PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1QJ7FHV
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1QJ7FHV
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 55 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 313
Class IB PI3K non-lipid kinase events 212
Signaling events mediated by Stem cell factor receptor (c-Kit) 208
Signaling mediated by p38-alpha and p38-beta 207
Reelin signaling pathway 189
Aurora B signaling 160
FOXA2 and FOXA3 transcription factor networks 147
EGFR-dependent Endothelin signaling events 146
PLK1 signaling events 139
Glucocorticoid receptor regulatory network 121
Results
Summary Table

The following list describes the columns found in ##REF##406.

  • 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 313 16005 51 -0.081 0.8 1000 -1000 -0.047 -1000
Class IB PI3K non-lipid kinase events 212 636 3 -0.14 -1000 1000 -1000 -0.014 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 208 16274 78 -0.57 0.18 1000 -1000 -0.05 -1000
Signaling mediated by p38-alpha and p38-beta 207 9121 44 -0.33 0.024 1000 -1000 -0.018 -1000
Reelin signaling pathway 189 10608 56 -0.35 0.058 1000 -1000 -0.038 -1000
Aurora B signaling 160 10751 67 -0.22 0.29 1000 -1000 -0.031 -1000
FOXA2 and FOXA3 transcription factor networks 147 6765 46 -1.1 0.034 1000 -1000 -0.04 -1000
EGFR-dependent Endothelin signaling events 146 3078 21 -0.21 0.034 1000 -1000 -0.035 -1000
PLK1 signaling events 139 11830 85 -0.074 0.25 1000 -1000 -0.025 -1000
Glucocorticoid receptor regulatory network 121 13801 114 -0.79 0.3 1000 -1000 -0.045 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 121 8273 68 -0.36 0.16 1000 -1000 -0.043 -1000
HIF-1-alpha transcription factor network 120 9130 76 -0.51 0.035 1000 -1000 -0.047 -1000
EPHB forward signaling 119 10115 85 -0.24 0.16 1000 -1000 -0.068 -1000
p75(NTR)-mediated signaling 118 14779 125 -0.26 0.1 1000 -1000 -0.06 -1000
Endothelins 108 10419 96 -0.37 0.18 1000 -1000 -0.031 -1000
Ephrin B reverse signaling 103 4976 48 -0.24 0.11 1000 -1000 -0.024 -1000
Angiopoietin receptor Tie2-mediated signaling 103 9135 88 -0.29 0.13 1000 -1000 -0.063 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 96 5205 54 -0.35 0.055 1000 -1000 -0.039 -1000
IL4-mediated signaling events 96 8823 91 -0.71 0.27 1000 -1000 -0.046 -1000
Noncanonical Wnt signaling pathway 95 2482 26 -0.11 0.024 1000 -1000 -0.035 -1000
Wnt signaling 95 667 7 -0.11 0.02 1000 -1000 -0.01 -1000
IL23-mediated signaling events 93 5639 60 -0.33 0.08 1000 -1000 -0.037 -1000
IGF1 pathway 85 4888 57 -0.12 0.043 1000 -1000 -0.04 -1000
Arf6 signaling events 81 5072 62 -0.21 0.055 1000 -1000 -0.027 -1000
BMP receptor signaling 76 6176 81 -0.4 0.11 1000 -1000 -0.05 -1000
Nongenotropic Androgen signaling 75 3901 52 -0.27 0.14 1000 -1000 -0.024 -1000
Neurotrophic factor-mediated Trk receptor signaling 74 8946 120 -0.4 0.18 1000 -1000 -0.046 -1000
Visual signal transduction: Rods 74 3850 52 -0.37 0.059 1000 -1000 -0.021 -1000
Plasma membrane estrogen receptor signaling 72 6195 86 -0.11 0.091 1000 -1000 -0.051 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 70 6007 85 -0.26 0.027 1000 -1000 -0.036 -1000
Signaling events mediated by PTP1B 69 5250 76 -0.47 0.08 1000 -1000 -0.026 -1000
Calcium signaling in the CD4+ TCR pathway 69 2162 31 -0.2 0.027 1000 -1000 -0.035 -1000
Signaling events regulated by Ret tyrosine kinase 68 5633 82 -0.064 0.11 1000 -1000 -0.059 -1000
Aurora C signaling 65 456 7 0 0.15 1000 -1000 -0.012 -1000
S1P1 pathway 65 2364 36 -0.34 0.024 1000 -1000 -0.025 -1000
ErbB2/ErbB3 signaling events 64 4182 65 -0.31 0.034 1000 -1000 -0.055 -1000
Effects of Botulinum toxin 64 1687 26 -0.004 0.11 1000 -1000 -0.005 -1000
amb2 Integrin signaling 62 5153 82 -0.37 0.13 1000 -1000 -0.031 -1000
Glypican 1 network 60 2905 48 -0.21 0.045 1000 -1000 -0.024 -1000
IL6-mediated signaling events 58 4354 75 -0.2 0.058 1000 -1000 -0.027 -1000
Syndecan-1-mediated signaling events 57 1960 34 -0.079 0.19 1000 -1000 -0.031 -1000
Ephrin A reverse signaling 57 402 7 -0.035 0.023 1000 -1000 -0.004 -1000
Integrins in angiogenesis 57 4802 84 -0.21 0.13 1000 -1000 -0.041 -1000
TCR signaling in naïve CD8+ T cells 55 5125 93 -0.098 0.093 1000 -1000 -0.047 -1000
LPA receptor mediated events 53 5436 102 -0.19 0.12 1000 -1000 -0.08 -1000
Signaling events mediated by the Hedgehog family 52 2707 52 -0.13 0.033 1000 -1000 -0.031 -1000
Visual signal transduction: Cones 49 1885 38 -0.035 0.18 1000 -1000 -0.009 -1000
ErbB4 signaling events 47 3255 69 -0.31 0.065 1000 -1000 -0.043 -1000
E-cadherin signaling in keratinocytes 47 2061 43 -0.19 0.032 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 46 2393 52 -0.12 0.075 1000 -1000 -0.036 -1000
Fc-epsilon receptor I signaling in mast cells 45 4380 97 -0.17 0.033 1000 -1000 -0.056 -1000
PDGFR-alpha signaling pathway 45 2010 44 -0.33 0.037 1000 -1000 -0.033 -1000
Canonical Wnt signaling pathway 45 2316 51 -0.3 0.12 1000 -1000 -0.044 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 44 1475 33 -0.42 0.057 1000 -1000 -0.027 -1000
Syndecan-3-mediated signaling events 43 1534 35 -0.24 0.055 1000 -1000 -0.016 -1000
Presenilin action in Notch and Wnt signaling 42 2609 61 -0.29 0.12 1000 -1000 -0.038 -1000
IL12-mediated signaling events 40 3549 87 -0.36 0.067 1000 -1000 -0.057 -1000
Nephrin/Neph1 signaling in the kidney podocyte 39 1349 34 -0.023 0.061 1000 -1000 -0.025 -1000
FAS signaling pathway (CD95) 39 1835 47 -0.45 0.04 1000 -1000 -0.032 -1000
Rapid glucocorticoid signaling 37 747 20 -0.11 0.028 1000 -1000 -0.004 -1000
Signaling events mediated by HDAC Class III 36 1441 40 -0.35 0.045 1000 -1000 -0.025 -1000
Glypican 2 network 36 146 4 0.032 0.055 1000 -1000 0.014 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2623 74 -0.2 0.05 1000 -1000 -0.057 -1000
LPA4-mediated signaling events 34 416 12 -0.12 0.005 1000 -1000 -0.024 -1000
Aurora A signaling 34 2053 60 -0.091 0.19 1000 -1000 -0.027 -1000
TCGA08_rtk_signaling 33 865 26 -0.19 0.039 1000 -1000 -0.014 -1000
Syndecan-4-mediated signaling events 33 2254 67 -0.21 0.12 1000 -1000 -0.039 -1000
Ras signaling in the CD4+ TCR pathway 33 577 17 -0.067 0.023 1000 -1000 -0.027 -1000
Nectin adhesion pathway 32 2036 63 -0.041 0.047 1000 -1000 -0.034 -1000
Coregulation of Androgen receptor activity 29 2233 76 -0.16 0.062 1000 -1000 -0.02 -1000
Regulation of Telomerase 29 3035 102 -0.21 0.15 1000 -1000 -0.029 -1000
Regulation of Androgen receptor activity 29 2086 70 -0.19 0.11 1000 -1000 -0.039 -1000
BCR signaling pathway 28 2799 99 -0.093 0.057 1000 -1000 -0.052 -1000
Insulin Pathway 28 2137 74 -0.11 0.063 1000 -1000 -0.044 -1000
Thromboxane A2 receptor signaling 27 2917 105 -0.19 0.036 1000 -1000 -0.036 -1000
Regulation of p38-alpha and p38-beta 27 1493 54 -0.25 0.052 1000 -1000 -0.048 -1000
TCGA08_retinoblastoma 27 222 8 -0.017 0.058 1000 -1000 -0.002 -1000
Signaling events mediated by PRL 27 941 34 -0.14 0.035 1000 -1000 -0.035 -1000
Regulation of nuclear SMAD2/3 signaling 26 3650 136 -0.23 0.075 1000 -1000 -0.036 -1000
IL27-mediated signaling events 26 1326 51 -0.2 0.072 1000 -1000 -0.026 -1000
Syndecan-2-mediated signaling events 25 1728 69 -0.11 0.13 1000 -1000 -0.023 -1000
IL2 signaling events mediated by STAT5 25 557 22 0.009 0.12 1000 -1000 -0.029 -1000
Osteopontin-mediated events 22 852 38 -0.17 0.094 1000 -1000 -0.028 -1000
TCGA08_p53 21 151 7 -0.01 0.02 1000 -1000 -0.004 -1000
Signaling mediated by p38-gamma and p38-delta 21 317 15 -0.024 0.024 1000 -1000 -0.032 -1000
Arf6 trafficking events 21 1543 71 -0.28 0.041 1000 -1000 -0.025 -1000
Caspase cascade in apoptosis 19 1428 74 -0.031 0.057 1000 -1000 -0.032 -1000
Ceramide signaling pathway 19 1461 76 -0.11 0.065 1000 -1000 -0.033 -1000
FoxO family signaling 18 1158 64 -0.019 0.26 1000 -1000 -0.032 -1000
S1P4 pathway 18 461 25 -0.014 0.041 1000 -1000 -0.019 -1000
S1P5 pathway 17 300 17 -0.007 0.032 1000 -1000 -0.011 -1000
Hedgehog signaling events mediated by Gli proteins 16 1089 65 -0.084 0.055 1000 -1000 -0.029 -1000
Cellular roles of Anthrax toxin 15 591 39 -0.08 0.028 1000 -1000 -0.02 -1000
Class I PI3K signaling events mediated by Akt 15 1024 68 -0.17 0.043 1000 -1000 -0.031 -1000
HIF-2-alpha transcription factor network 15 664 43 -0.16 0.17 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 15 886 58 -0.001 0.069 1000 -1000 -0.024 -1000
JNK signaling in the CD4+ TCR pathway 13 221 17 0.004 0.059 1000 -1000 -0.024 -1000
mTOR signaling pathway 13 701 53 -0.029 0.028 1000 -1000 -0.036 -1000
E-cadherin signaling in the nascent adherens junction 13 1046 76 -0.024 0.051 1000 -1000 -0.05 -1000
PLK2 and PLK4 events 12 38 3 0.016 0.035 1000 -1000 -0.008 -1000
ceramide signaling pathway 12 606 49 -0.004 0.037 1000 -1000 -0.03 -1000
S1P3 pathway 12 545 42 -0.013 0.042 1000 -1000 -0.026 -1000
BARD1 signaling events 11 632 57 -0.053 0.12 1000 -1000 -0.033 -1000
Retinoic acid receptors-mediated signaling 11 676 58 -0.052 0.053 1000 -1000 -0.038 -1000
a4b1 and a4b7 Integrin signaling 10 50 5 0.024 0.04 1000 -1000 0.014 -1000
TRAIL signaling pathway 10 502 48 -0.014 0.042 1000 -1000 -0.035 -1000
E-cadherin signaling events 10 52 5 0.011 0.032 1000 -1000 0.011 -1000
PDGFR-beta signaling pathway 9 918 97 -0.033 0.057 1000 -1000 -0.054 -1000
Sphingosine 1-phosphate (S1P) pathway 8 240 28 -0.007 0.05 1000 -1000 -0.018 -1000
IFN-gamma pathway 8 560 68 -0.011 0.078 1000 -1000 -0.046 -1000
IL1-mediated signaling events 8 542 62 -0.009 0.065 1000 -1000 -0.04 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 8 363 45 0.004 0.055 1000 -1000 -0.033 -1000
Class I PI3K signaling events 8 596 73 -0.018 0.046 1000 -1000 -0.037 -1000
p38 MAPK signaling pathway 8 368 44 -0.018 0.058 1000 -1000 -0.017 -1000
EPO signaling pathway 7 428 55 0.011 0.082 1000 -1000 -0.029 -1000
Insulin-mediated glucose transport 7 247 32 -0.13 0.039 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 295 37 -0.008 0.066 1000 -1000 -0.025 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 633 83 -0.018 0.047 1000 -1000 -0.031 -1000
Canonical NF-kappaB pathway 6 255 39 0 0.052 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 6 504 75 -0.026 0.062 1000 -1000 -0.035 -1000
VEGFR1 specific signals 6 348 56 -0.1 0.058 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class I 4 490 104 -0.061 0.058 1000 -1000 -0.035 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 571 125 -0.1 0.057 1000 -1000 -0.038 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 3 74 23 -0.003 0.043 1000 -1000 -0.028 -1000
Arf6 downstream pathway 3 132 43 -0.053 0.054 1000 -1000 -0.021 -1000
Paxillin-dependent events mediated by a4b1 3 115 36 -0.047 0.051 1000 -1000 -0.031 -1000
Circadian rhythm pathway 2 63 22 -0.007 0.053 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 2 65 31 0 0.033 1000 -1000 -0.016 -1000
Arf1 pathway 1 70 54 -0.001 0.045 1000 -1000 -0.019 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 19 27 -0.009 0.056 1000 -1000 -0.041 -1000
Alternative NF-kappaB pathway 0 5 13 0 0.067 1000 -1000 0 -1000
Total 6462 381953 7203 -21 -990 131000 -131000 -4.1 -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 1 379 -0.98 2 381
PLK1 0.41 0.26 0.67 323 -0.87 1 324
BIRC5 0.43 0.27 0.64 416 -0.78 4 420
HSPA1B 0.67 0.39 1 370 -0.99 2 372
MAP2K1 0.19 0.12 0.32 317 -10000 0 317
BRCA2 0.68 0.41 1 383 -0.93 3 386
FOXM1 0.79 0.51 1.2 425 -1.2 2 427
XRCC1 0.67 0.4 1 387 -0.99 2 389
FOXM1B/p19 0.1 0.26 0.81 52 -1.1 2 54
Cyclin D1/CDK4 0.58 0.38 0.9 382 -0.94 2 384
CDC2 0.73 0.45 1.1 424 -1 2 426
TGFA 0.58 0.4 0.91 393 -0.96 5 398
SKP2 0.67 0.4 1 388 -0.99 2 390
CCNE1 0.095 0.097 0.31 128 -10000 0 128
CKS1B 0.72 0.43 1.1 408 -0.99 2 410
RB1 0.34 0.33 0.7 311 -0.65 5 316
FOXM1C/SP1 0.6 0.36 0.92 360 -1.2 3 363
AURKB 0.35 0.31 0.64 334 -0.74 14 348
CENPF 0.78 0.47 1.1 434 -0.99 2 436
CDK4 0.092 0.057 0.23 39 -10000 0 39
MYC 0.38 0.39 0.85 252 -1 4 256
CHEK2 0.18 0.12 0.33 290 -10000 0 290
ONECUT1 0.61 0.4 0.95 391 -1 2 393
CDKN2A -0.081 0.12 0.22 8 -0.24 206 214
LAMA4 0.67 0.4 1 382 -0.99 2 384
FOXM1B/HNF6 0.62 0.4 0.98 363 -1.2 2 365
FOS 0.32 0.66 1 268 -1 44 312
SP1 0.023 0.025 -10000 0 -0.24 1 1
CDC25B 0.67 0.4 1 384 -0.99 2 386
response to radiation 0.13 0.089 0.24 253 -10000 0 253
CENPB 0.67 0.4 1 375 -0.99 2 377
CENPA 0.74 0.45 1.1 411 -0.99 2 413
NEK2 0.8 0.46 1.1 452 -0.95 2 454
HIST1H2BA 0.66 0.39 1 364 -0.99 2 366
CCNA2 0.16 0.13 0.31 345 -10000 0 345
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.71 0.44 1.1 375 -1.1 2 377
CCNB2 0.74 0.45 1.1 416 -0.99 2 418
CCNB1 0.74 0.47 1.1 403 -1 2 405
ETV5 0.67 0.41 1 384 -0.99 2 386
ESR1 0.54 0.55 1 341 -0.98 11 352
CCND1 0.62 0.42 0.97 397 -0.96 2 399
GSK3A 0.16 0.094 0.28 221 -10000 0 221
Cyclin A-E1/CDK1-2 0.25 0.17 0.41 380 -10000 0 380
CDK2 0.063 0.03 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.17 0.12 0.28 347 -10000 0 347
FOXM1B/Cbp/p300 0.24 0.3 0.73 68 -1.1 2 70
GAS1 0.61 0.49 1 363 -1.1 23 386
MMP2 0.66 0.41 1 380 -1.1 7 387
RB1/FOXM1C 0.53 0.4 0.9 358 -0.98 2 360
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 0.6 212 -10000 0 212
PI3K Class IB/PDE3B -0.14 0.27 -10000 0 -0.6 212 212
PDE3B -0.14 0.27 -10000 0 -0.6 212 212
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 -0.38 346 348
CRKL -0.17 0.21 -10000 0 -0.4 365 365
HRAS -0.12 0.18 -10000 0 -0.36 225 225
mol:PIP3 -0.14 0.2 -10000 0 -0.37 275 275
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 -0.42 372 372
FOXO3 -0.14 0.2 0.51 1 -0.38 245 246
AKT1 -0.16 0.21 0.35 1 -0.39 321 322
BAD -0.14 0.2 0.33 1 -0.38 250 251
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 372 372
GSK3B -0.14 0.2 0.51 1 -0.38 250 251
RAF1 -0.096 0.16 0.25 2 -0.35 55 57
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 368 368
STAT1 -0.44 0.52 -10000 0 -1 377 377
HRAS/SPRED1 -0.093 0.16 -10000 0 -0.35 52 52
cell proliferation -0.18 0.22 -10000 0 -0.41 374 374
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 -0.41 376 376
HRAS/SPRED2 -0.093 0.16 -10000 0 -0.35 55 55
LYN/TEC/p62DOK -0.14 0.22 -10000 0 -0.4 306 306
MAPK3 -0.066 0.12 0.32 4 -0.29 21 25
STAP1 -0.18 0.22 -10000 0 -0.42 375 375
GRAP2 0.016 0.073 0.26 3 -0.6 11 14
JAK2 -0.37 0.45 -10000 0 -0.84 377 377
STAT1 (dimer) -0.43 0.51 -10000 0 -0.98 377 377
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 307 307
actin filament polymerization -0.18 0.22 0.33 1 -0.41 371 372
LYN 0.021 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 378 378
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.38 322 322
PI3K -0.15 0.22 -10000 0 -0.39 352 352
PTEN 0.023 0.031 -10000 0 -0.6 2 2
SCF/KIT/EPO/EPOR -0.51 0.64 -10000 0 -1.2 374 374
MAPK8 -0.18 0.22 -10000 0 -0.42 374 374
STAT3 (dimer) -0.18 0.22 -10000 0 -0.41 368 368
positive regulation of transcription -0.052 0.11 0.24 11 -0.24 18 29
mol:GDP -0.13 0.19 -10000 0 -0.37 234 234
PIK3C2B -0.16 0.2 -10000 0 -0.42 287 287
CBL/CRKL -0.16 0.2 -10000 0 -0.38 356 356
FER -0.18 0.22 -10000 0 -0.42 375 375
SH2B3 -0.18 0.22 -10000 0 -0.42 375 375
PDPK1 -0.12 0.19 0.33 6 -0.35 242 248
SNAI2 -0.17 0.22 0.28 4 -0.42 329 333
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 379 379
KITLG -0.002 0.059 0.26 10 -0.55 4 14
cell motility -0.32 0.39 -10000 0 -0.73 379 379
PTPN6 0.032 0.018 0.28 2 -10000 0 2
EPOR -0.11 0.19 -10000 0 -1 11 11
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 378 378
SOCS1 0.024 0.031 0.26 6 -0.6 1 7
cell migration 0.18 0.22 0.42 377 -10000 0 377
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.045 0.097 0.25 137 -10000 0 137
VAV1 0.024 0.025 0.26 2 -0.6 1 3
GRB10 -0.18 0.22 -10000 0 -0.42 370 370
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 376 376
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.14 0.3 5 -0.3 26 31
CBL 0.022 0.007 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 376 376
MAP2K2 -0.074 0.14 0.35 4 -0.3 31 35
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 267 267
STAT5A -0.27 0.34 -10000 0 -0.62 378 378
GRB2 0.023 0.006 -10000 0 -10000 0 0
response to radiation -0.17 0.21 0.28 4 -0.41 328 332
SHC/GRAP2 0.023 0.053 -10000 0 -0.38 11 11
PTPRO -0.18 0.22 -10000 0 -0.42 372 372
SH2B2 -0.18 0.22 -10000 0 -0.42 371 371
DOK1 0.024 0.002 -10000 0 -10000 0 0
MATK -0.19 0.23 -10000 0 -0.43 377 377
CREBBP -0.027 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 -1.1 273 276
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.087 0.18 -10000 0 -0.34 266 266
ATF2/c-Jun -0.084 0.16 -10000 0 -0.45 69 69
MAPK11 -0.082 0.18 -10000 0 -0.35 242 242
MITF -0.11 0.21 -10000 0 -0.41 267 267
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 272 272
KRT8 -0.1 0.2 -10000 0 -0.4 252 252
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 -0.53 267 267
CEBPB -0.1 0.2 0.29 1 -0.4 249 250
SLC9A1 -0.11 0.21 -10000 0 -0.41 266 266
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.39 259 259
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.45 244 244
JUN -0.084 0.16 -10000 0 -0.44 69 69
PPARGC1A -0.21 0.34 0.27 2 -0.57 325 327
USF1 -0.1 0.19 0.32 3 -0.38 253 256
RAB5/GDP/GDI1 -0.081 0.16 -10000 0 -0.3 267 267
NOS2 -0.11 0.22 -10000 0 -0.57 65 65
DDIT3 -0.11 0.2 -10000 0 -0.4 267 267
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.096 0.17 0.28 3 -0.33 256 259
p38alpha-beta/HBP1 -0.1 0.25 -10000 0 -0.45 244 244
CREB1 -0.12 0.22 -10000 0 -0.42 266 266
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.4 243 243
RPS6KA4 -0.11 0.21 -10000 0 -0.4 266 266
PLA2G4A -0.13 0.22 -10000 0 -0.43 265 265
GDI1 -0.11 0.21 -10000 0 -0.4 271 271
TP53 -0.15 0.26 -10000 0 -0.52 255 255
RPS6KA5 -0.12 0.21 -10000 0 -0.4 273 273
ESR1 -0.15 0.24 0.29 1 -0.42 291 292
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 269 269
MEF2A -0.11 0.21 0.29 1 -0.4 267 268
EIF4EBP1 -0.12 0.22 -10000 0 -0.43 255 255
KRT19 -0.11 0.21 0.39 1 -0.41 252 253
ELK4 -0.1 0.19 0.31 3 -0.38 256 259
ATF6 -0.1 0.19 0.32 3 -0.38 257 260
ATF1 -0.12 0.22 -10000 0 -0.42 268 268
p38alpha-beta/MAPKAPK2 -0.096 0.22 -10000 0 -0.42 230 230
p38alpha-beta/MAPKAPK3 -0.1 0.25 -10000 0 -0.45 244 244
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 0.01 0.089 -10000 0 -0.6 17 17
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 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 -0.39 499 499
MAPK8IP1/MKK7/MAP3K11/JNK1 0.058 0.034 -10000 0 -0.34 1 1
AKT1 -0.16 0.14 -10000 0 -0.28 434 434
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 0.26 48 -10000 0 48
RELN/LRP8/DAB1 -0.18 0.2 0.36 5 -0.34 486 491
LRPAP1/LRP8 0.051 0.052 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.16 0.2 0.32 4 -0.32 475 479
DAB1/alpha3/beta1 Integrin -0.15 0.18 -10000 0 -0.33 343 343
long-term memory -0.21 0.23 0.35 4 -0.38 475 479
DAB1/LIS1 -0.16 0.2 0.3 4 -0.32 477 481
DAB1/CRLK/C3G -0.16 0.19 -10000 0 -0.33 400 400
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.2 0.31 4 -0.33 473 477
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 0.26 10 -0.6 80 90
CDK5R1 0.029 0.037 0.26 19 -10000 0 19
RELN -0.35 0.31 0.26 3 -0.6 496 499
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.2 0.21 -10000 0 -0.38 478 478
GRIN2A/RELN/LRP8/DAB1/Fyn -0.18 0.23 0.34 3 -0.37 447 450
MAPK8 0.024 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.2 0.33 2 -0.36 485 487
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.2 0.18 0.22 1 -0.34 486 487
RELN/LRP8 -0.2 0.21 -10000 0 -0.38 489 489
GRIN2B/RELN/LRP8/DAB1/Fyn -0.19 0.22 0.37 3 -0.35 500 503
PI3K 0.033 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 -0.32 329 330
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.034 0.26 3 -0.6 2 5
CRLK/C3G 0.034 0.009 -10000 0 -10000 0 0
GRIN2B -0.032 0.17 0.26 1 -0.6 69 70
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.091 0.12 0.23 1 -0.36 46 47
neuron adhesion -0.16 0.15 0.33 2 -0.52 15 17
LRP8 0.051 0.077 0.26 94 -10000 0 94
GSK3B -0.15 0.14 -10000 0 -0.27 424 424
RELN/VLDLR/DAB1/Fyn -0.18 0.2 0.32 2 -0.34 475 477
MAP3K11 0.024 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.16 -10000 0 -0.29 470 470
CDK5 0.024 0.009 0.26 1 -10000 0 1
MAPT -0.02 0.2 0.89 14 -0.55 74 88
neuron migration -0.2 0.18 0.28 1 -0.36 394 395
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.092 0.12 0.23 1 -0.36 46 47
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 487 487
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 0.24 274 -0.26 2 276
STMN1 0.083 0.083 0.28 53 -10000 0 53
Aurora B/RasGAP/Survivin 0.2 0.14 0.34 397 -10000 0 397
Chromosomal passenger complex/Cul3 protein complex 0.012 0.15 0.2 158 -0.25 98 256
BIRC5 0.19 0.12 0.27 558 -10000 0 558
DES -0.16 0.32 -10000 0 -0.58 215 215
Aurora C/Aurora B/INCENP 0.11 0.081 0.33 6 -0.31 1 7
Aurora B/TACC1 0.077 0.097 0.19 4 -0.37 13 17
Aurora B/PP2A 0.11 0.085 0.21 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.028 0.14 9 -10000 0 9
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 -0.39 313 313
KIF2C 0.16 0.11 0.25 462 -10000 0 462
PEBP1 0.028 0.004 -10000 0 -10000 0 0
KIF20A 0.21 0.098 0.26 649 -10000 0 649
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.085 -10000 0 -10000 0 0
SEPT1 0.027 0.031 0.26 13 -10000 0 13
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.027 0.029 0.26 12 -10000 0 12
NSUN2/NPM1/Nucleolin 0.081 0.19 0.3 40 -0.44 76 116
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 0.065 0.24 32 -10000 0 32
AURKB 0.15 0.12 0.26 436 -10000 0 436
AURKC 0.026 0.035 0.26 10 -0.6 1 11
CDCA8 0.12 0.12 0.27 294 -10000 0 294
cytokinesis 0.15 0.15 0.33 269 -0.36 5 274
Aurora B/Septin1 0.19 0.18 0.38 301 -0.34 4 305
AURKA 0.12 0.12 0.26 360 -10000 0 360
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.3 -10000 0 -0.6 321 321
BUB1 0.2 0.11 0.26 601 -10000 0 601
hSgo1/Aurora B/Survivin 0.29 0.19 0.43 507 -10000 0 507
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.2 0.15 0.36 304 -10000 0 304
SGOL1 0.19 0.11 0.26 561 -10000 0 561
CENPA 0.19 0.15 0.31 434 -0.19 1 435
NCAPG 0.15 0.12 0.26 440 -10000 0 440
Aurora B/HC8 Proteasome 0.12 0.084 -10000 0 -10000 0 0
NCAPD2 0.024 0.01 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.084 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.13 0.12 0.26 350 -10000 0 350
NPM1 0.073 0.13 0.27 4 -0.41 22 26
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 0.084 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.22 0.16 0.38 355 -10000 0 355
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
NSUN2 0.079 0.12 0.28 18 -0.33 21 39
MYLK 0.035 0.13 0.24 6 -0.32 73 79
KIF23 0.11 0.12 0.27 267 -10000 0 267
VIM 0.083 0.09 0.38 26 -0.43 2 28
RACGAP1 0.045 0.055 0.28 42 -10000 0 42
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.07 0.14 -10000 0 -0.36 45 45
Chromosomal passenger complex 0.19 0.13 0.29 476 -10000 0 476
Chromosomal passenger complex/EVI5 0.25 0.17 0.41 399 -10000 0 399
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
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.25 0.27 -10000 0 -0.72 116 116
PCK1 -0.94 0.64 -10000 0 -1.4 496 496
HNF4A -0.24 0.28 -10000 0 -0.81 63 63
KCNJ11 -0.28 0.3 -10000 0 -0.82 103 103
AKT1 -0.17 0.16 -10000 0 -0.46 38 38
response to starvation 0.004 0.011 -10000 0 -10000 0 0
DLK1 -0.46 0.48 -10000 0 -1.1 263 263
NKX2-1 -0.04 0.16 0.52 3 -0.54 1 4
ACADM -0.26 0.27 -10000 0 -0.7 130 130
TAT -1.1 0.63 -10000 0 -1.5 605 605
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 -0.75 227 227
PKLR -0.23 0.27 0.56 2 -0.74 87 89
APOA1 -0.29 0.32 -10000 0 -0.88 79 79
CPT1C -0.25 0.27 0.6 1 -0.74 103 104
ALAS1 -0.16 0.16 -10000 0 -0.72 7 7
TFRC -0.42 0.27 -10000 0 -0.73 231 231
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 0.26 7 -10000 0 7
CPT1A -0.24 0.27 -10000 0 -0.74 99 99
HMGCS1 -0.25 0.27 -10000 0 -0.74 103 103
NR3C1 -0.12 0.12 -10000 0 -0.24 282 282
CPT1B -0.25 0.27 -10000 0 -0.76 96 96
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.024 -10000 0 -10000 0 0
GCK -0.29 0.34 -10000 0 -0.9 124 124
CREB1 -0.074 0.092 -10000 0 -0.22 94 94
IGFBP1 -0.44 0.55 -10000 0 -1.4 195 195
PDX1 -0.13 0.16 0.51 1 -0.6 3 4
UCP2 -0.25 0.27 0.56 1 -0.76 88 89
ALDOB -0.28 0.29 -10000 0 -0.83 88 88
AFP -0.58 0.52 0.33 2 -0.84 558 560
BDH1 -0.25 0.27 -10000 0 -0.73 106 106
HADH -0.28 0.29 -10000 0 -0.76 122 122
F2 -0.29 0.31 -10000 0 -0.87 76 76
HNF1A 0.034 0.032 0.26 7 -10000 0 7
G6PC -0.18 0.12 -10000 0 -0.58 7 7
SLC2A2 -0.16 0.17 -10000 0 -0.96 1 1
INS 0.02 0.08 0.23 20 -10000 0 20
FOXA1 -0.22 0.23 0.28 15 -0.34 555 570
FOXA3 -0.37 0.22 0.3 10 -0.46 637 647
FOXA2 -0.33 0.33 -10000 0 -0.82 162 162
ABCC8 -0.33 0.39 0.59 1 -0.96 164 165
ALB -0.8 0.55 0.37 1 -1.1 569 570
EGFR-dependent Endothelin signaling events

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
HRAS 0.024 0.01 0.26 1 -10000 0 1
EGFR -0.19 0.29 -10000 0 -0.6 277 277
EGF/EGFR -0.16 0.24 -10000 0 -0.39 384 384
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.21 -10000 0 -0.38 287 287
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 -0.09 0.24 0.26 2 -0.6 151 153
EGF/EGFR dimer/SHC -0.16 0.23 -10000 0 -0.43 311 311
mol:GDP -0.12 0.2 -10000 0 -0.37 287 287
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.02 0.16 0.26 1 -0.6 58 59
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.35 286 286
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.12 0.2 -10000 0 -0.36 286 286
FRAP1 -0.15 0.17 0.16 3 -0.36 287 290
EGF/EGFR dimer -0.21 0.27 -10000 0 -0.48 397 397
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0 0.12 -10000 0 -0.44 60 60
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 0.1 3 -0.11 489 492
BUB1B 0.095 0.069 0.16 369 -10000 0 369
PLK1 0.055 0.04 0.099 241 -10000 0 241
PLK1S1 0.028 0.036 0.13 10 -0.16 18 28
KIF2A 0.045 0.037 0.21 5 -10000 0 5
regulation of mitotic centrosome separation 0.055 0.04 0.11 133 -10000 0 133
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.25 0.15 0.33 589 -10000 0 589
WEE1 0.048 0.063 0.22 2 -0.27 19 21
cytokinesis 0.14 0.078 0.22 263 -0.35 1 264
PP2A-alpha B56 0.12 0.12 -10000 0 -0.44 19 19
AURKA 0.072 0.053 0.12 369 -0.15 2 371
PICH/PLK1 0.11 0.093 0.22 279 -10000 0 279
CENPE 0.072 0.059 0.17 77 -10000 0 77
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 0.055 0.14 260 -10000 0 260
PAK1 0.022 0.016 0.26 3 -10000 0 3
SPC24 0.17 0.12 0.26 499 -10000 0 499
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.082 0.072 0.14 382 -0.19 17 399
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.016 39 -10000 0 39
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.025 0.019 0.056 128 -10000 0 128
G2 phase of mitotic cell cycle 0.001 0.003 0.015 14 -10000 0 14
STAG2 0.024 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 0.11 133 -10000 0 133
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.12 0.13 -10000 0 -0.47 24 24
TPT1 0.015 0.058 0.13 1 -0.17 63 64
CDC25C 0.12 0.071 0.17 391 -0.22 10 401
CDC25B 0.03 0.033 0.27 14 -10000 0 14
SGOL1 0.074 0.05 0.11 489 -0.1 3 492
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.074 0.07 0.26 19 -10000 0 19
CDC14B -0.011 0.075 -10000 0 -0.45 23 23
CDC20 0.16 0.12 0.26 448 -10000 0 448
PLK1/PBIP1 0.043 0.052 0.15 133 -10000 0 133
mitosis -0.005 0.005 0.024 2 -10000 0 2
FBXO5 0.034 0.037 0.16 13 -10000 0 13
CDC2 0.004 0.004 0.011 177 -10000 0 177
NDC80 0.17 0.12 0.26 514 -10000 0 514
metaphase plate congression 0.032 0.054 0.15 1 -0.19 37 38
ERCC6L 0.1 0.09 0.25 155 -10000 0 155
NLP/gamma Tubulin 0.026 0.025 0.08 29 -0.084 7 36
microtubule cytoskeleton organization 0.015 0.058 0.13 1 -0.16 63 64
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 7 -10000 0 7
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 7 -10000 0 7
PLK1/PRC1-2 0.22 0.12 0.28 628 -10000 0 628
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 0.036 0.1 136 -10000 0 136
mitotic prometaphase 0.002 0.005 0.023 38 -10000 0 38
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.053 -10000 0 -0.34 2 2
microtubule-based process 0.18 0.087 0.23 647 -10000 0 647
Golgi organization 0.055 0.04 0.11 133 -10000 0 133
Cohesin/SA2 0.059 0.03 0.14 5 -10000 0 5
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.21 0.099 0.26 649 -10000 0 649
APC/C/CDC20 0.15 0.1 0.24 447 -10000 0 447
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.043 0.051 0.15 133 -10000 0 133
PRC1 0.087 0.11 0.26 218 -10000 0 218
ECT2 0.055 0.059 0.21 59 -10000 0 59
C13orf34 0.045 0.034 0.096 134 -10000 0 134
NUDC 0.032 0.054 0.15 1 -0.19 37 38
regulation of attachment of spindle microtubules to kinetochore 0.095 0.069 0.16 369 -10000 0 369
spindle assembly 0.04 0.031 0.093 93 -10000 0 93
spindle stabilization 0.028 0.036 0.13 10 -0.16 18 28
APC/C/HCDH1 0.01 0.068 -10000 0 -0.37 25 25
MKLP2/PLK1 0.19 0.088 0.23 647 -10000 0 647
CCNB1 0.078 0.1 0.27 182 -10000 0 182
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 0.12 5 -0.16 30 35
G2/M transition of mitotic cell cycle 0.047 0.048 0.2 10 -10000 0 10
MLF1IP 0.028 0.053 0.14 142 -10000 0 142
INCENP 0.024 0.005 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory 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
PCK2 0.098 0.11 0.5 4 -10000 0 4
SMARCC2 0.024 0.013 -10000 0 -0.18 2 2
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.13 0.22 0.4 5 -0.76 54 59
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 0.26 4 -10000 0 4
FKBP5 0.017 0.073 0.26 3 -0.6 11 14
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.31 101 -0.3 8 109
PRL -0.067 0.12 0.58 2 -10000 0 2
cortisol/GR alpha (dimer)/TIF2 0.2 0.27 0.53 266 -0.48 4 270
RELA -0.04 0.1 0.3 1 -0.26 21 22
FGG 0.22 0.24 0.5 259 -0.55 1 260
GR beta/TIF2 0.1 0.14 0.32 110 -0.41 7 117
IFNG -0.32 0.36 0.49 3 -0.7 325 328
apoptosis -0.27 0.31 0.86 1 -0.65 247 248
CREB1 0.064 0.057 -10000 0 -10000 0 0
histone acetylation 0.031 0.14 0.37 47 -0.39 14 61
BGLAP -0.09 0.14 -10000 0 -0.46 24 24
GR/PKAc 0.14 0.13 0.37 63 -0.36 1 64
NF kappa B1 p50/RelA -0.066 0.18 0.49 2 -0.34 132 134
SMARCD1 0.025 0.011 -10000 0 -10000 0 0
MDM2 0.1 0.11 0.22 273 -10000 0 273
GATA3 0.014 0.12 0.26 27 -0.6 27 54
AKT1 0.019 0.012 -10000 0 -10000 0 0
CSF2 -0.026 0.11 0.4 2 -0.45 7 9
GSK3B -0.001 0.024 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.8 1 -0.62 122 123
CSN2 0.17 0.19 0.39 225 -0.51 1 226
BRG1/BAF155/BAF170/BAF60A 0.061 0.041 -10000 0 -0.48 4 4
NFATC1 0.023 0.022 -10000 0 -0.6 1 1
POU2F1 0.023 0.016 0.26 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 0.26 8 -0.6 10 18
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.33 75 -0.28 8 83
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.38 0.4 0.62 2 -0.81 346 348
JUN -0.27 0.29 0.37 6 -0.55 347 353
IL4 -0.12 0.15 -10000 0 -0.53 8 8
CDK5R1 0.022 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 -0.5 405 405
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.33 68 -0.3 5 73
cortisol/GR alpha (monomer) 0.3 0.32 0.61 348 -0.52 2 350
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.21 0.3 -10000 0 -0.62 261 261
AP-1/NFAT1-c-4 -0.46 0.46 0.47 6 -0.84 436 442
AFP -0.55 0.65 0.45 2 -1.4 287 289
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.17 0.16 0.46 58 -10000 0 58
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 -1.4 400 400
KRT14 -0.77 0.67 -10000 0 -1.4 465 465
TBP 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.16 0.14 0.3 388 -10000 0 388
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 0.47 6 -0.84 437 443
MAPK14 0.002 0.023 -10000 0 -10000 0 0
MAPK10 -0.092 0.22 -10000 0 -0.6 125 125
MAPK11 -0.002 0.038 -10000 0 -0.61 2 2
KRT5 -0.79 0.72 0.45 1 -1.4 455 456
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 0.36 337 -10000 0 337
MAPK3 0 0.022 -10000 0 -10000 0 0
MAPK1 0.002 0.022 -10000 0 -10000 0 0
ICAM1 -0.2 0.24 0.52 3 -0.51 241 244
NFKB1 -0.04 0.1 0.27 2 -0.24 31 33
MAPK8 -0.2 0.22 0.32 4 -0.42 334 338
MAPK9 0.002 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.33 0.86 1 -0.69 248 249
BAX 0.016 0.062 -10000 0 -10000 0 0
POMC -0.17 0.29 -10000 0 -0.9 62 62
EP300 0.16 0.14 0.3 381 -10000 0 381
cortisol/GR alpha (dimer)/p53 0.23 0.26 0.53 283 -0.55 1 284
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.11 0.27 132 -10000 0 132
SGK1 0.2 0.2 0.5 11 -1.1 4 15
IL13 -0.27 0.28 0.51 4 -0.61 213 217
IL6 -0.46 0.53 0.64 1 -1.1 321 322
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.23 0.23 0.57 1 -0.66 55 56
IL2 -0.35 0.36 0.49 2 -0.72 331 333
CDK5 0.016 0.016 0.26 1 -10000 0 1
PRKACB 0.034 0.066 0.26 42 -0.6 3 45
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.2 0.29 0.55 2 -0.65 150 152
CDK5R1/CDK5 0.016 0.037 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.021 0.16 0.41 2 -0.39 22 24
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.5 334 -0.51 1 335
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.16 0.16 0.36 203 -10000 0 203
NF kappa B1 p50/RelA/Cbp 0.07 0.19 0.42 54 -0.41 11 65
JUN (dimer) -0.27 0.29 0.37 6 -0.55 348 354
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.14 0.21 -10000 0 -0.61 82 82
NR3C1 0.18 0.2 0.4 280 -0.32 1 281
NR4A1 -0.034 0.19 -10000 0 -0.58 87 87
TIF2/SUV420H1 0.024 0.046 -10000 0 -0.45 7 7
MAPKKK cascade -0.27 0.31 0.86 1 -0.65 247 248
cortisol/GR alpha (dimer)/Src-1 0.26 0.27 0.53 330 -0.55 1 331
PBX1 0.023 0.016 0.26 1 -10000 0 1
POU1F1 0.022 0.014 0.26 1 -10000 0 1
SELE -0.2 0.3 0.64 1 -0.7 144 145
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.16 0.36 202 -10000 0 202
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.5 334 -0.51 1 335
mol:cortisol 0.17 0.19 0.35 360 -0.25 3 363
MMP1 0.047 0.31 0.45 1 -0.93 62 63
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.1 0.13 0.32 223 -0.18 3 226
NFATC2 -0.011 0.22 0.49 10 -0.63 53 63
NFATC3 -0.048 0.13 -10000 0 -0.28 146 146
CD40LG -0.31 0.52 0.75 7 -1 248 255
ITCH -0.005 0.087 -10000 0 -10000 0 0
CBLB -0.004 0.087 -10000 0 -0.28 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.079 0.38 0.66 37 -1 54 91
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 82 82
TLE4 -0.016 0.18 0.37 1 -0.67 39 40
Jun/NFAT1-c-4/p21SNFT -0.18 0.44 0.67 8 -0.84 204 212
AP-1/NFAT1-c-4 -0.33 0.63 0.79 15 -1.2 246 261
IKZF1 -0.005 0.15 0.5 7 -0.5 39 46
T-helper 2 cell differentiation -0.069 0.26 0.53 1 -0.85 48 49
AP-1/NFAT1 -0.11 0.28 0.45 16 -0.49 227 243
CALM1 0.009 0.066 -10000 0 -10000 0 0
EGR2 -0.25 0.55 0.67 4 -1.4 118 122
EGR3 -0.35 0.64 0.6 6 -1.2 259 265
NFAT1/FOXP3 0.064 0.22 0.48 84 -0.48 49 133
EGR1 -0.18 0.29 -10000 0 -0.6 276 276
JUN 0.014 0.066 0.22 2 -0.61 7 9
EGR4 0.036 0.054 0.27 43 -10000 0 43
mol:Ca2+ -0.012 0.057 -10000 0 -0.18 81 81
GBP3 -0.014 0.17 0.36 4 -0.55 48 52
FOSL1 0.027 0.045 0.26 15 -0.6 2 17
NFAT1-c-4/MAF/IRF4 -0.2 0.46 0.65 7 -0.86 227 234
DGKA -0.008 0.15 0.59 1 -0.52 34 35
CREM 0.023 0.009 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.49 0.65 3 -0.94 248 251
CTLA4 0.048 0.21 0.43 104 -0.53 35 139
NFAT1-c-4 (dimer)/EGR1 -0.3 0.53 0.67 3 -1 258 261
NFAT1-c-4 (dimer)/EGR4 -0.19 0.45 0.64 5 -0.84 233 238
FOS -0.17 0.29 -10000 0 -0.6 259 259
IFNG -0.043 0.27 0.51 15 -0.76 60 75
T cell activation -0.15 0.3 0.69 4 -0.68 134 138
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 0.64 235 -0.63 3 238
TNF -0.27 0.46 0.57 4 -0.91 248 252
FASLG -0.32 0.62 0.76 4 -1.2 252 256
TBX21 0.017 0.14 0.38 9 -0.6 33 42
BATF3 0.021 0.009 -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 -0.2 0.44 0.59 3 -0.84 233 236
GATA3 0.011 0.12 0.26 25 -0.6 27 52
T-helper 1 cell differentiation -0.041 0.26 0.5 16 -0.72 65 81
IL2RA -0.08 0.36 0.65 35 -0.93 58 93
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.007 0.15 0.37 1 -0.51 35 36
E2F1 0.1 0.11 0.27 262 -10000 0 262
PPARG -0.12 0.26 -10000 0 -0.6 186 186
SLC3A2 -0.008 0.15 0.35 2 -0.48 43 45
IRF4 -0.022 0.17 0.26 11 -0.6 64 75
PTGS2 -0.36 0.56 0.65 6 -1.1 274 280
CSF2 -0.3 0.5 0.69 9 -0.97 246 255
JunB/Fra1/NFAT1-c-4 -0.18 0.43 0.63 3 -0.82 225 228
IL4 -0.073 0.27 0.53 1 -0.91 47 48
IL5 -0.3 0.5 0.64 7 -0.97 246 253
IL2 -0.16 0.31 0.69 4 -0.71 121 125
IL3 -0.054 0.13 -10000 0 -0.79 18 18
RNF128 -0.047 0.22 0.28 5 -0.69 84 89
NFATC1 -0.16 0.34 0.63 3 -0.64 235 238
CDK4 0.12 0.24 0.58 80 -0.59 3 83
PTPRK -0.01 0.16 0.39 2 -0.56 37 39
IL8 -0.3 0.51 0.62 10 -0.98 244 254
POU2F1 0.021 0.012 0.26 1 -10000 0 1
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.26 0.37 -10000 0 -0.82 166 166
HDAC7 0.025 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.33 -10000 0 -0.8 106 106
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.26 0.37 -10000 0 -0.82 165 165
AP1 -0.12 0.23 -10000 0 -0.45 264 264
ABCG2 -0.28 0.39 -10000 0 -0.86 164 164
HIF1A -0.051 0.081 -10000 0 -0.22 24 24
TFF3 -0.27 0.41 0.7 3 -0.84 185 188
GATA2 0.01 0.096 0.26 10 -0.6 18 28
AKT1 -0.06 0.093 -10000 0 -0.3 9 9
response to hypoxia -0.065 0.083 -10000 0 -0.22 71 71
MCL1 -0.26 0.36 -10000 0 -0.81 160 160
NDRG1 -0.24 0.36 -10000 0 -0.82 141 141
SERPINE1 -0.26 0.38 0.7 2 -0.82 167 169
FECH -0.26 0.37 -10000 0 -0.82 164 164
FURIN -0.26 0.37 -10000 0 -0.82 163 163
NCOA2 0.019 0.059 -10000 0 -0.6 7 7
EP300 -0.065 0.13 0.32 1 -0.35 81 82
HMOX1 -0.26 0.38 -10000 0 -0.82 165 165
BHLHE40 -0.26 0.37 -10000 0 -0.82 165 165
BHLHE41 -0.26 0.38 -10000 0 -0.84 165 165
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.026 0.11 -10000 0 -10000 0 0
ENG -0.021 0.11 0.4 2 -10000 0 2
JUN 0.016 0.058 -10000 0 -0.6 7 7
RORA -0.26 0.37 -10000 0 -0.81 170 170
ABCB1 -0.26 0.45 -10000 0 -1.1 165 165
TFRC -0.26 0.37 0.64 1 -0.82 165 166
CXCR4 -0.26 0.38 -10000 0 -0.83 158 158
TF -0.44 0.46 -10000 0 -0.91 313 313
CITED2 -0.26 0.37 -10000 0 -0.82 165 165
HIF1A/ARNT -0.29 0.42 0.73 1 -0.95 147 148
LDHA -0.042 0.13 -10000 0 -0.73 21 21
ETS1 -0.26 0.37 -10000 0 -0.82 165 165
PGK1 -0.26 0.37 -10000 0 -0.82 165 165
NOS2 -0.26 0.37 -10000 0 -0.82 160 160
ITGB2 -0.26 0.38 -10000 0 -0.82 164 164
ALDOA -0.26 0.37 -10000 0 -0.85 144 144
Cbp/p300/CITED2 -0.27 0.4 -10000 0 -0.92 137 137
FOS -0.17 0.29 -10000 0 -0.6 254 254
HK2 -0.26 0.37 -10000 0 -0.82 165 165
SP1 0.001 0.059 -10000 0 -10000 0 0
GCK -0.14 0.36 0.54 1 -1.4 56 57
HK1 -0.26 0.37 -10000 0 -0.83 156 156
NPM1 -0.26 0.37 -10000 0 -0.82 166 166
EGLN1 -0.25 0.36 -10000 0 -0.81 160 160
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.26 0.37 -10000 0 -0.82 166 166
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.2 0.37 -10000 0 -1.1 100 100
IGFBP1 -0.33 0.43 -10000 0 -0.9 218 218
VEGFA -0.17 0.29 -10000 0 -0.71 91 91
HIF1A/JAB1 -0.008 0.067 -10000 0 -10000 0 0
CP -0.32 0.46 0.68 1 -0.94 217 218
CXCL12 -0.28 0.4 -10000 0 -0.88 164 164
COPS5 0.024 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.01 -10000 0 -10000 0 0
BNIP3 -0.26 0.37 0.77 1 -0.82 162 163
EGLN3 -0.25 0.38 0.7 2 -0.84 148 150
CA9 -0.22 0.4 0.67 6 -0.82 155 161
TERT -0.25 0.38 0.7 2 -0.82 158 160
ENO1 -0.26 0.37 -10000 0 -0.83 159 159
PFKL -0.26 0.37 -10000 0 -0.82 161 161
NCOA1 0.025 0.022 -10000 0 -0.6 1 1
ADM -0.28 0.4 -10000 0 -0.86 188 188
ARNT -0.039 0.069 -10000 0 -10000 0 0
HNF4A 0.017 0.042 0.27 11 -10000 0 11
ADFP -0.27 0.36 0.57 1 -0.81 173 174
SLC2A1 -0.18 0.29 -10000 0 -0.7 92 92
LEP -0.51 0.41 -10000 0 -0.89 349 349
HIF1A/ARNT/Cbp/p300 -0.22 0.34 -10000 0 -0.79 121 121
EPO -0.097 0.26 0.62 4 -0.76 22 26
CREBBP -0.055 0.12 0.32 1 -0.35 60 61
HIF1A/ARNT/Cbp/p300/HDAC7 -0.21 0.33 -10000 0 -0.82 95 95
PFKFB3 -0.26 0.38 -10000 0 -0.83 161 161
NT5E -0.26 0.38 -10000 0 -0.83 166 166
EPHB forward 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
Ephrin A5/EPHB2 -0.006 0.12 -10000 0 -0.37 81 81
cell-cell adhesion 0.15 0.16 0.32 343 -10000 0 343
Ephrin B/EPHB2/RasGAP 0.031 0.11 -10000 0 -0.34 59 59
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 0.2 -10000 0 -0.38 352 352
HRAS/GDP -0.14 0.19 -10000 0 -0.44 139 139
Ephrin B/EPHB1/GRB7 -0.13 0.22 -10000 0 -0.38 328 328
Endophilin/SYNJ1 -0.028 0.087 0.23 2 -0.32 58 60
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.13 0.22 -10000 0 -0.38 344 344
endothelial cell migration 0.044 0.02 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PAK1 -0.033 0.1 0.35 2 -0.35 64 66
HRAS 0.024 0.01 0.26 1 -10000 0 1
RRAS -0.028 0.088 0.23 2 -0.32 58 60
DNM1 0.021 0.049 0.26 1 -0.6 5 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.19 0.35 2 -0.36 363 365
lamellipodium assembly -0.15 0.16 -10000 0 -0.32 343 343
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.17 -10000 0 -0.33 265 265
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
EPHB2 0.028 0.033 0.26 15 -10000 0 15
EPHB3 0.025 0.015 0.26 3 -10000 0 3
EPHB1 -0.24 0.31 0.26 1 -0.6 352 353
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.14 0.18 -10000 0 -0.44 134 134
Ephrin B/EPHB2 0.021 0.1 -10000 0 -0.34 59 59
Ephrin B/EPHB3 0.019 0.1 -10000 0 -0.34 55 55
JNK cascade -0.14 0.16 0.36 6 -0.33 349 355
Ephrin B/EPHB1 -0.14 0.22 -10000 0 -0.37 363 363
RAP1/GDP -0.11 0.17 -10000 0 -0.41 118 118
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EFNB3 -0.024 0.16 -10000 0 -0.6 61 61
EFNB1 0.025 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.12 0.2 -10000 0 -0.35 350 350
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 -0.43 130 130
Rap1/GTP -0.13 0.18 -10000 0 -0.34 274 274
axon guidance -0.006 0.12 -10000 0 -0.37 81 81
MAPK3 -0.099 0.15 -10000 0 -0.4 87 87
MAPK1 -0.1 0.15 -10000 0 -0.4 89 89
Rac1/GDP -0.12 0.17 -10000 0 -0.42 127 127
actin cytoskeleton reorganization -0.13 0.13 -10000 0 -0.38 88 88
CDC42/GDP -0.12 0.17 -10000 0 -0.41 129 129
PI3K 0.048 0.022 -10000 0 -10000 0 0
EFNA5 -0.035 0.18 -10000 0 -0.6 77 77
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.091 -10000 0 -0.29 59 59
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.13 0.18 -10000 0 -0.5 54 54
PTK2 0.16 0.28 0.69 172 -10000 0 172
MAP4K4 -0.15 0.16 0.36 6 -0.34 349 355
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 61 68
MAP2K1 -0.11 0.16 -10000 0 -0.42 91 91
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.21 -10000 0 -0.35 349 349
cell migration -0.12 0.19 0.31 5 -0.44 111 116
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.028 0.088 0.23 2 -0.32 58 60
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.2 0.18 0.22 2 -0.34 477 479
HRAS/GTP -0.12 0.2 -10000 0 -0.34 354 354
Ephrin B1/EPHB1-2 -0.12 0.2 -10000 0 -0.35 350 350
cell adhesion mediated by integrin 0.009 0.091 0.3 56 -0.25 6 62
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.13 0.21 -10000 0 -0.35 362 362
RAC1-CDC42/GTP -0.15 0.16 -10000 0 -0.33 323 323
RASA1 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.17 -10000 0 -0.4 121 121
ruffle organization -0.15 0.17 0.37 4 -0.52 53 57
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.031 0.091 0.22 2 -0.33 59 61
Ephrin B/EPHB2/KALRN 0.025 0.12 -10000 0 -0.36 69 69
ROCK1 0.017 0.029 0.2 4 -10000 0 4
RAS family/GDP -0.12 0.12 -10000 0 -0.38 81 81
Rac1/GTP -0.14 0.18 -10000 0 -0.34 342 342
Ephrin B/EPHB1/Src/Paxillin -0.13 0.19 -10000 0 -0.33 347 347
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.34 240 240
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.26 0.35 1 -0.43 307 308
NT-4/5 (dimer)/p75(NTR) -0.26 0.31 -10000 0 -0.53 433 433
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.092 0.17 0.36 1 -0.34 226 227
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.018 0.17 0.26 19 -0.6 63 82
MGDIs/NGR/p75(NTR)/LINGO1 -0.058 0.21 0.35 6 -0.37 233 239
FURIN 0.024 0.01 0.26 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.22 -10000 0 -0.42 266 266
LINGO1 0.075 0.099 0.26 175 -10000 0 175
Sortilin/TRAF6/NRIF 0.023 0.027 -10000 0 -0.59 1 1
proBDNF (dimer) -0.018 0.17 0.26 19 -0.6 63 82
NTRK1 0.025 0.049 0.26 20 -0.6 2 22
RTN4R 0.029 0.038 0.26 20 -10000 0 20
neuron apoptosis -0.092 0.21 0.35 8 -0.53 65 73
IRAK1 0.025 0.012 0.26 2 -10000 0 2
SHC1 -0.096 0.17 -10000 0 -0.39 186 186
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.071 0.19 -10000 0 -0.36 236 236
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.082 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 0.086 0.26 7 -0.6 15 22
MAGED1 0.025 0.012 0.26 2 -10000 0 2
APP 0.024 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.21 0.3 -10000 0 -0.6 313 313
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 0.26 7 -0.6 15 22
cell cycle arrest -0.084 0.17 0.3 14 -0.32 236 250
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 -0.49 390 390
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 0.26 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 -0.44 238 238
BEX1 -0.02 0.24 0.26 137 -0.6 111 248
mol:GDP -0.12 0.18 -10000 0 -0.38 247 247
NGF (dimer) -0.002 0.14 0.34 1 -0.36 103 104
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.041 0.2 0.34 5 -0.34 221 226
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.075 0.17 -10000 0 -0.34 240 240
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 0.2 -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) -0.065 0.22 0.26 11 -0.6 121 132
TP53 -0.1 0.18 0.39 5 -0.35 251 256
PRDM4 -0.1 0.17 -10000 0 -0.36 236 236
BDNF (dimer) 0.018 0.21 0.34 16 -0.37 149 165
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 -0.36 234 234
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.15 0.22 0.33 3 -0.43 248 251
DIABLO 0.024 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 -0.39 241 241
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 -0.48 322 322
MAPK8 -0.11 0.19 0.3 8 -0.38 227 235
MAPK9 -0.11 0.19 0.3 6 -0.38 220 226
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.065 0.22 0.26 11 -0.6 121 132
NTF4 -0.21 0.3 -10000 0 -0.6 313 313
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 -0.079 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 0.26 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 0.26 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.099 0.18 0.28 13 -0.36 232 245
BAD -0.13 0.2 0.42 6 -0.4 235 241
RIPK2 0.02 0.018 0.26 3 -10000 0 3
NGFR -0.16 0.28 -10000 0 -0.6 238 238
CYCS -0.098 0.16 0.36 2 -0.34 232 234
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 0.42 6 -0.4 234 240
BDNF (dimer)/p75(NTR) -0.14 0.25 -10000 0 -0.46 285 285
PI3K -0.071 0.19 -10000 0 -0.36 229 229
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.071 0.19 -10000 0 -0.36 237 237
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) -0.12 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 -0.36 238 238
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 0.019 0.02 0.26 5 -10000 0 5
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 0.26 1 -10000 0 1
NGFRAP1 0.023 0.031 -10000 0 -0.6 2 2
CASP3 -0.12 0.19 0.4 6 -0.38 237 243
E2F1 0.1 0.11 0.26 262 -10000 0 262
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.01 0.12 -10000 0 -0.43 15 15
NGF (dimer)/TRKA 0.025 0.073 0.2 23 -0.42 17 40
MMP7 -0.041 0.2 0.26 24 -0.6 92 116
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.06 0.19 -10000 0 -0.35 231 231
MMP3 0.1 0.14 0.26 293 -0.6 9 302
APAF-1/Caspase 9 -0.098 0.12 -10000 0 -0.48 10 10
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.073 0.13 -10000 0 -0.43 70 70
PTK2B 0.02 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.17 -10000 0 -0.73 31 31
EDN1 -0.076 0.17 -10000 0 -0.58 69 69
EDN3 -0.24 0.3 0.26 1 -0.6 339 340
EDN2 0.078 0.11 0.26 197 -0.6 4 201
HRAS/GDP -0.095 0.19 -10000 0 -0.5 96 96
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.06 0.14 -10000 0 -0.4 74 74
ADCY4 -0.13 0.2 0.29 3 -0.44 203 206
ADCY5 -0.22 0.25 -10000 0 -0.46 358 358
ADCY6 -0.12 0.19 0.29 3 -0.42 199 202
ADCY7 -0.12 0.19 0.29 3 -0.42 197 200
ADCY1 -0.12 0.2 0.26 2 -0.42 205 207
ADCY2 -0.14 0.22 0.28 9 -0.47 216 225
ADCY3 -0.12 0.19 0.28 2 -0.42 197 199
ADCY8 -0.1 0.18 0.28 3 -0.42 150 153
ADCY9 -0.12 0.18 0.28 1 -0.42 188 189
arachidonic acid secretion -0.17 0.27 0.32 1 -0.5 278 279
ETB receptor/Endothelin-1/Gq/GTP -0.048 0.15 -10000 0 -0.37 107 107
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
HRAS 0.023 0.01 0.26 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP -0.059 0.13 -10000 0 -0.4 70 70
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.44 203 203
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.061 0.15 0.39 8 -0.44 68 76
EDNRB -0.019 0.16 -10000 0 -0.59 61 61
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.073 0.15 0.29 1 -0.47 74 75
CYSLTR1 -0.078 0.14 -10000 0 -0.48 69 69
SLC9A1 -0.046 0.095 -10000 0 -0.29 76 76
mol:GDP -0.1 0.2 0.34 2 -0.5 112 114
SLC9A3 -0.1 0.27 -10000 0 -0.64 130 130
RAF1 -0.14 0.23 0.32 1 -0.47 210 211
JUN -0.05 0.18 -10000 0 -0.77 32 32
JAK2 -0.071 0.13 -10000 0 -0.43 72 72
mol:IP3 -0.073 0.16 -10000 0 -0.45 83 83
ETA receptor/Endothelin-1 -0.084 0.16 0.34 5 -0.5 73 78
PLCB1 -0.012 0.14 -10000 0 -0.6 43 43
PLCB2 0.013 0.03 0.26 1 -0.6 1 2
ETA receptor/Endothelin-3 -0.2 0.22 -10000 0 -0.46 344 344
FOS -0.31 0.46 -10000 0 -0.94 276 276
Gai/GDP -0.1 0.3 -10000 0 -0.75 130 130
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.19 -10000 0 -0.53 101 101
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.075 0.16 -10000 0 -0.43 92 92
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 -0.6 174 174
Gs family/GDP -0.15 0.24 -10000 0 -0.51 195 195
ETA receptor/Endothelin-1/Gq/GTP -0.047 0.12 -10000 0 -0.39 50 50
MAPK14 -0.062 0.15 -10000 0 -0.43 82 82
TRPC6 -0.051 0.18 -10000 0 -0.78 31 31
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.16 -10000 0 -0.42 101 101
ETB receptor/Endothelin-2 0.032 0.15 0.25 14 -0.42 65 79
ETB receptor/Endothelin-3 -0.2 0.25 -10000 0 -0.46 375 375
ETB receptor/Endothelin-1 -0.073 0.18 -10000 0 -0.49 115 115
MAPK3 -0.26 0.39 -10000 0 -0.79 279 279
MAPK1 -0.27 0.4 -10000 0 -0.81 281 281
Rac1/GDP -0.094 0.19 -10000 0 -0.48 106 106
cAMP biosynthetic process -0.16 0.22 0.52 1 -0.48 204 205
MAPK8 -0.054 0.19 -10000 0 -0.68 44 44
SRC 0.023 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.065 0.17 -10000 0 -0.38 142 142
p130Cas/CRK/Src/PYK2 -0.096 0.21 0.49 1 -0.56 91 92
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.094 0.19 -10000 0 -0.48 105 105
COL1A2 -0.083 0.19 0.4 7 -0.48 107 114
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.026 0.095 0.26 11 -0.35 7 18
mol:DAG -0.073 0.16 -10000 0 -0.45 83 83
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 0.057 -10000 0 -0.24 9 9
positive regulation of muscle contraction -0.063 0.11 -10000 0 -0.39 65 65
Gq family/GDP -0.059 0.19 -10000 0 -0.51 63 63
HRAS/GTP -0.1 0.2 0.34 1 -0.48 119 120
PRKCH -0.074 0.16 -10000 0 -0.45 79 79
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.07 0.17 0.3 3 -0.48 84 87
PRKCB -0.071 0.17 -10000 0 -0.46 82 82
PRKCE -0.078 0.16 -10000 0 -0.45 80 80
PRKCD -0.075 0.16 -10000 0 -0.45 77 77
PRKCG -0.076 0.16 0.27 1 -0.45 82 83
regulation of vascular smooth muscle contraction -0.37 0.53 -10000 0 -1.1 273 273
PRKCQ -0.083 0.18 -10000 0 -0.49 95 95
PLA2G4A -0.19 0.3 0.33 1 -0.55 278 279
GNA14 0.015 0.068 0.26 19 -0.6 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 -0.059 0.13 -10000 0 -0.4 70 70
MMP1 0.18 0.13 0.42 57 -10000 0 57
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.26 15 -10000 0 15
EFNB1 -0.005 0.037 0.17 1 -0.45 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.1 0.19 -10000 0 -0.32 343 343
Ephrin B2/EPHB1-2 -0.12 0.19 -10000 0 -0.35 350 350
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.3 344 344
Ephrin B1/EPHB1-2/Tiam1 -0.11 0.19 -10000 0 -0.34 347 347
DNM1 0.02 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 -0.11 0.19 -10000 0 -0.34 349 349
PI3K 0.007 0.13 -10000 0 -0.54 40 40
mol:GDP -0.11 0.19 -10000 0 -0.33 347 347
ITGA2B 0.031 0.062 0.26 35 -0.6 3 38
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 0.015 0.26 3 -10000 0 3
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.005 0.12 -10000 0 -0.45 50 50
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 -0.026 0.14 -10000 0 -0.63 38 38
SRC -0.022 0.17 -10000 0 -0.75 41 41
ITGB3 0.015 0.08 0.26 4 -0.6 13 17
EPHB1 -0.24 0.31 0.27 1 -0.6 352 353
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 0.032 0.076 -10000 0 -0.44 16 16
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 0.33 349 -10000 0 349
MAPK8 -0.025 0.12 -10000 0 -0.52 40 40
Ephrin B1/EPHB1-2/RGS3 -0.11 0.19 -10000 0 -0.34 349 349
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 -0.71 20 20
regulation of focal adhesion formation 0.11 0.19 0.33 349 -10000 0 349
chemotaxis 0.11 0.19 0.33 349 -10000 0 349
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.1 0.18 -10000 0 -0.31 343 343
angiogenesis -0.026 0.14 -10000 0 -0.62 39 39
LCK -0.023 0.17 -10000 0 -0.77 40 40
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 -0.079 0.16 -10000 0 -0.41 147 147
NCK1/Dok-R -0.14 0.43 -10000 0 -1 146 146
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.036 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 0.036 0.11 0.27 133 -10000 0 133
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.41 -10000 0 -0.98 146 146
FN1 0.13 0.12 0.26 366 -10000 0 366
PLD2 -0.17 0.44 -10000 0 -1.1 146 146
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.014 0.19 0.26 117 -0.6 58 175
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 0.26 3 -10000 0 3
Tie2/Ang1/alpha5/beta1 Integrin -0.075 0.45 -10000 0 -1 146 146
CDKN1A -0.089 0.25 -10000 0 -0.63 102 102
ITGA5 0.024 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 0.44 -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 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
ANGPT2 -0.13 0.27 -10000 0 -0.7 107 107
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 -0.68 128 128
ANGPT4 -0.17 0.28 -10000 0 -0.6 251 251
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 -0.6 309 309
STAT5A (dimer) -0.12 0.32 -10000 0 -0.79 122 122
mol:L-citrulline -0.083 0.27 -10000 0 -0.64 147 147
AGTR1 -0.087 0.26 0.27 52 -0.6 168 220
MAPK14 -0.16 0.44 -10000 0 -1.1 147 147
Tie2/SHP2 -0.075 0.29 -10000 0 -1.1 56 56
TEK -0.083 0.32 -10000 0 -1.2 56 56
RPS6KB1 -0.1 0.35 -10000 0 -0.83 147 147
Angiotensin II/AT1 -0.065 0.2 0.18 52 -0.44 171 223
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 -1.1 147 147
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 -1.2 147 147
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 -0.78 127 127
DOK2 0.019 0.024 -10000 0 -0.6 1 1
negative regulation of cell cycle -0.079 0.22 -10000 0 -0.57 105 105
ETS1 -0.013 0.1 -10000 0 -0.26 108 108
PXN -0.067 0.3 0.43 2 -0.67 146 148
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.099 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 -0.29 114 129
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 0.45 -10000 0 -1.1 147 147
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.072 0.24 0.38 1 -0.57 147 148
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
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.01 0.089 -10000 0 -0.6 17 17
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.2 0.21 -10000 0 -0.38 489 489
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 -0.35 487 488
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.037 0.057 0.26 48 -10000 0 48
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.025 0.07 0.26 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 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.029 0.037 0.26 19 -10000 0 19
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.084 0.26 114 -10000 0 114
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.22 0.22 0.35 2 -0.39 485 487
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.15 0.16 0.33 2 -0.34 49 51
MAP1B 0 0.039 -10000 0 -0.32 12 12
RAC1 0.01 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.18 0.15 0.23 2 -0.32 393 395
RELN -0.35 0.31 0.26 3 -0.6 496 499
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 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.16 0.17 -10000 0 -0.31 418 418
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.17 0.15 0.31 3 -0.36 53 56
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.043 0.064 0.26 63 -10000 0 63
PAFAH1B2 0.022 0.008 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.014 0.041 -10000 0 -0.36 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.14 0.16 0.33 2 -0.34 43 45
LRP8 0.051 0.077 0.26 94 -10000 0 94
NDEL1/Katanin 60 -0.15 0.16 0.33 2 -0.34 51 53
P39/CDK5 -0.18 0.16 0.28 7 -0.32 358 365
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 -0.33 482 484
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 -0.34 481 482
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 487 487
CDC42 0.01 0.005 -10000 0 -10000 0 0
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 0.78 8 -1.2 164 172
STAT6 (cleaved dimer) -0.3 0.58 -10000 0 -1.2 196 196
IGHG1 -0.032 0.26 0.5 44 -0.4 31 75
IGHG3 -0.24 0.57 0.67 11 -1.1 189 200
AKT1 -0.092 0.34 0.6 11 -0.77 63 74
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.054 0.29 0.58 11 -0.89 27 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.093 0.35 0.61 13 -0.81 56 69
THY1 -0.25 0.6 0.8 8 -1.2 158 166
MYB 0.013 0.082 0.26 2 -0.6 14 16
HMGA1 0.031 0.041 0.26 24 -10000 0 24
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.12 0.41 0.65 37 -0.73 132 169
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.085 0.35 0.62 12 -0.84 44 56
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 -1.2 188 194
SOCS1 -0.14 0.4 0.67 8 -0.75 135 143
SOCS3 -0.099 0.35 0.65 8 -0.82 55 63
FCER2 -0.41 0.74 0.79 14 -1.3 278 292
PARP14 0.016 0.033 0.25 3 -10000 0 3
CCL17 -0.23 0.62 0.86 26 -1.2 176 202
GRB2 0.023 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.048 0.29 0.56 14 -0.77 27 41
T cell proliferation -0.27 0.61 0.75 6 -1.2 179 185
IL4R/JAK1 -0.26 0.59 0.73 1 -1.2 174 175
EGR2 -0.37 0.74 0.86 5 -1.4 205 210
JAK2 0.009 0.075 -10000 0 -10000 0 0
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 5 -1.1 10 15
CCL26 -0.25 0.61 0.78 10 -1.2 165 175
IL4R -0.25 0.66 0.87 18 -1.3 171 189
PTPN6 0.015 0.036 0.22 1 -10000 0 1
IL13RA2 -0.25 0.6 0.79 11 -1.2 169 180
IL13RA1 0.009 0.076 -10000 0 -10000 0 0
IRF4 -0.14 0.5 0.62 12 -1.4 91 103
ARG1 -0.008 0.21 0.62 2 -10000 0 2
CBL -0.12 0.38 0.61 18 -0.7 131 149
GTF3A 0.056 0.051 0.27 1 -10000 0 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.021 0.11 0.29 21 -10000 0 21
IRF4/BCL6 -0.12 0.45 0.57 1 -1.3 90 91
CD40LG -0.012 0.14 0.32 13 -0.59 41 54
MAPK14 -0.12 0.38 0.62 17 -0.73 108 125
mitosis -0.085 0.33 0.59 13 -0.72 63 76
STAT6 -0.28 0.74 0.95 30 -1.4 185 215
SPI1 0.027 0.018 0.27 4 -10000 0 4
RPS6KB1 -0.066 0.32 0.57 17 -0.7 56 73
STAT6 (dimer) -0.28 0.74 0.96 29 -1.4 185 214
STAT6 (dimer)/PARP14 -0.31 0.66 0.76 5 -1.2 201 206
mast cell activation 0.001 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.1 0.36 0.62 12 -0.82 61 73
FRAP1 -0.092 0.34 0.6 11 -0.77 63 74
LTA -0.23 0.62 0.88 21 -1.2 157 178
FES 0.021 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 0.74 24 -1.1 158 182
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.081 0.34 0.61 13 -0.81 49 62
IL2RG 0.024 0.073 0.28 32 -0.6 5 37
IL10 -0.22 0.6 0.83 12 -1.2 151 163
IRS1 0.002 0.12 -10000 0 -0.6 29 29
IRS2 0 0.12 -10000 0 -0.6 29 29
IL4 -0.019 0.27 0.63 9 -1.1 19 28
IL5 -0.25 0.6 0.79 1 -1.2 151 152
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.51 0.81 29 -0.91 155 184
COL1A1 -0.006 0.36 0.64 40 -0.95 41 81
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.27 0.61 -10000 0 -1.3 148 148
IL2R gamma/JAK3 0.036 0.071 0.4 14 -0.44 4 18
TFF3 -0.3 0.71 0.86 14 -1.4 191 205
ALOX15 -0.32 0.7 0.81 10 -1.3 204 214
MYBL1 0.042 0.07 0.26 73 -10000 0 73
T-helper 2 cell differentiation -0.2 0.52 0.72 15 -0.97 177 192
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 0.58 15 -0.75 65 80
mol:PI-3-4-5-P3 -0.092 0.34 0.61 11 -0.77 63 74
PI3K -0.1 0.36 0.63 9 -0.83 63 72
DOK2 0.019 0.024 -10000 0 -0.6 1 1
ETS1 0.006 0.048 -10000 0 -0.56 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.037 0.27 0.53 18 -0.73 21 39
ITGB3 -0.25 0.62 0.78 7 -1.2 162 169
PIGR -0.71 0.78 0.82 12 -1.3 484 496
IGHE -0.015 0.087 0.18 28 -0.21 32 60
MAPKKK cascade -0.036 0.27 0.53 18 -0.7 22 40
BCL6 0.025 0.034 -10000 0 -0.58 2 2
OPRM1 -0.25 0.6 0.81 8 -1.2 164 172
RETNLB -0.25 0.6 0.76 11 -1.2 171 182
SELP -0.38 0.77 0.81 12 -1.4 242 254
AICDA -0.24 0.57 0.77 8 -1.1 164 172
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.006 0.13 -10000 0 -0.6 37 37
GNB1/GNG2 -0.089 0.22 -10000 0 -0.48 132 132
mol:DAG -0.089 0.19 0.24 1 -0.45 124 125
PLCG1 -0.092 0.2 0.24 1 -0.47 124 125
YES1 -0.11 0.2 0.21 1 -0.39 221 222
FZD3 0.018 0.039 -10000 0 -0.6 3 3
FZD6 0.015 0.049 -10000 0 -0.6 5 5
G protein -0.076 0.21 0.3 2 -0.48 120 122
MAP3K7 -0.081 0.16 0.38 1 -0.42 94 95
mol:Ca2+ -0.086 0.19 0.24 1 -0.44 124 125
mol:IP3 -0.089 0.19 0.24 1 -0.45 124 125
NLK -0.013 0.14 -10000 0 -0.84 21 21
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.083 0.18 0.39 1 -0.45 99 100
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.22 0.23 1 -0.4 244 245
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
GNAS -0.1 0.2 0.21 1 -0.39 215 216
GO:0007205 -0.092 0.19 0.23 1 -0.45 124 125
WNT6 -0.1 0.26 0.26 20 -0.6 171 191
WNT4 0.015 0.095 0.26 15 -0.6 17 32
NFAT1/CK1 alpha -0.095 0.21 -10000 0 -0.49 124 124
GNG2 0.019 0.053 -10000 0 -0.6 6 6
WNT5A 0.02 0.066 0.26 9 -0.6 8 17
WNT11 -0.1 0.25 0.26 9 -0.6 165 174
CDC42 -0.095 0.2 -10000 0 -0.49 115 115
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.11 0.22 0.23 1 -0.4 244 245
FZD6 0.015 0.049 -10000 0 -0.6 5 5
WNT6 -0.1 0.26 0.26 20 -0.6 171 191
WNT4 0.015 0.095 0.26 15 -0.6 17 32
FZD3 0.018 0.039 -10000 0 -0.6 3 3
WNT5A 0.02 0.066 0.26 9 -0.6 8 17
WNT11 -0.1 0.25 0.26 9 -0.6 165 174
IL23-mediated signaling events

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
CCL2 -0.039 0.5 0.81 39 -1.1 63 102
IL23A -0.049 0.5 0.84 32 -1.1 64 96
NF kappa B1 p50/RelA/I kappa B alpha -0.08 0.46 0.74 7 -0.88 133 140
positive regulation of T cell mediated cytotoxicity -0.043 0.56 0.87 57 -0.95 138 195
ITGA3 -0.034 0.49 0.83 31 -1.1 60 91
IL17F -0.019 0.37 0.61 55 -0.69 62 117
IL12B 0.08 0.15 0.37 142 -10000 0 142
STAT1 (dimer) -0.057 0.52 0.77 39 -0.92 138 177
CD4 -0.033 0.5 0.82 40 -1 64 104
IL23 -0.035 0.49 0.83 38 -1.1 60 98
IL23R 0.047 0.2 0.56 25 -0.96 11 36
IL1B -0.05 0.51 0.84 34 -1.1 64 98
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.001 0.5 0.87 49 -1 58 107
TYK2 0.025 0.061 0.22 3 -10000 0 3
STAT4 0 0.12 0.26 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 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.036 0.089 0.33 26 -0.49 1 27
IL23R/JAK2 0.059 0.22 0.54 32 -0.92 10 42
positive regulation of chronic inflammatory response -0.043 0.56 0.87 57 -0.95 138 195
natural killer cell activation -0.004 0.016 -10000 0 -0.052 32 32
JAK2 0.037 0.085 0.27 28 -10000 0 28
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.01 -10000 0 -10000 0 0
RELA 0.026 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.028 0.48 0.82 40 -0.99 60 100
ALOX12B -0.035 0.49 0.84 34 -1 62 96
CXCL1 -0.22 0.72 0.85 40 -1.2 234 274
T cell proliferation -0.043 0.56 0.87 57 -0.95 138 195
NFKBIA 0.026 0.01 -10000 0 -10000 0 0
IL17A 0.012 0.32 0.57 68 -0.55 49 117
PI3K -0.074 0.48 0.69 22 -0.89 135 157
IFNG 0.027 0.072 0.18 110 -0.12 10 120
STAT3 (dimer) -0.077 0.45 0.73 9 -0.88 120 129
IL18R1 0.019 0.072 -10000 0 -0.6 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 0.025 0.35 0.66 63 -0.63 47 110
IL18/IL18R 0.041 0.11 0.32 7 -0.39 40 47
macrophage activation -0.001 0.03 0.054 88 -0.044 50 138
TNF -0.049 0.51 0.86 32 -1.1 64 96
STAT3/STAT4 -0.074 0.5 0.69 24 -0.92 141 165
STAT4 (dimer) -0.069 0.53 0.75 35 -0.95 141 176
IL18 0.031 0.04 0.27 21 -10000 0 21
IL19 0.006 0.5 0.82 62 -1 60 122
STAT5A (dimer) -0.061 0.51 0.74 35 -0.92 139 174
STAT1 0.029 0.035 0.26 18 -10000 0 18
SOCS3 0.02 0.044 -10000 0 -0.6 4 4
CXCL9 -0.007 0.53 0.86 62 -1.1 63 125
MPO -0.065 0.56 0.82 43 -1.2 92 135
positive regulation of humoral immune response -0.043 0.56 0.87 57 -0.95 138 195
IL23/IL23R/JAK2/TYK2 -0.051 0.58 0.87 57 -1 138 195
IL6 -0.33 0.76 0.82 27 -1.2 315 342
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
IL2 0.024 0.043 0.31 9 -10000 0 9
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.016 -10000 0 -0.052 32 32
CD3E -0.048 0.52 0.85 42 -1.2 68 110
keratinocyte proliferation -0.043 0.56 0.87 57 -0.95 138 195
NOS2 -0.034 0.5 0.82 40 -1.1 62 102
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 -0.35 183 183
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.024 0.01 0.26 1 -10000 0 1
IRS1/Crk -0.065 0.17 -10000 0 -0.35 187 187
IGF-1R heterotetramer/IGF1/PTP1B -0.048 0.17 -10000 0 -0.38 163 163
AKT1 -0.069 0.14 0.25 2 -0.32 139 141
BAD -0.067 0.13 0.24 2 -0.47 25 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.072 0.16 -10000 0 -0.35 187 187
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.062 0.17 -10000 0 -0.36 187 187
RAF1 -0.051 0.14 -10000 0 -0.5 32 32
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.036 0.17 -10000 0 -0.34 171 171
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.066 0.18 -10000 0 -0.37 198 198
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.064 0.13 0.25 2 -0.33 128 130
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.031 0.13 0.33 6 -0.41 28 34
PXN 0.024 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 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.042 0.13 -10000 0 -0.33 123 123
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.014 0.14 -10000 0 -0.32 119 119
IGF-1R heterotetramer -0.012 0.1 0.2 1 -0.67 14 15
IGF-1R heterotetramer/IGF1/IRS/Nck -0.049 0.17 -10000 0 -0.36 184 184
Crk/p130 Cas/Paxillin -0.041 0.16 -10000 0 -0.33 176 176
IGF1R -0.012 0.1 0.2 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 -0.036 0.17 -10000 0 -0.34 178 178
apoptosis 0.043 0.11 0.39 21 -0.27 4 25
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
PRKCD -0.083 0.18 -10000 0 -0.41 180 180
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 -0.42 21 25
PRKCZ -0.069 0.14 0.25 2 -0.32 151 153
Crk/p130 Cas/Paxillin/FAK1 -0.028 0.11 -10000 0 -0.41 24 24
PTPN1 0.024 0.022 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.085 0.19 -10000 0 -0.42 187 187
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.027 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 -0.35 184 184
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 -0.37 197 197
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 0.006 -10000 0 -10000 0 0
PDPK1 -0.071 0.14 0.28 1 -0.33 155 156
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.093 0.2 -10000 0 -0.44 185 185
SHC1 0.02 0.009 -10000 0 -10000 0 0
Arf6 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
CENTA1/KIF3B 0.025 0.036 -10000 0 -0.49 3 3
ARNO/beta Arrestin1-2 -0.077 0.18 -10000 0 -0.58 41 41
EGFR -0.19 0.3 -10000 0 -0.6 277 277
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 -0.48 397 397
ARRB2 -0.045 0.13 -10000 0 -0.38 114 114
mol:GTP 0.01 0.053 0.15 19 -0.21 19 38
ARRB1 0.021 0.031 -10000 0 -0.6 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR -0.001 0.12 0.26 3 -0.6 33 36
EGF -0.09 0.24 0.26 2 -0.6 151 153
somatostatin receptor activity 0 0 0.001 1 -0.001 212 213
ARAP2 0.02 0.049 -10000 0 -0.6 5 5
mol:GDP -0.12 0.17 -10000 0 -0.34 222 222
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 137 137
ITGA2B 0.031 0.062 0.26 35 -0.6 3 38
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.042 -10000 0 -0.35 5 5
ADAP1 0.023 0.034 0.26 3 -0.6 2 5
KIF13B 0.019 0.032 -10000 0 -0.6 2 2
HGF/MET -0.071 0.21 -10000 0 -0.47 171 171
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.14 0.18 1 -0.29 228 229
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.24 -10000 0 -0.42 387 387
ADRB2 -0.12 0.26 -10000 0 -0.6 193 193
receptor agonist activity 0 0 0 1 0 197 198
actin filament binding 0 0 0 2 -0.001 217 219
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.014 0.08 0.26 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 -0.001 123 124
ARF6/GDP -0.042 0.16 0.25 2 -0.46 72 74
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.43 163 163
alphaIIb/beta3 Integrin/paxillin/GIT1 0.055 0.068 -10000 0 -0.35 16 16
ACAP1 0.024 0.067 0.26 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 -0.011 0.14 -10000 0 -0.6 46 46
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 0 167 168
endosomal lumen acidification 0 0 0.001 5 0 184 189
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.012 0.15 -10000 0 -0.6 48 48
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 0 129 129
MET -0.079 0.23 -10000 0 -0.6 136 136
GNA14 0.025 0.065 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 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 -0.001 166 167
GNA11 0.024 0.004 -10000 0 -10000 0 0
LHCGR -0.074 0.21 -10000 0 -0.6 114 114
AGTR1 -0.089 0.26 0.26 52 -0.6 168 220
desensitization of G-protein coupled receptor protein signaling pathway -0.06 0.18 -10000 0 -0.51 114 114
IPCEF1/ARNO -0.14 0.2 -10000 0 -0.64 50 50
alphaIIb/beta3 Integrin 0.032 0.076 -10000 0 -0.44 16 16
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.066 0.16 0.32 8 -0.36 77 85
SMAD6-7/SMURF1 0.046 0.016 -10000 0 -10000 0 0
NOG 0.013 0.095 0.26 15 -0.6 17 32
SMAD9 -0.082 0.25 -10000 0 -0.64 121 121
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.03 0.15 -10000 0 -0.44 61 61
BMP7/USAG1 -0.21 0.26 -10000 0 -0.45 417 417
SMAD5/SKI -0.025 0.16 -10000 0 -0.45 58 58
SMAD1 0.013 0.061 -10000 0 -0.41 5 5
BMP2 -0.083 0.24 0.26 1 -0.6 141 142
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 0.26 343 -0.6 17 360
BMPR1A-1B/BAMBI 0.086 0.13 0.35 9 -0.35 41 50
AHSG 0.02 0.021 0.26 6 -10000 0 6
CER1 0.019 0.013 0.26 2 -10000 0 2
BMP2-4/CER1 -0.053 0.19 -10000 0 -0.41 168 168
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.044 0.17 -10000 0 -0.43 86 86
BMP2-4 (homodimer) -0.074 0.21 -10000 0 -0.47 173 173
RGMB 0.023 0.022 -10000 0 -0.6 1 1
BMP6/BMPR2/BMPR1A-1B 0.069 0.15 -10000 0 -0.33 79 79
RGMA -0.057 0.21 -10000 0 -0.6 107 107
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 99 100
BMP2-4/USAG1 -0.24 0.28 -10000 0 -0.47 446 446
SMAD6/SMURF1/SMAD5 -0.025 0.16 -10000 0 -0.45 60 60
SOSTDC1 -0.27 0.31 0.26 2 -0.6 393 395
BMP7/BMPR2/BMPR1A-1B 0.073 0.14 0.31 6 -0.34 64 70
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.024 0.17 0.26 1 -0.6 63 64
HFE2 0.021 0.022 0.26 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 -0.052 0.21 -10000 0 -0.43 170 170
SMAD5/SMAD5/SMAD4 -0.025 0.16 -10000 0 -0.45 58 58
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.03 0.16 -10000 0 -0.39 94 94
BMP7 (homodimer) -0.01 0.16 0.26 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 0.079 -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 -0.42 167 168
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.042 0.1 0.26 90 -0.6 10 100
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) 0.091 0.11 -10000 0 -0.45 17 17
CHRDL1 -0.4 0.29 -10000 0 -0.6 565 565
ENDOFIN/SMAD1 0.018 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 0.26 29 -0.6 26 55
SMURF2 0.022 0.008 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.28 -10000 0 -0.48 568 568
BMP2-4/GREM1 -0.04 0.21 -10000 0 -0.42 174 174
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.075 0.25 -10000 0 -0.64 115 115
SMAD1/SMAD6 0.018 0.081 -10000 0 -0.48 8 8
TAK1/SMAD6 0.034 0.01 -10000 0 -10000 0 0
BMP7 -0.01 0.16 0.26 25 -0.6 52 77
BMP6 -0.024 0.17 0.26 1 -0.6 63 64
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.044 0.17 -10000 0 -0.44 101 101
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 0.024 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 -0.053 0.2 0.24 1 -0.48 107 108
CHRD 0.024 0.096 0.26 38 -0.6 14 52
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.058 0.19 -10000 0 -0.5 99 99
BMP4 -0.011 0.14 0.26 1 -0.6 46 47
FST 0.005 0.11 0.26 3 -0.6 26 29
BMP2-4/NOG -0.055 0.2 -10000 0 -0.43 164 164
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.077 0.14 0.34 2 -0.32 64 66
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.002 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 83 83
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
HRAS 0.023 0.01 0.26 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 -0.007 0.14 -10000 0 -0.6 41 41
mol:GDP -0.054 0.15 -10000 0 -0.48 91 91
cell proliferation -0.14 0.22 -10000 0 -0.45 241 241
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FOS -0.27 0.39 -10000 0 -0.82 269 269
mol:Ca2+ -0.013 0.028 -10000 0 -0.073 108 108
MAPK3 -0.1 0.17 0.26 3 -0.47 72 75
MAPK1 -0.084 0.15 -10000 0 -0.39 85 85
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 262 262
cAMP biosynthetic process 0.004 0.021 -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 -0.004 262 262
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 -0.004 262 262
PI3K 0.03 0.009 -10000 0 -10000 0 0
apoptosis 0.14 0.22 0.44 269 -10000 0 269
T-DHT/AR/PELP1 -0.02 0.13 -10000 0 -0.39 90 90
HRAS/GDP -0.044 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 -0.018 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 81 81
T-DHT/AR/PELP1/Src/PI3K -0.017 0.097 -10000 0 -0.3 83 83
GNAZ 0.018 0.053 -10000 0 -0.6 6 6
SHBG 0.022 0.011 0.26 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.049 0.16 -10000 0 -0.47 73 73
mol:T-DHT -0.001 0.001 0.002 1 -0.004 60 61
RAC1 0.024 0.004 -10000 0 -10000 0 0
GNRH1 0.001 0.027 -10000 0 -0.44 3 3
Gi family/GTP -0.034 0.098 -10000 0 -0.29 72 72
CDC42 0.023 0.005 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.075 0.12 -10000 0 -0.3 75 75
NT3 (dimer)/TRKC -0.19 0.28 -10000 0 -0.5 346 346
NT3 (dimer)/TRKB -0.32 0.33 -10000 0 -0.56 485 485
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 0.26 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 0.025 0.049 0.26 20 -0.6 2 22
NTRK2 -0.29 0.31 -10000 0 -0.6 420 420
NTRK3 -0.18 0.3 0.26 5 -0.6 274 279
NT-4/5 (dimer)/TRKB -0.4 0.36 -10000 0 -0.62 547 547
neuron apoptosis 0.18 0.23 0.48 245 -10000 0 245
SHC 2-3/Grb2 -0.2 0.25 -10000 0 -0.52 245 245
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.2 0.26 -10000 0 -0.56 235 235
SHC3 -0.19 0.24 -10000 0 -0.52 229 229
STAT3 (dimer) 0.034 0.045 -10000 0 -0.37 3 3
NT3 (dimer)/TRKA -0.12 0.23 -10000 0 -0.44 242 242
RIN/GDP -0.05 0.12 0.29 4 -0.26 67 71
GIPC1 0.024 0.004 -10000 0 -10000 0 0
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.089 0.16 -10000 0 -0.34 209 209
RIN/GTP 0.014 0.009 0.18 2 -10000 0 2
CCND1 0.025 0.098 0.44 32 -0.85 3 35
MAGED1 0.025 0.012 0.26 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.21 0.3 -10000 0 -0.6 313 313
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.03 0.088 -10000 0 -0.36 31 31
TRKA/NEDD4-2 0.032 0.038 0.2 19 -0.36 3 22
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 0.26 7 -0.6 15 22
HRAS 0.024 0.01 0.26 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 0.26 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.26 2 -10000 0 2
DNM1 0.021 0.049 0.26 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 -0.082 0.16 -10000 0 -0.33 232 232
mol:GDP -0.081 0.17 0.34 5 -0.38 88 93
NGF (dimer) 0.015 0.086 0.26 7 -0.6 15 22
RhoG/GDP 0.018 0.002 -10000 0 -10000 0 0
RIT1/GDP -0.049 0.11 0.37 2 -0.27 55 57
TIAM1 0.025 0.015 0.26 3 -10000 0 3
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.2 0.24 -10000 0 -0.41 444 444
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 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.065 0.22 0.26 11 -0.6 121 132
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 0.26 19 -0.6 63 82
ubiquitin-dependent protein catabolic process 0.035 0.067 -10000 0 -0.35 18 18
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 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.05 -10000 0 -0.28 7 7
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 -0.5 497 497
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.01 -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 -0.47 497 497
MAPK3 0.004 0.094 0.24 4 -0.37 25 29
MAPK1 0.006 0.096 0.24 4 -0.37 25 29
CDC42/GDP -0.048 0.12 0.29 5 -0.26 60 65
NTF3 -0.065 0.22 0.26 11 -0.6 121 132
NTF4 -0.21 0.3 -10000 0 -0.6 313 313
NGF (dimer)/TRKA/FAIM 0.036 0.067 -10000 0 -0.36 17 17
PI3K 0.033 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 -0.086 0.17 0.25 2 -0.34 225 227
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.17 0.23 0.21 1 -0.44 328 329
RGS19 0.023 0.011 0.26 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.013 0.098 0.4 1 -0.45 8 9
Rac1/GDP -0.049 0.12 0.33 3 -0.26 63 66
NGF (dimer)/TRKA/GRIT 0.024 0.063 0.18 23 -0.36 17 40
neuron projection morphogenesis -0.081 0.22 -10000 0 -0.78 38 38
NGF (dimer)/TRKA/NEDD4-2 0.035 0.067 -10000 0 -0.35 18 18
MAP2K1 0.031 0.087 0.36 14 -10000 0 14
NGFR -0.16 0.28 -10000 0 -0.6 238 238
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.053 -10000 0 -0.3 16 16
RAS family/GTP/PI3K 0.019 0.011 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.063 0.027 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.01 -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 -0.043 0.14 -10000 0 -0.66 34 34
RASA1 0.024 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.033 0.037 -10000 0 -0.45 2 2
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.18 0.23 -10000 0 -0.38 437 437
NGF (dimer)/TRKA/p62/Atypical PKCs 0.051 0.067 -10000 0 -0.34 15 15
MATK 0.015 0.09 0.26 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 -0.21 53 53
NGF (dimer)/TRKA -0.096 0.17 -10000 0 -0.35 249 249
Rac1/GTP -0.092 0.13 -10000 0 -0.29 178 178
FRS2 family/SHP2/CRK family 0.061 0.029 -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 0.017 0.019 0.18 11 -10000 0 11
Metarhodopsin II/Arrestin 0.037 0.039 0.33 2 -10000 0 2
PDE6G/GNAT1/GTP 0.035 0.032 -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 0.26 11 -10000 0 11
GRK1 0.019 0.018 0.26 4 -10000 0 4
CNG Channel -0.064 0.17 -10000 0 -0.32 238 238
mol:Na + -0.061 0.17 -10000 0 -0.32 240 240
mol:ADP 0.019 0.018 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.009 0.13 -10000 0 -0.38 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.055 0.18 0.29 3 -0.32 238 241
CNGB1 0.031 0.053 0.26 40 -10000 0 40
RDH5 -0.37 0.3 -10000 0 -0.6 518 518
SAG 0.032 0.053 0.26 41 -10000 0 41
mol:Ca2+ -0.095 0.15 0.36 11 -0.32 205 216
Na + (4 Units) -0.064 0.16 -10000 0 -0.3 235 235
RGS9 -0.035 0.18 0.26 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 0.26 10 -0.6 1 11
GNGT1 0.059 0.091 0.26 134 -10000 0 134
GUCY2F 0.019 0.012 0.26 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 -0.33 13 14
mol:11-cis-retinal -0.37 0.3 -10000 0 -0.6 518 518
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 0.23 -10000 0 -0.44 521 521
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.16 0.29 0.26 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 0.054 0.26 44 -10000 0 44
Metarhodopsin II/Transducin 0.025 0.034 0.18 4 -10000 0 4
GCAP Family/Ca ++ 0.045 0.043 -10000 0 -0.36 4 4
PDE6A/B 0.028 0.068 -10000 0 -0.4 17 17
mol:Pi 0.008 0.13 -10000 0 -0.38 76 76
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.06 0.055 0.33 1 -10000 0 1
PDE6B 0.013 0.081 0.26 1 -0.6 14 15
PDE6A 0.028 0.031 0.26 14 -10000 0 14
PDE6G 0.031 0.043 0.26 27 -10000 0 27
RHO 0.025 0.031 0.26 13 -10000 0 13
PDE6 0.026 0.13 0.31 2 -0.33 84 86
GUCA1A 0.034 0.052 0.26 39 -10000 0 39
GC2/GCAP Family 0.056 0.045 -10000 0 -0.36 4 4
GUCA1C 0.018 0.009 0.26 1 -10000 0 1
GUCA1B 0.021 0.044 -10000 0 -0.6 4 4
Plasma membrane estrogen 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
GNB1/GNG2 0.004 0.16 -10000 0 -0.34 129 129
ER alpha/Gai/GDP/Gbeta gamma -0.078 0.22 -10000 0 -0.48 152 152
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 -0.36 47 49
IGF1R 0.013 0.081 0.26 1 -0.6 14 15
E2/ER alpha (dimer)/Striatin -0.004 0.15 -10000 0 -0.37 111 111
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.091 0.3 0.75 141 -10000 0 141
RhoA/GTP -0.014 0.1 -10000 0 -0.3 84 84
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.06 0.21 0.32 5 -0.48 137 142
regulation of stress fiber formation 0.017 0.1 -10000 0 -0.32 6 6
E2/ERA-ERB (dimer) -0.017 0.16 -10000 0 -0.38 130 130
KRAS 0.023 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 6 -10000 0 6
E2/ER alpha (dimer)/PELP1 -0.008 0.15 -10000 0 -0.38 107 107
GRB2 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.019 0.053 -10000 0 -0.6 6 6
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
HRAS 0.024 0.01 0.26 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.079 0.23 -10000 0 -0.52 157 157
E2/ER beta (dimer) 0.004 0.077 -10000 0 -0.42 25 25
mol:GDP -0.035 0.17 0.25 12 -0.41 125 137
mol:NADP -0.079 0.23 -10000 0 -0.52 157 157
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.025 0.11 0.27 2 -0.38 47 49
IGF-1R heterotetramer 0.013 0.081 0.26 1 -0.6 14 15
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 -0.52 157 157
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.64 124 124
JNK cascade 0.004 0.077 -10000 0 -0.42 25 25
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.006 0.1 -10000 0 -0.6 23 23
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
ESR1 -0.025 0.24 0.26 108 -0.6 106 214
Gq family/GDP/Gbeta gamma -0.008 0.16 -10000 0 -0.8 28 28
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.014 0.13 -10000 0 -0.54 18 18
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.053 0.2 0.31 5 -0.49 113 118
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
E2/ER alpha (dimer) -0.022 0.17 0.18 108 -0.43 111 219
STRN 0.024 0.003 -10000 0 -10000 0 0
GNAL -0.11 0.25 -10000 0 -0.6 174 174
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 -0.001 0.07 -10000 0 -0.4 24 24
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
HBEGF -0.047 0.21 0.34 21 -0.5 91 112
cAMP biosynthetic process -0.089 0.19 -10000 0 -0.34 264 264
SRC -0.072 0.22 0.3 8 -0.46 147 155
PI3K 0.033 0.01 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.017 0.16 -10000 0 -0.39 101 101
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.45 162 162
Gs family/GTP -0.086 0.2 -10000 0 -0.35 264 264
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.015 -10000 0 -10000 0 0
vasodilation -0.074 0.22 0.24 1 -0.49 157 158
mol:DAG -0.025 0.11 0.27 2 -0.38 47 49
Gs family/GDP/Gbeta gamma -0.089 0.18 -10000 0 -0.37 199 199
MSN -0.018 0.11 0.33 6 -0.28 1 7
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 0.49 157 -0.24 1 158
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.019 0.17 0.27 9 -0.39 123 132
NOS3 -0.085 0.25 -10000 0 -0.55 157 157
GNA11 0.024 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.065 0.25 0.32 3 -0.59 135 138
E2/ER alpha (dimer)/PELP1/Src -0.063 0.22 0.33 8 -0.5 140 148
ruffle organization -0.017 0.1 0.32 6 -10000 0 6
ROCK2 -0.017 0.11 0.34 6 -0.29 73 79
GNA14 0.025 0.065 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 3 -0.6 1 4
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.039 0.21 0.36 27 -0.49 88 115
MMP2 -0.065 0.2 0.28 10 -0.44 146 156
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.046 0.18 -10000 0 -0.43 143 143
CRKL -0.051 0.15 0.36 1 -0.42 70 71
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 -0.42 60 61
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.047 0.19 -10000 0 -0.41 162 162
MAP3K5 -0.043 0.15 0.36 1 -0.45 50 51
HGF/MET/CIN85/CBL/ENDOPHILINS -0.034 0.18 -10000 0 -0.38 168 168
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) -0.052 0.16 -10000 0 -0.48 64 64
GAB1/CRKL/SHP2/PI3K -0.021 0.16 -10000 0 -0.46 36 36
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.039 0.15 0.34 1 -0.42 59 60
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 0.28 21 -0.22 103 124
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.028 0.093 -10000 0 -0.26 58 58
PAK1 0.027 0.08 0.37 8 -0.72 1 9
HGF/MET/RANBP10 -0.049 0.19 -10000 0 -0.41 170 170
HRAS -0.11 0.27 -10000 0 -0.65 149 149
DOCK1 -0.049 0.15 0.52 1 -0.42 61 62
GAB1 -0.054 0.16 -10000 0 -0.37 128 128
CRK -0.052 0.15 0.36 1 -0.42 70 71
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.26 -10000 0 -0.59 177 177
JUN 0.019 0.057 -10000 0 -0.6 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.054 0.13 -10000 0 -0.3 170 170
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.051 0.17 0.38 5 -0.47 62 67
GRB2/SHC -0.019 0.11 -10000 0 -0.29 96 96
FOS -0.17 0.29 -10000 0 -0.6 252 252
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.032 0.099 0.28 21 -0.22 103 124
HGF/MET/MUC20 -0.059 0.18 -10000 0 -0.41 171 171
cell migration -0.019 0.11 -10000 0 -0.29 96 96
GRB2 0.023 0.006 -10000 0 -10000 0 0
CBL 0.022 0.007 -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 -0.35 135 135
MET/MUC20 -0.06 0.17 -10000 0 -0.43 143 143
RAP1B -0.043 0.14 0.29 3 -0.44 38 41
RAP1A -0.048 0.14 0.41 2 -0.4 57 59
HGF/MET/RANBP9 -0.047 0.19 -10000 0 -0.4 170 170
RAF1 -0.1 0.25 -10000 0 -0.62 149 149
STAT3 -0.052 0.16 -10000 0 -0.49 64 64
cell proliferation -0.046 0.19 0.33 7 -0.44 122 129
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 -0.42 36 37
SRC -0.057 0.14 -10000 0 -0.43 61 61
PI3K -0.027 0.13 -10000 0 -0.29 135 135
MET/Glomulin -0.052 0.15 -10000 0 -0.39 137 137
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 -0.44 70 71
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.094 0.23 0.47 1 -0.57 148 149
BAD 0.012 0.061 0.36 3 -0.72 1 4
MAP2K4 -0.04 0.14 0.34 1 -0.43 42 43
SHP2/GRB2/SOS1/GAB1 -0.044 0.18 -10000 0 -0.41 138 138
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.05 0.12 -10000 0 -0.28 153 153
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.6 46 46
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 -0.025 0.13 -10000 0 -0.28 161 161
PDPK1 0.017 0.067 0.44 2 -0.8 1 3
HGF/MET/SHIP -0.047 0.19 -10000 0 -0.41 169 169
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
Jak2/Leptin Receptor -0.1 0.19 0.27 1 -0.41 191 192
PTP1B/AKT1 -0.064 0.13 -10000 0 -0.34 91 91
FYN 0.022 0.023 -10000 0 -0.6 1 1
p210 bcr-abl/PTP1B -0.08 0.14 0.22 2 -0.36 113 115
EGFR -0.2 0.3 -10000 0 -0.61 277 277
EGF/EGFR -0.2 0.25 -10000 0 -0.43 393 393
CSF1 0.022 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 -0.36 102 116
Insulin Receptor/Insulin -0.041 0.11 -10000 0 -0.36 37 37
HCK 0.027 0.029 0.26 12 -10000 0 12
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.076 0.13 0.41 1 -0.35 103 104
EGF -0.11 0.24 0.26 2 -0.61 151 153
YES1 0.023 0.022 -10000 0 -0.6 1 1
CAV1 -0.16 0.21 0.27 2 -0.44 233 235
TXN 0.016 0.016 0.26 1 -10000 0 1
PTP1B/IRS1/GRB2 -0.069 0.15 -10000 0 -0.37 105 105
cell migration 0.08 0.14 0.36 113 -0.22 2 115
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.026 0.022 0.26 6 -10000 0 6
ITGA2B 0.029 0.062 0.26 35 -0.6 3 38
CSF1R 0.024 0.004 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.035 0.029 0.32 1 -10000 0 1
FGR 0.024 0.01 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.066 0.13 -10000 0 -0.35 99 99
Crk/p130 Cas -0.059 0.13 -10000 0 -0.36 77 77
DOK1 -0.066 0.12 0.23 2 -0.35 83 85
JAK2 -0.047 0.12 -10000 0 -0.5 37 37
Jak2/Leptin Receptor/Leptin -0.28 0.16 -10000 0 -0.39 412 412
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
PTPN1 -0.08 0.14 0.22 2 -0.36 113 115
LYN 0.021 0.009 -10000 0 -10000 0 0
CDH2 0.068 0.1 0.26 159 -0.6 2 161
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 -0.095 0.19 0.35 3 -0.47 113 116
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 -0.39 23 23
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.25 0.15 -10000 0 -0.36 358 358
negative regulation of transcription -0.046 0.12 -10000 0 -0.49 37 37
FCGR2A 0.02 0.009 -10000 0 -10000 0 0
FER 0.012 0.05 -10000 0 -0.61 5 5
alphaIIb/beta3 Integrin 0.029 0.076 -10000 0 -0.45 16 16
BLK 0.046 0.085 0.26 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 -0.6 182 182
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.006 -10000 0 -10000 0 0
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.049 0.18 0.34 4 -0.45 80 84
PRL 0.009 0.036 0.27 10 -10000 0 10
SOCS3 0.008 0.16 -10000 0 -1.2 13 13
SPRY2 -0.041 0.18 -10000 0 -0.61 76 76
Insulin Receptor/Insulin/IRS1 0.027 0.079 -10000 0 -0.38 29 29
CSF1/CSF1R -0.061 0.14 -10000 0 -0.36 92 92
Ras protein signal transduction 0.053 0.16 0.63 51 -10000 0 51
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 -0.6 652 652
STAT5B -0.068 0.14 0.2 3 -0.37 97 100
STAT5A -0.069 0.14 0.2 3 -0.36 107 110
GRB2 0.023 0.006 -10000 0 -10000 0 0
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 -0.59 8 8
YBX1 0.027 0.018 -10000 0 -10000 0 0
LCK 0.024 0.077 0.26 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 S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.005 0.042 0.24 5 -0.38 1 6
NFATC2 -0.013 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 0.55 17 -0.58 190 207
PTGS2 -0.2 0.35 0.54 13 -0.67 249 262
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 0.012 0.062 -10000 0 -0.61 7 7
mol:Ca2+ -0.002 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.027 0.045 0.26 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 -0.42 28 42
FOS -0.18 0.29 -10000 0 -0.59 262 262
IFNG -0.11 0.3 0.51 34 -0.56 164 198
AP-1/NFAT1-c-4 -0.14 0.35 0.59 31 -0.63 197 228
FASLG -0.12 0.28 0.57 19 -0.56 147 166
NFAT1-c-4/ICER1 -0.005 0.11 0.33 8 -0.36 34 42
IL2RA -0.12 0.29 0.53 27 -0.56 168 195
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.28 0.56 15 -0.54 187 202
JunB/Fra1/NFAT1-c-4 0.008 0.12 0.38 10 -0.36 35 45
IL4 -0.13 0.28 0.53 13 -0.56 170 183
IL2 -0.017 0.16 -10000 0 -0.95 23 23
IL3 -0.02 0.12 -10000 0 -0.72 22 22
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 0.26 1 -10000 0 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.003 0.089 -10000 0 -0.56 12 12
Crk/p130 Cas/Paxillin -0.054 0.12 -10000 0 -0.36 82 82
JUN -0.01 0.12 0.25 1 -0.42 21 22
HRAS 0.024 0.01 0.26 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 0.051 0.2 0.35 45 -0.36 127 172
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.051 0.2 0.35 45 -0.36 125 170
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 -0.006 0.16 0.33 4 -0.35 127 131
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.026 0.17 0.29 30 -0.33 126 156
GRB7 0.02 0.023 -10000 0 -0.6 1 1
RET51/GFRalpha1/GDNF 0.05 0.2 0.35 44 -0.36 125 169
MAPKKK cascade 0.005 0.15 0.29 8 -0.35 92 100
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.018 0.18 0.33 3 -0.4 136 139
lamellipodium assembly -0.029 0.13 -10000 0 -0.32 95 95
RET51/GFRalpha1/GDNF/SHC 0.042 0.18 0.36 37 -0.36 96 133
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.005 0.14 0.33 4 -0.35 95 99
RET9/GFRalpha1/GDNF/Shank3 -0.009 0.16 0.33 4 -0.35 127 131
MAPK3 -0.028 0.13 -10000 0 -0.33 98 98
DOK1 0.024 0.002 -10000 0 -10000 0 0
DOK6 0.019 0.065 0.26 6 -0.6 8 14
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.028 0.13 -10000 0 -0.46 13 13
DOK5 0.012 0.088 0.26 5 -0.6 16 21
GFRA1 -0.064 0.24 0.26 51 -0.6 136 187
MAPK8 -0.003 0.13 0.22 3 -0.3 100 103
HRAS/GTP 0.035 0.19 0.3 43 -0.36 120 163
tube development -0.002 0.15 0.35 9 -0.34 121 130
MAPK1 -0.027 0.14 0.34 1 -0.33 99 100
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.12 0.26 1 -0.28 118 119
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 0.046 0.2 0.34 41 -0.35 129 170
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.034 0.19 0.35 31 -0.36 126 157
RET51/GFRalpha1/GDNF/Dok5 0.034 0.2 0.36 40 -0.36 134 174
PRKCA 0.009 0.092 0.26 2 -0.6 18 20
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
CREB1 -0.007 0.13 0.23 15 -0.33 72 87
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.016 0.1 0.26 1 -0.28 85 86
RET51/GFRalpha1/GDNF/Grb7 0.05 0.19 0.34 59 -0.36 100 159
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.11 0.14 0.26 312 -0.6 11 323
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.008 0.12 0.25 1 -0.41 21 22
RET9/GFRalpha1/GDNF/FRS2 -0.008 0.16 0.33 4 -0.35 128 132
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 -0.017 0.11 0.26 1 -0.28 89 90
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.013 0.14 0.26 11 -0.3 100 111
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.008 0.14 0.26 3 -0.31 100 103
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.017 0.14 0.26 16 -0.32 74 90
PI3K -0.02 0.21 0.29 8 -0.49 96 104
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.001 0.15 0.32 3 -0.34 121 124
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity 0.004 0.13 0.26 5 -0.41 12 17
RET51/GFRalpha1/GDNF/FRS2 0.048 0.2 0.35 48 -0.36 126 174
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 0.017 0.14 0.26 16 -0.32 74 90
RET51/GFRalpha1/GDNF/PKC alpha 0.031 0.2 0.36 37 -0.36 135 172
GRB2 0.023 0.006 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.034 0.056 0.26 46 -10000 0 46
RAC1 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.037 0.22 0.35 43 -0.41 137 180
Rac1/GTP -0.015 0.16 0.24 5 -0.39 95 100
RET9/GFRalpha1/GDNF -0.021 0.16 0.33 4 -0.37 136 140
GFRalpha1/GDNF -0.027 0.19 0.38 4 -0.43 136 140
Aurora C signaling

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
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 0.02 0.018 -10000 0 -0.3 1 1
AURKB 0.15 0.12 0.26 436 -10000 0 436
AURKC 0.026 0.035 0.26 10 -0.6 1 11
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.76 11 11
mol:S1P -0.023 0.096 0.4 1 -0.68 11 12
S1P1/S1P/Gi -0.13 0.23 0.32 2 -0.44 267 269
GNAO1 0.006 0.097 0.25 27 -0.61 15 42
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.22 0.38 3 -0.41 238 241
PLCG1 -0.13 0.22 0.33 3 -0.42 248 251
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.033 -10000 0 -0.6 2 2
GNAI2 0.009 0.024 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.021 0.14 -10000 0 -0.61 41 41
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 0.098 0.28 2 -0.5 12 14
negative regulation of cAMP metabolic process -0.13 0.23 0.32 2 -0.42 267 269
MAPK3 -0.18 0.3 0.31 13 -0.58 273 286
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 -0.6 1 1
PLCB2 -0.026 0.097 0.32 5 -0.44 13 18
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.081 -10000 0 -0.42 12 12
receptor internalization -0.035 0.088 -10000 0 -0.46 12 12
PTGS2 -0.34 0.5 0.4 2 -1 280 282
Rac1/GTP -0.032 0.081 -10000 0 -0.42 12 12
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 0.32 2 -0.42 267 269
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 0.36 2 -0.62 286 288
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.32 3 -0.5 11 14
ABCC1 0.012 0.019 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.009 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.02 0.15 0.32 1 -0.34 12 13
NFATC4 -0.065 0.12 0.27 4 -10000 0 4
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.07 0.15 -10000 0 -0.32 183 183
JUN -0.008 0.1 0.24 22 -0.48 2 24
HRAS 0.024 0.01 0.27 1 -10000 0 1
DOCK7 -0.081 0.14 0.28 2 -0.32 71 73
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.055 0.16 -10000 0 -0.35 154 154
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.075 0.12 0.22 6 -0.28 107 113
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.074 0.17 -10000 0 -0.34 183 183
RAF1 -0.015 0.15 0.36 10 -0.34 8 18
ErbB2/ErbB3/neuregulin 2 -0.17 0.19 -10000 0 -0.37 362 362
STAT3 -0.004 0.16 -10000 0 -0.86 29 29
cell migration -0.058 0.1 0.26 8 -0.26 63 71
mol:PI-3-4-5-P3 -0.002 0.003 -10000 0 -10000 0 0
cell proliferation -0.042 0.26 0.46 10 -0.52 86 96
FOS -0.11 0.3 0.34 39 -0.5 269 308
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.15 -10000 0 -0.32 183 183
MAPK3 -0.012 0.21 0.43 10 -0.53 23 33
MAPK1 -0.024 0.22 0.44 10 -0.57 36 46
JAK2 -0.079 0.14 0.26 1 -0.32 71 72
NF2 -0.002 0.061 -10000 0 -0.68 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.14 0.23 3 -0.3 156 159
NRG1 -0.14 0.28 0.26 3 -0.6 219 222
GRB2/SOS1 0.034 0.01 -10000 0 -10000 0 0
MAPK8 -0.078 0.15 0.25 2 -0.3 182 184
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 0.096 -10000 0 -0.24 71 71
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.016 -10000 0 -10000 0 0
CHRNA1 0.024 0.19 0.37 58 -0.4 18 76
myelination -0.061 0.12 0.34 8 -10000 0 8
PPP3CB -0.075 0.13 0.27 2 -0.3 68 70
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.27 119 119
NRG2 -0.31 0.31 -10000 0 -0.6 435 435
mol:GDP -0.053 0.14 0.23 3 -0.29 159 162
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.013 0.15 0.34 13 -0.31 39 52
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 -0.32 70 72
MAP2K1 -0.049 0.23 0.44 6 -0.53 66 72
heart morphogenesis -0.07 0.15 -10000 0 -0.32 183 183
RAS family/GDP -0.021 0.14 0.3 1 -0.34 12 13
GRB2 0.023 0.007 -10000 0 -10000 0 0
PRKACA -0.003 0.072 -10000 0 -0.67 9 9
CHRNE 0.005 0.028 0.12 3 -0.22 2 5
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.07 0.15 -10000 0 -0.32 183 183
CDC42 0.023 0.005 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.01 0.025 0.14 29 -10000 0 29
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.11 -10000 0 -0.45 35 35
STXBP1 0.022 0.038 -10000 0 -0.6 3 3
ACh/CHRNA1 0.081 0.095 0.2 294 -0.16 5 299
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 0.26 90 -0.6 35 125
mol:ACh -0.004 0.038 0.091 11 -0.14 36 47
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.02 0.087 0.24 1 -0.3 29 30
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.081 0.094 0.2 294 -0.16 5 299
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.26 305 -10000 0 305
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.034 0.12 0.2 156 -0.38 32 188
SNAP25 -0.001 0.063 0.1 49 -0.31 28 77
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.05 0.16 0.26 163 -0.6 29 192
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.031 -10000 0 -0.38 3 3
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.087 0.24 1 -0.3 29 30
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.003 0.07 -10000 0 -0.35 7 7
alphaM/beta2 Integrin/GPIbA 0.005 0.078 0.35 4 -0.43 6 10
alphaM/beta2 Integrin/proMMP-9 0.069 0.11 0.35 10 -0.44 1 11
PLAUR 0.042 0.063 0.26 60 -10000 0 60
HMGB1 -0.004 0.041 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.006 0.063 -10000 0 -10000 0 0
AGER -0.008 0.054 0.24 1 -0.65 2 3
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.14 0.32 2 -0.38 11 13
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 324 -0.6 1 325
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 -0.37 36 36
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.25 -10000 0 -0.6 168 168
MYH2 -0.013 0.15 0.26 13 -0.44 44 57
MST1R 0.021 0.057 0.26 6 -0.6 6 12
leukocyte activation during inflammatory response -0.21 0.17 -10000 0 -0.35 473 473
APOB -0.37 0.3 -10000 0 -0.6 521 521
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 0.022 0.063 0.26 16 -0.6 6 22
alphaM/beta2 Integrin/CTGF 0.001 0.077 -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 0.26 10 -10000 0 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.13 0.24 7 -0.34 58 65
cell adhesion 0.005 0.078 0.34 4 -0.43 6 10
NFKB1 -0.11 0.21 0.44 3 -0.38 261 264
THY1 0.024 0.022 0.26 6 -10000 0 6
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.24 0.2 -10000 0 -0.38 526 526
alphaM/beta2 Integrin/LRP/tPA 0.004 0.091 -10000 0 -0.4 20 20
IL6 -0.28 0.4 0.36 1 -0.79 312 313
ITGB2 -0.005 0.051 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.028 0.085 0.33 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 0.26 13 -0.38 80 93
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 0.041 0.26 25 -10000 0 25
PLAT 0.007 0.089 -10000 0 -0.6 17 17
actin filament polymerization -0.012 0.15 0.26 14 -0.43 41 55
MST1 0.018 0.062 0.26 1 -0.6 8 9
alphaM/beta2 Integrin/lipoprotein(a) -0.21 0.18 -10000 0 -0.35 473 473
TNF -0.11 0.2 0.4 2 -0.75 15 17
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 0.027 0.029 0.26 12 -10000 0 12
dendritic cell antigen processing and presentation -0.011 0.13 0.24 7 -0.34 58 65
VTN 0.033 0.071 0.26 46 -0.6 4 50
alphaM/beta2 Integrin/CYR61 -0.014 0.11 -10000 0 -0.41 44 44
LPA 0.019 0.02 0.26 5 -10000 0 5
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 0.26 366 -10000 0 366
alphaM/beta2 Integrin/Thy1 0.007 0.064 -10000 0 -10000 0 0
MPO -0.015 0.15 0.26 1 -0.6 49 50
KNG1 0.022 0.027 0.26 10 -10000 0 10
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.014 0.16 0.26 22 -0.42 52 74
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.019 0.02 0.26 5 -10000 0 5
CTGF 0.017 0.066 0.26 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 -0.38 149 149
HP -0.074 0.24 0.26 28 -0.6 136 164
leukocyte adhesion -0.044 0.14 -10000 0 -0.48 23 23
SELP -0.11 0.25 -10000 0 -0.6 168 168
Glypican 1 network

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
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 -0.04 0.19 0.26 1 -0.6 84 85
PRNP 0.015 0.072 -10000 0 -0.6 11 11
GPC1/SLIT2 0 0.12 -10000 0 -0.43 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 91 91
TDGF1 0.01 0.09 0.26 2 -0.6 17 19
CRIPTO/GPC1 0.025 0.07 -10000 0 -0.45 17 17
APP/GPC1 0.035 0.012 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0 0.058 -10000 0 -0.39 17 17
FLT1 0.023 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.037 0.067 -10000 0 -0.38 19 19
SERPINC1 0.029 0.047 0.26 30 -10000 0 30
FYN 0 0.059 -10000 0 -0.38 18 18
FGR 0.001 0.058 -10000 0 -0.39 17 17
positive regulation of MAPKKK cascade 0.001 0.095 0.28 2 -0.39 29 31
SLIT2 -0.021 0.16 -10000 0 -0.6 58 58
GPC1/NRG -0.11 0.21 -10000 0 -0.45 219 219
NRG1 -0.14 0.27 0.26 3 -0.6 219 222
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.022 -10000 0 -10000 0 0
LYN 0.001 0.052 -10000 0 -0.39 13 13
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 0.012 -10000 0 -0.26 2 2
SRC 0.001 0.055 -10000 0 -0.39 15 15
TGFBR1 0.024 0.009 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.16 0.29 0.26 19 -0.6 252 271
GPC1 0.025 0.012 0.26 2 -10000 0 2
TGFBR1 (dimer) 0.024 0.009 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 5 -10000 0 5
BLK 0.013 0.076 -10000 0 -0.38 18 18
HCK 0.003 0.059 -10000 0 -0.39 16 16
FGF2 -0.21 0.3 -10000 0 -0.6 309 309
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 0.22 -10000 0 -0.43 269 269
LCK 0 0.074 -10000 0 -0.39 26 26
neuron differentiation -0.11 0.21 -10000 0 -0.45 219 219
PrPc/Cu2+ 0.011 0.053 -10000 0 -0.44 11 11
APP 0.024 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.01 0.094 -10000 0 -0.6 19 19
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.017 0.23 0.55 6 -0.63 21 27
CRP 0.003 0.24 0.57 22 -0.64 18 40
cell cycle arrest -0.027 0.25 0.56 9 -0.66 34 43
TIMP1 -0.012 0.22 0.53 7 -0.59 21 28
IL6ST -0.003 0.14 -10000 0 -0.59 43 43
Rac1/GDP -0.058 0.19 0.32 6 -0.39 116 122
AP1 -0.079 0.22 -10000 0 -0.48 95 95
GAB2 0.022 0.008 -10000 0 -10000 0 0
TNFSF11 -0.004 0.24 0.56 17 -0.61 23 40
HSP90B1 0.027 0.1 -10000 0 -0.77 8 8
GAB1 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.086 0.17 -10000 0 -0.5 59 59
AKT1 0.027 0.057 -10000 0 -0.52 4 4
FOXO1 0.028 0.058 0.43 1 -0.49 3 4
MAP2K6 -0.087 0.18 0.28 1 -0.39 125 126
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.042 0.2 0.39 9 -0.47 54 63
MITF -0.079 0.19 0.28 8 -0.39 125 133
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 -0.004 0.18 -10000 0 -1.2 20 20
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.012 0.13 -10000 0 -0.49 28 28
STAT3 -0.033 0.27 0.56 9 -0.7 37 46
STAT1 0.015 0.093 -10000 0 -0.84 7 7
CEBPD -0.002 0.24 0.56 12 -0.67 22 34
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.035 0.011 -10000 0 -10000 0 0
JUN 0.018 0.057 -10000 0 -0.6 7 7
PIAS3/MITF -0.065 0.18 0.33 1 -0.39 108 109
MAPK11 -0.085 0.17 -10000 0 -0.5 59 59
STAT3 (dimer)/FOXO1 -0.012 0.22 0.48 14 -0.54 32 46
GRB2/SOS1/GAB family -0.049 0.17 -10000 0 -0.44 53 53
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.092 0.18 -10000 0 -0.33 234 234
GRB2 0.023 0.007 -10000 0 -10000 0 0
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.16 0.46 0.56 20 -0.93 187 207
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 -0.93 28 49
FGG -0.014 0.24 0.62 8 -0.66 17 25
macrophage differentiation -0.027 0.25 0.56 9 -0.66 34 43
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.089 0.21 -10000 0 -0.36 265 265
JUNB -0.021 0.22 0.53 6 -0.63 17 23
FOS -0.17 0.29 -10000 0 -0.6 252 252
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.082 0.19 0.3 8 -0.37 167 175
STAT1/PIAS1 -0.05 0.2 0.35 8 -0.38 123 131
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.061 -10000 0 -0.53 5 5
STAT3 (dimer) -0.032 0.26 0.56 9 -0.71 34 43
PRKCD -0.025 0.2 0.44 16 -0.5 38 54
IL6R 0.007 0.099 -10000 0 -0.6 21 21
SOCS3 -0.082 0.19 -10000 0 -0.64 36 36
gp130 (dimer)/JAK1/JAK1/LMO4 0.035 0.11 -10000 0 -0.37 44 44
Rac1/GTP -0.052 0.2 0.35 7 -0.41 94 101
HCK 0.027 0.029 0.26 12 -10000 0 12
MAPKKK cascade 0.004 0.13 -10000 0 -0.58 25 25
bone resorption -0.002 0.24 0.55 18 -0.57 25 43
IRF1 -0.021 0.23 0.55 6 -0.64 19 25
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 -0.39 128 136
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.094 0.19 -10000 0 -0.55 64 64
PTPN11 0.012 0.083 -10000 0 -0.86 6 6
IL6/IL6RA -0.13 0.23 -10000 0 -0.45 262 262
gp130 (dimer)/TYK2/TYK2/LMO4 0.029 0.1 -10000 0 -0.37 46 46
gp130 (dimer)/JAK2/JAK2/LMO4 0.029 0.1 -10000 0 -0.37 44 44
IL6 -0.2 0.3 0.28 1 -0.6 302 303
PIAS3 0.023 0.005 -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 -0.097 0.18 0.23 1 -0.33 241 242
LMO4 0.028 0.043 0.29 2 -0.6 3 5
STAT3 (dimer)/PIAS3 -0.037 0.25 0.54 7 -0.66 39 46
MCL1 0.058 0.095 0.49 1 -0.48 4 5
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CCL5 0.03 0.048 0.26 26 -0.6 1 27
SDCBP 0.021 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.067 0.13 0.3 21 -0.41 12 33
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.051 0.13 0.27 7 -0.39 16 23
Syndecan-1/Syntenin 0.055 0.12 0.3 11 -0.41 12 23
MAPK3 0.051 0.12 0.27 11 -0.38 12 23
HGF/MET -0.07 0.21 -10000 0 -0.47 171 171
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 15 27
Syndecan-1/Syntenin/PIP2 0.05 0.12 0.28 11 -0.4 12 23
LAMA5 0.023 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.049 0.12 0.27 10 -0.39 12 22
MMP7 -0.041 0.2 0.26 24 -0.6 92 116
HGF -0.011 0.14 -10000 0 -0.6 46 46
Syndecan-1/CASK 0.046 0.12 0.25 16 -0.38 16 32
Syndecan-1/HGF/MET -0.004 0.21 0.3 7 -0.48 83 90
regulation of cell adhesion 0.044 0.11 0.28 6 -0.42 7 13
HPSE 0.028 0.04 0.26 16 -0.6 1 17
positive regulation of cell migration 0.067 0.13 0.3 21 -0.41 12 33
SDC1 0.069 0.12 0.3 20 -0.42 9 29
Syndecan-1/Collagen 0.067 0.13 0.3 21 -0.41 12 33
PPIB 0.024 0.009 0.26 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 0.26 324 -0.6 1 325
MAPK1 0.052 0.12 0.28 11 -0.38 11 22
homophilic cell adhesion 0.067 0.13 0.3 21 -0.4 13 34
MMP1 0.19 0.11 0.26 589 -10000 0 589
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.009 0.12 -10000 0 -0.37 82 82
EFNA5 -0.035 0.18 -10000 0 -0.6 77 77
FYN -0.027 0.11 -10000 0 -0.35 76 76
neuron projection morphogenesis -0.009 0.12 -10000 0 -0.37 82 82
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.009 0.12 -10000 0 -0.37 82 82
EPHA5 0.023 0.015 0.26 3 -10000 0 3
Integrins in angiogenesis

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
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 0.081 0.26 1 -0.6 14 15
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.071 0.26 5 -0.6 10 15
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.045 0.12 -10000 0 -0.54 26 26
VEGFA 0.025 0.019 0.26 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 -0.49 21 22
PTK2B -0.009 0.06 0.36 2 -0.36 13 15
alphaV/beta3 Integrin/JAM-A -0.078 0.18 0.3 1 -0.34 219 220
CBL 0.022 0.007 -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 -0.048 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 -0.38 14 14
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.28 -10000 0 -0.48 257 257
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 -0.46 224 227
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.57 276 276
GPR124 0.016 0.049 -10000 0 -0.6 5 5
MAPK1 -0.2 0.3 -10000 0 -0.58 289 289
PXN 0.024 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 -0.39 164 164
cell adhesion 0.027 0.071 0.26 1 -0.37 23 24
ANGPTL3 0.022 0.018 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.025 -10000 0 -0.39 1 1
IGF-1R heterotetramer 0.013 0.081 0.26 1 -0.6 14 15
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 0.26 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 -0.4 13 13
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.023 0.022 -10000 0 -0.6 1 1
alphaV/beta3 Integrin/CD47 0.039 0.058 -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 0.022 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 0.32 5 -0.39 24 29
alphaV beta3/Integrin/ppsTEM5 0.031 0.063 -10000 0 -0.4 13 13
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.033 0.071 0.26 46 -0.6 4 50
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.6 309 309
F11R -0.13 0.21 -10000 0 -0.45 237 237
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 -0.44 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.032 -10000 0 -0.35 2 2
HSP90AA1 0.024 0.004 -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 0.26 366 -10000 0 366
alphaV/beta3 Integrin/Pyk2 0.03 0.059 -10000 0 -0.36 13 13
SDC1 0.039 0.064 0.26 55 -0.6 1 56
VAV3 -0.01 0.037 -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 24 29
cell migration -0.036 0.12 0.3 6 -0.37 20 26
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.065 0.17 -10000 0 -0.33 192 192
SPP1 0.091 0.11 0.26 231 -10000 0 231
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 -0.099 0.25 0.26 4 -0.6 163 167
angiogenesis -0.18 0.3 0.3 1 -0.58 263 264
Rac1/GTP 0.022 0.031 -10000 0 -0.31 4 4
EDIL3 0.012 0.1 0.26 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 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
GRB2/SOS1/SHC 0.044 0.18 0.31 98 -0.5 42 140
FYN 0.021 0.2 0.39 33 -0.62 44 77
LAT/GRAP2/SLP76 0.025 0.18 0.38 30 -0.54 45 75
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.023 0.16 0.33 62 -0.41 52 114
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.016 0.061 0.17 51 -0.14 14 65
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
mol:Ca2+ -0.025 0.035 -10000 0 -0.095 144 144
integrin-mediated signaling pathway 0.025 0.025 -10000 0 -0.38 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.21 0.44 27 -0.56 60 87
TRPV6 -0.098 0.29 1.2 14 -0.6 158 172
CD28 0.024 0.05 0.27 7 -0.6 4 11
SHC1 0.027 0.22 0.33 104 -0.63 46 150
receptor internalization -0.013 0.23 0.42 22 -0.53 96 118
PRF1 -0.012 0.25 0.61 6 -1 33 39
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
COT/AKT1 0.032 0.14 0.3 59 -0.35 44 103
LAT 0.012 0.21 0.38 37 -0.65 46 83
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 -0.6 20 54
RASGRP2 -0.001 0.052 0.17 9 -0.17 55 64
RASGRP1 0.026 0.16 0.38 33 -0.44 44 77
HLA-A 0.025 0.015 0.27 2 -10000 0 2
RASSF5 0.019 0.033 0.26 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 0.18 129 -0.13 23 152
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.057 -10000 0 -0.22 32 32
PRKCA 0.012 0.1 0.24 34 -0.28 41 75
GRAP2 0.016 0.073 0.26 3 -0.6 11 14
mol:IP3 0.017 0.14 0.27 106 -0.39 43 149
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.009 0.19 0.35 23 -0.67 43 66
ORAI1 0.039 0.18 0.65 3 -0.98 13 16
CSK 0.007 0.21 0.41 24 -0.66 46 70
B7 family/CD28 0.064 0.22 0.48 31 -0.67 37 68
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.001 0.24 0.43 24 -0.67 59 83
PTPN6 0.007 0.2 0.39 28 -0.67 44 72
VAV1 0.002 0.21 0.42 24 -0.65 47 71
Monovalent TCR/CD3 -0.002 0.15 0.31 23 -0.55 41 64
CBL 0.022 0.007 -10000 0 -10000 0 0
LCK 0.017 0.21 0.4 30 -0.68 42 72
PAG1 0.02 0.21 0.36 44 -0.64 46 90
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0 0.23 0.41 25 -0.71 51 76
CD80 0.093 0.11 0.27 236 -10000 0 236
CD86 0.026 0.018 0.27 4 -10000 0 4
PDK1/CARD11/BCL10/MALT1 -0.006 0.073 0.2 1 -0.26 32 33
HRAS 0.024 0.01 0.26 1 -10000 0 1
GO:0035030 0.022 0.17 0.38 28 -0.54 38 66
CD8A 0.028 0.065 0.28 21 -0.61 5 26
CD8B 0.009 0.12 0.28 20 -0.61 29 49
PTPRC 0.023 0.038 0.27 12 -0.61 1 13
PDK1/PKC theta 0.024 0.2 0.39 60 -0.52 47 107
CSK/PAG1 0.024 0.21 0.35 44 -0.64 43 87
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 0.45 21 -0.62 48 69
STIM1 0.028 0.11 1.3 4 -10000 0 4
RAS family/GTP 0.045 0.097 0.23 72 -0.18 29 101
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.018 0.25 0.42 22 -0.57 96 118
mol:DAG -0.016 0.1 0.14 16 -0.36 44 60
RAP1A/GDP 0.021 0.039 0.1 72 -0.066 6 78
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 0.58 7 -0.96 33 40
RAP1A/GTP -0.002 0.018 -10000 0 -0.065 51 51
mol:PI-3-4-5-P3 0.017 0.18 0.4 30 -0.46 60 90
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.022 0.18 0.3 96 -0.51 43 139
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 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.005 0.16 0.49 8 -0.53 44 52
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 0.26 16 -0.6 2 18
PRKCB 0.014 0.11 0.28 34 -0.28 36 70
PRKCE 0.018 0.098 0.23 39 -0.27 35 74
PRKCQ 0.013 0.21 0.45 27 -0.59 51 78
LCP2 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.027 0.15 0.31 64 -0.35 51 115
IKK complex 0.037 0.087 0.22 96 -0.12 10 106
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.026 0.11 0.25 64 -0.27 39 103
PDPK1 0.028 0.16 0.36 62 -0.39 46 108
TCR/CD3/MHC I/CD8/Fyn -0.027 0.25 0.45 19 -0.78 57 76
LPA receptor mediated events

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
GNB1/GNG2 0.037 0.066 -10000 0 -0.36 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.13 -10000 0 -0.33 72 72
AP1 -0.11 0.21 -10000 0 -0.36 307 307
mol:PIP3 -0.12 0.19 -10000 0 -0.35 301 301
AKT1 0.011 0.071 0.31 3 -0.42 4 7
PTK2B -0.029 0.1 -10000 0 -0.35 42 42
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 0.25 1 -0.3 84 85
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 -0.33 105 105
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 75 75
endothelial cell migration 0.004 0.073 -10000 0 -0.45 19 19
ADCY4 -0.019 0.11 -10000 0 -0.48 29 29
ADCY5 -0.075 0.15 -10000 0 -0.49 57 57
ADCY6 -0.011 0.091 -10000 0 -0.46 21 21
ADCY7 -0.011 0.092 -10000 0 -0.48 21 21
ADCY1 -0.012 0.098 -10000 0 -0.44 25 25
ADCY2 -0.025 0.12 -10000 0 -0.5 32 32
ADCY3 -0.011 0.091 -10000 0 -0.46 21 21
ADCY8 -0.01 0.083 -10000 0 -0.44 19 19
ADCY9 -0.012 0.091 -10000 0 -0.46 21 21
GSK3B -0.029 0.1 0.28 3 -0.35 38 41
arachidonic acid secretion -0.017 0.099 -10000 0 -0.4 34 34
GNG2 0.019 0.053 -10000 0 -0.6 6 6
TRIP6 0.017 0.017 -10000 0 -0.42 1 1
GNAO1 0.004 0.076 -10000 0 -0.36 31 31
HRAS 0.024 0.01 0.26 1 -10000 0 1
NFKBIA -0.021 0.13 -10000 0 -0.35 88 88
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.03 0.11 -10000 0 -0.82 14 14
JUN 0.019 0.057 -10000 0 -0.6 7 7
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.015 0.13 -10000 0 -0.97 14 14
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 -0.015 0.11 0.25 1 -0.3 84 85
PLCB3 0.026 0.046 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 252 252
positive regulation of mitosis -0.017 0.099 -10000 0 -0.4 34 34
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 -0.39 30 30
GNAZ 0.005 0.061 -10000 0 -0.34 24 24
EGFR/PI3K-beta/Gab1 -0.12 0.2 -10000 0 -0.37 301 301
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 0.066 -10000 0 -0.32 10 10
GNAI2 0.008 0.051 -10000 0 -0.32 18 18
GNAI3 0.008 0.051 -10000 0 -0.33 18 18
GNAI1 -0.011 0.11 -10000 0 -0.4 53 53
LPA/LPA3 -0.029 0.15 0.18 30 -0.43 97 127
LPA/LPA2 0.019 0.014 0.18 1 -10000 0 1
LPA/LPA1 0.013 0.061 -10000 0 -0.36 20 20
HB-EGF/EGFR -0.077 0.21 0.27 1 -0.37 253 254
HBEGF 0.066 0.079 0.27 21 -0.45 3 24
mol:DAG -0.015 0.11 0.25 1 -0.3 84 85
cAMP biosynthetic process -0.031 0.11 0.4 1 -0.4 43 44
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.27 5 -0.34 67 72
GNAQ -0.023 0.11 0.21 1 -0.33 95 96
LPAR2 0.025 0.009 0.26 1 -10000 0 1
LPAR3 -0.038 0.2 0.26 30 -0.6 93 123
LPAR1 0.016 0.074 -10000 0 -0.6 11 11
IL8 -0.13 0.24 0.37 22 -0.43 226 248
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 -0.34 105 105
EGFR -0.19 0.3 -10000 0 -0.6 277 277
PLCG1 -0.025 0.12 0.21 3 -0.34 94 97
PLD2 -0.029 0.12 0.25 1 -0.34 100 101
G12/G13 0.038 0.053 -10000 0 -0.32 14 14
PI3K-beta 0.005 0.065 -10000 0 -0.43 6 6
cell migration 0.002 0.062 -10000 0 -0.26 11 11
SLC9A3R2 0.023 0.007 -10000 0 -10000 0 0
PXN -0.018 0.11 -10000 0 -0.39 30 30
HRAS/GTP -0.017 0.1 -10000 0 -0.41 34 34
RAC1 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 324 -0.6 1 325
PRKCE 0.024 0.022 -10000 0 -0.6 1 1
PRKCD -0.016 0.11 -10000 0 -0.3 71 71
Gi(beta/gamma) -0.01 0.099 -10000 0 -0.44 28 28
mol:LPA 0.001 0.016 -10000 0 -0.18 4 4
TRIP6/p130 Cas/FAK1/Paxillin -0.015 0.12 -10000 0 -0.46 18 18
MAPKKK cascade -0.017 0.099 -10000 0 -0.4 34 34
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 -0.32 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 -0.32 93 94
Rac1/GTP 0.031 0.12 -10000 0 -0.89 13 13
MMP2 0.004 0.073 -10000 0 -0.45 19 19
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 0.42 4 -0.66 81 85
IHH 0.017 0.081 0.27 25 -0.24 9 34
SHH Np/Cholesterol/GAS1 -0.001 0.081 -10000 0 -0.35 39 39
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.001 0.08 0.35 39 -10000 0 39
SMO/beta Arrestin2 -0.015 0.2 -10000 0 -0.63 67 67
SMO -0.039 0.21 -10000 0 -0.66 69 69
AKT1 0 0.12 -10000 0 -0.58 16 16
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 -10000 0 -0.64 69 69
STIL 0.012 0.17 0.3 26 -0.49 62 88
DHH N/PTCH2 -0.018 0.16 -10000 0 -0.46 86 86
DHH N/PTCH1 -0.024 0.2 0.29 1 -0.52 102 103
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DHH 0.008 0.1 0.26 1 -0.6 22 23
PTHLH -0.056 0.29 0.57 1 -0.84 84 85
determination of left/right symmetry -0.038 0.2 -10000 0 -0.64 69 69
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
skeletal system development -0.055 0.29 0.57 1 -0.83 84 85
IHH N/Hhip 0.029 0.057 0.36 1 -0.49 1 2
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 -10000 0 -0.64 69 69
pancreas development 0.024 0.033 0.26 8 -0.6 1 9
HHAT 0.02 0.023 -10000 0 -0.6 1 1
PI3K 0.033 0.01 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.6 44 44
somite specification -0.038 0.2 -10000 0 -0.64 69 69
SHH Np/Cholesterol/PTCH1 -0.022 0.16 0.28 2 -0.51 65 67
SHH Np/Cholesterol/PTCH2 -0.011 0.097 -10000 0 -0.35 56 56
SHH Np/Cholesterol/Megalin -0.064 0.16 0.28 3 -0.35 170 173
SHH -0.001 0.037 0.36 4 -0.45 1 5
catabolic process -0.028 0.2 0.35 1 -0.57 87 88
SMO/Vitamin D3 -0.005 0.2 0.37 11 -0.58 64 75
SHH Np/Cholesterol/Hhip 0.016 0.034 0.28 6 -0.36 2 8
LRP2 -0.13 0.28 0.26 20 -0.6 206 226
receptor-mediated endocytosis -0.078 0.22 0.31 7 -0.62 79 86
SHH Np/Cholesterol/BOC -0.006 0.091 -10000 0 -0.35 49 49
SHH Np/Cholesterol/CDO 0.013 0.043 -10000 0 -0.36 9 9
mesenchymal cell differentiation -0.016 0.034 0.36 2 -0.28 6 8
mol:Vitamin D3 0.006 0.18 0.35 16 -0.51 65 81
IHH N/PTCH2 -0.014 0.15 -10000 0 -0.5 69 69
CDON 0.015 0.065 -10000 0 -0.6 9 9
IHH N/PTCH1 -0.019 0.21 0.36 3 -0.58 87 90
Megalin/LRPAP1 -0.083 0.21 -10000 0 -0.44 209 209
PTCH2 -0.028 0.17 -10000 0 -0.6 69 69
SHH Np/Cholesterol 0.01 0.016 -10000 0 -0.35 1 1
PTCH1 -0.028 0.2 0.35 1 -0.58 87 88
HHIP 0.024 0.033 0.26 8 -0.6 1 9
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.031 0.049 -10000 0 -0.33 12 12
RGS9BP 0.037 0.054 0.26 44 -10000 0 44
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.018 0.26 4 -10000 0 4
mol:Na + 0.039 0.048 -10000 0 -10000 0 0
mol:ADP -0.006 0.026 0.25 4 -10000 0 4
GNAT2 0.024 0.013 0.26 2 -10000 0 2
RGS9-1/Gbeta5/R9AP 0.009 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 0.019 0.26 5 -10000 0 5
CNGB3 0.022 0.039 0.26 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 0.3 157 -10000 0 157
Cone PDE6 0.023 0.12 0.31 2 -0.34 73 75
Cone Metarhodopsin II 0.026 0.017 0.17 5 -10000 0 5
Na + (4 Units) 0.12 0.096 0.32 58 -10000 0 58
GNAT2/GDP 0.018 0.12 0.27 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 0.26 519 -10000 0 519
GNB3/GNGT2 0.024 0.06 -10000 0 -0.43 13 13
GNB3 0.015 0.076 0.26 2 -0.6 12 14
GNAT2/GTP 0.018 0.009 0.18 2 -10000 0 2
CNGA3 0.049 0.074 0.26 87 -10000 0 87
ARR3 0.021 0.021 0.26 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 0.046 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.17 0.12 0.26 519 -10000 0 519
RGS9 -0.035 0.18 0.26 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 0.26 4 -10000 0 4
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.018 0.082 -10000 0 -0.35 2 2
epithelial cell differentiation 0.035 0.078 0.4 1 -10000 0 1
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.028 0.1 0.48 8 -10000 0 8
FYN 0.022 0.023 -10000 0 -0.6 1 1
EGFR -0.19 0.29 -10000 0 -0.6 277 277
PRL 0.023 0.027 0.26 10 -10000 0 10
neuron projection morphogenesis -0.05 0.15 0.36 8 -0.38 19 27
PTPRZ1 -0.3 0.31 0.26 6 -0.6 431 437
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.15 -10000 0 -0.41 22 22
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.09 0.16 -10000 0 -0.36 174 174
ADAM17 0.031 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.075 0.4 8 -10000 0 8
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 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 -0.4 45 45
GRIN2B -0.11 0.17 -10000 0 -0.48 52 52
ErbB4/ErbB2/betacellulin 0.015 0.1 -10000 0 -0.43 4 4
STAT1 0.029 0.035 0.26 18 -10000 0 18
HBEGF 0.023 0.031 -10000 0 -0.6 2 2
PRLR 0.026 0.021 0.26 6 -10000 0 6
E4ICDs/ETO2 0.009 0.089 0.36 1 -0.44 7 8
axon guidance 0.061 0.12 0.41 7 -0.39 1 8
NEDD4 0.03 0.017 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.035 0.024 -10000 0 -10000 0 0
CBFA2T3 0.013 0.076 0.26 3 -0.6 12 15
ErbB4/ErbB2/HBEGF 0.033 0.073 -10000 0 -10000 0 0
MAPK3 -0.054 0.14 -10000 0 -0.39 21 21
STAT1 (dimer) 0.022 0.082 -10000 0 -10000 0 0
MAPK1 -0.053 0.15 0.39 2 -0.39 20 22
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.074 0.16 -10000 0 -0.4 43 43
NRG1 -0.12 0.2 -10000 0 -0.45 216 216
NRG3 -0.008 0.15 0.26 18 -0.6 48 66
NRG2 -0.31 0.31 -10000 0 -0.6 435 435
NRG4 0.026 0.027 0.26 10 -10000 0 10
heart development 0.061 0.12 0.41 7 -0.39 1 8
neural crest cell migration -0.073 0.16 -10000 0 -0.4 43 43
ERBB2 0.037 0.074 0.27 75 -10000 0 75
WWOX/E4ICDs 0.014 0.077 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.092 0.17 -10000 0 -0.34 187 187
apoptosis 0.016 0.14 0.51 35 -10000 0 35
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.18 0.19 -10000 0 -0.37 323 323
ErbB4/ErbB2/epiregulin 0.006 0.14 0.36 11 -0.41 7 18
ErbB4/ErbB4/betacellulin/betacellulin -0.002 0.11 -10000 0 -0.38 31 31
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.044 0.084 0.4 1 -10000 0 1
MDM2 0.014 0.086 0.35 7 -10000 0 7
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.087 0.15 -10000 0 -0.39 40 40
STAT5A 0.054 0.11 0.37 10 -10000 0 10
ErbB4/EGFR/neuregulin 1 beta -0.19 0.24 -10000 0 -0.54 202 202
DLG4 0.022 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.015 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.013 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 0.4 2 -10000 0 2
LRIG1 0.023 0.022 -10000 0 -0.6 1 1
EREG -0.03 0.21 0.26 61 -0.6 93 154
BTC -0.008 0.14 0.26 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 0.075 0.4 8 -10000 0 8
STAT5B 0.022 0.031 -10000 0 -0.6 2 2
YAP1 -0.011 0.11 0.23 3 -0.38 54 57
GRB2 0.023 0.006 -10000 0 -10000 0 0
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 0.26 1 -10000 0 1
cell proliferation -0.038 0.18 0.37 4 -0.55 17 21
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.058 0.22 1 -0.32 2 3
adherens junction organization -0.015 0.095 -10000 0 -0.34 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.083 0.16 0.34 3 -0.3 237 240
FMN1 -0.013 0.09 -10000 0 -0.32 44 44
mol:IP3 0.001 0.048 -10000 0 -0.25 2 2
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 -0.54 31 31
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.079 -10000 0 -0.31 36 36
VASP -0.01 0.084 -10000 0 -0.31 39 39
ZYX -0.009 0.084 -10000 0 -0.31 39 39
JUB -0.01 0.086 -10000 0 -0.31 41 41
EGFR(dimer) -0.11 0.18 -10000 0 -0.34 271 271
E-cadherin/beta catenin-gamma catenin 0.032 0.06 -10000 0 -0.37 14 14
mol:PI-3-4-5-P3 0.018 0.07 -10000 0 -0.26 8 8
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.018 0.071 -10000 0 -0.26 8 8
FYN -0.003 0.063 0.22 1 -0.31 7 8
mol:Ca2+ 0.001 0.047 -10000 0 -0.24 2 2
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:DAG 0.001 0.048 -10000 0 -0.25 2 2
CDH1 0.011 0.081 -10000 0 -0.6 14 14
RhoA/GDP -0.082 0.16 0.36 2 -0.3 238 240
establishment of polarity of embryonic epithelium -0.01 0.082 -10000 0 -0.3 39 39
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 0.29 -10000 0 -0.6 277 277
CASR -0.001 0.051 0.22 2 -10000 0 2
RhoA/GTP 0.015 0.053 -10000 0 -10000 0 0
AKT2 0.002 0.061 -10000 0 -0.29 2 2
actin cable formation -0.016 0.088 0.25 2 -0.32 44 46
apoptosis -0.006 0.07 0.28 13 -0.23 6 19
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.098 0.15 -10000 0 -0.32 241 241
PIP5K1A -0.01 0.08 -10000 0 -0.32 36 36
PLCG1 0.001 0.048 -10000 0 -0.25 2 2
Rac1/GTP -0.092 0.18 -10000 0 -0.32 269 269
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.036 0.1 1.1 1 -10000 0 1
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.028 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 0.19 -10000 0 -0.38 201 201
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 0.023 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.038 0.039 -10000 0 -0.33 7 7
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.075 0.18 0.62 81 -10000 0 81
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 0.02 0.023 0.26 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 0.027 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.026 0.16 -10000 0 -0.33 165 165
NR4A1 -0.032 0.18 -10000 0 -0.6 75 75
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 -0.6 186 186
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 -0.009 0.12 -10000 0 -0.43 13 13
PPARA 0.021 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 -0.32 213 213
SREBF1 -0.01 0.11 -10000 0 -0.58 1 1
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 -0.35 164 164
BCL2 0.007 0.098 -10000 0 -0.6 21 21
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.022 -10000 0 -0.6 1 1
LAT2 -0.021 0.1 -10000 0 -0.37 39 39
AP1 -0.069 0.19 -10000 0 -0.45 94 94
mol:PIP3 0.007 0.17 0.35 32 -0.43 38 70
IKBKB 0.033 0.13 0.28 89 -0.27 17 106
AKT1 0.011 0.17 0.32 106 -0.43 13 119
IKBKG 0.014 0.11 0.24 55 -0.27 22 77
MS4A2 -0.022 0.16 0.26 4 -0.58 59 63
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 0.33 12 -0.41 18 30
mol:Ca2+ 0.012 0.14 0.31 37 -0.32 38 75
LYN 0.021 0.014 -10000 0 -10000 0 0
CBLB -0.02 0.1 -10000 0 -0.36 39 39
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.007 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 99 -0.34 113 212
PTPN13 -0.017 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 0.011 0.13 0.32 25 -0.35 18 43
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.03 0.13 -10000 0 -0.37 78 78
LAT -0.021 0.1 -10000 0 -0.37 40 40
PAK2 0.012 0.13 0.32 15 -0.45 18 33
NFATC2 -0.035 0.13 -10000 0 -0.6 36 36
HRAS 0.007 0.13 0.28 14 -0.48 20 34
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 -0.42 121 121
Antigen/IgE/Fc epsilon R1 -0.024 0.15 -10000 0 -0.38 119 119
mol:GDP -0.016 0.11 -10000 0 -0.49 19 19
JUN 0.019 0.057 -10000 0 -0.6 7 7
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 -0.6 252 252
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.018 0.11 -10000 0 -0.37 42 42
CHUK 0.014 0.11 0.24 54 -0.27 21 75
KLRG1 -0.019 0.097 -10000 0 -0.33 40 40
VAV1 -0.021 0.1 -10000 0 -0.37 39 39
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.019 0.1 -10000 0 -0.36 38 38
negative regulation of mast cell degranulation -0.008 0.1 -10000 0 -0.39 19 19
BTK -0.014 0.11 -10000 0 -0.5 20 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.034 0.14 -10000 0 -0.34 115 115
GAB2/PI3K/SHP2 -0.049 0.1 -10000 0 -0.34 60 60
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.026 0.11 -10000 0 -0.29 94 94
RAF1 0 0.12 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.006 0.16 -10000 0 -0.37 118 118
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 -0.015 0.15 -10000 0 -0.36 114 114
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 -0.6 50 50
DUSP1 -0.054 0.21 -10000 0 -0.6 103 103
NF-kappa-B/RelA 0.008 0.06 0.14 3 -0.18 11 14
actin cytoskeleton reorganization -0.009 0.15 -10000 0 -0.62 26 26
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.11 -10000 0 -0.45 18 18
FER -0.021 0.11 -10000 0 -0.37 41 41
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 0.005 0.13 0.29 6 -0.49 19 25
cytokine secretion -0.003 0.036 -10000 0 -10000 0 0
SPHK1 -0.02 0.1 -10000 0 -0.36 40 40
PTK2 -0.011 0.16 -10000 0 -0.66 26 26
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.026 0.14 -10000 0 -0.38 78 78
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.003 0.17 0.33 29 -0.42 44 73
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 -0.37 20 20
MAP2K4 -0.074 0.29 -10000 0 -0.84 103 103
Fc epsilon R1/FcgammaRIIB -0.014 0.16 -10000 0 -0.39 118 118
mol:Choline -0.009 0.18 0.33 99 -0.34 113 212
SHC/Grb2/SOS1 0.01 0.11 -10000 0 -0.35 35 35
FYN 0.022 0.023 -10000 0 -0.6 1 1
DOK1 0.024 0.002 -10000 0 -10000 0 0
PXN -0.011 0.15 -10000 0 -0.59 26 26
HCLS1 -0.02 0.1 -10000 0 -0.37 38 38
PRKCB 0.012 0.14 0.28 53 -0.32 42 95
FCGR2B 0.018 0.039 0.26 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 0.26 1 -10000 0 1
PLA2G4A -0.046 0.14 -10000 0 -0.37 100 100
RASA1 0.024 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.18 0.33 99 -0.34 113 212
IKK complex 0.031 0.11 0.27 72 -0.21 11 83
WIPF1 0.024 0.004 -10000 0 -10000 0 0
PDGFR-alpha 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
PDGFRA -0.034 0.15 -10000 0 -0.62 47 47
PDGF/PDGFRA/CRKL -0.012 0.11 -10000 0 -0.45 46 46
positive regulation of JUN kinase activity 0.023 0.086 -10000 0 -0.35 35 35
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.015 0.11 -10000 0 -0.44 48 48
AP1 -0.33 0.46 -10000 0 -0.98 267 267
mol:IP3 -0.037 0.11 -10000 0 -0.48 43 43
PLCG1 -0.037 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+ -0.037 0.11 -10000 0 -0.48 43 43
CAV3 0.02 0.013 0.26 2 -10000 0 2
CAV1 -0.1 0.25 -10000 0 -0.6 164 164
SHC/Grb2/SOS1 0.024 0.087 -10000 0 -0.36 35 35
PDGF/PDGFRA/Shf -0.012 0.12 -10000 0 -0.45 47 47
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 0.006 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:DAG -0.037 0.11 -10000 0 -0.48 43 43
PDGF/PDGFRA -0.034 0.15 -10000 0 -0.62 47 47
actin cytoskeleton reorganization -0.012 0.11 -10000 0 -0.45 46 46
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.016 0.098 -10000 0 -0.39 44 44
PDGF/PDGFRA/Crk/C3G 0.015 0.099 -10000 0 -0.38 46 46
JAK1 -0.027 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 0.26 1 -10000 0 1
SHF 0.023 0.024 0.26 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 0.086 -10000 0 -0.35 35 35
PDGF/PDGFRA/SHB -0.012 0.11 -10000 0 -0.45 46 46
PDGF/PDGFRA/Caveolin-1 -0.1 0.23 -10000 0 -0.5 188 188
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 -0.45 46 46
JAK-STAT cascade -0.027 0.1 0.23 1 -0.44 46 47
cell proliferation -0.012 0.11 -10000 0 -0.45 47 47
Canonical Wnt signaling pathway

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
HDAC1 0.022 0.021 0.25 2 -10000 0 2
AES 0.022 0.019 0.22 1 -10000 0 1
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.014 0.082 0.26 2 -0.6 14 16
TLE1 0.019 0.053 0.22 2 -0.61 5 7
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.3 34 -0.37 3 37
WIF1 -0.3 0.31 0.26 9 -0.6 421 430
beta catenin/RanBP3 0.018 0.087 0.42 26 -0.4 1 27
KREMEN2 0.12 0.12 0.26 343 -10000 0 343
DKK1 0.023 0.17 0.26 107 -0.6 43 150
beta catenin/beta TrCP1 0.11 0.096 0.3 29 -0.41 1 30
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.026 0.24 0.59 72 -1.3 13 85
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 0.3 7 -0.61 18 25
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 -0.36 3 5
HNF1A 0.025 0.03 0.26 9 -10000 0 9
CTBP1 0.021 0.019 0.24 2 -10000 0 2
MYC 0.12 0.35 0.57 221 -1.4 20 241
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.095 0.35 1 -0.35 11 12
NKD1 0.021 0.062 0.26 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 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.003 0.13 0.47 25 -0.52 15 40
LEF1 0.057 0.087 0.26 119 -10000 0 119
DVL1 0.055 0.055 -10000 0 -0.36 2 2
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.15 0.31 5 -0.68 19 24
DKK1/LRP6/Kremen 2 0.096 0.14 0.35 51 -0.34 43 94
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 0.26 1 -10000 0 1
CCND1 0.094 0.26 0.62 141 -1.2 5 146
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 0.059 0.29 6 -0.29 9 15
APC 0.016 0.059 0.36 7 -10000 0 7
WNT1/LRP6/FZD1 0.12 0.11 0.23 400 -0.25 1 401
CREBBP 0.021 0.018 0.23 1 -10000 0 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.42 0.28 -10000 0 -0.6 581 581
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.26 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.049 -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 0.26 119 -10000 0 119
ARNT/IPAS -0.28 0.21 -10000 0 -0.4 587 587
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 0.032 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 -0.3 4 4
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.05 -10000 0 -0.28 11 11
EGLN3 0.043 0.065 0.26 65 -10000 0 65
EGLN2 0.025 0.015 0.26 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 -0.51 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.051 0.074 0.24 31 -0.27 11 42
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.083 0.17 -10000 0 -0.32 217 217
Syndecan-3/Neurocan 0.026 0.075 0.28 13 -0.38 16 29
POMC 0.018 0.091 0.26 18 -0.6 15 33
EGFR -0.19 0.29 -10000 0 -0.6 277 277
Syndecan-3/EGFR -0.089 0.16 -10000 0 -0.33 240 240
AGRP 0.021 0.024 0.26 7 -10000 0 7
NCSTN 0.021 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.009 0.26 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 0.26 48 -10000 0 48
long-term memory 0.035 0.063 -10000 0 -0.36 12 12
Syndecan-3/IL8 0.021 0.087 0.28 9 -0.35 29 38
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 0.26 12 -10000 0 12
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.24 0.31 0.26 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 -0.49 20 24
Syndecan-3/AgRP 0.015 0.061 -10000 0 -0.37 17 17
Syndecan-3/AgRP/MC4R 0.038 0.07 0.34 1 -0.36 16 17
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 29 38
IL8 0.027 0.11 0.26 52 -0.6 16 68
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 12 12
Syndecan-3/CASK 0 0.056 -10000 0 -0.38 17 17
alpha-MSH/MC4R 0.029 0.073 0.38 2 -0.45 15 17
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.023 0.076 -10000 0 -0.39 18 18
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.034 0.18 -10000 0 -0.6 77 77
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.049 -10000 0 -0.6 5 5
AP1 -0.087 0.16 -10000 0 -0.33 241 241
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 -0.65 12 12
NICD/RBPSUH 0.021 0.074 -10000 0 -0.38 21 21
WIF1 -0.29 0.31 0.26 9 -0.6 421 430
NOTCH1 0.01 0.065 -10000 0 -0.39 20 20
PSENEN 0.024 0.009 0.26 1 -10000 0 1
KREMEN2 0.12 0.12 0.26 343 -10000 0 343
DKK1 0.023 0.17 0.26 107 -0.6 43 150
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 0.012 0.042 -10000 0 -0.3 6 6
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 252 252
JUN 0.019 0.057 -10000 0 -0.6 7 7
MAP3K7 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 -0.003 0.071 0.24 2 -0.38 6 8
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.095 0.35 1 -0.35 11 12
HNF1A 0.026 0.022 0.26 7 -10000 0 7
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 0.26 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 -0.43 22 22
apoptosis -0.086 0.16 -10000 0 -0.33 241 241
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 0.014 0.099 -10000 0 -0.85 10 10
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 0.095 0.14 0.35 51 -0.34 43 94
LRP6 0.023 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 0.26 1 -10000 0 1
Axin1/APC/beta catenin 0.01 0.1 0.34 3 -0.43 16 19
DKK2 0.014 0.082 0.26 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 -0.006 0.12 -10000 0 -0.43 22 22
PPP2R5D -0.006 0.065 0.29 6 -0.35 19 25
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.2 -10000 0 -0.36 406 406
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 S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.03 0.15 0.37 43 -0.35 46 89
TBX21 -0.006 0.36 0.81 14 -1.3 41 55
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 16 -0.85 28 44
IL12RB2 0.022 0.16 0.28 93 -0.59 37 130
GADD45G 0.032 0.25 0.67 17 -0.8 29 46
natural killer cell activation 0.005 0.025 -10000 0 -10000 0 0
RELB 0.026 0.019 0.26 5 -10000 0 5
RELA 0.024 0.004 -10000 0 -10000 0 0
IL18 0.033 0.042 0.28 21 -10000 0 21
IL2RA 0.029 0.089 0.26 46 -0.6 10 56
IFNG 0.058 0.086 0.26 120 -10000 0 120
STAT3 (dimer) 0.018 0.24 0.59 27 -0.67 42 69
HLA-DRB5 0.019 0.08 0.25 50 -0.61 5 55
FASLG 0.038 0.29 0.77 23 -0.96 29 52
NF kappa B2 p52/RelB 0.004 0.25 0.76 3 -0.75 45 48
CD4 0.008 0.025 -10000 0 -10000 0 0
SOCS1 0.024 0.031 0.26 6 -0.6 1 7
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D 0.005 0.1 0.27 29 -0.61 15 44
CD3E 0.005 0.098 0.28 23 -0.61 15 38
CD3G 0.003 0.11 0.27 34 -0.61 20 54
IL12Rbeta2/JAK2 0.03 0.13 0.3 25 -0.45 37 62
CCL3 0.016 0.28 0.76 15 -0.99 26 41
CCL4 0.018 0.27 0.76 15 -0.96 24 39
HLA-A 0.026 0.016 0.27 2 -10000 0 2
IL18/IL18R 0.056 0.12 0.41 11 -0.4 40 51
NOS2 0.016 0.28 0.74 15 -0.96 28 43
IL12/IL12R/TYK2/JAK2/SPHK2 0.028 0.15 0.36 42 -0.35 51 93
IL1R1 0.006 0.3 0.74 15 -1 33 48
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 0.42 20 -0.83 44 64
RAB7A 0.032 0.23 0.65 14 -0.79 18 32
lysosomal transport 0.034 0.22 0.63 15 -0.74 18 33
FOS -0.36 0.64 0.65 9 -1.2 288 297
STAT4 (dimer) 0.044 0.28 0.61 27 -0.85 38 65
STAT5A (dimer) 0.033 0.28 0.65 31 -0.76 44 75
GZMA 0.009 0.29 0.72 22 -1.1 25 47
GZMB 0.008 0.32 0.74 22 -1.2 33 55
HLX 0.021 0.013 0.26 1 -10000 0 1
LCK 0.011 0.3 0.7 25 -0.84 47 72
TCR/CD3/MHC II/CD4 -0.057 0.18 0.31 15 -0.49 78 93
IL2/IL2R 0.067 0.1 0.44 29 -0.38 13 42
MAPK14 0.027 0.26 0.67 17 -0.84 30 47
CCR5 0.023 0.27 0.74 22 -0.85 28 50
IL1B 0.016 0.073 0.3 2 -0.61 8 10
STAT6 0.033 0.12 0.41 28 -0.52 5 33
STAT4 0 0.12 0.26 1 -0.6 32 33
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.035 0.26 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 0.29 154 -10000 0 154
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 -0.03 0.15 0.35 46 -0.37 43 89
IL2RB 0.033 0.048 0.26 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.26 0.59 31 -0.76 38 69
IL2RG 0.03 0.068 0.26 32 -0.6 5 37
IL12 0.04 0.16 0.32 54 -0.45 48 102
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
CD247 0.003 0.087 0.28 12 -0.6 13 25
IL2 0.023 0.026 0.26 9 -10000 0 9
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.011 0.16 0.3 11 -0.61 47 58
IL12/IL12R/TYK2/JAK2 0.017 0.3 0.73 28 -0.85 45 73
MAP2K3 0.021 0.27 0.67 17 -0.82 36 53
RIPK2 0.02 0.018 0.26 3 -10000 0 3
MAP2K6 0.026 0.26 0.66 18 -0.81 33 51
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.006 0.037 0.27 1 -0.6 1 2
IL18RAP 0.007 0.12 0.29 4 -0.6 31 35
IL12Rbeta1/TYK2 0.036 0.068 0.32 20 -0.5 1 21
EOMES -0.017 0.19 -10000 0 -1.1 21 21
STAT1 (dimer) 0.054 0.26 0.64 45 -0.73 30 75
T cell proliferation 0.035 0.21 0.52 19 -0.62 36 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.073 -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 -0.68 37 41
ATF2 0.026 0.25 0.63 17 -0.77 30 47
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.023 0.13 0.44 48 -0.23 7 55
KIRREL -0.013 0.15 -10000 0 -0.6 49 49
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.023 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 0.013 0.08 0.24 1 -0.29 39 40
FYN 0.022 0.12 0.27 93 -0.33 45 138
mol:Ca2+ 0.038 0.11 0.28 4 -0.34 44 48
mol:DAG 0.039 0.11 0.28 4 -0.34 44 48
NPHS2 0.017 0.031 0.27 5 -10000 0 5
mol:IP3 0.039 0.11 0.28 4 -0.34 44 48
regulation of endocytosis 0.029 0.097 0.25 5 -0.31 45 50
Nephrin/NEPH1/podocin/Cholesterol 0.031 0.1 0.26 9 -0.34 46 55
establishment of cell polarity 0.023 0.13 0.23 7 -0.44 48 55
Nephrin/NEPH1/podocin/NCK1-2 0.052 0.11 0.32 1 -0.32 44 45
Nephrin/NEPH1/beta Arrestin2 0.033 0.1 0.26 5 -0.31 45 50
NPHS1 0.061 0.091 0.27 126 -10000 0 126
Nephrin/NEPH1/podocin 0.032 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 0.29 4 -0.34 44 48
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.039 0.11 0.29 4 -0.34 43 47
GRB2 0.023 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.021 0.13 0.29 85 -0.33 50 135
cytoskeleton organization 0.01 0.1 0.26 15 -0.34 41 56
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 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
SPTAN1 -0.004 0.044 0.22 22 -10000 0 22
RFC1 -0.004 0.042 0.22 21 -10000 0 21
PRKDC 0.016 0.08 0.23 88 -10000 0 88
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 -0.32 5 12
MAP2K4 -0.089 0.18 0.39 2 -0.45 66 68
mol:ceramide -0.023 0.096 -10000 0 -0.41 12 12
GSN -0.009 0.062 0.22 23 -0.37 11 34
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.072 -10000 0 -0.41 6 6
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 0.01 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 -0.43 176 176
ARHGDIB -0.001 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 -0.6 16 16
MAPK8 -0.16 0.26 0.56 2 -0.47 306 308
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 -0.4 112 112
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.036 0.26 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 -0.004 0.042 0.22 20 -10000 0 20
CHUK -0.043 0.11 -10000 0 -0.57 14 14
FASLG 0.009 0.078 0.26 32 -0.62 6 38
FAS/FADD 0.008 0.038 -10000 0 -0.35 2 2
HGF -0.011 0.14 -10000 0 -0.6 46 46
LMNA -0.003 0.058 0.2 39 -10000 0 39
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 -0.45 0.63 -10000 0 -1.2 319 319
MET -0.079 0.23 -10000 0 -0.6 136 136
ICAD/CAD -0.006 0.035 0.2 10 -10000 0 10
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 0.021 -10000 0 -10000 0 0
PAK2 -0.002 0.055 0.24 30 -10000 0 30
BCL2 0.008 0.098 -10000 0 -0.6 21 21
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.043 0.16 -10000 0 -0.34 175 175
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 -0.063 0.15 -10000 0 -0.34 185 185
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 0.086 185 -10000 0 185
GNAL -0.11 0.25 -10000 0 -0.6 174 174
GNG2 0.019 0.053 -10000 0 -0.6 6 6
CRH 0.018 0.024 0.26 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
Signaling events mediated by HDAC Class III

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
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 0.064 0.45 1 -0.27 11 12
CDKN1A -0.009 0.028 -10000 0 -0.8 1 1
KAT2B 0.024 0.003 -10000 0 -10000 0 0
BAX 0.024 0.003 -10000 0 -10000 0 0
FOXO3 -0.005 0.011 -10000 0 -0.21 2 2
FOXO1 0.021 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 0.26 22 -0.6 499 521
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 0.26 9 -0.6 166 175
FHL2 0.021 0.05 0.26 2 -0.6 5 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.018 0.064 0.27 11 -0.45 1 12
SIRT1/FOXO3a 0.015 0.026 -10000 0 -0.2 3 3
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 0.028 0.044 -10000 0 -0.21 6 6
apoptosis -0.044 0.014 -10000 0 -10000 0 0
SIRT1/PGC1A -0.055 0.17 -10000 0 -0.36 183 183
p53/SIRT1 0.027 0.017 0.41 1 -10000 0 1
SIRT1/FOXO4 0.022 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.037 0.04 -10000 0 -0.35 6 6
HIST1H1E 0.02 0.03 0.21 5 -10000 0 5
SIRT1/p300 0.033 0.01 -10000 0 -10000 0 0
muscle cell differentiation -0.03 0.022 -10000 0 -10000 0 0
TP53 0.02 0.01 0.21 1 -10000 0 1
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 -0.45 499 499
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 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
MDK 0.032 0.043 0.26 27 -10000 0 27
GPC2 0.047 0.083 0.26 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
Stabilization and expansion of the E-cadherin adherens junction

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
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 0.029 0.044 0.26 21 -0.6 1 22
ENAH -0.004 0.06 0.27 8 -10000 0 8
EGFR -0.19 0.29 -10000 0 -0.6 277 277
EPHA2 0.02 0.049 -10000 0 -0.6 5 5
MYO6 -0.013 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 0.33 1 -0.52 340 341
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 48 48
EGF -0.09 0.24 0.26 2 -0.6 151 153
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.018 0.12 0.29 1 -0.48 42 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 -0.29 16 16
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.042 -10000 0 -0.35 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.049 -10000 0 -0.3 14 14
PVRL2 0.024 0.009 0.26 1 -10000 0 1
ZYX -0.013 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 0.2 -10000 0 -0.35 386 386
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 0.081 0.26 1 -0.6 14 15
GIT1 0.023 0.007 -10000 0 -10000 0 0
IGF1R 0.013 0.081 0.26 1 -0.6 14 15
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
DIAPH1 0.025 0.1 -10000 0 -0.59 6 6
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 16 16
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.015 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 -0.31 17 17
SEC6/SEC8 -0.023 0.041 -10000 0 -0.3 15 15
MGAT3 -0.027 0.081 -10000 0 -0.33 48 48
HGF/MET -0.044 0.16 -10000 0 -0.34 176 176
HGF -0.011 0.14 -10000 0 -0.6 46 46
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 0.29 33 -0.29 2 35
KIAA1543 -0.013 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 -0.013 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 -0.025 0.1 0.28 2 -0.63 13 15
IGF-1R heterotetramer/IGF1 -0.047 0.16 -10000 0 -0.32 183 183
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.023 -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 0.041 -10000 0 -0.35 5 5
establishment of epithelial cell apical/basal polarity -0.009 0.065 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
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.02 0.068 -10000 0 -0.38 28 28
ADCY5 -0.12 0.17 -10000 0 -0.39 249 249
ADCY6 -0.008 0.013 -10000 0 -0.38 1 1
ADCY7 -0.007 0.013 -10000 0 -0.38 1 1
ADCY1 -0.008 0.064 -10000 0 -0.38 19 19
ADCY2 -0.03 0.1 0.25 6 -0.38 62 68
ADCY3 -0.008 0.014 -10000 0 -0.38 1 1
ADCY8 -0.004 0.024 0.23 5 -10000 0 5
PRKCE 0.005 0.016 -10000 0 -0.44 1 1
ADCY9 -0.007 0.013 -10000 0 -0.38 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.01 0.091 0.23 15 -0.27 27 42
Aurora A 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
Aurora A/GADD45A 0.047 0.044 -10000 0 -10000 0 0
BIRC5 0.19 0.12 0.26 558 -10000 0 558
NFKBIA 0.027 0.044 0.29 7 -10000 0 7
CPEB1 -0.091 0.24 -10000 0 -0.6 151 151
AKT1 0.027 0.043 0.29 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.035 0.037 0.21 1 -10000 0 1
NDEL1/TACC3 0.067 0.069 0.26 15 -10000 0 15
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.005 0.027 -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 0.069 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 0.26 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 0.041 0.049 0.25 1 -10000 0 1
AURKB 0.093 0.078 0.18 356 -10000 0 356
CDC25B 0.034 0.04 0.22 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 -0.32 150 150
Aurora A/CPEB -0.031 0.14 -10000 0 -0.32 150 150
Aurora A/TACC1/TRAP/chTOG 0.047 0.067 -10000 0 -0.32 12 12
BRCA1 0.024 0.01 0.26 1 -10000 0 1
centrosome duplication 0.043 0.045 0.26 2 -10000 0 2
regulation of centrosome cycle 0.065 0.067 0.25 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 0.14 0.091 0.28 20 -10000 0 20
CENPA 0.1 0.085 0.19 370 -0.21 3 373
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 0.042 0.049 0.25 1 -10000 0 1
TACC1 0.01 0.078 -10000 0 -0.6 13 13
TACC3 0.057 0.084 0.26 116 -10000 0 116
Aurora A/Antizyme1 0.056 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.046 0.044 -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 0.069 0.27 23 -10000 0 23
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.074 0.26 19 -10000 0 19
PAK1 0.023 0.017 0.26 3 -10000 0 3
CKAP5 0.024 0.003 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.011 0.14 -10000 0 -0.6 46 46
HRAS 0.024 0.01 0.26 1 -10000 0 1
EGFR -0.19 0.29 -10000 0 -0.6 277 277
AKT -0.012 0.12 0.32 5 -0.28 69 74
FOXO3 0.022 0.023 -10000 0 -0.6 1 1
AKT1 0.024 0.005 -10000 0 -10000 0 0
FOXO1 0.021 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 0.059 0.26 3 -0.6 7 10
PIK3R3 0.024 0.009 0.26 1 -10000 0 1
PIK3R2 0.024 0.003 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.058 0.14 0.21 4 -0.34 122 126
ERBB2 0.021 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.005 0.095 0.35 38 -0.27 1 39
PI3K -0.045 0.15 0.28 11 -0.33 124 135
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.039 0.058 0.28 7 -0.17 1 8
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.092 0.11 0.28 36 -0.63 6 42
Syndecan-4/Syndesmos 0.099 0.11 0.38 6 -0.64 5 11
positive regulation of JNK cascade 0.088 0.14 0.37 6 -0.6 6 12
Syndecan-4/ADAM12 0.11 0.12 0.36 37 -0.68 5 42
CCL5 0.03 0.048 0.26 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 0.024 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
PLG -0.01 0.034 0.26 5 -10000 0 5
ADAM12 0.04 0.071 0.26 62 -0.6 2 64
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.011 0.26 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 0.39 4 -0.68 6 10
Syndecan-4/CXCL12/CXCR4 0.093 0.14 0.39 6 -0.65 6 12
Syndecan-4/Laminin alpha3 0.04 0.16 0.39 4 -0.67 6 10
MDK 0.032 0.043 0.26 27 -10000 0 27
Syndecan-4/FZD7 0.099 0.12 0.38 6 -0.68 5 11
Syndecan-4/Midkine 0.11 0.11 0.38 13 -0.65 5 18
FZD7 0.013 0.083 -10000 0 -0.6 15 15
Syndecan-4/FGFR1/FGF -0.011 0.16 -10000 0 -0.54 13 13
THBS1 0.023 0.022 -10000 0 -0.6 1 1
integrin-mediated signaling pathway 0.097 0.12 0.37 7 -0.66 6 13
positive regulation of MAPKKK cascade 0.088 0.14 0.37 6 -0.6 6 12
Syndecan-4/TACI 0.1 0.12 0.38 11 -0.67 5 16
CXCR4 0.031 0.04 0.26 23 -10000 0 23
cell adhesion 0.067 0.09 0.26 69 -0.27 18 87
Syndecan-4/Dynamin 0.1 0.11 0.39 5 -0.68 5 10
Syndecan-4/TSP1 0.1 0.11 0.38 6 -0.67 5 11
Syndecan-4/GIPC 0.1 0.11 0.38 5 -0.68 5 10
Syndecan-4/RANTES 0.1 0.11 0.36 12 -0.67 5 17
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.04 0.19 0.26 1 -0.6 84 85
LAMA3 -0.11 0.26 -10000 0 -0.6 182 182
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.023 0.23 0.7 76 -0.56 17 93
Syndecan-4/alpha-Actinin 0.1 0.11 0.39 5 -0.68 5 10
TFPI -0.001 0.12 -10000 0 -0.6 33 33
F2 0.024 0.033 0.28 7 -10000 0 7
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.005 0.18 0.38 3 -0.56 22 25
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.091 0.26 5 -0.6 17 22
Syndecan-4/CXCL12 0.081 0.14 0.39 5 -0.68 6 11
FGF6 0.015 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 0.022 0.087 0.26 32 -0.6 11 43
FGF2 -0.21 0.3 -10000 0 -0.6 309 309
FGFR1 0.016 0.049 -10000 0 -0.6 5 5
Syndecan-4/PI-4-5-P2 0.079 0.1 0.34 2 -0.68 5 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 362 -10000 0 362
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.011 0.027 -10000 0 -10000 0 0
vasculogenesis 0.1 0.1 0.37 7 -0.64 5 12
SDC4 0.092 0.1 0.37 7 -0.76 4 11
Syndecan-4/Tenascin C 0.099 0.12 0.38 6 -0.69 6 12
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.089 0.11 0.37 5 -0.68 5 10
MMP9 0.12 0.12 0.26 324 -0.59 1 325
Rac1/GTP 0.067 0.091 0.26 69 -0.28 18 87
cytoskeleton organization 0.098 0.1 0.37 7 -0.62 5 12
GIPC1 0.024 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.093 0.13 0.39 5 -0.64 6 11
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.067 0.21 0.32 1 -0.54 50 51
MAP3K8 0.009 0.047 -10000 0 -0.6 4 4
FOS -0.026 0.15 0.32 2 -0.46 37 39
PRKCA -0.004 0.093 0.24 2 -0.61 18 20
PTPN7 0.019 0.06 0.25 43 -10000 0 43
HRAS 0.023 0.01 0.26 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 0.022 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 -0.53 32 32
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 -0.011 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
Nectin adhesion pathway

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
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 -0.43 63 63
positive regulation of JNK cascade -0.012 0.12 -10000 0 -0.32 72 72
CDC42/GDP -0.005 0.16 0.43 1 -0.43 75 76
Rac1/GDP -0.006 0.16 -10000 0 -0.43 76 76
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 71 71
nectin-3/I-afadin -0.004 0.13 -10000 0 -0.44 65 65
RAPGEF1 -0.022 0.15 0.46 1 -0.47 63 64
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.035 0.16 -10000 0 -0.52 70 70
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 61 61
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.023 -10000 0 -0.35 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.004 0.13 -10000 0 -0.44 65 65
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.024 0.19 0.46 1 -0.52 80 81
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.11 -10000 0 -0.34 63 63
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 81 81
PVRL1 0.022 0.007 -10000 0 -10000 0 0
PVRL3 -0.024 0.17 -10000 0 -0.6 63 63
PVRL2 0.024 0.009 0.26 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 0.26 20 -0.6 32 52
JAM-A/CLDN1 0.011 0.13 -10000 0 -0.38 68 68
SRC -0.041 0.18 -10000 0 -0.56 76 76
ITGB3 0.015 0.08 0.26 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 75 76
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) 0.012 0.12 -10000 0 -0.38 64 64
nectin-1/I-afadin 0.03 0.024 -10000 0 -0.28 3 3
nectin-2/I-afadin 0.032 0.023 -10000 0 -0.28 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.009 0.12 -10000 0 -0.39 64 64
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.012 0.12 -10000 0 -0.32 72 72
alphaV/beta3 Integrin/Talin 0.004 0.089 0.27 1 -0.42 17 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.023 -10000 0 -0.28 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.023 -10000 0 -0.28 3 3
PIP5K1C -0.014 0.071 -10000 0 -0.24 62 62
VAV2 -0.023 0.19 0.44 1 -0.55 77 78
RAP1/GDP -0.003 0.14 -10000 0 -0.4 72 72
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.012 0.12 -10000 0 -0.38 64 64
nectin-3(dimer)/I-afadin/I-afadin -0.004 0.13 -10000 0 -0.44 65 65
Rac1/GTP -0.01 0.15 -10000 0 -0.41 79 79
PTPRM -0.01 0.079 -10000 0 -0.26 64 64
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 0.023 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
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 0.19 69 -10000 0 69
JMJD2C -0.004 0.043 0.12 12 -0.14 69 81
T-DHT/AR/Ubc9 -0.029 0.14 -10000 0 -0.4 90 90
CARM1 0.018 0.016 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.014 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 0.24 14 -0.57 8 22
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 -0.4 113 113
FHL2 0.003 0.12 -10000 0 -0.9 7 7
RANBP9 0.012 0.034 -10000 0 -10000 0 0
JMJD1A -0.01 0.056 0.12 32 -0.14 113 145
CDK6 0.023 0.045 0.26 2 -0.6 4 6
TGFB1I1 0.009 0.05 -10000 0 -0.6 3 3
T-DHT/AR/CyclinD1 -0.037 0.14 -10000 0 -0.38 100 100
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 -10000 0 -10000 0 0
TCF4 0.028 0.056 -10000 0 -0.59 5 5
CDKN2A 0.062 0.089 0.27 119 -10000 0 119
SRF 0.033 0.024 -10000 0 -10000 0 0
NKX3-1 -0.061 0.21 0.37 3 -0.62 67 70
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 -0.39 90 90
AR -0.059 0.2 0.22 1 -0.61 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 0.016 -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 -0.32 103 103
RPS6KA3 0.01 0.048 -10000 0 -0.6 2 2
T-DHT/AR/ARA70 -0.033 0.14 -10000 0 -0.37 103 103
LATS2 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.016 0.14 0.19 7 -0.34 101 108
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.015 0.057 0.26 12 -0.6 3 15
KLK2 -0.089 0.3 0.36 2 -1 72 74
CASP8 0.027 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.025 0.13 -10000 0 -0.37 80 80
TMPRSS2 -0.13 0.34 -10000 0 -1 107 107
CCND1 0.011 0.044 0.26 1 -0.6 3 4
PIAS1 0.009 0.045 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.032 0.061 2 -0.072 146 148
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.002 0.064 -10000 0 -0.2 12 12
T-DHT/AR/CDK6 -0.029 0.15 -10000 0 -0.4 95 95
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 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.02 -10000 0 -10000 0 0
FKBP4 0.013 0.038 0.26 4 -10000 0 4
Regulation of Telomerase

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
Telomerase catalytic core complex 0.055 0.14 0.46 11 -0.53 2 13
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.11 0.23 -10000 0 -0.44 263 263
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 0 0.091 -10000 0 -0.46 6 6
ER alpha/Oestrogen -0.019 0.17 0.18 108 -0.43 111 219
NFX1/SIN3/HDAC complex 0.022 0.059 0.25 1 -0.32 13 14
EGF -0.089 0.24 0.26 2 -0.6 151 153
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.04 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.051 0.12 0.43 3 -0.5 2 5
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 0.27 430 -10000 0 430
WRN 0.02 0.009 -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 0.045 0.1 -10000 0 -0.47 2 2
Mad/Max 0.04 0.015 -10000 0 -10000 0 0
TERT 0.055 0.14 0.5 7 -0.54 2 9
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 0.024 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 -0.7 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 0.26 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 0.02 0.057 -10000 0 -0.6 7 7
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 -0.6 252 252
IFN-gamma/IRF1 0.066 0.068 0.39 2 -0.33 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.048 0.072 0.26 82 -10000 0 82
Telomerase 0.028 0.077 0.26 2 -0.67 3 5
IRF1 0.028 0.019 0.27 2 -10000 0 2
ESR1 -0.024 0.24 0.27 108 -0.6 106 214
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 0.027 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 0.001 0.013 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.01 0.26 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 0.48 2 -0.63 4 6
NR2F2 0.012 0.042 -10000 0 -0.61 3 3
MAPK3 0.006 0.022 -10000 0 -10000 0 0
MAPK1 0.006 0.022 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.02 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 -0.18 0.29 -10000 0 -0.6 277 277
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.21 0.27 -10000 0 -0.47 396 396
MYC 0.006 0.091 -10000 0 -0.6 18 18
IL2 0.03 0.029 0.27 9 -10000 0 9
KU 0.034 0.01 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.021 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 0.46 4 -0.5 2 6
SP1/HDAC2 0.045 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.01 -10000 0 -10000 0 0
Telomerase/EST1A 0.042 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 0.27 120 -0.2 3 123
Telomerase/PinX1 0.033 0.098 -10000 0 -0.46 2 2
Telomerase/AKT1/mTOR/p70S6K 0.025 0.1 0.31 4 -0.54 13 17
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 -0.42 1 1
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.046 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 0.27 262 -10000 0 262
ZNFX1 0.024 0.007 -10000 0 -10000 0 0
PIF1 0.066 0.092 0.26 146 -10000 0 146
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.012 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 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 -0.41 22 23
JUN 0.017 0.058 -10000 0 -0.6 7 7
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 0.066 -10000 0 -0.45 16 16
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 0.002 0.088 0.25 1 -0.6 16 17
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 51 51
NCOA2 0.013 0.058 -10000 0 -0.6 7 7
CEBPA 0.019 0.057 -10000 0 -0.6 7 7
EHMT2 0.02 0.012 -10000 0 -10000 0 0
cell proliferation 0.004 0.15 0.35 28 -0.47 17 45
NR0B1 0.028 0.045 0.26 29 -10000 0 29
EGR1 -0.19 0.29 -10000 0 -0.6 277 277
RXRs/9cRA -0.047 0.16 -10000 0 -0.35 165 165
AR/RACK1/Src -0.016 0.11 0.32 7 -0.38 17 24
AR/GR -0.021 0.11 0.29 1 -0.29 92 93
GNB2L1 0.023 0.007 -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 -0.016 5 5
MAPK8 0 0.023 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.006 0.098 0.32 1 -0.36 18 19
SRC -0.018 0.063 0.21 3 -0.37 12 15
NR3C1 0.019 0.053 -10000 0 -0.6 6 6
KLK3 -0.16 0.4 0.4 1 -1.1 108 109
APPBP2 0.015 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.02 0.26 1 -10000 0 1
T-DHT/AR/TIP60 -0.012 0.092 0.34 2 -0.39 15 17
TMPRSS2 -0.13 0.37 -10000 0 -1.1 107 107
RXRG -0.11 0.25 0.26 1 -0.6 167 168
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.023 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.021 0.011 -10000 0 -10000 0 0
NR2C2 0.024 0.004 -10000 0 -10000 0 0
KLK2 -0.052 0.21 0.33 5 -0.7 69 74
AR -0.036 0.1 -10000 0 -0.31 91 91
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -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 0.013 0.095 0.26 10 -0.6 18 28
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.26 334 -10000 0 334
T-DHT/AR/RACK1/Src -0.01 0.1 0.34 9 -0.38 15 24
positive regulation of transcription 0.013 0.095 0.26 10 -0.6 18 28
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 0.25 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 0.34 2 -0.39 15 17
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 0.056 0.23 1 -0.38 14 15
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.026 0.015 -10000 0 -10000 0 0
POU2F1 0.009 0.051 -10000 0 -0.19 11 11
T-DHT/AR/DAX-1 -0.012 0.096 0.32 4 -0.39 16 20
CREBBP 0.023 0.007 -10000 0 -10000 0 0
SMARCE1 0.017 0.018 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.017 0.13 0.32 11 -0.38 40 51
IKBKB 0.022 0.091 0.32 6 -0.32 7 13
AKT1 0.036 0.11 0.28 54 -0.24 16 70
IKBKG 0.027 0.075 0.32 5 -0.28 3 8
CALM1 0 0.1 -10000 0 -0.45 16 16
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.016 0.17 0.34 13 -0.53 40 53
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0.11 -10000 0 -0.4 27 27
DOK1 0.024 0.002 -10000 0 -10000 0 0
AP-1 -0.031 0.1 0.26 6 -0.25 48 54
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 -0.45 55 66
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 46 46
GO:0007205 0 0.11 -10000 0 -0.41 26 26
SYK 0.024 0.004 -10000 0 -10000 0 0
ELK1 -0.001 0.11 -10000 0 -0.47 15 15
NFATC1 0.026 0.14 0.29 22 -0.43 31 53
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 0.024 0.047 0.16 10 -0.13 20 30
HRAS 0.009 0.11 0.28 7 -0.43 19 26
NFKBIA 0.025 0.046 0.17 8 -0.12 13 21
NF-kappa-B/RelA/I kappa B beta 0.028 0.042 0.17 8 -10000 0 8
RasGAP/Csk 0.023 0.13 0.33 9 -0.39 58 67
mol:GDP 0.002 0.1 -10000 0 -0.46 15 15
PTEN 0.022 0.031 -10000 0 -0.6 2 2
CD79B 0.005 0.11 0.26 8 -0.6 25 33
NF-kappa-B/RelA/I kappa B alpha 0.028 0.041 0.17 8 -10000 0 8
GRB2 0.023 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.018 0.17 0.34 11 -0.49 45 56
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.11 -10000 0 -0.38 37 37
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.093 0.17 -10000 0 -0.45 67 67
CHUK 0.023 0.082 0.32 5 -0.31 10 15
IBTK 0.023 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 -0.44 50 59
RELA 0.024 0.004 -10000 0 -10000 0 0
BCL2A1 0.025 0.036 0.16 11 -10000 0 11
VAV2 0.009 0.15 0.29 12 -0.59 26 38
ubiquitin-dependent protein catabolic process 0.026 0.047 0.17 8 -0.12 22 30
BTK 0.015 0.07 -10000 0 -0.97 4 4
CD19 -0.003 0.14 0.29 18 -0.44 52 70
MAP4K1 0.029 0.051 0.26 24 -0.6 2 26
CD72 0.028 0.04 0.26 16 -0.6 1 17
PAG1 0.02 0.016 0.26 2 -10000 0 2
MAPK14 0.018 0.15 0.34 15 -0.45 39 54
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 59 62
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 0.26 51 -0.6 65 116
re-entry into mitotic cell cycle -0.03 0.1 0.26 6 -0.25 47 53
RASA1 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.015 0.1 0.28 19 -0.38 11 30
MAPK1 0.008 0.096 0.27 8 -0.38 14 22
CD72/SHP1 0.022 0.15 0.37 15 -0.55 27 42
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.15 0.33 16 -0.45 40 56
actin cytoskeleton organization 0.024 0.14 0.31 20 -0.5 26 46
NF-kappa-B/RelA 0.057 0.08 0.3 8 -0.21 1 9
Calcineurin 0.015 0.096 -10000 0 -0.41 13 13
PI3K -0.015 0.099 -10000 0 -0.37 45 45
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.002 0.12 -10000 0 -0.4 44 44
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.003 0.21 0.45 6 -0.72 45 51
DAPP1 -0.026 0.22 -10000 0 -0.8 46 46
cytokine secretion 0.027 0.13 0.27 32 -0.4 31 63
mol:DAG 0 0.11 -10000 0 -0.38 37 37
PLCG2 0.021 0.025 0.26 1 -0.6 1 2
MAP2K1 0.008 0.1 0.28 8 -0.42 14 22
B-cell antigen/BCR complex/FcgammaRIIB 0.006 0.14 0.35 8 -0.37 80 88
mol:PI-3-4-5-P3 0.005 0.094 0.23 18 -0.33 19 37
ETS1 -0.001 0.093 0.28 1 -0.4 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 0.28 8 -0.44 65 73
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.017 0.15 0.3 17 -0.54 26 43
B-cell antigen/BCR complex/LYN/SYK 0.006 0.14 0.37 11 -0.46 49 60
CARD11 0.001 0.11 0.32 2 -0.47 17 19
FCGR2B 0.018 0.039 0.26 1 -0.6 3 4
PPP3CA 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.15 44 -0.13 2 46
PTPRC 0.023 0.038 0.26 12 -0.6 1 13
PDPK1 0.019 0.084 0.23 35 -0.23 17 52
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
Insulin Pathway

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
CBL/APS/CAP -0.043 0.17 -10000 0 -0.34 188 188
TC10/GTP -0.035 0.15 -10000 0 -0.31 177 177
Insulin Receptor/Insulin/IRS1/Shp2 0.045 0.079 -10000 0 -0.36 27 27
HRAS 0.024 0.01 0.26 1 -10000 0 1
APS homodimer 0.032 0.043 0.26 27 -10000 0 27
GRB14 0.014 0.19 0.26 117 -0.6 58 175
FOXO3 -0.02 0.16 -10000 0 -0.6 56 56
AKT1 -0.015 0.11 0.33 6 -0.31 61 67
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.057 0.051 0.44 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.11 0.26 -10000 0 -0.6 182 182
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.026 -10000 0 -10000 0 0
CAV1 -0.085 0.15 -10000 0 -0.37 174 174
CBL/APS/CAP/Crk-II/C3G -0.023 0.17 -10000 0 -0.33 180 180
Insulin Receptor/Insulin/IRS1/NCK2 0.045 0.078 -10000 0 -0.37 26 26
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 12 12
RPS6KB1 -0.015 0.099 0.32 6 -0.51 1 7
PARD6A 0.023 0.017 0.26 3 -10000 0 3
CBL 0.022 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.035 -10000 0 -0.55 3 3
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.011 0.095 -10000 0 -0.3 15 15
HRAS/GTP -0.02 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 0.072 -10000 0 -0.34 19 19
PRKCI 0.013 0.059 -10000 0 -0.47 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.001 0.11 -10000 0 -0.31 78 78
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.035 -10000 0 -0.47 3 3
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 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
AKT2 -0.016 0.11 0.3 5 -0.3 68 73
PRKCZ 0.005 0.085 -10000 0 -0.49 11 11
SH2B2 0.032 0.043 0.26 27 -10000 0 27
SHC/SHIP 0.012 0.06 -10000 0 -0.33 21 21
F2RL2 0.053 0.12 0.26 134 -0.6 12 146
TRIP10 0.024 0.003 -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 0.034 -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 -0.033 0.17 -10000 0 -0.35 181 181
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.05 0.028 -10000 0 -10000 0 0
INPP5D -0.019 0.063 -10000 0 -0.34 27 27
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.017 0.14 -10000 0 -0.68 33 33
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 0.035 -10000 0 -0.47 3 3
INS 0.02 0.01 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.34 27 27
GRB2 0.023 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.093 0.31 2 -0.51 1 3
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 0.03 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
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.028 0.032 0.27 14 -10000 0 14
GNB1/GNG2 -0.013 0.046 -10000 0 -0.19 42 42
AKT1 0.025 0.093 0.35 11 -0.28 19 30
EGF -0.09 0.24 0.26 2 -0.6 151 153
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.057 0.25 2 -0.27 3 5
mol:Ca2+ 0.025 0.11 0.41 10 -0.3 52 62
LYN 0.012 0.053 0.25 2 -0.26 1 3
RhoA/GTP 0.01 0.044 0.14 4 -0.14 18 22
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.022 0.12 0.42 11 -0.34 44 55
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 -0.007 0.13 -10000 0 -0.6 29 29
G beta5/gamma2 -0.011 0.063 -10000 0 -0.26 41 41
PRKCH 0.021 0.12 0.4 11 -0.35 45 56
DNM1 0.021 0.049 0.26 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 0.26 6 -0.6 21 27
G12 family/GTP 0.003 0.086 -10000 0 -0.3 44 44
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 0.37 22 -0.35 7 29
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 0.44 10 -0.37 53 63
cell morphogenesis 0.031 0.008 -10000 0 -10000 0 0
PLCB2 0.015 0.16 0.55 6 -0.51 53 59
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.023 0.069 0.25 6 -0.27 4 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.059 0.25 4 -0.28 3 7
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.025 0.009 0.26 1 -10000 0 1
PRKCB1 0.022 0.13 0.42 10 -0.36 51 61
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 0.51 8 -0.52 46 54
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 43 43
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.26 20 20
MAPK14 0.021 0.088 0.36 12 -0.23 40 52
TGM2/GTP 0.019 0.14 0.49 9 -0.42 49 58
MAPK11 0.019 0.089 0.35 13 -0.24 40 53
ARHGEF1 0.013 0.065 0.27 10 -0.18 36 46
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.024 0.13 0.45 10 -0.38 46 56
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.025 0.1 0.38 12 -0.28 43 55
cAMP biosynthetic process 0.02 0.12 0.41 10 -0.35 51 61
Gq family/GTP/EBP50 0.016 0.042 0.23 3 -0.3 3 6
actin cytoskeleton reorganization 0.031 0.008 -10000 0 -10000 0 0
SRC 0.012 0.056 0.25 2 -0.28 3 5
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.048 0.11 0.24 3 -0.29 56 59
VCAM1 0.023 0.11 0.39 11 -0.31 42 53
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.13 -10000 0 -0.6 29 29
platelet activation 0.026 0.11 0.42 13 -0.3 44 57
PGI2/IP 0.018 0.006 0.18 1 -10000 0 1
PRKACA 0.009 0.051 -10000 0 -0.3 21 21
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.49 26 26
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 0.45 10 -0.41 51 61
EGFR -0.19 0.29 -10000 0 -0.6 277 277
TXA2/TP alpha 0.02 0.16 0.5 8 -0.48 52 60
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 -0.43 22 28
SLC9A3R1 0.036 0.057 0.26 47 -10000 0 47
FYN 0.013 0.056 0.26 1 -0.29 4 5
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.024 0.027 0.26 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 -0.39 6 6
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.024 0.13 0.41 12 -0.38 40 52
PRKCB 0.025 0.13 0.41 11 -0.36 44 55
PRKCE 0.022 0.12 0.42 10 -0.35 44 54
PRKCD 0.021 0.12 0.42 10 -0.38 43 53
PRKCG 0.023 0.13 0.43 10 -0.38 47 57
muscle contraction 0.019 0.16 0.49 9 -0.48 49 58
PRKCZ 0.021 0.12 0.42 10 -0.34 44 54
ARR3 0.021 0.021 0.26 6 -10000 0 6
TXA2/TP beta 0.024 0.055 -10000 0 -0.27 21 21
PRKCQ 0.019 0.13 0.4 13 -0.39 48 61
MAPKKK cascade 0.019 0.15 0.46 9 -0.45 52 61
SELE 0.02 0.12 0.39 11 -0.39 42 53
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.064 -10000 0 -0.39 6 6
ROCK1 0.024 0.004 -10000 0 -10000 0 0
GNA14 0.025 0.065 0.26 19 -0.6 6 25
chemotaxis 0.018 0.18 0.59 6 -0.6 44 50
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.087 0.26 1 -0.6 16 17
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.095 0.13 -10000 0 -0.25 317 317
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 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.041 0.098 -10000 0 -0.35 55 55
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 62 62
apoptosis -0.039 0.093 -10000 0 -0.33 54 54
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 0.26 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 0.008 -10000 0 -10000 0 0
MAPK11 -0.011 0.13 0.33 4 -0.39 44 48
BLK 0.046 0.085 0.26 95 -0.6 2 97
HCK 0.027 0.029 0.26 12 -10000 0 12
MAP2K3 0.022 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.013 0.26 1 -10000 0 1
TRAF6/MEKK3 0.028 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.006 0.13 0.35 3 -0.39 49 52
positive regulation of innate immune response -0.013 0.15 0.37 4 -0.45 47 51
LCK 0.024 0.077 0.26 23 -0.6 9 32
p38alpha-beta/MKP7 -0.004 0.14 0.44 2 -0.44 41 43
p38alpha-beta/MKP5 -0.005 0.14 0.44 2 -0.46 36 38
PGK/cGMP 0.001 0.088 -10000 0 -0.44 31 31
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.04 0.18 0.44 2 -0.45 72 74
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.25 0.31 -10000 0 -0.6 366 366
TCGA08_retinoblastoma

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
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 0.26 119 -10000 0 119
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 33 -0.31 12 45
Signaling events mediated by PRL

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
CCNE1 0.061 0.088 0.26 128 -10000 0 128
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 0.016 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.08 0.24 34 -0.45 11 45
AGT 0.031 0.099 0.26 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 -0.44 276 277
CDK2/Cyclin E1 0.009 0.12 -10000 0 -0.5 13 13
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 0.019 0.013 0.26 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 -0.025 0.083 -10000 0 -0.42 17 17
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 -0.027 0.089 -10000 0 -0.44 20 20
RHOA -0.029 0.098 -10000 0 -0.47 24 24
cell motility -0.032 0.1 -10000 0 -0.39 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 -0.33 2 2
ROCK1 -0.031 0.1 -10000 0 -0.39 28 28
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.11 0.16 -10000 0 -0.34 244 244
ATF5 0.025 0.015 0.26 3 -10000 0 3
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.015 0.17 0.3 4 -0.42 105 109
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 0.081 0.26 104 -10000 0 104
muscle cell differentiation -0.025 0.064 0.35 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.057 0.074 -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 0.049 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 -1.2 7 7
AP1 -0.066 0.18 -10000 0 -0.33 230 230
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 9 9
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.034 0.069 0.27 57 -10000 0 57
SMAD3/SMAD4/GR 0.021 0.072 -10000 0 -0.39 7 7
GATA3 0.013 0.12 0.27 25 -0.58 28 53
SKI/SIN3/HDAC complex/NCoR1 0.004 0.078 -10000 0 -0.35 28 28
MEF2C/TIF2 0.03 0.076 0.31 3 -0.54 1 4
endothelial cell migration -0.029 0.086 0.52 10 -10000 0 10
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.022 0.26 7 -10000 0 7
RBBP4 0.024 0.004 -10000 0 -10000 0 0
RUNX2 0.027 0.028 0.26 11 -10000 0 11
RUNX3 0.023 0.033 0.26 2 -0.6 2 4
RUNX1 0.023 0.022 -10000 0 -0.6 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.016 0.055 -10000 0 -0.6 6 6
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.016 0.069 -10000 0 -0.96 2 2
KAT2B 0.025 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.045 0.077 -10000 0 -0.29 12 12
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.03 0.086 -10000 0 -0.54 9 9
SMAD3/SMAD4/ATF2 0.03 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.024 0.16 -10000 0 -0.42 96 96
SAP30 0.024 0.015 0.26 3 -10000 0 3
Cbp/p300/PIAS3 0.047 0.029 -10000 0 -10000 0 0
JUN -0.075 0.17 0.29 1 -0.32 229 230
SMAD3/SMAD4/IRF7 0.043 0.08 0.34 16 -10000 0 16
TFE3 0.029 0.01 -10000 0 -0.2 1 1
COL1A2 0.049 0.087 0.42 1 -0.52 4 5
mesenchymal cell differentiation -0.031 0.062 -10000 0 -10000 0 0
DLX1 0.053 0.11 0.26 121 -0.6 8 129
TCF3 0.024 0.005 -10000 0 -10000 0 0
FOS -0.16 0.29 -10000 0 -0.6 253 253
SMAD3/SMAD4/Max 0.024 0.061 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.045 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.006 -10000 0 -10000 0 0
LAMC1 0.01 0.04 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.058 -10000 0 -10000 0 0
IRF7 0.04 0.06 0.28 46 -10000 0 46
ESR1 -0.031 0.24 0.26 108 -0.6 106 214
HNF4A 0.023 0.03 0.26 12 -10000 0 12
MEF2C 0.05 0.096 0.4 10 -0.45 2 12
SMAD2-3/SMAD4 0.029 0.068 -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 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.027 0.027 0.26 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 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 -0.44 336 336
SMAD2 0.02 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 0.021 0.051 0.24 9 -0.41 2 11
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
NCOA1 0.023 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 0.075 0.33 28 -10000 0 28
SMAD3/SMAD4/MEF2C 0.065 0.09 0.33 1 -0.55 1 2
CITED1 -0.23 0.31 0.26 9 -0.6 336 345
SMAD2-3/SMAD4/ARC105 0.037 0.069 -10000 0 -10000 0 0
RBL1 0.024 0.01 0.26 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.063 -10000 0 -0.45 7 7
RUNX1-3/PEBPB2 0.041 0.037 -10000 0 -0.55 2 2
SMAD7 -0.044 0.15 -10000 0 -0.53 9 9
MYC/MIZ-1 0.013 0.071 -10000 0 -0.45 18 18
SMAD3/SMAD4 0.029 0.075 0.3 20 -0.36 3 23
IL10 0.004 0.088 0.32 4 -0.39 24 28
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 0.002 0.089 -10000 0 -0.38 26 26
CDK4 0.026 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.053 0.2 -10000 0 -0.6 97 97
SMAD3/SMAD4/SP1 0.044 0.066 -10000 0 -10000 0 0
FOXG1 0.017 0.069 0.26 55 -10000 0 55
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 0.26 9 -10000 0 9
SMAD3/SMAD4/HNF4 0.029 0.062 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.025 0.1 -10000 0 -0.42 28 28
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.027 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.04 0.072 -10000 0 -0.52 2 2
SMAD3/SMAD4/SP1-3 0.055 0.068 -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 8 -0.39 1 9
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 0.26 1 -0.6 90 91
negative regulation of cell growth -0.003 0.086 -10000 0 -0.35 10 10
SMAD3/SMAD4/MYOD 0.028 0.06 -10000 0 -10000 0 0
E2F5 0.022 0.023 0.26 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 -0.051 0.19 -10000 0 -0.33 229 229
SMAD3/SMAD4/RUNX2 0.032 0.062 -10000 0 -10000 0 0
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.024 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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
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 0.52 4 -0.59 2 6
IL27/IL27R/JAK1 0.055 0.15 0.8 3 -1.1 2 5
TBX21 0.007 0.17 0.5 10 -0.56 30 40
IL12B 0.072 0.098 0.27 156 -10000 0 156
IL12A -0.017 0.11 0.15 11 -0.44 47 58
IL6ST -0.008 0.14 -10000 0 -0.6 43 43
IL27RA/JAK1 0.023 0.076 0.65 1 -1.2 2 3
IL27 0.045 0.074 0.28 74 -10000 0 74
TYK2 0.03 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.1 0.17 1.1 1 -0.81 2 3
T-helper 2 cell differentiation -0.023 0.11 0.52 4 -0.59 2 6
T cell proliferation during immune response -0.023 0.11 0.52 4 -0.59 2 6
MAPKKK cascade 0.023 0.11 0.59 2 -0.52 4 6
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.029 0.038 0.27 18 -10000 0 18
IL12RB1 0.032 0.048 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 0.46 24 -0.54 40 64
IL27/IL27R/JAK2/TYK2 0.023 0.11 0.6 2 -0.52 4 6
positive regulation of T cell mediated cytotoxicity 0.023 0.11 0.59 2 -0.52 4 6
STAT1 (dimer) 0.051 0.2 0.67 18 -0.7 11 29
JAK2 0.028 0.013 -10000 0 -10000 0 0
JAK1 0.023 0.011 -10000 0 -10000 0 0
STAT2 (dimer) 0.035 0.11 0.5 2 -0.5 4 6
T cell proliferation -0.096 0.19 0.38 2 -0.48 53 55
IL12/IL12R/TYK2/JAK2 0.055 0.19 0.44 9 -0.72 25 34
IL17A -0.11 0.17 1.1 1 -0.81 2 3
mast cell activation -0.023 0.11 0.52 4 -0.59 2 6
IFNG 0.024 0.048 0.13 104 -0.1 5 109
T cell differentiation 0 0.006 0.015 1 -0.025 2 3
STAT3 (dimer) 0.034 0.11 0.5 2 -0.5 4 6
STAT5A (dimer) 0.032 0.12 0.5 2 -0.5 8 10
STAT4 (dimer) 0.022 0.13 0.5 2 -0.46 15 17
STAT4 0 0.12 0.26 1 -0.6 32 33
T cell activation -0.005 0.011 0.12 2 -0.12 4 6
IL27R/JAK2/TYK2 0.034 0.12 -10000 0 -1.2 2 2
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 0.25 44 -0.4 5 49
IL27RA 0.011 0.078 0.75 1 -1.3 2 3
IL6 -0.2 0.3 0.26 1 -0.6 302 303
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 0.045 0.45 2 -0.54 1 3
IL1B 0.002 0.045 0.14 2 -0.44 8 10
EBI3 0.024 0.052 0.27 7 -0.6 4 11
TNF 0.005 0.046 0.15 6 -0.44 7 13
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.11 0.11 0.32 82 -0.37 2 84
EPHB2 0.028 0.033 0.26 15 -10000 0 15
Syndecan-2/TACI 0.019 0.061 0.32 3 -0.35 13 16
LAMA1 -0.04 0.19 0.26 1 -0.6 84 85
Syndecan-2/alpha2 ITGB1 -0.036 0.15 -10000 0 -0.34 137 137
HRAS 0.024 0.01 0.26 1 -10000 0 1
Syndecan-2/CASK 0.005 0.019 -10000 0 -0.38 2 2
ITGA5 0.024 0.002 -10000 0 -10000 0 0
BAX -0.002 0.022 -10000 0 -0.34 1 1
EPB41 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.02 -10000 0 -0.34 2 2
LAMA3 -0.11 0.26 -10000 0 -0.6 182 182
EZR 0.024 0.013 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.051 0.2 -10000 0 -0.6 99 99
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 0.21 15 -0.38 2 17
Syndecan-2/GM-CSF 0.02 0.035 0.32 2 -0.38 2 4
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 0.076 0.24 4 -0.35 2 6
MAPK1 0.039 0.08 0.23 6 -0.34 2 8
Syndecan-2/RACK1 0.028 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 0.006 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 0.032 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 0.017 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 0.32 82 -0.37 2 84
Syndecan-2/Caveolin-2/Ras -0.011 0.12 -10000 0 -0.36 73 73
Syndecan-2/Laminin alpha3 -0.058 0.15 -10000 0 -0.38 130 130
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 0.26 1 -10000 0 1
Syndecan-2 dimer 0.021 0.035 0.21 15 -0.38 2 17
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 0.022 0.087 0.26 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 0.044 0.074 0.22 5 -0.35 2 7
FN1 0.13 0.12 0.26 366 -10000 0 366
Syndecan-2/IL8 0.024 0.076 0.32 14 -0.38 14 28
SDC2 0.006 0.022 -10000 0 -0.44 2 2
KNG1 0.022 0.027 0.26 10 -10000 0 10
Syndecan-2/Neurofibromin 0.017 0.023 -10000 0 -0.38 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.025 0.034 0.26 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 0.02 -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 0.2 4 -0.34 2 6
angiogenesis 0.024 0.076 0.32 14 -0.38 14 28
MMP2 0.019 0.044 -10000 0 -0.6 4 4
IL8 0.027 0.11 0.26 52 -0.6 16 68
calcineurin-NFAT signaling pathway 0.019 0.061 0.32 3 -0.35 13 16
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.008 -10000 0 -10000 0 0
ELF1 0.032 0.052 -10000 0 -0.37 7 7
CCNA2 0.12 0.12 0.26 345 -10000 0 345
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.029 0.26 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 0.33 15 -0.55 7 22
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.026 0.032 -10000 0 -0.37 5 5
IL2RA 0.022 0.11 0.44 8 -0.77 10 18
IL2RB 0.033 0.048 0.26 33 -10000 0 33
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.26 32 -0.6 5 37
G1/S transition of mitotic cell cycle 0.053 0.12 0.33 2 -0.79 10 12
PTPN11 0.025 0.002 -10000 0 -10000 0 0
CCND2 0.009 0.072 0.36 2 -0.8 6 8
LCK 0.024 0.077 0.26 23 -0.6 9 32
GRB2 0.023 0.006 -10000 0 -10000 0 0
IL2 0.024 0.026 0.26 9 -10000 0 9
CDK6 0.022 0.045 0.26 2 -0.6 4 6
CCND3 0.048 0.1 0.37 8 -0.64 3 11
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.05 0.064 -10000 0 -0.32 13 13
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.079 0.34 10 -0.33 1 11
alphaV/beta3 Integrin/Osteopontin/Src 0.086 0.076 0.24 16 -10000 0 16
AP1 -0.043 0.18 -10000 0 -0.53 20 20
ILK 0.038 0.067 -10000 0 -0.34 11 11
bone resorption 0.031 0.062 0.28 1 -0.52 1 2
PTK2B 0.02 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.074 0.088 0.33 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 0.033 0.025 -10000 0 -0.45 2 2
alphaV/beta3 Integrin/Osteopontin 0.087 0.093 0.35 4 -0.37 13 17
MAP3K1 0.037 0.068 0.26 11 -0.34 13 24
JUN 0.019 0.057 -10000 0 -0.6 7 7
MAPK3 0.027 0.065 0.27 11 -0.33 10 21
MAPK1 0.028 0.065 0.27 11 -0.32 10 21
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.065 0.26 13 -0.32 13 26
ITGB3 0.017 0.08 0.27 4 -0.6 13 17
NFKBIA 0.025 0.066 0.32 6 -0.32 9 15
FOS -0.17 0.29 -10000 0 -0.6 252 252
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.027 0.099 0.46 5 -0.56 2 7
NF kappa B1 p50/RelA 0.072 0.072 0.37 4 -10000 0 4
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 0.062 -10000 0 -0.44 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.038 0.067 0.26 11 -0.34 13 24
VAV3 0.017 0.07 0.26 15 -0.33 12 27
MAP3K14 0.039 0.068 0.26 9 -0.34 13 22
ROCK2 0.023 0.031 -10000 0 -0.6 2 2
SPP1 0.094 0.11 0.27 231 -10000 0 231
RAC1 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.036 0.061 0.33 1 -0.3 11 12
MMP2 -0.059 0.15 0.36 3 -0.51 19 22
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 0.14 119 -10000 0 119
TP53 0.009 0.019 -10000 0 -0.19 2 2
Senescence 0.009 0.019 -10000 0 -0.19 2 2
Apoptosis 0.009 0.019 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.01 0.062 0.29 26 -10000 0 26
MDM4 0.02 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
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 0.004 0.077 0.21 57 -0.35 19 76
CCND1 0.011 0.05 -10000 0 -0.38 6 6
p38 gamma/SNTA1 0.022 0.075 0.33 2 -0.33 17 19
MAP2K3 0.022 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.078 0.21 61 -0.35 19 80
MAP2K6 -0.004 0.056 -10000 0 -0.36 19 19
MAPT -0.024 0.12 0.26 13 -0.33 90 103
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
Arf6 trafficking events

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
SLC2A4 -0.28 0.31 -10000 0 -0.6 400 400
CLTC 0.026 0.071 0.28 1 -0.45 10 11
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 -0.34 8 8
CPE 0.006 0.048 0.15 1 -0.38 12 13
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.018 -10000 0 -10000 0 0
CTNND1 0.009 0.059 0.2 34 -10000 0 34
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.047 0.22 2 -0.34 7 9
TSHR -0.005 0.078 0.15 3 -0.38 33 36
INS -0.003 0.095 -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 -10000 0 0
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 -0.4 7 7
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 0.26 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 0.068 0.35 8 -10000 0 8
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 0.014 0.044 -10000 0 -0.34 8 8
clathrin heavy chain/ACAP1 0.025 0.067 0.28 6 -0.36 10 16
JIP4/KLC1 0.041 0.017 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.019 0.036 -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 0.06 0.19 81 -10000 0 81
NME1 0.012 0.013 0.15 7 -10000 0 7
clathrin coat assembly 0.029 0.074 0.28 3 -0.44 10 13
IL2RA 0.02 0.056 -10000 0 -0.31 12 12
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.13 0.15 -10000 0 -0.29 328 328
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 0.19 1 -0.36 6 7
SDC1 0.02 0.045 0.21 1 -0.33 7 8
ARF6/GDP 0.02 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 -0.36 8 8
mol:Phosphatidic acid 0.011 0.018 -10000 0 -10000 0 0
endocytosis -0.039 0.04 0.31 9 -10000 0 9
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.049 0.15 0.25 2 -0.32 155 157
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 -0.31 266 270
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
Caspase cascade in apoptosis

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.006 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 0.24 1 -0.41 39 40
SPTAN1 -0.005 0.11 0.3 3 -0.52 25 28
LIMK1 -0.004 0.11 0.27 4 -0.51 26 30
BIRC3 0.024 0.041 0.26 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.024 0.003 -10000 0 -10000 0 0
CASP10 -0.013 0.098 0.3 3 -0.47 27 30
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 -0.001 0.13 0.24 1 -0.48 35 36
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.11 0.28 4 -0.5 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 -0.69 24 24
BID 0.003 0.055 0.21 2 -0.27 26 28
MAP3K1 -0.007 0.1 -10000 0 -0.4 43 43
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.11 0.25 3 -0.5 26 29
CASP9 0.023 0.005 -10000 0 -10000 0 0
DNA repair -0.015 0.045 0.25 4 -0.21 3 7
neuron apoptosis 0.005 0.11 -10000 0 -0.71 17 17
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 -0.53 22 22
CASP7 0.001 0.062 0.27 4 -0.39 4 8
KRT18 0.016 0.07 -10000 0 -0.65 6 6
apoptosis -0.001 0.12 0.32 2 -0.46 38 40
DFFA -0.006 0.11 0.24 2 -0.51 26 28
DFFB -0.006 0.11 0.25 1 -0.52 25 26
PARP1 0.015 0.045 0.21 3 -0.25 4 7
actin filament polymerization 0.002 0.11 0.49 25 -0.3 6 31
TNF 0.024 0.067 0.26 17 -0.6 7 24
CYCS 0.004 0.052 0.19 7 -0.2 32 39
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 0.064 -10000 0 -0.25 30 30
CASP2 0.002 0.066 0.3 2 -0.39 5 7
JNK cascade 0.007 0.1 0.4 43 -10000 0 43
CASP3 -0.003 0.12 0.27 2 -0.53 26 28
LMNB2 -0.003 0.14 0.33 2 -0.53 36 38
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 -0.68 24 24
stress fiber formation -0.004 0.11 0.26 3 -0.5 25 28
GZMB 0.009 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 0.005 0.12 -10000 0 -0.72 17 17
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.001 -10000 0 -10000 0 0
VIM 0.001 0.13 0.3 4 -0.45 42 46
LMNA 0.007 0.086 0.32 2 -0.38 21 23
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.07 -10000 0 -0.3 19 19
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.004 0.11 0.29 2 -0.52 24 26
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.62 29 29
nuclear fragmentation during apoptosis 0.001 0.11 0.24 1 -0.4 39 40
CFL2 -0.002 0.11 0.3 6 -0.5 25 31
GAS2 -0.031 0.15 0.28 4 -0.4 79 83
positive regulation of apoptosis 0.013 0.12 0.28 7 -0.5 28 35
PRF1 0.015 0.087 0.26 8 -0.6 15 23
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0.008 -10000 0 -10000 0 0
MAP4K4 0.002 0.061 -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 -0.26 15 15
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.26 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 -0.016 0.05 0.19 3 -0.26 13 16
SMPD1 0.014 0.059 0.23 8 -0.24 14 22
RB1 -0.017 0.048 -10000 0 -0.29 9 9
FADD/Caspase 8 0.028 0.092 0.27 12 -0.38 6 18
MAP2K4 -0.017 0.046 -10000 0 -0.32 6 6
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 0.2 22 -0.31 6 28
EGF -0.09 0.24 0.26 2 -0.6 151 153
mol:ceramide -0.016 0.052 0.15 1 -0.26 14 15
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 0.26 3 -10000 0 3
negative regulation of cell cycle -0.017 0.048 -10000 0 -0.28 9 9
cell proliferation -0.05 0.13 0.28 1 -0.28 161 162
BID -0.025 0.18 -10000 0 -0.67 49 49
MAP3K1 -0.017 0.048 -10000 0 -0.25 14 14
EIF2A -0.015 0.051 0.29 3 -0.25 6 9
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.008 0.057 0.28 3 -0.3 6 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.061 0.28 3 -0.33 5 8
Cathepsin D/ceramide 0.004 0.062 0.18 28 -0.24 13 41
FADD 0.024 0.084 0.27 1 -0.39 3 4
KSR1 -0.01 0.058 0.2 19 -0.25 12 31
MAPK8 -0.014 0.056 -10000 0 -0.28 10 10
PRKRA -0.017 0.05 0.2 1 -0.25 14 15
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 14 15
CTSD 0.032 0.045 0.26 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 -0.052 0.14 0.3 1 -0.3 160 161
PRKCD 0.024 0.01 0.26 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 0.047 -10000 0 -0.38 6 6
mol:Sphingosine-1-phosphate 0.01 0.008 -10000 0 -10000 0 0
MAP2K1 -0.011 0.057 0.26 4 -0.31 5 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
CYCS -0.002 0.051 0.18 14 -0.23 12 26
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 -0.38 5 5
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 0.26 4 -0.3 6 10
SMPD3 -0.002 0.1 0.28 4 -0.29 74 78
TNF 0.024 0.067 0.26 17 -0.6 7 24
PKC zeta/PAR4 0.034 0.019 -10000 0 -0.45 1 1
mol:PHOSPHOCHOLINE 0.044 0.1 0.24 150 -0.24 2 152
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 -0.21 15 29
BCL2 0.007 0.098 -10000 0 -0.6 21 21
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.014 0.059 -10000 0 -10000 0 0
PLK1 0.28 0.19 0.59 68 -0.58 1 69
CDKN1B 0.17 0.14 0.4 49 -0.48 4 53
FOXO3 0.22 0.17 0.48 166 -0.63 1 167
KAT2B 0.061 0.03 -10000 0 -10000 0 0
FOXO1/SIRT1 0.009 0.053 -10000 0 -0.36 2 2
CAT 0.21 0.17 0.52 51 -0.89 3 54
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.062 0.031 -10000 0 -10000 0 0
FOXO1 0.019 0.061 -10000 0 -0.35 3 3
MAPK10 -0.019 0.13 0.21 9 -0.31 123 132
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.037 0.086 0.41 3 -0.35 1 4
response to oxidative stress 0.04 0.029 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.19 0.14 0.4 136 -0.61 1 137
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.069 0.085 -10000 0 -0.7 6 6
FOXO1/SKP2 0.028 0.057 -10000 0 -0.33 3 3
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 0.021 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 0.033 0.027 0.21 10 -10000 0 10
MAPK9 0.033 0.027 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 0.52 4 -0.62 53 57
RAL/GDP 0.059 0.023 -10000 0 -10000 0 0
CHUK 0.061 0.03 -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 0.022 -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 0.035 -10000 0 -10000 0 0
CCNB1 0.23 0.18 0.53 152 -0.58 1 153
FOXO1-3a-4/beta catenin 0.16 0.13 0.43 34 -0.38 1 35
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.057 -10000 0 -0.32 3 3
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
SGK1 0.057 0.05 -10000 0 -0.58 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 0.26 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 0.007 -10000 0 -10000 0 0
FBXO32 0.26 0.22 0.62 107 -1.2 3 110
BCL6 0.18 0.15 0.55 3 -0.78 5 8
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
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
CDC42/GTP -0.006 0.099 -10000 0 -0.31 41 41
PLCG1 -0.014 0.09 -10000 0 -0.32 40 40
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 -0.007 0.097 -10000 0 -0.3 41 41
S1PR5 0.026 0.042 0.26 12 -0.6 2 14
S1PR4 0.024 0.063 0.26 16 -0.6 6 22
MAPK3 -0.01 0.084 -10000 0 -0.32 33 33
MAPK1 -0.009 0.086 -10000 0 -0.33 35 35
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.29 62 62
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -10000 0 -0.31 3 3
RHOA 0.005 0.061 0.24 1 -0.33 6 7
S1P/S1P4/Gi -0.006 0.096 -10000 0 -0.3 68 68
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 0.023 0.005 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.091 0.3 35 -10000 0 35
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -10000 0 -0.31 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.095 0.26 27 -0.6 15 42
RhoA/GTP -0.004 0.093 -10000 0 -0.3 35 35
negative regulation of cAMP metabolic process -0.004 0.088 -10000 0 -0.28 62 62
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 0.042 0.26 12 -0.6 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.29 62 62
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.039 0.058 -10000 0 -0.41 12 12
forebrain development -0.044 0.21 0.35 1 -0.54 99 100
GNAO1 0.017 0.095 0.26 27 -0.6 15 42
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 0.022 0.009 -10000 0 -10000 0 0
SIN3/HDAC complex 0.055 0.023 -10000 0 -10000 0 0
GNAI1 -0.008 0.14 -10000 0 -0.6 41 41
XPO1 0.023 0.014 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.19 -10000 0 -0.6 56 56
SAP30 0.024 0.015 0.26 3 -10000 0 3
mol:GDP 0.017 0.058 -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 0.008 -10000 0 -10000 0 0
GLI2 0.008 0.066 -10000 0 -0.35 9 9
GLI3 0.009 0.089 0.29 1 -0.49 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 -0.008 0.099 -10000 0 -0.3 69 69
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 -0.45 19 19
GLI2/Su(fu) 0.011 0.083 -10000 0 -0.41 15 15
FOXA2 0.01 0.11 0.43 1 -0.66 15 16
neural tube patterning -0.044 0.21 0.35 1 -0.54 99 100
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 -0.044 0.21 0.35 1 -0.54 99 100
SUFU 0.015 0.025 -10000 0 -0.22 7 7
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 -0.046 0.22 0.35 1 -0.55 99 100
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 0.26 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 -0.013 0.11 -10000 0 -0.41 33 33
PTCH1 -0.084 0.32 -10000 0 -1.1 64 64
MIM/GLI1 -0.032 0.2 -10000 0 -0.62 54 54
CREBBP -0.001 0.098 -10000 0 -0.37 54 54
Su(fu)/SIN3/HDAC complex 0.005 0.093 -10000 0 -0.43 26 26
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.025 0.009 0.26 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 37 39
MAP2K2 0 0.091 -10000 0 -0.58 20 20
MAP2K1 -0.004 0.007 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 0.12 1 -10000 0 1
MAP2K6 -0.01 0.045 -10000 0 -0.33 16 16
CYAA -0.009 0.032 -10000 0 -0.33 8 8
MAP2K4 -0.004 0.007 -10000 0 -10000 0 0
IL1B -0.007 0.043 0.22 2 -0.27 18 20
Channel 0.027 0.039 -10000 0 -0.35 8 8
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 0.069 -10000 0 -0.39 24 24
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 -0.08 0.14 0.2 2 -0.33 204 206
PA/Cellular Receptors 0.028 0.042 -10000 0 -0.38 8 8
apoptosis -0.002 0.008 -10000 0 -0.075 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.036 -10000 0 -0.31 9 9
macrophage activation -0.006 0.009 0.14 1 -10000 0 1
TNF 0.024 0.067 0.26 17 -0.6 7 24
VCAM1 0.006 0.08 0.26 2 -0.34 37 39
platelet activation -0.002 0.069 -10000 0 -0.39 24 24
MAPKKK cascade -0.002 0.028 0.1 12 -0.13 7 19
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 0.069 -10000 0 -0.4 24 24
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 -10000 0 -0.33 8 8
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.01 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.029 0.018 -10000 0 -10000 0 0
CDKN1B 0.009 0.059 -10000 0 -0.62 2 2
CDKN1A 0.009 0.064 -10000 0 -0.62 3 3
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
FOXO3 0.012 0.061 -10000 0 -0.46 6 6
AKT1 0.005 0.059 -10000 0 -0.38 15 15
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 0.008 0.062 -10000 0 -0.62 3 3
AKT1/ASK1 0.032 0.07 -10000 0 -0.55 3 3
BAD/YWHAZ 0.036 0.022 -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 0.39 7 -10000 0 7
TSC1 0.01 0.053 -10000 0 -0.61 2 2
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.074 -10000 0 -0.61 3 3
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.063 -10000 0 -0.37 16 16
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.057 0.32 1 -0.62 2 3
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 0.064 -10000 0 -0.62 3 3
CASP9 0.011 0.048 -10000 0 -0.4 3 3
YWHAB 0.023 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.076 0.37 2 -0.54 3 5
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 0.011 0.062 0.25 3 -0.52 4 7
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.055 -10000 0 -0.33 17 17
CHUK 0.009 0.058 -10000 0 -0.61 2 2
BAD/BCL-XL 0.037 0.072 0.29 1 -0.58 3 4
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 -0.45 17 23
PDPK1 0.023 0.007 -10000 0 -10000 0 0
MDM2 0.011 0.068 0.27 2 -0.44 7 9
MAPKKK cascade -0.036 0.073 0.6 3 -10000 0 3
MDM2/Cbp/p300 0.043 0.077 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.07 0.32 2 -0.59 3 5
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.073 0.32 4 -0.53 3 7
glucose import -0.17 0.16 0.21 3 -0.33 396 399
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.052 -10000 0 -0.41 4 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.17 0.16 0.21 3 -0.33 396 399
GSK3A 0.009 0.062 -10000 0 -0.62 3 3
FOXO1 0.011 0.045 -10000 0 -0.44 3 3
GSK3B 0.009 0.063 -10000 0 -0.62 3 3
SFN 0.018 0.073 0.26 8 -0.6 10 18
G1/S transition of mitotic cell cycle 0.014 0.068 0.33 2 -0.6 3 5
p27Kip1/14-3-3 family 0.018 0.053 0.38 1 -0.45 3 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.086 -10000 0 -0.67 5 5
oxygen homeostasis 0.012 0.013 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.26 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.088 0.082 0.36 4 -0.33 1 5
EPO 0.16 0.18 0.56 52 -0.51 2 54
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 0.58 18 -0.57 2 20
FLT1 -0.012 0.16 -10000 0 -0.66 26 26
ADORA2A 0.17 0.17 0.53 46 -0.54 2 48
germ cell development 0.14 0.15 0.56 20 -0.55 2 22
SLC11A2 0.14 0.15 0.55 15 -0.57 2 17
BHLHE40 0.14 0.16 0.56 14 -0.59 3 17
HIF1AN 0.033 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.13 0.13 0.43 38 -0.38 1 39
ETS1 0.028 0.024 -10000 0 -0.62 1 1
CITED2 0.017 0.085 -10000 0 -0.55 9 9
KDR -0.008 0.15 -10000 0 -0.78 13 13
PGK1 0.15 0.15 0.55 15 -0.56 2 17
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 0.17 0.65 11 -0.57 4 15
EPAS1 0.078 0.088 0.31 41 -0.36 1 42
SP1 0.029 0.01 -10000 0 -10000 0 0
ABCG2 0.13 0.2 0.56 15 -0.58 23 38
EFNA1 0.12 0.14 0.55 7 -0.57 2 9
FXN 0.16 0.15 0.49 33 -0.55 2 35
POU5F1 0.15 0.16 0.57 20 -0.57 2 22
neuron apoptosis -0.16 0.17 0.56 4 -0.64 11 15
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 0.26 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 0.49 41 -0.55 2 43
TWIST1 0.14 0.18 0.49 33 -0.54 23 56
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 0.58 14 -0.57 2 16
CREBBP 0.023 0.007 -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 -0.68 2 2
UGCG 0.017 0.097 -10000 0 -0.64 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.048 0.12 0.28 15 -0.43 22 37
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 39 45
FOXO3 0.038 0.14 0.32 15 -0.51 24 39
AKT1 0.038 0.14 0.32 14 -0.53 27 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 0.054 0.1 0.34 3 -0.47 10 13
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 0.3 18 -0.46 12 30
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 19 -0.44 12 31
Rac1/GDP 0.018 0.013 0.19 1 -10000 0 1
T cell proliferation 0.043 0.099 0.3 13 -0.51 6 19
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 0.091 2 -0.076 14 16
PRKCZ 0.042 0.098 0.31 11 -0.54 6 17
NF kappa B1 p50/RelA 0.051 0.14 0.32 6 -0.44 31 37
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.026 0.072 0.28 18 -0.62 3 21
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.09 0.26 46 -0.6 10 56
IL2RB 0.033 0.048 0.27 33 -10000 0 33
TERT 0.049 0.075 0.26 89 -10000 0 89
E2F1 0.056 0.095 0.34 1 -0.4 16 17
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 -0.042 2 16
PTPN11 0.023 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 -0.51 6 19
GRB2 0.022 0.009 -10000 0 -10000 0 0
IL2 0.023 0.028 0.27 9 -10000 0 9
PIK3CA 0.024 0.008 -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 0.4 3 -0.81 29 32
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.052 0.074 0.44 6 -0.41 11 17
MAP4K1 0.029 0.051 0.26 24 -0.6 2 26
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
PRKCB 0.018 0.078 0.26 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 0.055 0.27 1 -0.32 11 12
JUN 0.004 0.12 -10000 0 -0.6 27 27
MAP3K7 0.013 0.056 0.22 4 -0.3 12 16
GRAP2 0.016 0.073 0.26 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 0.26 7 -0.6 2 9
LCP2 0.024 0.01 0.26 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 0.061 0.26 3 -0.32 14 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.059 0.074 0.43 6 -0.39 11 17
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.015 0.061 0.26 1 -0.3 30 31
FRAP1 -0.002 0.081 0.26 1 -0.46 19 20
AKT1 -0.006 0.062 0.19 2 -0.28 21 23
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 0.062 0.23 1 -0.32 2 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.003 0.034 -10000 0 -0.24 1 1
TSC2 0.023 0.007 -10000 0 -10000 0 0
RHEB/GDP 0.008 0.041 -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 42 42
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.044 -10000 0 -0.25 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.011 0.072 0.26 5 -0.3 18 23
MAP3K5 0 0.045 0.2 9 -0.19 34 43
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0 0.045 0.2 9 -0.19 34 43
mol:LY294002 0 0 -10000 0 -0.001 37 37
EIF4B 0.009 0.066 0.27 3 -0.28 13 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.063 0.23 1 -0.28 10 11
eIF4E/eIF4G1/eIF4A1 0.004 0.051 -10000 0 -0.28 18 18
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.02 0.073 -10000 0 -0.3 36 36
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.05 0.21 10 -0.2 2 12
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.028 0.055 -10000 0 -0.28 2 2
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 0.056 0.19 2 -0.29 24 26
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.52 48 48
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.002 0.05 -10000 0 -10000 0 0
TSC1/TSC2 0.027 0.068 0.26 2 -0.34 2 4
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 -0.01 0.078 -10000 0 -0.33 43 43
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 0.2 4 -0.3 18 22
EIF4EBP1 -0.029 0.24 -10000 0 -1 41 41
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D -0.001 0.078 0.32 3 -0.41 19 22
peptide biosynthetic process -0.011 0.017 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 13 -10000 0 13
EEF2 -0.011 0.017 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.018 0.22 -10000 0 -0.97 41 41
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.02 0.11 -10000 0 -0.41 36 36
KLHL20 0.016 0.069 0.22 12 -0.22 15 27
CYFIP2 0.029 0.044 0.26 21 -0.6 1 22
Rac1/GDP 0 0.087 0.26 9 -0.31 16 25
ENAH -0.017 0.11 -10000 0 -0.4 33 33
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 -0.25 14 14
ABI1/Sra1/Nap1 -0.013 0.033 -10000 0 -0.16 10 10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.068 -10000 0 -0.36 16 16
RAPGEF1 -0.019 0.11 0.26 1 -0.4 26 27
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.12 -10000 0 -0.41 43 43
CRK -0.017 0.1 -10000 0 -0.42 29 29
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 -0.024 0.12 -10000 0 -0.41 41 41
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.028 -10000 0 -0.19 13 13
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
ARF6/GTP/NME1/Tiam1 0.043 0.023 -10000 0 -10000 0 0
PI3K -0.002 0.042 -10000 0 -0.24 13 13
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 -0.34 24 24
TIAM1 0.025 0.015 0.26 3 -10000 0 3
E-cadherin(dimer)/Ca2+ 0.04 0.058 -10000 0 -0.34 14 14
AKT1 -0.007 0.034 -10000 0 -10000 0 0
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 0.26 9 -0.31 15 24
actin cytoskeleton organization 0.015 0.056 0.19 19 -0.16 13 32
CDC42/GDP 0 0.086 0.26 9 -0.31 15 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.045 -10000 0 -0.28 16 16
ITGB7 0.027 0.045 0.26 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 -0.33 14 14
mol:GDP -0.014 0.094 0.27 9 -0.35 17 26
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 0.089 0.26 5 -0.32 14 19
RAC1/GTP/IQGAP1 0.031 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.05 0.18 34 -0.25 3 37
NME1 0.024 0.024 0.26 7 -10000 0 7
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.12 -10000 0 -0.41 38 38
regulation of cell-cell adhesion 0.003 0.041 -10000 0 -0.22 14 14
WASF2 0.007 0.028 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.059 0.25 1 -0.28 14 15
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.069 -10000 0 -0.34 16 16
CCND1 0.015 0.058 0.21 31 -0.32 3 34
VAV2 -0.021 0.16 -10000 0 -0.55 35 35
RAP1/GDP 0.005 0.072 0.26 3 -0.29 14 17
adherens junction assembly -0.022 0.11 -10000 0 -0.4 38 38
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 -0.024 0.12 -10000 0 -0.41 42 42
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.095 0.27 27 -0.35 21 48
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 -0.023 0.13 -10000 0 -0.42 43 43
PLK2 and PLK4 events

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
PLK2 0.023 0.005 -10000 0 -9999 0 0
PLK4 0.035 0.05 0.26 37 -9999 0 37
regulation of centriole replication 0.016 0.028 0.26 1 -9999 0 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 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 0.26 10 -0.6 2 12
BAX 0.005 0.043 0.25 3 -0.18 4 7
EnzymeConsortium:3.1.4.12 0.001 0.027 0.085 4 -0.094 22 26
IKBKB 0.014 0.1 0.34 4 -0.41 17 21
MAP2K2 0.008 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 -0.16 10 12
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 0.2 1 -10000 0 1
protein ubiquitination 0.002 0.1 0.34 4 -0.41 21 25
EnzymeConsortium:2.7.1.37 0.007 0.056 0.23 13 -0.29 1 14
response to UV 0 0.001 0.002 15 -0.003 2 17
RAF1 0.008 0.054 0.2 29 -0.24 2 31
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.005 0.042 0.14 6 -0.16 13 19
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 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 -0.19 3 4
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.01 0.054 0.22 13 -0.25 2 15
MAPK1 0.006 0.061 0.22 13 -0.25 3 16
p50/RELA/I-kappa-B-alpha 0.035 0.009 -10000 0 -10000 0 0
FADD 0.022 0.12 0.28 9 -0.42 21 30
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 0.003 2 -10000 0 2
CHUK -0.004 0.097 -10000 0 -0.41 22 22
TNF R/SODD 0.028 0.016 -10000 0 -10000 0 0
TNF 0.024 0.067 0.26 17 -0.6 7 24
CYCS 0.007 0.047 0.19 11 -0.18 3 14
IKBKG -0.004 0.099 0.43 1 -0.41 23 24
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.11 -10000 0 -0.42 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 0.045 0.18 11 -0.19 3 14
TNF/TNF R/SODD 0.037 0.047 -10000 0 -0.38 6 6
TNFRSF1A 0.023 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.003 2 -10000 0 2
CASP8 0.01 0.11 -10000 0 -0.63 22 22
NSMAF 0.015 0.11 0.26 8 -0.4 24 32
response to hydrogen peroxide 0 0.001 0.002 15 -0.003 2 17
BCL2 0.007 0.098 -10000 0 -0.6 21 21
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 -0.013 0.097 -10000 0 -0.3 68 68
GNAO1 0.018 0.095 0.27 27 -0.6 15 42
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.092 -10000 0 -0.47 23 23
AKT3 -0.011 0.16 -10000 0 -0.99 17 17
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 -0.007 0.14 -10000 0 -0.6 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.023 0.27 6 -10000 0 6
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.098 -10000 0 -0.36 37 37
MAPK3 -0.009 0.091 0.27 1 -0.41 20 21
MAPK1 -0.006 0.091 0.27 1 -0.42 21 22
JAK2 -0.009 0.1 -10000 0 -0.42 27 27
CXCR4 -0.008 0.095 -10000 0 -0.42 21 21
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 -0.011 0.094 -10000 0 -0.42 20 20
S1P/S1P3/Gi -0.002 0.099 -10000 0 -0.36 37 37
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.1 -10000 0 -0.4 22 22
VEGFA 0.026 0.021 0.27 5 -10000 0 5
S1P/S1P2/Gi -0.003 0.092 -10000 0 -0.29 63 63
VEGFR1 homodimer/VEGFA homodimer 0.035 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 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 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 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.1 -10000 0 -0.4 22 22
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 0.071 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 -0.52 11 11
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.024 0.01 0.26 1 -10000 0 1
CCNE1 0.061 0.088 0.26 128 -10000 0 128
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 0.26 146 -10000 0 146
DNA repair 0.035 0.084 0.31 3 -0.38 4 7
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 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.064 -10000 0 -0.27 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 0.26 1 -10000 0 1
BARD1 0.024 0.009 0.26 1 -10000 0 1
PCNA 0.024 0.013 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.047 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.046 0.016 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.1 0.075 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 0.26 2 -0.26 1 3
BARD1/EWS 0.034 0.011 -10000 0 -10000 0 0
RBBP8 0.01 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 0.057 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 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.12 0.12 0.26 319 -10000 0 319
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
Retinoic acid receptors-mediated signaling

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.017 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.062 -10000 0 -0.41 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 -0.35 16 16
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.022 0.068 -10000 0 -0.45 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 0.023 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.002 -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 0.007 0.1 -10000 0 -0.49 19 19
RARA 0.014 0.055 0.2 10 -0.29 16 26
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.063 -10000 0 -0.42 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 9 -0.36 155 164
RXRA 0.023 0.064 -10000 0 -0.3 17 17
RXRB 0.015 0.064 0.25 9 -0.35 18 27
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.032 0.076 0.26 43 -0.6 6 49
CRBP1/9-cic-RA 0.023 0.054 0.18 43 -0.44 6 49
RARB 0.019 0.061 -10000 0 -0.6 8 8
PRKCG 0.031 0.043 0.27 26 -10000 0 26
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.54 20 20
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.009 0.1 -10000 0 -0.47 20 20
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.08 0.25 7 -0.39 12 19
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 0.01 0.12 0.54 1 -0.82 7 8
RXRs/RARs 0.009 0.12 -10000 0 -0.53 22 22
RXRs/RXRs/DNA/9cRA -0.015 0.093 -10000 0 -0.5 19 19
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 0.053 0.055 -10000 0 -0.36 2 2
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.015 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.26 15 -0.6 2 17
ITGA4 0.027 0.027 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.04 0.041 0.23 21 -0.45 2 23
alpha4/beta1 Integrin 0.037 0.019 -10000 0 -10000 0 0
TRAIL 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
TNFSF10 0.02 0.049 -10000 0 -0.6 5 5
positive regulation of NF-kappaB transcription factor activity -0.007 0.12 -10000 0 -0.34 82 82
MAP2K4 0.015 0.045 -10000 0 -0.41 2 2
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 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.014 0.14 0.26 1 -0.6 45 46
TRAIL/TRAILR2 0.025 0.039 -10000 0 -0.39 6 6
TRAIL/TRAILR3 0.026 0.046 -10000 0 -0.38 7 7
TRAIL/TRAILR1 0.024 0.045 -10000 0 -0.43 6 6
TRAIL/TRAILR4 -0.007 0.12 -10000 0 -0.34 82 82
TRAIL/TRAILR1/DAP3/GTP 0.028 0.037 -10000 0 -0.34 4 4
IKK complex 0.01 0.042 -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) -0.014 0.14 0.26 1 -0.6 45 46
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 -0.42 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 0.009 0.061 -10000 0 -0.44 5 5
TRAF2 0.024 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.022 0.025 0.26 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 0.082 0.28 44 -0.34 1 45
JNK cascade -0.007 0.12 -10000 0 -0.34 82 82
TRAIL (trimer) 0.02 0.049 -10000 0 -0.6 5 5
TNFRSF10C 0.022 0.025 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.037 -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 -0.42 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 events

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
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 -0.34 24 24
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
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.073 0.31 3 -0.37 10 13
PDGFB-D/PDGFRB/SLAP 0.028 0.029 0.2 1 -0.33 2 3
PDGFB-D/PDGFRB/APS/CBL 0.048 0.038 -10000 0 -0.38 2 2
AKT1 0.028 0.093 0.34 29 -10000 0 29
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.03 0.083 0.33 4 -0.41 10 14
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FGR 0.001 0.1 -10000 0 -0.53 16 16
mol:Ca2+ 0.023 0.087 0.29 4 -0.42 14 18
MYC 0.055 0.18 0.37 28 -0.77 22 50
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.034 0.044 -10000 0 -0.32 2 2
LRP1/PDGFRB/PDGFB 0.042 0.054 -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 0.3 3 -0.42 14 17
PTEN 0.022 0.031 -10000 0 -0.6 2 2
GRB2 0.023 0.006 -10000 0 -10000 0 0
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 0.2 1 -0.33 2 3
HRAS 0.024 0.01 0.26 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 -0.37 8 16
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 -0.39 5 7
positive regulation of MAPKKK cascade 0.035 0.025 -10000 0 -0.44 2 2
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.089 0.31 3 -0.43 14 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 0.26 1 -10000 0 1
BLK -0.033 0.17 0.29 3 -0.41 115 118
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 0.33 4 -0.44 16 20
CBL 0.022 0.007 -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 -0.52 22 22
PDGFRB 0.023 0.032 -10000 0 -0.6 2 2
ACP1 0.024 0.004 -10000 0 -10000 0 0
HCK 0.017 0.06 -10000 0 -0.55 4 4
ABL1 0.019 0.093 0.29 5 -0.39 17 22
PDGFB-D/PDGFRB/CBL 0.02 0.1 0.3 2 -0.46 19 21
PTPN1 0.024 0.022 0.26 6 -10000 0 6
SNX15 0.024 0.004 -10000 0 -10000 0 0
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.035 0.26 18 -10000 0 18
cell proliferation 0.056 0.16 0.36 31 -0.68 22 53
SLA 0.021 0.025 0.26 7 -10000 0 7
actin cytoskeleton reorganization 0.034 0.051 0.33 2 -0.32 1 3
SRC 0.013 0.054 -10000 0 -0.5 4 4
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 0.043 0.26 27 -10000 0 27
PLCgamma1/SPHK1 0.03 0.085 0.33 4 -0.42 10 14
LYN 0.01 0.065 -10000 0 -0.52 8 8
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 -0.31 2 2
SPHK1 0.024 0.039 0.26 7 -0.6 2 9
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.023 0.089 0.31 3 -0.43 14 17
PLCG1 0.023 0.09 0.33 2 -0.44 14 16
NHERF/PDGFRB 0.049 0.046 -10000 0 -0.38 2 2
YES1 0.001 0.11 -10000 0 -0.55 23 23
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 0.036 0.057 0.26 47 -10000 0 47
NHERF1-2/PDGFRB/PTEN 0.057 0.052 -10000 0 -0.35 4 4
FYN -0.002 0.1 -10000 0 -0.41 33 33
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 0.022 0.12 0.32 4 -0.52 24 28
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 0.098 0.36 29 -0.32 2 31
RASA1 0.02 0.05 -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 0.02 0.091 0.28 5 -0.38 17 22
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
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.024 0.038 0.26 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 0.018 0.095 0.26 27 -0.6 15 42
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 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.005 0.025 -10000 0 -0.25 5 5
S1PR5 0.026 0.042 0.26 12 -0.6 2 14
S1PR4 0.024 0.063 0.26 16 -0.6 6 22
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
S1P/S1P5/G12 0.045 0.042 -10000 0 -0.27 4 4
S1P/S1P3/Gq 0.027 0.062 -10000 0 -0.34 14 14
S1P/S1P4/Gi -0.002 0.1 0.26 1 -0.34 39 40
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 0.26 19 -0.6 6 25
GNA15 0.024 0.027 0.26 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 0.004 -10000 0 -10000 0 0
ABCC1 0.023 0.006 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.048 0.02 -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 0.048 -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 0.058 0.3 8 -10000 0 8
MAP2K1 0.007 0.044 0.28 3 -10000 0 3
MAP3K11 0.023 0.043 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 0.1 -10000 0 -0.48 5 5
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 0.36 2 -0.5 6 8
STAT3 0.023 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.073 0.1 -10000 0 -0.72 8 8
STAT1 0.026 0.049 0.3 4 -10000 0 4
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.058 0.086 0.26 120 -10000 0 120
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 0.063 0.25 3 -0.33 5 8
mol:Ca2+ 0.067 0.05 -10000 0 -10000 0 0
MAPK3 0.02 0.085 -10000 0 -0.56 12 12
STAT1 (dimer) 0.027 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 0.34 3 -0.34 2 5
SMAD7 0.017 0.035 0.18 3 -10000 0 3
CBL/CRKL/C3G 0.046 0.04 0.3 2 -10000 0 2
PI3K 0.06 0.044 -10000 0 -10000 0 0
IFNG 0.058 0.086 0.26 120 -10000 0 120
apoptosis 0.022 0.078 0.33 2 -0.41 11 13
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.005 -10000 0 -10000 0 0
CAMK2A 0.03 0.039 0.26 22 -10000 0 22
CAMK2B -0.011 0.17 0.26 32 -0.6 59 91
FRAP1 0.011 0.054 0.29 8 -10000 0 8
PRKCD 0.014 0.06 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 0.3 9 -10000 0 9
STAT1 (dimer)/PIASy 0.04 0.047 0.29 3 -10000 0 3
SOCS1 0.012 0.12 -10000 0 -1 10 10
mol:GDP 0.042 0.037 0.28 2 -10000 0 2
CASP1 0.016 0.04 0.23 5 -0.27 2 7
PTGES2 0.024 0.003 -10000 0 -10000 0 0
IRF9 0.028 0.042 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 0.023 -10000 0 -10000 0 0
CBL 0.011 0.045 0.27 3 -10000 0 3
MAP3K1 0.022 0.041 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 0.045 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 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
UBC13/UEV1A 0.03 0.01 -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 0.05 -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 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.023 0.1 0.38 3 -0.45 33 36
IL1A 0.028 0.032 0.26 15 -10000 0 15
IL1B 0.005 0.051 0.26 1 -0.46 9 10
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.041 -10000 0 -0.32 1 1
IL1R2 0.004 0.13 0.26 17 -0.6 33 50
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 0.36 5 -0.38 1 6
JUN -0.009 0.066 0.29 4 -0.3 20 24
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.045 0.066 -10000 0 -0.35 18 18
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 0.064 -10000 0 -0.38 18 18
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.004 0.065 0.33 3 -0.3 14 17
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 0.033 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.054 -10000 0 -0.31 12 12
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.026 0.064 -10000 0 -0.38 18 18
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 0.06 -10000 0 -0.33 18 18
IRAK3 0.005 0.11 0.26 1 -0.6 25 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.047 0.066 -10000 0 -0.35 18 18
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 -0.38 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 0.26 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.036 -10000 0 -10000 0 0
IL1RAP 0.024 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.018 0.053 -10000 0 -0.63 1 1
CASP1 0.021 0.023 -10000 0 -0.6 1 1
IL1RN/IL1R2 0.025 0.11 0.38 2 -0.45 35 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.037 0.064 -10000 0 -0.36 18 18
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 -0.34 21 21
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.054 0.26 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 14 18
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.041 0.061 -10000 0 -0.53 2 2
NEF 0.004 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 -0.43 6 6
CYCS 0.037 0.076 0.25 19 -0.34 6 25
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.018 0.091 0.31 12 -0.62 13 25
MAP2K7 0.042 0.13 0.32 1 -0.71 14 15
protein ubiquitination 0.014 0.085 0.31 4 -0.38 10 14
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 0.051 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 0.051 0.034 -10000 0 -0.32 2 2
MAPK8 0.04 0.12 0.46 2 -0.67 13 15
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.015 0.26 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 -0.35 8 12
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.097 0.27 1 -0.44 16 17
CHUK 0.014 0.088 0.32 4 -0.41 9 13
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.039 -10000 0 -0.4 2 2
TCRz/NEF 0.017 0.08 0.32 7 -0.45 17 24
TNF 0.024 0.067 0.26 17 -0.6 7 24
FASLG 0.014 0.1 0.3 32 -0.52 17 49
NFKB1 0.025 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.037 0.047 -10000 0 -0.38 6 6
CASP6 0.052 0.11 -10000 0 -0.51 18 18
CASP7 0.04 0.1 0.35 7 -0.5 8 15
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.35 4 -0.52 7 11
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 0.016 0.093 0.36 2 -0.4 16 18
APAF-1/Caspase 9 0.034 0.063 0.26 5 -0.4 5 10
BCL2 0.033 0.12 0.47 4 -0.56 16 20
Class I PI3K 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
ARF5/GTP -0.014 0.041 0.29 4 -10000 0 4
DAPP1 0.014 0.1 0.28 7 -0.35 30 37
Src family/SYK family/BLNK-LAT/BTK-ITK 0.01 0.14 0.3 9 -0.5 29 38
mol:DAG 0.016 0.079 0.24 26 -0.28 6 32
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 0.055 0.27 1 -0.37 4 5
PLCG2 0.021 0.025 0.26 1 -0.6 1 2
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.009 0.26 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 -0.3 2 4
ARAP3 -0.011 0.043 0.32 6 -0.3 1 7
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.035 0.26 17 -10000 0 17
ARHGEF6 0.021 0.049 -10000 0 -0.6 5 5
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.024 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 0.26 1 -10000 0 1
mol:Ca2+ 0.011 0.05 0.24 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 3 -10000 0 3
ZAP70 0.018 0.1 0.26 26 -0.6 18 44
mol:IP3 0.011 0.062 0.2 31 -0.19 4 35
LYN 0.021 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.025 0.055 0.33 2 -0.34 5 7
RhoA/GDP 0.033 0.042 -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 0.067 0.32 9 -0.32 3 12
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 0.021 0.032 -10000 0 -0.58 2 2
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.042 0.29 5 -0.29 1 6
RhoA/GTP -0.012 0.043 0.36 4 -0.29 1 5
Src family/SYK family/BLNK-LAT 0.021 0.094 0.27 9 -0.42 13 22
BLK 0.046 0.085 0.26 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 0.027 0.029 0.26 12 -10000 0 12
CYTH3 -0.012 0.04 0.36 2 -0.29 1 3
CYTH2 -0.012 0.041 0.33 3 -0.29 1 4
KRAS 0.024 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.012 0.052 0.31 1 -0.56 3 4
SGK1 0.007 0.074 -10000 0 -0.54 4 4
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.018 0.057 0.26 4 -0.34 6 10
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 0.31 9 -0.3 1 10
mol:PI-3-4-5-P3 -0.012 0.037 0.27 4 -0.3 1 5
ARAP3/RAP1A/GTP -0.012 0.036 0.21 2 -0.3 1 3
VAV1 0.024 0.025 0.26 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 0.031 0.054 0.27 1 -0.37 4 5
LAT 0.024 0.038 0.26 7 -0.6 2 9
Rac1/GTP 0.018 0.042 -10000 0 -0.33 5 5
ITK -0.018 0.068 0.36 4 -0.33 21 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.015 0.097 0.27 26 -0.35 10 36
LCK 0.024 0.077 0.26 23 -0.6 9 32
BTK -0.011 0.044 0.36 4 -0.29 1 5
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 -0.27 2 2
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.018 0.11 0.27 1 -0.37 37 38
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.011 0.097 0.3 1 -0.36 27 28
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.037 0.054 0.26 44 -10000 0 44
TXN 0.006 0.004 0.12 1 -10000 0 1
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 0.023 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 0.032 0.023 -10000 0 -0.28 3 3
TAK1/TAB family -0.001 0.02 0.18 1 -0.2 1 2
RAC1/OSM/MEKK3 0.041 0.016 -10000 0 -10000 0 0
TRAF2 0.024 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.092 -10000 0 -0.31 28 28
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 -0.011 0.17 0.26 32 -0.6 59 91
CCM2 0.024 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.007 0.11 -10000 0 -0.38 60 60
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 60 60
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
EPO signaling pathway

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.053 0.079 -10000 0 -10000 0 0
CRKL 0.023 0.048 0.29 6 -10000 0 6
mol:DAG 0.038 0.053 0.33 1 -10000 0 1
HRAS 0.034 0.08 0.3 17 -10000 0 17
MAPK8 0.045 0.068 0.25 26 -10000 0 26
RAP1A 0.024 0.047 0.29 5 -10000 0 5
GAB1 0.024 0.047 0.29 5 -10000 0 5
MAPK14 0.044 0.068 0.25 23 -10000 0 23
EPO 0.064 0.09 0.26 137 -10000 0 137
PLCG1 0.038 0.052 -10000 0 -10000 0 0
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 0.064 0.064 -10000 0 -0.36 4 4
GAB1/SHC/GRB2/SOS1 0.041 0.042 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.063 0.061 -10000 0 -10000 0 0
IRS2 0.011 0.075 0.29 4 -0.31 29 33
STAT1 0.046 0.065 0.32 4 -10000 0 4
STAT5B 0.04 0.06 0.33 1 -0.36 1 2
cell proliferation 0.027 0.075 0.24 30 -10000 0 30
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) 0.046 0.065 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.082 0.063 0.34 2 -10000 0 2
EPO/EPOR 0.063 0.061 -10000 0 -10000 0 0
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.047 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 0.062 0.056 -10000 0 -10000 0 0
mol:IP3 0.038 0.053 0.33 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.075 0.29 2 -0.31 21 23
SH2B3 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.044 0.068 0.26 26 -10000 0 26
EPO/EPOR (dimer)/JAK2/SOCS3 0.026 0.044 -10000 0 -0.2 5 5
PTPN6 0.023 0.039 0.3 2 -10000 0 2
TEC/VAV2/GRB2 0.047 0.049 0.28 3 -0.31 1 4
EPOR 0.026 0.01 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.042 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.021 0.025 0.26 1 -0.6 1 2
CRKL/CBL/C3G 0.047 0.048 -10000 0 -10000 0 0
VAV2 0.024 0.048 0.29 6 -10000 0 6
CBL 0.023 0.047 0.29 5 -10000 0 5
SHC/Grb2/SOS1 0.035 0.038 -10000 0 -10000 0 0
STAT5A 0.038 0.066 0.33 1 -0.36 5 6
GRB2 0.023 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.051 0.081 0.34 1 -0.43 3 4
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 0.28 7 -10000 0 7
BCL2 0.035 0.16 -10000 0 -0.86 23 23
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.42 57 57
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 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.15 0.4 1 -0.42 73 74
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 0.01 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 0.26 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 0.014 0.24 3 -10000 0 3
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.065 0.26 1 -0.34 8 9
VAMP2 0.022 0.008 -10000 0 -10000 0 0
SLC2A4 -0.13 0.17 0.41 1 -0.46 78 79
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 0.26 8 -0.6 10 18
LNPEP 0.021 0.038 -10000 0 -0.6 3 3
YWHAE 0.022 0.007 -10000 0 -10000 0 0
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 0.018 0.026 0.22 5 -0.32 1 6
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.027 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.066 0.05 0.39 6 -0.36 2 8
EPO 0.063 0.09 0.26 137 -10000 0 137
alpha4/beta7 Integrin 0.04 0.041 0.23 21 -0.45 2 23
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 0.062 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.07 -10000 0 -0.54 9 9
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.033 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 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
MADCAM1 0.031 0.045 0.26 29 -10000 0 29
cell adhesion 0.063 0.049 0.38 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 0.26 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 -0.3 6 7
VCAM1 0.021 0.057 0.26 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 -0.32 6 8
EPOR 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.072 -10000 0 -0.56 9 9
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.021 0.087 0.38 2 -0.46 7 9
NFATC2 -0.001 0.067 0.21 1 -0.26 23 24
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 0.01 0.096 0.35 1 -0.41 19 20
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.089 -10000 0 -0.46 8 8
BCL2/BAX 0.021 0.077 -10000 0 -0.42 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 0.003 -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 0.018 0.086 -10000 0 -0.44 11 11
Calcineurin A alpha-beta B1/BCL2 0.007 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 0.43 11 -10000 0 11
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.038 0.062 0.26 56 -10000 0 56
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.018 0.073 0.26 8 -0.6 10 18
MAP3K8 0.019 0.044 -10000 0 -0.6 4 4
NFAT4/CK1 alpha 0.017 0.027 -10000 0 -0.27 1 1
MEF2D/NFAT1/Cbp/p300 0.011 0.11 -10000 0 -0.31 53 53
CABIN1 0.011 0.096 0.35 1 -0.41 18 19
CALM1 0.02 0.014 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.005 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.26 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 0.043 0.038 -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 0.099 0.32 1 -0.47 8 9
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 0.029 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.04 -10000 0 -0.32 3 3
PRKCB 0.018 0.078 0.26 13 -0.6 11 24
PRKCE 0.024 0.022 -10000 0 -0.6 1 1
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 0.26 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.02 0.025 -10000 0 -0.6 1 1
PRKCA 0.009 0.092 0.26 2 -0.6 18 20
PRKCG 0.029 0.043 0.26 26 -10000 0 26
PRKCQ 0.004 0.12 0.26 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 0.032 0.086 0.34 1 -0.47 5 6
CaM/Ca2+/FKBP38 0.027 0.018 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.008 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.034 -10000 0 -10000 0 0
NFATc/ERK1 0.031 0.086 0.34 1 -0.47 5 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.038 0.095 -10000 0 -0.45 11 11
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 0.037 0.056 0.26 46 -10000 0 46
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 0.031 0.085 0.34 1 -0.47 5 6
CREBBP 0.019 0.016 -10000 0 -10000 0 0
BCL2 0.007 0.098 -10000 0 -0.6 21 21
Canonical NF-kappaB pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.11 0.28 13 -0.33 16 29
ERC1 0.023 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.032 0.38 1 -10000 0 1
NFKBIA 0.01 0.02 -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 0.26 3 -10000 0 3
IKBKG 0.019 0.029 -10000 0 -10000 0 0
IKK complex/A20 0.023 0.12 -10000 0 -0.42 25 25
NEMO/A20/RIP2 0.02 0.018 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.015 0.12 -10000 0 -0.41 36 36
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 -0.41 24 24
BCL10/MALT1/TRAF6 0.045 0.015 -10000 0 -10000 0 0
NOD2 0.028 0.039 0.26 21 -10000 0 21
NFKB1 0.025 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 -0.44 7 7
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.009 0.092 0.26 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 0.26 17 -0.6 7 24
NF kappa B1 p50/RelA 0.052 0.014 -10000 0 -10000 0 0
BCL10 0.024 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.02 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.017 0.12 -10000 0 -0.42 31 31
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.014 0.13 -10000 0 -0.45 31 31
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.051 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 -10000 0 -0.45 1 1
GATA1/HDAC5 0.035 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 0.026 0.073 -10000 0 -0.45 18 18
HDAC5/BCL6/BCoR 0.044 0.03 -10000 0 -0.39 3 3
HDAC9 0.023 0.06 0.26 11 -0.6 6 17
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.039 -10000 0 -0.38 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 0.013 0.095 0.26 10 -0.6 18 28
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 -0.44 6 6
Histones 0.016 0.051 -10000 0 -0.32 8 8
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 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.034 0.009 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.26 31 -10000 0 31
Tubulin/HDAC6 0.048 0.013 -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 0.025 0.26 9 -10000 0 9
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.019 0.053 -10000 0 -0.6 6 6
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.31 1 1
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 -10000 0 -10000 0 0
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 -0.009 0.18 -10000 0 -0.44 110 110
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.051 -10000 0 -0.32 8 8
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 0.26 108 -0.6 106 214
HDAC6/HDAC11 0.036 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 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 0.062 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 0.26 2 -10000 0 2
HDAC11 0.024 0.009 0.26 1 -10000 0 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.024 0.004 -10000 0 -10000 0 0
nuclear import -0.026 0.018 0.35 1 -10000 0 1
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 0.02 -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+ 0.024 0.03 -10000 0 -0.39 2 2
HIF1A 0.027 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 0.016 0.055 -10000 0 -0.53 2 2
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:NO 0.02 0.065 0.3 1 -0.45 5 6
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 0.032 0.068 -10000 0 -0.44 6 6
endothelial cell proliferation 0.012 0.084 0.36 6 -0.58 3 9
mol:Ca2+ 0.011 0.031 -10000 0 -0.41 2 2
MAPK3 -0.014 0.055 -10000 0 -0.35 17 17
MAPK1 -0.015 0.055 -10000 0 -0.34 17 17
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 -0.1 0.25 -10000 0 -0.6 164 164
VEGFA homodimer 0.025 0.019 0.26 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 17 17
PI3K 0.046 0.031 -10000 0 -0.39 2 2
PRKCA -0.014 0.058 0.25 1 -0.36 17 18
PRKCB -0.011 0.053 -10000 0 -0.36 12 12
VEGFR1 homodimer/PLGF homodimer 0.025 0.025 -10000 0 -0.45 2 2
VEGFA 0.025 0.019 0.26 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 0.03 -10000 0 -0.46 1 1
NRP2 0.024 0.009 0.26 1 -10000 0 1
VEGFR1 homodimer 0.013 0.021 -10000 0 -0.58 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 19 19
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 0.02 0.065 0.3 1 -0.45 5 6
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 0.036 -10000 0 -0.38 2 2
PDPK1 -0.002 0.045 -10000 0 -0.37 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.038 0.025 -10000 0 -0.48 1 1
mol:NADP 0.02 0.065 0.3 1 -0.45 5 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.029 -10000 0 -0.43 1 1
VEGFR1 homodimer/NRP2 0.026 0.026 -10000 0 -0.64 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.05 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 -0.38 5 5
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.022 0.015 0.26 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 0.049 -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 0.039 -10000 0 -0.45 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 0.038 -10000 0 -0.46 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.31 7 7
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 0.013 0.095 0.26 10 -0.6 18 28
GATA1 0.025 0.025 0.26 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 0.26 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 0.055 0.023 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.015 0.26 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 -0.28 10 10
PPARG -0.061 0.16 -10000 0 -0.36 170 170
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 0.038 -10000 0 -0.46 1 1
MBD3L2 0.018 0.012 0.26 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.021 0.07 -10000 0 -0.36 14 14
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.018 0.029 -10000 0 -0.51 1 1
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 0.26 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.037 0.048 -10000 0 -0.27 5 5
YY1/SAP30/HDAC1 0.037 0.048 -10000 0 -0.26 5 5
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 -0.28 10 10
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 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 0.024 0.067 -10000 0 -0.37 15 15
GATA1/HDAC1 0.036 0.018 -10000 0 -10000 0 0
GATA1/HDAC3 0.031 0.042 -10000 0 -0.48 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.051 -10000 0 -0.44 7 7
SIN3/HDAC complex/Mad/Max 0.014 0.058 -10000 0 -0.28 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 0.26 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 -0.28 10 10
Ran/GTP/Exportin 1 0.034 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 0.024 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
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 0.077 0.35 3 -0.62 2 5
PTK2B 0.009 0.062 0.35 1 -0.66 2 3
VEGFR2 homodimer/Frs2 0.028 0.035 -10000 0 -0.63 2 2
CAV1 -0.1 0.25 -10000 0 -0.6 164 164
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.042 0.037 -10000 0 -0.59 2 2
endothelial cell proliferation 0.046 0.11 0.37 20 -0.66 3 23
mol:Ca2+ 0.016 0.037 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.053 0.038 -10000 0 -0.56 2 2
RP11-342D11.1 0.006 0.034 -10000 0 -0.54 2 2
CDH5 0.02 0.032 -10000 0 -0.6 2 2
VEGFA homodimer 0.049 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.008 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 0.26 64 -0.6 1 65
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.045 0.083 -10000 0 -0.54 6 6
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.047 0.056 -10000 0 -0.53 2 2
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 -0.54 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.006 -10000 0 -10000 0 0
PAK1 0.023 0.017 0.26 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.056 0.051 -10000 0 -0.66 2 2
HRAS 0.024 0.01 0.26 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 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.051 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 -0.61 1 1
mol:NADP 0.026 0.082 0.56 1 -0.48 7 8
eNOS/Hsp90 0.038 0.079 0.55 1 -0.47 6 7
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 0.26 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 -0.65 3 4
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 0.26 2 -10000 0 2
EPAS1 0.028 0.019 -10000 0 -0.34 2 2
mol:L-citrulline 0.026 0.082 0.56 1 -0.48 7 8
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 0.05 0.04 -10000 0 -0.56 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 0.065 -10000 0 -0.67 2 2
MAPK1 0.01 0.067 -10000 0 -0.66 2 2
VEGFA145/NRP2 0.036 0.018 -10000 0 -0.2 1 1
VEGFR1/2 heterodimer 0.026 0.038 -10000 0 -0.69 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 0.39 2 -0.65 2 4
PI3K 0.029 0.049 -10000 0 -0.64 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 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.019 0.14 -10000 0 -0.5 12 12
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 0.004 -10000 0 -10000 0 0
CDC42 0.017 0.037 -10000 0 -0.56 2 2
actin cytoskeleton reorganization 0.047 0.056 -10000 0 -0.52 2 2
PTK2 0.011 0.062 -10000 0 -0.71 3 3
EDG1 0.006 0.034 -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 -0.003 0.04 -10000 0 -0.53 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 0.039 -10000 0 -0.56 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 0.03 0.079 0.35 3 -0.66 2 5
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 0.026 0.082 0.56 1 -0.48 7 8
PXN 0.024 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 0.26 4 -0.6 13 17
NOS3 0.026 0.09 0.57 1 -0.55 7 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.069 -10000 0 -0.37 21 21
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.008 0.065 0.35 1 -0.66 2 3
PRKCB -0.005 0.057 -10000 0 -0.91 1 1
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 0.036 0.018 -10000 0 -0.2 1 1
MAPKKK cascade 0.052 0.071 0.33 9 -0.58 1 10
NRP2 0.024 0.009 0.26 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 -0.65 3 5
MAP3K13 0.016 0.036 -10000 0 -0.56 2 2
PDPK1 0.017 0.044 -10000 0 -0.62 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.039 0.21 1 -0.35 1 2
SMAD3 0.021 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.066 -10000 0 -0.48 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 0.045 -10000 0 -0.28 5 5
MAP3K1 0.023 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 0.26 56 -10000 0 56
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.041 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 -0.16 4 4
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 0.009 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 0.044 0.34 1 -10000 0 1
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.048 -10000 0 -10000 0 0
ARF1/GDP 0.024 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 0.016 0.26 3 -10000 0 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.032 0.047 0.21 9 -10000 0 9
actin filament bundle formation -0.032 0.051 0.24 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 -0.16 3 3
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 -0.16 3 3
ARF6/GTP 0.023 0.032 -10000 0 -0.16 3 3
RhoA/GTP 0.034 0.029 -10000 0 -10000 0 0
mol:GDP 0.02 0.049 0.2 2 -0.22 5 7
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 -0.16 3 3
PLD2 0.02 0.025 -10000 0 -10000 0 0
PIP5K1A 0.01 0.026 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.009 0.036 -10000 0 -0.36 5 5
Rac1/GTP 0.017 0.06 -10000 0 -0.36 6 6
Paxillin-dependent events mediated by a4b1

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
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 0.26 10 -10000 0 10
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.041 0.23 21 -0.45 2 23
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 0.042 0.036 0.34 4 -0.36 2 6
lamellipodium assembly -0.001 0.08 -10000 0 -0.41 21 21
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.033 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 0.046 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 0.018 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.26 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 0.26 6 -0.6 6 12
alpha4/beta1 Integrin/Paxillin/Talin 0.051 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 0.007 -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 0.051 0.022 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.088 -10000 0 -0.46 20 20
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.26 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 0.26 3 -10000 0 3
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 0.044 -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 0.024 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 -0.32 1 1
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.033 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 0.023 0.045 -10000 0 -0.3 1 1
NF kappa B1 p105/c-Rel 0.021 0.013 -10000 0 -10000 0 0
LCK 0.024 0.077 0.26 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 -0.19 3 3
AP2 0.035 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.01 -10000 0 -10000 0 0
CLTB 0.024 0.009 0.26 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.013 0.009 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.005 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 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.017 -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 -10000 0 0
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 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 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.025 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.008 0.016 -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 0.016 -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 0.015 -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 -0.31 1 1
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 0.056 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.037 -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 2 3
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 0.26 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 824 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 0.26 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 0.063 -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/2587659/0.mRNAseq_preprocessor.Finished/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BRCA-TP/2660865/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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