIF1A -0.007 0.056 -10000 0 -0.33 13 13
COPS5 0.025 0.01 -10000 0 0 77 77
VHL/Elongin B/Elongin C/RBX1/CUL2 0.076 0.053 -10000 0 -10000 0 0
FIH (dimer) 0.028 0.005 -10000 0 0 20 20
CDKN2A 0.011 0.014 -10000 0 0 339 339
ARNT/IPAS 0.039 0.014 -10000 0 -10000 0 0
HIF1AN 0.028 0.005 -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 0.023 0.012 -10000 0 0 113 113
OS9 0.028 0.005 -10000 0 0 17 17
RACK1/Elongin B/Elongin C 0.053 0.019 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.01 0.066 0.24 1 -0.32 13 14
PHD1-3/OS9 0.061 0.047 -10000 0 -0.14 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.032 0.071 0.25 1 -0.32 14 15
VHL 0.029 0.004 -10000 0 0 9 9
HSP90AA1 0.028 0.005 -10000 0 0 20 20
HIF1A/JAB1 -0.01 0.064 0.24 1 -0.32 13 14
EGLN3 0.026 0.01 -10000 0 0 70 70
EGLN2 0.027 0.007 -10000 0 0 39 39
EGLN1 0.028 0.007 -10000 0 0 33 33
TP53 0.024 0.011 -10000 0 0 101 101
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.034 0.075 -10000 0 -0.62 5 5
ARNT 0.027 0.007 -10000 0 0 37 37
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.008 -10000 0 0 50 50
HIF1A/p19ARF -0.007 0.05 0.24 1 -0.32 8 9
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.002 0.086 0.24 10 -0.33 10 20
PDGFB-D/PDGFRB/SLAP 0.022 0.032 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/APS/CBL 0.034 0.022 -10000 0 -0.13 5 5
AKT1 -0.039 0.11 0.26 24 -0.25 5 29
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.088 0.27 6 -0.36 10 16
PIK3CA 0.02 0.014 -10000 0 0 172 172
FGR -0.002 0.082 0.32 1 -0.38 12 13
mol:Ca2+ -0.001 0.083 0.27 3 -0.39 10 13
MYC -0.026 0.24 0.38 7 -0.68 59 66
SHC1 0.028 0.006 -10000 0 0 21 21
HRAS/GDP -0.036 0.056 0.16 41 -10000 0 41
LRP1/PDGFRB/PDGFB 0.047 0.037 -10000 0 -0.15 13 13
GRB10 0.029 0.004 -10000 0 0 12 12
PTPN11 0.029 0.003 -10000 0 0 8 8
GO:0007205 -0.001 0.083 0.27 3 -0.4 10 13
PTEN 0.028 0.007 -10000 0 0 31 31
GRB2 0.028 0.005 -10000 0 0 20 20
GRB7 0.027 0.008 -10000 0 0 41 41
PDGFB-D/PDGFRB/SHP2 0.033 0.031 -10000 0 -0.16 5 5
PDGFB-D/PDGFRB/GRB10 0.033 0.031 -10000 0 -0.16 5 5
cell cycle arrest 0.022 0.032 -10000 0 -0.16 5 5
HRAS 0.028 0.006 -10000 0 0 27 27
HIF1A -0.044 0.1 0.23 24 -0.23 5 29
GAB1 -0.009 0.097 0.3 3 -0.35 15 18
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.01 0.1 0.28 12 -0.34 12 24
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 0.031 0.031 -10000 0 -0.16 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.025 0.098 0.26 6 -0.31 21 27
positive regulation of MAPKKK cascade 0.033 0.031 -10000 0 -0.16 5 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.001 0.084 0.27 3 -0.4 10 13
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 0.03 0.035 -10000 0 -0.16 8 8
SHB 0.029 0.003 -10000 0 0 8 8
BLK -0.059 0.16 0.32 1 -0.39 89 90
PTPN2 0.014 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.031 -10000 0 -0.16 5 5
BCAR1 0.026 0.009 -10000 0 0 56 56
VAV2 -0.022 0.12 0.3 4 -0.37 29 33
CBL 0.029 0.005 -10000 0 0 14 14
PDGFB-D/PDGFRB/DEP1 0.033 0.031 -10000 0 -0.16 5 5
LCK -0.001 0.075 0.32 1 -0.38 9 10
PDGFRB 0.009 0.03 -10000 0 -10000 0 0
ACP1 0.026 0.009 -10000 0 0 57 57
HCK 0.002 0.053 0.32 1 -10000 0 1
ABL1 -0.01 0.087 0.29 3 -0.29 15 18
PDGFB-D/PDGFRB/CBL -0.009 0.1 0.33 1 -0.43 13 14
PTPN1 0.011 0.027 -10000 0 -10000 0 0
SNX15 0.029 0.003 -10000 0 0 5 5
STAT3 0.027 0.007 -10000 0 0 37 37
STAT1 0.013 0.015 -10000 0 0 316 316
cell proliferation -0.019 0.22 0.35 9 -0.6 59 68
SLA 0.02 0.014 -10000 0 0 170 170
actin cytoskeleton reorganization -0.023 0.1 0.29 20 -10000 0 20
SRC 0.001 0.064 0.32 1 -0.88 1 2
PI3K -0.072 0.068 -10000 0 -0.22 37 37
PDGFB-D/PDGFRB/GRB7/SHC 0.048 0.032 -10000 0 -0.15 8 8
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.006 0.09 0.28 5 -0.37 10 15
LYN -0.009 0.087 0.31 1 -0.49 11 12
LRP1 0.028 0.006 -10000 0 0 21 21
SOS1 0.028 0.007 -10000 0 0 35 35
STAT5B 0.028 0.007 -10000 0 0 33 33
STAT5A 0.028 0.007 -10000 0 0 34 34
NCK1-2/p130 Cas 0.053 0.068 -10000 0 -0.15 6 6
SPHK1 0.015 0.026 -10000 0 -10000 0 0
EDG1 -0.001 0.003 0.019 1 -10000 0 1
mol:DAG -0.001 0.084 0.27 3 -0.4 10 13
PLCG1 -0.001 0.085 0.3 2 -0.41 10 12
NHERF/PDGFRB -0.014 0.1 -10000 0 -0.16 170 170
YES1 -0.001 0.083 0.31 1 -0.52 7 8
cell migration -0.014 0.1 -10000 0 -0.16 170 170
SHC/Grb2/SOS1 0.06 0.06 -10000 0 -0.15 4 4
SLC9A3R2 0.024 0.011 -10000 0 0 93 93
SLC9A3R1 0.022 0.013 -10000 0 0 141 141
NHERF1-2/PDGFRB/PTEN -0.006 0.11 -10000 0 -0.16 170 170
FYN -0.066 0.16 -10000 0 -0.42 88 88
DOK1 -0.028 0.06 0.16 50 -10000 0 50
HRAS/GTP 0.021 0.005 -10000 0 -10000 0 0
PDGFB 0.027 0.008 -10000 0 0 46 46
RAC1 -0.058 0.2 0.41 1 -0.53 62 63
PRKCD -0.029 0.061 0.16 49 -10000 0 49
FER -0.028 0.06 0.16 47 -10000 0 47
MAPKKK cascade -0.025 0.082 0.33 10 -10000 0 10
RASA1 -0.028 0.057 0.16 43 -10000 0 43
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 51 -10000 0 51
PDGFB-D/PDGFRB/SHB 0.034 0.031 -10000 0 -0.16 5 5
chemotaxis -0.01 0.085 0.28 3 -0.28 15 18
STAT1-3-5/STAT1-3-5 0.06 0.065 -10000 0 -0.16 7 7
Bovine Papilomavirus E5/PDGFRB 0.013 0.023 -10000 0 -0.15 5 5
PTPRJ 0.029 0.003 -10000 0 0 8 8
Noncanonical Wnt signaling pathway

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.025 0.01 -10000 0 0 76 76
GNB1/GNG2 0.043 0.08 0.2 4 -0.22 9 13
mol:DAG -0.009 0.075 0.17 23 -0.22 9 32
PLCG1 -0.01 0.076 0.17 23 -0.22 9 32
YES1 -0.008 0.066 0.2 16 -0.22 9 25
FZD3 0.022 0.013 -10000 0 0 139 139
FZD6 0.024 0.011 -10000 0 0 105 105
G protein 0.016 0.1 0.21 64 -0.26 2 66
MAP3K7 -0.025 0.067 0.19 10 -0.24 2 12
mol:Ca2+ -0.009 0.074 0.17 23 -0.21 9 32
mol:IP3 -0.009 0.075 0.17 23 -0.22 9 32
NLK -0.02 0.16 -10000 0 -0.79 24 24
GNB1 0.028 0.006 -10000 0 0 24 24
CAMK2A -0.017 0.071 0.2 11 -0.22 4 15
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 -0.007 0.072 0.2 13 -0.22 7 20
WNT6 0.029 0.003 -10000 0 0 7 7
WNT4 0.029 0.004 -10000 0 0 11 11
NFAT1/CK1 alpha -0.007 0.092 0.24 20 -0.27 2 22
GNG2 0.029 0.004 -10000 0 0 12 12
WNT5A 0.028 0.005 -10000 0 0 17 17
WNT11 0.025 0.01 -10000 0 0 74 74
CDC42 -0.005 0.068 0.19 22 -0.23 3 25
Arf6 signaling events

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
CENTA1/KIF3B 0.01 0.03 -10000 0 -0.12 26 26
ARNO/beta Arrestin1-2 0.025 0.029 -10000 0 -0.1 6 6
EGFR 0.027 0.009 -10000 0 0 54 54
EPHA2 0.029 0.005 -10000 0 0 16 16
USP6 0.028 0.006 -10000 0 0 25 25
IQSEC1 0.029 0.003 -10000 0 0 8 8
EGFR/EGFR/EGF/EGF 0.024 0.055 -10000 0 -0.16 43 43
ARRB2 0.006 0.002 -10000 0 -10000 0 0
mol:GTP 0.001 0.02 0.11 4 -0.069 14 18
ARRB1 0.027 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 40 40
somatostatin receptor activity 0 0 0 6 -0.001 30 36
ARAP2 0 0 0 7 0 25 32
mol:GDP -0.009 0.071 0.14 2 -0.24 24 26
mol:PI-3-4-5-P3 0 0 0 5 -0.001 28 33
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 0.067 0.04 -10000 0 -10000 0 0
ADAP1 0 0 0 2 0 17 19
KIF13B 0.024 0.012 -10000 0 0 111 111
HGF/MET 0.032 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 26 34
actin filament binding 0 0 0 5 0 30 35
SRC 0.028 0.007 -10000 0 0 31 31
ITGB3 0.024 0.011 -10000 0 0 98 98
GNAQ 0.028 0.007 -10000 0 -0.001 29 29
EFA6/PI-4-5-P2 0 0 0.001 15 -0.001 20 35
ARF6/GDP -0.003 0.072 0.16 9 -0.28 20 29
ARF6/GDP/GULP/ACAP1 -0.005 0.088 -10000 0 -0.24 30 30
alphaIIb/beta3 Integrin/paxillin/GIT1 0.041 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 46 46
HGF 0.028 0.005 -10000 0 0 17 17
CYTH3 0 0 0 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 6 0 21 27
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 0.018 0.006 -10000 0 -0.015 9 9
mol:Phosphatidic acid 0 0 0 5 0 26 31
PIP3-E 0 0 0 6 0 27 33
MET 0.025 0.011 -10000 0 0 87 87
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GIT1 0.028 0.007 -10000 0 0 31 31
mol:PI-4-5-P2 0 0 0.001 9 -0.001 26 35
GNA11 0.025 0.01 -10000 0 0 83 83
LHCGR 0.028 0.007 -10000 0 -0.005 23 23
AGTR1 0.027 0.008 -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
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.033 0.018 -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 -0.18 78 83
RAPGEF1 0.028 0.005 -10000 0 0 17 17
BDNF 0.029 0.004 -10000 0 0 13 13
PIK3CA 0.02 0.014 -10000 0 0 172 172
DYNLT1 0.025 0.01 -10000 0 0 82 82
NTRK1 0.029 0.005 -10000 0 0 15 15
NTRK2 0.028 0.005 -10000 0 0 19 19
NTRK3 0.028 0.006 -10000 0 0 21 21
NT-4/5 (dimer)/TRKB 0.037 0.009 -10000 0 -10000 0 0
neuron apoptosis 0.018 0.11 0.28 45 -10000 0 45
SHC 2-3/Grb2 -0.02 0.12 -10000 0 -0.31 45 45
SHC1 0.028 0.006 -10000 0 0 21 21
SHC2 -0.041 0.15 -10000 0 -0.39 73 73
SHC3 0.001 0.09 -10000 0 -0.41 16 16
STAT3 (dimer) -0.052 0.14 -10000 0 -0.28 142 142
NT3 (dimer)/TRKA 0.044 0.026 -10000 0 -10000 0 0
RIN/GDP 0.042 0.079 0.2 29 -0.26 11 40
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 -0.16 0.21 -10000 0 -0.52 141 141
MAGED1 0.028 0.006 -10000 0 0 21 21
PTPN11 0.029 0.003 -10000 0 0 8 8
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.052 0.02 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 0 20 20
NGF (dimer)/TRKA/MATK 0.036 0.012 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.038 0.016 -10000 0 -0.16 1 1
ELMO1 0.028 0.007 -10000 0 0 30 30
RhoG/GTP/ELMO1/DOCK1 0.036 0.013 -10000 0 -0.13 1 1
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.028 0.006 -10000 0 0 27 27
DOCK1 0.028 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 65 65
FRS2 0.028 0.007 -10000 0 0 30 30
DNM1 0.029 0.005 -10000 0 0 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.007 -10000 0 0 36 36
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.009 0.065 0.22 1 -0.17 12 13
mol:GDP 0.041 0.1 0.25 28 -0.37 13 41
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.021 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.035 0.074 0.21 19 -0.24 11 30
TIAM1 0.028 0.005 -10000 0 0 20 20
PIK3R1 0.021 0.013 -10000 0 0 159 159
BDNF (dimer)/TRKB 0.053 0.019 -10000 0 -10000 0 0
KIDINS220/CRKL/C3G 0.04 0.012 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.02 -10000 0 -0.16 3 3
FRS2 family/SHP2 0.053 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.067 0.035 -10000 0 -0.14 2 2
RIT1/GTP 0.019 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.023 0.012 -10000 0 0 116 116
RAP1/GDP 0.032 0.064 0.15 24 -0.23 11 35
KIDINS220/CRKL 0.028 0.007 -10000 0 0 31 31
BDNF (dimer) 0.029 0.004 -10000 0 0 13 13
ubiquitin-dependent protein catabolic process 0.035 0.014 -10000 0 -0.13 1 1
Schwann cell development -0.01 0.013 -10000 0 -0.055 3 3
EHD4 0.027 0.007 -10000 0 0 39 39
FRS2 family/GRB2/SOS1 0.066 0.033 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.002 0.059 -10000 0 -0.25 16 16
RAP1B 0.028 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 0.028 0.005 -10000 0 0 20 20
SH2B family/GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
Rap1/GTP 0.002 0.073 -10000 0 -0.26 22 22
STAT3 -0.052 0.14 -10000 0 -0.28 142 142
axon guidance -0.04 0.051 0.1 53 -10000 0 53
MAPK3 -0.028 0.035 0.18 15 -10000 0 15
MAPK1 -0.027 0.033 0.18 13 -10000 0 13
CDC42/GDP 0.044 0.08 0.2 34 -0.26 11 45
NTF3 0.023 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 -0.001 0.068 -10000 0 -0.16 76 76
FRS3 0.028 0.006 -10000 0 0 26 26
FAIM 0.027 0.007 -10000 0 0 39 39
GAB1 0.028 0.006 -10000 0 0 24 24
RASGRF1 -0.014 0.057 0.18 2 -0.17 9 11
SOS1 0.028 0.007 -10000 0 0 35 35
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 5 -0.35 7 12
Rac1/GDP 0.042 0.079 0.2 35 -0.26 11 46
NGF (dimer)/TRKA/GRIT 0.019 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.24 -10000 0 -0.86 37 37
NGF (dimer)/TRKA/NEDD4-2 0.035 0.014 -10000 0 -0.13 1 1
MAP2K1 -0.029 0.069 0.17 43 -10000 0 43
NGFR 0.028 0.005 -10000 0 0 18 18
NGF (dimer)/TRKA/GIPC/GAIP -0.008 0.051 -10000 0 -0.18 37 37
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 0.039 0.013 -10000 0 -10000 0 0
PRKCI 0.014 0.015 -10000 0 0 289 289
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCZ 0.028 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 49 49
TRKA/c-Abl 0.04 0.018 -10000 0 -0.16 3 3
SQSTM1 0.028 0.005 -10000 0 0 20 20
BDNF (dimer)/TRKB/GIPC 0.044 0.059 -10000 0 -0.14 32 32
NGF (dimer)/TRKA/p62/Atypical PKCs 0.064 0.05 -10000 0 -10000 0 0
MATK 0.027 0.008 -10000 0 0 44 44
NEDD4L 0.027 0.008 -10000 0 0 47 47
RAS family/GDP -0.012 0.033 -10000 0 -0.18 13 13
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 0.068 0.044 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.029 0.005 -10000 0 0 15 15
Jak2/Leptin Receptor 0.009 0.11 -10000 0 -0.36 30 30
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 -0.008 0.089 -10000 0 -0.34 7 7
EGFR 0.018 0.025 -10000 0 -10000 0 0
EGF/EGFR 0.006 0.1 -10000 0 -0.3 15 15
CSF1 0.028 0.006 -10000 0 0 27 27
AKT1 0.012 0.027 -10000 0 -10000 0 0
INSR 0.015 0.023 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.006 0.092 -10000 0 -0.32 11 11
Insulin Receptor/Insulin 0.003 0.098 -10000 0 -0.32 7 7
HCK 0.027 0.008 -10000 0 0 47 47
CRK 0.027 0.007 -10000 0 0 36 36
TYK2 0 0.1 0.27 16 -0.35 6 22
EGF 0.017 0.027 -10000 0 -10000 0 0
YES1 0.027 0.008 -10000 0 0 40 40
CAV1 -0.031 0.1 0.22 2 -0.34 24 26
TXN 0.014 0.026 -10000 0 -0.059 1 1
PTP1B/IRS1/GRB2 -0.059 0.1 -10000 0 -0.31 25 25
cell migration 0.008 0.089 0.34 7 -10000 0 7
STAT3 0.015 0.024 -10000 0 -10000 0 0
PRLR 0.017 0.023 0.15 1 -10000 0 1
ITGA2B 0.008 0.028 -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 0.093 -10000 0 -0.33 7 7
Crk/p130 Cas 0.005 0.1 -10000 0 -0.33 7 7
DOK1 -0.017 0.087 0.28 1 -0.35 8 9
JAK2 -0.003 0.11 -10000 0 -0.37 31 31
Jak2/Leptin Receptor/Leptin -0.003 0.12 0.27 2 -0.35 12 14
PIK3R1 0.021 0.013 -10000 0 0 159 159
PTPN1 -0.008 0.09 -10000 0 -0.34 7 7
LYN 0.027 0.009 -10000 0 0 52 52
CDH2 0.019 0.014 -10000 0 0 187 187
SRC 0.009 0.092 -10000 0 -0.5 13 13
ITGB3 0.011 0.025 -10000 0 -0.045 1 1
CAT1/PTP1B -0.02 0.12 0.26 10 -0.41 14 24
CAPN1 0.001 0.03 -10000 0 -10000 0 0
CSK 0.028 0.006 -10000 0 0 21 21
PI3K -0.013 0.096 -10000 0 -0.32 8 8
mol:H2O2 0 0.003 0.019 2 -0.037 1 3
STAT3 (dimer) -0.017 0.11 0.32 2 -0.32 12 14
negative regulation of transcription -0.002 0.11 -10000 0 -0.37 31 31
FCGR2A 0.028 0.006 -10000 0 0 27 27
FER 0.014 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 0 100 100
Insulin Receptor/Insulin/Shc 0.035 0.057 -10000 0 -0.15 42 42
RHOA 0.001 0.03 -10000 0 -10000 0 0
LEPR 0.025 0.016 -10000 0 -0.03 38 38
BCAR1 0.026 0.009 -10000 0 0 56 56
p210 bcr-abl/Grb2 0.028 0.005 -10000 0 0 20 20
mol:NADPH -0.001 0.002 -10000 0 -0.031 1 1
TRPV6 -0.031 0.13 0.23 4 -0.38 30 34
PRL 0.018 0.023 0.15 1 -10000 0 1
SOCS3 0 0.15 0.66 2 -1.1 9 11
SPRY2 -0.011 0.023 -10000 0 -0.065 1 1
Insulin Receptor/Insulin/IRS1 -0.077 0.1 -10000 0 -0.16 337 337
CSF1/CSF1R 0.004 0.1 -10000 0 -0.33 8 8
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 0.013 0.027 -10000 0 -10000 0 0
LEP 0.013 0.026 -10000 0 -10000 0 0
STAT5B -0.009 0.11 0.19 1 -0.36 24 25
STAT5A -0.009 0.11 0.19 1 -0.36 23 24
GRB2 0.028 0.005 -10000 0 0 20 20
PDGFB-D/PDGFRB 0 0.095 -10000 0 -0.34 7 7
CSN2 0.007 0.076 0.63 1 -10000 0 1
PIK3CA 0.02 0.014 -10000 0 0 172 172
LAT 0.012 0.087 -10000 0 -0.47 14 14
YBX1 -0.001 0.033 -10000 0 -10000 0 0
LCK 0.028 0.006 -10000 0 0 26 26
SHC1 0.028 0.006 -10000 0 0 21 21
NOX4 -0.002 0.024 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.006 -10000 0 0 21 21
Syndecan-3/Src/Cortactin 0.027 0.095 -10000 0 -0.42 16 16
Syndecan-3/Neurocan 0.007 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 54 54
Syndecan-3/EGFR 0.007 0.091 -10000 0 -0.48 17 17
AGRP 0.026 0.009 -10000 0 0 55 55
NCSTN 0.028 0.005 -10000 0 0 18 18
PSENEN 0.025 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 69 69
APH1A 0.028 0.007 -10000 0 0 31 31
NCAN 0.027 0.008 -10000 0 0 51 51
long-term memory 0.006 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 -0.006 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 0.015 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 0.087 -10000 0 -0.45 17 17
IL8 0.024 0.011 -10000 0 0 94 94
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 0.021 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.043 0.077 -10000 0 -0.14 65 65
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.009 -10000 0 0 61 61
Caspase 8 (4 units) 0.025 0.06 -10000 0 -0.26 2 2
NEF -0.004 0.001 -10000 0 -10000 0 0
NFKBIA -0.031 0.039 0.17 15 -10000 0 15
BIRC3 -0.083 0.1 0.16 8 -0.31 80 88
CYCS -0.024 0.043 0.17 6 -0.25 2 8
RIPK1 0.027 0.007 -10000 0 0 38 38
CD247 -0.031 0.004 -10000 0 -10000 0 0
MAP2K7 -0.023 0.15 -10000 0 -0.62 26 26
protein ubiquitination -0.034 0.096 0.23 4 -0.3 32 36
CRADD 0.029 0.004 -10000 0 0 13 13
DAXX 0.028 0.005 -10000 0 0 17 17
FAS 0.027 0.008 -10000 0 0 43 43
BID -0.021 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 0.009 -10000 0 0 63 63
MAP3K5 0.028 0.007 -10000 0 0 32 32
CFLAR 0.029 0.004 -10000 0 0 10 10
FADD 0.028 0.005 -10000 0 0 19 19
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.011 0.097 -10000 0 -0.21 84 84
MAPK8 -0.029 0.14 -10000 0 -0.58 26 26
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 23 23
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.009 0.037 0.16 5 -0.25 1 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.034 0.11 0.2 12 -0.35 35 47
CHUK -0.036 0.1 0.23 4 -0.32 32 36
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.066 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 0.041 0.039 -10000 0 -0.14 15 15
CASP6 0.006 0.15 -10000 0 -0.52 36 36
CASP7 -0.075 0.16 0.38 15 -0.41 79 94
RELA -0.033 0.04 0.17 16 -0.11 1 17
CASP2 0.027 0.008 -10000 0 0 44 44
CASP3 -0.086 0.17 0.38 15 -0.42 85 100
TNFRSF1A 0.025 0.01 -10000 0 0 78 78
TNFR1A/BAG4 0.029 0.036 -10000 0 -0.16 15 15
CASP8 0.029 0.003 -10000 0 0 8 8
CASP9 0.029 0.004 -10000 0 0 13 13
MAP3K14 -0.037 0.1 0.23 2 -0.35 32 34
APAF-1/Caspase 9 -0.083 0.086 0.16 1 -0.27 59 60
BCL2 -0.045 0.13 -10000 0 -0.53 26 26
E-cadherin signaling in the nascent adherens junction

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 -0.047 0.1 -10000 0 -0.32 63 63
KLHL20 -0.058 0.077 0.48 1 -0.28 15 16
CYFIP2 0.028 0.006 -10000 0 0 24 24
Rac1/GDP -0.046 0.078 0.24 5 -0.25 21 26
ENAH -0.048 0.1 -10000 0 -0.32 65 65
AP1M1 0.026 0.01 -10000 0 0 67 67
RAP1B 0.028 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CTNNB1 0.028 0.007 -10000 0 -0.013 13 13
CDC42/GTP -0.059 0.05 0.12 21 -0.23 2 23
ABI1/Sra1/Nap1 -0.053 0.045 -10000 0 -0.17 33 33
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.047 -10000 0 -0.14 9 9
RAPGEF1 -0.047 0.098 0.24 4 -0.31 54 58
CTNND1 0.029 0.004 -10000 0 -0.005 6 6
regulation of calcium-dependent cell-cell adhesion -0.024 0.11 -10000 0 -0.32 67 67
CRK -0.047 0.1 -10000 0 -0.32 60 60
E-cadherin/gamma catenin/alpha catenin 0.043 0.044 -10000 0 -0.16 20 20
alphaE/beta7 Integrin 0.04 0.014 -10000 0 -0.16 1 1
IQGAP1 0.028 0.006 -10000 0 0 25 25
NCKAP1 0.028 0.005 -10000 0 0 17 17
Rap1/GTP/I-afadin 0.04 0.042 -10000 0 -0.13 21 21
DLG1 -0.033 0.1 0.19 1 -0.32 53 54
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.044 0.042 -10000 0 -0.16 8 8
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 0.07 0.13 60 -10000 0 60
PIK3R1 0.021 0.013 -10000 0 0 159 159
CDH1 0.025 0.011 -10000 0 -0.002 77 77
RhoA/GDP -0.045 0.077 0.24 4 -0.25 20 24
actin cytoskeleton organization -0.043 0.058 0.41 1 -0.23 5 6
CDC42/GDP -0.045 0.078 0.24 5 -0.25 19 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.015 0.058 -10000 0 -0.19 36 36
ITGB7 0.029 0.004 -10000 0 0 9 9
RAC1 0.028 0.007 -10000 0 -0.001 28 28
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.056 0.046 -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 0.24 5 -0.27 22 27
CDC42/GTP/IQGAP1 0.037 0.014 -10000 0 -0.13 2 2
JUP 0.027 0.008 -10000 0 0 42 42
p120 catenin/RhoA/GDP -0.048 0.081 0.23 5 -0.26 18 23
RAC1/GTP/IQGAP1 0.036 0.015 -10000 0 -0.13 2 2
PIP5K1C/AP1M1 0.036 0.016 -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 0.005 -10000 0 -0.002 12 12
positive regulation of S phase of mitotic cell cycle -0.045 0.056 0.12 1 -0.13 141 142
NME1 0.027 0.008 -10000 0 0 43 43
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.048 0.1 -10000 0 -0.32 67 67
regulation of cell-cell adhesion -0.055 0.041 0.083 20 -0.21 2 22
WASF2 -0.031 0.035 0.09 4 -0.1 30 34
Rap1/GTP -0.055 0.057 0.25 2 -0.25 2 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.063 -10000 0 -0.15 20 20
CCND1 -0.055 0.069 0.13 1 -0.16 141 142
VAV2 -0.039 0.16 -10000 0 -0.66 23 23
RAP1/GDP -0.047 0.065 0.25 3 -0.25 4 7
adherens junction assembly -0.047 0.1 -10000 0 -0.31 67 67
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 43 43
regulation of heterotypic cell-cell adhesion -0.06 0.03 0.17 4 -0.23 2 6
E-cadherin/beta catenin -0.022 0.046 -10000 0 -0.18 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.046 0.1 -10000 0 -0.32 61 61
PIK3CA 0.02 0.014 -10000 0 0 172 172
Rac1/GTP -0.089 0.11 0.57 1 -0.4 33 34
E-cadherin/beta catenin/alpha catenin 0.048 0.032 -10000 0 -0.15 9 9
ITGAE 0.028 0.007 -10000 0 0 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.024 0.12 -10000 0 -0.33 67 67
EPHB forward signaling

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
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 0.059 0.065 -10000 0 -0.14 26 26
ITSN1 0.029 0.004 -10000 0 0 9 9
PIK3CA 0.02 0.014 -10000 0 0 172 172
SHC1 0.028 0.006 -10000 0 0 21 21
Ephrin B1/EPHB3 0.031 0.017 -10000 0 -0.13 1 1
Ephrin B1/EPHB1 0.036 0.013 -10000 0 -0.13 1 1
HRAS/GDP -0.069 0.069 0.12 4 -0.22 38 42
Ephrin B/EPHB1/GRB7 0.062 0.061 -10000 0 -0.14 23 23
Endophilin/SYNJ1 -0.038 0.056 0.18 19 -10000 0 19
KRAS 0.024 0.011 -10000 0 0 99 99
Ephrin B/EPHB1/Src 0.062 0.059 -10000 0 -0.14 21 21
endothelial cell migration 0.006 0.067 -10000 0 -0.14 81 81
GRB2 0.028 0.005 -10000 0 0 20 20
GRB7 0.027 0.008 -10000 0 0 41 41
PAK1 -0.039 0.067 0.31 4 -10000 0 4
HRAS 0.028 0.006 -10000 0 0 27 27
RRAS -0.035 0.057 0.18 19 -0.22 3 22
DNM1 0.029 0.005 -10000 0 0 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.029 0.066 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 0 159 159
EPHB2 0.028 0.006 -10000 0 0 21 21
EPHB3 0.024 0.012 -10000 0 0 106 106
EPHB1 0.028 0.007 -10000 0 0 35 35
EPHB4 0.028 0.005 -10000 0 0 19 19
mol:GDP -0.046 0.078 0.22 5 -0.24 21 26
Ephrin B/EPHB2 0.053 0.05 -10000 0 -0.13 23 23
Ephrin B/EPHB3 0.044 0.051 -10000 0 -0.13 21 21
JNK cascade -0.013 0.099 0.28 37 -10000 0 37
Ephrin B/EPHB1 0.053 0.049 -10000 0 -0.13 21 21
RAP1/GDP -0.058 0.089 0.21 10 -0.27 9 19
EFNB2 0.026 0.009 -10000 0 0 57 57
EFNB3 0.028 0.007 -10000 0 0 30 30
EFNB1 0.029 0.004 -10000 0 0 9 9
Ephrin B2/EPHB1-2 0.041 0.039 -10000 0 -0.13 18 18
RAP1B 0.028 0.006 -10000 0 0 22 22
RAP1A 0.029 0.003 -10000 0 0 7 7
CDC42/GTP -0.049 0.063 0.14 30 -10000 0 30
Rap1/GTP -0.068 0.039 0.066 12 -10000 0 12
axon guidance 0.034 0.017 -10000 0 -0.13 3 3
MAPK3 -0.026 0.05 0.15 5 -0.25 5 10
MAPK1 -0.02 0.047 0.16 10 -0.22 1 11
Rac1/GDP -0.054 0.087 0.23 7 -0.26 11 18
actin cytoskeleton reorganization -0.036 0.05 -10000 0 -0.19 3 3
CDC42/GDP -0.055 0.088 0.22 8 -0.26 11 19
PI3K 0.022 0.078 -10000 0 -0.14 81 81
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 0.001 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 0.56 150 -10000 0 150
MAP4K4 -0.014 0.099 0.28 37 -10000 0 37
SRC 0.028 0.007 -10000 0 0 31 31
KALRN 0.028 0.006 -10000 0 0 23 23
Intersectin/N-WASP 0.041 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.044 0.085 0.26 20 -10000 0 20
MAP2K1 -0.017 0.048 0.16 5 -0.22 4 9
WASL 0.028 0.006 -10000 0 0 22 22
Ephrin B1/EPHB1-2/NCK1 0.073 0.033 -10000 0 -0.14 1 1
cell migration -0.022 0.073 0.24 5 -0.28 6 11
NRAS 0.014 0.015 -10000 0 0 300 300
SYNJ1 -0.039 0.056 0.18 19 -10000 0 19
PXN 0.029 0.005 -10000 0 0 14 14
TF -0.044 0.053 0.16 17 -10000 0 17
HRAS/GTP -0.052 0.052 0.12 40 -10000 0 40
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 3 -0.19 22 25
RAC1 0.028 0.006 -10000 0 0 27 27
mol:GTP -0.044 0.058 0.14 44 -10000 0 44
RAC1-CDC42/GTP -0.062 0.04 -10000 0 -10000 0 0
RASA1 0.027 0.008 -10000 0 0 49 49
RAC1-CDC42/GDP -0.059 0.088 0.22 9 -0.27 9 18
ruffle organization -0.049 0.079 0.27 11 -10000 0 11
NCK1 0.026 0.009 -10000 0 0 63 63
receptor internalization -0.046 0.054 0.16 19 -0.22 1 20
Ephrin B/EPHB2/KALRN 0.064 0.06 -10000 0 -0.14 23 23
ROCK1 0.006 0.082 0.17 107 -10000 0 107
RAS family/GDP -0.038 0.051 -10000 0 -0.2 9 9
Rac1/GTP -0.066 0.032 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0 0.053 -10000 0 -0.21 2 2
IL12-mediated signaling events

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.016 0.11 0.37 12 -0.3 10 22
TBX21 -0.11 0.27 0.8 8 -0.8 3 11
B2M 0.027 0.007 -10000 0 -10000 0 0
TYK2 -0.013 0.051 0.18 9 -10000 0 9
IL12RB1 -0.014 0.051 0.18 9 -10000 0 9
GADD45B -0.079 0.26 0.78 8 -0.73 12 20
IL12RB2 -0.016 0.055 0.19 11 -10000 0 11
GADD45G -0.074 0.26 0.72 7 -0.96 11 18
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 -0.012 0.027 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 -0.67 24 35
HLA-DRB5 0.017 0.025 0.082 16 -0.046 50 66
FASLG -0.1 0.27 0.82 7 -1 1 8
NF kappa B2 p52/RelB -0.098 0.26 0.59 6 -0.6 26 32
CD4 0.02 0.027 0.082 20 -0.047 55 75
SOCS1 0.028 0.007 -10000 0 0 31 31
EntrezGene:6955 0 0.015 0.06 25 -0.041 7 32
CD3D 0.02 0.027 0.092 18 -0.053 47 65
CD3E 0.022 0.027 0.083 18 -0.046 60 78
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 16 -1 1 17
CCL4 -0.1 0.27 0.78 10 -0.71 6 16
HLA-A 0.028 0.005 -10000 0 -10000 0 0
IL18/IL18R 0.015 0.068 0.43 4 -10000 0 4
NOS2 -0.082 0.25 0.77 10 -0.66 4 14
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.11 0.37 12 -0.3 5 17
IL1R1 -0.36 0.53 0.78 4 -1 198 202
IL4 0.027 0.051 -10000 0 -0.19 10 10
JAK2 -0.013 0.052 0.18 9 -10000 0 9
EntrezGene:6957 0 0.013 0.052 22 -0.037 5 27
TCR/CD3/MHC I/CD8 -0.012 0.08 -10000 0 -0.44 4 4
RAB7A -0.063 0.23 0.7 6 -0.69 5 11
lysosomal transport -0.059 0.23 0.7 6 -0.65 5 11
FOS -0.14 0.43 0.74 21 -1.1 72 93
STAT4 (dimer) -0.058 0.26 0.72 10 -0.69 7 17
STAT5A (dimer) -0.11 0.25 0.6 5 -0.6 24 29
GZMA -0.11 0.28 0.88 7 -0.93 3 10
GZMB -0.1 0.28 0.83 13 -1 1 14
HLX 0.028 0.006 -10000 0 0 22 22
LCK -0.12 0.27 0.72 9 -0.7 9 18
TCR/CD3/MHC II/CD4 -0.024 0.15 0.34 23 -0.38 51 74
IL2/IL2R 0.049 0.061 -10000 0 -0.14 28 28
MAPK14 -0.074 0.26 0.72 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 -0.026 0.14 0.47 9 -0.7 8 17
STAT4 0.028 0.005 -10000 0 0 17 17
STAT3 0.027 0.007 -10000 0 0 37 37
STAT1 0.013 0.015 -10000 0 0 316 316
NFKB1 0.027 0.008 -10000 0 0 45 45
NFKB2 0.029 0.005 -10000 0 0 15 15
IL12B -0.016 0.055 0.19 12 -10000 0 12
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 0.008 -10000 0 0 51 51
proteasomal ubiquitin-dependent protein catabolic process -0.052 0.25 0.7 11 -0.64 7 18
IL2RG 0.026 0.009 -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 34 34
CD247 0.023 0.027 0.084 19 -0.047 62 81
IL2 0.028 0.007 -10000 0 0 33 33
SPHK2 0.028 0.005 -10000 0 0 20 20
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 -0.79 6 14
MAP2K3 -0.085 0.27 0.72 9 -0.77 17 26
RIPK2 0.019 0.014 -10000 0 0 199 199
MAP2K6 -0.069 0.25 0.73 9 -0.76 10 19
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.027 0.093 22 -0.056 34 56
IL18RAP -0.011 0.033 0.11 4 -10000 0 4
IL12Rbeta1/TYK2 0.005 0.066 0.23 8 -10000 0 8
EOMES 0.007 0.073 -10000 0 -0.5 3 3
STAT1 (dimer) -0.051 0.22 0.64 11 -0.65 6 17
T cell proliferation -0.039 0.22 0.64 11 -0.55 6 17
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.011 0.033 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
HIF-1-alpha transcription factor network

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
PKM2 0.33 0.46 0.9 8 -0.92 3 11
HDAC7 -0.004 0.005 -10000 0 -0.078 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.024 0.29 0.7 49 -0.74 2 51
SMAD4 -0.029 0.007 -10000 0 -10000 0 0
ID2 0.33 0.46 0.9 4 -0.92 3 7
AP1 0.02 0.072 0.24 11 -0.17 60 71
ABCG2 0.28 0.46 0.91 3 -0.92 3 6
HIF1A 0.12 0.15 0.34 72 -10000 0 72
TFF3 0.029 0.37 0.9 6 -0.9 5 11
GATA2 0.031 0.029 0.21 12 -0.067 1 13
AKT1 0.15 0.18 0.41 97 -10000 0 97
response to hypoxia 0.082 0.16 0.34 119 -10000 0 119
MCL1 0.31 0.45 0.9 7 -0.92 3 10
NDRG1 0.2 0.42 0.91 2 -1 2 4
SERPINE1 0.24 0.44 0.91 3 -0.92 3 6
FECH 0.32 0.46 0.9 7 -0.92 3 10
FURIN 0.32 0.46 0.9 10 -0.88 4 14
NCOA2 0.027 0.008 -10000 0 -10000 0 0
EP300 0.23 0.3 0.69 110 -0.4 2 112
HMOX1 0.31 0.45 0.91 2 -0.92 3 5
BHLHE40 0.1 0.39 0.8 79 -0.91 3 82
BHLHE41 0.1 0.39 0.8 79 -0.91 3 82
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.19 0.41 83 -10000 0 83
ENG 0.12 0.18 0.47 2 -10000 0 2
JUN 0.029 0.017 0.13 11 -0.047 1 12
RORA 0.33 0.46 0.91 3 -0.92 3 6
ABCB1 -0.009 0.065 0.64 1 -10000 0 1
TFRC 0.12 0.38 0.9 4 -0.92 3 7
CXCR4 0.33 0.46 0.91 3 -0.92 3 6
TF 0.31 0.45 0.91 3 -0.92 3 6
CITED2 0.31 0.46 0.9 8 -0.92 4 12
HIF1A/ARNT -0.042 0.26 0.84 12 -1 3 15
LDHA 0.017 0.14 0.64 22 -0.71 3 25
ETS1 0.31 0.45 0.89 13 -0.92 3 16
PGK1 0.13 0.39 0.9 2 -0.92 3 5
NOS2 0.1 0.39 0.8 79 -0.91 3 82
ITGB2 0.32 0.46 0.9 4 -0.92 3 7
ALDOA 0.33 0.46 0.89 12 -0.92 3 15
Cbp/p300/CITED2 0.24 0.45 0.9 74 -0.98 3 77
FOS 0.026 0.021 0.14 13 -0.029 1 14
HK2 0.34 0.46 0.9 4 -0.92 3 7
SP1 -0.03 0.022 0.22 4 -10000 0 4
GCK 0.29 0.34 0.87 72 -10000 0 72
HK1 0.33 0.46 0.89 13 -0.92 3 16
NPM1 0.33 0.46 0.9 10 -0.92 3 13
EGLN1 0.32 0.45 0.88 20 -0.92 3 23
CREB1 0.083 0.1 0.27 126 -10000 0 126
PGM1 0.28 0.44 0.9 7 -0.92 3 10
SMAD3 -0.03 0.005 -10000 0 -10000 0 0
EDN1 0.19 0.26 0.82 30 -1.1 1 31
IGFBP1 0.33 0.46 0.91 3 -0.92 3 6
VEGFA 0.25 0.4 0.84 78 -0.67 1 79
HIF1A/JAB1 0.07 0.1 0.26 14 -10000 0 14
CP 0.06 0.35 0.9 8 -0.94 4 12
CXCL12 0.28 0.46 0.91 3 -0.95 3 6
COPS5 0.02 0.018 -10000 0 -0.029 51 51
SMAD3/SMAD4 0.037 0.017 -10000 0 -0.17 1 1
BNIP3 0.29 0.45 0.9 7 -0.92 3 10
EGLN3 0.28 0.45 0.9 4 -0.9 4 8
CA9 0.26 0.44 0.9 7 -0.92 3 10
TERT 0.28 0.45 0.9 4 -0.92 3 7
ENO1 0.33 0.46 0.9 10 -0.92 3 13
PFKL 0.32 0.46 0.91 1 -0.92 3 4
NCOA1 0.019 0.021 -10000 0 -0.029 86 86
ADM 0.26 0.44 0.91 3 -0.92 3 6
ARNT 0.12 0.15 0.33 93 -10000 0 93
HNF4A 0.027 0.007 -10000 0 -10000 0 0
ADFP 0.1 0.39 0.8 79 -0.91 3 82
SLC2A1 0.25 0.4 0.84 64 -0.67 1 65
LEP 0.32 0.45 0.9 7 -0.92 3 10
HIF1A/ARNT/Cbp/p300 0.015 0.29 0.72 44 -0.73 3 47
EPO 0.26 0.36 0.8 43 -0.71 2 45
CREBBP 0.24 0.29 0.68 115 -10000 0 115
HIF1A/ARNT/Cbp/p300/HDAC7 -0.004 0.25 0.67 33 -0.7 4 37
PFKFB3 0.3 0.46 0.89 12 -0.89 5 17
NT5E 0.24 0.44 0.88 24 -1 3 27
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.007 -10000 0 0 38 38
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 0.008 -10000 0 0 50 50
RAC1-CDC42/GTP/PAK family -0.032 0.066 -10000 0 -0.25 9 9
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 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 -0.048 0.093 -10000 0 -0.32 41 41
PRKG1 0.029 0.003 -10000 0 0 5 5
DUSP8 0.028 0.006 -10000 0 0 25 25
PGK/cGMP/p38 alpha -0.027 0.11 0.16 3 -0.36 31 34
apoptosis -0.047 0.089 -10000 0 -0.3 42 42
RAL/GTP 0.038 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 0.062 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 27 27
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 0.037 0.01 -10000 0 -10000 0 0
MAPK11 -0.05 0.12 0.2 3 -0.35 37 40
BLK 0.024 0.011 -10000 0 0 100 100
HCK 0.027 0.008 -10000 0 0 47 47
MAP2K3 0.027 0.008 -10000 0 0 44 44
DUSP16 0.026 0.009 -10000 0 0 58 58
DUSP10 0.027 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 0.19 3 -0.39 31 34
positive regulation of innate immune response -0.051 0.13 0.22 3 -0.42 36 39
LCK 0.028 0.006 -10000 0 0 26 26
p38alpha-beta/MKP7 -0.045 0.13 0.21 1 -0.41 32 33
p38alpha-beta/MKP5 -0.044 0.13 0.24 2 -0.41 34 36
PGK/cGMP 0.022 0.002 -10000 0 -10000 0 0
PAK2 0.024 0.011 -10000 0 0 93 93
p38alpha-beta/MKP1 -0.054 0.14 0.24 2 -0.4 42 44
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 0.02 0.013 -10000 0 0 169 169
ErbB2/ErbB3 signaling events

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
USP8 -0.021 0.026 0.18 8 -10000 0 8
RAS family/GTP 0.029 0.11 0.36 34 -0.23 3 37
NFATC4 -0.024 0.088 0.24 28 -10000 0 28
ERBB2IP 0.011 0.028 -10000 0 -0.048 7 7
HSP90 (dimer) 0.028 0.005 -10000 0 0 20 20
mammary gland morphogenesis -0.02 0.1 0.3 27 -10000 0 27
JUN 0.033 0.14 0.43 45 -10000 0 45
HRAS 0.023 0.02 0.064 4 -0.031 59 63
DOCK7 -0.023 0.089 0.26 20 -10000 0 20
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.015 0.078 0.19 30 -10000 0 30
AKT1 -0.015 0.009 0.013 33 -10000 0 33
BAD -0.025 0.007 -10000 0 -10000 0 0
MAPK10 -0.017 0.075 0.19 32 -10000 0 32
mol:GTP 0.001 0.004 0.018 19 -10000 0 19
ErbB2/ErbB3/neuregulin 1 beta -0.02 0.11 0.32 27 -10000 0 27
RAF1 0.092 0.17 0.39 83 -10000 0 83
ErbB2/ErbB3/neuregulin 2 -0.02 0.064 0.16 33 -0.15 1 34
STAT3 -0.027 0.23 -10000 0 -0.87 37 37
cell migration -0.014 0.077 0.23 22 -10000 0 22
mol:PI-3-4-5-P3 -0.001 0.002 0.013 2 -10000 0 2
cell proliferation 0.067 0.25 0.68 48 -0.61 5 53
FOS 0.045 0.27 0.67 53 -0.42 53 106
NRAS 0.012 0.017 -10000 0 -0.031 21 21
mol:Ca2+ -0.02 0.1 0.3 27 -10000 0 27
MAPK3 0.071 0.23 0.65 43 -0.54 4 47
MAPK1 0.065 0.23 0.62 46 -0.61 6 52
JAK2 -0.024 0.088 0.26 19 -10000 0 19
NF2 -0.001 0.064 -10000 0 -0.64 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.001 0.061 0.17 14 -0.19 26 40
NRG1 -0.006 0.03 0.07 8 -10000 0 8
GRB2/SOS1 0.04 0.014 -10000 0 -10000 0 0
MAPK8 -0.019 0.1 0.32 13 -0.24 18 31
MAPK9 -0.016 0.076 0.19 37 -10000 0 37
ERBB2 -0.027 0.02 0.26 1 -10000 0 1
ERBB3 -0.007 0.03 0.072 7 -10000 0 7
SHC1 0.023 0.019 0.063 6 -0.03 56 62
RAC1 0.028 0.006 -10000 0 0 27 27
apoptosis 0.017 0.01 -10000 0 -10000 0 0
STAT3 (dimer) -0.025 0.22 -10000 0 -0.85 37 37
RNF41 -0.028 0.026 0.15 9 -10000 0 9
FRAP1 -0.012 0.005 0.003 43 -10000 0 43
RAC1-CDC42/GTP -0.036 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 -0.017 0.098 0.25 38 -10000 0 38
PPP3CB -0.024 0.087 0.25 20 -10000 0 20
KRAS 0.02 0.02 0.062 3 -0.031 47 50
RAC1-CDC42/GDP 0.018 0.081 0.19 5 -0.19 26 31
NRG2 0.029 0.003 -10000 0 0 7 7
mol:GDP -0.001 0.061 0.17 14 -0.19 26 40
SOS1 0.022 0.019 0.061 2 -0.03 57 59
MAP2K2 0.062 0.17 0.41 67 -10000 0 67
SRC 0.028 0.007 -10000 0 0 31 31
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.027 0.086 0.24 19 -10000 0 19
MAP2K1 0.085 0.22 0.62 46 -0.6 5 51
heart morphogenesis -0.02 0.1 0.3 27 -10000 0 27
RAS family/GDP 0.048 0.09 0.32 18 -0.23 3 21
GRB2 0.023 0.019 0.061 2 -0.03 60 62
PRKACA 0.005 0.065 -10000 0 -0.67 5 5
CHRNE 0.011 0.057 0.18 37 -10000 0 37
HSP90AA1 0.028 0.005 -10000 0 0 20 20
activation of caspase activity 0.015 0.009 -10000 0 -0.013 33 33
nervous system development -0.02 0.1 0.3 27 -10000 0 27
CDC42 0.029 0.004 -10000 0 0 11 11
Caspase cascade in apoptosis

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
TOP1 0.01 0.1 0.28 5 -0.38 20 25
ACTA1 -0.005 0.082 0.23 11 -0.25 8 19
NUMA1 0.012 0.1 0.28 5 -0.37 22 27
SPTAN1 -0.007 0.079 0.24 8 -0.25 7 15
LIMK1 -0.004 0.082 0.25 11 -0.25 7 18
BIRC3 0.023 0.013 -10000 0 -0.001 125 125
BIRC2 0.02 0.014 -10000 0 -0.03 7 7
BAX 0.028 0.006 -10000 0 0 21 21
CASP10 -0.029 0.052 0.17 29 -0.15 12 41
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 0.001 4 -0.001 44 48
PTK2 -0.001 0.11 0.28 5 -0.37 28 33
DIABLO 0.018 0.016 -10000 0 -0.002 205 205
apoptotic nuclear changes -0.007 0.078 0.24 8 -0.24 7 15
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 0.27 6 -0.25 11 17
MADD 0.029 0.003 -10000 0 0 8 8
TFAP2A 0.026 0.12 -10000 0 -0.8 9 9
BID -0.015 0.043 0.11 27 -0.14 28 55
MAP3K1 -0.02 0.12 -10000 0 -0.39 49 49
TRADD 0.026 0.009 -10000 0 0 63 63
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.005 0.1 0.27 31 -0.25 6 37
CASP9 0.026 0.013 -10000 0 -0.029 28 28
DNA repair -0.025 0.062 0.22 4 -0.18 22 26
neuron apoptosis -0.006 0.15 -10000 0 -0.72 21 21
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.098 0.28 5 -0.34 18 23
APAF1 0.024 0.015 -10000 0 -0.016 62 62
CASP6 -0.018 0.24 -10000 0 -0.89 35 35
TRAF2 0.028 0.006 -10000 0 0 23 23
ICAD/CAD -0.013 0.078 0.26 8 -0.25 6 14
CASP7 0.028 0.096 0.21 25 -0.27 17 42
KRT18 0.015 0.068 -10000 0 -0.66 3 3
apoptosis -0.013 0.14 0.33 10 -0.44 29 39
DFFA -0.005 0.079 0.26 7 -0.25 6 13
DFFB -0.004 0.079 0.25 7 -0.25 6 13
PARP1 0.025 0.063 0.18 22 -0.23 4 26
actin filament polymerization 0.012 0.08 0.24 6 -0.28 8 14
TNF 0.029 0.005 -10000 0 0 15 15
CYCS -0.009 0.053 0.15 8 -0.22 15 23
SATB1 -0.055 0.22 -10000 0 -0.87 35 35
SLK -0.006 0.081 0.29 8 -0.25 7 15
p15 BID/BAX -0.021 0.049 0.12 16 -0.2 5 21
CASP2 -0.028 0.087 0.18 17 -0.27 36 53
JNK cascade 0.02 0.12 0.39 49 -10000 0 49
CASP3 0.004 0.084 0.29 6 -0.25 7 13
LMNB2 -0.028 0.18 0.24 12 -0.48 58 70
RIPK1 0.027 0.007 -10000 0 0 38 38
CASP4 0.027 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 0.026 0.12 -10000 0 -0.78 9 9
stress fiber formation -0.005 0.081 0.29 8 -0.24 7 15
GZMB -0.021 0.047 0.19 25 -10000 0 25
CASP1 -0.02 0.085 -10000 0 -0.26 55 55
LMNB1 0.013 0.14 0.27 9 -0.43 31 40
APP -0.006 0.15 -10000 0 -0.73 21 21
TNFRSF1A 0.025 0.01 -10000 0 0 78 78
response to stress 0 0 0.001 12 -0.001 8 20
CASP8 -0.017 0.002 0 8 -10000 0 8
VIM -0.004 0.14 0.3 12 -0.44 31 43
LMNA -0.003 0.12 0.27 6 -0.41 31 37
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.023 0.088 -10000 0 -0.27 40 40
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.007 0.078 0.26 6 -0.25 6 12
APAF-1/Caspase 9 -0.032 0.17 -10000 0 -0.59 12 12
nuclear fragmentation during apoptosis 0.012 0.1 0.28 5 -0.37 22 27
CFL2 -0.013 0.08 0.28 8 -0.25 6 14
GAS2 -0.003 0.085 0.27 14 -0.25 6 20
positive regulation of apoptosis -0.002 0.15 0.25 13 -0.46 38 51
PRF1 0.026 0.013 -10000 0 -0.014 45 45
ceramide signaling pathway

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
MAP4K4 -0.05 0.13 0.24 2 -0.4 42 44
BAG4 0.026 0.009 -10000 0 0 61 61
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 0.012 -10000 0 -0.029 2 2
BAX -0.027 0.046 0.18 4 -0.16 24 28
EnzymeConsortium:3.1.4.12 -0.012 0.03 0.068 1 -0.089 41 42
IKBKB -0.049 0.13 0.26 5 -0.39 40 45
MAP2K2 -0.047 0.051 0.15 5 -0.2 13 18
MAP2K1 -0.04 0.046 0.14 5 -0.19 9 14
SMPD1 -0.017 0.037 -10000 0 -0.13 27 27
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.044 0.13 0.22 5 -0.39 41 46
MAP2K4 -0.034 0.04 -10000 0 -0.18 15 15
protein ubiquitination -0.051 0.12 0.27 2 -0.39 41 43
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 17 23
CRADD 0.02 0.02 -10000 0 -0.029 78 78
mol:ceramide -0.02 0.045 -10000 0 -0.15 34 34
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.027 -10000 0 -0.13 13 13
MADD 0.02 0.021 -10000 0 -0.029 82 82
MAP3K1 -0.027 0.043 -10000 0 -0.16 25 25
TRADD 0.019 0.02 -10000 0 -0.029 68 68
RELA/p50 0.029 0.003 -10000 0 0 6 6
MAPK3 -0.046 0.052 0.17 1 -0.2 17 18
MAPK1 -0.048 0.056 0.17 1 -0.22 23 24
p50/RELA/I-kappa-B-alpha 0.037 0.032 -10000 0 -0.16 13 13
FADD -0.048 0.13 0.23 5 -0.39 42 47
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 0.027 0.011 -10000 0 -0.029 15 15
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.052 0.12 0.23 2 -0.38 42 44
TNF R/SODD 0.029 0.036 -10000 0 -0.16 15 15
TNF 0.02 0.02 -10000 0 -0.029 79 79
CYCS -0.015 0.054 0.14 8 -0.16 15 23
IKBKG -0.051 0.12 0.23 7 -0.37 42 49
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.04 0.13 -10000 0 -0.39 47 47
RELA 0.029 0.003 -10000 0 0 6 6
RIPK1 0.026 0.011 -10000 0 -0.029 13 13
AIFM1 -0.011 0.055 0.13 13 -0.16 12 25
TNF/TNF R/SODD 0.041 0.039 -10000 0 -0.14 15 15
TNFRSF1A 0.024 0.013 -10000 0 -0.029 13 13
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 39 47
response to hydrogen peroxide 0 0 -10000 0 -0.002 4 4
BCL2 0.023 0.012 -10000 0 0 122 122
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.044 0.043 -9999 0 -0.16 19 19
E-cadherin/beta catenin 0.035 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 42 42
CDH1 0.026 0.01 -9999 0 0 71 71
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.006 0.078 0.38 3 -0.63 1 4
epithelial cell differentiation -0.022 0.067 0.24 1 -0.63 1 2
ITCH -0.008 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 54 54
PRL 0.027 0.007 -10000 0 0 39 39
neuron projection morphogenesis -0.032 0.083 0.28 10 -0.51 1 11
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 0.037 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 -0.028 0.092 0.41 1 -0.4 4 5
NCOR1 0.027 0.008 -10000 0 0 40 40
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.024 0.075 0.29 1 -0.56 1 2
GRIN2B -0.029 0.073 0.25 4 -0.54 1 5
ErbB4/ErbB2/betacellulin -0.009 0.073 0.35 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 0.037 0.016 -10000 0 -10000 0 0
CBFA2T3 0.026 0.009 -10000 0 0 64 64
ErbB4/ErbB2/HBEGF -0.009 0.075 0.35 3 -0.56 1 4
MAPK3 -0.023 0.088 0.28 12 -0.52 1 13
STAT1 (dimer) -0.001 0.049 -10000 0 -0.48 1 1
MAPK1 -0.021 0.084 0.29 10 -0.52 1 11
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 79 -10000 0 79
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 45 45
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 0.007 0.078 0.18 89 -10000 0 89
WWOX/E4ICDs 0.004 0.074 0.36 2 -0.63 1 3
SHC1 0.028 0.006 -10000 0 0 21 21
ErbB4/EGFR/neuregulin 4 0.003 0.089 0.35 3 -0.61 1 4
apoptosis 0.18 0.17 0.38 91 -0.43 1 92
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 0.35 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 0.029 0.088 0.38 1 -0.58 1 2
MDM2 -0.014 0.075 0.36 4 -0.63 1 5
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 0.063 0.38 3 -0.68 1 4
ErbB4/EGFR/neuregulin 1 beta -0.019 0.074 0.32 2 -0.56 1 3
DLG4 0.028 0.006 -10000 0 0 22 22
GRB2/SHC 0.04 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.002 0.068 0.26 1 -0.6 1 2
STAT5A (dimer) 0.012 0.079 0.35 1 -0.69 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.013 0.072 0.38 3 -0.68 1 4
LRIG1 0.028 0.007 -10000 0 0 32 32
EREG 0.027 0.007 -10000 0 0 39 39
BTC 0.027 0.008 -10000 0 0 46 46
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.061 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 33 33
YAP1 0.013 0.05 -10000 0 -0.48 4 4
GRB2 0.028 0.005 -10000 0 0 20 20
ErbB4/ErbB2/neuregulin 4 -0.01 0.077 0.35 3 -0.56 1 4
glial cell differentiation -0.002 0.068 0.59 1 -0.26 1 2
WWOX 0.026 0.009 -10000 0 0 64 64
cell proliferation -0.01 0.078 0.3 4 -0.57 1 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.032 -10000 0 -0.16 11 11
CRKL -0.006 0.11 -10000 0 -0.46 21 21
mol:PIP3 0.013 0.075 -10000 0 -0.83 4 4
AKT1 -0.004 0.072 -10000 0 -0.7 4 4
PTK2B 0.024 0.011 -10000 0 0 98 98
RAPGEF1 -0.014 0.1 -10000 0 -0.44 20 20
RANBP10 0.026 0.009 -10000 0 0 58 58
PIK3CA 0.02 0.014 -10000 0 0 172 172
HGF/MET/SHIP2 0.045 0.035 -10000 0 -0.14 11 11
MAP3K5 -0.007 0.11 0.25 1 -0.45 21 22
HGF/MET/CIN85/CBL/ENDOPHILINS 0.068 0.047 -10000 0 -0.14 12 12
AP1 -0.021 0.071 0.14 32 -0.16 46 78
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.006 -10000 0 0 21 21
apoptosis -0.069 0.27 -10000 0 -0.71 82 82
STAT3 (dimer) -0.001 0.078 0.17 11 -0.26 17 28
GAB1/CRKL/SHP2/PI3K -0.009 0.11 -10000 0 -0.44 20 20
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.01 0.11 0.3 2 -0.44 20 22
PTPN11 0.029 0.003 -10000 0 0 8 8
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 0.049 0.15 4 -0.22 7 11
PAK1 0.002 0.087 0.38 1 -0.68 4 5
HGF/MET/RANBP10 0.041 0.037 -10000 0 -0.15 12 12
HRAS 0.004 0.1 -10000 0 -0.47 22 22
DOCK1 -0.012 0.1 0.34 2 -0.44 21 23
GAB1 0.002 0.11 -10000 0 -0.46 22 22
CRK -0.003 0.11 0.28 3 -0.45 21 24
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.095 -10000 0 -0.41 21 21
JUN 0.028 0.007 -10000 0 0 34 34
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0 0.033 0.092 3 -0.18 14 17
PIK3R1 0.021 0.013 -10000 0 0 159 159
cell morphogenesis 0.001 0.13 0.29 16 -0.37 15 31
GRB2/SHC 0.04 0.052 0.2 3 -0.18 13 16
FOS 0.024 0.011 -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 0.039 0.051 0.19 3 -0.18 13 16
GRB2 0.028 0.005 -10000 0 0 20 20
CBL 0.029 0.005 -10000 0 0 14 14
MET/RANBP10 0.029 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 -0.017 0.099 0.25 1 -0.43 19 20
RAP1A -0.022 0.097 0.33 1 -0.43 20 21
HGF/MET/RANBP9 0.044 0.036 -10000 0 -0.14 11 11
RAF1 -0.002 0.1 -10000 0 -0.45 22 22
STAT3 -0.002 0.077 0.17 11 -0.26 17 28
cell proliferation -0.007 0.095 0.28 9 -0.35 14 23
RPS6KB1 0.019 0.047 -10000 0 -0.24 8 8
MAPK3 0.025 0.16 0.64 28 -10000 0 28
MAPK1 0.041 0.19 0.65 41 -10000 0 41
RANBP9 0.027 0.007 -10000 0 0 39 39
MAPK8 -0.01 0.1 0.25 1 -0.43 18 19
SRC -0.021 0.054 0.18 1 -0.26 8 9
PI3K 0.007 0.066 0.21 1 -0.18 19 20
MET/Glomulin 0.027 0.034 0.12 1 -0.072 21 22
SOS1 0.028 0.007 -10000 0 0 35 35
MAP2K1 -0.01 0.095 -10000 0 -0.42 22 22
MET 0.025 0.011 -10000 0 0 87 87
MAP4K1 0 0.11 0.27 1 -0.48 21 22
PTK2 0.021 0.013 -10000 0 0 164 164
MAP2K2 -0.021 0.097 0.27 1 -0.44 21 22
BAD -0.013 0.069 -10000 0 -0.68 4 4
MAP2K4 -0.014 0.099 -10000 0 -0.42 21 21
SHP2/GRB2/SOS1/GAB1 0.015 0.1 -10000 0 -0.38 25 25
INPPL1 0.028 0.006 -10000 0 0 21 21
PXN 0.029 0.005 -10000 0 0 14 14
SH3KBP1 0.028 0.005 -10000 0 0 17 17
HGS -0.009 0.042 0.17 1 -0.18 14 15
PLCgamma1/PKC 0.021 0.005 -10000 0 -10000 0 0
HGF 0.028 0.005 -10000 0 0 17 17
RASA1 0.027 0.008 -10000 0 0 49 49
NCK1 0.026 0.009 -10000 0 0 63 63
PTPRJ 0.029 0.003 -10000 0 0 8 8
NCK/PLCgamma1 0.038 0.05 0.2 3 -0.18 14 17
PDPK1 0.002 0.068 -10000 0 -0.73 4 4
HGF/MET/SHIP 0.03 0.028 -10000 0 -0.13 12 12
Glypican 1 network

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
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 0 109 109
PRNP 0.027 0.008 -10000 0 0 44 44
GPC1/SLIT2 0.021 0.058 -10000 0 -0.16 48 48
SMAD2 -0.043 0.026 0.17 6 -10000 0 6
GPC1/PrPc/Cu2+ 0.033 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 0.008 -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 -0.036 0.012 -10000 0 -10000 0 0
FLT1 0.028 0.006 -10000 0 0 28 28
GPC1/TGFB/TGFBR1/TGFBR2 0.053 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 -0.038 0.009 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.027 0.075 0.24 8 -0.27 12 20
SLIT2 0.025 0.011 -10000 0 0 89 89
GPC1/NRG 0.036 0.016 -10000 0 -10000 0 0
NRG1 0.025 0.01 -10000 0 0 78 78
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.023 -10000 0 -10000 0 0
LYN -0.035 0.013 -10000 0 -10000 0 0
mol:Spermine -0.017 0.003 -10000 0 -10000 0 0
cell growth 0.04 0.047 -10000 0 -0.15 26 26
BMP signaling pathway -0.028 0.005 0 17 -10000 0 17
SRC -0.036 0.011 -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 0.028 0.005 -10000 0 0 17 17
TGFBR1 (dimer) 0.028 0.005 -10000 0 0 16 16
VEGFA 0.026 0.01 -10000 0 0 71 71
BLK -0.032 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 43 43
FGFR1 0.025 0.01 -10000 0 0 74 74
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 0.041 0.01 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.043 0.1 -10000 0 -0.16 227 227
LCK -0.037 0.011 -10000 0 -10000 0 0
neuron differentiation 0.036 0.016 -10000 0 -10000 0 0
PrPc/Cu2+ 0.018 0.022 -10000 0 -0.15 9 9
APP 0.028 0.006 -10000 0 0 27 27
TGFBR2 (dimer) 0.029 0.005 -10000 0 0 14 14
Syndecan-2-mediated 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
Syndecan-2/Fibronectin -0.02 0.03 0.16 2 -0.24 1 3
EPHB2 0.028 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 0 109 109
Syndecan-2/alpha2 ITGB1 0.022 0.064 -10000 0 -0.14 57 57
HRAS 0.028 0.006 -10000 0 0 27 27
Syndecan-2/CASK -0.015 0.017 -10000 0 -0.12 13 13
ITGA5 0.028 0.005 -10000 0 0 20 20
BAX -0.027 0.027 -10000 0 -10000 0 0
EPB41 0.027 0.007 -10000 0 0 37 37
positive regulation of cell-cell adhesion -0.023 0.018 -10000 0 -0.12 14 14
LAMA3 0.025 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 -0.034 0.045 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 0.026 0.031 0.15 3 -0.12 13 16
NF1 0.026 0.009 -10000 0 0 61 61
FGFR/FGF/Syndecan-2 -0.015 0.006 -10000 0 -10000 0 0
ITGA2 0.026 0.009 -10000 0 0 60 60
MAPK8 -0.022 0.024 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.027 0.049 -10000 0 -0.14 26 26
Syndecan-2/Kininogen -0.022 0.025 0.16 3 -10000 0 3
ITGB1 0.028 0.006 -10000 0 0 22 22
SRC -0.019 0.066 0.17 55 -10000 0 55
Syndecan-2/CASK/Protein 4.1 -0.022 0.017 -10000 0 -0.12 11 11
extracellular matrix organization -0.039 0.047 0.16 4 -0.24 5 9
actin cytoskeleton reorganization -0.02 0.03 0.16 2 -0.24 1 3
Syndecan-2/Caveolin-2/Ras 0.025 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 0.16 3 -0.13 15 18
alpha5/beta1 Integrin 0.04 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 0.027 0.007 -10000 0 0 36 36
TNFRSF13B 0.027 0.007 -10000 0 0 37 37
RASA1 0.027 0.008 -10000 0 0 49 49
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 0.023 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 0 213 213
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 89 89
Syndecan-2/Neurofibromin -0.025 0.026 0.16 2 -10000 0 2
TRAPPC4 0.027 0.008 -10000 0 0 49 49
CSF2 0.028 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 -0.12 1 1
Syndecan-2/Ezrin -0.024 0.017 -10000 0 -0.12 13 13
PRKACA -0.013 0.061 0.18 45 -10000 0 45
angiogenesis -0.021 0.025 0.16 4 -10000 0 4
MMP2 0.022 0.013 -10000 0 0 134 134
IL8 0.024 0.011 -10000 0 0 94 94
calcineurin-NFAT signaling pathway -0.025 0.024 0.16 3 -10000 0 3
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.032 0.11 0.24 3 -0.38 28 31
IKBKB 0.006 0.079 0.28 6 -0.31 7 13
AKT1 -0.001 0.099 0.26 36 -0.23 4 40
IKBKG 0.004 0.065 0.28 2 -0.26 7 9
CALM1 -0.01 0.064 -10000 0 -0.29 8 8
PIK3CA 0.02 0.014 -10000 0 0 172 172
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 0.22 5 -0.22 20 25
LYN 0.027 0.009 -10000 0 0 52 52
BLNK 0.028 0.007 -10000 0 0 31 31
SHC1 0.028 0.006 -10000 0 0 21 21
BCR complex 0.04 0.012 -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 0.027 0.008 -10000 0 0 40 40
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.063 0.037 -10000 0 -0.23 2 2
GO:0007205 -0.004 0.071 0.2 1 -0.29 12 13
SYK 0.028 0.006 -10000 0 0 23 23
ELK1 -0.008 0.077 0.28 5 -0.28 12 17
NFATC1 -0.029 0.09 0.25 3 -0.37 15 18
B-cell antigen/BCR complex 0.04 0.012 -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 31 33
HRAS -0.017 0.069 0.18 3 -0.29 13 16
NFKBIA 0.01 0.046 0.16 2 -0.13 24 26
NF-kappa-B/RelA/I kappa B beta 0.013 0.042 0.13 6 -0.11 23 29
RasGAP/Csk 0.068 0.052 -10000 0 -0.14 4 4
mol:GDP -0.005 0.069 0.19 1 -0.28 12 13
PTEN 0.028 0.007 -10000 0 0 31 31
CD79B 0.028 0.006 -10000 0 -0.004 16 16
NF-kappa-B/RelA/I kappa B alpha 0.013 0.042 0.12 8 -0.1 18 26
GRB2 0.028 0.005 -10000 0 0 20 20
PI3K/BCAP/CD19 -0.07 0.15 0.3 1 -0.42 32 33
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.004 0.071 0.2 1 -0.28 13 14
CSK 0.028 0.006 -10000 0 0 21 21
FOS -0.017 0.084 0.24 7 -0.28 15 22
CHUK 0.001 0.082 0.28 2 -0.31 16 18
IBTK 0.028 0.007 -10000 0 0 30 30
CARD11/BCL10/MALT1/TAK1 0.01 0.082 0.21 1 -0.28 8 9
PTPN6 -0.037 0.085 0.21 4 -0.3 22 26
RELA 0.029 0.003 -10000 0 0 6 6
BCL2A1 0.007 0.031 0.1 5 -0.11 3 8
VAV2 -0.019 0.097 0.25 2 -0.38 18 20
ubiquitin-dependent protein catabolic process 0.009 0.047 0.14 3 -0.12 46 49
BTK 0.018 0.044 -10000 0 -0.98 1 1
CD19 -0.015 0.08 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 44 44
MAPK14 -0.027 0.13 0.28 5 -0.4 33 38
SH3BP5 0.029 0.004 -10000 0 0 12 12
PIK3AP1 -0.008 0.07 0.25 3 -0.29 11 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.001 0.088 -10000 0 -0.37 19 19
RAF1 -0.024 0.067 0.24 2 -0.28 13 15
RasGAP/p62DOK/SHIP 0.056 0.046 -10000 0 -0.14 6 6
CD79A 0.027 0.007 -10000 0 0 36 36
re-entry into mitotic cell cycle -0.022 0.073 0.22 5 -0.22 19 24
RASA1 0.027 0.008 -10000 0 0 49 49
MAPK3 -0.038 0.062 0.25 3 -0.27 11 14
MAPK1 -0.033 0.065 0.25 4 -0.27 10 14
CD72/SHP1 -0.023 0.11 0.26 21 -0.32 16 37
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.029 0.12 0.29 2 -0.41 31 33
actin cytoskeleton organization -0.022 0.093 0.26 5 -0.35 17 22
NF-kappa-B/RelA 0.022 0.087 0.26 3 -0.26 10 13
Calcineurin 0.008 0.082 -10000 0 -0.27 10 10
PI3K -0.054 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 35 35
Bam32/HPK1 -0.019 0.21 -10000 0 -0.69 40 40
DAPP1 -0.036 0.23 -10000 0 -0.79 39 39
cytokine secretion -0.027 0.086 0.25 3 -0.35 15 18
mol:DAG -0.004 0.071 0.2 1 -0.28 13 14
PLCG2 0.026 0.009 -10000 0 0 63 63
MAP2K1 -0.03 0.065 0.25 2 -0.28 12 14
B-cell antigen/BCR complex/FcgammaRIIB 0.05 0.024 -10000 0 -0.15 1 1
mol:PI-3-4-5-P3 -0.011 0.11 0.25 36 -0.26 7 43
ETS1 -0.021 0.072 0.23 2 -0.28 8 10
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.061 0.061 -10000 0 -0.15 24 24
B-cell antigen/BCR complex/LYN 0.005 0.083 0.21 1 -0.31 19 20
MALT1 0.025 0.01 -10000 0 0 75 75
TRAF6 0.028 0.006 -10000 0 -0.029 3 3
RAC1 -0.024 0.093 0.23 4 -0.37 15 19
B-cell antigen/BCR complex/LYN/SYK -0.006 0.12 0.33 5 -0.3 13 18
CARD11 -0.013 0.069 0.19 3 -0.28 12 15
FCGR2B 0.027 0.008 -10000 0 0 47 47
PPP3CA 0.027 0.008 -10000 0 0 43 43
BCL10 0.029 0.004 -10000 0 0 10 10
IKK complex 0.011 0.045 0.15 22 -0.12 5 27
PTPRC 0.024 0.011 -10000 0 0 102 102
PDPK1 -0.007 0.094 0.23 40 -0.19 7 47
PPP3CB 0.029 0.004 -10000 0 0 13 13
PPP3CC 0.024 0.011 -10000 0 0 101 101
POU2F2 0.007 0.03 0.15 4 -0.12 2 6
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.027 0.095 0.18 1 -0.28 22 23
adherens junction organization -0.03 0.097 -10000 0 -0.36 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.028 0.1 0.22 5 -0.26 10 15
FMN1 -0.031 0.092 -10000 0 -0.32 31 31
mol:IP3 -0.031 0.071 0.12 45 -0.22 16 61
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.022 0.098 0.15 1 -0.28 44 45
CTNNB1 0.001 0.032 0.046 10 -10000 0 10
AKT1 -0.035 0.076 0.19 2 -0.22 30 32
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.02 0.099 -10000 0 -0.31 32 32
CTNND1 -0.008 0.031 0.044 7 -10000 0 7
mol:PI-4-5-P2 -0.028 0.091 0.22 4 -0.3 32 36
VASP -0.031 0.091 -10000 0 -0.28 43 43
ZYX -0.039 0.095 -10000 0 -0.31 39 39
JUB -0.022 0.092 0.14 1 -0.27 44 45
EGFR(dimer) -0.013 0.1 -10000 0 -0.3 37 37
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 -0.23 33 34
PIK3CA -0.017 0.02 -10000 0 -10000 0 0
PI3K -0.018 0.081 0.21 1 -0.23 33 34
FYN -0.048 0.12 0.16 3 -0.3 71 74
mol:Ca2+ -0.03 0.07 0.12 45 -0.21 16 61
JUP -0.002 0.03 0.048 1 -10000 0 1
PIK3R1 -0.002 0.027 -10000 0 -10000 0 0
mol:DAG -0.031 0.071 0.12 45 -0.22 16 61
CDH1 -0.004 0.029 -10000 0 -10000 0 0
RhoA/GDP -0.027 0.1 0.22 5 -0.26 10 15
establishment of polarity of embryonic epithelium -0.031 0.09 -10000 0 -0.3 32 32
SRC 0.028 0.007 -10000 0 0 31 31
RAC1 0.028 0.006 -10000 0 0 27 27
RHOA 0.029 0.003 -10000 0 0 6 6
EGFR 0.027 0.009 -10000 0 0 54 54
CASR -0.024 0.083 0.18 2 -0.23 12 14
RhoA/GTP -0.021 0.087 0.18 2 -0.23 11 13
AKT2 -0.036 0.078 0.19 2 -0.23 32 34
actin cable formation -0.038 0.089 0.18 6 -0.35 22 28
apoptosis 0.021 0.096 0.25 31 -0.2 5 36
CTNNA1 -0.008 0.031 0.044 6 -10000 0 6
mol:GDP -0.03 0.09 0.18 2 -0.25 15 17
PIP5K1A -0.029 0.091 0.17 6 -0.28 43 49
PLCG1 -0.031 0.072 0.18 1 -0.22 16 17
Rac1/GTP -0.012 0.11 -10000 0 -0.29 36 36
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.005 -10000 0 0 19 19
VLDLR 0.026 0.009 -10000 0 0 60 60
LRPAP1 0.028 0.007 -10000 0 0 33 33
NUDC 0.028 0.005 -10000 0 0 18 18
RELN/LRP8 0.018 0.075 -10000 0 -0.15 88 88
CaM/Ca2+ 0.018 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 -0.041 0.071 0.16 48 -0.23 1 49
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 0.01 -10000 0 0 83 83
CALM1 0.028 0.006 -10000 0 0 26 26
DYNLT1 0.025 0.01 -10000 0 0 82 82
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.039 0.017 -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 0.027 0.007 -10000 0 0 37 37
LIS1/Poliovirus Protein 3A -0.024 0.009 -10000 0 -10000 0 0
CDK5R2 0.029 0.003 -10000 0 0 7 7
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.014 0.077 -10000 0 -0.15 98 98
YWHAE 0.027 0.008 -10000 0 0 40 40
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 -0.014 0.04 -10000 0 -0.26 14 14
p35/CDK5 -0.036 0.086 0.2 22 -0.22 1 23
RELN 0.022 0.012 -10000 0 0 131 131
PAFAH/LIS1 -0.031 0.017 -10000 0 -10000 0 0
LIS1/CLIP170 -0.036 0.012 -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 -10000 0 13
LIS1/IQGAP1 -0.036 0.014 -10000 0 -0.15 2 2
RHOA -0.009 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 0.028 0.005 -10000 0 0 18 18
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 0.028 0.005 -10000 0 0 20 20
NDEL1/Katanin 60 -0.035 0.099 0.28 16 -0.25 1 17
P39/CDK5 -0.038 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 -0.036 0.077 0.18 17 -0.23 1 18
PPP2R5D 0.028 0.006 -10000 0 0 26 26
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.03 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.008 -10000 0 0 40 40
RELN/VLDLR/DAB1/LIS1 0.02 0.079 -10000 0 -0.14 85 85
RELN/VLDLR 0.027 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 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
ANTXR1 0.028 0.006 -10000 0 0 26 26
ANTXR2 0.027 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 -10000 0 -0.35 76 76
MAP2K2 -0.13 0.26 -10000 0 -0.63 122 122
MAP2K1 -0.016 0.01 0.15 1 -0.062 2 3
MAP2K7 -0.016 0.007 -10000 0 -10000 0 0
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 0.027 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 -10000 0 0
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 0.029 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 -0.023 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 0.099 3 -0.11 10 13
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 -0.037 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
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.008 -10000 0 0 46 46
LAT2 -0.009 0.075 0.14 4 -0.27 23 27
AP1 0.026 0.1 0.24 1 -0.38 11 12
mol:PIP3 -0.018 0.092 0.24 12 -0.31 18 30
IKBKB -0.01 0.071 0.2 22 -0.19 15 37
AKT1 -0.008 0.13 0.26 52 -0.25 8 60
IKBKG -0.012 0.066 0.19 16 -0.19 12 28
MS4A2 -0.011 0.031 0.056 14 -10000 0 14
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.007 0.024 -10000 0 -10000 0 0
MAP3K1 0.015 0.11 0.24 40 -0.31 14 54
mol:Ca2+ -0.013 0.077 0.21 14 -0.25 14 28
LYN -0.011 0.03 0.061 3 -10000 0 3
CBLB -0.007 0.074 0.14 5 -0.26 22 27
SHC1 0.028 0.006 -10000 0 -0.001 22 22
RasGAP/p62DOK 0.013 0.073 -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 -0.031 0.089 0.28 16 -0.2 3 19
PTPN13 -0.021 0.11 -10000 0 -0.46 11 11
PTPN11 -0.009 0.034 0.055 48 -10000 0 48
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.013 0.11 0.28 17 -0.32 4 21
SYK -0.008 0.031 0.057 5 -10000 0 5
GRB2 0.024 0.017 -10000 0 -0.03 43 43
LAT/PLCgamma1/GRB2/SLP76/GADs -0.025 0.075 0.16 1 -0.3 20 21
LAT -0.007 0.073 0.14 4 -0.26 23 27
PAK2 0.023 0.12 0.23 65 -0.33 14 79
NFATC2 -0.02 0.072 -10000 0 -0.39 20 20
HRAS 0.003 0.094 0.21 12 -0.33 18 30
GAB2 0.026 0.009 -10000 0 0 62 62
PLA2G1B -0.004 0.066 -10000 0 -0.91 2 2
Fc epsilon R1 0.038 0.046 -10000 0 -0.12 30 30
Antigen/IgE/Fc epsilon R1 0.036 0.041 -10000 0 -0.12 23 23
mol:GDP 0.01 0.092 0.2 8 -0.35 17 25
JUN 0.028 0.007 -10000 0 0 34 34
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.017 -10000 0 -10000 0 0
FOS 0.024 0.011 -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 0.17 17 -0.19 13 30
KLRG1 -0.011 0.062 -10000 0 -0.27 14 14
VAV1 -0.006 0.074 0.14 6 -0.27 20 26
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.008 0.075 0.14 4 -0.27 23 27
negative regulation of mast cell degranulation -0.02 0.051 -10000 0 -0.26 13 13
BTK 0.013 0.088 0.21 2 -0.36 14 16
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.001 0.068 0.19 24 -0.18 17 41
GAB2/PI3K/SHP2 -0.059 0.063 -10000 0 -0.19 50 50
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.058 0.12 1 -0.2 22 23
RAF1 0.02 0.063 -10000 0 -0.96 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.057 0.049 -10000 0 -0.12 28 28
FCER1G -0.016 0.025 0.064 1 -10000 0 1
FCER1A -0.01 0.031 0.052 2 -10000 0 2
Antigen/IgE/Fc epsilon R1/Fyn 0.034 0.078 -10000 0 -0.14 78 78
MAPK3 -0.004 0.067 -10000 0 -0.89 2 2
MAPK1 -0.007 0.071 -10000 0 -0.95 2 2
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.003 0.16 -10000 0 -0.52 28 28
DUSP1 0.023 0.012 -10000 0 0 125 125
NF-kappa-B/RelA -0.012 0.054 0.13 21 -0.15 10 31
actin cytoskeleton reorganization -0.006 0.1 -10000 0 -0.5 7 7
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.03 0.091 0.19 1 -0.36 16 17
FER -0.006 0.073 0.14 4 -0.27 21 25
RELA 0.029 0.003 -10000 0 0 6 6
ITK 0.002 0.043 0.12 6 -0.23 12 18
SOS1 0.028 0.007 -10000 0 0 35 35
PLCG1 0.006 0.095 0.25 10 -0.34 14 24
cytokine secretion -0.013 0.034 0.069 12 -0.1 15 27
SPHK1 -0.007 0.073 0.14 5 -0.27 21 26
PTK2 -0.006 0.1 -10000 0 -0.55 6 6
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.002 0.083 -10000 0 -0.31 20 20
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.021 0.096 0.23 10 -0.3 23 33
MAP2K2 -0.009 0.067 -10000 0 -0.91 2 2
MAP2K1 0.006 0.061 -10000 0 -0.91 2 2
MAP2K7 0.027 0.007 -10000 0 0 37 37
KLRG1/SHP2 -0.007 0.072 0.18 37 -0.25 13 50
MAP2K4 -0.063 0.3 -10000 0 -0.87 63 63
Fc epsilon R1/FcgammaRIIB 0.061 0.053 -10000 0 -0.12 28 28
mol:Choline -0.03 0.088 0.27 16 -0.2 3 19
SHC/Grb2/SOS1 0.05 0.083 -10000 0 -0.26 17 17
FYN 0.024 0.011 -10000 0 0 99 99
DOK1 0.029 0.004 -10000 0 0 10 10
PXN -0.015 0.099 -10000 0 -0.49 7 7
HCLS1 -0.007 0.076 0.15 9 -0.28 21 30
PRKCB -0.015 0.076 0.19 16 -0.24 20 36
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 13 13
LCP2 0.024 0.015 -10000 0 -0.03 33 33
PLA2G4A -0.045 0.089 0.14 7 -0.3 28 35
RASA1 0.027 0.008 -10000 0 0 49 49
mol:Phosphatidic acid -0.03 0.088 0.27 16 -0.2 3 19
IKK complex -0.009 0.067 0.2 21 -0.17 2 23
WIPF1 0.029 0.005 -10000 0 0 14 14
IL27-mediated signaling events

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
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 -0.001 0.14 0.57 7 -0.39 25 32
IL27/IL27R/JAK1 0.057 0.13 0.53 8 -0.94 3 11
TBX21 0.046 0.14 0.4 39 -0.56 3 42
IL12B 0.031 0.014 0.091 26 -10000 0 26
IL12A -0.012 0.015 0.046 23 -10000 0 23
IL6ST -0.011 0.035 0.097 26 -10000 0 26
IL27RA/JAK1 0.012 0.11 0.36 3 -1 3 6
IL27 -0.011 0.036 0.097 26 -10000 0 26
TYK2 -0.012 0.041 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 -0.001 0.14 0.57 7 -0.39 25 32
T cell proliferation during immune response -0.001 0.14 0.57 7 -0.39 25 32
MAPKKK cascade 0.001 0.14 0.39 25 -0.57 7 32
STAT3 0.027 0.007 -10000 0 0 37 37
STAT2 0.025 0.01 -10000 0 0 76 76
STAT1 -0.011 0.016 0.062 3 -10000 0 3
IL12RB1 0.028 0.011 0.059 26 0 48 74
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.041 0.14 0.44 25 -0.56 3 28
IL27/IL27R/JAK2/TYK2 0.002 0.14 0.4 25 -0.58 7 32
positive regulation of T cell mediated cytotoxicity 0.001 0.14 0.39 25 -0.57 7 32
STAT1 (dimer) 0.074 0.13 0.55 2 -0.78 3 5
JAK2 -0.008 0.038 0.12 24 -10000 0 24
JAK1 -0.024 0.018 0.065 6 -10000 0 6
STAT2 (dimer) 0.01 0.13 0.36 17 -0.51 7 24
T cell proliferation -0.014 0.13 0.36 26 -0.59 6 32
IL12/IL12R/TYK2/JAK2 0.018 0.18 0.48 25 -0.72 24 49
IL17A -0.029 0.091 -10000 0 -10000 0 0
mast cell activation -0.001 0.14 0.57 7 -0.39 25 32
IFNG 0.016 0.064 0.28 27 -0.12 2 29
T cell differentiation -0.001 0.006 0.027 19 -0.022 3 22
STAT3 (dimer) 0.015 0.14 0.36 24 -0.54 8 32
STAT5A (dimer) 0.016 0.14 0.36 25 -0.53 8 33
STAT4 (dimer) 0.016 0.14 0.36 23 -0.51 8 31
STAT4 0.028 0.005 -10000 0 0 17 17
T cell activation -0.001 0.012 0.11 1 -0.25 1 2
IL27R/JAK2/TYK2 0.047 0.12 0.42 26 -0.95 3 29
GATA3 0.009 0.13 0.59 22 -10000 0 22
IL18 -0.012 0.013 0.003 137 -10000 0 137
positive regulation of mast cell cytokine production 0.015 0.14 0.35 24 -0.53 8 32
IL27/EBI3 0.045 0.032 0.18 7 -10000 0 7
IL27RA 0.019 0.12 0.43 5 -1.1 3 8
IL6 0.026 0.01 -10000 0 -10000 0 0
STAT5A 0.028 0.007 -10000 0 0 34 34
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 0.034 0.095 27 -10000 0 27
TNF -0.015 0.007 0.009 40 -10000 0 40
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.2 0.31 0.78 1 -0.84 62 63
CRP -0.2 0.3 -10000 0 -0.85 64 64
cell cycle arrest -0.24 0.37 -10000 0 -1 73 73
TIMP1 -0.2 0.31 -10000 0 -0.81 75 75
IL6ST 0.002 0.036 -10000 0 -0.09 2 2
Rac1/GDP -0.067 0.11 -10000 0 -0.4 7 7
AP1 -0.001 0.13 0.42 6 -0.53 16 22
GAB2 0.025 0.016 0.099 1 -0.032 20 21
TNFSF11 -0.21 0.3 -10000 0 -0.85 64 64
HSP90B1 -0.025 0.13 -10000 0 -0.79 12 12
GAB1 0.026 0.014 0.093 1 -0.031 25 26
MAPK14 -0.025 0.082 0.36 1 -0.44 3 4
AKT1 -0.014 0.088 0.59 1 -0.53 2 3
FOXO1 -0.023 0.084 0.54 1 -0.51 2 3
MAP2K6 -0.027 0.086 -10000 0 -0.34 4 4
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.1 0.15 0.44 3 -0.48 13 16
MITF -0.055 0.091 0.34 2 -0.36 8 10
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 0.3 1 -0.43 15 16
STAT3 -0.26 0.41 0.61 1 -1.1 74 75
STAT1 0.045 0.071 -10000 0 -0.88 1 1
CEBPD -0.25 0.38 0.64 1 -0.98 91 92
PIK3CA 0.018 0.016 -10000 0 -0.029 18 18
PI3K -0.001 0.068 -10000 0 -0.16 76 76
JUN 0.025 0.014 -10000 0 -0.03 24 24
PIAS3/MITF -0.055 0.094 0.35 1 -0.36 6 7
MAPK11 -0.019 0.076 0.36 1 -0.44 3 4
STAT3 (dimer)/FOXO1 -0.2 0.28 0.54 1 -0.77 63 64
GRB2/SOS1/GAB family 0.016 0.1 -10000 0 -0.31 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.018 0.068 0.24 1 -0.27 8 9
GRB2 0.026 0.014 0.093 1 -0.031 24 25
JAK2 0.027 0.008 -10000 0 0 46 46
LBP -0.14 0.24 0.63 5 -0.71 21 26
PIK3R1 0.019 0.016 0.093 1 -0.029 17 18
JAK1 0.004 0.035 0.13 1 -0.072 5 6
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 73 73
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.091 -10000 0 -0.2 4 4
JUNB -0.27 0.41 -10000 0 -0.94 139 139
FOS 0.021 0.016 -10000 0 -0.03 25 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.044 0.1 -10000 0 -0.38 8 8
STAT1/PIAS1 -0.033 0.13 0.4 3 -0.38 9 12
GRB2/SOS1/GAB family/SHP2/PI3K -0.003 0.086 0.48 1 -0.4 7 8
STAT3 (dimer) -0.26 0.4 0.61 1 -1.1 74 75
PRKCD -0.14 0.2 0.53 2 -0.57 41 43
IL6R 0.004 0.035 0.13 1 -0.065 3 4
SOCS3 -0.011 0.094 0.46 1 -0.85 2 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.008 0.069 -10000 0 -0.18 7 7
Rac1/GTP -0.078 0.12 0.36 3 -0.43 10 13
HCK 0.026 0.01 -10000 0 -0.033 6 6
MAPKKK cascade -0.002 0.12 0.44 1 -0.54 17 18
bone resorption -0.2 0.29 -10000 0 -0.79 64 64
IRF1 -0.21 0.32 0.74 2 -0.86 66 68
mol:GDP -0.056 0.098 -10000 0 -0.38 8 8
SOS1 0.026 0.015 -10000 0 -0.031 23 23
VAV1 -0.058 0.097 0.32 1 -0.38 9 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.006 0.063 -10000 0 -0.42 4 4
PTPN11 0.005 0.08 -10000 0 -0.78 5 5
IL6/IL6RA 0.007 0.053 0.24 1 -0.18 9 10
gp130 (dimer)/TYK2/TYK2/LMO4 0.01 0.059 -10000 0 -0.15 11 11
gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.06 -10000 0 -0.15 11 11
IL6 0.002 0.037 0.16 1 -0.09 2 3
PIAS3 0.028 0.005 -10000 0 0 17 17
PTPRE 0.033 0.026 0.12 1 -0.13 3 4
PIAS1 0.029 0.005 -10000 0 0 14 14
RAC1 0.007 0.029 -10000 0 -0.036 11 11
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.021 0.07 -10000 0 -0.28 11 11
LMO4 0.002 0.038 0.16 1 -0.09 2 3
STAT3 (dimer)/PIAS3 -0.24 0.36 0.58 2 -0.99 74 76
MCL1 -0.011 0.098 0.71 1 -0.59 1 2
EGFR-dependent Endothelin signaling events

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
HRAS 0.028 0.006 -10000 0 0 27 27
EGFR 0.027 0.009 -10000 0 0 54 54
EGF/EGFR 0.032 0.052 -10000 0 -0.12 41 41
EGF/EGFR dimer/SHC/GRB2/SOS1 0.058 0.067 -10000 0 -0.14 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.028 0.006 -10000 0 0 27 27
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.027 0.008 -10000 0 0 40 40
EGF/EGFR dimer/SHC 0.038 0.055 -10000 0 -0.15 41 41
mol:GDP 0.052 0.064 -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 0.039 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.056 0.03 -10000 0 -0.14 36 36
SHC1 0.028 0.006 -10000 0 0 21 21
HRAS/GDP 0.047 0.065 -10000 0 -0.14 36 36
FRAP1 -0.046 0.039 0.1 21 -10000 0 21
EGF/EGFR dimer 0.024 0.055 -10000 0 -0.16 43 43
SOS1 0.028 0.007 -10000 0 0 35 35
GRB2 0.028 0.005 -10000 0 0 20 20
ETA receptor/Endothelin-1 0.038 0.017 -10000 0 -0.16 1 1
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.029 0.003 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.039 0.029 -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 0 136 136
AURKC 0.028 0.006 -9999 0 0 27 27
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.12 0.25 0.6 19 -0.77 1 20
PCK1 0.17 0.24 0.62 67 -10000 0 67
HNF4A 0.15 0.3 0.72 53 -0.77 1 54
KCNJ11 0.12 0.27 0.62 3 -0.82 1 4
AKT1 0.095 0.19 0.39 56 -0.4 1 57
response to starvation 0 0.01 0.17 2 -10000 0 2
DLK1 0.14 0.29 0.77 24 -0.82 1 25
NKX2-1 0.11 0.18 0.66 4 -10000 0 4
ACADM 0.12 0.25 0.6 17 -0.77 1 18
TAT 0.12 0.19 0.48 32 -10000 0 32
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 0.74 9 -10000 0 9
PKLR 0.13 0.26 0.65 26 -0.77 1 27
APOA1 0.2 0.37 0.92 55 -1 1 56
CPT1C 0.12 0.26 0.66 26 -0.77 1 27
ALAS1 0.088 0.19 0.86 3 -0.63 1 4
TFRC 0.25 0.36 0.76 142 -10000 0 142
FOXF1 0.026 0.01 -10000 0 -10000 0 0
NF1 0.027 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 0.6 18 -0.85 2 20
HMGCS1 0.14 0.29 0.69 48 -0.77 1 49
NR3C1 -0.028 0.006 -10000 0 -10000 0 0
CPT1B 0.1 0.24 0.59 14 -0.77 1 15
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.028 0.012 -10000 0 -0.25 1 1
GCK 0.12 0.25 0.59 19 -0.77 1 20
CREB1 0.041 0.092 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 0.62 22 -0.78 53 75
ALDOB 0.13 0.27 0.62 3 -0.82 1 4
AFP 0.041 0.064 0.57 1 -10000 0 1
BDH1 0.15 0.28 0.7 41 -0.79 1 42
HADH 0.11 0.28 0.61 7 -0.95 4 11
F2 0.17 0.31 0.78 27 -0.96 1 28
HNF1A -0.03 0.01 -10000 0 -0.25 1 1
G6PC 0.05 0.083 -10000 0 -10000 0 0
SLC2A2 0.12 0.2 0.59 7 -10000 0 7
INS 0.027 0.023 -10000 0 -0.24 4 4
FOXA1 -0.028 0.026 0.35 2 -10000 0 2
FOXA3 0.098 0.16 0.29 179 -10000 0 179
FOXA2 0.19 0.36 0.82 49 -0.92 1 50
ABCC8 0.12 0.27 0.63 1 -0.82 1 2
ALB 0.042 0.066 0.52 2 -10000 0 2
Syndecan-4-mediated signaling events

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
PTK2 0.075 0.11 0.26 17 -0.39 11 28
Syndecan-4/Syndesmos 0.072 0.1 0.31 5 -0.44 1 6
positive regulation of JNK cascade 0.061 0.11 0.3 5 -0.42 1 6
Syndecan-4/ADAM12 0.038 0.085 0.29 2 -0.45 1 3
CCL5 0.025 0.01 -10000 0 0 82 82
Rac1/GDP 0.021 0.005 -10000 0 -10000 0 0
DNM2 0.026 0.009 -10000 0 0 56 56
ITGA5 0.028 0.005 -10000 0 0 20 20
SDCBP 0.027 0.007 -10000 0 0 36 36
PLG -0.009 0.039 -10000 0 -0.083 26 26
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 26 26
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 0.096 0.32 3 -0.45 1 4
Syndecan-4/CXCL12/CXCR4 0.064 0.12 0.31 5 -0.44 1 6
Syndecan-4/Laminin alpha3 0.064 0.098 0.31 5 -0.44 1 6
MDK 0.029 0.003 -10000 0 0 7 7
Syndecan-4/FZD7 0.07 0.1 0.32 4 -0.45 1 5
Syndecan-4/Midkine 0.073 0.1 0.31 5 -0.44 1 6
FZD7 0.028 0.006 -10000 0 0 27 27
Syndecan-4/FGFR1/FGF 0.066 0.1 0.31 4 -0.43 1 5
THBS1 0.024 0.011 -10000 0 0 95 95
integrin-mediated signaling pathway 0.04 0.082 0.28 2 -0.43 1 3
positive regulation of MAPKKK cascade 0.061 0.11 0.3 5 -0.42 1 6
Syndecan-4/TACI 0.073 0.099 0.31 5 -0.44 1 6
CXCR4 0.028 0.005 -10000 0 0 17 17
cell adhesion 0.02 0.065 0.14 19 -0.19 12 31
Syndecan-4/Dynamin 0.069 0.098 0.31 5 -0.45 1 6
Syndecan-4/TSP1 0.063 0.1 0.31 5 -0.45 1 6
Syndecan-4/GIPC 0.064 0.097 0.31 5 -0.45 1 6
Syndecan-4/RANTES 0.067 0.1 0.31 5 -0.44 1 6
ITGB1 0.028 0.006 -10000 0 0 22 22
LAMA1 0.024 0.012 -10000 0 0 109 109
LAMA3 0.025 0.01 -10000 0 0 74 74
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA -0.027 0.09 0.6 9 -10000 0 9
Syndecan-4/alpha-Actinin 0.073 0.1 0.31 5 -0.44 1 6
TFPI 0.027 0.009 -10000 0 0 52 52
F2 0.018 0.032 0.078 1 -0.049 2 3
alpha5/beta1 Integrin 0.04 0.011 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.038 0.094 0.24 49 -0.44 1 50
ACTN1 0.028 0.006 -10000 0 0 21 21
TNC 0.02 0.013 -10000 0 0 168 168
Syndecan-4/CXCL12 0.065 0.11 0.31 5 -0.45 1 6
FGF6 0.026 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 0.027 0.007 -10000 0 0 37 37
FGF2 0.027 0.008 -10000 0 0 43 43
FGFR1 0.025 0.01 -10000 0 0 74 74
Syndecan-4/PI-4-5-P2 0.04 0.087 -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 -0.075 30 30
vasculogenesis 0.062 0.1 0.3 5 -0.43 1 6
SDC4 0.049 0.093 0.34 2 -0.46 1 3
Syndecan-4/Tenascin C 0.041 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 0.069 0.099 0.31 5 -0.45 1 6
MMP9 0.007 0.027 -10000 0 -0.053 2 2
Rac1/GTP 0.012 0.062 0.15 19 -0.19 12 31
cytoskeleton organization 0.07 0.098 0.3 5 -0.43 1 6
GIPC1 0.025 0.01 -10000 0 0 80 80
Syndecan-4/TFPI 0.066 0.1 0.32 3 -0.45 1 4
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 -0.3 37 39
JUN 0.028 0.007 -10000 0 0 34 34
EP300 0.027 0.008 -10000 0 0 50 50
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 0.027 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.13 0.12 0.32 2 -0.32 31 33
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 0.28 1 -0.37 44 45
NR0B1 0.027 0.007 -10000 0 0 38 38
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 0.19 1 -0.21 261 262
GNB2L1 0.029 0.005 -10000 0 -10000 0 0
PKN1 0.025 0.01 -10000 0 0 80 80
RCHY1 0.027 0.008 -10000 0 0 47 47
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 0.37 1 -0.29 2 3
SRC -0.053 0.065 0.24 1 -10000 0 1
NR3C1 0.029 0.005 -10000 0 0 15 15
KLK3 -0.048 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 -0.081 0.068 0.12 2 -0.2 20 22
TMPRSS2 -0.39 0.45 -10000 0 -0.9 244 244
RXRG 0.028 0.006 -10000 0 0 27 27
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.028 0.007 -10000 0 0 31 31
RXRB 0.028 0.005 -10000 0 0 16 16
CARM1 0.026 0.009 -10000 0 -10000 0 0
NR2C2 0.029 0.003 -10000 0 0 8 8
KLK2 -0.062 0.079 0.32 1 -0.34 4 5
AR -0.11 0.11 0.17 1 -0.22 252 253
SENP1 0.028 0.007 -10000 0 0 30 30
HSP90AA1 0.028 0.005 -10000 0 0 20 20
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 -0.029 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.055 0.3 3 -0.22 17 20
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 -0.28 26 28
T-DHT/AR/Hsp90 -0.079 0.088 0.26 5 -0.26 4 9
GSK3B -0.006 0.031 -10000 0 -10000 0 0
NR2C1 0.029 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.046 0.07 0.27 1 -0.2 1 2
SIRT1 0.029 0.003 -10000 0 0 7 7
ZMIZ2 0.029 0.004 -10000 0 -10000 0 0
POU2F1 -0.057 0.072 -10000 0 -0.19 31 31
T-DHT/AR/DAX-1 -0.076 0.09 0.26 6 -0.24 3 9
CREBBP 0.027 0.008 -10000 0 0 41 41
SMARCE1 0.028 0.007 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
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 0.38 11 -0.36 6 17
mol:PIP3 0.008 0.13 0.4 16 -0.43 2 18
SPRED1 0.027 0.008 -10000 0 0 40 40
SPRED2 0.029 0.004 -10000 0 0 10 10
GAB1 -0.009 0.12 0.42 15 -0.41 2 17
FOXO3 -0.013 0.13 0.39 16 -0.43 9 25
AKT1 -0.005 0.14 0.4 16 -0.45 10 26
BAD -0.013 0.13 0.38 16 -0.42 10 26
megakaryocyte differentiation -0.006 0.13 0.45 15 -0.41 2 17
GSK3B -0.007 0.14 0.39 18 -0.43 9 27
RAF1 -0.02 0.11 0.33 15 -0.32 4 19
SHC1 0.028 0.006 -10000 0 0 21 21
STAT3 -0.011 0.12 0.42 13 -0.41 2 15
STAT1 -0.012 0.23 0.59 15 -0.61 22 37
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 0.01 0.022 -10000 0 -0.029 102 102
TEC 0.026 0.009 -10000 0 0 55 55
RPS6KB1 0.001 0.14 0.43 16 -0.43 3 19
HRAS/SPRED2 -0.012 0.11 0.34 13 -0.32 4 17
LYN/TEC/p62DOK 0.013 0.13 0.4 10 -0.36 4 14
MAPK3 -0.028 0.092 0.28 13 -0.3 5 18
STAP1 -0.008 0.12 0.42 15 -0.41 2 17
GRAP2 0.027 0.008 -10000 0 0 47 47
JAK2 -0.021 0.22 0.57 15 -0.66 12 27
STAT1 (dimer) -0.01 0.23 0.59 16 -0.6 22 38
mol:Gleevec 0.001 0.009 -10000 0 -0.035 18 18
GRB2/SOCS1/VAV1 0.014 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) -0.03 0.18 0.47 14 -0.5 18 32
PIK3R1 0.016 0.019 -10000 0 -0.029 46 46
CBL/CRKL/GRB2 -0.016 0.13 0.37 14 -0.32 1 15
PI3K -0.017 0.12 0.41 9 -0.38 4 13
PTEN 0.022 0.018 -10000 0 -0.03 55 55
SCF/KIT/EPO/EPOR 0.006 0.23 0.62 10 -0.67 6 16
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 0.27 13 -0.25 4 17
mol:GDP -0.018 0.12 0.37 9 -0.35 4 13
PIK3C2B -0.01 0.13 0.45 15 -0.41 2 17
CBL/CRKL -0.017 0.12 0.37 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 -0.32 2 17
PDPK1 0.001 0.12 0.39 17 -0.39 2 19
SNAI2 -0.01 0.12 0.42 14 -0.38 3 17
positive regulation of cell proliferation -0.017 0.2 0.54 15 -0.55 15 30
KITLG 0.018 0.041 0.12 16 -10000 0 16
cell motility -0.017 0.2 0.54 15 -0.55 15 30
PTPN6 -0.001 0.035 -10000 0 -0.076 15 15
EPOR -0.029 0.2 0.99 1 -0.73 18 19
STAT5A (dimer) -0.021 0.18 0.5 15 -0.52 16 31
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 35 35
EPO 0.02 0.031 0.09 9 -0.043 68 77
VAV1 0.027 0.008 -10000 0 0 41 41
GRB10 -0.009 0.12 0.42 15 -0.41 2 17
PTPN11 0 0.034 -10000 0 -0.064 18 18
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 0.3 15 -0.27 2 17
CBL 0.029 0.005 -10000 0 0 14 14
KIT -0.011 0.21 0.69 17 -0.7 13 30
MAP2K2 -0.027 0.091 0.3 13 -0.3 2 15
SHC/Grb2/SOS1 0.018 0.13 0.42 11 -0.41 2 13
STAT5A -0.02 0.19 0.5 15 -0.53 16 31
GRB2 0.028 0.005 -10000 0 0 20 20
response to radiation -0.007 0.13 0.42 16 -0.37 3 19
SHC/GRAP2 0.038 0.014 -10000 0 -10000 0 0
PTPRO -0.007 0.12 0.45 15 -0.41 2 17
SH2B2 -0.001 0.12 0.43 15 -0.4 2 17
DOK1 0.029 0.004 -10000 0 0 10 10
MATK -0.011 0.12 0.43 13 -0.41 2 15
CREBBP 0 0.084 0.36 16 -10000 0 16
BCL2 -0.18 0.45 0.95 1 -1.1 103 104
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.007 0.13 0.59 1 -0.45 2 3
CRKL -0.026 0.092 0.27 13 -0.21 5 18
mol:DAG -0.034 0.075 0.36 2 -0.28 7 9
HRAS -0.033 0.1 0.26 28 -10000 0 28
MAPK8 -0.019 0.076 0.15 77 -10000 0 77
RAP1A -0.025 0.095 0.27 16 -0.21 5 21
GAB1 -0.025 0.095 0.27 16 -0.21 5 21
MAPK14 -0.019 0.076 0.15 76 -0.17 1 77
EPO -0.02 0.034 0.073 8 -10000 0 8
PLCG1 -0.034 0.076 0.36 2 -0.29 7 9
EPOR/TRPC2/IP3 Receptors -0.023 0.029 0.071 3 -10000 0 3
RAPGEF1 0.028 0.005 -10000 0 0 17 17
EPO/EPOR (dimer)/SOCS3 0.035 0.048 0.19 1 -0.16 2 3
GAB1/SHC/GRB2/SOS1 -0.037 0.098 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 16 -0.21 5 21
STAT1 -0.025 0.076 0.48 2 -0.34 3 5
STAT5B -0.045 0.095 0.44 2 -0.31 8 10
cell proliferation -0.024 0.082 0.18 41 -10000 0 41
GAB1/SHIP/PIK3R1/SHP2/SHC -0.065 0.078 0.17 1 -0.23 17 18
TEC -0.021 0.092 0.26 15 -0.21 4 19
SOCS3 0.028 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 0.069 10 -10000 0 10
PIK3R1 0.021 0.013 -10000 0 0 159 159
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 0.015 0.028 0.09 2 -0.047 83 85
TEC/VAV2 -0.032 0.088 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration -0.023 0.029 0.071 3 -10000 0 3
SHC1 0.028 0.006 -10000 0 0 21 21
EPO/EPOR (dimer)/LYN 0.027 0.059 0.3 2 -0.16 9 11
mol:IP3 -0.034 0.075 0.36 2 -0.28 7 9
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.049 0.09 0.25 9 -0.23 13 22
SH2B3 -0.018 0.035 0.067 15 -10000 0 15
NFKB1 -0.019 0.075 0.15 71 -0.22 3 74
EPO/EPOR (dimer)/JAK2/SOCS3 0.008 0.03 0.2 1 -0.19 4 5
PTPN6 -0.033 0.076 0.28 6 -0.21 5 11
TEC/VAV2/GRB2 -0.03 0.099 0.28 11 -10000 0 11
EPOR -0.023 0.029 0.071 3 -10000 0 3
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 35 35
PLCG2 0.026 0.009 -10000 0 0 63 63
CRKL/CBL/C3G -0.04 0.095 0.26 10 -10000 0 10
VAV2 -0.026 0.093 0.27 15 -0.21 5 20
CBL -0.024 0.095 0.27 16 -0.21 5 21
SHC/Grb2/SOS1 -0.052 0.065 0.27 2 -0.22 3 5
STAT5A -0.046 0.097 0.44 2 -0.32 11 13
GRB2 0.028 0.005 -10000 0 0 20 20
STAT5 (dimer) -0.076 0.14 0.57 2 -0.38 64 66
LYN/PLCgamma2 0.02 0.042 -10000 0 -0.16 12 12
PTPN11 0.029 0.003 -10000 0 0 8 8
BTK -0.024 0.095 0.27 16 -0.21 5 21
BCL2 -0.071 0.26 0.5 1 -0.64 84 85
Ceramide signaling 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
SPHK2 -0.03 0.011 -10000 0 -10000 0 0
MAP4K4 -0.035 0.086 0.17 2 -0.28 39 41
BAG4 0.026 0.009 -10000 0 0 61 61
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 0.058 -10000 0 -0.33 15 15
RIPK1 0.027 0.007 -10000 0 0 38 38
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 0.064 0.18 6 -0.2 28 34
RB1 0.006 0.043 0.18 20 -0.18 10 30
FADD/Caspase 8 -0.035 0.097 0.22 7 -0.32 34 41
MAP2K4 -0.009 0.027 -10000 0 -0.19 9 9
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 -0.19 9 19
EGF 0.027 0.008 -10000 0 0 40 40
mol:ceramide 0.012 0.03 -10000 0 -0.18 10 10
MADD 0.029 0.003 -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 0.024 0.011 -10000 0 0 93 93
negative regulation of cell cycle 0.006 0.043 0.18 20 -0.18 10 30
cell proliferation -0.034 0.054 0.18 6 -0.22 8 14
BID -0.038 0.18 -10000 0 -0.63 41 41
MAP3K1 0 0.027 -10000 0 -0.18 10 10
EIF2A 0.066 0.1 0.23 79 -0.2 1 80
TRADD 0.026 0.009 -10000 0 0 63 63
CRADD 0.029 0.004 -10000 0 0 13 13
MAPK3 -0.023 0.048 0.19 4 -0.24 6 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.025 0.05 0.19 4 -0.24 5 9
Cathepsin D/ceramide 0.029 0.032 -10000 0 -0.18 10 10
FADD -0.036 0.088 0.18 4 -0.29 34 38
KSR1 0.002 0.035 0.22 5 -0.18 10 15
MAPK8 0 0.041 -10000 0 -10000 0 0
PRKRA 0.006 0.045 0.21 16 -0.18 10 26
PDGFA 0.027 0.008 -10000 0 0 46 46
TRAF2 0.028 0.006 -10000 0 0 23 23
IGF1 0.028 0.007 -10000 0 0 32 32
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.012 0.029 -10000 0 -0.18 10 10
CTSD 0.028 0.007 -10000 0 0 29 29
regulation of nitric oxide biosynthetic process 0.037 0.025 -10000 0 -0.16 7 7
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.035 0.058 0.2 6 -0.24 8 14
PRKCD 0.029 0.005 -10000 0 0 15 15
PRKCZ 0.028 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 0.025 -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 0.091 -10000 0 -0.28 38 38
TNFR1A/BAG4/TNF-alpha 0.041 0.039 -10000 0 -0.14 15 15
mol:Sphingosine-1-phosphate -0.03 0.011 -10000 0 -10000 0 0
MAP2K1 -0.014 0.038 0.18 9 -0.2 1 10
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 0 6 6
CYCS 0.024 0.057 0.15 12 -0.17 8 20
TNFRSF1A 0.025 0.01 -10000 0 0 78 78
NFKB1 0.027 0.008 -10000 0 0 45 45
TNFR1A/BAG4 0.029 0.036 -10000 0 -0.16 15 15
EIF2AK2 0.06 0.089 0.22 42 -0.19 4 46
TNF-alpha/TNFR1A/FAN 0.043 0.038 -10000 0 -0.15 14 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.017 0.11 -10000 0 -0.41 32 32
MAP2K2 -0.026 0.046 0.18 8 -0.22 5 13
SMPD3 -0.026 0.11 0.18 4 -0.31 58 62
TNF 0.029 0.005 -10000 0 0 15 15
PKC zeta/PAR4 0.041 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.011 0.036 0.14 2 -0.15 8 10
NF kappa B1/RelA/I kappa B alpha 0.064 0.057 -10000 0 -0.15 17 17
AIFM1 0.03 0.062 0.2 15 -0.17 7 22
BCL2 0.023 0.012 -10000 0 0 122 122
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.039 0.021 -10000 0 -0.2 3 3
FBXW11 0.028 0.005 -10000 0 0 18 18
NF kappa B1 p50/c-Rel -0.037 0.016 0.16 1 -0.15 4 5
NF kappa B1 p50/RelA/I kappa B alpha -0.029 0.053 0.18 2 -0.23 9 11
NFKBIA -0.005 0.039 -10000 0 -10000 0 0
MAPK14 0.028 0.005 -10000 0 0 19 19
NF kappa B1 p105/p50 -0.037 0.017 0.16 1 -0.15 5 6
ARRB2 0.006 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 -0.15 7 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.038 0.017 0.16 1 -0.15 6 7
PIK3CA 0.02 0.014 -10000 0 0 172 172
NF kappa B1 p50 dimer -0.032 0.016 -10000 0 -0.16 5 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
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 0.041 -10000 0 -0.21 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.032 0.054 -10000 0 -0.24 9 9
SRC 0.028 0.007 -10000 0 0 31 31
PI3K -0.001 0.068 -10000 0 -0.16 76 76
NF kappa B1 p50/RelA -0.007 0.041 -10000 0 -0.21 4 4
IKBKB 0.027 0.007 -10000 0 0 39 39
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 0 18 18
SYK 0.028 0.006 -10000 0 0 23 23
I kappa B alpha/PIK3R1 0.005 0.053 -10000 0 -0.22 15 15
cell death -0.031 0.052 -10000 0 -0.23 9 9
NF kappa B1 p105/c-Rel -0.037 0.016 0.16 1 -0.15 4 5
LCK 0.028 0.006 -10000 0 0 26 26
BCL3 0.028 0.007 -10000 0 0 35 35
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.011 0.11 0.3 16 -0.36 11 27
FYN -0.022 0.13 0.3 16 -0.39 21 37
LAT/GRAP2/SLP76 -0.02 0.1 0.28 9 -0.36 12 21
IKBKB 0.027 0.007 -10000 0 0 39 39
AKT1 -0.021 0.1 0.28 10 -0.32 20 30
B2M 0.021 0.021 0.11 1 -0.053 2 3
IKBKG -0.019 0.04 0.12 11 -0.13 4 15
MAP3K8 0.029 0.005 -10000 0 0 16 16
mol:Ca2+ -0.026 0.013 0.08 1 -10000 0 1
integrin-mediated signaling pathway 0.038 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.027 0.12 0.32 9 -0.41 24 33
TRPV6 0.075 0.33 1.3 37 -10000 0 37
CD28 0.019 0.023 -10000 0 -10000 0 0
SHC1 -0.013 0.11 0.3 12 -0.38 15 27
receptor internalization -0.012 0.096 0.3 6 -0.37 18 24
PRF1 -0.024 0.19 0.8 1 -0.92 19 20
KRAS 0.024 0.011 -10000 0 0 99 99
GRB2 0.028 0.005 -10000 0 0 20 20
COT/AKT1 -0.018 0.09 0.26 11 -0.28 16 27
LAT -0.017 0.1 0.31 9 -0.39 14 23
EntrezGene:6955 -0.001 0.004 0.07 1 -0.023 7 8
CD3D 0.023 0.017 0.11 1 -0.054 1 2
CD3E -0.005 0.03 -10000 0 -10000 0 0
CD3G 0.016 0.024 -10000 0 -0.052 7 7
RASGRP2 -0.003 0.016 0.069 1 -0.14 2 3
RASGRP1 -0.052 0.13 0.28 7 -0.35 40 47
HLA-A -0.005 0.03 0.11 1 -10000 0 1
RASSF5 0.029 0.004 -10000 0 0 11 11
RAP1A/GTP/RAPL 0.038 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.05 0.16 12 -0.12 8 20
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.036 0.045 -10000 0 -0.17 22 22
PRKCA -0.025 0.065 0.21 12 -0.22 6 18
GRAP2 0.027 0.008 -10000 0 0 47 47
mol:IP3 -0.031 0.076 -10000 0 -0.28 13 13
EntrezGene:6957 0 0.005 0.076 1 -0.022 8 9
TCR/CD3/MHC I/CD8 -0.014 0.089 0.32 4 -0.34 21 25
ORAI1 -0.091 0.28 -10000 0 -1.1 37 37
CSK -0.014 0.1 0.32 8 -0.4 12 20
B7 family/CD28 0.013 0.11 0.39 3 -0.41 14 17
CHUK 0.027 0.007 -10000 0 0 36 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.015 0.1 0.32 4 -0.39 17 21
PTPN6 -0.01 0.11 0.32 9 -0.37 15 24
VAV1 -0.014 0.1 0.31 9 -0.39 13 22
Monovalent TCR/CD3 -0.013 0.062 0.38 1 -0.18 50 51
CBL 0.029 0.005 -10000 0 0 14 14
LCK -0.01 0.12 0.3 13 -0.38 17 30
PAG1 -0.01 0.11 0.29 12 -0.39 13 25
RAP1A 0.029 0.003 -10000 0 0 7 7
TCR/CD3/MHC I/CD8/LCK -0.015 0.1 0.27 8 -0.38 18 26
CD80 0.018 0.023 -10000 0 -10000 0 0
CD86 0.017 0.023 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.03 0.059 0.095 1 -0.2 21 22
HRAS 0.028 0.006 -10000 0 0 27 27
GO:0035030 -0.029 0.09 0.28 5 -0.35 15 20
CD8A 0.021 0.022 0.11 1 -0.051 3 4
CD8B -0.004 0.031 0.11 1 -10000 0 1
PTPRC 0.017 0.02 -10000 0 -10000 0 0
PDK1/PKC theta -0.03 0.11 0.31 11 -0.37 20 31
CSK/PAG1 -0.016 0.11 0.3 11 -0.41 11 22
SOS1 0.028 0.007 -10000 0 0 35 35
peptide-MHC class I 0.035 0.03 0.18 1 -0.17 6 7
GRAP2/SLP76 0.012 0.11 0.32 7 -0.38 15 22
STIM1 -0.036 0.069 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.071 0.18 33 -0.18 7 40
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.013 0.099 0.3 6 -0.39 18 24
mol:DAG -0.04 0.058 -10000 0 -0.25 16 16
RAP1A/GDP -0.002 0.026 0.08 10 -0.066 2 12
PLCG1 0.028 0.007 -10000 0 0 31 31
CD247 0.017 0.025 0.1 1 -0.052 6 7
cytotoxic T cell degranulation -0.022 0.18 0.79 1 -0.88 19 20
RAP1A/GTP -0.004 0.008 -10000 0 -0.057 2 2
mol:PI-3-4-5-P3 -0.022 0.11 0.3 10 -0.37 19 29
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.032 0.097 0.21 4 -0.37 11 15
NRAS 0.014 0.015 -10000 0 0 300 300
ZAP70 0.028 0.009 -10000 0 -0.029 12 12
GRB2/SOS1 0.039 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.028 0.098 0.27 9 -0.36 11 20
MALT1 0.025 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 35 35
PRKCB -0.034 0.039 -10000 0 -0.18 16 16
PRKCE -0.026 0.064 0.21 11 -0.23 5 16
PRKCQ -0.027 0.12 0.31 9 -0.4 20 29
LCP2 0.027 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 0.09 0.25 12 -0.29 17 29
IKK complex -0.004 0.043 0.16 18 -0.12 1 19
RAS family/GDP -0.004 0.009 -10000 0 -0.038 9 9
MAP3K14 -0.022 0.071 0.21 11 -0.22 16 27
PDPK1 -0.024 0.097 0.28 11 -0.31 18 29
TCR/CD3/MHC I/CD8/Fyn -0.016 0.11 0.48 1 -0.42 21 22
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.056 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 0.087 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 -0.028 0.068 0.13 3 -0.23 27 30
CaM/Ca2+ 0.051 0.067 0.32 8 -0.2 1 9
RAP1A 0.029 0.003 -10000 0 0 7 7
STAT1 (dimer)/SHP2 -0.016 0.05 0.25 2 -10000 0 2
AKT1 0 0.12 0.29 30 -0.23 5 35
MAP2K1 -0.033 0.076 0.31 14 -10000 0 14
MAP3K11 -0.027 0.083 0.33 16 -10000 0 16
IFNGR1 -0.019 0.031 0.078 15 -10000 0 15
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.009 0.092 0.21 1 -0.28 41 42
Rap1/GTP -0.064 0.042 -10000 0 -0.19 1 1
CRKL/C3G 0.04 0.012 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.068 0.062 0.26 8 -0.15 8 16
CEBPB -0.036 0.15 0.39 7 -0.61 19 26
STAT3 0.027 0.007 -10000 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.02 0.19 -10000 0 -0.85 22 22
STAT1 -0.018 0.047 0.38 2 -10000 0 2
CALM1 0.027 0.009 -10000 0 -0.006 33 33
IFN-gamma (dimer) -0.024 0.025 0.07 7 -10000 0 7
PIK3CA 0.02 0.014 -10000 0 0 173 173
STAT1 (dimer)/PIAS1 -0.02 0.051 0.37 2 -10000 0 2
CEBPB/PTGES2/Cbp/p300 -0.054 0.094 -10000 0 -0.4 19 19
mol:Ca2+ 0.051 0.061 0.33 8 -0.17 2 10
MAPK3 -0.039 0.16 0.45 3 -0.68 25 28
STAT1 (dimer) -0.03 0.1 0.5 3 -0.36 12 15
MAPK1 -0.053 0.19 0.44 4 -0.71 36 40
JAK2 -0.02 0.03 0.076 14 -10000 0 14
PIK3R1 0.021 0.014 -10000 0 -0.001 164 164
JAK1 -0.02 0.031 0.079 14 -10000 0 14
CAMK2D 0.026 0.01 -10000 0 -0.004 50 50
DAPK1 -0.023 0.1 0.42 5 -0.42 13 18
SMAD7 0.025 0.11 0.37 31 -10000 0 31
CBL/CRKL/C3G -0.037 0.088 0.33 14 -10000 0 14
PI3K 0.018 0.083 0.25 6 -0.23 7 13
IFNG -0.024 0.025 0.07 7 -10000 0 7
apoptosis 0.003 0.097 0.47 4 -0.41 2 6
CAMK2G 0.028 0.008 -10000 0 -0.01 21 21
STAT3 (dimer) 0.027 0.007 -10000 0 0 37 37
CAMK2A 0.028 0.008 -10000 0 -0.012 17 17
CAMK2B 0.028 0.007 -10000 0 -0.009 17 17
FRAP1 -0.004 0.1 0.27 30 -0.22 6 36
PRKCD 0 0.12 0.29 31 -0.24 2 33
RAP1B 0.028 0.006 -10000 0 0 22 22
negative regulation of cell growth -0.028 0.068 0.13 3 -0.23 27 30
PTPN2 0.027 0.011 -10000 0 -0.012 37 37
EP300 0.025 0.016 0.072 13 -0.035 20 33
IRF1 0 0.094 0.2 21 -0.33 11 32
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 -0.037 0.083 0.31 14 -10000 0 14
CASP1 0.001 0.081 0.28 5 -0.23 5 10
PTGES2 0.029 0.005 -10000 0 0 16 16
IRF9 -0.023 0.063 0.29 12 -0.19 5 17
mol:PI-3-4-5-P3 -0.034 0.065 0.14 9 -0.22 7 16
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 14 14
PIAS4 0.027 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.028 0.068 0.13 3 -0.23 27 30
PTPN11 -0.018 0.084 0.35 15 -10000 0 15
CREBBP 0.026 0.016 0.071 14 -0.035 20 34
RAPGEF1 0.028 0.005 -10000 0 0 17 17
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.011 0.057 -10000 0 -0.2 27 27
epithelial cell differentiation 0.047 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 54 54
EPHA2 0.029 0.005 -10000 0 0 16 16
MYO6 -0.047 0.026 0.16 3 -0.22 1 4
CTNNB1 0.029 0.003 -10000 0 0 7 7
ABI1/Sra1/Nap1 0.051 0.03 -10000 0 -0.15 9 9
AQP5 -0.012 0.049 -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 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.045 0.027 -10000 0 -10000 0 0
EGF 0.027 0.008 -10000 0 0 40 40
NCKAP1 0.028 0.005 -10000 0 0 17 17
AQP3 -0.13 0.17 -10000 0 -0.4 138 138
cortical microtubule organization 0.047 0.041 -10000 0 -0.13 9 9
GO:0000145 -0.043 0.025 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.053 0.043 -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 0.067 0.04 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.051 0.065 -10000 0 -0.23 59 59
PVRL2 0.028 0.007 -10000 0 0 32 32
ZYX -0.042 0.026 -10000 0 -0.22 1 1
ARF6/GTP 0.071 0.044 -10000 0 -10000 0 0
CDH1 0.026 0.01 -10000 0 0 71 71
EGFR/EGFR/EGF/EGF -0.062 0.032 0.094 7 -0.22 2 9
RhoA/GDP 0.047 0.044 -10000 0 -0.13 10 10
actin cytoskeleton organization -0.051 0.027 -10000 0 -0.22 1 1
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 32 32
DIAPH1 0.028 0.13 -10000 0 -0.55 20 20
Wnt receptor signaling pathway -0.047 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 -0.052 0.028 -10000 0 -0.23 1 1
EFNA1 0.027 0.008 -10000 0 0 46 46
LPP -0.048 0.033 0.14 4 -0.3 1 5
Ephrin A1/EPHA2 -0.05 0.033 0.094 21 -10000 0 21
SEC6/SEC8 -0.064 0.034 -10000 0 -0.23 1 1
MGAT3 -0.045 0.027 -10000 0 -10000 0 0
HGF/MET -0.044 0.048 0.094 49 -10000 0 49
HGF 0.028 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 27 27
actin cable formation -0.031 0.086 0.28 12 -0.28 7 19
KIAA1543 -0.047 0.022 -10000 0 -10000 0 0
KIFC3 -0.047 0.023 -10000 0 -10000 0 0
NCK1 0.026 0.009 -10000 0 0 63 63
EXOC3 0.026 0.009 -10000 0 0 60 60
ACTN1 -0.048 0.026 0.16 4 -0.22 1 5
NCK1/GIT1 0.036 0.016 -10000 0 -10000 0 0
mol:GDP 0.047 0.041 -10000 0 -0.13 9 9
EXOC4 0.028 0.007 -10000 0 0 34 34
STX4 -0.049 0.024 -10000 0 -10000 0 0
PIP5K1C -0.046 0.027 -10000 0 -10000 0 0
LIMA1 0.028 0.005 -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 -0.064 0.099 0.22 1 -0.58 13 14
IGF-1R heterotetramer/IGF1 -0.075 0.042 0.094 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 -10000 0 -10000 0 0
mol:GTP 0.065 0.039 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.044 0.09 0.28 15 -10000 0 15
cortical actin cytoskeleton stabilization -0.011 0.057 -10000 0 -0.2 27 27
regulation of cell-cell adhesion -0.051 0.027 -10000 0 -0.22 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.011 0.058 -10000 0 -0.2 27 27
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.028 0.005 -10000 0 0 20 20
SPHK1 0.028 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 44 44
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 0.033 0.038 0.17 1 -0.26 3 4
GNAI3 0.024 0.011 -10000 0 0 98 98
G12/G13 0.04 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 0.029 -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 0.017 0.035 0.16 1 -0.26 3 4
S1P/S1P3/Gq -0.009 0.082 -10000 0 -0.32 25 25
S1P/S1P4/Gi 0.009 0.062 0.18 2 -0.22 17 19
GNAQ 0.028 0.006 -10000 0 0 28 28
GNAZ 0.027 0.008 -10000 0 0 47 47
GNA14 0.028 0.005 -10000 0 0 19 19
GNA15 0.027 0.008 -10000 0 0 46 46
GNA12 0.028 0.007 -10000 0 0 33 33
GNA13 0.029 0.005 -10000 0 0 14 14
GNA11 0.025 0.01 -10000 0 0 83 83
ABCC1 0.028 0.005 -10000 0 0 17 17
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.027 0.014 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.032 0.022 -10000 0 -10000 0 0
CDKN1B 0.02 0.075 0.27 10 -0.34 6 16
CDKN1A 0.008 0.064 0.28 3 -0.33 7 10
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.011 -10000 0 0 98 98
FOXO3 0.007 0.055 -10000 0 -0.33 6 6
AKT1 0.014 0.056 -10000 0 -0.34 9 9
BAD 0.029 0.002 -10000 0 0 4 4
AKT3 -0.1 0.11 -10000 0 -0.21 281 281
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.059 -10000 0 -0.33 8 8
AKT1/ASK1 0.034 0.063 -10000 0 -0.32 9 9
BAD/YWHAZ 0.044 0.026 -10000 0 -10000 0 0
RICTOR 0.027 0.007 -10000 0 0 39 39
RAF1 0.029 0.003 -10000 0 0 7 7
JNK cascade -0.032 0.061 0.31 9 -10000 0 9
TSC1 0.007 0.05 -10000 0 -0.32 5 5
YWHAZ 0.025 0.01 -10000 0 0 79 79
AKT1/RAF1 0.037 0.065 -10000 0 -0.33 9 9
EP300 0.027 0.008 -10000 0 0 50 50
mol:GDP 0.014 0.056 -10000 0 -0.33 9 9
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.005 0.056 -10000 0 -0.33 8 8
YWHAQ 0.029 0.005 -10000 0 0 15 15
TBC1D4 -0.014 0.011 0.19 1 -10000 0 1
MAP3K5 0.028 0.007 -10000 0 0 32 32
MAPKAP1 0.028 0.005 -10000 0 0 17 17
negative regulation of cell cycle -0.018 0.064 0.3 7 -0.17 4 11
YWHAH 0.027 0.008 -10000 0 0 42 42
AKT1S1 0.005 0.059 -10000 0 -0.33 9 9
CASP9 0.007 0.056 -10000 0 -0.32 7 7
YWHAB 0.027 0.008 -10000 0 0 44 44
p27Kip1/KPNA1 0.021 0.087 0.27 16 -0.34 7 23
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.053 0.019 -10000 0 -10000 0 0
YWHAE 0.027 0.008 -10000 0 0 40 40
SRC 0.028 0.007 -10000 0 0 31 31
AKT2/p21CIP1 0.002 0.06 0.27 3 -0.3 8 11
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.032 -10000 0 -0.28 3 3
CHUK 0.011 0.063 0.24 8 -0.32 7 15
BAD/BCL-XL -0.006 0.06 -10000 0 -0.33 8 8
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 0.083 0.25 2 -0.38 9 11
PDPK1 0.028 0.005 -10000 0 0 18 18
MDM2 0.011 0.068 0.28 3 -0.33 9 12
MAPKKK cascade -0.036 0.064 0.32 9 -10000 0 9
MDM2/Cbp/p300 0.039 0.074 0.32 5 -0.33 9 14
TSC1/TSC2 -0.004 0.062 0.27 5 -0.33 9 14
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.071 0.3 5 -0.32 9 14
glucose import -0.021 0.035 0.19 11 -10000 0 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.012 0.045 0.2 4 -0.2 7 11
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.018 0.031 0.19 11 -10000 0 11
GSK3A 0.009 0.061 0.28 4 -0.32 7 11
FOXO1 0.006 0.05 -10000 0 -0.32 5 5
GSK3B 0.008 0.062 0.28 1 -0.34 8 9
SFN 0.027 0.007 -10000 0 0 38 38
G1/S transition of mitotic cell cycle 0.006 0.077 0.29 14 -0.33 8 22
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 0.028 0.005 -10000 0 0 18 18
HSP90AA1 0.028 0.005 -10000 0 0 20 20
YWHAG 0.029 0.004 -10000 0 0 12 12
RHEB 0.027 0.009 -10000 0 0 53 53
CREBBP 0.027 0.008 -10000 0 0 41 41
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.028 0.084 -10000 0 -0.25 25 25
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 -10000 0 -0.32 26 26
SUMO1 0.029 0.003 -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 0.028 0.006 -10000 0 0 23 23
Histones 0.054 0.062 -10000 0 -0.22 13 13
YY1/LSF 0 0.063 -10000 0 -0.22 20 20
SMG5 0.028 0.006 -10000 0 0 24 24
RAN 0.029 0.004 -10000 0 0 12 12
I kappa B alpha/HDAC3 -0.023 0.042 -10000 0 -0.31 6 6
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 0.074 0.25 1 -0.37 8 9
HDAC1/Smad7 0.05 0.022 -10000 0 -10000 0 0
RANGAP1 0.027 0.008 -10000 0 0 47 47
HDAC3/TR2 0.026 0.052 -10000 0 -0.22 14 14
NuRD/MBD3 Complex 0.003 0.066 0.24 1 -0.25 16 17
NF kappa B1 p50/RelA 0.002 0.092 0.22 1 -0.33 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 0.041 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.01 0.085 0.24 1 -0.34 18 19
RBBP7 0.028 0.005 -10000 0 0 19 19
NPC 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.027 0.007 -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 0.028 0.005 -10000 0 0 18 18
NFKBIA 0 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 -0.002 0.068 0.18 4 -0.26 18 22
SIN3 complex 0.053 0.042 -10000 0 -10000 0 0
SMURF1 0.028 0.005 -10000 0 0 20 20
CHD3 0.028 0.007 -10000 0 0 35 35
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 40 40
YY1/HDAC3 -0.011 0.062 -10000 0 -0.28 15 15
YY1/HDAC2 0.003 0.062 -10000 0 -0.23 21 21
YY1/HDAC1 0.002 0.061 -10000 0 -0.2 25 25
NuRD/MBD2 Complex (MeCP1) 0.005 0.065 0.18 5 -0.27 12 17
PPARG -0.002 0.078 0.28 1 -0.26 22 23
HDAC8/hEST1B 0.047 0.025 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 0 23 23
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 0 18 18
TNFRSF1A 0.025 0.01 -10000 0 0 78 78
HDAC3/SMRT (N-CoR2) 0.026 0.052 -10000 0 -0.22 14 14
MBD3L2 0.027 0.007 -10000 0 0 37 37
ubiquitin-dependent protein catabolic process 0.05 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.008 -10000 0 0 41 41
NuRD/MBD3/MBD3L2 Complex -0.003 0.086 0.21 2 -0.32 21 23
HDAC1 0.027 0.008 -10000 0 0 50 50
HDAC3 0.005 0.032 -10000 0 -0.32 3 3
HDAC2 0.027 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 0.028 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 45 45
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.004 -10000 0 0 10 10
YY1/LSF/HDAC1 0.013 0.065 -10000 0 -0.21 19 19
YY1/SAP30/HDAC1 0.014 0.065 -10000 0 -0.21 19 19
EP300 0.027 0.008 -10000 0 0 50 50
STAT3 (dimer non-phopshorylated) 0.003 0.04 -10000 0 -0.23 15 15
proteasomal ubiquitin-dependent protein catabolic process 0 0.051 -10000 0 -0.31 12 12
histone deacetylation 0.005 0.065 0.18 5 -0.27 12 17
STAT3 (dimer non-phopshorylated)/HDAC3 -0.001 0.068 -10000 0 -0.3 13 13
nuclear export -0.046 0.024 -10000 0 -10000 0 0
PRKACA 0.025 0.01 -10000 0 0 80 80
GATAD2B 0.028 0.006 -10000 0 0 22 22
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 0.026 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 0.19 5 -0.3 15 20
NuRD Complex -0.006 0.084 0.25 1 -0.34 16 17
positive regulation of chromatin silencing 0.051 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 0.028 0.005 -10000 0 0 18 18
XPO1 0.027 0.008 -10000 0 0 51 51
SUMO1/HDAC1 0.022 0.051 0.16 1 -0.22 11 12
HDAC complex 0.065 0.039 -10000 0 -0.14 2 2
GATA1/Fog1 0.036 0.016 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.049 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 0.19 5 -0.3 15 20
NuRD/MBD2/PRMT5 Complex 0.005 0.065 0.18 5 -0.27 12 17
Ran/GTP/Exportin 1 0.021 0.052 -10000 0 -0.22 12 12
NF kappa B/RelA/I kappa B alpha -0.017 0.075 -10000 0 -0.3 28 28
SIN3/HDAC complex/NCoR1 -0.008 0.083 0.16 6 -0.33 22 28
TFCP2 0.027 0.008 -10000 0 0 42 42
NR2C1 0.029 0.005 -10000 0 0 14 14
MBD3 0.027 0.008 -10000 0 0 51 51
MBD2 0.028 0.007 -10000 0 0 35 35
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.049 0.16 0.51 22 -10000 0 22
PTGS2 -0.059 0.15 0.51 20 -10000 0 20
JUNB 0.019 0.014 -10000 0 0 189 189
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.031 0.09 29 -0.16 6 35
CaM/Ca2+ -0.017 0.031 0.09 29 -0.16 6 35
CALM1 -0.024 0.027 0.092 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 0.011 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 8 8
Jun/NFAT1-c-4/p21SNFT -0.045 0.11 0.35 27 -10000 0 27
FOS -0.021 0.025 0.092 5 -10000 0 5
IFNG -0.069 0.12 0.46 9 -10000 0 9
AP-1/NFAT1-c-4 -0.071 0.13 0.5 17 -10000 0 17
FASLG -0.052 0.16 0.5 25 -10000 0 25
NFAT1-c-4/ICER1 -0.038 0.1 0.3 30 -10000 0 30
IL2RA -0.052 0.15 0.47 23 -10000 0 23
FKBP12/FK506 0.02 0.006 -10000 0 -10000 0 0
CSF2 -0.049 0.16 0.63 9 -10000 0 9
JunB/Fra1/NFAT1-c-4 -0.059 0.098 0.3 19 -10000 0 19
IL4 -0.05 0.16 0.5 27 -10000 0 27
IL2 -0.035 0.21 -10000 0 -0.93 29 29
IL3 0 0.11 -10000 0 -0.66 14 14
FKBP1A 0.027 0.007 -10000 0 0 39 39
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
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 -10000 0 53
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 0.044 -10000 0 -0.16 25 25
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.032 0.022 -10000 0 -10000 0 0
CLTB 0.029 0.005 -10000 0 0 14 14
coatomer protein complex/ARF1/GTP/ER cargo protein -0.014 0.039 0.12 1 -0.18 23 24
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 -0.016 0.031 -10000 0 -0.16 21 21
mol:Choline -0.005 0.024 0.092 7 -0.15 1 8
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.019 0.024 0.044 12 -10000 0 12
DDEF1 -0.003 0.023 0.093 7 -0.16 1 8
ARF1/GDP -0.002 0.013 -10000 0 -0.095 5 5
AP2M1 0.024 0.011 -10000 0 0 97 97
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 0.011 -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 0.026 11 -10000 0 11
COPA 0.028 0.005 -10000 0 0 19 19
RAC1 0.028 0.006 -10000 0 0 27 27
ARF1/GTP/coatomer protein complex -0.001 0.04 -10000 0 -0.16 23 23
ARF1/GTP/ARHGAP10 0.012 0.031 -10000 0 -0.13 25 25
GGA3 0.028 0.005 -10000 0 0 19 19
ARF1/GTP/Membrin 0.006 0.053 -10000 0 -0.17 41 41
AP2A1 0.027 0.008 -10000 0 0 48 48
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.01 0.035 -10000 0 -0.16 27 27
ARF1/GDP/Membrin 0.012 0.058 -10000 0 -0.26 17 17
Arfaptin 2/Rac/GDP 0.033 0.019 -10000 0 -10000 0 0
CYTH2 -0.004 0.004 0.012 4 -0.022 25 29
ARF1/GTP/GGA3 0.028 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 0.092 7 -0.15 1 8
ARF-GAP1/v-SNARE -0.015 0.005 0 61 -10000 0 61
PIP5K1A -0.004 0.024 0.093 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 0.092 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 0.051 -10000 0 -0.35 11 11
GBF1 0.001 0.052 -10000 0 -0.34 12 12
ARF1/GTP/Arfaptin 2 0.027 0.041 -10000 0 -0.15 25 25
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.035 0.044 -10000 0 -0.15 20 20
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.04 0.021 0.2 1 -10000 0 1
KIRREL -0.022 0.03 0.048 80 -10000 0 80
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.04 0.021 -10000 0 -0.2 1 1
PLCG1 0.028 0.007 -10000 0 0 31 31
ARRB2 0.028 0.006 -10000 0 0 25 25
WASL 0.028 0.006 -10000 0 0 22 22
Nephrin/NEPH1/podocin/CD2AP 0.064 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 -0.22 1 77
mol:Ca2+ 0.061 0.038 -10000 0 -0.17 1 1
mol:DAG 0.062 0.039 -10000 0 -0.17 1 1
NPHS2 -0.02 0.033 0.05 96 -10000 0 96
mol:IP3 0.062 0.039 -10000 0 -0.17 1 1
regulation of endocytosis 0.031 0.052 -10000 0 -0.21 1 1
Nephrin/NEPH1/podocin/Cholesterol 0.051 0.03 0.15 2 -0.16 1 3
establishment of cell polarity 0.04 0.021 -10000 0 -0.2 1 1
Nephrin/NEPH1/podocin/NCK1-2 0.081 0.047 -10000 0 -0.16 1 1
Nephrin/NEPH1/beta Arrestin2 0.033 0.054 -10000 0 -0.21 1 1
NPHS1 -0.024 0.027 0.05 52 -10000 0 52
Nephrin/NEPH1/podocin 0.03 0.049 0.19 3 -0.22 1 4
TJP1 0.027 0.007 -10000 0 0 38 38
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 0.063 0.04 -10000 0 -0.17 1 1
CD2AP 0.028 0.007 -10000 0 0 31 31
Nephrin/NEPH1/podocin/GRB2 0.064 0.039 0.2 1 -0.17 1 2
GRB2 0.028 0.005 -10000 0 0 20 20
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.013 0.072 0.15 82 -10000 0 82
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
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.064 0.037 -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 0.012 -10000 0 -10000 0 0
GATA1/HDAC5 0.038 0.021 -10000 0 -0.16 4 4
GATA2/HDAC5 0.037 0.028 -10000 0 -0.16 9 9
HDAC5/BCL6/BCoR 0.041 0.04 -10000 0 -0.15 15 15
HDAC9 0.027 0.008 -10000 0 0 50 50
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.03 -10000 0 -0.15 8 8
HDAC4/ANKRA2 0.039 0.014 -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 0.014 -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 0.012 -10000 0 0 130 130
HDAC5 0.028 0.007 -10000 0 0 29 29
GNB1/GNG2 0.041 0.013 -10000 0 -0.16 1 1
Histones -0.02 0.069 -10000 0 -0.23 28 28
ADRBK1 0.029 0.003 -10000 0 0 7 7
HDAC4 0.029 0.005 -10000 0 0 16 16
XPO1 0.027 0.008 -10000 0 0 51 51
HDAC5/ANKRA2 0.037 0.022 -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 0.036 0.023 -10000 0 -0.16 4 4
CAMK4 0.027 0.007 -10000 0 0 39 39
Tubulin/HDAC6 0.052 0.02 -10000 0 -10000 0 0
SUMO1 0.029 0.003 -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 0.027 0.008 -10000 0 0 40 40
NR3C1 0.029 0.005 -10000 0 0 15 15
SUMO1/HDAC4 0.023 0.054 -10000 0 -0.22 13 13
SRF 0.028 0.007 -10000 0 0 30 30
HDAC4/YWHAB 0.039 0.013 -10000 0 -10000 0 0
Tubulin 0.04 0.012 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.039 0.015 -10000 0 -0.16 1 1
GNB1 0.028 0.006 -10000 0 0 24 24
RANGAP1 0.027 0.008 -10000 0 0 47 47
BCL6/BCoR 0.031 0.033 -10000 0 -0.16 12 12
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 0.029 -10000 0 -0.15 9 9
HDAC4/SRF 0.051 0.023 -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 0.068 -10000 0 -0.23 28 28
cell motility 0.051 0.02 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.028 0.006 -10000 0 0 23 23
HDAC7/HDAC3 0.021 0.002 -10000 0 -10000 0 0
BCL6 0.024 0.011 -10000 0 0 99 99
HDAC4/CaMK II delta B 0.028 0.005 -10000 0 0 16 16
Hsp90/HDAC6 0.04 0.012 -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 0.021 0.052 -10000 0 -0.22 12 12
NPC 0.017 0.002 -10000 0 -10000 0 0
MEF2C 0.026 0.009 -10000 0 0 65 65
RAN 0.029 0.004 -10000 0 0 12 12
HDAC4/MEF2C 0.058 0.064 -10000 0 -0.14 29 29
GNG2 0.029 0.004 -10000 0 0 12 12
NCOR2 0.028 0.005 -10000 0 0 17 17
TUBB2A 0.027 0.008 -10000 0 0 41 41
HDAC11 0.029 0.003 -10000 0 0 7 7
HSP90AA1 0.028 0.005 -10000 0 0 20 20
RANBP2 0.029 0.004 -10000 0 0 10 10
ANKRA2 0.026 0.009 -10000 0 0 55 55
RFXANK 0.027 0.009 -10000 0 0 53 53
nuclear import -0.016 0.038 0.19 5 -10000 0 5
JNK signaling in the CD4+ TCR 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
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 -0.27 9 9
JUN -0.002 0.064 0.24 1 -0.57 4 5
MAP3K7 -0.014 0.045 0.15 3 -0.21 9 12
GRAP2 0.027 0.008 -10000 0 0 47 47
CRK 0.027 0.007 -10000 0 0 36 36
MAP2K4 -0.027 0.083 0.26 1 -0.37 18 19
LAT 0.029 0.003 -10000 0 0 8 8
LCP2 0.028 0.007 -10000 0 0 35 35
MAPK8 0.003 0.056 -10000 0 -0.59 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.06 -10000 0 -0.28 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55 0.059 0.055 -10000 0 -0.14 12 12
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.008 -10000 0 -10000 0 0
HDAC2 0.028 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.051 0.023 -10000 0 -0.16 1 1
forebrain development -0.004 0.086 -10000 0 -0.46 7 7
GNAO1 0.022 0.018 -10000 0 -0.035 40 40
SMO/beta Arrestin2 0.033 0.025 -10000 0 -10000 0 0
SMO 0.022 0.019 -10000 0 -0.038 47 47
ARRB2 0.023 0.017 -10000 0 -0.034 39 39
GLI3/SPOP 0.017 0.089 0.23 6 -0.34 14 20
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.005 -10000 0 0 19 19
GNAI2 0.024 0.017 -10000 0 -0.035 42 42
SIN3/HDAC complex 0.054 0.042 -10000 0 -10000 0 0
GNAI1 0.023 0.017 -10000 0 -0.034 41 41
XPO1 0.006 0.028 -10000 0 -0.045 34 34
GLI1/Su(fu) -0.001 0.089 -10000 0 -0.53 6 6
SAP30 0.027 0.008 -10000 0 -10000 0 0
mol:GDP 0.022 0.019 -10000 0 -0.038 47 47
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 0.076 0.22 1 -0.34 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 45 45
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 0.026 0.009 -10000 0 -10000 0 0
SIN3A 0.029 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) -0.001 0.096 0.22 3 -0.4 14 17
GLI2/Su(fu) -0.009 0.087 0.19 1 -0.38 18 19
FOXA2 -0.036 0.21 -10000 0 -0.79 37 37
neural tube patterning -0.004 0.086 -10000 0 -0.46 7 7
SPOP 0.029 0.005 -10000 0 0 16 16
Su(fu)/PIAS1 0.018 0.043 -10000 0 -0.19 15 15
GNB1 0.028 0.006 -10000 0 0 24 24
CSNK1G2 0.027 0.008 -10000 0 0 45 45
CSNK1G3 0.028 0.006 -10000 0 0 21 21
MTSS1 0.013 0.036 -10000 0 -0.13 29 29
embryonic limb morphogenesis -0.004 0.086 -10000 0 -0.46 7 7
SUFU 0.006 0.016 -10000 0 -10000 0 0
LGALS3 0.026 0.009 -10000 0 0 56 56
catabolic process 0.006 0.11 0.25 1 -0.43 18 19
GLI3A/CBP -0.031 0.01 -10000 0 -10000 0 0
KIF3A 0.028 0.005 -10000 0 0 17 17
GLI1 -0.005 0.087 -10000 0 -0.47 7 7
RAB23 0.028 0.005 -10000 0 0 20 20
CSNK1A1 0.029 0.004 -10000 0 0 13 13
IFT172 0.028 0.005 -10000 0 0 17 17
RBBP7 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.016 0.044 -10000 0 -0.19 13 13
GNAZ 0.022 0.017 -10000 0 -0.035 38 38
RBBP4 0.027 0.008 -10000 0 -10000 0 0
CSNK1G1 0.029 0.004 -10000 0 0 13 13
PIAS1 0.029 0.005 -10000 0 0 14 14
PRKACA 0.025 0.01 -10000 0 0 80 80
GLI2/SPOP 0.005 0.084 0.21 1 -0.36 15 16
STK36 0.007 0.029 -10000 0 -0.044 40 40
Gi family/GNB1/GNG2/GDP 0.003 0.064 -10000 0 -0.25 13 13
PTCH1 -0.018 0.13 -10000 0 -0.91 9 9
MIM/GLI1 -0.007 0.11 -10000 0 -0.5 8 8
CREBBP -0.031 0.01 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex -0.001 0.098 0.18 6 -0.4 20 26
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.001 0.093 0.6 12 -10000 0 12
regulation of axonogenesis 0.002 0.05 0.28 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 30 40
mol:GM1 0.01 0.034 0.2 13 -0.13 7 20
mol:Choline -0.011 0.041 0.16 25 -0.14 5 30
lamellipodium assembly 0.005 0.068 0.35 12 -0.38 6 18
MAPK3 -0.005 0.063 0.39 13 -10000 0 13
ARF6/GTP/NME1/Tiam1 0.048 0.054 0.31 13 -0.15 1 14
ARF1 0.026 0.009 -10000 0 0 55 55
ARF6/GDP 0.021 0.061 0.35 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 0.004 -10000 0 0 13 13
TIAM1 -0.021 0.023 0.064 13 -10000 0 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.004 0.063 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 0.025 0.059 0.3 12 -0.23 7 19
NME1 -0.02 0.023 0.062 14 -10000 0 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 27 27
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 0.056 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 0.007 -10000 0 0 29 29
tube morphogenesis 0.005 0.068 0.35 12 -0.38 6 18
ruffle organization -0.002 0.05 0.21 12 -0.28 6 18
regulation of epithelial cell migration 0.027 0.038 0.23 12 -0.18 7 19
PLD2 -0.008 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 0.041 0.16 25 -0.14 5 30
Rac1/GTP 0.005 0.069 0.35 12 -0.38 6 18
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 0.056 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 44 44
RhoA/GTP 0.021 0.057 0.17 1 -0.19 9 10
negative regulation of cAMP metabolic process 0.011 0.052 0.18 1 -0.18 14 15
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 33 33
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.011 0.052 0.18 1 -0.19 14 15
RhoA/GDP 0.021 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 mediated by p38-alpha and p38-beta

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
PTGS2 0.001 0.096 0.53 9 -0.85 3 12
MKNK1 0.029 0.005 -10000 0 0 14 14
MAPK14 -0.01 0.059 0.2 24 -0.3 3 27
ATF2/c-Jun -0.038 0.055 -10000 0 -0.27 4 4
MAPK11 -0.017 0.052 0.2 19 -0.3 3 22
MITF -0.001 0.049 0.22 18 -0.34 3 21
MAPKAPK5 -0.001 0.049 0.22 18 -0.34 3 21
KRT8 -0.001 0.05 0.22 18 -0.3 4 22
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 0.067 0.27 18 -0.42 3 21
CEBPB 0 0.046 0.22 18 -0.25 3 21
SLC9A1 -0.001 0.048 0.22 18 -0.34 3 21
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.002 0.073 0.35 19 -0.33 3 22
p38alpha-beta/MNK1 0.045 0.054 0.25 18 -0.35 3 21
JUN -0.037 0.055 -10000 0 -0.27 4 4
PPARGC1A 0 0.049 0.22 17 -0.34 3 20
USF1 0 0.051 0.23 18 -0.34 3 21
RAB5/GDP/GDI1 -0.005 0.071 -10000 0 -0.2 10 10
NOS2 0 0.048 0.22 18 -0.33 3 21
DDIT3 0.011 0.066 0.23 20 -0.34 3 23
RAB5A 0.029 0.003 -10000 0 0 8 8
HSPB1 -0.011 0.044 0.2 12 -0.29 3 15
p38alpha-beta/HBP1 0.043 0.054 0.25 17 -0.35 3 20
CREB1 -0.027 0.098 0.25 9 -0.35 3 12
RAB5/GDP 0.021 0.003 -10000 0 -10000 0 0
EIF4E -0.035 0.054 0.18 16 -0.32 3 19
RPS6KA4 -0.001 0.049 0.22 18 -0.34 3 21
PLA2G4A -0.018 0.046 0.18 6 -0.38 3 9
GDI1 -0.001 0.051 0.23 18 -0.29 5 23
TP53 -0.022 0.061 0.26 9 -0.46 3 12
RPS6KA5 -0.001 0.049 0.22 18 -0.34 3 21
ESR1 -0.025 0.08 0.22 15 -0.22 60 75
HBP1 0.027 0.007 -10000 0 0 37 37
MEF2C -0.006 0.058 0.22 16 -0.26 13 29
MEF2A -0.002 0.047 0.22 17 -0.34 3 20
EIF4EBP1 -0.023 0.093 0.24 10 -0.36 3 13
KRT19 -0.008 0.062 0.22 18 -0.24 20 38
ELK4 -0.001 0.049 0.23 17 -0.34 3 20
ATF6 -0.001 0.05 0.23 18 -0.34 3 21
ATF1 -0.027 0.099 0.24 10 -0.35 3 13
p38alpha-beta/MAPKAPK2 0.045 0.053 0.25 16 -0.35 3 19
p38alpha-beta/MAPKAPK3 0.046 0.054 0.25 18 -0.35 3 21
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.068 -10000 0 -0.17 67 67
AKT1 -0.049 0.11 -10000 0 -0.4 6 6
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 0.33 3 -0.38 4 7
mol:Ca2+ -0.047 0.081 0.32 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.01 0.09 0.28 1 -0.24 1 2
RP11-342D11.1 -0.047 0.069 0.33 2 -10000 0 2
CDH5 0.026 0.009 -10000 0 0 57 57
VEGFA homodimer 0.067 0.036 -10000 0 -0.14 1 1
SHC1 0.028 0.006 -10000 0 0 21 21
SHC2 0.025 0.01 -10000 0 0 80 80
HRAS/GDP -0.068 0.065 -10000 0 -10000 0 0
SH2D2A 0.029 0.005 -10000 0 0 15 15
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.023 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 0.021 0.096 -10000 0 -10000 0 0
GRB10 -0.049 0.082 0.32 4 -10000 0 4
PTPN11 0.029 0.003 -10000 0 0 8 8
GRB2 0.028 0.005 -10000 0 0 20 20
PAK1 0.027 0.008 -10000 0 0 47 47
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.013 0.096 0.28 1 -0.24 1 2
HRAS 0.028 0.006 -10000 0 0 27 27
VEGF/Rho/ROCK1/Integrin Complex -0.026 0.093 0.29 1 -0.28 36 37
HIF1A 0.028 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 0.035 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.07 0.06 0.28 1 -0.24 16 17
mol:GDP -0.061 0.07 0.21 1 -10000 0 1
mol:NADP -0.02 0.086 0.3 1 -0.47 3 4
eNOS/Hsp90 -0.021 0.088 0.29 2 -0.45 3 5
PIK3R1 0.021 0.013 -10000 0 0 159 159
mol:IP3 -0.047 0.081 0.32 4 -10000 0 4
HIF1A/ARNT 0.039 0.015 -10000 0 -0.16 1 1
SHB 0.029 0.003 -10000 0 0 8 8
VEGFA -0.026 0.01 -10000 0 -10000 0 0
VEGFC 0.023 0.012 -10000 0 0 112 112
FAK1/Vinculin -0.038 0.12 0.34 5 -0.38 10 15
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 -0.001 0.1 0.28 1 -0.24 28 29
PTPN6 0.026 0.009 -10000 0 0 59 59
EPAS1 -0.025 0.015 -10000 0 -10000 0 0
mol:L-citrulline -0.02 0.086 0.3 1 -0.47 3 4
ITGAV 0.028 0.007 -10000 0 0 33 33
PIK3CA 0.02 0.014 -10000 0 0 172 172
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.014 0.087 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 0.049 -10000 0 -10000 0 0
VEGFB 0.028 0.006 -10000 0 0 24 24
MAPK11 -0.044 0.09 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 0.035 0.017 -10000 0 -10000 0 0
VEGFR1/2 heterodimer -0.063 0.049 -10000 0 -10000 0 0
KDR -0.062 0.064 0.4 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 0.088 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.056 0.052 0.28 1 -10000 0 1
FES -0.049 0.083 0.33 4 -10000 0 4
GAB1 -0.048 0.093 0.35 1 -0.38 2 3
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 35 35
ARNT 0.027 0.007 -10000 0 0 37 37
eNOS/Caveolin-1 -0.025 0.091 0.28 1 -0.47 3 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.057 0.05 0.28 1 -10000 0 1
PI3K/GAB1 -0.058 0.14 0.29 1 -0.37 23 24
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.023 0.09 0.28 1 -10000 0 1
PRKACA 0.025 0.01 -10000 0 0 80 80
VEGFR2/3 heterodimer/VEGFC homodimer -0.074 0.058 0.28 1 -0.24 16 17
HSP90AA1 0.028 0.005 -10000 0 0 20 20
CDC42 -0.05 0.084 0.33 4 -10000 0 4
actin cytoskeleton reorganization -0.06 0.05 0.27 1 -10000 0 1
PTK2 -0.046 0.11 0.35 3 -0.38 11 14
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+ -0.05 0.081 0.3 3 -10000 0 3
MAP2K3 -0.042 0.078 0.34 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.062 0.062 0.22 4 -10000 0 4
PLCG1 -0.048 0.082 0.33 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.014 0.087 0.28 1 -10000 0 1
IQGAP1 0.028 0.006 -10000 0 0 25 25
YES1 0.027 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 0.084 -10000 0 -10000 0 0
FYN 0.024 0.011 -10000 0 0 99 99
VEGFB/NRP1 -0.05 0.081 0.3 4 -10000 0 4
mol:NO -0.02 0.086 0.3 1 -0.47 3 4
PXN 0.029 0.005 -10000 0 0 14 14
HRAS/GTP -0.075 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 0.056 0.28 1 -0.24 5 6
RAC1 0.028 0.006 -10000 0 0 27 27
PRKCA -0.049 0.084 0.32 6 -10000 0 6
PRKCB -0.043 0.08 0.31 7 -10000 0 7
VCL 0.029 0.004 -10000 0 0 13 13
VEGFA165/NRP1 -0.053 0.058 0.27 1 -10000 0 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.061 0.051 0.28 1 -10000 0 1
VEGFA165/NRP2 0.035 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.07 0.076 0.27 4 -10000 0 4
NRP2 0.028 0.007 -10000 0 0 35 35
VEGFC homodimer 0.023 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 -0.04 0.13 0.34 5 -0.38 11 16
MAP3K13 -0.041 0.08 0.33 4 -10000 0 4
PDPK1 -0.045 0.081 -10000 0 -10000 0 0
VEGFR1 specific signals

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
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 0.031 0.006 -10000 0 -10000 0 0
GAB1 0.028 0.006 -10000 0 0 24 24
AKT1 -0.029 0.089 0.24 2 -10000 0 2
PLCG1 -0.041 0.021 0.17 3 -10000 0 3
NOS3 -0.018 0.055 -10000 0 -0.3 2 2
CBL 0.029 0.005 -10000 0 0 14 14
mol:NO -0.012 0.065 0.4 2 -0.29 2 4
FLT1 -0.03 0.008 -10000 0 -10000 0 0
PGF 0.028 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 0.02 0.014 -10000 0 0 172 172
eNOS/Hsp90 -0.009 0.074 0.32 1 -10000 0 1
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 0 159 159
PLGF homodimer 0.028 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 71 71
VEGFR1 homodimer/VEGFA homodimer -0.034 0.015 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.053 0.047 0.3 1 -10000 0 1
PI3K 0.017 0.074 -10000 0 -10000 0 0
PRKCA -0.045 0.028 -10000 0 -10000 0 0
PRKCB -0.038 0.019 0.16 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer -0.038 0.01 -10000 0 -10000 0 0
VEGFA 0.026 0.01 -10000 0 0 71 71
VEGFB 0.028 0.006 -10000 0 0 24 24
mol:IP3 -0.041 0.021 0.17 3 -10000 0 3
RASA1 -0.044 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 0.081 0.39 2 -0.32 4 6
PTPN11 0.029 0.003 -10000 0 0 8 8
mol:PI-3-4-5-P3 0.016 0.073 -10000 0 -10000 0 0
mol:L-citrulline -0.012 0.065 0.4 2 -0.29 2 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.052 0.037 -10000 0 -10000 0 0
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 0.09 0.32 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.039 0.017 -10000 0 -10000 0 0
mol:NADP -0.012 0.065 0.4 2 -0.29 2 4
HSP90AA1 0.028 0.005 -10000 0 0 20 20
ubiquitin-dependent protein catabolic process 0.05 0.036 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.036 0.012 -10000 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0.018 0.014 -10000 0 -0.1 7 7
TRAF2/ASK1 0.036 0.013 -10000 0 -0.13 1 1
ATM 0.028 0.007 -10000 0 0 30 30
MAP2K3 -0.021 0.099 -10000 0 -0.31 39 39
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.015 0.089 0.18 1 -0.37 17 18
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.028 0.006 -10000 0 0 22 22
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 49 49
MAP3K1 0.027 0.008 -10000 0 0 51 51
MAP3K6 0.028 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 0.014 -10000 0 -0.16 1 1
TAK1/TAB family 0.016 0.028 -10000 0 -0.14 2 2
RAC1/OSM/MEKK3 0.051 0.02 -10000 0 -10000 0 0
TRAF2 0.028 0.006 -10000 0 0 23 23
RAC1/OSM/MEKK3/MKK3 0.003 0.096 -10000 0 -0.27 38 38
TRAF6 0.003 0 -10000 0 -10000 0 0
RAC1 0.028 0.006 -10000 0 0 27 27
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 0.035 0.022 -10000 0 -0.13 8 8
MAPK11 0.023 0.012 -10000 0 0 130 130
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 0.006 0.002 -10000 0 -10000 0 0
TAOK2 0.006 0.002 -10000 0 -10000 0 0
TAOK3 0.006 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.028 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 0.015 0.039 -10000 0 -0.17 23 23
GADD45/MTK1/MTK1 0.055 0.047 -10000 0 -0.13 7 7
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 0.008 -10000 0 0 50 50
HDAC4 0.029 0.005 -10000 0 0 16 16
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.015 0.023 -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 0.028 0.006 -10000 0 0 21 21
FOXO3 0.004 0.013 0.26 1 -10000 0 1
FOXO1 0.027 0.007 -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 49 49
TAT 0.026 0.009 -10000 0 0 58 58
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 25 25
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 0.023 0.16 12 -10000 0 12
SIRT1/Histone H1b 0.007 0.068 -10000 0 -0.21 22 22
apoptosis -0.053 0.029 -10000 0 -0.16 12 12
SIRT1/PGC1A 0.04 0.019 0.14 14 -10000 0 14
p53/SIRT1 0.022 0.088 0.34 13 -0.17 73 86
SIRT1/FOXO4 0.005 0.065 -10000 0 -0.22 20 20
FOXO1/FHL2/SIRT1 0.05 0.031 0.15 11 -0.13 3 14
HIST1H1E 0.001 0.03 0.13 8 -0.19 10 18
SIRT1/p300 0.042 0.024 0.15 13 -0.17 1 14
muscle cell differentiation 0.024 0.025 -10000 0 -0.12 15 15
TP53 -0.02 0.035 0.18 14 -10000 0 14
KU70/SIRT1/BAX 0.054 0.029 0.16 12 -10000 0 12
CREBBP 0.027 0.008 -10000 0 0 41 41
MEF2D 0.029 0.005 -10000 0 0 15 15
HIV-1 Tat/SIRT1 0.041 0.021 0.15 10 -10000 0 10
ACSS2 -0.029 0.026 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 -0.028 0.005 0 17 -9999 0 17
PI3K Class IB/PDE3B 0.028 0.005 -9999 0 0 17 17
PDE3B 0.028 0.005 -9999 0 0 17 17
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.044 0.02 -10000 0 -10000 0 0
RGS9BP 0.026 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 + 0.035 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 0.027 0.007 -10000 0 0 39 39
CNGB3 0.027 0.008 -10000 0 0 47 47
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 0.058 0.05 -10000 0 -0.14 5 5
Cone Metarhodopsin II 0.018 0.005 -10000 0 -10000 0 0
Na + (4 Units) 0.046 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 0.048 0.022 -10000 0 -10000 0 0
SLC24A2 0.028 0.007 -10000 0 0 30 30
GNB3/GNGT2 0.038 0.015 -10000 0 -10000 0 0
GNB3 0.026 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 0.047 0.03 -10000 0 -0.15 6 6
Cone CNG Channel 0.055 0.035 -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 30 30
RGS9 0.029 0.005 -10000 0 0 15 15
PDE6C 0.028 0.005 -10000 0 0 18 18
GNGT2 0.028 0.005 -10000 0 0 18 18
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.026 0.009 -10000 0 0 55 55
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.028 0.006 -9999 0 0 22 22
ITGB7 0.029 0.004 -9999 0 0 9 9
ITGA4 0.027 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 0.013 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
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 0.053 -10000 0 -0.22 13 13
HDAC4 0.029 0.005 -10000 0 0 16 16
Ran/GTP/Exportin 1/HDAC1 -0.037 0.021 -10000 0 -0.14 3 3
SUMO1 0.029 0.003 -10000 0 0 8 8
NPC/RanGAP1/SUMO1 0.002 0.02 0.091 2 -0.2 5 7
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 0.054 -10000 0 -0.22 13 13
SUMO1/HDAC1 0.022 0.051 0.16 1 -0.22 11 12
RANGAP1 0.027 0.008 -10000 0 0 47 47
MDM2/SUMO1/SUMO1 0.063 0.034 -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 0.048 -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 0.028 0.006 -10000 0 0 23 23
Ran/GTP/Exportin 1 -0.014 0.062 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 14 14
EntrezGene:9972 0 0 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.027 0.008 -10000 0 0 44 44
CDC42/GTP 0.02 0.058 0.17 1 -0.19 10 11
PLCG1 -0.01 0.052 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 0.04 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 -0.011 0.051 0.16 1 -0.2 8 9
MAPK1 -0.006 0.046 0.16 1 -0.21 4 5
S1P/S1P5/Gi 0.011 0.052 0.18 1 -0.19 14 15
GNAI1 0.028 0.006 -10000 0 0 27 27
CDC42/GDP 0.021 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.019 0.005 -10000 0 -10000 0 0
RHOA -0.029 0.029 0.2 8 -10000 0 8
S1P/S1P4/Gi 0.011 0.052 0.18 1 -0.19 14 15
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 33 33
GNA13 0.029 0.005 -10000 0 0 14 14
CDC42 0.029 0.004 -10000 0 0 11 11
Alternative NF-kappaB 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
IKK alpha homodimer 0.039 0.013 -9999 0 -10000 0 0
FBXW11 0.028 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 0.028 0.005 -9999 0 0 18 18
CHUK 0.027 0.007 -9999 0 0 36 36
NF kappa B2 p100/RelB 0.073 0.044 -9999 0 -0.14 2 2
NFKB1 0.027 0.008 -9999 0 0 45 45
MAP3K14 0.028 0.006 -9999 0 0 21 21
NF kappa B1 p50/RelB 0.036 0.027 -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 0.036 0.014 -9999 0 -0.13 2 2
regulation of B cell activation 0.036 0.014 -9999 0 -0.13 2 2
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 0.034 0.018 -10000 0 -0.13 3 3
EPHA5 0.028 0.007 -10000 0 0 29 29
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.038 0.12 0.81 3 -10000 0 3
NCK1/PAK1/Dok-R -0.044 0.055 -10000 0 -0.32 2 2
NCK1/Dok-R 0.015 0.07 0.71 1 -10000 0 1
PIK3CA 0.019 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 0.025 0.016 0.074 1 -10000 0 1
Rac/GDP 0.021 0.005 -10000 0 -10000 0 0
F2 0.012 0.044 -10000 0 -0.23 11 11
TNIP2 0.028 0.007 -10000 0 0 34 34
NF kappa B/RelA 0.03 0.078 0.68 1 -10000 0 1
FN1 0.018 0.014 -10000 0 0 213 213
PLD2 -0.011 0.059 0.82 1 -10000 0 1
PTPN11 0.029 0.003 -10000 0 0 8 8
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 41 41
PAK1 0.027 0.008 -10000 0 0 47 47
Tie2/Ang1/alpha5/beta1 Integrin 0.034 0.072 -10000 0 -10000 0 0
CDKN1A -0.04 0.16 0.72 5 -0.72 16 21
ITGA5 0.028 0.005 -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 0.027 0.007 -10000 0 0 36 36
mol:NO -0.031 0.12 0.63 5 -10000 0 5
PLG -0.012 0.057 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 0.028 0.005 -10000 0 0 20 20
PIK3R1 0.018 0.018 0.075 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 -0.042 0.12 0.69 6 -10000 0 6
ANGPT4 0.022 0.02 0.081 6 -10000 0 6
response to hypoxia -0.002 0.009 0.084 3 -10000 0 3
Tie2/Ang1/GRB14 -0.004 0.067 0.75 1 -10000 0 1
alpha5/beta1 Integrin 0.04 0.011 -10000 0 -10000 0 0
FGF2 0.024 0.016 -10000 0 -0.079 5 5
STAT5A (dimer) -0.04 0.15 0.73 5 -0.67 4 9
mol:L-citrulline -0.031 0.12 0.63 5 -10000 0 5
AGTR1 0.026 0.015 0.11 5 -0.033 16 21
MAPK14 0 0.092 0.79 2 -0.76 1 3
Tie2/SHP2 0.005 0.089 -10000 0 -10000 0 0
TEK -0.001 0.089 0.87 1 -10000 0 1
RPS6KB1 -0.039 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 0.056 -10000 0 -10000 0 0
NFKB1 0.027 0.008 -10000 0 0 45 45
MAPK8 -0.011 0.062 0.82 1 -10000 0 1
PI3K -0.035 0.12 0.9 2 -0.6 1 3
FES -0.004 0.1 0.8 2 -0.71 3 5
Crk/Dok-R 0.017 0.072 0.71 1 -10000 0 1
Tie2/Ang1/ABIN2 -0.003 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 0.8 3 -10000 0 3
STAT5A 0.026 0.012 -10000 0 -0.01 49 49
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0 0.14 0.76 3 -0.55 1 4
Tie2/Ang2 -0.035 0.13 0.75 5 -10000 0 5
Tie2/Ang1 0.002 0.064 0.96 1 -10000 0 1
FOXO1 -0.036 0.12 0.82 3 -10000 0 3
ELF1 -0.011 0.032 0.26 1 -10000 0 1
ELF2 -0.002 0.061 0.92 1 -10000 0 1
mol:Choline -0.01 0.062 0.81 1 -10000 0 1
cell migration -0.024 0.036 -10000 0 -0.18 1 1
FYN -0.045 0.13 0.7 6 -10000 0 6
DOK2 0.024 0.011 -10000 0 0 104 104
negative regulation of cell cycle -0.036 0.15 0.71 5 -0.64 16 21
ETS1 -0.01 0.034 0.2 5 -10000 0 5
PXN 0 0.14 0.72 3 -10000 0 3
ITGB1 0.028 0.006 -10000 0 0 22 22
NOS3 -0.034 0.12 0.76 3 -10000 0 3
RAC1 0.028 0.006 -10000 0 0 27 27
TNF -0.008 0.038 0.22 7 -10000 0 7
MAPKKK cascade -0.01 0.062 0.81 1 -10000 0 1
RASA1 0.027 0.008 -10000 0 0 49 49
Tie2/Ang1/Shc 0.002 0.071 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 -0.01 0.062 0.81 1 -10000 0 1
mol:Angiotensin II 0.001 0.009 0.085 6 -10000 0 6
mol:NADP -0.031 0.12 0.63 5 -10000 0 5
Rac1/GTP -0.032 0.11 0.65 1 -0.52 2 3
MMP2 -0.007 0.073 0.82 1 -10000 0 1
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.038 0.019 -10000 0 -10000 0 0
PDGFRB 0.023 0.02 0.071 1 -10000 0 1
SPHK1 0.004 0.083 -10000 0 -0.67 8 8
mol:S1P 0 0.079 0.25 1 -0.58 8 9
S1P1/S1P/Gi 0.001 0.098 0.48 12 -0.33 7 19
GNAO1 0.019 0.024 0.087 11 -0.045 3 14
PDGFB-D/PDGFRB/PLCgamma1 0.004 0.1 0.44 13 -0.35 4 17
PLCG1 -0.004 0.096 0.45 12 -0.32 6 18
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.02 0.071 1 -10000 0 1
GNAI2 0.02 0.024 0.087 11 -0.045 3 14
GNAI3 -0.008 0.028 0.078 10 -10000 0 10
GNAI1 -0.004 0.03 0.078 11 -10000 0 11
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.01 0.049 0.14 50 -10000 0 50
S1P1/S1P -0.011 0.069 0.28 10 -0.4 8 18
negative regulation of cAMP metabolic process 0.002 0.097 0.48 12 -0.32 7 19
MAPK3 -0.003 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 0.021 0.007 -10000 0 -0.15 1 1
KDR 0.028 0.01 0.064 2 -0.033 8 10
PLCB2 0 0.084 0.28 16 -0.36 8 24
RAC1 0.028 0.006 -10000 0 0 27 27
RhoA/GTP -0.021 0.048 -10000 0 -0.35 8 8
receptor internalization -0.011 0.065 0.27 10 -0.37 8 18
PTGS2 0.002 0.13 0.65 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 0.025 0.013 0.067 1 -0.034 7 8
negative regulation of T cell proliferation 0.002 0.097 0.48 12 -0.32 7 19
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.005 0.029 0.076 10 -10000 0 10
MAPK1 0.001 0.1 0.55 10 -0.48 4 14
S1P1/S1P/PDGFB-D/PDGFRB 0.002 0.09 0.32 17 -0.34 8 25
ABCC1 0.022 0.02 -10000 0 -0.042 1 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 25 25
CLTC 0.011 0.068 -10000 0 -0.42 8 8
calcium ion-dependent exocytosis 0 0.031 0.16 1 -0.2 7 8
Dynamin 2/GTP -0.024 0.036 0.14 23 -10000 0 23
EXOC4 0.028 0.007 -10000 0 0 34 34
CD59 -0.001 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 0.026 0.009 -10000 0 0 56 56
mol:PI-4-5-P2 0.001 0.05 -10000 0 -0.24 11 11
TSHR -0.025 0.007 -10000 0 -10000 0 0
INS -0.003 0.098 -10000 0 -0.47 22 22
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 -0.004 0.049 -10000 0 -0.4 6 6
ASAP2/amphiphysin II 0.035 0.013 -10000 0 -0.12 2 2
ARF6/GTP 0.021 0.003 -10000 0 -10000 0 0
CDH1 -0.006 0.054 -10000 0 -0.46 6 6
clathrin-independent pinocytosis 0.021 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.028 0.006 -10000 0 0 24 24
positive regulation of endocytosis 0.021 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.008 -10000 0 0 48 48
substrate adhesion-dependent cell spreading 0.007 0.052 0.18 1 -0.26 8 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.028 0.005 -10000 0 0 17 17
regulation of calcium-dependent cell-cell adhesion -0.026 0.064 0.34 7 -0.21 1 8
positive regulation of phagocytosis -0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.037 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 0.047 -10000 0 -0.35 7 7
clathrin heavy chain/ACAP1 -0.002 0.061 0.2 5 -0.34 9 14
JIP4/KLC1 0.051 0.02 -10000 0 -10000 0 0
EXOC1 0.028 0.006 -10000 0 0 25 25
exocyst 0.007 0.052 0.19 1 -0.26 8 9
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 0.009 0.072 -10000 0 -0.39 11 11
IL2RA 0.002 0.052 -10000 0 -0.38 7 7
VAMP3 -0.026 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.027 0.065 0.18 1 -0.32 10 11
EXOC6 0.027 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 -0.001 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 0.066 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 0.028 0.005 -10000 0 0 19 19
ADRB2 0.001 0.07 0.22 4 -0.41 9 13
EXOC3 0.026 0.009 -10000 0 0 60 60
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.028 0.018 0.17 2 -10000 0 2
KLC1 0.028 0.006 -10000 0 0 22 22
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 0.064 -10000 0 -0.34 7 7
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 15 15
GNAT1/GTP 0.021 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 0.003 -10000 0 0 8 8
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.055 0.02 0.094 2 -10000 0 2
mol:Na + -0.061 0.028 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 -0.15 8 8
CNGB1 0.027 0.007 -10000 0 0 39 39
RDH5 0.028 0.007 -10000 0 0 31 31
SAG 0.029 0.004 -10000 0 0 10 10
mol:Ca2+ -0.049 0.086 0.31 21 -10000 0 21
Na + (4 Units) -0.067 0.026 0.076 2 -10000 0 2
RGS9 0.029 0.005 -10000 0 0 15 15
GNB1/GNGT1 0.04 0.014 -10000 0 -0.16 1 1
GNAT1/GDP 0.053 0.037 -10000 0 -0.13 6 6
GUCY2D 0.028 0.006 -10000 0 0 27 27
GNGT1 0.028 0.006 -10000 0 0 22 22
GUCY2F 0.029 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 0.047 0.028 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 0 24 24
Rhodopsin 0.04 0.012 -10000 0 -10000 0 0
SLC24A1 0.029 0.005 -10000 0 0 15 15
CNGA1 0.028 0.006 -10000 0 0 26 26
Metarhodopsin II 0.018 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.064 0.031 -10000 0 -10000 0 0
RGS9BP 0.026 0.009 -10000 0 0 57 57
Metarhodopsin II/Transducin 0.005 0.026 -10000 0 -0.18 2 2
GCAP Family/Ca ++ 0.051 0.017 -10000 0 -10000 0 0
PDE6A/B 0.039 0.013 -10000 0 -10000 0 0
mol:Pi 0.047 0.03 -10000 0 -0.15 6 6
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.05 0.021 -10000 0 -0.13 1 1
PDE6B 0.027 0.008 -10000 0 0 43 43
PDE6A 0.029 0.004 -10000 0 0 13 13
PDE6G 0.028 0.006 -10000 0 0 21 21
RHO 0.028 0.005 -10000 0 0 19 19
PDE6 0.061 0.051 -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 -0.025 0.18 0.42 11 -0.54 4 15
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 -0.01 0.18 0.64 13 -0.54 4 17
JUNB 0.019 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 -10000 0 -0.53 38 38
Jun/NFAT1-c-4/p21SNFT -0.012 0.16 0.56 4 -0.7 1 5
AP-1/NFAT1-c-4 -0.028 0.21 0.66 5 -0.81 1 6
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 -0.02 0.15 0.38 9 -0.37 7 16
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 0.77 4 -0.68 2 6
NFAT1/FOXP3 -0.014 0.14 0.43 9 -0.39 4 13
EGR1 -0.015 0.018 0.15 1 -10000 0 1
JUN -0.013 0.052 0.15 18 -10000 0 18
EGR4 -0.015 0.026 0.15 1 -10000 0 1
mol:Ca2+ -0.011 0.003 -10000 0 -10000 0 0
GBP3 -0.03 0.17 0.44 21 -0.54 25 46
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 0.42 7 -0.39 2 9
CREM 0.029 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.006 0.16 0.49 6 -0.72 1 7
CTLA4 -0.026 0.11 0.47 8 -0.34 4 12
NFAT1-c-4 (dimer)/EGR1 -0.054 0.15 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 0.15 15 -10000 0 15
IFNG 0.004 0.18 0.58 25 -0.62 8 33
T cell activation 0 0.16 0.7 3 -10000 0 3
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 -0.68 6 7
TNF -0.057 0.15 0.64 3 -0.76 1 4
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 -10000 0 -0.4 3 3
NFAT1-c-4/ICER1 -0.005 0.16 0.49 6 -0.72 1 7
GATA3 0.027 0.007 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.014 0.18 0.57 27 -0.61 8 35
IL2RA -0.018 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 0.43 8 -0.4 3 11
E2F1 0.028 0.015 0.18 4 -10000 0 4
PPARG 0.029 0.004 -10000 0 -10000 0 0
SLC3A2 -0.026 0.12 0.42 2 -0.4 3 5
IRF4 0.027 0.008 -10000 0 -10000 0 0
PTGS2 -0.018 0.2 0.62 8 -0.74 1 9
CSF2 -0.007 0.22 0.73 10 -0.74 1 11
JunB/Fra1/NFAT1-c-4 0.014 0.16 0.57 2 -0.77 1 3
IL4 0.001 0.15 -10000 0 -0.66 3 3
IL5 -0.007 0.22 0.69 13 -0.74 1 14
IL2 0 0.16 0.76 2 -10000 0 2
IL3 -0.008 0.082 -10000 0 -0.52 12 12
RNF128 -0.034 0.048 0.32 9 -10000 0 9
NFATC1 0.006 0.13 0.69 6 -1 1 7
CDK4 0.004 0.14 0.8 3 -0.79 2 5
PTPRK -0.027 0.13 0.38 5 -0.45 9 14
IL8 -0.052 0.15 0.57 2 -0.74 1 3
POU2F1 0.029 0.004 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.029 0.003 -9999 0 0 7 7
GPC2 0.028 0.006 -9999 0 0 21 21
GPC2/Midkine 0.042 0.009 -9999 0 -9999 0 0
neuron projection morphogenesis 0.041 0.009 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.046 0.021 -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 0.037 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 0.003 -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 0.028 0.005 -9999 0 0 19 19
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 0.001 -9999 0 -10000 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 -0.025 0.011 0.18 1 -10000 0 1
ADCY5 -0.025 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 -0.026 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 -0.017 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 0.2 41 -0.24 1 42
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 0.06 -0.002 0.011 -0.026
47_PPARGC1A 0.029 0.029 0.029 0.029
105_BMP4 0.029 0.029 0.029 0.029
105_BMP6 0.029 0.029 0.029 0.029
105_BMP7 0 0.029 0.029 0.029
105_BMP2 0 0.029 0.029 0.029
131_RELN/VLDLR 0.076 0.076 0.076 0.076
30_TGFB1/TGF beta receptor Type II 0.029 0.029 0 0.029
84_STAT5B 0.037 -0.026 -0.026 0.067
84_STAT5A 0.037 -0.026 -0.026 0.067
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/3024492/2.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_Analysis/OV-TP/3140895/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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