Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 53 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 324
Class IB PI3K non-lipid kinase events 212
Signaling mediated by p38-alpha and p38-beta 211
Signaling events mediated by Stem cell factor receptor (c-Kit) 211
Reelin signaling pathway 192
Aurora B signaling 159
EGFR-dependent Endothelin signaling events 151
PLK1 signaling events 150
FOXA2 and FOXA3 transcription factor networks 141
EPHB forward signaling 129
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXM1 transcription factor network 324 16562 51 -0.084 0.81 1000 -1000 -0.039 -1000
Class IB PI3K non-lipid kinase events 212 636 3 -0.14 -1000 1000 -1000 -0.016 -1000
Signaling mediated by p38-alpha and p38-beta 211 9327 44 -0.33 0.024 1000 -1000 -0.014 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 211 16516 78 -0.57 0.18 1000 -1000 -0.039 -1000
Reelin signaling pathway 192 10794 56 -0.35 0.058 1000 -1000 -0.028 -1000
Aurora B signaling 159 10704 67 -0.22 0.29 1000 -1000 -0.035 -1000
EGFR-dependent Endothelin signaling events 151 3184 21 -0.21 0.034 1000 -1000 -0.034 -1000
PLK1 signaling events 150 12829 85 -0.074 0.25 1000 -1000 -0.025 -1000
FOXA2 and FOXA3 transcription factor networks 141 6489 46 -1.1 0.034 1000 -1000 -0.035 -1000
EPHB forward signaling 129 11031 85 -0.24 0.16 1000 -1000 -0.06 -1000
HIF-1-alpha transcription factor network 128 9761 76 -0.51 0.035 1000 -1000 -0.043 -1000
Glucocorticoid receptor regulatory network 121 13801 114 -0.79 0.3 1000 -1000 -0.049 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 120 8161 68 -0.36 0.16 1000 -1000 -0.057 -1000
p75(NTR)-mediated signaling 118 14814 125 -0.26 0.1 1000 -1000 -0.068 -1000
Endothelins 110 10621 96 -0.37 0.18 1000 -1000 -0.042 -1000
Angiopoietin receptor Tie2-mediated signaling 105 9287 88 -0.29 0.13 1000 -1000 -0.059 -1000
Ephrin B reverse signaling 104 5014 48 -0.24 0.12 1000 -1000 -0.024 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 102 5536 54 -0.35 0.055 1000 -1000 -0.038 -1000
IL4-mediated signaling events 97 8906 91 -0.71 0.27 1000 -1000 -0.058 -1000
Noncanonical Wnt signaling pathway 96 2511 26 -0.11 0.024 1000 -1000 -0.04 -1000
Wnt signaling 96 675 7 -0.11 0.02 1000 -1000 -0.01 -1000
IL23-mediated signaling events 94 5689 60 -0.33 0.08 1000 -1000 -0.022 -1000
IGF1 pathway 87 5001 57 -0.12 0.043 1000 -1000 -0.036 -1000
Arf6 signaling events 80 5013 62 -0.21 0.055 1000 -1000 -0.019 -1000
BMP receptor signaling 79 6436 81 -0.4 0.11 1000 -1000 -0.034 -1000
ErbB2/ErbB3 signaling events 77 5029 65 -0.31 0.034 1000 -1000 -0.043 -1000
Nongenotropic Androgen signaling 76 3968 52 -0.26 0.14 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 75 6448 85 -0.26 0.027 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 75 3918 52 -0.37 0.059 1000 -1000 -0.023 -1000
Plasma membrane estrogen receptor signaling 74 6411 86 -0.11 0.091 1000 -1000 -0.05 -1000
Neurotrophic factor-mediated Trk receptor signaling 74 8934 120 -0.4 0.18 1000 -1000 -0.041 -1000
Signaling events regulated by Ret tyrosine kinase 70 5749 82 -0.063 0.11 1000 -1000 -0.048 -1000
Signaling events mediated by PTP1B 69 5260 76 -0.47 0.08 1000 -1000 -0.029 -1000
Effects of Botulinum toxin 66 1740 26 -0.004 0.11 1000 -1000 -0.003 -1000
Aurora C signaling 65 459 7 0 0.15 1000 -1000 -0.013 -1000
Syndecan-1-mediated signaling events 64 2183 34 -0.079 0.19 1000 -1000 -0.027 -1000
S1P1 pathway 64 2310 36 -0.34 0.024 1000 -1000 -0.029 -1000
Calcium signaling in the CD4+ TCR pathway 64 2013 31 -0.2 0.027 1000 -1000 -0.04 -1000
amb2 Integrin signaling 62 5147 82 -0.37 0.13 1000 -1000 -0.02 -1000
ErbB4 signaling events 61 4221 69 -0.31 0.065 1000 -1000 -0.027 -1000
Glypican 1 network 60 2903 48 -0.21 0.045 1000 -1000 -0.023 -1000
Ephrin A reverse signaling 57 403 7 -0.034 0.024 1000 -1000 -0.009 -1000
Integrins in angiogenesis 56 4785 84 -0.21 0.13 1000 -1000 -0.033 -1000
TCR signaling in naïve CD8+ T cells 55 5138 93 -0.1 0.095 1000 -1000 -0.05 -1000
LPA receptor mediated events 55 5630 102 -0.19 0.12 1000 -1000 -0.045 -1000
IL6-mediated signaling events 53 4017 75 -0.2 0.058 1000 -1000 -0.031 -1000
Signaling events mediated by the Hedgehog family 51 2658 52 -0.13 0.034 1000 -1000 -0.034 -1000
Visual signal transduction: Cones 49 1882 38 -0.035 0.18 1000 -1000 -0.006 -1000
RXR and RAR heterodimerization with other nuclear receptor 49 2584 52 -0.12 0.076 1000 -1000 -0.029 -1000
Fc-epsilon receptor I signaling in mast cells 46 4526 97 -0.17 0.034 1000 -1000 -0.054 -1000
PDGFR-alpha signaling pathway 46 2027 44 -0.33 0.037 1000 -1000 -0.046 -1000
Canonical Wnt signaling pathway 45 2300 51 -0.3 0.12 1000 -1000 -0.038 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 44 1457 33 -0.42 0.057 1000 -1000 -0.03 -1000
Presenilin action in Notch and Wnt signaling 42 2598 61 -0.3 0.12 1000 -1000 -0.041 -1000
Ras signaling in the CD4+ TCR pathway 41 701 17 -0.066 0.023 1000 -1000 -0.015 -1000
IL12-mediated signaling events 40 3558 87 -0.36 0.067 1000 -1000 -0.062 -1000
Nephrin/Neph1 signaling in the kidney podocyte 39 1353 34 -0.024 0.063 1000 -1000 -0.023 -1000
FAS signaling pathway (CD95) 39 1844 47 -0.46 0.041 1000 -1000 -0.027 -1000
TCGA08_rtk_signaling 39 1020 26 -0.19 0.039 1000 -1000 -0.014 -1000
E-cadherin signaling in keratinocytes 39 1705 43 -0.19 0.032 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 37 1510 40 -0.35 0.045 1000 -1000 -0.025 -1000
Syndecan-3-mediated signaling events 37 1322 35 -0.24 0.055 1000 -1000 -0.025 -1000
Rapid glucocorticoid signaling 37 747 20 -0.11 0.028 1000 -1000 -0.004 -1000
LPA4-mediated signaling events 36 443 12 -0.12 0.005 1000 -1000 -0.016 -1000
Glypican 2 network 36 146 4 0.032 0.055 1000 -1000 0.013 -1000
Stabilization and expansion of the E-cadherin adherens junction 35 2639 74 -0.2 0.05 1000 -1000 -0.063 -1000
Aurora A signaling 34 2086 60 -0.09 0.19 1000 -1000 -0.015 -1000
Signaling events mediated by PRL 34 1188 34 -0.14 0.035 1000 -1000 -0.033 -1000
Syndecan-4-mediated signaling events 32 2180 67 -0.21 0.12 1000 -1000 -0.033 -1000
Syndecan-2-mediated signaling events 31 2177 69 -0.12 0.13 1000 -1000 -0.03 -1000
Nectin adhesion pathway 31 1987 63 -0.041 0.047 1000 -1000 -0.036 -1000
Regulation of Telomerase 30 3094 102 -0.21 0.15 1000 -1000 -0.036 -1000
Regulation of p38-alpha and p38-beta 29 1573 54 -0.26 0.052 1000 -1000 -0.045 -1000
Insulin Pathway 29 2179 74 -0.11 0.063 1000 -1000 -0.046 -1000
Regulation of Androgen receptor activity 29 2082 70 -0.19 0.11 1000 -1000 -0.046 -1000
Coregulation of Androgen receptor activity 28 2178 76 -0.16 0.062 1000 -1000 -0.021 -1000
Thromboxane A2 receptor signaling 28 2958 105 -0.19 0.037 1000 -1000 -0.036 -1000
IL27-mediated signaling events 28 1434 51 -0.2 0.072 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 27 3688 136 -0.23 0.075 1000 -1000 -0.031 -1000
TCGA08_retinoblastoma 27 217 8 -0.017 0.058 1000 -1000 -0.002 -1000
BCR signaling pathway 26 2634 99 -0.092 0.058 1000 -1000 -0.075 -1000
IL2 signaling events mediated by STAT5 25 558 22 0.009 0.13 1000 -1000 -0.031 -1000
Osteopontin-mediated events 23 877 38 -0.17 0.094 1000 -1000 -0.032 -1000
Arf6 trafficking events 22 1593 71 -0.28 0.041 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 21 915 43 -0.16 0.17 1000 -1000 -0.037 -1000
TCGA08_p53 21 151 7 -0.009 0.02 1000 -1000 -0.003 -1000
Caspase cascade in apoptosis 20 1486 74 -0.032 0.057 1000 -1000 -0.028 -1000
Signaling mediated by p38-gamma and p38-delta 20 312 15 -0.024 0.024 1000 -1000 -0.028 -1000
Ceramide signaling pathway 19 1471 76 -0.11 0.065 1000 -1000 -0.022 -1000
FoxO family signaling 19 1248 64 -0.019 0.26 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 18 1272 68 -0.17 0.043 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 16 641 39 -0.081 0.028 1000 -1000 -0.026 -1000
PLK2 and PLK4 events 13 39 3 0.016 0.035 1000 -1000 -0.007 -1000
JNK signaling in the CD4+ TCR pathway 13 225 17 0.004 0.059 1000 -1000 -0.024 -1000
Hedgehog signaling events mediated by Gli proteins 13 876 65 -0.083 0.056 1000 -1000 -0.042 -1000
mTOR signaling pathway 13 711 53 -0.028 0.028 1000 -1000 -0.04 -1000
ceramide signaling pathway 13 669 49 -0.005 0.037 1000 -1000 -0.028 -1000
IL2 signaling events mediated by PI3K 13 790 58 -0.001 0.069 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 13 1058 76 -0.025 0.051 1000 -1000 -0.051 -1000
S1P4 pathway 13 348 25 -0.014 0.041 1000 -1000 -0.024 -1000
S1P5 pathway 12 208 17 -0.007 0.032 1000 -1000 -0.015 -1000
Retinoic acid receptors-mediated signaling 12 714 58 -0.052 0.054 1000 -1000 -0.026 -1000
BARD1 signaling events 11 640 57 -0.053 0.12 1000 -1000 -0.032 -1000
S1P3 pathway 11 481 42 -0.013 0.042 1000 -1000 -0.027 -1000
TRAIL signaling pathway 10 503 48 -0.014 0.042 1000 -1000 -0.033 -1000
E-cadherin signaling events 10 52 5 0.011 0.032 1000 -1000 0.013 -1000
Sphingosine 1-phosphate (S1P) pathway 8 224 28 -0.007 0.05 1000 -1000 -0.019 -1000
EPO signaling pathway 8 484 55 0.011 0.083 1000 -1000 -0.026 -1000
IFN-gamma pathway 8 560 68 -0.012 0.078 1000 -1000 -0.052 -1000
IL1-mediated signaling events 8 535 62 -0.01 0.065 1000 -1000 -0.035 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 8 673 83 -0.019 0.047 1000 -1000 -0.025 -1000
Class I PI3K signaling events 8 616 73 -0.018 0.046 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 8 856 97 -0.035 0.058 1000 -1000 -0.053 -1000
p38 MAPK signaling pathway 8 358 44 -0.018 0.058 1000 -1000 -0.026 -1000
Canonical NF-kappaB pathway 7 294 39 -0.004 0.052 1000 -1000 -0.025 -1000
Arf6 downstream pathway 7 316 43 -0.053 0.054 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 7 232 32 -0.13 0.039 1000 -1000 -0.019 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 280 37 -0.008 0.066 1000 -1000 -0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 7 356 45 0.005 0.055 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class II 6 507 75 -0.026 0.063 1000 -1000 -0.035 -1000
a4b1 and a4b7 Integrin signaling 6 33 5 0.024 0.04 1000 -1000 0.015 -1000
VEGFR1 specific signals 6 359 56 -0.1 0.058 1000 -1000 -0.036 -1000
Signaling events mediated by VEGFR1 and VEGFR2 5 658 125 -0.1 0.057 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class I 4 472 104 -0.061 0.058 1000 -1000 -0.034 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 3 78 23 -0.003 0.043 1000 -1000 -0.018 -1000
Circadian rhythm pathway 2 64 22 -0.007 0.053 1000 -1000 -0.036 -1000
Paxillin-dependent events mediated by a4b1 2 99 36 -0.047 0.052 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 2 73 31 0 0.034 1000 -1000 -0.011 -1000
Arf1 pathway 1 63 54 -0.001 0.045 1000 -1000 -0.019 -1000
Alternative NF-kappaB pathway 1 19 13 0 0.067 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 23 27 -0.009 0.057 1000 -1000 -0.04 -1000
Total 6590 390709 7203 -21 -990 131000 -131000 -4 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.67 0.4 1 397 -0.98 2 399
PLK1 0.42 0.27 0.64 413 -0.86 1 414
BIRC5 0.44 0.27 0.68 350 -0.87 3 353
HSPA1B 0.67 0.39 1 391 -0.99 2 393
MAP2K1 0.19 0.12 0.33 316 -10000 0 316
BRCA2 0.68 0.41 1 426 -0.93 3 429
FOXM1 0.8 0.52 1.2 441 -1.2 2 443
XRCC1 0.68 0.4 1 388 -0.99 2 390
FOXM1B/p19 0.062 0.2 0.83 18 -1.1 2 20
Cyclin D1/CDK4 0.59 0.38 0.92 370 -0.94 2 372
CDC2 0.74 0.45 1.1 438 -1 2 440
TGFA 0.58 0.4 0.91 403 -0.96 5 408
SKP2 0.68 0.4 1 380 -0.99 2 382
CCNE1 0.095 0.097 0.31 127 -10000 0 127
CKS1B 0.72 0.43 1.1 417 -0.99 2 419
RB1 0.34 0.33 0.7 322 -0.65 5 327
FOXM1C/SP1 0.6 0.36 0.91 385 -1.2 3 388
AURKB 0.36 0.31 0.66 309 -0.8 11 320
CENPF 0.78 0.48 1.1 461 -0.99 2 463
CDK4 0.093 0.058 0.25 21 -10000 0 21
MYC 0.39 0.39 0.85 262 -1 4 266
CHEK2 0.19 0.13 0.32 311 -10000 0 311
ONECUT1 0.62 0.4 0.95 405 -1 2 407
CDKN2A -0.084 0.12 0.24 5 -0.26 179 184
LAMA4 0.68 0.4 1 406 -0.99 2 408
FOXM1B/HNF6 0.62 0.41 0.98 383 -1.2 2 385
FOS 0.33 0.66 1 284 -0.99 47 331
SP1 0.023 0.025 -10000 0 -0.21 6 6
CDC25B 0.68 0.4 1 399 -0.99 2 401
response to radiation 0.13 0.09 0.24 296 -10000 0 296
CENPB 0.68 0.4 1 409 -0.99 2 411
CENPA 0.74 0.45 1.1 426 -0.99 2 428
NEK2 0.81 0.47 1.1 468 -0.95 2 470
HIST1H2BA 0.67 0.39 1 393 -0.99 2 395
CCNA2 0.16 0.14 0.32 348 -10000 0 348
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.71 0.44 1.1 397 -1.1 2 399
CCNB2 0.75 0.45 1.1 435 -0.99 2 437
CCNB1 0.75 0.47 1.1 426 -1 2 428
ETV5 0.68 0.41 1 398 -0.99 2 400
ESR1 0.54 0.55 1 360 -0.98 11 371
CCND1 0.62 0.42 0.98 399 -0.96 2 401
GSK3A 0.16 0.095 0.28 210 -10000 0 210
Cyclin A-E1/CDK1-2 0.26 0.17 0.41 389 -10000 0 389
CDK2 0.064 0.03 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.17 0.12 0.28 391 -10000 0 391
FOXM1B/Cbp/p300 0.24 0.3 0.73 82 -1.1 2 84
GAS1 0.62 0.49 1 398 -1.1 25 423
MMP2 0.67 0.42 1 390 -1.2 6 396
RB1/FOXM1C 0.54 0.4 0.91 360 -0.98 2 362
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 mediated by p38-alpha and p38-beta

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
PTGS2 -0.33 0.52 0.41 3 -1.1 275 278
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.088 0.18 -10000 0 -0.34 268 268
ATF2/c-Jun -0.085 0.17 -10000 0 -0.45 71 71
MAPK11 -0.083 0.18 -10000 0 -0.35 250 250
MITF -0.12 0.21 -10000 0 -0.41 271 271
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 276 276
KRT8 -0.11 0.21 -10000 0 -0.4 259 259
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 -0.52 276 276
CEBPB -0.1 0.2 0.29 1 -0.4 253 254
SLC9A1 -0.11 0.21 -10000 0 -0.41 270 270
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.4 262 262
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.44 269 269
JUN -0.085 0.17 -10000 0 -0.45 71 71
PPARGC1A -0.21 0.34 0.28 2 -0.56 332 334
USF1 -0.1 0.19 0.33 3 -0.38 256 259
RAB5/GDP/GDI1 -0.082 0.16 -10000 0 -0.3 270 270
NOS2 -0.11 0.22 -10000 0 -0.57 67 67
DDIT3 -0.11 0.21 -10000 0 -0.4 271 271
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.097 0.17 0.28 3 -0.34 259 262
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 248 248
CREB1 -0.12 0.22 -10000 0 -0.42 273 273
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.41 246 246
RPS6KA4 -0.11 0.21 -10000 0 -0.4 270 270
PLA2G4A -0.13 0.22 -10000 0 -0.43 267 267
GDI1 -0.11 0.21 -10000 0 -0.4 275 275
TP53 -0.15 0.27 0.27 1 -0.53 257 258
RPS6KA5 -0.12 0.21 -10000 0 -0.4 277 277
ESR1 -0.15 0.24 0.29 1 -0.42 306 307
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 273 273
MEF2A -0.11 0.21 0.29 1 -0.4 269 270
EIF4EBP1 -0.12 0.22 -10000 0 -0.43 262 262
KRT19 -0.11 0.21 0.4 1 -0.41 260 261
ELK4 -0.1 0.19 0.32 3 -0.38 260 263
ATF6 -0.1 0.19 0.33 3 -0.38 261 264
ATF1 -0.12 0.22 -10000 0 -0.42 275 275
p38alpha-beta/MAPKAPK2 -0.096 0.22 -10000 0 -0.42 234 234
p38alpha-beta/MAPKAPK3 -0.11 0.25 -10000 0 -0.44 266 266
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.16 0.2 0.33 2 -0.38 347 349
CRKL -0.17 0.21 -10000 0 -0.4 362 362
HRAS -0.12 0.18 -10000 0 -0.36 211 211
mol:PIP3 -0.14 0.2 -10000 0 -0.38 265 265
SPRED1 0.024 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 372 372
FOXO3 -0.14 0.2 0.51 1 -0.37 313 314
AKT1 -0.16 0.21 0.35 1 -0.38 351 352
BAD -0.15 0.2 0.33 1 -0.37 320 321
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 374 374
GSK3B -0.14 0.2 0.51 1 -0.37 320 321
RAF1 -0.096 0.16 -10000 0 -0.35 53 53
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 370 370
STAT1 -0.44 0.53 -10000 0 -1 379 379
HRAS/SPRED1 -0.093 0.16 -10000 0 -0.35 55 55
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 -0.41 378 378
HRAS/SPRED2 -0.093 0.16 -10000 0 -0.35 52 52
LYN/TEC/p62DOK -0.14 0.22 -10000 0 -0.4 309 309
MAPK3 -0.065 0.13 0.32 4 -0.28 23 27
STAP1 -0.18 0.22 -10000 0 -0.42 374 374
GRAP2 0.016 0.073 0.27 3 -0.6 11 14
JAK2 -0.37 0.45 -10000 0 -0.84 378 378
STAT1 (dimer) -0.43 0.51 -10000 0 -0.98 379 379
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 311 311
actin filament polymerization -0.18 0.22 0.33 1 -0.41 373 374
LYN 0.021 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 380 380
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.38 322 322
PI3K -0.15 0.22 -10000 0 -0.39 350 350
PTEN 0.023 0.031 -10000 0 -0.6 2 2
SCF/KIT/EPO/EPOR -0.51 0.64 -10000 0 -1.2 376 376
MAPK8 -0.18 0.22 -10000 0 -0.42 374 374
STAT3 (dimer) -0.18 0.22 -10000 0 -0.41 370 370
positive regulation of transcription -0.052 0.11 0.24 10 -0.24 19 29
mol:GDP -0.13 0.19 -10000 0 -0.38 232 232
PIK3C2B -0.16 0.2 -10000 0 -0.42 286 286
CBL/CRKL -0.16 0.2 -10000 0 -0.38 352 352
FER -0.18 0.22 -10000 0 -0.42 376 376
SH2B3 -0.18 0.22 -10000 0 -0.42 376 376
PDPK1 -0.12 0.19 0.34 5 -0.36 234 239
SNAI2 -0.17 0.22 0.28 4 -0.42 329 333
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 380 380
KITLG -0.003 0.059 0.26 10 -0.55 4 14
cell motility -0.32 0.39 -10000 0 -0.73 380 380
PTPN6 0.032 0.018 0.28 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -0.96 14 14
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 380 380
SOCS1 0.024 0.031 0.27 6 -0.6 1 7
cell migration 0.18 0.22 0.42 377 -10000 0 377
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.045 0.098 0.26 139 -10000 0 139
VAV1 0.024 0.025 0.27 2 -0.6 1 3
GRB10 -0.18 0.22 -10000 0 -0.42 372 372
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 377 377
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.14 0.32 4 -0.3 31 35
CBL 0.022 0.008 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 378 378
MAP2K2 -0.074 0.14 0.35 4 -0.3 25 29
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 267 267
STAT5A -0.27 0.34 -10000 0 -0.62 380 380
GRB2 0.023 0.011 0.27 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 329 333
SHC/GRAP2 0.023 0.053 -10000 0 -0.36 13 13
PTPRO -0.18 0.22 -10000 0 -0.42 374 374
SH2B2 -0.18 0.22 -10000 0 -0.42 372 372
DOK1 0.024 0.003 -10000 0 -10000 0 0
MATK -0.19 0.23 -10000 0 -0.43 377 377
CREBBP -0.028 0.073 -10000 0 -10000 0 0
BCL2 -0.15 0.3 -10000 0 -1.2 45 45
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.028 -10000 0 -10000 0 0
VLDLR 0.011 0.089 -10000 0 -0.6 17 17
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
ITGA3 0.021 0.023 -10000 0 -0.6 1 1
RELN/VLDLR/Fyn -0.22 0.22 -10000 0 -0.4 486 486
MAPK8IP1/MKK7/MAP3K11/JNK1 0.058 0.035 -10000 0 -0.34 1 1
AKT1 -0.16 0.14 -10000 0 -0.28 436 436
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.037 0.057 0.27 48 -10000 0 48
RELN/LRP8/DAB1 -0.18 0.2 0.36 5 -0.34 489 494
LRPAP1/LRP8 0.051 0.052 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.16 0.2 0.32 4 -0.33 478 482
DAB1/alpha3/beta1 Integrin -0.16 0.18 -10000 0 -0.32 413 413
long-term memory -0.21 0.23 0.35 4 -0.38 473 477
DAB1/LIS1 -0.16 0.2 0.31 4 -0.32 484 488
DAB1/CRLK/C3G -0.16 0.19 -10000 0 -0.32 470 470
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.2 0.31 4 -0.33 483 487
ARHGEF2 0.021 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.035 0.19 0.27 10 -0.6 80 90
CDK5R1 0.029 0.037 0.27 19 -10000 0 19
RELN -0.35 0.31 0.27 3 -0.6 499 502
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.2 0.21 -10000 0 -0.38 481 481
GRIN2A/RELN/LRP8/DAB1/Fyn -0.18 0.23 0.34 3 -0.37 448 451
MAPK8 0.024 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.2 0.33 2 -0.36 488 490
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.2 0.18 0.23 1 -0.34 489 490
RELN/LRP8 -0.21 0.21 -10000 0 -0.38 492 492
GRIN2B/RELN/LRP8/DAB1/Fyn -0.19 0.22 0.37 3 -0.35 503 506
PI3K 0.034 0.01 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.024 -10000 0 -0.28 3 3
RAP1A -0.18 0.16 0.36 1 -0.32 331 332
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.034 0.27 3 -0.6 2 5
CRLK/C3G 0.034 0.009 -10000 0 -10000 0 0
GRIN2B -0.031 0.17 0.27 1 -0.6 69 70
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.092 0.12 0.23 1 -0.36 47 48
neuron adhesion -0.16 0.15 0.33 2 -0.52 15 17
LRP8 0.052 0.077 0.27 95 -10000 0 95
GSK3B -0.15 0.14 -10000 0 -0.27 426 426
RELN/VLDLR/DAB1/Fyn -0.18 0.2 0.32 2 -0.34 478 480
MAP3K11 0.024 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.16 -10000 0 -0.29 472 472
CDK5 0.024 0.01 0.27 1 -10000 0 1
MAPT -0.02 0.2 0.89 14 -0.55 73 87
neuron migration -0.2 0.18 0.28 1 -0.36 397 398
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.092 0.12 0.23 1 -0.36 47 48
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 490 490
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.12 0.11 0.25 274 -0.26 2 276
STMN1 0.084 0.084 0.28 54 -10000 0 54
Aurora B/RasGAP/Survivin 0.2 0.14 0.34 398 -10000 0 398
Chromosomal passenger complex/Cul3 protein complex 0.012 0.15 0.21 157 -0.25 98 255
BIRC5 0.19 0.12 0.27 560 -10000 0 560
DES -0.16 0.32 -10000 0 -0.59 212 212
Aurora C/Aurora B/INCENP 0.11 0.082 0.33 6 -0.31 1 7
Aurora B/TACC1 0.077 0.097 -10000 0 -0.37 13 13
Aurora B/PP2A 0.12 0.085 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.029 0.14 10 -10000 0 10
mitotic metaphase/anaphase transition -0.007 0.006 -10000 0 -10000 0 0
NDC80 0.16 0.13 0.28 394 -10000 0 394
Cul3 protein complex -0.12 0.21 -10000 0 -0.39 316 316
KIF2C 0.17 0.11 0.25 490 -10000 0 490
PEBP1 0.028 0.004 -10000 0 -10000 0 0
KIF20A 0.21 0.098 0.26 652 -10000 0 652
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.085 -10000 0 -10000 0 0
SEPT1 0.027 0.031 0.27 13 -10000 0 13
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.027 0.029 0.27 12 -10000 0 12
NSUN2/NPM1/Nucleolin 0.081 0.2 0.32 25 -0.45 73 98
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.075 0.066 0.24 32 -10000 0 32
AURKB 0.15 0.12 0.26 437 -10000 0 437
AURKC 0.026 0.036 0.27 11 -0.6 1 12
CDCA8 0.12 0.12 0.28 296 -10000 0 296
cytokinesis 0.16 0.16 0.33 295 -0.36 5 300
Aurora B/Septin1 0.19 0.18 0.38 302 -0.34 4 306
AURKA 0.13 0.12 0.26 360 -10000 0 360
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.3 -10000 0 -0.6 324 324
BUB1 0.2 0.11 0.26 605 -10000 0 605
hSgo1/Aurora B/Survivin 0.29 0.19 0.43 509 -10000 0 509
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.2 0.15 0.37 290 -10000 0 290
SGOL1 0.19 0.11 0.27 565 -10000 0 565
CENPA 0.19 0.15 0.32 416 -10000 0 416
NCAPG 0.15 0.12 0.27 442 -10000 0 442
Aurora B/HC8 Proteasome 0.12 0.085 -10000 0 -10000 0 0
NCAPD2 0.024 0.01 0.27 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.085 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.13 0.12 0.27 350 -10000 0 350
NPM1 0.074 0.13 0.27 4 -0.56 10 14
RASA1 0.024 0.005 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.085 -10000 0 -10000 0 0
PPP1CC 0.025 0.002 -10000 0 -10000 0 0
Centraspindlin 0.22 0.16 0.39 345 -10000 0 345
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
NSUN2 0.08 0.12 0.28 18 -0.4 9 27
MYLK 0.035 0.13 0.24 6 -0.32 74 80
KIF23 0.11 0.12 0.28 269 -10000 0 269
VIM 0.083 0.09 0.38 26 -0.43 2 28
RACGAP1 0.045 0.056 0.28 43 -10000 0 43
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.07 0.14 -10000 0 -0.5 21 21
Chromosomal passenger complex 0.2 0.13 0.3 470 -10000 0 470
Chromosomal passenger complex/EVI5 0.25 0.18 0.42 389 -10000 0 389
TACC1 0.01 0.078 -10000 0 -0.6 13 13
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.024 0.01 0.27 1 -10000 0 1
EGFR -0.19 0.3 -10000 0 -0.6 281 281
EGF/EGFR -0.17 0.24 -10000 0 -0.4 388 388
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.21 -10000 0 -0.38 290 290
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.024 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.091 0.24 0.27 2 -0.6 153 155
EGF/EGFR dimer/SHC -0.16 0.23 -10000 0 -0.38 389 389
mol:GDP -0.12 0.21 -10000 0 -0.38 290 290
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.021 0.16 0.27 1 -0.6 60 61
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.35 289 289
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.12 0.2 -10000 0 -0.36 289 289
FRAP1 -0.15 0.17 -10000 0 -0.36 290 290
EGF/EGFR dimer -0.21 0.27 -10000 0 -0.48 400 400
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
ETA receptor/Endothelin-1 -0.001 0.13 -10000 0 -0.45 60 60
PLK1 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
regulation of centriole-centriole cohesion -0.074 0.05 0.11 2 -0.11 405 407
BUB1B 0.096 0.069 0.15 453 -10000 0 453
PLK1 0.055 0.04 0.098 252 -10000 0 252
PLK1S1 0.029 0.036 0.14 9 -0.17 16 25
KIF2A 0.046 0.038 0.19 7 -10000 0 7
regulation of mitotic centrosome separation 0.055 0.04 0.098 252 -10000 0 252
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 20 22
cytokinesis 0.14 0.079 0.22 221 -0.35 1 222
PP2A-alpha B56 0.12 0.12 -10000 0 -0.44 18 18
AURKA 0.072 0.054 0.12 378 -0.15 2 380
PICH/PLK1 0.11 0.094 0.22 280 -10000 0 280
CENPE 0.072 0.059 0.14 261 -10000 0 261
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.046 0.037 0.19 7 -10000 0 7
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.089 0.056 0.13 496 -0.14 1 497
PAK1 0.022 0.017 0.26 3 -10000 0 3
SPC24 0.17 0.12 0.27 500 -10000 0 500
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.083 0.073 0.15 313 -0.19 16 329
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 41 -10000 0 41
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.025 0.02 0.055 137 -10000 0 137
G2 phase of mitotic cell cycle 0.001 0.003 0.014 16 -10000 0 16
STAG2 0.025 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.084 -10000 0 -0.5 21 21
spindle elongation 0.055 0.04 0.098 252 -10000 0 252
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 -0.16 69 70
CDC25C 0.12 0.071 0.16 509 -0.21 11 520
CDC25B 0.03 0.033 0.27 14 -10000 0 14
SGOL1 0.074 0.05 0.11 405 -0.11 2 407
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.074 0.071 0.26 19 -10000 0 19
CDC14B -0.011 0.075 -10000 0 -0.45 23 23
CDC20 0.16 0.12 0.27 450 -10000 0 450
PLK1/PBIP1 0.048 0.051 0.15 136 -10000 0 136
mitosis -0.005 0.005 0.024 2 -10000 0 2
FBXO5 0.034 0.037 0.15 16 -0.12 1 17
CDC2 0.004 0.004 0.011 178 -10000 0 178
NDC80 0.17 0.12 0.27 516 -10000 0 516
metaphase plate congression 0.032 0.055 0.15 1 -0.2 33 34
ERCC6L 0.1 0.09 0.25 153 -10000 0 153
NLP/gamma Tubulin 0.026 0.025 0.078 33 -0.083 9 42
microtubule cytoskeleton organization 0.015 0.058 0.13 1 -0.16 69 70
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 12 -10000 0 12
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 12 -10000 0 12
PLK1/PRC1-2 0.22 0.13 0.3 532 -10000 0 532
GRASP65/GM130/RAB1/GTP/PLK1 0.073 0.032 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.047 0.037 0.088 251 -10000 0 251
mitotic prometaphase 0.002 0.005 0.023 40 -10000 0 40
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.053 -10000 0 -0.34 2 2
microtubule-based process 0.19 0.088 0.23 648 -10000 0 648
Golgi organization 0.055 0.04 0.098 252 -10000 0 252
Cohesin/SA2 0.059 0.03 0.15 4 -10000 0 4
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.22 0.1 0.27 652 -10000 0 652
APC/C/CDC20 0.15 0.1 0.24 451 -10000 0 451
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.043 0.052 0.15 136 -10000 0 136
PRC1 0.088 0.11 0.27 220 -10000 0 220
ECT2 0.055 0.059 0.23 52 -10000 0 52
C13orf34 0.045 0.034 0.083 255 -10000 0 255
NUDC 0.032 0.055 0.15 1 -0.2 33 34
regulation of attachment of spindle microtubules to kinetochore 0.096 0.069 0.15 454 -10000 0 454
spindle assembly 0.04 0.031 0.092 100 -10000 0 100
spindle stabilization 0.029 0.036 0.14 9 -0.17 16 25
APC/C/HCDH1 0.01 0.068 -10000 0 -0.37 25 25
MKLP2/PLK1 0.19 0.088 0.23 648 -10000 0 648
CCNB1 0.078 0.1 0.27 183 -10000 0 183
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.041 0.052 0.23 1 -0.28 11 12
TUBG1 0.025 0.041 0.13 3 -0.16 27 30
G2/M transition of mitotic cell cycle 0.047 0.048 0.21 10 -10000 0 10
MLF1IP 0.027 0.054 0.14 143 -10000 0 143
INCENP 0.024 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.25 0.27 -10000 0 -0.74 102 102
PCK1 -0.93 0.64 -10000 0 -1.4 499 499
HNF4A -0.24 0.28 -10000 0 -0.78 74 74
KCNJ11 -0.28 0.3 -10000 0 -0.79 120 120
AKT1 -0.17 0.16 -10000 0 -0.44 56 56
response to starvation 0.004 0.011 -10000 0 -10000 0 0
DLK1 -0.45 0.48 0.58 1 -1.1 274 275
NKX2-1 -0.038 0.16 0.51 5 -0.54 1 6
ACADM -0.26 0.27 -10000 0 -0.74 104 104
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 -0.74 242 242
PKLR -0.23 0.27 0.56 2 -0.7 111 113
APOA1 -0.28 0.32 -10000 0 -0.86 86 86
CPT1C -0.25 0.27 0.56 2 -0.74 103 105
ALAS1 -0.15 0.16 -10000 0 -0.76 6 6
TFRC -0.42 0.27 -10000 0 -0.76 199 199
FOXF1 0.017 0.048 0.26 6 -0.6 3 9
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.032 0.27 6 -10000 0 6
CPT1A -0.24 0.27 -10000 0 -0.74 98 98
HMGCS1 -0.25 0.27 -10000 0 -0.72 111 111
NR3C1 -0.12 0.12 -10000 0 -0.3 128 128
CPT1B -0.25 0.27 -10000 0 -0.75 102 102
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.024 -10000 0 -10000 0 0
GCK -0.28 0.34 -10000 0 -0.9 124 124
CREB1 -0.074 0.092 -10000 0 -0.23 76 76
IGFBP1 -0.43 0.55 -10000 0 -1.4 197 197
PDX1 -0.12 0.16 0.52 1 -0.6 3 4
UCP2 -0.25 0.27 0.56 1 -0.71 117 118
ALDOB -0.28 0.29 -10000 0 -0.78 117 117
AFP -0.59 0.52 0.37 1 -0.91 495 496
BDH1 -0.25 0.27 -10000 0 -0.74 99 99
HADH -0.28 0.29 -10000 0 -0.79 104 104
F2 -0.28 0.31 -10000 0 -0.86 81 81
HNF1A 0.034 0.032 0.27 6 -10000 0 6
G6PC -0.18 0.12 -10000 0 -0.57 8 8
SLC2A2 -0.16 0.17 -10000 0 -0.96 1 1
INS 0.02 0.08 0.23 23 -10000 0 23
FOXA1 -0.22 0.23 0.29 15 -0.37 460 475
FOXA3 -0.37 0.22 0.3 9 -0.47 611 620
FOXA2 -0.33 0.33 -10000 0 -0.82 159 159
ABCC8 -0.32 0.39 0.6 1 -0.99 149 150
ALB -0.8 0.55 0.37 1 -1.1 577 578
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.006 0.12 -10000 0 -0.38 77 77
cell-cell adhesion 0.15 0.16 0.32 344 -10000 0 344
Ephrin B/EPHB2/RasGAP 0.03 0.11 -10000 0 -0.34 60 60
ITSN1 0.023 0.031 -10000 0 -0.6 2 2
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.15 0.21 -10000 0 -0.38 355 355
HRAS/GDP -0.14 0.19 -10000 0 -0.34 351 351
Ephrin B/EPHB1/GRB7 -0.13 0.22 -10000 0 -0.38 331 331
Endophilin/SYNJ1 -0.028 0.087 0.23 2 -0.32 59 61
KRAS 0.024 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.13 0.23 -10000 0 -0.38 347 347
endothelial cell migration 0.044 0.02 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PAK1 -0.034 0.1 0.35 2 -0.35 65 67
HRAS 0.024 0.01 0.27 1 -10000 0 1
RRAS -0.028 0.089 0.23 2 -0.32 59 61
DNM1 0.021 0.049 0.27 1 -0.6 5 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.19 0.35 2 -0.36 366 368
lamellipodium assembly -0.15 0.16 -10000 0 -0.32 344 344
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.11 0.17 -10000 0 -0.33 275 275
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
EPHB2 0.028 0.033 0.27 15 -10000 0 15
EPHB3 0.025 0.015 0.27 3 -10000 0 3
EPHB1 -0.24 0.31 0.27 1 -0.6 355 356
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.14 0.18 -10000 0 -0.44 143 143
Ephrin B/EPHB2 0.02 0.1 -10000 0 -0.34 60 60
Ephrin B/EPHB3 0.019 0.1 -10000 0 -0.34 56 56
JNK cascade -0.15 0.16 0.36 6 -0.33 352 358
Ephrin B/EPHB1 -0.14 0.22 -10000 0 -0.38 366 366
RAP1/GDP -0.11 0.17 -10000 0 -0.4 125 125
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.025 0.16 -10000 0 -0.6 62 62
EFNB1 0.025 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.12 0.2 -10000 0 -0.35 353 353
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 -0.43 132 132
Rap1/GTP -0.13 0.18 -10000 0 -0.34 305 305
axon guidance -0.006 0.12 -10000 0 -0.38 77 77
MAPK3 -0.099 0.15 -10000 0 -0.4 89 89
MAPK1 -0.1 0.15 -10000 0 -0.4 91 91
Rac1/GDP -0.12 0.17 -10000 0 -0.41 137 137
actin cytoskeleton reorganization -0.13 0.13 -10000 0 -0.34 127 127
CDC42/GDP -0.12 0.17 -10000 0 -0.41 137 137
PI3K 0.049 0.022 -10000 0 -10000 0 0
EFNA5 -0.034 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 -0.006 0.091 -10000 0 -0.29 60 60
CDC42 0.024 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.13 0.18 -10000 0 -0.33 282 282
PTK2 0.16 0.28 0.69 174 -10000 0 174
MAP4K4 -0.15 0.17 0.36 6 -0.34 352 358
SRC 0.024 0.005 -10000 0 -10000 0 0
KALRN 0.014 0.081 -10000 0 -0.6 14 14
Intersectin/N-WASP 0.034 0.025 -10000 0 -0.45 2 2
neuron projection morphogenesis -0.12 0.15 0.29 7 -0.44 62 69
MAP2K1 -0.11 0.16 -10000 0 -0.32 258 258
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.21 -10000 0 -0.36 352 352
cell migration -0.12 0.19 0.31 5 -0.36 240 245
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.029 0.089 0.23 2 -0.32 59 61
PXN 0.025 0.002 -10000 0 -10000 0 0
TF -0.2 0.18 0.22 2 -0.34 478 480
HRAS/GTP -0.12 0.2 -10000 0 -0.34 349 349
Ephrin B1/EPHB1-2 -0.12 0.2 -10000 0 -0.35 353 353
cell adhesion mediated by integrin 0.009 0.091 0.3 60 -0.21 16 76
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.13 0.21 -10000 0 -0.35 365 365
RAC1-CDC42/GTP -0.15 0.16 -10000 0 -0.34 285 285
RASA1 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.12 0.17 -10000 0 -0.4 128 128
ruffle organization -0.15 0.17 0.37 4 -0.53 54 58
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.032 0.092 0.22 2 -0.33 60 62
Ephrin B/EPHB2/KALRN 0.025 0.12 -10000 0 -0.36 70 70
ROCK1 0.018 0.03 -10000 0 -10000 0 0
RAS family/GDP -0.12 0.13 -10000 0 -0.35 112 112
Rac1/GTP -0.14 0.19 -10000 0 -0.34 344 344
Ephrin B/EPHB1/Src/Paxillin -0.14 0.19 -10000 0 -0.34 353 353
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.26 0.38 -10000 0 -0.8 179 179
HDAC7 0.025 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.34 0.68 1 -0.76 125 126
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.26 0.37 -10000 0 -0.8 176 176
AP1 -0.12 0.23 -10000 0 -0.45 264 264
ABCG2 -0.27 0.39 -10000 0 -0.82 193 193
HIF1A -0.05 0.082 -10000 0 -0.22 17 17
TFF3 -0.27 0.41 0.7 3 -0.82 202 205
GATA2 0.01 0.097 0.26 11 -0.6 18 29
AKT1 -0.059 0.093 -10000 0 -0.26 29 29
response to hypoxia -0.065 0.083 0.19 1 -0.21 98 99
MCL1 -0.25 0.36 -10000 0 -0.81 164 164
NDRG1 -0.24 0.36 -10000 0 -0.81 149 149
SERPINE1 -0.25 0.38 0.71 3 -0.81 171 174
FECH -0.26 0.37 -10000 0 -0.81 172 172
FURIN -0.26 0.37 -10000 0 -0.8 173 173
NCOA2 0.019 0.059 -10000 0 -0.6 7 7
EP300 -0.065 0.13 0.33 1 -0.34 90 91
HMOX1 -0.26 0.38 -10000 0 -0.8 175 175
BHLHE40 -0.26 0.37 -10000 0 -0.8 176 176
BHLHE41 -0.26 0.38 -10000 0 -0.82 174 174
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.025 0.11 -10000 0 -10000 0 0
ENG -0.02 0.11 0.4 2 -10000 0 2
JUN 0.016 0.062 -10000 0 -0.6 8 8
RORA -0.26 0.38 -10000 0 -0.81 174 174
ABCB1 -0.26 0.45 -10000 0 -1.1 165 165
TFRC -0.26 0.37 0.73 1 -0.81 172 173
CXCR4 -0.26 0.38 -10000 0 -0.81 172 172
TF -0.43 0.46 -10000 0 -0.88 339 339
CITED2 -0.26 0.37 -10000 0 -0.81 171 171
HIF1A/ARNT -0.29 0.42 0.78 1 -0.91 167 168
LDHA -0.041 0.13 -10000 0 -0.73 21 21
ETS1 -0.26 0.37 -10000 0 -0.81 171 171
PGK1 -0.26 0.38 -10000 0 -0.8 176 176
NOS2 -0.26 0.37 -10000 0 -0.81 168 168
ITGB2 -0.26 0.38 -10000 0 -0.8 175 175
ALDOA -0.25 0.37 -10000 0 -0.82 163 163
Cbp/p300/CITED2 -0.27 0.4 -10000 0 -0.91 144 144
FOS -0.17 0.29 -10000 0 -0.6 254 254
HK2 -0.26 0.38 -10000 0 -0.81 172 172
SP1 0.001 0.059 -10000 0 -0.21 7 7
GCK -0.14 0.36 -10000 0 -1.4 54 54
HK1 -0.26 0.38 -10000 0 -0.81 173 173
NPM1 -0.26 0.38 -10000 0 -0.81 173 173
EGLN1 -0.25 0.36 -10000 0 -0.8 167 167
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.26 0.37 -10000 0 -0.8 176 176
SMAD3 0.025 0.004 -10000 0 -10000 0 0
EDN1 -0.2 0.38 -10000 0 -1.1 103 103
IGFBP1 -0.33 0.43 -10000 0 -0.89 227 227
VEGFA -0.17 0.3 -10000 0 -0.69 99 99
HIF1A/JAB1 -0.008 0.067 -10000 0 -10000 0 0
CP -0.32 0.46 0.68 2 -0.92 228 230
CXCL12 -0.28 0.4 -10000 0 -0.84 192 192
COPS5 0.024 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.01 -10000 0 -10000 0 0
BNIP3 -0.26 0.38 0.77 1 -0.81 176 177
EGLN3 -0.25 0.38 0.75 2 -0.8 172 174
CA9 -0.22 0.4 0.69 7 -0.79 171 178
TERT -0.25 0.38 0.71 2 -0.8 169 171
ENO1 -0.26 0.38 -10000 0 -0.8 177 177
PFKL -0.26 0.38 -10000 0 -0.8 177 177
NCOA1 0.025 0.022 -10000 0 -0.6 1 1
ADM -0.28 0.41 -10000 0 -0.86 193 193
ARNT -0.038 0.069 -10000 0 -10000 0 0
HNF4A 0.017 0.041 0.27 10 -0.18 1 11
ADFP -0.27 0.36 -10000 0 -0.8 181 181
SLC2A1 -0.17 0.3 -10000 0 -0.7 97 97
LEP -0.51 0.41 -10000 0 -0.88 361 361
HIF1A/ARNT/Cbp/p300 -0.22 0.34 -10000 0 -0.78 129 129
EPO -0.095 0.26 0.7 4 -0.73 25 29
CREBBP -0.055 0.12 0.33 1 -0.34 64 65
HIF1A/ARNT/Cbp/p300/HDAC7 -0.2 0.33 -10000 0 -0.8 104 104
PFKFB3 -0.26 0.38 -10000 0 -0.82 169 169
NT5E -0.26 0.38 -10000 0 -0.81 178 178
Glucocorticoid receptor regulatory 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
PCK2 0.098 0.11 0.5 4 -10000 0 4
SMARCC2 0.025 0.013 -10000 0 -0.2 1 1
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.13 0.22 0.4 5 -0.68 67 72
SUMO2 0 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.034 0.037 0.28 18 -10000 0 18
FKBP4 0.025 0.018 0.27 4 -10000 0 4
FKBP5 0.017 0.073 0.27 3 -0.6 11 14
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.33 68 -0.33 5 73
PRL -0.067 0.12 0.54 3 -0.4 9 12
cortisol/GR alpha (dimer)/TIF2 0.2 0.27 0.53 270 -0.48 4 274
RELA -0.041 0.1 0.3 1 -0.25 28 29
FGG 0.22 0.24 0.48 297 -0.55 1 298
GR beta/TIF2 0.1 0.14 0.33 92 -0.41 7 99
IFNG -0.33 0.37 0.49 3 -0.72 304 307
apoptosis -0.27 0.31 0.86 1 -0.65 247 248
CREB1 0.065 0.057 -10000 0 -10000 0 0
histone acetylation 0.03 0.13 0.38 42 -0.42 11 53
BGLAP -0.09 0.14 -10000 0 -0.48 19 19
GR/PKAc 0.14 0.13 0.36 68 -0.36 1 69
NF kappa B1 p50/RelA -0.068 0.18 0.49 2 -0.34 144 146
SMARCD1 0.025 0.011 -10000 0 -10000 0 0
MDM2 0.1 0.11 0.22 280 -10000 0 280
GATA3 0.014 0.12 0.27 27 -0.6 27 54
AKT1 0.019 0.012 -10000 0 -10000 0 0
CSF2 -0.026 0.11 0.49 1 -0.57 2 3
GSK3B -0.001 0.024 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.8 1 -0.59 156 157
CSN2 0.17 0.19 0.38 283 -0.42 2 285
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 0.024 0.016 0.27 1 -10000 0 1
CDKN1A 0.016 0.079 -10000 0 -1.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN 0.018 0.073 0.27 8 -0.6 10 18
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.35 45 -0.33 3 48
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.38 0.4 0.62 2 -0.81 345 347
JUN -0.27 0.3 0.37 6 -0.55 350 356
IL4 -0.12 0.15 -10000 0 -0.48 23 23
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 -0.5 410 410
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.35 49 -0.31 4 53
cortisol/GR alpha (monomer) 0.3 0.32 0.61 357 -0.52 2 359
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.2 0.3 -10000 0 -0.62 261 261
AP-1/NFAT1-c-4 -0.46 0.46 0.48 6 -0.84 447 453
AFP -0.56 0.66 0.47 1 -1.4 285 286
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.17 0.16 0.46 60 -10000 0 60
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 0.42 1 -1.4 399 400
KRT14 -0.77 0.67 -10000 0 -1.4 466 466
TBP 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.16 0.14 0.3 360 -10000 0 360
HDAC1 0.023 0.009 -10000 0 -10000 0 0
HDAC2 0.021 0.01 -10000 0 -10000 0 0
AP-1 -0.47 0.46 0.48 6 -0.84 447 453
MAPK14 0.002 0.023 -10000 0 -10000 0 0
MAPK10 -0.094 0.22 -10000 0 -0.6 128 128
MAPK11 -0.003 0.038 -10000 0 -0.61 2 2
KRT5 -0.79 0.72 0.45 1 -1.4 457 458
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 -0.5 17 17
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.16 0.18 0.37 280 -10000 0 280
MAPK3 0 0.022 -10000 0 -10000 0 0
MAPK1 0.002 0.022 -10000 0 -10000 0 0
ICAM1 -0.2 0.25 0.61 2 -0.54 212 214
NFKB1 -0.041 0.1 0.27 2 -0.23 45 47
MAPK8 -0.2 0.22 0.32 4 -0.42 334 338
MAPK9 0.002 0.023 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.33 0.86 1 -0.69 248 249
BAX 0.016 0.063 -10000 0 -10000 0 0
POMC -0.17 0.29 -10000 0 -1.1 43 43
EP300 0.16 0.14 0.31 284 -10000 0 284
cortisol/GR alpha (dimer)/p53 0.23 0.26 0.53 301 -0.55 1 302
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.11 0.26 140 -10000 0 140
SGK1 0.2 0.2 0.5 12 -1.1 4 16
IL13 -0.27 0.28 0.51 4 -0.63 183 187
IL6 -0.46 0.53 0.64 1 -1.1 329 330
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.23 0.23 0.52 2 -0.54 156 158
IL2 -0.36 0.36 0.49 2 -0.71 350 352
CDK5 0.016 0.016 0.26 1 -10000 0 1
PRKACB 0.034 0.066 0.27 42 -0.6 3 45
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
IL8 -0.2 0.29 0.55 2 -0.64 163 165
CDK5R1/CDK5 0.016 0.038 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.022 0.16 0.42 2 -0.36 33 35
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.51 328 -0.52 1 329
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.16 0.16 0.36 208 -10000 0 208
NF kappa B1 p50/RelA/Cbp 0.068 0.19 0.43 44 -0.42 12 56
JUN (dimer) -0.27 0.29 0.37 6 -0.55 351 357
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 0.42 234 -0.32 1 235
NR4A1 -0.035 0.19 -10000 0 -0.58 88 88
TIF2/SUV420H1 0.024 0.046 -10000 0 -0.45 7 7
MAPKKK cascade -0.27 0.31 0.86 1 -0.65 247 248
cortisol/GR alpha (dimer)/Src-1 0.26 0.27 0.53 333 -0.55 1 334
PBX1 0.023 0.016 0.27 1 -10000 0 1
POU1F1 0.022 0.014 0.27 1 -10000 0 1
SELE -0.2 0.3 0.64 1 -0.66 169 170
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.16 0.36 205 -10000 0 205
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.26 0.51 328 -0.52 1 329
mol:cortisol 0.17 0.19 0.35 363 -0.25 3 366
MMP1 0.047 0.31 0.43 4 -0.92 65 69
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.1 0.13 0.32 224 -0.18 4 228
NFATC2 -0.011 0.22 0.51 8 -0.63 52 60
NFATC3 -0.048 0.13 -10000 0 -0.29 134 134
CD40LG -0.31 0.52 0.75 7 -1 246 253
ITCH -0.005 0.087 -10000 0 -0.27 79 79
CBLB -0.004 0.087 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.078 0.38 0.66 38 -1 52 90
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 -0.65 42 43
Jun/NFAT1-c-4/p21SNFT -0.18 0.44 0.72 6 -0.85 204 210
AP-1/NFAT1-c-4 -0.33 0.63 0.8 14 -1.2 245 259
IKZF1 -0.005 0.15 0.5 7 -0.5 39 46
T-helper 2 cell differentiation -0.069 0.26 0.5 2 -0.84 50 52
AP-1/NFAT1 -0.11 0.28 0.5 11 -0.49 224 235
CALM1 0.009 0.066 -10000 0 -10000 0 0
EGR2 -0.25 0.55 0.67 4 -1.3 139 143
EGR3 -0.35 0.64 0.7 3 -1.3 236 239
NFAT1/FOXP3 0.064 0.22 0.49 81 -0.49 46 127
EGR1 -0.18 0.3 -10000 0 -0.6 278 278
JUN 0.013 0.07 0.22 2 -0.61 8 10
EGR4 0.036 0.055 0.27 44 -10000 0 44
mol:Ca2+ -0.012 0.057 -10000 0 -0.19 1 1
GBP3 -0.013 0.17 0.39 2 -0.56 47 49
FOSL1 0.027 0.045 0.27 15 -0.6 2 17
NFAT1-c-4/MAF/IRF4 -0.2 0.46 0.65 7 -0.86 226 233
DGKA -0.007 0.15 0.59 1 -0.52 34 35
CREM 0.023 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.49 0.66 3 -0.94 247 250
CTLA4 0.049 0.21 0.46 86 -0.57 29 115
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 -0.84 229 234
FOS -0.17 0.29 0.21 2 -0.6 259 261
IFNG -0.043 0.27 0.54 11 -0.78 55 66
T cell activation -0.16 0.3 0.64 5 -0.68 143 148
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 0.64 220 -0.64 3 223
TNF -0.27 0.46 0.58 4 -0.9 253 257
FASLG -0.32 0.62 0.82 3 -1.2 247 250
TBX21 0.017 0.14 0.38 9 -0.6 33 42
BATF3 0.021 0.01 -10000 0 -10000 0 0
PRKCQ 0.007 0.12 0.29 10 -0.6 30 40
PTPN1 -0.006 0.15 0.42 4 -0.5 39 43
NFAT1-c-4/ICER1 -0.2 0.44 0.59 3 -0.84 230 233
GATA3 0.011 0.12 0.27 27 -0.6 27 54
T-helper 1 cell differentiation -0.041 0.26 0.54 11 -0.76 55 66
IL2RA -0.079 0.36 0.65 36 -0.94 56 92
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.007 0.15 0.35 2 -0.48 43 45
E2F1 0.1 0.11 0.27 263 -10000 0 263
PPARG -0.12 0.26 -10000 0 -0.6 186 186
SLC3A2 -0.008 0.15 0.37 1 -0.52 35 36
IRF4 -0.022 0.17 0.27 11 -0.6 65 76
PTGS2 -0.36 0.56 0.65 6 -1.1 274 280
CSF2 -0.3 0.5 0.7 9 -0.98 241 250
JunB/Fra1/NFAT1-c-4 -0.18 0.43 0.63 3 -0.82 219 222
IL4 -0.073 0.27 0.53 1 -0.9 48 49
IL5 -0.3 0.5 0.64 7 -0.97 247 254
IL2 -0.16 0.31 0.74 3 -0.69 139 142
IL3 -0.054 0.13 -10000 0 -0.8 18 18
RNF128 -0.047 0.22 0.29 5 -0.69 84 89
NFATC1 -0.16 0.34 0.64 3 -0.65 220 223
CDK4 0.12 0.24 0.61 64 -0.64 2 66
PTPRK -0.01 0.16 0.39 2 -0.54 42 44
IL8 -0.3 0.5 0.63 9 -0.99 242 251
POU2F1 0.021 0.012 0.27 1 -10000 0 1
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 -0.062 0.19 -10000 0 -0.35 240 240
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.25 0.35 1 -0.43 306 307
NT-4/5 (dimer)/p75(NTR) -0.26 0.31 -10000 0 -0.53 436 436
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.092 0.17 0.36 1 -0.34 225 226
IKBKG 0.025 0.002 -10000 0 -10000 0 0
BDNF -0.019 0.17 0.27 19 -0.6 64 83
MGDIs/NGR/p75(NTR)/LINGO1 -0.057 0.21 0.35 6 -0.37 238 244
FURIN 0.024 0.01 0.27 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.22 -10000 0 -0.42 267 267
LINGO1 0.076 0.1 0.27 177 -10000 0 177
Sortilin/TRAF6/NRIF 0.023 0.027 -10000 0 -0.59 1 1
proBDNF (dimer) -0.019 0.17 0.27 19 -0.6 64 83
NTRK1 0.026 0.045 0.27 21 -0.6 1 22
RTN4R 0.029 0.038 0.27 20 -10000 0 20
neuron apoptosis -0.092 0.21 0.35 8 -0.48 89 97
IRAK1 0.025 0.012 0.27 2 -10000 0 2
SHC1 -0.096 0.17 -10000 0 -0.4 186 186
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.07 0.19 -10000 0 -0.36 236 236
MAGEH1 0.025 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.081 0.21 -10000 0 -0.38 242 242
Mammalian IAPs/DIABLO 0.057 0.035 -10000 0 -0.36 2 2
proNGF (dimer) 0.015 0.086 0.27 7 -0.6 15 22
MAGED1 0.025 0.012 0.27 2 -10000 0 2
APP 0.024 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.22 0.3 -10000 0 -0.6 316 316
ZNF274 0.024 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.079 0.17 -10000 0 -0.34 228 228
NGF 0.015 0.087 0.27 7 -0.6 15 22
cell cycle arrest -0.085 0.17 0.3 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 -0.49 392 392
NCSTN 0.021 0.009 -10000 0 -10000 0 0
mol:GTP -0.084 0.2 -10000 0 -0.39 240 240
PSENEN 0.024 0.009 0.27 1 -10000 0 1
mol:ceramide -0.1 0.17 -10000 0 -0.36 237 237
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.052 0.11 -10000 0 -0.37 29 29
p75(NTR)/beta APP -0.11 0.22 -10000 0 -0.44 248 248
BEX1 -0.018 0.24 0.27 139 -0.6 109 248
mol:GDP -0.12 0.18 -10000 0 -0.39 242 242
NGF (dimer) -0.002 0.14 0.35 1 -0.36 104 105
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.041 0.2 0.35 5 -0.34 221 226
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.075 0.17 -10000 0 -0.34 240 240
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) -0.067 0.22 0.27 11 -0.6 124 135
TP53 -0.1 0.18 0.36 6 -0.35 255 261
PRDM4 -0.1 0.17 -10000 0 -0.36 236 236
BDNF (dimer) 0.017 0.21 0.34 16 -0.38 150 166
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 0.025 0.002 -10000 0 -10000 0 0
MAPK10 -0.15 0.21 0.33 3 -0.43 249 252
DIABLO 0.025 0.002 -10000 0 -10000 0 0
SMPD2 -0.1 0.17 -10000 0 -0.36 237 237
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.087 0.2 -10000 0 -0.4 240 240
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.17 0.27 -10000 0 -0.48 325 325
MAPK8 -0.11 0.19 0.3 8 -0.38 227 235
MAPK9 -0.11 0.19 0.3 6 -0.38 222 228
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.067 0.23 0.27 11 -0.6 124 135
NTF4 -0.22 0.3 -10000 0 -0.6 316 316
NDN 0.005 0.1 -10000 0 -0.6 24 24
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.056 0.18 -10000 0 -0.32 237 237
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.024 -10000 0 -0.36 1 1
RhoA-B-C/GTP -0.084 0.2 -10000 0 -0.39 240 240
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.079 0.21 -10000 0 -0.37 256 256
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.09 0.21 -10000 0 -0.39 258 258
PRKACB 0.034 0.066 0.27 42 -0.6 3 45
proBDNF (dimer)/p75 ECD 0.001 0.13 -10000 0 -0.44 66 66
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.18 0.28 13 -0.38 196 209
BAD -0.13 0.2 0.4 7 -0.4 242 249
RIPK2 0.02 0.018 0.27 3 -10000 0 3
NGFR -0.16 0.28 -10000 0 -0.6 238 238
CYCS -0.098 0.16 0.36 2 -0.35 232 234
ADAM17 0.024 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.06 0.17 -10000 0 -0.36 170 170
BCL2L11 -0.13 0.2 0.4 7 -0.4 241 248
BDNF (dimer)/p75(NTR) -0.14 0.25 -10000 0 -0.46 286 286
PI3K -0.071 0.19 -10000 0 -0.36 228 228
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.071 0.19 -10000 0 -0.36 235 235
NDNL2 0.024 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.11 0.22 -10000 0 -0.44 256 256
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.07 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 0.018 0.018 0.27 4 -10000 0 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.12 0.2 -10000 0 -0.4 267 267
SQSTM1 0.024 0.009 0.27 1 -10000 0 1
NGFRAP1 0.023 0.031 -10000 0 -0.6 2 2
CASP3 -0.12 0.19 0.4 6 -0.37 246 252
E2F1 0.1 0.11 0.27 263 -10000 0 263
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.009 0.12 -10000 0 -0.43 14 14
NGF (dimer)/TRKA 0.026 0.071 -10000 0 -0.42 16 16
MMP7 -0.041 0.2 0.27 24 -0.6 93 117
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.06 0.19 -10000 0 -0.35 231 231
MMP3 0.1 0.14 0.27 295 -0.6 9 304
APAF-1/Caspase 9 -0.098 0.12 -10000 0 -0.49 10 10
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 -0.074 0.13 -10000 0 -0.44 71 71
PTK2B 0.02 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.17 -10000 0 -0.77 29 29
EDN1 -0.077 0.17 -10000 0 -0.63 64 64
EDN3 -0.24 0.3 0.27 1 -0.6 341 342
EDN2 0.079 0.11 0.27 199 -0.6 4 203
HRAS/GDP -0.095 0.19 0.28 1 -0.48 111 112
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.061 0.14 -10000 0 -0.39 83 83
ADCY4 -0.13 0.2 0.29 3 -0.44 205 208
ADCY5 -0.22 0.25 -10000 0 -0.47 356 356
ADCY6 -0.12 0.19 0.29 3 -0.42 200 203
ADCY7 -0.12 0.19 0.29 3 -0.42 199 202
ADCY1 -0.12 0.2 0.28 1 -0.43 199 200
ADCY2 -0.14 0.23 0.3 7 -0.47 218 225
ADCY3 -0.12 0.19 0.28 2 -0.42 199 201
ADCY8 -0.1 0.18 0.28 3 -0.43 150 153
ADCY9 -0.12 0.18 0.28 1 -0.42 190 191
arachidonic acid secretion -0.17 0.27 0.3 2 -0.5 278 280
ETB receptor/Endothelin-1/Gq/GTP -0.048 0.15 -10000 0 -0.37 107 107
GNAO1 0.019 0.095 0.27 28 -0.6 15 43
HRAS 0.023 0.01 0.27 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP -0.06 0.13 -10000 0 -0.41 68 68
ETA receptor/Endothelin-1/Gs/GTP -0.13 0.2 -10000 0 -0.44 201 201
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.062 0.16 0.39 8 -0.44 70 78
EDNRB -0.018 0.16 -10000 0 -0.6 60 60
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.074 0.15 -10000 0 -0.47 75 75
CYSLTR1 -0.079 0.15 -10000 0 -0.48 71 71
SLC9A1 -0.048 0.099 -10000 0 -0.32 66 66
mol:GDP -0.1 0.2 0.31 3 -0.49 125 128
SLC9A3 -0.1 0.27 -10000 0 -0.64 134 134
RAF1 -0.14 0.23 0.32 1 -0.46 229 230
JUN -0.051 0.19 -10000 0 -0.78 33 33
JAK2 -0.073 0.13 -10000 0 -0.44 69 69
mol:IP3 -0.074 0.16 -10000 0 -0.44 90 90
ETA receptor/Endothelin-1 -0.085 0.16 0.34 5 -0.5 75 80
PLCB1 -0.012 0.14 -10000 0 -0.6 43 43
PLCB2 0.013 0.03 0.27 1 -0.6 1 2
ETA receptor/Endothelin-3 -0.2 0.22 -10000 0 -0.46 346 346
FOS -0.31 0.45 -10000 0 -0.94 276 276
Gai/GDP -0.1 0.3 -10000 0 -0.76 128 128
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 0.28 1 -0.53 104 105
BCAR1 0.022 0.009 -10000 0 -10000 0 0
PRKCB1 -0.076 0.16 -10000 0 -0.42 102 102
GNAQ 0.012 0.036 -10000 0 -0.61 2 2
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNAL -0.11 0.25 -10000 0 -0.6 174 174
Gs family/GDP -0.15 0.24 0.27 1 -0.49 220 221
ETA receptor/Endothelin-1/Gq/GTP -0.048 0.12 -10000 0 -0.39 51 51
MAPK14 -0.063 0.15 -10000 0 -0.42 91 91
TRPC6 -0.052 0.19 -10000 0 -0.82 29 29
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 -0.063 0.16 -10000 0 -0.42 105 105
ETB receptor/Endothelin-2 0.034 0.15 0.25 14 -0.42 64 78
ETB receptor/Endothelin-3 -0.2 0.25 -10000 0 -0.46 381 381
ETB receptor/Endothelin-1 -0.074 0.18 -10000 0 -0.49 116 116
MAPK3 -0.26 0.39 -10000 0 -0.79 279 279
MAPK1 -0.27 0.4 0.31 1 -0.81 281 282
Rac1/GDP -0.095 0.19 0.28 1 -0.48 110 111
cAMP biosynthetic process -0.16 0.22 0.52 1 -0.49 196 197
MAPK8 -0.055 0.19 -10000 0 -0.69 45 45
SRC 0.024 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.066 0.17 -10000 0 -0.47 87 87
p130Cas/CRK/Src/PYK2 -0.097 0.21 0.49 1 -0.56 95 96
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.094 0.19 0.28 1 -0.47 111 112
COL1A2 -0.083 0.19 0.4 7 -0.48 108 115
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.026 0.096 0.26 11 -0.38 6 17
mol:DAG -0.074 0.16 -10000 0 -0.44 91 91
MAP2K2 -0.2 0.3 0.32 3 -0.59 281 284
MAP2K1 -0.2 0.3 0.32 2 -0.58 280 282
EDNRA -0.034 0.058 -10000 0 -0.25 9 9
positive regulation of muscle contraction -0.064 0.12 -10000 0 -0.39 67 67
Gq family/GDP -0.059 0.19 -10000 0 -0.48 78 78
HRAS/GTP -0.1 0.2 0.29 2 -0.47 126 128
PRKCH -0.075 0.16 -10000 0 -0.43 91 91
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.07 0.18 0.29 5 -0.46 99 104
PRKCB -0.072 0.17 0.24 1 -0.45 91 92
PRKCE -0.079 0.16 -10000 0 -0.43 97 97
PRKCD -0.076 0.16 -10000 0 -0.43 91 91
PRKCG -0.077 0.16 0.27 1 -0.44 90 91
regulation of vascular smooth muscle contraction -0.37 0.53 -10000 0 -1.1 274 274
PRKCQ -0.084 0.18 -10000 0 -0.48 102 102
PLA2G4A -0.19 0.3 0.31 2 -0.55 279 281
GNA14 0.015 0.068 0.26 19 -0.6 6 25
GNA15 0.022 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 -0.06 0.13 -10000 0 -0.41 68 68
MMP1 0.18 0.13 0.41 67 -10000 0 67
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.12 0.36 -10000 0 -0.87 147 147
NCK1/PAK1/Dok-R -0.078 0.15 -10000 0 -0.41 147 147
NCK1/Dok-R -0.14 0.42 -10000 0 -1 147 147
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.035 0.092 0.24 134 -10000 0 134
RELA 0.024 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.035 0.11 0.27 133 -10000 0 133
TNIP2 0.024 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.41 -10000 0 -0.98 147 147
FN1 0.13 0.12 0.27 367 -10000 0 367
PLD2 -0.16 0.44 -10000 0 -1.1 146 146
PTPN11 0.025 0.002 -10000 0 -10000 0 0
GRB14 0.014 0.19 0.27 117 -0.6 59 176
ELK1 -0.14 0.39 -10000 0 -0.96 147 147
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PAK1 0.023 0.017 0.27 3 -10000 0 3
Tie2/Ang1/alpha5/beta1 Integrin -0.075 0.45 -10000 0 -1 147 147
CDKN1A -0.089 0.24 -10000 0 -0.6 126 126
ITGA5 0.025 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.43 -10000 0 -1 147 147
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.083 0.27 0.38 1 -0.64 147 148
PLG -0.17 0.43 -10000 0 -1.1 147 147
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.34 -10000 0 -0.83 147 147
GRB2 0.023 0.011 0.27 1 -10000 0 1
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
ANGPT2 -0.13 0.27 -10000 0 -0.68 116 116
BMX -0.29 0.48 -10000 0 -1.3 147 147
ANGPT1 -0.19 0.46 -10000 0 -1.2 134 134
tube development -0.1 0.27 -10000 0 -0.66 142 142
ANGPT4 -0.18 0.28 -10000 0 -0.6 254 254
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 -0.6 311 311
STAT5A (dimer) -0.12 0.31 -10000 0 -0.76 140 140
mol:L-citrulline -0.083 0.27 0.38 1 -0.64 147 148
AGTR1 -0.086 0.26 0.27 52 -0.6 167 219
MAPK14 -0.16 0.44 -10000 0 -1.1 148 148
Tie2/SHP2 -0.075 0.29 -10000 0 -1.1 56 56
TEK -0.084 0.32 -10000 0 -1.2 56 56
RPS6KB1 -0.1 0.35 -10000 0 -0.83 147 147
Angiotensin II/AT1 -0.064 0.2 0.18 52 -0.44 170 222
Tie2/Ang1/GRB2 -0.16 0.45 -10000 0 -1.1 147 147
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 -1.1 147 147
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 -1 147 147
Tie2/Ang1/ABIN2 -0.16 0.46 -10000 0 -1.1 147 147
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 -0.9 140 140
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 -0.76 139 139
DOK2 0.019 0.024 -10000 0 -0.6 1 1
negative regulation of cell cycle -0.079 0.22 -10000 0 -0.55 127 127
ETS1 -0.013 0.1 -10000 0 -0.27 108 108
PXN -0.066 0.3 0.43 2 -0.67 146 148
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.098 0.3 -10000 0 -0.73 147 147
RAC1 0.024 0.004 -10000 0 -10000 0 0
TNF -0.017 0.13 0.27 15 -0.28 133 148
MAPKKK cascade -0.16 0.41 -10000 0 -1 146 146
RASA1 0.024 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.16 0.44 -10000 0 -1.1 147 147
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.072 0.24 0.37 2 -0.57 147 149
mol:Phosphatidic acid -0.16 0.41 -10000 0 -1 146 146
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.083 0.27 0.38 1 -0.64 147 148
Rac1/GTP -0.1 0.32 -10000 0 -0.78 147 147
MMP2 -0.17 0.44 -10000 0 -1.1 147 147
Ephrin B reverse signaling

Figure 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
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.27 15 -10000 0 15
EFNB1 -0.006 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 -0.32 345 345
Ephrin B2/EPHB1-2 -0.12 0.2 -10000 0 -0.35 353 353
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.31 346 346
Ephrin B1/EPHB1-2/Tiam1 -0.11 0.19 -10000 0 -0.34 350 350
DNM1 0.021 0.049 0.28 1 -0.6 5 6
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.024 0.12 -10000 0 -0.56 37 37
YES1 -0.025 0.17 -10000 0 -0.77 41 41
Ephrin B1/EPHB1-2/NCK2 -0.12 0.2 -10000 0 -0.34 352 352
PI3K 0.007 0.13 -10000 0 -0.54 40 40
mol:GDP -0.11 0.19 -10000 0 -0.33 350 350
ITGA2B 0.032 0.063 0.27 36 -0.6 3 39
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.027 0.17 -10000 0 -0.76 41 41
MAP3K7 -0.025 0.13 -10000 0 -0.58 39 39
FGR -0.024 0.17 -10000 0 -0.77 40 40
TIAM1 0.025 0.017 0.27 4 -10000 0 4
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.005 0.12 0.26 1 -0.45 52 53
LYN -0.023 0.17 -10000 0 -0.75 41 41
Ephrin B1/EPHB1-2/Src Family Kinases -0.028 0.16 -10000 0 -0.71 41 41
Ephrin B1/EPHB1-2 -0.025 0.14 -10000 0 -0.63 38 38
SRC -0.022 0.17 -10000 0 -0.75 41 41
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
EPHB1 -0.24 0.31 0.28 1 -0.6 355 356
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.033 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 0.12 0.19 0.33 352 -10000 0 352
MAPK8 -0.025 0.12 -10000 0 -0.52 40 40
Ephrin B1/EPHB1-2/RGS3 -0.11 0.2 -10000 0 -0.34 352 352
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 0.12 0.19 0.33 352 -10000 0 352
chemotaxis 0.11 0.19 0.33 352 -10000 0 352
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.1 0.18 -10000 0 -0.31 345 345
angiogenesis -0.026 0.14 -10000 0 -0.62 39 39
LCK -0.023 0.17 -10000 0 -0.77 40 40
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 0.011 0.089 -10000 0 -0.6 17 17
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
NUDC 0.024 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.21 0.21 -10000 0 -0.38 492 492
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.21 0.17 0.25 1 -0.35 490 491
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.037 0.057 0.27 48 -10000 0 48
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.025 0.07 0.27 22 -0.6 7 29
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.051 0.052 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.025 0.002 -10000 0 -10000 0 0
CDK5R1 0.029 0.037 0.27 19 -10000 0 19
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.085 0.27 116 -10000 0 116
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.22 0.22 0.35 2 -0.39 488 490
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 0.24 1 -0.32 394 395
RELN -0.35 0.31 0.27 3 -0.6 499 502
PAFAH/LIS1 0.024 0.049 0.32 2 -0.39 7 9
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.13 0.13 -10000 0 -0.3 14 14
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.16 0.17 -10000 0 -0.31 422 422
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.17 0.15 0.31 3 -0.31 343 346
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 0.065 0.27 64 -10000 0 64
PAFAH1B2 0.022 0.008 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.014 0.041 -10000 0 -0.36 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.14 0.16 0.33 2 -0.34 47 49
LRP8 0.052 0.077 0.27 95 -10000 0 95
NDEL1/Katanin 60 -0.15 0.16 0.33 2 -0.34 53 55
P39/CDK5 -0.18 0.16 0.32 4 -0.32 359 363
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.2 0.16 0.24 1 -0.33 480 481
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.18 0.2 0.34 1 -0.34 484 485
RELN/VLDLR -0.19 0.21 -10000 0 -0.36 490 490
CDC42 0.01 0.005 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.6 0.77 11 -1.2 160 171
STAT6 (cleaved dimer) -0.31 0.58 -10000 0 -1.2 195 195
IGHG1 -0.032 0.26 0.51 43 -0.56 6 49
IGHG3 -0.24 0.57 0.67 11 -1.1 187 198
AKT1 -0.093 0.34 0.59 13 -0.79 59 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.054 0.29 0.57 13 -0.8 37 50
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.093 0.35 0.6 15 -0.82 55 70
THY1 -0.25 0.6 0.79 12 -1.2 161 173
MYB 0.013 0.082 0.27 2 -0.6 14 16
HMGA1 0.031 0.04 0.27 23 -10000 0 23
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.12 0.41 0.65 37 -0.74 131 168
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.085 0.35 0.6 16 -0.82 48 64
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 0.7 7 -1.2 184 191
SOCS1 -0.15 0.4 0.64 11 -0.76 128 139
SOCS3 -0.1 0.35 0.64 10 -0.81 58 68
FCER2 -0.41 0.74 0.78 16 -1.3 276 292
PARP14 0.016 0.033 0.27 2 -10000 0 2
CCL17 -0.23 0.62 0.88 24 -1.2 151 175
GRB2 0.023 0.011 0.27 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.048 0.29 0.51 28 -0.72 33 61
T cell proliferation -0.27 0.61 0.74 7 -1.2 174 181
IL4R/JAK1 -0.26 0.59 0.74 1 -1.2 174 175
EGR2 -0.37 0.74 0.8 13 -1.4 212 225
JAK2 0.009 0.076 -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 7 -1.1 10 17
CCL26 -0.25 0.61 0.78 12 -1.2 161 173
IL4R -0.25 0.66 0.86 23 -1.3 169 192
PTPN6 0.015 0.036 0.22 2 -10000 0 2
IL13RA2 -0.25 0.6 0.79 10 -1.2 150 160
IL13RA1 0.009 0.077 -10000 0 -10000 0 0
IRF4 -0.14 0.5 0.62 12 -1.4 90 102
ARG1 -0.008 0.22 0.62 2 -10000 0 2
CBL -0.12 0.38 0.59 24 -0.7 127 151
GTF3A 0.056 0.052 0.27 1 -10000 0 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.021 0.11 0.29 21 -10000 0 21
IRF4/BCL6 -0.12 0.45 0.58 1 -1.3 90 91
CD40LG -0.012 0.14 0.33 13 -0.62 39 52
MAPK14 -0.12 0.38 0.59 24 -0.73 109 133
mitosis -0.085 0.33 0.58 14 -0.73 59 73
STAT6 -0.28 0.74 0.96 30 -1.4 183 213
SPI1 0.027 0.018 0.27 4 -10000 0 4
RPS6KB1 -0.066 0.32 0.57 19 -0.72 53 72
STAT6 (dimer) -0.28 0.74 0.96 30 -1.4 183 213
STAT6 (dimer)/PARP14 -0.31 0.66 0.76 5 -1.3 196 201
mast cell activation 0.001 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.1 0.36 0.59 17 -0.76 80 97
FRAP1 -0.093 0.34 0.59 13 -0.79 59 72
LTA -0.23 0.62 0.87 24 -1.2 158 182
FES 0.022 0.038 -10000 0 -0.6 3 3
T-helper 1 cell differentiation 0.27 0.71 1.3 184 -0.95 30 214
CCL11 -0.18 0.59 0.74 28 -1.1 157 185
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.081 0.34 0.58 20 -0.78 57 77
IL2RG 0.024 0.073 0.28 32 -0.6 5 37
IL10 -0.22 0.6 0.83 12 -1.2 139 151
IRS1 0.002 0.12 -10000 0 -0.6 29 29
IRS2 0.001 0.12 -10000 0 -0.6 29 29
IL4 -0.018 0.27 0.62 13 -1.1 19 32
IL5 -0.25 0.6 0.77 11 -1.2 171 182
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.51 0.81 31 -0.9 159 190
COL1A1 -0.005 0.36 0.64 42 -0.95 41 83
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.27 0.61 -10000 0 -1.3 150 150
IL2R gamma/JAK3 0.036 0.071 0.35 19 -0.39 5 24
TFF3 -0.3 0.71 0.86 15 -1.3 199 214
ALOX15 -0.32 0.7 0.8 15 -1.3 210 225
MYBL1 0.042 0.07 0.27 73 -10000 0 73
T-helper 2 cell differentiation -0.2 0.52 0.69 26 -0.96 179 205
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 0.57 17 -0.75 65 82
mol:PI-3-4-5-P3 -0.092 0.34 0.6 13 -0.79 59 72
PI3K -0.1 0.36 0.62 11 -0.85 59 70
DOK2 0.019 0.024 -10000 0 -0.6 1 1
ETS1 0.005 0.048 -10000 0 -0.56 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.038 0.27 0.49 34 -0.66 28 62
ITGB3 -0.25 0.62 0.78 10 -1.2 160 170
PIGR -0.71 0.78 0.8 17 -1.3 478 495
IGHE -0.015 0.087 0.18 28 -0.21 30 58
MAPKKK cascade -0.036 0.27 0.49 36 -0.64 28 64
BCL6 0.025 0.034 -10000 0 -0.59 2 2
OPRM1 -0.25 0.6 0.81 8 -1.2 155 163
RETNLB -0.25 0.6 0.78 6 -1.2 145 151
SELP -0.38 0.77 0.8 15 -1.4 239 254
AICDA -0.24 0.57 0.77 8 -1.2 155 163
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 -0.005 0.13 -10000 0 -0.6 37 37
GNB1/GNG2 -0.091 0.22 -10000 0 -0.48 134 134
mol:DAG -0.091 0.19 0.24 1 -0.45 126 127
PLCG1 -0.094 0.2 0.24 1 -0.47 126 127
YES1 -0.11 0.2 0.21 1 -0.39 225 226
FZD3 0.018 0.039 -10000 0 -0.6 3 3
FZD6 0.015 0.049 -10000 0 -0.6 5 5
G protein -0.077 0.21 0.3 2 -0.48 122 124
MAP3K7 -0.082 0.16 0.38 1 -0.42 93 94
mol:Ca2+ -0.088 0.19 0.24 1 -0.44 126 127
mol:IP3 -0.091 0.19 0.24 1 -0.45 126 127
NLK -0.013 0.14 -10000 0 -0.84 21 21
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.084 0.18 0.39 1 -0.45 101 102
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.22 0.23 1 -0.4 248 249
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
GNAS -0.1 0.2 0.21 1 -0.4 216 217
GO:0007205 -0.094 0.19 0.23 1 -0.45 125 126
WNT6 -0.1 0.26 0.27 20 -0.6 172 192
WNT4 0.015 0.095 0.27 15 -0.6 17 32
NFAT1/CK1 alpha -0.096 0.21 -10000 0 -0.49 125 125
GNG2 0.019 0.053 -10000 0 -0.6 6 6
WNT5A 0.02 0.07 0.27 9 -0.6 9 18
WNT11 -0.1 0.25 0.27 9 -0.6 167 176
CDC42 -0.096 0.2 -10000 0 -0.49 116 116
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 -0.4 248 249
FZD6 0.015 0.049 -10000 0 -0.6 5 5
WNT6 -0.1 0.26 0.27 20 -0.6 172 192
WNT4 0.015 0.095 0.27 15 -0.6 17 32
FZD3 0.018 0.039 -10000 0 -0.6 3 3
WNT5A 0.02 0.07 0.27 9 -0.6 9 18
WNT11 -0.1 0.25 0.27 9 -0.6 167 176
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 -0.04 0.5 0.82 37 -1.1 66 103
IL23A -0.051 0.5 0.89 24 -1.1 66 90
NF kappa B1 p50/RelA/I kappa B alpha -0.081 0.46 0.78 5 -0.88 137 142
positive regulation of T cell mediated cytotoxicity -0.044 0.56 0.88 54 -0.96 139 193
ITGA3 -0.035 0.49 0.84 29 -1.1 65 94
IL17F -0.02 0.37 0.62 52 -0.6 130 182
IL12B 0.08 0.15 0.37 151 -10000 0 151
STAT1 (dimer) -0.058 0.52 0.77 38 -0.93 139 177
CD4 -0.035 0.5 0.84 36 -1 67 103
IL23 -0.036 0.5 0.85 34 -1.1 62 96
IL23R 0.048 0.2 0.62 16 -0.96 11 27
IL1B -0.052 0.51 0.86 31 -1.1 67 98
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0 0.5 0.88 48 -1 60 108
TYK2 0.025 0.061 0.22 3 -10000 0 3
STAT4 0 0.12 0.27 1 -0.6 32 33
STAT3 0.024 0.006 -10000 0 -10000 0 0
IL18RAP 0.005 0.12 0.28 4 -0.6 31 35
IL12RB1 0.032 0.09 0.4 25 -0.64 1 26
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.036 0.089 0.33 28 -0.49 1 29
IL23R/JAK2 0.06 0.22 0.57 24 -0.92 10 34
positive regulation of chronic inflammatory response -0.044 0.56 0.88 54 -0.96 139 193
natural killer cell activation -0.004 0.016 -10000 0 -0.053 31 31
JAK2 0.037 0.086 0.28 24 -10000 0 24
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 -0.03 0.48 0.83 37 -1 62 99
ALOX12B -0.036 0.49 0.85 33 -1 66 99
CXCL1 -0.22 0.72 0.85 39 -1.2 235 274
T cell proliferation -0.044 0.56 0.88 54 -0.96 139 193
NFKBIA 0.026 0.01 -10000 0 -10000 0 0
IL17A 0.011 0.32 0.56 70 -0.53 63 133
PI3K -0.077 0.48 0.7 21 -0.89 138 159
IFNG 0.027 0.072 0.18 109 -0.12 8 117
STAT3 (dimer) -0.079 0.46 0.76 7 -0.86 138 145
IL18R1 0.019 0.072 -10000 0 -0.6 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 0.024 0.36 0.67 62 -0.64 50 112
IL18/IL18R 0.041 0.11 0.32 7 -0.39 40 47
macrophage activation -0.001 0.03 0.059 73 -0.044 52 125
TNF -0.051 0.51 0.87 31 -1.1 69 100
STAT3/STAT4 -0.076 0.5 0.7 21 -0.92 142 163
STAT4 (dimer) -0.071 0.53 0.76 34 -0.96 142 176
IL18 0.031 0.04 0.27 21 -10000 0 21
IL19 0.005 0.5 0.85 52 -1 61 113
STAT5A (dimer) -0.063 0.51 0.75 34 -0.93 140 174
STAT1 0.03 0.035 0.27 18 -10000 0 18
SOCS3 0.02 0.044 -10000 0 -0.6 4 4
CXCL9 -0.009 0.53 0.87 58 -1.1 64 122
MPO -0.066 0.56 0.85 35 -1.2 94 129
positive regulation of humoral immune response -0.044 0.56 0.88 54 -0.96 139 193
IL23/IL23R/JAK2/TYK2 -0.053 0.58 0.89 53 -1 139 192
IL6 -0.33 0.76 0.83 27 -1.2 320 347
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
IL2 0.023 0.042 0.32 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.016 -10000 0 -0.053 31 31
CD3E -0.049 0.52 0.86 41 -1.1 72 113
keratinocyte proliferation -0.044 0.56 0.88 54 -0.96 139 193
NOS2 -0.035 0.5 0.83 37 -1.1 64 101
IGF1 pathway

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.071 0.16 -10000 0 -0.36 183 183
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.024 0.01 0.27 1 -10000 0 1
IRS1/Crk -0.065 0.17 -10000 0 -0.36 187 187
IGF-1R heterotetramer/IGF1/PTP1B -0.047 0.18 -10000 0 -0.39 163 163
AKT1 -0.069 0.14 0.25 2 -0.32 148 150
BAD -0.067 0.13 0.24 2 -0.31 130 132
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.071 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 -0.51 32 32
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.035 0.17 -10000 0 -0.34 171 171
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.065 0.18 -10000 0 -0.37 197 197
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.064 0.13 0.25 2 -0.33 127 129
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.031 0.13 0.31 8 -0.41 28 36
PXN 0.025 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
HRAS/GTP -0.042 0.14 -10000 0 -0.33 123 123
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.013 0.14 -10000 0 -0.32 119 119
IGF-1R heterotetramer -0.011 0.1 0.26 1 -0.67 14 15
IGF-1R heterotetramer/IGF1/IRS/Nck -0.048 0.18 -10000 0 -0.36 184 184
Crk/p130 Cas/Paxillin -0.04 0.16 -10000 0 -0.33 177 177
IGF1R -0.011 0.1 0.26 1 -0.67 14 15
IGF1 -0.12 0.27 -10000 0 -0.62 178 178
IRS2/Crk -0.073 0.18 -10000 0 -0.36 197 197
PI3K -0.035 0.17 -10000 0 -0.34 177 177
apoptosis 0.043 0.11 0.39 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 -0.045 0.11 0.28 4 -0.42 21 25
PRKCZ -0.069 0.14 0.25 2 -0.32 148 150
Crk/p130 Cas/Paxillin/FAK1 -0.028 0.11 -10000 0 -0.41 24 24
PTPN1 0.025 0.022 0.27 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.085 0.19 -10000 0 -0.42 187 187
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.026 0.15 -10000 0 -0.34 138 138
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.057 0.17 -10000 0 -0.36 184 184
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.071 0.16 -10000 0 -0.36 187 187
IRS1 -0.075 0.18 -10000 0 -0.37 194 194
IRS2 -0.082 0.18 -10000 0 -0.38 197 197
IGF-1R heterotetramer/IGF1 -0.082 0.22 -10000 0 -0.47 189 189
GRB2 0.023 0.011 0.27 1 -10000 0 1
PDPK1 -0.071 0.14 0.28 1 -0.34 154 155
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 -0.6 281 281
EPHA2 0.02 0.049 -10000 0 -0.6 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.27 -10000 0 -0.48 401 401
ARRB2 -0.045 0.13 -10000 0 -0.38 114 114
mol:GTP 0.01 0.053 0.16 14 -0.22 17 31
ARRB1 0.021 0.031 -10000 0 -0.6 2 2
FBXO8 0.024 0.005 -10000 0 -10000 0 0
TSHR 0 0.12 0.27 3 -0.6 32 35
EGF -0.091 0.24 0.27 2 -0.6 153 155
somatostatin receptor activity 0 0 0.001 1 -0.001 190 191
ARAP2 0.021 0.044 -10000 0 -0.6 4 4
mol:GDP -0.12 0.17 -10000 0 -0.34 222 222
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 134 134
ITGA2B 0.032 0.063 0.27 36 -0.6 3 39
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 0.033 0.27 2 -0.6 2 4
KIF13B 0.019 0.032 -10000 0 -0.6 2 2
HGF/MET -0.07 0.21 -10000 0 -0.47 174 174
PXN 0.025 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 -10000 0 -0.3 218 218
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.24 -10000 0 -0.43 385 385
ADRB2 -0.12 0.26 -10000 0 -0.6 193 193
receptor agonist activity 0 0 0 1 0 201 202
actin filament binding 0 0 0 2 -0.001 196 198
SRC 0.024 0.005 -10000 0 -10000 0 0
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
GNAQ 0.022 0.031 -10000 0 -0.6 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 109 110
ARF6/GDP -0.042 0.16 0.25 2 -0.46 73 75
ARF6/GDP/GULP/ACAP1 -0.11 0.2 -10000 0 -0.42 175 175
alphaIIb/beta3 Integrin/paxillin/GIT1 0.055 0.068 -10000 0 -0.35 16 16
ACAP1 0.024 0.067 0.27 22 -0.6 6 28
ACAP2 0.024 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.06 0.18 -10000 0 -0.51 114 114
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 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 0 161 162
endosomal lumen acidification 0 0 0.001 5 0 182 187
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.013 0.15 -10000 0 -0.6 50 50
GNAQ/ARNO 0.017 0.1 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 131 131
MET -0.079 0.23 -10000 0 -0.6 136 136
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GIT1 0.023 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 159 160
GNA11 0.024 0.005 -10000 0 -10000 0 0
LHCGR -0.074 0.21 -10000 0 -0.6 114 114
AGTR1 -0.087 0.26 0.27 52 -0.6 167 219
desensitization of G-protein coupled receptor protein signaling pathway -0.06 0.18 -10000 0 -0.51 114 114
IPCEF1/ARNO -0.14 0.21 -10000 0 -0.62 55 55
alphaIIb/beta3 Integrin 0.033 0.076 -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 0.34 4 -0.36 77 81
SMAD6-7/SMURF1 0.046 0.016 -10000 0 -10000 0 0
NOG 0.012 0.097 0.27 14 -0.6 18 32
SMAD9 -0.082 0.25 -10000 0 -0.64 122 122
SMAD4 0.024 0.005 -10000 0 -10000 0 0
SMAD5 -0.03 0.15 -10000 0 -0.43 64 64
BMP7/USAG1 -0.21 0.26 -10000 0 -0.45 415 415
SMAD5/SKI -0.024 0.16 -10000 0 -0.42 69 69
SMAD1 0.013 0.061 -10000 0 -0.41 5 5
BMP2 -0.083 0.24 0.27 1 -0.6 142 143
SMAD1/SMAD1/SMAD4 0.018 0.072 -10000 0 -0.42 8 8
BMPR1A 0.024 0.004 -10000 0 -10000 0 0
BMPR1B 0.11 0.16 0.27 346 -0.6 17 363
BMPR1A-1B/BAMBI 0.087 0.13 0.35 9 -0.35 41 50
AHSG 0.02 0.022 0.27 6 -10000 0 6
CER1 0.019 0.013 0.27 2 -10000 0 2
BMP2-4/CER1 -0.053 0.19 -10000 0 -0.41 174 174
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.044 0.17 -10000 0 -0.4 109 109
BMP2-4 (homodimer) -0.074 0.21 0.2 1 -0.46 181 182
RGMB 0.023 0.022 -10000 0 -0.6 1 1
BMP6/BMPR2/BMPR1A-1B 0.07 0.15 -10000 0 -0.33 79 79
RGMA -0.058 0.21 -10000 0 -0.6 108 108
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.043 0.17 0.24 1 -0.43 101 102
BMP2-4/USAG1 -0.24 0.28 -10000 0 -0.46 468 468
SMAD6/SMURF1/SMAD5 -0.025 0.16 -10000 0 -0.43 70 70
SOSTDC1 -0.28 0.31 0.27 2 -0.6 396 398
BMP7/BMPR2/BMPR1A-1B 0.074 0.15 0.31 6 -0.34 64 70
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.023 0.17 0.27 1 -0.6 63 64
HFE2 0.021 0.022 0.27 6 -10000 0 6
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.051 0.21 -10000 0 -0.41 183 183
SMAD5/SMAD5/SMAD4 -0.025 0.16 -10000 0 -0.43 70 70
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.03 0.16 -10000 0 -0.39 96 96
BMP7 (homodimer) -0.01 0.16 0.27 25 -0.6 52 77
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.006 0.13 -10000 0 -0.43 68 68
SMAD1/SKI 0.019 0.078 -10000 0 -0.44 9 9
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 -0.4 181 182
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.043 0.1 0.27 92 -0.6 10 102
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.017 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.092 0.11 -10000 0 -0.45 17 17
CHRDL1 -0.4 0.29 -10000 0 -0.6 568 568
ENDOFIN/SMAD1 0.019 0.08 -10000 0 -0.44 10 10
SMAD6-7/SMURF1/SMAD1 0.035 0.085 -10000 0 -0.44 9 9
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.013 0.12 0.27 29 -0.6 26 55
SMURF2 0.022 0.008 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.28 -10000 0 -0.48 585 585
BMP2-4/GREM1 -0.04 0.21 -10000 0 -0.42 178 178
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.075 0.25 -10000 0 -0.62 125 125
SMAD1/SMAD6 0.018 0.081 -10000 0 -0.45 10 10
TAK1/SMAD6 0.034 0.01 -10000 0 -10000 0 0
BMP7 -0.01 0.16 0.27 25 -0.6 52 77
BMP6 -0.023 0.17 0.27 1 -0.6 63 64
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.045 0.17 -10000 0 -0.44 104 104
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.076 -10000 0 -0.43 10 10
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.007 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.053 0.2 0.24 1 -0.49 107 108
CHRD 0.025 0.097 0.27 39 -0.6 14 53
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.059 0.19 -10000 0 -0.4 161 161
BMP4 -0.01 0.14 0.27 1 -0.6 46 47
FST 0.005 0.11 0.27 3 -0.6 26 29
BMP2-4/NOG -0.056 0.2 -10000 0 -0.41 182 182
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.077 0.14 0.34 2 -0.32 64 66
ErbB2/ErbB3 signaling events

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
USP8 -0.009 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.02 0.15 0.29 2 -0.3 48 50
NFATC4 -0.066 0.12 0.27 4 -0.27 67 71
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.071 0.16 -10000 0 -0.32 185 185
JUN -0.008 0.1 0.24 26 -0.48 2 28
HRAS 0.025 0.01 0.27 1 -10000 0 1
DOCK7 -0.082 0.14 0.28 2 -0.31 182 184
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.055 0.16 -10000 0 -0.35 153 153
AKT1 -0.004 0.008 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.075 0.12 0.22 6 -0.28 108 114
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.075 0.17 -10000 0 -0.34 185 185
RAF1 -0.015 0.15 0.36 10 -0.3 42 52
ErbB2/ErbB3/neuregulin 2 -0.17 0.19 -10000 0 -0.37 364 364
STAT3 -0.003 0.16 -10000 0 -0.86 29 29
cell migration -0.059 0.1 0.25 10 -0.26 68 78
mol:PI-3-4-5-P3 -0.002 0.003 -10000 0 -10000 0 0
cell proliferation -0.041 0.26 0.46 10 -0.52 87 97
FOS -0.11 0.3 0.33 50 -0.5 269 319
NRAS 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.071 0.16 -10000 0 -0.32 185 185
MAPK3 -0.012 0.21 0.43 10 -0.55 22 32
MAPK1 -0.023 0.23 0.44 10 -0.49 67 77
JAK2 -0.079 0.14 0.26 1 -0.31 182 183
NF2 -0.003 0.066 -10000 0 -0.69 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.14 0.23 3 -0.3 154 157
NRG1 -0.14 0.28 0.26 3 -0.6 220 223
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
MAPK8 -0.079 0.15 0.25 2 -0.3 183 185
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 -0.16 6 6
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 -0.24 169 169
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.017 -10000 0 -10000 0 0
CHRNA1 0.025 0.19 0.37 56 -0.41 18 74
myelination -0.062 0.12 0.33 9 -0.26 66 75
PPP3CB -0.076 0.13 0.27 2 -0.29 179 181
KRAS 0.024 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.27 118 118
NRG2 -0.31 0.31 -10000 0 -0.6 438 438
mol:GDP -0.053 0.13 0.23 3 -0.3 154 157
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.013 0.15 0.37 10 -0.31 42 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 -0.31 184 186
MAP2K1 -0.049 0.24 0.44 6 -0.54 64 70
heart morphogenesis -0.071 0.16 -10000 0 -0.32 185 185
RAS family/GDP -0.021 0.14 0.3 1 -0.29 47 48
GRB2 0.024 0.011 0.26 1 -10000 0 1
PRKACA -0.004 0.076 -10000 0 -0.68 10 10
CHRNE 0.005 0.028 0.14 2 -0.22 2 4
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.004 0.008 -10000 0 -10000 0 0
nervous system development -0.071 0.16 -10000 0 -0.32 185 185
CDC42 0.024 0.005 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.002 0.005 -10000 0 -10000 0 0
GNB1/GNG2 -0.002 0.13 -10000 0 -0.36 95 95
regulation of S phase of mitotic cell cycle -0.017 0.097 -10000 0 -0.3 82 82
GNAO1 0.018 0.095 0.27 28 -0.6 15 43
HRAS 0.023 0.01 0.27 1 -10000 0 1
SHBG/T-DHT 0.015 0.007 0.16 1 -10000 0 1
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.069 0.12 -10000 0 -0.36 81 81
T-DHT/AR -0.035 0.14 0.18 1 -0.45 91 92
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 265 265
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 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 0.27 2 -0.44 250 252
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FOS -0.26 0.39 -10000 0 -0.82 269 269
mol:Ca2+ -0.012 0.028 -10000 0 -0.074 107 107
MAPK3 -0.1 0.17 0.26 3 -0.42 102 105
MAPK1 -0.083 0.15 -10000 0 -0.38 91 91
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 264 264
cAMP biosynthetic process 0.003 0.021 -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 -0.004 264 264
HRAS/GTP -0.026 0.12 -10000 0 -0.35 88 88
actin cytoskeleton reorganization 0.033 0.013 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 264 264
PI3K 0.031 0.01 -10000 0 -10000 0 0
apoptosis 0.14 0.22 0.44 270 -10000 0 270
T-DHT/AR/PELP1 -0.019 0.13 -10000 0 -0.39 90 90
HRAS/GDP -0.043 0.15 -10000 0 -0.46 90 90
CREB1 -0.15 0.24 -10000 0 -0.47 270 270
RAC1-CDC42/GTP 0.041 0.017 -10000 0 -10000 0 0
AR -0.045 0.2 0.26 1 -0.6 90 91
GNB1 0.024 0.005 -10000 0 -10000 0 0
RAF1 -0.06 0.11 -10000 0 -0.35 84 84
RAC1-CDC42/GDP -0.017 0.15 -10000 0 -0.44 90 90
T-DHT/AR/PELP1/Src -0.018 0.12 -10000 0 -0.36 89 89
MAP2K2 -0.07 0.12 -10000 0 -0.36 81 81
T-DHT/AR/PELP1/Src/PI3K -0.017 0.097 -10000 0 -0.3 82 82
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
SHBG 0.022 0.011 0.27 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.049 0.16 -10000 0 -0.5 65 65
mol:T-DHT -0.001 0.001 0.002 1 -0.004 83 84
RAC1 0.024 0.004 -10000 0 -10000 0 0
GNRH1 0.001 0.027 -10000 0 -0.45 3 3
Gi family/GTP -0.033 0.098 -10000 0 -0.29 70 70
CDC42 0.024 0.005 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.045 0.18 -10000 0 -0.43 143 143
CRKL -0.051 0.15 0.36 1 -0.41 74 75
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 -0.4 70 71
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 -0.4 169 169
MAP3K5 -0.044 0.15 0.36 1 -0.41 67 68
HGF/MET/CIN85/CBL/ENDOPHILINS -0.034 0.18 -10000 0 -0.38 168 168
AP1 -0.13 0.21 -10000 0 -0.42 256 256
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 -0.36 134 134
GAB1/CRKL/SHP2/PI3K -0.02 0.16 -10000 0 -0.41 58 58
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.039 0.15 0.34 1 -0.4 68 69
PTPN11 0.025 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.024 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
ELK1 -0.032 0.1 0.27 26 -0.22 103 129
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.027 0.093 -10000 0 -0.26 59 59
PAK1 0.027 0.08 0.37 8 -0.72 1 9
HGF/MET/RANBP10 -0.049 0.19 -10000 0 -0.41 168 168
HRAS -0.11 0.27 -10000 0 -0.65 150 150
DOCK1 -0.049 0.15 0.53 1 -0.4 69 70
GAB1 -0.054 0.16 -10000 0 -0.37 132 132
CRK -0.052 0.15 0.36 1 -0.36 121 122
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.26 -10000 0 -0.59 178 178
JUN 0.018 0.061 -10000 0 -0.6 8 8
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.054 0.13 -10000 0 -0.3 170 170
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.051 0.17 0.38 5 -0.46 67 72
GRB2/SHC -0.019 0.11 -10000 0 -0.27 115 115
FOS -0.17 0.29 -10000 0 -0.6 251 251
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.032 0.099 0.27 26 -0.22 103 129
HGF/MET/MUC20 -0.059 0.18 -10000 0 -0.41 171 171
cell migration -0.019 0.11 -10000 0 -0.27 115 115
GRB2 0.023 0.011 0.27 1 -10000 0 1
CBL 0.022 0.008 -10000 0 -10000 0 0
MET/RANBP10 -0.047 0.18 -10000 0 -0.44 138 138
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.051 0.15 -10000 0 -0.35 136 136
MET/MUC20 -0.06 0.17 -10000 0 -0.43 143 143
RAP1B -0.043 0.14 0.29 3 -0.4 59 62
RAP1A -0.048 0.14 0.41 2 -0.4 60 62
HGF/MET/RANBP9 -0.047 0.19 -10000 0 -0.41 165 165
RAF1 -0.1 0.25 -10000 0 -0.62 149 149
STAT3 -0.052 0.16 -10000 0 -0.37 133 133
cell proliferation -0.046 0.19 0.29 20 -0.44 123 143
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 0.67 43 -10000 0 43
RANBP9 0.024 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.13 0.44 1 -0.42 35 36
SRC -0.057 0.14 0.2 1 -0.34 135 136
PI3K -0.027 0.13 -10000 0 -0.29 135 135
MET/Glomulin -0.052 0.15 -10000 0 -0.39 138 138
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.094 0.23 0.47 1 -0.57 148 149
MET -0.079 0.23 -10000 0 -0.6 136 136
MAP4K1 -0.047 0.16 0.38 1 -0.43 72 73
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.094 0.23 0.47 1 -0.57 149 150
BAD 0.012 0.061 0.36 3 -0.72 1 4
MAP2K4 -0.04 0.14 0.34 1 -0.42 46 47
SHP2/GRB2/SOS1/GAB1 -0.044 0.18 -10000 0 -0.41 142 142
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.025 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.049 0.12 -10000 0 -0.28 154 154
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.01 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 -0.28 160 160
PDPK1 0.017 0.067 0.44 2 -0.8 1 3
HGF/MET/SHIP -0.047 0.19 -10000 0 -0.41 169 169
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.02 0.18 11 -10000 0 11
Metarhodopsin II/Arrestin 0.038 0.04 0.19 33 -10000 0 33
PDE6G/GNAT1/GTP 0.035 0.033 0.18 37 -10000 0 37
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.029 0.27 11 -10000 0 11
GRK1 0.019 0.018 0.27 4 -10000 0 4
CNG Channel -0.064 0.17 -10000 0 -0.33 238 238
mol:Na + -0.061 0.17 -10000 0 -0.32 238 238
mol:ADP 0.019 0.018 0.27 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 -0.33 237 240
CNGB1 0.031 0.054 0.27 40 -10000 0 40
RDH5 -0.37 0.3 -10000 0 -0.6 520 520
SAG 0.033 0.054 0.27 42 -10000 0 42
mol:Ca2+ -0.095 0.15 0.36 11 -0.32 204 215
Na + (4 Units) -0.064 0.16 -10000 0 -0.31 225 225
RGS9 -0.035 0.18 0.27 7 -0.6 78 85
GNB1/GNGT1 0.056 0.062 -10000 0 -10000 0 0
GNAT1/GDP 0.018 0.12 0.31 3 -0.33 76 79
GUCY2D 0.024 0.035 0.27 10 -0.6 1 11
GNGT1 0.059 0.091 0.27 133 -10000 0 133
GUCY2F 0.019 0.013 0.27 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.018 0.053 0.22 1 -0.33 13 14
mol:11-cis-retinal -0.37 0.3 -10000 0 -0.6 520 520
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 -0.44 522 522
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.16 0.29 0.27 4 -0.6 246 250
Metarhodopsin II 0.027 0.022 0.17 7 -10000 0 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.056 0.051 -10000 0 -0.36 5 5
RGS9BP 0.037 0.055 0.27 44 -10000 0 44
Metarhodopsin II/Transducin 0.025 0.034 0.18 7 -0.17 1 8
GCAP Family/Ca ++ 0.045 0.042 -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 0.061 0.055 0.33 1 -10000 0 1
PDE6B 0.013 0.081 0.27 1 -0.6 14 15
PDE6A 0.027 0.03 0.27 13 -10000 0 13
PDE6G 0.031 0.044 0.27 27 -10000 0 27
RHO 0.025 0.031 0.27 13 -10000 0 13
PDE6 0.027 0.13 0.31 2 -0.33 84 86
GUCA1A 0.034 0.051 0.27 38 -10000 0 38
GC2/GCAP Family 0.056 0.045 -10000 0 -0.36 4 4
GUCA1C 0.018 0.009 0.27 1 -10000 0 1
GUCA1B 0.021 0.044 -10000 0 -0.6 4 4
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.004 0.16 -10000 0 -0.34 129 129
ER alpha/Gai/GDP/Gbeta gamma -0.079 0.22 -10000 0 -0.48 151 151
AKT1 -0.098 0.32 -10000 0 -0.79 140 140
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.096 0.33 -10000 0 -0.8 140 140
mol:Ca2+ -0.021 0.1 0.27 2 -0.47 20 22
IGF1R 0.013 0.082 0.27 2 -0.6 14 16
E2/ER alpha (dimer)/Striatin -0.003 0.16 -10000 0 -0.37 111 111
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.091 0.31 0.75 140 -10000 0 140
RhoA/GTP -0.013 0.1 -10000 0 -0.31 84 84
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.06 0.21 0.32 5 -0.48 138 143
regulation of stress fiber formation 0.017 0.1 0.26 73 -0.32 7 80
E2/ERA-ERB (dimer) -0.017 0.16 0.18 98 -0.37 134 232
KRAS 0.024 0.005 -10000 0 -10000 0 0
G13/GTP -0.005 0.14 -10000 0 -0.34 106 106
pseudopodium formation -0.017 0.1 0.32 7 -0.26 73 80
E2/ER alpha (dimer)/PELP1 -0.008 0.15 -10000 0 -0.38 107 107
GRB2 0.023 0.011 0.27 1 -10000 0 1
GNG2 0.019 0.053 -10000 0 -0.6 6 6
GNAO1 0.019 0.095 0.27 28 -0.6 15 43
HRAS 0.024 0.01 0.27 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.079 0.23 -10000 0 -0.52 158 158
E2/ER beta (dimer) 0.004 0.077 -10000 0 -0.42 25 25
mol:GDP -0.035 0.17 0.26 12 -0.41 126 138
mol:NADP -0.079 0.23 -10000 0 -0.52 158 158
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.025 0.11 0.27 2 -0.49 20 22
IGF-1R heterotetramer 0.013 0.082 0.27 2 -0.6 14 16
PLCB1 -0.021 0.11 0.28 2 -0.38 46 48
PLCB2 -0.004 0.083 -10000 0 -0.54 11 11
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
mol:L-citrulline -0.079 0.23 -10000 0 -0.52 158 158
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.67 108 108
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 0.27 109 -0.6 106 215
Gq family/GDP/Gbeta gamma -0.009 0.16 -10000 0 -0.78 30 30
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.013 0.13 -10000 0 -0.54 18 18
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.054 0.2 0.32 5 -0.49 114 119
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
E2/ER alpha (dimer) -0.022 0.17 0.18 109 -0.43 111 220
STRN 0.024 0.003 -10000 0 -10000 0 0
GNAL -0.11 0.25 -10000 0 -0.6 174 174
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 -0.001 0.07 -10000 0 -0.39 25 25
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 0.35 20 -0.58 64 84
cAMP biosynthetic process -0.089 0.19 -10000 0 -0.34 269 269
SRC -0.073 0.22 0.3 8 -0.46 146 154
PI3K 0.034 0.01 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.016 0.16 -10000 0 -0.38 119 119
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 -0.085 0.2 -10000 0 -0.35 269 269
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.016 -10000 0 -10000 0 0
vasodilation -0.074 0.22 0.24 1 -0.49 158 159
mol:DAG -0.025 0.11 0.27 2 -0.49 20 22
Gs family/GDP/Gbeta gamma -0.089 0.18 -10000 0 -0.37 206 206
MSN -0.019 0.11 0.32 7 -0.27 73 80
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 0.49 158 -0.24 1 159
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
RhoA/GDP -0.018 0.17 0.27 9 -0.39 125 134
NOS3 -0.085 0.25 -10000 0 -0.55 158 158
GNA11 0.024 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.065 0.25 0.32 2 -0.59 135 137
E2/ER alpha (dimer)/PELP1/Src -0.063 0.22 0.35 6 -0.5 139 145
ruffle organization -0.017 0.1 0.32 7 -0.26 73 80
ROCK2 -0.016 0.12 0.35 6 -0.29 79 85
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.039 0.21 0.38 21 -0.56 64 85
MMP2 -0.066 0.2 0.29 9 -0.57 67 76
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.076 0.12 -10000 0 -0.3 79 79
NT3 (dimer)/TRKC -0.19 0.28 -10000 0 -0.5 351 351
NT3 (dimer)/TRKB -0.32 0.33 -10000 0 -0.56 488 488
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 -0.019 0.17 0.27 19 -0.6 64 83
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.026 0.045 0.27 21 -0.6 1 22
NTRK2 -0.3 0.31 -10000 0 -0.6 422 422
NTRK3 -0.18 0.3 0.27 5 -0.6 276 281
NT-4/5 (dimer)/TRKB -0.4 0.36 -10000 0 -0.63 538 538
neuron apoptosis 0.18 0.23 0.47 247 -10000 0 247
SHC 2-3/Grb2 -0.2 0.25 -10000 0 -0.52 247 247
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.2 0.26 -10000 0 -0.56 237 237
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 -0.44 245 245
RIN/GDP -0.05 0.12 0.29 4 -0.26 76 80
GIPC1 0.024 0.004 -10000 0 -10000 0 0
KRAS 0.024 0.005 -10000 0 -10000 0 0
DNAJA3 -0.088 0.16 -10000 0 -0.33 221 221
RIN/GTP 0.014 0.009 0.18 2 -10000 0 2
CCND1 0.025 0.098 0.44 31 -0.85 3 34
MAGED1 0.025 0.012 0.27 2 -10000 0 2
PTPN11 0.025 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.22 0.3 -10000 0 -0.6 316 316
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.031 0.087 -10000 0 -0.4 25 25
TRKA/NEDD4-2 0.033 0.035 -10000 0 -0.32 2 2
ELMO1 0.024 0.003 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.032 0.007 -10000 0 -10000 0 0
NGF 0.015 0.087 0.27 7 -0.6 15 22
HRAS 0.024 0.01 0.27 1 -10000 0 1
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.022 0.008 -10000 0 -10000 0 0
RIT2 0.019 0.013 0.27 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.27 2 -10000 0 2
DNM1 0.021 0.049 0.27 1 -0.6 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.076 0.17 -10000 0 -0.33 239 239
mol:GDP -0.081 0.17 0.36 4 -0.38 87 91
NGF (dimer) 0.015 0.086 0.27 7 -0.6 15 22
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.049 0.11 0.37 2 -0.27 54 56
TIAM1 0.025 0.017 0.27 4 -10000 0 4
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.2 0.24 -10000 0 -0.42 443 443
KIDINS220/CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.015 -10000 0 -10000 0 0
FRS2 family/SHP2 0.047 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.047 0.029 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.067 0.22 0.27 11 -0.6 124 135
RAP1/GDP -0.045 0.098 -10000 0 -0.23 59 59
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.019 0.17 0.27 19 -0.6 64 83
ubiquitin-dependent protein catabolic process 0.036 0.065 -10000 0 -0.38 14 14
Schwann cell development -0.051 0.039 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.051 -10000 0 -0.27 8 8
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.29 0.3 -10000 0 -0.51 488 488
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
Rap1/GTP -0.083 0.13 -10000 0 -0.47 43 43
STAT3 0.034 0.045 -10000 0 -0.37 3 3
axon guidance -0.28 0.28 -10000 0 -0.48 501 501
MAPK3 0.005 0.094 0.25 3 -0.37 24 27
MAPK1 0.006 0.096 0.25 3 -0.37 24 27
CDC42/GDP -0.048 0.12 0.29 5 -0.26 60 65
NTF3 -0.067 0.23 0.27 11 -0.6 124 135
NTF4 -0.22 0.3 -10000 0 -0.6 316 316
NGF (dimer)/TRKA/FAIM 0.037 0.066 -10000 0 -0.39 14 14
PI3K 0.034 0.01 -10000 0 -10000 0 0
FRS3 0.024 0.005 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.024 0.004 -10000 0 -10000 0 0
RASGRF1 -0.085 0.17 0.26 2 -0.34 225 227
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.17 0.24 0.21 1 -0.44 335 336
RGS19 0.023 0.011 0.27 1 -10000 0 1
CDC42 0.024 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.014 0.098 0.4 1 -0.45 8 9
Rac1/GDP -0.049 0.12 0.33 3 -0.27 60 63
NGF (dimer)/TRKA/GRIT 0.024 0.062 -10000 0 -0.36 16 16
neuron projection morphogenesis -0.079 0.22 -10000 0 -0.78 37 37
NGF (dimer)/TRKA/NEDD4-2 0.036 0.066 -10000 0 -0.39 14 14
MAP2K1 0.031 0.088 0.36 15 -10000 0 15
NGFR -0.16 0.28 -10000 0 -0.6 238 238
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.052 -10000 0 -0.31 15 15
RAS family/GTP/PI3K 0.019 0.011 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.064 0.027 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.012 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
MAPKKK cascade -0.042 0.14 -10000 0 -0.65 33 33
RASA1 0.024 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.034 0.034 -10000 0 -0.45 1 1
SQSTM1 0.024 0.009 0.27 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.18 0.23 -10000 0 -0.38 439 439
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.066 -10000 0 -0.34 14 14
MATK 0.015 0.091 0.27 10 -0.6 16 26
NEDD4L 0.023 0.022 -10000 0 -0.6 1 1
RAS family/GDP -0.06 0.073 -10000 0 -0.21 54 54
NGF (dimer)/TRKA -0.096 0.17 -10000 0 -0.34 249 249
Rac1/GTP -0.092 0.12 -10000 0 -0.29 183 183
FRS2 family/SHP2/CRK family 0.061 0.029 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.002 0.088 -10000 0 -0.44 23 23
Crk/p130 Cas/Paxillin -0.053 0.12 -10000 0 -0.34 97 97
JUN -0.01 0.12 0.25 1 -0.42 21 22
HRAS 0.024 0.01 0.27 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 0.053 0.2 0.36 46 -0.36 126 172
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.27 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.052 0.2 0.36 45 -0.36 124 169
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.005 0.16 0.33 4 -0.35 126 130
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.027 0.17 0.29 31 -0.33 125 156
GRB7 0.02 0.023 -10000 0 -0.6 1 1
RET51/GFRalpha1/GDNF 0.052 0.2 0.36 45 -0.36 126 171
MAPKKK cascade 0.005 0.15 0.29 9 -0.35 92 101
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.017 0.18 0.33 3 -0.4 135 138
lamellipodium assembly -0.027 0.13 -10000 0 -0.32 94 94
RET51/GFRalpha1/GDNF/SHC 0.043 0.18 0.36 37 -0.36 97 134
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.005 0.14 0.33 4 -0.35 94 98
RET9/GFRalpha1/GDNF/Shank3 -0.008 0.16 0.33 4 -0.35 126 130
MAPK3 -0.028 0.13 0.23 2 -0.33 99 101
DOK1 0.024 0.003 -10000 0 -10000 0 0
DOK6 0.019 0.065 0.27 6 -0.6 8 14
PXN 0.025 0.002 -10000 0 -10000 0 0
neurite development -0.028 0.13 -10000 0 -0.32 96 96
DOK5 0.012 0.088 0.27 5 -0.6 16 21
GFRA1 -0.063 0.24 0.27 51 -0.6 135 186
MAPK8 -0.002 0.13 0.22 3 -0.46 18 21
HRAS/GTP 0.036 0.19 0.3 43 -0.36 118 161
tube development -0.001 0.15 0.35 10 -0.34 120 130
MAPK1 -0.027 0.13 0.27 3 -0.33 99 102
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.018 0.12 0.26 1 -0.28 121 122
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.047 0.2 0.35 42 -0.35 128 170
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.035 0.19 0.35 32 -0.36 125 157
RET51/GFRalpha1/GDNF/Dok5 0.035 0.2 0.36 41 -0.37 133 174
PRKCA 0.009 0.092 0.27 2 -0.6 18 20
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
CREB1 -0.007 0.13 0.24 7 -0.33 71 78
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.015 0.1 0.26 1 -0.27 88 89
RET51/GFRalpha1/GDNF/Grb7 0.051 0.19 0.34 59 -0.36 99 158
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.11 0.14 0.27 314 -0.6 11 325
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.008 0.12 0.25 1 -0.41 21 22
RET9/GFRalpha1/GDNF/FRS2 -0.007 0.16 0.33 4 -0.35 127 131
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.1 0.26 1 -0.28 88 89
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.014 0.14 0.25 16 -0.3 99 115
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.009 0.14 0.26 3 -0.31 99 102
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.018 0.14 0.26 16 -0.32 73 89
PI3K -0.018 0.21 0.3 9 -0.49 95 104
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0 0.15 0.32 3 -0.34 120 123
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity 0.005 0.13 0.25 9 -0.28 96 105
RET51/GFRalpha1/GDNF/FRS2 0.049 0.2 0.35 49 -0.36 127 176
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
IRS2 0.001 0.12 -10000 0 -0.6 29 29
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.018 0.14 0.26 16 -0.32 73 89
RET51/GFRalpha1/GDNF/PKC alpha 0.032 0.2 0.36 37 -0.36 137 174
GRB2 0.023 0.011 0.27 1 -10000 0 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.035 0.057 0.27 47 -10000 0 47
RAC1 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.038 0.22 0.35 44 -0.41 136 180
Rac1/GTP -0.014 0.16 0.24 5 -0.39 94 99
RET9/GFRalpha1/GDNF -0.02 0.16 0.33 4 -0.37 136 140
GFRalpha1/GDNF -0.026 0.19 0.38 4 -0.43 136 140
Signaling events mediated by PTP1B

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
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
Jak2/Leptin Receptor -0.1 0.2 0.27 1 -0.41 193 194
PTP1B/AKT1 -0.064 0.13 0.22 1 -0.34 98 99
FYN 0.022 0.023 -10000 0 -0.6 1 1
p210 bcr-abl/PTP1B -0.08 0.14 0.22 2 -0.36 115 117
EGFR -0.2 0.3 -10000 0 -0.61 281 281
EGF/EGFR -0.2 0.25 -10000 0 -0.44 396 396
CSF1 0.023 0.031 -10000 0 -0.6 2 2
AKT1 0.024 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.042 0.16 0.24 18 -0.36 102 120
Insulin Receptor/Insulin -0.041 0.11 -10000 0 -0.37 37 37
HCK 0.028 0.029 0.27 12 -10000 0 12
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.076 0.13 0.31 2 -0.35 103 105
EGF -0.11 0.24 0.26 2 -0.61 154 156
YES1 0.023 0.022 -10000 0 -0.6 1 1
CAV1 -0.16 0.21 0.27 2 -0.44 238 240
TXN 0.016 0.016 0.26 1 -10000 0 1
PTP1B/IRS1/GRB2 -0.07 0.15 -10000 0 -0.37 107 107
cell migration 0.08 0.14 0.36 115 -0.22 2 117
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.026 0.022 0.26 6 -10000 0 6
ITGA2B 0.03 0.063 0.26 36 -0.6 3 39
CSF1R 0.024 0.004 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.036 0.029 0.33 1 -10000 0 1
FGR 0.024 0.01 0.27 1 -10000 0 1
PTP1B/p130 Cas -0.066 0.13 0.22 1 -0.35 107 108
Crk/p130 Cas -0.059 0.13 -10000 0 -0.35 95 95
DOK1 -0.066 0.12 0.23 2 -0.38 65 67
JAK2 -0.047 0.12 -10000 0 -0.49 38 38
Jak2/Leptin Receptor/Leptin -0.28 0.16 -10000 0 -0.4 376 376
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
PTPN1 -0.081 0.14 0.22 2 -0.36 115 117
LYN 0.021 0.009 -10000 0 -10000 0 0
CDH2 0.069 0.1 0.27 160 -0.6 2 162
SRC -0.018 0.1 -10000 0 -0.62 18 18
ITGB3 0.013 0.08 0.26 4 -0.6 13 17
CAT1/PTP1B -0.097 0.19 0.35 3 -0.48 112 115
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 -0.38 26 26
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.25 0.15 -10000 0 -0.37 331 331
negative regulation of transcription -0.046 0.12 -10000 0 -0.49 38 38
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 0.086 0.27 95 -0.6 2 97
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.11 0.26 -10000 0 -0.6 183 183
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.011 0.27 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.051 0.18 0.38 3 -0.46 78 81
PRL 0.009 0.036 0.27 10 -10000 0 10
SOCS3 0.008 0.16 -10000 0 -1.2 13 13
SPRY2 -0.04 0.18 -10000 0 -0.61 76 76
Insulin Receptor/Insulin/IRS1 0.027 0.08 -10000 0 -0.39 28 28
CSF1/CSF1R -0.061 0.14 -10000 0 -0.35 99 99
Ras protein signal transduction 0.054 0.16 0.63 52 -10000 0 52
IRS1 0.002 0.12 -10000 0 -0.6 29 29
INS 0.01 0.016 -10000 0 -10000 0 0
LEP -0.47 0.25 -10000 0 -0.6 653 653
STAT5B -0.069 0.14 0.2 3 -0.36 106 109
STAT5A -0.07 0.14 0.2 3 -0.36 108 111
GRB2 0.023 0.011 0.27 1 -10000 0 1
PDGFB-D/PDGFRB -0.07 0.14 0.22 1 -0.36 103 104
CSN2 0.026 0.059 0.4 1 -10000 0 1
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 0.27 23 -0.6 9 32
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.027 0.26 8 -10000 0 8
Effects of Botulinum toxin

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
STX1A 0.01 0.025 0.14 30 -10000 0 30
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.11 -10000 0 -0.44 36 36
STXBP1 0.022 0.038 -10000 0 -0.6 3 3
ACh/CHRNA1 0.081 0.096 0.2 296 -0.16 5 301
RAB3GAP2/RIMS1/UNC13B 0.035 0.093 -10000 0 -0.33 35 35
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 0.024 0.15 0.27 91 -0.6 35 126
mol:ACh -0.004 0.039 0.079 31 -0.14 38 69
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.02 0.088 0.24 1 -0.29 33 34
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.081 0.095 0.2 296 -0.16 5 301
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.27 307 -10000 0 307
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.035 0.12 0.2 157 -0.38 32 189
SNAP25 -0.001 0.064 0.1 50 -0.31 29 79
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.05 0.16 0.27 164 -0.6 29 193
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.031 -10000 0 -0.38 3 3
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.088 0.24 1 -0.29 33 34
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.022 -10000 0 -0.3 2 2
AURKB 0.15 0.12 0.27 437 -10000 0 437
AURKC 0.026 0.036 0.27 11 -0.6 1 12
Syndecan-1-mediated 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
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CCL5 0.03 0.048 0.27 26 -0.6 1 27
SDCBP 0.021 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.067 0.13 0.25 57 -0.4 13 70
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 0.28 7 -0.39 16 23
Syndecan-1/Syntenin 0.054 0.12 0.29 13 -0.41 12 25
MAPK3 0.05 0.12 0.27 13 -0.38 12 25
HGF/MET -0.07 0.21 -10000 0 -0.47 174 174
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 0.31 36 -0.4 16 52
Syndecan-1/CD147 0.067 0.13 0.3 12 -0.37 15 27
Syndecan-1/Syntenin/PIP2 0.05 0.12 0.27 13 -0.4 12 25
LAMA5 0.023 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.048 0.12 0.26 12 -0.39 12 24
MMP7 -0.041 0.2 0.27 24 -0.6 93 117
HGF -0.01 0.14 -10000 0 -0.6 46 46
Syndecan-1/CASK 0.046 0.12 0.21 40 -0.36 19 59
Syndecan-1/HGF/MET -0.005 0.21 0.3 7 -0.48 84 91
regulation of cell adhesion 0.044 0.11 0.26 11 -0.4 8 19
HPSE 0.028 0.04 0.27 16 -0.6 1 17
positive regulation of cell migration 0.067 0.13 0.25 57 -0.4 13 70
SDC1 0.07 0.12 0.26 44 -0.34 16 60
Syndecan-1/Collagen 0.067 0.13 0.25 57 -0.4 13 70
PPIB 0.024 0.009 0.27 1 -10000 0 1
MET -0.079 0.23 -10000 0 -0.6 136 136
PRKACA 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.27 327 -0.6 1 328
MAPK1 0.051 0.12 0.27 13 -0.37 13 26
homophilic cell adhesion 0.067 0.13 0.26 45 -0.39 14 59
MMP1 0.19 0.11 0.27 589 -10000 0 589
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.037 -10000 0 -0.33 2 2
PDGFRB 0.019 0.033 -10000 0 -0.61 2 2
SPHK1 -0.021 0.099 -10000 0 -0.75 12 12
mol:S1P -0.023 0.097 0.4 1 -0.66 12 13
S1P1/S1P/Gi -0.13 0.23 0.33 2 -0.45 252 254
GNAO1 0.007 0.097 0.26 28 -0.61 15 43
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.22 0.38 3 -0.42 223 226
PLCG1 -0.13 0.22 0.37 2 -0.43 241 243
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.033 -10000 0 -0.61 2 2
GNAI2 0.009 0.024 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.02 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 -0.035 0.098 0.28 2 -0.48 13 15
negative regulation of cAMP metabolic process -0.13 0.23 0.32 2 -0.44 252 254
MAPK3 -0.18 0.3 0.31 13 -0.58 274 287
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
KDR 0.013 0.029 -10000 0 -0.61 1 1
PLCB2 -0.026 0.098 0.32 5 -0.43 14 19
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.082 -10000 0 -0.41 13 13
receptor internalization -0.036 0.088 -10000 0 -0.45 13 13
PTGS2 -0.34 0.5 0.4 2 -1 282 284
Rac1/GTP -0.032 0.082 -10000 0 -0.41 13 13
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.26 5 -10000 0 5
negative regulation of T cell proliferation -0.13 0.23 0.32 2 -0.44 252 254
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.005 0.057 -10000 0 -0.61 6 6
MAPK1 -0.2 0.33 0.33 3 -0.63 288 291
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
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.005 0.042 0.24 5 -0.38 1 6
NFATC2 -0.012 0.092 0.24 4 -0.4 37 41
NFATC3 0.007 0.038 0.24 5 -10000 0 5
CD40LG -0.14 0.3 0.55 17 -0.62 157 174
PTGS2 -0.2 0.36 0.54 13 -0.68 248 261
JUNB 0.024 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.029 0.17 4 -10000 0 4
CaM/Ca2+ 0.009 0.029 0.17 4 -10000 0 4
CALM1 0.017 0.023 -10000 0 -10000 0 0
JUN 0.011 0.066 -10000 0 -0.61 8 8
mol:Ca2+ -0.002 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.013 -10000 0 -10000 0 0
FOSL1 0.027 0.045 0.27 15 -0.6 2 17
CREM 0.023 0.007 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.006 0.14 0.49 14 -0.42 28 42
FOS -0.18 0.29 -10000 0 -0.59 263 263
IFNG -0.11 0.3 0.52 35 -0.57 148 183
AP-1/NFAT1-c-4 -0.13 0.35 0.59 32 -0.66 177 209
FASLG -0.12 0.28 0.57 20 -0.58 134 154
NFAT1-c-4/ICER1 -0.005 0.11 0.35 9 -0.36 34 43
IL2RA -0.12 0.29 0.54 27 -0.59 147 174
FKBP12/FK506 0.018 0.004 -10000 0 -10000 0 0
CSF2 -0.13 0.28 0.57 15 -0.58 151 166
JunB/Fra1/NFAT1-c-4 0.008 0.12 0.38 10 -0.36 33 43
IL4 -0.13 0.28 0.54 13 -0.57 157 170
IL2 -0.017 0.16 -10000 0 -0.95 23 23
IL3 -0.019 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 0.27 1 -10000 0 1
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.003 0.071 -10000 0 -0.35 7 7
alphaM/beta2 Integrin/GPIbA 0.005 0.079 0.35 4 -0.43 6 10
alphaM/beta2 Integrin/proMMP-9 0.069 0.11 0.35 10 -0.44 1 11
PLAUR 0.041 0.062 0.27 59 -10000 0 59
HMGB1 -0.005 0.041 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.006 0.063 -10000 0 -10000 0 0
AGER -0.009 0.054 0.24 1 -0.65 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 -0.033 0.14 0.33 2 -0.37 12 14
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.27 327 -0.6 1 328
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 -0.38 33 33
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.25 -10000 0 -0.6 169 169
MYH2 -0.013 0.15 0.3 6 -0.44 44 50
MST1R 0.021 0.057 0.27 6 -0.6 6 12
leukocyte activation during inflammatory response -0.21 0.17 -10000 0 -0.35 475 475
APOB -0.37 0.3 -10000 0 -0.6 524 524
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.019 0.044 -10000 0 -0.6 4 4
JAM3 0.02 0.032 -10000 0 -0.6 2 2
GP1BA 0.023 0.064 0.27 17 -0.6 6 23
alphaM/beta2 Integrin/CTGF 0.001 0.078 -10000 0 -0.43 9 9
alphaM/beta2 Integrin -0.013 0.13 0.22 5 -0.35 57 62
JAM3 homodimer 0.02 0.032 -10000 0 -0.6 2 2
ICAM2 0.018 0.049 -10000 0 -0.6 5 5
ICAM1 0.027 0.027 0.27 10 -10000 0 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.01 0.13 0.24 8 -0.38 47 55
cell adhesion 0.005 0.078 0.34 4 -0.43 6 10
NFKB1 -0.11 0.21 0.44 3 -0.38 270 273
THY1 0.024 0.022 0.27 6 -10000 0 6
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.24 0.2 -10000 0 -0.38 531 531
alphaM/beta2 Integrin/LRP/tPA 0.004 0.091 -10000 0 -0.38 22 22
IL6 -0.28 0.4 0.35 2 -0.79 316 318
ITGB2 -0.005 0.051 0.27 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.028 0.085 0.34 15 -10000 0 15
alphaM/beta2 Integrin/JAM2/JAM3 -0.003 0.1 -10000 0 -0.39 34 34
JAM2 -0.006 0.13 -10000 0 -0.6 39 39
alphaM/beta2 Integrin/ICAM1 0.017 0.089 0.36 2 -0.36 14 16
alphaM/beta2 Integrin/uPA/Plg 0.016 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.018 0.16 0.26 13 -0.38 80 93
positive regulation of phagocytosis -0.003 0.11 0.32 3 -0.35 23 26
Ron/MSP 0.028 0.067 -10000 0 -0.44 15 15
alphaM/beta2 Integrin/uPAR/uPA 0.029 0.087 0.34 15 -10000 0 15
alphaM/beta2 Integrin/uPAR 0.016 0.079 0.36 3 -10000 0 3
PLAU 0.031 0.042 0.27 25 -10000 0 25
PLAT 0.007 0.089 -10000 0 -0.6 17 17
actin filament polymerization -0.012 0.15 0.29 7 -0.42 44 51
MST1 0.018 0.062 0.27 1 -0.6 8 9
alphaM/beta2 Integrin/lipoprotein(a) -0.21 0.18 -10000 0 -0.35 475 475
TNF -0.11 0.2 0.37 4 -0.73 17 21
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.011 0.069 -10000 0 -10000 0 0
fibrinolysis 0.014 0.069 -10000 0 -10000 0 0
HCK 0.028 0.029 0.27 12 -10000 0 12
dendritic cell antigen processing and presentation -0.01 0.13 0.24 8 -0.38 47 55
VTN 0.034 0.072 0.27 48 -0.6 4 52
alphaM/beta2 Integrin/CYR61 -0.014 0.11 -10000 0 -0.4 45 45
LPA 0.019 0.018 0.27 4 -10000 0 4
LRP1 0.019 0.061 -10000 0 -0.6 8 8
cell migration 0.041 0.085 0.28 10 -0.37 6 16
FN1 0.13 0.12 0.27 367 -10000 0 367
alphaM/beta2 Integrin/Thy1 0.007 0.064 -10000 0 -10000 0 0
MPO -0.015 0.15 0.27 1 -0.6 49 50
KNG1 0.022 0.027 0.27 10 -10000 0 10
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.014 0.16 0.29 10 -0.48 38 48
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.018 0.27 4 -10000 0 4
CTGF 0.017 0.066 0.27 2 -0.6 9 11
alphaM/beta2 Integrin/Hck 0.008 0.068 0.37 3 -10000 0 3
ITGAM -0.005 0.044 0.25 3 -10000 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.055 0.17 -10000 0 -0.38 152 152
HP -0.075 0.24 0.27 27 -0.6 137 164
leukocyte adhesion -0.044 0.14 0.28 2 -0.4 39 41
SELP -0.11 0.25 -10000 0 -0.6 169 169
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.019 0.081 0.29 1 -0.35 2 3
epithelial cell differentiation 0.035 0.078 0.41 1 -10000 0 1
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.028 0.1 0.49 8 -10000 0 8
FYN 0.022 0.023 -10000 0 -0.6 1 1
EGFR -0.19 0.3 -10000 0 -0.6 281 281
PRL 0.023 0.027 0.27 10 -10000 0 10
neuron projection morphogenesis -0.05 0.15 0.36 8 -0.37 27 35
PTPRZ1 -0.3 0.31 0.27 6 -0.6 435 441
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.15 -10000 0 -0.38 36 36
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.09 0.16 -10000 0 -0.36 184 184
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.075 0.4 8 -0.31 3 11
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.12 -10000 0 -0.39 36 36
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.083 0.16 -10000 0 -0.34 171 171
GRIN2B -0.11 0.17 -10000 0 -0.46 61 61
ErbB4/ErbB2/betacellulin 0.015 0.1 -10000 0 -0.34 24 24
STAT1 0.03 0.035 0.27 18 -10000 0 18
HBEGF 0.023 0.031 -10000 0 -0.6 2 2
PRLR 0.026 0.021 0.27 6 -10000 0 6
E4ICDs/ETO2 0.009 0.088 0.36 1 -0.44 7 8
axon guidance 0.061 0.12 0.32 39 -0.39 1 40
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.035 0.024 -10000 0 -10000 0 0
CBFA2T3 0.013 0.076 0.27 3 -0.6 12 15
ErbB4/ErbB2/HBEGF 0.033 0.073 -10000 0 -0.32 2 2
MAPK3 -0.054 0.14 -10000 0 -0.38 27 27
STAT1 (dimer) 0.023 0.082 0.28 3 -10000 0 3
MAPK1 -0.053 0.15 0.39 2 -0.38 29 31
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.074 0.16 -10000 0 -0.34 161 161
NRG1 -0.12 0.2 -10000 0 -0.45 218 218
NRG3 -0.007 0.15 0.27 18 -0.6 48 66
NRG2 -0.31 0.31 -10000 0 -0.6 438 438
NRG4 0.026 0.027 0.27 10 -10000 0 10
heart development 0.061 0.12 0.32 39 -0.39 1 40
neural crest cell migration -0.072 0.16 -10000 0 -0.34 161 161
ERBB2 0.037 0.074 0.27 75 -10000 0 75
WWOX/E4ICDs 0.014 0.076 0.29 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.093 0.17 -10000 0 -0.34 191 191
apoptosis 0.016 0.14 0.51 36 -10000 0 36
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.18 0.19 -10000 0 -0.37 340 340
ErbB4/ErbB2/epiregulin 0.007 0.14 0.36 11 -0.33 60 71
ErbB4/ErbB4/betacellulin/betacellulin -0.001 0.11 0.29 1 -0.37 33 34
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.045 0.084 0.41 1 -0.31 2 3
MDM2 0.015 0.086 0.32 14 -10000 0 14
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.088 0.15 -10000 0 -0.34 210 210
STAT5A 0.054 0.11 0.36 11 -0.38 1 12
ErbB4/EGFR/neuregulin 1 beta -0.19 0.24 -10000 0 -0.46 321 321
DLG4 0.022 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.017 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.014 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.064 0.1 0.47 1 -10000 0 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.065 0.11 0.36 6 -0.38 2 8
LRIG1 0.023 0.022 -10000 0 -0.6 1 1
EREG -0.03 0.21 0.27 62 -0.6 94 156
BTC -0.008 0.14 0.27 2 -0.6 43 45
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.052 0.11 0.32 38 -0.4 1 39
ERBB4 -0.003 0.074 0.4 8 -0.31 3 11
STAT5B 0.022 0.031 -10000 0 -0.6 2 2
YAP1 -0.011 0.11 -10000 0 -0.38 54 54
GRB2 0.023 0.011 0.27 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.035 0.072 0.32 1 -10000 0 1
glial cell differentiation -0.013 0.07 -10000 0 -10000 0 0
WWOX 0.022 0.012 0.27 1 -10000 0 1
cell proliferation -0.038 0.18 0.35 10 -0.47 34 44
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.11 0.2 -10000 0 -0.39 247 247
fibroblast growth factor receptor signaling pathway -0.11 0.2 -10000 0 -0.39 247 247
LAMA1 -0.039 0.19 0.27 1 -0.6 83 84
PRNP 0.015 0.072 -10000 0 -0.6 11 11
GPC1/SLIT2 0 0.12 -10000 0 -0.43 63 63
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 -0.45 83 83
TDGF1 0.009 0.092 0.27 1 -0.6 18 19
CRIPTO/GPC1 0.024 0.072 -10000 0 -0.45 18 18
APP/GPC1 0.035 0.012 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0 0.059 -10000 0 -0.39 18 18
FLT1 0.023 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.037 0.067 -10000 0 -0.39 19 19
SERPINC1 0.029 0.047 0.27 30 -10000 0 30
FYN -0.001 0.06 -10000 0 -0.38 19 19
FGR 0 0.059 -10000 0 -0.39 18 18
positive regulation of MAPKKK cascade 0 0.097 0.28 2 -0.39 30 32
SLIT2 -0.02 0.16 -10000 0 -0.6 58 58
GPC1/NRG -0.11 0.21 -10000 0 -0.45 220 220
NRG1 -0.14 0.28 0.27 3 -0.6 220 223
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.022 -10000 0 -10000 0 0
LYN 0 0.054 -10000 0 -0.39 14 14
mol:Spermine 0.006 0.007 -10000 0 -10000 0 0
cell growth -0.11 0.2 -10000 0 -0.39 247 247
BMP signaling pathway -0.025 0.013 -10000 0 -0.27 2 2
SRC 0 0.056 -10000 0 -0.39 16 16
TGFBR1 0.025 0.009 0.27 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.16 0.29 0.27 19 -0.6 254 273
GPC1 0.025 0.013 0.27 2 -10000 0 2
TGFBR1 (dimer) 0.025 0.009 0.27 1 -10000 0 1
VEGFA 0.025 0.019 0.27 5 -10000 0 5
BLK 0.012 0.078 -10000 0 -0.38 19 19
HCK 0.002 0.06 -10000 0 -0.39 17 17
FGF2 -0.21 0.3 -10000 0 -0.6 311 311
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 0.036 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.23 -10000 0 -0.45 254 254
LCK 0 0.076 -10000 0 -0.39 27 27
neuron differentiation -0.11 0.21 -10000 0 -0.45 220 220
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
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 -0.034 0.18 -10000 0 -0.6 77 77
FYN -0.026 0.11 -10000 0 -0.36 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 0.024 0.018 0.27 4 -10000 0 4
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 -0.4 298 298
PTK2 -0.054 0.15 0.32 2 -0.48 29 31
IGF1R 0.013 0.082 0.27 2 -0.6 14 16
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.071 0.27 5 -0.6 10 15
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.045 0.12 -10000 0 -0.49 31 31
VEGFA 0.025 0.019 0.27 5 -10000 0 5
ILK -0.042 0.12 -10000 0 -0.5 24 24
ROCK1 0.024 0.004 -10000 0 -10000 0 0
AKT1 -0.043 0.1 0.33 1 -0.5 20 21
PTK2B -0.009 0.06 0.36 2 -0.36 13 15
alphaV/beta3 Integrin/JAM-A -0.078 0.18 0.3 1 -0.35 219 220
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.038 0.058 -10000 0 -0.39 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.047 0.2 -10000 0 -0.4 187 187
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.053 -10000 0 -0.44 3 3
alphaV/beta3 Integrin/Syndecan-1 0.049 0.07 -10000 0 -0.38 14 14
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.28 -10000 0 -0.48 255 255
PI4 Kinase 0.029 0.015 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.079 0.091 0.35 3 -0.38 13 16
RPS6KB1 -0.16 0.23 0.42 3 -0.57 132 135
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.57 281 281
GPR124 0.016 0.049 -10000 0 -0.6 5 5
MAPK1 -0.2 0.3 -10000 0 -0.57 302 302
PXN 0.025 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.042 0.18 -10000 0 -0.39 163 163
cell adhesion 0.027 0.071 0.26 1 -0.37 23 24
ANGPTL3 0.022 0.018 0.27 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.025 -10000 0 -0.39 1 1
IGF-1R heterotetramer 0.013 0.082 0.27 2 -0.6 14 16
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.01 0.094 -10000 0 -0.6 19 19
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
RAC1 0.024 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.03 0.062 -10000 0 -0.41 12 12
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.022 -10000 0 -0.6 1 1
alphaV/beta3 Integrin/CD47 0.04 0.059 -10000 0 -0.39 14 14
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.1 -10000 0 -0.47 27 27
CSF1 0.023 0.031 -10000 0 -0.6 2 2
PIK3C2A -0.041 0.11 -10000 0 -0.48 22 22
PI4 Kinase/Pyk2 -0.079 0.15 -10000 0 -0.32 186 186
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.051 0.061 -10000 0 -0.38 13 13
FAK1/Vinculin -0.036 0.13 0.34 4 -0.4 24 28
alphaV beta3/Integrin/ppsTEM5 0.031 0.063 -10000 0 -0.41 12 12
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.034 0.072 0.27 48 -0.6 4 52
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.21 0.3 -10000 0 -0.6 311 311
F11R -0.13 0.21 -10000 0 -0.44 251 251
alphaV/beta3 Integrin/Lactadherin 0.035 0.076 0.35 1 -0.4 22 23
alphaV/beta3 Integrin/TGFBR2 0.031 0.093 -10000 0 -0.45 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.051 0.032 -10000 0 -0.35 2 2
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.038 0.051 -10000 0 -0.35 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.13 0.12 0.27 367 -10000 0 367
alphaV/beta3 Integrin/Pyk2 0.03 0.059 -10000 0 -0.36 13 13
SDC1 0.04 0.064 0.27 55 -0.6 1 56
VAV3 -0.01 0.038 -10000 0 -0.34 5 5
PTPN11 0.025 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 25 30
cell migration -0.036 0.12 0.31 5 -0.36 23 28
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.065 0.17 -10000 0 -0.32 206 206
SPP1 0.092 0.11 0.27 232 -10000 0 232
KDR 0.023 0.022 -10000 0 -0.6 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.097 0.25 0.27 4 -0.6 162 166
angiogenesis -0.18 0.3 0.3 1 -0.57 279 280
Rac1/GTP 0.022 0.032 -10000 0 -0.31 4 4
EDIL3 0.012 0.1 0.27 15 -0.6 21 36
cell proliferation 0.03 0.092 -10000 0 -0.44 27 27
TCR signaling in naïve CD8+ T cells

Figure 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 0.043 0.18 0.31 96 -0.5 41 137
FYN 0.02 0.2 0.39 34 -0.62 44 78
LAT/GRAP2/SLP76 0.024 0.18 0.41 25 -0.54 45 70
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.023 0.16 0.33 59 -0.4 55 114
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.016 0.062 0.17 52 -0.14 14 66
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
mol:Ca2+ -0.025 0.035 -10000 0 -0.097 138 138
integrin-mediated signaling pathway 0.026 0.025 -10000 0 -0.38 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.21 0.44 27 -0.56 61 88
TRPV6 -0.1 0.29 1.2 14 -0.6 161 175
CD28 0.024 0.05 0.28 7 -0.6 4 11
SHC1 0.027 0.22 0.33 107 -0.6 51 158
receptor internalization -0.014 0.23 0.4 25 -0.52 101 126
PRF1 -0.012 0.25 0.57 8 -1 35 43
KRAS 0.024 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
COT/AKT1 0.032 0.14 0.31 56 -0.35 43 99
LAT 0.012 0.21 0.38 37 -0.64 47 84
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 0.28 34 -0.6 20 54
RASGRP2 -0.001 0.052 0.17 9 -0.17 55 64
RASGRP1 0.025 0.16 0.38 34 -0.44 44 78
HLA-A 0.026 0.016 0.27 2 -10000 0 2
RASSF5 0.019 0.033 0.27 1 -0.6 2 3
RAP1A/GTP/RAPL 0.026 0.025 -10000 0 -0.38 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.084 0.18 120 -0.14 16 136
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.057 -10000 0 -0.22 34 34
PRKCA 0.012 0.1 0.25 30 -0.28 42 72
GRAP2 0.016 0.073 0.26 3 -0.6 11 14
mol:IP3 0.017 0.15 0.27 107 -0.39 43 150
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.19 0.35 23 -0.67 43 66
ORAI1 0.04 0.18 0.65 3 -0.98 13 16
CSK 0.006 0.21 0.41 24 -0.66 46 70
B7 family/CD28 0.064 0.22 0.45 38 -0.66 38 76
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.24 0.43 25 -0.65 62 87
PTPN6 0.006 0.21 0.38 30 -0.66 45 75
VAV1 0.002 0.21 0.42 24 -0.64 49 73
Monovalent TCR/CD3 -0.002 0.15 0.28 29 -0.53 43 72
CBL 0.022 0.008 -10000 0 -10000 0 0
LCK 0.017 0.21 0.41 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 -0.001 0.23 0.42 25 -0.66 58 83
CD80 0.095 0.11 0.27 240 -10000 0 240
CD86 0.026 0.018 0.28 4 -10000 0 4
PDK1/CARD11/BCL10/MALT1 -0.007 0.073 0.17 2 -0.26 34 36
HRAS 0.024 0.01 0.27 1 -10000 0 1
GO:0035030 0.022 0.17 0.37 31 -0.53 40 71
CD8A 0.028 0.065 0.28 21 -0.61 5 26
CD8B 0.01 0.12 0.28 20 -0.61 29 49
PTPRC 0.024 0.038 0.27 12 -0.61 1 13
PDK1/PKC theta 0.024 0.2 0.39 61 -0.52 47 108
CSK/PAG1 0.023 0.21 0.35 45 -0.64 43 88
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 0.029 0.11 1.3 4 -10000 0 4
RAS family/GTP 0.046 0.097 0.23 73 -0.18 32 105
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.019 0.25 0.4 25 -0.56 101 126
mol:DAG -0.017 0.1 0.14 18 -0.36 44 62
RAP1A/GDP 0.021 0.039 0.11 59 -10000 0 59
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 0.54 9 -0.92 36 45
RAP1A/GTP -0.001 0.018 -10000 0 -0.066 48 48
mol:PI-3-4-5-P3 0.017 0.18 0.41 29 -0.46 61 90
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.022 0.18 0.3 97 -0.52 42 139
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 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.005 0.17 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 0.27 16 -0.6 2 18
PRKCB 0.014 0.11 0.31 29 -0.29 34 63
PRKCE 0.018 0.099 0.24 35 -0.26 37 72
PRKCQ 0.012 0.21 0.44 28 -0.58 52 80
LCP2 0.024 0.01 0.26 1 -10000 0 1
BCL10 0.024 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.027 0.15 0.31 63 -0.35 52 115
IKK complex 0.037 0.088 0.22 96 -0.12 11 107
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.026 0.11 0.27 56 -0.29 31 87
PDPK1 0.028 0.16 0.36 60 -0.39 46 106
TCR/CD3/MHC I/CD8/Fyn -0.027 0.26 0.45 19 -0.78 56 75
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 0.038 0.065 -10000 0 -0.35 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.13 -10000 0 -0.32 75 75
AP1 -0.11 0.21 -10000 0 -0.36 307 307
mol:PIP3 -0.13 0.19 -10000 0 -0.35 305 305
AKT1 0.012 0.07 0.31 3 -0.4 5 8
PTK2B -0.03 0.1 -10000 0 -0.33 52 52
RHOA 0.003 0.066 0.22 6 -0.32 23 29
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.11 0.24 2 -0.3 84 86
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 -0.33 102 105
NF kappa B1 p50/RelA -0.012 0.13 -10000 0 -0.34 88 88
endothelial cell migration 0.004 0.071 -10000 0 -0.45 18 18
ADCY4 -0.019 0.11 -10000 0 -0.49 28 28
ADCY5 -0.075 0.15 -10000 0 -0.49 56 56
ADCY6 -0.011 0.09 -10000 0 -0.46 20 20
ADCY7 -0.01 0.091 -10000 0 -0.47 20 20
ADCY1 -0.011 0.098 -10000 0 -0.45 24 24
ADCY2 -0.024 0.12 -10000 0 -0.5 31 31
ADCY3 -0.011 0.09 -10000 0 -0.46 20 20
ADCY8 -0.009 0.082 -10000 0 -0.44 18 18
ADCY9 -0.011 0.09 -10000 0 -0.46 20 20
GSK3B -0.029 0.1 0.28 3 -0.35 39 42
arachidonic acid secretion -0.016 0.098 -10000 0 -0.38 37 37
GNG2 0.019 0.053 -10000 0 -0.6 6 6
TRIP6 0.017 0.017 -10000 0 -0.42 1 1
GNAO1 0.005 0.076 -10000 0 -0.36 30 30
HRAS 0.024 0.01 0.27 1 -10000 0 1
NFKBIA -0.021 0.13 0.26 1 -0.35 88 89
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.12 -10000 0 -0.82 15 15
JUN 0.018 0.061 -10000 0 -0.6 8 8
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.014 0.14 -10000 0 -0.96 15 15
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 -0.015 0.11 0.24 2 -0.3 84 86
PLCB3 0.026 0.047 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 251 251
positive regulation of mitosis -0.016 0.098 -10000 0 -0.38 37 37
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 -0.36 38 38
GNAZ 0.006 0.059 -10000 0 -0.34 23 23
EGFR/PI3K-beta/Gab1 -0.12 0.2 -10000 0 -0.37 306 306
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 0.18 1 -0.16 1 2
ARHGEF1 0.021 0.065 -10000 0 -0.3 12 12
GNAI2 0.009 0.049 -10000 0 -0.32 17 17
GNAI3 0.009 0.05 -10000 0 -0.33 17 17
GNAI1 -0.011 0.1 -10000 0 -0.4 52 52
LPA/LPA3 -0.029 0.15 0.18 29 -0.43 97 126
LPA/LPA2 0.019 0.014 0.19 1 -10000 0 1
LPA/LPA1 0.014 0.059 -10000 0 -0.36 19 19
HB-EGF/EGFR -0.078 0.21 0.27 1 -0.37 257 258
HBEGF 0.067 0.079 0.27 21 -0.45 3 24
mol:DAG -0.015 0.11 0.24 2 -0.3 84 86
cAMP biosynthetic process -0.03 0.11 0.4 1 -0.41 40 41
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.26 24 -0.34 68 92
GNAQ -0.023 0.11 0.21 1 -0.33 95 96
LPAR2 0.025 0.009 0.27 1 -10000 0 1
LPAR3 -0.038 0.2 0.27 29 -0.6 93 122
LPAR1 0.017 0.071 -10000 0 -0.6 10 10
IL8 -0.13 0.24 0.37 21 -0.43 227 248
PTK2 -0.023 0.1 0.25 1 -0.34 69 70
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 -0.6 281 281
PLCG1 -0.025 0.12 0.2 4 -0.34 94 98
PLD2 -0.029 0.12 0.25 1 -0.34 103 104
G12/G13 0.038 0.052 -10000 0 -0.31 13 13
PI3K-beta 0.005 0.064 -10000 0 -0.37 11 11
cell migration 0.002 0.063 -10000 0 -0.25 17 17
SLC9A3R2 0.023 0.007 -10000 0 -10000 0 0
PXN -0.018 0.11 -10000 0 -0.37 38 38
HRAS/GTP -0.017 0.1 -10000 0 -0.37 46 46
RAC1 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.27 327 -0.6 1 328
PRKCE 0.024 0.022 -10000 0 -0.6 1 1
PRKCD -0.016 0.11 0.24 1 -0.3 73 74
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 -0.34 60 60
MAPKKK cascade -0.016 0.098 -10000 0 -0.38 37 37
contractile ring contraction involved in cytokinesis 0.002 0.067 0.22 6 -0.31 24 30
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.022 0.12 0.19 2 -0.33 97 99
GNA15 -0.022 0.11 0.18 4 -0.32 98 102
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 -0.34 102 105
GNA11 -0.022 0.11 0.21 1 -0.32 93 94
Rac1/GTP 0.03 0.12 -10000 0 -0.87 15 15
MMP2 0.004 0.072 -10000 0 -0.46 18 18
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.017 0.23 0.56 6 -0.64 19 25
CRP 0.003 0.25 0.57 22 -0.67 15 37
cell cycle arrest -0.027 0.25 0.56 9 -0.68 31 40
TIMP1 -0.011 0.22 0.54 7 -0.62 15 22
IL6ST -0.003 0.14 -10000 0 -0.59 43 43
Rac1/GDP -0.058 0.19 0.32 6 -0.47 61 67
AP1 -0.079 0.22 -10000 0 -0.58 44 44
GAB2 0.022 0.008 -10000 0 -10000 0 0
TNFSF11 -0.004 0.24 0.62 8 -0.72 10 18
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 60 60
AKT1 0.026 0.058 -10000 0 -0.52 4 4
FOXO1 0.027 0.059 0.43 1 -0.57 2 3
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 0.4 8 -0.48 49 57
MITF -0.08 0.19 0.28 8 -0.4 124 132
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.004 -10000 0 -10000 0 0
A2M -0.003 0.18 -10000 0 -1.2 20 20
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.013 0.13 -10000 0 -0.51 27 27
STAT3 -0.034 0.27 0.56 9 -0.74 32 41
STAT1 0.016 0.093 -10000 0 -0.84 7 7
CEBPD -0.002 0.24 0.57 12 -0.71 18 30
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.035 0.011 -10000 0 -10000 0 0
JUN 0.018 0.061 -10000 0 -0.6 8 8
PIAS3/MITF -0.065 0.18 0.33 1 -0.46 63 64
MAPK11 -0.085 0.17 -10000 0 -0.49 63 63
STAT3 (dimer)/FOXO1 -0.012 0.22 0.52 9 -0.58 22 31
GRB2/SOS1/GAB family -0.049 0.17 -10000 0 -0.46 47 47
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.093 0.18 -10000 0 -0.34 230 230
GRB2 0.024 0.011 0.27 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.15 0.46 0.56 19 -0.94 187 206
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.026 0.009 -10000 0 -10000 0 0
MYC 0.009 0.28 0.57 21 -1 24 45
FGG -0.014 0.24 0.58 13 -0.66 17 30
macrophage differentiation -0.027 0.25 0.56 9 -0.68 31 40
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.089 0.21 -10000 0 -0.36 266 266
JUNB -0.02 0.22 0.53 6 -0.62 19 25
FOS -0.17 0.29 -10000 0 -0.6 251 251
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.082 0.19 0.31 8 -0.41 129 137
STAT1/PIAS1 -0.05 0.2 0.36 7 -0.43 78 85
GRB2/SOS1/GAB family/SHP2/PI3K 0.027 0.062 -10000 0 -0.53 5 5
STAT3 (dimer) -0.032 0.26 0.56 9 -0.73 31 40
PRKCD -0.025 0.2 0.47 11 -0.52 32 43
IL6R 0.007 0.099 -10000 0 -0.6 21 21
SOCS3 -0.083 0.19 -10000 0 -0.63 38 38
gp130 (dimer)/JAK1/JAK1/LMO4 0.035 0.1 -10000 0 -0.37 43 43
Rac1/GTP -0.052 0.2 0.36 6 -0.47 61 67
HCK 0.027 0.029 0.27 12 -10000 0 12
MAPKKK cascade 0.004 0.14 -10000 0 -0.6 24 24
bone resorption -0.001 0.24 0.6 9 -0.66 11 20
IRF1 -0.021 0.23 0.56 6 -0.66 17 23
mol:GDP -0.074 0.19 0.3 8 -0.39 125 133
SOS1 0.025 0.004 -10000 0 -10000 0 0
VAV1 -0.076 0.19 0.3 8 -0.4 125 133
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.094 0.19 -10000 0 -0.55 64 64
PTPN11 0.013 0.083 -10000 0 -0.86 6 6
IL6/IL6RA -0.13 0.23 0.22 1 -0.41 318 319
gp130 (dimer)/TYK2/TYK2/LMO4 0.03 0.1 0.24 1 -0.38 44 45
gp130 (dimer)/JAK2/JAK2/LMO4 0.029 0.1 -10000 0 -0.38 43 43
IL6 -0.2 0.3 0.28 1 -0.6 305 306
PIAS3 0.023 0.006 -10000 0 -10000 0 0
PTPRE 0.007 0.034 -10000 0 -0.6 1 1
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.098 0.18 0.23 1 -0.33 241 242
LMO4 0.028 0.043 0.29 2 -0.6 3 5
STAT3 (dimer)/PIAS3 -0.037 0.25 0.55 7 -0.68 35 42
MCL1 0.058 0.096 0.49 1 -0.62 1 2
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.038 0.22 0.43 4 -0.65 82 86
IHH 0.017 0.081 0.29 6 -0.25 1 7
SHH Np/Cholesterol/GAS1 -0.001 0.081 -10000 0 -0.35 39 39
LRPAP1 0.024 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 -0.64 66 66
SMO -0.039 0.21 -10000 0 -0.67 67 67
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 -0.65 67 67
STIL 0.013 0.18 0.3 26 -0.5 59 85
DHH N/PTCH2 -0.017 0.16 -10000 0 -0.47 86 86
DHH N/PTCH1 -0.023 0.2 -10000 0 -0.56 87 87
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DHH 0.008 0.1 0.27 1 -0.6 22 23
PTHLH -0.055 0.29 0.44 10 -0.84 85 95
determination of left/right symmetry -0.038 0.2 -10000 0 -0.65 67 67
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
skeletal system development -0.054 0.29 0.44 10 -0.83 85 95
IHH N/Hhip 0.029 0.056 -10000 0 -0.49 1 1
DHH N/Hhip 0.023 0.081 -10000 0 -0.44 23 23
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.038 0.2 -10000 0 -0.65 67 67
pancreas development 0.024 0.031 0.27 7 -0.6 1 8
HHAT 0.02 0.023 -10000 0 -0.6 1 1
PI3K 0.034 0.01 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.6 44 44
somite specification -0.038 0.2 -10000 0 -0.65 67 67
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 -0.36 170 173
SHH -0.002 0.037 0.36 4 -0.45 1 5
catabolic process -0.028 0.2 0.35 1 -0.58 86 87
SMO/Vitamin D3 -0.005 0.2 0.37 12 -0.59 62 74
SHH Np/Cholesterol/Hhip 0.016 0.033 0.29 5 -0.36 2 7
LRP2 -0.13 0.28 0.27 20 -0.6 206 226
receptor-mediated endocytosis -0.078 0.22 0.31 8 -0.64 72 80
SHH Np/Cholesterol/BOC -0.006 0.091 -10000 0 -0.35 49 49
SHH Np/Cholesterol/CDO 0.012 0.042 -10000 0 -0.36 9 9
mesenchymal cell differentiation -0.016 0.033 0.36 2 -0.28 5 7
mol:Vitamin D3 0.006 0.18 0.35 17 -0.52 64 81
IHH N/PTCH2 -0.014 0.15 -10000 0 -0.49 71 71
CDON 0.015 0.065 -10000 0 -0.6 9 9
IHH N/PTCH1 -0.019 0.21 0.36 3 -0.58 86 89
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 0.015 -10000 0 -0.36 1 1
PTCH1 -0.028 0.2 0.35 1 -0.58 86 87
HHIP 0.024 0.032 0.27 7 -0.6 1 8
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.031 0.049 -10000 0 -0.33 12 12
RGS9BP 0.037 0.055 0.27 44 -10000 0 44
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.018 0.27 4 -10000 0 4
mol:Na + 0.039 0.048 -10000 0 -10000 0 0
mol:ADP -0.007 0.027 0.25 4 -10000 0 4
GNAT2 0.024 0.013 0.27 2 -10000 0 2
RGS9-1/Gbeta5/R9AP 0.009 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 0.02 0.27 5 -10000 0 5
CNGB3 0.023 0.039 0.27 20 -10000 0 20
Cone Metarhodopsin II/X-Arrestin 0.016 0.014 0.18 6 -10000 0 6
mol:Ca2+ 0.14 0.11 0.3 154 -10000 0 154
Cone PDE6 0.024 0.12 0.34 1 -0.34 73 74
Cone Metarhodopsin II 0.026 0.018 -10000 0 -10000 0 0
Na + (4 Units) 0.12 0.097 0.32 58 -10000 0 58
GNAT2/GDP 0.018 0.12 0.28 1 -0.33 76 77
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.035 -10000 0 -10000 0 0
Cone Transducin 0.034 0.052 -10000 0 -0.35 12 12
SLC24A2 0.18 0.12 0.27 522 -10000 0 522
GNB3/GNGT2 0.024 0.06 -10000 0 -0.43 13 13
GNB3 0.015 0.076 0.27 2 -0.6 12 14
GNAT2/GTP 0.018 0.009 0.18 2 -10000 0 2
CNGA3 0.049 0.074 0.27 87 -10000 0 87
ARR3 0.021 0.021 0.27 6 -10000 0 6
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.039 0.048 -10000 0 -10000 0 0
mol:Pi 0.008 0.13 -10000 0 -0.38 76 76
Cone CNG Channel 0.05 0.047 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.18 0.12 0.27 522 -10000 0 522
RGS9 -0.035 0.18 0.27 7 -0.6 78 85
PDE6C 0.02 0.004 -10000 0 -10000 0 0
GNGT2 0.021 0.023 -10000 0 -0.6 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.018 0.27 4 -10000 0 4
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.036 0.11 0.39 23 -10000 0 23
VDR 0.024 0.003 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.028 0.12 0.26 3 -0.27 159 162
RXRs/LXRs/DNA/Oxysterols -0.009 0.12 0.3 3 -0.43 13 16
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 0.004 0.081 -10000 0 -0.33 37 37
RXRs/NUR77 -0.057 0.2 -10000 0 -0.38 202 202
RXRs/PPAR -0.1 0.18 -10000 0 -0.33 271 271
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.049 0.041 -10000 0 -0.34 7 7
RARA 0.022 0.007 -10000 0 -10000 0 0
NCOA1 0.024 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.038 0.039 -10000 0 -0.34 7 7
RARG 0.025 0.002 -10000 0 -10000 0 0
RPS6KB1 0.076 0.19 0.62 83 -10000 0 83
RARs/THRs/DNA/SMRT 0.005 0.076 -10000 0 -0.31 36 36
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.033 0.16 -10000 0 -0.34 165 165
NR1H4 0.021 0.023 0.27 7 -10000 0 7
RXRs/LXRs/DNA -0.011 0.16 -10000 0 -0.33 151 151
NR1H2 0.027 0.013 -10000 0 -10000 0 0
NR1H3 0.028 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.026 0.16 -10000 0 -0.33 165 165
NR4A1 -0.033 0.18 -10000 0 -0.6 76 76
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.032 0.11 -10000 0 -0.24 143 143
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 0.37 3 -1 8 11
mol:Oxysterols 0.003 0.009 -10000 0 -10000 0 0
cholesterol transport -0.008 0.12 0.3 3 -0.43 13 16
PPARA 0.022 0.031 -10000 0 -0.6 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.018 0.061 -10000 0 -0.6 8 8
RXRs/NUR77/BCL2 -0.074 0.16 -10000 0 -0.32 214 214
SREBF1 -0.009 0.11 -10000 0 -0.52 3 3
RXRs/RXRs/DNA/9cRA -0.033 0.16 -10000 0 -0.34 165 165
ABCA1 -0.013 0.13 -10000 0 -0.75 7 7
RARs/THRs 0.045 0.091 -10000 0 -0.36 34 34
RXRs/FXR -0.029 0.16 -10000 0 -0.35 165 165
BCL2 0.008 0.098 -10000 0 -0.6 21 21
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.022 -10000 0 -0.6 1 1
LAT2 -0.021 0.1 -10000 0 -0.36 41 41
AP1 -0.069 0.19 -10000 0 -0.47 81 81
mol:PIP3 0.007 0.17 0.34 38 -0.37 72 110
IKBKB 0.034 0.13 0.27 95 -0.26 19 114
AKT1 0.011 0.17 0.31 118 -0.42 14 132
IKBKG 0.015 0.11 0.24 58 -0.27 21 79
MS4A2 -0.022 0.16 0.26 4 -0.59 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 0.3 17 -0.41 18 35
mol:Ca2+ 0.013 0.14 0.29 46 -0.32 39 85
LYN 0.022 0.014 -10000 0 -10000 0 0
CBLB -0.021 0.1 -10000 0 -0.36 39 39
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.006 0.13 -10000 0 -0.35 102 102
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.009 0.18 0.33 101 -0.34 113 214
PTPN13 -0.016 0.16 -10000 0 -0.59 33 33
PTPN11 0.022 0.019 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.011 0.13 0.31 30 -0.34 22 52
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.03 0.13 -10000 0 -0.37 79 79
LAT -0.021 0.1 -10000 0 -0.36 41 41
PAK2 0.012 0.13 0.3 22 -0.45 18 40
NFATC2 -0.035 0.13 -10000 0 -0.6 36 36
HRAS 0.008 0.13 0.28 15 -0.48 20 35
GAB2 0.022 0.008 -10000 0 -10000 0 0
PLA2G1B 0 0.11 -10000 0 -0.85 12 12
Fc epsilon R1 -0.029 0.17 -10000 0 -0.42 122 122
Antigen/IgE/Fc epsilon R1 -0.024 0.15 -10000 0 -0.38 122 122
mol:GDP -0.016 0.11 -10000 0 -0.49 19 19
JUN 0.018 0.061 -10000 0 -0.6 8 8
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 251 251
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.018 0.11 -10000 0 -0.35 47 47
CHUK 0.014 0.11 0.24 61 -0.27 22 83
KLRG1 -0.019 0.097 -10000 0 -0.33 40 40
VAV1 -0.021 0.1 -10000 0 -0.36 41 41
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.019 0.1 -10000 0 -0.36 37 37
negative regulation of mast cell degranulation -0.008 0.1 -10000 0 -0.39 20 20
BTK -0.014 0.11 -10000 0 -0.51 18 18
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.035 0.14 -10000 0 -0.34 116 116
GAB2/PI3K/SHP2 -0.05 0.1 -10000 0 -0.33 79 79
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 -0.37 119 119
FCER1G 0.019 0.019 0.26 1 -10000 0 1
FCER1A -0.053 0.2 -10000 0 -0.61 95 95
Antigen/IgE/Fc epsilon R1/Fyn -0.015 0.15 -10000 0 -0.36 115 115
MAPK3 0 0.11 -10000 0 -0.86 12 12
MAPK1 -0.004 0.11 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.021 0.18 -10000 0 -0.59 51 51
DUSP1 -0.054 0.21 -10000 0 -0.6 103 103
NF-kappa-B/RelA 0.008 0.06 0.16 1 -0.18 8 9
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 -0.022 0.11 -10000 0 -0.37 40 40
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 0.28 8 -0.49 19 27
cytokine secretion -0.003 0.036 -10000 0 -10000 0 0
SPHK1 -0.02 0.1 -10000 0 -0.37 39 39
PTK2 -0.01 0.16 -10000 0 -0.66 26 26
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.026 0.14 -10000 0 -0.38 82 82
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.004 0.17 0.33 33 -0.43 43 76
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 -0.01 0.097 -10000 0 -0.37 21 21
MAP2K4 -0.075 0.3 -10000 0 -0.84 105 105
Fc epsilon R1/FcgammaRIIB -0.015 0.16 -10000 0 -0.39 119 119
mol:Choline -0.009 0.18 0.33 101 -0.34 113 214
SHC/Grb2/SOS1 0.01 0.11 -10000 0 -0.43 18 18
FYN 0.022 0.023 -10000 0 -0.6 1 1
DOK1 0.024 0.003 -10000 0 -10000 0 0
PXN -0.01 0.15 -10000 0 -0.59 26 26
HCLS1 -0.021 0.1 -10000 0 -0.37 37 37
PRKCB 0.012 0.14 0.27 60 -0.32 44 104
FCGR2B 0.018 0.039 0.27 1 -0.6 3 4
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.008 0.1 -10000 0 -0.39 20 20
LCP2 0.024 0.01 0.27 1 -10000 0 1
PLA2G4A -0.046 0.14 -10000 0 -0.38 94 94
RASA1 0.024 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.18 0.33 101 -0.34 113 214
IKK complex 0.031 0.11 0.25 92 -0.21 11 103
WIPF1 0.024 0.004 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.034 0.15 -10000 0 -0.62 47 47
PDGF/PDGFRA/CRKL -0.012 0.11 -10000 0 -0.44 48 48
positive regulation of JUN kinase activity 0.023 0.087 -10000 0 -0.35 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 -0.049 0.11 -10000 0 -0.48 43 43
PLCG1 -0.049 0.11 -10000 0 -0.48 43 43
PDGF/PDGFRA/alphaV Integrin -0.012 0.11 -10000 0 -0.44 48 48
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.1 -10000 0 -0.48 43 43
CAV3 0.02 0.013 0.27 2 -10000 0 2
CAV1 -0.1 0.25 -10000 0 -0.6 164 164
SHC/Grb2/SOS1 0.025 0.088 -10000 0 -0.36 35 35
PDGF/PDGFRA/Shf -0.012 0.12 -10000 0 -0.45 48 48
FOS -0.33 0.45 -10000 0 -0.97 267 267
JUN -0.041 0.05 -10000 0 -0.44 7 7
oligodendrocyte development -0.012 0.11 -10000 0 -0.44 48 48
GRB2 0.023 0.011 0.27 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:DAG -0.049 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 -0.43 49 49
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.017 0.098 -10000 0 -0.39 44 44
PDGF/PDGFRA/Crk/C3G 0.016 0.099 -10000 0 -0.39 46 46
JAK1 -0.028 0.1 0.23 1 -0.45 46 47
ELK1/SRF -0.036 0.093 0.32 1 -0.38 44 45
SHB 0.024 0.009 0.27 1 -10000 0 1
SHF 0.023 0.024 0.27 1 -0.6 1 2
CSNK2A1 0.037 0.024 -10000 0 -10000 0 0
GO:0007205 -0.048 0.11 0.22 1 -0.48 47 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.023 0.087 -10000 0 -0.35 35 35
PDGF/PDGFRA/SHB -0.012 0.11 -10000 0 -0.43 49 49
PDGF/PDGFRA/Caveolin-1 -0.1 0.23 -10000 0 -0.51 188 188
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 -0.44 48 48
JAK-STAT cascade -0.027 0.1 0.23 1 -0.45 46 47
cell proliferation -0.012 0.11 -10000 0 -0.45 48 48
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.021 0.25 2 -10000 0 2
AES 0.022 0.019 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.024 0.005 -10000 0 -10000 0 0
DKK2 0.014 0.082 0.27 2 -0.6 14 16
TLE1 0.019 0.053 0.22 2 -0.61 5 7
MACF1 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.11 0.1 0.32 27 -0.46 1 28
WIF1 -0.3 0.31 0.27 9 -0.6 424 433
beta catenin/RanBP3 0.018 0.087 0.42 26 -0.4 1 27
KREMEN2 0.12 0.12 0.27 346 -10000 0 346
DKK1 0.024 0.17 0.27 110 -0.6 43 153
beta catenin/beta TrCP1 0.11 0.097 0.31 22 -0.41 1 23
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.027 0.24 0.59 74 -1.3 13 87
AXIN1 0.024 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 0.31 5 -0.61 18 23
Axin1/APC/GSK3 0.046 0.056 0.24 1 -0.32 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.041 0.063 0.31 2 -0.37 3 5
HNF1A 0.025 0.028 0.26 8 -10000 0 8
CTBP1 0.021 0.019 0.24 2 -10000 0 2
MYC 0.12 0.35 0.58 215 -1.4 20 235
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.096 0.35 1 -0.35 11 12
NKD1 0.021 0.062 0.27 14 -0.6 6 20
TCF4 0.018 0.052 0.23 2 -0.6 5 7
TCF3 0.022 0.02 0.23 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.057 0.024 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.002 0.13 0.47 25 -0.52 15 40
LEF1 0.057 0.087 0.26 119 -10000 0 119
DVL1 0.055 0.056 -10000 0 -0.36 2 2
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.15 0.3 8 -0.65 21 29
DKK1/LRP6/Kremen 2 0.097 0.14 0.35 54 -0.36 37 91
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.25 2 -10000 0 2
NLK 0.023 0.013 0.27 1 -10000 0 1
CCND1 0.094 0.27 0.62 142 -1.2 5 147
WNT1 0.024 0.01 0.27 1 -10000 0 1
GSK3A 0.025 0.004 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.06 0.3 5 -0.3 8 13
APC 0.016 0.06 0.36 7 -10000 0 7
WNT1/LRP6/FZD1 0.12 0.11 0.23 399 -10000 0 399
CREBBP 0.021 0.018 0.23 1 -10000 0 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.42 0.28 -10000 0 -0.6 584 584
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.27 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
HIF1A/p53 0.031 0.05 -10000 0 -0.27 12 12
HIF1A 0.018 0.04 -10000 0 -0.27 8 8
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.034 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.057 0.086 0.27 118 -10000 0 118
ARNT/IPAS -0.28 0.21 -10000 0 -0.41 590 590
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.047 -10000 0 -0.28 12 12
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.039 0.023 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.033 0.05 -10000 0 -0.28 12 12
PHD1-3/OS9 0.056 0.049 -10000 0 -0.36 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.052 -10000 0 -0.3 4 4
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.027 0.05 -10000 0 -0.28 11 11
EGLN3 0.043 0.066 0.27 65 -10000 0 65
EGLN2 0.025 0.015 0.27 3 -10000 0 3
EGLN1 0.019 0.024 -10000 0 -0.6 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.071 -10000 0 -0.52 12 12
ARNT 0.02 0.01 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.051 0.074 0.27 10 -0.27 11 21
Presenilin action in Notch and Wnt signaling

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.023 0.076 -10000 0 -0.39 18 18
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.006 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.034 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 -0.61 5 5
AP1 -0.087 0.16 -10000 0 -0.33 239 239
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 0.022 0.074 -10000 0 -0.38 20 20
WIF1 -0.3 0.31 0.27 9 -0.6 424 433
NOTCH1 0.01 0.064 -10000 0 -0.39 20 20
PSENEN 0.025 0.009 0.27 1 -10000 0 1
KREMEN2 0.12 0.12 0.27 346 -10000 0 346
DKK1 0.024 0.17 0.27 110 -0.6 43 153
beta catenin/beta TrCP1 0.006 0.071 -10000 0 -0.36 6 6
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.061 -10000 0 -0.46 7 7
CtBP/CBP/TCF1/TLE1/AES 0.012 0.043 -10000 0 -0.31 5 5
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.17 0.29 -10000 0 -0.6 251 251
JUN 0.018 0.061 -10000 0 -0.6 8 8
MAP3K7 0.021 0.01 -10000 0 -10000 0 0
CTNNB1 -0.003 0.071 0.25 1 -0.38 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.096 0.35 1 -0.35 11 12
HNF1A 0.026 0.021 0.26 6 -10000 0 6
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.017 0.22 -10000 0 -1.3 23 23
NKD1 0.021 0.062 0.27 14 -0.6 6 20
FZD1 0.024 0.003 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.008 0.12 -10000 0 -0.44 19 19
apoptosis -0.086 0.16 -10000 0 -0.33 239 239
Delta 1/NOTCHprecursor 0.02 0.076 -10000 0 -0.39 18 18
DLL1 0.021 0.031 -10000 0 -0.6 2 2
PPARD 0.013 0.1 -10000 0 -0.84 11 11
Gamma Secretase 0.055 0.035 -10000 0 -0.34 1 1
APC 0.003 0.086 -10000 0 -0.48 18 18
DVL1 -0.032 0.082 -10000 0 -0.4 26 26
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.097 0.14 0.35 54 -0.36 37 91
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.01 -10000 0 -10000 0 0
CCND1 0.021 0.1 -10000 0 -1.1 5 5
WNT1 0.023 0.01 0.27 1 -10000 0 1
Axin1/APC/beta catenin 0.01 0.1 0.34 3 -0.47 12 15
DKK2 0.014 0.082 0.27 2 -0.6 14 16
NOTCH1 precursor/DVL1 -0.022 0.11 -10000 0 -0.61 17 17
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.12 -10000 0 -0.45 19 19
PPP2R5D -0.006 0.065 0.3 5 -0.37 16 21
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.2 -10000 0 -0.36 409 409
RBPJ 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.066 0.21 0.3 2 -0.4 157 159
MAP3K8 0.009 0.047 -10000 0 -0.61 4 4
FOS -0.025 0.15 0.32 2 -0.44 43 45
PRKCA -0.004 0.094 0.25 2 -0.61 18 20
PTPN7 0.019 0.061 0.25 44 -10000 0 44
HRAS 0.023 0.01 0.27 1 -10000 0 1
PRKCB 0.005 0.081 0.26 14 -0.61 11 25
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.035 -10000 0 -10000 0 0
MAPK3 0.006 0.095 -10000 0 -0.81 5 5
MAP2K1 -0.014 0.12 -10000 0 -0.51 35 35
ELK1 0.005 0.03 -10000 0 -10000 0 0
BRAF -0.015 0.1 -10000 0 -0.49 33 33
mol:GTP -0.002 0.003 -10000 0 -0.006 267 267
MAPK1 -0.01 0.12 -10000 0 -0.45 33 33
RAF1 -0.014 0.1 -10000 0 -0.51 30 30
KRAS 0.022 0.006 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.031 0.15 0.36 48 -0.35 48 96
TBX21 -0.005 0.36 0.78 17 -1.3 41 58
B2M 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.021 0.037 -10000 0 -10000 0 0
IL12RB1 0.028 0.07 0.35 25 -0.64 1 26
GADD45B 0.021 0.26 0.68 17 -0.89 25 42
IL12RB2 0.023 0.16 0.28 93 -0.6 36 129
GADD45G 0.032 0.26 0.67 18 -0.91 20 38
natural killer cell activation 0.005 0.025 0.17 1 -10000 0 1
RELB 0.026 0.019 0.27 5 -10000 0 5
RELA 0.024 0.004 -10000 0 -10000 0 0
IL18 0.033 0.043 0.28 21 -10000 0 21
IL2RA 0.029 0.089 0.27 46 -0.6 10 56
IFNG 0.058 0.086 0.27 119 -10000 0 119
STAT3 (dimer) 0.02 0.25 0.59 27 -0.7 37 64
HLA-DRB5 0.019 0.081 0.26 50 -0.61 5 55
FASLG 0.039 0.3 0.8 21 -1 24 45
NF kappa B2 p52/RelB 0.004 0.25 0.76 3 -0.82 35 38
CD4 0.008 0.025 -10000 0 -10000 0 0
SOCS1 0.024 0.031 0.27 6 -0.6 1 7
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D 0.005 0.1 0.27 29 -0.61 15 44
CD3E 0.005 0.098 0.28 24 -0.61 15 39
CD3G 0.003 0.11 0.28 33 -0.61 20 53
IL12Rbeta2/JAK2 0.031 0.13 0.31 25 -0.45 36 61
CCL3 0.017 0.28 0.75 17 -0.99 26 43
CCL4 0.019 0.27 0.76 16 -0.99 22 38
HLA-A 0.026 0.016 0.27 2 -10000 0 2
IL18/IL18R 0.057 0.12 0.41 11 -0.4 40 51
NOS2 0.017 0.28 0.73 17 -1 24 41
IL12/IL12R/TYK2/JAK2/SPHK2 0.029 0.15 0.36 47 -0.35 52 99
IL1R1 0.007 0.3 0.74 16 -1.1 30 46
IL4 -0.009 0.038 -10000 0 -10000 0 0
JAK2 0.021 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 0.37 29 -0.67 63 92
RAB7A 0.032 0.23 0.64 15 -0.8 17 32
lysosomal transport 0.034 0.23 0.62 18 -0.76 17 35
FOS -0.36 0.64 0.62 12 -1.2 289 301
STAT4 (dimer) 0.045 0.28 0.61 29 -0.86 37 66
STAT5A (dimer) 0.033 0.28 0.64 33 -0.82 36 69
GZMA 0.01 0.3 0.72 24 -1.1 25 49
GZMB 0.009 0.33 0.74 23 -1.2 31 54
HLX 0.021 0.013 0.27 1 -10000 0 1
LCK 0.012 0.3 0.71 26 -0.9 39 65
TCR/CD3/MHC II/CD4 -0.057 0.18 0.3 18 -0.44 96 114
IL2/IL2R 0.067 0.1 0.44 29 -0.38 13 42
MAPK14 0.027 0.27 0.68 17 -0.87 28 45
CCR5 0.024 0.27 0.75 22 -0.86 27 49
IL1B 0.016 0.077 0.3 2 -0.61 9 11
STAT6 0.033 0.12 0.42 28 -0.52 5 33
STAT4 0 0.12 0.27 1 -0.6 32 33
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.035 0.27 18 -10000 0 18
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.004 -10000 0 -10000 0 0
IL12B 0.067 0.11 0.29 157 -10000 0 157
CD8A 0.029 0.065 0.29 21 -0.6 5 26
CD8B 0.01 0.12 0.28 20 -0.6 29 49
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.031 0.15 0.35 48 -0.36 48 96
IL2RB 0.033 0.048 0.27 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process 0.05 0.27 0.59 33 -0.77 37 70
IL2RG 0.03 0.068 0.27 32 -0.6 5 37
IL12 0.04 0.16 0.32 56 -0.45 48 104
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
CD247 0.003 0.087 0.28 12 -0.61 13 25
IL2 0.023 0.025 0.27 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.011 0.16 0.31 11 -0.61 47 58
IL12/IL12R/TYK2/JAK2 0.018 0.31 0.75 28 -0.92 37 65
MAP2K3 0.021 0.27 0.67 18 -0.87 32 50
RIPK2 0.02 0.018 0.27 3 -10000 0 3
MAP2K6 0.026 0.26 0.67 18 -0.86 29 47
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.006 0.037 0.24 2 -0.6 1 3
IL18RAP 0.007 0.12 0.3 4 -0.6 31 35
IL12Rbeta1/TYK2 0.037 0.068 0.32 21 -0.5 1 22
EOMES -0.017 0.19 -10000 0 -0.98 24 24
STAT1 (dimer) 0.054 0.27 0.64 48 -0.76 27 75
T cell proliferation 0.035 0.22 0.52 21 -0.67 29 50
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 -0.73 30 34
ATF2 0.026 0.25 0.64 17 -0.8 28 45
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.024 0.13 0.44 48 -0.24 7 55
KIRREL -0.013 0.15 -10000 0 -0.6 49 49
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.024 0.13 0.24 7 -0.44 48 55
PLCG1 0.024 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.042 0.11 0.29 4 -0.34 46 50
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.081 0.24 1 -0.29 39 40
FYN 0.023 0.13 0.28 87 -0.33 45 132
mol:Ca2+ 0.039 0.11 0.29 3 -0.34 44 47
mol:DAG 0.04 0.11 0.29 4 -0.34 44 48
NPHS2 0.017 0.032 0.27 5 -10000 0 5
mol:IP3 0.04 0.11 0.29 4 -0.34 44 48
regulation of endocytosis 0.03 0.097 0.25 5 -0.31 45 50
Nephrin/NEPH1/podocin/Cholesterol 0.032 0.11 0.26 9 -0.34 46 55
establishment of cell polarity 0.024 0.13 0.24 7 -0.44 48 55
Nephrin/NEPH1/podocin/NCK1-2 0.052 0.11 0.33 1 -0.32 44 45
Nephrin/NEPH1/beta Arrestin2 0.033 0.1 0.26 4 -0.31 45 49
NPHS1 0.063 0.093 0.27 130 -10000 0 130
Nephrin/NEPH1/podocin 0.033 0.1 0.31 4 -0.33 45 49
TJP1 0.023 0.022 -10000 0 -0.6 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.041 0.11 0.29 4 -0.34 44 48
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.039 0.11 0.3 5 -0.34 43 48
GRB2 0.023 0.011 0.27 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.022 0.13 0.29 86 -0.33 50 136
cytoskeleton organization 0.011 0.1 0.28 15 -0.34 41 56
Nephrin/NEPH1 0.023 0.097 0.19 7 -0.32 47 54
Nephrin/NEPH1/ZO-1 0.033 0.11 -10000 0 -0.37 47 47
FAS signaling pathway (CD95)

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
SPTAN1 -0.004 0.044 0.22 23 -10000 0 23
RFC1 -0.004 0.042 0.22 21 -10000 0 21
PRKDC 0.016 0.08 0.23 89 -10000 0 89
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.02 0.1 -10000 0 -0.64 18 18
FASLG/FAS/FADD/FAF1 -0.005 0.056 0.23 7 -0.32 5 12
MAP2K4 -0.09 0.18 0.39 2 -0.45 68 70
mol:ceramide -0.023 0.096 -10000 0 -0.41 12 12
GSN -0.009 0.062 0.22 23 -0.38 11 34
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.072 -10000 0 -0.42 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 0.009 0.02 -10000 0 -10000 0 0
RB1 -0.004 0.041 0.22 20 -10000 0 20
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET -0.056 0.2 -10000 0 -0.43 179 179
ARHGDIB -0.002 0.049 0.23 28 -10000 0 28
FADD 0.005 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.068 0.37 11 -0.22 23 34
NFKB1 -0.049 0.12 -10000 0 -0.6 16 16
MAPK8 -0.16 0.26 0.56 2 -0.47 313 315
DFFA -0.004 0.042 0.22 20 -0.19 5 25
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 0.041 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.036 0.27 17 -10000 0 17
FAF1 0.002 0.03 -10000 0 -10000 0 0
PARP1 -0.001 0.054 0.25 27 -10000 0 27
DFFB -0.005 0.042 0.22 20 -0.19 5 25
CHUK -0.044 0.11 -10000 0 -0.57 14 14
FASLG 0.009 0.079 0.26 33 -0.62 6 39
FAS/FADD 0.008 0.038 -10000 0 -0.35 2 2
HGF -0.01 0.14 -10000 0 -0.6 46 46
LMNA -0.003 0.058 0.39 1 -10000 0 1
CASP6 -0.004 0.041 0.22 20 -10000 0 20
CASP10 0.003 0.041 -10000 0 -0.62 2 2
CASP3 0 0.046 0.28 20 -10000 0 20
PTPN13 0.009 0.096 -10000 0 -0.6 20 20
CASP8 -0.021 0.025 -10000 0 -10000 0 0
IL6 -0.46 0.63 -10000 0 -1.2 323 323
MET -0.079 0.23 -10000 0 -0.6 136 136
ICAD/CAD -0.006 0.037 0.2 16 -10000 0 16
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.097 -10000 0 -0.42 12 12
activation of caspase activity by cytochrome c -0.019 0.022 -10000 0 -10000 0 0
PAK2 -0.002 0.054 0.24 31 -0.19 11 42
BCL2 0.008 0.098 -10000 0 -0.6 21 21
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.011 0.14 -10000 0 -0.6 46 46
HRAS 0.024 0.01 0.27 1 -10000 0 1
EGFR -0.19 0.3 -10000 0 -0.6 281 281
AKT -0.012 0.12 0.32 5 -0.28 78 83
FOXO3 0.022 0.023 -10000 0 -0.6 1 1
AKT1 0.024 0.005 -10000 0 -10000 0 0
FOXO1 0.022 0.023 -10000 0 -0.6 1 1
AKT3 0.014 0.062 -10000 0 -0.6 8 8
FOXO4 0.025 0.001 -10000 0 -10000 0 0
MET -0.079 0.23 -10000 0 -0.6 136 136
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.02 0.06 0.27 4 -0.6 7 11
PIK3R3 0.024 0.009 0.27 1 -10000 0 1
PIK3R2 0.024 0.004 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.059 0.14 0.21 4 -0.25 258 262
ERBB2 0.021 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.005 0.096 0.35 38 -0.27 1 39
PI3K -0.046 0.15 0.27 12 -0.33 128 140
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
KRAS 0.024 0.005 -10000 0 -10000 0 0
FOXO 0.039 0.058 0.28 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
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.003 0.058 -10000 0 -0.32 2 2
adherens junction organization -0.015 0.095 -10000 0 -0.34 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.084 0.16 0.34 3 -0.35 79 82
FMN1 -0.013 0.091 -10000 0 -0.32 44 44
mol:IP3 0 0.048 -10000 0 -0.26 1 1
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 0.025 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.079 -10000 0 -0.31 36 36
VASP -0.011 0.084 -10000 0 -0.31 39 39
ZYX -0.01 0.085 -10000 0 -0.31 39 39
JUB -0.01 0.086 -10000 0 -0.31 41 41
EGFR(dimer) -0.11 0.19 -10000 0 -0.35 275 275
E-cadherin/beta catenin-gamma catenin 0.032 0.06 -10000 0 -0.37 14 14
mol:PI-3-4-5-P3 0.018 0.07 -10000 0 -0.31 2 2
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.018 0.071 -10000 0 -0.31 2 2
FYN -0.003 0.063 -10000 0 -0.38 3 3
mol:Ca2+ 0.001 0.047 -10000 0 -0.25 1 1
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:DAG 0 0.048 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
RhoA/GDP -0.084 0.16 0.36 2 -0.35 81 83
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 0.3 -10000 0 -0.6 281 281
CASR -0.001 0.051 0.23 1 -10000 0 1
RhoA/GTP 0.015 0.053 -10000 0 -10000 0 0
AKT2 0.002 0.061 -10000 0 -0.3 2 2
actin cable formation -0.015 0.089 0.25 2 -0.34 31 33
apoptosis -0.006 0.07 0.32 5 -0.23 6 11
CTNNA1 0.025 0.005 -10000 0 -10000 0 0
mol:GDP -0.099 0.16 -10000 0 -0.32 243 243
PIP5K1A -0.01 0.08 -10000 0 -0.32 36 36
PLCG1 0 0.048 -10000 0 -10000 0 0
Rac1/GTP -0.093 0.18 -10000 0 -0.33 264 264
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
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 0.065 0.45 1 -0.27 12 13
CDKN1A -0.009 0.028 -10000 0 -0.8 1 1
KAT2B 0.024 0.003 -10000 0 -10000 0 0
BAX 0.024 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.011 -10000 0 -0.26 1 1
FOXO1 0.022 0.023 -10000 0 -0.6 1 1
FOXO4 0.011 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.35 0.31 0.27 22 -0.6 500 522
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.009 0.019 -10000 0 -10000 0 0
PPARGC1A -0.1 0.25 0.27 9 -0.6 167 176
FHL2 0.021 0.05 0.27 2 -0.6 5 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.033 0.011 -10000 0 -10000 0 0
HIST2H4A 0.018 0.065 0.27 12 -0.45 1 13
SIRT1/FOXO3a 0.015 0.027 -10000 0 -0.2 4 4
SIRT1 0.022 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.025 -10000 0 -0.39 1 1
SIRT1/Histone H1b 0.028 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 -0.38 167 167
p53/SIRT1 0.027 0.017 0.41 1 -10000 0 1
SIRT1/FOXO4 0.023 0.037 -10000 0 -0.21 1 1
FOXO1/FHL2/SIRT1 0.038 0.04 -10000 0 -0.36 6 6
HIST1H1E 0.02 0.03 0.23 3 -10000 0 3
SIRT1/p300 0.033 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.03 0.022 -10000 0 -10000 0 0
TP53 0.02 0.01 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 -0.41 585 585
ACSS2 -0.008 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.03 0.023 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.083 0.17 -10000 0 -0.52 20 20
Syndecan-3/Neurocan 0.026 0.075 0.28 13 -0.38 16 29
POMC 0.018 0.091 0.27 18 -0.6 15 33
EGFR -0.19 0.3 -10000 0 -0.6 281 281
Syndecan-3/EGFR -0.09 0.17 -10000 0 -0.33 221 221
AGRP 0.021 0.024 0.27 7 -10000 0 7
NCSTN 0.021 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.009 0.27 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.022 -10000 0 -0.6 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.057 0.27 48 -10000 0 48
long-term memory 0.035 0.063 -10000 0 -0.36 12 12
Syndecan-3/IL8 0.021 0.087 0.29 9 -0.35 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 0.27 12 -10000 0 12
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.24 0.31 0.27 1 -0.6 355 356
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 0.039 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 0.27 51 -0.6 16 67
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 12 12
Syndecan-3/CASK 0 0.056 -10000 0 -0.38 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
Rapid glucocorticoid signaling

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
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 0.27 7 -10000 0 7
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.001 -10000 0 -10000 0 0
MAPK11 0.005 0.018 -10000 0 -0.37 2 2
LPA4-mediated signaling events

Figure 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 0.18 -10000 0 -0.39 250 250
ADCY6 -0.008 0.013 -10000 0 -0.38 1 1
ADCY7 -0.007 0.013 -10000 0 -0.38 1 1
ADCY1 -0.007 0.064 -10000 0 -0.39 19 19
ADCY2 -0.031 0.11 0.25 6 -0.39 63 69
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 -0.45 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 0.2 30 -0.25 37 67
Glypican 2 network

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
MDK 0.032 0.043 0.27 27 -10000 0 27
GPC2 0.047 0.084 0.27 86 -0.6 3 89
GPC2/Midkine 0.055 0.071 0.38 12 -0.45 3 15
neuron projection morphogenesis 0.055 0.071 0.38 12 -0.45 3 15
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.011 0.045 -10000 0 -0.27 16 16
epithelial cell differentiation 0.036 0.056 -10000 0 -0.33 14 14
CYFIP2 0.03 0.045 0.27 22 -0.6 1 23
ENAH -0.005 0.06 0.27 8 -10000 0 8
EGFR -0.19 0.3 -10000 0 -0.6 281 281
EPHA2 0.02 0.049 -10000 0 -0.6 5 5
MYO6 -0.014 0.052 -10000 0 -0.32 15 15
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.032 -10000 0 -0.39 1 1
AQP5 -0.2 0.27 0.34 1 -0.52 341 342
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 -0.027 0.08 -10000 0 -0.32 48 48
EGF -0.091 0.24 0.27 2 -0.6 153 155
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.019 0.12 0.29 1 -0.48 43 44
cortical microtubule organization 0.036 0.056 -10000 0 -0.33 14 14
GO:0000145 -0.013 0.047 -10000 0 -0.3 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.058 -10000 0 -0.34 14 14
MLLT4 0.022 0.023 -10000 0 -0.6 1 1
ARF6/GDP -0.022 0.042 -10000 0 -0.3 16 16
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.043 -10000 0 -0.35 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.049 -10000 0 -0.31 14 14
PVRL2 0.024 0.009 0.27 1 -10000 0 1
ZYX -0.014 0.05 -10000 0 -0.32 14 14
ARF6/GTP 0.048 0.044 -10000 0 -0.33 5 5
CDH1 0.011 0.081 -10000 0 -0.6 14 14
EGFR/EGFR/EGF/EGF -0.15 0.21 -10000 0 -0.35 390 390
RhoA/GDP 0.037 0.055 -10000 0 -0.32 14 14
actin cytoskeleton organization -0.015 0.049 -10000 0 -0.31 15 15
IGF-1R heterotetramer 0.013 0.082 0.27 2 -0.6 14 16
GIT1 0.023 0.007 -10000 0 -10000 0 0
IGF1R 0.013 0.082 0.27 2 -0.6 14 16
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
DIAPH1 0.025 0.1 -10000 0 -0.54 14 14
Wnt receptor signaling pathway -0.036 0.056 0.33 14 -10000 0 14
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.042 -10000 0 -0.3 15 15
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.016 0.05 -10000 0 -0.32 15 15
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.015 0.05 -10000 0 -0.31 15 15
Ephrin A1/EPHA2 0.024 0.057 -10000 0 -0.32 17 17
SEC6/SEC8 -0.023 0.041 -10000 0 -0.3 15 15
MGAT3 -0.027 0.081 -10000 0 -0.33 48 48
HGF/MET -0.043 0.16 -10000 0 -0.34 176 176
HGF -0.01 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 0.31 27 -0.3 1 28
KIAA1543 -0.014 0.051 -10000 0 -0.33 14 14
KIFC3 -0.014 0.048 -10000 0 -0.32 14 14
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.013 0.05 -10000 0 -0.32 14 14
NCK1/GIT1 0.033 0.011 -10000 0 -10000 0 0
mol:GDP 0.036 0.056 -10000 0 -0.33 14 14
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.013 0.05 -10000 0 -0.32 14 14
PIP5K1C -0.014 0.051 -10000 0 -0.32 14 14
LIMA1 0.024 0.022 -10000 0 -0.6 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.015 0.088 0.3 20 -10000 0 20
adherens junction assembly -0.026 0.11 0.28 2 -0.63 14 16
IGF-1R heterotetramer/IGF1 -0.047 0.16 -10000 0 -0.33 183 183
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.033 0.024 -10000 0 -0.28 3 3
MET -0.079 0.23 -10000 0 -0.6 136 136
PLEKHA7 -0.014 0.054 -10000 0 -0.34 14 14
mol:GTP 0.042 0.042 -10000 0 -0.35 5 5
establishment of epithelial cell apical/basal polarity -0.009 0.066 0.35 5 -10000 0 5
cortical actin cytoskeleton stabilization 0.011 0.045 -10000 0 -0.27 16 16
regulation of cell-cell adhesion -0.015 0.049 -10000 0 -0.31 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.046 -10000 0 -0.27 16 16
Aurora A signaling

Figure 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
Aurora A/GADD45A 0.047 0.044 -10000 0 -10000 0 0
BIRC5 0.19 0.12 0.27 560 -10000 0 560
NFKBIA 0.028 0.046 0.29 7 -10000 0 7
CPEB1 -0.09 0.24 -10000 0 -0.6 151 151
AKT1 0.028 0.045 0.29 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.035 0.037 0.22 1 -10000 0 1
NDEL1/TACC3 0.068 0.07 0.26 15 -10000 0 15
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.005 0.028 -10000 0 -10000 0 0
PAK1/Aurora A 0.043 0.045 0.26 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.1 0.07 0.27 23 -10000 0 23
TP53 0.023 0.054 0.19 2 -0.22 10 12
DLG7 0.025 0.033 0.18 1 -10000 0 1
AURKAIP1 0.024 0.01 0.27 1 -10000 0 1
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.072 0.074 0.28 15 -10000 0 15
G2/M transition of mitotic cell cycle 0.035 0.037 0.21 1 -10000 0 1
AURKA 0.042 0.05 0.25 1 -10000 0 1
AURKB 0.093 0.079 0.18 357 -10000 0 357
CDC25B 0.035 0.041 0.23 4 -10000 0 4
G2/M transition checkpoint 0.021 0.03 -10000 0 -10000 0 0
mRNA polyadenylation -0.03 0.14 -10000 0 -0.32 151 151
Aurora A/CPEB -0.03 0.14 -10000 0 -0.32 151 151
Aurora A/TACC1/TRAP/chTOG 0.047 0.067 -10000 0 -0.32 12 12
BRCA1 0.024 0.01 0.27 1 -10000 0 1
centrosome duplication 0.043 0.045 0.26 2 -10000 0 2
regulation of centrosome cycle 0.066 0.068 0.26 15 -10000 0 15
spindle assembly 0.046 0.066 -10000 0 -0.32 12 12
TDRD7 0.024 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.15 0.091 0.28 24 -10000 0 24
CENPA 0.1 0.086 0.2 359 -0.2 3 362
Aurora A/PP2A 0.047 0.045 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.033 0.042 0.24 1 -10000 0 1
negative regulation of DNA binding 0.02 0.064 0.19 2 -0.22 10 12
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.021 0.03 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.051 0.25 1 -10000 0 1
TACC1 0.01 0.078 -10000 0 -0.6 13 13
TACC3 0.058 0.085 0.27 118 -10000 0 118
Aurora A/Antizyme1 0.056 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.047 0.045 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.004 0.028 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.023 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.1 0.07 0.27 23 -10000 0 23
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.1 0.075 0.25 28 -10000 0 28
PAK1 0.023 0.017 0.27 3 -10000 0 3
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.061 0.088 0.27 127 -10000 0 127
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.022 0.031 -10000 0 -0.6 2 2
CDKN1A -0.036 0.098 -10000 0 -0.45 23 23
PRL-3/alpha Tubulin 0.029 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.081 0.24 35 -0.45 11 46
AGT 0.031 0.1 0.27 66 -0.6 11 77
CCNA2 -0.074 0.15 0.26 1 -10000 0 1
TUBA1B 0.025 0.002 -10000 0 -10000 0 0
EGR1 -0.14 0.21 -10000 0 -0.44 278 278
CDK2/Cyclin E1 0.009 0.12 -10000 0 -0.51 12 12
MAPK3 0.009 0.014 0.26 2 -10000 0 2
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.009 0.016 0.26 3 -10000 0 3
PTP4A1 -0.11 0.16 -10000 0 -0.34 246 246
PTP4A3 0.02 0.013 0.27 1 -10000 0 1
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.009 0.014 0.26 2 -10000 0 2
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 -0.025 0.082 -10000 0 -0.42 16 16
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.087 0.16 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.011 -10000 0 -0.18 1 1
RHOC -0.026 0.088 -10000 0 -0.44 19 19
RHOA -0.029 0.097 -10000 0 -0.48 23 23
cell motility -0.032 0.1 -10000 0 -0.38 30 30
PRL-1/alpha Tubulin -0.088 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.025 -10000 0 -0.34 2 2
ROCK1 -0.031 0.1 -10000 0 -0.39 28 28
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.025 0.002 -10000 0 -10000 0 0
mitosis -0.11 0.16 -10000 0 -0.34 246 246
ATF5 0.025 0.015 0.27 3 -10000 0 3
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.093 0.11 0.29 17 -0.63 6 23
Syndecan-4/Syndesmos 0.1 0.11 0.38 6 -0.64 5 11
positive regulation of JNK cascade 0.089 0.14 0.36 9 -0.57 7 16
Syndecan-4/ADAM12 0.11 0.12 0.37 25 -0.68 5 30
CCL5 0.03 0.048 0.27 26 -0.6 1 27
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.025 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
PLG -0.01 0.033 0.27 4 -10000 0 4
ADAM12 0.041 0.072 0.27 63 -0.6 2 65
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.011 0.27 1 -10000 0 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.07 0.15 0.4 3 -0.68 6 9
Syndecan-4/CXCL12/CXCR4 0.093 0.14 0.39 6 -0.65 6 12
Syndecan-4/Laminin alpha3 0.039 0.16 0.4 4 -0.63 7 11
MDK 0.032 0.043 0.27 27 -10000 0 27
Syndecan-4/FZD7 0.1 0.12 0.38 6 -0.68 5 11
Syndecan-4/Midkine 0.11 0.11 0.38 12 -0.65 5 17
FZD7 0.013 0.083 -10000 0 -0.6 15 15
Syndecan-4/FGFR1/FGF -0.011 0.17 0.36 1 -0.53 14 15
THBS1 0.023 0.022 -10000 0 -0.6 1 1
integrin-mediated signaling pathway 0.098 0.12 0.38 7 -0.66 6 13
positive regulation of MAPKKK cascade 0.089 0.14 0.36 9 -0.57 7 16
Syndecan-4/TACI 0.1 0.12 0.38 13 -0.67 5 18
CXCR4 0.031 0.04 0.27 23 -10000 0 23
cell adhesion 0.067 0.09 0.3 43 -0.27 18 61
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 0.39 5 -0.68 5 10
Syndecan-4/RANTES 0.1 0.11 0.37 7 -0.67 5 12
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.039 0.19 0.27 1 -0.6 83 84
LAMA3 -0.12 0.26 -10000 0 -0.6 185 185
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.024 0.23 0.7 78 -0.57 17 95
Syndecan-4/alpha-Actinin 0.1 0.11 0.39 5 -0.68 5 10
TFPI -0.001 0.12 -10000 0 -0.6 33 33
F2 0.024 0.034 0.28 7 -10000 0 7
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.005 0.18 0.4 2 -0.56 22 24
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.091 0.27 5 -0.6 17 22
Syndecan-4/CXCL12 0.081 0.14 0.39 5 -0.64 7 12
FGF6 0.016 0.031 -10000 0 -0.6 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.02 0.16 -10000 0 -0.6 58 58
TNFRSF13B 0.023 0.087 0.27 32 -0.6 11 43
FGF2 -0.21 0.3 -10000 0 -0.6 311 311
FGFR1 0.016 0.049 -10000 0 -0.6 5 5
Syndecan-4/PI-4-5-P2 0.08 0.1 0.34 2 -0.68 5 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 362 -10000 0 362
cell migration -0.02 0.013 -10000 0 -10000 0 0
PRKCD 0.011 0.028 -10000 0 -10000 0 0
vasculogenesis 0.1 0.1 0.38 6 -0.64 5 11
SDC4 0.093 0.1 0.42 3 -0.76 4 7
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 0.09 0.11 0.37 5 -0.68 5 10
MMP9 0.12 0.12 0.27 327 -0.59 1 328
Rac1/GTP 0.068 0.091 0.3 43 -0.28 18 61
cytoskeleton organization 0.098 0.1 0.38 6 -0.62 5 11
GIPC1 0.024 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.094 0.13 0.39 5 -0.64 6 11
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.11 0.11 0.32 83 -0.37 2 85
EPHB2 0.028 0.033 0.27 15 -10000 0 15
Syndecan-2/TACI 0.019 0.062 0.32 4 -0.35 13 17
LAMA1 -0.039 0.19 0.27 1 -0.6 83 84
Syndecan-2/alpha2 ITGB1 -0.037 0.15 -10000 0 -0.34 139 139
HRAS 0.024 0.01 0.27 1 -10000 0 1
Syndecan-2/CASK 0.005 0.019 -10000 0 -0.38 2 2
ITGA5 0.025 0.002 -10000 0 -10000 0 0
BAX -0.002 0.022 -10000 0 -10000 0 0
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.02 -10000 0 -0.34 2 2
LAMA3 -0.12 0.26 -10000 0 -0.6 185 185
EZR 0.024 0.013 0.27 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.051 0.2 -10000 0 -0.6 100 100
Syndecan-2/MMP2 0.014 0.039 -10000 0 -0.4 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.026 0.064 -10000 0 -0.42 16 16
dendrite morphogenesis 0.021 0.035 0.32 3 -0.38 2 5
Syndecan-2/GM-CSF 0.02 0.035 0.32 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 0.077 0.26 3 -0.35 2 5
MAPK1 0.039 0.08 0.19 86 -0.34 2 88
Syndecan-2/RACK1 0.027 0.025 -10000 0 -0.33 2 2
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.022 -10000 0 -0.44 2 2
ITGA2 0.012 0.086 -10000 0 -0.6 16 16
MAPK8 0.005 0.025 0.24 4 -0.37 2 6
Syndecan-2/alpha2/beta1 Integrin 0.001 0.12 -10000 0 -0.38 61 61
Syndecan-2/Kininogen 0.018 0.033 0.32 3 -0.38 2 5
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.043 0.072 0.35 5 -0.32 2 7
Syndecan-2/CASK/Protein 4.1 0.016 0.021 -10000 0 -0.35 2 2
extracellular matrix organization 0.018 0.022 -10000 0 -0.38 2 2
actin cytoskeleton reorganization 0.11 0.11 0.32 83 -0.37 2 85
Syndecan-2/Caveolin-2/Ras -0.011 0.12 -10000 0 -0.36 73 73
Syndecan-2/Laminin alpha3 -0.059 0.15 -10000 0 -0.32 187 187
Syndecan-2/RasGAP 0.036 0.03 -10000 0 -0.32 2 2
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
PRKCD 0.024 0.01 0.27 1 -10000 0 1
Syndecan-2 dimer 0.021 0.035 0.32 3 -0.38 2 5
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.026 -10000 0 -0.31 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
TNFRSF13B 0.023 0.087 0.27 32 -0.6 11 43
RASA1 0.024 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.026 0.064 -10000 0 -0.42 16 16
Syndecan-2/Synbindin 0.017 0.022 -10000 0 -0.37 2 2
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CASP3 0.045 0.074 0.19 162 -0.35 2 164
FN1 0.13 0.12 0.27 367 -10000 0 367
Syndecan-2/IL8 0.024 0.077 0.32 15 -0.34 18 33
SDC2 0.006 0.022 -10000 0 -0.44 2 2
KNG1 0.022 0.027 0.27 10 -10000 0 10
Syndecan-2/Neurofibromin 0.017 0.023 -10000 0 -0.38 2 2
TRAPPC4 0.022 0.008 -10000 0 -10000 0 0
CSF2 0.025 0.034 0.27 16 -10000 0 16
Syndecan-2/TGFB1 0.018 0.022 -10000 0 -0.38 2 2
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.021 -10000 0 -0.35 2 2
Syndecan-2/Ezrin 0.028 0.028 0.3 1 -0.35 2 3
PRKACA 0.047 0.076 0.19 173 -0.34 2 175
angiogenesis 0.024 0.076 0.32 15 -0.34 18 33
MMP2 0.019 0.044 -10000 0 -0.6 4 4
IL8 0.027 0.11 0.27 51 -0.6 16 67
calcineurin-NFAT signaling pathway 0.019 0.061 0.32 4 -0.35 13 17
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.031 -10000 0 -0.6 2 2
alphaV beta3 Integrin 0.027 0.062 -10000 0 -0.45 13 13
PTK2 -0.029 0.13 -10000 0 -0.47 49 49
positive regulation of JNK cascade -0.013 0.12 -10000 0 -0.32 72 72
CDC42/GDP -0.005 0.16 0.44 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 -0.45 64 64
RAPGEF1 -0.023 0.15 0.46 1 -0.47 62 63
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.035 0.16 -10000 0 -0.53 63 63
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 60 60
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 -0.45 64 64
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 -0.53 78 79
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 -0.33 63 63
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.03 0.024 -10000 0 -0.45 1 1
positive regulation of lamellipodium assembly -0.011 0.12 -10000 0 -0.34 78 78
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.023 0.17 -10000 0 -0.6 63 63
PVRL2 0.024 0.009 0.27 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
CLDN1 0.006 0.13 0.27 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 73 73
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
nectin-1(dimer)/I-afadin/I-afadin 0.03 0.024 -10000 0 -0.45 1 1
FARP2 -0.023 0.19 0.46 1 -0.54 73 74
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 -0.39 63 63
nectin-1/I-afadin 0.03 0.024 -10000 0 -0.45 1 1
nectin-2/I-afadin 0.033 0.024 -10000 0 -0.28 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.009 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 0.01 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.013 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 0.033 0.024 -10000 0 -0.28 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.033 0.024 -10000 0 -0.28 3 3
PIP5K1C -0.014 0.07 -10000 0 -0.24 62 62
VAV2 -0.023 0.19 0.44 1 -0.55 76 77
RAP1/GDP -0.003 0.14 -10000 0 -0.4 70 70
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 -0.39 63 63
nectin-3(dimer)/I-afadin/I-afadin -0.004 0.13 -10000 0 -0.45 64 64
Rac1/GTP -0.01 0.15 -10000 0 -0.42 77 77
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 0.024 0.005 -10000 0 -10000 0 0
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0.055 0.14 0.51 6 -0.53 2 8
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.11 0.23 -10000 0 -0.44 260 260
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 0 0.091 -10000 0 -0.24 75 75
ER alpha/Oestrogen -0.019 0.17 0.18 109 -0.43 111 220
NFX1/SIN3/HDAC complex 0.022 0.059 0.25 1 -0.32 13 14
EGF -0.09 0.24 0.27 2 -0.6 153 155
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.023 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.052 0.12 0.44 2 -0.5 2 4
SAP18 0.023 0.007 -10000 0 -10000 0 0
MRN complex 0.035 0.023 -10000 0 -10000 0 0
WT1 0.15 0.12 0.27 431 -10000 0 431
WRN 0.02 0.01 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.006 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.1 -10000 0 -0.51 1 1
Mad/Max 0.041 0.015 -10000 0 -10000 0 0
TERT 0.055 0.14 0.52 5 -0.6 1 6
CCND1 0.079 0.17 0.55 18 -1.1 3 21
MAX 0.026 0.007 -10000 0 -10000 0 0
RBBP7 0.027 0.023 0.27 7 -10000 0 7
RBBP4 0.025 0.005 -10000 0 -10000 0 0
TERF2 0.021 0.014 -10000 0 -10000 0 0
PTGES3 0.025 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.038 0.054 -10000 0 -0.38 5 5
CDKN1B 0.029 0.057 -10000 0 -0.71 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.016 0.27 3 -10000 0 3
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.019 0.061 -10000 0 -0.6 8 8
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.16 0.29 -10000 0 -0.6 251 251
IFN-gamma/IRF1 0.066 0.068 0.4 2 -0.33 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.048 0.073 0.27 83 -10000 0 83
Telomerase 0.028 0.077 0.26 2 -0.67 3 5
IRF1 0.028 0.019 0.28 2 -0.19 3 5
ESR1 -0.024 0.24 0.27 109 -0.6 106 215
KU/TER 0.034 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 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 -0.006 0.012 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.01 0.27 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.058 0.13 0.52 1 -0.63 4 5
NR2F2 0.012 0.042 -10000 0 -0.61 3 3
MAPK3 0.005 0.021 -10000 0 -10000 0 0
MAPK1 0.005 0.021 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.011 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.016 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.3 -10000 0 -0.6 281 281
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.21 0.27 -10000 0 -0.48 400 400
MYC 0.006 0.091 -10000 0 -0.6 18 18
IL2 0.03 0.028 0.27 8 -10000 0 8
KU 0.034 0.01 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
TGFB1 0.021 0.011 -10000 0 -10000 0 0
TRF2/BLM 0.045 0.05 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.065 0.13 0.48 3 -0.56 1 4
SP1/HDAC2 0.046 0.027 -10000 0 -10000 0 0
PINX1 0.02 0.01 -10000 0 -10000 0 0
Telomerase/EST1A 0.043 0.1 -10000 0 -0.5 1 1
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 0.088 0.27 119 -0.2 1 120
Telomerase/PinX1 0.034 0.099 -10000 0 -0.5 1 1
Telomerase/AKT1/mTOR/p70S6K 0.025 0.1 0.32 3 -0.54 13 16
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 -10000 0 0
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 0.046 0.1 -10000 0 -0.51 1 1
E2F1 0.1 0.12 0.27 263 -10000 0 263
ZNFX1 0.024 0.007 -10000 0 -10000 0 0
PIF1 0.067 0.093 0.27 146 -10000 0 146
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.012 0.27 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.029 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.087 0.27 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 -0.096 0.13 -10000 0 -0.25 321 321
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.01 0.27 1 -10000 0 1
p38 alpha/TAB1 -0.041 0.098 -10000 0 -0.34 57 57
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 -0.35 71 71
apoptosis -0.04 0.094 -10000 0 -0.33 57 57
RAL/GTP 0.032 0.007 -10000 0 -10000 0 0
LYN 0.021 0.009 -10000 0 -10000 0 0
DUSP1 -0.054 0.21 -10000 0 -0.6 103 103
PAK1 0.023 0.017 0.27 3 -10000 0 3
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.025 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.031 0.009 -10000 0 -10000 0 0
MAPK11 -0.012 0.13 0.33 4 -0.37 52 56
BLK 0.046 0.086 0.27 95 -0.6 2 97
HCK 0.028 0.029 0.27 12 -10000 0 12
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.024 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.013 0.27 1 -10000 0 1
TRAF6/MEKK3 0.028 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.007 0.13 0.31 4 -0.38 54 58
positive regulation of innate immune response -0.014 0.15 0.32 6 -0.43 54 60
LCK 0.024 0.077 0.27 23 -0.6 9 32
p38alpha-beta/MKP7 -0.005 0.15 0.38 3 -0.42 49 52
p38alpha-beta/MKP5 -0.006 0.14 0.44 2 -0.43 44 46
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 -0.041 0.18 0.44 2 -0.42 90 92
CDC42 0.024 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.26 0.31 -10000 0 -0.6 370 370
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 -0.044 0.17 -10000 0 -0.34 189 189
TC10/GTP -0.036 0.15 -10000 0 -0.31 178 178
Insulin Receptor/Insulin/IRS1/Shp2 0.045 0.079 -10000 0 -0.37 27 27
HRAS 0.024 0.01 0.27 1 -10000 0 1
APS homodimer 0.032 0.042 0.27 26 -10000 0 26
GRB14 0.014 0.19 0.27 117 -0.6 59 176
FOXO3 -0.02 0.16 -10000 0 -0.6 57 57
AKT1 -0.015 0.11 0.33 6 -0.31 62 68
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.058 0.051 0.37 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.11 0.26 -10000 0 -0.6 183 183
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.002 0.026 -10000 0 -10000 0 0
CAV1 -0.085 0.15 -10000 0 -0.37 174 174
CBL/APS/CAP/Crk-II/C3G -0.024 0.17 -10000 0 -0.33 181 181
Insulin Receptor/Insulin/IRS1/NCK2 0.045 0.078 -10000 0 -0.37 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 -0.4 6 6
RPS6KB1 -0.015 0.099 0.32 6 -0.51 1 7
PARD6A 0.023 0.017 0.27 3 -10000 0 3
CBL 0.022 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.041 -10000 0 -0.56 4 4
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.011 0.096 -10000 0 -0.29 55 55
HRAS/GTP -0.021 0.046 -10000 0 -0.3 18 18
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.072 -10000 0 -0.35 19 19
PRKCI 0.013 0.06 -10000 0 -0.47 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.002 0.11 -10000 0 -0.32 76 76
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.039 -10000 0 -0.47 4 4
PI3K 0.043 0.07 -10000 0 -0.33 24 24
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.007 0.18 1 -10000 0 1
AKT2 -0.016 0.11 0.3 5 -0.31 62 67
PRKCZ 0.004 0.085 -10000 0 -0.49 11 11
SH2B2 0.032 0.042 0.27 26 -10000 0 26
SHC/SHIP 0.012 0.06 -10000 0 -0.33 21 21
F2RL2 0.054 0.12 0.27 135 -0.6 12 147
TRIP10 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.038 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.035 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.034 0.17 -10000 0 -0.35 182 182
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.05 0.029 -10000 0 -10000 0 0
INPP5D -0.019 0.063 -10000 0 -0.34 27 27
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.018 0.14 -10000 0 -0.68 34 34
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.002 -10000 0 -10000 0 0
IRS1 0.002 0.12 -10000 0 -0.6 29 29
p62DOK/RasGAP 0.042 0.04 -10000 0 -0.48 4 4
INS 0.02 0.01 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.34 27 27
GRB2 0.023 0.011 0.27 1 -10000 0 1
EIF4EBP1 -0.02 0.092 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 0.031 0.075 -10000 0 -0.36 28 28
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
Regulation of Androgen receptor activity

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
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 -0.037 0.11 0.37 1 -0.42 21 22
JUN 0.016 0.062 -10000 0 -0.6 8 8
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.024 0.003 -10000 0 -10000 0 0
KAT5 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.01 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 40 41
MAP2K6 0.002 0.088 0.26 1 -0.61 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 49 49
NCOA2 0.013 0.058 -10000 0 -0.6 7 7
CEBPA 0.019 0.057 -10000 0 -0.6 7 7
EHMT2 0.021 0.012 -10000 0 -10000 0 0
cell proliferation 0.003 0.15 0.37 23 -0.46 18 41
NR0B1 0.029 0.045 0.27 29 -10000 0 29
EGR1 -0.19 0.29 -10000 0 -0.6 279 279
RXRs/9cRA -0.047 0.16 -10000 0 -0.36 165 165
AR/RACK1/Src -0.016 0.11 0.32 8 -0.37 19 27
AR/GR -0.021 0.11 0.29 1 -0.3 88 89
GNB2L1 0.023 0.008 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.015 6 6
MAPK8 -0.001 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 0.2 4 -0.37 12 16
NR3C1 0.02 0.053 -10000 0 -0.6 6 6
KLK3 -0.15 0.4 -10000 0 -1.2 107 107
APPBP2 0.015 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.02 0.27 1 -10000 0 1
T-DHT/AR/TIP60 -0.012 0.092 0.34 2 -0.39 15 17
TMPRSS2 -0.13 0.37 -10000 0 -1.1 109 109
RXRG -0.11 0.25 0.26 1 -0.6 167 168
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.024 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.022 0.012 -10000 0 -10000 0 0
NR2C2 0.024 0.004 -10000 0 -10000 0 0
KLK2 -0.052 0.21 0.34 5 -0.7 69 74
AR -0.036 0.1 -10000 0 -0.3 92 92
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
MDM2 0.026 0.015 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 102 -0.025 20 122
GATA2 0.014 0.096 0.27 11 -0.6 18 29
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.26 335 -10000 0 335
T-DHT/AR/RACK1/Src -0.01 0.1 0.34 9 -0.38 15 24
positive regulation of transcription 0.014 0.096 0.27 11 -0.6 18 29
DNAJA1 0.016 0.021 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.011 -10000 0 -10000 0 0
NCOA1 0.021 0.032 -10000 0 -0.63 1 1
SPDEF -0.011 0.14 0.26 11 -0.6 44 55
T-DHT/AR/TIF2 0.006 0.088 0.32 4 -0.37 11 15
T-DHT/AR/Hsp90 -0.013 0.091 0.34 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 0.027 0.015 -10000 0 -10000 0 0
POU2F1 0.009 0.052 -10000 0 -0.2 5 5
T-DHT/AR/DAX-1 -0.012 0.097 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
Coregulation of Androgen receptor activity

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
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 0.21 12 -10000 0 12
JMJD2C -0.004 0.043 0.12 12 -0.14 69 81
T-DHT/AR/Ubc9 -0.029 0.14 -10000 0 -0.39 94 94
CARM1 0.019 0.016 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.014 0.03 -10000 0 -10000 0 0
AKT1 0.028 0.018 -10000 0 -10000 0 0
PTK2B 0.011 0.027 -10000 0 -10000 0 0
MED1 0.026 0.02 -10000 0 -10000 0 0
MAK 0.037 0.084 0.26 8 -0.57 8 16
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.012 0.035 -10000 0 -10000 0 0
GSN 0.002 0.082 -10000 0 -0.6 12 12
NCOA2 0.01 0.059 -10000 0 -0.6 7 7
NCOA6 0.012 0.034 -10000 0 -10000 0 0
DNA-PK 0.051 0.053 -10000 0 -10000 0 0
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.014 0.029 -10000 0 -10000 0 0
cell proliferation 0.006 0.11 -10000 0 -0.56 19 19
XRCC5 0.027 0.015 -10000 0 -10000 0 0
UBE3A 0.008 0.045 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.039 0.16 -10000 0 -0.4 112 112
FHL2 0.003 0.12 -10000 0 -0.9 7 7
RANBP9 0.012 0.034 -10000 0 -10000 0 0
JMJD1A -0.01 0.057 0.12 32 -0.14 115 147
CDK6 0.023 0.045 0.27 2 -0.6 4 6
TGFB1I1 0.009 0.05 -10000 0 -0.6 3 3
T-DHT/AR/CyclinD1 -0.038 0.14 -10000 0 -0.4 92 92
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 0.036 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.035 0.19 1 -10000 0 1
TCF4 0.028 0.056 -10000 0 -0.59 5 5
CDKN2A 0.062 0.089 0.28 118 -10000 0 118
SRF 0.033 0.024 -10000 0 -10000 0 0
NKX3-1 -0.062 0.21 0.37 3 -0.62 68 71
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 -0.37 103 103
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 0.019 0.017 -10000 0 -10000 0 0
PRKDC 0.024 0.016 -10000 0 -10000 0 0
PA2G4 0.032 0.026 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.019 0.13 -10000 0 -0.35 92 92
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 0.22 1 -0.34 100 101
Cyclin D3/CDK11 p58 0.019 0.006 -10000 0 -10000 0 0
VAV3 0.016 0.058 0.26 16 -0.6 3 19
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 79 79
TMPRSS2 -0.13 0.35 -10000 0 -0.99 111 111
CCND1 0.012 0.044 0.27 1 -0.6 3 4
PIAS1 0.009 0.045 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.032 0.062 2 -0.072 148 150
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.002 0.064 -10000 0 -0.2 10 10
T-DHT/AR/CDK6 -0.029 0.15 -10000 0 -0.38 103 103
CMTM2 0.023 0.013 0.26 1 -10000 0 1
SNURF 0.01 0.091 -10000 0 -0.6 18 18
ZMIZ1 0.009 0.043 -10000 0 -10000 0 0
CCND3 0.025 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.02 -10000 0 -10000 0 0
FKBP4 0.013 0.038 0.27 4 -10000 0 4
Thromboxane A2 receptor signaling

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.028 0.032 0.27 14 -10000 0 14
GNB1/GNG2 -0.014 0.046 -10000 0 -0.19 44 44
AKT1 0.024 0.094 0.34 12 -0.27 28 40
EGF -0.091 0.24 0.27 2 -0.6 153 155
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.058 0.25 2 -0.27 3 5
mol:Ca2+ 0.025 0.11 0.42 10 -0.3 53 63
LYN 0.012 0.054 0.25 2 -0.26 1 3
RhoA/GTP 0.01 0.044 0.14 4 -0.14 18 22
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.022 0.12 0.42 11 -0.34 45 56
GNG2 0.019 0.053 -10000 0 -0.6 6 6
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.6 30 30
G beta5/gamma2 -0.011 0.063 -10000 0 -0.26 42 42
PRKCH 0.021 0.12 0.41 11 -0.35 46 57
DNM1 0.021 0.049 0.27 1 -0.6 5 6
TXA2/TP beta/beta Arrestin3 0.007 0.032 -10000 0 -0.4 2 2
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
PTGDR 0.01 0.1 0.27 6 -0.6 21 27
G12 family/GTP 0.002 0.086 -10000 0 -0.3 42 42
ADRBK1 0.023 0.007 -10000 0 -10000 0 0
ADRBK2 0.022 0.031 -10000 0 -0.6 2 2
RhoA/GTP/ROCK1 0.032 0.008 -10000 0 -10000 0 0
mol:GDP -0.012 0.099 0.36 24 -0.33 8 32
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 0.001 0.12 -10000 0 -0.6 31 31
mol:IP3 0.023 0.13 0.44 10 -0.37 54 64
cell morphogenesis 0.032 0.008 -10000 0 -10000 0 0
PLCB2 0.015 0.17 0.55 6 -0.5 55 61
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.023 0.069 0.26 7 -0.28 4 11
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 0.27 1 -10000 0 1
PRKCB1 0.022 0.13 0.43 10 -0.37 50 60
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 0.54 7 -0.52 47 54
LCK 0.015 0.072 0.25 2 -0.35 11 13
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 -0.43 42 42
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.26 20 20
MAPK14 0.021 0.089 0.36 12 -0.23 41 53
TGM2/GTP 0.019 0.14 0.51 8 -0.42 48 56
MAPK11 0.019 0.09 0.36 13 -0.24 43 56
ARHGEF1 0.013 0.066 0.28 9 -0.18 37 46
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.024 0.13 0.45 10 -0.39 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 0.43 9 -0.35 51 60
Gq family/GTP/EBP50 0.016 0.042 0.22 4 -0.23 9 13
actin cytoskeleton reorganization 0.032 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 -0.049 0.11 0.23 4 -0.29 60 64
VCAM1 0.023 0.11 0.41 10 -0.31 43 53
TP beta/Gq family/GDP/G beta5/gamma2 -0.008 0.13 -10000 0 -0.6 30 30
platelet activation 0.026 0.12 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 22 22
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.48 27 27
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 52 62
EGFR -0.19 0.3 -10000 0 -0.6 281 281
TXA2/TP alpha 0.019 0.16 0.53 7 -0.48 52 59
Gq family/GTP 0.002 0.049 0.25 1 -0.26 16 17
YES1 0.014 0.059 0.25 2 -0.28 4 6
GNAI2/GTP 0.014 0.048 -10000 0 -0.25 21 21
PGD2/DP 0.007 0.075 0.18 6 -0.43 22 28
SLC9A3R1 0.037 0.057 0.27 47 -10000 0 47
FYN 0.012 0.057 0.26 1 -0.29 4 5
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.024 0.027 0.27 3 -0.6 1 4
PGK/cGMP 0.017 0.079 -10000 0 -0.38 31 31
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.036 0.066 -10000 0 -0.38 7 7
NOS3 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.025 0.13 0.41 12 -0.38 41 53
PRKCB 0.024 0.13 0.41 11 -0.37 44 55
PRKCE 0.021 0.12 0.43 10 -0.35 47 57
PRKCD 0.02 0.12 0.42 10 -0.38 44 54
PRKCG 0.023 0.13 0.44 10 -0.38 45 55
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 0.27 6 -10000 0 6
TXA2/TP beta 0.024 0.055 -10000 0 -0.27 21 21
PRKCQ 0.018 0.14 0.42 12 -0.39 48 60
MAPKKK cascade 0.019 0.15 0.48 8 -0.45 52 60
SELE 0.019 0.12 0.39 11 -0.39 43 54
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.064 -10000 0 -0.39 6 6
ROCK1 0.024 0.004 -10000 0 -10000 0 0
GNA14 0.025 0.065 0.27 19 -0.6 6 25
chemotaxis 0.018 0.18 0.59 6 -0.61 43 49
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.5 3 7
IL27/IL27R/JAK1 0.056 0.15 0.62 6 -0.72 5 11
TBX21 0.007 0.17 0.45 16 -0.54 35 51
IL12B 0.072 0.099 0.28 156 -10000 0 156
IL12A -0.017 0.11 0.15 11 -0.45 47 58
IL6ST -0.008 0.14 -10000 0 -0.6 43 43
IL27RA/JAK1 0.023 0.076 0.65 1 -1.2 2 3
IL27 0.046 0.075 0.28 75 -10000 0 75
TYK2 0.031 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.11 0.17 0.76 2 -0.56 8 10
T-helper 2 cell differentiation -0.023 0.11 0.52 4 -0.5 3 7
T cell proliferation during immune response -0.023 0.11 0.52 4 -0.5 3 7
MAPKKK cascade 0.023 0.11 0.5 3 -0.52 4 7
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.025 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.038 0.27 18 -10000 0 18
IL12RB1 0.032 0.049 0.28 25 -0.6 1 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.019 0.19 0.42 41 -0.54 41 82
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 0.5 3 -0.52 4 7
STAT1 (dimer) 0.051 0.2 0.59 30 -0.66 13 43
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 -0.097 0.19 0.35 3 -0.44 78 81
IL12/IL12R/TYK2/JAK2 0.054 0.19 0.45 7 -0.74 24 31
IL17A -0.11 0.17 0.76 2 -0.56 8 10
mast cell activation -0.023 0.11 0.52 4 -0.5 3 7
IFNG 0.024 0.048 0.13 106 -0.11 4 110
T cell differentiation 0 0.006 0.014 18 -0.02 5 23
STAT3 (dimer) 0.035 0.11 0.5 2 -0.5 4 6
STAT5A (dimer) 0.032 0.12 0.5 2 -0.48 9 11
STAT4 (dimer) 0.023 0.13 0.5 2 -0.43 21 23
STAT4 0 0.12 0.27 1 -0.6 32 33
T cell activation -0.005 0.011 0.12 2 -0.12 4 6
IL27R/JAK2/TYK2 0.035 0.12 -10000 0 -0.92 3 3
GATA3 -0.027 0.27 0.6 30 -1.3 27 57
IL18 0.009 0.022 0.14 21 -10000 0 21
positive regulation of mast cell cytokine production 0.034 0.11 0.5 2 -0.49 4 6
IL27/EBI3 0.05 0.072 0.28 16 -0.45 4 20
IL27RA 0.011 0.078 0.75 1 -1.3 2 3
IL6 -0.2 0.3 0.27 1 -0.6 305 306
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.015 0.044 0.45 2 -0.54 1 3
IL1B 0.002 0.047 0.14 2 -0.45 9 11
EBI3 0.024 0.052 0.27 7 -0.6 4 11
TNF 0.005 0.046 0.14 17 -0.45 7 24
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 -0.014 0.17 0.3 4 -0.41 106 110
AKT1 0.025 0.009 -10000 0 -10000 0 0
GSC -0.041 0.3 -10000 0 -1.4 38 38
NKX2-5 0.052 0.082 0.27 104 -10000 0 104
muscle cell differentiation -0.025 0.064 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.057 0.075 -10000 0 -10000 0 0
SMAD4 0.009 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 -0.38 321 322
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 -0.84 16 16
AP1 -0.067 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 10 10
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.035 0.07 0.27 59 -10000 0 59
SMAD3/SMAD4/GR 0.022 0.072 -10000 0 -0.42 6 6
GATA3 0.013 0.12 0.27 27 -0.58 28 55
SKI/SIN3/HDAC complex/NCoR1 0.004 0.078 -10000 0 -0.35 28 28
MEF2C/TIF2 0.03 0.077 0.31 3 -0.37 4 7
endothelial cell migration -0.03 0.088 0.56 6 -10000 0 6
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.022 0.27 7 -10000 0 7
RBBP4 0.024 0.005 -10000 0 -10000 0 0
RUNX2 0.027 0.028 0.27 11 -10000 0 11
RUNX3 0.023 0.033 0.27 2 -0.6 2 4
RUNX1 0.023 0.022 -10000 0 -0.6 1 1
CTBP1 0.024 0.005 -10000 0 -10000 0 0
NR3C1 0.016 0.055 -10000 0 -0.6 6 6
VDR 0.024 0.003 -10000 0 -10000 0 0
CDKN1A 0.016 0.07 -10000 0 -0.96 2 2
KAT2B 0.025 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.046 0.077 -10000 0 -0.27 22 22
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.024 0.005 -10000 0 -10000 0 0
SERPINE1 0.03 0.088 -10000 0 -0.56 6 6
SMAD3/SMAD4/ATF2 0.03 0.06 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.023 0.16 -10000 0 -0.42 96 96
SAP30 0.024 0.015 0.27 3 -10000 0 3
Cbp/p300/PIAS3 0.047 0.03 -10000 0 -10000 0 0
JUN -0.075 0.17 0.29 1 -0.32 229 230
SMAD3/SMAD4/IRF7 0.044 0.08 0.34 16 -10000 0 16
TFE3 0.029 0.01 -10000 0 -10000 0 0
COL1A2 0.049 0.088 0.43 1 -0.52 4 5
mesenchymal cell differentiation -0.032 0.062 -10000 0 -10000 0 0
DLX1 0.053 0.11 0.27 122 -0.6 8 130
TCF3 0.024 0.005 -10000 0 -10000 0 0
FOS -0.16 0.29 -10000 0 -0.6 253 253
SMAD3/SMAD4/Max 0.025 0.061 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.045 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.01 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.058 -10000 0 -10000 0 0
IRF7 0.041 0.061 0.28 47 -10000 0 47
ESR1 -0.031 0.24 0.27 109 -0.6 106 215
HNF4A 0.023 0.029 0.27 11 -10000 0 11
MEF2C 0.051 0.096 0.4 10 -0.45 2 12
SMAD2-3/SMAD4 0.029 0.069 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.046 0.027 -10000 0 -0.39 1 1
IGHV3OR16-13 0.004 0.043 -10000 0 -0.35 11 11
TGIF2/HDAC complex 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.027 0.027 0.27 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.039 0.064 -10000 0 -0.49 1 1
MSG1/HSC70 -0.16 0.24 -10000 0 -0.44 339 339
SMAD2 0.021 0.032 -10000 0 -10000 0 0
SMAD3 0.011 0.043 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.041 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 0.022 0.05 0.24 9 -0.29 3 12
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
NCOA1 0.024 0.022 -10000 0 -0.6 1 1
MYOD/E2A 0.032 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.075 0.066 -10000 0 -10000 0 0
IFNB1 0.018 0.076 0.33 28 -10000 0 28
SMAD3/SMAD4/MEF2C 0.066 0.091 -10000 0 -0.55 1 1
CITED1 -0.23 0.31 0.27 9 -0.6 338 347
SMAD2-3/SMAD4/ARC105 0.037 0.07 -10000 0 -10000 0 0
RBL1 0.024 0.01 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.063 -10000 0 -0.41 10 10
RUNX1-3/PEBPB2 0.041 0.037 -10000 0 -0.55 2 2
SMAD7 -0.044 0.15 -10000 0 -0.54 8 8
MYC/MIZ-1 0.013 0.071 -10000 0 -0.45 18 18
SMAD3/SMAD4 0.029 0.074 0.3 21 -0.36 3 24
IL10 0.004 0.088 0.34 2 -0.39 24 26
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.024 0.006 -10000 0 -10000 0 0
CDK2 0.026 0.007 -10000 0 -10000 0 0
IL5 0.003 0.09 0.29 4 -0.38 26 30
CDK4 0.026 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.052 0.2 -10000 0 -0.6 96 96
SMAD3/SMAD4/SP1 0.044 0.067 -10000 0 -10000 0 0
FOXG1 0.017 0.069 0.27 54 -10000 0 54
FOXO3 0.01 0.02 -10000 0 -0.32 2 2
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 0.05 0.092 0.3 2 -0.41 8 10
MYOD1 0.021 0.026 0.27 9 -10000 0 9
SMAD3/SMAD4/HNF4 0.029 0.061 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.026 0.11 -10000 0 -0.42 28 28
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.027 0.27 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.04 0.072 -10000 0 -0.52 2 2
SMAD3/SMAD4/SP1-3 0.055 0.069 -10000 0 -10000 0 0
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.069 0.09 0.34 9 -0.39 1 10
ITGB5 0.014 0.044 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.012 0.064 -10000 0 -0.3 21 21
SMAD3/SMAD4/AR -0.016 0.15 -10000 0 -0.42 89 89
AR -0.043 0.2 0.27 1 -0.6 90 91
negative regulation of cell growth -0.002 0.086 -10000 0 -0.32 17 17
SMAD3/SMAD4/MYOD 0.028 0.061 -10000 0 -10000 0 0
E2F5 0.022 0.023 0.27 6 -10000 0 6
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.06 0.072 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.051 -10000 0 -0.35 9 9
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.052 0.19 -10000 0 -0.33 229 229
SMAD3/SMAD4/RUNX2 0.032 0.062 -10000 0 -10000 0 0
TGIF2 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.024 0.003 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.024 0.016 0.27 1 -10000 0 1
CDKN2C 0.015 0.03 -10000 0 -0.58 1 1
CDKN2A 0.058 0.085 0.27 113 -10000 0 113
CCND2 -0.015 0.037 0.18 1 -0.25 9 10
RB1 0.014 0.049 0.29 11 -0.24 6 17
CDK4 -0.017 0.045 0.21 1 -0.34 8 9
CDK6 -0.016 0.049 0.26 5 -0.25 15 20
G1/S progression -0.009 0.063 0.19 34 -0.31 12 46
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.018 0.13 0.32 11 -0.4 33 44
IKBKB 0.023 0.091 0.3 8 -0.32 7 15
AKT1 0.036 0.11 0.26 69 -0.24 16 85
IKBKG 0.027 0.075 0.32 5 -0.28 3 8
CALM1 0 0.1 0.26 1 -0.46 15 16
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.017 0.17 0.36 10 -0.53 39 49
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0.11 -10000 0 -0.46 17 17
DOK1 0.024 0.003 -10000 0 -10000 0 0
AP-1 -0.03 0.1 0.24 8 -0.25 46 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 -0.47 50 61
CAMK2G 0.001 0.1 0.3 1 -0.44 14 15
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 45 45
GO:0007205 0 0.11 -10000 0 -0.47 17 17
SYK 0.024 0.004 -10000 0 -10000 0 0
ELK1 0 0.11 0.26 1 -0.47 15 16
NFATC1 0.027 0.14 0.3 19 -0.45 28 47
B-cell antigen/BCR complex -0.006 0.17 0.38 8 -0.48 78 86
PAG1/CSK 0.029 0.017 -10000 0 -10000 0 0
NFKBIB 0.025 0.047 0.16 11 -0.13 17 28
HRAS 0.009 0.11 0.27 11 -0.46 16 27
NFKBIA 0.025 0.046 0.16 12 -0.12 16 28
NF-kappa-B/RelA/I kappa B beta 0.028 0.042 0.17 9 -10000 0 9
RasGAP/Csk 0.023 0.13 0.33 9 -0.39 58 67
mol:GDP 0.002 0.1 -10000 0 -0.46 15 15
PTEN 0.023 0.031 -10000 0 -0.6 2 2
CD79B 0.005 0.11 0.27 8 -0.6 25 33
NF-kappa-B/RelA/I kappa B alpha 0.029 0.041 0.17 9 -10000 0 9
GRB2 0.023 0.011 0.27 1 -10000 0 1
PI3K/BCAP/CD19 0.019 0.17 0.35 9 -0.5 40 49
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.11 -10000 0 -0.48 17 17
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.092 0.17 -10000 0 -0.45 67 67
CHUK 0.024 0.083 0.32 5 -0.31 9 14
IBTK 0.024 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.016 0.1 -10000 0 -0.42 15 15
PTPN6 -0.02 0.13 0.29 9 -0.58 27 36
RELA 0.024 0.004 -10000 0 -10000 0 0
BCL2A1 0.026 0.036 0.16 12 -10000 0 12
VAV2 0.009 0.15 0.29 12 -0.59 26 38
ubiquitin-dependent protein catabolic process 0.027 0.047 0.16 11 -0.12 21 32
BTK 0.015 0.07 -10000 0 -0.97 4 4
CD19 -0.002 0.14 0.29 19 -0.46 47 66
MAP4K1 0.03 0.051 0.27 24 -0.6 2 26
CD72 0.028 0.04 0.27 16 -0.6 1 17
PAG1 0.021 0.016 0.27 2 -10000 0 2
MAPK14 0.019 0.15 0.36 11 -0.46 36 47
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0 0.12 -10000 0 -0.46 25 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.002 0.14 0.28 3 -0.44 58 61
RAF1 0.008 0.11 0.28 5 -0.45 14 19
RasGAP/p62DOK/SHIP 0.023 0.13 0.31 8 -0.38 58 66
CD79A -0.01 0.18 0.27 52 -0.6 65 117
re-entry into mitotic cell cycle -0.03 0.1 0.25 7 -0.26 39 46
RASA1 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.1 0.28 20 -0.38 11 31
MAPK1 0.008 0.096 0.27 8 -0.38 14 22
CD72/SHP1 0.023 0.15 0.38 15 -0.55 27 42
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.15 0.34 14 -0.45 38 52
actin cytoskeleton organization 0.025 0.14 0.31 21 -0.51 25 46
NF-kappa-B/RelA 0.058 0.08 0.29 10 -0.21 1 11
Calcineurin 0.015 0.096 -10000 0 -0.41 13 13
PI3K -0.015 0.1 -10000 0 -0.45 22 22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.003 0.12 -10000 0 -0.47 27 27
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.003 0.21 0.45 6 -0.72 45 51
DAPP1 -0.025 0.22 -10000 0 -0.8 46 46
cytokine secretion 0.028 0.13 0.28 25 -0.42 28 53
mol:DAG 0 0.11 -10000 0 -0.48 17 17
PLCG2 0.021 0.025 0.27 1 -0.6 1 2
MAP2K1 0.008 0.1 0.28 7 -0.42 14 21
B-cell antigen/BCR complex/FcgammaRIIB 0.006 0.14 0.35 8 -0.44 59 67
mol:PI-3-4-5-P3 0.005 0.094 0.23 22 -0.33 19 41
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 0.29 8 -0.47 56 64
MALT1 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.017 0.15 0.3 17 -0.55 25 42
B-cell antigen/BCR complex/LYN/SYK 0.006 0.14 0.37 11 -0.46 48 59
CARD11 0.002 0.11 0.3 3 -0.47 17 20
FCGR2B 0.018 0.039 0.27 1 -0.6 3 4
PPP3CA 0.024 0.009 0.27 1 -10000 0 1
BCL10 0.024 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.15 45 -0.13 2 47
PTPRC 0.023 0.038 0.27 12 -0.6 1 13
PDPK1 0.02 0.085 0.21 53 -0.23 17 70
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
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 0.13 0.12 0.27 348 -10000 0 348
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.029 0.27 12 -10000 0 12
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.049 0.1 0.32 16 -0.53 8 24
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.027 0.032 -10000 0 -0.37 5 5
IL2RA 0.022 0.11 0.44 8 -0.77 10 18
IL2RB 0.033 0.048 0.27 33 -10000 0 33
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.27 32 -0.6 5 37
G1/S transition of mitotic cell cycle 0.054 0.12 0.33 2 -0.79 10 12
PTPN11 0.025 0.002 -10000 0 -10000 0 0
CCND2 0.009 0.072 0.36 2 -0.81 6 8
LCK 0.024 0.077 0.27 23 -0.6 9 32
GRB2 0.024 0.011 0.27 1 -10000 0 1
IL2 0.023 0.025 0.27 8 -10000 0 8
CDK6 0.022 0.045 0.27 2 -0.6 4 6
CCND3 0.048 0.1 0.4 4 -0.64 3 7
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 0.051 0.065 0.28 1 -0.33 11 12
NF kappa B1 p50/RelA/I kappa B alpha 0.054 0.08 0.34 11 -10000 0 11
alphaV/beta3 Integrin/Osteopontin/Src 0.086 0.076 0.24 16 -10000 0 16
AP1 -0.042 0.18 -10000 0 -0.54 20 20
ILK 0.038 0.067 -10000 0 -0.34 11 11
bone resorption 0.03 0.062 0.28 1 -0.33 9 10
PTK2B 0.02 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.074 0.088 0.31 7 -0.31 12 19
ITGAV 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.034 0.025 -10000 0 -0.45 2 2
alphaV/beta3 Integrin/Osteopontin 0.088 0.094 0.34 5 -0.37 13 18
MAP3K1 0.038 0.068 0.26 13 -0.34 13 26
JUN 0.018 0.061 -10000 0 -0.6 8 8
MAPK3 0.027 0.065 0.27 11 -0.33 10 21
MAPK1 0.028 0.066 0.27 12 -0.32 10 22
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.066 0.26 14 -0.32 13 27
ITGB3 0.017 0.08 0.27 4 -0.6 13 17
NFKBIA 0.026 0.068 0.34 8 -0.32 6 14
FOS -0.17 0.29 -10000 0 -0.6 251 251
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.028 0.1 0.46 5 -0.56 2 7
NF kappa B1 p50/RelA 0.072 0.073 0.36 6 -10000 0 6
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.033 0.062 0.24 1 -0.44 13 14
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.038 0.068 0.26 12 -0.34 13 25
VAV3 0.017 0.071 0.26 16 -0.33 13 29
MAP3K14 0.039 0.068 0.26 10 -0.34 13 23
ROCK2 0.023 0.031 -10000 0 -0.6 2 2
SPP1 0.094 0.11 0.27 232 -10000 0 232
RAC1 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.036 0.062 0.32 2 -0.31 11 13
MMP2 -0.059 0.15 0.36 3 -0.52 18 21
Arf6 trafficking events

Figure 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
SLC2A4 -0.28 0.31 -10000 0 -0.6 401 401
CLTC 0.027 0.071 0.24 8 -0.45 10 18
calcium ion-dependent exocytosis 0.009 0.023 -10000 0 -0.25 1 1
Dynamin 2/GTP 0.021 0.012 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.017 0.046 -10000 0 -0.33 9 9
CPE 0.006 0.048 -10000 0 -0.39 12 12
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.018 -10000 0 -0.17 2 2
CTNND1 0.009 0.06 0.2 34 -10000 0 34
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.047 0.22 2 -0.32 8 10
TSHR -0.004 0.077 -10000 0 -0.39 32 32
INS -0.002 0.094 -10000 0 -0.48 29 29
BIN1 0.018 0.061 -10000 0 -0.6 8 8
mol:Choline 0.011 0.018 -10000 0 -0.17 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.014 0.15 8 -10000 0 8
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 -0.35 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.058 -10000 0 -0.28 20 20
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.029 0.27 12 -10000 0 12
substrate adhesion-dependent cell spreading 0.016 0.041 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.069 0.34 9 -10000 0 9
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.014 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.015 0.045 -10000 0 -0.34 8 8
clathrin heavy chain/ACAP1 0.025 0.067 0.28 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 0.018 0.037 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.009 0.061 0.19 82 -10000 0 82
NME1 0.012 0.014 0.15 8 -10000 0 8
clathrin coat assembly 0.029 0.074 0.24 10 -0.44 10 20
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 -0.29 332 332
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.027 -10000 0 -0.31 5 5
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.043 0.2 1 -0.34 7 8
SDC1 0.021 0.046 0.21 1 -0.33 7 8
ARF6/GDP 0.021 0.012 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.041 0.071 -10000 0 -0.35 9 9
mol:Phosphatidic acid 0.011 0.018 -10000 0 -0.17 2 2
endocytosis -0.039 0.04 0.35 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.049 0.15 0.25 2 -0.32 168 170
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.022 -10000 0 -0.6 1 1
Dynamin 2/GDP 0.025 0.015 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.1 0.17 0.29 3 -0.31 267 270
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
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.023 0.087 -10000 0 -0.62 7 7
oxygen homeostasis 0.012 0.013 -10000 0 -10000 0 0
TCEB2 0.024 0.016 0.27 3 -10000 0 3
TCEB1 0.02 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.089 0.083 0.34 9 -0.33 1 10
EPO 0.16 0.18 0.54 68 -0.51 2 70
FIH (dimer) 0.034 0.02 -10000 0 -10000 0 0
APEX1 0.035 0.024 -10000 0 -10000 0 0
SERPINE1 0.15 0.16 0.53 35 -0.57 2 37
FLT1 -0.012 0.16 -10000 0 -0.77 16 16
ADORA2A 0.17 0.17 0.5 71 -0.49 4 75
germ cell development 0.15 0.16 0.52 35 -0.55 2 37
SLC11A2 0.15 0.16 0.5 33 -0.53 3 36
BHLHE40 0.14 0.16 0.5 36 -0.55 4 40
HIF1AN 0.034 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.13 0.13 0.42 49 -0.38 1 50
ETS1 0.028 0.025 -10000 0 -0.62 1 1
CITED2 0.016 0.085 -10000 0 -0.61 5 5
KDR -0.008 0.15 -10000 0 -0.76 14 14
PGK1 0.15 0.16 0.5 38 -0.5 4 42
SIRT1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0.002 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.62 15 -0.57 4 19
EPAS1 0.079 0.09 0.31 44 -0.36 1 45
SP1 0.029 0.01 -10000 0 -10000 0 0
ABCG2 0.13 0.2 0.5 37 -0.57 24 61
EFNA1 0.12 0.14 0.53 9 -0.53 3 12
FXN 0.16 0.16 0.48 45 -0.55 2 47
POU5F1 0.15 0.16 0.52 35 -0.57 2 37
neuron apoptosis -0.16 0.17 0.56 4 -0.62 15 19
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.052 0.07 0.28 65 -10000 0 65
EGLN2 0.035 0.024 0.27 3 -10000 0 3
EGLN1 0.027 0.03 -10000 0 -0.61 1 1
VHL/Elongin B/Elongin C 0.039 0.023 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.03 0.024 -10000 0 -10000 0 0
SLC2A1 0.16 0.16 0.48 51 -0.51 3 54
TWIST1 0.15 0.18 0.48 41 -0.53 24 65
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.11 0.11 0.45 8 -0.38 1 9
VEGFA 0.14 0.16 0.51 32 -0.53 3 35
CREBBP 0.023 0.007 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.025 0.048 0.14 118 -10000 0 118
TP53 0.009 0.019 -10000 0 -0.19 2 2
Senescence 0.008 0.022 -10000 0 -0.19 2 2
Apoptosis 0.008 0.022 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.009 0.063 0.29 27 -10000 0 27
MDM4 0.02 0.01 -10000 0 -10000 0 0
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 0.24 5 -0.5 27 32
NUMA1 0 0.11 0.24 1 -0.41 39 40
SPTAN1 -0.005 0.11 0.28 5 -0.51 26 31
LIMK1 -0.004 0.11 0.28 3 -0.52 25 28
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.024 0.004 -10000 0 -10000 0 0
CASP10 -0.013 0.098 0.22 11 -0.47 27 38
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
PTK2 0 0.13 0.24 2 -0.45 40 42
DIABLO 0.025 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.11 0.27 5 -0.5 26 31
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 0.28 3 -0.5 34 37
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.011 0.14 -10000 0 -0.7 24 24
BID 0.003 0.055 0.19 3 -0.27 26 29
MAP3K1 -0.007 0.1 -10000 0 -0.41 42 42
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.11 0.25 3 -0.5 26 29
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair -0.016 0.045 0.25 4 -0.21 3 7
neuron apoptosis 0.004 0.12 -10000 0 -0.71 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.004 0.12 0.25 1 -0.46 33 34
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 -0.5 25 25
CASP7 0.002 0.062 0.27 3 -0.7 1 4
KRT18 0.016 0.07 -10000 0 -0.65 6 6
apoptosis -0.001 0.12 0.29 4 -0.46 40 44
DFFA -0.006 0.11 0.24 2 -0.51 26 28
DFFB -0.006 0.11 0.24 2 -0.51 26 28
PARP1 0.016 0.045 0.21 3 -0.25 4 7
actin filament polymerization 0.002 0.11 0.51 23 -0.3 6 29
TNF 0.024 0.067 0.27 17 -0.6 7 24
CYCS 0.004 0.052 0.22 5 -0.23 18 23
SATB1 -0.011 0.16 -10000 0 -0.79 27 27
SLK -0.005 0.11 0.26 3 -0.51 26 29
p15 BID/BAX 0.011 0.063 -10000 0 -0.25 30 30
CASP2 0.001 0.067 0.3 2 -0.28 18 20
JNK cascade 0.007 0.1 0.4 42 -10000 0 42
CASP3 -0.003 0.12 0.27 2 -0.53 26 28
LMNB2 -0.003 0.14 0.3 3 -0.51 40 43
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.035 -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 26 29
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 0.29 8 -0.47 30 38
APP 0.004 0.12 -10000 0 -0.72 18 18
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.002 -10000 0 -10000 0 0
VIM 0.001 0.13 0.29 5 -0.45 42 47
LMNA 0.007 0.086 0.32 2 -0.38 21 23
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.071 -10000 0 -0.28 25 25
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.004 0.11 0.27 3 -0.5 26 29
APAF-1/Caspase 9 -0.003 0.12 -10000 0 -0.62 28 28
nuclear fragmentation during apoptosis 0.001 0.11 0.24 1 -0.4 39 40
CFL2 -0.002 0.11 0.3 6 -0.52 23 29
GAS2 -0.032 0.15 0.27 5 -0.4 81 86
positive regulation of apoptosis 0.013 0.12 0.27 8 -0.48 30 38
PRF1 0.015 0.087 0.27 8 -0.6 15 23
Signaling mediated by p38-gamma and p38-delta

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
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 58 -0.35 19 77
CCND1 0.011 0.05 -10000 0 -0.38 6 6
p38 gamma/SNTA1 0.022 0.075 0.33 2 -0.34 17 19
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.006 0.078 0.21 62 -0.35 19 81
MAP2K6 -0.004 0.056 -10000 0 -0.37 19 19
MAPT -0.024 0.12 0.26 13 -0.34 83 96
MAPK13 0.01 0.013 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.023 -10000 0 -0.36 3 3
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0.008 -10000 0 -10000 0 0
MAP4K4 0.002 0.062 -10000 0 -0.28 18 18
BAG4 0.02 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.003 0.057 -10000 0 -0.26 16 16
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BAX 0 0.044 -10000 0 -0.35 10 10
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.068 0.68 8 -10000 0 8
BAD -0.017 0.051 0.19 3 -0.27 11 14
SMPD1 0.014 0.059 0.21 11 -0.22 19 30
RB1 -0.017 0.048 -10000 0 -0.26 12 12
FADD/Caspase 8 0.028 0.092 0.27 13 -0.39 6 19
MAP2K4 -0.017 0.047 -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 0.23 8 -0.31 6 14
EGF -0.091 0.24 0.27 2 -0.6 153 155
mol:ceramide -0.016 0.052 0.15 1 -0.26 15 16
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.012 -10000 0 -0.2 1 1
ASAH1 0.021 0.018 0.27 3 -10000 0 3
negative regulation of cell cycle -0.018 0.048 -10000 0 -0.26 12 12
cell proliferation -0.05 0.13 0.28 1 -0.28 162 163
BID -0.025 0.17 -10000 0 -0.66 51 51
MAP3K1 -0.017 0.049 -10000 0 -0.27 11 11
EIF2A -0.016 0.052 0.29 3 -0.25 6 9
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.009 0.057 0.32 2 -0.32 5 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.061 0.32 2 -0.36 4 6
Cathepsin D/ceramide 0.004 0.062 0.18 28 -0.24 14 42
FADD 0.023 0.084 0.27 1 -0.39 3 4
KSR1 -0.01 0.058 0.2 19 -0.27 10 29
MAPK8 -0.014 0.056 -10000 0 -0.29 9 9
PRKRA -0.017 0.05 0.2 1 -0.27 11 12
PDGFA 0.024 0.005 -10000 0 -10000 0 0
TRAF2 0.024 0.004 -10000 0 -10000 0 0
IGF1 -0.11 0.26 -10000 0 -0.6 177 177
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.016 0.052 0.15 1 -0.26 15 16
CTSD 0.033 0.046 0.27 30 -10000 0 30
regulation of nitric oxide biosynthetic process 0.035 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.053 0.14 0.3 1 -0.3 161 162
PRKCD 0.024 0.01 0.27 1 -10000 0 1
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.012 -10000 0 -0.2 1 1
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 -0.34 7 7
TNFR1A/BAG4/TNF-alpha 0.037 0.048 -10000 0 -0.38 6 6
mol:Sphingosine-1-phosphate 0.01 0.008 -10000 0 -10000 0 0
MAP2K1 -0.011 0.057 0.32 2 -0.34 4 6
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
CYCS -0.002 0.051 0.18 14 -0.25 9 23
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 -10000 0 -0.28 7 7
TNF-alpha/TNFR1A/FAN 0.04 0.045 -10000 0 -0.33 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.076 -10000 0 -0.39 20 20
MAP2K2 -0.012 0.057 0.32 2 -0.31 5 7
SMPD3 -0.003 0.1 0.28 4 -0.29 80 84
TNF 0.024 0.067 0.27 17 -0.6 7 24
PKC zeta/PAR4 0.034 0.019 -10000 0 -0.45 1 1
mol:PHOSPHOCHOLINE 0.044 0.1 0.25 151 -0.24 2 153
NF kappa B1/RelA/I kappa B alpha 0.065 0.027 -10000 0 -0.34 1 1
AIFM1 -0.003 0.051 0.18 14 -0.22 13 27
BCL2 0.008 0.098 -10000 0 -0.6 21 21
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.014 0.059 -10000 0 -10000 0 0
PLK1 0.28 0.2 0.54 182 -0.58 1 183
CDKN1B 0.17 0.14 0.4 54 -0.42 6 60
FOXO3 0.22 0.17 0.48 160 -0.63 1 161
KAT2B 0.061 0.03 -10000 0 -10000 0 0
FOXO1/SIRT1 0.01 0.053 -10000 0 -0.33 3 3
CAT 0.21 0.17 0.65 13 -0.89 3 16
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.062 0.032 -10000 0 -10000 0 0
FOXO1 0.019 0.061 -10000 0 -0.33 4 4
MAPK10 -0.019 0.13 0.21 9 -0.32 124 133
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 0.41 128 -0.61 1 129
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.07 0.085 -10000 0 -0.65 8 8
FOXO1/SKP2 0.028 0.057 -10000 0 -0.35 2 2
mol:GDP 0.04 0.029 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.14 0.13 0.48 3 -0.53 9 12
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.022 0.13 -10000 0 -0.53 27 27
MST1 0.054 0.067 0.3 1 -0.54 8 9
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.13 -10000 0 -0.46 38 38
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.034 0.027 0.21 10 -10000 0 10
MAPK9 0.033 0.028 0.22 6 -10000 0 6
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 0.45 21 -0.44 2 23
RBL2 0.12 0.26 0.57 2 -0.62 56 58
RAL/GDP 0.06 0.024 -10000 0 -10000 0 0
CHUK 0.062 0.031 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.06 0.023 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.074 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 0.051 0.036 -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 0.45 26 -0.38 2 28
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.057 -10000 0 -0.35 2 2
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 0.27 8 -0.6 10 18
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.068 0.11 0.36 1 -0.42 13 14
CREBBP 0.022 0.007 -10000 0 -10000 0 0
FBXO32 0.26 0.22 0.6 123 -1.2 3 126
BCL6 0.18 0.15 0.55 3 -0.74 6 9
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
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.01 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.029 0.019 -10000 0 -10000 0 0
CDKN1B 0.009 0.06 -10000 0 -0.34 15 15
CDKN1A 0.008 0.064 -10000 0 -0.35 17 17
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
FOXO3 0.011 0.062 -10000 0 -0.37 13 13
AKT1 0.004 0.06 -10000 0 -0.37 16 16
BAD 0.024 0.005 -10000 0 -10000 0 0
AKT3 0.006 0.037 -10000 0 -0.36 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.063 -10000 0 -0.35 17 17
AKT1/ASK1 0.032 0.071 -10000 0 -0.33 18 18
BAD/YWHAZ 0.036 0.023 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.031 0.068 0.32 18 -10000 0 18
TSC1 0.01 0.054 -10000 0 -0.34 12 12
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.075 0.27 1 -0.35 16 17
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.064 -10000 0 -0.36 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.006 0.058 0.32 1 -0.34 16 17
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.004 0.006 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.08 0.31 19 -0.26 4 23
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.066 -10000 0 -0.36 16 16
CASP9 0.011 0.048 -10000 0 -0.33 9 9
YWHAB 0.023 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.076 0.34 3 -0.38 8 11
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.018 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.01 0.062 0.25 3 -0.48 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.056 -10000 0 -0.32 18 18
CHUK 0.009 0.059 -10000 0 -0.34 15 15
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 -0.42 21 27
PDPK1 0.023 0.007 -10000 0 -10000 0 0
MDM2 0.011 0.069 0.27 2 -0.35 18 20
MAPKKK cascade -0.036 0.074 0.34 17 -0.26 1 18
MDM2/Cbp/p300 0.043 0.078 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.071 0.26 29 -0.59 3 32
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.074 0.32 4 -0.53 3 7
glucose import -0.17 0.16 0.21 3 -0.33 397 400
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.052 0.18 1 -0.41 4 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.17 0.16 0.21 3 -0.34 397 400
GSK3A 0.009 0.063 -10000 0 -0.36 16 16
FOXO1 0.011 0.046 -10000 0 -0.37 6 6
GSK3B 0.008 0.063 -10000 0 -0.36 16 16
SFN 0.018 0.073 0.27 8 -0.6 10 18
G1/S transition of mitotic cell cycle 0.013 0.069 0.33 2 -0.6 3 5
p27Kip1/14-3-3 family 0.018 0.053 0.38 1 -0.46 3 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.025 0.009 0.27 1 -10000 0 1
ANTXR2 0.018 0.061 -10000 0 -0.6 8 8
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.075 9 9
monocyte activation 0.006 0.08 0.26 2 -0.34 38 40
MAP2K2 -0.001 0.093 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.007 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 0.12 1 -10000 0 1
MAP2K6 -0.01 0.045 -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 -0.008 0.045 0.22 2 -0.27 19 21
Channel 0.027 0.039 -10000 0 -0.33 9 9
NLRP1 -0.007 0.032 -10000 0 -0.32 8 8
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.07 -10000 0 -0.39 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.075 9 -10000 0 9
MAPK3 -0.004 0.007 -10000 0 -10000 0 0
MAPK1 -0.004 0.008 0.12 1 -10000 0 1
PGR -0.081 0.14 0.065 51 -0.33 207 258
PA/Cellular Receptors 0.028 0.042 -10000 0 -0.36 9 9
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 0.12 2 -10000 0 2
TNF 0.024 0.067 0.27 17 -0.6 7 24
VCAM1 0.006 0.081 0.26 2 -0.34 38 40
platelet activation -0.002 0.07 -10000 0 -0.39 25 25
MAPKKK cascade -0.002 0.028 0.14 3 -0.13 7 10
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 -0.21 10 10
mol:cAMP -0.002 0.071 -10000 0 -0.4 25 25
necrosis -0.002 0.008 -10000 0 -0.075 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.037 -10000 0 -0.31 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.005 -10000 0 -9999 0 0
PLK4 0.035 0.051 0.27 38 -9999 0 38
regulation of centriole replication 0.016 0.029 0.26 1 -9999 0 1
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.052 0.075 0.44 6 -0.42 11 17
MAP4K1 0.03 0.051 0.27 24 -0.6 2 26
MAP3K8 0.021 0.044 -10000 0 -0.6 4 4
PRKCB 0.019 0.079 0.27 14 -0.6 11 25
DBNL 0.024 0.004 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.013 0.056 0.23 3 -0.32 11 14
JUN 0.004 0.12 -10000 0 -0.59 28 28
MAP3K7 0.013 0.057 0.24 2 -0.3 12 14
GRAP2 0.016 0.073 0.27 3 -0.6 11 14
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.012 0.067 0.26 1 -0.39 9 10
LAT 0.024 0.038 0.27 7 -0.6 2 9
LCP2 0.024 0.01 0.27 1 -10000 0 1
MAPK8 0.01 0.13 -10000 0 -0.64 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.062 0.26 3 -0.31 16 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.059 0.074 0.43 6 -0.4 11 17
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.039 0.058 -10000 0 -0.42 12 12
forebrain development -0.044 0.21 0.35 1 -0.63 61 62
GNAO1 0.018 0.096 0.27 28 -0.6 15 43
SMO/beta Arrestin2 0.027 0.048 -10000 0 -0.45 7 7
SMO 0.017 0.059 -10000 0 -0.6 7 7
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.021 0.086 0.28 1 -0.5 10 11
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.023 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 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) -0.035 0.19 -10000 0 -0.66 44 44
SAP30 0.025 0.015 0.27 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 0.009 -10000 0 -10000 0 0
GLI2 0.008 0.066 -10000 0 -0.3 18 18
GLI3 0.009 0.089 0.29 1 -0.49 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 0.098 -10000 0 -0.34 43 43
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.014 0.092 -10000 0 -0.46 18 18
GLI2/Su(fu) 0.011 0.083 -10000 0 -0.41 15 15
FOXA2 0.01 0.11 0.44 1 -0.66 15 16
neural tube patterning -0.044 0.21 0.35 1 -0.63 61 62
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 -0.63 61 62
SUFU 0.015 0.025 -10000 0 -0.24 1 1
LGALS3 0.018 0.061 -10000 0 -0.6 8 8
catabolic process 0.023 0.1 0.29 1 -0.55 15 16
GLI3A/CBP -0.001 0.098 -10000 0 -0.37 54 54
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.046 0.22 0.35 1 -0.66 60 61
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
IFT172 0.024 0.022 -10000 0 -0.6 1 1
RBBP7 0.026 0.022 0.27 7 -10000 0 7
Su(fu)/Galectin3 0.018 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 -0.45 26 26
PTCH1 -0.083 0.32 -10000 0 -1.1 62 62
MIM/GLI1 -0.032 0.2 -10000 0 -0.67 43 43
CREBBP -0.001 0.098 -10000 0 -0.37 54 54
Su(fu)/SIN3/HDAC complex 0.006 0.093 -10000 0 -0.47 21 21
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.015 0.061 0.22 2 -0.3 31 33
FRAP1 -0.003 0.083 0.26 1 -0.46 20 21
AKT1 -0.006 0.063 0.19 2 -0.28 22 24
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0.024 0.063 0.23 2 -0.28 3 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.24 1 1
TSC2 0.023 0.007 -10000 0 -10000 0 0
RHEB/GDP 0.007 0.042 -10000 0 -0.28 2 2
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.006 0.076 -10000 0 -0.31 43 43
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.045 -10000 0 -0.23 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.011 0.073 0.29 3 -0.3 19 22
MAP3K5 0 0.045 0.2 9 -0.19 35 44
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0 0.045 0.2 9 -0.19 35 44
mol:LY294002 0 0 -10000 0 -0.001 37 37
EIF4B 0.009 0.067 0.27 4 -0.3 12 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.064 -10000 0 -0.29 7 7
eIF4E/eIF4G1/eIF4A1 0.004 0.052 -10000 0 -0.29 18 18
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.019 0.073 -10000 0 -0.31 34 34
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.051 0.21 10 -0.2 2 12
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.028 0.055 0.21 1 -0.28 2 3
mol:Amino Acids 0 0 -10000 0 -0.001 37 37
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.017 0.057 0.19 2 -0.29 24 26
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.006 0.14 -10000 0 -0.52 49 49
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.002 0.051 -10000 0 -10000 0 0
TSC1/TSC2 0.027 0.069 0.26 3 -0.34 2 5
tumor necrosis factor receptor activity 0 0 0.001 37 -10000 0 37
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.011 0.078 -10000 0 -0.33 44 44
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.031 -10000 0 -0.6 2 2
PDK2 -0.015 0.054 0.2 4 -0.3 18 22
EIF4EBP1 -0.028 0.23 -10000 0 -1 41 41
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D -0.001 0.08 0.32 3 -0.42 20 23
peptide biosynthetic process -0.011 0.017 -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
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.005 0.1 0.26 2 -0.4 29 31
BAG4 0.02 0.01 -10000 0 -10000 0 0
BAD 0.005 0.041 0.2 6 -0.19 4 10
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.024 0.041 0.27 10 -0.6 2 12
BAX 0.004 0.043 0.24 4 -0.18 5 9
EnzymeConsortium:3.1.4.12 0.001 0.027 0.085 4 -0.091 27 31
IKBKB 0.014 0.11 0.3 7 -0.4 20 27
MAP2K2 0.007 0.053 0.23 12 -0.27 1 13
MAP2K1 0.008 0.054 0.23 14 -0.27 1 15
SMPD1 0.001 0.033 0.14 4 -0.15 13 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.29 13 -0.41 23 36
MAP2K4 0.005 0.034 0.2 1 -10000 0 1
protein ubiquitination 0.001 0.1 0.34 4 -0.39 26 30
EnzymeConsortium:2.7.1.37 0.007 0.056 0.23 13 -0.3 1 14
response to UV 0 0.001 0.002 15 -0.003 2 17
RAF1 0.008 0.054 0.2 29 -0.24 2 31
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.005 0.042 0.13 8 -0.14 22 30
I-kappa-B-alpha/RELA/p50/ubiquitin 0.032 0.008 -10000 0 -10000 0 0
MADD 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.003 0.039 0.21 1 -0.18 4 5
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.009 0.054 0.22 13 -0.25 2 15
MAPK1 0.006 0.061 0.22 13 -0.25 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 22 31
KSR1 0.009 0.052 0.19 25 -0.22 4 29
MAPK8 0.002 0.04 0.26 4 -10000 0 4
TRAF2 0.024 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 7 -10000 0 7
CHUK -0.005 0.097 -10000 0 -0.4 24 24
TNF R/SODD 0.028 0.016 -10000 0 -10000 0 0
TNF 0.024 0.067 0.27 17 -0.6 7 24
CYCS 0.007 0.047 0.19 11 -0.18 3 14
IKBKG -0.005 0.1 0.43 1 -0.41 23 24
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.11 -10000 0 -0.43 28 28
RELA 0.024 0.004 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.006 0.046 0.18 11 -0.17 6 17
TNF/TNF R/SODD 0.037 0.047 -10000 0 -0.38 6 6
TNFRSF1A 0.024 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 7 -10000 0 7
CASP8 0.01 0.11 -10000 0 -0.64 22 22
NSMAF 0.014 0.11 0.26 9 -0.4 25 34
response to hydrogen peroxide 0 0.001 0.002 15 -0.003 2 17
BCL2 0.008 0.098 -10000 0 -0.6 21 21
IL2 signaling events mediated by PI3K

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
BCL2L1 0.022 0.075 -10000 0 -0.68 2 2
UGCG 0.018 0.097 -10000 0 -0.64 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.049 0.12 0.3 9 -0.47 18 27
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 5 -0.44 29 34
FRAP1 0.034 0.15 0.34 5 -0.48 37 42
FOXO3 0.038 0.14 0.34 10 -0.52 23 33
AKT1 0.038 0.15 0.35 6 -0.56 24 30
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 0.38 2 -0.47 10 12
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.035 0.014 -10000 0 -10000 0 0
RPS6KB1 0.012 0.097 -10000 0 -0.84 9 9
mol:sphingomyelin 0.007 0.076 -10000 0 -0.76 7 7
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.028 0.03 0.27 12 -10000 0 12
PIK3R1 0.024 0.009 -10000 0 -10000 0 0
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.069 0.2 0.44 4 -0.93 23 27
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 0.33 11 -0.52 9 20
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 0.33 11 -0.51 9 20
Rac1/GDP 0.018 0.013 0.19 1 -10000 0 1
T cell proliferation 0.043 0.1 0.3 13 -0.47 8 21
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 0.092 2 -0.076 14 16
PRKCZ 0.042 0.1 0.32 10 -0.49 8 18
NF kappa B1 p50/RelA 0.052 0.14 0.33 2 -0.54 15 17
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.026 0.071 0.31 11 -0.62 3 14
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.09 0.27 46 -0.6 10 56
IL2RB 0.033 0.049 0.27 33 -10000 0 33
TERT 0.049 0.076 0.27 89 -10000 0 89
E2F1 0.057 0.095 0.34 1 -0.43 12 13
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.034 14 -0.043 2 16
PTPN11 0.024 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.27 32 -0.6 5 37
actin cytoskeleton organization 0.043 0.1 0.3 13 -0.47 8 21
GRB2 0.023 0.012 0.27 1 -10000 0 1
IL2 0.022 0.027 0.27 8 -10000 0 8
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.042 0.021 -10000 0 -10000 0 0
LCK 0.024 0.077 0.27 23 -0.6 9 32
BCL2 0.023 0.19 0.42 2 -0.79 30 32
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 -0.021 0.11 -10000 0 -0.41 36 36
KLHL20 0.016 0.069 0.23 10 -0.22 16 26
CYFIP2 0.03 0.045 0.27 22 -0.6 1 23
Rac1/GDP -0.001 0.087 0.26 9 -0.31 16 25
ENAH -0.018 0.11 -10000 0 -0.4 34 34
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 -0.15 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.068 -10000 0 -0.36 16 16
RAPGEF1 -0.02 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 -0.023 0.12 -10000 0 -0.42 43 43
CRK -0.017 0.1 -10000 0 -0.42 30 30
E-cadherin/gamma catenin/alpha catenin 0.032 0.063 -10000 0 -0.39 14 14
alphaE/beta7 Integrin 0.035 0.034 -10000 0 -0.45 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.023 -10000 0 -0.36 1 1
DLG1 -0.025 0.12 -10000 0 -0.41 41 41
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 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 0.024 -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 0.026 0.017 0.27 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.04 0.058 -10000 0 -0.34 14 14
AKT1 -0.007 0.034 0.15 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
CDH1 0.011 0.081 -10000 0 -0.6 14 14
RhoA/GDP 0 0.087 0.26 9 -0.31 17 26
actin cytoskeleton organization 0.015 0.056 0.19 18 -0.16 13 31
CDC42/GDP 0 0.087 0.26 9 -0.31 16 25
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.045 -10000 0 -0.28 16 16
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
RAC1 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.044 0.062 -10000 0 -0.36 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.03 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 0.09 0.26 5 -0.32 15 20
RAC1/GTP/IQGAP1 0.032 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.008 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.024 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.053 0.2 35 -0.25 3 38
NME1 0.024 0.025 0.27 8 -10000 0 8
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.12 -10000 0 -0.42 38 38
regulation of cell-cell adhesion 0.002 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 0.059 0.22 29 -0.32 3 32
VAV2 -0.021 0.16 -10000 0 -0.54 37 37
RAP1/GDP 0.005 0.072 0.26 3 -0.29 14 17
adherens junction assembly -0.023 0.12 -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 -0.025 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 -0.024 0.13 -10000 0 -0.42 43 43
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.095 0.27 28 -0.6 15 43
CDC42/GTP -0.007 0.099 -10000 0 -0.37 22 22
PLCG1 -0.014 0.09 -10000 0 -0.38 21 21
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 -0.36 22 22
S1PR5 0.026 0.043 0.27 12 -0.6 2 14
S1PR4 0.024 0.063 0.27 16 -0.6 6 22
MAPK3 -0.01 0.084 0.27 1 -0.32 32 33
MAPK1 -0.009 0.086 -10000 0 -0.33 35 35
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.33 34 34
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 -0.38 2 2
RHOA 0.005 0.062 0.24 1 -0.33 6 7
S1P/S1P4/Gi -0.005 0.096 -10000 0 -0.34 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
S1P/S1P4/G12/G13 0.041 0.042 -10000 0 -0.35 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.024 0.005 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.091 0.36 17 -10000 0 17
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.028 -10000 0 -0.38 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.095 0.27 28 -0.6 15 43
RhoA/GTP -0.004 0.093 -10000 0 -0.36 17 17
negative regulation of cAMP metabolic process -0.007 0.092 -10000 0 -0.33 34 34
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.026 0.043 0.27 12 -0.6 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.089 -10000 0 -0.33 34 34
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
Retinoic acid receptors-mediated signaling

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.017 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.061 -10000 0 -0.4 9 9
KAT2B 0.024 0.003 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.007 0.065 0.2 2 -0.36 12 14
RAR alpha/9cRA/Cyclin H 0.049 0.075 -10000 0 -0.36 16 16
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.022 0.067 -10000 0 -0.44 10 10
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.026 0.052 -10000 0 -0.24 18 18
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.008 0.11 -10000 0 -0.54 20 20
NCOA2 0.015 0.058 -10000 0 -0.6 7 7
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.024 0.022 -10000 0 -0.6 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARG 0.025 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.007 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.025 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.1 -10000 0 -0.48 20 20
RARA 0.014 0.055 0.18 23 -0.28 17 40
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.016 0.062 -10000 0 -0.41 9 9
PRKCA 0.011 0.092 0.27 2 -0.6 18 20
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.12 0.45 1 -0.53 21 22
RXRG -0.052 0.16 0.24 12 -0.36 155 167
RXRA 0.023 0.065 0.35 1 -0.3 18 19
RXRB 0.015 0.065 0.25 10 -0.35 18 28
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.032 0.076 0.27 43 -0.6 6 49
CRBP1/9-cic-RA 0.023 0.054 0.18 43 -0.44 6 49
RARB 0.019 0.061 -10000 0 -0.6 8 8
PRKCG 0.031 0.045 0.27 28 -10000 0 28
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.52 22 22
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.01 0.1 -10000 0 -0.45 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.08 0.25 7 -0.4 11 18
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.12 0.45 1 -0.53 22 23
positive regulation of DNA binding 0.033 0.065 -10000 0 -0.33 17 17
NRIP1 0.011 0.12 0.54 1 -0.73 9 10
RXRs/RARs 0.01 0.12 -10000 0 -0.52 23 23
RXRs/RXRs/DNA/9cRA -0.015 0.093 -10000 0 -0.49 20 20
PRKACA 0.024 0.003 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.054 0.056 -10000 0 -0.3 4 4
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.015 -10000 0 -10000 0 0
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 -0.46 16 16
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.024 0.01 0.27 1 -10000 0 1
CCNE1 0.061 0.088 0.27 127 -10000 0 127
CDK2/Cyclin E1 0.06 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.035 0.012 -10000 0 -10000 0 0
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
FANCA 0.064 0.094 0.27 146 -10000 0 146
DNA repair 0.034 0.084 0.3 4 -0.37 5 9
BRCA1/BARD1/ubiquitin 0.035 0.012 -10000 0 -10000 0 0
BARD1/DNA-PK 0.051 0.026 -10000 0 -10000 0 0
FANCL 0.024 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.033 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.017 0.064 -10000 0 -0.28 6 6
BRCA1/BACH1/BARD1/TopBP1 0.047 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.055 0.024 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.044 0.019 -10000 0 -10000 0 0
BRCA1/BACH1 0.024 0.01 0.27 1 -10000 0 1
BARD1 0.025 0.009 0.27 1 -10000 0 1
PCNA 0.024 0.013 0.27 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.047 0.015 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.046 0.017 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.1 0.076 0.32 2 -10000 0 2
BARD1/DNA-PK/P53 0.055 0.033 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.035 0.012 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.035 0.017 -10000 0 -10000 0 0
FA complex 0.036 0.041 0.25 3 -0.26 1 4
BARD1/EWS 0.034 0.011 -10000 0 -10000 0 0
RBBP8 0.009 0.006 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.053 0.023 -10000 0 -10000 0 0
BRCA1/BARD1 0.077 0.058 0.34 2 -10000 0 2
CSTF1 0.023 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.018 0.006 0.18 1 -10000 0 1
CDK2 0.025 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.12 0.12 0.27 320 -10000 0 320
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.035 0.012 -10000 0 -10000 0 0
EWSR1 0.023 0.006 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.31 66 66
GNAO1 0.019 0.096 0.27 28 -0.6 15 43
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.005 0.094 -10000 0 -0.47 24 24
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 -0.006 0.14 -10000 0 -0.6 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.023 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.098 -10000 0 -0.44 21 21
MAPK3 -0.008 0.092 0.27 2 -0.42 20 22
MAPK1 -0.006 0.091 0.27 1 -0.42 21 22
JAK2 -0.009 0.1 -10000 0 -0.42 26 26
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 -0.44 21 21
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.1 -10000 0 -0.42 19 19
VEGFA 0.026 0.021 0.27 5 -10000 0 5
S1P/S1P2/Gi -0.003 0.092 -10000 0 -0.35 34 34
VEGFR1 homodimer/VEGFA homodimer 0.036 0.023 -10000 0 -0.21 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.038 -10000 0 -0.31 9 9
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
GNAZ 0.019 0.054 -10000 0 -0.6 6 6
G12/G13 0.032 0.012 -10000 0 -10000 0 0
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.1 -10000 0 -0.41 21 21
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.046 -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 0.025 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.014 0.14 0.27 1 -0.6 45 46
TRAIL/TRAILR2 0.025 0.039 -10000 0 -0.43 5 5
TRAIL/TRAILR3 0.026 0.046 -10000 0 -0.46 5 5
TRAIL/TRAILR1 0.024 0.045 -10000 0 -0.34 10 10
TRAIL/TRAILR4 -0.007 0.12 -10000 0 -0.34 82 82
TRAIL/TRAILR1/DAP3/GTP 0.028 0.038 -10000 0 -0.34 4 4
IKK complex 0.01 0.043 -10000 0 -0.43 1 1
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.037 0.26 1 -0.4 6 7
MAP3K1 0.017 0.063 -10000 0 -0.49 6 6
TRAILR4 (trimer) -0.014 0.14 0.27 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 -0.43 5 5
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.007 0.037 0.26 1 -0.45 5 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.041 0.046 -10000 0 -0.32 4 4
mol:ceramide 0.007 0.028 -10000 0 -0.36 4 4
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.008 0.061 -10000 0 -0.47 4 4
TRAF2 0.024 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.022 0.025 0.27 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.04 -10000 0 -0.37 4 4
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.034 0.082 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 0.27 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.038 -10000 0 -0.32 2 2
TRAIL/TRAILR2/FADD 0.031 0.038 -10000 0 -0.37 4 4
cell death 0.007 0.028 -10000 0 -0.36 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.044 -10000 0 -0.43 5 5
TRAILR2 (trimer) 0.02 0.01 -10000 0 -10000 0 0
CASP8 0.013 0.045 -10000 0 -0.54 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.042 0.045 -10000 0 -0.32 4 4
E-cadherin signaling events

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
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
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.024 0.038 0.27 7 -0.6 2 9
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.011 0.02 0.23 1 -0.3 2 3
GNAO1 0.019 0.095 0.27 28 -0.6 15 43
mol:Sphinganine-1-P 0.01 0.026 -10000 0 -0.45 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.05 0.037 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.012 -10000 0 -10000 0 0
S1PR3 0.026 0.022 0.27 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.005 0.025 -10000 0 -0.25 5 5
S1PR5 0.026 0.043 0.27 12 -0.6 2 14
S1PR4 0.024 0.063 0.27 16 -0.6 6 22
GNAI1 -0.007 0.14 -10000 0 -0.6 41 41
S1P/S1P5/G12 0.045 0.043 -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 -0.41 22 23
GNAQ 0.023 0.031 -10000 0 -0.6 2 2
GNAZ 0.019 0.053 -10000 0 -0.6 6 6
GNA14 0.025 0.065 0.27 19 -0.6 6 25
GNA15 0.024 0.027 0.27 3 -0.6 1 4
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.024 0.005 -10000 0 -10000 0 0
ABCC1 0.023 0.006 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.053 0.08 -10000 0 -10000 0 0
CRKL 0.024 0.048 0.27 9 -10000 0 9
mol:DAG 0.038 0.054 0.33 1 -10000 0 1
HRAS 0.034 0.08 0.3 17 -10000 0 17
MAPK8 0.045 0.069 0.25 28 -10000 0 28
RAP1A 0.024 0.048 0.26 8 -10000 0 8
GAB1 0.024 0.047 0.26 8 -10000 0 8
MAPK14 0.045 0.068 0.25 28 -10000 0 28
EPO 0.065 0.091 0.26 139 -10000 0 139
PLCG1 0.038 0.054 0.33 1 -10000 0 1
EPOR/TRPC2/IP3 Receptors 0.026 0.01 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.065 0.064 -10000 0 -0.37 4 4
GAB1/SHC/GRB2/SOS1 0.042 0.043 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.063 0.062 0.24 3 -10000 0 3
IRS2 0.011 0.076 0.27 6 -0.31 29 35
STAT1 0.046 0.066 0.32 4 -10000 0 4
STAT5B 0.04 0.061 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 0.26 8 -0.32 1 9
SOCS3 0.02 0.044 -10000 0 -0.6 4 4
STAT1 (dimer) 0.046 0.066 0.32 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 0.083 0.064 0.34 3 -10000 0 3
EPO/EPOR 0.063 0.062 0.24 3 -10000 0 3
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.048 0.26 6 -0.31 1 7
elevation of cytosolic calcium ion concentration 0.026 0.01 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.063 0.057 -10000 0 -10000 0 0
mol:IP3 0.038 0.054 0.33 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.076 0.29 2 -0.31 21 23
SH2B3 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.045 0.069 0.25 28 -10000 0 28
EPO/EPOR (dimer)/JAK2/SOCS3 0.026 0.045 -10000 0 -0.2 7 7
PTPN6 0.023 0.039 0.3 2 -10000 0 2
TEC/VAV2/GRB2 0.047 0.049 0.27 4 -0.31 1 5
EPOR 0.026 0.01 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.043 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.021 0.025 0.27 1 -0.6 1 2
CRKL/CBL/C3G 0.047 0.048 0.28 5 -10000 0 5
VAV2 0.025 0.048 0.27 9 -10000 0 9
CBL 0.023 0.047 0.26 8 -10000 0 8
SHC/Grb2/SOS1 0.036 0.038 -10000 0 -10000 0 0
STAT5A 0.038 0.067 0.33 1 -0.36 5 6
GRB2 0.023 0.011 0.27 1 -10000 0 1
STAT5 (dimer) 0.051 0.082 0.34 1 -0.36 9 10
LYN/PLCgamma2 0.027 0.024 -10000 0 -0.45 1 1
PTPN11 0.025 0.002 -10000 0 -10000 0 0
BTK 0.025 0.049 0.29 6 -10000 0 6
BCL2 0.035 0.16 -10000 0 -0.86 23 23
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.07 0.053 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.056 0.048 0.36 3 -10000 0 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.049 0.021 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.043 -10000 0 -10000 0 0
CaM/Ca2+ 0.068 0.049 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.044 0.045 0.29 2 -10000 0 2
AKT1 0.013 0.059 0.3 8 -10000 0 8
MAP2K1 0.007 0.045 0.28 3 -10000 0 3
MAP3K11 0.013 0.047 0.28 3 -10000 0 3
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.014 0.11 -10000 0 -0.48 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 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.073 0.1 -10000 0 -0.67 10 10
STAT1 0.026 0.05 0.28 5 -10000 0 5
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.058 0.086 0.27 119 -10000 0 119
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.042 0.047 0.3 4 -10000 0 4
CEBPB/PTGES2/Cbp/p300 0.027 0.062 0.25 3 -0.37 2 5
mol:Ca2+ 0.066 0.051 -10000 0 -10000 0 0
MAPK3 0.02 0.085 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.06 -10000 0 -10000 0 0
MAPK1 -0.008 0.17 -10000 0 -0.67 47 47
JAK2 0.026 0.008 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.038 -10000 0 -0.6 3 3
DAPK1 0.026 0.071 0.37 2 -0.34 2 4
SMAD7 0.016 0.035 0.18 3 -10000 0 3
CBL/CRKL/C3G 0.046 0.04 0.3 2 -10000 0 2
PI3K 0.06 0.045 -10000 0 -10000 0 0
IFNG 0.058 0.086 0.27 119 -10000 0 119
apoptosis 0.023 0.078 0.33 2 -0.41 11 13
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.04 0.27 23 -10000 0 23
CAMK2B -0.012 0.17 0.27 32 -0.6 60 92
FRAP1 0.011 0.054 0.29 8 -10000 0 8
PRKCD 0.014 0.061 0.3 9 -10000 0 9
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.043 -10000 0 -10000 0 0
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 0.021 0.059 0.3 9 -0.33 1 10
STAT1 (dimer)/PIASy 0.04 0.047 0.29 3 -10000 0 3
SOCS1 0.013 0.12 -10000 0 -1 10 10
mol:GDP 0.042 0.037 0.28 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 0.041 0.22 9 -10000 0 9
mol:PI-3-4-5-P3 0.045 0.034 -10000 0 -10000 0 0
RAP1/GDP 0.036 0.024 -10000 0 -10000 0 0
CBL 0.011 0.046 0.27 3 -10000 0 3
MAP3K1 0.022 0.042 0.28 3 -10000 0 3
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.043 -10000 0 -10000 0 0
PTPN11 0.026 0.046 0.29 3 -10000 0 3
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.031 0.011 -10000 0 -10000 0 0
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.051 -10000 0 -0.38 6 6
IRAK/TOLLIP 0.024 0.014 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.025 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.023 0.1 0.38 2 -0.45 33 35
IL1A 0.028 0.031 0.27 14 -10000 0 14
IL1B 0.004 0.053 0.26 1 -0.46 10 11
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.041 -10000 0 -0.32 1 1
IL1R2 0.004 0.13 0.27 16 -0.6 33 49
IL1R1 0.017 0.068 -10000 0 -0.6 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.061 0.26 3 -0.31 12 15
TOLLIP 0.024 0.005 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.033 0.073 0.34 7 -0.38 1 8
JUN -0.01 0.066 0.29 4 -0.3 20 24
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.045 0.068 -10000 0 -0.35 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88 0.056 0.052 -10000 0 -0.36 10 10
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.065 0.052 -10000 0 -0.34 10 10
IL1 beta fragment/IL1R1/IL1RAP 0.026 0.065 -10000 0 -0.38 19 19
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 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 0.034 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.055 -10000 0 -0.4 4 4
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.026 0.065 -10000 0 -0.38 19 19
IL1 beta/IL1R2 0.01 0.098 -10000 0 -0.4 42 42
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.061 -10000 0 -0.33 19 19
IRAK3 0.005 0.11 0.27 1 -0.6 25 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.046 0.067 -10000 0 -0.35 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.04 -10000 0 -0.28 10 10
IL1 alpha/IL1R1/IL1RAP 0.045 0.053 -10000 0 -0.39 10 10
RELA 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.009 0.27 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.037 -10000 0 -10000 0 0
IL1RAP 0.024 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.018 0.054 -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 0.066 -10000 0 -0.36 19 19
TMEM189-UBE2V1 0.019 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.07 -10000 0 -0.36 15 15
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.054 0.27 29 -0.6 2 31
TRAF6/TAK1/TAB1/TAB2 0.039 0.018 -10000 0 -10000 0 0
MAP2K6 -0.002 0.071 0.39 4 -0.32 14 18
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.021 0.089 0.31 5 -0.42 10 15
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 0.011 0.097 0.28 2 -0.38 24 26
Exportin 1/Ran/NUP214 0.047 0.012 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.09 -10000 0 -0.46 8 8
BCL2/BAX 0.022 0.077 -10000 0 -0.43 23 23
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.014 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.014 -10000 0 -10000 0 0
BAX 0.024 0.004 -10000 0 -10000 0 0
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.019 0.086 -10000 0 -0.43 12 12
Calcineurin A alpha-beta B1/BCL2 0.008 0.098 -10000 0 -0.6 21 21
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.085 0.42 12 -10000 0 12
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.038 0.062 0.27 56 -10000 0 56
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.018 0.073 0.27 8 -0.6 10 18
MAP3K8 0.019 0.044 -10000 0 -0.6 4 4
NFAT4/CK1 alpha 0.017 0.028 -10000 0 -0.27 1 1
MEF2D/NFAT1/Cbp/p300 0.011 0.11 -10000 0 -0.31 54 54
CABIN1 0.012 0.096 0.28 2 -0.37 23 25
CALM1 0.02 0.014 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.024 0.005 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.27 31 -10000 0 31
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.044 0.039 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.012 -10000 0 -10000 0 0
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.023 0.1 0.32 1 -0.45 11 12
PRKCH 0.023 0.022 -10000 0 -0.6 1 1
CABIN1/Cbp/p300 0.027 0.023 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.009 -10000 0 -10000 0 0
apoptosis 0.012 0.03 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.04 -10000 0 -0.32 3 3
PRKCB 0.019 0.079 0.27 14 -0.6 11 25
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 0.27 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.019 0.025 -10000 0 -0.6 1 1
PRKCA 0.009 0.092 0.27 2 -0.6 18 20
PRKCG 0.03 0.045 0.27 28 -10000 0 28
PRKCQ 0.004 0.12 0.27 10 -0.6 30 40
FKBP38/BCL2 0.021 0.077 -10000 0 -0.43 23 23
EP300 0.019 0.017 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.031 0.087 0.34 1 -0.41 9 10
CaM/Ca2+/FKBP38 0.027 0.018 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.004 -10000 0 -10000 0 0
CSNK1A1 0.008 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.033 0.034 -10000 0 -10000 0 0
NFATc/ERK1 0.03 0.087 0.34 1 -0.41 9 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.039 0.095 -10000 0 -0.43 12 12
NR4A1 -0.012 0.18 -10000 0 -0.54 72 72
GSK3B 0.021 0.012 -10000 0 -10000 0 0
positive T cell selection 0.014 0.018 -10000 0 -0.42 1 1
NFAT1/CK1 alpha 0.003 0.051 -10000 0 -0.3 4 4
RCH1/ KPNB1 0.042 0.044 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.038 0.056 0.27 47 -10000 0 47
MEF2D 0.017 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.086 0.34 1 -0.42 8 9
CREBBP 0.019 0.016 -10000 0 -10000 0 0
BCL2 0.008 0.098 -10000 0 -0.6 21 21
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.014 0.041 0.35 2 -0.29 1 3
DAPP1 0.013 0.1 0.28 7 -0.37 25 32
Src family/SYK family/BLNK-LAT/BTK-ITK 0.01 0.14 0.3 9 -0.49 31 40
mol:DAG 0.016 0.079 0.24 27 -0.26 8 35
HRAS 0.025 0.011 0.26 1 -10000 0 1
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.03 0.057 0.27 1 -0.36 5 6
PLCG2 0.021 0.025 0.27 1 -0.6 1 2
PLCG1 0.024 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.009 0.27 1 -10000 0 1
mol:GTP -0.011 0.044 0.38 4 -0.3 1 5
ARF1/GTP -0.004 0.034 0.29 4 -0.3 1 5
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
RAP1A/GTP -0.012 0.036 0.21 2 -0.3 1 3
ADAP1 -0.013 0.041 0.36 2 -0.31 2 4
ARAP3 -0.011 0.044 0.38 4 -0.3 1 5
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.036 0.27 18 -10000 0 18
ARHGEF6 0.021 0.049 -10000 0 -0.6 5 5
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.01 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.023 -10000 0 -0.6 1 1
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.01 0.27 1 -10000 0 1
mol:Ca2+ 0.01 0.05 0.24 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.017 0.27 4 -10000 0 4
ZAP70 0.018 0.1 0.27 26 -0.6 18 44
mol:IP3 0.01 0.062 0.2 31 -0.19 5 36
LYN 0.021 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.056 0.33 2 -0.36 5 7
RhoA/GDP 0.033 0.043 -10000 0 -0.3 1 1
PDK1/Src/Hsp90 0.043 0.018 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.018 0.068 0.37 6 -0.32 3 9
SRC 0.024 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.01 0.23 1 -10000 0 1
RAC1 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.032 -10000 0 -0.58 2 2
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.042 0.29 5 -0.29 1 6
RhoA/GTP -0.012 0.044 0.36 4 -0.29 1 5
Src family/SYK family/BLNK-LAT 0.02 0.095 0.27 9 -0.42 13 22
BLK 0.046 0.086 0.27 95 -0.6 2 97
PDPK1 0.023 0.007 -10000 0 -10000 0 0
CYTH1 -0.011 0.043 0.36 4 -0.29 1 5
HCK 0.028 0.029 0.27 12 -10000 0 12
CYTH3 -0.013 0.04 0.36 2 -0.29 1 3
CYTH2 -0.012 0.041 0.33 3 -0.29 1 4
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.012 0.053 0.31 1 -0.42 7 8
SGK1 0.006 0.075 -10000 0 -0.35 29 29
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.059 0.34 2 -0.35 6 8
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.021 0.051 0.39 5 -0.3 1 6
mol:PI-3-4-5-P3 -0.012 0.037 0.27 4 -0.3 1 5
ARAP3/RAP1A/GTP -0.012 0.037 0.21 2 -0.3 1 3
VAV1 0.024 0.025 0.27 2 -0.6 1 3
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.035 0.029 -10000 0 -0.3 1 1
PLEKHA1 -0.01 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.056 0.27 1 -0.35 5 6
LAT 0.024 0.038 0.27 7 -0.6 2 9
Rac1/GTP 0.018 0.043 -10000 0 -0.33 5 5
ITK -0.018 0.068 0.36 4 -0.34 21 25
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.014 0.097 0.27 26 -0.35 10 36
LCK 0.024 0.077 0.27 23 -0.6 9 32
BTK -0.012 0.044 0.36 4 -0.29 1 5
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.024 0.073 0.31 3 -0.41 6 9
PDGFB-D/PDGFRB/SLAP 0.028 0.03 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/APS/CBL 0.047 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 0.084 0.33 4 -0.42 9 13
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.52 17 17
mol:Ca2+ 0.023 0.088 0.33 2 -0.41 15 17
MYC 0.055 0.18 0.39 18 -0.79 21 39
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.32 2 2
LRP1/PDGFRB/PDGFB 0.042 0.055 -10000 0 -0.47 8 8
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.025 0.002 -10000 0 -10000 0 0
GO:0007205 0.023 0.088 0.32 2 -0.42 15 17
PTEN 0.022 0.031 -10000 0 -0.6 2 2
GRB2 0.023 0.011 0.27 1 -10000 0 1
GRB7 0.02 0.023 -10000 0 -0.6 1 1
PDGFB-D/PDGFRB/SHP2 0.035 0.025 -10000 0 -0.45 2 2
PDGFB-D/PDGFRB/GRB10 0.035 0.025 -10000 0 -0.45 2 2
cell cycle arrest 0.028 0.029 -10000 0 -0.33 2 2
HRAS 0.024 0.01 0.27 1 -10000 0 1
HIF1A 0.024 0.087 0.32 30 -10000 0 30
GAB1 0.025 0.093 0.32 3 -0.42 13 16
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.086 0.33 7 -0.43 4 11
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 -0.42 4 6
positive regulation of MAPKKK cascade 0.035 0.025 -10000 0 -0.45 2 2
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.089 0.33 2 -0.42 15 17
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.032 -10000 0 -0.45 3 3
SHB 0.024 0.009 0.27 1 -10000 0 1
BLK -0.035 0.17 0.3 1 -0.41 115 116
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.035 0.025 -10000 0 -0.44 2 2
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.027 0.1 0.34 3 -0.44 16 19
CBL 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.035 0.025 -10000 0 -0.45 2 2
LCK 0.004 0.1 -10000 0 -0.49 26 26
PDGFRB 0.023 0.032 -10000 0 -0.61 2 2
ACP1 0.024 0.004 -10000 0 -10000 0 0
HCK 0.016 0.064 -10000 0 -0.56 5 5
ABL1 0.019 0.093 0.33 2 -0.39 17 19
PDGFB-D/PDGFRB/CBL 0.02 0.1 0.32 1 -0.46 18 19
PTPN1 0.024 0.022 0.26 6 -10000 0 6
SNX15 0.024 0.004 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.035 0.27 18 -10000 0 18
cell proliferation 0.056 0.16 0.38 22 -0.69 21 43
SLA 0.021 0.025 0.27 7 -10000 0 7
actin cytoskeleton reorganization 0.032 0.052 0.33 2 -0.31 2 4
SRC 0.013 0.054 -10000 0 -0.47 5 5
PI3K -0.013 0.023 -10000 0 -0.3 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.035 -10000 0 -0.39 3 3
SH2B2 0.032 0.042 0.27 26 -10000 0 26
PLCgamma1/SPHK1 0.03 0.085 0.33 4 -0.43 9 13
LYN 0.01 0.065 -10000 0 -0.52 8 8
LRP1 0.019 0.061 -10000 0 -0.6 8 8
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.031 -10000 0 -0.6 2 2
STAT5A 0.02 0.049 -10000 0 -0.6 5 5
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.32 2 2
SPHK1 0.024 0.039 0.27 7 -0.6 2 9
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.023 0.089 0.33 2 -0.42 15 17
PLCG1 0.023 0.091 0.33 2 -0.44 13 15
NHERF/PDGFRB 0.049 0.046 -10000 0 -0.38 2 2
YES1 0.001 0.11 -10000 0 -0.52 27 27
cell migration 0.049 0.045 -10000 0 -0.38 2 2
SHC/Grb2/SOS1 0.049 0.042 -10000 0 -0.32 2 2
SLC9A3R2 0.023 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.037 0.057 0.27 47 -10000 0 47
NHERF1-2/PDGFRB/PTEN 0.058 0.052 -10000 0 -0.36 4 4
FYN -0.002 0.1 -10000 0 -0.66 7 7
DOK1 0.021 0.05 -10000 0 -0.35 2 2
HRAS/GTP 0.018 0.007 0.18 1 -10000 0 1
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.021 0.12 0.34 2 -0.53 22 24
PRKCD 0.021 0.052 0.34 1 -0.35 2 3
FER 0.018 0.057 -10000 0 -0.36 6 6
MAPKKK cascade 0.039 0.099 0.36 30 -0.32 2 32
RASA1 0.02 0.051 -10000 0 -0.35 2 2
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.035 0.042 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/SHB 0.034 0.027 -10000 0 -0.36 3 3
chemotaxis 0.019 0.091 0.29 4 -0.38 17 21
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
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 -0.38 22 23
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.037 0.055 0.27 45 -10000 0 45
TXN 0.006 0.004 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 0.024 0.005 -10000 0 -10000 0 0
MAP3K6 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.033 0.021 -10000 0 -0.45 1 1
TAK1/TAB family -0.001 0.02 0.19 1 -0.2 1 2
RAC1/OSM/MEKK3 0.041 0.017 -10000 0 -10000 0 0
TRAF2 0.024 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.093 -10000 0 -0.32 22 22
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.012 0.17 0.27 32 -0.6 60 92
CCM2 0.024 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.007 0.11 -10000 0 -0.38 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 61 61
OSM/MEKK3 0.032 0.012 -10000 0 -10000 0 0
TAOK1 0.008 0.032 -10000 0 -0.36 6 6
TAOK2 0.01 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.008 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.021 -10000 0 -0.37 1 1
GADD45/MTK1/MTK1 0.058 0.036 -10000 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.025 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.11 0.28 14 -0.32 20 34
ERC1 0.023 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.032 0.38 1 -10000 0 1
NFKBIA -0.004 0.022 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.018 0.27 3 -10000 0 3
IKBKG 0.019 0.028 -10000 0 -10000 0 0
IKK complex/A20 0.022 0.13 -10000 0 -0.4 34 34
NEMO/A20/RIP2 0.02 0.018 0.27 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.015 0.13 0.28 1 -0.41 39 40
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 0.033 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.012 0.11 -10000 0 -0.39 32 32
BCL10/MALT1/TRAF6 0.046 0.015 -10000 0 -10000 0 0
NOD2 0.028 0.039 0.27 21 -10000 0 21
NFKB1 0.026 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
MALT1 0.024 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.034 0.051 -10000 0 -0.45 7 7
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.009 0.092 0.27 2 -0.6 18 20
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.067 0.27 17 -0.6 7 24
NF kappa B1 p50/RelA 0.052 0.014 -10000 0 -10000 0 0
BCL10 0.024 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.022 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.016 0.12 -10000 0 -0.41 35 35
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.43 40 40
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.04 0.073 0.34 10 -10000 0 10
regulation of axonogenesis -0.01 0.026 0.24 4 -10000 0 4
myoblast fusion -0.025 0.048 -10000 0 -10000 0 0
mol:GTP 0.023 0.032 -10000 0 -0.15 8 8
regulation of calcium-dependent cell-cell adhesion -0.053 0.044 -10000 0 -0.33 1 1
ARF1/GTP 0.03 0.029 -10000 0 -10000 0 0
mol:GM1 0.012 0.025 -10000 0 -10000 0 0
mol:Choline 0.009 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 0.19 59 -10000 0 59
ARF6/GTP/NME1/Tiam1 0.054 0.045 0.34 1 -10000 0 1
ARF1 0.02 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.048 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.048 -10000 0 -0.26 2 2
ARF6 0.032 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.018 0.26 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.032 0.047 0.19 60 -10000 0 60
actin filament bundle formation -0.032 0.051 0.25 3 -10000 0 3
KALRN 0.009 0.056 -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 0.026 0.27 8 -10000 0 8
Rac1/GDP 0.033 0.052 -10000 0 -0.25 3 3
substrate adhesion-dependent cell spreading 0.023 0.032 -10000 0 -0.15 8 8
cortical actin cytoskeleton organization 0.017 0.06 -10000 0 -0.36 6 6
RAC1 0.024 0.004 -10000 0 -10000 0 0
liver development 0.023 0.032 -10000 0 -0.15 8 8
ARF6/GTP 0.023 0.032 -10000 0 -0.15 8 8
RhoA/GTP 0.034 0.029 -10000 0 -10000 0 0
mol:GDP 0.02 0.049 0.18 51 -0.22 5 56
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.043 -10000 0 -0.42 5 5
RAB11FIP3 0.023 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.06 -10000 0 -0.36 6 6
ruffle organization 0.01 0.026 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.023 0.032 -10000 0 -0.15 8 8
PLD2 0.02 0.025 -10000 0 -10000 0 0
PIP5K1A 0.01 0.026 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.009 0.036 -10000 0 -0.36 5 5
Rac1/GTP 0.017 0.06 -10000 0 -0.36 6 6
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.42 54 54
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.005 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.15 0.41 1 -0.43 66 67
YWHAZ 0.019 0.011 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.009 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.021 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.022 0.016 0.27 3 -10000 0 3
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.009 0.016 0.24 4 -10000 0 4
PRKCZ 0.023 0.022 -10000 0 -0.6 1 1
TRIP10 0.024 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.065 0.26 1 -0.3 14 15
VAMP2 0.022 0.008 -10000 0 -10000 0 0
SLC2A4 -0.13 0.17 0.42 1 -0.48 66 67
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.017 0.005 -10000 0 -10000 0 0
SFN 0.018 0.073 0.27 8 -0.6 10 18
LNPEP 0.022 0.038 -10000 0 -0.6 3 3
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 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 0.27 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.066 0.05 0.4 6 -0.36 2 8
EPO 0.064 0.091 0.27 139 -10000 0 139
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.019 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.061 0.063 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.07 -10000 0 -0.54 9 9
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.035 0.033 -10000 0 -10000 0 0
PXN 0.025 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
MADCAM1 0.031 0.045 0.27 29 -10000 0 29
cell adhesion 0.064 0.049 0.39 6 -0.36 2 8
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC -0.008 0.044 -10000 0 -0.36 6 6
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.047 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 0.27 6 -0.6 6 12
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.025 -10000 0 -10000 0 0
BCAR1 -0.008 0.045 0.38 2 -0.33 6 8
EPOR 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.072 -10000 0 -0.56 9 9
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.041 0.062 -10000 0 -0.53 2 2
NEF 0.005 0.02 -10000 0 -0.18 4 4
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.019 0.056 0.28 10 -0.43 6 16
CYCS 0.038 0.076 0.26 18 -0.74 1 19
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.018 0.091 0.31 12 -0.62 13 25
MAP2K7 0.041 0.13 -10000 0 -0.75 14 14
protein ubiquitination 0.013 0.086 0.33 3 -0.38 10 13
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 0.038 0.073 0.24 2 -0.36 6 8
NF-kappa-B/RelA/I kappa B alpha 0.052 0.034 -10000 0 -0.29 3 3
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.023 0.022 -10000 0 -0.6 1 1
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.052 0.034 -10000 0 -0.29 3 3
MAPK8 0.039 0.12 0.46 2 -0.68 14 16
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.015 0.27 3 -10000 0 3
TRAF2 0.024 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.026 0.06 0.26 2 -0.36 8 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.097 0.27 1 -0.48 12 13
CHUK 0.013 0.089 0.34 3 -0.41 9 12
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.039 -10000 0 -0.4 2 2
TCRz/NEF 0.018 0.08 0.33 7 -0.45 17 24
TNF 0.024 0.067 0.27 17 -0.6 7 24
FASLG 0.015 0.1 0.31 33 -0.52 17 50
NFKB1 0.025 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.037 0.048 -10000 0 -0.38 6 6
CASP6 0.053 0.11 -10000 0 -0.53 14 14
CASP7 0.04 0.1 0.35 7 -0.51 8 15
RELA 0.026 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.34 5 -0.5 8 13
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.028 0.016 -10000 0 -10000 0 0
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.005 -10000 0 -10000 0 0
MAP3K14 0.015 0.093 0.36 2 -0.45 11 13
APAF-1/Caspase 9 0.034 0.063 0.26 5 -0.4 5 10
BCL2 0.033 0.13 0.47 4 -0.57 17 21
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 0.074 -10000 0 -0.45 18 18
HDAC5/BCL6/BCoR 0.044 0.03 -10000 0 -0.39 3 3
HDAC9 0.023 0.06 0.27 11 -0.6 6 17
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.039 -10000 0 -0.38 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 0.014 0.096 0.27 11 -0.6 18 29
HDAC4/RFXANK 0.034 0.019 -10000 0 -0.45 1 1
BCOR 0.024 0.022 -10000 0 -0.6 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.006 -10000 0 -10000 0 0
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.031 0.042 -10000 0 -0.44 6 6
Histones 0.016 0.052 -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 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.025 0.002 -10000 0 -10000 0 0
HDAC6 0.025 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.034 0.009 -10000 0 -10000 0 0
CAMK4 0.033 0.046 0.27 31 -10000 0 31
Tubulin/HDAC6 0.048 0.014 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
GATA1 0.025 0.026 0.27 9 -10000 0 9
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.02 0.053 -10000 0 -0.6 6 6
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.24 4 4
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.02 -10000 0 -0.45 1 1
Tubulin 0.035 0.011 -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 -0.008 0.18 -10000 0 -0.45 107 107
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.014 0.054 -10000 0 -0.32 8 8
cell motility 0.048 0.013 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
HDAC7/HDAC3 0.036 0.006 -10000 0 -10000 0 0
BCL6 0.022 0.031 -10000 0 -0.6 2 2
HDAC4/CaMK II delta B 0.023 0.022 -10000 0 -0.6 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.025 0.24 0.27 109 -0.6 106 215
HDAC6/HDAC11 0.036 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.039 -10000 0 -0.24 3 3
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.022 -10000 0 -0.6 1 1
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.063 0.032 -10000 0 -0.33 2 2
GNG2 0.019 0.053 -10000 0 -0.6 6 6
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.024 0.013 0.27 2 -10000 0 2
HDAC11 0.025 0.012 0.27 2 -10000 0 2
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.024 0.004 -10000 0 -10000 0 0
nuclear import -0.026 0.018 0.35 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
ITGA4 0.027 0.027 0.27 10 -10000 0 10
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
alpha4/beta1 Integrin 0.037 0.019 -10000 0 -10000 0 0
VEGFR1 specific signals

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.025 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+ 0.025 0.031 -10000 0 -0.39 2 2
HIF1A 0.028 0.013 -10000 0 -0.32 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.012 0.04 -10000 0 -0.44 1 1
PLCG1 0.011 0.032 -10000 0 -0.41 2 2
NOS3 0.015 0.058 0.28 3 -0.51 3 6
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:NO 0.019 0.067 0.29 2 -0.45 6 8
FLT1 0.013 0.021 -10000 0 -0.59 1 1
PGF 0.023 0.022 -10000 0 -0.6 1 1
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.029 -10000 0 -0.6 1 1
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.031 0.07 -10000 0 -0.43 7 7
endothelial cell proliferation 0.013 0.085 0.36 6 -0.58 3 9
mol:Ca2+ 0.011 0.032 -10000 0 -0.41 2 2
MAPK3 -0.015 0.055 -10000 0 -0.35 17 17
MAPK1 -0.015 0.055 -10000 0 -0.35 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 0.27 5 -10000 0 5
VEGFR1 homodimer/VEGFA homodimer 0.026 0.024 -10000 0 -0.51 1 1
platelet activating factor biosynthetic process -0.016 0.053 -10000 0 -0.34 16 16
PI3K 0.046 0.031 -10000 0 -0.39 2 2
PRKCA -0.014 0.058 0.25 1 -0.36 17 18
PRKCB -0.01 0.053 -10000 0 -0.37 12 12
VEGFR1 homodimer/PLGF homodimer 0.025 0.025 -10000 0 -0.45 2 2
VEGFA 0.025 0.019 0.27 5 -10000 0 5
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.011 0.032 -10000 0 -0.41 2 2
RASA1 0.012 0.031 -10000 0 -0.46 1 1
NRP2 0.025 0.009 0.27 1 -10000 0 1
VEGFR1 homodimer 0.013 0.021 -10000 0 -0.59 1 1
VEGFB homodimer 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.032 0.14 0.3 1 -0.47 21 22
PTPN11 0.025 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.045 0.03 -10000 0 -0.39 2 2
mol:L-citrulline 0.019 0.067 0.29 2 -0.45 6 8
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.03 -10000 0 -0.44 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.038 0.025 -10000 0 -0.48 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.058 0.037 -10000 0 -0.38 2 2
PDPK1 -0.002 0.046 -10000 0 -0.43 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.038 0.025 -10000 0 -0.48 1 1
mol:NADP 0.019 0.067 0.29 2 -0.45 6 8
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.029 -10000 0 -0.44 1 1
VEGFR1 homodimer/NRP2 0.026 0.026 -10000 0 -0.64 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.027 0.062 -10000 0 -0.45 13 13
AKT1 0.034 0.078 0.35 3 -0.54 3 6
PTK2B 0.009 0.062 0.35 1 -0.38 12 13
VEGFR2 homodimer/Frs2 0.028 0.035 -10000 0 -0.64 2 2
CAV1 -0.1 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 0.038 -10000 0 -0.59 2 2
endothelial cell proliferation 0.046 0.11 0.36 22 -0.66 3 25
mol:Ca2+ 0.016 0.036 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.053 0.038 -10000 0 -0.57 2 2
RP11-342D11.1 0.006 0.033 -10000 0 -0.54 2 2
CDH5 0.02 0.032 -10000 0 -0.6 2 2
VEGFA homodimer 0.049 0.029 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.009 0.096 -10000 0 -0.6 20 20
HRAS/GDP 0.032 0.032 -10000 0 -0.58 1 1
SH2D2A 0.039 0.07 0.27 64 -0.6 1 65
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.044 0.085 -10000 0 -0.47 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.047 0.056 -10000 0 -0.45 3 3
VEGFR1 homodimer 0.023 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.043 -10000 0 -0.64 1 1
GRB10 0.017 0.036 -10000 0 -0.54 2 2
PTPN11 0.025 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.011 0.27 1 -10000 0 1
PAK1 0.023 0.017 0.27 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.056 0.051 -10000 0 -0.49 4 4
HRAS 0.024 0.01 0.27 1 -10000 0 1
VEGF/Rho/ROCK1/Integrin Complex 0.014 0.058 -10000 0 -0.53 3 3
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.013 0.27 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.052 0.037 -10000 0 -0.56 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.031 -10000 0 -0.6 2 2
Nck/Pak 0.032 0.016 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.04 0.045 -10000 0 -0.73 2 2
mol:GDP 0.041 0.037 -10000 0 -0.62 1 1
mol:NADP 0.025 0.084 0.56 1 -0.42 12 13
eNOS/Hsp90 0.037 0.081 0.55 1 -0.41 10 11
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.016 0.037 -10000 0 -0.55 2 2
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.009 0.27 1 -10000 0 1
VEGFA 0.026 0.019 0.27 5 -10000 0 5
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.027 0.085 0.35 1 -0.65 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 0.27 2 -10000 0 2
EPAS1 0.029 0.019 -10000 0 -0.34 2 2
mol:L-citrulline 0.025 0.084 0.56 1 -0.42 12 13
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.051 0.041 -10000 0 -0.57 2 2
VEGFR2 homodimer/VEGFA homodimer 0.044 0.036 -10000 0 -0.59 2 2
VEGFR2/3 heterodimer 0.027 0.045 -10000 0 -0.65 3 3
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.007 0.05 -10000 0 -0.59 2 2
VEGFR2 homodimer 0.015 0.037 -10000 0 -0.71 2 2
FLT1 0.023 0.007 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.008 0.066 0.32 1 -0.68 2 3
MAPK1 0.01 0.067 -10000 0 -0.66 2 2
VEGFA145/NRP2 0.037 0.018 -10000 0 -0.2 1 1
VEGFR1/2 heterodimer 0.026 0.038 -10000 0 -0.7 2 2
KDR 0.015 0.037 -10000 0 -0.72 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.044 0.038 -10000 0 -0.6 2 2
SRC 0.024 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.017 0.075 0.34 4 -0.55 3 7
PI3K 0.029 0.049 -10000 0 -0.65 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.043 0.036 -10000 0 -0.59 2 2
FES 0.015 0.041 -10000 0 -0.42 5 5
GAB1 0.016 0.047 -10000 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.041 0.037 -10000 0 -0.59 2 2
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.02 0.14 -10000 0 -0.41 26 26
VEGFR2 homodimer/VEGFA homodimer/Yes 0.041 0.039 -10000 0 -0.51 3 3
PI3K/GAB1 0.043 0.063 0.31 1 -0.54 2 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.057 0.042 -10000 0 -0.47 2 2
PRKACA 0.024 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.045 -10000 0 -0.61 3 3
HSP90AA1 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.017 0.037 -10000 0 -0.56 2 2
actin cytoskeleton reorganization 0.047 0.056 -10000 0 -0.45 3 3
PTK2 0.011 0.062 -10000 0 -0.71 3 3
EDG1 0.006 0.033 -10000 0 -0.54 2 2
mol:DAG 0.016 0.037 -10000 0 -0.55 2 2
CaM/Ca2+ 0.03 0.039 -10000 0 -0.51 2 2
MAP2K3 -0.004 0.04 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.042 0.037 -10000 0 -0.56 2 2
PLCG1 0.016 0.037 -10000 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.052 0.04 -10000 0 -0.57 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.022 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.043 0.036 -10000 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.042 0.037 -10000 0 -0.59 2 2
cell migration 0.029 0.079 0.35 3 -0.66 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 0.025 0.084 0.56 1 -0.42 12 13
PXN 0.025 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.026 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.034 -10000 0 -0.56 2 2
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.015 0.08 0.27 4 -0.6 13 17
NOS3 0.025 0.092 0.57 1 -0.47 12 13
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 -0.36 17 18
PRKCB -0.005 0.057 -10000 0 -0.39 9 9
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.025 0.035 -10000 0 -0.54 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.04 0.04 -10000 0 -0.65 2 2
VEGFA165/NRP2 0.037 0.018 -10000 0 -0.2 1 1
MAPKKK cascade 0.052 0.071 0.34 9 -0.58 1 10
NRP2 0.025 0.009 0.27 1 -10000 0 1
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.024 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.028 0.087 0.42 2 -0.65 3 5
MAP3K13 0.016 0.036 -10000 0 -0.56 2 2
PDPK1 0.016 0.044 -10000 0 -0.62 1 1
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.051 0.062 -10000 0 -0.4 6 6
Ran/GTP/Exportin 1/HDAC1 -0.01 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.063 -10000 0 -0.35 7 7
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.022 0.015 0.27 2 -10000 0 2
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.052 0.043 -10000 0 -0.44 1 1
YY1/LSF 0.024 0.05 -10000 0 -0.3 5 5
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.032 -10000 0 -0.32 5 5
I kappa B alpha/HDAC1 0.029 0.04 -10000 0 -0.46 1 1
SAP18 0.023 0.007 -10000 0 -10000 0 0
RELA 0.019 0.038 -10000 0 -0.33 5 5
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.03 0.039 -10000 0 -0.46 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.39 3 3
NF kappa B1 p50/RelA 0.026 0.065 0.38 1 -0.36 5 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.014 0.096 0.27 11 -0.6 18 29
GATA1 0.025 0.026 0.27 9 -10000 0 9
Mad/Max 0.035 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.015 0.083 -10000 0 -0.37 18 18
RBBP7 0.026 0.022 0.27 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.024 0.004 -10000 0 -10000 0 0
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.028 -10000 0 -0.27 5 5
KAT2B 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.03 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.023 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.008 -10000 0 -10000 0 0
SAP30 0.025 0.015 0.27 3 -10000 0 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.048 -10000 0 -0.39 3 3
YY1/HDAC2 0.025 0.046 -10000 0 -0.3 4 4
YY1/HDAC1 0.025 0.048 -10000 0 -0.29 5 5
NuRD/MBD2 Complex (MeCP1) 0.024 0.055 -10000 0 -0.28 10 10
PPARG -0.061 0.16 -10000 0 -0.36 173 173
HDAC8/hEST1B 0.042 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.03 0.039 -10000 0 -0.46 1 1
MBD3L2 0.018 0.013 0.27 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.046 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.021 0.071 -10000 0 -0.36 13 13
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.018 0.029 -10000 0 -0.27 6 6
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.006 -10000 0 -10000 0 0
HDAC8 0.025 0.001 -10000 0 -10000 0 0
SMAD7 0.024 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.009 0.27 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.037 0.049 -10000 0 -0.27 5 5
YY1/SAP30/HDAC1 0.037 0.048 -10000 0 -0.27 3 3
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.028 -10000 0 -0.27 5 5
histone deacetylation 0.024 0.055 -10000 0 -0.28 10 10
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.037 -10000 0 -0.35 2 2
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GATAD2B 0.021 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.025 0.068 -10000 0 -0.35 18 18
GATA1/HDAC1 0.036 0.018 -10000 0 -10000 0 0
GATA1/HDAC3 0.031 0.042 -10000 0 -0.48 1 1
CHD4 0.024 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.051 -10000 0 -0.45 7 7
SIN3/HDAC complex/Mad/Max 0.014 0.058 -10000 0 -0.41 4 4
NuRD Complex 0.023 0.068 -10000 0 -0.36 10 10
positive regulation of chromatin silencing 0.05 0.042 -10000 0 -0.43 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.24 3 3
HDAC complex 0.058 0.023 -10000 0 -10000 0 0
GATA1/Fog1 0.032 0.023 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.016 -10000 0 -10000 0 0
TNF 0.024 0.067 0.27 17 -0.6 7 24
negative regulation of cell growth 0.014 0.057 -10000 0 -0.4 4 4
NuRD/MBD2/PRMT5 Complex 0.024 0.055 -10000 0 -0.28 10 10
Ran/GTP/Exportin 1 0.035 0.039 -10000 0 -0.24 3 3
NF kappa B/RelA/I kappa B alpha 0.018 0.052 -10000 0 -0.36 7 7
SIN3/HDAC complex/NCoR1 0.006 0.068 -10000 0 -0.32 23 23
TFCP2 0.025 0.002 -10000 0 -10000 0 0
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.005 -10000 0 -10000 0 0
MBD2 0.024 0.005 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.024 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.039 0.21 1 -0.35 1 2
SMAD3 0.022 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.066 -10000 0 -0.46 8 8
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.062 -10000 0 -0.28 2 2
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.046 -10000 0 -0.27 6 6
MAP3K1 0.024 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.034 0.025 -10000 0 -0.45 2 2
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.023 0.031 -10000 0 -0.6 2 2
UBE2I 0.023 0.007 -10000 0 -10000 0 0
NUP153 0.024 0.004 -10000 0 -10000 0 0
KPNA2 0.038 0.062 0.27 56 -10000 0 56
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.037 -10000 0 -10000 0 0
CLOCK 0.026 0.004 -10000 0 -10000 0 0
TIMELESS/CRY2 0.032 0.023 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.013 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.016 0.014 -10000 0 -10000 0 0
ARNTL 0.026 0.005 -10000 0 -10000 0 0
TIMELESS 0.018 0.022 -10000 0 -10000 0 0
NPAS2 0.023 0.044 0.27 1 -0.6 4 5
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.007 -10000 0 -0.097 5 5
CHEK1 0.029 0.042 0.27 24 -10000 0 24
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 0.045 0.038 -10000 0 -10000 0 0
mol:NADPH 0.007 0.007 0.097 5 -10000 0 5
PER1/TIMELESS 0.025 0.049 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.015 0.27 3 -10000 0 3
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.011 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.027 0.27 10 -10000 0 10
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.041 0.38 4 -0.45 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.02 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.043 0.037 0.34 4 -0.36 2 6
lamellipodium assembly -0.001 0.081 -10000 0 -0.41 21 21
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.004 -10000 0 -10000 0 0
PXN 0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.047 0.022 -10000 0 -10000 0 0
cell adhesion 0.05 0.021 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.019 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.027 0.045 0.27 15 -0.6 2 17
ARF6/GDP 0.022 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.041 -10000 0 -0.34 6 6
p130Cas/Crk/Dock1 0.041 0.02 -10000 0 -10000 0 0
VCAM1 0.021 0.057 0.27 6 -0.6 6 12
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.022 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.024 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.047 0.023 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.023 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.022 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.088 -10000 0 -0.45 21 21
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.035 0.008 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.045 -10000 0 -0.27 1 1
NFKBIA 0.014 0.037 -10000 0 -0.24 9 9
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.024 0.022 -10000 0 -0.6 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.015 0.011 0.25 1 -10000 0 1
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.009 0.013 0.26 2 -10000 0 2
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.025 0.046 -10000 0 -0.26 7 7
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.047 -10000 0 -0.32 1 1
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.025 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 -0.23 11 11
cell death 0.022 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 0.27 23 -0.6 9 32
BCL3 0.024 0.004 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.033 -10000 0 -10000 0 0
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 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.01 -10000 0 -10000 0 0
CLTB 0.024 0.01 0.27 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.013 0.009 -10000 0 -10000 0 0
CD4 0.023 0.006 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.017 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.011 0.2 2 -10000 0 2
mol:Choline 0.007 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.017 -10000 0 -10000 0 0
ARF1/GDP 0 0.023 0.19 2 -10000 0 2
AP2M1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.017 -10000 0 -10000 0 0
ARFIP2 0.014 0.018 -10000 0 -10000 0 0
COPA 0.021 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.025 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0.044 -10000 0 -0.24 18 18
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.026 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.011 0.053 -10000 0 -0.27 21 21
Arfaptin 2/Rac/GDP 0.028 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.016 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.025 -10000 0 -10000 0 0
PLD2 0.007 0.017 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.008 0.017 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.022 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.017 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.009 0.027 -10000 0 -0.31 5 5
USO1 0.009 0.022 -10000 0 -0.32 3 3
GBF1 0.01 0.022 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.016 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.024 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.014 0.2 4 -9999 0 4
RELB 0.026 0.019 0.27 5 -9999 0 5
NFKB2 0.024 0.004 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.033 0.013 0.18 5 -9999 0 5
regulation of B cell activation 0.033 0.013 0.18 5 -9999 0 5
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.012 -10000 0 -0.28 1 1
MDM2/SUMO1 0.033 0.041 -10000 0 -0.24 3 3
HDAC4 0.023 0.022 -10000 0 -0.6 1 1
Ran/GTP/Exportin 1/HDAC1 -0.009 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.019 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.24 4 4
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.24 3 3
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.057 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.037 -10000 0 -0.24 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.039 0.25 1 -0.24 3 4
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Inferred Pathway Levels Matrix

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

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

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/2843240/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BRCA-TP/2859781/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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