PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1X34VDQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1X34VDQ
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 53 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 321
Class IB PI3K non-lipid kinase events 211
Signaling events mediated by Stem cell factor receptor (c-Kit) 210
Signaling mediated by p38-alpha and p38-beta 208
Reelin signaling pathway 195
Aurora B signaling 162
EGFR-dependent Endothelin signaling events 148
FOXA2 and FOXA3 transcription factor networks 146
PLK1 signaling events 138
HIF-1-alpha transcription factor network 125
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 321 16418 51 -0.084 0.81 1000 -1000 -0.035 -1000
Class IB PI3K non-lipid kinase events 211 633 3 -0.14 -1000 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 210 16436 78 -0.57 0.18 1000 -1000 -0.044 -1000
Signaling mediated by p38-alpha and p38-beta 208 9186 44 -0.33 0.024 1000 -1000 -0.021 -1000
Reelin signaling pathway 195 10945 56 -0.35 0.058 1000 -1000 -0.025 -1000
Aurora B signaling 162 10862 67 -0.22 0.29 1000 -1000 -0.03 -1000
EGFR-dependent Endothelin signaling events 148 3116 21 -0.21 0.034 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 146 6743 46 -1.1 0.034 1000 -1000 -0.037 -1000
PLK1 signaling events 138 11802 85 -0.074 0.25 1000 -1000 -0.033 -1000
HIF-1-alpha transcription factor network 125 9527 76 -0.51 0.035 1000 -1000 -0.034 -1000
Glucocorticoid receptor regulatory network 125 14299 114 -0.79 0.3 1000 -1000 -0.051 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 122 8345 68 -0.36 0.16 1000 -1000 -0.053 -1000
p75(NTR)-mediated signaling 118 14835 125 -0.26 0.1 1000 -1000 -0.065 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 117 6346 54 -0.35 0.055 1000 -1000 -0.031 -1000
EPHB forward signaling 112 9566 85 -0.24 0.16 1000 -1000 -0.066 -1000
Endothelins 111 10686 96 -0.37 0.18 1000 -1000 -0.046 -1000
Angiopoietin receptor Tie2-mediated signaling 104 9168 88 -0.29 0.13 1000 -1000 -0.063 -1000
Ephrin B reverse signaling 103 4973 48 -0.24 0.11 1000 -1000 -0.027 -1000
IL4-mediated signaling events 100 9108 91 -0.71 0.27 1000 -1000 -0.05 -1000
Wnt signaling 96 674 7 -0.11 0.019 1000 -1000 -0.014 -1000
IL23-mediated signaling events 94 5674 60 -0.33 0.08 1000 -1000 -0.031 -1000
Noncanonical Wnt signaling pathway 92 2400 26 -0.11 0.024 1000 -1000 -0.036 -1000
IGF1 pathway 88 5023 57 -0.12 0.043 1000 -1000 -0.032 -1000
ErbB2/ErbB3 signaling events 84 5502 65 -0.31 0.034 1000 -1000 -0.057 -1000
Arf6 signaling events 80 4972 62 -0.21 0.056 1000 -1000 -0.025 -1000
BMP receptor signaling 77 6255 81 -0.4 0.11 1000 -1000 -0.047 -1000
Nongenotropic Androgen signaling 75 3948 52 -0.26 0.14 1000 -1000 -0.028 -1000
Visual signal transduction: Rods 74 3851 52 -0.37 0.059 1000 -1000 -0.023 -1000
Neurotrophic factor-mediated Trk receptor signaling 73 8825 120 -0.4 0.18 1000 -1000 -0.043 -1000
Signaling events mediated by PTP1B 72 5522 76 -0.47 0.08 1000 -1000 -0.026 -1000
Calcium signaling in the CD4+ TCR pathway 72 2255 31 -0.2 0.027 1000 -1000 -0.038 -1000
Plasma membrane estrogen receptor signaling 70 6054 86 -0.11 0.091 1000 -1000 -0.053 -1000
amb2 Integrin signaling 68 5580 82 -0.37 0.13 1000 -1000 -0.021 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 67 5751 85 -0.26 0.027 1000 -1000 -0.039 -1000
Signaling events regulated by Ret tyrosine kinase 67 5563 82 -0.063 0.11 1000 -1000 -0.052 -1000
Aurora C signaling 65 458 7 0 0.15 1000 -1000 -0.02 -1000
Syndecan-1-mediated signaling events 64 2199 34 -0.079 0.19 1000 -1000 -0.027 -1000
S1P1 pathway 64 2337 36 -0.34 0.024 1000 -1000 -0.033 -1000
Effects of Botulinum toxin 64 1670 26 -0.004 0.11 1000 -1000 -0.008 -1000
Glypican 1 network 63 3030 48 -0.21 0.045 1000 -1000 -0.025 -1000
ErbB4 signaling events 60 4185 69 -0.31 0.065 1000 -1000 -0.036 -1000
IL6-mediated signaling events 58 4368 75 -0.2 0.058 1000 -1000 -0.031 -1000
Ephrin A reverse signaling 56 398 7 -0.034 0.024 1000 -1000 -0.004 -1000
Integrins in angiogenesis 55 4652 84 -0.21 0.13 1000 -1000 -0.046 -1000
TCR signaling in naïve CD8+ T cells 55 5133 93 -0.1 0.094 1000 -1000 -0.05 -1000
Signaling events mediated by the Hedgehog family 53 2791 52 -0.13 0.034 1000 -1000 -0.029 -1000
LPA receptor mediated events 53 5493 102 -0.19 0.12 1000 -1000 -0.049 -1000
Syndecan-3-mediated signaling events 50 1751 35 -0.24 0.054 1000 -1000 -0.015 -1000
Visual signal transduction: Cones 49 1887 38 -0.035 0.18 1000 -1000 -0.011 -1000
PDGFR-alpha signaling pathway 46 2024 44 -0.33 0.037 1000 -1000 -0.041 -1000
RXR and RAR heterodimerization with other nuclear receptor 46 2404 52 -0.12 0.076 1000 -1000 -0.026 -1000
Canonical Wnt signaling pathway 45 2304 51 -0.3 0.12 1000 -1000 -0.039 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 45 1487 33 -0.42 0.057 1000 -1000 -0.029 -1000
Presenilin action in Notch and Wnt signaling 42 2594 61 -0.3 0.12 1000 -1000 -0.037 -1000
IL12-mediated signaling events 41 3577 87 -0.36 0.068 1000 -1000 -0.066 -1000
Fc-epsilon receptor I signaling in mast cells 41 4030 97 -0.17 0.034 1000 -1000 -0.057 -1000
E-cadherin signaling in keratinocytes 41 1764 43 -0.19 0.032 1000 -1000 -0.034 -1000
Ras signaling in the CD4+ TCR pathway 40 693 17 -0.066 0.023 1000 -1000 -0.013 -1000
Nephrin/Neph1 signaling in the kidney podocyte 39 1350 34 -0.024 0.063 1000 -1000 -0.029 -1000
FAS signaling pathway (CD95) 39 1852 47 -0.46 0.041 1000 -1000 -0.027 -1000
TCGA08_rtk_signaling 39 1017 26 -0.19 0.039 1000 -1000 -0.007 -1000
Syndecan-2-mediated signaling events 38 2682 69 -0.12 0.13 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 38 1523 40 -0.35 0.045 1000 -1000 -0.025 -1000
Glypican 2 network 36 146 4 0.032 0.055 1000 -1000 0.013 -1000
Rapid glucocorticoid signaling 36 739 20 -0.11 0.028 1000 -1000 -0.004 -1000
LPA4-mediated signaling events 35 420 12 -0.12 0.006 1000 -1000 -0.017 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2606 74 -0.2 0.05 1000 -1000 -0.065 -1000
Aurora A signaling 34 2049 60 -0.09 0.19 1000 -1000 -0.019 -1000
Syndecan-4-mediated signaling events 32 2173 67 -0.21 0.12 1000 -1000 -0.034 -1000
Insulin Pathway 31 2332 74 -0.11 0.063 1000 -1000 -0.044 -1000
Nectin adhesion pathway 30 1930 63 -0.041 0.047 1000 -1000 -0.039 -1000
Regulation of Telomerase 30 3111 102 -0.21 0.15 1000 -1000 -0.028 -1000
Regulation of Androgen receptor activity 30 2145 70 -0.19 0.11 1000 -1000 -0.036 -1000
Coregulation of Androgen receptor activity 28 2150 76 -0.16 0.062 1000 -1000 -0.018 -1000
IL27-mediated signaling events 28 1437 51 -0.2 0.072 1000 -1000 -0.044 -1000
Regulation of nuclear SMAD2/3 signaling 27 3749 136 -0.23 0.075 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 27 2886 105 -0.19 0.037 1000 -1000 -0.038 -1000
Regulation of p38-alpha and p38-beta 27 1504 54 -0.26 0.052 1000 -1000 -0.048 -1000
IL2 signaling events mediated by STAT5 27 601 22 0.009 0.12 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 27 222 8 -0.017 0.058 1000 -1000 -0.003 -1000
BCR signaling pathway 26 2650 99 -0.092 0.058 1000 -1000 -0.052 -1000
Osteopontin-mediated events 22 846 38 -0.17 0.094 1000 -1000 -0.028 -1000
Arf6 trafficking events 22 1566 71 -0.28 0.041 1000 -1000 -0.026 -1000
TCGA08_p53 21 151 7 -0.009 0.02 1000 -1000 -0.008 -1000
HIF-2-alpha transcription factor network 20 866 43 -0.16 0.17 1000 -1000 -0.031 -1000
FoxO family signaling 20 1334 64 -0.018 0.26 1000 -1000 -0.045 -1000
Signaling mediated by p38-gamma and p38-delta 20 308 15 -0.024 0.024 1000 -1000 -0.028 -1000
Signaling events mediated by PRL 20 694 34 -0.14 0.035 1000 -1000 -0.039 -1000
Caspase cascade in apoptosis 19 1411 74 -0.032 0.057 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 18 1279 68 -0.17 0.043 1000 -1000 -0.03 -1000
Ceramide signaling pathway 18 1402 76 -0.11 0.065 1000 -1000 -0.026 -1000
S1P4 pathway 18 451 25 -0.013 0.041 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 17 1127 65 -0.083 0.056 1000 -1000 -0.032 -1000
S1P5 pathway 17 301 17 -0.006 0.032 1000 -1000 -0.007 -1000
Cellular roles of Anthrax toxin 15 606 39 -0.081 0.028 1000 -1000 -0.02 -1000
IL2 signaling events mediated by PI3K 15 878 58 -0.001 0.069 1000 -1000 -0.027 -1000
mTOR signaling pathway 14 767 53 -0.028 0.028 1000 -1000 -0.03 -1000
ceramide signaling pathway 13 638 49 -0.005 0.037 1000 -1000 -0.031 -1000
PLK2 and PLK4 events 12 38 3 0.016 0.035 1000 -1000 -0.005 -1000
JNK signaling in the CD4+ TCR pathway 12 217 17 0.004 0.059 1000 -1000 -0.022 -1000
Retinoic acid receptors-mediated signaling 12 709 58 -0.052 0.054 1000 -1000 -0.031 -1000
S1P3 pathway 12 537 42 -0.012 0.042 1000 -1000 -0.029 -1000
BARD1 signaling events 11 643 57 -0.053 0.12 1000 -1000 -0.026 -1000
TRAIL signaling pathway 10 490 48 -0.013 0.042 1000 -1000 -0.024 -1000
E-cadherin signaling in the nascent adherens junction 10 774 76 -0.025 0.051 1000 -1000 -0.056 -1000
PDGFR-beta signaling pathway 9 915 97 -0.035 0.058 1000 -1000 -0.052 -1000
Canonical NF-kappaB pathway 8 318 39 -0.004 0.052 1000 -1000 -0.027 -1000
Sphingosine 1-phosphate (S1P) pathway 8 233 28 -0.005 0.05 1000 -1000 -0.019 -1000
IFN-gamma pathway 8 553 68 -0.012 0.078 1000 -1000 -0.048 -1000
IL1-mediated signaling events 8 550 62 -0.01 0.065 1000 -1000 -0.039 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 8 696 83 -0.018 0.047 1000 -1000 -0.024 -1000
Class I PI3K signaling events 8 622 73 -0.018 0.046 1000 -1000 -0.034 -1000
E-cadherin signaling events 8 42 5 0.011 0.032 1000 -1000 0.007 -1000
p38 MAPK signaling pathway 8 357 44 -0.018 0.058 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class II 7 532 75 -0.026 0.063 1000 -1000 -0.032 -1000
EPO signaling pathway 7 420 55 0.011 0.083 1000 -1000 -0.029 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 273 37 -0.008 0.066 1000 -1000 -0.033 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 7 356 45 0.005 0.055 1000 -1000 -0.039 -1000
a4b1 and a4b7 Integrin signaling 6 33 5 0.024 0.04 1000 -1000 0.009 -1000
Insulin-mediated glucose transport 6 208 32 -0.13 0.039 1000 -1000 -0.029 -1000
VEGFR1 specific signals 6 354 56 -0.099 0.058 1000 -1000 -0.039 -1000
Arf6 downstream pathway 5 257 43 -0.053 0.054 1000 -1000 -0.018 -1000
Signaling events mediated by VEGFR1 and VEGFR2 5 652 125 -0.099 0.057 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class I 4 469 104 -0.061 0.058 1000 -1000 -0.034 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 3 73 23 -0.003 0.043 1000 -1000 -0.024 -1000
Circadian rhythm pathway 2 63 22 -0.007 0.053 1000 -1000 -0.025 -1000
Paxillin-dependent events mediated by a4b1 2 97 36 -0.047 0.052 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 2 67 31 0 0.034 1000 -1000 -0.012 -1000
Arf1 pathway 1 73 54 -0.001 0.045 1000 -1000 -0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 23 27 -0.009 0.057 1000 -1000 -0.039 -1000
Alternative NF-kappaB pathway 0 5 13 0 0.067 1000 -1000 0 -1000
Total 6591 389620 7203 -21 -990 131000 -131000 -4 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.67 0.39 1 385 -0.98 2 387
PLK1 0.42 0.27 0.63 433 -0.86 1 434
BIRC5 0.44 0.27 0.66 401 -0.78 4 405
HSPA1B 0.67 0.39 1 389 -0.99 2 391
MAP2K1 0.19 0.12 0.33 309 -10000 0 309
BRCA2 0.68 0.41 1 385 -0.93 3 388
FOXM1 0.8 0.52 1.2 430 -1.2 2 432
XRCC1 0.68 0.4 1 378 -0.99 2 380
FOXM1B/p19 0.089 0.24 0.83 41 -1.1 2 43
Cyclin D1/CDK4 0.59 0.38 0.92 369 -0.94 2 371
CDC2 0.74 0.45 1.1 430 -1 2 432
TGFA 0.58 0.4 0.92 389 -0.95 4 393
SKP2 0.68 0.4 1 389 -0.99 2 391
CCNE1 0.095 0.097 0.31 127 -10000 0 127
CKS1B 0.72 0.43 1.1 419 -0.99 2 421
RB1 0.34 0.33 0.68 337 -0.56 5 342
FOXM1C/SP1 0.6 0.36 0.92 374 -1.2 3 377
AURKB 0.36 0.31 0.65 330 -0.73 14 344
CENPF 0.78 0.48 1.1 444 -0.99 2 446
CDK4 0.093 0.058 0.22 51 -10000 0 51
MYC 0.39 0.39 0.85 262 -1 4 266
CHEK2 0.19 0.13 0.32 316 -10000 0 316
ONECUT1 0.62 0.4 0.96 390 -1 2 392
CDKN2A -0.084 0.12 0.24 5 -0.26 179 184
LAMA4 0.68 0.4 1 394 -0.99 2 396
FOXM1B/HNF6 0.62 0.41 0.99 365 -1.2 2 367
FOS 0.33 0.66 1 275 -0.99 47 322
SP1 0.023 0.025 -10000 0 -0.21 6 6
CDC25B 0.68 0.4 1 380 -0.99 2 382
response to radiation 0.13 0.09 0.24 269 -10000 0 269
CENPB 0.68 0.4 1 388 -0.99 2 390
CENPA 0.74 0.45 1.1 410 -0.99 2 412
NEK2 0.81 0.46 1.1 466 -0.95 2 468
HIST1H2BA 0.67 0.39 1 392 -0.99 2 394
CCNA2 0.16 0.14 0.32 347 -10000 0 347
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.71 0.44 1.1 389 -1.1 2 391
CCNB2 0.75 0.45 1.1 420 -0.99 2 422
CCNB1 0.75 0.47 1.1 413 -1 2 415
ETV5 0.68 0.41 1 388 -0.99 2 390
ESR1 0.54 0.55 1.1 341 -0.98 11 352
CCND1 0.62 0.42 0.98 396 -0.96 2 398
GSK3A 0.16 0.095 0.27 270 -10000 0 270
Cyclin A-E1/CDK1-2 0.26 0.17 0.42 381 -10000 0 381
CDK2 0.064 0.03 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.17 0.12 0.28 372 -10000 0 372
FOXM1B/Cbp/p300 0.24 0.3 0.73 80 -1.1 2 82
GAS1 0.62 0.49 1 379 -1.1 25 404
MMP2 0.67 0.42 1 395 -1.1 7 402
RB1/FOXM1C 0.54 0.4 0.9 362 -0.98 2 364
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.14 0.27 0.6 211 -10000 0 211
PI3K Class IB/PDE3B -0.14 0.27 -10000 0 -0.6 211 211
PDE3B -0.14 0.27 -10000 0 -0.6 211 211
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.33 2 -0.38 356 358
CRKL -0.17 0.21 -10000 0 -0.4 367 367
HRAS -0.12 0.18 -10000 0 -0.36 236 236
mol:PIP3 -0.14 0.2 -10000 0 -0.38 265 265
SPRED1 0.024 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 374 374
FOXO3 -0.14 0.2 0.51 1 -0.38 252 253
AKT1 -0.16 0.21 0.35 1 -0.39 346 347
BAD -0.15 0.2 0.33 1 -0.38 254 255
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 374 374
GSK3B -0.14 0.2 0.51 1 -0.38 255 256
RAF1 -0.096 0.16 0.25 2 -0.34 59 61
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 370 370
STAT1 -0.44 0.53 -10000 0 -1 379 379
HRAS/SPRED1 -0.093 0.16 -10000 0 -0.34 64 64
cell proliferation -0.18 0.22 -10000 0 -0.41 375 375
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.023 0.031 -10000 0 -0.6 2 2
RPS6KB1 -0.17 0.22 -10000 0 -0.41 381 381
HRAS/SPRED2 -0.093 0.16 -10000 0 -0.35 57 57
LYN/TEC/p62DOK -0.14 0.22 -10000 0 -0.4 309 309
MAPK3 -0.065 0.13 0.32 4 -0.28 26 30
STAP1 -0.18 0.22 -10000 0 -0.42 376 376
GRAP2 0.016 0.073 0.27 3 -0.6 11 14
JAK2 -0.37 0.45 -10000 0 -0.84 379 379
STAT1 (dimer) -0.43 0.51 -10000 0 -0.98 379 379
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.41 300 300
actin filament polymerization -0.18 0.22 0.33 1 -0.41 375 376
LYN 0.021 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 380 380
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.38 319 319
PI3K -0.15 0.22 -10000 0 -0.39 353 353
PTEN 0.023 0.031 -10000 0 -0.6 2 2
SCF/KIT/EPO/EPOR -0.51 0.64 -10000 0 -1.2 376 376
MAPK8 -0.18 0.22 -10000 0 -0.42 375 375
STAT3 (dimer) -0.18 0.22 -10000 0 -0.41 370 370
positive regulation of transcription -0.052 0.11 0.23 12 -0.24 19 31
mol:GDP -0.13 0.19 -10000 0 -0.38 232 232
PIK3C2B -0.16 0.2 -10000 0 -0.42 286 286
CBL/CRKL -0.16 0.2 -10000 0 -0.38 358 358
FER -0.18 0.22 -10000 0 -0.42 378 378
SH2B3 -0.18 0.22 -10000 0 -0.42 376 376
PDPK1 -0.12 0.19 0.33 6 -0.35 243 249
SNAI2 -0.17 0.22 0.28 4 -0.42 330 334
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 381 381
KITLG -0.003 0.059 0.26 10 -0.55 4 14
cell motility -0.32 0.39 -10000 0 -0.73 381 381
PTPN6 0.032 0.018 0.28 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -1 12 12
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 380 380
SOCS1 0.024 0.031 0.27 6 -0.6 1 7
cell migration 0.18 0.22 0.42 378 -10000 0 378
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.045 0.098 0.26 139 -10000 0 139
VAV1 0.024 0.025 0.27 2 -0.6 1 3
GRB10 -0.18 0.22 -10000 0 -0.42 372 372
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 378 378
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.14 0.3 5 -0.29 37 42
CBL 0.022 0.008 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 378 378
MAP2K2 -0.074 0.14 0.29 7 -0.29 40 47
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 268 268
STAT5A -0.27 0.34 -10000 0 -0.62 380 380
GRB2 0.023 0.011 0.27 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 330 334
SHC/GRAP2 0.023 0.054 -10000 0 -0.36 13 13
PTPRO -0.18 0.22 -10000 0 -0.42 374 374
SH2B2 -0.18 0.22 -10000 0 -0.42 375 375
DOK1 0.024 0.003 -10000 0 -10000 0 0
MATK -0.19 0.23 -10000 0 -0.43 378 378
CREBBP -0.028 0.072 -10000 0 -10000 0 0
BCL2 -0.15 0.3 -10000 0 -1.2 43 43
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.33 0.52 0.41 3 -1.1 274 277
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.088 0.18 -10000 0 -0.34 267 267
ATF2/c-Jun -0.085 0.17 -10000 0 -0.41 92 92
MAPK11 -0.082 0.18 -10000 0 -0.35 247 247
MITF -0.11 0.21 -10000 0 -0.41 268 268
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 273 273
KRT8 -0.11 0.21 -10000 0 -0.4 255 255
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.01 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.53 265 265
CEBPB -0.1 0.2 0.29 1 -0.4 250 251
SLC9A1 -0.11 0.21 -10000 0 -0.41 267 267
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.4 260 260
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.45 245 245
JUN -0.085 0.17 -10000 0 -0.41 92 92
PPARGC1A -0.21 0.34 0.28 1 -0.57 327 328
USF1 -0.1 0.19 0.33 3 -0.39 254 257
RAB5/GDP/GDI1 -0.082 0.16 -10000 0 -0.3 260 260
NOS2 -0.11 0.22 -10000 0 -0.57 66 66
DDIT3 -0.11 0.21 -10000 0 -0.4 269 269
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.096 0.17 0.28 3 -0.34 248 251
p38alpha-beta/HBP1 -0.1 0.25 -10000 0 -0.45 245 245
CREB1 -0.12 0.22 -10000 0 -0.43 267 267
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.41 241 241
RPS6KA4 -0.11 0.21 -10000 0 -0.41 267 267
PLA2G4A -0.13 0.22 -10000 0 -0.44 266 266
GDI1 -0.11 0.21 -10000 0 -0.4 272 272
TP53 -0.15 0.27 -10000 0 -0.53 254 254
RPS6KA5 -0.12 0.21 -10000 0 -0.4 274 274
ESR1 -0.15 0.24 0.29 1 -0.43 289 290
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 270 270
MEF2A -0.11 0.21 0.29 1 -0.4 268 269
EIF4EBP1 -0.12 0.22 -10000 0 -0.43 258 258
KRT19 -0.11 0.22 0.4 1 -0.41 256 257
ELK4 -0.1 0.19 0.32 3 -0.38 257 260
ATF6 -0.1 0.19 0.33 3 -0.38 258 261
ATF1 -0.12 0.22 -10000 0 -0.42 269 269
p38alpha-beta/MAPKAPK2 -0.096 0.22 -10000 0 -0.42 231 231
p38alpha-beta/MAPKAPK3 -0.1 0.25 -10000 0 -0.45 245 245
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.028 -10000 0 -10000 0 0
VLDLR 0.011 0.086 -10000 0 -0.6 16 16
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
ITGA3 0.021 0.023 -10000 0 -0.6 1 1
RELN/VLDLR/Fyn -0.22 0.22 -10000 0 -0.38 511 511
MAPK8IP1/MKK7/MAP3K11/JNK1 0.058 0.035 -10000 0 -0.34 1 1
AKT1 -0.16 0.14 -10000 0 -0.28 436 436
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.037 0.057 0.27 48 -10000 0 48
RELN/LRP8/DAB1 -0.18 0.2 0.36 5 -0.34 491 496
LRPAP1/LRP8 0.051 0.052 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.16 0.2 0.32 4 -0.33 478 482
DAB1/alpha3/beta1 Integrin -0.16 0.18 -10000 0 -0.32 416 416
long-term memory -0.21 0.23 0.35 4 -0.38 476 480
DAB1/LIS1 -0.16 0.2 0.31 4 -0.32 487 491
DAB1/CRLK/C3G -0.16 0.19 -10000 0 -0.32 474 474
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.2 0.31 4 -0.33 484 488
ARHGEF2 0.021 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.035 0.19 0.27 10 -0.6 80 90
CDK5R1 0.029 0.037 0.27 19 -10000 0 19
RELN -0.35 0.31 0.27 3 -0.6 499 502
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.2 0.21 -10000 0 -0.38 490 490
GRIN2A/RELN/LRP8/DAB1/Fyn -0.18 0.23 0.34 3 -0.37 449 452
MAPK8 0.024 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.2 0.33 2 -0.35 511 513
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.2 0.18 0.23 1 -0.34 489 490
RELN/LRP8 -0.21 0.21 -10000 0 -0.38 492 492
GRIN2B/RELN/LRP8/DAB1/Fyn -0.19 0.22 0.37 3 -0.35 502 505
PI3K 0.034 0.01 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.024 -10000 0 -0.28 3 3
RAP1A -0.18 0.16 0.36 1 -0.32 371 372
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.034 0.27 3 -0.6 2 5
CRLK/C3G 0.034 0.009 -10000 0 -10000 0 0
GRIN2B -0.031 0.17 0.27 1 -0.6 68 69
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.092 0.12 0.23 1 -0.36 47 48
neuron adhesion -0.16 0.15 0.33 2 -0.52 14 16
LRP8 0.051 0.077 0.27 94 -10000 0 94
GSK3B -0.15 0.14 -10000 0 -0.27 435 435
RELN/VLDLR/DAB1/Fyn -0.18 0.2 0.32 2 -0.34 478 480
MAP3K11 0.024 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.15 -10000 0 -0.29 473 473
CDK5 0.024 0.01 0.27 1 -10000 0 1
MAPT -0.02 0.2 0.89 14 -0.55 73 87
neuron migration -0.2 0.18 0.28 1 -0.35 429 430
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.093 0.12 0.23 1 -0.36 47 48
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 490 490
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.12 0.11 0.25 274 -0.26 2 276
STMN1 0.084 0.084 0.28 54 -10000 0 54
Aurora B/RasGAP/Survivin 0.2 0.14 0.34 398 -10000 0 398
Chromosomal passenger complex/Cul3 protein complex 0.012 0.15 0.21 153 -0.25 97 250
BIRC5 0.19 0.12 0.27 560 -10000 0 560
DES -0.16 0.32 0.36 2 -0.58 219 221
Aurora C/Aurora B/INCENP 0.11 0.082 0.33 6 -0.32 1 7
Aurora B/TACC1 0.077 0.097 -10000 0 -0.37 13 13
Aurora B/PP2A 0.12 0.085 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.029 0.14 10 -10000 0 10
mitotic metaphase/anaphase transition -0.007 0.006 -10000 0 -10000 0 0
NDC80 0.16 0.13 0.28 394 -10000 0 394
Cul3 protein complex -0.12 0.21 -10000 0 -0.39 316 316
KIF2C 0.17 0.11 0.25 494 -10000 0 494
PEBP1 0.028 0.004 -10000 0 -10000 0 0
KIF20A 0.21 0.098 0.26 652 -10000 0 652
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.085 -10000 0 -10000 0 0
SEPT1 0.027 0.031 0.27 13 -10000 0 13
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.027 0.029 0.27 12 -10000 0 12
NSUN2/NPM1/Nucleolin 0.081 0.2 0.33 24 -0.45 73 97
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.075 0.066 0.24 32 -10000 0 32
AURKB 0.15 0.12 0.26 437 -10000 0 437
AURKC 0.026 0.035 0.27 10 -0.6 1 11
CDCA8 0.12 0.12 0.28 296 -10000 0 296
cytokinesis 0.16 0.16 0.32 335 -0.36 5 340
Aurora B/Septin1 0.19 0.18 0.38 317 -0.34 4 321
AURKA 0.13 0.12 0.26 360 -10000 0 360
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.31 -10000 0 -0.6 324 324
BUB1 0.2 0.11 0.26 604 -10000 0 604
hSgo1/Aurora B/Survivin 0.29 0.19 0.43 509 -10000 0 509
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.2 0.15 0.36 307 -10000 0 307
SGOL1 0.19 0.11 0.27 565 -10000 0 565
CENPA 0.19 0.15 0.32 426 -10000 0 426
NCAPG 0.15 0.12 0.27 442 -10000 0 442
Aurora B/HC8 Proteasome 0.12 0.085 -10000 0 -10000 0 0
NCAPD2 0.024 0.01 0.27 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.085 0.21 6 -10000 0 6
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.13 0.12 0.27 350 -10000 0 350
NPM1 0.073 0.13 0.26 5 -0.36 32 37
RASA1 0.024 0.005 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.085 -10000 0 -10000 0 0
PPP1CC 0.025 0.002 -10000 0 -10000 0 0
Centraspindlin 0.22 0.16 0.38 375 -10000 0 375
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
NSUN2 0.08 0.12 0.28 18 -0.41 8 26
MYLK 0.036 0.13 0.24 6 -0.33 72 78
KIF23 0.11 0.12 0.28 269 -10000 0 269
VIM 0.083 0.09 0.38 26 -0.44 2 28
RACGAP1 0.045 0.056 0.28 43 -10000 0 43
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.07 0.14 -10000 0 -0.46 26 26
Chromosomal passenger complex 0.2 0.13 0.29 480 -10000 0 480
Chromosomal passenger complex/EVI5 0.25 0.18 0.42 389 -10000 0 389
TACC1 0.01 0.078 -10000 0 -0.6 13 13
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.024 0.01 0.27 1 -10000 0 1
EGFR -0.19 0.3 -10000 0 -0.6 281 281
EGF/EGFR -0.17 0.24 -10000 0 -0.4 388 388
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.21 -10000 0 -0.38 290 290
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.024 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.091 0.24 0.27 2 -0.6 153 155
EGF/EGFR dimer/SHC -0.16 0.23 -10000 0 -0.43 314 314
mol:GDP -0.12 0.21 -10000 0 -0.38 290 290
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.021 0.16 0.27 1 -0.6 60 61
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.35 289 289
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.12 0.2 -10000 0 -0.36 289 289
FRAP1 -0.15 0.17 0.16 3 -0.36 290 293
EGF/EGFR dimer -0.21 0.27 -10000 0 -0.48 401 401
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
ETA receptor/Endothelin-1 -0.001 0.13 -10000 0 -0.44 63 63
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.25 0.27 -10000 0 -0.7 128 128
PCK1 -0.93 0.64 -10000 0 -1.4 500 500
HNF4A -0.24 0.28 -10000 0 -0.81 61 61
KCNJ11 -0.28 0.3 -10000 0 -0.77 135 135
AKT1 -0.17 0.16 -10000 0 -0.43 62 62
response to starvation 0.004 0.011 -10000 0 -10000 0 0
DLK1 -0.45 0.48 -10000 0 -1.1 277 277
NKX2-1 -0.038 0.16 0.53 3 -0.54 1 4
ACADM -0.25 0.27 -10000 0 -0.74 105 105
TAT -1.1 0.63 -10000 0 -1.5 607 607
CEBPB 0.024 0.009 -10000 0 -10000 0 0
CEBPA 0.02 0.058 -10000 0 -0.6 7 7
TTR -0.41 0.28 -10000 0 -0.76 214 214
PKLR -0.23 0.27 0.56 2 -0.7 110 112
APOA1 -0.28 0.32 -10000 0 -0.88 75 75
CPT1C -0.25 0.27 0.56 2 -0.71 125 127
ALAS1 -0.15 0.16 -10000 0 -0.72 7 7
TFRC -0.42 0.27 -10000 0 -0.73 235 235
FOXF1 0.017 0.048 0.26 6 -0.6 3 9
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.032 0.27 6 -10000 0 6
CPT1A -0.24 0.27 -10000 0 -0.73 107 107
HMGCS1 -0.25 0.27 -10000 0 -0.72 111 111
NR3C1 -0.12 0.12 -10000 0 -0.26 222 222
CPT1B -0.25 0.27 -10000 0 -0.71 132 132
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.024 -10000 0 -10000 0 0
GCK -0.28 0.33 -10000 0 -0.82 158 158
CREB1 -0.074 0.092 -10000 0 -0.22 86 86
IGFBP1 -0.43 0.55 -10000 0 -1.4 197 197
PDX1 -0.12 0.16 0.52 1 -0.55 7 8
UCP2 -0.25 0.27 0.56 1 -0.72 113 114
ALDOB -0.28 0.29 -10000 0 -0.78 115 115
AFP -0.59 0.52 0.37 1 -0.86 541 542
BDH1 -0.25 0.27 -10000 0 -0.72 116 116
HADH -0.28 0.29 -10000 0 -0.75 137 137
F2 -0.28 0.31 -10000 0 -0.87 78 78
HNF1A 0.034 0.032 0.27 6 -10000 0 6
G6PC -0.18 0.12 -10000 0 -0.63 4 4
SLC2A2 -0.16 0.17 -10000 0 -0.96 1 1
INS 0.02 0.08 0.23 25 -10000 0 25
FOXA1 -0.22 0.23 0.29 15 -0.38 432 447
FOXA3 -0.37 0.22 0.4 1 -0.49 567 568
FOXA2 -0.33 0.33 -10000 0 -0.81 169 169
ABCC8 -0.32 0.39 0.6 1 -0.94 170 171
ALB -0.8 0.55 0.37 1 -1.2 557 558
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.074 0.05 0.11 2 -0.11 406 408
BUB1B 0.096 0.069 0.16 384 -10000 0 384
PLK1 0.055 0.04 0.11 132 -10000 0 132
PLK1S1 0.029 0.036 0.14 8 -0.17 16 24
KIF2A 0.046 0.038 0.21 5 -10000 0 5
regulation of mitotic centrosome separation 0.055 0.04 0.11 132 -10000 0 132
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.25 0.15 0.34 554 -10000 0 554
WEE1 0.048 0.063 0.22 2 -0.27 19 21
cytokinesis 0.14 0.079 0.22 251 -0.35 1 252
PP2A-alpha B56 0.12 0.12 -10000 0 -0.48 8 8
AURKA 0.072 0.054 0.13 371 -0.18 1 372
PICH/PLK1 0.11 0.094 0.22 278 -10000 0 278
CENPE 0.072 0.059 0.14 258 -10000 0 258
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.046 0.037 0.21 5 -10000 0 5
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.089 0.056 0.13 403 -0.14 1 404
PAK1 0.022 0.017 0.26 3 -10000 0 3
SPC24 0.17 0.12 0.27 500 -10000 0 500
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.082 0.073 0.15 392 -0.19 18 410
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 41 -10000 0 41
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.025 0.02 0.056 128 -10000 0 128
G2 phase of mitotic cell cycle 0.001 0.003 0.014 16 -10000 0 16
STAG2 0.025 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.084 -10000 0 -0.5 21 21
spindle elongation 0.055 0.04 0.11 132 -10000 0 132
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.12 0.13 -10000 0 -0.49 15 15
TPT1 0.015 0.058 0.13 1 -0.17 63 64
CDC25C 0.12 0.071 0.17 409 -0.22 10 419
CDC25B 0.03 0.033 0.27 14 -10000 0 14
SGOL1 0.074 0.05 0.11 406 -0.11 2 408
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.074 0.071 0.32 9 -10000 0 9
CDC14B -0.011 0.075 -10000 0 -0.45 23 23
CDC20 0.16 0.12 0.27 450 -10000 0 450
PLK1/PBIP1 0.048 0.051 0.15 132 -10000 0 132
mitosis -0.005 0.005 0.024 2 -10000 0 2
FBXO5 0.034 0.037 0.15 16 -0.12 1 17
CDC2 0.004 0.004 0.011 178 -10000 0 178
NDC80 0.17 0.12 0.27 515 -10000 0 515
metaphase plate congression 0.032 0.055 0.15 1 -0.19 39 40
ERCC6L 0.1 0.09 0.25 152 -10000 0 152
NLP/gamma Tubulin 0.026 0.025 0.08 29 -0.087 7 36
microtubule cytoskeleton organization 0.015 0.058 0.13 1 -0.17 63 64
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 12 -10000 0 12
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 12 -10000 0 12
PLK1/PRC1-2 0.22 0.13 0.29 580 -10000 0 580
GRASP65/GM130/RAB1/GTP/PLK1 0.073 0.032 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.047 0.037 0.1 136 -10000 0 136
mitotic prometaphase 0.002 0.005 0.023 40 -10000 0 40
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.053 -10000 0 -0.34 2 2
microtubule-based process 0.19 0.088 0.23 648 -10000 0 648
Golgi organization 0.055 0.04 0.11 132 -10000 0 132
Cohesin/SA2 0.059 0.03 0.15 3 -10000 0 3
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.22 0.1 0.27 652 -10000 0 652
APC/C/CDC20 0.15 0.1 0.24 449 -10000 0 449
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.043 0.052 0.15 132 -10000 0 132
PRC1 0.088 0.11 0.27 220 -10000 0 220
ECT2 0.055 0.059 0.23 50 -10000 0 50
C13orf34 0.045 0.034 0.097 132 -10000 0 132
NUDC 0.032 0.055 0.15 1 -0.19 39 40
regulation of attachment of spindle microtubules to kinetochore 0.096 0.069 0.16 385 -10000 0 385
spindle assembly 0.04 0.031 0.093 93 -10000 0 93
spindle stabilization 0.029 0.036 0.14 8 -0.17 16 24
APC/C/HCDH1 0.01 0.068 -10000 0 -0.39 23 23
MKLP2/PLK1 0.19 0.088 0.23 648 -10000 0 648
CCNB1 0.078 0.1 0.27 183 -10000 0 183
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.041 0.052 0.23 1 -0.28 11 12
TUBG1 0.025 0.041 0.13 3 -0.16 28 31
G2/M transition of mitotic cell cycle 0.047 0.048 0.21 10 -10000 0 10
MLF1IP 0.027 0.054 0.14 127 -10000 0 127
INCENP 0.024 0.005 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.26 0.38 -10000 0 -0.81 171 171
HDAC7 0.025 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.34 0.68 1 -0.76 126 127
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.26 0.37 -10000 0 -0.81 168 168
AP1 -0.12 0.23 -10000 0 -0.45 265 265
ABCG2 -0.27 0.39 -10000 0 -0.84 183 183
HIF1A -0.051 0.082 -10000 0 -0.24 11 11
TFF3 -0.27 0.41 0.7 3 -0.82 201 204
GATA2 0.01 0.097 0.26 11 -0.6 18 29
AKT1 -0.06 0.093 -10000 0 -0.26 25 25
response to hypoxia -0.065 0.083 -10000 0 -0.22 77 77
MCL1 -0.25 0.36 -10000 0 -0.81 162 162
NDRG1 -0.24 0.36 -10000 0 -0.82 145 145
SERPINE1 -0.25 0.38 0.7 2 -0.81 170 172
FECH -0.26 0.37 -10000 0 -0.82 165 165
FURIN -0.26 0.37 -10000 0 -0.81 168 168
NCOA2 0.019 0.059 -10000 0 -0.6 7 7
EP300 -0.065 0.13 0.33 1 -0.34 88 89
HMOX1 -0.26 0.38 -10000 0 -0.82 165 165
BHLHE40 -0.26 0.37 -10000 0 -0.82 169 169
BHLHE41 -0.26 0.38 -10000 0 -0.83 169 169
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.025 0.11 -10000 0 -10000 0 0
ENG -0.02 0.11 0.4 2 -10000 0 2
JUN 0.016 0.062 -10000 0 -0.6 8 8
RORA -0.26 0.38 -10000 0 -0.81 172 172
ABCB1 -0.26 0.45 -10000 0 -1.1 167 167
TFRC -0.26 0.38 0.64 1 -0.82 168 169
CXCR4 -0.26 0.38 -10000 0 -0.82 167 167
TF -0.43 0.46 -10000 0 -0.9 322 322
CITED2 -0.26 0.37 -10000 0 -0.82 168 168
HIF1A/ARNT -0.29 0.42 0.78 1 -0.93 156 157
LDHA -0.041 0.13 -10000 0 -0.74 21 21
ETS1 -0.26 0.37 -10000 0 -0.82 167 167
PGK1 -0.26 0.38 -10000 0 -0.81 170 170
NOS2 -0.26 0.37 -10000 0 -0.82 163 163
ITGB2 -0.26 0.38 -10000 0 -0.81 170 170
ALDOA -0.25 0.37 -10000 0 -0.82 161 161
Cbp/p300/CITED2 -0.27 0.4 -10000 0 -0.9 149 149
FOS -0.17 0.29 -10000 0 -0.6 254 254
HK2 -0.26 0.38 -10000 0 -0.81 171 171
SP1 0.001 0.059 -10000 0 -0.19 11 11
GCK -0.14 0.36 0.54 1 -1.4 56 57
HK1 -0.26 0.38 -10000 0 -0.82 166 166
NPM1 -0.26 0.38 -10000 0 -0.81 171 171
EGLN1 -0.25 0.36 -10000 0 -0.81 164 164
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.26 0.37 -10000 0 -0.81 170 170
SMAD3 0.025 0.004 -10000 0 -10000 0 0
EDN1 -0.2 0.38 -10000 0 -1.1 104 104
IGFBP1 -0.33 0.43 -10000 0 -0.9 223 223
VEGFA -0.17 0.3 -10000 0 -0.69 100 100
HIF1A/JAB1 -0.008 0.067 -10000 0 -10000 0 0
CP -0.32 0.46 0.68 2 -0.93 225 227
CXCL12 -0.28 0.4 -10000 0 -0.85 183 183
COPS5 0.024 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.01 -10000 0 -10000 0 0
BNIP3 -0.26 0.38 0.77 1 -0.82 170 171
EGLN3 -0.25 0.38 0.71 2 -0.81 168 170
CA9 -0.22 0.4 0.69 5 -0.81 161 166
TERT -0.25 0.38 0.71 2 -0.81 167 169
ENO1 -0.26 0.38 -10000 0 -0.81 171 171
PFKL -0.26 0.38 -10000 0 -0.81 169 169
NCOA1 0.025 0.022 -10000 0 -0.6 1 1
ADM -0.28 0.41 -10000 0 -0.86 190 190
ARNT -0.038 0.069 -10000 0 -10000 0 0
HNF4A 0.017 0.04 0.27 10 -10000 0 10
ADFP -0.27 0.36 0.57 1 -0.8 176 177
SLC2A1 -0.17 0.3 -10000 0 -0.69 100 100
LEP -0.51 0.41 -10000 0 -0.88 358 358
HIF1A/ARNT/Cbp/p300 -0.22 0.34 0.64 1 -0.78 129 130
EPO -0.095 0.26 0.68 4 -0.73 25 29
CREBBP -0.055 0.12 0.33 1 -0.34 65 66
HIF1A/ARNT/Cbp/p300/HDAC7 -0.2 0.33 0.62 1 -0.79 109 110
PFKFB3 -0.26 0.38 -10000 0 -0.83 163 163
NT5E -0.26 0.38 -10000 0 -0.82 172 172
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.098 0.11 0.47 5 -10000 0 5
SMARCC2 0.025 0.013 -10000 0 -0.2 1 1
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.13 0.22 0.39 6 -0.61 83 89
SUMO2 0 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.034 0.037 0.28 18 -10000 0 18
FKBP4 0.025 0.018 0.27 4 -10000 0 4
FKBP5 0.017 0.073 0.27 3 -0.6 11 14
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.32 81 -0.31 7 88
PRL -0.067 0.12 0.54 3 -0.45 1 4
cortisol/GR alpha (dimer)/TIF2 0.2 0.27 0.52 283 -0.48 4 287
RELA -0.041 0.1 0.27 2 -0.25 32 34
FGG 0.22 0.24 0.47 316 -0.45 2 318
GR beta/TIF2 0.1 0.14 0.31 128 -0.41 7 135
IFNG -0.33 0.37 0.49 3 -0.72 308 311
apoptosis -0.27 0.31 0.86 1 -0.63 265 266
CREB1 0.065 0.057 -10000 0 -10000 0 0
histone acetylation 0.03 0.13 0.38 43 -0.42 11 54
BGLAP -0.09 0.14 -10000 0 -0.55 7 7
GR/PKAc 0.14 0.13 0.36 73 -0.37 1 74
NF kappa B1 p50/RelA -0.068 0.18 0.49 2 -0.34 130 132
SMARCD1 0.025 0.011 -10000 0 -10000 0 0
MDM2 0.1 0.11 0.23 269 -10000 0 269
GATA3 0.014 0.12 0.27 26 -0.6 27 53
AKT1 0.019 0.012 -10000 0 -10000 0 0
CSF2 -0.026 0.11 0.49 1 -0.5 4 5
GSK3B -0.001 0.024 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.8 1 -0.57 185 186
CSN2 0.17 0.19 0.39 238 -0.51 1 239
BRG1/BAF155/BAF170/BAF60A 0.061 0.041 -10000 0 -0.48 4 4
NFATC1 0.023 0.023 -10000 0 -0.6 1 1
POU2F1 0.024 0.016 0.27 1 -10000 0 1
CDKN1A 0.016 0.079 -10000 0 -1.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN 0.018 0.073 0.27 8 -0.6 10 18
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.35 51 -0.32 4 55
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.38 0.4 0.62 2 -0.79 359 361
JUN -0.27 0.3 0.37 6 -0.54 364 370
IL4 -0.12 0.15 -10000 0 -0.46 36 36
CDK5R1 0.021 0.039 0.26 19 -10000 0 19
PRKACA 0.024 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.28 0.26 -10000 0 -0.51 400 400
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.34 51 -0.31 4 55
cortisol/GR alpha (monomer) 0.3 0.32 0.6 369 -0.52 2 371
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.2 0.3 -10000 0 -0.62 260 260
AP-1/NFAT1-c-4 -0.46 0.46 0.48 6 -0.84 442 448
AFP -0.56 0.66 0.47 1 -1.4 287 288
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.17 0.16 0.45 67 -10000 0 67
TP53 0.031 0.022 -10000 0 -0.52 1 1
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.7 0.7 -10000 0 -1.4 392 392
KRT14 -0.77 0.67 -10000 0 -1.4 467 467
TBP 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.16 0.14 0.3 399 -10000 0 399
HDAC1 0.023 0.009 -10000 0 -10000 0 0
HDAC2 0.021 0.01 -10000 0 -10000 0 0
AP-1 -0.47 0.46 0.48 6 -0.85 441 447
MAPK14 0.002 0.023 -10000 0 -10000 0 0
MAPK10 -0.092 0.22 -10000 0 -0.6 126 126
MAPK11 -0.002 0.038 -10000 0 -0.61 2 2
KRT5 -0.79 0.72 0.43 2 -1.4 457 459
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.022 -10000 0 -0.6 1 1
STAT1 0.034 0.037 0.28 18 -10000 0 18
CGA -0.058 0.18 -10000 0 -0.47 28 28
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.16 0.18 0.36 349 -10000 0 349
MAPK3 0 0.022 -10000 0 -10000 0 0
MAPK1 0.002 0.022 -10000 0 -10000 0 0
ICAM1 -0.2 0.25 0.52 3 -0.53 214 217
NFKB1 -0.041 0.1 0.3 1 -0.26 20 21
MAPK8 -0.2 0.22 0.32 4 -0.42 339 343
MAPK9 0.002 0.023 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.33 0.86 1 -0.66 273 274
BAX 0.016 0.063 -10000 0 -10000 0 0
POMC -0.17 0.29 0.46 1 -0.82 75 76
EP300 0.16 0.14 0.29 390 -10000 0 390
cortisol/GR alpha (dimer)/p53 0.23 0.26 0.52 306 -0.55 1 307
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.11 0.28 120 -10000 0 120
SGK1 0.2 0.2 0.5 12 -1.1 4 16
IL13 -0.27 0.28 0.55 2 -0.68 137 139
IL6 -0.46 0.54 0.64 1 -1.1 328 329
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.23 0.23 0.58 1 -0.65 64 65
IL2 -0.36 0.36 0.49 2 -0.71 352 354
CDK5 0.016 0.016 0.26 1 -10000 0 1
PRKACB 0.034 0.066 0.27 42 -0.6 3 45
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
IL8 -0.2 0.29 0.44 5 -0.59 208 213
CDK5R1/CDK5 0.015 0.038 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.022 0.16 0.42 2 -0.4 23 25
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.5 341 -0.51 1 342
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.16 0.16 0.34 260 -10000 0 260
NF kappa B1 p50/RelA/Cbp 0.069 0.19 0.42 51 -0.42 12 63
JUN (dimer) -0.27 0.3 0.37 6 -0.54 363 369
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.14 0.21 -10000 0 -0.58 91 91
NR3C1 0.18 0.2 0.4 292 -0.32 1 293
NR4A1 -0.035 0.19 -10000 0 -0.58 88 88
TIF2/SUV420H1 0.024 0.046 -10000 0 -0.45 7 7
MAPKKK cascade -0.27 0.31 0.86 1 -0.63 265 266
cortisol/GR alpha (dimer)/Src-1 0.26 0.27 0.52 359 -0.55 1 360
PBX1 0.023 0.016 0.27 1 -10000 0 1
POU1F1 0.022 0.014 0.27 1 -10000 0 1
SELE -0.2 0.3 0.64 1 -0.73 130 131
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.16 0.35 255 -10000 0 255
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.5 341 -0.51 1 342
mol:cortisol 0.17 0.19 0.34 379 -0.25 3 382
MMP1 0.047 0.31 0.43 4 -0.92 65 69
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.1 0.13 0.32 224 -0.21 1 225
NFATC2 -0.011 0.22 0.51 8 -0.65 49 57
NFATC3 -0.048 0.13 -10000 0 -0.28 142 142
CD40LG -0.31 0.52 0.69 9 -1 249 258
ITCH -0.005 0.087 -10000 0 -0.28 1 1
CBLB -0.004 0.087 -10000 0 -0.28 3 3
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.077 0.38 0.6 52 -0.95 62 114
JUNB 0.024 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.1 -10000 0 -0.31 84 84
T cell anergy -0.025 0.14 -10000 0 -0.43 81 81
TLE4 -0.016 0.18 0.37 1 -0.7 35 36
Jun/NFAT1-c-4/p21SNFT -0.18 0.44 0.68 8 -0.84 205 213
AP-1/NFAT1-c-4 -0.33 0.63 0.79 15 -1.2 247 262
IKZF1 -0.005 0.15 0.5 7 -0.58 22 29
T-helper 2 cell differentiation -0.069 0.26 0.5 2 -0.82 53 55
AP-1/NFAT1 -0.11 0.28 0.46 15 -0.49 224 239
CALM1 0.009 0.066 -10000 0 -10000 0 0
EGR2 -0.25 0.55 0.64 5 -1.2 155 160
EGR3 -0.35 0.63 0.66 4 -1.3 236 240
NFAT1/FOXP3 0.064 0.22 0.49 82 -0.51 41 123
EGR1 -0.18 0.3 -10000 0 -0.6 277 277
JUN 0.013 0.07 0.22 2 -0.61 8 10
EGR4 0.036 0.055 0.27 44 -10000 0 44
mol:Ca2+ -0.012 0.057 -10000 0 -0.18 80 80
GBP3 -0.013 0.17 0.39 2 -0.59 40 42
FOSL1 0.027 0.045 0.27 15 -0.6 2 17
NFAT1-c-4/MAF/IRF4 -0.2 0.46 0.65 7 -0.86 224 231
DGKA -0.007 0.15 0.59 1 -0.55 28 29
CREM 0.023 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.49 0.62 4 -0.94 248 252
CTLA4 0.048 0.21 0.44 104 -0.55 31 135
NFAT1-c-4 (dimer)/EGR1 -0.3 0.53 0.67 3 -1 259 262
NFAT1-c-4 (dimer)/EGR4 -0.18 0.45 0.64 5 -0.84 230 235
FOS -0.17 0.29 0.22 1 -0.6 259 260
IFNG -0.043 0.27 0.54 11 -0.78 55 66
T cell activation -0.16 0.3 0.61 6 -0.67 146 152
MAF 0.021 0.008 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.33 0.62 251 -0.6 4 255
TNF -0.27 0.46 0.57 4 -0.9 255 259
FASLG -0.32 0.62 0.77 4 -1.2 251 255
TBX21 0.017 0.14 0.38 9 -0.6 33 42
BATF3 0.021 0.01 -10000 0 -10000 0 0
PRKCQ 0.007 0.12 0.29 10 -0.6 30 40
PTPN1 -0.006 0.15 0.42 4 -0.52 34 38
NFAT1-c-4/ICER1 -0.19 0.44 0.59 3 -0.84 231 234
GATA3 0.011 0.12 0.27 26 -0.6 27 53
T-helper 1 cell differentiation -0.041 0.26 0.53 12 -0.76 55 67
IL2RA -0.078 0.36 0.63 39 -0.79 84 123
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.007 0.15 -10000 0 -0.58 23 23
E2F1 0.1 0.11 0.27 263 -10000 0 263
PPARG -0.12 0.26 -10000 0 -0.6 185 185
SLC3A2 -0.008 0.15 -10000 0 -0.58 23 23
IRF4 -0.021 0.17 0.27 11 -0.6 64 75
PTGS2 -0.36 0.56 0.63 7 -1.1 275 282
CSF2 -0.3 0.5 0.68 10 -0.97 247 257
JunB/Fra1/NFAT1-c-4 -0.18 0.43 0.63 3 -0.81 227 230
IL4 -0.073 0.27 0.5 2 -0.88 52 54
IL5 -0.3 0.5 0.62 8 -0.97 247 255
IL2 -0.16 0.31 0.64 5 -0.69 143 148
IL3 -0.053 0.13 -10000 0 -0.82 17 17
RNF128 -0.047 0.22 0.29 5 -0.69 84 89
NFATC1 -0.16 0.34 0.6 4 -0.63 251 255
CDK4 0.12 0.24 0.55 109 -0.59 3 112
PTPRK -0.01 0.16 0.39 2 -0.57 36 38
IL8 -0.3 0.5 0.6 11 -0.98 247 258
POU2F1 0.021 0.012 0.27 1 -10000 0 1
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.034 0.019 -10000 0 -0.45 1 1
Necdin/E2F1 0.065 0.11 -10000 0 -0.41 24 24
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.063 0.19 -10000 0 -0.35 240 240
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.26 0.35 1 -0.43 305 306
NT-4/5 (dimer)/p75(NTR) -0.26 0.31 -10000 0 -0.53 441 441
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.092 0.17 0.36 1 -0.34 225 226
IKBKG 0.025 0.002 -10000 0 -10000 0 0
BDNF -0.018 0.17 0.27 19 -0.6 63 82
MGDIs/NGR/p75(NTR)/LINGO1 -0.057 0.21 0.35 6 -0.37 233 239
FURIN 0.024 0.01 0.27 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.22 -10000 0 -0.42 266 266
LINGO1 0.076 0.099 0.27 177 -10000 0 177
Sortilin/TRAF6/NRIF 0.023 0.027 -10000 0 -0.6 1 1
proBDNF (dimer) -0.018 0.17 0.27 19 -0.6 63 82
NTRK1 0.026 0.045 0.27 21 -0.6 1 22
RTN4R 0.029 0.038 0.27 20 -10000 0 20
neuron apoptosis -0.092 0.21 0.35 8 -0.54 65 73
IRAK1 0.025 0.012 0.27 2 -10000 0 2
SHC1 -0.096 0.17 -10000 0 -0.4 186 186
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.054 0.035 -10000 0 -0.34 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.071 0.19 -10000 0 -0.37 236 236
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.081 0.21 -10000 0 -0.38 242 242
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.36 2 2
proNGF (dimer) 0.015 0.087 0.27 7 -0.6 15 22
MAGED1 0.025 0.012 0.27 2 -10000 0 2
APP 0.024 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.22 0.3 -10000 0 -0.6 316 316
ZNF274 0.024 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.08 0.17 -10000 0 -0.34 228 228
NGF 0.015 0.087 0.27 7 -0.6 15 22
cell cycle arrest -0.085 0.17 0.23 41 -0.32 236 277
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.063 0.13 -10000 0 -0.29 171 171
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.22 0.28 -10000 0 -0.46 434 434
NCSTN 0.021 0.009 -10000 0 -10000 0 0
mol:GTP -0.085 0.2 -10000 0 -0.39 240 240
PSENEN 0.024 0.009 0.27 1 -10000 0 1
mol:ceramide -0.1 0.17 -10000 0 -0.36 237 237
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.052 0.11 -10000 0 -0.37 29 29
p75(NTR)/beta APP -0.11 0.22 -10000 0 -0.44 248 248
BEX1 -0.018 0.24 0.27 139 -0.6 109 248
mol:GDP -0.12 0.18 -10000 0 -0.39 242 242
NGF (dimer) -0.002 0.14 0.35 1 -0.36 104 105
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.041 0.2 0.35 5 -0.34 221 226
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.075 0.17 -10000 0 -0.34 238 238
MYD88 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.085 0.21 -10000 0 -0.39 240 240
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.082 0.077 -10000 0 -10000 0 0
NT3 (dimer) -0.067 0.23 0.27 11 -0.6 124 135
TP53 -0.1 0.18 0.36 6 -0.36 251 257
PRDM4 -0.1 0.17 -10000 0 -0.36 236 236
BDNF (dimer) 0.018 0.21 0.34 16 -0.38 149 165
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.022 -10000 0 -0.6 1 1
activation of caspase activity -0.065 0.18 -10000 0 -0.34 240 240
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.07 0.19 -10000 0 -0.37 234 234
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
MAPK10 -0.15 0.21 0.33 3 -0.43 246 249
DIABLO 0.025 0.002 -10000 0 -10000 0 0
SMPD2 -0.1 0.17 -10000 0 -0.36 237 237
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.088 0.2 -10000 0 -0.4 240 240
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.17 0.27 -10000 0 -0.49 314 314
MAPK8 -0.11 0.19 0.3 8 -0.38 223 231
MAPK9 -0.11 0.19 0.3 6 -0.38 220 226
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.067 0.23 0.27 11 -0.6 124 135
NTF4 -0.22 0.3 -10000 0 -0.6 316 316
NDN 0.005 0.1 -10000 0 -0.6 24 24
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.056 0.18 -10000 0 -0.32 237 237
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.024 -10000 0 -0.36 1 1
RhoA-B-C/GTP -0.085 0.2 -10000 0 -0.39 240 240
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.078 0.21 -10000 0 -0.37 255 255
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.089 0.21 -10000 0 -0.39 257 257
PRKACB 0.034 0.066 0.27 42 -0.6 3 45
proBDNF (dimer)/p75 ECD 0.002 0.13 -10000 0 -0.44 65 65
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.18 0.28 13 -0.36 230 243
BAD -0.13 0.2 0.4 7 -0.4 236 243
RIPK2 0.02 0.018 0.27 3 -10000 0 3
NGFR -0.16 0.28 -10000 0 -0.6 238 238
CYCS -0.098 0.17 0.36 2 -0.35 232 234
ADAM17 0.024 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.06 0.17 -10000 0 -0.36 170 170
BCL2L11 -0.13 0.2 0.4 7 -0.4 235 242
BDNF (dimer)/p75(NTR) -0.14 0.25 -10000 0 -0.46 285 285
PI3K -0.071 0.19 -10000 0 -0.36 228 228
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.071 0.19 -10000 0 -0.36 235 235
NDNL2 0.024 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.22 -10000 0 -0.44 256 256
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.071 0.19 -10000 0 -0.37 238 238
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
PLG 0.018 0.018 0.27 4 -10000 0 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.12 0.2 -10000 0 -0.4 266 266
SQSTM1 0.024 0.009 0.27 1 -10000 0 1
NGFRAP1 0.023 0.031 -10000 0 -0.6 2 2
CASP3 -0.12 0.19 0.4 6 -0.38 236 242
E2F1 0.1 0.11 0.27 263 -10000 0 263
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.009 0.12 -10000 0 -0.43 14 14
NGF (dimer)/TRKA 0.026 0.071 -10000 0 -0.42 16 16
MMP7 -0.041 0.2 0.27 24 -0.6 93 117
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.06 0.19 -10000 0 -0.35 231 231
MMP3 0.1 0.14 0.27 295 -0.6 9 304
APAF-1/Caspase 9 -0.098 0.12 -10000 0 -0.49 10 10
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.011 0.086 -10000 0 -0.6 16 16
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
NUDC 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.21 0.21 -10000 0 -0.38 492 492
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.21 0.17 0.25 1 -0.35 490 491
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.037 0.057 0.27 48 -10000 0 48
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.025 0.07 0.27 22 -0.6 7 29
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.051 0.052 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.025 0.002 -10000 0 -10000 0 0
CDK5R1 0.029 0.037 0.27 19 -10000 0 19
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.085 0.27 116 -10000 0 116
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.22 0.22 0.35 2 -0.38 511 513
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.15 0.16 0.3 3 -0.3 340 343
MAP1B 0.001 0.038 -10000 0 -0.32 11 11
RAC1 0.01 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.18 0.15 0.23 2 -0.31 457 459
RELN -0.35 0.31 0.27 3 -0.6 499 502
PAFAH/LIS1 0.024 0.049 0.32 2 -0.39 7 9
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.13 0.13 -10000 0 -0.3 31 31
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.16 0.17 -10000 0 -0.31 422 422
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.17 0.15 0.29 4 -0.31 356 360
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.009 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.043 0.065 0.27 64 -10000 0 64
PAFAH1B2 0.022 0.008 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.014 0.04 -10000 0 -0.23 10 10
NDEL1/Katanin 60/Dynein heavy chain -0.14 0.16 0.33 2 -0.34 52 54
LRP8 0.051 0.077 0.27 94 -10000 0 94
NDEL1/Katanin 60 -0.15 0.16 0.33 2 -0.3 331 333
P39/CDK5 -0.18 0.16 0.28 7 -0.31 461 468
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.2 0.16 0.22 2 -0.33 485 487
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.18 0.2 0.34 1 -0.34 484 485
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 490 490
CDC42 0.01 0.005 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.005 0.12 -10000 0 -0.38 76 76
cell-cell adhesion 0.15 0.16 0.34 281 -10000 0 281
Ephrin B/EPHB2/RasGAP 0.03 0.11 -10000 0 -0.34 60 60
ITSN1 0.023 0.031 -10000 0 -0.6 2 2
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.15 0.21 -10000 0 -0.38 359 359
HRAS/GDP -0.14 0.2 -10000 0 -0.43 147 147
Ephrin B/EPHB1/GRB7 -0.13 0.22 -10000 0 -0.38 331 331
Endophilin/SYNJ1 -0.028 0.087 -10000 0 -0.32 58 58
KRAS 0.024 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.13 0.23 -10000 0 -0.38 346 346
endothelial cell migration 0.044 0.02 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PAK1 -0.034 0.1 0.35 2 -0.35 65 67
HRAS 0.024 0.01 0.27 1 -10000 0 1
RRAS -0.029 0.089 -10000 0 -0.32 58 58
DNM1 0.021 0.049 0.27 1 -0.6 5 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.19 0.35 2 -0.36 365 367
lamellipodium assembly -0.15 0.16 -10000 0 -0.34 281 281
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.11 0.17 -10000 0 -0.44 97 97
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
EPHB2 0.028 0.033 0.27 15 -10000 0 15
EPHB3 0.025 0.015 0.27 3 -10000 0 3
EPHB1 -0.24 0.31 0.27 1 -0.6 354 355
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.14 0.18 -10000 0 -0.45 131 131
Ephrin B/EPHB2 0.02 0.11 -10000 0 -0.34 60 60
Ephrin B/EPHB3 0.019 0.1 -10000 0 -0.34 56 56
JNK cascade -0.15 0.16 0.36 6 -0.33 351 357
Ephrin B/EPHB1 -0.14 0.22 -10000 0 -0.38 365 365
RAP1/GDP -0.11 0.17 -10000 0 -0.41 120 120
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.025 0.16 -10000 0 -0.6 62 62
EFNB1 0.025 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.12 0.2 -10000 0 -0.35 352 352
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.13 0.2 -10000 0 -0.5 81 81
Rap1/GTP -0.13 0.18 -10000 0 -0.34 274 274
axon guidance -0.006 0.12 -10000 0 -0.38 76 76
MAPK3 -0.099 0.15 -10000 0 -0.41 83 83
MAPK1 -0.1 0.15 -10000 0 -0.41 89 89
Rac1/GDP -0.12 0.17 -10000 0 -0.42 123 123
actin cytoskeleton reorganization -0.13 0.13 -10000 0 -0.36 105 105
CDC42/GDP -0.12 0.17 -10000 0 -0.42 124 124
PI3K 0.048 0.022 -10000 0 -10000 0 0
EFNA5 -0.034 0.18 -10000 0 -0.6 76 76
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.006 0.091 -10000 0 -0.54 4 4
CDC42 0.024 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.13 0.18 -10000 0 -0.34 282 282
PTK2 0.16 0.28 0.69 174 -10000 0 174
MAP4K4 -0.15 0.17 0.36 6 -0.34 351 357
SRC 0.024 0.005 -10000 0 -10000 0 0
KALRN 0.014 0.081 -10000 0 -0.6 14 14
Intersectin/N-WASP 0.034 0.025 -10000 0 -0.45 2 2
neuron projection morphogenesis -0.12 0.15 0.29 7 -0.44 62 69
MAP2K1 -0.11 0.16 -10000 0 -0.42 93 93
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.21 -10000 0 -0.36 351 351
cell migration -0.12 0.19 0.31 5 -0.47 96 101
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.029 0.089 -10000 0 -0.32 58 58
PXN 0.025 0.002 -10000 0 -10000 0 0
TF -0.2 0.18 -10000 0 -0.35 447 447
HRAS/GTP -0.12 0.2 -10000 0 -0.34 348 348
Ephrin B1/EPHB1-2 -0.12 0.2 -10000 0 -0.35 352 352
cell adhesion mediated by integrin 0.009 0.092 0.31 56 -0.27 4 60
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.13 0.21 -10000 0 -0.36 354 354
RAC1-CDC42/GTP -0.15 0.16 -10000 0 -0.51 55 55
RASA1 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.12 0.17 -10000 0 -0.44 94 94
ruffle organization -0.15 0.17 0.37 4 -0.53 54 58
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.032 0.092 -10000 0 -0.33 59 59
Ephrin B/EPHB2/KALRN 0.025 0.12 -10000 0 -0.36 70 70
ROCK1 0.018 0.03 0.2 4 -10000 0 4
RAS family/GDP -0.12 0.13 -10000 0 -0.38 84 84
Rac1/GTP -0.16 0.17 -10000 0 -0.35 281 281
Ephrin B/EPHB1/Src/Paxillin -0.14 0.19 -10000 0 -0.34 349 349
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.074 0.13 -10000 0 -0.44 71 71
PTK2B 0.02 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.17 -10000 0 -0.74 32 32
EDN1 -0.078 0.17 -10000 0 -0.59 71 71
EDN3 -0.24 0.3 0.27 1 -0.6 340 341
EDN2 0.079 0.11 0.27 199 -0.6 4 203
HRAS/GDP -0.095 0.19 0.28 1 -0.47 115 116
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.061 0.14 -10000 0 -0.4 76 76
ADCY4 -0.13 0.2 0.29 3 -0.45 203 206
ADCY5 -0.22 0.25 -10000 0 -0.47 351 351
ADCY6 -0.12 0.19 0.29 3 -0.42 198 201
ADCY7 -0.12 0.19 0.29 3 -0.42 197 200
ADCY1 -0.12 0.2 0.26 2 -0.43 199 201
ADCY2 -0.14 0.23 0.3 7 -0.47 217 224
ADCY3 -0.12 0.19 0.28 2 -0.42 197 199
ADCY8 -0.1 0.18 0.28 3 -0.43 147 150
ADCY9 -0.12 0.18 0.28 1 -0.42 188 189
arachidonic acid secretion -0.17 0.27 0.3 2 -0.5 282 284
ETB receptor/Endothelin-1/Gq/GTP -0.048 0.15 -10000 0 -0.36 115 115
GNAO1 0.019 0.096 0.27 28 -0.6 15 43
HRAS 0.023 0.01 0.27 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP -0.061 0.13 0.3 5 -0.4 72 77
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.44 198 198
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.063 0.16 0.39 8 -0.44 70 78
EDNRB -0.017 0.16 -10000 0 -0.6 59 59
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.074 0.15 -10000 0 -0.47 75 75
CYSLTR1 -0.079 0.15 -10000 0 -0.48 71 71
SLC9A1 -0.048 0.099 -10000 0 -0.31 73 73
mol:GDP -0.1 0.2 0.34 2 -0.49 123 125
SLC9A3 -0.1 0.27 -10000 0 -0.64 131 131
RAF1 -0.14 0.23 0.32 1 -0.46 225 226
JUN -0.052 0.19 -10000 0 -0.74 38 38
JAK2 -0.073 0.13 -10000 0 -0.43 74 74
mol:IP3 -0.074 0.16 -10000 0 -0.44 90 90
ETA receptor/Endothelin-1 -0.086 0.16 0.34 5 -0.5 75 80
PLCB1 -0.012 0.14 -10000 0 -0.6 43 43
PLCB2 0.013 0.03 0.27 1 -0.6 1 2
ETA receptor/Endothelin-3 -0.2 0.22 -10000 0 -0.46 345 345
FOS -0.31 0.46 -10000 0 -0.94 275 275
Gai/GDP -0.1 0.3 -10000 0 -0.76 127 127
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 0.28 1 -0.53 104 105
BCAR1 0.022 0.009 -10000 0 -10000 0 0
PRKCB1 -0.076 0.16 -10000 0 -0.42 102 102
GNAQ 0.012 0.036 -10000 0 -0.61 2 2
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNAL -0.11 0.25 -10000 0 -0.6 172 172
Gs family/GDP -0.15 0.24 -10000 0 -0.5 206 206
ETA receptor/Endothelin-1/Gq/GTP -0.049 0.12 -10000 0 -0.38 57 57
MAPK14 -0.062 0.15 -10000 0 -0.41 95 95
TRPC6 -0.052 0.19 -10000 0 -0.81 30 30
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.6 39 39
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.16 -10000 0 -0.41 109 109
ETB receptor/Endothelin-2 0.034 0.15 0.25 14 -0.42 63 77
ETB receptor/Endothelin-3 -0.2 0.25 -10000 0 -0.46 377 377
ETB receptor/Endothelin-1 -0.073 0.18 -10000 0 -0.49 118 118
MAPK3 -0.26 0.39 -10000 0 -0.79 279 279
MAPK1 -0.27 0.4 -10000 0 -0.81 281 281
Rac1/GDP -0.095 0.19 0.28 1 -0.48 107 108
cAMP biosynthetic process -0.16 0.22 0.52 1 -0.49 194 195
MAPK8 -0.056 0.19 -10000 0 -0.69 45 45
SRC 0.024 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.065 0.17 -10000 0 -0.37 145 145
p130Cas/CRK/Src/PYK2 -0.097 0.21 0.49 1 -0.55 99 100
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.094 0.19 0.28 1 -0.47 115 116
COL1A2 -0.083 0.19 0.4 7 -0.48 109 116
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.026 0.096 0.26 12 -0.38 6 18
mol:DAG -0.074 0.16 -10000 0 -0.44 90 90
MAP2K2 -0.2 0.3 0.34 2 -0.59 281 283
MAP2K1 -0.2 0.3 0.32 2 -0.58 279 281
EDNRA -0.034 0.058 -10000 0 -0.25 9 9
positive regulation of muscle contraction -0.064 0.12 -10000 0 -0.39 67 67
Gq family/GDP -0.059 0.19 -10000 0 -0.48 78 78
HRAS/GTP -0.1 0.2 0.34 1 -0.47 126 127
PRKCH -0.075 0.16 -10000 0 -0.43 91 91
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.07 0.18 0.29 5 -0.46 98 103
PRKCB -0.072 0.17 0.24 1 -0.45 94 95
PRKCE -0.078 0.16 -10000 0 -0.43 95 95
PRKCD -0.076 0.16 -10000 0 -0.44 89 89
PRKCG -0.077 0.16 0.27 1 -0.44 93 94
regulation of vascular smooth muscle contraction -0.37 0.53 -10000 0 -1.1 273 273
PRKCQ -0.084 0.18 -10000 0 -0.48 104 104
PLA2G4A -0.19 0.3 0.31 2 -0.55 282 284
GNA14 0.015 0.068 0.26 19 -0.61 6 25
GNA15 0.021 0.028 0.26 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.021 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.061 0.13 -10000 0 -0.41 68 68
MMP1 0.18 0.13 0.41 67 -10000 0 67
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.12 0.36 -10000 0 -0.87 147 147
NCK1/PAK1/Dok-R -0.078 0.15 -10000 0 -0.41 147 147
NCK1/Dok-R -0.14 0.42 -10000 0 -1 146 146
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.035 0.092 0.24 134 -10000 0 134
RELA 0.024 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.035 0.11 0.27 132 -10000 0 132
TNIP2 0.024 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.41 -10000 0 -0.99 146 146
FN1 0.13 0.12 0.27 367 -10000 0 367
PLD2 -0.16 0.44 -10000 0 -1.1 146 146
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.014 0.19 0.27 117 -0.6 59 176
ELK1 -0.14 0.39 -10000 0 -0.96 147 147
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PAK1 0.023 0.017 0.27 3 -10000 0 3
Tie2/Ang1/alpha5/beta1 Integrin -0.075 0.45 -10000 0 -1 146 146
CDKN1A -0.089 0.24 -10000 0 -0.62 110 110
ITGA5 0.025 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.43 -10000 0 -1 146 146
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.083 0.27 -10000 0 -0.64 147 147
PLG -0.17 0.43 -10000 0 -1.1 147 147
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.34 -10000 0 -0.83 147 147
GRB2 0.023 0.011 0.27 1 -10000 0 1
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
ANGPT2 -0.13 0.27 -10000 0 -0.71 106 106
BMX -0.29 0.48 -10000 0 -1.3 147 147
ANGPT1 -0.19 0.47 -10000 0 -1.2 134 134
tube development -0.1 0.27 -10000 0 -0.68 130 130
ANGPT4 -0.17 0.28 -10000 0 -0.6 252 252
response to hypoxia -0.011 0.026 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.48 -10000 0 -1.1 146 146
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.6 310 310
STAT5A (dimer) -0.12 0.31 -10000 0 -0.79 122 122
mol:L-citrulline -0.083 0.27 -10000 0 -0.64 147 147
AGTR1 -0.086 0.26 0.27 52 -0.6 167 219
MAPK14 -0.16 0.44 -10000 0 -1.1 147 147
Tie2/SHP2 -0.076 0.29 -10000 0 -1.1 56 56
TEK -0.084 0.32 -10000 0 -1.2 56 56
RPS6KB1 -0.1 0.35 -10000 0 -0.83 147 147
Angiotensin II/AT1 -0.064 0.2 0.18 52 -0.44 170 222
Tie2/Ang1/GRB2 -0.16 0.45 -10000 0 -1.1 146 146
MAPK3 -0.15 0.4 -10000 0 -0.98 146 146
MAPK1 -0.15 0.4 -10000 0 -1 146 146
Tie2/Ang1/GRB7 -0.16 0.45 -10000 0 -1.1 146 146
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.17 0.44 -10000 0 -1.1 146 146
PI3K -0.14 0.41 -10000 0 -1 147 147
FES -0.16 0.44 -10000 0 -1.1 148 148
Crk/Dok-R -0.14 0.43 -10000 0 -1 146 146
Tie2/Ang1/ABIN2 -0.16 0.46 -10000 0 -1.1 146 146
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.1 0.32 -10000 0 -0.77 147 147
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.09 0.35 0.47 1 -0.81 146 147
Tie2/Ang2 -0.15 0.37 -10000 0 -0.94 125 125
Tie2/Ang1 -0.18 0.48 -10000 0 -1.2 146 146
FOXO1 -0.1 0.32 0.47 1 -0.78 147 148
ELF1 0.016 0.032 -10000 0 -10000 0 0
ELF2 -0.16 0.43 -10000 0 -1.1 146 146
mol:Choline -0.16 0.41 -10000 0 -1 146 146
cell migration -0.029 0.097 -10000 0 -0.23 147 147
FYN -0.12 0.31 -10000 0 -0.78 128 128
DOK2 0.019 0.024 -10000 0 -0.6 1 1
negative regulation of cell cycle -0.079 0.22 -10000 0 -0.56 110 110
ETS1 -0.013 0.1 -10000 0 -0.27 108 108
PXN -0.066 0.3 0.43 2 -0.67 146 148
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.098 0.3 -10000 0 -0.73 147 147
RAC1 0.024 0.004 -10000 0 -10000 0 0
TNF -0.017 0.13 0.27 15 -0.28 133 148
MAPKKK cascade -0.16 0.41 -10000 0 -1 146 146
RASA1 0.024 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.16 0.44 -10000 0 -1.1 145 145
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.072 0.24 0.37 2 -0.57 147 149
mol:Phosphatidic acid -0.16 0.41 -10000 0 -1 146 146
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.083 0.27 -10000 0 -0.64 147 147
Rac1/GTP -0.1 0.32 -10000 0 -0.78 147 147
MMP2 -0.17 0.44 -10000 0 -1.1 147 147
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.27 15 -10000 0 15
EFNB1 -0.007 0.037 -10000 0 -0.45 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.1 0.19 -10000 0 -0.32 342 342
Ephrin B2/EPHB1-2 -0.12 0.2 -10000 0 -0.35 352 352
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.31 342 342
Ephrin B1/EPHB1-2/Tiam1 -0.11 0.2 -10000 0 -0.34 349 349
DNM1 0.021 0.049 0.28 1 -0.6 5 6
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.024 0.12 -10000 0 -0.56 37 37
YES1 -0.025 0.17 -10000 0 -0.77 41 41
Ephrin B1/EPHB1-2/NCK2 -0.12 0.2 -10000 0 -0.34 351 351
PI3K 0.007 0.13 -10000 0 -0.54 40 40
mol:GDP -0.11 0.19 -10000 0 -0.33 349 349
ITGA2B 0.032 0.058 0.27 35 -0.6 2 37
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.027 0.17 -10000 0 -0.76 41 41
MAP3K7 -0.025 0.13 -10000 0 -0.58 39 39
FGR -0.024 0.17 -10000 0 -0.77 40 40
TIAM1 0.025 0.017 0.27 4 -10000 0 4
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.004 0.12 -10000 0 -0.5 38 38
LYN -0.023 0.17 -10000 0 -0.75 41 41
Ephrin B1/EPHB1-2/Src Family Kinases -0.028 0.16 -10000 0 -0.71 41 41
Ephrin B1/EPHB1-2 -0.025 0.14 -10000 0 -0.63 38 38
SRC -0.022 0.17 -10000 0 -0.75 41 41
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
EPHB1 -0.24 0.31 0.28 1 -0.6 354 355
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.033 0.074 -10000 0 -0.44 15 15
BLK -0.024 0.18 -10000 0 -0.78 39 39
HCK -0.022 0.17 -10000 0 -0.75 41 41
regulation of stress fiber formation 0.11 0.19 0.34 351 -10000 0 351
MAPK8 -0.025 0.12 -10000 0 -0.52 39 39
Ephrin B1/EPHB1-2/RGS3 -0.11 0.2 -10000 0 -0.34 350 350
endothelial cell migration -0.019 0.11 -10000 0 -0.51 35 35
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.72 20 20
regulation of focal adhesion formation 0.11 0.19 0.34 351 -10000 0 351
chemotaxis 0.11 0.19 0.34 350 -10000 0 350
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.1 0.18 -10000 0 -0.31 342 342
angiogenesis -0.026 0.14 -10000 0 -0.62 39 39
LCK -0.023 0.17 -10000 0 -0.77 40 40
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.6 0.77 11 -1.2 164 175
STAT6 (cleaved dimer) -0.31 0.58 -10000 0 -1.2 192 192
IGHG1 -0.032 0.26 0.51 43 -0.54 7 50
IGHG3 -0.24 0.57 0.67 11 -1.1 187 198
AKT1 -0.092 0.34 0.58 15 -0.74 71 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.054 0.29 0.55 16 -0.72 49 65
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.093 0.35 0.56 26 -0.73 77 103
THY1 -0.25 0.6 0.8 9 -1.2 156 165
MYB 0.013 0.082 0.27 2 -0.6 14 16
HMGA1 0.031 0.04 0.27 23 -10000 0 23
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.12 0.41 0.65 38 -0.71 151 189
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.085 0.35 0.58 18 -0.78 56 74
SP1 0.035 0.028 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.016 0.043 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.27 0.6 0.71 6 -1.2 182 188
SOCS1 -0.15 0.4 0.66 9 -0.75 141 150
SOCS3 -0.1 0.35 0.63 10 -0.81 58 68
FCER2 -0.41 0.74 0.78 16 -1.3 275 291
PARP14 0.016 0.033 0.25 3 -10000 0 3
CCL17 -0.23 0.62 0.87 26 -1.2 157 183
GRB2 0.023 0.011 0.27 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.048 0.29 0.54 18 -0.72 33 51
T cell proliferation -0.27 0.61 0.74 7 -1.2 179 186
IL4R/JAK1 -0.26 0.59 0.74 1 -1.2 175 176
EGR2 -0.37 0.74 0.83 8 -1.4 210 218
JAK2 0.009 0.076 0.22 1 -10000 0 1
JAK3 0.022 0.039 0.29 12 -10000 0 12
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.016 0.041 -10000 0 -10000 0 0
COL1A2 -0.024 0.26 0.57 7 -1.1 10 17
CCL26 -0.25 0.61 0.79 8 -1.2 156 164
IL4R -0.25 0.66 0.86 22 -1.2 174 196
PTPN6 0.015 0.036 0.22 2 -10000 0 2
IL13RA2 -0.25 0.6 0.79 10 -1.2 157 167
IL13RA1 0.009 0.077 -10000 0 -10000 0 0
IRF4 -0.14 0.5 0.63 11 -1.4 89 100
ARG1 -0.008 0.21 0.62 2 -10000 0 2
CBL -0.12 0.38 0.57 31 -0.69 133 164
GTF3A 0.056 0.052 0.27 1 -10000 0 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.021 0.11 0.29 27 -10000 0 27
IRF4/BCL6 -0.11 0.45 0.58 1 -1.3 89 90
CD40LG -0.012 0.14 0.33 13 -0.62 39 52
MAPK14 -0.12 0.38 0.59 24 -0.71 126 150
mitosis -0.085 0.33 0.56 18 -0.7 69 87
STAT6 -0.28 0.74 0.95 30 -1.4 184 214
SPI1 0.027 0.018 0.27 4 -10000 0 4
RPS6KB1 -0.066 0.32 0.55 23 -0.69 62 85
STAT6 (dimer) -0.28 0.74 0.96 30 -1.4 184 214
STAT6 (dimer)/PARP14 -0.31 0.66 0.76 5 -1.3 200 205
mast cell activation 0.001 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.1 0.36 0.58 19 -0.73 90 109
FRAP1 -0.093 0.34 0.58 15 -0.74 71 86
LTA -0.23 0.62 0.86 24 -1.2 160 184
FES 0.022 0.038 -10000 0 -0.6 3 3
T-helper 1 cell differentiation 0.27 0.71 1.3 185 -0.95 30 215
CCL11 -0.18 0.59 0.76 19 -1.2 149 168
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.081 0.34 0.58 20 -0.74 65 85
IL2RG 0.024 0.073 0.28 32 -0.6 5 37
IL10 -0.22 0.6 0.82 15 -1.2 149 164
IRS1 0.002 0.12 -10000 0 -0.6 29 29
IRS2 0 0.12 -10000 0 -0.6 29 29
IL4 -0.018 0.27 0.58 22 -1.1 20 42
IL5 -0.25 0.6 0.78 7 -1.2 155 162
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.51 0.81 29 -0.91 157 186
COL1A1 -0.005 0.36 0.64 39 -0.96 40 79
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.27 0.61 -10000 0 -1.3 156 156
IL2R gamma/JAK3 0.036 0.071 0.4 14 -0.4 5 19
TFF3 -0.3 0.71 0.86 15 -1.3 202 217
ALOX15 -0.32 0.7 0.8 15 -1.3 217 232
MYBL1 0.042 0.07 0.27 73 -10000 0 73
T-helper 2 cell differentiation -0.2 0.52 0.7 23 -0.97 179 202
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.024 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.09 0.34 0.54 27 -0.72 74 101
mol:PI-3-4-5-P3 -0.092 0.34 0.58 15 -0.74 71 86
PI3K -0.1 0.36 0.59 14 -0.8 72 86
DOK2 0.019 0.024 -10000 0 -0.6 1 1
ETS1 0.005 0.048 -10000 0 -0.56 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.037 0.27 0.49 33 -0.64 30 63
ITGB3 -0.25 0.62 0.78 7 -1.2 161 168
PIGR -0.71 0.78 0.81 15 -1.3 484 499
IGHE -0.015 0.088 0.18 22 -0.22 21 43
MAPKKK cascade -0.036 0.27 0.49 33 -0.63 30 63
BCL6 0.025 0.034 -10000 0 -0.59 2 2
OPRM1 -0.25 0.6 0.81 9 -1.2 163 172
RETNLB -0.25 0.6 -10000 0 -1.2 145 145
SELP -0.38 0.77 0.82 10 -1.5 227 237
AICDA -0.24 0.57 0.78 7 -1.2 152 159
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.11 0.22 0.23 1 -0.4 248 249
FZD6 0.015 0.049 -10000 0 -0.6 5 5
WNT6 -0.1 0.26 0.27 20 -0.6 172 192
WNT4 0.015 0.095 0.27 15 -0.6 17 32
FZD3 0.018 0.039 -10000 0 -0.6 3 3
WNT5A 0.019 0.07 0.27 9 -0.6 9 18
WNT11 -0.1 0.25 0.27 9 -0.6 166 175
IL23-mediated signaling events

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
CCL2 -0.04 0.5 0.82 37 -1.1 64 101
IL23A -0.051 0.5 0.86 29 -1.1 66 95
NF kappa B1 p50/RelA/I kappa B alpha -0.081 0.46 0.73 7 -0.88 135 142
positive regulation of T cell mediated cytotoxicity -0.044 0.56 0.88 56 -0.96 138 194
ITGA3 -0.035 0.49 0.83 31 -1.1 66 97
IL17F -0.02 0.37 0.6 61 -0.64 94 155
IL12B 0.08 0.15 0.38 142 -10000 0 142
STAT1 (dimer) -0.058 0.52 0.77 38 -0.93 138 176
CD4 -0.035 0.5 0.86 32 -1 63 95
IL23 -0.036 0.5 0.84 37 -1.1 62 99
IL23R 0.047 0.2 0.6 18 -0.96 11 29
IL1B -0.052 0.51 0.85 33 -1.1 67 100
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0 0.5 0.88 49 -1 60 109
TYK2 0.025 0.061 0.23 1 -10000 0 1
STAT4 0 0.12 0.27 1 -0.6 32 33
STAT3 0.024 0.006 -10000 0 -10000 0 0
IL18RAP 0.005 0.12 0.28 4 -0.6 31 35
IL12RB1 0.032 0.09 0.4 25 -0.64 1 26
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.036 0.089 0.34 25 -0.49 1 26
IL23R/JAK2 0.059 0.22 0.57 24 -0.92 10 34
positive regulation of chronic inflammatory response -0.044 0.56 0.88 56 -0.96 138 194
natural killer cell activation -0.004 0.016 -10000 0 -0.053 31 31
JAK2 0.037 0.086 0.27 31 -10000 0 31
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.01 -10000 0 -10000 0 0
RELA 0.026 0.01 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.03 0.48 0.83 37 -0.99 64 101
ALOX12B -0.036 0.49 0.84 34 -1 65 99
CXCL1 -0.22 0.72 0.84 41 -1.2 235 276
T cell proliferation -0.044 0.56 0.88 56 -0.96 138 194
NFKBIA 0.026 0.01 -10000 0 -10000 0 0
IL17A 0.011 0.32 0.56 72 -0.53 61 133
PI3K -0.077 0.48 0.69 21 -0.9 137 158
IFNG 0.027 0.072 0.18 109 -0.12 10 119
STAT3 (dimer) -0.078 0.46 0.74 8 -0.86 135 143
IL18R1 0.019 0.072 -10000 0 -0.6 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 0.024 0.36 0.67 63 -0.64 49 112
IL18/IL18R 0.041 0.11 0.32 7 -0.39 40 47
macrophage activation -0.001 0.03 0.058 74 -0.044 50 124
TNF -0.051 0.51 0.85 35 -1.1 69 104
STAT3/STAT4 -0.076 0.5 0.7 22 -0.92 141 163
STAT4 (dimer) -0.071 0.53 0.76 34 -0.96 141 175
IL18 0.031 0.04 0.27 21 -10000 0 21
IL19 0.005 0.5 0.85 54 -1 60 114
STAT5A (dimer) -0.063 0.51 0.75 34 -0.93 139 173
STAT1 0.03 0.035 0.27 18 -10000 0 18
SOCS3 0.02 0.044 -10000 0 -0.6 4 4
CXCL9 -0.009 0.53 0.87 58 -1.1 63 121
MPO -0.066 0.56 0.82 42 -1.2 96 138
positive regulation of humoral immune response -0.044 0.56 0.88 56 -0.96 138 194
IL23/IL23R/JAK2/TYK2 -0.053 0.58 0.88 55 -1 138 193
IL6 -0.33 0.76 0.83 27 -1.2 319 346
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
IL2 0.023 0.042 0.32 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.016 -10000 0 -0.053 31 31
CD3E -0.049 0.52 0.86 41 -1.1 72 113
keratinocyte proliferation -0.044 0.56 0.88 56 -0.96 138 194
NOS2 -0.035 0.5 0.84 35 -1.1 62 97
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.005 0.13 -10000 0 -0.6 37 37
GNB1/GNG2 -0.09 0.22 -10000 0 -0.48 133 133
mol:DAG -0.091 0.19 0.24 1 -0.45 125 126
PLCG1 -0.094 0.2 0.24 1 -0.47 125 126
YES1 -0.11 0.2 0.21 1 -0.39 225 226
FZD3 0.018 0.039 -10000 0 -0.6 3 3
FZD6 0.015 0.049 -10000 0 -0.6 5 5
G protein -0.077 0.21 0.3 2 -0.48 120 122
MAP3K7 -0.082 0.16 0.38 1 -0.42 93 94
mol:Ca2+ -0.088 0.19 0.24 1 -0.44 125 126
mol:IP3 -0.091 0.19 0.24 1 -0.45 125 126
NLK -0.013 0.14 -10000 0 -0.84 21 21
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.085 0.18 0.31 2 -0.43 111 113
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.22 0.23 1 -0.4 248 249
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
GNAS -0.1 0.2 0.21 1 -0.5 122 123
GO:0007205 -0.094 0.19 0.23 1 -0.45 125 126
WNT6 -0.1 0.26 0.27 20 -0.6 172 192
WNT4 0.015 0.095 0.27 15 -0.6 17 32
NFAT1/CK1 alpha -0.096 0.21 -10000 0 -0.52 106 106
GNG2 0.019 0.053 -10000 0 -0.6 6 6
WNT5A 0.019 0.07 0.27 9 -0.6 9 18
WNT11 -0.1 0.25 0.27 9 -0.6 166 175
CDC42 -0.096 0.2 -10000 0 -0.49 115 115
IGF1 pathway

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
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.071 0.16 -10000 0 -0.36 183 183
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.024 0.01 0.27 1 -10000 0 1
IRS1/Crk -0.065 0.17 -10000 0 -0.36 187 187
IGF-1R heterotetramer/IGF1/PTP1B -0.048 0.18 -10000 0 -0.39 163 163
AKT1 -0.069 0.14 0.25 2 -0.32 151 153
BAD -0.067 0.13 0.24 2 -0.31 146 148
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.072 0.16 -10000 0 -0.36 187 187
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.062 0.17 -10000 0 -0.36 187 187
RAF1 -0.051 0.14 -10000 0 -0.51 32 32
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.035 0.17 -10000 0 -0.34 171 171
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.065 0.18 -10000 0 -0.37 197 197
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.064 0.13 0.25 2 -0.33 132 134
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.031 0.13 0.31 8 -0.41 28 36
PXN 0.025 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
HRAS/GTP -0.042 0.14 -10000 0 -0.33 123 123
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.013 0.14 -10000 0 -0.33 119 119
IGF-1R heterotetramer -0.011 0.1 0.26 1 -0.67 14 15
IGF-1R heterotetramer/IGF1/IRS/Nck -0.048 0.18 -10000 0 -0.36 184 184
Crk/p130 Cas/Paxillin -0.04 0.16 -10000 0 -0.33 176 176
IGF1R -0.011 0.1 0.26 1 -0.67 14 15
IGF1 -0.12 0.27 -10000 0 -0.62 178 178
IRS2/Crk -0.073 0.18 -10000 0 -0.36 197 197
PI3K -0.035 0.17 -10000 0 -0.34 177 177
apoptosis 0.043 0.11 0.38 23 -0.27 4 27
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
PRKCD -0.083 0.18 -10000 0 -0.41 177 177
RAF1/14-3-3 E -0.025 0.13 0.3 1 -0.43 32 33
BAD/14-3-3 -0.046 0.11 0.28 4 -0.41 23 27
PRKCZ -0.069 0.14 0.25 2 -0.32 154 156
Crk/p130 Cas/Paxillin/FAK1 -0.028 0.11 -10000 0 -0.41 24 24
PTPN1 0.025 0.022 0.27 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.085 0.19 -10000 0 -0.43 185 185
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.026 0.15 -10000 0 -0.35 133 133
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.057 0.17 -10000 0 -0.36 184 184
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.071 0.16 -10000 0 -0.36 187 187
IRS1 -0.075 0.18 -10000 0 -0.37 194 194
IRS2 -0.083 0.18 -10000 0 -0.38 197 197
IGF-1R heterotetramer/IGF1 -0.083 0.22 -10000 0 -0.47 189 189
GRB2 0.023 0.011 0.27 1 -10000 0 1
PDPK1 -0.071 0.14 0.28 1 -0.33 156 157
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.093 0.2 -10000 0 -0.44 182 182
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.009 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.02 0.15 0.27 5 -0.27 116 121
NFATC4 -0.066 0.12 0.27 4 -0.26 176 180
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.071 0.16 -10000 0 -0.32 185 185
JUN -0.008 0.1 0.24 22 -0.48 2 24
HRAS 0.025 0.01 0.27 1 -10000 0 1
DOCK7 -0.082 0.14 0.28 2 -0.31 184 186
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.055 0.16 -10000 0 -0.35 153 153
AKT1 -0.004 0.008 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.075 0.11 0.22 6 -0.28 106 112
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.075 0.17 -10000 0 -0.34 185 185
RAF1 -0.015 0.15 0.34 13 -0.3 47 60
ErbB2/ErbB3/neuregulin 2 -0.17 0.19 -10000 0 -0.37 363 363
STAT3 -0.004 0.16 -10000 0 -0.86 29 29
cell migration -0.058 0.1 0.24 10 -0.26 62 72
mol:PI-3-4-5-P3 -0.002 0.003 -10000 0 -10000 0 0
cell proliferation -0.042 0.26 0.39 34 -0.5 104 138
FOS -0.11 0.3 0.34 42 -0.5 269 311
NRAS 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.071 0.16 -10000 0 -0.32 185 185
MAPK3 -0.012 0.21 0.43 10 -0.44 62 72
MAPK1 -0.024 0.23 0.38 22 -0.47 79 101
JAK2 -0.079 0.14 0.26 1 -0.31 184 185
NF2 -0.003 0.066 -10000 0 -0.69 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.14 0.23 3 -0.29 177 180
NRG1 -0.14 0.28 0.26 3 -0.6 220 223
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
MAPK8 -0.079 0.15 0.24 3 -0.3 189 192
MAPK9 -0.044 0.085 0.21 8 -10000 0 8
ERBB2 0.003 0.074 0.24 73 -10000 0 73
ERBB3 0.023 0.022 -10000 0 -0.6 1 1
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
apoptosis 0.022 0.027 -10000 0 -0.17 4 4
STAT3 (dimer) -0.003 0.16 -10000 0 -0.84 29 29
RNF41 -0.013 0.011 -10000 0 -10000 0 0
FRAP1 -0.005 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.073 0.097 -10000 0 -0.24 177 177
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.017 -10000 0 -10000 0 0
CHRNA1 0.025 0.19 0.37 58 -0.37 31 89
myelination -0.062 0.12 0.33 9 -0.26 164 173
PPP3CB -0.076 0.13 0.27 2 -0.29 180 182
KRAS 0.024 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.29 43 43
NRG2 -0.31 0.31 -10000 0 -0.6 436 436
mol:GDP -0.053 0.13 0.23 3 -0.28 177 180
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.013 0.15 0.28 30 -0.31 47 77
SRC 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.081 0.14 0.28 2 -0.31 184 186
MAP2K1 -0.049 0.24 0.44 6 -0.52 72 78
heart morphogenesis -0.071 0.16 -10000 0 -0.32 185 185
RAS family/GDP -0.021 0.14 0.3 1 -0.27 115 116
GRB2 0.024 0.011 0.26 1 -10000 0 1
PRKACA -0.004 0.076 -10000 0 -0.68 10 10
CHRNE 0.005 0.028 0.14 2 -0.22 2 4
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.004 0.008 -10000 0 -10000 0 0
nervous system development -0.071 0.16 -10000 0 -0.32 185 185
CDC42 0.024 0.005 -10000 0 -10000 0 0
Arf6 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
CENTA1/KIF3B 0.025 0.036 0.18 2 -0.49 3 5
ARNO/beta Arrestin1-2 -0.076 0.18 -10000 0 -0.58 41 41
EGFR -0.19 0.3 -10000 0 -0.6 281 281
EPHA2 0.02 0.049 -10000 0 -0.6 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.27 -10000 0 -0.48 401 401
ARRB2 -0.045 0.13 -10000 0 -0.38 114 114
mol:GTP 0.01 0.053 0.14 28 -0.18 27 55
ARRB1 0.021 0.031 -10000 0 -0.6 2 2
FBXO8 0.024 0.005 -10000 0 -10000 0 0
TSHR 0 0.12 0.27 3 -0.6 32 35
EGF -0.091 0.24 0.27 2 -0.6 153 155
somatostatin receptor activity 0 0 0.001 1 -0.001 189 190
ARAP2 0.021 0.044 -10000 0 -0.6 4 4
mol:GDP -0.12 0.17 -10000 0 -0.35 219 219
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 114 114
ITGA2B 0.032 0.058 0.27 35 -0.6 2 37
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.043 -10000 0 -0.36 5 5
ADAP1 0.023 0.033 0.27 2 -0.6 2 4
KIF13B 0.019 0.032 -10000 0 -0.6 2 2
HGF/MET -0.07 0.21 -10000 0 -0.47 173 173
PXN 0.025 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 -10000 0 -0.3 218 218
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.24 -10000 0 -0.42 389 389
ADRB2 -0.12 0.26 -10000 0 -0.6 191 191
receptor agonist activity 0 0 0 1 0 182 183
actin filament binding 0 0 0 2 -0.001 199 201
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
GNAQ 0.022 0.031 -10000 0 -0.6 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 103 104
ARF6/GDP -0.042 0.16 0.25 2 -0.44 78 80
ARF6/GDP/GULP/ACAP1 -0.11 0.2 -10000 0 -0.41 182 182
alphaIIb/beta3 Integrin/paxillin/GIT1 0.056 0.066 -10000 0 -0.35 15 15
ACAP1 0.024 0.067 0.27 22 -0.6 6 28
ACAP2 0.024 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.06 0.18 -10000 0 -0.51 114 114
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.01 0.14 -10000 0 -0.6 45 45
CYTH3 0.002 0.005 -10000 0 -10000 0 0
CYTH2 0.005 0.11 -10000 0 -1 9 9
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 152 153
endosomal lumen acidification 0 0 0.001 4 0 180 184
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.014 0.15 -10000 0 -0.6 50 50
GNAQ/ARNO 0.017 0.1 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 121 121
MET -0.079 0.23 -10000 0 -0.6 136 136
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GIT1 0.023 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 152 153
GNA11 0.024 0.005 -10000 0 -10000 0 0
LHCGR -0.074 0.21 -10000 0 -0.6 114 114
AGTR1 -0.087 0.26 0.27 52 -0.6 167 219
desensitization of G-protein coupled receptor protein signaling pathway -0.06 0.18 -10000 0 -0.51 114 114
IPCEF1/ARNO -0.14 0.21 -10000 0 -0.62 55 55
alphaIIb/beta3 Integrin 0.033 0.074 -10000 0 -0.44 15 15
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.066 0.16 0.34 4 -0.36 77 81
SMAD6-7/SMURF1 0.046 0.016 -10000 0 -10000 0 0
NOG 0.012 0.097 0.27 14 -0.6 18 32
SMAD9 -0.082 0.25 -10000 0 -0.64 122 122
SMAD4 0.024 0.005 -10000 0 -10000 0 0
SMAD5 -0.03 0.15 -10000 0 -0.43 62 62
BMP7/USAG1 -0.21 0.26 -10000 0 -0.45 412 412
SMAD5/SKI -0.024 0.16 -10000 0 -0.45 57 57
SMAD1 0.013 0.061 -10000 0 -0.43 4 4
BMP2 -0.083 0.24 0.27 1 -0.6 142 143
SMAD1/SMAD1/SMAD4 0.018 0.072 -10000 0 -0.43 7 7
BMPR1A 0.024 0.004 -10000 0 -10000 0 0
BMPR1B 0.11 0.16 0.27 346 -0.6 17 363
BMPR1A-1B/BAMBI 0.087 0.13 0.35 9 -0.35 41 50
AHSG 0.02 0.022 0.27 6 -10000 0 6
CER1 0.019 0.013 0.27 2 -10000 0 2
BMP2-4/CER1 -0.053 0.19 -10000 0 -0.41 173 173
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.044 0.17 -10000 0 -0.42 94 94
BMP2-4 (homodimer) -0.074 0.21 -10000 0 -0.46 180 180
RGMB 0.023 0.022 -10000 0 -0.6 1 1
BMP6/BMPR2/BMPR1A-1B 0.069 0.15 -10000 0 -0.34 79 79
RGMA -0.058 0.21 -10000 0 -0.6 108 108
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.043 0.17 0.24 1 -0.43 100 101
BMP2-4/USAG1 -0.24 0.28 -10000 0 -0.46 464 464
SMAD6/SMURF1/SMAD5 -0.025 0.16 -10000 0 -0.45 58 58
SOSTDC1 -0.27 0.31 0.27 2 -0.6 393 395
BMP7/BMPR2/BMPR1A-1B 0.074 0.15 0.31 6 -0.34 64 70
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.024 0.17 0.27 1 -0.6 63 64
HFE2 0.021 0.022 0.27 6 -10000 0 6
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.051 0.21 -10000 0 -0.43 175 175
SMAD5/SMAD5/SMAD4 -0.025 0.16 -10000 0 -0.45 60 60
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.03 0.16 -10000 0 -0.39 92 92
BMP7 (homodimer) -0.01 0.16 0.27 25 -0.6 52 77
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.006 0.13 -10000 0 -0.43 68 68
SMAD1/SKI 0.019 0.078 -10000 0 -0.46 8 8
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.053 0.19 0.35 1 -0.41 173 174
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.043 0.1 0.27 91 -0.6 10 101
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.017 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.092 0.11 -10000 0 -0.45 17 17
CHRDL1 -0.4 0.29 -10000 0 -0.6 568 568
ENDOFIN/SMAD1 0.019 0.08 -10000 0 -0.48 8 8
SMAD6-7/SMURF1/SMAD1 0.034 0.085 -10000 0 -0.46 8 8
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.013 0.12 0.27 29 -0.6 26 55
SMURF2 0.022 0.008 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.28 -10000 0 -0.49 571 571
BMP2-4/GREM1 -0.04 0.21 -10000 0 -0.42 177 177
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.075 0.25 -10000 0 -0.62 123 123
SMAD1/SMAD6 0.018 0.081 -10000 0 -0.49 8 8
TAK1/SMAD6 0.034 0.01 -10000 0 -10000 0 0
BMP7 -0.01 0.16 0.27 25 -0.6 52 77
BMP6 -0.024 0.17 0.27 1 -0.6 63 64
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.045 0.17 -10000 0 -0.44 103 103
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.076 -10000 0 -0.48 7 7
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.007 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.052 0.2 0.24 1 -0.48 106 107
CHRD 0.025 0.097 0.27 39 -0.6 14 53
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.059 0.19 -10000 0 -0.51 99 99
BMP4 -0.01 0.14 0.27 1 -0.6 45 46
FST 0.005 0.11 0.27 3 -0.6 26 29
BMP2-4/NOG -0.056 0.2 -10000 0 -0.41 181 181
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.077 0.14 0.34 2 -0.33 63 65
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.002 0.005 -10000 0 -10000 0 0
GNB1/GNG2 -0.003 0.13 -10000 0 -0.36 94 94
regulation of S phase of mitotic cell cycle -0.017 0.097 -10000 0 -0.3 82 82
GNAO1 0.018 0.096 0.27 28 -0.6 15 43
HRAS 0.023 0.01 0.27 1 -10000 0 1
SHBG/T-DHT 0.015 0.007 0.16 1 -10000 0 1
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.069 0.12 -10000 0 -0.36 81 81
T-DHT/AR -0.035 0.14 0.18 1 -0.45 91 92
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 265 265
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.6 39 39
mol:GDP -0.054 0.15 -10000 0 -0.48 91 91
cell proliferation -0.14 0.22 0.27 2 -0.44 250 252
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FOS -0.26 0.39 -10000 0 -0.82 269 269
mol:Ca2+ -0.012 0.027 -10000 0 -0.073 105 105
MAPK3 -0.1 0.17 0.26 3 -0.43 94 97
MAPK1 -0.083 0.15 -10000 0 -0.38 89 89
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 264 264
cAMP biosynthetic process 0.003 0.02 -10000 0 -10000 0 0
GNG2 0.019 0.053 -10000 0 -0.6 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 264 264
HRAS/GTP -0.026 0.12 -10000 0 -0.35 88 88
actin cytoskeleton reorganization 0.033 0.013 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 264 264
PI3K 0.031 0.01 -10000 0 -10000 0 0
apoptosis 0.14 0.22 0.44 269 -10000 0 269
T-DHT/AR/PELP1 -0.019 0.13 -10000 0 -0.39 90 90
HRAS/GDP -0.043 0.15 -10000 0 -0.46 90 90
CREB1 -0.15 0.24 -10000 0 -0.47 269 269
RAC1-CDC42/GTP 0.041 0.017 -10000 0 -10000 0 0
AR -0.045 0.2 0.26 1 -0.6 90 91
GNB1 0.024 0.005 -10000 0 -10000 0 0
RAF1 -0.06 0.11 -10000 0 -0.35 84 84
RAC1-CDC42/GDP -0.017 0.15 -10000 0 -0.44 90 90
T-DHT/AR/PELP1/Src -0.018 0.12 -10000 0 -0.36 89 89
MAP2K2 -0.07 0.12 -10000 0 -0.36 83 83
T-DHT/AR/PELP1/Src/PI3K -0.017 0.097 -10000 0 -0.3 82 82
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
SHBG 0.022 0.011 0.27 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.048 0.16 -10000 0 -0.49 64 64
mol:T-DHT -0.001 0.001 0.002 1 -0.004 80 81
RAC1 0.024 0.004 -10000 0 -10000 0 0
GNRH1 0.001 0.027 -10000 0 -0.45 3 3
Gi family/GTP -0.032 0.097 -10000 0 -0.28 69 69
CDC42 0.024 0.005 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.02 0.18 11 -10000 0 11
Metarhodopsin II/Arrestin 0.038 0.04 0.33 2 -10000 0 2
PDE6G/GNAT1/GTP 0.035 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.029 0.27 11 -10000 0 11
GRK1 0.019 0.018 0.27 4 -10000 0 4
CNG Channel -0.064 0.18 -10000 0 -0.33 238 238
mol:Na + -0.061 0.17 0.25 2 -0.32 240 242
mol:ADP 0.019 0.018 0.27 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.008 0.13 -10000 0 -0.38 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.056 0.18 0.29 3 -0.33 239 242
CNGB1 0.031 0.054 0.27 40 -10000 0 40
RDH5 -0.37 0.3 -10000 0 -0.6 519 519
SAG 0.033 0.054 0.27 42 -10000 0 42
mol:Ca2+ -0.095 0.15 0.36 11 -0.32 205 216
Na + (4 Units) -0.064 0.16 -10000 0 -0.31 236 236
RGS9 -0.035 0.18 0.27 7 -0.6 78 85
GNB1/GNGT1 0.056 0.062 -10000 0 -10000 0 0
GNAT1/GDP 0.018 0.12 0.31 3 -0.33 76 79
GUCY2D 0.024 0.035 0.27 10 -0.6 1 11
GNGT1 0.059 0.091 0.27 133 -10000 0 133
GUCY2F 0.019 0.013 0.27 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.018 0.053 0.22 1 -0.34 13 14
mol:11-cis-retinal -0.37 0.3 -10000 0 -0.6 519 519
mol:cGMP 0.043 0.047 -10000 0 -0.35 5 5
GNB1 0.024 0.005 -10000 0 -10000 0 0
Rhodopsin -0.27 0.24 -10000 0 -0.44 523 523
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.16 0.29 0.27 4 -0.6 246 250
Metarhodopsin II 0.027 0.022 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.056 0.051 -10000 0 -0.36 5 5
RGS9BP 0.037 0.055 0.27 44 -10000 0 44
Metarhodopsin II/Transducin 0.025 0.034 0.18 6 -10000 0 6
GCAP Family/Ca ++ 0.045 0.042 -10000 0 -0.36 4 4
PDE6A/B 0.028 0.068 -10000 0 -0.45 14 14
mol:Pi 0.008 0.13 -10000 0 -0.38 76 76
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.061 0.055 0.33 1 -10000 0 1
PDE6B 0.013 0.081 0.27 1 -0.6 14 15
PDE6A 0.027 0.03 0.27 13 -10000 0 13
PDE6G 0.031 0.044 0.27 27 -10000 0 27
RHO 0.025 0.031 0.27 13 -10000 0 13
PDE6 0.026 0.13 0.31 2 -0.34 80 82
GUCA1A 0.034 0.051 0.27 38 -10000 0 38
GC2/GCAP Family 0.056 0.045 -10000 0 -0.36 4 4
GUCA1C 0.018 0.009 0.27 1 -10000 0 1
GUCA1B 0.021 0.044 -10000 0 -0.6 4 4
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.076 0.12 -10000 0 -0.3 79 79
NT3 (dimer)/TRKC -0.19 0.28 -10000 0 -0.5 343 343
NT3 (dimer)/TRKB -0.32 0.33 -10000 0 -0.57 469 469
SHC/Grb2/SOS1/GAB1/PI3K 0.017 0.021 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.018 0.17 0.27 19 -0.6 63 82
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.026 0.045 0.27 21 -0.6 1 22
NTRK2 -0.3 0.31 -10000 0 -0.6 422 422
NTRK3 -0.18 0.3 0.27 5 -0.6 276 281
NT-4/5 (dimer)/TRKB -0.4 0.36 -10000 0 -0.62 549 549
neuron apoptosis 0.18 0.23 0.48 241 -10000 0 241
SHC 2-3/Grb2 -0.2 0.25 -10000 0 -0.53 240 240
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.2 0.26 -10000 0 -0.56 236 236
SHC3 -0.19 0.24 -10000 0 -0.53 228 228
STAT3 (dimer) 0.034 0.045 -10000 0 -0.37 3 3
NT3 (dimer)/TRKA -0.12 0.23 -10000 0 -0.44 243 243
RIN/GDP -0.05 0.12 0.32 3 -0.27 60 63
GIPC1 0.024 0.004 -10000 0 -10000 0 0
KRAS 0.024 0.005 -10000 0 -10000 0 0
DNAJA3 -0.088 0.16 -10000 0 -0.33 221 221
RIN/GTP 0.014 0.009 0.18 2 -10000 0 2
CCND1 0.025 0.098 0.44 31 -0.85 3 34
MAGED1 0.025 0.012 0.27 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.22 0.3 -10000 0 -0.6 316 316
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.031 0.087 -10000 0 -0.4 25 25
TRKA/NEDD4-2 0.033 0.035 -10000 0 -0.33 2 2
ELMO1 0.024 0.003 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.032 0.007 -10000 0 -10000 0 0
NGF 0.015 0.087 0.27 7 -0.6 15 22
HRAS 0.024 0.01 0.27 1 -10000 0 1
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.022 0.008 -10000 0 -10000 0 0
RIT2 0.019 0.013 0.27 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.27 2 -10000 0 2
DNM1 0.021 0.049 0.27 1 -0.6 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.076 0.17 -10000 0 -0.32 245 245
mol:GDP -0.081 0.17 0.4 3 -0.39 79 82
NGF (dimer) 0.015 0.087 0.27 7 -0.6 15 22
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.049 0.11 0.37 2 -0.27 54 56
TIAM1 0.025 0.017 0.27 4 -10000 0 4
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.2 0.24 -10000 0 -0.42 442 442
KIDINS220/CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.015 -10000 0 -10000 0 0
FRS2 family/SHP2 0.047 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.047 0.029 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.067 0.23 0.27 11 -0.6 124 135
RAP1/GDP -0.045 0.098 -10000 0 -0.23 59 59
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.018 0.17 0.27 19 -0.6 63 82
ubiquitin-dependent protein catabolic process 0.036 0.065 -10000 0 -0.38 14 14
Schwann cell development -0.051 0.039 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.051 -10000 0 -0.27 8 8
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.29 0.3 -10000 0 -0.51 480 480
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
Rap1/GTP -0.083 0.13 -10000 0 -0.45 49 49
STAT3 0.034 0.045 -10000 0 -0.37 3 3
axon guidance -0.28 0.28 -10000 0 -0.49 480 480
MAPK3 0.005 0.094 0.25 3 -0.37 24 27
MAPK1 0.006 0.096 0.24 4 -0.37 24 28
CDC42/GDP -0.048 0.12 0.29 5 -0.27 55 60
NTF3 -0.067 0.23 0.27 11 -0.6 124 135
NTF4 -0.22 0.3 -10000 0 -0.6 316 316
NGF (dimer)/TRKA/FAIM 0.037 0.066 -10000 0 -0.39 14 14
PI3K 0.034 0.01 -10000 0 -10000 0 0
FRS3 0.024 0.005 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.024 0.004 -10000 0 -10000 0 0
RASGRF1 -0.085 0.17 0.25 2 -0.34 229 231
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.17 0.24 0.21 1 -0.44 333 334
RGS19 0.023 0.011 0.27 1 -10000 0 1
CDC42 0.024 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.098 0.4 1 -0.45 8 9
Rac1/GDP -0.049 0.12 0.33 3 -0.27 56 59
NGF (dimer)/TRKA/GRIT 0.024 0.062 -10000 0 -0.36 16 16
neuron projection morphogenesis -0.079 0.22 -10000 0 -0.78 37 37
NGF (dimer)/TRKA/NEDD4-2 0.036 0.066 -10000 0 -0.39 14 14
MAP2K1 0.031 0.088 0.36 15 -10000 0 15
NGFR -0.16 0.28 -10000 0 -0.6 238 238
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.052 -10000 0 -0.31 15 15
RAS family/GTP/PI3K 0.019 0.011 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.064 0.027 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
MAPKKK cascade -0.042 0.14 -10000 0 -0.65 33 33
RASA1 0.024 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.034 0.034 -10000 0 -0.45 1 1
SQSTM1 0.024 0.009 0.27 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.18 0.23 -10000 0 -0.38 438 438
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.066 -10000 0 -0.34 14 14
MATK 0.015 0.091 0.27 10 -0.6 16 26
NEDD4L 0.023 0.022 -10000 0 -0.6 1 1
RAS family/GDP -0.06 0.073 -10000 0 -0.22 32 32
NGF (dimer)/TRKA -0.096 0.17 -10000 0 -0.35 249 249
Rac1/GTP -0.092 0.12 -10000 0 -0.29 182 182
FRS2 family/SHP2/CRK family 0.061 0.029 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
Jak2/Leptin Receptor -0.11 0.2 0.27 1 -0.41 199 200
PTP1B/AKT1 -0.064 0.13 0.22 1 -0.34 102 103
FYN 0.022 0.023 -10000 0 -0.6 1 1
p210 bcr-abl/PTP1B -0.08 0.14 0.22 2 -0.36 115 117
EGFR -0.2 0.3 -10000 0 -0.61 281 281
EGF/EGFR -0.2 0.25 -10000 0 -0.44 397 397
CSF1 0.023 0.031 -10000 0 -0.6 2 2
AKT1 0.024 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.042 0.16 0.24 14 -0.35 107 121
Insulin Receptor/Insulin -0.041 0.11 -10000 0 -0.36 41 41
HCK 0.028 0.029 0.27 12 -10000 0 12
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.077 0.13 0.41 1 -0.36 102 103
EGF -0.11 0.24 0.26 2 -0.61 154 156
YES1 0.023 0.022 -10000 0 -0.6 1 1
CAV1 -0.16 0.21 0.27 2 -0.44 236 238
TXN 0.012 0.019 0.26 1 -10000 0 1
PTP1B/IRS1/GRB2 -0.07 0.15 -10000 0 -0.38 104 104
cell migration 0.08 0.14 0.36 115 -0.22 2 117
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.026 0.022 0.26 6 -10000 0 6
ITGA2B 0.03 0.059 0.26 35 -0.6 2 37
CSF1R 0.024 0.004 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.036 0.029 0.33 1 -10000 0 1
FGR 0.024 0.01 0.27 1 -10000 0 1
PTP1B/p130 Cas -0.066 0.13 -10000 0 -0.35 106 106
Crk/p130 Cas -0.059 0.13 -10000 0 -0.35 91 91
DOK1 -0.066 0.12 0.25 1 -0.38 63 64
JAK2 -0.047 0.12 -10000 0 -0.48 41 41
Jak2/Leptin Receptor/Leptin -0.28 0.16 -10000 0 -0.36 587 587
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
PTPN1 -0.081 0.14 0.22 2 -0.36 115 117
LYN 0.021 0.009 -10000 0 -10000 0 0
CDH2 0.069 0.1 0.27 160 -0.6 2 162
SRC -0.018 0.1 -10000 0 -0.62 18 18
ITGB3 0.013 0.08 0.26 4 -0.6 13 17
CAT1/PTP1B -0.097 0.19 0.35 3 -0.47 120 123
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.033 0.11 -10000 0 -0.37 30 30
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.25 0.15 -10000 0 -0.36 360 360
negative regulation of transcription -0.046 0.12 -10000 0 -0.47 41 41
FCGR2A 0.02 0.009 -10000 0 -10000 0 0
FER 0.008 0.051 -10000 0 -0.61 5 5
alphaIIb/beta3 Integrin 0.029 0.074 -10000 0 -0.45 15 15
BLK 0.046 0.086 0.27 95 -0.6 2 97
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.11 0.26 -10000 0 -0.6 183 183
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.011 0.27 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.051 0.18 0.3 7 -0.44 88 95
PRL 0.009 0.036 0.27 10 -10000 0 10
SOCS3 0.008 0.16 -10000 0 -1.2 13 13
SPRY2 -0.04 0.18 -10000 0 -0.61 76 76
Insulin Receptor/Insulin/IRS1 0.027 0.08 -10000 0 -0.38 29 29
CSF1/CSF1R -0.061 0.14 -10000 0 -0.36 93 93
Ras protein signal transduction 0.054 0.16 0.63 52 -10000 0 52
IRS1 0.002 0.12 -10000 0 -0.6 29 29
INS 0.01 0.016 -10000 0 -10000 0 0
LEP -0.47 0.25 -10000 0 -0.6 653 653
STAT5B -0.069 0.14 0.2 3 -0.36 106 109
STAT5A -0.07 0.14 0.2 3 -0.36 108 111
GRB2 0.023 0.011 0.27 1 -10000 0 1
PDGFB-D/PDGFRB -0.07 0.14 -10000 0 -0.36 103 103
CSN2 0.026 0.059 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
LAT -0.009 0.077 -10000 0 -0.6 8 8
YBX1 0.027 0.018 -10000 0 -10000 0 0
LCK 0.024 0.077 0.27 23 -0.6 9 32
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.027 0.26 8 -10000 0 8
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.005 0.042 0.24 5 -0.38 1 6
NFATC2 -0.012 0.092 0.24 4 -0.4 37 41
NFATC3 0.007 0.038 0.24 5 -10000 0 5
CD40LG -0.14 0.3 0.54 18 -0.57 198 216
PTGS2 -0.2 0.36 0.54 13 -0.67 250 263
JUNB 0.024 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.029 0.17 4 -10000 0 4
CaM/Ca2+ 0.009 0.029 0.17 4 -10000 0 4
CALM1 0.017 0.023 -10000 0 -10000 0 0
JUN 0.011 0.066 -10000 0 -0.61 8 8
mol:Ca2+ -0.002 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.013 -10000 0 -10000 0 0
FOSL1 0.027 0.045 0.27 15 -0.6 2 17
CREM 0.023 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.006 0.14 0.49 14 -0.39 36 50
FOS -0.18 0.29 -10000 0 -0.59 263 263
IFNG -0.11 0.3 0.52 35 -0.55 171 206
AP-1/NFAT1-c-4 -0.13 0.35 0.58 33 -0.62 202 235
FASLG -0.12 0.28 0.56 20 -0.56 145 165
NFAT1-c-4/ICER1 -0.005 0.11 0.35 9 -0.36 34 43
IL2RA -0.12 0.29 0.52 29 -0.54 193 222
FKBP12/FK506 0.018 0.004 -10000 0 -10000 0 0
CSF2 -0.13 0.28 0.56 16 -0.54 194 210
JunB/Fra1/NFAT1-c-4 0.008 0.12 0.35 14 -0.36 36 50
IL4 -0.13 0.28 0.54 13 -0.54 189 202
IL2 -0.017 0.16 -10000 0 -0.95 23 23
IL3 -0.019 0.12 -10000 0 -0.73 21 21
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
BATF3 0.02 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.27 1 -10000 0 1
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.005 0.16 -10000 0 -0.34 128 128
ER alpha/Gai/GDP/Gbeta gamma -0.078 0.22 -10000 0 -0.48 149 149
AKT1 -0.098 0.32 -10000 0 -0.79 140 140
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.096 0.33 -10000 0 -0.8 140 140
mol:Ca2+ -0.021 0.1 0.27 2 -0.47 20 22
IGF1R 0.013 0.082 0.27 2 -0.6 14 16
E2/ER alpha (dimer)/Striatin -0.003 0.16 -10000 0 -0.37 111 111
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.091 0.31 0.75 140 -10000 0 140
RhoA/GTP -0.014 0.1 -10000 0 -0.31 84 84
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.06 0.21 0.32 5 -0.49 131 136
regulation of stress fiber formation 0.017 0.1 0.26 79 -0.32 7 86
E2/ERA-ERB (dimer) -0.016 0.16 -10000 0 -0.38 127 127
KRAS 0.024 0.005 -10000 0 -10000 0 0
G13/GTP -0.005 0.14 -10000 0 -0.34 106 106
pseudopodium formation -0.017 0.1 0.32 7 -0.26 79 86
E2/ER alpha (dimer)/PELP1 -0.008 0.15 -10000 0 -0.38 107 107
GRB2 0.023 0.011 0.27 1 -10000 0 1
GNG2 0.019 0.053 -10000 0 -0.6 6 6
GNAO1 0.019 0.096 0.27 28 -0.6 15 43
HRAS 0.024 0.01 0.27 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.079 0.23 -10000 0 -0.53 147 147
E2/ER beta (dimer) 0.005 0.075 -10000 0 -0.44 23 23
mol:GDP -0.035 0.17 0.26 10 -0.41 124 134
mol:NADP -0.079 0.23 -10000 0 -0.53 147 147
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.024 0.11 0.27 2 -0.5 20 22
IGF-1R heterotetramer 0.013 0.082 0.27 2 -0.6 14 16
PLCB1 -0.021 0.11 0.28 2 -0.38 46 48
PLCB2 -0.004 0.083 -10000 0 -0.54 11 11
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
mol:L-citrulline -0.079 0.23 -10000 0 -0.53 147 147
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.66 107 107
JNK cascade 0.005 0.075 -10000 0 -0.43 23 23
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.007 0.1 -10000 0 -0.6 22 22
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
ESR1 -0.025 0.24 0.27 109 -0.6 106 215
Gq family/GDP/Gbeta gamma -0.009 0.16 -10000 0 -0.8 29 29
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.013 0.13 -10000 0 -0.54 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.053 0.2 0.32 5 -0.49 108 113
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
E2/ER alpha (dimer) -0.022 0.17 0.18 109 -0.43 111 220
STRN 0.024 0.003 -10000 0 -10000 0 0
GNAL -0.11 0.25 -10000 0 -0.6 172 172
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 -0.001 0.069 -10000 0 -0.4 23 23
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.6 39 39
HBEGF -0.047 0.21 0.35 19 -0.59 59 78
cAMP biosynthetic process -0.088 0.19 -10000 0 -0.35 260 260
SRC -0.072 0.22 0.3 8 -0.61 65 73
PI3K 0.034 0.01 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.016 0.16 -10000 0 -0.4 101 101
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.46 152 152
Gs family/GTP -0.084 0.2 -10000 0 -0.35 260 260
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.016 -10000 0 -10000 0 0
vasodilation -0.074 0.22 -10000 0 -0.5 149 149
mol:DAG -0.024 0.11 0.27 2 -0.5 20 22
Gs family/GDP/Gbeta gamma -0.088 0.18 -10000 0 -0.38 183 183
MSN -0.019 0.11 0.32 7 -0.27 79 86
Gq family/GTP 0.001 0.087 -10000 0 -0.57 10 10
mol:PI-3-4-5-P3 -0.09 0.31 -10000 0 -0.77 140 140
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.074 0.22 0.5 149 -10000 0 149
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
RhoA/GDP -0.018 0.17 0.27 9 -0.4 118 127
NOS3 -0.084 0.25 -10000 0 -0.56 147 147
GNA11 0.024 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.064 0.25 0.32 2 -0.59 134 136
E2/ER alpha (dimer)/PELP1/Src -0.062 0.22 0.35 6 -0.5 137 143
ruffle organization -0.017 0.1 0.32 7 -0.26 79 86
ROCK2 -0.016 0.12 0.34 7 -0.29 82 89
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.039 0.21 0.4 19 -0.58 58 77
MMP2 -0.065 0.2 0.29 7 -0.59 61 68
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.003 0.071 -10000 0 -0.35 7 7
alphaM/beta2 Integrin/GPIbA 0.006 0.079 0.35 4 -0.43 6 10
alphaM/beta2 Integrin/proMMP-9 0.069 0.11 0.35 10 -0.44 1 11
PLAUR 0.041 0.062 0.27 59 -10000 0 59
HMGB1 -0.005 0.041 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.006 0.063 -10000 0 -10000 0 0
AGER -0.009 0.054 0.24 1 -0.49 3 4
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.14 0.32 2 -0.36 13 15
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.27 326 -0.6 1 327
CYR61 -0.008 0.14 -10000 0 -0.6 42 42
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.12 -10000 0 -0.36 37 37
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.25 -10000 0 -0.6 169 169
MYH2 -0.013 0.15 0.25 17 -0.36 74 91
MST1R 0.021 0.057 0.27 6 -0.6 6 12
leukocyte activation during inflammatory response -0.21 0.17 -10000 0 -0.34 496 496
APOB -0.37 0.3 -10000 0 -0.6 524 524
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.019 0.044 -10000 0 -0.6 4 4
JAM3 0.02 0.032 -10000 0 -0.6 2 2
GP1BA 0.023 0.064 0.27 17 -0.6 6 23
alphaM/beta2 Integrin/CTGF 0.001 0.078 -10000 0 -0.43 9 9
alphaM/beta2 Integrin -0.013 0.13 0.22 6 -0.34 60 66
JAM3 homodimer 0.02 0.032 -10000 0 -0.6 2 2
ICAM2 0.018 0.049 -10000 0 -0.6 5 5
ICAM1 0.027 0.027 0.27 10 -10000 0 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.01 0.13 0.24 8 -0.34 61 69
cell adhesion 0.005 0.078 0.34 4 -0.43 6 10
NFKB1 -0.11 0.21 0.44 3 -0.38 275 278
THY1 0.024 0.022 0.27 6 -10000 0 6
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.24 0.2 -10000 0 -0.38 531 531
alphaM/beta2 Integrin/LRP/tPA 0.004 0.091 -10000 0 -0.4 20 20
IL6 -0.28 0.4 0.35 2 -0.79 315 317
ITGB2 -0.005 0.051 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.028 0.085 0.34 15 -10000 0 15
alphaM/beta2 Integrin/JAM2/JAM3 -0.003 0.1 -10000 0 -0.39 34 34
JAM2 -0.006 0.13 -10000 0 -0.6 39 39
alphaM/beta2 Integrin/ICAM1 0.017 0.089 0.36 2 -0.36 14 16
alphaM/beta2 Integrin/uPA/Plg 0.016 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.018 0.16 0.24 17 -0.38 83 100
positive regulation of phagocytosis -0.003 0.11 0.32 3 -0.35 23 26
Ron/MSP 0.027 0.067 -10000 0 -0.4 18 18
alphaM/beta2 Integrin/uPAR/uPA 0.03 0.087 0.34 15 -10000 0 15
alphaM/beta2 Integrin/uPAR 0.016 0.079 0.36 3 -10000 0 3
PLAU 0.031 0.042 0.27 25 -10000 0 25
PLAT 0.007 0.089 -10000 0 -0.6 17 17
actin filament polymerization -0.012 0.15 0.25 19 -0.35 75 94
MST1 0.018 0.062 0.27 1 -0.6 8 9
alphaM/beta2 Integrin/lipoprotein(a) -0.21 0.18 -10000 0 -0.35 495 495
TNF -0.11 0.2 0.37 4 -0.37 235 239
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.011 0.069 -10000 0 -10000 0 0
fibrinolysis 0.015 0.069 -10000 0 -10000 0 0
HCK 0.028 0.029 0.27 12 -10000 0 12
dendritic cell antigen processing and presentation -0.01 0.13 0.24 8 -0.34 61 69
VTN 0.034 0.072 0.27 48 -0.6 4 52
alphaM/beta2 Integrin/CYR61 -0.014 0.11 -10000 0 -0.4 45 45
LPA 0.019 0.018 0.27 4 -10000 0 4
LRP1 0.018 0.061 -10000 0 -0.6 8 8
cell migration 0.041 0.085 0.28 10 -0.37 6 16
FN1 0.13 0.12 0.27 367 -10000 0 367
alphaM/beta2 Integrin/Thy1 0.007 0.064 -10000 0 -10000 0 0
MPO -0.015 0.15 0.27 1 -0.6 49 50
KNG1 0.022 0.027 0.27 10 -10000 0 10
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.014 0.16 0.26 22 -0.38 69 91
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.018 0.27 4 -10000 0 4
CTGF 0.017 0.066 0.27 2 -0.6 9 11
alphaM/beta2 Integrin/Hck 0.008 0.068 0.37 3 -10000 0 3
ITGAM -0.005 0.044 0.25 3 -10000 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.055 0.17 -10000 0 -0.38 150 150
HP -0.075 0.24 0.27 27 -0.6 137 164
leukocyte adhesion -0.044 0.14 0.28 2 -0.4 39 41
SELP -0.11 0.25 -10000 0 -0.6 169 169
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.046 0.18 -10000 0 -0.43 143 143
CRKL -0.051 0.15 0.36 1 -0.44 59 60
mol:PIP3 0.006 0.043 0.59 2 -0.86 1 3
AKT1 0.014 0.064 0.4 3 -0.75 1 4
PTK2B 0.02 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.05 0.15 0.34 1 -0.47 40 41
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.046 0.19 -10000 0 -0.41 161 161
MAP3K5 -0.043 0.15 0.36 1 -0.48 41 42
HGF/MET/CIN85/CBL/ENDOPHILINS -0.034 0.18 -10000 0 -0.38 167 167
AP1 -0.13 0.21 -10000 0 -0.42 257 257
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.26 0.38 -10000 0 -0.77 293 293
STAT3 (dimer) -0.051 0.16 -10000 0 -0.48 65 65
GAB1/CRKL/SHP2/PI3K -0.02 0.16 -10000 0 -0.49 29 29
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.039 0.15 0.34 1 -0.48 37 38
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
ELK1 -0.032 0.1 0.29 19 -0.22 100 119
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.027 0.093 -10000 0 -0.32 31 31
PAK1 0.027 0.08 0.37 8 -0.72 1 9
HGF/MET/RANBP10 -0.048 0.19 -10000 0 -0.41 169 169
HRAS -0.11 0.27 -10000 0 -0.66 148 148
DOCK1 -0.049 0.15 0.52 1 -0.47 40 41
GAB1 -0.053 0.16 -10000 0 -0.44 71 71
CRK -0.052 0.15 0.36 1 -0.44 61 62
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.26 -10000 0 -0.59 174 174
JUN 0.018 0.061 -10000 0 -0.6 8 8
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.054 0.13 -10000 0 -0.3 169 169
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.051 0.17 0.38 5 -0.48 60 65
GRB2/SHC -0.019 0.11 -10000 0 -0.29 96 96
FOS -0.17 0.29 -10000 0 -0.6 251 251
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.032 0.099 0.29 19 -0.22 100 119
HGF/MET/MUC20 -0.059 0.18 -10000 0 -0.4 173 173
cell migration -0.019 0.11 -10000 0 -0.29 96 96
GRB2 0.023 0.011 0.27 1 -10000 0 1
CBL 0.022 0.008 -10000 0 -10000 0 0
MET/RANBP10 -0.047 0.18 -10000 0 -0.43 143 143
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.051 0.15 -10000 0 -0.35 136 136
MET/MUC20 -0.06 0.17 -10000 0 -0.43 143 143
RAP1B -0.043 0.14 0.32 1 -0.45 37 38
RAP1A -0.048 0.14 0.41 2 -0.45 37 39
HGF/MET/RANBP9 -0.046 0.19 -10000 0 -0.41 164 164
RAF1 -0.1 0.25 -10000 0 -0.62 149 149
STAT3 -0.052 0.16 -10000 0 -0.48 65 65
cell proliferation -0.045 0.19 0.34 8 -0.44 122 130
RPS6KB1 -0.016 0.066 -10000 0 -0.24 28 28
MAPK3 -0.043 0.1 0.72 6 -10000 0 6
MAPK1 -0.013 0.18 0.68 42 -10000 0 42
RANBP9 0.024 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.13 0.44 1 -0.47 23 24
SRC -0.056 0.14 0.2 1 -0.43 62 63
PI3K -0.026 0.13 -10000 0 -0.27 157 157
MET/Glomulin -0.052 0.16 -10000 0 -0.39 138 138
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.094 0.23 0.47 1 -0.57 148 149
MET -0.079 0.23 -10000 0 -0.6 136 136
MAP4K1 -0.046 0.16 0.38 1 -0.5 47 48
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.094 0.23 0.47 1 -0.57 149 150
BAD 0.012 0.061 0.36 3 -0.72 1 4
MAP2K4 -0.04 0.14 0.34 1 -0.45 33 34
SHP2/GRB2/SOS1/GAB1 -0.043 0.18 -10000 0 -0.42 126 126
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.025 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.049 0.12 -10000 0 -0.28 156 156
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.01 0.14 -10000 0 -0.6 45 45
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.024 0.13 -10000 0 -0.28 160 160
PDPK1 0.017 0.067 0.44 2 -0.8 1 3
HGF/MET/SHIP -0.047 0.19 -10000 0 -0.41 168 168
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.003 0.089 -10000 0 -0.56 12 12
Crk/p130 Cas/Paxillin -0.053 0.12 -10000 0 -0.35 97 97
JUN -0.01 0.12 0.25 1 -0.42 21 22
HRAS 0.024 0.01 0.27 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 0.052 0.2 0.36 46 -0.36 126 172
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.27 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.052 0.2 0.36 45 -0.36 124 169
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.005 0.16 0.33 4 -0.35 126 130
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.027 0.17 0.29 31 -0.33 125 156
GRB7 0.02 0.023 -10000 0 -0.6 1 1
RET51/GFRalpha1/GDNF 0.051 0.2 0.36 45 -0.36 126 171
MAPKKK cascade 0.005 0.15 0.29 9 -0.35 92 101
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.018 0.18 0.33 3 -0.4 135 138
lamellipodium assembly -0.027 0.13 -10000 0 -0.32 94 94
RET51/GFRalpha1/GDNF/SHC 0.043 0.18 0.36 37 -0.36 97 134
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.005 0.14 0.33 4 -0.35 94 98
RET9/GFRalpha1/GDNF/Shank3 -0.008 0.16 0.33 4 -0.35 126 130
MAPK3 -0.028 0.13 -10000 0 -0.33 99 99
DOK1 0.024 0.003 -10000 0 -10000 0 0
DOK6 0.019 0.065 0.27 6 -0.6 8 14
PXN 0.025 0.002 -10000 0 -10000 0 0
neurite development -0.028 0.13 -10000 0 -0.47 13 13
DOK5 0.012 0.088 0.27 5 -0.6 16 21
GFRA1 -0.063 0.24 0.27 51 -0.6 135 186
MAPK8 -0.002 0.13 0.22 3 -0.46 18 21
HRAS/GTP 0.036 0.19 0.3 43 -0.36 120 163
tube development -0.001 0.15 0.35 10 -0.34 120 130
MAPK1 -0.027 0.14 0.34 1 -0.33 99 100
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.018 0.12 0.26 1 -0.28 117 118
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.047 0.2 0.35 42 -0.35 128 170
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.035 0.19 0.35 32 -0.36 127 159
RET51/GFRalpha1/GDNF/Dok5 0.035 0.2 0.36 41 -0.37 133 174
PRKCA 0.009 0.092 0.27 2 -0.6 18 20
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
CREB1 -0.007 0.13 0.24 8 -0.33 71 79
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.015 0.1 0.26 1 -0.28 84 85
RET51/GFRalpha1/GDNF/Grb7 0.051 0.19 0.34 59 -0.36 99 158
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.11 0.14 0.27 314 -0.6 11 325
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.009 0.12 0.25 1 -0.41 21 22
RET9/GFRalpha1/GDNF/FRS2 -0.007 0.16 0.33 4 -0.35 127 131
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.1 0.26 1 -0.28 84 85
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.014 0.14 0.25 16 -0.3 99 115
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.009 0.14 0.26 3 -0.31 99 102
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.018 0.14 0.26 16 -0.32 73 89
PI3K -0.018 0.21 0.29 12 -0.49 95 107
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0 0.15 0.32 3 -0.34 120 123
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity 0.005 0.13 0.25 9 -0.41 12 21
RET51/GFRalpha1/GDNF/FRS2 0.049 0.2 0.35 49 -0.36 127 176
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
IRS2 0 0.12 -10000 0 -0.6 29 29
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.018 0.14 0.26 16 -0.32 73 89
RET51/GFRalpha1/GDNF/PKC alpha 0.032 0.2 0.36 37 -0.36 137 174
GRB2 0.023 0.011 0.27 1 -10000 0 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.035 0.057 0.27 47 -10000 0 47
RAC1 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.038 0.22 0.35 44 -0.41 136 180
Rac1/GTP -0.014 0.16 0.24 5 -0.39 94 99
RET9/GFRalpha1/GDNF -0.02 0.16 0.33 4 -0.37 136 140
GFRalpha1/GDNF -0.026 0.19 0.38 4 -0.43 136 140
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.082 0.32 7 -0.32 1 8
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.022 -10000 0 -0.3 2 2
AURKB 0.15 0.12 0.27 437 -10000 0 437
AURKC 0.026 0.035 0.27 10 -0.6 1 11
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CCL5 0.03 0.048 0.27 26 -0.6 1 27
SDCBP 0.021 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.067 0.13 0.26 45 -0.34 20 65
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.05 0.13 0.28 7 -0.39 16 23
Syndecan-1/Syntenin 0.054 0.12 0.29 13 -0.41 12 25
MAPK3 0.05 0.12 0.28 11 -0.36 15 26
HGF/MET -0.07 0.21 -10000 0 -0.47 173 173
TGFB1/TGF beta receptor Type II 0.024 0.003 -10000 0 -10000 0 0
BSG 0.024 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.05 0.13 0.27 7 -0.38 16 23
Syndecan-1/RANTES 0.062 0.14 0.32 33 -0.4 16 49
Syndecan-1/CD147 0.067 0.13 0.3 12 -0.37 16 28
Syndecan-1/Syntenin/PIP2 0.05 0.12 0.27 13 -0.4 12 25
LAMA5 0.023 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.048 0.12 0.26 12 -0.39 12 24
MMP7 -0.041 0.2 0.27 24 -0.6 93 117
HGF -0.01 0.14 -10000 0 -0.6 45 45
Syndecan-1/CASK 0.045 0.12 0.21 52 -0.32 26 78
Syndecan-1/HGF/MET -0.005 0.21 0.29 8 -0.47 86 94
regulation of cell adhesion 0.043 0.11 0.26 11 -0.4 8 19
HPSE 0.028 0.04 0.27 16 -0.6 1 17
positive regulation of cell migration 0.067 0.13 0.26 45 -0.34 20 65
SDC1 0.069 0.12 0.25 56 -0.27 39 95
Syndecan-1/Collagen 0.067 0.13 0.26 45 -0.34 20 65
PPIB 0.024 0.009 0.27 1 -10000 0 1
MET -0.079 0.23 -10000 0 -0.6 136 136
PRKACA 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.27 326 -0.6 1 327
MAPK1 0.051 0.12 0.28 11 -0.36 14 25
homophilic cell adhesion 0.067 0.13 0.3 23 -0.38 15 38
MMP1 0.19 0.11 0.27 589 -10000 0 589
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.036 -10000 0 -0.33 2 2
PDGFRB 0.019 0.033 -10000 0 -0.61 2 2
SPHK1 -0.02 0.098 -10000 0 -0.73 12 12
mol:S1P -0.023 0.096 0.4 1 -0.64 12 13
S1P1/S1P/Gi -0.13 0.23 0.33 2 -0.44 257 259
GNAO1 0.006 0.098 0.26 28 -0.59 16 44
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.22 0.38 3 -0.41 238 241
PLCG1 -0.13 0.22 0.33 3 -0.43 241 244
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.033 -10000 0 -0.61 2 2
GNAI2 0.009 0.024 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.019 0.13 -10000 0 -0.61 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.013 0.024 0.2 1 -0.28 2 3
S1P1/S1P -0.034 0.097 0.28 2 -0.46 13 15
negative regulation of cAMP metabolic process -0.13 0.23 0.3 3 -0.43 257 260
MAPK3 -0.18 0.3 0.31 13 -0.58 272 285
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
KDR 0.013 0.029 -10000 0 -0.61 1 1
PLCB2 -0.026 0.097 0.32 5 -0.41 14 19
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.081 -10000 0 -0.39 13 13
receptor internalization -0.035 0.087 0.19 1 -0.43 13 14
PTGS2 -0.34 0.5 0.4 2 -1 280 282
Rac1/GTP -0.032 0.081 -10000 0 -0.39 13 13
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.26 5 -10000 0 5
negative regulation of T cell proliferation -0.13 0.23 0.3 3 -0.43 257 260
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.005 0.057 -10000 0 -0.61 6 6
MAPK1 -0.2 0.33 0.33 3 -0.63 287 290
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.11 0.32 3 -0.5 10 13
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.01 0.025 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.11 -10000 0 -0.44 36 36
STXBP1 0.022 0.038 -10000 0 -0.6 3 3
ACh/CHRNA1 0.081 0.096 0.2 296 -0.16 5 301
RAB3GAP2/RIMS1/UNC13B 0.035 0.093 -10000 0 -0.39 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.15 0.27 91 -0.6 35 126
mol:ACh -0.004 0.039 0.091 11 -0.14 38 49
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.02 0.088 0.24 1 -0.3 29 30
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.081 0.095 0.2 296 -0.16 5 301
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.27 307 -10000 0 307
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.035 0.12 0.2 157 -0.38 31 188
SNAP25 -0.001 0.064 0.1 50 -0.31 29 79
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.051 0.16 0.27 164 -0.6 28 192
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.031 -10000 0 -0.38 3 3
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.088 0.24 1 -0.3 29 30
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.11 0.2 -10000 0 -0.39 246 246
fibroblast growth factor receptor signaling pathway -0.11 0.2 -10000 0 -0.39 246 246
LAMA1 -0.039 0.19 0.27 1 -0.6 83 84
PRNP 0.015 0.072 -10000 0 -0.6 11 11
GPC1/SLIT2 0 0.12 -10000 0 -0.44 61 61
SMAD2 -0.019 0.055 0.25 1 -0.35 19 20
GPC1/PrPc/Cu2+ 0.026 0.049 -10000 0 -0.38 11 11
GPC1/Laminin alpha1 -0.016 0.15 -10000 0 -0.43 90 90
TDGF1 0.009 0.092 0.27 1 -0.6 18 19
CRIPTO/GPC1 0.024 0.072 -10000 0 -0.45 18 18
APP/GPC1 0.035 0.012 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0 0.059 -10000 0 -0.39 18 18
FLT1 0.023 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.037 0.067 -10000 0 -0.39 19 19
SERPINC1 0.029 0.047 0.27 30 -10000 0 30
FYN -0.001 0.06 -10000 0 -0.39 19 19
FGR 0 0.059 -10000 0 -0.39 18 18
positive regulation of MAPKKK cascade 0 0.097 0.28 2 -0.39 30 32
SLIT2 -0.02 0.16 -10000 0 -0.6 58 58
GPC1/NRG -0.11 0.21 -10000 0 -0.39 283 283
NRG1 -0.14 0.28 0.27 3 -0.6 220 223
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.022 -10000 0 -10000 0 0
LYN 0 0.054 -10000 0 -0.39 14 14
mol:Spermine 0.006 0.007 -10000 0 -10000 0 0
cell growth -0.11 0.2 -10000 0 -0.39 246 246
BMP signaling pathway -0.025 0.013 -10000 0 -0.27 2 2
SRC 0 0.056 -10000 0 -0.39 16 16
TGFBR1 0.025 0.009 0.27 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.16 0.29 0.27 19 -0.6 254 273
GPC1 0.025 0.013 0.27 2 -10000 0 2
TGFBR1 (dimer) 0.024 0.009 0.27 1 -10000 0 1
VEGFA 0.025 0.019 0.27 5 -10000 0 5
BLK 0.012 0.078 -10000 0 -0.39 19 19
HCK 0.002 0.06 -10000 0 -0.39 17 17
FGF2 -0.21 0.3 -10000 0 -0.6 310 310
FGFR1 0.016 0.049 -10000 0 -0.6 5 5
VEGFR1 homodimer 0.023 0.007 -10000 0 -10000 0 0
TGFBR2 0.01 0.094 -10000 0 -0.6 19 19
cell death 0.035 0.012 -10000 0 -10000 0 0
ATIII/GPC1 0.036 0.035 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.23 -10000 0 -0.45 254 254
LCK 0 0.076 -10000 0 -0.39 27 27
neuron differentiation -0.11 0.21 -10000 0 -0.39 283 283
PrPc/Cu2+ 0.011 0.053 -10000 0 -0.45 11 11
APP 0.024 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.01 0.094 -10000 0 -0.6 19 19
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.019 0.081 0.29 1 -0.35 2 3
epithelial cell differentiation 0.035 0.078 0.41 1 -10000 0 1
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.028 0.1 0.49 8 -10000 0 8
FYN 0.022 0.023 -10000 0 -0.6 1 1
EGFR -0.19 0.3 -10000 0 -0.6 281 281
PRL 0.023 0.027 0.27 10 -10000 0 10
neuron projection morphogenesis -0.05 0.15 0.36 8 -0.38 21 29
PTPRZ1 -0.3 0.31 0.27 6 -0.6 435 441
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.15 -10000 0 -0.4 29 29
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.09 0.16 -10000 0 -0.36 184 184
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.075 0.4 8 -0.31 3 11
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.001 0.12 -10000 0 -0.39 36 36
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.083 0.16 -10000 0 -0.34 172 172
GRIN2B -0.11 0.17 -10000 0 -0.36 200 200
ErbB4/ErbB2/betacellulin 0.015 0.1 -10000 0 -0.34 24 24
STAT1 0.03 0.035 0.27 18 -10000 0 18
HBEGF 0.023 0.031 -10000 0 -0.6 2 2
PRLR 0.026 0.021 0.27 6 -10000 0 6
E4ICDs/ETO2 0.009 0.088 0.32 2 -0.44 7 9
axon guidance 0.061 0.12 0.4 8 -0.4 1 9
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.035 0.024 -10000 0 -10000 0 0
CBFA2T3 0.013 0.076 0.27 3 -0.6 12 15
ErbB4/ErbB2/HBEGF 0.033 0.073 -10000 0 -0.32 2 2
MAPK3 -0.054 0.14 -10000 0 -0.39 22 22
STAT1 (dimer) 0.023 0.082 0.29 1 -10000 0 1
MAPK1 -0.053 0.15 0.39 2 -0.39 22 24
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.075 0.16 -10000 0 -0.35 161 161
NRG1 -0.12 0.2 -10000 0 -0.45 217 217
NRG3 -0.007 0.15 0.27 18 -0.6 47 65
NRG2 -0.31 0.31 -10000 0 -0.6 436 436
NRG4 0.026 0.027 0.27 10 -10000 0 10
heart development 0.061 0.12 0.4 8 -0.4 1 9
neural crest cell migration -0.073 0.16 -10000 0 -0.34 161 161
ERBB2 0.037 0.074 0.27 75 -10000 0 75
WWOX/E4ICDs 0.014 0.077 0.29 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.094 0.17 -10000 0 -0.34 196 196
apoptosis 0.015 0.13 0.5 35 -10000 0 35
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.18 0.19 -10000 0 -0.37 338 338
ErbB4/ErbB2/epiregulin 0.006 0.14 0.36 11 -0.33 62 73
ErbB4/ErbB4/betacellulin/betacellulin -0.001 0.11 0.29 1 -0.38 32 33
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.045 0.084 0.41 1 -10000 0 1
MDM2 0.015 0.086 0.32 14 -10000 0 14
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.088 0.15 -10000 0 -0.34 179 179
STAT5A 0.054 0.11 0.37 10 -0.38 1 11
ErbB4/EGFR/neuregulin 1 beta -0.19 0.24 -10000 0 -0.46 321 321
DLG4 0.022 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.017 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.014 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.064 0.1 0.47 1 -10000 0 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.065 0.11 0.36 6 -0.38 2 8
LRIG1 0.023 0.022 -10000 0 -0.6 1 1
EREG -0.03 0.21 0.27 62 -0.6 94 156
BTC -0.008 0.14 0.27 2 -0.6 43 45
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.052 0.11 0.41 7 -0.4 1 8
ERBB4 -0.003 0.074 0.4 8 -0.31 3 11
STAT5B 0.022 0.031 -10000 0 -0.6 2 2
YAP1 -0.011 0.11 -10000 0 -0.45 33 33
GRB2 0.023 0.011 0.27 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.035 0.072 0.32 1 -10000 0 1
glial cell differentiation -0.013 0.07 -10000 0 -10000 0 0
WWOX 0.022 0.012 0.27 1 -10000 0 1
cell proliferation -0.038 0.18 0.35 10 -0.47 33 43
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.017 0.23 0.55 6 -0.63 21 27
CRP 0.003 0.25 0.58 16 -0.69 13 29
cell cycle arrest -0.027 0.25 0.57 8 -0.68 31 39
TIMP1 -0.012 0.22 0.54 7 -0.6 20 27
IL6ST -0.003 0.14 -10000 0 -0.6 43 43
Rac1/GDP -0.058 0.19 0.32 6 -0.43 79 85
AP1 -0.08 0.22 0.36 1 -0.52 70 71
GAB2 0.022 0.008 -10000 0 -10000 0 0
TNFSF11 -0.004 0.24 0.6 10 -0.65 17 27
HSP90B1 0.027 0.1 -10000 0 -0.81 7 7
GAB1 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.086 0.17 -10000 0 -0.49 63 63
AKT1 0.026 0.058 -10000 0 -0.52 4 4
FOXO1 0.027 0.058 0.42 1 -0.57 2 3
MAP2K6 -0.087 0.18 0.26 2 -0.39 128 130
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.042 0.2 0.39 9 -0.46 57 66
MITF -0.08 0.19 0.28 8 -0.39 129 137
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.004 -10000 0 -10000 0 0
A2M -0.003 0.18 -10000 0 -1.2 20 20
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.013 0.13 -10000 0 -0.51 27 27
STAT3 -0.034 0.27 0.59 6 -0.75 30 36
STAT1 0.015 0.093 -10000 0 -0.84 7 7
CEBPD -0.002 0.24 0.57 12 -0.71 18 30
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.035 0.011 -10000 0 -10000 0 0
JUN 0.018 0.061 -10000 0 -0.6 8 8
PIAS3/MITF -0.065 0.18 0.33 1 -0.38 120 121
MAPK11 -0.085 0.17 -10000 0 -0.49 62 62
STAT3 (dimer)/FOXO1 -0.012 0.22 0.48 14 -0.56 27 41
GRB2/SOS1/GAB family -0.049 0.17 -10000 0 -0.46 48 48
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.093 0.18 -10000 0 -0.33 237 237
GRB2 0.023 0.011 0.27 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.16 0.46 0.56 19 -0.94 187 206
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.026 0.009 -10000 0 -10000 0 0
MYC 0.009 0.28 0.57 21 -0.96 26 47
FGG -0.014 0.24 0.57 15 -0.63 21 36
macrophage differentiation -0.027 0.25 0.57 8 -0.68 31 39
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.089 0.21 -10000 0 -0.36 268 268
JUNB -0.021 0.22 0.53 6 -0.63 17 23
FOS -0.17 0.29 -10000 0 -0.6 251 251
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.082 0.19 0.31 8 -0.34 231 239
STAT1/PIAS1 -0.05 0.2 0.36 7 -0.38 121 128
GRB2/SOS1/GAB family/SHP2/PI3K 0.027 0.062 -10000 0 -0.53 5 5
STAT3 (dimer) -0.033 0.26 0.6 6 -0.73 31 37
PRKCD -0.025 0.2 0.43 19 -0.51 37 56
IL6R 0.007 0.099 -10000 0 -0.6 21 21
SOCS3 -0.082 0.19 -10000 0 -0.63 38 38
gp130 (dimer)/JAK1/JAK1/LMO4 0.035 0.1 0.26 1 -0.37 43 44
Rac1/GTP -0.053 0.2 0.35 7 -0.45 71 78
HCK 0.027 0.029 0.27 12 -10000 0 12
MAPKKK cascade 0.003 0.14 -10000 0 -0.6 25 25
bone resorption -0.002 0.24 0.56 16 -0.62 17 33
IRF1 -0.021 0.23 0.55 6 -0.66 16 22
mol:GDP -0.074 0.19 0.3 8 -0.39 129 137
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.076 0.19 0.3 8 -0.39 129 137
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.094 0.19 -10000 0 -0.55 65 65
PTPN11 0.012 0.083 -10000 0 -0.86 6 6
IL6/IL6RA -0.13 0.23 -10000 0 -0.41 310 310
gp130 (dimer)/TYK2/TYK2/LMO4 0.03 0.1 0.24 1 -0.37 45 46
gp130 (dimer)/JAK2/JAK2/LMO4 0.029 0.1 0.24 1 -0.38 44 45
IL6 -0.2 0.3 0.28 1 -0.6 304 305
PIAS3 0.023 0.006 -10000 0 -10000 0 0
PTPRE 0.007 0.034 -10000 0 -0.6 1 1
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.098 0.18 0.23 1 -0.32 263 264
LMO4 0.028 0.043 0.29 2 -0.6 3 5
STAT3 (dimer)/PIAS3 -0.037 0.25 0.56 6 -0.69 33 39
MCL1 0.058 0.096 0.49 1 -0.51 3 4
Ephrin A reverse 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
MAPKKK cascade -0.008 0.12 -10000 0 -0.37 81 81
EFNA5 -0.034 0.18 -10000 0 -0.6 76 76
FYN -0.026 0.11 -10000 0 -0.36 75 75
neuron projection morphogenesis -0.008 0.12 -10000 0 -0.37 81 81
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.008 0.12 -10000 0 -0.37 81 81
EPHA5 0.024 0.018 0.27 4 -10000 0 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.035 0.024 -10000 0 -0.32 2 2
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.4 297 297
PTK2 -0.054 0.15 0.32 2 -0.5 25 27
IGF1R 0.013 0.082 0.27 2 -0.6 14 16
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.071 0.27 5 -0.6 10 15
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.044 0.12 -10000 0 -0.56 24 24
VEGFA 0.025 0.019 0.27 5 -10000 0 5
ILK -0.042 0.12 -10000 0 -0.5 24 24
ROCK1 0.024 0.004 -10000 0 -10000 0 0
AKT1 -0.043 0.1 0.33 1 -0.5 20 21
PTK2B -0.009 0.06 0.36 2 -0.36 13 15
alphaV/beta3 Integrin/JAM-A -0.078 0.18 0.3 1 -0.35 219 220
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.038 0.058 -10000 0 -0.39 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.047 0.2 -10000 0 -0.4 187 187
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.053 -10000 0 -0.44 3 3
alphaV/beta3 Integrin/Syndecan-1 0.049 0.07 -10000 0 -0.39 14 14
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.28 -10000 0 -0.48 255 255
PI4 Kinase 0.029 0.015 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.079 0.091 0.35 3 -0.38 13 16
RPS6KB1 -0.16 0.23 0.42 3 -0.57 132 135
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.59 261 261
GPR124 0.016 0.049 -10000 0 -0.6 5 5
MAPK1 -0.2 0.3 -10000 0 -0.59 273 273
PXN 0.025 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.042 0.18 -10000 0 -0.39 163 163
cell adhesion 0.027 0.071 0.26 1 -0.37 23 24
ANGPTL3 0.022 0.018 0.27 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.025 -10000 0 -0.39 1 1
IGF-1R heterotetramer 0.013 0.082 0.27 2 -0.6 14 16
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.01 0.094 -10000 0 -0.6 19 19
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
RAC1 0.024 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.03 0.062 -10000 0 -0.41 12 12
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.022 -10000 0 -0.6 1 1
alphaV/beta3 Integrin/CD47 0.039 0.059 -10000 0 -0.39 14 14
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.1 -10000 0 -0.47 27 27
CSF1 0.023 0.031 -10000 0 -0.6 2 2
PIK3C2A -0.041 0.11 -10000 0 -0.48 22 22
PI4 Kinase/Pyk2 -0.079 0.15 -10000 0 -0.32 186 186
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.051 0.061 -10000 0 -0.38 13 13
FAK1/Vinculin -0.036 0.13 0.34 4 -0.41 20 24
alphaV beta3/Integrin/ppsTEM5 0.031 0.063 -10000 0 -0.42 12 12
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.034 0.072 0.27 48 -0.6 4 52
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.6 310 310
F11R -0.13 0.21 -10000 0 -0.45 238 238
alphaV/beta3 Integrin/Lactadherin 0.035 0.076 0.35 1 -0.4 22 23
alphaV/beta3 Integrin/TGFBR2 0.03 0.093 -10000 0 -0.45 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.051 0.032 -10000 0 -0.35 2 2
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.038 0.051 -10000 0 -0.35 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.12 0.27 367 -10000 0 367
alphaV/beta3 Integrin/Pyk2 0.03 0.059 -10000 0 -0.36 13 13
SDC1 0.04 0.064 0.27 55 -0.6 1 56
VAV3 -0.01 0.038 -10000 0 -0.34 5 5
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
FAK1/Paxillin -0.036 0.13 0.33 5 -0.4 23 28
cell migration -0.036 0.12 0.31 5 -0.37 19 24
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.065 0.17 -10000 0 -0.33 190 190
SPP1 0.092 0.11 0.27 232 -10000 0 232
KDR 0.023 0.022 -10000 0 -0.6 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.098 0.25 0.27 4 -0.6 162 166
angiogenesis -0.18 0.3 -10000 0 -0.59 248 248
Rac1/GTP 0.022 0.032 -10000 0 -0.31 4 4
EDIL3 0.012 0.1 0.27 15 -0.6 21 36
cell proliferation 0.03 0.092 -10000 0 -0.44 27 27
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.043 0.18 0.31 90 -0.52 37 127
FYN 0.02 0.2 0.37 39 -0.62 44 83
LAT/GRAP2/SLP76 0.024 0.18 0.38 31 -0.54 45 76
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.023 0.16 0.33 63 -0.41 52 115
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.016 0.062 0.17 53 -0.14 14 67
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
mol:Ca2+ -0.025 0.035 -10000 0 -0.096 144 144
integrin-mediated signaling pathway 0.026 0.025 -10000 0 -0.38 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.21 0.44 27 -0.57 59 86
TRPV6 -0.1 0.29 1.2 14 -0.6 161 175
CD28 0.024 0.05 0.28 7 -0.61 4 11
SHC1 0.027 0.22 0.33 104 -0.64 44 148
receptor internalization -0.014 0.23 0.4 25 -0.53 97 122
PRF1 -0.013 0.25 0.62 6 -1.1 31 37
KRAS 0.024 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
COT/AKT1 0.031 0.14 0.3 62 -0.35 45 107
LAT 0.012 0.21 0.38 37 -0.66 45 82
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D 0.021 0.098 0.28 29 -0.61 15 44
CD3E 0.019 0.096 0.28 24 -0.61 15 39
CD3G 0.017 0.11 0.27 34 -0.59 21 55
RASGRP2 -0.001 0.052 0.17 9 -0.17 54 63
RASGRP1 0.025 0.16 0.4 30 -0.44 42 72
HLA-A 0.025 0.016 0.27 2 -10000 0 2
RASSF5 0.019 0.033 0.27 1 -0.6 2 3
RAP1A/GTP/RAPL 0.026 0.025 -10000 0 -0.38 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.084 0.18 120 -0.14 15 135
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.057 -10000 0 -0.22 35 35
PRKCA 0.012 0.1 0.24 32 -0.28 42 74
GRAP2 0.016 0.073 0.26 3 -0.6 11 14
mol:IP3 0.017 0.15 0.27 108 -0.39 43 151
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.19 0.35 23 -0.67 43 66
ORAI1 0.04 0.18 0.65 3 -0.98 13 16
CSK 0.006 0.21 0.41 24 -0.67 45 69
B7 family/CD28 0.064 0.22 0.45 38 -0.66 38 76
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.24 0.43 25 -0.71 53 78
PTPN6 0.006 0.21 0.38 30 -0.67 44 74
VAV1 0.002 0.21 0.42 24 -0.66 46 70
Monovalent TCR/CD3 -0.002 0.15 0.3 25 -0.55 41 66
CBL 0.022 0.008 -10000 0 -10000 0 0
LCK 0.017 0.21 0.39 33 -0.68 42 75
PAG1 0.02 0.21 0.36 44 -0.66 44 88
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.23 0.42 25 -0.71 51 76
CD80 0.094 0.11 0.27 238 -10000 0 238
CD86 0.026 0.018 0.28 4 -10000 0 4
PDK1/CARD11/BCL10/MALT1 -0.007 0.073 0.17 2 -0.26 34 36
HRAS 0.024 0.01 0.27 1 -10000 0 1
GO:0035030 0.022 0.17 0.37 31 -0.54 38 69
CD8A 0.028 0.065 0.28 21 -0.61 5 26
CD8B 0.01 0.12 0.28 20 -0.61 29 49
PTPRC 0.024 0.038 0.27 12 -0.61 1 13
PDK1/PKC theta 0.024 0.2 0.39 62 -0.52 47 109
CSK/PAG1 0.023 0.21 0.34 47 -0.65 42 89
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.037 0.017 -10000 0 -10000 0 0
GRAP2/SLP76 0.018 0.21 0.44 23 -0.62 48 71
STIM1 0.029 0.11 1.3 4 -10000 0 4
RAS family/GTP 0.045 0.097 0.23 73 -0.18 29 102
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.019 0.25 0.41 24 -0.56 98 122
mol:DAG -0.017 0.1 0.14 18 -0.36 43 61
RAP1A/GDP 0.021 0.039 0.11 58 -10000 0 58
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.015 0.085 0.28 12 -0.61 13 25
cytotoxic T cell degranulation -0.009 0.24 0.59 7 -0.96 33 40
RAP1A/GTP -0.001 0.017 -10000 0 -0.066 49 49
mol:PI-3-4-5-P3 0.017 0.18 0.37 39 -0.47 58 97
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.022 0.18 0.3 100 -0.52 43 143
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.019 0.1 0.27 26 -0.6 18 44
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.005 0.17 0.44 10 -0.53 44 54
MALT1 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.028 0.12 0.39 15 -0.52 29 44
CARD11 0.027 0.046 0.27 16 -0.6 2 18
PRKCB 0.013 0.11 0.3 30 -0.29 34 64
PRKCE 0.018 0.099 0.24 37 -0.26 37 74
PRKCQ 0.012 0.21 0.44 28 -0.59 50 78
LCP2 0.024 0.01 0.26 1 -10000 0 1
BCL10 0.024 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.026 0.15 0.31 65 -0.35 52 117
IKK complex 0.037 0.088 0.22 97 -0.12 13 110
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.026 0.11 0.25 65 -0.27 39 104
PDPK1 0.028 0.16 0.35 66 -0.38 49 115
TCR/CD3/MHC I/CD8/Fyn -0.027 0.26 0.45 19 -0.79 55 74
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.038 0.22 0.43 4 -0.66 81 85
IHH 0.017 0.081 0.27 24 -0.21 50 74
SHH Np/Cholesterol/GAS1 0 0.08 -10000 0 -0.35 38 38
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.001 0.079 0.35 38 -10000 0 38
SMO/beta Arrestin2 -0.015 0.2 -10000 0 -0.63 67 67
SMO -0.039 0.21 -10000 0 -0.65 70 70
AKT1 0 0.12 -10000 0 -0.56 17 17
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.02 0.16 -10000 0 -0.6 58 58
ADRBK1 0.023 0.007 -10000 0 -10000 0 0
heart looping -0.038 0.2 0.29 1 -0.64 71 72
STIL 0.013 0.18 0.3 26 -0.5 61 87
DHH N/PTCH2 -0.017 0.16 -10000 0 -0.45 90 90
DHH N/PTCH1 -0.023 0.2 0.29 1 -0.52 102 103
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DHH 0.008 0.1 0.27 1 -0.6 22 23
PTHLH -0.056 0.29 0.44 10 -0.84 85 95
determination of left/right symmetry -0.038 0.2 0.29 1 -0.64 71 72
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
skeletal system development -0.054 0.29 0.44 10 -0.83 85 95
IHH N/Hhip 0.029 0.056 -10000 0 -0.49 1 1
DHH N/Hhip 0.023 0.081 -10000 0 -0.44 23 23
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.038 0.2 0.29 1 -0.64 71 72
pancreas development 0.024 0.031 0.27 7 -0.6 1 8
HHAT 0.02 0.024 -10000 0 -0.6 1 1
PI3K 0.034 0.01 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.14 -10000 0 -0.6 43 43
somite specification -0.038 0.2 0.29 1 -0.64 71 72
SHH Np/Cholesterol/PTCH1 -0.022 0.16 0.28 2 -0.51 66 68
SHH Np/Cholesterol/PTCH2 -0.01 0.097 -10000 0 -0.36 55 55
SHH Np/Cholesterol/Megalin -0.064 0.16 0.28 3 -0.36 170 173
SHH -0.002 0.037 0.36 4 -0.45 1 5
catabolic process -0.028 0.2 0.32 2 -0.57 89 91
SMO/Vitamin D3 -0.005 0.2 0.35 15 -0.58 64 79
SHH Np/Cholesterol/Hhip 0.016 0.033 0.29 5 -0.36 2 7
LRP2 -0.13 0.28 0.27 20 -0.6 206 226
receptor-mediated endocytosis -0.078 0.22 0.31 8 -0.62 79 87
SHH Np/Cholesterol/BOC -0.006 0.091 -10000 0 -0.35 49 49
SHH Np/Cholesterol/CDO 0.012 0.042 -10000 0 -0.36 9 9
mesenchymal cell differentiation -0.016 0.033 0.36 2 -0.28 5 7
mol:Vitamin D3 0.006 0.18 0.35 17 -0.51 65 82
IHH N/PTCH2 -0.014 0.15 -10000 0 -0.49 71 71
CDON 0.015 0.065 -10000 0 -0.6 9 9
IHH N/PTCH1 -0.019 0.21 0.36 3 -0.57 89 92
Megalin/LRPAP1 -0.083 0.21 -10000 0 -0.44 209 209
PTCH2 -0.027 0.17 -10000 0 -0.6 68 68
SHH Np/Cholesterol 0.01 0.015 -10000 0 -0.36 1 1
PTCH1 -0.028 0.2 0.32 2 -0.57 89 91
HHIP 0.024 0.032 0.27 7 -0.6 1 8
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.065 -10000 0 -0.35 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.13 -10000 0 -0.32 75 75
AP1 -0.11 0.21 -10000 0 -0.36 307 307
mol:PIP3 -0.13 0.19 -10000 0 -0.35 303 303
AKT1 0.012 0.07 0.31 3 -0.43 4 7
PTK2B -0.03 0.1 -10000 0 -0.36 39 39
RHOA 0.003 0.066 0.26 2 -0.32 23 25
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.11 0.24 2 -0.3 87 89
MAGI3 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
apoptosis -0.026 0.12 -10000 0 -0.34 103 103
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
positive regulation of microtubule depolymerization -0.053 0.13 0.26 3 -0.34 91 94
NF kappa B1 p50/RelA -0.012 0.13 -10000 0 -0.34 83 83
endothelial cell migration 0.004 0.072 -10000 0 -0.46 18 18
ADCY4 -0.019 0.11 -10000 0 -0.49 28 28
ADCY5 -0.075 0.15 -10000 0 -0.49 56 56
ADCY6 -0.011 0.09 -10000 0 -0.46 20 20
ADCY7 -0.01 0.091 -10000 0 -0.47 20 20
ADCY1 -0.012 0.098 -10000 0 -0.46 23 23
ADCY2 -0.023 0.12 -10000 0 -0.51 29 29
ADCY3 -0.011 0.09 -10000 0 -0.47 19 19
ADCY8 -0.009 0.082 -10000 0 -0.44 18 18
ADCY9 -0.011 0.09 -10000 0 -0.46 20 20
GSK3B -0.029 0.1 0.28 3 -0.35 39 42
arachidonic acid secretion -0.015 0.097 -10000 0 -0.41 31 31
GNG2 0.019 0.053 -10000 0 -0.6 6 6
TRIP6 0.017 0.017 -10000 0 -0.42 1 1
GNAO1 0.005 0.076 -10000 0 -0.36 30 30
HRAS 0.024 0.01 0.27 1 -10000 0 1
NFKBIA -0.021 0.13 0.26 1 -0.35 88 89
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.031 0.11 -10000 0 -0.82 14 14
JUN 0.018 0.061 -10000 0 -0.6 8 8
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.016 0.13 -10000 0 -0.96 14 14
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.015 0.11 0.24 2 -0.3 87 89
PLCB3 0.026 0.047 0.18 15 -10000 0 15
FOS -0.17 0.29 -10000 0 -0.6 251 251
positive regulation of mitosis -0.015 0.097 -10000 0 -0.41 31 31
LPA/LPA1-2-3 0.001 0.14 -10000 0 -0.36 104 104
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
stress fiber formation -0.017 0.1 -10000 0 -0.38 32 32
GNAZ 0.006 0.059 -10000 0 -0.34 23 23
EGFR/PI3K-beta/Gab1 -0.12 0.2 -10000 0 -0.37 303 303
positive regulation of dendritic cell cytokine production -0.001 0.14 -10000 0 -0.35 104 104
LPA/LPA2/MAGI-3 0.033 0.016 -10000 0 -10000 0 0
ARHGEF1 0.021 0.065 -10000 0 -0.32 9 9
GNAI2 0.009 0.049 -10000 0 -0.35 14 14
GNAI3 0.009 0.05 -10000 0 -0.33 16 16
GNAI1 -0.01 0.1 -10000 0 -0.41 50 50
LPA/LPA3 -0.029 0.15 0.18 29 -0.43 98 127
LPA/LPA2 0.019 0.014 0.19 1 -10000 0 1
LPA/LPA1 0.014 0.059 -10000 0 -0.36 19 19
HB-EGF/EGFR -0.079 0.21 0.27 1 -0.37 257 258
HBEGF 0.066 0.079 0.27 21 -0.45 3 24
mol:DAG -0.015 0.11 0.24 2 -0.3 87 89
cAMP biosynthetic process -0.03 0.11 0.4 1 -0.41 39 40
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.26 20 -0.35 64 84
GNAQ -0.023 0.11 0.21 1 -0.33 95 96
LPAR2 0.025 0.009 0.27 1 -10000 0 1
LPAR3 -0.038 0.2 0.27 29 -0.6 93 122
LPAR1 0.017 0.071 -10000 0 -0.6 10 10
IL8 -0.13 0.24 0.37 22 -0.42 258 280
PTK2 -0.023 0.1 0.25 1 -0.34 67 68
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.34 103 103
EGFR -0.19 0.3 -10000 0 -0.6 281 281
PLCG1 -0.025 0.12 0.2 4 -0.34 94 98
PLD2 -0.029 0.12 0.25 1 -0.34 100 101
G12/G13 0.038 0.052 -10000 0 -0.31 13 13
PI3K-beta 0.005 0.064 -10000 0 -0.46 5 5
cell migration 0.002 0.062 -10000 0 -0.25 14 14
SLC9A3R2 0.023 0.007 -10000 0 -10000 0 0
PXN -0.018 0.11 -10000 0 -0.39 31 31
HRAS/GTP -0.016 0.1 -10000 0 -0.42 31 31
RAC1 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.27 326 -0.6 1 327
PRKCE 0.024 0.003 -10000 0 -10000 0 0
PRKCD -0.016 0.11 0.24 1 -0.29 77 78
Gi(beta/gamma) -0.01 0.097 -10000 0 -0.46 25 25
mol:LPA 0.001 0.016 -10000 0 -0.16 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.015 0.12 -10000 0 -0.47 17 17
MAPKKK cascade -0.015 0.097 -10000 0 -0.41 31 31
contractile ring contraction involved in cytokinesis 0.002 0.067 0.26 2 -0.31 23 25
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.022 0.12 0.21 1 -0.33 97 98
GNA15 -0.022 0.11 0.21 1 -0.33 94 95
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.055 0.13 0.26 3 -0.35 91 94
GNA11 -0.022 0.11 0.21 1 -0.33 93 94
Rac1/GTP 0.031 0.12 -10000 0 -0.86 14 14
MMP2 0.004 0.072 -10000 0 -0.46 18 18
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.083 0.17 -10000 0 -0.32 216 216
Syndecan-3/Neurocan 0.026 0.075 0.28 13 -0.38 16 29
POMC 0.018 0.091 0.27 18 -0.6 15 33
EGFR -0.19 0.3 -10000 0 -0.6 281 281
Syndecan-3/EGFR -0.091 0.17 -10000 0 -0.33 243 243
AGRP 0.021 0.024 0.27 7 -10000 0 7
NCSTN 0.021 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.009 0.27 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.057 0.27 48 -10000 0 48
long-term memory 0.035 0.063 -10000 0 -0.36 12 12
Syndecan-3/IL8 0.021 0.087 0.29 9 -0.34 30 39
PSEN1 0.024 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
limb bud formation 0.001 0.057 -10000 0 -0.39 17 17
MC4R 0.024 0.03 0.27 12 -10000 0 12
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.24 0.31 0.27 1 -0.6 354 355
FGFR/FGF/Syndecan-3 0.001 0.057 -10000 0 -0.39 17 17
neuron projection morphogenesis -0.082 0.17 0.33 4 -0.32 201 205
Syndecan-3/AgRP 0.015 0.061 -10000 0 -0.36 18 18
Syndecan-3/AgRP/MC4R 0.039 0.07 0.34 1 -0.35 17 18
Fyn/Cortactin 0.029 0.017 -10000 0 -0.22 1 1
SDC3 0.001 0.058 -10000 0 -0.4 17 17
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.021 0.086 0.28 9 -0.34 31 40
IL8 0.026 0.11 0.27 51 -0.6 16 67
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 12 12
Syndecan-3/CASK 0 0.056 -10000 0 -0.36 19 19
alpha-MSH/MC4R 0.029 0.073 0.21 26 -0.45 15 41
Gamma Secretase 0.054 0.035 -10000 0 -0.34 1 1
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.031 0.049 -10000 0 -0.33 12 12
RGS9BP 0.037 0.055 0.27 44 -10000 0 44
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.018 0.27 4 -10000 0 4
mol:Na + 0.039 0.048 -10000 0 -10000 0 0
mol:ADP -0.007 0.027 0.25 4 -10000 0 4
GNAT2 0.024 0.013 0.27 2 -10000 0 2
RGS9-1/Gbeta5/R9AP 0.008 0.13 -10000 0 -0.38 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.015 -10000 0 -10000 0 0
GRK7 0.023 0.02 0.27 5 -10000 0 5
CNGB3 0.023 0.039 0.27 20 -10000 0 20
Cone Metarhodopsin II/X-Arrestin 0.016 0.014 0.18 6 -10000 0 6
mol:Ca2+ 0.14 0.11 0.3 158 -10000 0 158
Cone PDE6 0.024 0.12 0.31 2 -0.34 73 75
Cone Metarhodopsin II 0.026 0.018 -10000 0 -10000 0 0
Na + (4 Units) 0.12 0.097 0.32 58 -10000 0 58
GNAT2/GDP 0.018 0.12 0.28 1 -0.33 76 77
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.035 -10000 0 -10000 0 0
Cone Transducin 0.033 0.052 -10000 0 -0.35 12 12
SLC24A2 0.18 0.12 0.27 522 -10000 0 522
GNB3/GNGT2 0.024 0.06 -10000 0 -0.43 13 13
GNB3 0.015 0.076 0.27 2 -0.6 12 14
GNAT2/GTP 0.018 0.009 0.18 2 -10000 0 2
CNGA3 0.049 0.074 0.27 87 -10000 0 87
ARR3 0.021 0.021 0.27 6 -10000 0 6
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.039 0.048 -10000 0 -10000 0 0
mol:Pi 0.008 0.13 -10000 0 -0.38 76 76
Cone CNG Channel 0.05 0.047 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.18 0.12 0.27 522 -10000 0 522
RGS9 -0.035 0.18 0.27 7 -0.6 78 85
PDE6C 0.02 0.004 -10000 0 -10000 0 0
GNGT2 0.021 0.023 -10000 0 -0.6 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.018 0.27 4 -10000 0 4
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.034 0.15 -10000 0 -0.62 47 47
PDGF/PDGFRA/CRKL -0.012 0.11 -10000 0 -0.44 48 48
positive regulation of JUN kinase activity 0.023 0.087 -10000 0 -0.36 35 35
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.015 0.11 -10000 0 -0.45 48 48
AP1 -0.33 0.46 -10000 0 -0.99 267 267
mol:IP3 -0.05 0.11 -10000 0 -0.48 44 44
PLCG1 -0.049 0.11 -10000 0 -0.48 43 43
PDGF/PDGFRA/alphaV Integrin -0.012 0.11 -10000 0 -0.45 46 46
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.11 -10000 0 -0.48 44 44
CAV3 0.02 0.013 0.27 2 -10000 0 2
CAV1 -0.099 0.25 -10000 0 -0.6 163 163
SHC/Grb2/SOS1 0.025 0.088 -10000 0 -0.36 35 35
PDGF/PDGFRA/Shf -0.012 0.12 -10000 0 -0.45 48 48
FOS -0.33 0.45 -10000 0 -0.97 267 267
JUN -0.041 0.05 -10000 0 -0.44 7 7
oligodendrocyte development -0.012 0.11 -10000 0 -0.45 46 46
GRB2 0.023 0.011 0.27 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:DAG -0.05 0.11 -10000 0 -0.48 44 44
PDGF/PDGFRA -0.034 0.15 -10000 0 -0.62 47 47
actin cytoskeleton reorganization -0.012 0.11 -10000 0 -0.43 49 49
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.017 0.098 -10000 0 -0.39 44 44
PDGF/PDGFRA/Crk/C3G 0.016 0.099 -10000 0 -0.39 46 46
JAK1 -0.028 0.1 0.23 1 -0.45 46 47
ELK1/SRF -0.036 0.093 0.32 1 -0.38 44 45
SHB 0.024 0.009 0.27 1 -10000 0 1
SHF 0.023 0.024 0.27 1 -0.6 1 2
CSNK2A1 0.037 0.024 -10000 0 -10000 0 0
GO:0007205 -0.048 0.11 0.22 1 -0.48 47 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.023 0.087 -10000 0 -0.36 35 35
PDGF/PDGFRA/SHB -0.012 0.11 -10000 0 -0.43 49 49
PDGF/PDGFRA/Caveolin-1 -0.1 0.23 -10000 0 -0.51 187 187
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.056 0.11 -10000 0 -0.45 46 46
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.013 0.11 -10000 0 -0.44 48 48
JAK-STAT cascade -0.028 0.1 0.23 1 -0.45 46 47
cell proliferation -0.012 0.11 -10000 0 -0.45 48 48
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.036 0.11 0.55 4 -10000 0 4
VDR 0.024 0.003 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.028 0.12 -10000 0 -0.4 9 9
RXRs/LXRs/DNA/Oxysterols -0.009 0.12 -10000 0 -0.43 13 13
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.003 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0.003 0.081 -10000 0 -0.33 37 37
RXRs/NUR77 -0.057 0.2 -10000 0 -0.38 202 202
RXRs/PPAR -0.1 0.18 -10000 0 -0.33 271 271
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.049 0.041 -10000 0 -0.34 7 7
RARA 0.022 0.007 -10000 0 -10000 0 0
NCOA1 0.024 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.038 0.039 -10000 0 -0.34 7 7
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.076 0.19 0.62 83 -10000 0 83
RARs/THRs/DNA/SMRT 0.005 0.076 -10000 0 -0.31 36 36
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.033 0.16 -10000 0 -0.34 165 165
NR1H4 0.021 0.023 0.27 7 -10000 0 7
RXRs/LXRs/DNA -0.011 0.16 -10000 0 -0.33 151 151
NR1H2 0.027 0.013 -10000 0 -10000 0 0
NR1H3 0.028 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.026 0.16 -10000 0 -0.33 165 165
NR4A1 -0.033 0.18 -10000 0 -0.6 76 76
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.033 0.11 0.18 2 -0.24 143 145
RXRG -0.1 0.25 0.27 1 -0.6 167 168
RXR alpha/CCPG 0.035 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.013 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB 0.001 0.12 -10000 0 -0.6 31 31
PPARG -0.12 0.26 -10000 0 -0.6 185 185
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.013 0.15 -10000 0 -1 8 8
mol:Oxysterols 0.003 0.009 -10000 0 -10000 0 0
cholesterol transport -0.008 0.12 -10000 0 -0.43 13 13
PPARA 0.022 0.031 -10000 0 -0.6 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.018 0.061 -10000 0 -0.6 8 8
RXRs/NUR77/BCL2 -0.074 0.16 -10000 0 -0.32 215 215
SREBF1 -0.009 0.11 -10000 0 -0.52 3 3
RXRs/RXRs/DNA/9cRA -0.033 0.16 -10000 0 -0.34 165 165
ABCA1 -0.013 0.13 -10000 0 -0.81 6 6
RARs/THRs 0.045 0.091 -10000 0 -0.36 34 34
RXRs/FXR -0.029 0.16 -10000 0 -0.35 165 165
BCL2 0.008 0.098 -10000 0 -0.6 21 21
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.021 0.25 2 -10000 0 2
AES 0.022 0.019 0.21 2 -10000 0 2
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.024 0.005 -10000 0 -10000 0 0
DKK2 0.014 0.082 0.27 2 -0.6 14 16
TLE1 0.019 0.053 0.22 2 -0.61 5 7
MACF1 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.11 0.1 0.31 31 -0.39 2 33
WIF1 -0.3 0.31 0.27 9 -0.6 424 433
beta catenin/RanBP3 0.018 0.087 0.42 26 -0.4 1 27
KREMEN2 0.12 0.12 0.27 346 -10000 0 346
DKK1 0.024 0.17 0.27 110 -0.6 43 153
beta catenin/beta TrCP1 0.11 0.097 0.31 24 -0.41 1 25
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.027 0.24 0.59 74 -1.3 13 87
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.047 0.077 -10000 0 -0.54 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.067 0.13 0.32 4 -0.61 18 22
Axin1/APC/GSK3 0.046 0.056 0.24 1 -0.32 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.041 0.063 0.31 2 -0.37 3 5
HNF1A 0.025 0.028 0.26 8 -10000 0 8
CTBP1 0.021 0.019 0.24 2 -10000 0 2
MYC 0.12 0.35 0.57 223 -1.4 20 243
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.096 0.35 1 -0.35 11 12
NKD1 0.021 0.062 0.27 14 -0.6 6 20
TCF4 0.018 0.052 0.23 2 -0.6 5 7
TCF3 0.022 0.02 0.23 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.057 0.024 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.002 0.13 0.47 25 -0.52 15 40
LEF1 0.057 0.087 0.26 119 -10000 0 119
DVL1 0.055 0.056 -10000 0 -0.46 1 1
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.15 0.3 7 -0.68 19 26
DKK1/LRP6/Kremen 2 0.097 0.14 0.35 54 -0.36 37 91
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.25 2 -10000 0 2
NLK 0.023 0.013 0.27 1 -10000 0 1
CCND1 0.094 0.27 0.62 142 -1.2 5 147
WNT1 0.024 0.01 0.27 1 -10000 0 1
GSK3A 0.025 0.004 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.06 0.3 5 -0.3 8 13
APC 0.016 0.06 0.36 7 -10000 0 7
WNT1/LRP6/FZD1 0.12 0.11 0.23 390 -0.25 1 391
CREBBP 0.021 0.018 0.23 1 -10000 0 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.42 0.28 -10000 0 -0.6 584 584
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.27 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
HIF1A/p53 0.031 0.05 -10000 0 -0.27 12 12
HIF1A 0.018 0.04 -10000 0 -0.26 9 9
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.034 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.057 0.086 0.27 118 -10000 0 118
ARNT/IPAS -0.28 0.21 -10000 0 -0.41 590 590
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.047 -10000 0 -0.28 12 12
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.039 0.023 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.033 0.05 -10000 0 -0.28 12 12
PHD1-3/OS9 0.056 0.049 -10000 0 -0.36 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.052 -10000 0 -0.27 11 11
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.027 0.05 -10000 0 -0.28 12 12
EGLN3 0.043 0.065 0.27 65 -10000 0 65
EGLN2 0.025 0.015 0.27 3 -10000 0 3
EGLN1 0.019 0.024 -10000 0 -0.6 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.071 -10000 0 -0.52 12 12
ARNT 0.02 0.01 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.051 0.074 0.24 31 -0.27 11 42
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.023 0.076 -10000 0 -0.39 15 15
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.006 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.033 0.18 -10000 0 -0.6 76 76
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.049 -10000 0 -0.61 5 5
AP1 -0.087 0.16 -10000 0 -0.33 242 242
NCSTN 0.021 0.009 -10000 0 -10000 0 0
ADAM10 0.024 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.014 0.1 -10000 0 -0.68 11 11
NICD/RBPSUH 0.021 0.074 -10000 0 -0.38 17 17
WIF1 -0.3 0.31 0.27 9 -0.6 424 433
NOTCH1 0.01 0.064 -10000 0 -0.39 20 20
PSENEN 0.024 0.009 0.27 1 -10000 0 1
KREMEN2 0.12 0.12 0.27 346 -10000 0 346
DKK1 0.024 0.17 0.27 110 -0.6 43 153
beta catenin/beta TrCP1 0.006 0.071 -10000 0 -0.36 6 6
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.061 -10000 0 -0.46 7 7
CtBP/CBP/TCF1/TLE1/AES 0.011 0.043 -10000 0 -0.31 5 5
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 251 251
JUN 0.018 0.061 -10000 0 -0.6 8 8
MAP3K7 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 -0.003 0.071 0.25 1 -0.38 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.096 0.35 1 -0.35 11 12
HNF1A 0.026 0.021 0.26 6 -10000 0 6
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.017 0.22 -10000 0 -1.3 23 23
NKD1 0.021 0.062 0.27 14 -0.6 6 20
FZD1 0.024 0.003 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.008 0.12 -10000 0 -0.45 19 19
apoptosis -0.086 0.16 -10000 0 -0.33 242 242
Delta 1/NOTCHprecursor 0.02 0.076 -10000 0 -0.39 18 18
DLL1 0.021 0.031 -10000 0 -0.6 2 2
PPARD 0.013 0.1 -10000 0 -0.84 11 11
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
APC 0.003 0.086 -10000 0 -0.49 17 17
DVL1 -0.032 0.082 -10000 0 -0.4 26 26
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.097 0.14 0.35 54 -0.36 37 91
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.01 -10000 0 -10000 0 0
CCND1 0.021 0.1 -10000 0 -1.1 5 5
WNT1 0.023 0.01 0.27 1 -10000 0 1
Axin1/APC/beta catenin 0.01 0.1 0.34 3 -0.48 11 14
DKK2 0.014 0.082 0.27 2 -0.6 14 16
NOTCH1 precursor/DVL1 -0.022 0.11 -10000 0 -0.61 17 17
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.005 0.12 -10000 0 -0.45 19 19
PPP2R5D -0.006 0.065 0.3 5 -0.37 16 21
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.2 -10000 0 -0.36 409 409
RBPJ 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.031 0.15 0.37 45 -0.38 36 81
TBX21 -0.005 0.36 0.78 17 -1.2 44 61
B2M 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.021 0.037 -10000 0 -10000 0 0
IL12RB1 0.028 0.07 0.35 25 -0.64 1 26
GADD45B 0.021 0.26 0.68 17 -0.85 29 46
IL12RB2 0.023 0.16 0.28 93 -0.6 36 129
GADD45G 0.032 0.26 0.67 18 -0.88 22 40
natural killer cell activation 0.005 0.025 0.17 1 -10000 0 1
RELB 0.026 0.019 0.27 5 -10000 0 5
RELA 0.024 0.004 -10000 0 -10000 0 0
IL18 0.033 0.043 0.28 21 -10000 0 21
IL2RA 0.03 0.087 0.27 46 -0.6 9 55
IFNG 0.057 0.086 0.27 119 -10000 0 119
STAT3 (dimer) 0.02 0.25 0.57 32 -0.66 43 75
HLA-DRB5 0.019 0.081 0.26 46 -0.61 5 51
FASLG 0.039 0.3 0.76 25 -1 26 51
NF kappa B2 p52/RelB 0.004 0.25 0.76 3 -0.74 46 49
CD4 0.008 0.025 -10000 0 -10000 0 0
SOCS1 0.024 0.031 0.27 6 -0.6 1 7
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D 0.005 0.1 0.27 28 -0.61 15 43
CD3E 0.005 0.098 0.28 24 -0.61 15 39
CD3G 0.003 0.11 0.28 33 -0.61 20 53
IL12Rbeta2/JAK2 0.031 0.13 0.3 26 -0.44 38 64
CCL3 0.017 0.28 0.73 18 -0.95 29 47
CCL4 0.019 0.27 0.74 17 -0.93 26 43
HLA-A 0.026 0.016 0.27 2 -10000 0 2
IL18/IL18R 0.056 0.12 0.38 15 -0.4 40 55
NOS2 0.016 0.28 0.73 17 -1 24 41
IL12/IL12R/TYK2/JAK2/SPHK2 0.029 0.15 0.36 46 -0.35 51 97
IL1R1 0.006 0.3 0.73 16 -1.1 30 46
IL4 -0.009 0.038 -10000 0 -10000 0 0
JAK2 0.02 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.005 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.029 0.24 0.43 20 -0.94 36 56
RAB7A 0.032 0.23 0.64 16 -0.78 19 35
lysosomal transport 0.034 0.23 0.62 18 -0.73 19 37
FOS -0.36 0.64 0.62 12 -1.2 289 301
STAT4 (dimer) 0.045 0.28 0.61 29 -0.86 37 66
STAT5A (dimer) 0.033 0.28 0.61 41 -0.76 45 86
GZMA 0.009 0.3 0.7 27 -1.1 25 52
GZMB 0.008 0.33 0.71 27 -1.2 33 60
HLX 0.021 0.013 0.27 1 -10000 0 1
LCK 0.012 0.3 0.68 29 -0.83 48 77
TCR/CD3/MHC II/CD4 -0.057 0.18 0.32 15 -0.49 79 94
IL2/IL2R 0.068 0.099 0.44 29 -0.38 12 41
MAPK14 0.027 0.27 0.66 19 -0.85 30 49
CCR5 0.023 0.27 0.75 22 -0.86 27 49
IL1B 0.016 0.077 0.3 2 -0.61 9 11
STAT6 0.033 0.12 0.44 24 -0.52 5 29
STAT4 0 0.12 0.27 1 -0.6 32 33
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.035 0.27 18 -10000 0 18
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.004 -10000 0 -10000 0 0
IL12B 0.067 0.11 0.29 156 -10000 0 156
CD8A 0.028 0.065 0.29 21 -0.6 5 26
CD8B 0.01 0.12 0.28 20 -0.6 29 49
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.031 0.15 0.38 36 -0.37 45 81
IL2RB 0.033 0.048 0.27 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process 0.05 0.27 0.59 32 -0.77 37 69
IL2RG 0.03 0.068 0.27 32 -0.6 5 37
IL12 0.04 0.16 0.31 58 -0.45 48 106
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
CD247 0.003 0.087 0.28 12 -0.61 13 25
IL2 0.023 0.025 0.27 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.011 0.16 0.29 13 -0.61 47 60
IL12/IL12R/TYK2/JAK2 0.018 0.31 0.71 32 -0.86 45 77
MAP2K3 0.021 0.27 0.66 19 -0.83 36 55
RIPK2 0.02 0.018 0.27 3 -10000 0 3
MAP2K6 0.026 0.26 0.66 19 -0.83 32 51
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.006 0.037 0.24 2 -0.6 1 3
IL18RAP 0.007 0.12 0.3 4 -0.6 31 35
IL12Rbeta1/TYK2 0.037 0.068 0.32 20 -0.5 1 21
EOMES -0.017 0.19 -10000 0 -1.1 19 19
STAT1 (dimer) 0.053 0.27 0.65 46 -0.75 28 74
T cell proliferation 0.035 0.22 0.52 20 -0.66 31 51
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.074 -10000 0 -0.6 11 11
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.013 0.2 0.45 4 -0.73 30 34
ATF2 0.026 0.25 0.64 17 -0.79 29 46
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.022 -10000 0 -0.6 1 1
LAT2 -0.021 0.1 -10000 0 -0.37 37 37
AP1 -0.069 0.19 -10000 0 -0.45 93 93
mol:PIP3 0.008 0.17 0.36 31 -0.45 34 65
IKBKB 0.034 0.13 0.3 68 -0.27 16 84
AKT1 0.011 0.17 0.31 118 -0.43 13 131
IKBKG 0.015 0.11 0.28 35 -0.28 19 54
MS4A2 -0.021 0.16 0.26 4 -0.59 58 62
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.12 0.3 16 -0.41 18 34
mol:Ca2+ 0.013 0.14 0.31 36 -0.34 33 69
LYN 0.022 0.014 -10000 0 -10000 0 0
CBLB -0.02 0.1 -10000 0 -0.37 36 36
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.006 0.13 -10000 0 -0.35 102 102
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.009 0.18 0.33 101 -0.34 112 213
PTPN13 -0.016 0.16 -10000 0 -0.59 33 33
PTPN11 0.022 0.019 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.012 0.13 0.32 27 -0.34 22 49
SYK 0.025 0.011 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.029 0.13 -10000 0 -0.45 35 35
LAT -0.02 0.1 -10000 0 -0.38 37 37
PAK2 0.012 0.13 0.31 17 -0.46 18 35
NFATC2 -0.035 0.13 -10000 0 -0.55 41 41
HRAS 0.008 0.13 0.28 15 -0.48 20 35
GAB2 0.022 0.008 -10000 0 -10000 0 0
PLA2G1B 0 0.11 -10000 0 -0.85 12 12
Fc epsilon R1 -0.028 0.17 -10000 0 -0.42 118 118
Antigen/IgE/Fc epsilon R1 -0.024 0.15 -10000 0 -0.38 116 116
mol:GDP -0.015 0.11 -10000 0 -0.49 19 19
JUN 0.018 0.061 -10000 0 -0.6 8 8
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 251 251
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.38 38 38
CHUK 0.015 0.11 0.28 34 -0.28 19 53
KLRG1 -0.019 0.097 -10000 0 -0.41 20 20
VAV1 -0.021 0.1 -10000 0 -0.38 36 36
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.018 0.1 -10000 0 -0.37 35 35
negative regulation of mast cell degranulation -0.007 0.1 -10000 0 -0.39 19 19
BTK -0.013 0.11 -10000 0 -0.5 20 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.034 0.14 -10000 0 -0.36 92 92
GAB2/PI3K/SHP2 -0.05 0.1 -10000 0 -0.35 60 60
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.026 0.11 -10000 0 -0.48 21 21
RAF1 0 0.12 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.005 0.16 -10000 0 -0.37 117 117
FCER1G 0.019 0.019 0.26 1 -10000 0 1
FCER1A -0.052 0.2 -10000 0 -0.61 94 94
Antigen/IgE/Fc epsilon R1/Fyn -0.014 0.15 -10000 0 -0.36 113 113
MAPK3 0 0.11 -10000 0 -0.86 12 12
MAPK1 -0.005 0.11 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.021 0.18 -10000 0 -0.59 51 51
DUSP1 -0.054 0.21 -10000 0 -0.6 103 103
NF-kappa-B/RelA 0.008 0.06 0.15 4 -0.18 9 13
actin cytoskeleton reorganization -0.008 0.15 -10000 0 -0.62 26 26
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0 0.11 -10000 0 -0.45 18 18
FER -0.021 0.11 -10000 0 -0.38 39 39
RELA 0.024 0.004 -10000 0 -10000 0 0
ITK -0.012 0.092 -10000 0 -0.4 36 36
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.006 0.13 0.29 7 -0.49 19 26
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.019 0.1 -10000 0 -0.37 38 38
PTK2 -0.01 0.16 -10000 0 -0.66 26 26
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.026 0.14 -10000 0 -0.46 38 38
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.004 0.17 0.33 30 -0.44 40 70
MAP2K2 -0.004 0.11 -10000 0 -0.86 12 12
MAP2K1 -0.003 0.11 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.009 0.096 -10000 0 -0.38 19 19
MAP2K4 -0.075 0.3 -10000 0 -0.84 105 105
Fc epsilon R1/FcgammaRIIB -0.014 0.16 -10000 0 -0.39 117 117
mol:Choline -0.008 0.18 0.33 101 -0.34 112 213
SHC/Grb2/SOS1 0.01 0.11 -10000 0 -0.43 18 18
FYN 0.022 0.023 -10000 0 -0.6 1 1
DOK1 0.024 0.003 -10000 0 -10000 0 0
PXN -0.01 0.15 -10000 0 -0.59 26 26
HCLS1 -0.02 0.1 -10000 0 -0.37 36 36
PRKCB 0.013 0.14 0.32 34 -0.37 24 58
FCGR2B 0.018 0.039 0.27 1 -0.6 3 4
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.008 0.1 -10000 0 -0.4 19 19
LCP2 0.024 0.01 0.27 1 -10000 0 1
PLA2G4A -0.046 0.14 -10000 0 -0.39 90 90
RASA1 0.024 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.008 0.18 0.33 101 -0.34 112 213
IKK complex 0.031 0.11 0.28 67 -0.21 9 76
WIPF1 0.024 0.004 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.058 -10000 0 -0.32 2 2
adherens junction organization -0.015 0.095 -10000 0 -0.34 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.084 0.16 0.34 3 -0.35 79 82
FMN1 -0.013 0.091 -10000 0 -0.35 29 29
mol:IP3 0 0.048 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.008 0.091 -10000 0 -0.33 41 41
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.004 0.059 -10000 0 -0.28 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.56 28 28
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.079 -10000 0 -0.33 24 24
VASP -0.011 0.084 -10000 0 -0.33 25 25
ZYX -0.01 0.085 -10000 0 -0.34 25 25
JUB -0.01 0.086 -10000 0 -0.31 41 41
EGFR(dimer) -0.11 0.19 -10000 0 -0.35 275 275
E-cadherin/beta catenin-gamma catenin 0.032 0.06 -10000 0 -0.38 14 14
mol:PI-3-4-5-P3 0.018 0.07 -10000 0 -0.31 2 2
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.018 0.071 -10000 0 -0.31 2 2
FYN -0.003 0.063 -10000 0 -0.38 3 3
mol:Ca2+ 0.001 0.047 -10000 0 -10000 0 0
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:DAG 0 0.048 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
RhoA/GDP -0.084 0.16 0.36 2 -0.3 242 244
establishment of polarity of embryonic epithelium -0.01 0.082 -10000 0 -0.32 25 25
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.3 -10000 0 -0.6 281 281
CASR -0.001 0.051 0.23 1 -10000 0 1
RhoA/GTP 0.015 0.053 -10000 0 -10000 0 0
AKT2 0.002 0.061 -10000 0 -0.3 2 2
actin cable formation -0.015 0.089 0.25 2 -0.37 19 21
apoptosis -0.006 0.07 0.32 5 -0.23 6 11
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.099 0.16 -10000 0 -0.32 243 243
PIP5K1A -0.01 0.08 -10000 0 -0.34 24 24
PLCG1 0 0.048 -10000 0 -10000 0 0
Rac1/GTP -0.094 0.18 -10000 0 -0.33 260 260
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.066 0.21 0.3 2 -0.4 158 160
MAP3K8 0.009 0.047 -10000 0 -0.61 4 4
FOS -0.025 0.15 0.32 2 -0.44 41 43
PRKCA -0.004 0.094 0.25 2 -0.61 18 20
PTPN7 0.019 0.061 0.25 44 -10000 0 44
HRAS 0.023 0.01 0.27 1 -10000 0 1
PRKCB 0.004 0.081 0.26 13 -0.61 11 24
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.035 -10000 0 -10000 0 0
MAPK3 0.005 0.095 -10000 0 -0.81 5 5
MAP2K1 -0.014 0.12 -10000 0 -0.52 34 34
ELK1 0.005 0.03 -10000 0 -10000 0 0
BRAF -0.015 0.1 -10000 0 -0.51 30 30
mol:GTP -0.002 0.003 -10000 0 -0.006 267 267
MAPK1 -0.01 0.12 -10000 0 -0.46 31 31
RAF1 -0.014 0.1 -10000 0 -0.51 30 30
KRAS 0.022 0.006 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.024 0.13 0.44 48 -0.24 7 55
KIRREL -0.013 0.15 -10000 0 -0.6 49 49
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.024 0.13 0.24 7 -0.44 48 55
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.042 0.11 0.29 4 -0.34 46 50
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.081 0.24 1 -0.29 39 40
FYN 0.023 0.13 0.28 93 -0.33 45 138
mol:Ca2+ 0.039 0.11 0.28 4 -0.34 44 48
mol:DAG 0.04 0.11 0.29 4 -0.34 44 48
NPHS2 0.017 0.032 0.27 5 -10000 0 5
mol:IP3 0.04 0.11 0.29 4 -0.34 44 48
regulation of endocytosis 0.03 0.097 0.25 5 -0.31 45 50
Nephrin/NEPH1/podocin/Cholesterol 0.032 0.11 0.26 9 -0.34 46 55
establishment of cell polarity 0.024 0.13 0.24 7 -0.44 48 55
Nephrin/NEPH1/podocin/NCK1-2 0.052 0.11 0.33 1 -0.32 44 45
Nephrin/NEPH1/beta Arrestin2 0.033 0.1 0.26 5 -0.32 45 50
NPHS1 0.063 0.093 0.27 130 -10000 0 130
Nephrin/NEPH1/podocin 0.033 0.1 0.31 4 -0.33 45 49
TJP1 0.023 0.022 -10000 0 -0.6 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.041 0.11 0.28 6 -0.34 44 50
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.039 0.11 0.3 5 -0.34 43 48
GRB2 0.023 0.011 0.27 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.021 0.13 0.29 86 -0.33 50 136
cytoskeleton organization 0.01 0.1 0.28 13 -0.35 35 48
Nephrin/NEPH1 0.023 0.097 0.2 2 -0.32 47 49
Nephrin/NEPH1/ZO-1 0.033 0.11 -10000 0 -0.37 47 47
FAS signaling pathway (CD95)

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
SPTAN1 -0.004 0.044 0.22 23 -10000 0 23
RFC1 -0.004 0.042 0.22 21 -10000 0 21
PRKDC 0.016 0.08 0.23 89 -10000 0 89
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.02 0.1 -10000 0 -0.64 18 18
FASLG/FAS/FADD/FAF1 -0.005 0.056 0.23 7 -0.3 6 13
MAP2K4 -0.089 0.18 0.39 2 -0.41 89 91
mol:ceramide -0.023 0.096 -10000 0 -0.41 12 12
GSN -0.009 0.062 0.22 23 -0.38 11 34
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.072 -10000 0 -0.39 7 7
FAS 0.003 0.041 -10000 0 -0.62 2 2
BID -0.019 0.022 -10000 0 -10000 0 0
MAP3K1 -0.052 0.12 0.32 2 -0.48 23 25
MAP3K7 0.009 0.02 -10000 0 -10000 0 0
RB1 -0.004 0.041 0.22 20 -10000 0 20
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET -0.056 0.2 -10000 0 -0.43 178 178
ARHGDIB -0.002 0.049 0.23 28 -10000 0 28
FADD 0.005 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.068 0.37 11 -0.22 23 34
NFKB1 -0.049 0.12 -10000 0 -0.62 15 15
MAPK8 -0.16 0.26 0.56 2 -0.47 313 315
DFFA -0.004 0.042 0.22 20 -10000 0 20
DNA fragmentation during apoptosis -0.009 0.05 0.22 20 -10000 0 20
FAS/FADD/MET -0.044 0.15 -10000 0 -0.38 130 130
CFLAR/RIP1 0.041 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.036 0.27 17 -10000 0 17
FAF1 0.002 0.03 -10000 0 -10000 0 0
PARP1 -0.001 0.054 0.25 27 -10000 0 27
DFFB -0.005 0.042 0.22 20 -10000 0 20
CHUK -0.044 0.11 -10000 0 -0.57 14 14
FASLG 0.009 0.079 0.26 33 -0.62 6 39
FAS/FADD 0.008 0.038 -10000 0 -0.35 2 2
HGF -0.01 0.14 -10000 0 -0.6 45 45
LMNA -0.003 0.058 0.39 1 -10000 0 1
CASP6 -0.004 0.041 0.22 20 -10000 0 20
CASP10 0.003 0.041 -10000 0 -0.62 2 2
CASP3 0 0.046 0.28 20 -10000 0 20
PTPN13 0.009 0.096 -10000 0 -0.6 20 20
CASP8 -0.021 0.025 -10000 0 -10000 0 0
IL6 -0.46 0.63 -10000 0 -1.2 322 322
MET -0.079 0.23 -10000 0 -0.6 136 136
ICAD/CAD -0.006 0.037 0.21 9 -10000 0 9
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.097 -10000 0 -0.42 12 12
activation of caspase activity by cytochrome c -0.019 0.022 -10000 0 -10000 0 0
PAK2 -0.002 0.054 0.24 30 -10000 0 30
BCL2 0.008 0.098 -10000 0 -0.6 21 21
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.011 0.14 -10000 0 -0.6 46 46
HRAS 0.024 0.01 0.27 1 -10000 0 1
EGFR -0.19 0.3 -10000 0 -0.6 281 281
AKT -0.012 0.12 0.3 6 -0.28 71 77
FOXO3 0.022 0.023 -10000 0 -0.6 1 1
AKT1 0.024 0.005 -10000 0 -10000 0 0
FOXO1 0.022 0.023 -10000 0 -0.6 1 1
AKT3 0.014 0.062 -10000 0 -0.6 8 8
FOXO4 0.025 0.001 -10000 0 -10000 0 0
MET -0.079 0.23 -10000 0 -0.6 136 136
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.02 0.06 0.27 4 -0.6 7 11
PIK3R3 0.024 0.009 0.27 1 -10000 0 1
PIK3R2 0.024 0.004 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.059 0.14 0.21 4 -0.25 258 262
ERBB2 0.021 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.005 0.096 0.35 38 -0.27 1 39
PI3K -0.046 0.15 0.26 13 -0.33 128 141
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
KRAS 0.024 0.005 -10000 0 -10000 0 0
FOXO 0.039 0.058 0.26 9 -0.17 1 10
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.11 0.11 0.22 367 -0.37 2 369
EPHB2 0.028 0.033 0.27 15 -10000 0 15
Syndecan-2/TACI 0.019 0.062 0.32 4 -0.35 13 17
LAMA1 -0.039 0.19 0.27 1 -0.6 83 84
Syndecan-2/alpha2 ITGB1 -0.037 0.15 -10000 0 -0.34 139 139
HRAS 0.024 0.01 0.27 1 -10000 0 1
Syndecan-2/CASK 0.005 0.019 -10000 0 -0.38 2 2
ITGA5 0.025 0.002 -10000 0 -10000 0 0
BAX -0.002 0.022 -10000 0 -10000 0 0
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.02 -10000 0 -0.35 2 2
LAMA3 -0.12 0.26 -10000 0 -0.6 185 185
EZR 0.024 0.013 0.27 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.052 0.2 -10000 0 -0.6 100 100
Syndecan-2/MMP2 0.014 0.039 -10000 0 -0.4 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.026 0.064 -10000 0 -0.42 16 16
dendrite morphogenesis 0.021 0.035 0.32 3 -0.38 2 5
Syndecan-2/GM-CSF 0.02 0.035 0.21 16 -0.38 2 18
determination of left/right symmetry 0.006 0.022 -10000 0 -0.44 2 2
Syndecan-2/PKC delta 0.019 0.025 0.32 1 -0.38 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.034 0.077 0.26 3 -0.35 2 5
MAPK1 0.039 0.08 0.19 86 -0.34 2 88
Syndecan-2/RACK1 0.027 0.025 -10000 0 -0.33 2 2
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.022 -10000 0 -0.44 2 2
ITGA2 0.012 0.086 -10000 0 -0.6 16 16
MAPK8 0.005 0.025 0.24 4 -0.37 2 6
Syndecan-2/alpha2/beta1 Integrin 0.001 0.12 -10000 0 -0.38 61 61
Syndecan-2/Kininogen 0.018 0.033 0.23 10 -0.38 2 12
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.043 0.072 0.35 5 -0.32 2 7
Syndecan-2/CASK/Protein 4.1 0.016 0.021 -10000 0 -0.35 2 2
extracellular matrix organization 0.018 0.022 -10000 0 -0.38 2 2
actin cytoskeleton reorganization 0.11 0.11 0.22 367 -0.37 2 369
Syndecan-2/Caveolin-2/Ras -0.011 0.12 -10000 0 -0.36 74 74
Syndecan-2/Laminin alpha3 -0.059 0.15 -10000 0 -0.32 187 187
Syndecan-2/RasGAP 0.036 0.03 -10000 0 -0.32 2 2
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
PRKCD 0.024 0.01 0.27 1 -10000 0 1
Syndecan-2 dimer 0.021 0.035 0.32 3 -0.38 2 5
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.026 -10000 0 -0.31 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
TNFRSF13B 0.023 0.087 0.27 32 -0.6 11 43
RASA1 0.024 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.026 0.064 -10000 0 -0.42 16 16
Syndecan-2/Synbindin 0.017 0.022 -10000 0 -0.37 2 2
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CASP3 0.045 0.074 0.22 5 -0.35 2 7
FN1 0.13 0.12 0.27 367 -10000 0 367
Syndecan-2/IL8 0.024 0.077 0.23 51 -0.34 18 69
SDC2 0.006 0.022 -10000 0 -0.44 2 2
KNG1 0.022 0.027 0.27 10 -10000 0 10
Syndecan-2/Neurofibromin 0.017 0.023 -10000 0 -0.38 2 2
TRAPPC4 0.022 0.008 -10000 0 -10000 0 0
CSF2 0.025 0.034 0.27 16 -10000 0 16
Syndecan-2/TGFB1 0.018 0.022 -10000 0 -0.38 2 2
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.021 -10000 0 -0.35 2 2
Syndecan-2/Ezrin 0.028 0.028 0.3 1 -0.35 2 3
PRKACA 0.047 0.076 0.19 173 -0.34 2 175
angiogenesis 0.024 0.076 0.23 51 -0.34 18 69
MMP2 0.019 0.044 -10000 0 -0.6 4 4
IL8 0.026 0.11 0.27 51 -0.6 16 67
calcineurin-NFAT signaling pathway 0.019 0.061 0.32 4 -0.35 13 17
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.022 -10000 0 -0.6 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.018 0.065 0.45 1 -0.27 12 13
CDKN1A -0.009 0.028 -10000 0 -0.8 1 1
KAT2B 0.024 0.003 -10000 0 -10000 0 0
BAX 0.024 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.011 -10000 0 -0.26 1 1
FOXO1 0.022 0.023 -10000 0 -0.6 1 1
FOXO4 0.011 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.35 0.31 0.27 22 -0.6 500 522
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.009 0.019 -10000 0 -10000 0 0
PPARGC1A -0.1 0.25 0.27 9 -0.6 167 176
FHL2 0.021 0.05 0.27 2 -0.6 5 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.033 0.011 -10000 0 -10000 0 0
HIST2H4A 0.018 0.065 0.27 12 -0.45 1 13
SIRT1/FOXO3a 0.015 0.027 -10000 0 -0.2 4 4
SIRT1 0.022 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.025 -10000 0 -0.39 1 1
SIRT1/Histone H1b 0.027 0.044 -10000 0 -10000 0 0
apoptosis -0.044 0.014 -10000 0 -10000 0 0
SIRT1/PGC1A -0.056 0.17 -10000 0 -0.36 184 184
p53/SIRT1 0.027 0.017 0.41 1 -10000 0 1
SIRT1/FOXO4 0.023 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.038 0.04 -10000 0 -0.36 6 6
HIST1H1E 0.02 0.03 0.23 3 -10000 0 3
SIRT1/p300 0.033 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.03 0.022 -10000 0 -10000 0 0
TP53 0.02 0.01 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.28 0.22 -10000 0 -0.41 585 585
ACSS2 -0.008 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.03 0.023 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.032 0.043 0.27 27 -10000 0 27
GPC2 0.047 0.084 0.27 86 -0.6 3 89
GPC2/Midkine 0.055 0.071 0.38 12 -0.45 3 15
neuron projection morphogenesis 0.055 0.071 0.38 12 -0.45 3 15
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.042 0.16 -10000 0 -0.34 173 173
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.006 0.015 0.14 7 -10000 0 7
GNB1/GNG2 0.028 0.036 -10000 0 -0.38 6 6
GNB1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.062 0.15 -10000 0 -0.34 183 183
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.02 0.036 0.086 183 -10000 0 183
GNAL -0.11 0.25 -10000 0 -0.6 172 172
GNG2 0.019 0.053 -10000 0 -0.6 6 6
CRH 0.018 0.024 0.27 7 -10000 0 7
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.001 -10000 0 -10000 0 0
MAPK11 0.005 0.018 -10000 0 -0.37 2 2
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.02 0.068 -10000 0 -0.36 30 30
ADCY5 -0.12 0.17 -10000 0 -0.39 248 248
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.007 0.002 -10000 0 -10000 0 0
ADCY1 -0.007 0.063 -10000 0 -0.39 18 18
ADCY2 -0.03 0.1 0.25 6 -0.39 62 68
ADCY3 -0.007 0.004 -10000 0 -10000 0 0
ADCY8 -0.004 0.024 0.23 5 -10000 0 5
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.007 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.01 0.09 0.22 18 -0.25 33 51
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.011 0.045 -10000 0 -0.27 16 16
epithelial cell differentiation 0.036 0.056 -10000 0 -0.33 14 14
CYFIP2 0.03 0.045 0.27 22 -0.6 1 23
ENAH -0.005 0.06 0.27 8 -10000 0 8
EGFR -0.19 0.3 -10000 0 -0.6 281 281
EPHA2 0.02 0.049 -10000 0 -0.6 5 5
MYO6 -0.014 0.052 -10000 0 -0.32 15 15
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.032 -10000 0 -0.39 1 1
AQP5 -0.2 0.27 0.34 1 -0.52 339 340
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.05 -10000 0 -0.32 14 14
regulation of calcium-dependent cell-cell adhesion -0.026 0.08 -10000 0 -0.32 47 47
EGF -0.091 0.24 0.27 2 -0.6 153 155
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.019 0.12 -10000 0 -0.48 43 43
cortical microtubule organization 0.036 0.056 -10000 0 -0.33 14 14
GO:0000145 -0.013 0.047 -10000 0 -0.3 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.058 -10000 0 -0.34 14 14
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
ARF6/GDP -0.022 0.042 -10000 0 -0.3 16 16
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.043 -10000 0 -0.35 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.049 -10000 0 -0.43 1 1
PVRL2 0.024 0.009 0.27 1 -10000 0 1
ZYX -0.014 0.05 -10000 0 -0.32 14 14
ARF6/GTP 0.048 0.044 -10000 0 -0.33 5 5
CDH1 0.011 0.081 -10000 0 -0.6 14 14
EGFR/EGFR/EGF/EGF -0.15 0.21 -10000 0 -0.35 390 390
RhoA/GDP 0.037 0.055 -10000 0 -0.32 14 14
actin cytoskeleton organization -0.015 0.049 -10000 0 -0.31 15 15
IGF-1R heterotetramer 0.013 0.082 0.27 2 -0.6 14 16
GIT1 0.023 0.007 -10000 0 -10000 0 0
IGF1R 0.013 0.082 0.27 2 -0.6 14 16
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
DIAPH1 0.025 0.1 -10000 0 -0.67 2 2
Wnt receptor signaling pathway -0.036 0.056 0.33 14 -10000 0 14
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.042 -10000 0 -0.3 15 15
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.016 0.05 -10000 0 -0.32 15 15
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.015 0.05 -10000 0 -0.31 15 15
Ephrin A1/EPHA2 0.024 0.057 -10000 0 -0.32 17 17
SEC6/SEC8 -0.023 0.041 -10000 0 -0.3 15 15
MGAT3 -0.027 0.081 -10000 0 -0.33 47 47
HGF/MET -0.043 0.16 -10000 0 -0.34 174 174
HGF -0.01 0.14 -10000 0 -0.6 45 45
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.011 0.046 -10000 0 -0.27 16 16
actin cable formation 0.04 0.095 0.31 28 -0.3 1 29
KIAA1543 -0.014 0.051 -10000 0 -0.33 14 14
KIFC3 -0.014 0.048 -10000 0 -0.32 14 14
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.013 0.05 -10000 0 -0.32 14 14
NCK1/GIT1 0.033 0.011 -10000 0 -10000 0 0
mol:GDP 0.036 0.056 -10000 0 -0.33 14 14
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.013 0.05 -10000 0 -0.32 14 14
PIP5K1C -0.014 0.051 -10000 0 -0.32 14 14
LIMA1 0.024 0.022 -10000 0 -0.6 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.015 0.088 0.3 20 -10000 0 20
adherens junction assembly -0.026 0.11 0.28 1 -0.63 14 15
IGF-1R heterotetramer/IGF1 -0.047 0.16 -10000 0 -0.33 183 183
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.024 -10000 0 -0.28 3 3
MET -0.079 0.23 -10000 0 -0.6 136 136
PLEKHA7 -0.014 0.054 -10000 0 -0.34 14 14
mol:GTP 0.042 0.042 -10000 0 -0.35 5 5
establishment of epithelial cell apical/basal polarity -0.009 0.066 0.35 5 -10000 0 5
cortical actin cytoskeleton stabilization 0.011 0.045 -10000 0 -0.27 16 16
regulation of cell-cell adhesion -0.015 0.049 -10000 0 -0.31 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.046 -10000 0 -0.27 16 16
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.047 0.044 -10000 0 -10000 0 0
BIRC5 0.19 0.12 0.27 560 -10000 0 560
NFKBIA 0.028 0.046 0.29 7 -10000 0 7
CPEB1 -0.09 0.24 -10000 0 -0.6 151 151
AKT1 0.028 0.045 0.29 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.035 0.037 0.22 1 -10000 0 1
NDEL1/TACC3 0.067 0.07 0.26 15 -10000 0 15
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.005 0.028 -10000 0 -10000 0 0
PAK1/Aurora A 0.043 0.045 0.26 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.1 0.07 0.27 23 -10000 0 23
TP53 0.023 0.054 -10000 0 -10000 0 0
DLG7 0.025 0.033 0.18 1 -10000 0 1
AURKAIP1 0.024 0.01 0.27 1 -10000 0 1
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.071 0.073 0.28 15 -10000 0 15
G2/M transition of mitotic cell cycle 0.035 0.037 0.21 1 -10000 0 1
AURKA 0.042 0.05 0.25 1 -10000 0 1
AURKB 0.093 0.079 0.18 345 -10000 0 345
CDC25B 0.035 0.041 0.23 4 -10000 0 4
G2/M transition checkpoint 0.021 0.03 -10000 0 -10000 0 0
mRNA polyadenylation -0.031 0.14 -10000 0 -0.32 151 151
Aurora A/CPEB -0.031 0.14 -10000 0 -0.32 151 151
Aurora A/TACC1/TRAP/chTOG 0.047 0.067 -10000 0 -0.32 12 12
BRCA1 0.024 0.01 0.27 1 -10000 0 1
centrosome duplication 0.043 0.045 0.26 2 -10000 0 2
regulation of centrosome cycle 0.066 0.068 0.26 15 -10000 0 15
spindle assembly 0.046 0.066 -10000 0 -0.32 12 12
TDRD7 0.024 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.15 0.091 0.28 24 -10000 0 24
CENPA 0.1 0.086 0.2 359 -0.21 3 362
Aurora A/PP2A 0.047 0.045 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.033 0.042 0.24 1 -10000 0 1
negative regulation of DNA binding 0.02 0.064 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.021 0.03 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.051 0.25 1 -10000 0 1
TACC1 0.01 0.078 -10000 0 -0.6 13 13
TACC3 0.058 0.085 0.27 118 -10000 0 118
Aurora A/Antizyme1 0.056 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.047 0.045 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.004 0.028 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.023 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.1 0.07 0.27 23 -10000 0 23
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.075 0.25 27 -10000 0 27
PAK1 0.023 0.017 0.27 3 -10000 0 3
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.093 0.11 0.28 37 -0.63 6 43
Syndecan-4/Syndesmos 0.099 0.11 0.41 3 -0.64 5 8
positive regulation of JNK cascade 0.088 0.14 0.37 6 -0.6 6 12
Syndecan-4/ADAM12 0.11 0.12 0.41 6 -0.68 5 11
CCL5 0.03 0.048 0.27 26 -0.6 1 27
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.025 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
PLG -0.01 0.033 0.27 4 -10000 0 4
ADAM12 0.041 0.072 0.27 63 -0.6 2 65
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.011 0.27 1 -10000 0 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.069 0.15 0.42 2 -0.68 6 8
Syndecan-4/CXCL12/CXCR4 0.093 0.14 0.39 5 -0.65 6 11
Syndecan-4/Laminin alpha3 0.039 0.16 0.42 2 -0.67 6 8
MDK 0.032 0.043 0.27 27 -10000 0 27
Syndecan-4/FZD7 0.1 0.12 0.4 4 -0.68 5 9
Syndecan-4/Midkine 0.11 0.11 0.39 9 -0.65 5 14
FZD7 0.013 0.084 -10000 0 -0.6 15 15
Syndecan-4/FGFR1/FGF -0.011 0.17 -10000 0 -0.55 12 12
THBS1 0.023 0.022 -10000 0 -0.6 1 1
integrin-mediated signaling pathway 0.098 0.12 0.38 6 -0.66 6 12
positive regulation of MAPKKK cascade 0.088 0.14 0.37 6 -0.6 6 12
Syndecan-4/TACI 0.1 0.12 0.39 7 -0.67 5 12
CXCR4 0.031 0.04 0.27 23 -10000 0 23
cell adhesion 0.067 0.09 0.26 68 -0.27 18 86
Syndecan-4/Dynamin 0.1 0.11 0.41 3 -0.68 5 8
Syndecan-4/TSP1 0.1 0.11 0.39 5 -0.67 5 10
Syndecan-4/GIPC 0.1 0.11 0.42 2 -0.68 5 7
Syndecan-4/RANTES 0.1 0.11 0.38 5 -0.67 5 10
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.039 0.19 0.27 1 -0.6 83 84
LAMA3 -0.12 0.26 -10000 0 -0.6 185 185
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.024 0.23 0.7 78 -0.57 17 95
Syndecan-4/alpha-Actinin 0.1 0.11 0.41 3 -0.68 5 8
TFPI -0.001 0.12 -10000 0 -0.6 33 33
F2 0.024 0.034 0.28 7 -10000 0 7
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.006 0.18 0.4 2 -0.56 22 24
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.091 0.27 5 -0.6 17 22
Syndecan-4/CXCL12 0.081 0.14 0.4 4 -0.68 6 10
FGF6 0.016 0.031 -10000 0 -0.6 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.02 0.16 -10000 0 -0.6 58 58
TNFRSF13B 0.023 0.087 0.27 32 -0.6 11 43
FGF2 -0.21 0.3 -10000 0 -0.6 310 310
FGFR1 0.016 0.049 -10000 0 -0.6 5 5
Syndecan-4/PI-4-5-P2 0.08 0.1 0.34 2 -0.68 5 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 363 -10000 0 363
cell migration -0.02 0.013 -10000 0 -10000 0 0
PRKCD 0.011 0.028 -10000 0 -10000 0 0
vasculogenesis 0.1 0.1 0.39 5 -0.64 5 10
SDC4 0.092 0.1 0.41 3 -0.76 4 7
Syndecan-4/Tenascin C 0.099 0.12 0.39 5 -0.69 6 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.09 0.11 0.38 2 -0.68 5 7
MMP9 0.12 0.12 0.27 326 -0.59 1 327
Rac1/GTP 0.068 0.091 0.27 61 -0.28 18 79
cytoskeleton organization 0.098 0.1 0.39 5 -0.62 5 10
GIPC1 0.024 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.093 0.13 0.4 4 -0.64 6 10
Insulin Pathway

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
CBL/APS/CAP -0.044 0.17 -10000 0 -0.34 189 189
TC10/GTP -0.036 0.15 -10000 0 -0.31 178 178
Insulin Receptor/Insulin/IRS1/Shp2 0.045 0.079 -10000 0 -0.37 27 27
HRAS 0.024 0.01 0.27 1 -10000 0 1
APS homodimer 0.032 0.042 0.27 26 -10000 0 26
GRB14 0.014 0.19 0.27 117 -0.6 59 176
FOXO3 -0.02 0.16 -10000 0 -0.6 57 57
AKT1 -0.016 0.11 0.32 7 -0.3 70 77
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.058 0.051 0.37 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.11 0.26 -10000 0 -0.6 183 183
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.002 0.026 0.22 5 -10000 0 5
CAV1 -0.085 0.15 -10000 0 -0.37 174 174
CBL/APS/CAP/Crk-II/C3G -0.024 0.17 -10000 0 -0.33 181 181
Insulin Receptor/Insulin/IRS1/NCK2 0.045 0.078 -10000 0 -0.36 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.066 -10000 0 -0.32 24 24
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.068 -10000 0 -0.34 13 13
RPS6KB1 -0.015 0.099 0.3 7 -0.29 57 64
PARD6A 0.023 0.017 0.27 3 -10000 0 3
CBL 0.022 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.041 -10000 0 -0.56 4 4
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.011 0.096 -10000 0 -0.29 55 55
HRAS/GTP -0.021 0.046 -10000 0 -0.3 18 18
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.073 -10000 0 -0.35 19 19
PRKCI 0.013 0.06 -10000 0 -0.47 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.002 0.11 -10000 0 -0.32 78 78
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.039 -10000 0 -0.47 4 4
PI3K 0.043 0.07 -10000 0 -0.33 24 24
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
AKT2 -0.016 0.11 0.29 6 -0.3 72 78
PRKCZ 0.004 0.085 -10000 0 -0.49 11 11
SH2B2 0.032 0.042 0.27 26 -10000 0 26
SHC/SHIP 0.012 0.06 -10000 0 -0.33 21 21
F2RL2 0.054 0.12 0.27 135 -0.6 12 147
TRIP10 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.035 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.034 0.17 -10000 0 -0.35 182 182
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.05 0.029 -10000 0 -10000 0 0
INPP5D -0.019 0.063 0.19 1 -0.34 27 28
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.018 0.14 -10000 0 -0.68 34 34
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
p62DOK/RasGAP 0.042 0.04 -10000 0 -0.48 4 4
INS 0.02 0.01 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.063 0.19 1 -0.34 27 28
GRB2 0.023 0.011 0.27 1 -10000 0 1
EIF4EBP1 -0.02 0.092 0.28 3 -0.29 58 61
PTPRA 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.054 -10000 0 -0.29 20 20
Insulin Receptor/Insulin/IRS1 0.031 0.075 -10000 0 -0.35 29 29
Insulin Receptor/Insulin/IRS3 0.035 0.015 -10000 0 -10000 0 0
Par3/Par6 0.063 0.074 -10000 0 -0.33 12 12
Nectin adhesion pathway

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
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
alphaV beta3 Integrin 0.027 0.062 -10000 0 -0.45 13 13
PTK2 -0.028 0.13 -10000 0 -0.46 50 50
positive regulation of JNK cascade -0.012 0.12 -10000 0 -0.32 70 70
CDC42/GDP -0.005 0.16 0.43 1 -0.44 70 71
Rac1/GDP -0.006 0.16 -10000 0 -0.43 73 73
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.01 0.14 -10000 0 -0.4 66 66
nectin-3/I-afadin -0.003 0.13 -10000 0 -0.45 63 63
RAPGEF1 -0.022 0.15 0.46 1 -0.48 60 61
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.035 0.16 -10000 0 -0.54 60 60
PDGFB-D/PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
TLN1 -0.019 0.063 -10000 0 -0.42 7 7
Rap1/GTP -0.015 0.11 -10000 0 -0.34 58 58
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.023 -10000 0 -0.36 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.003 0.13 -10000 0 -0.45 63 63
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.023 0.19 0.46 1 -0.53 74 75
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.033 0.11 -10000 0 -0.34 62 62
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.03 0.024 -10000 0 -0.28 3 3
positive regulation of lamellipodium assembly -0.011 0.12 -10000 0 -0.34 74 74
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.023 0.16 -10000 0 -0.6 62 62
PVRL2 0.024 0.009 0.27 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
CLDN1 0.005 0.13 0.27 20 -0.6 32 52
JAM-A/CLDN1 0.011 0.13 -10000 0 -0.38 67 67
SRC -0.041 0.18 -10000 0 -0.59 63 63
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
nectin-1(dimer)/I-afadin/I-afadin 0.03 0.024 -10000 0 -0.28 3 3
FARP2 -0.023 0.19 0.46 1 -0.53 74 75
RAC1 0.024 0.004 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.013 0.12 -10000 0 -0.39 62 62
nectin-1/I-afadin 0.03 0.024 -10000 0 -0.28 3 3
nectin-2/I-afadin 0.032 0.024 -10000 0 -0.28 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.01 0.12 -10000 0 -0.39 63 63
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.01 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.012 0.12 -10000 0 -0.32 70 70
alphaV/beta3 Integrin/Talin 0.004 0.089 -10000 0 -0.42 17 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.024 -10000 0 -0.28 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.024 -10000 0 -0.28 3 3
PIP5K1C -0.014 0.07 -10000 0 -0.24 61 61
VAV2 -0.023 0.19 0.44 1 -0.56 72 73
RAP1/GDP -0.003 0.14 -10000 0 -0.4 67 67
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.013 0.12 -10000 0 -0.39 62 62
nectin-3(dimer)/I-afadin/I-afadin -0.003 0.13 -10000 0 -0.45 63 63
Rac1/GTP -0.01 0.15 -10000 0 -0.42 73 73
PTPRM -0.01 0.079 -10000 0 -0.26 63 63
E-cadherin/beta catenin/alpha catenin 0.047 0.064 -10000 0 -0.33 15 15
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.024 0.005 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.055 0.14 0.47 9 -0.53 2 11
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.11 0.23 -10000 0 -0.44 265 265
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 0 0.091 -10000 0 -0.24 75 75
ER alpha/Oestrogen -0.019 0.17 0.18 109 -0.43 111 220
NFX1/SIN3/HDAC complex 0.022 0.059 0.25 1 -0.32 13 14
EGF -0.09 0.24 0.27 2 -0.6 153 155
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.023 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.051 0.12 0.44 2 -0.5 2 4
SAP18 0.023 0.007 -10000 0 -10000 0 0
MRN complex 0.035 0.023 -10000 0 -10000 0 0
WT1 0.15 0.12 0.27 431 -10000 0 431
WRN 0.02 0.01 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.006 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.1 -10000 0 -0.47 2 2
Mad/Max 0.04 0.015 -10000 0 -10000 0 0
TERT 0.055 0.14 0.51 6 -0.54 2 8
CCND1 0.079 0.17 0.54 21 -1.1 3 24
MAX 0.026 0.007 -10000 0 -10000 0 0
RBBP7 0.027 0.023 0.27 7 -10000 0 7
RBBP4 0.025 0.005 -10000 0 -10000 0 0
TERF2 0.021 0.014 -10000 0 -10000 0 0
PTGES3 0.025 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.038 0.054 -10000 0 -0.38 5 5
CDKN1B 0.029 0.057 -10000 0 -0.71 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.016 0.27 3 -10000 0 3
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.019 0.061 -10000 0 -0.6 8 8
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.16 0.29 -10000 0 -0.6 251 251
IFN-gamma/IRF1 0.066 0.068 0.4 2 -0.33 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.048 0.073 0.27 83 -10000 0 83
Telomerase 0.028 0.077 0.26 2 -0.67 3 5
IRF1 0.028 0.019 0.28 2 -10000 0 2
ESR1 -0.024 0.24 0.27 109 -0.6 106 215
KU/TER 0.034 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.026 0.054 0.24 1 -0.33 6 7
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.055 0.24 1 -0.34 6 7
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.013 -10000 0 -10000 0 0
ATM 0.013 0.016 -10000 0 -10000 0 0
SMAD3 -0.007 0.012 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.01 0.27 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.058 0.13 0.52 1 -0.63 4 5
NR2F2 0.012 0.042 -10000 0 -0.61 3 3
MAPK3 0.005 0.021 -10000 0 -10000 0 0
MAPK1 0.005 0.021 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.011 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.016 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.3 -10000 0 -0.6 281 281
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.21 0.27 -10000 0 -0.48 400 400
MYC 0.006 0.091 -10000 0 -0.6 18 18
IL2 0.03 0.028 0.27 8 -10000 0 8
KU 0.034 0.01 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
TGFB1 0.021 0.011 -10000 0 -10000 0 0
TRF2/BLM 0.045 0.049 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.065 0.13 0.48 3 -0.51 2 5
SP1/HDAC2 0.046 0.027 -10000 0 -10000 0 0
PINX1 0.02 0.01 -10000 0 -10000 0 0
Telomerase/EST1A 0.043 0.1 -10000 0 -0.46 2 2
Smad3/Myc 0.005 0.061 -10000 0 -0.39 18 18
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.061 0.087 0.27 119 -0.2 1 120
Telomerase/PinX1 0.033 0.099 -10000 0 -0.5 1 1
Telomerase/AKT1/mTOR/p70S6K 0.025 0.1 0.31 4 -0.52 14 18
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.04 0.098 -10000 0 -0.43 1 1
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.045 0.034 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.045 0.1 -10000 0 -0.47 2 2
E2F1 0.1 0.12 0.27 263 -10000 0 263
ZNFX1 0.024 0.007 -10000 0 -10000 0 0
PIF1 0.067 0.093 0.27 146 -10000 0 146
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.012 0.27 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0.011 -10000 0 -10000 0 0
SMARCC1 0.004 0.031 -10000 0 -0.59 1 1
REL 0.025 0.024 -10000 0 -0.6 1 1
HDAC7 -0.036 0.11 0.37 1 -0.38 34 35
JUN 0.016 0.062 -10000 0 -0.6 8 8
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.024 0.003 -10000 0 -10000 0 0
KAT5 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.009 0.064 -10000 0 -0.46 15 15
FOXO1 0.021 0.023 -10000 0 -0.6 1 1
T-DHT/AR -0.023 0.12 0.38 1 -0.39 39 40
MAP2K6 0.003 0.086 0.26 1 -0.61 15 16
BRM/BAF57 0.025 0.027 -10000 0 -10000 0 0
MAP2K4 0.013 0.021 -10000 0 -10000 0 0
SMARCA2 0.017 0.019 -10000 0 -10000 0 0
PDE9A -0.065 0.27 -10000 0 -1.1 49 49
NCOA2 0.013 0.058 -10000 0 -0.6 7 7
CEBPA 0.019 0.057 -10000 0 -0.6 7 7
EHMT2 0.021 0.012 -10000 0 -10000 0 0
cell proliferation 0.004 0.15 0.37 22 -0.47 17 39
NR0B1 0.029 0.045 0.27 29 -10000 0 29
EGR1 -0.19 0.29 -10000 0 -0.6 278 278
RXRs/9cRA -0.047 0.16 -10000 0 -0.36 165 165
AR/RACK1/Src -0.015 0.11 0.32 9 -0.37 19 28
AR/GR -0.021 0.11 0.29 1 -0.3 92 93
GNB2L1 0.023 0.008 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.013 11 11
MAPK8 -0.001 0.023 -10000 0 -0.21 1 1
T-DHT/AR/TIF2/CARM1 -0.005 0.098 0.32 1 -0.36 18 19
SRC -0.017 0.062 0.19 23 -0.37 11 34
NR3C1 0.02 0.053 -10000 0 -0.6 6 6
KLK3 -0.15 0.4 0.37 5 -1.1 113 118
APPBP2 0.015 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.02 0.27 1 -10000 0 1
T-DHT/AR/TIP60 -0.012 0.092 0.31 3 -0.39 14 17
TMPRSS2 -0.13 0.37 -10000 0 -1.1 109 109
RXRG -0.11 0.25 0.26 1 -0.6 167 168
mol:9cRA -0.001 0.002 -10000 0 -0.011 5 5
RXRA 0.024 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.021 0.012 -10000 0 -10000 0 0
NR2C2 0.024 0.004 -10000 0 -10000 0 0
KLK2 -0.052 0.21 0.3 16 -0.69 71 87
AR -0.035 0.1 -10000 0 -0.3 93 93
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
MDM2 0.026 0.015 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 102 -0.025 20 122
GATA2 0.014 0.096 0.27 11 -0.6 18 29
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.26 335 -10000 0 335
T-DHT/AR/RACK1/Src -0.01 0.1 0.32 11 -0.39 14 25
positive regulation of transcription 0.014 0.096 0.27 11 -0.6 18 29
DNAJA1 0.016 0.021 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.011 -10000 0 -10000 0 0
NCOA1 0.021 0.032 -10000 0 -0.63 1 1
SPDEF -0.011 0.14 0.26 11 -0.6 44 55
T-DHT/AR/TIF2 0.006 0.088 0.32 4 -0.37 11 15
T-DHT/AR/Hsp90 -0.013 0.091 0.31 3 -0.39 15 18
GSK3B 0.021 0.012 -10000 0 -10000 0 0
NR2C1 0.025 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.023 0.055 0.23 1 -0.38 13 14
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.027 0.015 -10000 0 -10000 0 0
POU2F1 0.009 0.052 -10000 0 -0.21 1 1
T-DHT/AR/DAX-1 -0.012 0.096 0.3 5 -0.39 15 20
CREBBP 0.023 0.007 -10000 0 -10000 0 0
SMARCE1 0.017 0.018 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.01 0.043 -10000 0 -0.6 1 1
SVIL 0.01 0.051 -10000 0 -0.6 3 3
ZNF318 0.041 0.055 0.23 1 -10000 0 1
JMJD2C -0.004 0.043 0.12 12 -0.14 69 81
T-DHT/AR/Ubc9 -0.029 0.14 -10000 0 -0.4 88 88
CARM1 0.019 0.016 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.014 0.03 -10000 0 -10000 0 0
AKT1 0.028 0.018 -10000 0 -10000 0 0
PTK2B 0.011 0.027 -10000 0 -10000 0 0
MED1 0.026 0.02 -10000 0 -10000 0 0
MAK 0.037 0.084 0.26 8 -0.57 8 16
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.012 0.035 -10000 0 -10000 0 0
GSN 0.002 0.082 -10000 0 -0.6 12 12
NCOA2 0.01 0.059 -10000 0 -0.6 7 7
NCOA6 0.012 0.034 -10000 0 -10000 0 0
DNA-PK 0.051 0.053 -10000 0 -10000 0 0
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.014 0.029 -10000 0 -10000 0 0
cell proliferation 0.006 0.11 -10000 0 -0.56 19 19
XRCC5 0.027 0.015 -10000 0 -10000 0 0
UBE3A 0.008 0.045 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.039 0.16 -10000 0 -0.43 101 101
FHL2 0.003 0.12 -10000 0 -0.7 11 11
RANBP9 0.012 0.034 -10000 0 -10000 0 0
JMJD1A -0.01 0.057 0.12 32 -0.14 115 147
CDK6 0.023 0.045 0.27 2 -0.6 4 6
TGFB1I1 0.009 0.05 -10000 0 -0.6 3 3
T-DHT/AR/CyclinD1 -0.038 0.14 -10000 0 -0.41 90 90
XRCC6 0.026 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.035 0.17 -10000 0 -0.41 102 102
CTDSP1 0.017 0.02 -10000 0 -10000 0 0
CTDSP2 0.035 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.035 0.19 1 -10000 0 1
TCF4 0.028 0.056 -10000 0 -0.59 5 5
CDKN2A 0.062 0.089 0.28 118 -10000 0 118
SRF 0.033 0.024 -10000 0 -10000 0 0
NKX3-1 -0.062 0.21 0.3 18 -0.62 68 86
KLK3 -0.16 0.47 -10000 0 -1.4 102 102
TMF1 0.018 0.016 -10000 0 -10000 0 0
HNRNPA1 0.03 0.02 -10000 0 -10000 0 0
AOF2 -0.008 0.023 -10000 0 -0.069 102 102
APPL1 0.013 0.036 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.022 0.15 -10000 0 -0.4 90 90
AR -0.059 0.2 0.22 1 -0.62 90 91
UBA3 0.017 0.02 -10000 0 -10000 0 0
PATZ1 0.028 0.02 -10000 0 -10000 0 0
PAWR 0.018 0.017 -10000 0 -10000 0 0
PRKDC 0.024 0.016 -10000 0 -10000 0 0
PA2G4 0.032 0.026 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.019 0.13 -10000 0 -0.35 93 93
RPS6KA3 0.01 0.048 -10000 0 -0.6 2 2
T-DHT/AR/ARA70 -0.033 0.14 -10000 0 -0.4 91 91
LATS2 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.016 0.14 0.22 1 -0.36 92 93
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.016 0.058 0.27 14 -0.6 3 17
KLK2 -0.089 0.3 0.3 12 -1 73 85
CASP8 0.027 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.025 0.13 -10000 0 -0.37 79 79
TMPRSS2 -0.13 0.35 -10000 0 -1 109 109
CCND1 0.012 0.044 0.27 1 -0.6 3 4
PIAS1 0.009 0.045 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.032 0.062 2 -0.072 149 151
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.002 0.064 -10000 0 -0.19 16 16
T-DHT/AR/CDK6 -0.029 0.15 -10000 0 -0.38 104 104
CMTM2 0.023 0.013 0.26 1 -10000 0 1
SNURF 0.01 0.091 -10000 0 -0.6 18 18
ZMIZ1 0.009 0.043 -10000 0 -10000 0 0
CCND3 0.025 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.02 -10000 0 -10000 0 0
FKBP4 0.013 0.038 0.27 4 -10000 0 4
IL27-mediated signaling events

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
TGFB1 0.025 0.008 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.023 0.11 0.48 5 -0.6 2 7
IL27/IL27R/JAK1 0.056 0.15 0.8 3 -0.72 5 8
TBX21 0.007 0.17 0.45 16 -0.54 36 52
IL12B 0.072 0.099 0.28 156 -10000 0 156
IL12A -0.017 0.11 0.15 11 -0.45 47 58
IL6ST -0.008 0.14 0.2 1 -0.6 43 44
IL27RA/JAK1 0.023 0.076 0.65 1 -1.2 2 3
IL27 0.046 0.075 0.28 76 -10000 0 76
TYK2 0.031 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.11 0.17 0.76 2 -0.56 8 10
T-helper 2 cell differentiation -0.023 0.11 0.48 5 -0.6 2 7
T cell proliferation during immune response -0.023 0.11 0.48 5 -0.6 2 7
MAPKKK cascade 0.023 0.11 0.6 2 -0.48 5 7
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.025 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.038 0.27 18 -10000 0 18
IL12RB1 0.032 0.049 0.28 25 -0.6 1 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.018 0.19 0.45 27 -0.54 41 68
IL27/IL27R/JAK2/TYK2 0.023 0.11 0.6 2 -0.48 5 7
positive regulation of T cell mediated cytotoxicity 0.023 0.11 0.6 2 -0.48 5 7
STAT1 (dimer) 0.051 0.2 0.6 29 -0.68 12 41
JAK2 0.028 0.013 -10000 0 -10000 0 0
JAK1 0.023 0.013 -10000 0 -10000 0 0
STAT2 (dimer) 0.035 0.11 0.5 2 -0.5 4 6
T cell proliferation -0.097 0.19 0.35 3 -0.44 78 81
IL12/IL12R/TYK2/JAK2 0.053 0.19 0.46 3 -0.74 24 27
IL17A -0.11 0.17 0.76 2 -0.56 8 10
mast cell activation -0.023 0.11 0.48 5 -0.6 2 7
IFNG 0.024 0.048 0.13 106 -0.11 4 110
T cell differentiation 0 0.006 0.014 17 -0.019 8 25
STAT3 (dimer) 0.035 0.11 0.5 2 -0.5 4 6
STAT5A (dimer) 0.032 0.12 0.5 2 -0.48 9 11
STAT4 (dimer) 0.023 0.13 0.5 2 -0.43 22 24
STAT4 0 0.12 0.27 1 -0.6 32 33
T cell activation -0.005 0.011 0.12 2 -0.12 4 6
IL27R/JAK2/TYK2 0.035 0.12 -10000 0 -0.92 3 3
GATA3 -0.027 0.27 0.6 30 -1.3 27 57
IL18 0.009 0.022 0.14 21 -10000 0 21
positive regulation of mast cell cytokine production 0.034 0.11 0.5 2 -0.49 4 6
IL27/EBI3 0.05 0.072 0.26 36 -0.45 4 40
IL27RA 0.011 0.078 0.75 1 -1.3 2 3
IL6 -0.2 0.3 0.27 1 -0.6 304 305
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.015 0.044 0.45 2 -0.54 1 3
IL1B 0.002 0.048 0.14 2 -0.45 9 11
EBI3 0.024 0.052 0.27 7 -0.61 4 11
TNF 0.005 0.046 0.14 17 -0.45 7 24
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.014 0.17 0.31 3 -0.42 105 108
AKT1 0.025 0.009 -10000 0 -10000 0 0
GSC -0.041 0.3 -10000 0 -1.4 38 38
NKX2-5 0.052 0.082 0.27 104 -10000 0 104
muscle cell differentiation -0.025 0.064 0.34 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.056 0.075 -10000 0 -10000 0 0
SMAD4 0.008 0.048 -10000 0 -10000 0 0
CBFB 0.022 0.008 -10000 0 -10000 0 0
SAP18 0.023 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.21 0.27 1 -0.38 320 321
SMAD3/SMAD4/VDR 0.048 0.065 -10000 0 -0.36 1 1
MYC 0.003 0.091 -10000 0 -0.6 18 18
CDKN2B -0.046 0.17 -10000 0 -0.75 21 21
AP1 -0.067 0.18 -10000 0 -0.33 241 241
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.088 -10000 0 -0.36 25 25
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.057 -10000 0 -0.35 10 10
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.035 0.07 0.27 59 -10000 0 59
SMAD3/SMAD4/GR 0.022 0.072 -10000 0 -0.42 6 6
GATA3 0.013 0.12 0.27 26 -0.58 28 54
SKI/SIN3/HDAC complex/NCoR1 0.004 0.078 -10000 0 -0.35 28 28
MEF2C/TIF2 0.03 0.077 0.31 3 -0.39 3 6
endothelial cell migration -0.029 0.087 0.53 9 -10000 0 9
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.022 0.27 7 -10000 0 7
RBBP4 0.024 0.005 -10000 0 -10000 0 0
RUNX2 0.027 0.028 0.27 11 -10000 0 11
RUNX3 0.023 0.033 0.27 2 -0.6 2 4
RUNX1 0.023 0.022 -10000 0 -0.6 1 1
CTBP1 0.024 0.005 -10000 0 -10000 0 0
NR3C1 0.016 0.055 -10000 0 -0.6 6 6
VDR 0.024 0.003 -10000 0 -10000 0 0
CDKN1A 0.016 0.07 -10000 0 -0.96 2 2
KAT2B 0.025 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.046 0.077 -10000 0 -0.29 12 12
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.024 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.087 -10000 0 -0.54 8 8
SMAD3/SMAD4/ATF2 0.03 0.06 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.023 0.16 -10000 0 -0.43 95 95
SAP30 0.024 0.015 0.27 3 -10000 0 3
Cbp/p300/PIAS3 0.046 0.03 -10000 0 -10000 0 0
JUN -0.075 0.17 0.29 1 -0.32 235 236
SMAD3/SMAD4/IRF7 0.044 0.08 0.34 16 -10000 0 16
TFE3 0.029 0.01 -10000 0 -0.21 1 1
COL1A2 0.049 0.088 0.29 48 -0.52 4 52
mesenchymal cell differentiation -0.032 0.062 -10000 0 -10000 0 0
DLX1 0.053 0.11 0.27 122 -0.6 8 130
TCF3 0.024 0.005 -10000 0 -10000 0 0
FOS -0.16 0.29 -10000 0 -0.6 253 253
SMAD3/SMAD4/Max 0.025 0.061 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.045 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.01 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.058 -10000 0 -10000 0 0
IRF7 0.04 0.061 0.28 47 -10000 0 47
ESR1 -0.031 0.24 0.27 109 -0.6 106 215
HNF4A 0.023 0.029 0.27 11 -10000 0 11
MEF2C 0.051 0.096 0.4 10 -0.45 2 12
SMAD2-3/SMAD4 0.029 0.069 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.046 0.027 -10000 0 -0.39 1 1
IGHV3OR16-13 0.004 0.043 -10000 0 -0.35 11 11
TGIF2/HDAC complex 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.027 0.027 0.27 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.039 0.064 -10000 0 -0.49 1 1
MSG1/HSC70 -0.16 0.24 -10000 0 -0.45 338 338
SMAD2 0.021 0.032 -10000 0 -10000 0 0
SMAD3 0.011 0.043 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.041 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 0.022 0.05 0.25 7 -0.34 2 9
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
NCOA1 0.024 0.022 -10000 0 -0.6 1 1
MYOD/E2A 0.032 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.075 0.066 -10000 0 -10000 0 0
IFNB1 0.018 0.076 0.33 28 -10000 0 28
SMAD3/SMAD4/MEF2C 0.066 0.091 -10000 0 -0.55 1 1
CITED1 -0.23 0.31 0.27 9 -0.6 337 346
SMAD2-3/SMAD4/ARC105 0.037 0.07 -10000 0 -10000 0 0
RBL1 0.024 0.01 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.063 -10000 0 -0.43 8 8
RUNX1-3/PEBPB2 0.041 0.037 -10000 0 -0.55 2 2
SMAD7 -0.044 0.15 -10000 0 -0.45 25 25
MYC/MIZ-1 0.013 0.071 -10000 0 -0.45 18 18
SMAD3/SMAD4 0.029 0.074 0.31 17 -0.36 3 20
IL10 0.004 0.088 0.34 2 -0.39 24 26
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.024 0.006 -10000 0 -10000 0 0
CDK2 0.026 0.007 -10000 0 -10000 0 0
IL5 0.003 0.09 0.3 1 -0.38 26 27
CDK4 0.026 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.051 0.2 -10000 0 -0.6 95 95
SMAD3/SMAD4/SP1 0.044 0.067 -10000 0 -10000 0 0
FOXG1 0.017 0.069 0.27 54 -10000 0 54
FOXO3 0.01 0.02 -10000 0 -0.45 1 1
FOXO1 0.009 0.023 -10000 0 -0.45 1 1
FOXO4 0.012 0.009 -10000 0 -10000 0 0
heart looping 0.05 0.095 0.4 10 -0.45 2 12
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.049 0.092 0.3 2 -0.41 8 10
MYOD1 0.021 0.026 0.27 9 -10000 0 9
SMAD3/SMAD4/HNF4 0.029 0.061 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.025 0.11 -10000 0 -0.42 28 28
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.027 0.27 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.04 0.072 -10000 0 -0.53 2 2
SMAD3/SMAD4/SP1-3 0.055 0.069 -10000 0 -10000 0 0
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.069 0.09 0.35 7 -0.39 1 8
ITGB5 0.014 0.044 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.012 0.064 -10000 0 -0.3 22 22
SMAD3/SMAD4/AR -0.016 0.15 -10000 0 -0.42 88 88
AR -0.043 0.2 0.27 1 -0.6 90 91
negative regulation of cell growth -0.002 0.086 -10000 0 -0.34 12 12
SMAD3/SMAD4/MYOD 0.028 0.061 -10000 0 -10000 0 0
E2F5 0.022 0.023 0.27 6 -10000 0 6
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.06 0.072 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.051 -10000 0 -0.35 9 9
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.052 0.19 -10000 0 -0.33 235 235
SMAD3/SMAD4/RUNX2 0.032 0.062 -10000 0 -10000 0 0
TGIF2 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.024 0.003 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.028 0.032 0.27 14 -10000 0 14
GNB1/GNG2 -0.014 0.046 -10000 0 -0.19 42 42
AKT1 0.024 0.094 0.35 11 -0.28 23 34
EGF -0.091 0.24 0.27 2 -0.6 153 155
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.058 0.25 2 -0.27 3 5
mol:Ca2+ 0.025 0.11 0.41 10 -0.3 53 63
LYN 0.012 0.054 0.25 2 -0.26 1 3
RhoA/GTP 0.01 0.044 0.14 4 -0.14 19 23
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.022 0.12 0.44 10 -0.35 44 54
GNG2 0.019 0.053 -10000 0 -0.6 6 6
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.61 29 29
G beta5/gamma2 -0.011 0.063 -10000 0 -0.26 42 42
PRKCH 0.021 0.12 0.42 10 -0.35 46 56
DNM1 0.021 0.049 0.27 1 -0.6 5 6
TXA2/TP beta/beta Arrestin3 0.007 0.032 -10000 0 -0.4 2 2
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
PTGDR 0.01 0.1 0.27 6 -0.6 21 27
G12 family/GTP 0.002 0.086 -10000 0 -0.31 41 41
ADRBK1 0.023 0.007 -10000 0 -10000 0 0
ADRBK2 0.022 0.031 -10000 0 -0.6 2 2
RhoA/GTP/ROCK1 0.032 0.008 -10000 0 -10000 0 0
mol:GDP -0.012 0.099 0.36 24 -0.33 8 32
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 0.001 0.12 -10000 0 -0.6 31 31
mol:IP3 0.023 0.13 0.47 8 -0.37 54 62
cell morphogenesis 0.031 0.008 -10000 0 -10000 0 0
PLCB2 0.015 0.17 0.59 5 -0.51 54 59
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.023 0.069 0.26 6 -0.28 3 9
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.059 0.26 3 -0.31 1 4
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.025 0.009 0.27 1 -10000 0 1
PRKCB1 0.022 0.13 0.43 10 -0.37 49 59
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.019 0.16 0.61 5 -0.53 45 50
LCK 0.015 0.072 0.25 2 -0.36 10 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.26 21 21
TXA2-R family/G12 family/GDP/G beta/gamma 0.005 0.11 -10000 0 -0.42 44 44
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.26 19 19
MAPK14 0.021 0.089 0.37 11 -0.23 41 52
TGM2/GTP 0.019 0.14 0.51 8 -0.42 50 58
MAPK11 0.019 0.09 0.36 13 -0.24 40 53
ARHGEF1 0.012 0.066 0.28 9 -0.18 34 43
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.024 0.13 0.45 10 -0.39 45 55
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.025 0.1 0.4 11 -0.28 43 54
cAMP biosynthetic process 0.02 0.12 0.43 9 -0.35 51 60
Gq family/GTP/EBP50 0.016 0.042 0.22 4 -0.3 3 7
actin cytoskeleton reorganization 0.031 0.008 -10000 0 -10000 0 0
SRC 0.012 0.056 0.25 2 -0.31 1 3
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.049 0.11 0.26 2 -0.29 58 60
VCAM1 0.023 0.11 0.41 10 -0.31 43 53
TP beta/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.61 29 29
platelet activation 0.026 0.12 0.43 12 -0.31 43 55
PGI2/IP 0.018 0.006 0.18 1 -10000 0 1
PRKACA 0.009 0.051 -10000 0 -0.3 22 22
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.54 21 21
TXA2/TP beta/beta Arrestin2 -0.008 0.068 -10000 0 -0.43 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.045 -10000 0 -0.28 20 20
mol:DAG 0.022 0.14 0.48 8 -0.42 50 58
EGFR -0.19 0.3 -10000 0 -0.6 281 281
TXA2/TP alpha 0.019 0.16 0.53 7 -0.48 51 58
Gq family/GTP 0.002 0.049 0.25 1 -0.22 31 32
YES1 0.014 0.059 0.25 2 -0.28 4 6
GNAI2/GTP 0.014 0.048 -10000 0 -0.27 10 10
PGD2/DP 0.007 0.075 0.18 6 -0.44 22 28
SLC9A3R1 0.037 0.057 0.27 47 -10000 0 47
FYN 0.012 0.057 0.26 1 -0.29 4 5
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.024 0.027 0.27 3 -0.6 1 4
PGK/cGMP 0.017 0.079 -10000 0 -0.38 31 31
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.036 0.066 -10000 0 -0.38 7 7
NOS3 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.024 0.13 0.42 11 -0.39 40 51
PRKCB 0.024 0.13 0.41 11 -0.37 44 55
PRKCE 0.022 0.12 0.44 9 -0.35 45 54
PRKCD 0.02 0.12 0.46 8 -0.38 42 50
PRKCG 0.023 0.13 0.47 8 -0.38 45 53
muscle contraction 0.019 0.16 0.54 7 -0.48 49 56
PRKCZ 0.021 0.12 0.42 10 -0.34 44 54
ARR3 0.021 0.021 0.27 6 -10000 0 6
TXA2/TP beta 0.024 0.055 -10000 0 -0.27 21 21
PRKCQ 0.018 0.14 0.43 11 -0.39 47 58
MAPKKK cascade 0.019 0.15 0.5 7 -0.45 52 59
SELE 0.019 0.12 0.39 11 -0.39 43 54
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.064 -10000 0 -0.4 6 6
ROCK1 0.024 0.004 -10000 0 -10000 0 0
GNA14 0.025 0.065 0.27 19 -0.6 6 25
chemotaxis 0.018 0.18 0.64 5 -0.61 43 48
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.084 0.27 1 -0.6 15 16
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.096 0.13 -10000 0 -0.25 321 321
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.01 0.27 1 -10000 0 1
p38 alpha/TAB1 -0.041 0.098 -10000 0 -0.35 56 56
PRKG1 0.001 0.12 -10000 0 -0.6 31 31
DUSP8 0.021 0.038 -10000 0 -0.6 3 3
PGK/cGMP/p38 alpha -0.014 0.13 -10000 0 -0.36 63 63
apoptosis -0.04 0.094 -10000 0 -0.33 56 56
RAL/GTP 0.032 0.007 -10000 0 -10000 0 0
LYN 0.021 0.009 -10000 0 -10000 0 0
DUSP1 -0.054 0.21 -10000 0 -0.6 103 103
PAK1 0.023 0.017 0.27 3 -10000 0 3
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.025 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.031 0.009 -10000 0 -10000 0 0
MAPK11 -0.012 0.13 0.33 4 -0.4 42 46
BLK 0.046 0.086 0.27 95 -0.6 2 97
HCK 0.028 0.029 0.27 12 -10000 0 12
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.013 0.27 1 -10000 0 1
TRAF6/MEKK3 0.028 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.007 0.13 0.31 4 -0.39 50 54
positive regulation of innate immune response -0.013 0.15 0.37 4 -0.45 48 52
LCK 0.024 0.077 0.27 23 -0.6 9 32
p38alpha-beta/MKP7 -0.005 0.15 0.44 2 -0.45 40 42
p38alpha-beta/MKP5 -0.006 0.14 0.44 2 -0.46 36 38
PGK/cGMP 0.001 0.088 -10000 0 -0.45 31 31
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.041 0.18 0.38 3 -0.45 71 74
CDC42 0.024 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.26 0.31 -10000 0 -0.6 370 370
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.022 0.008 -10000 0 -10000 0 0
ELF1 0.032 0.05 -10000 0 -0.37 6 6
CCNA2 0.12 0.12 0.27 347 -10000 0 347
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.029 0.27 12 -10000 0 12
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.049 0.1 0.32 16 -0.53 8 24
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.027 0.032 -10000 0 -0.37 5 5
IL2RA 0.023 0.11 0.3 52 -0.76 9 61
IL2RB 0.033 0.048 0.27 33 -10000 0 33
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.27 32 -0.6 5 37
G1/S transition of mitotic cell cycle 0.054 0.12 0.32 3 -0.79 10 13
PTPN11 0.025 0.002 -10000 0 -10000 0 0
CCND2 0.009 0.072 0.36 2 -0.81 6 8
LCK 0.024 0.077 0.27 23 -0.6 9 32
GRB2 0.024 0.011 0.27 1 -10000 0 1
IL2 0.023 0.025 0.27 8 -10000 0 8
CDK6 0.022 0.045 0.27 2 -0.6 4 6
CCND3 0.048 0.1 0.39 5 -0.64 3 8
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.024 0.016 0.27 1 -10000 0 1
CDKN2C 0.015 0.03 -10000 0 -0.58 1 1
CDKN2A 0.058 0.085 0.27 118 -10000 0 118
CCND2 -0.015 0.037 0.18 1 -0.25 9 10
RB1 0.014 0.049 0.29 11 -0.24 6 17
CDK4 -0.017 0.045 0.21 1 -0.34 8 9
CDK6 -0.016 0.049 0.26 5 -0.25 15 20
G1/S progression -0.009 0.063 0.19 34 -0.32 12 46
BCR signaling pathway

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
JUN 0.018 0.13 0.32 11 -0.4 34 45
IKBKB 0.023 0.091 0.31 7 -0.32 7 14
AKT1 0.036 0.11 0.27 56 -0.25 11 67
IKBKG 0.027 0.075 0.32 5 -0.28 3 8
CALM1 0 0.1 0.26 1 -0.46 15 16
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.017 0.17 0.36 10 -0.53 39 49
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0.11 -10000 0 -0.36 40 40
DOK1 0.024 0.003 -10000 0 -10000 0 0
AP-1 -0.03 0.1 0.26 6 -0.26 40 46
LYN 0.021 0.009 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
BCR complex -0.006 0.17 0.38 8 -0.48 78 86
CD22 -0.02 0.14 0.3 11 -0.47 50 61
CAMK2G 0.001 0.1 0.3 1 -0.43 15 16
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.003 0.096 -10000 0 -0.36 41 41
GO:0007205 0 0.11 -10000 0 -0.37 40 40
SYK 0.024 0.004 -10000 0 -10000 0 0
ELK1 0 0.11 0.26 1 -0.45 17 18
NFATC1 0.027 0.14 0.31 16 -0.45 28 44
B-cell antigen/BCR complex -0.006 0.17 0.38 8 -0.48 78 86
PAG1/CSK 0.029 0.017 -10000 0 -10000 0 0
NFKBIB 0.025 0.047 0.17 9 -0.13 16 25
HRAS 0.009 0.11 0.27 11 -0.39 25 36
NFKBIA 0.025 0.046 0.17 9 -0.13 9 18
NF-kappa-B/RelA/I kappa B beta 0.028 0.042 0.17 9 -10000 0 9
RasGAP/Csk 0.023 0.13 0.34 8 -0.39 58 66
mol:GDP 0.002 0.1 -10000 0 -0.44 17 17
PTEN 0.023 0.031 -10000 0 -0.6 2 2
CD79B 0.005 0.11 0.27 8 -0.6 25 33
NF-kappa-B/RelA/I kappa B alpha 0.028 0.041 0.17 9 -10000 0 9
GRB2 0.023 0.011 0.27 1 -10000 0 1
PI3K/BCAP/CD19 0.019 0.17 0.35 9 -0.5 40 49
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.11 -10000 0 -0.37 40 40
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.092 0.17 -10000 0 -0.45 67 67
CHUK 0.024 0.083 0.32 5 -0.29 14 19
IBTK 0.024 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.016 0.1 -10000 0 -0.42 15 15
PTPN6 -0.02 0.13 0.29 9 -0.58 27 36
RELA 0.024 0.004 -10000 0 -10000 0 0
BCL2A1 0.026 0.036 0.16 11 -10000 0 11
VAV2 0.009 0.15 0.3 10 -0.59 26 36
ubiquitin-dependent protein catabolic process 0.027 0.047 0.17 9 -0.13 17 26
BTK 0.015 0.07 -10000 0 -0.97 4 4
CD19 -0.002 0.14 0.29 19 -0.46 47 66
MAP4K1 0.03 0.051 0.27 24 -0.6 2 26
CD72 0.028 0.04 0.27 16 -0.6 1 17
PAG1 0.02 0.016 0.27 2 -10000 0 2
MAPK14 0.019 0.15 0.36 11 -0.45 37 48
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0 0.12 -10000 0 -0.45 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.003 0.14 0.28 3 -0.44 58 61
RAF1 0.008 0.11 0.28 5 -0.43 16 21
RasGAP/p62DOK/SHIP 0.023 0.13 0.31 8 -0.38 58 66
CD79A -0.01 0.18 0.27 52 -0.6 65 117
re-entry into mitotic cell cycle -0.03 0.1 0.26 6 -0.26 39 45
RASA1 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.1 0.33 7 -0.38 11 18
MAPK1 0.008 0.096 0.28 6 -0.38 14 20
CD72/SHP1 0.023 0.15 0.38 15 -0.55 27 42
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.15 0.34 14 -0.45 38 52
actin cytoskeleton organization 0.025 0.14 0.32 18 -0.53 23 41
NF-kappa-B/RelA 0.058 0.08 0.3 9 -0.21 1 10
Calcineurin 0.015 0.096 -10000 0 -0.41 13 13
PI3K -0.015 0.1 -10000 0 -0.46 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.003 0.12 -10000 0 -0.4 44 44
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.003 0.21 0.46 5 -0.73 43 48
DAPP1 -0.025 0.22 -10000 0 -0.81 45 45
cytokine secretion 0.028 0.13 0.3 19 -0.42 28 47
mol:DAG 0 0.11 -10000 0 -0.37 40 40
PLCG2 0.021 0.025 0.27 1 -0.6 1 2
MAP2K1 0.008 0.1 0.28 7 -0.42 14 21
B-cell antigen/BCR complex/FcgammaRIIB 0.006 0.14 0.35 8 -0.45 58 66
mol:PI-3-4-5-P3 0.005 0.094 0.23 21 -0.33 19 40
ETS1 -0.001 0.093 0.28 1 -0.41 15 16
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.025 0.14 0.33 9 -0.39 60 69
B-cell antigen/BCR complex/LYN -0.018 0.14 0.31 5 -0.47 55 60
MALT1 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.017 0.15 0.31 15 -0.57 23 38
B-cell antigen/BCR complex/LYN/SYK 0.006 0.14 0.37 11 -0.46 48 59
CARD11 0.002 0.11 0.32 2 -0.47 17 19
FCGR2B 0.018 0.039 0.27 1 -0.6 3 4
PPP3CA 0.024 0.009 0.27 1 -10000 0 1
BCL10 0.024 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.15 44 -0.13 2 46
PTPRC 0.023 0.038 0.27 12 -0.6 1 13
PDPK1 0.02 0.085 0.23 38 -0.23 17 55
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.01 -10000 0 -10000 0 0
POU2F2 0.022 0.033 0.17 9 -10000 0 9
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.05 0.065 0.28 1 -0.32 13 14
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.08 0.34 11 -0.33 1 12
alphaV/beta3 Integrin/Osteopontin/Src 0.086 0.076 0.25 2 -10000 0 2
AP1 -0.043 0.18 -10000 0 -0.53 21 21
ILK 0.038 0.067 -10000 0 -0.34 11 11
bone resorption 0.03 0.062 -10000 0 -0.52 1 1
PTK2B 0.02 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.074 0.088 0.34 2 -0.32 11 13
ITGAV 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.034 0.025 -10000 0 -0.45 2 2
alphaV/beta3 Integrin/Osteopontin 0.088 0.094 0.35 4 -0.37 13 17
MAP3K1 0.038 0.068 0.26 12 -0.34 13 25
JUN 0.018 0.061 -10000 0 -0.6 8 8
MAPK3 0.027 0.065 0.27 11 -0.33 10 21
MAPK1 0.028 0.066 0.28 9 -0.33 10 19
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.066 0.26 14 -0.33 11 25
ITGB3 0.017 0.08 0.27 4 -0.6 13 17
NFKBIA 0.026 0.068 0.34 8 -0.32 9 17
FOS -0.17 0.29 -10000 0 -0.6 251 251
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.028 0.1 0.45 6 -0.56 2 8
NF kappa B1 p50/RelA 0.072 0.073 0.36 6 -10000 0 6
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.032 0.063 -10000 0 -0.44 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.038 0.068 0.26 12 -0.34 13 25
VAV3 0.017 0.071 0.26 15 -0.33 12 27
MAP3K14 0.039 0.068 0.26 10 -0.34 13 23
ROCK2 0.023 0.031 -10000 0 -0.6 2 2
SPP1 0.094 0.11 0.27 232 -10000 0 232
RAC1 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.036 0.062 0.32 2 -0.31 11 13
MMP2 -0.059 0.15 0.36 3 -0.52 18 21
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.28 0.31 -10000 0 -0.6 401 401
CLTC 0.027 0.071 0.24 8 -0.45 10 18
calcium ion-dependent exocytosis 0.009 0.023 -10000 0 -0.25 1 1
Dynamin 2/GTP 0.021 0.012 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.016 0.046 -10000 0 -0.33 9 9
CPE 0.006 0.048 0.15 1 -0.39 12 13
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.018 -10000 0 -0.17 2 2
CTNND1 0.009 0.06 0.2 34 -10000 0 34
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.047 0.22 2 -0.32 8 10
TSHR -0.004 0.077 0.15 3 -0.39 32 35
INS -0.002 0.094 -10000 0 -0.48 29 29
BIN1 0.018 0.061 -10000 0 -0.6 8 8
mol:Choline 0.011 0.018 -10000 0 -0.17 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.013 0.15 7 -10000 0 7
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.012 -10000 0 -10000 0 0
JUP 0.017 0.039 0.24 1 -0.32 5 6
ASAP2/amphiphysin II 0.041 0.04 -10000 0 -0.31 9 9
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.058 -10000 0 -0.28 20 20
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.029 0.27 12 -10000 0 12
substrate adhesion-dependent cell spreading 0.016 0.041 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.069 0.34 9 -10000 0 9
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.014 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.015 0.045 -10000 0 -0.34 8 8
clathrin heavy chain/ACAP1 0.025 0.067 0.25 12 -0.36 10 22
JIP4/KLC1 0.041 0.017 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.018 0.037 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.009 0.061 0.36 2 -10000 0 2
NME1 0.012 0.013 0.15 7 -10000 0 7
clathrin coat assembly 0.029 0.074 0.24 10 -0.44 10 20
IL2RA 0.02 0.055 0.19 1 -0.29 16 17
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.13 0.15 -10000 0 -0.28 346 346
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.027 -10000 0 -0.31 5 5
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.043 0.2 1 -0.34 7 8
SDC1 0.02 0.046 0.2 2 -0.33 7 9
ARF6/GDP 0.021 0.012 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.041 0.071 -10000 0 -0.35 9 9
mol:Phosphatidic acid 0.011 0.018 -10000 0 -0.17 2 2
endocytosis -0.039 0.04 0.31 9 -10000 0 9
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.048 0.15 0.25 2 -0.32 167 169
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.022 -10000 0 -0.6 1 1
Dynamin 2/GDP 0.024 0.015 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.1 0.17 0.28 4 -0.31 288 292
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.07 0.32 2 -0.37 5 7
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.025 0.048 0.14 118 -10000 0 118
TP53 0.009 0.019 -10000 0 -0.19 2 2
Senescence 0.008 0.022 -10000 0 -0.19 2 2
Apoptosis 0.008 0.022 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.063 0.29 27 -10000 0 27
MDM4 0.02 0.01 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.023 0.087 -10000 0 -0.62 7 7
oxygen homeostasis 0.012 0.013 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.27 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.089 0.083 0.34 8 -0.33 1 9
EPO 0.16 0.18 0.54 68 -0.51 2 70
FIH (dimer) 0.033 0.019 -10000 0 -10000 0 0
APEX1 0.034 0.024 -10000 0 -10000 0 0
SERPINE1 0.15 0.16 0.53 31 -0.57 2 33
FLT1 -0.012 0.16 -10000 0 -0.66 26 26
ADORA2A 0.17 0.17 0.5 71 -0.55 2 73
germ cell development 0.14 0.16 0.52 31 -0.55 2 33
SLC11A2 0.15 0.15 0.51 28 -0.57 2 30
BHLHE40 0.14 0.16 0.54 17 -0.59 3 20
HIF1AN 0.033 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.13 0.13 0.42 49 -0.38 1 50
ETS1 0.027 0.027 -10000 0 -0.46 2 2
CITED2 0.016 0.085 -10000 0 -0.55 9 9
KDR -0.008 0.15 -10000 0 -0.67 21 21
PGK1 0.15 0.16 0.49 36 -0.52 3 39
SIRT1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0.002 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.62 15 -0.57 4 19
EPAS1 0.079 0.089 0.3 45 -0.36 1 46
SP1 0.029 0.01 -10000 0 -10000 0 0
ABCG2 0.13 0.2 0.51 29 -0.58 23 52
EFNA1 0.12 0.14 0.54 8 -0.57 2 10
FXN 0.16 0.15 0.48 45 -0.49 4 49
POU5F1 0.15 0.16 0.57 21 -0.57 2 23
neuron apoptosis -0.16 0.17 0.56 4 -0.62 15 19
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.052 0.07 0.28 65 -10000 0 65
EGLN2 0.035 0.024 0.27 3 -10000 0 3
EGLN1 0.027 0.03 -10000 0 -0.61 1 1
VHL/Elongin B/Elongin C 0.039 0.023 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.03 0.024 -10000 0 -10000 0 0
SLC2A1 0.16 0.16 0.48 51 -0.55 2 53
TWIST1 0.15 0.18 0.48 41 -0.54 23 64
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.11 0.11 0.46 7 -0.38 1 8
VEGFA 0.14 0.16 0.52 27 -0.57 2 29
CREBBP 0.023 0.007 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.014 0.059 -10000 0 -10000 0 0
PLK1 0.28 0.19 0.53 183 -0.58 1 184
CDKN1B 0.17 0.14 0.4 54 -0.48 4 58
FOXO3 0.22 0.17 0.48 167 -0.63 1 168
KAT2B 0.061 0.03 -10000 0 -10000 0 0
FOXO1/SIRT1 0.01 0.053 -10000 0 -0.36 2 2
CAT 0.21 0.17 0.52 52 -0.89 3 55
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.062 0.032 -10000 0 -10000 0 0
FOXO1 0.019 0.061 -10000 0 -0.38 2 2
MAPK10 -0.018 0.13 0.2 13 -0.32 122 135
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.037 0.086 0.39 4 -0.33 2 6
response to oxidative stress 0.04 0.029 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.19 0.14 0.4 149 -0.61 1 150
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.07 0.085 -10000 0 -0.7 6 6
FOXO1/SKP2 0.028 0.057 -10000 0 -0.4 1 1
mol:GDP 0.04 0.029 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.14 0.13 0.48 3 -0.53 9 12
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.022 0.13 -10000 0 -0.53 27 27
MST1 0.054 0.067 0.3 1 -0.54 8 9
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.13 -10000 0 -0.46 36 36
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.034 0.027 0.2 15 -10000 0 15
MAPK9 0.033 0.028 0.21 11 -10000 0 11
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
SIRT1 0.009 0.021 -10000 0 -10000 0 0
SOD2 0.16 0.14 0.49 13 -0.51 1 14
RBL2 0.12 0.26 0.57 2 -0.64 43 45
RAL/GDP 0.06 0.023 -10000 0 -10000 0 0
CHUK 0.062 0.031 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.06 0.023 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.073 0.14 -10000 0 -1.2 7 7
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.05 0.036 -10000 0 -10000 0 0
CCNB1 0.23 0.18 0.53 153 -0.58 1 154
FOXO1-3a-4/beta catenin 0.16 0.13 0.41 49 -0.38 2 51
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.057 -10000 0 -0.4 1 1
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
SGK1 0.057 0.05 -10000 0 -0.59 3 3
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.034 0.077 0.41 2 -10000 0 2
SFN 0.018 0.073 0.27 8 -0.6 10 18
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.068 0.11 0.36 1 -0.42 12 13
CREBBP 0.022 0.008 -10000 0 -10000 0 0
FBXO32 0.26 0.22 0.59 135 -1.2 3 138
BCL6 0.18 0.15 0.52 5 -0.74 6 11
RALB 0.025 0.004 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.009 0.013 0.23 2 -10000 0 2
SNTA1 0.024 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.037 0.3 7 -10000 0 7
MAPK12 0.005 0.076 0.21 58 -0.35 18 76
CCND1 0.011 0.05 -10000 0 -0.38 6 6
p38 gamma/SNTA1 0.022 0.074 0.33 2 -0.34 16 18
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.006 0.077 0.21 62 -0.35 18 80
MAP2K6 -0.004 0.054 -10000 0 -0.37 18 18
MAPT -0.024 0.12 0.26 13 -0.34 83 96
MAPK13 0.01 0.013 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.023 -10000 0 -0.36 3 3
Signaling events mediated by PRL

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
CCNE1 0.061 0.088 0.27 127 -10000 0 127
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.022 0.031 -10000 0 -0.6 2 2
CDKN1A -0.036 0.098 -10000 0 -0.45 23 23
PRL-3/alpha Tubulin 0.029 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.081 0.24 35 -0.45 11 46
AGT 0.031 0.1 0.27 66 -0.6 11 77
CCNA2 -0.074 0.15 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.14 0.21 0.18 1 -0.44 277 278
CDK2/Cyclin E1 0.009 0.12 -10000 0 -0.52 12 12
MAPK3 0.009 0.014 0.26 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.009 0.016 0.26 3 -10000 0 3
PTP4A1 -0.11 0.16 -10000 0 -10000 0 0
PTP4A3 0.02 0.013 0.27 1 -10000 0 1
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.009 0.014 0.26 2 -10000 0 2
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 -0.024 0.082 -10000 0 -0.42 16 16
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.087 0.16 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.011 -10000 0 -10000 0 0
RHOC -0.026 0.088 -10000 0 -0.44 19 19
RHOA -0.029 0.097 -10000 0 -0.48 23 23
cell motility -0.032 0.1 -10000 0 -0.38 30 30
PRL-1/alpha Tubulin -0.088 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.025 -10000 0 -0.34 2 2
ROCK1 -0.031 0.1 -10000 0 -0.39 28 28
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.025 0.002 -10000 0 -10000 0 0
mitosis -0.11 0.16 -10000 0 -10000 0 0
ATF5 0.025 0.015 0.27 3 -10000 0 3
Caspase cascade in apoptosis

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
TOP1 0.006 0.11 0.24 1 -0.42 35 36
ACTA1 0.01 0.12 0.25 4 -0.51 26 30
NUMA1 0 0.11 -10000 0 -0.42 35 35
SPTAN1 -0.005 0.11 0.3 3 -0.52 25 28
LIMK1 -0.004 0.11 0.3 2 -0.52 25 27
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.024 0.004 -10000 0 -10000 0 0
CASP10 -0.013 0.098 0.22 11 -0.47 27 38
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
PTK2 0 0.13 0.24 1 -0.47 37 38
DIABLO 0.025 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.11 0.28 4 -0.51 25 29
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.01 0.12 0.3 2 -0.5 34 36
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.011 0.14 -10000 0 -0.68 25 25
BID 0.003 0.055 0.19 3 -0.27 26 29
MAP3K1 -0.007 0.1 -10000 0 -0.42 40 40
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.11 0.26 2 -0.51 25 27
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair -0.016 0.045 0.25 4 -0.21 3 7
neuron apoptosis 0.004 0.12 -10000 0 -0.71 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.004 0.12 -10000 0 -0.5 27 27
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 -0.004 0.16 -10000 0 -0.91 22 22
TRAF2 0.024 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.007 0.11 -10000 0 -0.51 24 24
CASP7 0.002 0.062 0.27 4 -0.5 2 6
KRT18 0.016 0.07 -10000 0 -0.65 6 6
apoptosis -0.001 0.12 0.32 2 -0.46 39 41
DFFA -0.006 0.11 0.25 1 -0.51 26 27
DFFB -0.006 0.11 0.25 1 -0.52 25 26
PARP1 0.016 0.045 0.21 3 -0.25 4 7
actin filament polymerization 0.002 0.11 0.51 23 -0.3 6 29
TNF 0.024 0.067 0.27 17 -0.6 7 24
CYCS 0.004 0.052 0.22 5 -0.24 17 22
SATB1 -0.011 0.16 -10000 0 -0.79 27 27
SLK -0.005 0.11 0.27 2 -0.52 25 27
p15 BID/BAX 0.011 0.063 -10000 0 -0.29 17 17
CASP2 0.001 0.067 0.23 7 -0.28 18 25
JNK cascade 0.007 0.1 0.41 40 -10000 0 40
CASP3 -0.003 0.12 0.27 2 -0.53 26 28
LMNB2 -0.003 0.14 0.28 4 -0.51 40 44
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.36 2 2
negative regulation of DNA binding 0.012 0.13 -10000 0 -0.67 25 25
stress fiber formation -0.004 0.11 0.26 3 -0.51 25 28
GZMB 0.008 0.11 0.29 11 -0.53 26 37
CASP1 0.011 0.014 -10000 0 -0.36 1 1
LMNB1 0.02 0.12 0.31 6 -0.53 23 29
APP 0.004 0.12 -10000 0 -0.72 18 18
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.002 -10000 0 -10000 0 0
VIM 0.001 0.13 0.31 3 -0.46 41 44
LMNA 0.006 0.086 0.32 2 -0.38 22 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.071 -10000 0 -0.3 20 20
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.004 0.11 0.29 2 -0.52 24 26
APAF-1/Caspase 9 -0.003 0.12 -10000 0 -0.62 28 28
nuclear fragmentation during apoptosis 0.001 0.11 -10000 0 -0.42 35 35
CFL2 -0.002 0.11 0.3 6 -0.52 23 29
GAS2 -0.032 0.15 0.28 3 -0.4 78 81
positive regulation of apoptosis 0.013 0.12 0.27 8 -0.49 29 37
PRF1 0.015 0.087 0.27 8 -0.6 15 23
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.01 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.029 0.019 -10000 0 -10000 0 0
CDKN1B 0.009 0.06 -10000 0 -0.34 15 15
CDKN1A 0.008 0.064 -10000 0 -0.36 16 16
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
FOXO3 0.011 0.062 -10000 0 -0.37 13 13
AKT1 0.004 0.06 -10000 0 -0.37 16 16
BAD 0.024 0.005 -10000 0 -10000 0 0
AKT3 0.006 0.037 -10000 0 -0.36 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.063 -10000 0 -0.35 18 18
AKT1/ASK1 0.032 0.071 -10000 0 -0.34 14 14
BAD/YWHAZ 0.036 0.023 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.031 0.068 0.33 14 -10000 0 14
TSC1 0.01 0.054 -10000 0 -0.34 12 12
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.075 0.27 1 -0.35 17 18
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.064 -10000 0 -0.36 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.006 0.058 0.32 1 -0.34 16 17
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.004 0.006 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.08 0.33 15 -0.26 4 19
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.066 -10000 0 -0.36 16 16
CASP9 0.011 0.048 -10000 0 -0.32 10 10
YWHAB 0.023 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.076 0.34 3 -0.54 3 6
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.018 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.01 0.062 0.25 3 -0.48 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.056 -10000 0 -0.32 18 18
CHUK 0.009 0.059 -10000 0 -0.33 16 16
BAD/BCL-XL 0.037 0.072 0.29 1 -0.42 7 8
mTORC2 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.032 0.1 0.32 6 -0.44 18 24
PDPK1 0.023 0.007 -10000 0 -10000 0 0
MDM2 0.011 0.069 0.27 2 -0.35 17 19
MAPKKK cascade -0.036 0.074 0.34 17 -0.26 1 18
MDM2/Cbp/p300 0.043 0.078 0.35 3 -0.56 3 6
TSC1/TSC2 0.013 0.071 0.26 29 -0.36 12 41
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.074 0.34 3 -0.53 3 6
glucose import -0.17 0.16 0.21 3 -0.33 397 400
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.052 0.18 1 -0.41 4 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.17 0.16 0.21 3 -0.34 397 400
GSK3A 0.009 0.063 -10000 0 -0.36 16 16
FOXO1 0.011 0.046 -10000 0 -0.37 6 6
GSK3B 0.008 0.063 -10000 0 -0.35 17 17
SFN 0.018 0.073 0.27 8 -0.6 10 18
G1/S transition of mitotic cell cycle 0.013 0.069 0.31 3 -0.35 15 18
p27Kip1/14-3-3 family 0.018 0.053 0.38 1 -0.46 3 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Ceramide signaling pathway

Figure 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
SPHK2 0.01 0.008 -10000 0 -0.2 1 1
MAP4K4 0.002 0.062 -10000 0 -0.36 5 5
BAG4 0.02 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.003 0.057 -10000 0 -0.27 14 14
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BAX 0 0.044 -10000 0 -0.35 10 10
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.068 0.68 8 -10000 0 8
BAD -0.017 0.051 0.19 3 -0.27 11 14
SMPD1 0.014 0.059 0.23 8 -0.24 14 22
RB1 -0.017 0.048 -10000 0 -0.28 10 10
FADD/Caspase 8 0.028 0.092 0.27 10 -0.39 6 16
MAP2K4 -0.018 0.047 0.18 1 -0.3 7 8
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.059 0.27 4 -0.31 6 10
EGF -0.091 0.24 0.27 2 -0.6 153 155
mol:ceramide -0.016 0.052 0.15 1 -0.26 15 16
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.012 -10000 0 -10000 0 0
ASAH1 0.021 0.018 0.27 3 -10000 0 3
negative regulation of cell cycle -0.017 0.048 -10000 0 -0.27 10 10
cell proliferation -0.05 0.13 0.28 1 -0.29 161 162
BID -0.025 0.17 -10000 0 -0.66 51 51
MAP3K1 -0.017 0.049 -10000 0 -0.27 11 11
EIF2A -0.016 0.052 0.29 3 -0.25 7 10
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.009 0.057 0.32 2 -0.32 5 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.061 0.32 2 -0.36 4 6
Cathepsin D/ceramide 0.004 0.062 0.19 8 -0.24 14 22
FADD 0.023 0.084 0.27 1 -0.39 3 4
KSR1 -0.01 0.058 0.2 19 -0.31 7 26
MAPK8 -0.014 0.056 -10000 0 -0.29 9 9
PRKRA -0.017 0.05 0.2 1 -0.27 11 12
PDGFA 0.024 0.005 -10000 0 -10000 0 0
TRAF2 0.024 0.004 -10000 0 -10000 0 0
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.016 0.052 0.15 1 -0.26 15 16
CTSD 0.033 0.046 0.27 30 -10000 0 30
regulation of nitric oxide biosynthetic process 0.035 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.053 0.14 0.3 1 -0.31 161 162
PRKCD 0.024 0.01 0.27 1 -10000 0 1
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.012 -10000 0 -10000 0 0
RelA/NF kappa B1 0.035 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.048 -10000 0 -0.38 5 5
TNFR1A/BAG4/TNF-alpha 0.037 0.048 -10000 0 -0.38 6 6
mol:Sphingosine-1-phosphate 0.01 0.008 -10000 0 -0.2 1 1
MAP2K1 -0.011 0.057 0.32 2 -0.34 4 6
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
CYCS -0.002 0.051 0.24 3 -0.25 9 12
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.028 0.016 -10000 0 -10000 0 0
EIF2AK2 -0.018 0.046 0.18 2 -0.28 7 9
TNF-alpha/TNFR1A/FAN 0.04 0.045 -10000 0 -0.33 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.076 -10000 0 -0.4 19 19
MAP2K2 -0.012 0.057 0.32 2 -0.32 5 7
SMPD3 -0.003 0.1 0.28 4 -0.29 80 84
TNF 0.024 0.067 0.27 17 -0.6 7 24
PKC zeta/PAR4 0.034 0.019 -10000 0 -0.45 1 1
mol:PHOSPHOCHOLINE 0.044 0.1 0.25 151 -0.24 2 153
NF kappa B1/RelA/I kappa B alpha 0.065 0.027 -10000 0 -0.34 1 1
AIFM1 -0.003 0.051 0.18 14 -0.23 11 25
BCL2 0.008 0.098 -10000 0 -0.6 21 21
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.096 0.27 28 -0.6 15 43
CDC42/GTP -0.006 0.097 -10000 0 -0.31 36 36
PLCG1 -0.013 0.088 -10000 0 -0.32 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.012 -10000 0 -10000 0 0
cell migration -0.006 0.095 -10000 0 -0.31 36 36
S1PR5 0.026 0.043 0.27 12 -0.6 2 14
S1PR4 0.024 0.063 0.27 16 -0.6 6 22
MAPK3 -0.01 0.083 0.27 1 -0.32 30 31
MAPK1 -0.009 0.084 -10000 0 -0.32 34 34
S1P/S1P5/Gi -0.003 0.086 -10000 0 -0.28 60 60
GNAI1 -0.005 0.13 -10000 0 -0.6 39 39
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 0.18 10 -0.31 3 13
RHOA 0.005 0.062 0.24 1 -0.33 6 7
S1P/S1P4/Gi -0.004 0.093 -10000 0 -0.29 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
S1P/S1P4/G12/G13 0.041 0.042 -10000 0 -0.35 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.024 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.039 0.058 -10000 0 -0.42 12 12
forebrain development -0.043 0.21 0.35 1 -0.52 105 106
GNAO1 0.018 0.096 0.27 28 -0.6 15 43
SMO/beta Arrestin2 0.027 0.048 -10000 0 -0.45 7 7
SMO 0.017 0.059 -10000 0 -0.6 7 7
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.021 0.086 0.28 1 -0.5 10 11
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.023 0.009 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 0.023 -10000 0 -10000 0 0
GNAI1 -0.006 0.13 -10000 0 -0.6 39 39
XPO1 0.023 0.014 -10000 0 -10000 0 0
GLI1/Su(fu) -0.035 0.19 -10000 0 -0.61 56 56
SAP30 0.025 0.015 0.27 3 -10000 0 3
mol:GDP 0.017 0.059 -10000 0 -0.6 7 7
MIM/GLI2A 0.022 0.027 0.28 4 -10000 0 4
IFT88 0.023 0.007 -10000 0 -10000 0 0
GNAI3 0.023 0.009 -10000 0 -10000 0 0
GLI2 0.008 0.066 -10000 0 -0.3 18 18
GLI3 0.009 0.089 0.29 1 -0.5 12 13
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.007 -10000 0 -10000 0 0
GNG2 0.019 0.053 -10000 0 -0.6 6 6
Gi family/GTP -0.006 0.096 -10000 0 -0.29 67 67
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.092 -10000 0 -0.46 18 18
GLI2/Su(fu) 0.011 0.083 -10000 0 -0.41 15 15
FOXA2 0.01 0.11 0.44 1 -0.66 15 16
neural tube patterning -0.043 0.21 0.35 1 -0.52 105 106
SPOP 0.022 0.008 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.043 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.022 0.027 0.28 4 -10000 0 4
embryonic limb morphogenesis -0.043 0.21 0.35 1 -0.52 105 106
SUFU 0.015 0.025 -10000 0 -0.24 1 1
LGALS3 0.018 0.061 -10000 0 -0.6 8 8
catabolic process 0.023 0.1 0.29 1 -0.55 15 16
GLI3A/CBP -0.001 0.098 -10000 0 -0.37 54 54
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.045 0.22 0.35 1 -0.54 105 106
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
IFT172 0.024 0.022 -10000 0 -0.6 1 1
RBBP7 0.026 0.022 0.27 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.059 -10000 0 -0.41 8 8
GNAZ 0.018 0.054 -10000 0 -0.6 6 6
RBBP4 0.024 0.005 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.016 0.07 -10000 0 -0.38 10 10
STK36 0.022 0.014 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.012 0.1 -10000 0 -0.39 32 32
PTCH1 -0.083 0.32 -10000 0 -1 70 70
MIM/GLI1 -0.032 0.2 0.37 1 -0.6 61 62
CREBBP -0.001 0.098 -10000 0 -0.37 54 54
Su(fu)/SIN3/HDAC complex 0.005 0.093 -10000 0 -0.41 28 28
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.089 0.29 33 -10000 0 33
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 0.18 10 -0.31 3 13
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.096 0.27 28 -0.6 15 43
RhoA/GTP -0.003 0.091 -10000 0 -0.3 33 33
negative regulation of cAMP metabolic process -0.006 0.089 -10000 0 -0.28 60 60
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.026 0.043 0.27 12 -0.6 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.003 0.086 -10000 0 -0.28 60 60
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.6 39 39
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.025 0.009 0.27 1 -10000 0 1
ANTXR2 0.018 0.061 -10000 0 -0.6 8 8
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.075 9 9
monocyte activation 0.006 0.08 0.26 2 -0.34 38 40
MAP2K2 -0.001 0.093 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.007 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 0.12 1 -10000 0 1
MAP2K6 -0.01 0.044 -10000 0 -0.33 15 15
CYAA -0.009 0.032 -10000 0 -0.31 9 9
MAP2K4 -0.004 0.007 -10000 0 -10000 0 0
IL1B -0.008 0.045 0.18 3 -0.27 19 22
Channel 0.027 0.039 0.17 1 -0.33 9 10
NLRP1 -0.007 0.032 -10000 0 -0.32 8 8
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.07 -10000 0 -0.39 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.075 9 -10000 0 9
MAPK3 -0.004 0.007 -10000 0 -10000 0 0
MAPK1 -0.004 0.008 0.12 1 -10000 0 1
PGR -0.081 0.14 0.2 2 -0.33 205 207
PA/Cellular Receptors 0.028 0.042 0.18 1 -0.36 9 10
apoptosis -0.002 0.008 -10000 0 -0.075 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.037 0.17 1 -0.31 9 10
macrophage activation -0.006 0.009 0.14 1 -10000 0 1
TNF 0.024 0.067 0.27 17 -0.6 7 24
VCAM1 0.006 0.081 0.26 2 -0.34 38 40
platelet activation -0.002 0.07 -10000 0 -0.39 25 25
MAPKKK cascade -0.002 0.027 0.1 11 -0.13 7 18
IL18 -0.003 0.025 -10000 0 -0.22 7 7
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.075 9 9
LEF -0.002 0.008 -10000 0 -0.076 9 9
CASP1 -0.003 0.026 -10000 0 -0.17 14 14
mol:cAMP -0.002 0.071 -10000 0 -0.4 25 25
necrosis -0.002 0.008 -10000 0 -0.075 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.037 0.17 1 -0.31 9 10
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.022 0.075 -10000 0 -0.59 3 3
UGCG 0.018 0.097 -10000 0 -0.64 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.049 0.12 0.3 9 -0.43 22 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.019 0.096 -10000 0 -0.63 15 15
mol:DAG 0.007 0.076 -10000 0 -0.76 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.04 0.13 0.31 6 -0.42 37 43
FRAP1 0.034 0.15 0.34 6 -0.47 41 47
FOXO3 0.038 0.14 0.34 10 -0.5 25 35
AKT1 0.039 0.15 0.32 12 -0.52 29 41
GAB2 0.021 0.01 -10000 0 -10000 0 0
SMPD1 0.009 0.11 -10000 0 -0.62 22 22
SGMS1 0.02 0.062 -10000 0 -0.58 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.007 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.055 0.1 0.38 2 -0.47 10 12
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.035 0.014 -10000 0 -10000 0 0
RPS6KB1 0.012 0.097 -10000 0 -0.84 9 9
mol:sphingomyelin 0.007 0.076 -10000 0 -0.76 7 7
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.028 0.03 0.27 12 -10000 0 12
PIK3R1 0.024 0.009 -10000 0 -10000 0 0
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.069 0.2 0.39 13 -0.93 23 36
MYB 0.036 0.18 -10000 0 -1.1 15 15
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.038 0.11 0.31 18 -0.46 13 31
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.092 -10000 0 -0.75 9 9
mol:PI-3-4-5-P3 0.043 0.11 0.3 18 -0.44 13 31
Rac1/GDP 0.018 0.013 -10000 0 -10000 0 0
T cell proliferation 0.043 0.099 0.3 13 -0.47 8 21
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 0.092 2 -0.076 14 16
PRKCZ 0.042 0.1 0.31 11 -0.49 8 19
NF kappa B1 p50/RelA 0.052 0.14 0.32 6 -0.45 28 34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.026 0.071 0.31 11 -0.62 3 14
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.087 0.27 46 -0.6 9 55
IL2RB 0.033 0.049 0.27 33 -10000 0 33
TERT 0.049 0.076 0.27 89 -10000 0 89
E2F1 0.057 0.095 0.34 1 -0.37 21 22
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.034 14 -0.043 2 16
PTPN11 0.024 0.008 -10000 0 -10000 0 0
IL2RG 0.03 0.068 0.27 32 -0.6 5 37
actin cytoskeleton organization 0.043 0.099 0.3 13 -0.47 8 21
GRB2 0.022 0.012 0.27 1 -10000 0 1
IL2 0.022 0.027 0.27 8 -10000 0 8
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.042 0.021 -10000 0 -10000 0 0
LCK 0.024 0.077 0.27 23 -0.6 9 32
BCL2 0.023 0.19 0.42 2 -0.79 30 32
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.015 0.061 0.22 2 -0.3 31 33
FRAP1 -0.003 0.083 0.26 1 -0.46 20 21
AKT1 -0.006 0.063 0.19 2 -0.28 22 24
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0.024 0.063 0.23 2 -0.23 20 22
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.2 5 5
TSC2 0.023 0.007 -10000 0 -10000 0 0
RHEB/GDP 0.007 0.042 -10000 0 -0.28 2 2
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.006 0.076 -10000 0 -0.31 43 43
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.045 -10000 0 -0.22 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.011 0.073 0.26 5 -0.3 19 24
MAP3K5 0 0.045 0.2 9 -0.19 31 40
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0 0.045 0.2 9 -0.19 31 40
mol:LY294002 0 0 -10000 0 -0.001 37 37
EIF4B 0.009 0.067 0.27 4 -0.3 12 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.064 0.22 2 -0.28 11 13
eIF4E/eIF4G1/eIF4A1 0.003 0.052 -10000 0 -0.28 19 19
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.019 0.073 -10000 0 -0.31 34 34
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.051 0.21 10 -0.2 2 12
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.028 0.055 0.21 1 -0.28 2 3
mol:Amino Acids 0 0 -10000 0 -0.001 37 37
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.017 0.057 0.17 7 -0.28 31 38
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.006 0.14 -10000 0 -0.53 45 45
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.002 0.051 -10000 0 -10000 0 0
TSC1/TSC2 0.027 0.069 0.26 3 -0.25 19 22
tumor necrosis factor receptor activity 0 0 0.001 37 -10000 0 37
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.011 0.078 -10000 0 -0.33 44 44
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
PDK2 -0.015 0.054 0.19 7 -0.3 18 25
EIF4EBP1 -0.028 0.23 -10000 0 -1 41 41
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D -0.001 0.08 0.32 3 -0.42 20 23
peptide biosynthetic process -0.011 0.017 0.18 1 -10000 0 1
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 16 -10000 0 16
EEF2 -0.011 0.017 0.18 1 -10000 0 1
eIF4E/4E-BP1 -0.018 0.22 -10000 0 -0.97 41 41
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.005 0.1 0.26 2 -0.41 28 30
BAG4 0.02 0.01 -10000 0 -10000 0 0
BAD 0.005 0.041 0.2 6 -0.19 4 10
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BAX 0.004 0.043 0.24 4 -0.18 4 8
EnzymeConsortium:3.1.4.12 0.001 0.027 0.085 4 -0.094 23 27
IKBKB 0.014 0.11 0.34 4 -0.41 18 22
MAP2K2 0.007 0.053 0.23 12 -0.27 1 13
MAP2K1 0.008 0.054 0.23 14 -0.27 1 15
SMPD1 0.001 0.033 0.17 2 -0.15 12 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.31 8 -0.43 19 27
MAP2K4 0.005 0.034 0.18 2 -0.18 2 4
protein ubiquitination 0.001 0.1 0.34 4 -0.39 26 30
EnzymeConsortium:2.7.1.37 0.007 0.056 0.23 13 -0.3 1 14
response to UV 0 0.001 0.002 15 -0.003 2 17
RAF1 0.008 0.054 0.2 29 -0.22 4 33
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.005 0.042 0.14 7 -0.15 20 27
I-kappa-B-alpha/RELA/p50/ubiquitin 0.032 0.008 -10000 0 -10000 0 0
MADD 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.003 0.039 0.21 1 -0.18 4 5
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.009 0.054 0.22 13 -0.25 2 15
MAPK1 0.006 0.061 0.22 13 -0.24 4 17
p50/RELA/I-kappa-B-alpha 0.035 0.009 -10000 0 -10000 0 0
FADD 0.021 0.12 0.28 9 -0.42 20 29
KSR1 0.009 0.052 0.19 25 -0.22 4 29
MAPK8 0.002 0.04 0.26 4 -10000 0 4
TRAF2 0.024 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 7 -10000 0 7
CHUK -0.005 0.097 0.25 1 -0.4 26 27
TNF R/SODD 0.028 0.016 -10000 0 -10000 0 0
TNF 0.024 0.067 0.27 17 -0.6 7 24
CYCS 0.007 0.047 0.19 11 -0.19 2 13
IKBKG -0.005 0.1 0.43 1 -0.41 23 24
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.11 -10000 0 -0.43 28 28
RELA 0.024 0.004 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.006 0.046 0.18 11 -0.19 3 14
TNF/TNF R/SODD 0.037 0.048 -10000 0 -0.38 6 6
TNFRSF1A 0.024 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 7 -10000 0 7
CASP8 0.01 0.11 -10000 0 -0.64 22 22
NSMAF 0.014 0.11 0.26 6 -0.43 20 26
response to hydrogen peroxide 0 0.001 0.002 15 -0.003 2 17
BCL2 0.008 0.098 -10000 0 -0.6 21 21
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.005 -10000 0 -9999 0 0
PLK4 0.035 0.05 0.27 37 -9999 0 37
regulation of centriole replication 0.016 0.028 0.26 1 -9999 0 1
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.052 0.075 0.44 6 -0.42 11 17
MAP4K1 0.03 0.051 0.27 24 -0.6 2 26
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
PRKCB 0.019 0.078 0.27 13 -0.6 11 24
DBNL 0.024 0.004 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.013 0.056 0.27 1 -0.32 11 12
JUN 0.004 0.12 -10000 0 -0.59 28 28
MAP3K7 0.013 0.057 0.27 1 -0.31 10 11
GRAP2 0.016 0.073 0.27 3 -0.6 11 14
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.012 0.067 0.26 1 -0.39 9 10
LAT 0.024 0.038 0.27 7 -0.6 2 9
LCP2 0.024 0.01 0.27 1 -10000 0 1
MAPK8 0.01 0.13 -10000 0 -0.64 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.062 0.26 3 -0.32 14 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.059 0.074 0.43 6 -0.4 11 17
Retinoic acid receptors-mediated signaling

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.017 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.061 -10000 0 -0.4 9 9
KAT2B 0.024 0.003 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.007 0.065 0.2 2 -0.36 12 14
RAR alpha/9cRA/Cyclin H 0.048 0.075 -10000 0 -0.36 16 16
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.022 0.067 -10000 0 -0.44 10 10
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.026 0.052 -10000 0 -0.24 18 18
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.007 0.11 -10000 0 -0.56 18 18
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.024 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARG 0.025 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.007 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.025 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.1 -10000 0 -0.49 19 19
RARA 0.014 0.055 0.18 25 -0.28 17 42
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.016 0.062 -10000 0 -0.41 9 9
PRKCA 0.01 0.092 0.27 2 -0.6 18 20
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.12 0.45 1 -0.54 20 21
RXRG -0.052 0.16 0.25 10 -0.36 155 165
RXRA 0.023 0.065 0.35 1 -0.3 17 18
RXRB 0.015 0.065 0.25 10 -0.36 18 28
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.032 0.076 0.27 43 -0.6 6 49
CRBP1/9-cic-RA 0.023 0.054 0.18 43 -0.45 6 49
RARB 0.019 0.061 -10000 0 -0.6 8 8
PRKCG 0.031 0.045 0.27 28 -10000 0 28
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.01 0.1 -10000 0 -0.53 21 21
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.01 0.1 -10000 0 -0.45 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.08 0.24 11 -0.39 12 23
RXRs/RARs/NRIP1/9cRA/HDAC3 0.01 0.12 0.45 1 -0.54 21 22
positive regulation of DNA binding 0.033 0.065 -10000 0 -0.34 16 16
NRIP1 0.011 0.12 0.54 1 -0.82 7 8
RXRs/RARs 0.01 0.12 -10000 0 -0.52 23 23
RXRs/RXRs/DNA/9cRA -0.015 0.093 -10000 0 -0.5 20 20
PRKACA 0.024 0.003 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.054 0.056 -10000 0 -0.3 4 4
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.015 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
mol:S1P 0 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.012 0.094 -10000 0 -0.3 66 66
GNAO1 0.019 0.096 0.27 28 -0.6 15 43
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.093 -10000 0 -0.47 24 24
AKT3 -0.011 0.16 -10000 0 -1.1 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.008 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.6 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.023 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.096 -10000 0 -0.36 35 35
MAPK3 -0.008 0.091 0.27 2 -0.41 19 21
MAPK1 -0.005 0.089 0.27 1 -0.35 32 33
JAK2 -0.008 0.1 -10000 0 -0.42 25 25
CXCR4 -0.008 0.093 -10000 0 -0.42 19 19
FLT1 0.023 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.01 0.093 -10000 0 -0.42 19 19
S1P/S1P3/Gi -0.001 0.097 -10000 0 -0.36 35 35
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.1 -10000 0 -0.4 20 20
VEGFA 0.026 0.021 0.27 5 -10000 0 5
S1P/S1P2/Gi -0.002 0.089 -10000 0 -0.29 61 61
VEGFR1 homodimer/VEGFA homodimer 0.036 0.023 -10000 0 -0.21 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.038 -10000 0 -0.31 9 9
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
GNAZ 0.019 0.054 -10000 0 -0.6 6 6
G12/G13 0.032 0.012 -10000 0 -10000 0 0
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.1 -10000 0 -0.41 19 19
BARD1 signaling events

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.033 0.013 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.018 -10000 0 -10000 0 0
protein ubiquitination 0.07 0.053 0.32 2 -10000 0 2
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.035 0.023 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.013 0.094 -10000 0 -0.43 19 19
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.024 0.01 0.27 1 -10000 0 1
CCNE1 0.061 0.088 0.27 127 -10000 0 127
CDK2/Cyclin E1 0.06 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.035 0.012 -10000 0 -10000 0 0
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
FANCA 0.064 0.094 0.27 146 -10000 0 146
DNA repair 0.034 0.084 0.3 4 -0.37 5 9
BRCA1/BARD1/ubiquitin 0.035 0.012 -10000 0 -10000 0 0
BARD1/DNA-PK 0.051 0.026 -10000 0 -10000 0 0
FANCL 0.024 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.033 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.064 -10000 0 -0.28 6 6
BRCA1/BACH1/BARD1/TopBP1 0.047 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.055 0.024 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.044 0.019 -10000 0 -10000 0 0
BRCA1/BACH1 0.024 0.01 0.27 1 -10000 0 1
BARD1 0.024 0.009 0.27 1 -10000 0 1
PCNA 0.024 0.013 0.27 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.047 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.046 0.017 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.1 0.076 0.32 2 -10000 0 2
BARD1/DNA-PK/P53 0.055 0.033 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.035 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.035 0.017 -10000 0 -10000 0 0
FA complex 0.036 0.041 0.25 3 -0.26 1 4
BARD1/EWS 0.034 0.011 -10000 0 -10000 0 0
RBBP8 0.009 0.006 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.053 0.023 -10000 0 -10000 0 0
BRCA1/BARD1 0.077 0.058 0.34 2 -10000 0 2
CSTF1 0.023 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.018 0.006 0.18 1 -10000 0 1
CDK2 0.025 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.12 0.12 0.27 320 -10000 0 320
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.035 0.012 -10000 0 -10000 0 0
EWSR1 0.023 0.006 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.049 -10000 0 -0.6 5 5
positive regulation of NF-kappaB transcription factor activity -0.006 0.12 -10000 0 -0.34 80 80
MAP2K4 0.015 0.046 0.22 1 -0.41 2 3
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.01 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.024 -10000 0 -0.6 1 1
SMPD1 0.007 0.028 -10000 0 -0.36 4 4
IKBKG 0.025 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.013 0.14 0.27 1 -0.6 43 44
TRAIL/TRAILR2 0.025 0.039 -10000 0 -0.43 5 5
TRAIL/TRAILR3 0.026 0.046 -10000 0 -0.39 7 7
TRAIL/TRAILR1 0.024 0.045 -10000 0 -0.43 6 6
TRAIL/TRAILR4 -0.006 0.12 -10000 0 -0.34 80 80
TRAIL/TRAILR1/DAP3/GTP 0.028 0.038 -10000 0 -0.34 4 4
IKK complex 0.01 0.043 -10000 0 -0.43 1 1
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.037 0.26 1 -0.44 5 6
MAP3K1 0.017 0.063 -10000 0 -0.49 6 6
TRAILR4 (trimer) -0.013 0.14 0.27 1 -0.6 43 44
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.024 -10000 0 -0.6 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.045 -10000 0 -0.43 5 5
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.007 0.037 0.26 1 -0.45 5 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.041 0.046 -10000 0 -0.32 4 4
mol:ceramide 0.007 0.028 -10000 0 -0.36 4 4
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.008 0.061 -10000 0 -0.44 5 5
TRAF2 0.024 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.022 0.025 0.27 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.04 -10000 0 -0.37 4 4
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.034 0.081 0.28 42 -0.34 1 43
JNK cascade -0.006 0.12 -10000 0 -0.34 80 80
TRAIL (trimer) 0.02 0.049 -10000 0 -0.6 5 5
TNFRSF10C 0.022 0.025 0.27 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.038 -10000 0 -0.32 2 2
TRAIL/TRAILR2/FADD 0.031 0.038 -10000 0 -0.37 4 4
cell death 0.007 0.028 -10000 0 -0.36 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.044 -10000 0 -0.43 5 5
TRAILR2 (trimer) 0.02 0.01 -10000 0 -10000 0 0
CASP8 0.013 0.045 -10000 0 -0.54 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.042 0.045 -10000 0 -0.32 4 4
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.021 0.11 -10000 0 -0.44 27 27
KLHL20 0.016 0.069 0.24 9 -0.23 9 18
CYFIP2 0.03 0.045 0.27 22 -0.6 1 23
Rac1/GDP -0.001 0.087 -10000 0 -0.32 13 13
ENAH -0.018 0.11 -10000 0 -0.44 22 22
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.049 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.033 -10000 0 -0.17 5 5
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.068 -10000 0 -0.36 16 16
RAPGEF1 -0.02 0.11 -10000 0 -0.41 23 23
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.023 0.12 -10000 0 -0.44 34 34
CRK -0.017 0.1 -10000 0 -0.44 24 24
E-cadherin/gamma catenin/alpha catenin 0.032 0.063 -10000 0 -0.39 14 14
alphaE/beta7 Integrin 0.035 0.034 -10000 0 -0.45 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.023 -10000 0 -0.36 1 1
DLG1 -0.025 0.12 -10000 0 -0.44 29 29
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.028 -10000 0 -10000 0 0
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
ARF6/GTP/NME1/Tiam1 0.043 0.024 -10000 0 -10000 0 0
PI3K -0.002 0.042 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.02 0.068 -10000 0 -0.45 14 14
TIAM1 0.025 0.017 0.27 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.04 0.058 -10000 0 -0.34 14 14
AKT1 -0.007 0.034 0.15 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
RhoA/GDP 0 0.087 -10000 0 -0.32 14 14
actin cytoskeleton organization 0.015 0.056 0.19 18 -0.17 6 24
CDC42/GDP 0 0.087 -10000 0 -0.32 13 13
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.045 -10000 0 -0.28 16 16
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
RAC1 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.044 0.062 -10000 0 -0.36 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.029 0.054 -10000 0 -0.34 14 14
mol:GDP -0.014 0.094 -10000 0 -0.36 14 14
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.006 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.004 0.09 -10000 0 -0.32 14 14
RAC1/GTP/IQGAP1 0.032 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.008 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.024 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.053 0.2 36 -0.25 3 39
NME1 0.024 0.024 0.27 7 -10000 0 7
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.12 -10000 0 -0.45 27 27
regulation of cell-cell adhesion 0.002 0.041 -10000 0 -10000 0 0
WASF2 0.007 0.028 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.059 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.069 -10000 0 -0.34 16 16
CCND1 0.015 0.059 0.21 31 -0.32 3 34
VAV2 -0.021 0.16 -10000 0 -0.62 21 21
RAP1/GDP 0.005 0.072 -10000 0 -0.31 2 2
adherens junction assembly -0.023 0.12 -10000 0 -0.44 27 27
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.024 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.039 0.065 -10000 0 -0.33 16 16
E-cadherin/beta catenin 0 0.062 -10000 0 -0.35 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.025 0.12 -10000 0 -0.45 28 28
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.095 0.27 27 -0.35 20 47
E-cadherin/beta catenin/alpha catenin 0.033 0.062 -10000 0 -0.39 14 14
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.024 0.13 -10000 0 -0.45 33 33
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.073 0.31 3 -0.37 10 13
PDGFB-D/PDGFRB/SLAP 0.028 0.03 -10000 0 -0.45 1 1
PDGFB-D/PDGFRB/APS/CBL 0.047 0.038 -10000 0 -0.38 2 2
AKT1 0.028 0.093 0.34 30 -10000 0 30
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.03 0.084 0.33 4 -0.39 12 16
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.44 31 31
mol:Ca2+ 0.023 0.088 0.29 4 -0.41 15 19
MYC 0.055 0.18 0.37 26 -0.77 22 48
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.32 2 2
LRP1/PDGFRB/PDGFB 0.042 0.055 -10000 0 -0.47 8 8
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.023 0.088 0.32 2 -0.42 15 17
PTEN 0.022 0.031 -10000 0 -0.6 2 2
GRB2 0.023 0.011 0.27 1 -10000 0 1
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PDGFB-D/PDGFRB/SHP2 0.035 0.025 -10000 0 -0.45 2 2
PDGFB-D/PDGFRB/GRB10 0.035 0.025 -10000 0 -0.45 2 2
cell cycle arrest 0.028 0.029 -10000 0 -0.45 1 1
HRAS 0.024 0.01 0.27 1 -10000 0 1
HIF1A 0.024 0.087 0.32 30 -10000 0 30
GAB1 0.025 0.093 0.32 3 -0.42 13 16
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.086 0.32 8 -0.36 10 18
PDGFB-D/PDGFRB 0.043 0.031 -10000 0 -0.39 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.035 0.025 -10000 0 -0.45 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.02 0.064 0.3 2 -0.38 6 8
positive regulation of MAPKKK cascade 0.035 0.025 -10000 0 -0.45 2 2
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.089 0.33 2 -0.42 15 17
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.032 -10000 0 -0.45 3 3
SHB 0.024 0.009 0.27 1 -10000 0 1
BLK -0.035 0.17 0.3 1 -0.43 91 92
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.035 0.025 -10000 0 -0.44 2 2
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.027 0.1 0.34 3 -0.44 16 19
CBL 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.035 0.025 -10000 0 -0.45 2 2
LCK 0.004 0.1 -10000 0 -0.48 29 29
PDGFRB 0.023 0.032 -10000 0 -0.61 2 2
ACP1 0.024 0.004 -10000 0 -10000 0 0
HCK 0.016 0.064 -10000 0 -0.56 5 5
ABL1 0.019 0.093 0.29 5 -0.38 18 23
PDGFB-D/PDGFRB/CBL 0.02 0.1 0.32 1 -0.46 19 20
PTPN1 0.024 0.022 0.26 6 -10000 0 6
SNX15 0.024 0.004 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.035 0.27 18 -10000 0 18
cell proliferation 0.056 0.16 0.36 31 -0.68 22 53
SLA 0.021 0.025 0.27 7 -10000 0 7
actin cytoskeleton reorganization 0.032 0.053 0.33 2 -0.32 1 3
SRC 0.013 0.054 -10000 0 -0.47 5 5
PI3K -0.013 0.023 -10000 0 -0.3 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.035 -10000 0 -0.39 3 3
SH2B2 0.032 0.042 0.27 26 -10000 0 26
PLCgamma1/SPHK1 0.03 0.085 0.33 4 -0.4 12 16
LYN 0.01 0.065 -10000 0 -0.57 6 6
LRP1 0.018 0.061 -10000 0 -0.6 8 8
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.031 -10000 0 -0.6 2 2
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.32 2 2
SPHK1 0.024 0.039 0.27 7 -0.61 2 9
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.023 0.089 0.33 2 -0.42 15 17
PLCG1 0.023 0.091 0.33 2 -0.43 15 17
NHERF/PDGFRB 0.049 0.046 -10000 0 -0.39 2 2
YES1 0.001 0.11 -10000 0 -0.51 28 28
cell migration 0.049 0.045 -10000 0 -0.38 2 2
SHC/Grb2/SOS1 0.049 0.042 -10000 0 -0.32 2 2
SLC9A3R2 0.023 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.037 0.057 0.27 47 -10000 0 47
NHERF1-2/PDGFRB/PTEN 0.058 0.052 -10000 0 -0.36 4 4
FYN -0.002 0.1 -10000 0 -0.43 28 28
DOK1 0.021 0.05 -10000 0 -0.35 2 2
HRAS/GTP 0.018 0.007 0.18 1 -10000 0 1
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.021 0.12 0.34 2 -0.53 22 24
PRKCD 0.021 0.052 0.34 1 -0.35 2 3
FER 0.018 0.057 -10000 0 -0.36 6 6
MAPKKK cascade 0.039 0.099 0.36 30 -0.32 2 32
RASA1 0.02 0.051 -10000 0 -0.35 2 2
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.035 0.042 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/SHB 0.034 0.027 -10000 0 -0.45 2 2
chemotaxis 0.019 0.091 0.28 5 -0.38 18 23
STAT1-3-5/STAT1-3-5 0.048 0.05 -10000 0 -0.36 7 7
Bovine Papilomavirus E5/PDGFRB 0.017 0.024 -10000 0 -0.45 2 2
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.11 0.28 14 -0.32 21 35
ERC1 0.023 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.032 0.38 1 -10000 0 1
NFKBIA -0.004 0.022 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.018 0.27 3 -10000 0 3
IKBKG 0.019 0.028 -10000 0 -10000 0 0
IKK complex/A20 0.022 0.13 -10000 0 -0.4 35 35
NEMO/A20/RIP2 0.02 0.018 0.27 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.015 0.13 0.28 1 -0.37 60 61
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.032 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.012 0.11 -10000 0 -0.39 33 33
BCL10/MALT1/TRAF6 0.046 0.015 -10000 0 -10000 0 0
NOD2 0.028 0.039 0.27 21 -10000 0 21
NFKB1 0.026 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
MALT1 0.024 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.034 0.051 -10000 0 -0.45 7 7
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.009 0.092 0.27 2 -0.6 18 20
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.067 0.27 17 -0.6 7 24
NF kappa B1 p50/RelA 0.052 0.014 -10000 0 -10000 0 0
BCL10 0.024 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.022 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.016 0.12 -10000 0 -0.41 35 35
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.43 40 40
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.024 0.038 0.27 7 -0.6 2 9
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.011 0.02 0.23 1 -0.3 2 3
GNAO1 0.019 0.096 0.27 28 -0.6 15 43
mol:Sphinganine-1-P 0.01 0.026 -10000 0 -0.45 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.05 0.037 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.012 -10000 0 -10000 0 0
S1PR3 0.026 0.022 0.27 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.005 0.025 -10000 0 -0.25 5 5
S1PR5 0.026 0.043 0.27 12 -0.6 2 14
S1PR4 0.024 0.063 0.27 16 -0.6 6 22
GNAI1 -0.005 0.13 -10000 0 -0.6 39 39
S1P/S1P5/G12 0.045 0.043 -10000 0 -0.26 5 5
S1P/S1P3/Gq 0.027 0.062 -10000 0 -0.38 9 9
S1P/S1P4/Gi -0.001 0.098 0.26 1 -0.34 37 38
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.005 -10000 0 -10000 0 0
ABCC1 0.023 0.006 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.07 0.053 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.056 0.048 0.36 3 -10000 0 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.049 0.021 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.043 -10000 0 -10000 0 0
CaM/Ca2+ 0.068 0.049 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.044 0.045 0.29 2 -10000 0 2
AKT1 0.013 0.059 0.3 8 -10000 0 8
MAP2K1 0.007 0.045 0.28 3 -10000 0 3
MAP3K11 0.013 0.047 0.28 3 -10000 0 3
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.014 0.11 -10000 0 -0.41 10 10
Rap1/GTP 0.013 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.078 0.056 -10000 0 -10000 0 0
CEBPB 0.027 0.097 0.4 1 -0.5 6 7
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.073 0.1 -10000 0 -0.7 9 9
STAT1 0.025 0.05 0.3 4 -10000 0 4
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.058 0.086 0.27 119 -10000 0 119
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.042 0.047 0.29 4 -10000 0 4
CEBPB/PTGES2/Cbp/p300 0.027 0.062 0.25 3 -0.35 3 6
mol:Ca2+ 0.066 0.051 -10000 0 -10000 0 0
MAPK3 0.02 0.085 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.06 -10000 0 -10000 0 0
MAPK1 -0.009 0.17 -10000 0 -0.67 47 47
JAK2 0.026 0.008 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.038 -10000 0 -0.6 3 3
DAPK1 0.026 0.071 0.37 2 -0.35 1 3
SMAD7 0.016 0.035 0.18 3 -10000 0 3
CBL/CRKL/C3G 0.046 0.04 0.32 1 -10000 0 1
PI3K 0.06 0.044 -10000 0 -10000 0 0
IFNG 0.058 0.086 0.27 119 -10000 0 119
apoptosis 0.022 0.078 0.33 2 -0.41 11 13
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.04 0.27 23 -10000 0 23
CAMK2B -0.012 0.17 0.27 32 -0.6 60 92
FRAP1 0.011 0.054 0.29 8 -10000 0 8
PRKCD 0.014 0.061 0.3 9 -10000 0 9
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.043 -10000 0 -10000 0 0
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 0.021 0.059 0.31 6 -10000 0 6
STAT1 (dimer)/PIASy 0.04 0.047 0.29 3 -10000 0 3
SOCS1 0.013 0.12 -10000 0 -1 10 10
mol:GDP 0.042 0.037 0.3 1 -10000 0 1
CASP1 0.016 0.04 0.26 3 -0.27 2 5
PTGES2 0.024 0.003 -10000 0 -10000 0 0
IRF9 0.028 0.041 0.22 9 -10000 0 9
mol:PI-3-4-5-P3 0.045 0.034 -10000 0 -10000 0 0
RAP1/GDP 0.036 0.024 -10000 0 -10000 0 0
CBL 0.011 0.046 0.3 2 -10000 0 2
MAP3K1 0.021 0.042 0.28 3 -10000 0 3
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.043 -10000 0 -10000 0 0
PTPN11 0.026 0.046 0.29 3 -10000 0 3
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.031 0.011 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.051 -10000 0 -0.38 6 6
IRAK/TOLLIP 0.024 0.014 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.025 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.023 0.1 0.38 2 -0.45 32 34
IL1A 0.028 0.031 0.27 14 -10000 0 14
IL1B 0.004 0.053 0.26 1 -0.46 10 11
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.041 -10000 0 -0.32 1 1
IL1R2 0.005 0.13 0.27 16 -0.6 32 48
IL1R1 0.017 0.068 -10000 0 -0.6 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.061 0.26 3 -0.31 12 15
TOLLIP 0.024 0.005 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.033 0.073 0.34 7 -0.38 1 8
JUN -0.01 0.066 0.29 4 -0.3 19 23
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.045 0.068 -10000 0 -0.35 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88 0.056 0.052 -10000 0 -0.36 10 10
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.065 0.052 -10000 0 -0.34 10 10
IL1 beta fragment/IL1R1/IL1RAP 0.026 0.065 -10000 0 -0.38 19 19
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.004 0.064 0.33 3 -0.3 13 16
IRAK1 -0.001 0.019 0.21 2 -10000 0 2
IL1RN/IL1R1 0.035 0.066 -10000 0 -0.45 12 12
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.055 -10000 0 -0.31 12 12
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.026 0.065 -10000 0 -0.38 19 19
IL1 beta/IL1R2 0.011 0.097 -10000 0 -0.4 41 41
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.061 -10000 0 -0.33 19 19
IRAK3 0.005 0.11 0.27 1 -0.6 25 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.046 0.067 -10000 0 -0.35 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.04 -10000 0 -0.28 10 10
IL1 alpha/IL1R1/IL1RAP 0.045 0.053 -10000 0 -0.39 10 10
RELA 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.009 0.27 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.037 -10000 0 -10000 0 0
IL1RAP 0.024 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.017 0.054 -10000 0 -0.32 15 15
CASP1 0.021 0.023 -10000 0 -0.6 1 1
IL1RN/IL1R2 0.025 0.11 0.38 2 -0.45 34 36
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.037 0.066 -10000 0 -0.36 19 19
TMEM189-UBE2V1 0.019 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.07 -10000 0 -0.36 15 15
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.054 0.27 29 -0.6 2 31
TRAF6/TAK1/TAB1/TAB2 0.039 0.018 -10000 0 -10000 0 0
MAP2K6 -0.001 0.07 0.39 4 -0.32 13 17
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.021 0.089 0.31 5 -0.41 11 16
NFATC2 -0.001 0.067 0.21 1 -0.26 24 25
NFATC3 0.014 0.018 -10000 0 -0.42 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.096 0.28 2 -0.33 34 36
Exportin 1/Ran/NUP214 0.047 0.012 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.09 -10000 0 -0.46 8 8
BCL2/BAX 0.022 0.077 -10000 0 -0.43 23 23
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.014 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.014 -10000 0 -10000 0 0
BAX 0.024 0.004 -10000 0 -10000 0 0
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.019 0.086 -10000 0 -0.37 17 17
Calcineurin A alpha-beta B1/BCL2 0.008 0.098 -10000 0 -0.6 21 21
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.085 0.37 17 -10000 0 17
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.038 0.062 0.27 56 -10000 0 56
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.018 0.073 0.27 8 -0.6 10 18
MAP3K8 0.019 0.044 -10000 0 -0.6 4 4
NFAT4/CK1 alpha 0.017 0.028 -10000 0 -0.27 1 1
MEF2D/NFAT1/Cbp/p300 0.011 0.11 -10000 0 -0.31 47 47
CABIN1 0.012 0.096 0.28 2 -0.33 33 35
CALM1 0.02 0.014 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.024 0.005 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.27 31 -10000 0 31
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.044 0.039 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.012 -10000 0 -10000 0 0
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.023 0.1 0.32 1 -0.45 11 12
PRKCH 0.023 0.022 -10000 0 -0.6 1 1
CABIN1/Cbp/p300 0.027 0.023 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.009 -10000 0 -10000 0 0
apoptosis 0.012 0.03 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.04 -10000 0 -0.32 3 3
PRKCB 0.019 0.078 0.27 13 -0.6 11 24
PRKCE 0.024 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.007 0.06 -10000 0 -0.39 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.024 0.01 0.27 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.019 0.025 -10000 0 -0.6 1 1
PRKCA 0.009 0.092 0.27 2 -0.6 18 20
PRKCG 0.03 0.045 0.27 28 -10000 0 28
PRKCQ 0.004 0.12 0.27 10 -0.6 30 40
FKBP38/BCL2 0.021 0.077 -10000 0 -0.43 23 23
EP300 0.019 0.016 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.031 0.087 0.34 1 -0.41 9 10
CaM/Ca2+/FKBP38 0.027 0.018 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.004 -10000 0 -10000 0 0
CSNK1A1 0.008 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.033 0.034 -10000 0 -10000 0 0
NFATc/ERK1 0.03 0.087 0.34 1 -0.42 8 9
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.039 0.095 -10000 0 -0.42 13 13
NR4A1 -0.012 0.18 -10000 0 -0.54 72 72
GSK3B 0.021 0.012 -10000 0 -10000 0 0
positive T cell selection 0.014 0.018 -10000 0 -0.42 1 1
NFAT1/CK1 alpha 0.003 0.051 -10000 0 -0.3 4 4
RCH1/ KPNB1 0.042 0.044 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.038 0.056 0.27 47 -10000 0 47
MEF2D 0.017 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.03 0.086 0.34 1 -0.42 8 9
CREBBP 0.019 0.016 -10000 0 -10000 0 0
BCL2 0.008 0.098 -10000 0 -0.6 21 21
Class I PI3K signaling events

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.014 0.041 0.35 2 -10000 0 2
DAPP1 0.013 0.1 0.28 7 -0.37 25 32
Src family/SYK family/BLNK-LAT/BTK-ITK 0.009 0.14 0.3 10 -0.49 31 41
mol:DAG 0.016 0.079 0.24 27 -0.28 6 33
HRAS 0.025 0.011 0.26 1 -10000 0 1
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.03 0.057 0.27 1 -0.36 5 6
PLCG2 0.021 0.025 0.27 1 -0.6 1 2
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.009 0.27 1 -10000 0 1
mol:GTP -0.011 0.044 0.32 6 -0.3 1 7
ARF1/GTP -0.004 0.034 0.29 4 -0.3 1 5
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
RAP1A/GTP -0.012 0.036 0.21 2 -0.3 1 3
ADAP1 -0.013 0.041 0.36 2 -0.31 2 4
ARAP3 -0.011 0.044 0.32 6 -0.3 1 7
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.036 0.27 18 -10000 0 18
ARHGEF6 0.021 0.049 -10000 0 -0.6 5 5
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.01 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.01 0.27 1 -10000 0 1
mol:Ca2+ 0.01 0.05 0.24 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.017 0.27 4 -10000 0 4
ZAP70 0.018 0.1 0.27 26 -0.6 18 44
mol:IP3 0.01 0.062 0.2 31 -0.19 6 37
LYN 0.021 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.056 0.33 2 -0.34 6 8
RhoA/GDP 0.033 0.043 -10000 0 -0.3 1 1
PDK1/Src/Hsp90 0.043 0.018 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.018 0.068 0.37 6 -0.32 3 9
SRC 0.024 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.01 0.23 1 -10000 0 1
RAC1 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.032 -10000 0 -0.58 2 2
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.042 0.29 5 -0.29 1 6
RhoA/GTP -0.012 0.044 0.36 4 -0.29 1 5
Src family/SYK family/BLNK-LAT 0.02 0.095 0.27 9 -0.42 13 22
BLK 0.046 0.086 0.27 95 -0.6 2 97
PDPK1 0.023 0.007 -10000 0 -10000 0 0
CYTH1 -0.011 0.043 0.36 4 -0.29 1 5
HCK 0.028 0.029 0.27 12 -10000 0 12
CYTH3 -0.013 0.04 0.36 2 -0.29 1 3
CYTH2 -0.012 0.041 0.33 3 -0.29 1 4
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.012 0.053 0.31 1 -0.42 7 8
SGK1 0.006 0.075 -10000 0 -0.35 29 29
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.059 0.26 4 -0.33 7 11
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.021 0.051 0.39 5 -0.3 1 6
mol:PI-3-4-5-P3 -0.012 0.037 0.27 4 -0.3 1 5
ARAP3/RAP1A/GTP -0.012 0.037 0.21 2 -0.3 1 3
VAV1 0.024 0.025 0.27 2 -0.6 1 3
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.035 0.029 -10000 0 -0.3 1 1
PLEKHA1 -0.01 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.056 0.27 1 -0.35 5 6
LAT 0.024 0.038 0.27 7 -0.6 2 9
Rac1/GTP 0.018 0.043 -10000 0 -0.34 4 4
ITK -0.018 0.068 0.36 4 -0.34 21 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.014 0.097 0.27 26 -0.35 10 36
LCK 0.024 0.077 0.27 23 -0.6 9 32
BTK -0.012 0.044 0.36 4 -0.29 1 5
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.032 0.063 -9999 0 -0.39 14 14
E-cadherin/beta catenin 0.021 0.068 -9999 0 -0.45 14 14
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.006 -9999 0 -10000 0 0
CDH1 0.011 0.081 -9999 0 -0.6 14 14
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.016 -10000 0 -0.32 1 1
TRAF2/ASK1 0.03 0.018 -10000 0 -0.38 1 1
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.018 0.11 0.27 1 -0.38 34 35
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.011 0.097 0.3 1 -0.38 22 23
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.037 0.055 0.27 45 -10000 0 45
TXN 0.006 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.024 0.005 -10000 0 -10000 0 0
MAP3K6 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.033 0.021 -10000 0 -0.45 1 1
TAK1/TAB family -0.001 0.02 0.19 1 -0.2 1 2
RAC1/OSM/MEKK3 0.041 0.017 -10000 0 -10000 0 0
TRAF2 0.024 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.093 -10000 0 -0.31 25 25
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.012 0.17 0.27 32 -0.6 60 92
CCM2 0.024 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.007 0.11 -10000 0 -0.38 61 61
MAPK11 0.021 0.031 -10000 0 -0.6 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.019 0.11 -10000 0 -0.35 61 61
OSM/MEKK3 0.032 0.012 -10000 0 -10000 0 0
TAOK1 0.008 0.032 -10000 0 -0.36 6 6
TAOK2 0.01 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.021 -10000 0 -0.37 1 1
GADD45/MTK1/MTK1 0.058 0.036 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.051 0.041 -10000 0 -0.35 6 6
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.01 -10000 0 -0.3 1 1
GATA1/HDAC4 0.035 0.024 0.2 8 -0.45 1 9
GATA1/HDAC5 0.035 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 0.026 0.074 -10000 0 -0.45 18 18
HDAC5/BCL6/BCoR 0.044 0.03 -10000 0 -0.39 3 3
HDAC9 0.023 0.06 0.27 11 -0.6 6 17
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.039 -10000 0 -0.39 6 6
HDAC4/ANKRA2 0.034 0.019 -10000 0 -0.45 1 1
HDAC5/YWHAB 0.033 0.011 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
GATA2 0.014 0.096 0.27 11 -0.6 18 29
HDAC4/RFXANK 0.034 0.019 -10000 0 -0.45 1 1
BCOR 0.024 0.022 -10000 0 -0.6 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.006 -10000 0 -10000 0 0
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.042 -10000 0 -0.45 6 6
Histones 0.016 0.052 -10000 0 -0.29 13 13
ADRBK1 0.023 0.007 -10000 0 -10000 0 0
HDAC4 0.023 0.022 -10000 0 -0.6 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.01 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.02 -10000 0 -0.45 1 1
HDAC7 0.024 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.025 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.034 0.009 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.27 31 -10000 0 31
Tubulin/HDAC6 0.048 0.014 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
GATA1 0.025 0.026 0.27 9 -10000 0 9
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.02 0.053 -10000 0 -0.6 6 6
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.24 4 4
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.02 -10000 0 -0.45 1 1
Tubulin 0.035 0.011 0.2 2 -10000 0 2
HDAC4/14-3-3 E 0.032 0.02 -10000 0 -0.45 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.033 0.03 -10000 0 -0.45 3 3
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.019 -10000 0 -0.39 1 1
HDAC4/SRF 0.051 0.034 -10000 0 -0.39 1 1
HDAC4/ER alpha -0.008 0.18 -10000 0 -0.44 112 112
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.014 0.054 -10000 0 -0.28 13 13
cell motility 0.047 0.013 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
HDAC7/HDAC3 0.036 0.006 -10000 0 -10000 0 0
BCL6 0.022 0.031 -10000 0 -0.6 2 2
HDAC4/CaMK II delta B 0.023 0.022 -10000 0 -0.6 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.025 0.24 0.27 109 -0.6 106 215
HDAC6/HDAC11 0.036 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.039 -10000 0 -0.24 3 3
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.022 -10000 0 -0.6 1 1
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.063 0.032 -10000 0 -0.33 2 2
GNG2 0.019 0.053 -10000 0 -0.6 6 6
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.024 0.013 0.27 2 -10000 0 2
HDAC11 0.025 0.012 0.27 2 -10000 0 2
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.024 0.004 -10000 0 -10000 0 0
nuclear import -0.026 0.018 0.35 1 -10000 0 1
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.053 0.08 -10000 0 -10000 0 0
CRKL 0.024 0.048 0.29 6 -10000 0 6
mol:DAG 0.038 0.054 0.33 1 -10000 0 1
HRAS 0.034 0.08 0.3 17 -10000 0 17
MAPK8 0.045 0.069 0.26 23 -10000 0 23
RAP1A 0.024 0.048 0.29 5 -10000 0 5
GAB1 0.024 0.047 0.29 5 -10000 0 5
MAPK14 0.045 0.068 0.26 23 -10000 0 23
EPO 0.065 0.091 0.26 139 -10000 0 139
PLCG1 0.038 0.054 0.33 1 -10000 0 1
EPOR/TRPC2/IP3 Receptors 0.026 0.01 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.065 0.064 -10000 0 -0.37 4 4
GAB1/SHC/GRB2/SOS1 0.042 0.043 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.063 0.062 -10000 0 -10000 0 0
IRS2 0.011 0.076 0.29 4 -0.31 29 33
STAT1 0.046 0.066 0.33 3 -10000 0 3
STAT5B 0.04 0.061 0.33 1 -0.36 1 2
cell proliferation 0.027 0.075 0.25 26 -10000 0 26
GAB1/SHIP/PIK3R1/SHP2/SHC 0.035 0.032 -10000 0 -10000 0 0
TEC 0.023 0.049 0.29 5 -0.32 1 6
SOCS3 0.02 0.044 -10000 0 -0.6 4 4
STAT1 (dimer) 0.045 0.066 0.33 3 -10000 0 3
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.083 0.064 0.34 3 -10000 0 3
EPO/EPOR 0.063 0.062 -10000 0 -10000 0 0
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.048 0.28 3 -0.31 1 4
elevation of cytosolic calcium ion concentration 0.026 0.01 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.063 0.057 -10000 0 -10000 0 0
mol:IP3 0.038 0.054 0.33 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.076 0.29 2 -0.31 21 23
SH2B3 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.045 0.069 0.26 23 -10000 0 23
EPO/EPOR (dimer)/JAK2/SOCS3 0.026 0.045 -10000 0 -0.2 7 7
PTPN6 0.023 0.039 0.3 2 -10000 0 2
TEC/VAV2/GRB2 0.047 0.049 -10000 0 -0.31 1 1
EPOR 0.026 0.01 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.043 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.021 0.025 0.27 1 -0.6 1 2
CRKL/CBL/C3G 0.047 0.048 -10000 0 -10000 0 0
VAV2 0.025 0.048 0.29 6 -10000 0 6
CBL 0.023 0.047 0.29 5 -10000 0 5
SHC/Grb2/SOS1 0.036 0.038 -10000 0 -10000 0 0
STAT5A 0.038 0.067 0.33 1 -0.36 5 6
GRB2 0.023 0.011 0.27 1 -10000 0 1
STAT5 (dimer) 0.051 0.082 0.34 1 -0.4 4 5
LYN/PLCgamma2 0.027 0.024 -10000 0 -0.45 1 1
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.025 0.049 0.29 6 -10000 0 6
BCL2 0.035 0.16 -10000 0 -0.86 23 23
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 0.026 -10000 0 -0.32 1 1
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.027 0.27 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.066 0.05 0.4 6 -0.36 2 8
EPO 0.064 0.091 0.27 139 -10000 0 139
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.019 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.061 0.063 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.07 -10000 0 -0.51 10 10
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.035 0.033 -10000 0 -10000 0 0
PXN 0.025 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
MADCAM1 0.031 0.045 0.27 29 -10000 0 29
cell adhesion 0.063 0.049 0.39 6 -0.36 2 8
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC -0.008 0.044 -10000 0 -0.36 6 6
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.046 0.044 -10000 0 -0.39 6 6
p130Cas/Crk/Dock1 0.027 0.041 0.35 1 -0.32 2 3
VCAM1 0.021 0.057 0.27 6 -0.6 6 12
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.025 -10000 0 -10000 0 0
BCAR1 -0.008 0.045 0.38 2 -0.33 6 8
EPOR 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.072 -10000 0 -0.53 10 10
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.041 0.062 -10000 0 -0.53 2 2
NEF 0.005 0.02 -10000 0 -0.18 4 4
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.019 0.056 -10000 0 -0.56 3 3
CYCS 0.038 0.076 0.26 18 -0.74 1 19
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.018 0.091 0.31 12 -0.52 17 29
MAP2K7 0.041 0.13 0.32 1 -0.72 15 16
protein ubiquitination 0.013 0.086 0.31 4 -0.37 11 15
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.004 -10000 0 -10000 0 0
FAS 0.023 0.031 -10000 0 -0.6 2 2
BID 0.037 0.073 0.24 2 -0.36 6 8
NF-kappa-B/RelA/I kappa B alpha 0.052 0.034 -10000 0 -0.32 2 2
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.052 0.034 -10000 0 -0.32 2 2
MAPK8 0.039 0.12 0.46 2 -0.68 14 16
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.015 0.27 3 -10000 0 3
TRAF2 0.024 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.026 0.06 0.24 4 -0.36 8 12
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.097 0.27 1 -0.44 16 17
CHUK 0.013 0.089 0.32 4 -0.4 10 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.039 -10000 0 -0.4 2 2
TCRz/NEF 0.018 0.08 0.27 12 -0.45 17 29
TNF 0.024 0.067 0.27 17 -0.6 7 24
FASLG 0.015 0.1 0.31 33 -0.52 17 50
NFKB1 0.025 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.037 0.048 -10000 0 -0.38 6 6
CASP6 0.053 0.11 -10000 0 -0.53 14 14
CASP7 0.04 0.1 0.38 4 -0.51 8 12
RELA 0.026 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.36 3 -0.52 7 10
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.028 0.016 -10000 0 -10000 0 0
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.005 -10000 0 -10000 0 0
MAP3K14 0.015 0.093 0.36 2 -0.44 12 14
APAF-1/Caspase 9 0.034 0.063 0.27 4 -0.4 5 9
BCL2 0.033 0.13 0.47 4 -0.57 17 21
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 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
ITGA4 0.027 0.027 0.27 10 -10000 0 10
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
alpha4/beta1 Integrin 0.037 0.019 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.43 50 50
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.005 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.16 0.41 1 -0.45 59 60
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.009 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.021 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.022 0.016 0.27 3 -10000 0 3
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.009 0.016 0.24 4 -10000 0 4
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
TRIP10 0.024 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.065 0.26 1 -0.34 8 9
VAMP2 0.022 0.008 -10000 0 -10000 0 0
SLC2A4 -0.13 0.17 0.42 1 -0.5 59 60
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.017 0.005 -10000 0 -10000 0 0
SFN 0.018 0.073 0.27 8 -0.6 10 18
LNPEP 0.022 0.038 -10000 0 -0.6 3 3
YWHAE 0.022 0.007 -10000 0 -10000 0 0
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.025 0.021 -10000 0 -0.5 1 1
VEGFR1 homodimer/NRP1 0.009 0.018 -10000 0 -0.51 1 1
mol:DAG 0.011 0.032 -10000 0 -0.41 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.022 -10000 0 -0.47 1 1
CaM/Ca2+ 0.025 0.031 -10000 0 -0.39 2 2
HIF1A 0.028 0.013 -10000 0 -0.32 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.012 0.04 -10000 0 -0.39 2 2
PLCG1 0.011 0.032 -10000 0 -0.41 2 2
NOS3 0.015 0.058 -10000 0 -0.51 3 3
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:NO 0.019 0.067 0.3 1 -0.45 6 7
FLT1 0.013 0.021 -10000 0 -0.59 1 1
PGF 0.023 0.022 -10000 0 -0.6 1 1
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.029 -10000 0 -0.6 1 1
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.031 0.07 -10000 0 -0.43 7 7
endothelial cell proliferation 0.013 0.085 0.35 7 -0.58 3 10
mol:Ca2+ 0.011 0.032 -10000 0 -0.41 2 2
MAPK3 -0.015 0.056 -10000 0 -0.35 17 17
MAPK1 -0.015 0.055 0.23 1 -0.35 17 18
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.023 0.022 -10000 0 -0.6 1 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.099 0.25 -10000 0 -0.6 163 163
VEGFA homodimer 0.025 0.019 0.27 5 -10000 0 5
VEGFR1 homodimer/VEGFA homodimer 0.026 0.024 -10000 0 -0.51 1 1
platelet activating factor biosynthetic process -0.016 0.053 -10000 0 -0.34 16 16
PI3K 0.046 0.031 -10000 0 -0.4 2 2
PRKCA -0.014 0.058 0.25 1 -0.36 17 18
PRKCB -0.011 0.053 -10000 0 -0.37 12 12
VEGFR1 homodimer/PLGF homodimer 0.025 0.025 -10000 0 -0.45 2 2
VEGFA 0.025 0.019 0.27 5 -10000 0 5
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.011 0.032 -10000 0 -0.41 2 2
RASA1 0.012 0.031 -10000 0 -0.46 1 1
NRP2 0.025 0.009 0.27 1 -10000 0 1
VEGFR1 homodimer 0.013 0.021 -10000 0 -0.59 1 1
VEGFB homodimer 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.032 0.14 -10000 0 -0.48 20 20
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.045 0.03 -10000 0 -0.39 2 2
mol:L-citrulline 0.019 0.067 0.3 1 -0.45 6 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.03 -10000 0 -0.44 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.038 0.025 -10000 0 -0.48 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.058 0.037 -10000 0 -0.38 2 2
PDPK1 -0.002 0.046 -10000 0 -0.37 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.038 0.025 -10000 0 -0.48 1 1
mol:NADP 0.019 0.067 0.3 1 -0.45 6 7
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.029 -10000 0 -0.44 1 1
VEGFR1 homodimer/NRP2 0.026 0.026 -10000 0 -0.64 1 1
Arf6 downstream 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
PLAUR 0.04 0.073 0.37 2 -10000 0 2
regulation of axonogenesis -0.01 0.026 0.24 4 -10000 0 4
myoblast fusion -0.025 0.048 -10000 0 -10000 0 0
mol:GTP 0.023 0.032 -10000 0 -0.15 8 8
regulation of calcium-dependent cell-cell adhesion -0.053 0.044 -10000 0 -0.33 1 1
ARF1/GTP 0.03 0.029 -10000 0 -10000 0 0
mol:GM1 0.012 0.025 -10000 0 -10000 0 0
mol:Choline 0.008 0.036 -10000 0 -0.36 5 5
lamellipodium assembly 0.017 0.06 -10000 0 -0.36 6 6
MAPK3 0.032 0.047 0.21 9 -10000 0 9
ARF6/GTP/NME1/Tiam1 0.054 0.045 0.34 1 -10000 0 1
ARF1 0.02 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.048 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.048 -10000 0 -0.26 2 2
ARF6 0.032 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.018 0.26 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.032 0.047 0.19 60 -10000 0 60
actin filament bundle formation -0.032 0.051 0.25 3 -10000 0 3
KALRN 0.009 0.057 -10000 0 -0.33 15 15
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.051 -10000 0 -0.25 3 3
NME1 0.026 0.024 0.27 7 -10000 0 7
Rac1/GDP 0.033 0.052 -10000 0 -0.25 3 3
substrate adhesion-dependent cell spreading 0.023 0.032 -10000 0 -0.15 8 8
cortical actin cytoskeleton organization 0.017 0.06 -10000 0 -0.36 6 6
RAC1 0.024 0.004 -10000 0 -10000 0 0
liver development 0.023 0.032 -10000 0 -0.15 8 8
ARF6/GTP 0.023 0.032 -10000 0 -0.15 8 8
RhoA/GTP 0.034 0.029 -10000 0 -10000 0 0
mol:GDP 0.02 0.049 0.18 51 -0.22 5 56
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.043 -10000 0 -0.42 5 5
RAB11FIP3 0.023 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.06 -10000 0 -0.36 6 6
ruffle organization 0.01 0.026 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.023 0.032 -10000 0 -0.15 8 8
PLD2 0.02 0.025 -10000 0 -10000 0 0
PIP5K1A 0.01 0.026 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.008 0.036 -10000 0 -0.36 5 5
Rac1/GTP 0.017 0.06 -10000 0 -0.36 6 6
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.027 0.062 -10000 0 -0.45 13 13
AKT1 0.034 0.078 0.35 3 -0.54 3 6
PTK2B 0.009 0.062 0.35 1 -0.38 12 13
VEGFR2 homodimer/Frs2 0.028 0.035 -10000 0 -0.64 2 2
CAV1 -0.099 0.25 -10000 0 -0.6 163 163
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.042 0.038 -10000 0 -0.59 2 2
endothelial cell proliferation 0.046 0.11 0.36 22 -0.52 5 27
mol:Ca2+ 0.016 0.036 -10000 0 -0.55 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.053 0.038 -10000 0 -0.57 2 2
RP11-342D11.1 0.006 0.033 -10000 0 -0.54 2 2
CDH5 0.02 0.032 -10000 0 -0.6 2 2
VEGFA homodimer 0.049 0.029 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.009 0.096 -10000 0 -0.6 20 20
HRAS/GDP 0.032 0.032 -10000 0 -0.58 1 1
SH2D2A 0.039 0.07 0.27 64 -0.6 1 65
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.044 0.085 -10000 0 -0.48 9 9
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.047 0.056 -10000 0 -0.45 3 3
VEGFR1 homodimer 0.023 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.043 -10000 0 -0.64 1 1
GRB10 0.017 0.036 -10000 0 -0.55 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
PAK1 0.023 0.017 0.27 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.056 0.051 -10000 0 -0.49 4 4
HRAS 0.024 0.01 0.27 1 -10000 0 1
VEGF/Rho/ROCK1/Integrin Complex 0.014 0.058 -10000 0 -0.53 3 3
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.27 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.052 0.037 -10000 0 -0.56 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.031 -10000 0 -0.6 2 2
Nck/Pak 0.032 0.016 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.04 0.045 -10000 0 -0.73 2 2
mol:GDP 0.041 0.037 -10000 0 -0.62 1 1
mol:NADP 0.025 0.084 0.56 1 -0.45 9 10
eNOS/Hsp90 0.037 0.081 0.55 1 -0.43 8 9
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.016 0.037 -10000 0 -0.55 2 2
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.009 0.27 1 -10000 0 1
VEGFA 0.026 0.019 0.27 5 -10000 0 5
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.027 0.085 0.35 1 -0.58 4 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.065 -10000 0 -0.39 14 14
PTPN6 0.024 0.013 0.27 2 -10000 0 2
EPAS1 0.029 0.019 -10000 0 -0.34 2 2
mol:L-citrulline 0.025 0.084 0.56 1 -0.45 9 10
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.051 0.041 -10000 0 -0.57 2 2
VEGFR2 homodimer/VEGFA homodimer 0.044 0.036 -10000 0 -0.59 2 2
VEGFR2/3 heterodimer 0.027 0.045 -10000 0 -0.65 3 3
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.007 0.05 -10000 0 -0.59 2 2
VEGFR2 homodimer 0.015 0.037 -10000 0 -0.71 2 2
FLT1 0.023 0.007 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.008 0.066 0.27 5 -0.55 3 8
MAPK1 0.01 0.067 0.26 3 -0.66 2 5
VEGFA145/NRP2 0.037 0.018 -10000 0 -0.2 1 1
VEGFR1/2 heterodimer 0.026 0.038 -10000 0 -0.7 2 2
KDR 0.015 0.037 -10000 0 -0.72 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.044 0.038 -10000 0 -0.6 2 2
SRC 0.024 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.017 0.075 0.31 6 -0.55 3 9
PI3K 0.029 0.049 -10000 0 -0.65 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.042 0.036 -10000 0 -0.59 2 2
FES 0.015 0.041 -10000 0 -0.42 5 5
GAB1 0.016 0.047 -10000 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.041 0.037 -10000 0 -0.59 2 2
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.02 0.14 -10000 0 -0.44 19 19
VEGFR2 homodimer/VEGFA homodimer/Yes 0.041 0.039 -10000 0 -0.51 3 3
PI3K/GAB1 0.043 0.063 0.31 1 -0.54 2 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.057 0.042 -10000 0 -0.47 2 2
PRKACA 0.024 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.045 -10000 0 -0.61 3 3
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.016 0.037 -10000 0 -0.56 2 2
actin cytoskeleton reorganization 0.047 0.056 -10000 0 -0.45 3 3
PTK2 0.011 0.062 -10000 0 -0.71 3 3
EDG1 0.006 0.033 -10000 0 -0.54 2 2
mol:DAG 0.016 0.037 -10000 0 -0.55 2 2
CaM/Ca2+ 0.03 0.039 -10000 0 -0.51 2 2
MAP2K3 -0.004 0.04 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.042 0.037 -10000 0 -0.56 2 2
PLCG1 0.016 0.037 -10000 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.052 0.04 -10000 0 -0.57 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.043 0.036 -10000 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.042 0.037 -10000 0 -0.59 2 2
cell migration 0.029 0.079 0.35 3 -0.57 3 6
mol:PI-3-4-5-P3 0.028 0.046 -10000 0 -0.59 2 2
FYN 0.022 0.023 -10000 0 -0.6 1 1
VEGFB/NRP1 0.021 0.034 -10000 0 -0.51 2 2
mol:NO 0.025 0.084 0.56 1 -0.45 9 10
PXN 0.025 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.026 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.034 -10000 0 -0.56 2 2
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
NOS3 0.025 0.092 0.57 1 -0.52 9 10
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.07 -10000 0 -0.37 21 21
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.008 0.065 0.35 1 -0.36 17 18
PRKCB -0.006 0.057 -10000 0 -0.38 10 10
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.025 0.035 -10000 0 -0.54 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.04 0.04 -10000 0 -0.65 2 2
VEGFA165/NRP2 0.037 0.018 -10000 0 -0.2 1 1
MAPKKK cascade 0.052 0.071 0.33 10 -0.58 1 11
NRP2 0.025 0.009 0.27 1 -10000 0 1
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.024 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.028 0.087 0.42 2 -0.58 4 6
MAP3K13 0.016 0.036 -10000 0 -0.56 2 2
PDPK1 0.016 0.044 -10000 0 -0.62 1 1
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.051 0.062 -10000 0 -0.4 6 6
Ran/GTP/Exportin 1/HDAC1 -0.01 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.063 -10000 0 -0.37 6 6
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.022 0.015 0.27 2 -10000 0 2
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.052 0.043 -10000 0 -0.44 1 1
YY1/LSF 0.024 0.05 -10000 0 -0.3 5 5
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.032 -10000 0 -0.32 5 5
I kappa B alpha/HDAC1 0.029 0.04 -10000 0 -0.46 1 1
SAP18 0.023 0.007 -10000 0 -10000 0 0
RELA 0.019 0.038 -10000 0 -0.33 5 5
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.03 0.039 -10000 0 -0.46 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.39 3 3
NF kappa B1 p50/RelA 0.026 0.065 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.014 0.096 0.27 11 -0.6 18 29
GATA1 0.025 0.026 0.27 9 -10000 0 9
Mad/Max 0.035 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.015 0.083 -10000 0 -0.37 18 18
RBBP7 0.026 0.022 0.27 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.024 0.004 -10000 0 -10000 0 0
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.028 -10000 0 -0.27 5 5
KAT2B 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.03 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.023 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.008 -10000 0 -10000 0 0
SAP30 0.025 0.015 0.27 3 -10000 0 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.048 -10000 0 -0.39 3 3
YY1/HDAC2 0.025 0.046 -10000 0 -0.3 4 4
YY1/HDAC1 0.025 0.048 -10000 0 -0.29 5 5
NuRD/MBD2 Complex (MeCP1) 0.024 0.055 -10000 0 -0.41 2 2
PPARG -0.061 0.16 -10000 0 -0.36 171 171
HDAC8/hEST1B 0.042 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.03 0.039 -10000 0 -0.46 1 1
MBD3L2 0.018 0.013 0.27 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.046 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.021 0.071 -10000 0 -0.36 13 13
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.018 0.029 -10000 0 -0.27 6 6
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.006 -10000 0 -10000 0 0
HDAC8 0.025 0.001 -10000 0 -10000 0 0
SMAD7 0.024 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.009 0.27 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.037 0.049 -10000 0 -0.28 4 4
YY1/SAP30/HDAC1 0.037 0.048 -10000 0 -0.27 3 3
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.028 -10000 0 -0.27 5 5
histone deacetylation 0.024 0.055 -10000 0 -0.4 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.018 0.037 -10000 0 -0.44 1 1
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GATAD2B 0.021 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.025 0.068 -10000 0 -0.35 18 18
GATA1/HDAC1 0.036 0.018 -10000 0 -10000 0 0
GATA1/HDAC3 0.031 0.042 -10000 0 -0.48 1 1
CHD4 0.024 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.051 -10000 0 -0.45 7 7
SIN3/HDAC complex/Mad/Max 0.014 0.058 -10000 0 -0.29 18 18
NuRD Complex 0.023 0.068 -10000 0 -0.36 10 10
positive regulation of chromatin silencing 0.05 0.042 -10000 0 -0.43 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.24 3 3
HDAC complex 0.058 0.023 -10000 0 -10000 0 0
GATA1/Fog1 0.032 0.023 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.016 -10000 0 -10000 0 0
TNF 0.024 0.067 0.27 17 -0.6 7 24
negative regulation of cell growth 0.014 0.057 -10000 0 -0.28 18 18
NuRD/MBD2/PRMT5 Complex 0.024 0.055 -10000 0 -0.41 2 2
Ran/GTP/Exportin 1 0.035 0.039 -10000 0 -0.24 3 3
NF kappa B/RelA/I kappa B alpha 0.018 0.052 -10000 0 -0.38 6 6
SIN3/HDAC complex/NCoR1 0.006 0.068 -10000 0 -0.32 23 23
TFCP2 0.025 0.002 -10000 0 -10000 0 0
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.005 -10000 0 -10000 0 0
MBD2 0.024 0.005 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.024 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.039 -10000 0 -0.35 1 1
SMAD3 0.022 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.066 -10000 0 -0.49 7 7
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.062 -10000 0 -10000 0 0
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.046 -10000 0 -0.28 5 5
MAP3K1 0.024 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.033 0.025 -10000 0 -0.45 2 2
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.023 0.031 -10000 0 -0.6 2 2
UBE2I 0.023 0.007 -10000 0 -10000 0 0
NUP153 0.024 0.004 -10000 0 -10000 0 0
KPNA2 0.038 0.062 0.27 56 -10000 0 56
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.037 -10000 0 -10000 0 0
CLOCK 0.026 0.004 -10000 0 -10000 0 0
TIMELESS/CRY2 0.032 0.023 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.013 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.016 0.014 -10000 0 -10000 0 0
ARNTL 0.026 0.005 -10000 0 -10000 0 0
TIMELESS 0.018 0.022 -10000 0 -10000 0 0
NPAS2 0.023 0.044 0.27 1 -0.6 4 5
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.007 -10000 0 -0.097 5 5
CHEK1 0.029 0.041 0.27 23 -10000 0 23
mol:HEME 0.007 0.007 0.097 5 -10000 0 5
PER1 0.012 0.078 -10000 0 -0.6 13 13
BMAL/CLOCK/NPAS2 0.053 0.034 -10000 0 -0.38 4 4
BMAL1/CLOCK 0.022 0.051 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.044 0.037 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.044 0.037 -10000 0 -10000 0 0
mol:NADPH 0.007 0.007 0.097 5 -10000 0 5
PER1/TIMELESS 0.025 0.049 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.015 0.27 3 -10000 0 3
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.011 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.027 0.27 10 -10000 0 10
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.02 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.043 0.037 0.34 4 -0.36 2 6
lamellipodium assembly -0.001 0.081 -10000 0 -0.41 20 20
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.004 -10000 0 -10000 0 0
PXN 0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.047 0.022 -10000 0 -10000 0 0
cell adhesion 0.05 0.021 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.019 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
ARF6/GDP 0.022 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.041 -10000 0 -0.34 6 6
p130Cas/Crk/Dock1 0.041 0.02 -10000 0 -10000 0 0
VCAM1 0.021 0.057 0.27 6 -0.6 6 12
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.022 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.023 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.047 0.023 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.022 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.088 -10000 0 -0.46 20 20
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.035 0.008 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.045 -10000 0 -0.27 1 1
NFKBIA 0.014 0.037 -10000 0 -0.24 9 9
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.024 0.022 -10000 0 -0.6 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.015 0.011 0.25 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.009 0.013 0.26 2 -10000 0 2
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.025 0.046 -10000 0 -0.26 7 7
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.047 -10000 0 -0.28 2 2
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.024 0.046 -10000 0 -0.26 7 7
IKBKB 0.02 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
SYK 0.024 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.026 0.048 -10000 0 -0.26 3 3
cell death 0.022 0.045 -10000 0 -0.27 2 2
NF kappa B1 p105/c-Rel 0.021 0.013 -10000 0 -10000 0 0
LCK 0.024 0.077 0.27 23 -0.6 9 32
BCL3 0.024 0.004 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.033 0.18 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.049 -10000 0 -0.18 4 4
AP2 0.035 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.01 -10000 0 -10000 0 0
CLTB 0.024 0.01 0.27 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.013 0.009 -10000 0 -10000 0 0
CD4 0.023 0.006 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.011 0.2 2 -10000 0 2
mol:Choline 0.007 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.017 -10000 0 -10000 0 0
ARF1/GDP 0 0.023 0.19 2 -10000 0 2
AP2M1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.017 -10000 0 -10000 0 0
ARFIP2 0.014 0.018 -10000 0 -10000 0 0
COPA 0.021 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.025 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0.044 -10000 0 -0.24 18 18
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.026 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.011 0.053 -10000 0 -0.26 26 26
Arfaptin 2/Rac/GDP 0.028 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.016 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.024 -10000 0 -10000 0 0
PLD2 0.007 0.017 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.008 0.017 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.022 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.017 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.009 0.027 -10000 0 -0.31 5 5
USO1 0.009 0.022 -10000 0 -0.32 3 3
GBF1 0.009 0.022 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.016 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.012 -10000 0 -0.28 1 1
MDM2/SUMO1 0.033 0.041 -10000 0 -0.24 3 3
HDAC4 0.023 0.022 -10000 0 -0.6 1 1
Ran/GTP/Exportin 1/HDAC1 -0.009 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.019 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.24 4 4
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.24 3 3
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.057 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.037 -10000 0 -0.24 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.039 0.25 1 -0.24 3 4
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.067 0.024 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.014 -10000 0 -9999 0 0
RELB 0.026 0.019 0.27 5 -9999 0 5
NFKB2 0.024 0.004 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.033 0.013 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.013 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 828 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.HN.A2NL TCGA.GM.A3NY TCGA.GM.A2DO TCGA.GM.A2DN
109_MAP3K5 0.024 0.024 0.097 0.024
47_PPARGC1A 0.27 0.025 0.025 0.025
105_BMP4 -0.6 0.025 -0.6 0.025
105_BMP6 0.025 0.025 0.025 0.025
105_BMP7 0.025 0.025 0.025 0.025
105_BMP2 0.025 0.025 0.025 0.025
131_RELN/VLDLR 0.064 -0.67 -0.36 -0.36
30_TGFB1/TGF beta receptor Type II 0.027 0.024 0.024 0.024
84_STAT5B 0.064 -0.063 -0.13 0.011
84_STAT5A 0.064 -0.063 -0.13 0.011
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/3025930/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BRCA-TP/3139796/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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