PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C12J6B0M
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C12J6B0M
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 58 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 325
Class IB PI3K non-lipid kinase events 287
Signaling events mediated by Stem cell factor receptor (c-Kit) 287
Signaling mediated by p38-alpha and p38-beta 276
Reelin signaling pathway 228
EGFR-dependent Endothelin signaling events 199
Aurora B signaling 195
PLK1 signaling events 177
FOXA2 and FOXA3 transcription factor networks 172
HIF-1-alpha transcription factor network 165
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 1093 . Pathway is significant if Significance.Ratio > 0.05 .

  • 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. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 1093 ).

Pathway.Name Significance.Ratio 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 0.2973 325 16602 51 -0.053 0.69 1000 -1000 -0.037 -1000
Class IB PI3K non-lipid kinase events 0.2626 287 861 3 -0.13 -1000 1000 -1000 -0.009 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2626 287 22406 78 -0.57 0.18 1000 -1000 -0.039 -1000
Signaling mediated by p38-alpha and p38-beta 0.2525 276 12146 44 -0.32 0.024 1000 -1000 -0.016 -1000
Reelin signaling pathway 0.2086 228 12794 56 -0.32 0.054 1000 -1000 -0.029 -1000
EGFR-dependent Endothelin signaling events 0.1821 199 4192 21 -0.21 0.034 1000 -1000 -0.036 -1000
Aurora B signaling 0.1784 195 13094 67 -0.21 0.27 1000 -1000 -0.038 -1000
PLK1 signaling events 0.1619 177 15062 85 -0.063 0.23 1000 -1000 -0.02 -1000
FOXA2 and FOXA3 transcription factor networks 0.1574 172 7956 46 -1.1 0.034 1000 -1000 -0.045 -1000
HIF-1-alpha transcription factor network 0.1510 165 12540 76 -0.48 0.035 1000 -1000 -0.037 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1500 164 14448 88 -0.32 0.11 1000 -1000 -0.057 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1418 155 10563 68 -0.34 0.15 1000 -1000 -0.057 -1000
Endothelins 0.1336 146 14041 96 -0.34 0.17 1000 -1000 -0.037 -1000
Glucocorticoid receptor regulatory network 0.1308 143 16316 114 -0.72 0.28 1000 -1000 -0.041 -1000
p75(NTR)-mediated signaling 0.1299 142 17866 125 -0.22 0.096 1000 -1000 -0.058 -1000
EPHB forward signaling 0.1226 134 11433 85 -0.2 0.14 1000 -1000 -0.062 -1000
Ephrin B reverse signaling 0.1125 123 5945 48 -0.2 0.089 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1107 121 6587 54 -0.32 0.054 1000 -1000 -0.034 -1000
Wnt signaling 0.1089 119 836 7 -0.097 0.017 1000 -1000 -0.01 -1000
IL4-mediated signaling events 0.1080 118 10781 91 -0.66 0.25 1000 -1000 -0.073 -1000
Noncanonical Wnt signaling pathway 0.1043 114 2978 26 -0.097 0.024 1000 -1000 -0.038 -1000
IGF1 pathway 0.1034 113 6456 57 -0.11 0.044 1000 -1000 -0.032 -1000
Arf6 signaling events 0.1006 110 6876 62 -0.21 0.05 1000 -1000 -0.033 -1000
Nongenotropic Androgen signaling 0.0970 106 5528 52 -0.25 0.13 1000 -1000 -0.021 -1000
ErbB2/ErbB3 signaling events 0.0933 102 6663 65 -0.26 0.034 1000 -1000 -0.043 -1000
Signaling events regulated by Ret tyrosine kinase 0.0924 101 8343 82 -0.07 0.097 1000 -1000 -0.046 -1000
BMP receptor signaling 0.0897 98 7987 81 -0.38 0.1 1000 -1000 -0.043 -1000
Plasma membrane estrogen receptor signaling 0.0878 96 8331 86 -0.12 0.11 1000 -1000 -0.048 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0860 94 8038 85 -0.24 0.024 1000 -1000 -0.03 -1000
IL23-mediated signaling events 0.0860 94 5662 60 -0.3 0.084 1000 -1000 -0.039 -1000
Signaling events mediated by PTP1B 0.0851 93 7096 76 -0.44 0.082 1000 -1000 -0.027 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0842 92 11148 120 -0.35 0.17 1000 -1000 -0.04 -1000
Calcium signaling in the CD4+ TCR pathway 0.0833 91 2843 31 -0.19 0.027 1000 -1000 -0.035 -1000
Visual signal transduction: Rods 0.0814 89 4650 52 -0.33 0.055 1000 -1000 -0.015 -1000
S1P1 pathway 0.0805 88 3180 36 -0.33 0.024 1000 -1000 -0.026 -1000
Aurora C signaling 0.0769 84 588 7 0 0.14 1000 -1000 -0.016 -1000
TCR signaling in naïve CD8+ T cells 0.0769 84 7876 93 -0.089 0.084 1000 -1000 -0.037 -1000
Effects of Botulinum toxin 0.0732 80 2091 26 -0.003 0.1 1000 -1000 -0.001 -1000
IL6-mediated signaling events 0.0732 80 6014 75 -0.18 0.053 1000 -1000 -0.046 -1000
Glypican 1 network 0.0723 79 3806 48 -0.2 0.045 1000 -1000 -0.026 -1000
Integrins in angiogenesis 0.0723 79 6644 84 -0.2 0.11 1000 -1000 -0.031 -1000
ErbB4 signaling events 0.0714 78 5398 69 -0.27 0.06 1000 -1000 -0.026 -1000
Signaling events mediated by the Hedgehog family 0.0704 77 4025 52 -0.12 0.028 1000 -1000 -0.021 -1000
amb2 Integrin signaling 0.0695 76 6241 82 -0.33 0.12 1000 -1000 -0.029 -1000
Syndecan-1-mediated signaling events 0.0659 72 2452 34 -0.073 0.18 1000 -1000 -0.03 -1000
LPA receptor mediated events 0.0659 72 7396 102 -0.19 0.12 1000 -1000 -0.071 -1000
IL12-mediated signaling events 0.0631 69 6023 87 -0.32 0.072 1000 -1000 -0.065 -1000
Ephrin A reverse signaling 0.0622 68 481 7 -0.028 0.023 1000 -1000 -0.008 -1000
Syndecan-3-mediated signaling events 0.0595 65 2277 35 -0.23 0.054 1000 -1000 -0.011 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0576 63 2146 34 -0.024 0.058 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 0.0567 62 2742 44 -0.3 0.036 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0549 60 3159 52 -0.12 0.071 1000 -1000 -0.046 -1000
Visual signal transduction: Cones 0.0531 58 2238 38 -0.024 0.16 1000 -1000 -0.006 -1000
Fc-epsilon receptor I signaling in mast cells 0.0531 58 5717 97 -0.14 0.033 1000 -1000 -0.06 -1000
Canonical Wnt signaling pathway 0.0531 58 3001 51 -0.28 0.12 1000 -1000 -0.035 -1000
Syndecan-2-mediated signaling events 0.0512 56 3930 69 -0.12 0.11 1000 -1000 -0.027 -1000
Presenilin action in Notch and Wnt signaling 0.0503 55 3403 61 -0.27 0.12 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0503 55 1841 33 -0.38 0.059 1000 -1000 -0.03 -1000
Nectin adhesion pathway 0.0494 54 3439 63 -0.056 0.047 1000 -1000 -0.036 -1000
Glypican 2 network 0.0467 51 207 4 0.033 0.058 1000 -1000 0.016 -1000
Rapid glucocorticoid signaling 0.0467 51 1030 20 -0.11 0.026 1000 -1000 -0.003 -1000
Ras signaling in the CD4+ TCR pathway 0.0467 51 870 17 -0.056 0.025 1000 -1000 -0.017 -1000
FAS signaling pathway (CD95) 0.0457 50 2357 47 -0.43 0.039 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class III 0.0421 46 1866 40 -0.32 0.045 1000 -1000 -0.023 -1000
TCGA08_rtk_signaling 0.0421 46 1205 26 -0.19 0.037 1000 -1000 -0.01 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0421 46 3419 74 -0.19 0.049 1000 -1000 -0.063 -1000
LPA4-mediated signaling events 0.0403 44 534 12 -0.11 0.006 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 0.0384 42 3222 76 -0.14 0.063 1000 -1000 -0.031 -1000
Aurora A signaling 0.0384 42 2562 60 -0.079 0.18 1000 -1000 -0.015 -1000
Syndecan-4-mediated signaling events 0.0384 42 2820 67 -0.2 0.12 1000 -1000 -0.036 -1000
Regulation of Androgen receptor activity 0.0384 42 2986 70 -0.16 0.11 1000 -1000 -0.041 -1000
Insulin Pathway 0.0375 41 3100 74 -0.12 0.06 1000 -1000 -0.041 -1000
TCGA08_retinoblastoma 0.0348 38 309 8 -0.018 0.06 1000 -1000 -0.001 -1000
Regulation of Telomerase 0.0348 38 3952 102 -0.2 0.14 1000 -1000 -0.023 -1000
Regulation of p38-alpha and p38-beta 0.0329 36 1974 54 -0.24 0.052 1000 -1000 -0.049 -1000
IL27-mediated signaling events 0.0329 36 1853 51 -0.18 0.075 1000 -1000 -0.042 -1000
Thromboxane A2 receptor signaling 0.0320 35 3744 105 -0.19 0.036 1000 -1000 -0.041 -1000
BCR signaling pathway 0.0320 35 3527 99 -0.077 0.056 1000 -1000 -0.049 -1000
Regulation of nuclear SMAD2/3 signaling 0.0311 34 4668 136 -0.19 0.077 1000 -1000 -0.031 -1000
Osteopontin-mediated events 0.0311 34 1323 38 -0.14 0.086 1000 -1000 -0.035 -1000
E-cadherin signaling in keratinocytes 0.0311 34 1490 43 -0.19 0.033 1000 -1000 -0.032 -1000
IL2 signaling events mediated by STAT5 0.0293 32 711 22 0.006 0.11 1000 -1000 -0.023 -1000
TCGA08_p53 0.0265 29 207 7 -0.011 0.02 1000 -1000 -0.004 -1000
S1P4 pathway 0.0256 28 722 25 -0.012 0.044 1000 -1000 -0.018 -1000
HIF-2-alpha transcription factor network 0.0238 26 1138 43 -0.15 0.16 1000 -1000 -0.031 -1000
S1P5 pathway 0.0229 25 431 17 -0.007 0.033 1000 -1000 -0.01 -1000
Signaling events mediated by PRL 0.0229 25 852 34 -0.12 0.035 1000 -1000 -0.034 -1000
Ceramide signaling pathway 0.0220 24 1854 76 -0.1 0.063 1000 -1000 -0.03 -1000
Caspase cascade in apoptosis 0.0210 23 1749 74 -0.025 0.057 1000 -1000 -0.039 -1000
IL2 signaling events mediated by PI3K 0.0210 23 1341 58 -0.001 0.065 1000 -1000 -0.024 -1000
Hedgehog signaling events mediated by Gli proteins 0.0201 22 1433 65 -0.087 0.056 1000 -1000 -0.032 -1000
mTOR signaling pathway 0.0192 21 1156 53 -0.022 0.029 1000 -1000 -0.031 -1000
BARD1 signaling events 0.0183 20 1164 57 -0.046 0.1 1000 -1000 -0.038 -1000
Cellular roles of Anthrax toxin 0.0183 20 808 39 -0.079 0.027 1000 -1000 -0.018 -1000
Class I PI3K signaling events mediated by Akt 0.0183 20 1424 68 -0.16 0.043 1000 -1000 -0.029 -1000
Arf6 trafficking events 0.0174 19 1372 71 -0.27 0.042 1000 -1000 -0.026 -1000
JNK signaling in the CD4+ TCR pathway 0.0165 18 311 17 0.002 0.064 1000 -1000 -0.025 -1000
S1P3 pathway 0.0165 18 795 42 -0.014 0.042 1000 -1000 -0.035 -1000
FoxO family signaling 0.0156 17 1118 64 -0.016 0.23 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0156 17 986 58 -0.051 0.051 1000 -1000 -0.03 -1000
ceramide signaling pathway 0.0146 16 786 49 -0.001 0.036 1000 -1000 -0.033 -1000
Signaling mediated by p38-gamma and p38-delta 0.0146 16 251 15 -0.026 0.024 1000 -1000 -0.022 -1000
PLK2 and PLK4 events 0.0128 14 44 3 0.016 0.033 1000 -1000 -0.003 -1000
TRAIL signaling pathway 0.0128 14 711 48 -0.015 0.043 1000 -1000 -0.023 -1000
IL1-mediated signaling events 0.0128 14 904 62 -0.015 0.061 1000 -1000 -0.031 -1000
E-cadherin signaling in the nascent adherens junction 0.0119 13 998 76 -0.023 0.054 1000 -1000 -0.053 -1000
PDGFR-beta signaling pathway 0.0119 13 1283 97 -0.024 0.056 1000 -1000 -0.052 -1000
p38 MAPK signaling pathway 0.0119 13 606 44 -0.018 0.067 1000 -1000 -0.019 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0110 12 357 28 -0.007 0.051 1000 -1000 -0.013 -1000
EPO signaling pathway 0.0101 11 615 55 0.014 0.08 1000 -1000 -0.034 -1000
IFN-gamma pathway 0.0101 11 760 68 -0.006 0.076 1000 -1000 -0.043 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0101 11 414 37 -0.009 0.067 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0101 11 510 45 0.003 0.054 1000 -1000 -0.045 -1000
Class I PI3K signaling events 0.0101 11 819 73 -0.018 0.051 1000 -1000 -0.036 -1000
Insulin-mediated glucose transport 0.0091 10 337 32 -0.12 0.039 1000 -1000 -0.013 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0091 10 870 83 -0.019 0.047 1000 -1000 -0.023 -1000
E-cadherin signaling events 0.0091 10 54 5 0.012 0.033 1000 -1000 0.013 -1000
Signaling events mediated by HDAC Class II 0.0082 9 701 75 -0.035 0.062 1000 -1000 -0.029 -1000
a4b1 and a4b7 Integrin signaling 0.0082 9 48 5 0.024 0.041 1000 -1000 0.008 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 9 1248 125 -0.1 0.053 1000 -1000 -0.034 -1000
Canonical NF-kappaB pathway 0.0073 8 337 39 0 0.051 1000 -1000 -0.031 -1000
VEGFR1 specific signals 0.0073 8 472 56 -0.1 0.052 1000 -1000 -0.033 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0046 5 123 23 -0.004 0.043 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 0.0046 5 621 104 -0.06 0.057 1000 -1000 -0.03 -1000
Atypical NF-kappaB pathway 0.0046 5 167 31 0 0.028 1000 -1000 -0.014 -1000
Circadian rhythm pathway 0.0037 4 97 22 -0.007 0.049 1000 -1000 -0.03 -1000
Paxillin-dependent events mediated by a4b1 0.0037 4 179 36 -0.047 0.051 1000 -1000 -0.023 -1000
Arf6 downstream pathway 0.0027 3 133 43 -0.055 0.056 1000 -1000 -0.022 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0009 1 28 27 -0.008 0.056 1000 -1000 -0.036 -1000
Arf1 pathway 0.0009 1 91 54 -0.001 0.045 1000 -1000 -0.013 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 0 0.067 1000 -1000 0 -1000
Total NA 8421 498341 7203 -20 -990 131000 -131000 -3.9 -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 0.57 0.39 0.98 378 -1 3 381
PLK1 0.35 0.24 0.61 370 -0.9 1 371
BIRC5 0.37 0.24 0.61 383 -0.79 4 387
HSPA1B 0.57 0.39 0.97 399 -1 3 402
MAP2K1 0.16 0.11 0.31 293 -10000 0 293
BRCA2 0.58 0.4 0.99 382 -0.99 4 386
FOXM1 0.66 0.48 1.1 442 -1.3 3 445
XRCC1 0.57 0.39 0.98 378 -1 3 381
FOXM1B/p19 0.12 0.26 0.82 49 -1.2 3 52
Cyclin D1/CDK4 0.5 0.37 0.89 374 -0.99 3 377
CDC2 0.62 0.43 1 438 -1.1 3 441
TGFA 0.5 0.39 0.88 400 -0.95 7 407
SKP2 0.58 0.39 0.98 398 -1 3 401
CCNE1 0.089 0.094 0.29 179 -10000 0 179
CKS1B 0.57 0.39 0.94 442 -1 3 445
RB1 0.29 0.3 0.67 324 -0.62 6 330
FOXM1C/SP1 0.52 0.36 0.89 362 -1.1 5 367
AURKB 0.29 0.3 0.65 229 -0.86 16 245
CENPF 0.66 0.45 1.1 484 -0.99 3 487
CDK4 0.08 0.053 0.23 32 -10000 0 32
MYC 0.34 0.36 0.82 266 -0.96 6 272
CHEK2 0.15 0.11 0.29 363 -10000 0 363
ONECUT1 0.53 0.39 0.92 392 -1.1 3 395
CDKN2A -0.053 0.11 0.23 18 -0.22 194 212
LAMA4 0.57 0.4 0.98 394 -1.1 6 400
FOXM1B/HNF6 0.53 0.4 0.96 356 -1.3 3 359
FOS 0.27 0.64 0.99 310 -1 74 384
SP1 0.024 0.021 -10000 0 -0.2 5 5
CDC25B 0.58 0.39 0.99 377 -1 3 380
response to radiation 0.11 0.084 0.24 214 -10000 0 214
CENPB 0.57 0.39 0.97 401 -1 3 404
CENPA 0.62 0.43 1.1 433 -1 3 436
NEK2 0.69 0.44 1.1 497 -0.97 3 500
HIST1H2BA 0.57 0.39 0.98 368 -1 3 371
CCNA2 0.14 0.13 0.3 401 -10000 0 401
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.6 0.42 1.1 369 -1.2 3 372
CCNB2 0.63 0.43 1 452 -1 3 455
CCNB1 0.63 0.45 1.1 417 -1.1 3 420
ETV5 0.58 0.4 1 378 -1 3 381
ESR1 0.44 0.55 1 359 -1 18 377
CCND1 0.52 0.41 0.95 391 -1 3 394
GSK3A 0.13 0.089 0.26 258 -10000 0 258
Cyclin A-E1/CDK1-2 0.23 0.16 0.4 417 -10000 0 417
CDK2 0.056 0.028 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.14 0.11 0.27 341 -10000 0 341
FOXM1B/Cbp/p300 0.26 0.29 0.73 78 -1.1 3 81
GAS1 0.52 0.49 0.96 391 -1.1 38 429
MMP2 0.56 0.41 0.97 392 -1.2 10 402
RB1/FOXM1C 0.46 0.38 0.88 367 -1 3 370
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 0.13 0.26 0.56 287 -10000 0 287
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.56 287 287
PDE3B -0.13 0.26 -10000 0 -0.57 287 287
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.32 4 -0.38 476 480
CRKL -0.17 0.21 0.26 1 -0.4 484 485
HRAS -0.12 0.18 -10000 0 -0.35 319 319
mol:PIP3 -0.14 0.2 0.28 2 -0.37 365 367
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 -0.42 490 490
FOXO3 -0.14 0.2 0.53 1 -0.37 344 345
AKT1 -0.16 0.21 0.37 1 -0.38 449 450
BAD -0.15 0.2 0.34 2 -0.37 345 347
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 491 491
GSK3B -0.14 0.2 0.53 1 -0.37 343 344
RAF1 -0.097 0.16 0.25 4 -0.3 274 278
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 489 489
STAT1 -0.44 0.52 -10000 0 -0.99 499 499
HRAS/SPRED1 -0.094 0.16 -10000 0 -0.3 299 299
cell proliferation -0.18 0.22 -10000 0 -0.41 494 494
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.031 -10000 0 -0.57 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 498 498
HRAS/SPRED2 -0.094 0.16 -10000 0 -0.3 303 303
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.4 411 411
MAPK3 -0.066 0.12 0.39 3 -0.27 35 38
STAP1 -0.18 0.22 -10000 0 -0.42 493 493
GRAP2 0.017 0.063 0.26 3 -0.57 12 15
JAK2 -0.37 0.44 -10000 0 -0.84 495 495
STAT1 (dimer) -0.43 0.51 -10000 0 -0.97 499 499
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.15 0.22 -10000 0 -0.4 417 417
actin filament polymerization -0.18 0.22 0.33 1 -0.41 491 492
LYN 0.021 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.59 497 497
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 439 439
PI3K -0.15 0.22 -10000 0 -0.4 465 465
PTEN 0.023 0.019 -10000 0 -0.57 1 1
SCF/KIT/EPO/EPOR -0.51 0.63 -10000 0 -1.2 492 492
MAPK8 -0.19 0.22 -10000 0 -0.42 494 494
STAT3 (dimer) -0.18 0.22 0.27 1 -0.41 489 490
positive regulation of transcription -0.052 0.1 0.25 11 -0.23 24 35
mol:GDP -0.13 0.19 -10000 0 -0.37 336 336
PIK3C2B -0.17 0.21 -10000 0 -0.42 385 385
CBL/CRKL -0.16 0.2 0.26 1 -0.38 479 480
FER -0.18 0.22 -10000 0 -0.42 494 494
SH2B3 -0.18 0.22 -10000 0 -0.42 495 495
PDPK1 -0.12 0.19 0.34 9 -0.35 334 343
SNAI2 -0.18 0.21 0.28 4 -0.42 444 448
positive regulation of cell proliferation -0.32 0.38 -10000 0 -0.72 501 501
KITLG -0.004 0.058 0.25 10 -0.59 5 15
cell motility -0.32 0.38 -10000 0 -0.72 501 501
PTPN6 0.032 0.017 0.27 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -1 15 15
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 497 497
SOCS1 0.025 0.033 0.26 14 -0.57 1 15
cell migration 0.18 0.22 0.41 495 -10000 0 495
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.041 0.091 0.24 169 -10000 0 169
VAV1 0.023 0.033 0.26 2 -0.57 3 5
GRB10 -0.18 0.22 -10000 0 -0.42 490 490
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 496 496
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.13 0.3 7 -0.28 45 52
CBL 0.022 0.007 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 493 493
MAP2K2 -0.075 0.13 0.33 6 -0.28 43 49
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 360 360
STAT5A -0.27 0.33 -10000 0 -0.62 497 497
GRB2 0.023 0.009 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 445 449
SHC/GRAP2 0.024 0.046 -10000 0 -0.29 17 17
PTPRO -0.18 0.22 -10000 0 -0.42 491 491
SH2B2 -0.18 0.22 -10000 0 -0.42 491 491
DOK1 0.025 0.014 0.26 4 -10000 0 4
MATK -0.19 0.22 -10000 0 -0.42 495 495
CREBBP -0.027 0.072 -10000 0 -10000 0 0
BCL2 -0.16 0.32 -10000 0 -1.3 58 58
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.32 0.5 0.42 4 -1 357 361
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.088 0.18 -10000 0 -0.35 327 327
ATF2/c-Jun -0.081 0.16 -10000 0 -0.38 126 126
MAPK11 -0.082 0.18 -10000 0 -0.35 324 324
MITF -0.12 0.22 0.28 1 -0.41 351 352
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 358 358
KRT8 -0.11 0.21 -10000 0 -0.4 338 338
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.52 356 356
CEBPB -0.1 0.2 0.28 1 -0.4 332 333
SLC9A1 -0.11 0.21 -10000 0 -0.41 352 352
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.39 351 351
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.45 325 325
JUN -0.081 0.16 -10000 0 -0.38 126 126
PPARGC1A -0.2 0.33 0.26 1 -0.56 419 420
USF1 -0.1 0.19 0.31 3 -0.38 335 338
RAB5/GDP/GDI1 -0.081 0.16 -10000 0 -0.3 351 351
NOS2 -0.11 0.22 -10000 0 -0.55 93 93
DDIT3 -0.11 0.2 -10000 0 -0.4 351 351
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.094 0.17 0.28 4 -0.33 328 332
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 323 323
CREB1 -0.12 0.22 -10000 0 -0.43 358 358
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.4 322 322
RPS6KA4 -0.11 0.21 -10000 0 -0.4 351 351
PLA2G4A -0.13 0.22 -10000 0 -0.42 353 353
GDI1 -0.11 0.21 -10000 0 -0.4 358 358
TP53 -0.15 0.27 0.28 1 -0.52 337 338
RPS6KA5 -0.12 0.22 -10000 0 -0.41 362 362
ESR1 -0.15 0.24 0.28 1 -0.42 409 410
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 354 354
MEF2A -0.11 0.21 0.28 1 -0.4 354 355
EIF4EBP1 -0.12 0.22 0.28 1 -0.43 340 341
KRT19 -0.11 0.21 0.31 1 -0.4 328 329
ELK4 -0.1 0.19 0.3 3 -0.38 338 341
ATF6 -0.1 0.19 0.31 3 -0.38 339 342
ATF1 -0.12 0.22 -10000 0 -0.43 360 360
p38alpha-beta/MAPKAPK2 -0.095 0.22 -10000 0 -0.41 310 310
p38alpha-beta/MAPKAPK3 -0.1 0.25 -10000 0 -0.45 325 325
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 0.027 -10000 0 -10000 0 0
VLDLR 0.007 0.096 -10000 0 -0.57 29 29
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
ITGA3 0.022 0.021 0.26 1 -0.57 1 2
RELN/VLDLR/Fyn -0.19 0.21 -10000 0 -0.37 604 604
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.044 -10000 0 -0.32 7 7
AKT1 -0.15 0.14 -10000 0 -0.27 550 550
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.26 61 -10000 0 61
RELN/LRP8/DAB1 -0.16 0.19 0.32 4 -0.32 608 612
LRPAP1/LRP8 0.048 0.047 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.14 0.18 0.31 4 -0.3 592 596
DAB1/alpha3/beta1 Integrin -0.14 0.17 -10000 0 -0.3 528 528
long-term memory -0.18 0.22 0.33 5 -0.35 576 581
DAB1/LIS1 -0.14 0.19 0.3 4 -0.3 603 607
DAB1/CRLK/C3G -0.14 0.18 -10000 0 -0.3 587 587
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.14 0.19 0.3 4 -0.3 604 608
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 -0.033 0.18 0.26 13 -0.57 107 120
CDK5R1 0.028 0.034 0.26 23 -10000 0 23
RELN -0.32 0.29 0.26 2 -0.57 619 621
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RELN/LRP8/Fyn -0.18 0.2 -10000 0 -0.35 596 596
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 0.33 4 -0.35 557 561
MAPK8 0.02 0.051 -10000 0 -0.57 8 8
RELN/VLDLR/DAB1 -0.17 0.19 0.32 2 -0.34 608 610
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.18 0.22 2 -0.32 611 613
RELN/LRP8 -0.18 0.2 -10000 0 -0.35 612 612
GRIN2B/RELN/LRP8/DAB1/Fyn -0.16 0.2 0.36 3 -0.32 614 617
PI3K 0.028 0.049 -10000 0 -0.38 14 14
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.021 -10000 0 -0.42 1 1
RAP1A -0.16 0.15 0.33 4 -0.33 125 129
PAFAH1B1 0.022 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.029 0.26 4 -0.57 2 6
CRLK/C3G 0.033 0.01 -10000 0 -10000 0 0
GRIN2B -0.018 0.14 0.26 1 -0.57 70 71
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.086 0.12 -10000 0 -0.35 78 78
neuron adhesion -0.14 0.15 0.34 6 -0.47 24 30
LRP8 0.046 0.068 0.26 103 -10000 0 103
GSK3B -0.14 0.14 -10000 0 -0.38 79 79
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.31 2 -0.32 594 596
MAP3K11 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.15 0.16 -10000 0 -0.28 591 591
CDK5 0.025 0.015 0.26 4 -10000 0 4
MAPT -0.021 0.2 0.88 21 -0.51 106 127
neuron migration -0.18 0.18 0.27 2 -0.34 505 507
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.087 0.12 -10000 0 -0.35 78 78
RELN/VLDLR -0.17 0.2 -10000 0 -0.33 612 612
EGFR-dependent Endothelin signaling events

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
HRAS 0.026 0.022 0.26 9 -10000 0 9
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EGF/EGFR -0.16 0.22 -10000 0 -0.36 518 518
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.35 395 395
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.027 0.26 1 -0.57 2 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.082 0.23 0.26 2 -0.57 194 196
EGF/EGFR dimer/SHC -0.15 0.22 -10000 0 -0.4 422 422
mol:GDP -0.12 0.19 -10000 0 -0.35 395 395
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.017 0.15 0.26 1 -0.57 74 75
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.32 394 394
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.11 0.18 -10000 0 -0.33 394 394
FRAP1 -0.14 0.16 0.16 3 -0.33 395 398
EGF/EGFR dimer -0.21 0.25 -10000 0 -0.45 526 526
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
ETA receptor/Endothelin-1 0.002 0.12 -10000 0 -0.42 76 76
Aurora B signaling

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
Condensin I complex 0.1 0.099 0.23 313 -0.26 2 315
STMN1 0.078 0.078 0.26 68 -10000 0 68
Aurora B/RasGAP/Survivin 0.19 0.14 0.33 504 -10000 0 504
Chromosomal passenger complex/Cul3 protein complex 0.006 0.14 0.19 189 -0.24 134 323
BIRC5 0.18 0.11 0.26 711 -10000 0 711
DES -0.16 0.32 -10000 0 -0.59 256 256
Aurora C/Aurora B/INCENP 0.11 0.078 0.3 11 -0.3 1 12
Aurora B/TACC1 0.072 0.098 0.18 30 -0.33 25 55
Aurora B/PP2A 0.11 0.082 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.031 0.026 0.14 8 -10000 0 8
mitotic metaphase/anaphase transition -0.006 0.005 -10000 0 -10000 0 0
NDC80 0.14 0.12 0.26 484 -10000 0 484
Cul3 protein complex -0.11 0.2 -10000 0 -0.36 415 415
KIF2C 0.15 0.1 0.24 587 -10000 0 587
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.25 790 -10000 0 790
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.082 -10000 0 -10000 0 0
SEPT1 0.03 0.042 0.26 35 -10000 0 35
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.021 0.26 9 -10000 0 9
NSUN2/NPM1/Nucleolin 0.074 0.19 0.32 26 -0.46 89 115
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.006 -10000 0 -10000 0 0
H3F3B 0.07 0.06 0.23 33 -10000 0 33
AURKB 0.14 0.12 0.25 560 -10000 0 560
AURKC 0.026 0.032 0.26 14 -0.57 1 15
CDCA8 0.11 0.11 0.26 355 -10000 0 355
cytokinesis 0.14 0.14 0.31 336 -0.33 6 342
Aurora B/Septin1 0.18 0.17 0.36 382 -0.33 3 385
AURKA 0.11 0.11 0.25 428 -10000 0 428
INCENP 0.03 0.008 -10000 0 -10000 0 0
KLHL13 -0.21 0.29 -10000 0 -0.57 424 424
BUB1 0.17 0.11 0.25 709 -10000 0 709
hSgo1/Aurora B/Survivin 0.27 0.18 0.41 630 -10000 0 630
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.14 0.35 340 -10000 0 340
SGOL1 0.16 0.11 0.26 656 -10000 0 656
CENPA 0.16 0.14 0.3 497 -0.28 1 498
NCAPG 0.13 0.12 0.26 505 -10000 0 505
Aurora B/HC8 Proteasome 0.11 0.082 -10000 0 -10000 0 0
NCAPD2 0.024 0.009 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.11 0.081 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.11 0.11 0.26 407 -10000 0 407
NPM1 0.067 0.12 0.26 4 -0.38 27 31
RASA1 0.024 0.004 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.081 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.2 0.15 0.36 416 -10000 0 416
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 0.073 0.12 0.27 21 -0.48 5 26
MYLK 0.02 0.14 0.23 8 -0.31 128 136
KIF23 0.098 0.11 0.26 319 -10000 0 319
VIM 0.078 0.084 0.37 32 -0.41 2 34
RACGAP1 0.04 0.046 0.27 41 -10000 0 41
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.062 0.14 -10000 0 -0.74 14 14
Chromosomal passenger complex 0.17 0.12 0.28 572 -10000 0 572
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 505 -10000 0 505
TACC1 0.006 0.089 -10000 0 -0.57 25 25
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
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 -0.063 0.048 0.11 6 -0.1 565 571
BUB1B 0.082 0.066 0.15 427 -10000 0 427
PLK1 0.049 0.038 0.094 279 -10000 0 279
PLK1S1 0.025 0.034 0.13 11 -0.16 20 31
KIF2A 0.041 0.039 0.24 9 -10000 0 9
regulation of mitotic centrosome separation 0.048 0.038 0.094 279 -10000 0 279
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.23 0.14 0.31 752 -10000 0 752
WEE1 0.043 0.06 0.23 2 -0.27 24 26
cytokinesis 0.12 0.086 0.21 290 -0.37 2 292
PP2A-alpha B56 0.11 0.12 -10000 0 -0.44 32 32
AURKA 0.063 0.052 0.12 431 -0.14 4 435
PICH/PLK1 0.096 0.087 0.21 310 -10000 0 310
CENPE 0.061 0.054 0.14 199 -10000 0 199
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.041 0.038 0.24 9 -10000 0 9
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.078 0.054 0.12 562 -0.14 2 564
PAK1 0.022 0.019 0.25 6 -10000 0 6
SPC24 0.17 0.11 0.26 664 -10000 0 664
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.071 0.069 0.14 438 -0.19 23 461
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 55 -10000 0 55
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.022 0.019 0.053 151 -10000 0 151
G2 phase of mitotic cell cycle 0.001 0.003 0.015 13 -10000 0 13
STAG2 0.024 0.018 -10000 0 -0.57 1 1
GRASP65/GM130/RAB1/GTP 0.011 0.08 -10000 0 -0.5 25 25
spindle elongation 0.048 0.038 0.094 279 -10000 0 279
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.1 0.13 -10000 0 -0.48 36 36
TPT1 0.013 0.056 0.12 2 -0.17 78 80
CDC25C 0.11 0.067 0.16 481 -0.2 15 496
CDC25B 0.029 0.031 0.26 18 -10000 0 18
SGOL1 0.063 0.048 0.1 565 -0.11 6 571
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.068 0.064 0.31 11 -10000 0 11
CDC14B -0.01 0.075 -10000 0 -0.42 34 34
CDC20 0.14 0.12 0.26 565 -10000 0 565
PLK1/PBIP1 0.036 0.045 0.14 139 -10000 0 139
mitosis -0.004 0.005 0.027 4 -10000 0 4
FBXO5 0.03 0.035 0.14 22 -0.11 2 24
CDC2 0.003 0.004 0.011 192 -10000 0 192
NDC80 0.16 0.12 0.26 619 -10000 0 619
metaphase plate congression 0.028 0.054 0.14 2 -0.19 48 50
ERCC6L 0.087 0.083 0.24 168 -10000 0 168
NLP/gamma Tubulin 0.023 0.024 0.071 44 -0.083 12 56
microtubule cytoskeleton organization 0.013 0.056 0.12 2 -0.17 78 80
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 13 -10000 0 13
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 13 -10000 0 13
PLK1/PRC1-2 0.2 0.12 0.27 759 -10000 0 759
GRASP65/GM130/RAB1/GTP/PLK1 0.069 0.03 -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 0.041 0.035 0.084 283 -10000 0 283
mitotic prometaphase 0.002 0.005 0.022 51 -10000 0 51
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.051 -10000 0 -0.31 3 3
microtubule-based process 0.17 0.089 0.22 789 -10000 0 789
Golgi organization 0.048 0.038 0.094 279 -10000 0 279
Cohesin/SA2 0.053 0.031 0.14 5 -0.3 1 6
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.26 790 -10000 0 790
APC/C/CDC20 0.14 0.099 0.23 560 -10000 0 560
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.03 0.046 0.14 139 -10000 0 139
PRC1 0.079 0.099 0.26 257 -10000 0 257
ECT2 0.049 0.057 0.26 45 -10000 0 45
C13orf34 0.04 0.033 0.091 163 -10000 0 163
NUDC 0.028 0.054 0.14 2 -0.19 48 50
regulation of attachment of spindle microtubules to kinetochore 0.082 0.066 0.15 428 -10000 0 428
spindle assembly 0.035 0.029 0.085 127 -10000 0 127
spindle stabilization 0.025 0.034 0.13 11 -0.16 20 31
APC/C/HCDH1 0.009 0.067 -10000 0 -0.36 34 34
MKLP2/PLK1 0.17 0.089 0.22 789 -10000 0 789
CCNB1 0.069 0.091 0.26 205 -10000 0 205
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.026 0.086 0.23 1 -0.38 39 40
TUBG1 0.023 0.038 0.13 3 -0.16 34 37
G2/M transition of mitotic cell cycle 0.041 0.043 0.2 11 -10000 0 11
MLF1IP 0.023 0.045 0.14 147 -10000 0 147
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 -0.24 0.27 -10000 0 -0.75 105 105
PCK1 -0.92 0.63 -10000 0 -1.4 655 655
HNF4A -0.23 0.28 0.66 2 -0.79 78 80
KCNJ11 -0.28 0.29 -10000 0 -0.77 158 158
AKT1 -0.16 0.16 0.37 1 -0.43 63 64
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.44 0.47 -10000 0 -1.1 347 347
NKX2-1 -0.044 0.16 0.39 19 -0.38 37 56
ACADM -0.25 0.27 0.52 1 -0.72 132 133
TAT -1.1 0.63 -10000 0 -1.4 761 761
CEBPB 0.024 0.01 -10000 0 -10000 0 0
CEBPA 0.02 0.058 -10000 0 -0.57 10 10
TTR -0.4 0.29 0.57 1 -0.74 317 318
PKLR -0.22 0.27 0.57 6 -0.7 124 130
APOA1 -0.28 0.31 0.79 1 -0.88 86 87
CPT1C -0.24 0.27 0.55 2 -0.73 126 128
ALAS1 -0.15 0.16 -10000 0 -0.79 5 5
TFRC -0.42 0.26 -10000 0 -0.75 242 242
FOXF1 0.02 0.041 0.26 6 -0.57 4 10
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.032 0.27 8 -10000 0 8
CPT1A -0.23 0.27 0.53 2 -0.75 105 107
HMGCS1 -0.24 0.27 0.62 2 -0.7 145 147
NR3C1 -0.12 0.12 -10000 0 -0.3 174 174
CPT1B -0.24 0.27 0.52 1 -0.73 125 126
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.023 -10000 0 -10000 0 0
GCK -0.27 0.32 0.52 1 -0.85 156 157
CREB1 -0.076 0.093 -10000 0 -0.21 163 163
IGFBP1 -0.41 0.54 -10000 0 -1.4 240 240
PDX1 -0.12 0.15 -10000 0 -0.57 4 4
UCP2 -0.24 0.27 0.52 2 -0.72 124 126
ALDOB -0.28 0.28 0.68 1 -0.77 137 138
AFP -0.56 0.5 -10000 0 -1 478 478
BDH1 -0.24 0.26 0.52 1 -0.72 123 124
HADH -0.27 0.28 -10000 0 -0.77 130 130
F2 -0.28 0.3 0.79 1 -0.88 82 83
HNF1A 0.034 0.032 0.27 8 -10000 0 8
G6PC -0.18 0.12 -10000 0 -0.55 10 10
SLC2A2 -0.16 0.17 0.62 1 -0.78 2 3
INS 0.018 0.077 0.23 21 -10000 0 21
FOXA1 -0.22 0.23 0.27 18 -0.39 516 534
FOXA3 -0.36 0.21 0.34 2 -0.47 767 769
FOXA2 -0.32 0.32 0.77 1 -0.8 205 206
ABCC8 -0.32 0.38 -10000 0 -0.96 198 198
ALB -0.76 0.54 0.35 1 -1.1 712 713
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.26 0.36 0.54 1 -0.77 236 237
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.34 0.66 3 -0.76 149 152
SMAD4 0.024 0.006 -10000 0 -10000 0 0
ID2 -0.24 0.37 -10000 0 -0.79 221 221
AP1 -0.1 0.21 -10000 0 -0.42 320 320
ABCG2 -0.26 0.39 -10000 0 -0.8 252 252
HIF1A -0.048 0.084 -10000 0 -0.23 30 30
TFF3 -0.25 0.41 0.65 6 -0.79 263 269
GATA2 0.009 0.095 0.25 13 -0.57 26 39
AKT1 -0.055 0.094 -10000 0 -0.26 29 29
response to hypoxia -0.062 0.084 0.19 2 -0.2 140 142
MCL1 -0.24 0.35 -10000 0 -0.78 214 214
NDRG1 -0.22 0.36 -10000 0 -0.79 196 196
SERPINE1 -0.24 0.38 0.65 4 -0.78 223 227
FECH -0.24 0.37 -10000 0 -0.78 223 223
FURIN -0.24 0.37 -10000 0 -0.78 222 222
NCOA2 -0.002 0.12 -10000 0 -0.56 48 48
EP300 -0.06 0.13 0.34 2 -0.34 104 106
HMOX1 -0.24 0.37 0.65 1 -0.79 221 222
BHLHE40 -0.24 0.37 -10000 0 -0.79 222 222
BHLHE41 -0.25 0.38 -10000 0 -0.8 222 222
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.019 0.11 -10000 0 -0.3 1 1
ENG -0.016 0.11 0.38 3 -10000 0 3
JUN 0.018 0.046 -10000 0 -0.57 6 6
RORA -0.25 0.37 -10000 0 -0.78 228 228
ABCB1 -0.26 0.45 -10000 0 -1.1 220 220
TFRC -0.24 0.37 -10000 0 -0.79 220 220
CXCR4 -0.24 0.37 0.65 1 -0.79 222 223
TF -0.4 0.45 -10000 0 -0.86 430 430
CITED2 -0.25 0.37 -10000 0 -0.79 221 221
HIF1A/ARNT -0.27 0.42 0.74 4 -0.89 210 214
LDHA -0.037 0.12 -10000 0 -0.73 23 23
ETS1 -0.25 0.37 -10000 0 -0.79 223 223
PGK1 -0.24 0.37 -10000 0 -0.79 223 223
NOS2 -0.24 0.37 -10000 0 -0.79 216 216
ITGB2 -0.24 0.37 0.65 1 -0.79 219 220
ALDOA -0.24 0.37 -10000 0 -0.79 213 213
Cbp/p300/CITED2 -0.25 0.39 -10000 0 -0.88 186 186
FOS -0.15 0.27 -10000 0 -0.57 306 306
HK2 -0.24 0.37 -10000 0 -0.78 224 224
SP1 0.002 0.057 -10000 0 -0.2 4 4
GCK -0.12 0.33 0.57 1 -1.3 60 61
HK1 -0.24 0.37 -10000 0 -0.78 222 222
NPM1 -0.24 0.37 -10000 0 -0.78 222 222
EGLN1 -0.24 0.36 -10000 0 -0.78 214 214
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.25 0.37 -10000 0 -0.78 223 223
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.36 -10000 0 -1.1 117 117
IGFBP1 -0.31 0.42 -10000 0 -0.86 290 290
VEGFA -0.16 0.29 0.56 1 -0.67 130 131
HIF1A/JAB1 -0.009 0.067 -10000 0 -0.27 1 1
CP -0.3 0.45 0.64 2 -0.88 305 307
CXCL12 -0.26 0.4 -10000 0 -0.82 244 244
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.012 -10000 0 -0.17 1 1
BNIP3 -0.24 0.37 0.72 1 -0.78 226 227
EGLN3 -0.24 0.38 0.68 2 -0.79 218 220
CA9 -0.21 0.39 0.66 6 -0.78 215 221
TERT -0.23 0.37 0.66 4 -0.78 219 223
ENO1 -0.25 0.37 -10000 0 -0.79 222 222
PFKL -0.24 0.37 -10000 0 -0.78 222 222
NCOA1 0.024 0.019 -10000 0 -0.57 1 1
ADM -0.26 0.4 -10000 0 -0.83 244 244
ARNT -0.035 0.07 -10000 0 -10000 0 0
HNF4A 0.019 0.041 0.26 19 -0.17 1 20
ADFP -0.26 0.36 0.54 1 -0.77 236 237
SLC2A1 -0.16 0.29 0.62 3 -0.67 132 135
LEP -0.48 0.41 -10000 0 -0.84 462 462
HIF1A/ARNT/Cbp/p300 -0.2 0.34 0.64 2 -0.76 162 164
EPO -0.11 0.26 0.64 4 -0.72 57 61
CREBBP -0.05 0.12 0.34 2 -0.35 72 74
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 0.72 1 -0.77 135 136
PFKFB3 -0.24 0.37 -10000 0 -0.8 214 214
NT5E -0.25 0.37 -10000 0 -0.79 227 227
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.16 0.39 -10000 0 -0.86 241 241
NCK1/PAK1/Dok-R -0.096 0.17 -10000 0 -0.41 241 241
NCK1/Dok-R -0.19 0.46 -10000 0 -1 241 241
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.044 0.099 0.24 212 -10000 0 212
RELA 0.023 0.005 -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 0.048 0.11 0.27 213 -10000 0 213
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.17 0.44 -10000 0 -0.97 240 240
FN1 0.11 0.11 0.26 421 -10000 0 421
PLD2 -0.22 0.47 -10000 0 -1.1 240 240
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.011 0.18 0.26 142 -0.57 80 222
ELK1 -0.19 0.42 -10000 0 -0.96 241 241
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 0.023 0.019 0.26 6 -10000 0 6
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.49 -10000 0 -1 241 241
CDKN1A -0.11 0.26 -10000 0 -0.62 174 174
ITGA5 0.024 0.007 0.26 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.19 0.46 -10000 0 -1 240 240
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.11 0.29 0.39 1 -0.64 241 242
PLG -0.22 0.47 -10000 0 -1.1 241 241
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.16 0.36 -10000 0 -0.82 241 241
GRB2 0.023 0.009 0.26 1 -10000 0 1
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
ANGPT2 -0.15 0.28 -10000 0 -0.71 153 153
BMX -0.32 0.51 -10000 0 -1.2 242 242
ANGPT1 -0.23 0.5 -10000 0 -1.2 212 212
tube development -0.13 0.29 -10000 0 -0.66 223 223
ANGPT4 -0.15 0.26 -10000 0 -0.57 305 305
response to hypoxia -0.014 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.22 0.51 -10000 0 -1.1 240 240
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
STAT5A (dimer) -0.15 0.34 -10000 0 -0.78 203 203
mol:L-citrulline -0.11 0.29 0.39 1 -0.64 241 242
AGTR1 -0.097 0.26 0.26 59 -0.57 244 303
MAPK14 -0.21 0.47 -10000 0 -1.1 243 243
Tie2/SHP2 -0.1 0.32 -10000 0 -1.1 90 90
TEK -0.11 0.35 -10000 0 -1.2 91 91
RPS6KB1 -0.14 0.38 -10000 0 -0.82 241 241
Angiotensin II/AT1 -0.071 0.19 0.18 59 -0.41 247 306
Tie2/Ang1/GRB2 -0.21 0.49 -10000 0 -1.1 241 241
MAPK3 -0.19 0.43 -10000 0 -0.98 240 240
MAPK1 -0.2 0.43 -10000 0 -0.99 240 240
Tie2/Ang1/GRB7 -0.22 0.49 -10000 0 -1.1 241 241
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.22 0.48 -10000 0 -1.1 241 241
PI3K -0.19 0.44 -10000 0 -0.99 241 241
FES -0.21 0.47 -10000 0 -1.1 243 243
Crk/Dok-R -0.19 0.46 -10000 0 -1 241 241
Tie2/Ang1/ABIN2 -0.21 0.5 -10000 0 -1.1 241 241
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.14 0.34 -10000 0 -0.77 241 241
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.38 0.47 1 -0.8 240 241
Tie2/Ang2 -0.18 0.4 -10000 0 -0.93 208 208
Tie2/Ang1 -0.23 0.52 -10000 0 -1.2 241 241
FOXO1 -0.14 0.35 0.47 1 -0.78 241 242
ELF1 0.011 0.037 -10000 0 -10000 0 0
ELF2 -0.21 0.47 -10000 0 -1.1 240 240
mol:Choline -0.2 0.45 -10000 0 -1 240 240
cell migration -0.04 0.1 0.097 1 -0.23 241 242
FYN -0.15 0.33 -10000 0 -0.76 212 212
DOK2 0.02 0.03 0.26 4 -0.57 2 6
negative regulation of cell cycle -0.1 0.24 -10000 0 -0.56 175 175
ETS1 -0.023 0.11 -10000 0 -0.27 172 172
PXN -0.1 0.32 0.42 2 -0.67 240 242
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.13 0.33 -10000 0 -0.73 241 241
RAC1 0.024 0.003 -10000 0 -10000 0 0
TNF -0.026 0.13 0.26 20 -0.27 200 220
MAPKKK cascade -0.2 0.45 -10000 0 -1 240 240
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.21 0.48 -10000 0 -1.1 241 241
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.099 0.26 0.37 2 -0.57 241 243
mol:Phosphatidic acid -0.2 0.45 -10000 0 -1 240 240
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.11 0.29 0.39 1 -0.64 241 242
Rac1/GTP -0.14 0.35 -10000 0 -0.77 241 241
MMP2 -0.22 0.48 -10000 0 -1.1 241 241
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.099 0.13 0.3 282 -0.22 2 284
NFATC2 -0.025 0.23 0.48 8 -0.59 101 109
NFATC3 -0.04 0.12 -10000 0 -0.28 169 169
CD40LG -0.29 0.5 0.65 6 -0.98 312 318
ITCH -0.002 0.082 -10000 0 -10000 0 0
CBLB -0.002 0.083 -10000 0 -0.26 99 99
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.093 0.39 0.59 53 -0.99 93 146
JUNB 0.025 0.01 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.1 -10000 0 -0.3 105 105
T cell anergy -0.026 0.14 0.33 1 -0.42 102 103
TLE4 -0.026 0.19 0.36 1 -0.6 70 71
Jun/NFAT1-c-4/p21SNFT -0.17 0.43 0.67 6 -0.85 255 261
AP-1/NFAT1-c-4 -0.31 0.61 0.74 15 -1.1 309 324
IKZF1 -0.017 0.16 0.47 7 -0.49 63 70
T-helper 2 cell differentiation -0.084 0.28 0.48 1 -0.83 84 85
AP-1/NFAT1 -0.098 0.26 0.44 13 -0.46 287 300
CALM1 0.011 0.063 -10000 0 -0.19 1 1
EGR2 -0.25 0.55 0.69 2 -1.4 160 162
EGR3 -0.33 0.62 0.58 4 -1.2 313 317
NFAT1/FOXP3 0.05 0.22 0.46 109 -0.45 83 192
EGR1 -0.16 0.27 -10000 0 -0.56 336 336
JUN 0.015 0.054 0.2 2 -0.57 6 8
EGR4 0.04 0.06 0.26 75 -10000 0 75
mol:Ca2+ -0.01 0.054 -10000 0 -0.18 3 3
GBP3 -0.021 0.17 0.38 3 -0.54 62 65
FOSL1 0.027 0.048 0.26 26 -0.57 3 29
NFAT1-c-4/MAF/IRF4 -0.19 0.45 0.59 7 -0.87 279 286
DGKA -0.017 0.16 0.56 1 -0.5 56 57
CREM 0.023 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.26 0.48 0.6 3 -0.94 302 305
CTLA4 0.038 0.21 0.42 125 -0.51 45 170
NFAT1-c-4 (dimer)/EGR1 -0.28 0.51 0.61 4 -1 315 319
NFAT1-c-4 (dimer)/EGR4 -0.18 0.45 0.59 6 -0.85 279 285
FOS -0.15 0.27 -10000 0 -0.57 310 310
IFNG -0.054 0.27 0.51 10 -0.75 81 91
T cell activation -0.15 0.29 0.62 4 -0.65 202 206
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 0.15 0.33 0.66 264 -0.61 2 266
TNF -0.25 0.44 0.54 4 -0.9 303 307
FASLG -0.32 0.63 0.79 2 -1.2 309 311
TBX21 0.021 0.12 0.35 15 -0.57 36 51
BATF3 0.021 0.015 0.26 3 -10000 0 3
PRKCQ 0.006 0.11 0.28 8 -0.57 39 47
PTPN1 -0.017 0.16 0.39 3 -0.48 63 66
NFAT1-c-4/ICER1 -0.19 0.44 0.55 3 -0.84 284 287
GATA3 0.01 0.11 0.26 28 -0.57 35 63
T-helper 1 cell differentiation -0.052 0.27 0.51 10 -0.73 83 93
IL2RA -0.094 0.37 0.59 47 -0.85 118 165
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.16 0.36 1 -0.48 64 65
E2F1 0.096 0.11 0.26 320 -10000 0 320
PPARG -0.11 0.25 -10000 0 -0.57 252 252
SLC3A2 -0.018 0.16 0.36 1 -0.48 65 66
IRF4 -0.019 0.16 0.26 13 -0.57 83 96
PTGS2 -0.34 0.54 0.63 4 -1 344 348
CSF2 -0.28 0.48 0.64 9 -0.95 311 320
JunB/Fra1/NFAT1-c-4 -0.17 0.43 0.58 5 -0.82 280 285
IL4 -0.089 0.29 -10000 0 -0.89 81 81
IL5 -0.28 0.48 0.58 7 -0.96 308 315
IL2 -0.15 0.3 0.62 4 -0.66 199 203
IL3 -0.05 0.13 -10000 0 -0.82 18 18
RNF128 -0.041 0.2 0.27 5 -0.65 105 110
NFATC1 -0.15 0.34 0.61 2 -0.67 262 264
CDK4 0.12 0.24 0.59 110 -0.57 2 112
PTPRK -0.02 0.17 0.42 3 -0.52 67 70
IL8 -0.28 0.49 0.58 9 -0.97 306 315
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.073 0.14 -10000 0 -0.43 96 96
PTK2B 0.02 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.2 -10000 0 -0.84 44 44
EDN1 -0.073 0.16 -10000 0 -0.59 81 81
EDN3 -0.22 0.29 0.26 3 -0.57 442 445
EDN2 0.073 0.11 0.26 245 -0.57 5 250
HRAS/GDP -0.093 0.2 0.28 1 -0.49 143 144
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.14 -10000 0 -0.41 104 104
ADCY4 -0.13 0.2 0.28 2 -0.42 279 281
ADCY5 -0.21 0.24 -10000 0 -0.45 467 467
ADCY6 -0.12 0.19 0.28 2 -0.4 270 272
ADCY7 -0.12 0.18 0.28 2 -0.4 269 271
ADCY1 -0.12 0.2 0.26 1 -0.41 272 273
ADCY2 -0.14 0.22 0.29 6 -0.45 291 297
ADCY3 -0.12 0.18 0.26 1 -0.4 269 270
ADCY8 -0.1 0.17 0.27 2 -0.4 207 209
ADCY9 -0.11 0.18 0.26 1 -0.4 256 257
arachidonic acid secretion -0.16 0.28 0.31 2 -0.51 354 356
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.36 153 153
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.025 0.022 0.25 9 -10000 0 9
ETA receptor/Endothelin-1/G12/GTP -0.059 0.14 -10000 0 -0.4 96 96
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.42 271 271
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.064 0.16 0.37 10 -0.44 97 107
EDNRB -0.029 0.17 -10000 0 -0.56 100 100
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.078 0.16 -10000 0 -0.5 106 106
CYSLTR1 -0.081 0.16 -10000 0 -0.49 102 102
SLC9A1 -0.045 0.093 -10000 0 -0.28 108 108
mol:GDP -0.1 0.21 0.33 2 -0.5 159 161
SLC9A3 -0.11 0.28 -10000 0 -0.66 178 178
RAF1 -0.14 0.24 0.33 1 -0.47 282 283
JUN -0.05 0.18 -10000 0 -0.7 56 56
JAK2 -0.072 0.14 -10000 0 -0.44 96 96
mol:IP3 -0.075 0.17 -10000 0 -0.45 125 125
ETA receptor/Endothelin-1 -0.083 0.16 -10000 0 -0.49 106 106
PLCB1 -0.019 0.15 -10000 0 -0.57 74 74
PLCB2 0.014 0.026 0.26 1 -0.57 1 2
ETA receptor/Endothelin-3 -0.19 0.21 0.24 1 -0.43 451 452
FOS -0.29 0.44 -10000 0 -0.93 336 336
Gai/GDP -0.1 0.29 -10000 0 -0.75 165 165
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.21 -10000 0 -0.54 141 141
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.43 134 134
GNAQ 0.013 0.036 -10000 0 -0.57 3 3
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNAL -0.11 0.24 -10000 0 -0.57 235 235
Gs family/GDP -0.15 0.24 0.26 1 -0.5 265 266
ETA receptor/Endothelin-1/Gq/GTP -0.047 0.12 -10000 0 -0.4 71 71
MAPK14 -0.066 0.16 -10000 0 -0.43 123 123
TRPC6 -0.057 0.21 -10000 0 -0.93 42 42
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.17 -10000 0 -0.42 145 145
ETB receptor/Endothelin-2 0.022 0.15 0.24 17 -0.4 103 120
ETB receptor/Endothelin-3 -0.19 0.24 0.24 1 -0.44 496 497
ETB receptor/Endothelin-1 -0.078 0.18 -10000 0 -0.47 167 167
MAPK3 -0.25 0.38 -10000 0 -0.79 340 340
MAPK1 -0.26 0.4 -10000 0 -0.81 343 343
Rac1/GDP -0.094 0.19 0.28 1 -0.48 148 149
cAMP biosynthetic process -0.16 0.22 0.4 2 -0.47 267 269
MAPK8 -0.058 0.21 -10000 0 -0.74 66 66
SRC 0.023 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.068 0.17 -10000 0 -0.38 189 189
p130Cas/CRK/Src/PYK2 -0.097 0.22 0.49 1 -0.58 121 122
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.093 0.19 -10000 0 -0.49 142 142
COL1A2 -0.089 0.2 0.37 9 -0.48 154 163
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.021 0.097 0.25 15 -0.38 11 26
mol:DAG -0.075 0.17 -10000 0 -0.45 126 126
MAP2K2 -0.19 0.3 0.34 2 -0.59 346 348
MAP2K1 -0.19 0.3 0.32 2 -0.59 344 346
EDNRA -0.035 0.07 0.28 1 -0.3 25 26
positive regulation of muscle contraction -0.063 0.12 -10000 0 -0.38 94 94
Gq family/GDP -0.059 0.19 -10000 0 -0.5 102 102
HRAS/GTP -0.1 0.2 0.3 2 -0.48 167 169
PRKCH -0.077 0.16 -10000 0 -0.45 116 116
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.073 0.18 0.28 3 -0.48 121 124
PRKCB -0.074 0.18 -10000 0 -0.46 124 124
PRKCE -0.08 0.16 -10000 0 -0.46 116 116
PRKCD -0.076 0.16 -10000 0 -0.44 119 119
PRKCG -0.078 0.17 0.27 1 -0.44 126 127
regulation of vascular smooth muscle contraction -0.34 0.51 -10000 0 -1.1 333 333
PRKCQ -0.084 0.18 -10000 0 -0.48 136 136
PLA2G4A -0.18 0.31 0.31 2 -0.56 356 358
GNA14 0.014 0.067 0.25 19 -0.57 10 29
GNA15 0.022 0.027 0.25 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.037 -10000 0 -0.57 4 4
Rac1/GTP -0.059 0.14 -10000 0 -0.4 96 96
MMP1 0.17 0.13 0.41 66 -10000 0 66
Glucocorticoid receptor regulatory network

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
PCK2 0.09 0.1 0.38 9 -10000 0 9
SMARCC2 0.024 0.013 -10000 0 -0.19 1 1
SMARCC1 0.024 0.012 -10000 0 -0.16 1 1
TBX21 -0.12 0.21 0.4 5 -0.72 64 69
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.032 0.26 19 -10000 0 19
FKBP4 0.025 0.017 0.26 5 -10000 0 5
FKBP5 0.015 0.078 0.26 5 -0.57 18 23
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.32 96 -0.35 7 103
PRL -0.062 0.12 0.56 2 -0.49 1 3
cortisol/GR alpha (dimer)/TIF2 0.18 0.28 0.53 314 -0.48 17 331
RELA -0.037 0.1 0.28 1 -0.26 36 37
FGG 0.21 0.24 0.49 331 -0.49 3 334
GR beta/TIF2 0.078 0.16 0.32 123 -0.4 42 165
IFNG -0.3 0.36 0.46 2 -0.7 385 387
apoptosis -0.26 0.3 0.85 1 -0.66 280 281
CREB1 0.06 0.053 -10000 0 -10000 0 0
histone acetylation 0.025 0.13 0.37 50 -0.43 15 65
BGLAP -0.08 0.14 0.39 2 -0.48 27 29
GR/PKAc 0.13 0.13 0.36 82 -0.33 3 85
NF kappa B1 p50/RelA -0.062 0.18 0.42 4 -0.34 179 183
SMARCD1 0.024 0.012 -10000 0 -10000 0 0
MDM2 0.098 0.11 0.23 308 -10000 0 308
GATA3 0.014 0.11 0.26 28 -0.56 35 63
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.024 0.1 0.47 1 -0.54 5 6
GSK3B 0.001 0.023 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.79 1 -0.62 140 141
CSN2 0.16 0.19 0.38 300 -0.43 4 304
BRG1/BAF155/BAF170/BAF60A 0.06 0.041 -10000 0 -0.44 6 6
NFATC1 0.023 0.026 -10000 0 -0.57 2 2
POU2F1 0.023 0.015 0.26 1 -10000 0 1
CDKN1A 0.016 0.086 -10000 0 -1.3 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.007 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.35 58 -0.32 6 64
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.39 0.62 2 -0.83 377 379
JUN -0.25 0.29 0.41 8 -0.54 433 441
IL4 -0.11 0.15 -10000 0 -0.55 14 14
CDK5R1 0.022 0.036 0.25 23 -10000 0 23
PRKACA 0.024 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.47 504 504
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.13 0.34 68 -0.34 5 73
cortisol/GR alpha (monomer) 0.28 0.32 0.61 416 -0.53 4 420
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.59 315 315
AP-1/NFAT1-c-4 -0.42 0.45 0.48 6 -0.81 543 549
AFP -0.53 0.64 0.5 1 -1.4 353 354
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.46 70 -10000 0 70
TP53 0.031 0.027 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.64 0.68 0.46 1 -1.4 468 469
KRT14 -0.69 0.66 -10000 0 -1.3 555 555
TBP 0.028 0.013 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.3 395 -10000 0 395
HDAC1 0.022 0.011 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.43 0.45 0.48 6 -0.82 544 550
MAPK14 0.004 0.022 -10000 0 -10000 0 0
MAPK10 -0.083 0.2 -10000 0 -0.57 158 158
MAPK11 -0.001 0.038 -10000 0 -0.58 3 3
KRT5 -0.72 0.7 0.43 2 -1.4 564 566
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.019 -10000 0 -0.56 1 1
STAT1 0.033 0.032 0.26 19 -10000 0 19
CGA -0.053 0.17 0.45 1 -0.55 7 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.36 364 -10000 0 364
MAPK3 0.001 0.022 -10000 0 -10000 0 0
MAPK1 0.003 0.022 -10000 0 -10000 0 0
ICAM1 -0.18 0.24 0.6 3 -0.55 229 232
NFKB1 -0.038 0.1 0.28 1 -0.24 49 50
MAPK8 -0.19 0.22 0.39 5 -0.42 417 422
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.27 0.32 0.86 1 -0.7 281 282
BAX 0.017 0.064 -10000 0 -10000 0 0
POMC -0.16 0.3 -10000 0 -0.96 72 72
EP300 0.14 0.14 0.31 280 -10000 0 280
cortisol/GR alpha (dimer)/p53 0.21 0.26 0.53 343 -0.5 3 346
proteasomal ubiquitin-dependent protein catabolic process 0.077 0.11 0.27 157 -10000 0 157
SGK1 0.19 0.2 0.51 13 -1.1 6 19
IL13 -0.25 0.28 0.55 3 -0.68 147 150
IL6 -0.43 0.52 0.49 2 -1.1 408 410
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.55 2 -0.68 56 58
IL2 -0.33 0.35 0.44 4 -0.69 448 452
CDK5 0.018 0.019 0.25 4 -10000 0 4
PRKACB 0.032 0.06 0.26 47 -0.57 4 51
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.52 4 -0.63 200 204
CDK5R1/CDK5 0.019 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.018 0.15 0.38 3 -0.36 48 51
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.51 385 -0.46 3 388
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.16 0.36 238 -0.63 1 239
NF kappa B1 p50/RelA/Cbp 0.061 0.19 0.42 49 -0.43 15 64
JUN (dimer) -0.25 0.29 0.41 8 -0.54 432 440
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.2 -10000 0 -0.56 118 118
NR3C1 0.17 0.2 0.42 291 -0.43 4 295
NR4A1 -0.03 0.18 -10000 0 -0.55 112 112
TIF2/SUV420H1 0.008 0.094 -10000 0 -0.42 48 48
MAPKKK cascade -0.26 0.3 0.85 1 -0.66 280 281
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.53 407 -0.5 3 410
PBX1 0.023 0.015 0.26 1 -10000 0 1
POU1F1 0.021 0.015 0.26 2 -10000 0 2
SELE -0.19 0.31 0.55 3 -0.7 192 195
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.36 237 -0.64 1 238
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.51 385 -0.46 3 388
mol:cortisol 0.16 0.19 0.35 432 -0.28 3 435
MMP1 0.03 0.31 -10000 0 -0.93 82 82
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.034 0.016 -10000 0 -0.42 1 1
Necdin/E2F1 0.061 0.11 -10000 0 -0.39 33 33
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.045 0.17 -10000 0 -0.32 289 289
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.24 0.34 1 -0.4 365 366
NT-4/5 (dimer)/p75(NTR) -0.22 0.29 -10000 0 -0.49 519 519
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.081 0.16 0.36 1 -0.32 274 275
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.012 0.16 0.26 24 -0.57 75 99
MGDIs/NGR/p75(NTR)/LINGO1 -0.037 0.2 0.34 7 -0.34 280 287
FURIN 0.024 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.087 0.2 -10000 0 -0.39 317 317
LINGO1 0.077 0.097 0.26 247 -10000 0 247
Sortilin/TRAF6/NRIF 0.024 0.024 -10000 0 -0.55 1 1
proBDNF (dimer) -0.012 0.16 0.26 24 -0.56 75 99
NTRK1 0.024 0.051 0.26 25 -0.57 4 29
RTN4R 0.032 0.044 0.26 40 -10000 0 40
neuron apoptosis -0.077 0.19 0.36 4 -0.52 67 71
IRAK1 0.025 0.014 0.26 4 -10000 0 4
SHC1 -0.079 0.15 -10000 0 -0.37 221 221
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.053 0.18 -10000 0 -0.34 285 285
MAGEH1 0.024 0.018 -10000 0 -0.57 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.063 0.19 -10000 0 -0.36 294 294
Mammalian IAPs/DIABLO 0.057 0.032 -10000 0 -0.33 2 2
proNGF (dimer) 0.017 0.074 0.26 8 -0.56 16 24
MAGED1 0.025 0.01 0.26 2 -10000 0 2
APP 0.024 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.56 363 363
ZNF274 0.024 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.063 0.15 -10000 0 -0.32 276 276
NGF 0.017 0.074 0.26 8 -0.57 16 24
cell cycle arrest -0.072 0.15 0.23 47 -0.29 285 332
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.052 0.12 -10000 0 -0.27 208 208
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.18 0.26 -10000 0 -0.44 484 484
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.067 0.19 -10000 0 -0.36 289 289
PSENEN 0.024 0.011 0.26 2 -10000 0 2
mol:ceramide -0.076 0.16 -10000 0 -0.33 284 284
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.043 0.11 -10000 0 -0.36 30 30
p75(NTR)/beta APP -0.089 0.2 -10000 0 -0.4 297 297
BEX1 -0.016 0.23 0.26 172 -0.57 139 311
mol:GDP -0.1 0.16 -10000 0 -0.36 291 291
NGF (dimer) 0.002 0.14 0.34 1 -0.34 133 134
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.021 0.18 0.34 6 -0.32 266 272
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RAC1/GTP -0.058 0.16 -10000 0 -0.31 285 285
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 -0.067 0.19 -10000 0 -0.36 289 289
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.077 0.073 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.56 157 169
TP53 -0.089 0.16 0.35 3 -0.33 306 309
PRDM4 -0.075 0.16 -10000 0 -0.34 285 285
BDNF (dimer) 0.023 0.2 0.33 21 -0.35 192 213
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.018 -10000 0 -0.57 1 1
activation of caspase activity -0.048 0.17 -10000 0 -0.32 289 289
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.18 -10000 0 -0.34 282 282
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.13 0.2 0.33 3 -0.41 287 290
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.076 0.16 -10000 0 -0.33 284 284
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.069 0.18 -10000 0 -0.37 287 287
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.14 0.25 -10000 0 -0.45 397 397
MAPK8 -0.094 0.18 0.3 8 -0.36 263 271
MAPK9 -0.092 0.17 0.3 6 -0.36 259 265
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.061 0.21 0.26 12 -0.57 157 169
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NDN 0.005 0.1 -10000 0 -0.57 34 34
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.041 0.16 -10000 0 -0.3 286 286
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.022 -10000 0 -0.33 1 1
RhoA-B-C/GTP -0.067 0.19 -10000 0 -0.36 289 289
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.059 0.19 -10000 0 -0.34 310 310
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.069 0.2 -10000 0 -0.36 312 312
PRKACB 0.032 0.06 0.26 47 -0.57 4 51
proBDNF (dimer)/p75 ECD 0.007 0.12 -10000 0 -0.4 79 79
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.086 0.17 0.28 14 -0.34 278 292
BAD -0.11 0.18 0.37 6 -0.38 270 276
RIPK2 0.02 0.016 0.26 3 -10000 0 3
NGFR -0.14 0.26 -10000 0 -0.57 286 286
CYCS -0.084 0.15 0.36 2 -0.32 275 277
ADAM17 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.044 0.16 -10000 0 -0.34 208 208
BCL2L11 -0.11 0.18 0.37 6 -0.39 267 273
BDNF (dimer)/p75(NTR) -0.11 0.23 -10000 0 -0.43 344 344
PI3K -0.056 0.18 -10000 0 -0.34 277 277
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.053 0.18 -10000 0 -0.34 285 285
NDNL2 0.023 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) -0.094 0.2 -10000 0 -0.41 306 306
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.052 0.18 -10000 0 -0.34 285 285
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
PLG 0.018 0.021 0.26 8 -10000 0 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.1 0.18 -10000 0 -0.37 323 323
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
NGFRAP1 0.023 0.031 -10000 0 -0.57 3 3
CASP3 -0.1 0.17 0.33 7 -0.36 276 283
E2F1 0.092 0.11 0.26 320 -10000 0 320
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.001 0.11 -10000 0 -0.4 18 18
NGF (dimer)/TRKA 0.026 0.066 -10000 0 -0.42 18 18
MMP7 -0.037 0.19 0.26 33 -0.57 121 154
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.042 0.17 -10000 0 -0.32 278 278
MMP3 0.096 0.14 0.26 380 -0.57 14 394
APAF-1/Caspase 9 -0.084 0.11 -10000 0 -0.44 10 10
EPHB forward 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
Ephrin A5/EPHB2 -0.002 0.11 -10000 0 -0.36 95 95
cell-cell adhesion 0.13 0.15 0.31 333 -10000 0 333
Ephrin B/EPHB2/RasGAP 0.031 0.11 -10000 0 -0.31 81 81
ITSN1 0.023 0.026 -10000 0 -0.57 2 2
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.12 0.19 -10000 0 -0.36 410 410
HRAS/GDP -0.11 0.18 -10000 0 -0.42 174 174
Ephrin B/EPHB1/GRB7 -0.1 0.2 -10000 0 -0.35 397 397
Endophilin/SYNJ1 -0.027 0.083 0.22 2 -0.3 79 81
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.21 -10000 0 -0.36 411 411
endothelial cell migration 0.04 0.042 -10000 0 -0.32 11 11
GRB2 0.023 0.009 0.26 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 -0.031 0.099 0.35 2 -0.33 83 85
HRAS 0.026 0.022 0.26 9 -10000 0 9
RRAS -0.027 0.084 0.23 2 -0.3 79 81
DNM1 0.02 0.048 0.26 1 -0.57 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.14 0.18 0.35 2 -0.34 416 418
lamellipodium assembly -0.13 0.15 -10000 0 -0.31 333 333
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.089 0.16 -10000 0 -0.32 311 311
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
EPHB2 0.027 0.031 0.26 19 -10000 0 19
EPHB3 0.025 0.02 0.26 8 -10000 0 8
EPHB1 -0.2 0.29 0.26 1 -0.57 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.11 0.17 -10000 0 -0.42 169 169
Ephrin B/EPHB2 0.021 0.1 -10000 0 -0.31 82 82
Ephrin B/EPHB3 0.02 0.097 -10000 0 -0.31 77 77
JNK cascade -0.12 0.15 0.36 9 -0.31 403 412
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.35 430 430
RAP1/GDP -0.093 0.16 -10000 0 -0.4 131 131
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.023 0.16 -10000 0 -0.57 82 82
EFNB1 0.024 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.098 0.18 -10000 0 -0.32 411 411
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.19 -10000 0 -0.42 152 152
Rap1/GTP -0.11 0.17 -10000 0 -0.48 71 71
axon guidance -0.003 0.11 -10000 0 -0.36 95 95
MAPK3 -0.084 0.14 -10000 0 -0.39 103 103
MAPK1 -0.089 0.14 -10000 0 -0.39 107 107
Rac1/GDP -0.1 0.16 -10000 0 -0.4 159 159
actin cytoskeleton reorganization -0.11 0.12 -10000 0 -0.36 114 114
CDC42/GDP -0.1 0.16 -10000 0 -0.39 166 166
PI3K 0.045 0.044 -10000 0 -0.32 11 11
EFNA5 -0.028 0.17 0.26 1 -0.57 95 96
Ephrin B2/EPHB4 0.03 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.089 -10000 0 -0.27 85 85
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.16 -10000 0 -0.47 71 71
PTK2 0.14 0.26 0.67 205 -10000 0 205
MAP4K4 -0.12 0.15 0.36 9 -0.31 403 412
SRC 0.023 0.005 -10000 0 -10000 0 0
KALRN 0.014 0.078 -10000 0 -0.57 19 19
Intersectin/N-WASP 0.034 0.021 -10000 0 -0.42 2 2
neuron projection morphogenesis -0.1 0.14 0.29 9 -0.42 81 90
MAP2K1 -0.086 0.15 -10000 0 -0.4 114 114
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.088 0.19 -10000 0 -0.33 409 409
cell migration -0.1 0.18 0.31 5 -0.44 128 133
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.084 0.23 2 -0.3 79 81
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.32 568 570
HRAS/GTP -0.099 0.19 -10000 0 -0.32 390 390
Ephrin B1/EPHB1-2 -0.096 0.18 -10000 0 -0.33 410 410
cell adhesion mediated by integrin 0.011 0.086 0.28 77 -0.21 20 97
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.33 414 414
RAC1-CDC42/GTP -0.13 0.15 -10000 0 -0.48 72 72
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.095 0.16 -10000 0 -0.38 156 156
ruffle organization -0.12 0.16 0.36 5 -0.49 71 76
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.086 0.22 2 -0.3 81 83
Ephrin B/EPHB2/KALRN 0.026 0.12 -10000 0 -0.34 92 92
ROCK1 0.017 0.031 0.19 30 -0.33 1 31
RAS family/GDP -0.1 0.12 -10000 0 -0.36 107 107
Rac1/GTP -0.12 0.17 -10000 0 -0.33 333 333
Ephrin B/EPHB1/Src/Paxillin -0.12 0.18 -10000 0 -0.32 416 416
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 0.031 0.26 19 -10000 0 19
EFNB1 0.002 0.036 -10000 0 -0.42 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.077 0.17 -10000 0 -0.3 399 399
Ephrin B2/EPHB1-2 -0.097 0.18 -10000 0 -0.32 411 411
neuron projection morphogenesis -0.083 0.16 -10000 0 -0.28 399 399
Ephrin B1/EPHB1-2/Tiam1 -0.088 0.18 -10000 0 -0.31 406 406
DNM1 0.02 0.048 0.27 1 -0.57 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.021 0.12 -10000 0 -0.56 45 45
YES1 -0.023 0.17 -10000 0 -0.77 50 50
Ephrin B1/EPHB1-2/NCK2 -0.089 0.18 -10000 0 -0.31 407 407
PI3K 0.006 0.13 -10000 0 -0.5 60 60
mol:GDP -0.088 0.18 -10000 0 -0.31 406 406
ITGA2B 0.033 0.06 0.26 54 -0.57 3 57
endothelial cell proliferation 0.029 0.011 -10000 0 -10000 0 0
FYN -0.024 0.16 -10000 0 -0.76 49 49
MAP3K7 -0.023 0.12 0.22 3 -0.57 48 51
FGR -0.02 0.16 -10000 0 -0.76 49 49
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.008 0.13 0.25 1 -0.44 82 83
LYN -0.021 0.16 -10000 0 -0.75 49 49
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.15 -10000 0 -0.71 50 50
Ephrin B1/EPHB1-2 -0.022 0.13 -10000 0 -0.63 45 45
SRC -0.019 0.16 -10000 0 -0.75 50 50
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
EPHB1 -0.2 0.29 0.26 1 -0.57 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.027 0.089 -10000 0 -0.41 36 36
BLK -0.019 0.17 -10000 0 -0.78 47 47
HCK -0.019 0.16 -10000 0 -0.75 50 50
regulation of stress fiber formation 0.089 0.18 0.31 407 -10000 0 407
MAPK8 -0.024 0.12 -10000 0 -0.51 54 54
Ephrin B1/EPHB1-2/RGS3 -0.088 0.18 -10000 0 -0.31 407 407
endothelial cell migration -0.017 0.11 -10000 0 -0.51 42 42
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.68 26 26
regulation of focal adhesion formation 0.089 0.18 0.31 407 -10000 0 407
chemotaxis 0.088 0.18 0.31 407 -10000 0 407
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.08 0.17 -10000 0 -0.29 399 399
angiogenesis -0.023 0.13 -10000 0 -0.62 47 47
LCK -0.02 0.17 -10000 0 -0.77 49 49
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 0.007 0.096 -10000 0 -0.57 29 29
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.18 0.2 -10000 0 -0.35 612 612
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 -0.18 0.17 -10000 0 -0.32 609 609
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.26 61 -10000 0 61
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.023 0.066 0.26 23 -0.57 10 33
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 0.048 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.028 0.034 0.26 23 -10000 0 23
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.054 0.083 0.26 155 -10000 0 155
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.19 0.21 0.34 2 -0.37 608 610
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.15 0.35 3 -0.32 60 63
MAP1B -0.001 0.045 -10000 0 -0.31 21 21
RAC1 0.011 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.15 0.15 -10000 0 -0.3 498 498
RELN -0.32 0.29 0.26 2 -0.57 619 621
PAFAH/LIS1 0.023 0.045 0.32 2 -0.36 9 11
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.13 -10000 0 -0.29 16 16
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.3 510 510
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.14 0.15 0.33 3 -0.34 66 69
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 0.051 0.074 0.26 123 -10000 0 123
PAFAH1B2 0.019 0.044 -10000 0 -0.57 6 6
MAP1B/LIS1/Dynein heavy chain 0.014 0.043 -10000 0 -0.22 18 18
NDEL1/Katanin 60/Dynein heavy chain -0.12 0.15 0.34 3 -0.32 56 59
LRP8 0.046 0.068 0.26 103 -10000 0 103
NDEL1/Katanin 60 -0.13 0.15 0.35 3 -0.33 63 66
P39/CDK5 -0.15 0.16 0.34 6 -0.3 449 455
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.18 0.15 -10000 0 -0.3 601 601
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 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.16 0.19 0.33 1 -0.32 602 603
RELN/VLDLR -0.17 0.2 -10000 0 -0.33 612 612
CDC42 0.01 0.005 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.097 0.21 0.22 1 -0.39 297 298
FZD6 0.014 0.054 -10000 0 -0.57 9 9
WNT6 -0.076 0.24 0.26 47 -0.57 200 247
WNT4 0.017 0.086 0.26 20 -0.57 20 40
FZD3 0.015 0.054 -10000 0 -0.57 9 9
WNT5A 0.017 0.073 0.26 9 -0.57 15 24
WNT11 -0.085 0.23 0.26 10 -0.57 199 209
IL4-mediated signaling events

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
BCL2L1 -0.23 0.61 0.85 4 -1.3 181 185
STAT6 (cleaved dimer) -0.3 0.57 -10000 0 -1.2 239 239
IGHG1 -0.025 0.26 0.49 77 -0.52 11 88
IGHG3 -0.23 0.57 0.67 16 -1.1 229 245
AKT1 -0.082 0.34 0.57 21 -0.77 78 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.044 0.29 0.54 24 -0.79 42 66
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.083 0.36 0.57 29 -0.84 67 96
THY1 -0.23 0.61 0.79 14 -1.2 186 200
MYB 0.011 0.086 0.26 1 -0.57 23 24
HMGA1 0.034 0.048 0.26 48 -10000 0 48
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.41 0.63 59 -0.76 149 208
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.075 0.35 0.57 29 -0.88 49 78
SP1 0.034 0.025 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.014 0.046 -10000 0 -0.54 1 1
STAT6 (dimer)/ETS1 -0.26 0.6 0.7 7 -1.2 214 221
SOCS1 -0.13 0.4 0.62 21 -0.76 159 180
SOCS3 -0.089 0.35 0.61 13 -0.82 69 82
FCER2 -0.37 0.73 0.82 21 -1.4 318 339
PARP14 0.017 0.031 0.24 3 -10000 0 3
CCL17 -0.22 0.62 0.85 41 -1.2 190 231
GRB2 0.023 0.009 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.039 0.29 0.53 32 -0.75 34 66
T cell proliferation -0.25 0.61 0.72 10 -1.2 206 216
IL4R/JAK1 -0.24 0.6 0.7 6 -1.2 200 206
EGR2 -0.34 0.74 0.84 15 -1.5 252 267
JAK2 0.012 0.076 0.26 1 -10000 0 1
JAK3 0.022 0.035 0.27 14 -10000 0 14
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
JAK1 0.017 0.041 -10000 0 -10000 0 0
COL1A2 -0.022 0.27 0.56 11 -1.1 18 29
CCL26 -0.23 0.61 0.81 17 -1.2 191 208
IL4R -0.24 0.66 0.86 32 -1.3 194 226
PTPN6 0.014 0.035 0.21 2 -10000 0 2
IL13RA2 -0.23 0.61 0.79 16 -1.2 190 206
IL13RA1 0.012 0.077 0.23 4 -10000 0 4
IRF4 -0.13 0.49 0.62 7 -1.4 116 123
ARG1 -0.004 0.22 0.57 6 -0.75 3 9
CBL -0.11 0.38 0.59 31 -0.73 140 171
GTF3A 0.055 0.048 0.26 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.025 0.11 0.28 40 -10000 0 40
IRF4/BCL6 -0.11 0.44 0.55 1 -1.3 116 117
CD40LG -0.01 0.13 0.31 12 -0.58 50 62
MAPK14 -0.1 0.38 0.6 31 -0.77 114 145
mitosis -0.075 0.33 0.56 25 -0.72 78 103
STAT6 -0.26 0.76 0.93 51 -1.4 213 264
SPI1 0.027 0.019 0.26 6 -10000 0 6
RPS6KB1 -0.058 0.32 0.55 30 -0.7 68 98
STAT6 (dimer) -0.26 0.76 0.94 50 -1.4 213 263
STAT6 (dimer)/PARP14 -0.29 0.66 0.73 13 -1.3 232 245
mast cell activation 0 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.088 0.35 0.58 27 -0.79 81 108
FRAP1 -0.082 0.34 0.57 21 -0.77 78 99
LTA -0.22 0.62 0.85 39 -1.2 187 226
FES 0.022 0.031 -10000 0 -0.57 3 3
T-helper 1 cell differentiation 0.25 0.72 1.4 215 -0.93 51 266
CCL11 -0.17 0.59 0.76 22 -1.2 171 193
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.069 0.34 0.57 32 -0.78 63 95
IL2RG 0.025 0.071 0.26 46 -0.56 7 53
IL10 -0.2 0.6 0.83 17 -1.2 172 189
IRS1 0.001 0.11 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
IL4 -0.008 0.26 0.65 13 -1.1 20 33
IL5 -0.23 0.61 0.84 7 -1.3 182 189
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.52 0.79 53 -0.93 185 238
COL1A1 0.003 0.36 0.69 32 -1 46 78
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.61 -10000 0 -1.3 177 177
IL2R gamma/JAK3 0.037 0.068 0.29 33 -0.38 7 40
TFF3 -0.28 0.7 0.85 26 -1.4 241 267
ALOX15 -0.3 0.69 0.85 13 -1.4 244 257
MYBL1 0.038 0.063 0.26 81 -10000 0 81
T-helper 2 cell differentiation -0.19 0.52 0.71 27 -0.99 208 235
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.079 0.34 0.55 33 -0.77 74 107
mol:PI-3-4-5-P3 -0.081 0.34 0.57 22 -0.77 78 100
PI3K -0.09 0.36 0.59 19 -0.83 78 97
DOK2 0.02 0.03 0.26 4 -0.57 2 6
ETS1 0.003 0.054 -10000 0 -0.53 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.029 0.27 0.51 35 -0.71 26 61
ITGB3 -0.25 0.63 0.85 4 -1.3 192 196
PIGR -0.66 0.8 0.84 13 -1.3 561 574
IGHE -0.015 0.086 0.18 26 -0.22 31 57
MAPKKK cascade -0.028 0.27 0.5 38 -0.69 26 64
BCL6 0.022 0.046 -10000 0 -0.56 6 6
OPRM1 -0.23 0.61 0.88 7 -1.3 184 191
RETNLB -0.23 0.6 0.81 7 -1.3 182 189
SELP -0.35 0.77 0.83 15 -1.5 283 298
AICDA -0.22 0.58 0.77 11 -1.2 177 188
Noncanonical Wnt signaling pathway

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
NFATC2 -0.026 0.16 -10000 0 -0.57 88 88
GNB1/GNG2 -0.076 0.21 -10000 0 -0.48 159 159
mol:DAG -0.077 0.18 0.24 1 -0.44 149 150
PLCG1 -0.08 0.19 0.24 1 -0.46 149 150
YES1 -0.095 0.19 -10000 0 -0.49 147 147
FZD3 0.015 0.054 -10000 0 -0.57 9 9
FZD6 0.014 0.054 -10000 0 -0.57 9 9
G protein -0.063 0.2 0.3 2 -0.46 145 147
MAP3K7 -0.071 0.15 0.23 2 -0.41 117 119
mol:Ca2+ -0.074 0.18 0.23 1 -0.43 149 150
mol:IP3 -0.077 0.18 0.24 1 -0.44 149 150
NLK -0.009 0.13 -10000 0 -0.84 24 24
GNB1 0.023 0.005 -10000 0 -10000 0 0
CAMK2A -0.072 0.17 0.24 3 -0.42 132 135
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.097 0.21 0.22 1 -0.39 297 298
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
GNAS -0.09 0.19 0.2 1 -0.38 264 265
GO:0007205 -0.081 0.18 0.22 2 -0.44 149 151
WNT6 -0.076 0.24 0.26 47 -0.57 200 247
WNT4 0.017 0.086 0.26 20 -0.57 20 40
NFAT1/CK1 alpha -0.09 0.2 0.32 2 -0.48 153 155
GNG2 0.017 0.065 -10000 0 -0.57 13 13
WNT5A 0.017 0.073 0.26 9 -0.57 15 24
WNT11 -0.085 0.23 0.26 10 -0.57 199 209
CDC42 -0.083 0.19 -10000 0 -0.47 139 139
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.067 0.15 -10000 0 -0.33 242 242
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.026 0.022 0.26 9 -10000 0 9
IRS1/Crk -0.061 0.16 -10000 0 -0.34 246 246
IGF-1R heterotetramer/IGF1/PTP1B -0.044 0.17 -10000 0 -0.36 213 213
AKT1 -0.067 0.14 0.25 2 -0.32 198 200
BAD -0.065 0.13 0.24 2 -0.45 48 50
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.16 -10000 0 -0.34 244 244
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.16 0.2 2 -0.34 246 248
RAF1 -0.047 0.13 0.28 2 -0.47 48 50
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.032 0.16 -10000 0 -0.33 214 214
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.062 0.17 -10000 0 -0.36 246 246
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.32 165 167
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.029 0.12 0.3 10 -0.4 43 53
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.13 -10000 0 -0.31 161 161
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.3 160 160
IGF-1R heterotetramer -0.011 0.098 0.22 3 -0.62 20 23
IGF-1R heterotetramer/IGF1/IRS/Nck -0.046 0.17 -10000 0 -0.34 243 243
Crk/p130 Cas/Paxillin -0.037 0.16 -10000 0 -0.32 230 230
IGF1R -0.011 0.098 0.22 3 -0.62 20 23
IGF1 -0.11 0.25 -10000 0 -0.59 233 233
IRS2/Crk -0.067 0.17 -10000 0 -0.35 245 245
PI3K -0.036 0.17 -10000 0 -0.33 236 236
apoptosis 0.044 0.11 0.37 40 -0.27 5 45
HRAS/GDP 0.019 0.015 0.18 9 -10000 0 9
PRKCD -0.078 0.17 -10000 0 -0.39 227 227
RAF1/14-3-3 E -0.024 0.13 0.3 1 -0.41 47 48
BAD/14-3-3 -0.046 0.11 0.28 5 -0.4 40 45
PRKCZ -0.067 0.14 0.25 2 -0.32 201 203
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.11 -10000 0 -0.41 39 39
PTPN1 0.024 0.018 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.18 -10000 0 -0.41 236 236
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.14 -10000 0 -0.32 176 176
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.054 0.16 -10000 0 -0.33 243 243
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.34 246 246
IRS1 -0.071 0.17 -10000 0 -0.36 246 246
IRS2 -0.076 0.17 -10000 0 -0.36 256 256
IGF-1R heterotetramer/IGF1 -0.078 0.21 -10000 0 -0.46 239 239
GRB2 0.023 0.009 0.26 1 -10000 0 1
PDPK1 -0.069 0.14 0.28 1 -0.33 206 207
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.19 -10000 0 -0.42 235 235
SHC1 0.02 0.009 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.027 0.029 -10000 0 -0.39 3 3
ARNO/beta Arrestin1-2 -0.063 0.16 -10000 0 -0.56 43 43
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EPHA2 0.02 0.04 -10000 0 -0.57 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 0.25 -10000 0 -0.45 526 526
ARRB2 -0.042 0.13 -10000 0 -0.36 146 146
mol:GTP 0.012 0.049 0.16 22 -0.21 18 40
ARRB1 0.021 0.026 -10000 0 -0.57 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR 0.001 0.12 0.26 4 -0.57 42 46
EGF -0.083 0.23 0.26 2 -0.57 194 196
somatostatin receptor activity 0 0 0.001 1 -0.001 278 279
ARAP2 0.021 0.04 -10000 0 -0.57 5 5
mol:GDP -0.12 0.16 -10000 0 -0.32 315 315
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 145 145
ITGA2B 0.033 0.06 0.26 54 -0.57 3 57
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
ADAP1 0.025 0.029 0.26 10 -0.57 1 11
KIF13B 0.019 0.027 -10000 0 -0.57 2 2
HGF/MET -0.066 0.2 -10000 0 -0.44 226 226
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 0.19 1 -0.28 310 311
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.17 0.23 -10000 0 -0.4 515 515
ADRB2 -0.1 0.24 -10000 0 -0.57 229 229
receptor agonist activity 0 0 0 1 0 282 283
actin filament binding 0 0 0 2 -0.001 279 281
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 172 173
ARF6/GDP -0.037 0.15 0.25 2 -0.44 87 89
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.4 221 221
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.079 -10000 0 -0.32 36 36
ACAP1 0.029 0.066 0.26 47 -0.57 6 53
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.055 0.17 -10000 0 -0.48 146 146
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 0.14 0.26 2 -0.57 65 67
CYTH3 0.004 0.018 -10000 0 -0.42 2 2
CYTH2 0.006 0.099 -10000 0 -1 10 10
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 238 239
endosomal lumen acidification 0 0 0.001 7 0 268 275
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.014 0.14 -10000 0 -0.57 69 69
GNAQ/ARNO 0.018 0.095 -10000 0 -0.95 10 10
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 234 234
MET -0.073 0.22 -10000 0 -0.57 177 177
GNA14 0.022 0.065 0.26 19 -0.57 10 29
GNA15 0.024 0.025 0.26 6 -0.57 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 234 235
GNA11 0.021 0.036 -10000 0 -0.57 4 4
LHCGR -0.069 0.2 -10000 0 -0.57 146 146
AGTR1 -0.098 0.26 0.26 59 -0.57 244 303
desensitization of G-protein coupled receptor protein signaling pathway -0.055 0.17 -10000 0 -0.48 146 146
IPCEF1/ARNO -0.13 0.19 -10000 0 -0.59 68 68
alphaIIb/beta3 Integrin 0.027 0.089 -10000 0 -0.41 36 36
Nongenotropic Androgen signaling

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
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.01 0.13 -10000 0 -0.33 152 152
regulation of S phase of mitotic cell cycle -0.024 0.11 -10000 0 -0.29 137 137
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.025 0.022 0.25 9 -10000 0 9
SHBG/T-DHT 0.015 0.005 -10000 0 -10000 0 0
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.069 0.11 -10000 0 -0.32 127 127
T-DHT/AR -0.042 0.15 0.17 1 -0.42 142 143
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 322 322
GNAI2 0.023 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
mol:GDP -0.063 0.16 -10000 0 -0.46 148 148
cell proliferation -0.14 0.21 0.27 3 -0.44 305 308
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.25 0.38 -10000 0 -0.81 326 326
mol:Ca2+ -0.013 0.028 -10000 0 -0.073 147 147
MAPK3 -0.1 0.16 0.26 4 -0.34 250 254
MAPK1 -0.08 0.14 -10000 0 -0.39 109 109
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 -0.001 0.002 -10000 0 -0.004 319 319
cAMP biosynthetic process 0.004 0.021 -10000 0 -10000 0 0
GNG2 0.017 0.065 -10000 0 -0.57 13 13
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 319 319
HRAS/GTP -0.028 0.12 -10000 0 -0.32 139 139
actin cytoskeleton reorganization 0.029 0.037 -10000 0 -0.3 12 12
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 319 319
PI3K 0.026 0.042 -10000 0 -0.33 14 14
apoptosis 0.13 0.21 0.43 330 -10000 0 330
T-DHT/AR/PELP1 -0.025 0.13 -10000 0 -0.36 141 141
HRAS/GDP -0.052 0.16 -10000 0 -0.45 144 144
CREB1 -0.14 0.23 -10000 0 -0.46 330 330
RAC1-CDC42/GTP 0.037 0.04 -10000 0 -0.3 12 12
AR -0.054 0.2 0.25 1 -0.57 141 142
GNB1 0.023 0.005 -10000 0 -10000 0 0
RAF1 -0.061 0.11 -10000 0 -0.32 134 134
RAC1-CDC42/GDP -0.028 0.16 -10000 0 -0.44 141 141
T-DHT/AR/PELP1/Src -0.022 0.13 -10000 0 -0.34 140 140
MAP2K2 -0.07 0.11 -10000 0 -0.32 127 127
T-DHT/AR/PELP1/Src/PI3K -0.025 0.11 -10000 0 -0.29 137 137
GNAZ 0.017 0.057 -10000 0 -0.57 10 10
SHBG 0.022 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.052 0.16 -10000 0 -0.48 95 95
mol:T-DHT -0.001 0.001 0.002 1 -0.004 98 99
RAC1 0.024 0.003 -10000 0 -10000 0 0
GNRH1 0.001 0.029 -10000 0 -0.42 5 5
Gi family/GTP -0.036 0.1 -10000 0 -0.28 102 102
CDC42 0.023 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.008 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.14 0.31 2 -0.3 60 62
NFATC4 -0.063 0.12 0.27 9 -0.25 197 206
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.068 0.15 -10000 0 -0.3 252 252
JUN -0.009 0.096 0.23 26 -0.45 3 29
HRAS 0.026 0.022 0.26 9 -10000 0 9
DOCK7 -0.079 0.14 0.28 2 -0.3 251 253
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.052 0.15 -10000 0 -0.33 206 206
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.006 -10000 0 -10000 0 0
MAPK10 -0.07 0.11 0.2 10 -0.27 139 149
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.073 0.16 -10000 0 -0.33 252 252
RAF1 -0.019 0.14 0.32 13 -0.3 50 63
ErbB2/ErbB3/neuregulin 2 -0.14 0.18 -10000 0 -0.34 437 437
STAT3 -0.001 0.16 -10000 0 -0.86 34 34
cell migration -0.055 0.1 0.23 16 -0.25 92 108
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.044 0.24 0.42 12 -0.49 121 133
FOS -0.1 0.28 0.37 12 -0.49 328 340
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.068 0.15 -10000 0 -0.3 252 252
MAPK3 -0.015 0.2 0.39 13 -0.43 62 75
MAPK1 -0.027 0.21 0.4 13 -0.56 48 61
JAK2 -0.077 0.14 0.26 1 -0.3 247 248
NF2 -0.002 0.057 -10000 0 -0.68 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.053 0.13 0.23 3 -0.29 210 213
NRG1 -0.14 0.26 0.25 4 -0.57 292 296
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.08 0.15 0.25 2 -0.3 256 258
MAPK9 -0.042 0.083 0.2 11 -0.26 3 14
ERBB2 0.001 0.071 0.24 85 -0.44 1 86
ERBB3 0.021 0.041 -10000 0 -0.57 5 5
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
apoptosis 0.019 0.025 -10000 0 -0.17 4 4
STAT3 (dimer) 0 0.15 -10000 0 -0.84 34 34
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.004 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.07 0.093 -10000 0 -0.22 246 246
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.02 -10000 0 -0.38 1 1
CHRNA1 0.017 0.18 0.35 58 -0.38 25 83
myelination -0.058 0.12 0.3 17 -0.25 84 101
PPP3CB -0.074 0.13 0.27 2 -0.28 248 250
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.26 195 195
NRG2 -0.26 0.29 -10000 0 -0.57 509 509
mol:GDP -0.053 0.13 0.23 3 -0.29 210 213
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.017 0.14 0.32 16 -0.31 48 64
SRC 0.023 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.079 0.14 0.28 2 -0.3 252 254
MAP2K1 -0.053 0.22 0.44 3 -0.52 80 83
heart morphogenesis -0.068 0.15 -10000 0 -0.3 252 252
RAS family/GDP -0.021 0.14 0.33 2 -0.3 54 56
GRB2 0.023 0.009 0.25 1 -10000 0 1
PRKACA -0.002 0.067 -10000 0 -0.68 10 10
CHRNE 0.004 0.027 0.12 4 -0.21 3 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.068 0.15 -10000 0 -0.3 252 252
CDC42 0.023 0.005 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.002 0.082 -10000 0 -0.55 14 14
Crk/p130 Cas/Paxillin -0.056 0.12 -10000 0 -0.33 146 146
JUN -0.015 0.12 0.23 2 -0.4 29 31
HRAS 0.026 0.022 0.26 9 -10000 0 9
RET51/GFRalpha1/GDNF/GRB10 0.041 0.19 0.34 53 -0.34 177 230
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.042 0.19 0.34 52 -0.34 176 228
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.011 0.15 0.32 5 -0.33 180 185
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.02 0.16 0.28 37 -0.3 179 216
GRB7 0.019 0.032 -10000 0 -0.57 3 3
RET51/GFRalpha1/GDNF 0.04 0.19 0.34 52 -0.34 176 228
MAPKKK cascade 0 0.15 0.28 11 -0.32 131 142
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.024 0.18 0.32 4 -0.36 209 213
lamellipodium assembly -0.033 0.13 -10000 0 -0.3 157 157
RET51/GFRalpha1/GDNF/SHC 0.036 0.18 0.34 43 -0.34 139 182
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.14 0.32 5 -0.28 188 193
RET9/GFRalpha1/GDNF/Shank3 -0.013 0.15 0.32 5 -0.32 189 194
MAPK3 -0.031 0.13 0.28 3 -0.3 141 144
DOK1 0.025 0.014 0.26 4 -10000 0 4
DOK6 0.017 0.07 0.26 7 -0.57 14 21
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.031 0.12 -10000 0 -0.3 126 126
DOK5 0.011 0.087 0.26 5 -0.57 23 28
GFRA1 -0.07 0.24 0.26 53 -0.57 192 245
MAPK8 -0.01 0.13 0.21 4 -0.28 143 147
HRAS/GTP 0.028 0.18 0.29 53 -0.34 169 222
tube development -0.006 0.14 0.34 11 -0.31 171 182
MAPK1 -0.031 0.13 0.28 4 -0.3 141 145
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.11 0.25 1 -0.26 171 172
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.037 0.19 0.33 49 -0.33 182 231
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.027 0.18 0.34 38 -0.34 179 217
RET51/GFRalpha1/GDNF/Dok5 0.024 0.2 0.34 48 -0.35 187 235
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
HRAS/GDP 0.019 0.015 0.18 9 -10000 0 9
CREB1 -0.014 0.13 0.22 11 -0.3 125 136
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.02 0.1 0.25 1 -0.26 127 128
RET51/GFRalpha1/GDNF/Grb7 0.041 0.18 0.33 66 -0.34 145 211
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.097 0.13 0.26 374 -0.57 13 387
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.014 0.12 0.24 1 -0.4 27 28
RET9/GFRalpha1/GDNF/FRS2 -0.012 0.15 0.32 5 -0.33 181 186
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.02 0.1 0.25 1 -0.26 127 128
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.005 0.14 0.24 16 -0.28 140 156
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.002 0.14 0.25 4 -0.29 142 146
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.01 0.13 0.25 15 -0.3 105 120
PI3K -0.029 0.2 0.28 13 -0.44 172 185
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.14 0.31 4 -0.31 171 175
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.005 0.12 0.24 8 -0.26 134 142
RET51/GFRalpha1/GDNF/FRS2 0.038 0.19 0.34 56 -0.34 178 234
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.13 0.25 15 -0.3 105 120
RET51/GFRalpha1/GDNF/PKC alpha 0.024 0.19 0.35 42 -0.34 185 227
GRB2 0.023 0.009 0.26 1 -10000 0 1
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.052 0.26 54 -10000 0 54
RAC1 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.027 0.22 0.34 50 -0.38 191 241
Rac1/GTP -0.022 0.16 0.23 4 -0.37 144 148
RET9/GFRalpha1/GDNF -0.026 0.16 0.18 91 -0.34 197 288
GFRalpha1/GDNF -0.033 0.18 0.2 91 -0.4 197 288
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.058 0.16 0.33 4 -0.35 114 118
SMAD6-7/SMURF1 0.046 0.015 -10000 0 -10000 0 0
NOG 0.012 0.095 0.26 19 -0.57 25 44
SMAD9 -0.088 0.25 -10000 0 -0.6 185 185
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.021 0.14 -10000 0 -0.42 73 73
BMP7/USAG1 -0.19 0.25 -10000 0 -0.42 532 532
SMAD5/SKI -0.015 0.15 0.26 3 -0.42 79 82
SMAD1 0.013 0.062 -10000 0 -0.41 8 8
BMP2 -0.074 0.22 0.26 2 -0.57 179 181
SMAD1/SMAD1/SMAD4 0.018 0.069 -10000 0 -0.39 10 10
BMPR1A 0.023 0.026 -10000 0 -0.57 2 2
BMPR1B 0.1 0.15 0.26 425 -0.57 23 448
BMPR1A-1B/BAMBI 0.083 0.12 0.34 9 -0.33 53 62
AHSG 0.021 0.029 0.26 16 -10000 0 16
CER1 0.018 0.013 0.26 3 -10000 0 3
BMP2-4/CER1 -0.046 0.18 -10000 0 -0.39 214 214
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.038 0.16 -10000 0 -0.42 98 98
BMP2-4 (homodimer) -0.066 0.2 -10000 0 -0.44 229 229
RGMB 0.023 0.019 -10000 0 -0.57 1 1
BMP6/BMPR2/BMPR1A-1B 0.07 0.14 -10000 0 -0.31 96 96
RGMA -0.053 0.2 -10000 0 -0.57 139 139
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.036 0.16 -10000 0 -0.42 120 120
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.44 577 577
SMAD6/SMURF1/SMAD5 -0.016 0.15 0.26 2 -0.42 79 81
SOSTDC1 -0.25 0.3 0.26 3 -0.57 507 510
BMP7/BMPR2/BMPR1A-1B 0.068 0.14 0.3 4 -0.32 90 94
SKI 0.023 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.016 0.15 0.26 2 -0.56 72 74
HFE2 0.018 0.023 0.26 9 -10000 0 9
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.043 0.2 -10000 0 -0.4 220 220
SMAD5/SMAD5/SMAD4 -0.016 0.15 0.26 2 -0.42 82 84
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.022 0.15 -10000 0 -0.38 110 110
BMP7 (homodimer) -0.011 0.16 0.26 30 -0.56 73 103
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.001 0.12 -10000 0 -0.42 71 71
SMAD1/SKI 0.02 0.076 -10000 0 -0.43 11 11
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.045 0.18 0.34 1 -0.39 216 217
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.036 0.095 0.26 94 -0.57 14 108
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.085 0.11 -10000 0 -0.41 25 25
CHRDL1 -0.38 0.28 -10000 0 -0.57 729 729
ENDOFIN/SMAD1 0.019 0.078 -10000 0 -0.45 11 11
SMAD6-7/SMURF1/SMAD1 0.036 0.081 -10000 0 -0.42 11 11
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.016 0.11 0.26 39 -0.57 30 69
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.26 -10000 0 -0.45 729 729
BMP2-4/GREM1 -0.037 0.2 -10000 0 -0.4 224 224
SMAD7 0.023 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.08 0.25 -10000 0 -0.57 193 193
SMAD1/SMAD6 0.019 0.078 -10000 0 -0.45 11 11
TAK1/SMAD6 0.033 0.01 -10000 0 -10000 0 0
BMP7 -0.011 0.16 0.26 30 -0.57 73 103
BMP6 -0.016 0.15 0.26 2 -0.57 72 74
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.034 0.17 -10000 0 -0.42 123 123
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.075 -10000 0 -0.45 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 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.047 0.2 0.23 1 -0.48 133 134
CHRD 0.026 0.095 0.26 58 -0.57 19 77
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.05 0.18 -10000 0 -0.48 122 122
BMP4 -0.01 0.14 0.26 1 -0.57 62 63
FST -0.001 0.12 0.26 3 -0.57 45 48
BMP2-4/NOG -0.047 0.19 0.34 1 -0.4 210 211
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.072 0.14 0.33 1 -0.3 89 90
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0 0.15 -10000 0 -0.32 176 176
ER alpha/Gai/GDP/Gbeta gamma -0.085 0.22 -10000 0 -0.47 211 211
AKT1 -0.12 0.33 -10000 0 -0.77 206 206
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.33 -10000 0 -0.78 204 204
mol:Ca2+ -0.026 0.1 0.26 2 -0.45 29 31
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
E2/ER alpha (dimer)/Striatin -0.016 0.16 -10000 0 -0.36 165 165
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.11 0.31 0.73 206 -10000 0 206
RhoA/GTP -0.015 0.1 -10000 0 -0.28 123 123
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.067 0.21 0.31 4 -0.46 199 203
regulation of stress fiber formation 0.023 0.1 0.43 3 -0.31 8 11
E2/ERA-ERB (dimer) -0.019 0.16 -10000 0 -0.36 170 170
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.009 0.13 -10000 0 -0.31 151 151
pseudopodium formation -0.023 0.1 0.31 8 -0.43 3 11
E2/ER alpha (dimer)/PELP1 -0.014 0.15 -10000 0 -0.36 151 151
GRB2 0.023 0.009 0.26 1 -10000 0 1
GNG2 0.017 0.065 -10000 0 -0.57 13 13
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.026 0.022 0.26 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.088 0.23 -10000 0 -0.51 213 213
E2/ER beta (dimer) 0.008 0.063 -10000 0 -0.4 24 24
mol:GDP -0.039 0.16 0.26 11 -0.39 169 180
mol:NADP -0.088 0.23 -10000 0 -0.51 213 213
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 -0.027 0.11 0.27 2 -0.47 28 30
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
PLCB1 -0.025 0.11 0.28 2 -0.45 33 35
PLCB2 -0.005 0.082 -10000 0 -0.49 17 17
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
mol:L-citrulline -0.088 0.23 -10000 0 -0.51 213 213
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.079 0.25 -10000 0 -0.64 158 158
JNK cascade 0.008 0.063 -10000 0 -0.4 24 24
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.011 0.085 -10000 0 -0.57 23 23
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
ESR1 -0.035 0.23 0.26 115 -0.57 151 266
Gq family/GDP/Gbeta gamma -0.01 0.16 -10000 0 -0.74 39 39
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.017 0.13 -10000 0 -0.56 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.059 0.2 0.31 5 -0.46 164 169
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
E2/ER alpha (dimer) -0.028 0.16 0.18 115 -0.41 157 272
STRN 0.013 0.08 -10000 0 -0.57 20 20
GNAL -0.11 0.24 -10000 0 -0.57 235 235
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.057 -10000 0 -0.36 26 26
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
HBEGF -0.056 0.21 0.34 20 -0.5 116 136
cAMP biosynthetic process -0.086 0.18 -10000 0 -0.32 348 348
SRC -0.079 0.21 0.29 7 -0.44 208 215
PI3K 0.028 0.049 -10000 0 -0.38 14 14
GNB1 0.023 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.16 -10000 0 -0.38 142 142
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.44 216 216
Gs family/GTP -0.083 0.18 -10000 0 -0.33 348 348
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.019 -10000 0 -10000 0 0
vasodilation -0.083 0.22 -10000 0 -0.49 213 213
mol:DAG -0.027 0.11 0.27 2 -0.47 28 30
Gs family/GDP/Gbeta gamma -0.09 0.18 -10000 0 -0.36 272 272
MSN -0.026 0.11 0.32 8 -0.46 3 11
Gq family/GTP -0.001 0.087 -10000 0 -0.51 16 16
mol:PI-3-4-5-P3 -0.11 0.32 -10000 0 -0.75 204 204
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.083 0.22 0.49 213 -10000 0 213
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.16 0.26 10 -0.38 166 176
NOS3 -0.094 0.25 -10000 0 -0.54 211 211
GNA11 0.022 0.036 -10000 0 -0.57 4 4
MAPKKK cascade -0.084 0.25 0.31 2 -0.56 207 209
E2/ER alpha (dimer)/PELP1/Src -0.071 0.22 0.34 5 -0.48 202 207
ruffle organization -0.023 0.1 0.31 8 -0.43 3 11
ROCK2 -0.025 0.12 0.34 8 -0.28 130 138
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.048 0.2 0.36 23 -0.49 110 133
MMP2 -0.07 0.2 0.28 9 -0.43 188 197
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.041 0.17 -10000 0 -0.41 177 177
CRKL -0.047 0.15 0.31 2 -0.4 92 94
mol:PIP3 0.002 0.059 0.56 1 -0.89 4 5
AKT1 0.01 0.074 0.37 3 -0.79 4 7
PTK2B 0.02 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.14 0.3 3 -0.38 88 91
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.042 0.18 -10000 0 -0.38 214 214
MAP3K5 -0.04 0.15 0.36 1 -0.43 70 71
HGF/MET/CIN85/CBL/ENDOPHILINS -0.03 0.17 -10000 0 -0.35 222 222
AP1 -0.11 0.19 -10000 0 -0.39 308 308
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.24 0.38 -10000 0 -0.77 356 356
STAT3 (dimer) -0.047 0.15 -10000 0 -0.34 178 178
GAB1/CRKL/SHP2/PI3K -0.02 0.15 -10000 0 -0.4 78 78
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.036 0.14 0.34 1 -0.42 64 65
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
ELK1 -0.03 0.096 0.29 28 -0.21 119 147
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.092 -10000 0 -0.26 75 75
PAK1 0.024 0.087 0.38 6 -0.75 4 10
HGF/MET/RANBP10 -0.045 0.18 -10000 0 -0.38 223 223
HRAS -0.11 0.26 -10000 0 -0.64 193 193
DOCK1 -0.046 0.14 0.52 1 -0.39 86 87
GAB1 -0.05 0.15 -10000 0 -0.42 96 96
CRK -0.049 0.15 0.36 1 -0.42 74 75
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.25 -10000 0 -0.57 232 232
JUN 0.02 0.044 -10000 0 -0.57 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.052 0.12 -10000 0 -0.28 226 226
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
cell morphogenesis -0.049 0.16 0.37 6 -0.45 89 95
GRB2/SHC -0.016 0.11 -10000 0 -0.28 123 123
FOS -0.14 0.27 -10000 0 -0.57 306 306
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.03 0.095 0.28 28 -0.21 120 148
HGF/MET/MUC20 -0.055 0.17 -10000 0 -0.38 225 225
cell migration -0.016 0.11 -10000 0 -0.28 123 123
GRB2 0.023 0.009 0.26 1 -10000 0 1
CBL 0.022 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.042 0.17 -10000 0 -0.41 177 177
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.047 0.14 -10000 0 -0.32 187 187
MET/MUC20 -0.055 0.16 -10000 0 -0.4 186 186
RAP1B -0.039 0.14 0.3 6 -0.39 69 75
RAP1A -0.045 0.13 0.32 3 -0.38 71 74
HGF/MET/RANBP9 -0.043 0.18 -10000 0 -0.38 218 218
RAF1 -0.099 0.24 -10000 0 -0.6 192 192
STAT3 -0.048 0.15 -10000 0 -0.34 178 178
cell proliferation -0.042 0.19 0.28 35 -0.42 159 194
RPS6KB1 -0.015 0.063 -10000 0 -0.26 24 24
MAPK3 -0.042 0.093 0.62 8 -10000 0 8
MAPK1 -0.011 0.17 0.68 53 -10000 0 53
RANBP9 0.023 0.005 -10000 0 -10000 0 0
MAPK8 -0.029 0.14 0.43 1 -0.43 59 60
SRC -0.052 0.13 0.2 1 -0.31 175 176
PI3K -0.028 0.13 -10000 0 -0.29 180 180
MET/Glomulin -0.047 0.14 -10000 0 -0.37 178 178
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.091 0.23 0.47 1 -0.55 192 193
MET -0.073 0.22 -10000 0 -0.57 177 177
MAP4K1 -0.042 0.15 0.38 1 -0.42 88 89
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.09 0.23 0.47 1 -0.55 192 193
BAD 0.008 0.071 0.36 3 -0.75 4 7
MAP2K4 -0.037 0.13 0.34 1 -0.4 60 61
SHP2/GRB2/SOS1/GAB1 -0.041 0.17 -10000 0 -0.4 174 174
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.048 0.11 -10000 0 -0.27 206 206
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 0.26 2 -0.57 65 67
RASA1 0.024 0.004 -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 -0.022 0.13 -10000 0 -0.26 211 211
PDPK1 0.012 0.077 0.42 1 -0.83 4 5
HGF/MET/SHIP -0.043 0.18 -10000 0 -0.38 224 224
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.02 0.48 0.81 41 -1.1 72 113
IL23A -0.031 0.48 0.89 24 -1.1 65 89
NF kappa B1 p50/RelA/I kappa B alpha -0.059 0.44 0.78 7 -1 80 87
positive regulation of T cell mediated cytotoxicity -0.023 0.54 0.88 60 -1.1 94 154
ITGA3 -0.016 0.47 0.79 42 -1 76 118
IL17F -0.007 0.36 0.6 67 -0.69 74 141
IL12B 0.084 0.15 0.35 215 -10000 0 215
STAT1 (dimer) -0.037 0.5 0.76 43 -1 103 146
CD4 -0.015 0.48 0.82 43 -1 74 117
IL23 -0.016 0.48 0.83 45 -1.1 64 109
IL23R 0.047 0.2 0.6 16 -0.94 16 32
IL1B -0.033 0.5 0.86 30 -1.2 70 100
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.018 0.48 0.84 58 -1 69 127
TYK2 0.026 0.058 0.21 6 -10000 0 6
STAT4 0.001 0.12 0.26 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.008 0.11 0.27 5 -0.56 35 40
IL12RB1 0.034 0.091 0.37 42 -0.58 2 44
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.087 0.31 44 -0.43 2 46
IL23R/JAK2 0.06 0.22 0.56 24 -0.86 15 39
positive regulation of chronic inflammatory response -0.023 0.54 0.88 60 -1.1 94 154
natural killer cell activation -0.004 0.015 -10000 0 -0.051 35 35
JAK2 0.038 0.081 0.26 28 -10000 0 28
PIK3R1 0.017 0.064 -10000 0 -0.56 13 13
NFKB1 0.026 0.009 -10000 0 -10000 0 0
RELA 0.026 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.01 0.47 0.81 48 -1 64 112
ALOX12B -0.017 0.47 0.83 40 -1 70 110
CXCL1 -0.18 0.69 0.85 41 -1.2 276 317
T cell proliferation -0.023 0.54 0.88 60 -1.1 94 154
NFKBIA 0.026 0.009 -10000 0 -10000 0 0
IL17A 0.02 0.31 0.56 86 -0.55 59 145
PI3K -0.055 0.46 0.7 17 -1.1 81 98
IFNG 0.025 0.067 0.17 133 -0.11 15 148
STAT3 (dimer) -0.056 0.44 0.77 8 -1 78 86
IL18R1 0.016 0.078 -10000 0 -0.56 19 19
IL23/IL23R/JAK2/TYK2/SOCS3 0.036 0.34 0.65 79 -0.68 38 117
IL18/IL18R 0.041 0.1 0.28 11 -0.36 52 63
macrophage activation 0 0.029 0.056 102 -0.044 52 154
TNF -0.03 0.49 0.86 32 -1.1 71 103
STAT3/STAT4 -0.054 0.48 0.68 23 -1 102 125
STAT4 (dimer) -0.049 0.51 0.75 36 -1.1 108 144
IL18 0.03 0.038 0.26 26 -10000 0 26
IL19 0.022 0.48 0.84 54 -1 66 120
STAT5A (dimer) -0.04 0.49 0.74 37 -1 112 149
STAT1 0.028 0.031 0.26 19 -10000 0 19
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
CXCL9 0.008 0.5 0.86 63 -1.1 73 136
MPO -0.045 0.54 0.82 39 -1.2 109 148
positive regulation of humoral immune response -0.023 0.54 0.88 60 -1.1 94 154
IL23/IL23R/JAK2/TYK2 -0.03 0.55 0.88 58 -1.2 81 139
IL6 -0.3 0.74 0.79 36 -1.2 395 431
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
IL2 0.021 0.037 0.3 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.015 -10000 0 -0.051 35 35
CD3E -0.027 0.5 0.84 48 -1.1 80 128
keratinocyte proliferation -0.023 0.54 0.88 60 -1.1 94 154
NOS2 -0.016 0.48 0.81 41 -1.1 71 112
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.41 240 241
PTP1B/AKT1 -0.067 0.13 0.22 1 -0.34 133 134
FYN 0.022 0.026 -10000 0 -0.57 2 2
p210 bcr-abl/PTP1B -0.082 0.14 0.22 2 -0.35 161 163
EGFR -0.2 0.28 -10000 0 -0.58 390 390
EGF/EGFR -0.2 0.24 -10000 0 -0.41 530 530
CSF1 0.021 0.044 -10000 0 -0.57 6 6
AKT1 0.023 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.048 0.16 0.23 17 -0.36 139 156
Insulin Receptor/Insulin -0.043 0.12 -10000 0 -0.38 51 51
HCK 0.027 0.026 0.26 13 -10000 0 13
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.078 0.14 0.28 3 -0.35 145 148
EGF -0.099 0.22 0.25 2 -0.58 194 196
YES1 0.023 0.019 -10000 0 -0.57 1 1
CAV1 -0.16 0.21 0.27 2 -0.42 332 334
TXN 0.017 0.017 0.25 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.072 0.15 -10000 0 -0.36 162 162
cell migration 0.082 0.14 0.35 161 -0.22 2 163
STAT3 0.022 0.004 -10000 0 -10000 0 0
PRLR 0.022 0.052 0.25 7 -0.57 7 14
ITGA2B 0.031 0.06 0.25 54 -0.57 3 57
CSF1R 0.024 0.008 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.031 0.043 0.31 1 -0.42 6 7
FGR 0.024 0.009 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.069 0.14 0.22 1 -0.35 147 148
Crk/p130 Cas -0.062 0.14 -10000 0 -0.35 132 132
DOK1 -0.067 0.13 0.23 2 -0.39 83 85
JAK2 -0.047 0.12 -10000 0 -0.45 55 55
Jak2/Leptin Receptor/Leptin -0.26 0.16 -10000 0 -0.39 453 453
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
PTPN1 -0.083 0.14 0.22 2 -0.36 161 163
LYN 0.021 0.008 -10000 0 -10000 0 0
CDH2 0.063 0.092 0.26 187 -0.57 2 189
SRC -0.018 0.098 -10000 0 -0.62 21 21
ITGB3 0.005 0.1 0.25 4 -0.57 33 37
CAT1/PTP1B -0.092 0.19 0.41 2 -0.47 146 148
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.038 0.12 -10000 0 -0.4 50 50
mol:H2O2 -0.004 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.24 0.14 -10000 0 -0.35 429 429
negative regulation of transcription -0.047 0.12 -10000 0 -0.45 55 55
FCGR2A 0.021 0.012 0.26 1 -10000 0 1
FER 0.011 0.058 -10000 0 -0.58 10 10
alphaIIb/beta3 Integrin 0.023 0.09 -10000 0 -0.42 36 36
BLK 0.051 0.087 0.26 151 -0.57 2 153
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.006 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.57 266 266
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.009 0.26 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.041 0.17 0.34 4 -0.47 91 95
PRL 0.007 0.032 0.26 10 -10000 0 10
SOCS3 0.01 0.16 -10000 0 -1.2 16 16
SPRY2 -0.041 0.18 -10000 0 -0.57 106 106
Insulin Receptor/Insulin/IRS1 0.026 0.08 -10000 0 -0.37 41 41
CSF1/CSF1R -0.064 0.14 -10000 0 -0.35 143 143
Ras protein signal transduction 0.051 0.15 0.64 60 -10000 0 60
IRS1 0.001 0.11 -10000 0 -0.57 42 42
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.44 0.24 -10000 0 -0.57 841 841
STAT5B -0.069 0.14 0.2 3 -0.35 143 146
STAT5A -0.07 0.14 0.2 3 -0.35 147 150
GRB2 0.023 0.009 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.073 0.14 0.22 1 -0.35 150 151
CSN2 0.025 0.057 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.009 0.072 -10000 0 -0.59 8 8
YBX1 0.027 0.015 0.22 1 -10000 0 1
LCK 0.026 0.075 0.26 40 -0.57 11 51
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.019 0.036 0.25 10 -0.57 2 12
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.069 0.11 -10000 0 -0.28 94 94
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.46 448 448
NT3 (dimer)/TRKB -0.29 0.3 -10000 0 -0.52 617 617
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.033 -10000 0 -0.26 8 8
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.012 0.16 0.26 24 -0.57 75 99
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.024 0.051 0.26 25 -0.57 4 29
NTRK2 -0.28 0.3 -10000 0 -0.57 552 552
NTRK3 -0.17 0.28 0.26 5 -0.57 347 352
NT-4/5 (dimer)/TRKB -0.35 0.33 -10000 0 -0.56 703 703
neuron apoptosis 0.17 0.22 0.47 289 -10000 0 289
SHC 2-3/Grb2 -0.18 0.24 -10000 0 -0.52 288 288
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.18 0.25 -10000 0 -0.54 287 287
SHC3 -0.17 0.23 -10000 0 -0.52 279 279
STAT3 (dimer) 0.033 0.043 -10000 0 -0.36 4 4
NT3 (dimer)/TRKA -0.1 0.21 -10000 0 -0.41 302 302
RIN/GDP -0.045 0.12 0.3 4 -0.26 75 79
GIPC1 0.024 0.008 0.26 1 -10000 0 1
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.078 0.15 -10000 0 -0.33 249 249
RIN/GTP 0.014 0.008 0.18 2 -10000 0 2
CCND1 0.025 0.094 0.43 39 -0.82 4 43
MAGED1 0.025 0.01 0.26 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.56 363 363
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.035 0.082 0.34 3 -0.38 29 32
TRKA/NEDD4-2 0.031 0.04 -10000 0 -0.37 5 5
ELMO1 0.024 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.008 -10000 0 -10000 0 0
NGF 0.017 0.074 0.26 8 -0.57 16 24
HRAS 0.026 0.022 0.26 9 -10000 0 9
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.021 0.019 -10000 0 -0.57 1 1
RIT2 0.018 0.011 0.26 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
DNM1 0.02 0.048 0.26 1 -0.57 7 8
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 -0.071 0.16 -10000 0 -0.32 280 280
mol:GDP -0.074 0.16 0.37 4 -0.37 106 110
NGF (dimer) 0.017 0.074 0.26 8 -0.56 16 24
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.044 0.11 0.38 2 -0.26 69 71
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
BDNF (dimer)/TRKB -0.18 0.23 -10000 0 -0.39 572 572
KIDINS220/CRKL/C3G 0.033 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.048 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.56 157 169
RAP1/GDP -0.041 0.093 -10000 0 -0.22 67 67
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.012 0.16 0.26 24 -0.56 75 99
ubiquitin-dependent protein catabolic process 0.036 0.061 -10000 0 -0.36 18 18
Schwann cell development -0.048 0.038 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.048 -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 -0.27 0.28 -10000 0 -0.46 647 647
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.077 0.13 -10000 0 -0.45 56 56
STAT3 0.033 0.043 -10000 0 -0.36 4 4
axon guidance -0.26 0.26 -10000 0 -0.44 647 647
MAPK3 0.024 0.085 0.24 3 -0.35 27 30
MAPK1 0.026 0.088 0.24 4 -0.35 28 32
CDC42/GDP -0.043 0.12 0.29 5 -0.26 81 86
NTF3 -0.061 0.21 0.26 12 -0.57 157 169
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NGF (dimer)/TRKA/FAIM 0.037 0.061 -10000 0 -0.36 18 18
PI3K 0.028 0.049 -10000 0 -0.38 14 14
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 -0.076 0.16 0.25 3 -0.33 268 271
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.41 427 428
RGS19 0.023 0.01 0.26 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.095 0.39 1 -0.44 9 10
Rac1/GDP -0.044 0.12 0.34 3 -0.26 77 80
NGF (dimer)/TRKA/GRIT 0.024 0.057 -10000 0 -0.36 18 18
neuron projection morphogenesis -0.068 0.21 -10000 0 -0.74 50 50
NGF (dimer)/TRKA/NEDD4-2 0.036 0.061 -10000 0 -0.36 18 18
MAP2K1 0.029 0.085 0.36 17 -10000 0 17
NGFR -0.14 0.26 -10000 0 -0.57 286 286
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.05 -10000 0 -0.29 21 21
RAS family/GTP/PI3K 0.017 0.03 -10000 0 -0.26 9 9
FRS2 family/SHP2/GRB2/SOS1 0.063 0.026 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -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 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAPKKK cascade -0.039 0.14 -10000 0 -0.65 41 41
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.039 -10000 0 -0.42 4 4
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.36 566 566
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.062 -10000 0 -0.31 18 18
MATK 0.02 0.086 0.26 30 -0.57 18 48
NEDD4L 0.023 0.019 -10000 0 -0.57 1 1
RAS family/GDP -0.055 0.069 -10000 0 -0.21 68 68
NGF (dimer)/TRKA -0.085 0.16 -10000 0 -0.34 297 297
Rac1/GTP -0.083 0.12 -10000 0 -0.28 219 219
FRS2 family/SHP2/CRK family 0.06 0.029 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.003 0.039 0.22 2 -0.37 2 4
NFATC2 -0.026 0.11 0.19 4 -0.37 88 92
NFATC3 0.006 0.034 0.22 2 -10000 0 2
CD40LG -0.14 0.29 0.48 15 -0.57 241 256
PTGS2 -0.19 0.33 0.47 13 -0.64 327 340
JUNB 0.024 0.01 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.027 0.15 2 -10000 0 2
CaM/Ca2+ 0.008 0.027 0.15 2 -10000 0 2
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.013 0.049 -10000 0 -0.57 6 6
mol:Ca2+ -0.003 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.027 0.048 0.26 26 -0.57 3 29
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.005 0.15 0.46 12 -0.42 48 60
FOS -0.15 0.27 -10000 0 -0.57 306 306
IFNG -0.11 0.28 0.46 40 -0.54 215 255
AP-1/NFAT1-c-4 -0.13 0.34 0.52 40 -0.62 251 291
FASLG -0.12 0.26 0.51 22 -0.55 195 217
NFAT1-c-4/ICER1 -0.018 0.12 0.28 9 -0.34 77 86
IL2RA -0.12 0.28 0.48 28 -0.55 228 256
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.27 0.47 20 -0.53 236 256
JunB/Fra1/NFAT1-c-4 -0.007 0.13 0.33 13 -0.34 77 90
IL4 -0.13 0.26 0.47 13 -0.54 224 237
IL2 -0.014 0.15 -10000 0 -0.94 27 27
IL3 -0.017 0.11 -10000 0 -0.72 23 23
FKBP1A 0.024 0.004 -10000 0 -10000 0 0
BATF3 0.021 0.015 0.26 3 -10000 0 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.18 14 -10000 0 14
Metarhodopsin II/Arrestin 0.036 0.037 0.32 2 -10000 0 2
PDE6G/GNAT1/GTP 0.035 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.027 0.26 14 -10000 0 14
GRK1 0.019 0.016 0.26 4 -10000 0 4
CNG Channel -0.048 0.16 -10000 0 -0.3 284 284
mol:Na + -0.047 0.16 0.24 5 -0.3 288 293
mol:ADP 0.019 0.016 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 86 87
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.041 0.16 0.28 5 -0.3 288 293
CNGB1 0.03 0.051 0.26 52 -10000 0 52
RDH5 -0.33 0.29 -10000 0 -0.57 641 641
SAG 0.032 0.052 0.26 54 -10000 0 54
mol:Ca2+ -0.08 0.14 0.36 18 -0.3 183 201
Na + (4 Units) -0.05 0.14 -10000 0 -0.28 278 278
RGS9 -0.024 0.16 0.26 11 -0.57 88 99
GNB1/GNGT1 0.054 0.059 -10000 0 -10000 0 0
GNAT1/GDP 0.025 0.11 0.3 5 -0.31 86 91
GUCY2D 0.024 0.044 0.26 19 -0.57 3 22
GNGT1 0.055 0.086 0.26 169 -10000 0 169
GUCY2F 0.018 0.011 0.26 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.02 0.049 0.2 3 -0.31 16 19
mol:11-cis-retinal -0.33 0.29 -10000 0 -0.56 641 641
mol:cGMP 0.042 0.044 -10000 0 -0.32 7 7
GNB1 0.023 0.005 -10000 0 -10000 0 0
Rhodopsin -0.24 0.22 -10000 0 -0.42 645 645
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.14 0.26 0.26 4 -0.57 294 298
Metarhodopsin II 0.026 0.019 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.05 -10000 0 -0.34 7 7
RGS9BP 0.036 0.052 0.26 57 -10000 0 57
Metarhodopsin II/Transducin 0.024 0.031 0.17 6 -0.17 1 7
GCAP Family/Ca ++ 0.044 0.037 -10000 0 -0.33 4 4
PDE6A/B 0.029 0.064 -10000 0 -0.42 18 18
mol:Pi 0.016 0.12 0.33 1 -0.36 86 87
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.058 0.053 0.32 2 -10000 0 2
PDE6B 0.014 0.077 0.26 3 -0.57 18 21
PDE6A 0.028 0.032 0.26 20 -10000 0 20
PDE6G 0.032 0.045 0.26 42 -10000 0 42
RHO 0.024 0.028 0.26 15 -10000 0 15
PDE6 0.035 0.12 0.3 8 -0.31 97 105
GUCA1A 0.031 0.045 0.26 42 -10000 0 42
GC2/GCAP Family 0.054 0.039 -10000 0 -0.34 4 4
GUCA1C 0.017 0.008 0.26 1 -10000 0 1
GUCA1B 0.022 0.036 -10000 0 -0.57 4 4
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.044 -10000 0 -0.39 6 6
PDGFRB 0.018 0.037 -10000 0 -0.57 4 4
SPHK1 -0.018 0.097 -10000 0 -0.75 14 14
mol:S1P -0.021 0.095 0.38 1 -0.66 14 15
S1P1/S1P/Gi -0.13 0.23 0.31 2 -0.43 363 365
GNAO1 0.006 0.092 0.24 32 -0.57 20 52
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.32 4 -0.4 316 320
PLCG1 -0.13 0.22 0.35 2 -0.41 345 347
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.037 -10000 0 -0.57 4 4
GNAI2 0.009 0.023 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.021 0.13 -10000 0 -0.58 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.03 -10000 0 -0.33 6 6
S1P1/S1P -0.034 0.097 0.34 1 -0.46 18 19
negative regulation of cAMP metabolic process -0.13 0.23 0.28 3 -0.42 363 366
MAPK3 -0.18 0.3 0.3 13 -0.58 357 370
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 0.003 -10000 0 -10000 0 0
KDR 0.011 0.044 -10000 0 -0.57 5 5
PLCB2 -0.025 0.097 0.29 7 -0.41 19 26
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.081 -10000 0 -0.39 18 18
receptor internalization -0.035 0.088 -10000 0 -0.42 19 19
PTGS2 -0.33 0.5 0.38 3 -1 367 370
Rac1/GTP -0.032 0.081 -10000 0 -0.39 18 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.25 7 -10000 0 7
negative regulation of T cell proliferation -0.13 0.23 0.28 3 -0.42 363 366
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.06 -10000 0 -0.57 10 10
MAPK1 -0.2 0.33 0.31 3 -0.62 372 375
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.31 4 -0.48 17 21
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.078 0.31 10 -0.3 1 11
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.019 -10000 0 -0.3 2 2
AURKB 0.14 0.12 0.26 560 -10000 0 560
AURKC 0.026 0.032 0.26 14 -0.57 1 15
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.043 0.17 0.3 131 -0.44 61 192
FYN 0.02 0.19 0.31 67 -0.48 83 150
LAT/GRAP2/SLP76 0.026 0.17 0.34 49 -0.5 57 106
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.022 0.15 0.3 86 -0.36 85 171
B2M 0.024 0.008 -10000 0 -10000 0 0
IKBKG 0.016 0.058 0.16 75 -0.13 29 104
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
mol:Ca2+ -0.022 0.032 -10000 0 -0.09 169 169
integrin-mediated signaling pathway 0.026 0.022 -10000 0 -0.29 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.2 0.34 55 -0.47 100 155
TRPV6 -0.089 0.26 1.2 15 -0.57 195 210
CD28 0.024 0.05 0.26 10 -0.57 6 16
SHC1 0.029 0.21 0.31 158 -0.44 110 268
receptor internalization -0.012 0.22 0.35 37 -0.47 146 183
PRF1 -0.011 0.24 0.55 7 -0.97 43 50
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
COT/AKT1 0.031 0.13 0.28 82 -0.3 78 160
LAT 0.012 0.2 0.32 72 -0.46 105 177
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.023 0.095 0.26 49 -0.57 19 68
CD3E 0.023 0.086 0.27 37 -0.58 16 53
CD3G 0.012 0.11 0.26 38 -0.57 33 71
RASGRP2 0 0.05 0.14 15 -0.17 69 84
RASGRP1 0.024 0.15 0.32 57 -0.39 65 122
HLA-A 0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.019 0.033 0.26 1 -0.57 3 4
RAP1A/GTP/RAPL 0.026 0.022 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.079 0.17 169 -0.12 38 207
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.055 -10000 0 -0.21 44 44
PRKCA 0.013 0.098 0.22 55 -0.27 53 108
GRAP2 0.017 0.063 0.25 3 -0.57 12 15
mol:IP3 0.014 0.14 0.26 132 -0.38 52 184
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.004 0.17 0.3 36 -0.6 55 91
ORAI1 0.037 0.17 0.64 4 -0.96 15 19
CSK 0.007 0.2 0.35 40 -0.45 112 152
B7 family/CD28 0.062 0.21 0.42 47 -0.59 53 100
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0 0.22 0.37 39 -0.49 123 162
PTPN6 0.003 0.19 0.33 46 -0.45 107 153
VAV1 0.003 0.2 0.34 43 -0.45 112 155
Monovalent TCR/CD3 -0.001 0.14 0.26 40 -0.49 57 97
CBL 0.022 0.007 -10000 0 -10000 0 0
LCK 0.017 0.2 0.31 69 -0.55 69 138
PAG1 0.02 0.2 0.31 75 -0.44 110 185
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.22 0.35 41 -0.48 122 163
CD80 0.084 0.1 0.26 279 -10000 0 279
CD86 0.026 0.018 0.26 6 -10000 0 6
PDK1/CARD11/BCL10/MALT1 -0.005 0.071 0.19 4 -0.25 44 48
HRAS 0.026 0.022 0.26 9 -10000 0 9
GO:0035030 0.021 0.16 0.32 44 -0.48 54 98
CD8A 0.029 0.057 0.27 29 -0.58 5 34
CD8B 0.014 0.11 0.27 30 -0.57 32 62
PTPRC 0.022 0.041 0.26 12 -0.57 3 15
PDK1/PKC theta 0.023 0.18 0.36 83 -0.45 76 159
CSK/PAG1 0.021 0.19 0.31 71 -0.44 99 170
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.01 -10000 0 -10000 0 0
GRAP2/SLP76 0.019 0.2 0.38 35 -0.47 94 129
STIM1 0.025 0.095 1.3 4 -10000 0 4
RAS family/GTP 0.044 0.091 0.22 85 -0.18 40 125
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.23 0.35 37 -0.5 146 183
mol:DAG -0.016 0.096 0.12 35 -0.32 64 99
RAP1A/GDP 0.021 0.038 0.1 85 -0.066 8 93
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.017 0.077 0.26 16 -0.57 15 31
cytotoxic T cell degranulation -0.009 0.22 0.54 7 -0.9 43 50
RAP1A/GTP -0.001 0.017 -10000 0 -0.064 66 66
mol:PI-3-4-5-P3 0.017 0.17 0.32 58 -0.41 92 150
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.021 0.17 0.29 119 -0.48 54 173
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.027 0.098 0.26 61 -0.57 20 81
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.006 0.16 0.32 22 -0.48 58 80
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.032 0.11 0.3 38 -0.48 32 70
CARD11 0.027 0.041 0.26 21 -0.57 2 23
PRKCB 0.014 0.1 0.26 51 -0.27 46 97
PRKCE 0.019 0.094 0.22 56 -0.26 41 97
PRKCQ 0.012 0.2 0.34 57 -0.46 101 158
LCP2 0.024 0.008 0.25 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.14 0.29 88 -0.3 85 173
IKK complex 0.035 0.08 0.2 132 -0.12 23 155
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.025 0.11 0.24 83 -0.26 49 132
PDPK1 0.027 0.15 0.33 86 -0.34 76 162
TCR/CD3/MHC I/CD8/Fyn -0.028 0.24 0.37 35 -0.54 129 164
Effects of Botulinum toxin

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
STX1A 0.01 0.024 0.13 40 -10000 0 40
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.031 0.11 -10000 0 -0.41 46 46
STXBP1 0.02 0.048 -10000 0 -0.57 7 7
ACh/CHRNA1 0.072 0.09 0.19 351 -0.16 8 359
RAB3GAP2/RIMS1/UNC13B 0.036 0.087 -10000 0 -0.36 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.14 0.26 117 -0.57 45 162
mol:ACh -0.003 0.036 0.089 12 -0.14 43 55
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.021 0.082 0.23 1 -0.27 42 43
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.072 0.09 0.19 351 -0.15 8 359
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.26 362 -10000 0 362
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.032 0.11 0.2 196 -0.36 43 239
SNAP25 0 0.058 0.094 59 -0.3 34 93
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.046 0.15 0.26 204 -0.57 39 243
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.036 -10000 0 -0.36 7 7
STX1A/SNAP25 fragment 1/VAMP2 0.021 0.082 0.23 1 -0.27 42 43
IL6-mediated signaling events

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
BCL2L1 -0.028 0.22 0.63 2 -0.66 25 27
CRP -0.007 0.24 0.56 23 -0.68 23 46
cell cycle arrest -0.039 0.25 0.54 13 -0.67 48 61
TIMP1 -0.021 0.21 0.51 11 -0.6 27 38
IL6ST -0.037 0.19 -10000 0 -0.56 120 120
Rac1/GDP -0.069 0.2 0.38 2 -0.48 101 103
AP1 -0.073 0.21 0.37 1 -0.47 112 113
GAB2 0.022 0.02 -10000 0 -0.57 1 1
TNFSF11 -0.018 0.24 0.59 12 -0.65 28 40
HSP90B1 0.022 0.11 -10000 0 -0.79 11 11
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.095 0.18 -10000 0 -0.51 97 97
AKT1 0.022 0.066 -10000 0 -0.66 4 4
FOXO1 0.023 0.068 0.43 1 -0.54 5 6
MAP2K6 -0.096 0.18 0.27 2 -0.41 180 182
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.053 0.2 0.38 13 -0.49 82 95
MITF -0.09 0.19 0.26 12 -0.41 179 191
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 25 25
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.018 0.13 -10000 0 -0.49 38 38
STAT3 -0.045 0.26 0.55 13 -0.72 50 63
STAT1 0.012 0.093 -10000 0 -0.83 10 10
CEBPD -0.014 0.23 0.57 9 -0.68 28 37
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.05 -10000 0 -0.38 14 14
JUN 0.02 0.044 -10000 0 -0.57 6 6
PIAS3/MITF -0.072 0.18 0.32 2 -0.46 101 103
MAPK11 -0.095 0.18 -10000 0 -0.51 99 99
STAT3 (dimer)/FOXO1 -0.026 0.22 0.51 14 -0.56 48 62
GRB2/SOS1/GAB family -0.061 0.18 -10000 0 -0.48 79 79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.19 0.24 1 -0.34 310 311
GRB2 0.023 0.009 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.17 0.46 0.53 29 -0.92 263 292
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.026 0.008 -10000 0 -10000 0 0
MYC -0.004 0.27 0.54 26 -0.92 36 62
FGG -0.026 0.23 0.6 12 -0.66 28 40
macrophage differentiation -0.039 0.25 0.54 13 -0.67 48 61
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.092 0.21 -10000 0 -0.35 356 356
JUNB -0.03 0.22 0.51 9 -0.63 28 37
FOS -0.14 0.27 -10000 0 -0.57 306 306
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.093 0.2 0.29 11 -0.42 182 193
STAT1/PIAS1 -0.061 0.2 0.35 10 -0.4 150 160
GRB2/SOS1/GAB family/SHP2/PI3K 0.023 0.07 -10000 0 -0.52 8 8
STAT3 (dimer) -0.044 0.26 0.55 13 -0.71 48 61
PRKCD -0.037 0.2 0.45 16 -0.52 57 73
IL6R 0.001 0.11 -10000 0 -0.56 38 38
SOCS3 -0.092 0.19 -10000 0 -0.6 67 67
gp130 (dimer)/JAK1/JAK1/LMO4 0.012 0.13 -10000 0 -0.35 120 120
Rac1/GTP -0.064 0.2 0.34 10 -0.48 97 107
HCK 0.026 0.026 0.26 13 -10000 0 13
MAPKKK cascade -0.002 0.14 -10000 0 -0.59 33 33
bone resorption -0.015 0.23 0.55 19 -0.6 30 49
IRF1 -0.031 0.22 0.63 2 -0.66 27 29
mol:GDP -0.084 0.19 0.28 12 -0.4 177 189
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.085 0.2 0.28 12 -0.41 177 189
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.2 -10000 0 -0.56 105 105
PTPN11 0.011 0.081 -10000 0 -0.84 8 8
IL6/IL6RA -0.12 0.22 0.22 1 -0.38 402 403
gp130 (dimer)/TYK2/TYK2/LMO4 0.007 0.13 -10000 0 -0.35 120 120
gp130 (dimer)/JAK2/JAK2/LMO4 0.007 0.13 -10000 0 -0.35 114 114
IL6 -0.18 0.28 0.27 1 -0.56 380 381
PIAS3 0.02 0.009 -10000 0 -10000 0 0
PTPRE 0.008 0.035 -10000 0 -0.57 2 2
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 -0.11 0.19 0.22 2 -0.33 330 332
LMO4 0.028 0.036 0.28 2 -0.56 3 5
STAT3 (dimer)/PIAS3 -0.049 0.24 0.53 10 -0.68 49 59
MCL1 0.053 0.098 0.49 1 -0.55 5 6
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.36 330 330
fibroblast growth factor receptor signaling pathway -0.1 0.18 -10000 0 -0.36 330 330
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
PRNP 0.015 0.072 -10000 0 -0.57 16 16
GPC1/SLIT2 -0.015 0.14 -10000 0 -0.42 116 116
SMAD2 -0.001 0.068 0.24 1 -0.33 42 43
GPC1/PrPc/Cu2+ 0.026 0.05 -10000 0 -0.36 17 17
GPC1/Laminin alpha1 -0.011 0.14 -10000 0 -0.4 114 114
TDGF1 0.019 0.048 0.26 1 -0.57 7 8
CRIPTO/GPC1 0.031 0.042 -10000 0 -0.42 8 8
APP/GPC1 0.035 0.02 -10000 0 -0.42 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.006 0.034 -10000 0 -0.36 8 8
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.031 0.082 -10000 0 -0.36 43 43
SERPINC1 0.031 0.05 0.26 50 -10000 0 50
FYN 0.005 0.037 -10000 0 -0.36 10 10
FGR 0.006 0.034 -10000 0 -0.36 8 8
positive regulation of MAPKKK cascade 0.011 0.079 0.28 3 -0.36 22 25
SLIT2 -0.04 0.18 -10000 0 -0.57 115 115
GPC1/NRG -0.11 0.2 -10000 0 -0.42 293 293
NRG1 -0.14 0.26 0.26 4 -0.57 292 296
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.025 -10000 0 -0.36 1 1
LYN 0.006 0.031 -10000 0 -0.36 6 6
mol:Spermine 0.006 0.016 -10000 0 -0.42 1 1
cell growth -0.1 0.18 -10000 0 -0.36 330 330
BMP signaling pathway -0.025 0.025 0.56 1 -0.26 6 7
SRC 0.006 0.034 -10000 0 -0.36 8 8
TGFBR1 0.024 0.008 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.27 0.26 26 -0.57 310 336
GPC1 0.025 0.025 0.26 6 -0.57 1 7
TGFBR1 (dimer) 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 7 -10000 0 7
BLK 0.021 0.062 -10000 0 -0.37 10 10
HCK 0.008 0.037 -10000 0 -0.36 8 8
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 42 42
cell death 0.035 0.02 -10000 0 -0.42 1 1
ATIII/GPC1 0.037 0.04 -10000 0 -0.42 1 1
PLA2G2A/GPC1 -0.098 0.21 -10000 0 -0.42 310 310
LCK 0.007 0.056 -10000 0 -0.36 19 19
neuron differentiation -0.11 0.2 -10000 0 -0.42 293 293
PrPc/Cu2+ 0.011 0.053 -10000 0 -0.42 16 16
APP 0.024 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.001 0.11 -10000 0 -0.56 42 42
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.035 -10000 0 -0.37 6 6
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.37 409 409
PTK2 -0.055 0.15 0.3 4 -0.47 59 63
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.067 0.26 6 -0.57 13 19
SRC 0.023 0.005 -10000 0 -10000 0 0
CDKN1B -0.044 0.12 -10000 0 -0.53 35 35
VEGFA 0.025 0.019 0.26 7 -10000 0 7
ILK -0.042 0.12 -10000 0 -0.49 32 32
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
AKT1 -0.043 0.1 -10000 0 -0.48 29 29
PTK2B -0.013 0.069 0.36 2 -0.33 33 35
alphaV/beta3 Integrin/JAM-A -0.076 0.17 0.3 1 -0.33 296 297
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.032 0.072 -10000 0 -0.36 33 33
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.19 -10000 0 -0.38 246 246
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.013 0.068 -10000 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 0.043 0.081 -10000 0 -0.36 33 33
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.45 359 359
PI4 Kinase 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.068 0.099 0.34 3 -0.35 33 36
RPS6KB1 -0.16 0.22 0.42 3 -0.54 187 190
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.54 402 402
GPR124 0.016 0.048 -10000 0 -0.57 7 7
MAPK1 -0.2 0.29 -10000 0 -0.55 409 409
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
alphaV/beta3 Integrin/Tumstatin -0.031 0.16 -10000 0 -0.37 197 197
cell adhesion 0.023 0.082 0.25 1 -0.36 42 43
ANGPTL3 0.021 0.015 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.032 -10000 0 -0.36 4 4
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 42 42
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
RAC1 0.024 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.025 0.077 -10000 0 -0.39 29 29
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.018 -10000 0 -0.57 1 1
alphaV/beta3 Integrin/CD47 0.034 0.072 -10000 0 -0.36 33 33
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.014 0.13 -10000 0 -0.45 72 72
CSF1 0.021 0.044 -10000 0 -0.57 6 6
PIK3C2A -0.04 0.11 -10000 0 -0.49 28 28
PI4 Kinase/Pyk2 -0.076 0.15 -10000 0 -0.32 184 184
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.078 -10000 0 -0.36 33 33
FAK1/Vinculin -0.037 0.13 0.31 6 -0.39 49 55
alphaV beta3/Integrin/ppsTEM5 0.026 0.077 -10000 0 -0.4 29 29
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.033 0.077 0.26 68 -0.57 8 76
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
F11R -0.12 0.19 -10000 0 -0.42 312 312
alphaV/beta3 Integrin/Lactadherin 0.03 0.087 0.34 1 -0.38 42 43
alphaV/beta3 Integrin/TGFBR2 0.02 0.12 -10000 0 -0.45 55 55
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.038 -10000 0 -0.33 6 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.065 -10000 0 -0.33 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.11 0.26 421 -10000 0 421
alphaV/beta3 Integrin/Pyk2 0.027 0.072 -10000 0 -0.33 33 33
SDC1 0.038 0.059 0.26 68 -0.57 1 69
VAV3 -0.011 0.041 -10000 0 -0.31 13 13
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
FAK1/Paxillin -0.037 0.13 0.31 6 -0.39 51 57
cell migration -0.036 0.12 0.29 8 -0.36 44 52
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.066 0.17 0.26 1 -0.31 289 290
SPP1 0.084 0.1 0.26 279 -10000 0 279
KDR 0.021 0.04 -10000 0 -0.57 5 5
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 -0.074 0.22 0.26 4 -0.57 179 183
angiogenesis -0.19 0.3 0.3 1 -0.56 373 374
Rac1/GTP 0.021 0.038 -10000 0 -0.29 12 12
EDIL3 -0.007 0.14 0.26 15 -0.57 62 77
cell proliferation 0.02 0.12 -10000 0 -0.45 55 55
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.081 0.28 1 -0.32 2 3
epithelial cell differentiation 0.032 0.08 0.39 1 -0.4 4 5
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.022 0.097 0.46 8 -10000 0 8
FYN 0.022 0.026 -10000 0 -0.57 2 2
EGFR -0.19 0.28 -10000 0 -0.57 390 390
PRL 0.022 0.023 0.26 10 -10000 0 10
neuron projection morphogenesis -0.041 0.14 0.37 13 -0.36 34 47
PTPRZ1 -0.27 0.3 0.26 6 -0.57 541 547
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.14 -10000 0 -0.38 42 42
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.087 0.15 -10000 0 -0.34 243 243
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.007 0.074 0.38 8 -0.3 6 14
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.002 0.11 -10000 0 -0.36 40 40
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.079 0.15 -10000 0 -0.32 232 232
GRIN2B -0.097 0.16 -10000 0 -0.4 85 85
ErbB4/ErbB2/betacellulin 0.013 0.097 -10000 0 -0.32 32 32
STAT1 0.028 0.031 0.26 19 -10000 0 19
HBEGF 0.023 0.026 -10000 0 -0.57 2 2
PRLR 0.021 0.051 0.26 7 -0.57 7 14
E4ICDs/ETO2 0.006 0.087 0.31 2 -0.4 11 13
axon guidance 0.054 0.11 0.31 51 -0.35 3 54
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.031 0.04 -10000 0 -0.39 7 7
CBFA2T3 0.014 0.071 0.26 4 -0.57 15 19
ErbB4/ErbB2/HBEGF 0.03 0.072 -10000 0 -0.34 3 3
MAPK3 -0.047 0.14 0.34 4 -0.36 41 45
STAT1 (dimer) 0.019 0.081 0.27 3 -10000 0 3
MAPK1 -0.047 0.14 0.36 5 -0.36 41 46
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.071 0.15 0.27 1 -0.32 221 222
NRG1 -0.1 0.19 -10000 0 -0.42 288 288
NRG3 0.001 0.13 0.26 24 -0.57 50 74
NRG2 -0.26 0.29 -10000 0 -0.57 509 509
NRG4 0.026 0.028 0.26 15 -10000 0 15
heart development 0.054 0.11 0.31 51 -0.35 3 54
neural crest cell migration -0.07 0.15 0.27 1 -0.32 221 222
ERBB2 0.035 0.071 0.27 87 -0.41 1 88
WWOX/E4ICDs 0.011 0.075 0.28 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.097 0.16 -10000 0 -0.32 279 279
apoptosis 0.012 0.12 0.48 41 -10000 0 41
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.15 0.17 -10000 0 -0.34 386 386
ErbB4/ErbB2/epiregulin 0.007 0.13 0.35 12 -0.31 76 88
ErbB4/ErbB4/betacellulin/betacellulin -0.004 0.11 0.28 1 -0.35 42 43
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.04 0.087 0.39 1 -0.4 6 7
MDM2 0.008 0.079 0.29 8 -10000 0 8
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.083 0.14 -10000 0 -0.32 239 239
STAT5A 0.049 0.11 0.36 13 -0.37 3 16
ErbB4/EGFR/neuregulin 1 beta -0.18 0.23 -10000 0 -0.43 426 426
DLG4 0.022 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.01 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.059 0.1 0.45 1 -0.46 3 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.11 0.34 8 -0.35 3 11
LRIG1 0.022 0.031 -10000 0 -0.57 3 3
EREG -0.024 0.2 0.26 77 -0.57 116 193
BTC -0.007 0.13 0.26 2 -0.57 57 59
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.044 0.11 0.31 40 -0.36 3 43
ERBB4 -0.007 0.074 0.38 8 -0.3 6 14
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
YAP1 -0.013 0.11 -10000 0 -0.39 74 74
GRB2 0.023 0.009 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.033 0.071 0.32 1 -0.41 1 2
glial cell differentiation -0.01 0.07 -10000 0 -10000 0 0
WWOX 0.021 0.013 0.26 2 -10000 0 2
cell proliferation -0.038 0.17 0.34 15 -0.46 44 59
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.04 0.22 0.41 5 -0.62 115 120
IHH 0.016 0.082 0.26 31 -0.2 93 124
SHH Np/Cholesterol/GAS1 0 0.075 -10000 0 -0.33 49 49
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0 0.075 0.33 49 -10000 0 49
SMO/beta Arrestin2 -0.019 0.21 0.3 1 -0.6 102 103
SMO -0.042 0.21 0.32 1 -0.58 121 122
AKT1 -0.004 0.13 -10000 0 -0.62 23 23
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.018 0.15 -10000 0 -0.57 76 76
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.041 0.21 0.32 1 -0.57 121 122
STIL 0.006 0.17 0.3 30 -0.46 92 122
DHH N/PTCH2 -0.008 0.14 -10000 0 -0.44 98 98
DHH N/PTCH1 -0.027 0.2 0.28 1 -0.5 146 147
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.008 0.096 0.26 2 -0.57 29 31
PTHLH -0.061 0.3 0.42 14 -0.82 123 137
determination of left/right symmetry -0.041 0.21 0.32 1 -0.57 121 122
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
skeletal system development -0.059 0.29 0.42 14 -0.81 123 137
IHH N/Hhip 0.027 0.056 0.21 7 -0.3 4 11
DHH N/Hhip 0.022 0.077 -10000 0 -0.41 31 31
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.041 0.21 0.32 1 -0.57 121 122
pancreas development 0.023 0.03 0.26 5 -0.56 2 7
HHAT 0.02 0.02 -10000 0 -0.57 1 1
PI3K 0.028 0.049 -10000 0 -0.38 14 14
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.57 61 61
somite specification -0.041 0.21 0.32 1 -0.57 121 122
SHH Np/Cholesterol/PTCH1 -0.024 0.16 0.25 5 -0.44 119 124
SHH Np/Cholesterol/PTCH2 -0.004 0.082 -10000 0 -0.33 59 59
SHH Np/Cholesterol/Megalin -0.06 0.15 0.28 3 -0.33 229 232
SHH 0 0.037 0.34 7 -0.42 1 8
catabolic process -0.033 0.21 0.29 3 -0.56 126 129
SMO/Vitamin D3 -0.009 0.2 0.34 21 -0.5 118 139
SHH Np/Cholesterol/Hhip 0.015 0.028 0.25 3 -0.33 3 6
LRP2 -0.12 0.26 0.26 26 -0.57 277 303
receptor-mediated endocytosis -0.079 0.22 0.3 11 -0.57 119 130
SHH Np/Cholesterol/BOC -0.004 0.083 -10000 0 -0.33 61 61
SHH Np/Cholesterol/CDO 0.013 0.04 -10000 0 -0.33 12 12
mesenchymal cell differentiation -0.015 0.028 0.33 3 -0.24 3 6
mol:Vitamin D3 0.002 0.18 0.33 24 -0.45 113 137
IHH N/PTCH2 -0.006 0.14 0.21 3 -0.46 79 82
CDON 0.015 0.065 -10000 0 -0.57 13 13
IHH N/PTCH1 -0.024 0.21 0.35 4 -0.57 126 130
Megalin/LRPAP1 -0.079 0.2 -10000 0 -0.42 277 277
PTCH2 -0.018 0.15 -10000 0 -0.57 76 76
SHH Np/Cholesterol 0.01 0.013 -10000 0 -0.33 1 1
PTCH1 -0.033 0.21 0.3 3 -0.57 126 129
HHIP 0.023 0.03 0.26 5 -0.57 2 7
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.006 0.07 0.34 1 -0.36 8 9
alphaM/beta2 Integrin/GPIbA 0.01 0.075 0.33 4 -0.4 6 10
alphaM/beta2 Integrin/proMMP-9 0.074 0.11 0.34 17 -0.41 1 18
PLAUR 0.042 0.062 0.26 83 -10000 0 83
HMGB1 -0.003 0.04 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.009 0.063 0.34 1 -10000 0 1
AGER -0.006 0.05 0.26 1 -0.62 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 -0.025 0.14 0.32 4 -0.36 14 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
CYR61 -0.004 0.12 -10000 0 -0.57 51 51
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.38 30 30
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.092 0.23 -10000 0 -0.56 206 206
MYH2 -0.013 0.14 0.29 8 -0.47 35 43
MST1R 0.022 0.053 0.26 10 -0.57 7 17
leukocyte activation during inflammatory response -0.18 0.17 0.29 1 -0.33 587 588
APOB -0.33 0.29 -10000 0 -0.57 647 647
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.048 0.26 1 -0.57 7 8
JAM3 0.019 0.041 -10000 0 -0.57 5 5
GP1BA 0.024 0.057 0.26 26 -0.57 6 32
alphaM/beta2 Integrin/CTGF 0.004 0.077 0.34 1 -0.4 13 14
alphaM/beta2 Integrin -0.012 0.12 0.21 5 -0.4 41 46
JAM3 homodimer 0.019 0.041 -10000 0 -0.56 5 5
ICAM2 0.019 0.041 -10000 0 -0.57 5 5
ICAM1 0.027 0.027 0.26 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.12 0.22 6 -0.39 42 48
cell adhesion 0.01 0.075 0.33 4 -0.4 6 10
NFKB1 -0.098 0.2 0.41 5 -0.38 330 335
THY1 0.024 0.021 0.26 8 -10000 0 8
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.21 0.19 -10000 0 -0.36 653 653
alphaM/beta2 Integrin/LRP/tPA 0.008 0.09 0.34 1 -0.38 27 28
IL6 -0.26 0.39 0.36 4 -0.76 391 395
ITGB2 -0.002 0.052 0.26 14 -10000 0 14
elevation of cytosolic calcium ion concentration 0.031 0.085 0.33 20 -10000 0 20
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 0.34 1 -0.38 47 48
JAM2 -0.007 0.13 -10000 0 -0.57 55 55
alphaM/beta2 Integrin/ICAM1 0.024 0.086 0.34 3 -0.33 16 19
alphaM/beta2 Integrin/uPA/Plg 0.019 0.07 0.33 1 -10000 0 1
RhoA/GTP -0.018 0.15 0.24 15 -0.48 41 56
positive regulation of phagocytosis -0.001 0.1 0.3 5 -0.36 18 23
Ron/MSP 0.03 0.061 0.36 1 -0.4 18 19
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.087 0.34 20 -10000 0 20
alphaM/beta2 Integrin/uPAR 0.02 0.079 0.38 4 -10000 0 4
PLAU 0.03 0.036 0.26 26 -10000 0 26
PLAT 0.006 0.091 0.26 1 -0.57 26 27
actin filament polymerization -0.011 0.14 0.29 8 -0.45 35 43
MST1 0.021 0.055 0.26 8 -0.57 8 16
alphaM/beta2 Integrin/lipoprotein(a) -0.18 0.17 0.32 1 -0.33 587 588
TNF -0.098 0.2 0.39 3 -0.76 17 20
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.013 0.068 0.34 1 -10000 0 1
fibrinolysis 0.017 0.069 0.32 1 -10000 0 1
HCK 0.027 0.026 0.26 13 -10000 0 13
dendritic cell antigen processing and presentation -0.011 0.12 0.22 6 -0.39 42 48
VTN 0.033 0.077 0.26 68 -0.57 8 76
alphaM/beta2 Integrin/CYR61 -0.008 0.1 0.34 1 -0.4 47 48
LPA 0.018 0.017 0.26 5 -10000 0 5
LRP1 0.018 0.062 -10000 0 -0.57 12 12
cell migration 0.043 0.083 0.28 15 -0.36 8 23
FN1 0.11 0.11 0.26 421 -10000 0 421
alphaM/beta2 Integrin/Thy1 0.01 0.063 0.34 1 -10000 0 1
MPO -0.01 0.13 0.26 2 -0.57 58 60
KNG1 0.023 0.032 0.26 20 -10000 0 20
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.012 0.15 0.29 13 -0.47 37 50
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.021 0.26 8 -10000 0 8
CTGF 0.016 0.068 0.26 3 -0.57 14 17
alphaM/beta2 Integrin/Hck 0.011 0.067 0.35 5 -10000 0 5
ITGAM -0.003 0.043 0.24 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.044 0.16 0.34 1 -0.36 186 187
HP -0.07 0.22 0.26 34 -0.57 178 212
leukocyte adhesion -0.039 0.14 0.33 1 -0.44 36 37
SELP -0.093 0.23 -10000 0 -0.57 206 206
Syndecan-1-mediated signaling 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
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CCL5 0.029 0.056 0.26 38 -0.57 4 42
SDCBP 0.021 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.063 0.12 0.27 24 -0.41 9 33
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.049 0.12 0.27 2 -0.37 17 19
Syndecan-1/Syntenin 0.051 0.12 0.29 7 -0.38 14 21
MAPK3 0.047 0.11 0.26 9 -0.36 13 22
HGF/MET -0.066 0.2 -10000 0 -0.44 226 226
TGFB1/TGF beta receptor Type II 0.025 0.013 0.26 3 -10000 0 3
BSG 0.024 0.009 0.26 1 -10000 0 1
keratinocyte migration 0.049 0.12 0.27 2 -0.36 17 19
Syndecan-1/RANTES 0.058 0.13 0.31 36 -0.4 18 54
Syndecan-1/CD147 0.063 0.12 0.3 9 -0.36 16 25
Syndecan-1/Syntenin/PIP2 0.047 0.11 0.27 7 -0.37 14 21
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.046 0.11 0.26 6 -0.36 14 20
MMP7 -0.037 0.19 0.26 33 -0.57 121 154
HGF -0.011 0.14 0.26 2 -0.57 65 67
Syndecan-1/CASK 0.042 0.12 0.22 19 -0.37 17 36
Syndecan-1/HGF/MET -0.004 0.2 0.3 7 -0.45 115 122
regulation of cell adhesion 0.041 0.11 0.26 8 -0.4 7 15
HPSE 0.027 0.035 0.26 18 -0.57 1 19
positive regulation of cell migration 0.063 0.12 0.27 24 -0.41 9 33
SDC1 0.065 0.12 0.27 23 -0.41 9 32
Syndecan-1/Collagen 0.063 0.12 0.27 24 -0.41 9 33
PPIB 0.024 0.013 0.26 3 -10000 0 3
MET -0.073 0.22 -10000 0 -0.57 177 177
PRKACA 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
MAPK1 0.048 0.11 0.27 9 -0.36 12 21
homophilic cell adhesion 0.061 0.12 0.27 24 -0.38 14 38
MMP1 0.18 0.11 0.26 739 -10000 0 739
LPA receptor mediated 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
GNB1/GNG2 0.033 0.077 -10000 0 -0.34 40 40
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.12 -10000 0 -0.41 17 17
AP1 -0.093 0.19 -10000 0 -0.33 392 392
mol:PIP3 -0.13 0.18 -10000 0 -0.34 416 416
AKT1 0.006 0.08 0.31 3 -0.42 13 16
PTK2B -0.027 0.1 -10000 0 -0.34 55 55
RHOA 0.003 0.061 0.23 4 -0.3 27 31
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.11 0.26 4 -0.28 108 112
MAGI3 0.023 0.018 -10000 0 -0.56 1 1
RELA 0.024 0.005 -10000 0 -10000 0 0
apoptosis -0.025 0.12 -10000 0 -0.32 143 143
HRAS/GDP 0.019 0.015 0.18 9 -10000 0 9
positive regulation of microtubule depolymerization -0.05 0.12 0.26 3 -0.32 113 116
NF kappa B1 p50/RelA -0.011 0.12 -10000 0 -0.33 96 96
endothelial cell migration 0.002 0.081 0.26 1 -0.42 33 34
ADCY4 -0.023 0.12 -10000 0 -0.5 44 44
ADCY5 -0.076 0.15 -10000 0 -0.49 83 83
ADCY6 -0.015 0.099 -10000 0 -0.47 34 34
ADCY7 -0.014 0.098 -10000 0 -0.48 33 33
ADCY1 -0.017 0.11 -10000 0 -0.5 37 37
ADCY2 -0.029 0.13 -10000 0 -0.51 50 50
ADCY3 -0.015 0.099 -10000 0 -0.46 34 34
ADCY8 -0.012 0.091 -10000 0 -0.45 30 30
ADCY9 -0.015 0.098 -10000 0 -0.47 34 34
GSK3B -0.026 0.099 0.28 3 -0.35 45 48
arachidonic acid secretion -0.019 0.11 -10000 0 -0.42 49 49
GNG2 0.017 0.065 -10000 0 -0.56 13 13
TRIP6 0.018 0.015 -10000 0 -0.4 1 1
GNAO1 0.002 0.083 -10000 0 -0.36 47 47
HRAS 0.026 0.022 0.26 9 -10000 0 9
NFKBIA -0.02 0.13 0.28 3 -0.34 99 102
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.027 0.12 -10000 0 -0.81 22 22
JUN 0.02 0.044 -10000 0 -0.57 6 6
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.012 0.14 -10000 0 -0.95 22 22
PIK3R1 0.016 0.065 -10000 0 -0.56 13 13
mol:IP3 -0.013 0.11 0.26 4 -0.28 108 112
PLCB3 0.025 0.045 0.2 3 -10000 0 3
FOS -0.14 0.27 -10000 0 -0.57 306 306
positive regulation of mitosis -0.019 0.11 -10000 0 -0.42 49 49
LPA/LPA1-2-3 0.002 0.14 -10000 0 -0.33 142 142
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 -0.016 0.1 -10000 0 -0.37 45 45
GNAZ 0.003 0.07 -10000 0 -0.34 40 40
EGFR/PI3K-beta/Gab1 -0.13 0.2 -10000 0 -0.35 416 416
positive regulation of dendritic cell cytokine production 0.001 0.13 -10000 0 -0.33 142 142
LPA/LPA2/MAGI-3 0.033 0.02 -10000 0 -0.35 1 1
ARHGEF1 0.018 0.07 -10000 0 -0.31 20 20
GNAI2 0.006 0.06 -10000 0 -0.33 32 32
GNAI3 0.006 0.06 -10000 0 -0.33 32 32
GNAI1 -0.013 0.11 -10000 0 -0.37 83 83
LPA/LPA3 -0.025 0.14 0.18 39 -0.4 123 162
LPA/LPA2 0.019 0.015 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.071 -10000 0 -0.38 33 33
HB-EGF/EGFR -0.079 0.2 0.27 2 -0.34 362 364
HBEGF 0.066 0.073 0.27 24 -0.42 3 27
mol:DAG -0.013 0.11 0.26 4 -0.28 108 112
cAMP biosynthetic process -0.033 0.11 0.4 1 -0.43 54 55
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.27 24 -0.34 83 107
GNAQ -0.02 0.11 0.18 4 -0.31 122 126
LPAR2 0.025 0.011 0.26 2 -10000 0 2
LPAR3 -0.034 0.19 0.26 39 -0.57 119 158
LPAR1 0.012 0.088 -10000 0 -0.5 28 28
IL8 -0.13 0.23 0.35 30 -0.41 348 378
PTK2 -0.022 0.1 0.24 1 -0.32 98 99
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.32 143 143
EGFR -0.19 0.28 -10000 0 -0.57 390 390
PLCG1 -0.022 0.11 0.2 4 -0.32 120 124
PLD2 -0.027 0.12 0.24 1 -0.31 140 141
G12/G13 0.036 0.061 -10000 0 -0.31 26 26
PI3K-beta 0 0.079 -10000 0 -0.47 14 14
cell migration 0.002 0.063 -10000 0 -0.26 20 20
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
PXN -0.017 0.1 -10000 0 -0.38 45 45
HRAS/GTP -0.02 0.11 -10000 0 -0.43 49 49
RAC1 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
PRKCE 0.024 0.003 -10000 0 -10000 0 0
PRKCD -0.014 0.1 0.3 2 -0.4 11 13
Gi(beta/gamma) -0.014 0.11 -10000 0 -0.45 44 44
mol:LPA 0.001 0.016 -10000 0 -0.18 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.013 0.12 -10000 0 -0.42 31 31
MAPKKK cascade -0.019 0.11 -10000 0 -0.42 49 49
contractile ring contraction involved in cytokinesis 0.002 0.063 0.23 4 -0.3 27 31
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.02 0.11 0.21 1 -0.31 127 128
GNA15 -0.018 0.1 0.18 5 -0.31 120 125
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.051 0.12 0.26 3 -0.33 113 116
GNA11 -0.02 0.1 0.19 2 -0.31 123 125
Rac1/GTP 0.028 0.13 -10000 0 -0.86 22 22
MMP2 0.002 0.081 0.26 1 -0.43 33 34
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.042 0.14 0.35 65 -0.36 42 107
TBX21 0.014 0.34 0.76 21 -1.2 49 70
B2M 0.025 0.012 -10000 0 -10000 0 0
TYK2 0.024 0.036 0.19 1 -10000 0 1
IL12RB1 0.031 0.071 0.32 41 -0.6 2 43
GADD45B 0.037 0.26 0.64 22 -0.91 30 52
IL12RB2 0.028 0.15 0.27 123 -0.57 42 165
GADD45G 0.055 0.26 0.65 28 -0.9 29 57
natural killer cell activation 0.007 0.025 0.081 53 -0.048 11 64
RELB 0.026 0.022 0.26 10 -10000 0 10
RELA 0.023 0.005 -10000 0 -10000 0 0
IL18 0.034 0.04 0.27 26 -10000 0 26
IL2RA 0.027 0.088 0.26 58 -0.57 15 73
IFNG 0.054 0.08 0.26 146 -10000 0 146
STAT3 (dimer) 0.035 0.24 0.56 39 -0.72 43 82
HLA-DRB5 -0.006 0.011 -10000 0 -0.025 251 251
FASLG 0.049 0.31 0.75 29 -1.1 37 66
NF kappa B2 p52/RelB 0.022 0.25 0.67 5 -0.81 47 52
CD4 0.009 0.024 -10000 0 -10000 0 0
SOCS1 0.025 0.033 0.26 14 -0.57 1 15
EntrezGene:6955 -0.006 0.016 0.023 57 -0.028 282 339
CD3D 0.009 0.098 0.26 49 -0.58 19 68
CD3E 0.009 0.089 0.26 37 -0.57 16 53
CD3G -0.001 0.12 0.26 37 -0.57 33 70
IL12Rbeta2/JAK2 0.037 0.12 0.29 31 -0.43 42 73
CCL3 0.033 0.28 0.69 21 -0.98 32 53
CCL4 0.035 0.27 0.69 21 -0.95 31 52
HLA-A 0.002 0.008 0.023 73 -0.044 14 87
IL18/IL18R 0.065 0.12 0.37 17 -0.37 52 69
NOS2 0.032 0.28 0.68 23 -1 32 55
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.14 0.35 61 -0.35 51 112
IL1R1 0.017 0.31 0.69 21 -1.2 42 63
IL4 -0.011 0.037 -10000 0 -10000 0 0
JAK2 0.023 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.005 0.014 0.023 58 -0.026 250 308
TCR/CD3/MHC I/CD8 -0.024 0.22 0.37 33 -0.66 75 108
RAB7A 0.052 0.24 0.62 22 -0.8 24 46
lysosomal transport 0.053 0.23 0.61 24 -0.75 24 48
FOS -0.32 0.62 0.58 15 -1.2 350 365
STAT4 (dimer) 0.062 0.28 0.58 41 -0.86 45 86
STAT5A (dimer) 0.047 0.28 0.62 45 -0.83 43 88
GZMA 0.025 0.29 0.7 27 -1.1 32 59
GZMB 0.023 0.32 0.69 31 -1.1 45 76
HLX 0.021 0.015 0.26 3 -10000 0 3
LCK 0.028 0.29 0.66 36 -0.93 45 81
TCR/CD3/MHC II/CD4 -0.054 0.17 0.24 27 -0.3 245 272
IL2/IL2R 0.065 0.098 0.41 39 -0.36 21 60
MAPK14 0.048 0.27 0.64 28 -0.9 34 62
CCR5 0.037 0.27 0.69 27 -0.93 30 57
IL1B 0.017 0.078 0.29 3 -0.58 14 17
STAT6 0.039 0.12 0.37 42 -0.6 7 49
STAT4 0.001 0.12 0.26 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 0.26 19 -10000 0 19
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.008 0.26 1 -10000 0 1
IL12B 0.072 0.11 0.28 227 -10000 0 227
CD8A 0.029 0.059 0.28 29 -0.57 5 34
CD8B 0.014 0.11 0.27 30 -0.57 32 62
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.042 0.14 0.36 42 -0.35 66 108
IL2RB 0.03 0.05 0.26 38 -0.57 2 40
proteasomal ubiquitin-dependent protein catabolic process 0.066 0.26 0.57 45 -0.78 45 90
IL2RG 0.03 0.067 0.26 46 -0.57 7 53
IL12 0.049 0.15 0.29 103 -0.42 58 161
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
CD247 0.006 0.079 0.26 16 -0.57 15 31
IL2 0.022 0.021 0.26 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.004 0.14 0.28 19 -0.58 57 76
IL12/IL12R/TYK2/JAK2 0.033 0.3 0.72 34 -0.96 43 77
MAP2K3 0.042 0.28 0.62 30 -0.87 42 72
RIPK2 0.02 0.016 0.26 3 -10000 0 3
MAP2K6 0.046 0.27 0.62 31 -0.86 38 69
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.013 -10000 0 -0.028 285 285
IL18RAP 0.012 0.11 0.28 5 -0.57 35 40
IL12Rbeta1/TYK2 0.04 0.068 0.29 35 -0.46 2 37
EOMES -0.021 0.18 -10000 0 -0.99 31 31
STAT1 (dimer) 0.067 0.26 0.62 62 -0.75 35 97
T cell proliferation 0.049 0.22 0.5 28 -0.66 40 68
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.08 -10000 0 -0.57 19 19
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.012 0.19 0.38 4 -0.72 39 43
ATF2 0.045 0.25 0.6 28 -0.82 35 63
Ephrin A reverse signaling

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
MAPKKK cascade -0.005 0.11 -10000 0 -0.36 95 95
EFNA5 -0.028 0.17 0.26 1 -0.57 95 96
FYN -0.023 0.098 -10000 0 -0.33 95 95
neuron projection morphogenesis -0.005 0.11 -10000 0 -0.36 95 95
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.004 0.11 -10000 0 -0.36 95 95
EPHA5 0.023 0.017 0.26 5 -10000 0 5
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.071 0.16 -10000 0 -0.3 282 282
Syndecan-3/Neurocan 0.027 0.073 0.27 18 -0.37 20 38
POMC 0.019 0.093 0.26 30 -0.57 22 52
EGFR -0.19 0.28 -10000 0 -0.57 390 390
Syndecan-3/EGFR -0.088 0.16 -10000 0 -0.3 335 335
AGRP 0.021 0.024 0.26 10 -10000 0 10
NCSTN 0.02 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.011 0.26 2 -10000 0 2
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.055 0.26 64 -10000 0 64
long-term memory 0.035 0.062 -10000 0 -0.35 16 16
Syndecan-3/IL8 0.021 0.081 0.28 9 -0.33 38 47
PSEN1 0.024 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
limb bud formation 0.002 0.055 -10000 0 -0.39 21 21
MC4R 0.023 0.026 0.26 13 -10000 0 13
SRC 0.023 0.005 -10000 0 -10000 0 0
PTN -0.23 0.29 0.26 2 -0.57 455 457
FGFR/FGF/Syndecan-3 0.002 0.056 -10000 0 -0.39 21 21
neuron projection morphogenesis -0.071 0.15 0.33 5 -0.29 261 266
Syndecan-3/AgRP 0.016 0.06 0.26 1 -0.36 22 23
Syndecan-3/AgRP/MC4R 0.038 0.068 0.3 2 -0.36 20 22
Fyn/Cortactin 0.028 0.021 -10000 0 -0.3 2 2
SDC3 0.002 0.056 -10000 0 -0.39 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.02 0.08 0.28 9 -0.33 38 47
IL8 0.025 0.099 0.26 60 -0.57 21 81
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 16 16
Syndecan-3/CASK 0 0.054 -10000 0 -0.36 23 23
alpha-MSH/MC4R 0.029 0.072 0.36 2 -0.41 22 24
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.014 0.14 0.42 85 -0.24 2 87
KIRREL -0.024 0.16 -10000 0 -0.57 87 87
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.014 0.14 0.24 2 -0.42 85 87
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.034 0.12 0.29 3 -0.32 84 87
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.008 0.088 0.24 1 -0.28 70 71
FYN 0.013 0.13 0.28 98 -0.3 83 181
mol:Ca2+ 0.031 0.11 0.31 1 -0.32 79 80
mol:DAG 0.032 0.11 0.29 2 -0.32 79 81
NPHS2 0.014 0.032 0.26 5 -10000 0 5
mol:IP3 0.032 0.11 0.29 2 -0.32 79 81
regulation of endocytosis 0.023 0.1 0.24 6 -0.29 83 89
Nephrin/NEPH1/podocin/Cholesterol 0.023 0.11 0.25 9 -0.32 84 93
establishment of cell polarity 0.014 0.14 0.24 2 -0.42 85 87
Nephrin/NEPH1/podocin/NCK1-2 0.043 0.11 0.32 1 -0.3 82 83
Nephrin/NEPH1/beta Arrestin2 0.026 0.11 0.25 6 -0.29 83 89
NPHS1 0.058 0.089 0.26 166 -10000 0 166
Nephrin/NEPH1/podocin 0.024 0.11 0.3 4 -0.31 83 87
TJP1 0.023 0.019 -10000 0 -0.57 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 0.033 0.12 0.3 2 -0.32 79 81
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.031 0.12 0.32 2 -0.32 81 83
GRB2 0.023 0.009 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.012 0.13 0.29 95 -0.31 89 184
cytoskeleton organization 0.003 0.11 0.29 12 -0.33 66 78
Nephrin/NEPH1 0.016 0.1 0.19 7 -0.3 85 92
Nephrin/NEPH1/ZO-1 0.025 0.12 -10000 0 -0.34 85 85
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 -0.033 0.15 -10000 0 -0.59 66 66
PDGF/PDGFRA/CRKL -0.011 0.11 -10000 0 -0.41 68 68
positive regulation of JUN kinase activity 0.024 0.083 -10000 0 -0.33 47 47
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.014 0.11 -10000 0 -0.43 66 66
AP1 -0.3 0.44 -10000 0 -0.96 323 323
mol:IP3 -0.036 0.11 -10000 0 -0.45 63 63
PLCG1 -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA/alphaV Integrin -0.011 0.11 -10000 0 -0.43 66 66
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.11 -10000 0 -0.45 63 63
CAV3 0.02 0.011 0.26 2 -10000 0 2
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
SHC/Grb2/SOS1 0.026 0.084 -10000 0 -0.33 47 47
PDGF/PDGFRA/Shf -0.011 0.11 -10000 0 -0.42 66 66
FOS -0.3 0.43 0.32 1 -0.94 323 324
JUN -0.038 0.044 -10000 0 -0.44 6 6
oligodendrocyte development -0.011 0.11 -10000 0 -0.42 66 66
GRB2 0.023 0.009 0.26 1 -10000 0 1
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:DAG -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA -0.033 0.15 -10000 0 -0.59 66 66
actin cytoskeleton reorganization -0.011 0.11 -10000 0 -0.42 66 66
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.012 0.11 -10000 0 -0.38 71 71
PDGF/PDGFRA/Crk/C3G 0.015 0.098 -10000 0 -0.36 66 66
JAK1 -0.027 0.1 0.23 1 -0.42 66 67
ELK1/SRF -0.035 0.091 0.32 1 -0.35 64 65
SHB 0.024 0.008 0.26 1 -10000 0 1
SHF 0.024 0.021 0.26 2 -0.57 1 3
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.047 0.11 0.22 1 -0.47 65 66
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.083 -10000 0 -0.33 47 47
PDGF/PDGFRA/SHB -0.011 0.11 -10000 0 -0.42 66 66
PDGF/PDGFRA/Caveolin-1 -0.099 0.22 -10000 0 -0.48 255 255
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.053 0.11 0.24 1 -0.43 65 66
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.012 0.11 -10000 0 -0.42 66 66
JAK-STAT cascade -0.027 0.1 0.23 1 -0.42 66 67
cell proliferation -0.011 0.11 -10000 0 -0.42 66 66
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.034 0.1 0.99 2 -10000 0 2
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.025 0.12 -10000 0 -0.38 10 10
RXRs/LXRs/DNA/Oxysterols -0.006 0.12 -10000 0 -0.43 13 13
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.004 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0 0.083 -10000 0 -0.3 62 62
RXRs/NUR77 -0.05 0.18 -10000 0 -0.35 265 265
RXRs/PPAR -0.1 0.17 -10000 0 -0.32 333 333
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 0.047 0.043 -10000 0 -0.31 12 12
RARA 0.023 0.012 0.26 2 -10000 0 2
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.036 0.041 -10000 0 -0.3 12 12
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.071 0.18 0.61 99 -10000 0 99
RARs/THRs/DNA/SMRT 0.002 0.079 -10000 0 -0.29 60 60
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 -0.028 0.15 -10000 0 -0.32 215 215
NR1H4 0.021 0.026 0.26 13 -10000 0 13
RXRs/LXRs/DNA -0.006 0.15 -10000 0 -0.3 195 195
NR1H2 0.027 0.012 -10000 0 -10000 0 0
NR1H3 0.028 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.021 0.14 -10000 0 -0.3 214 214
NR4A1 -0.028 0.17 -10000 0 -0.57 95 95
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.031 0.1 -10000 0 -0.23 190 190
RXRG -0.098 0.24 0.26 2 -0.56 219 221
RXR alpha/CCPG 0.035 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.012 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB -0.006 0.13 -10000 0 -0.57 55 55
PPARG -0.12 0.25 -10000 0 -0.57 252 252
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.009 0.14 -10000 0 -1.1 9 9
mol:Oxysterols 0.004 0.009 -10000 0 -0.12 1 1
cholesterol transport -0.005 0.12 -10000 0 -0.43 13 13
PPARA 0.02 0.044 -10000 0 -0.57 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.016 0.067 -10000 0 -0.57 14 14
RXRs/NUR77/BCL2 -0.069 0.15 -10000 0 -0.3 267 267
SREBF1 -0.006 0.11 0.44 1 -0.57 1 2
RXRs/RXRs/DNA/9cRA -0.028 0.15 -10000 0 -0.32 215 215
ABCA1 -0.01 0.13 -10000 0 -0.84 8 8
RARs/THRs 0.04 0.096 -10000 0 -0.33 60 60
RXRs/FXR -0.024 0.16 -10000 0 -0.33 214 214
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.033 0.043 -10000 0 -0.31 13 13
RGS9BP 0.036 0.052 0.26 57 -10000 0 57
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.016 0.26 4 -10000 0 4
mol:Na + 0.037 0.045 -10000 0 -10000 0 0
mol:ADP -0.006 0.025 0.25 5 -10000 0 5
GNAT2 0.024 0.015 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 86 87
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.015 0.18 5 -10000 0 5
GRK7 0.023 0.019 0.26 7 -10000 0 7
CNGB3 0.022 0.037 0.26 25 -10000 0 25
Cone Metarhodopsin II/X-Arrestin 0.015 0.014 0.18 8 -10000 0 8
mol:Ca2+ 0.12 0.1 0.29 177 -10000 0 177
Cone PDE6 0.031 0.11 0.32 2 -0.31 82 84
Cone Metarhodopsin II 0.025 0.017 -10000 0 -10000 0 0
Na + (4 Units) 0.11 0.092 0.31 69 -10000 0 69
GNAT2/GDP 0.025 0.1 0.28 3 -0.31 85 88
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.032 0.19 10 -10000 0 10
Cone Transducin 0.036 0.046 -10000 0 -0.33 13 13
SLC24A2 0.16 0.12 0.26 621 -10000 0 621
GNB3/GNGT2 0.026 0.053 -10000 0 -0.4 14 14
GNB3 0.018 0.064 0.26 5 -0.57 12 17
GNAT2/GTP 0.018 0.01 0.18 4 -10000 0 4
CNGA3 0.045 0.068 0.26 101 -10000 0 101
ARR3 0.021 0.021 0.26 8 -10000 0 8
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.038 0.045 -10000 0 -10000 0 0
mol:Pi 0.016 0.12 0.33 1 -0.36 86 87
Cone CNG Channel 0.049 0.043 0.28 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.16 0.12 0.26 621 -10000 0 621
RGS9 -0.024 0.16 0.26 11 -0.57 88 99
PDE6C 0.019 0.008 0.26 1 -10000 0 1
GNGT2 0.021 0.026 -10000 0 -0.57 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.26 5 -10000 0 5
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.022 0.026 -10000 0 -0.57 2 2
LAT2 -0.02 0.1 -10000 0 -0.36 57 57
AP1 -0.058 0.18 -10000 0 -0.44 121 121
mol:PIP3 0.009 0.17 0.34 48 -0.42 55 103
IKBKB 0.033 0.13 0.28 120 -0.26 28 148
AKT1 0.012 0.17 0.32 146 -0.44 22 168
IKBKG 0.016 0.11 0.25 75 -0.27 32 107
MS4A2 -0.022 0.15 0.25 5 -0.55 82 87
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.12 0.3 25 -0.39 32 57
mol:Ca2+ 0.014 0.14 0.3 57 -0.32 53 110
LYN 0.022 0.012 -10000 0 -10000 0 0
CBLB -0.019 0.1 -10000 0 -0.36 55 55
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0.001 0.12 -10000 0 -0.33 124 124
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.004 0.17 0.33 126 -0.33 136 262
PTPN13 -0.015 0.15 -10000 0 -0.55 44 44
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.012 0.13 0.32 40 -0.34 31 71
SYK 0.025 0.01 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.027 0.13 -10000 0 -0.43 57 57
LAT -0.019 0.1 -10000 0 -0.36 57 57
PAK2 0.012 0.13 0.29 31 -0.43 31 62
NFATC2 -0.049 0.16 -10000 0 -0.6 76 76
HRAS 0.008 0.13 0.27 20 -0.46 34 54
GAB2 0.021 0.019 -10000 0 -0.57 1 1
PLA2G1B 0.002 0.098 -10000 0 -0.84 12 12
Fc epsilon R1 -0.022 0.16 -10000 0 -0.4 145 145
Antigen/IgE/Fc epsilon R1 -0.018 0.14 -10000 0 -0.36 144 144
mol:GDP -0.014 0.12 0.25 1 -0.47 33 34
JUN 0.02 0.044 -10000 0 -0.57 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
FOS -0.14 0.27 -10000 0 -0.57 306 306
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.36 63 63
CHUK 0.015 0.11 0.25 74 -0.27 33 107
KLRG1 -0.018 0.097 -10000 0 -0.32 57 57
VAV1 -0.02 0.1 -10000 0 -0.37 57 57
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.1 -10000 0 -0.36 55 55
negative regulation of mast cell degranulation -0.007 0.098 -10000 0 -0.38 31 31
BTK -0.013 0.11 -10000 0 -0.48 32 32
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.03 0.13 -10000 0 -0.36 114 114
GAB2/PI3K/SHP2 -0.048 0.1 -10000 0 -0.33 89 89
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 -10000 0 -0.31 92 92
RAF1 0.002 0.1 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0.001 0.15 -10000 0 -0.35 146 146
FCER1G 0.019 0.017 0.25 1 -10000 0 1
FCER1A -0.044 0.18 -10000 0 -0.57 115 115
Antigen/IgE/Fc epsilon R1/Fyn -0.009 0.14 -10000 0 -0.34 140 140
MAPK3 0.003 0.099 -10000 0 -0.86 12 12
MAPK1 -0.002 0.1 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.18 -10000 0 -0.59 70 70
DUSP1 -0.045 0.19 -10000 0 -0.57 126 126
NF-kappa-B/RelA 0.007 0.058 0.14 5 -0.18 15 20
actin cytoskeleton reorganization -0.008 0.15 -10000 0 -0.57 37 37
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.12 -10000 0 -0.45 32 32
FER -0.021 0.11 -10000 0 -0.37 61 61
RELA 0.023 0.005 -10000 0 -10000 0 0
ITK -0.012 0.091 -10000 0 -0.4 48 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.004 0.13 0.28 9 -0.48 32 41
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.018 0.1 0.21 2 -0.36 57 59
PTK2 -0.009 0.15 -10000 0 -0.6 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.024 0.14 -10000 0 -0.44 59 59
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.006 0.16 0.32 45 -0.42 59 104
MAP2K2 -0.001 0.098 -10000 0 -0.85 12 12
MAP2K1 0 0.099 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.095 -10000 0 -0.36 32 32
MAP2K4 -0.072 0.29 -10000 0 -0.83 133 133
Fc epsilon R1/FcgammaRIIB -0.008 0.15 -10000 0 -0.37 146 146
mol:Choline -0.004 0.17 0.33 126 -0.32 136 262
SHC/Grb2/SOS1 0.011 0.11 -10000 0 -0.42 29 29
FYN 0.022 0.026 -10000 0 -0.57 2 2
DOK1 0.025 0.014 0.26 4 -10000 0 4
PXN -0.009 0.14 -10000 0 -0.55 36 36
HCLS1 -0.019 0.1 -10000 0 -0.36 58 58
PRKCB 0.013 0.14 0.28 72 -0.36 40 112
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.007 0.1 -10000 0 -0.38 31 31
LCP2 0.024 0.008 0.26 1 -10000 0 1
PLA2G4A -0.045 0.14 -10000 0 -0.36 131 131
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.17 0.33 126 -0.32 136 262
IKK complex 0.031 0.11 0.25 116 -0.21 20 136
WIPF1 0.024 0.003 -10000 0 -10000 0 0
Canonical Wnt signaling 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
HDAC1 0.022 0.021 0.24 2 -10000 0 2
AES 0.022 0.019 0.21 2 -10000 0 2
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.009 0.095 0.26 2 -0.57 28 30
TLE1 0.019 0.048 0.22 1 -0.57 6 7
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.3 42 -0.36 5 47
WIF1 -0.28 0.3 0.26 13 -0.56 544 557
beta catenin/RanBP3 0.02 0.089 0.42 37 -0.4 1 38
KREMEN2 0.12 0.12 0.26 473 -10000 0 473
DKK1 0.026 0.16 0.26 146 -0.57 54 200
beta catenin/beta TrCP1 0.11 0.094 0.3 36 -0.35 3 39
FZD1 0.024 0.004 -10000 0 -10000 0 0
AXIN2 0.016 0.26 0.6 83 -1.3 22 105
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.046 0.076 -10000 0 -0.56 12 12
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.13 0.29 10 -0.57 24 34
Axin1/APC/GSK3 0.047 0.053 0.24 2 -0.31 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.063 0.31 2 -0.4 4 6
HNF1A 0.025 0.028 0.25 11 -10000 0 11
CTBP1 0.021 0.02 0.25 2 -10000 0 2
MYC 0.11 0.33 0.57 261 -1.3 24 285
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.099 0.34 1 -0.33 22 23
NKD1 0.022 0.053 0.26 16 -0.57 6 22
TCF4 0.016 0.062 0.23 2 -0.56 11 13
TCF3 0.022 0.022 0.25 4 -10000 0 4
WNT1/LRP6/FZD1/Axin1 0.057 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.005 0.12 0.45 36 -0.5 15 51
LEF1 0.052 0.082 0.25 140 -0.53 1 141
DVL1 0.055 0.053 0.22 1 -0.36 2 3
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.14 0.32 3 -0.61 27 30
DKK1/LRP6/Kremen 2 0.099 0.14 0.34 80 -0.34 47 127
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.24 2 -10000 0 2
NLK 0.023 0.014 0.25 2 -10000 0 2
CCND1 0.091 0.26 0.61 181 -1.2 6 187
WNT1 0.024 0.011 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -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 0.055 0.29 5 -0.29 10 15
APC 0.016 0.056 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.22 518 -0.24 1 519
CREBBP 0.021 0.018 0.27 1 -10000 0 1
Syndecan-2-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
Syndecan-2/Fibronectin 0.094 0.1 0.21 421 -0.34 2 423
EPHB2 0.027 0.031 0.26 19 -10000 0 19
Syndecan-2/TACI 0.024 0.06 0.2 63 -0.33 14 77
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
Syndecan-2/alpha2 ITGB1 -0.038 0.15 -10000 0 -0.32 201 201
HRAS 0.026 0.022 0.26 9 -10000 0 9
Syndecan-2/CASK 0.005 0.016 -10000 0 -0.35 2 2
ITGA5 0.024 0.007 0.26 1 -10000 0 1
BAX 0.002 0.031 0.45 1 -10000 0 1
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.018 -10000 0 -0.32 2 2
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
EZR 0.023 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.052 0.2 -10000 0 -0.57 138 138
Syndecan-2/MMP2 0.015 0.038 0.18 1 -0.36 9 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.071 -10000 0 -0.42 26 26
dendrite morphogenesis 0.022 0.033 0.21 19 -0.35 2 21
Syndecan-2/GM-CSF 0.022 0.036 0.21 26 -0.36 2 28
determination of left/right symmetry 0.007 0.019 -10000 0 -0.41 2 2
Syndecan-2/PKC delta 0.019 0.021 0.31 1 -0.35 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.073 0.19 172 -0.32 2 174
MAPK1 0.037 0.076 0.19 196 -0.32 2 198
Syndecan-2/RACK1 0.03 0.026 0.26 2 -0.31 2 4
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.019 -10000 0 -0.41 2 2
ITGA2 0.008 0.094 -10000 0 -0.57 28 28
MAPK8 0.005 0.033 0.27 5 -0.35 6 11
Syndecan-2/alpha2/beta1 Integrin 0.004 0.12 -10000 0 -0.35 84 84
Syndecan-2/Kininogen 0.02 0.033 0.21 20 -0.36 2 22
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.069 0.24 18 -0.29 2 20
Syndecan-2/CASK/Protein 4.1 0.017 0.018 -10000 0 -0.32 2 2
extracellular matrix organization 0.02 0.023 0.24 3 -0.35 2 5
actin cytoskeleton reorganization 0.093 0.1 0.21 421 -0.34 2 423
Syndecan-2/Caveolin-2/Ras -0.009 0.11 0.27 2 -0.33 104 106
Syndecan-2/Laminin alpha3 -0.057 0.14 -10000 0 -0.35 190 190
Syndecan-2/RasGAP 0.038 0.03 0.26 2 -0.3 2 4
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.022 0.033 0.21 19 -0.35 2 21
GO:0007205 0.002 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.024 -10000 0 -0.29 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.028 0.084 0.26 63 -0.57 12 75
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.071 -10000 0 -0.42 26 26
Syndecan-2/Synbindin 0.018 0.02 -10000 0 -0.34 2 2
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CASP3 0.042 0.071 0.19 190 -0.32 2 192
FN1 0.11 0.11 0.26 421 -10000 0 421
Syndecan-2/IL8 0.023 0.07 0.21 60 -0.36 19 79
SDC2 0.007 0.019 -10000 0 -0.41 2 2
KNG1 0.023 0.032 0.26 20 -10000 0 20
Syndecan-2/Neurofibromin 0.018 0.02 -10000 0 -0.35 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.026 0.036 0.26 26 -10000 0 26
Syndecan-2/TGFB1 0.02 0.023 0.24 3 -0.35 2 5
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.018 -10000 0 -0.32 2 2
Syndecan-2/Ezrin 0.029 0.025 0.29 1 -0.32 2 3
PRKACA 0.044 0.072 0.19 203 -0.32 2 205
angiogenesis 0.023 0.07 0.21 60 -0.35 19 79
MMP2 0.018 0.048 0.26 1 -0.57 7 8
IL8 0.025 0.099 0.26 60 -0.57 21 81
calcineurin-NFAT signaling pathway 0.024 0.06 0.2 63 -0.32 14 77
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.084 -10000 0 -0.41 32 32
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.028 0.17 -10000 0 -0.57 95 95
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.044 -10000 0 -0.57 6 6
AP1 -0.074 0.15 -10000 0 -0.31 293 293
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.021 0.036 -10000 0 -0.57 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.1 -10000 0 -0.63 19 19
NICD/RBPSUH 0.02 0.081 -10000 0 -0.4 32 32
WIF1 -0.27 0.3 0.26 13 -0.57 544 557
NOTCH1 0.008 0.075 -10000 0 -0.43 29 29
PSENEN 0.024 0.011 0.26 2 -10000 0 2
KREMEN2 0.12 0.12 0.26 473 -10000 0 473
DKK1 0.026 0.16 0.26 146 -0.57 54 200
beta catenin/beta TrCP1 0.009 0.067 -10000 0 -0.34 6 6
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.061 0.25 1 -0.45 9 10
CtBP/CBP/TCF1/TLE1/AES 0.012 0.038 -10000 0 -0.29 6 6
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 306 306
JUN 0.02 0.044 -10000 0 -0.57 6 6
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 0 0.066 0.25 1 -0.37 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.099 0.34 1 -0.33 22 23
HNF1A 0.025 0.02 0.25 8 -10000 0 8
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.013 0.21 -10000 0 -1.3 27 27
NKD1 0.022 0.053 0.26 16 -0.57 6 22
FZD1 0.024 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.006 0.12 -10000 0 -0.44 32 32
apoptosis -0.074 0.15 -10000 0 -0.31 293 293
Delta 1/NOTCHprecursor 0.018 0.083 -10000 0 -0.4 32 32
DLL1 0.02 0.041 -10000 0 -0.57 5 5
PPARD 0.015 0.092 -10000 0 -0.82 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.31 1 1
APC 0.004 0.082 -10000 0 -0.46 23 23
DVL1 -0.029 0.077 -10000 0 -0.36 35 35
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.099 0.14 0.34 80 -0.34 47 127
LRP6 0.023 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.009 -10000 0 -10000 0 0
CCND1 0.02 0.1 -10000 0 -1.1 7 7
WNT1 0.023 0.011 0.26 2 -10000 0 2
Axin1/APC/beta catenin 0.013 0.098 0.32 5 -0.42 19 24
DKK2 0.009 0.095 0.26 2 -0.57 28 30
NOTCH1 precursor/DVL1 -0.02 0.11 -10000 0 -0.53 34 34
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.003 0.12 -10000 0 -0.44 32 32
PPP2R5D -0.004 0.057 0.29 5 -0.34 19 24
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.19 -10000 0 -0.33 526 526
RBPJ 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.38 0.28 -10000 0 -0.57 728 728
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.029 0.049 -10000 0 -0.28 10 10
HIF1A 0.004 0.029 -10000 0 -0.27 11 11
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.037 0.28 1 -10000 0 1
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.059 0.085 0.26 170 -10000 0 170
ARNT/IPAS -0.25 0.2 -10000 0 -0.38 728 728
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.046 -10000 0 -0.28 15 15
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.05 -10000 0 -0.28 16 16
PHD1-3/OS9 0.056 0.048 -10000 0 -0.33 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.042 0.054 0.31 1 -0.3 5 6
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.049 -10000 0 -0.28 14 14
EGLN3 0.04 0.063 0.26 77 -0.57 1 78
EGLN2 0.025 0.016 0.26 5 -10000 0 5
EGLN1 0.02 0.02 -10000 0 -0.57 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.065 -10000 0 -0.51 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.052 0.073 0.28 8 -0.27 14 22
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
alphaV beta3 Integrin 0.021 0.079 -10000 0 -0.42 33 33
PTK2 -0.04 0.16 -10000 0 -0.48 91 91
positive regulation of JNK cascade -0.021 0.12 -10000 0 -0.32 129 129
CDC42/GDP -0.018 0.17 0.42 1 -0.43 130 131
Rac1/GDP -0.018 0.17 -10000 0 -0.42 132 132
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 -0.022 0.15 -10000 0 -0.39 127 127
nectin-3/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
RAPGEF1 -0.036 0.17 0.37 2 -0.47 117 119
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.05 0.18 -10000 0 -0.52 121 121
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.56 4 4
TLN1 -0.024 0.071 -10000 0 -0.4 14 14
Rap1/GTP -0.024 0.12 -10000 0 -0.34 110 110
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.039 0.2 0.44 1 -0.52 135 136
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.018 0.13 -10000 0 -0.34 116 116
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.029 -10000 0 -0.42 3 3
positive regulation of lamellipodium assembly -0.02 0.13 -10000 0 -0.33 132 132
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.039 0.18 -10000 0 -0.57 114 114
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
CLDN1 0.007 0.12 0.26 23 -0.57 40 63
JAM-A/CLDN1 0.003 0.13 -10000 0 -0.35 112 112
SRC -0.056 0.21 -10000 0 -0.56 133 133
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.029 -10000 0 -0.42 3 3
FARP2 -0.038 0.2 0.43 1 -0.52 133 134
RAC1 0.024 0.003 -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) 0.002 0.13 -10000 0 -0.37 114 114
nectin-1/I-afadin 0.029 0.029 -10000 0 -0.42 3 3
nectin-2/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.001 0.13 -10000 0 -0.36 115 115
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.021 0.12 -10000 0 -0.32 129 129
alphaV/beta3 Integrin/Talin -0.006 0.1 0.26 2 -0.41 40 42
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
PIP5K1C -0.019 0.079 -10000 0 -0.43 14 14
VAV2 -0.038 0.21 0.43 1 -0.54 129 130
RAP1/GDP -0.014 0.16 0.39 1 -0.4 122 123
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.13 -10000 0 -0.37 114 114
nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
Rac1/GTP -0.022 0.16 -10000 0 -0.41 129 129
PTPRM -0.017 0.088 -10000 0 -0.25 116 116
E-cadherin/beta catenin/alpha catenin 0.047 0.062 -10000 0 -0.32 20 20
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.033 0.044 0.26 40 -10000 0 40
GPC2 0.049 0.081 0.26 126 -0.57 3 129
GPC2/Midkine 0.058 0.069 0.36 16 -0.42 3 19
neuron projection morphogenesis 0.057 0.069 0.36 16 -0.42 3 19
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.042 0.15 -10000 0 -0.32 238 238
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.13 9 -10000 0 9
GNB1/GNG2 0.026 0.043 -10000 0 -0.36 13 13
GNB1 0.023 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 -0.061 0.14 -10000 0 -0.31 251 251
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 0.034 0.081 251 -10000 0 251
GNAL -0.11 0.24 -10000 0 -0.57 235 235
GNG2 0.017 0.065 -10000 0 -0.57 13 13
CRH 0.017 0.023 0.26 9 -10000 0 9
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.031 -10000 0 -0.35 8 8
MAPK11 0.005 0.019 -10000 0 -0.35 3 3
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.056 0.2 -10000 0 -0.39 192 192
MAP3K8 0.009 0.051 -10000 0 -0.57 7 7
FOS -0.02 0.14 0.29 2 -0.45 50 52
PRKCA -0.002 0.086 0.24 1 -0.57 22 23
PTPN7 0.021 0.059 0.24 61 -10000 0 61
HRAS 0.024 0.022 0.25 9 -10000 0 9
PRKCB 0.006 0.079 0.25 19 -0.57 15 34
NRAS 0.023 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.036 -10000 0 -10000 0 0
MAPK3 0.008 0.09 -10000 0 -0.81 5 5
MAP2K1 -0.012 0.12 -10000 0 -0.5 45 45
ELK1 0.006 0.029 -10000 0 -10000 0 0
BRAF -0.012 0.099 -10000 0 -0.48 39 39
mol:GTP -0.002 0.003 -10000 0 -0.006 323 323
MAPK1 -0.009 0.12 -10000 0 -0.47 41 41
RAF1 -0.011 0.097 -10000 0 -0.48 39 39
KRAS 0.022 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.003 0.04 0.22 27 -10000 0 27
RFC1 -0.003 0.036 0.22 23 -10000 0 23
PRKDC 0.016 0.078 0.23 106 -10000 0 106
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.1 -10000 0 -0.63 22 22
FASLG/FAS/FADD/FAF1 -0.005 0.059 0.22 13 -0.28 15 28
MAP2K4 -0.084 0.18 0.39 2 -0.42 114 116
mol:ceramide -0.023 0.1 -10000 0 -0.38 28 28
GSN -0.006 0.053 0.22 26 -0.35 11 37
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.078 0.28 1 -0.37 17 18
FAS 0.003 0.044 -10000 0 -0.58 4 4
BID -0.018 0.02 -10000 0 -10000 0 0
MAP3K1 -0.047 0.12 0.31 2 -0.43 35 37
MAP3K7 0.011 0.019 -10000 0 -10000 0 0
RB1 -0.003 0.036 0.22 22 -10000 0 22
CFLAR 0.027 0.018 -10000 0 -0.54 1 1
HGF/MET -0.052 0.19 -10000 0 -0.4 233 233
ARHGDIB -0.001 0.042 0.22 33 -10000 0 33
FADD 0.006 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.059 0.35 11 -0.21 28 39
NFKB1 -0.044 0.12 -10000 0 -0.54 21 21
MAPK8 -0.15 0.26 0.56 2 -0.47 395 397
DFFA -0.004 0.036 0.22 22 -10000 0 22
DNA fragmentation during apoptosis -0.006 0.045 0.22 22 -10000 0 22
FAS/FADD/MET -0.038 0.14 -10000 0 -0.38 143 143
CFLAR/RIP1 0.039 0.018 -10000 0 -0.38 1 1
FAIM3 0.026 0.035 0.26 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.046 0.22 36 -10000 0 36
DFFB -0.004 0.037 0.22 22 -10000 0 22
CHUK -0.039 0.11 -10000 0 -0.53 17 17
FASLG 0.006 0.088 0.25 42 -0.58 15 57
FAS/FADD 0.009 0.039 -10000 0 -0.32 4 4
HGF -0.011 0.14 0.26 2 -0.57 65 67
LMNA -0.003 0.053 -10000 0 -10000 0 0
CASP6 -0.003 0.036 0.22 22 -10000 0 22
CASP10 0.004 0.04 -10000 0 -0.58 3 3
CASP3 0 0.042 0.27 22 -10000 0 22
PTPN13 0.01 0.091 -10000 0 -0.57 26 26
CASP8 -0.021 0.024 -10000 0 -10000 0 0
IL6 -0.43 0.62 -10000 0 -1.2 400 400
MET -0.073 0.22 -10000 0 -0.57 177 177
ICAD/CAD -0.006 0.032 0.2 11 -10000 0 11
FASLG/FAS/FADD/FAF1/Caspase 10 -0.024 0.1 -10000 0 -0.39 28 28
activation of caspase activity by cytochrome c -0.018 0.02 -10000 0 -10000 0 0
PAK2 -0.003 0.048 0.22 35 -10000 0 35
BCL2 0.008 0.094 -10000 0 -0.56 28 28
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.02 0.07 0.42 1 -0.26 51 52
CDKN1A -0.009 0.033 -10000 0 -0.76 2 2
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
BAX 0.025 0.014 0.26 4 -10000 0 4
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.02 0.041 -10000 0 -0.57 5 5
FOXO4 0.012 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 -0.32 0.3 0.26 26 -0.57 635 661
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.023 -10000 0 -0.42 1 1
PPARGC1A -0.09 0.24 0.26 10 -0.57 210 220
FHL2 0.022 0.041 0.26 1 -0.57 5 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.02 0.07 0.26 51 -0.42 1 52
SIRT1/FOXO3a 0.015 0.026 -10000 0 -0.2 3 3
SIRT1 0.022 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.023 -10000 0 -0.36 1 1
SIRT1/Histone H1b 0.028 0.043 -10000 0 -10000 0 0
apoptosis -0.044 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A -0.046 0.16 -10000 0 -0.36 208 208
p53/SIRT1 0.027 0.019 0.41 2 -10000 0 2
SIRT1/FOXO4 0.022 0.037 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.037 0.041 -10000 0 -0.33 10 10
HIST1H1E 0.021 0.03 0.2 6 -10000 0 6
SIRT1/p300 0.032 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.023 0.36 1 -10000 0 1
TP53 0.02 0.011 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.045 0.016 -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 -0.25 0.21 -10000 0 -0.42 628 628
ACSS2 -0.007 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.023 -10000 0 -0.36 1 1
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.012 0.14 -10000 0 -0.57 66 66
HRAS 0.026 0.022 0.26 9 -10000 0 9
EGFR -0.19 0.28 -10000 0 -0.57 390 390
AKT -0.014 0.12 0.28 7 -0.28 92 99
FOXO3 0.022 0.019 -10000 0 -0.57 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.041 -10000 0 -0.57 5 5
AKT3 0.014 0.06 -10000 0 -0.57 11 11
FOXO4 0.024 0.001 -10000 0 -10000 0 0
MET -0.073 0.22 -10000 0 -0.57 177 177
PIK3CA 0.023 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 0.016 0.073 0.26 4 -0.57 16 20
PIK3R3 0.024 0.008 0.26 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 -0.061 0.14 0.21 4 -0.34 162 166
ERBB2 0.02 0.02 -10000 0 -0.57 1 1
proliferation/survival/translation -0.006 0.089 0.32 49 -0.26 1 50
PI3K -0.05 0.14 0.25 13 -0.32 170 183
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.037 0.057 0.25 10 -0.16 2 12
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
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 0.012 0.041 -10000 0 -0.26 19 19
epithelial cell differentiation 0.037 0.052 -10000 0 -0.31 18 18
CYFIP2 0.028 0.048 0.26 26 -0.57 3 29
ENAH -0.003 0.059 0.3 11 -10000 0 11
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EPHA2 0.02 0.04 -10000 0 -0.57 5 5
MYO6 -0.011 0.05 0.36 1 -0.3 19 20
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.034 -10000 0 -0.36 3 3
AQP5 -0.18 0.26 0.31 2 -0.5 419 421
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.049 0.36 1 -0.3 18 19
regulation of calcium-dependent cell-cell adhesion -0.022 0.074 0.36 1 -0.29 62 63
EGF -0.082 0.23 0.26 2 -0.57 194 196
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.015 0.12 0.29 1 -0.47 55 56
cortical microtubule organization 0.037 0.052 -10000 0 -0.31 18 18
GO:0000145 -0.011 0.046 0.35 1 -0.28 18 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.041 0.053 -10000 0 -0.31 18 18
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
ARF6/GDP -0.02 0.037 -10000 0 -0.27 18 18
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0 0.048 -10000 0 -0.28 18 18
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.011 0.049 0.36 1 -0.3 18 19
ARF6/GTP 0.049 0.04 -10000 0 -0.31 5 5
CDH1 0.012 0.076 -10000 0 -0.57 18 18
EGFR/EGFR/EGF/EGF -0.14 0.2 -10000 0 -0.33 519 519
RhoA/GDP 0.038 0.051 -10000 0 -0.3 18 18
actin cytoskeleton organization -0.012 0.047 0.34 1 -0.29 19 20
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
DIAPH1 0.026 0.1 -10000 0 -0.64 4 4
Wnt receptor signaling pathway -0.037 0.052 0.31 18 -10000 0 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.037 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.013 0.048 0.35 1 -0.3 19 20
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.014 0.052 -10000 0 -0.29 25 25
Ephrin A1/EPHA2 0.026 0.051 -10000 0 -0.29 20 20
SEC6/SEC8 -0.021 0.04 -10000 0 -0.3 18 18
MGAT3 -0.022 0.075 0.36 1 -0.3 62 63
HGF/MET -0.039 0.15 -10000 0 -0.32 232 232
HGF -0.011 0.14 0.26 2 -0.57 65 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.012 0.042 -10000 0 -0.26 19 19
actin cable formation 0.042 0.094 0.3 45 -0.29 1 46
KIAA1543 -0.012 0.053 0.35 1 -0.33 18 19
KIFC3 -0.012 0.047 0.36 1 -0.3 18 19
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.011 0.048 -10000 0 -0.3 18 18
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.037 0.052 -10000 0 -0.31 18 18
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.011 0.047 0.36 1 -0.3 17 18
PIP5K1C -0.011 0.05 0.36 1 -0.3 18 19
LIMA1 0.024 0.018 -10000 0 -0.57 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.017 0.088 0.31 26 -10000 0 26
adherens junction assembly -0.021 0.1 0.3 3 -0.63 16 19
IGF-1R heterotetramer/IGF1 -0.041 0.15 -10000 0 -0.31 234 234
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
MET -0.073 0.22 -10000 0 -0.57 177 177
PLEKHA7 -0.012 0.056 0.36 1 -0.35 18 19
mol:GTP 0.043 0.037 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.007 0.066 0.37 7 -0.51 1 8
cortical actin cytoskeleton stabilization 0.012 0.041 -10000 0 -0.26 19 19
regulation of cell-cell adhesion -0.012 0.047 0.34 1 -0.29 19 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.012 0.042 -10000 0 -0.26 19 19
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.018 0.063 -10000 0 -0.36 36 36
ADCY5 -0.11 0.16 -10000 0 -0.36 328 328
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.009 0.062 -10000 0 -0.36 28 28
ADCY2 -0.03 0.1 0.24 8 -0.36 85 93
ADCY3 -0.007 0.003 -10000 0 -10000 0 0
ADCY8 -0.004 0.023 0.23 6 -10000 0 6
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.085 0.23 15 -0.26 28 43
Coregulation of Androgen receptor activity

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
NRIP1 0.012 0.04 -10000 0 -0.57 1 1
SVIL 0.01 0.052 -10000 0 -0.57 5 5
ZNF318 0.039 0.054 0.21 6 -10000 0 6
JMJD2C -0.001 0.042 0.11 32 -0.13 78 110
T-DHT/AR/Ubc9 -0.034 0.14 -10000 0 -0.36 149 149
CARM1 0.019 0.015 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.011 -10000 0 -10000 0 0
CTNNB1 0.014 0.029 -10000 0 -10000 0 0
AKT1 0.027 0.018 -10000 0 -10000 0 0
PTK2B 0.012 0.026 -10000 0 -10000 0 0
MED1 0.025 0.02 -10000 0 -10000 0 0
MAK 0.034 0.083 0.24 18 -0.54 11 29
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.01 0.052 -10000 0 -0.57 5 5
GSN 0.006 0.071 -10000 0 -0.57 12 12
NCOA2 -0.01 0.12 -10000 0 -0.57 48 48
NCOA6 0.013 0.033 -10000 0 -10000 0 0
DNA-PK 0.05 0.053 0.24 1 -10000 0 1
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.027 -10000 0 -10000 0 0
cell proliferation 0.004 0.11 0.35 1 -0.57 24 25
XRCC5 0.026 0.015 -10000 0 -10000 0 0
UBE3A 0.009 0.044 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.042 0.15 -10000 0 -0.38 161 161
FHL2 0.002 0.1 -10000 0 -0.86 7 7
RANBP9 0.013 0.033 -10000 0 -10000 0 0
JMJD1A -0.015 0.047 0.12 1 -0.14 131 132
CDK6 0.02 0.058 0.26 2 -0.57 10 12
TGFB1I1 0.01 0.046 -10000 0 -0.57 3 3
T-DHT/AR/CyclinD1 -0.042 0.14 -10000 0 -0.36 149 149
XRCC6 0.025 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.041 0.16 -10000 0 -0.35 177 177
CTDSP1 0.018 0.019 -10000 0 -10000 0 0
CTDSP2 0.034 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.039 -10000 0 -0.57 1 1
TCF4 0.024 0.066 -10000 0 -0.56 11 11
CDKN2A 0.063 0.088 0.26 170 -10000 0 170
SRF 0.032 0.023 -10000 0 -10000 0 0
NKX3-1 -0.047 0.096 -10000 0 -0.21 248 248
KLK3 -0.14 0.46 -10000 0 -1.4 126 126
TMF1 0.018 0.016 -10000 0 -10000 0 0
HNRNPA1 0.028 0.02 -10000 0 -10000 0 0
AOF2 -0.007 0.023 -10000 0 -0.069 126 126
APPL1 0.019 0.032 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.028 0.14 -10000 0 -0.35 154 154
AR -0.067 0.2 0.21 1 -0.58 141 142
UBA3 0.017 0.019 -10000 0 -10000 0 0
PATZ1 0.027 0.021 -10000 0 -10000 0 0
PAWR 0.018 0.024 -10000 0 -0.57 1 1
PRKDC 0.023 0.016 -10000 0 -10000 0 0
PA2G4 0.031 0.027 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.024 0.13 -10000 0 -0.32 141 141
RPS6KA3 0.008 0.062 -10000 0 -0.57 8 8
T-DHT/AR/ARA70 -0.037 0.14 -10000 0 -0.35 155 155
LATS2 0.027 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.022 0.14 -10000 0 -0.34 140 140
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.014 0.063 0.26 17 -0.57 7 24
KLK2 -0.076 0.27 0.34 1 -0.99 81 82
CASP8 0.026 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.041 0.15 -10000 0 -0.37 149 149
TMPRSS2 -0.13 0.33 -10000 0 -0.98 136 136
CCND1 0.012 0.042 0.26 1 -0.57 4 5
PIAS1 0.01 0.044 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.028 -10000 0 -0.07 166 166
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.003 0.063 -10000 0 -0.19 19 19
T-DHT/AR/CDK6 -0.035 0.14 -10000 0 -0.36 160 160
CMTM2 0.023 0.012 0.25 1 -10000 0 1
SNURF 0.012 0.082 -10000 0 -0.57 21 21
ZMIZ1 0.01 0.039 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.021 -10000 0 -10000 0 0
FKBP4 0.014 0.036 0.26 4 -10000 0 4
Aurora A signaling

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
Aurora A/GADD45A 0.044 0.041 -10000 0 -10000 0 0
BIRC5 0.18 0.11 0.26 711 -10000 0 711
NFKBIA 0.024 0.04 0.28 8 -10000 0 8
CPEB1 -0.079 0.22 0.26 1 -0.57 187 188
AKT1 0.023 0.04 0.29 7 -10000 0 7
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.033 0.036 0.2 1 -10000 0 1
NDEL1/TACC3 0.066 0.067 0.26 16 -10000 0 16
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.001 0.026 -10000 0 -10000 0 0
PAK1/Aurora A 0.04 0.043 0.27 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.09 0.067 0.27 26 -10000 0 26
TP53 0.022 0.051 -10000 0 -0.22 13 13
DLG7 0.022 0.03 0.18 1 -10000 0 1
AURKAIP1 0.026 0.024 0.26 11 -10000 0 11
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 0.069 0.071 0.28 16 -10000 0 16
G2/M transition of mitotic cell cycle 0.031 0.034 0.2 1 -10000 0 1
AURKA 0.037 0.045 0.24 1 -10000 0 1
AURKB 0.086 0.074 0.17 417 -10000 0 417
CDC25B 0.031 0.039 0.22 3 -10000 0 3
G2/M transition checkpoint 0.019 0.028 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.13 -10000 0 -0.3 177 177
Aurora A/CPEB -0.025 0.13 -10000 0 -0.3 177 177
Aurora A/TACC1/TRAP/chTOG 0.044 0.07 -10000 0 -0.3 22 22
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
centrosome duplication 0.04 0.043 0.27 2 -10000 0 2
regulation of centrosome cycle 0.064 0.066 0.26 16 -10000 0 16
spindle assembly 0.042 0.069 -10000 0 -0.3 22 22
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.087 0.28 29 -10000 0 29
CENPA 0.095 0.081 0.19 430 -0.21 3 433
Aurora A/PP2A 0.043 0.042 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.031 0.04 0.24 1 -10000 0 1
negative regulation of DNA binding 0.018 0.063 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.028 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.045 0.24 1 -10000 0 1
TACC1 0.006 0.089 -10000 0 -0.57 25 25
TACC3 0.058 0.083 0.26 162 -10000 0 162
Aurora A/Antizyme1 0.054 0.043 -10000 0 -10000 0 0
Aurora A/RasGAP 0.043 0.042 -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 -0.001 0.027 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.024 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.089 0.067 0.27 26 -10000 0 26
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.094 0.072 0.24 39 -10000 0 39
PAK1 0.023 0.019 0.26 6 -10000 0 6
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Syndecan-4-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
PTK2 0.083 0.1 0.3 6 -0.57 6 12
Syndecan-4/Syndesmos 0.094 0.1 0.37 7 -0.7 6 13
positive regulation of JNK cascade 0.083 0.13 0.36 8 -0.64 8 16
Syndecan-4/ADAM12 0.1 0.12 0.4 9 -0.72 6 15
CCL5 0.029 0.056 0.26 38 -0.57 4 42
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.007 0.26 1 -10000 0 1
SDCBP 0.021 0.008 -10000 0 -10000 0 0
PLG -0.008 0.034 0.25 8 -10000 0 8
ADAM12 0.036 0.061 0.26 64 -0.57 2 66
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.066 0.15 0.38 4 -0.74 8 12
Syndecan-4/CXCL12/CXCR4 0.087 0.14 0.38 6 -0.69 8 14
Syndecan-4/Laminin alpha3 0.033 0.15 0.38 5 -0.74 7 12
MDK 0.033 0.044 0.26 40 -10000 0 40
Syndecan-4/FZD7 0.094 0.12 0.38 6 -0.69 7 13
Syndecan-4/Midkine 0.1 0.11 0.38 11 -0.69 6 17
FZD7 0.013 0.082 -10000 0 -0.57 21 21
Syndecan-4/FGFR1/FGF -0.01 0.16 -10000 0 -0.54 18 18
THBS1 0.021 0.04 -10000 0 -0.57 5 5
integrin-mediated signaling pathway 0.092 0.12 0.36 7 -0.69 7 14
positive regulation of MAPKKK cascade 0.083 0.13 0.36 8 -0.64 8 16
Syndecan-4/TACI 0.098 0.12 0.37 13 -0.72 6 19
CXCR4 0.029 0.034 0.26 24 -10000 0 24
cell adhesion 0.06 0.083 0.25 83 -0.25 21 104
Syndecan-4/Dynamin 0.098 0.1 0.38 4 -0.73 6 10
Syndecan-4/TSP1 0.097 0.11 0.38 6 -0.72 6 12
Syndecan-4/GIPC 0.098 0.1 0.38 4 -0.73 6 10
Syndecan-4/RANTES 0.099 0.11 0.36 7 -0.72 6 13
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.024 0.22 0.7 96 -0.53 22 118
Syndecan-4/alpha-Actinin 0.098 0.1 0.38 5 -0.72 6 11
TFPI -0.005 0.13 0.26 1 -0.57 54 55
F2 0.025 0.034 0.26 13 -10000 0 13
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
positive regulation of cell adhesion 0 0.17 0.37 3 -0.55 32 35
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.092 0.26 11 -0.57 25 36
Syndecan-4/CXCL12 0.076 0.14 0.38 5 -0.72 8 13
FGF6 0.015 0.025 -10000 0 -0.57 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.019 0.15 -10000 0 -0.57 78 78
TNFRSF13B 0.028 0.084 0.26 63 -0.57 12 75
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
Syndecan-4/PI-4-5-P2 0.075 0.1 0.34 2 -0.72 6 8
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.25 416 -10000 0 416
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.012 0.025 -10000 0 -10000 0 0
vasculogenesis 0.095 0.1 0.37 6 -0.68 6 12
SDC4 0.087 0.1 0.37 6 -0.78 5 11
Syndecan-4/Tenascin C 0.093 0.12 0.38 6 -0.72 7 13
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.085 0.1 0.36 5 -0.7 6 11
MMP9 0.12 0.12 0.26 453 -0.56 1 454
Rac1/GTP 0.061 0.084 0.25 83 -0.25 21 104
cytoskeleton organization 0.092 0.1 0.36 7 -0.67 6 13
GIPC1 0.024 0.008 0.26 1 -10000 0 1
Syndecan-4/TFPI 0.085 0.13 0.38 5 -0.72 7 12
Regulation of Androgen receptor activity

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
HDAC1 0.008 0.01 -10000 0 -10000 0 0
SMARCC1 0.006 0.027 -10000 0 -0.5 2 2
REL 0.017 0.068 -10000 0 -0.57 14 14
HDAC7 -0.036 0.11 0.37 3 -0.39 47 50
JUN 0.019 0.044 -10000 0 -0.57 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.018 -10000 0 -0.57 1 1
KAT5 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.008 0.065 -10000 0 -0.43 23 23
FOXO1 0.019 0.041 -10000 0 -0.57 5 5
T-DHT/AR -0.023 0.12 0.33 1 -0.39 58 59
MAP2K6 0.002 0.088 0.24 1 -0.57 23 24
BRM/BAF57 0.026 0.027 -10000 0 -10000 0 0
MAP2K4 0.014 0.02 -10000 0 -10000 0 0
SMARCA2 0.018 0.018 -10000 0 -10000 0 0
PDE9A -0.061 0.26 -10000 0 -1 63 63
NCOA2 -0.008 0.12 -10000 0 -0.57 48 48
CEBPA 0.019 0.057 -10000 0 -0.57 10 10
EHMT2 0.021 0.012 -10000 0 -10000 0 0
cell proliferation 0.001 0.15 0.35 33 -0.44 27 60
NR0B1 0.027 0.042 0.26 35 -10000 0 35
EGR1 -0.16 0.27 -10000 0 -0.57 336 336
RXRs/9cRA -0.042 0.15 -10000 0 -0.33 215 215
AR/RACK1/Src -0.016 0.11 0.31 7 -0.36 36 43
AR/GR -0.028 0.12 0.29 1 -0.3 128 129
GNB2L1 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.016 5 5
MAPK8 -0.002 0.042 -10000 0 -0.43 8 8
T-DHT/AR/TIF2/CARM1 -0.017 0.12 0.32 1 -0.38 54 55
SRC -0.019 0.068 0.19 30 -0.34 27 57
NR3C1 0.018 0.06 -10000 0 -0.57 11 11
KLK3 -0.14 0.39 -10000 0 -1.2 130 130
APPBP2 0.016 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.015 0.097 0.42 1 -0.39 30 31
TMPRSS2 -0.12 0.36 -10000 0 -1 137 137
RXRG -0.1 0.24 0.26 2 -0.57 219 221
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.023 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.022 0.011 -10000 0 -10000 0 0
NR2C2 0.018 0.057 -10000 0 -0.57 10 10
KLK2 -0.051 0.2 0.32 5 -0.66 85 90
AR -0.04 0.11 -10000 0 -0.3 139 139
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.016 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 126 -0.023 42 168
GATA2 0.013 0.095 0.26 13 -0.57 26 39
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.25 444 -10000 0 444
T-DHT/AR/RACK1/Src -0.013 0.1 0.34 9 -0.38 31 40
positive regulation of transcription 0.013 0.094 0.26 13 -0.56 26 39
DNAJA1 0.017 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.022 0.029 -10000 0 -0.6 1 1
SPDEF -0.01 0.15 0.26 36 -0.57 68 104
T-DHT/AR/TIF2 -0.005 0.1 0.32 6 -0.38 29 35
T-DHT/AR/Hsp90 -0.016 0.097 0.33 3 -0.38 30 33
GSK3B 0.022 0.01 -10000 0 -10000 0 0
NR2C1 0.025 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.062 0.23 1 -0.35 28 29
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.025 0.016 -10000 0 -10000 0 0
POU2F1 0.009 0.05 -10000 0 -0.2 2 2
T-DHT/AR/DAX-1 -0.015 0.1 0.33 4 -0.39 31 35
CREBBP 0.022 0.007 -10000 0 -10000 0 0
SMARCE1 0.018 0.018 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.049 0.16 -10000 0 -0.32 275 275
TC10/GTP -0.039 0.14 -10000 0 -0.29 259 259
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.078 -10000 0 -0.34 41 41
HRAS 0.026 0.022 0.26 9 -10000 0 9
APS homodimer 0.034 0.046 0.26 45 -10000 0 45
GRB14 0.011 0.18 0.26 142 -0.57 80 222
FOXO3 -0.022 0.16 -10000 0 -0.6 74 74
AKT1 -0.02 0.11 0.32 8 -0.28 95 103
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.055 0.046 0.42 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.12 0.26 -10000 0 -0.57 267 267
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.024 -10000 0 -10000 0 0
CAV1 -0.083 0.15 -10000 0 -0.35 239 239
CBL/APS/CAP/Crk-II/C3G -0.028 0.16 -10000 0 -0.31 262 262
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.078 -10000 0 -0.34 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.075 -10000 0 -0.3 49 49
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.014 0.064 -10000 0 -0.36 14 14
RPS6KB1 -0.019 0.096 0.29 9 -0.48 1 10
PARD6A 0.023 0.019 0.26 6 -10000 0 6
CBL 0.022 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.038 -10000 0 -0.55 4 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.007 0.094 -10000 0 -0.28 20 20
HRAS/GTP -0.02 0.044 -10000 0 -0.28 24 24
Insulin Receptor 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.069 -10000 0 -0.32 26 26
PRKCI 0.013 0.059 -10000 0 -0.45 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.005 0.1 -10000 0 -0.29 117 117
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.035 -10000 0 -0.46 4 4
PI3K 0.037 0.079 -10000 0 -0.3 49 49
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 0.019 0.015 0.18 9 -10000 0 9
AKT2 -0.019 0.11 0.3 8 -0.28 99 107
PRKCZ 0.004 0.086 -10000 0 -0.48 17 17
SH2B2 0.034 0.046 0.26 45 -10000 0 45
SHC/SHIP 0.012 0.057 -10000 0 -0.3 28 28
F2RL2 0.046 0.12 0.26 155 -0.57 20 175
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.021 -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 0.033 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.039 0.17 -10000 0 -0.32 266 266
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.049 0.027 -10000 0 -10000 0 0
INPP5D -0.019 0.062 -10000 0 -0.31 41 41
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.02 0.14 -10000 0 -0.69 47 47
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
p62DOK/RasGAP 0.042 0.035 -10000 0 -0.47 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.31 41 41
GRB2 0.023 0.009 0.26 1 -10000 0 1
EIF4EBP1 -0.021 0.089 0.31 3 -0.48 1 4
PTPRA 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.052 -10000 0 -0.27 28 28
Insulin Receptor/Insulin/IRS1 0.029 0.074 -10000 0 -0.33 42 42
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.06 0.073 -10000 0 -0.31 20 20
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.025 0.26 2 -0.54 1 3
CDKN2C 0.014 0.028 -10000 0 -0.55 1 1
CDKN2A 0.06 0.085 0.26 170 -10000 0 170
CCND2 -0.016 0.036 0.2 2 -0.21 14 16
RB1 0.015 0.047 0.26 15 -0.23 8 23
CDK4 -0.017 0.037 0.21 2 -0.22 12 14
CDK6 -0.018 0.04 0.22 2 -0.2 24 26
G1/S progression -0.01 0.058 0.19 41 -0.27 15 56
Regulation of Telomerase

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
Telomerase catalytic core complex 0.058 0.13 0.45 12 -0.48 3 15
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.094 0.21 -10000 0 -0.41 319 319
IFNAR2 0.028 0.02 -10000 0 -0.57 1 1
AKT1 -0.003 0.088 -10000 0 -0.23 100 100
ER alpha/Oestrogen -0.026 0.16 0.18 115 -0.4 157 272
NFX1/SIN3/HDAC complex 0.023 0.058 0.24 1 -0.33 15 16
EGF -0.081 0.23 0.26 2 -0.56 194 196
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.055 0.12 0.41 5 -0.45 4 9
SAP18 0.024 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.022 -10000 0 -10000 0 0
WT1 0.14 0.12 0.26 533 -10000 0 533
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.005 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.051 0.1 -10000 0 -0.46 2 2
Mad/Max 0.041 0.014 -10000 0 -10000 0 0
TERT 0.058 0.13 0.46 11 -0.53 2 13
CCND1 0.081 0.16 0.51 29 -1 4 33
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.019 0.26 7 -10000 0 7
RBBP4 0.024 0.019 -10000 0 -0.56 1 1
TERF2 0.021 0.013 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.039 0.05 -10000 0 -0.4 4 4
CDKN1B 0.029 0.049 0.23 1 -0.67 3 4
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.015 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.022 0.044 -10000 0 -0.56 6 6
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.56 306 306
IFN-gamma/IRF1 0.064 0.063 0.38 2 -0.32 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.044 0.067 0.26 97 -10000 0 97
Telomerase 0.03 0.08 0.27 2 -0.6 6 8
IRF1 0.029 0.018 0.26 3 -10000 0 3
ESR1 -0.034 0.23 0.26 115 -0.56 151 266
KU/TER 0.034 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.056 0.23 1 -0.33 10 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.057 0.23 1 -0.34 10 11
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.012 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.014 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.008 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.06 0.13 0.44 3 -0.55 7 10
NR2F2 0.012 0.037 -10000 0 -0.57 3 3
MAPK3 0.006 0.019 -10000 0 -10000 0 0
MAPK1 0.006 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.022 0.014 0.25 3 -10000 0 3
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 0.012 0.016 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.56 390 390
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.2 0.25 -10000 0 -0.45 525 525
MYC 0.008 0.084 -10000 0 -0.57 22 22
IL2 0.029 0.024 0.26 8 -10000 0 8
KU 0.034 0.009 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.023 0.014 0.25 3 -10000 0 3
TRF2/BLM 0.043 0.045 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.068 0.12 0.44 6 -0.5 2 8
SP1/HDAC2 0.046 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.049 0.1 -10000 0 -0.46 2 2
Smad3/Myc 0.007 0.054 -10000 0 -0.36 20 20
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.058 0.081 0.26 146 -0.19 3 149
Telomerase/PinX1 0.041 0.097 -10000 0 -0.45 2 2
Telomerase/AKT1/mTOR/p70S6K 0.026 0.1 0.29 6 -0.55 15 21
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.045 0.095 -10000 0 -0.42 1 1
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.051 0.1 -10000 0 -0.46 2 2
E2F1 0.097 0.11 0.26 320 -10000 0 320
ZNFX1 0.024 0.006 -10000 0 -10000 0 0
PIF1 0.069 0.092 0.26 211 -10000 0 211
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.01 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.086 0.26 1 -0.57 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.091 0.12 -10000 0 -0.24 418 418
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 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 0.007 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.039 0.098 -10000 0 -0.36 67 67
PRKG1 -0.014 0.14 -10000 0 -0.57 69 69
DUSP8 0.022 0.031 -10000 0 -0.57 3 3
PGK/cGMP/p38 alpha -0.018 0.13 -10000 0 -0.36 83 83
apoptosis -0.038 0.093 -10000 0 -0.34 67 67
RAL/GTP 0.032 0.006 -10000 0 -10000 0 0
LYN 0.021 0.008 -10000 0 -10000 0 0
DUSP1 -0.045 0.19 -10000 0 -0.57 126 126
PAK1 0.023 0.019 0.26 6 -10000 0 6
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.024 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -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 0.008 0.26 1 -10000 0 1
RAC1-CDC42/GTP 0.031 0.008 -10000 0 -10000 0 0
MAPK11 -0.009 0.13 0.33 3 -0.42 45 48
BLK 0.051 0.087 0.26 151 -0.57 2 153
HCK 0.027 0.026 0.26 13 -10000 0 13
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.014 0.26 2 -10000 0 2
TRAF6/MEKK3 0.028 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.004 0.13 0.3 4 -0.4 60 64
positive regulation of innate immune response -0.01 0.15 0.35 4 -0.48 52 56
LCK 0.026 0.075 0.26 40 -0.57 11 51
p38alpha-beta/MKP7 -0.002 0.14 0.37 3 -0.47 47 50
p38alpha-beta/MKP5 -0.003 0.14 0.42 2 -0.48 42 44
PGK/cGMP -0.01 0.11 -10000 0 -0.42 69 69
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.032 0.17 0.42 2 -0.47 76 78
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.24 0.29 -10000 0 -0.57 478 478
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.014 0.26 3 -10000 0 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.012 0.12 0.49 7 -0.5 4 11
IL27/IL27R/JAK1 0.037 0.16 0.73 6 -0.87 5 11
TBX21 -0.001 0.17 0.5 15 -0.52 40 55
IL12B 0.075 0.098 0.26 227 -10000 0 227
IL12A -0.013 0.097 0.14 18 -0.42 57 75
IL6ST -0.041 0.19 -10000 0 -0.56 120 120
IL27RA/JAK1 0.022 0.079 0.64 1 -1.2 3 4
IL27 0.048 0.076 0.26 113 -10000 0 113
TYK2 0.03 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.097 0.16 1.1 1 -0.79 2 3
T-helper 2 cell differentiation -0.012 0.12 0.49 7 -0.5 4 11
T cell proliferation during immune response -0.012 0.12 0.49 7 -0.5 4 11
MAPKKK cascade 0.012 0.12 0.5 4 -0.49 7 11
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.033 0.26 19 -10000 0 19
IL12RB1 0.033 0.053 0.26 41 -0.57 2 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.009 0.18 0.47 32 -0.53 48 80
IL27/IL27R/JAK2/TYK2 0.012 0.12 0.51 4 -0.5 7 11
positive regulation of T cell mediated cytotoxicity 0.012 0.12 0.5 4 -0.49 7 11
STAT1 (dimer) 0.035 0.21 0.67 23 -0.67 18 41
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.024 0.12 0.44 4 -0.48 7 11
T cell proliferation -0.09 0.18 0.37 4 -0.48 70 74
IL12/IL12R/TYK2/JAK2 0.059 0.18 0.45 3 -0.73 27 30
IL17A -0.097 0.16 1.1 1 -0.79 2 3
mast cell activation -0.012 0.12 0.49 7 -0.5 4 11
IFNG 0.021 0.045 0.12 120 -0.11 5 125
T cell differentiation 0 0.006 0.022 4 -0.022 5 9
STAT3 (dimer) 0.023 0.12 0.44 4 -0.48 7 11
STAT5A (dimer) 0.021 0.12 0.47 3 -0.48 11 14
STAT4 (dimer) 0.011 0.14 0.44 4 -0.48 19 23
STAT4 0.001 0.12 0.26 1 -0.57 43 44
T cell activation -0.005 0.011 0.12 3 -0.1 6 9
IL27R/JAK2/TYK2 0.016 0.14 -10000 0 -1.1 3 3
GATA3 -0.023 0.27 0.62 37 -1.3 35 72
IL18 0.009 0.02 0.13 26 -10000 0 26
positive regulation of mast cell cytokine production 0.023 0.11 0.43 4 -0.47 7 11
IL27/EBI3 0.053 0.072 0.25 59 -0.35 7 66
IL27RA 0.01 0.081 0.74 1 -1.3 3 4
IL6 -0.18 0.28 0.26 1 -0.57 380 381
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.041 0.45 3 -0.52 1 4
IL1B 0.001 0.048 0.13 3 -0.42 14 17
EBI3 0.025 0.054 0.26 14 -0.57 6 20
TNF 0.006 0.043 0.14 10 -0.42 9 19
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 0.027 0.027 0.26 14 -10000 0 14
GNB1/GNG2 -0.016 0.048 -10000 0 -0.19 64 64
AKT1 0.023 0.092 0.36 10 -0.32 13 23
EGF -0.082 0.23 0.26 2 -0.57 194 196
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.06 0.25 2 -0.35 4 6
mol:Ca2+ 0.021 0.11 0.42 10 -0.31 66 76
LYN 0.013 0.056 0.25 2 -0.4 2 4
RhoA/GTP 0.009 0.045 0.13 3 -0.14 8 11
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.019 0.12 0.44 10 -0.35 62 72
GNG2 0.017 0.065 -10000 0 -0.57 13 13
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.58 39 39
G beta5/gamma2 -0.012 0.067 -10000 0 -0.26 62 62
PRKCH 0.017 0.12 0.45 8 -0.36 63 71
DNM1 0.02 0.048 0.26 1 -0.57 7 8
TXA2/TP beta/beta Arrestin3 0.008 0.031 -10000 0 -0.4 2 2
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.008 0.1 0.26 7 -0.57 32 39
G12 family/GTP 0 0.09 -10000 0 -0.31 59 59
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.02 0.041 -10000 0 -0.57 5 5
RhoA/GTP/ROCK1 0.031 0.014 -10000 0 -0.36 1 1
mol:GDP -0.011 0.099 0.37 33 -0.33 8 41
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 -0.014 0.14 -10000 0 -0.57 69 69
mol:IP3 0.019 0.14 0.46 9 -0.38 71 80
cell morphogenesis 0.031 0.014 -10000 0 -0.36 1 1
PLCB2 0.01 0.17 0.52 7 -0.52 74 81
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.026 0.072 0.25 7 -0.32 5 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.061 0.25 3 -0.37 3 6
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.026 0.021 0.26 9 -10000 0 9
PRKCB1 0.018 0.13 0.44 9 -0.38 64 73
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.014 0.17 0.54 7 -0.54 64 71
LCK 0.016 0.074 0.25 2 -0.38 12 14
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.32 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.1 -10000 0 -0.42 53 53
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.3 1 1
MAPK14 0.018 0.089 0.34 14 -0.24 30 44
TGM2/GTP 0.014 0.15 0.51 8 -0.44 58 66
MAPK11 0.017 0.089 0.34 14 -0.25 32 46
ARHGEF1 0.011 0.066 0.27 10 -0.19 27 37
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.02 0.13 0.47 9 -0.39 63 72
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.022 0.1 0.39 12 -0.28 59 71
cAMP biosynthetic process 0.016 0.13 0.43 9 -0.36 66 75
Gq family/GTP/EBP50 0.015 0.043 0.22 5 -0.22 17 22
actin cytoskeleton reorganization 0.031 0.014 -10000 0 -0.36 1 1
SRC 0.013 0.058 0.25 2 -0.32 5 7
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.047 0.1 0.26 2 -0.31 56 58
VCAM1 0.02 0.11 0.39 11 -0.31 62 73
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.58 39 39
platelet activation 0.023 0.12 0.43 12 -0.31 55 67
PGI2/IP 0.019 0.014 0.18 9 -10000 0 9
PRKACA 0.008 0.053 -10000 0 -0.28 32 32
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.48 35 35
TXA2/TP beta/beta Arrestin2 -0.006 0.066 -10000 0 -0.44 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.047 -10000 0 -0.26 30 30
mol:DAG 0.017 0.14 0.51 7 -0.43 64 71
EGFR -0.19 0.28 -10000 0 -0.57 390 390
TXA2/TP alpha 0.014 0.16 0.52 7 -0.49 68 75
Gq family/GTP 0.001 0.049 0.25 1 -0.22 45 46
YES1 0.014 0.061 0.25 2 -0.34 4 6
GNAI2/GTP 0.013 0.052 -10000 0 -0.28 17 17
PGD2/DP 0.005 0.076 0.18 7 -0.4 35 42
SLC9A3R1 0.036 0.054 0.26 60 -10000 0 60
FYN 0.012 0.059 0.26 1 -0.37 5 6
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.025 0.025 0.26 6 -0.57 1 7
PGK/cGMP 0.007 0.096 -10000 0 -0.36 69 69
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.034 0.072 -10000 0 -0.42 12 12
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.021 0.13 0.43 10 -0.38 59 69
PRKCB 0.02 0.13 0.41 11 -0.38 62 73
PRKCE 0.018 0.12 0.45 9 -0.36 60 69
PRKCD 0.017 0.13 0.46 8 -0.39 62 70
PRKCG 0.019 0.13 0.45 9 -0.39 62 71
muscle contraction 0.014 0.16 0.51 8 -0.5 64 72
PRKCZ 0.017 0.12 0.44 9 -0.35 62 71
ARR3 0.021 0.021 0.26 8 -10000 0 8
TXA2/TP beta 0.024 0.06 -10000 0 -0.3 17 17
PRKCQ 0.015 0.14 0.42 12 -0.39 65 77
MAPKKK cascade 0.014 0.15 0.5 7 -0.46 69 76
SELE 0.016 0.12 0.38 12 -0.39 61 73
TP beta/GNAI2/GDP/G beta/gamma 0.034 0.071 -10000 0 -0.42 13 13
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
GNA14 0.023 0.065 0.26 19 -0.57 10 29
chemotaxis 0.012 0.18 0.57 7 -0.61 63 70
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0.024 0.13 0.27 27 -0.38 42 69
IKBKB 0.024 0.09 0.36 5 -0.32 12 17
AKT1 0.04 0.11 0.27 81 -0.25 15 96
IKBKG 0.028 0.073 0.35 4 -0.31 5 9
CALM1 0.002 0.096 0.25 1 -0.42 21 22
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.025 0.16 0.36 12 -0.53 43 55
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.1 -10000 0 -0.35 46 46
DOK1 0.025 0.014 0.26 4 -10000 0 4
AP-1 -0.021 0.098 0.24 9 -0.24 60 69
LYN 0.021 0.008 -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 0.005 0.16 0.36 21 -0.44 95 116
CD22 -0.01 0.13 0.27 23 -0.44 64 87
CAMK2G 0.003 0.094 0.27 5 -0.41 18 23
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.086 -10000 0 -0.34 47 47
GO:0007205 0.002 0.1 -10000 0 -0.36 47 47
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0.002 0.1 0.26 1 -0.42 21 22
NFATC1 0.031 0.13 0.31 24 -0.45 33 57
B-cell antigen/BCR complex 0.005 0.16 0.36 21 -0.44 95 116
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.024 0.048 0.16 13 -0.12 46 59
HRAS 0.012 0.11 0.27 14 -0.38 29 43
NFKBIA 0.024 0.047 0.16 13 -0.12 45 58
NF-kappa-B/RelA/I kappa B beta 0.027 0.042 0.17 10 -10000 0 10
RasGAP/Csk 0.033 0.12 0.32 22 -0.36 68 90
mol:GDP 0.004 0.098 -10000 0 -0.34 41 41
PTEN 0.022 0.019 -10000 0 -0.57 1 1
CD79B 0.012 0.098 0.26 21 -0.57 27 48
NF-kappa-B/RelA/I kappa B alpha 0.028 0.042 0.17 10 -10000 0 10
GRB2 0.023 0.009 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.024 0.16 0.35 11 -0.49 52 63
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.003 0.1 -10000 0 -0.36 46 46
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.077 0.15 -10000 0 -0.43 82 82
CHUK 0.024 0.082 0.32 5 -0.32 16 21
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.019 0.095 -10000 0 -0.4 18 18
PTPN6 -0.012 0.12 0.28 9 -0.56 32 41
RELA 0.024 0.005 -10000 0 -10000 0 0
BCL2A1 0.025 0.035 0.16 10 -10000 0 10
VAV2 0.014 0.14 0.29 7 -0.6 28 35
ubiquitin-dependent protein catabolic process 0.026 0.047 0.16 13 -0.12 46 59
BTK 0.015 0.061 -10000 0 -0.97 4 4
CD19 0.006 0.14 0.27 33 -0.52 39 72
MAP4K1 0.033 0.054 0.26 48 -0.57 2 50
CD72 0.03 0.042 0.26 30 -0.57 1 31
PAG1 0.02 0.014 0.26 2 -10000 0 2
MAPK14 0.027 0.14 0.35 16 -0.46 40 56
SH3BP5 0.023 0.018 -10000 0 -0.57 1 1
PIK3AP1 0.004 0.11 -10000 0 -0.44 28 28
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.13 0.26 3 -0.42 74 77
RAF1 0.011 0.1 0.28 9 -0.41 19 28
RasGAP/p62DOK/SHIP 0.032 0.12 0.3 21 -0.35 68 89
CD79A -0.002 0.17 0.26 85 -0.57 81 166
re-entry into mitotic cell cycle -0.021 0.097 0.24 9 -0.24 60 69
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.097 0.27 26 -0.36 14 40
MAPK1 0.011 0.09 0.27 7 -0.36 17 24
CD72/SHP1 0.03 0.14 0.35 29 -0.54 31 60
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.025 0.14 0.34 17 -0.45 45 62
actin cytoskeleton organization 0.032 0.14 0.33 22 -0.51 28 50
NF-kappa-B/RelA 0.056 0.081 0.3 10 -0.21 1 11
Calcineurin 0.019 0.091 -10000 0 -0.39 16 16
PI3K -0.013 0.095 -10000 0 -0.44 28 28
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.006 0.11 -10000 0 -0.39 49 49
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.014 0.2 0.43 6 -0.7 50 56
DAPP1 -0.015 0.2 -10000 0 -0.79 51 51
cytokine secretion 0.032 0.13 0.3 26 -0.42 33 59
mol:DAG 0.003 0.1 -10000 0 -0.36 46 46
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
MAP2K1 0.011 0.097 0.28 10 -0.4 17 27
B-cell antigen/BCR complex/FcgammaRIIB 0.017 0.13 0.34 21 -0.41 68 89
mol:PI-3-4-5-P3 0.006 0.089 0.24 9 -0.32 24 33
ETS1 0.001 0.089 0.28 2 -0.39 19 21
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.13 0.33 21 -0.36 73 94
B-cell antigen/BCR complex/LYN -0.01 0.13 0.29 5 -0.45 67 72
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.14 0.32 18 -0.55 28 46
B-cell antigen/BCR complex/LYN/SYK 0.016 0.14 0.35 23 -0.44 58 81
CARD11 0.004 0.1 0.28 5 -0.44 21 26
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
PPP3CA 0.024 0.011 0.26 2 -10000 0 2
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 50 -0.14 4 54
PTPRC 0.021 0.041 0.26 12 -0.57 3 15
PDPK1 0.02 0.082 0.22 53 -0.23 20 73
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.009 -10000 0 -10000 0 0
POU2F2 0.021 0.033 0.17 10 -10000 0 10
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 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.016 0.16 0.3 3 -0.39 148 151
AKT1 0.025 0.01 -10000 0 -10000 0 0
GSC -0.03 0.27 -10000 0 -1.3 41 41
NKX2-5 0.001 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.026 0.066 0.32 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.068 0.065 -10000 0 -0.44 1 1
SMAD4 0.012 0.045 -10000 0 -10000 0 0
CBFB 0.022 0.008 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.099 0.19 0.26 1 -0.36 379 380
SMAD3/SMAD4/VDR 0.055 0.058 -10000 0 -0.34 1 1
MYC 0.005 0.084 -10000 0 -0.57 22 22
CDKN2B -0.042 0.17 -10000 0 -1 16 16
AP1 -0.05 0.16 -10000 0 -0.3 293 293
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.01 0.086 -10000 0 -0.35 32 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.013 0.058 -10000 0 -0.34 11 11
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.046 0.081 0.26 127 -10000 0 127
SMAD3/SMAD4/GR 0.023 0.072 -10000 0 -0.39 11 11
GATA3 0.013 0.11 0.26 28 -0.56 35 63
SKI/SIN3/HDAC complex/NCoR1 0.005 0.076 -10000 0 -0.35 34 34
MEF2C/TIF2 0.023 0.087 0.32 3 -0.31 21 24
endothelial cell migration -0.029 0.094 0.57 13 -10000 0 13
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.019 0.26 7 -10000 0 7
RBBP4 0.023 0.018 -10000 0 -0.57 1 1
RUNX2 0.027 0.028 0.26 15 -10000 0 15
RUNX3 0.022 0.043 0.26 5 -0.57 5 10
RUNX1 0.023 0.019 -10000 0 -0.57 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.014 0.061 -10000 0 -0.57 11 11
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.016 0.078 -10000 0 -1.1 3 3
KAT2B 0.024 0.019 -10000 0 -0.57 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.078 0.3 1 -0.26 22 23
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.094 -10000 0 -0.6 11 11
SMAD3/SMAD4/ATF2 0.033 0.061 -10000 0 -0.36 4 4
SMAD3/SMAD4/ATF3 -0.011 0.14 -10000 0 -0.39 112 112
SAP30 0.024 0.015 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.041 0.031 -10000 0 -10000 0 0
JUN -0.059 0.15 0.29 1 -0.29 278 279
SMAD3/SMAD4/IRF7 0.052 0.081 0.32 25 -10000 0 25
TFE3 0.028 0.009 -10000 0 -10000 0 0
COL1A2 0.045 0.094 0.39 4 -0.6 8 12
mesenchymal cell differentiation -0.035 0.058 -10000 0 -10000 0 0
DLX1 0.055 0.1 0.26 168 -0.57 9 177
TCF3 0.024 0.009 0.26 1 -10000 0 1
FOS -0.14 0.27 -10000 0 -0.57 307 307
SMAD3/SMAD4/Max 0.028 0.058 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.044 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.013 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.034 0.055 -10000 0 -10000 0 0
IRF7 0.048 0.072 0.27 102 -10000 0 102
ESR1 -0.04 0.23 0.25 115 -0.57 151 266
HNF4A 0.023 0.032 0.26 20 -10000 0 20
MEF2C 0.047 0.086 0.4 8 -0.44 3 11
SMAD2-3/SMAD4 0.034 0.065 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.36 1 1
IGHV3OR16-13 0.006 0.039 -10000 0 -0.34 12 12
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.023 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.023 0.26 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.043 0.061 -10000 0 -0.45 1 1
MSG1/HSC70 -0.13 0.22 -10000 0 -0.42 401 401
SMAD2 0.022 0.03 -10000 0 -10000 0 0
SMAD3 0.015 0.04 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.042 -10000 0 -0.37 2 2
SMAD2/SMAD2/SMAD4 0.026 0.058 0.25 9 -0.51 3 12
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
MYOD/E2A 0.032 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.064 -10000 0 -0.41 1 1
IFNB1 0.022 0.071 0.32 29 -10000 0 29
SMAD3/SMAD4/MEF2C 0.065 0.084 0.31 1 -0.42 3 4
CITED1 -0.19 0.29 0.26 15 -0.57 400 415
SMAD2-3/SMAD4/ARC105 0.042 0.066 -10000 0 -10000 0 0
RBL1 0.023 0.027 0.26 1 -0.57 2 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.017 0.065 -10000 0 -0.48 9 9
RUNX1-3/PEBPB2 0.04 0.039 -10000 0 -0.42 5 5
SMAD7 -0.032 0.14 -10000 0 -0.42 29 29
MYC/MIZ-1 0.015 0.065 -10000 0 -0.42 22 22
SMAD3/SMAD4 0.032 0.073 0.3 24 -0.37 3 27
IL10 0.007 0.08 0.3 5 -0.36 30 35
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.021 0.01 -10000 0 -10000 0 0
CDK2 0.025 0.008 -10000 0 -10000 0 0
IL5 0.004 0.083 0.36 1 -0.35 34 35
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.041 0.18 0.26 1 -0.57 112 113
SMAD3/SMAD4/SP1 0.047 0.064 -10000 0 -0.37 2 2
FOXG1 0.017 0.067 0.26 74 -10000 0 74
FOXO3 0.011 0.017 -10000 0 -0.42 1 1
FOXO1 0.009 0.031 -10000 0 -0.42 5 5
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.047 0.086 0.4 8 -0.43 3 11
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.054 0.089 0.28 6 -0.39 9 15
MYOD1 0.021 0.027 0.26 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.033 0.058 -10000 0 -0.21 1 1
SMAD3/SMAD4/GATA3 0.029 0.098 0.35 1 -0.39 36 37
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.023 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.069 -10000 0 -0.4 4 4
SMAD3/SMAD4/SP1-3 0.062 0.062 -10000 0 -0.44 1 1
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.03 0.015 -10000 0 -0.2 1 1
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 0.056 0.074 0.28 1 -0.25 13 14
ITGB5 0.016 0.042 -10000 0 -0.4 1 1
TGIF/SIN3/HDAC complex/CtBP 0.013 0.061 -10000 0 -0.3 24 24
SMAD3/SMAD4/AR -0.019 0.15 -10000 0 -0.38 140 140
AR -0.053 0.2 0.26 1 -0.57 141 142
negative regulation of cell growth 0 0.083 -10000 0 -0.32 25 25
SMAD3/SMAD4/MYOD 0.032 0.057 -10000 0 -0.21 1 1
E2F5 0.022 0.021 0.26 7 -10000 0 7
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.073 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.055 -10000 0 -0.37 11 11
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.035 0.17 -10000 0 -0.3 279 279
SMAD3/SMAD4/RUNX2 0.035 0.058 -10000 0 -10000 0 0
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.022 0.031 -10000 0 -0.57 3 3
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.043 0.072 0.32 1 -0.3 33 34
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.082 0.35 11 -0.33 2 13
alphaV/beta3 Integrin/Osteopontin/Src 0.081 0.071 0.23 16 -10000 0 16
AP1 -0.036 0.18 -10000 0 -0.54 33 33
ILK 0.03 0.074 0.29 1 -0.32 28 29
bone resorption 0.019 0.088 -10000 0 -0.5 12 12
PTK2B 0.02 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.068 0.092 0.3 8 -0.3 23 31
ITGAV 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.022 0.075 -10000 0 -0.42 30 30
alphaV/beta3 Integrin/Osteopontin 0.077 0.1 0.34 4 -0.34 33 37
MAP3K1 0.029 0.077 0.26 14 -0.32 33 47
JUN 0.021 0.044 -10000 0 -0.57 6 6
MAPK3 0.02 0.069 0.27 11 -0.3 25 36
MAPK1 0.021 0.07 0.26 12 -0.3 25 37
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.015 0.082 0.26 15 -0.36 31 46
ITGB3 0.009 0.1 0.26 4 -0.56 33 37
NFKBIA 0.018 0.068 0.28 8 -0.34 4 12
FOS -0.14 0.27 -10000 0 -0.57 306 306
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.022 0.098 0.45 6 -0.55 2 8
NF kappa B1 p50/RelA 0.063 0.076 0.37 5 -10000 0 5
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.026 0.08 0.23 1 -0.41 33 34
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.03 0.075 0.25 14 -0.32 33 47
VAV3 0.017 0.075 0.26 16 -0.3 31 47
MAP3K14 0.031 0.075 0.26 10 -0.31 33 43
ROCK2 0.007 0.099 -10000 0 -0.57 31 31
SPP1 0.086 0.1 0.26 279 -10000 0 279
RAC1 0.024 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.069 0.3 3 -0.28 29 32
MMP2 -0.054 0.14 0.32 4 -0.51 31 35
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.001 0.064 -10000 0 -0.32 11 11
adherens junction organization -0.013 0.091 -10000 0 -0.38 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.085 0.15 0.34 3 -0.34 109 112
FMN1 -0.011 0.085 -10000 0 -0.34 29 29
mol:IP3 -0.001 0.053 -10000 0 -0.28 10 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.087 -10000 0 -0.35 29 29
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.002 0.063 -10000 0 -0.28 13 13
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.012 0.13 -10000 0 -0.56 32 32
CTNND1 0.024 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.075 -10000 0 -0.33 27 27
VASP -0.009 0.08 -10000 0 -0.33 27 27
ZYX -0.009 0.081 -10000 0 -0.34 28 28
JUB -0.008 0.082 -10000 0 -0.34 29 29
EGFR(dimer) -0.1 0.18 -10000 0 -0.41 139 139
E-cadherin/beta catenin-gamma catenin 0.033 0.055 -10000 0 -0.35 18 18
mol:PI-3-4-5-P3 0.016 0.073 -10000 0 -0.3 13 13
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.016 0.075 -10000 0 -0.3 13 13
FYN -0.003 0.067 -10000 0 -0.38 5 5
mol:Ca2+ -0.001 0.053 -10000 0 -0.28 10 10
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
mol:DAG -0.001 0.053 -10000 0 -0.28 10 10
CDH1 0.012 0.076 -10000 0 -0.57 18 18
RhoA/GDP -0.084 0.15 0.36 2 -0.34 104 106
establishment of polarity of embryonic epithelium -0.009 0.079 -10000 0 -0.33 27 27
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.57 390 390
CASR -0.003 0.055 0.23 2 -0.31 2 4
RhoA/GTP 0.013 0.057 -10000 0 -0.3 2 2
AKT2 0.001 0.063 -10000 0 -0.29 11 11
actin cable formation -0.016 0.086 0.25 2 -0.34 31 33
apoptosis -0.005 0.073 0.31 13 -0.24 8 21
CTNNA1 0.024 0.006 -10000 0 -10000 0 0
mol:GDP -0.097 0.15 -10000 0 -0.36 110 110
PIP5K1A -0.008 0.077 -10000 0 -0.34 27 27
PLCG1 -0.001 0.054 -10000 0 -0.29 10 10
Rac1/GTP -0.092 0.17 -10000 0 -0.39 131 131
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
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 0.02 -10000 0 -0.57 1 1
ELF1 0.03 0.054 -10000 0 -0.36 12 12
CCNA2 0.11 0.11 0.26 401 -10000 0 401
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.027 0.026 0.26 14 -10000 0 14
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.046 0.1 0.33 11 -0.49 13 24
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.024 0.045 -10000 0 -0.38 12 12
IL2RA 0.02 0.12 0.43 11 -0.76 15 26
IL2RB 0.031 0.05 0.26 38 -0.57 2 40
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.067 0.26 46 -0.57 7 53
G1/S transition of mitotic cell cycle 0.042 0.14 0.35 3 -0.8 17 20
PTPN11 0.025 0.003 -10000 0 -10000 0 0
CCND2 0.006 0.087 0.43 1 -0.8 12 13
LCK 0.027 0.075 0.26 40 -0.57 11 51
GRB2 0.023 0.009 0.26 1 -10000 0 1
IL2 0.022 0.021 0.26 8 -10000 0 8
CDK6 0.019 0.058 0.26 2 -0.57 10 12
CCND3 0.047 0.1 0.42 5 -0.57 5 10
TCGA08_p53

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
CDKN2A 0.025 0.046 0.13 170 -10000 0 170
TP53 0.009 0.018 -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 -0.011 0.06 0.29 31 -10000 0 31
MDM4 0.02 0.009 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
CDC42/GTP -0.005 0.096 -10000 0 -0.3 52 52
PLCG1 -0.012 0.087 -10000 0 -0.31 49 49
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 0.033 0.011 -10000 0 -10000 0 0
cell migration -0.005 0.094 -10000 0 -0.29 53 53
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
S1PR4 0.029 0.062 0.26 38 -0.57 6 44
MAPK3 -0.008 0.082 0.26 1 -0.31 40 41
MAPK1 -0.008 0.084 -10000 0 -0.32 44 44
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.27 88 88
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 0.18 17 -0.28 3 20
RHOA 0.006 0.058 0.18 86 -0.31 6 92
S1P/S1P4/Gi -0.004 0.094 -10000 0 -0.28 92 92
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
S1P/S1P4/G12/G13 0.044 0.041 -10000 0 -0.33 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
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 0.024 0.088 -10000 0 -0.58 13 13
oxygen homeostasis 0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.087 0.087 0.36 9 -0.35 3 12
EPO 0.15 0.17 0.5 82 -0.49 4 86
FIH (dimer) 0.032 0.02 -10000 0 -10000 0 0
APEX1 0.033 0.025 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.49 43 -0.54 5 48
FLT1 -0.018 0.17 -10000 0 -0.76 28 28
ADORA2A 0.16 0.17 0.49 66 -0.52 4 70
germ cell development 0.14 0.16 0.49 43 -0.52 4 47
SLC11A2 0.14 0.16 0.51 18 -0.54 4 22
BHLHE40 0.13 0.16 0.47 35 -0.55 5 40
HIF1AN 0.032 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.13 0.4 61 -0.38 3 64
ETS1 0.026 0.039 -10000 0 -0.58 4 4
CITED2 0.015 0.09 -10000 0 -0.5 26 26
KDR -0.017 0.18 -10000 0 -0.74 35 35
PGK1 0.14 0.16 0.47 37 -0.54 4 41
SIRT1 0.025 0.004 -10000 0 -10000 0 0
response to hypoxia 0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.6 17 -0.57 6 23
EPAS1 0.068 0.088 0.29 48 -0.37 6 54
SP1 0.029 0.012 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.47 39 -0.55 43 82
EFNA1 0.11 0.14 0.49 10 -0.51 4 14
FXN 0.15 0.16 0.46 52 -0.52 4 56
POU5F1 0.14 0.16 0.5 39 -0.54 4 43
neuron apoptosis -0.15 0.18 0.56 6 -0.59 17 23
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.047 0.067 0.27 76 -0.58 1 77
EGLN2 0.033 0.026 0.26 5 -10000 0 5
EGLN1 0.027 0.028 -10000 0 -0.58 1 1
VHL/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.028 0.024 -10000 0 -10000 0 0
SLC2A1 0.14 0.16 0.46 58 -0.5 5 63
TWIST1 0.13 0.19 0.46 50 -0.55 39 89
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.41 9 -0.39 2 11
VEGFA 0.13 0.16 0.48 35 -0.52 5 40
CREBBP 0.023 0.007 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.09 0.29 47 -10000 0 47
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 0.18 17 -0.28 3 20
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
RhoA/GTP -0.003 0.091 -10000 0 -0.29 47 47
negative regulation of cAMP metabolic process -0.004 0.088 -10000 0 -0.27 88 88
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.27 88 88
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
Signaling events mediated by PRL

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
CCNE1 0.062 0.087 0.26 179 -10000 0 179
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.018 0.057 -10000 0 -0.57 10 10
CDKN1A -0.031 0.093 -10000 0 -0.43 30 30
PRL-3/alpha Tubulin 0.03 0.019 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.075 0.24 44 -0.42 13 57
AGT 0.029 0.089 0.26 73 -0.57 13 86
CCNA2 -0.065 0.14 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.12 0.2 -10000 0 -0.41 336 336
CDK2/Cyclin E1 0.016 0.11 -10000 0 -0.48 17 17
MAPK3 0.01 0.018 0.26 4 -10000 0 4
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.018 0.26 4 -10000 0 4
PTP4A1 -0.093 0.14 -10000 0 -10000 0 0
PTP4A3 0.021 0.02 0.26 6 -10000 0 6
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.017 0.26 3 -10000 0 3
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 -0.016 0.071 -10000 0 -0.43 12 12
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.072 0.15 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.015 -10000 0 -10000 0 0
RHOC -0.019 0.079 -10000 0 -0.55 9 9
RHOA -0.021 0.089 -10000 0 -0.47 24 24
cell motility -0.026 0.1 -10000 0 -0.39 33 33
PRL-1/alpha Tubulin -0.073 0.15 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.041 -10000 0 -0.33 10 10
ROCK1 -0.024 0.098 -10000 0 -0.39 29 29
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.093 0.14 -10000 0 -10000 0 0
ATF5 0.025 0.013 0.26 3 -10000 0 3
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0.004 0.059 -10000 0 -0.38 5 5
BAG4 0.018 0.032 -10000 0 -0.57 3 3
PKC zeta/ceramide -0.001 0.052 -10000 0 -0.25 16 16
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BAX 0.002 0.041 -10000 0 -0.35 11 11
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.068 0.7 10 -10000 0 10
BAD -0.015 0.046 0.19 4 -0.25 14 18
SMPD1 0.015 0.056 0.2 12 -0.24 17 29
RB1 -0.015 0.044 -10000 0 -0.25 13 13
FADD/Caspase 8 0.028 0.086 0.26 12 -0.4 6 18
MAP2K4 -0.016 0.044 0.18 5 -0.3 8 13
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.056 0.19 33 -0.3 7 40
EGF -0.082 0.23 0.26 2 -0.57 194 196
mol:ceramide -0.014 0.048 -10000 0 -0.25 15 15
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.009 -10000 0 -10000 0 0
ASAH1 0.021 0.015 0.26 3 -10000 0 3
negative regulation of cell cycle -0.016 0.044 -10000 0 -0.25 13 13
cell proliferation -0.044 0.12 0.27 1 -0.27 204 205
BID -0.02 0.17 -10000 0 -0.66 60 60
MAP3K1 -0.015 0.047 0.19 4 -0.24 16 20
EIF2A -0.014 0.049 0.26 4 -0.24 7 11
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.006 0.054 0.28 3 -0.29 7 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.059 0.26 4 -0.33 5 9
Cathepsin D/ceramide 0.004 0.057 0.17 31 -0.24 14 45
FADD 0.006 0.059 0.22 12 -0.39 4 16
KSR1 -0.009 0.055 0.2 24 -0.25 13 37
MAPK8 -0.014 0.058 -10000 0 -0.26 22 22
PRKRA -0.015 0.047 0.2 4 -0.24 15 19
PDGFA 0.024 0.008 0.26 1 -10000 0 1
TRAF2 0.025 0.015 0.26 4 -10000 0 4
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.047 -10000 0 -0.25 15 15
CTSD 0.031 0.041 0.26 34 -10000 0 34
regulation of nitric oxide biosynthetic process 0.034 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.047 0.13 0.29 1 -0.29 203 204
PRKCD 0.024 0.009 0.26 1 -10000 0 1
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.034 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.018 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.044 -10000 0 -0.35 5 5
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 11 11
mol:Sphingosine-1-phosphate 0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.009 0.055 0.24 5 -0.3 6 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
CYCS 0 0.049 0.2 9 -0.24 9 18
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.42 3 3
EIF2AK2 -0.016 0.043 0.19 5 -0.28 7 12
TNF-alpha/TNFR1A/FAN 0.04 0.044 -10000 0 -0.36 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.077 -10000 0 -0.37 31 31
MAP2K2 -0.01 0.055 0.28 3 -0.3 6 9
SMPD3 -0.002 0.098 0.26 4 -0.29 95 99
TNF 0.024 0.065 0.26 25 -0.57 9 34
PKC zeta/PAR4 0.033 0.021 -10000 0 -0.42 2 2
mol:PHOSPHOCHOLINE 0.042 0.097 0.24 195 -0.24 2 197
NF kappa B1/RelA/I kappa B alpha 0.063 0.03 -10000 0 -0.31 2 2
AIFM1 -0.001 0.049 0.19 11 -0.25 8 19
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.009 0.11 0.26 2 -0.42 41 43
ACTA1 0.012 0.11 0.26 7 -0.48 31 38
NUMA1 0.004 0.11 0.26 2 -0.39 47 49
SPTAN1 -0.002 0.11 0.27 7 -0.48 32 39
LIMK1 -0.001 0.11 0.27 5 -0.49 31 36
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.014 0.26 4 -10000 0 4
CASP10 -0.011 0.09 0.2 11 -0.44 33 44
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.004 0.12 0.25 3 -0.43 47 50
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.001 0.1 0.27 7 -0.47 32 39
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.006 0.12 0.28 4 -0.47 40 44
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.013 0.13 -10000 0 -0.67 30 30
BID 0.003 0.053 0.18 3 -0.26 32 35
MAP3K1 -0.003 0.093 -10000 0 -0.41 43 43
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.001 0.11 0.26 7 -0.48 31 38
CASP9 0.023 0.005 -10000 0 -10000 0 0
DNA repair -0.016 0.043 0.22 6 -0.2 6 12
neuron apoptosis 0.004 0.12 -10000 0 -0.69 25 25
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.11 0.27 1 -0.45 38 39
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 0 0.15 -10000 0 -0.9 25 25
TRAF2 0.025 0.015 0.26 4 -10000 0 4
ICAD/CAD -0.004 0.1 0.25 1 -0.48 30 31
CASP7 0.002 0.06 0.26 5 -0.35 6 11
KRT18 0.015 0.079 -10000 0 -0.72 9 9
apoptosis 0.002 0.12 0.32 4 -0.53 29 33
DFFA -0.003 0.1 0.25 3 -0.48 32 35
DFFB -0.003 0.1 0.25 3 -0.48 32 35
PARP1 0.016 0.043 0.2 6 -0.22 6 12
actin filament polymerization 0.001 0.1 0.46 31 -0.3 8 39
TNF 0.024 0.065 0.26 25 -0.57 9 34
CYCS 0.005 0.048 0.21 6 -0.22 23 29
SATB1 -0.008 0.15 -10000 0 -0.78 30 30
SLK -0.002 0.1 0.28 4 -0.49 31 35
p15 BID/BAX 0.013 0.062 0.24 2 -0.24 36 38
CASP2 0.003 0.063 0.23 7 -0.38 6 13
JNK cascade 0.002 0.093 0.41 43 -10000 0 43
CASP3 0 0.11 0.26 4 -0.5 33 37
LMNB2 0.001 0.13 0.28 4 -0.51 42 46
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 0.032 -10000 0 -0.33 2 2
negative regulation of DNA binding 0.014 0.13 -10000 0 -0.66 30 30
stress fiber formation -0.002 0.1 0.28 4 -0.48 31 35
GZMB 0.011 0.1 0.27 11 -0.49 32 43
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.02 0.12 0.29 8 -0.54 25 33
APP 0.004 0.12 -10000 0 -0.7 25 25
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM 0.004 0.12 0.29 5 -0.44 47 52
LMNA 0.009 0.08 0.32 2 -0.38 20 22
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.066 -10000 0 -0.3 20 20
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.001 0.1 0.27 4 -0.49 30 34
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.61 38 38
nuclear fragmentation during apoptosis 0.004 0.1 0.26 2 -0.38 47 49
CFL2 -0.001 0.11 0.3 8 -0.47 31 39
GAS2 -0.025 0.14 0.27 6 -0.38 95 101
positive regulation of apoptosis 0.014 0.11 0.27 8 -0.5 30 38
PRF1 0.016 0.077 0.26 8 -0.57 17 25
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.077 -10000 0 -0.66 3 3
UGCG 0.009 0.12 -10000 0 -0.67 30 30
AKT1/mTOR/p70S6K/Hsp90/TERT 0.048 0.12 0.29 13 -0.41 29 42
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.12 -10000 0 -0.66 30 30
mol:DAG 0.004 0.085 -10000 0 -0.76 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.13 0.3 6 -0.4 57 63
FRAP1 0.031 0.15 0.33 6 -0.46 59 65
FOXO3 0.036 0.14 0.33 12 -0.48 36 48
AKT1 0.037 0.14 0.31 13 -0.5 39 52
GAB2 0.021 0.02 -10000 0 -0.57 1 1
SMPD1 0.01 0.11 -10000 0 -0.64 25 25
SGMS1 0.018 0.065 -10000 0 -0.54 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.039 -10000 0 -0.33 14 14
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.046 0.11 0.28 8 -0.44 27 35
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.05 -10000 0 -0.39 14 14
RPS6KB1 0.012 0.091 -10000 0 -0.84 10 10
mol:sphingomyelin 0.004 0.085 -10000 0 -0.76 12 12
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.027 0.027 0.26 14 -10000 0 14
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.065 0.2 0.39 14 -0.9 29 43
MYB 0.028 0.19 0.48 2 -1.1 24 26
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.036 0.11 0.28 20 -0.41 26 46
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.088 -10000 0 -0.75 10 10
mol:PI-3-4-5-P3 0.04 0.11 0.28 20 -0.4 26 46
Rac1/GDP 0.014 0.039 -10000 0 -0.33 12 12
T cell proliferation 0.04 0.1 0.29 12 -0.49 12 24
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.013 0.1 3 -0.076 23 26
PRKCZ 0.04 0.1 0.3 10 -0.51 12 22
NF kappa B1 p50/RelA 0.048 0.14 0.32 6 -0.42 51 57
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.075 0.29 11 -0.52 8 19
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
IL2RA 0.027 0.088 0.26 58 -0.57 15 73
IL2RB 0.031 0.051 0.26 38 -0.57 2 40
TERT 0.054 0.08 0.26 147 -10000 0 147
E2F1 0.051 0.094 0.33 2 -0.36 31 33
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.033 23 -0.05 3 26
PTPN11 0.023 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.26 46 -0.57 7 53
actin cytoskeleton organization 0.04 0.1 0.29 12 -0.49 12 24
GRB2 0.023 0.011 0.26 1 -10000 0 1
IL2 0.021 0.023 0.26 8 -10000 0 8
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.043 -10000 0 -0.31 12 12
LCK 0.027 0.075 0.26 40 -0.57 11 51
BCL2 0.019 0.19 0.42 2 -0.79 44 46
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.062 -10000 0 -0.39 20 20
forebrain development -0.043 0.2 0.35 1 -0.52 128 129
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
SMO/beta Arrestin2 0.027 0.045 -10000 0 -0.42 9 9
SMO 0.017 0.055 -10000 0 -0.57 9 9
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.024 0.081 0.32 2 -0.49 11 13
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 0.022 -10000 0 -10000 0 0
GNAI1 -0.008 0.13 -10000 0 -0.57 57 57
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.19 -10000 0 -0.61 70 70
SAP30 0.024 0.015 0.26 4 -10000 0 4
mol:GDP 0.017 0.055 -10000 0 -0.57 9 9
MIM/GLI2A 0.021 0.02 0.26 2 -10000 0 2
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.022 0.009 -10000 0 -10000 0 0
GLI2 0.01 0.066 -10000 0 -0.3 23 23
GLI3 0.013 0.084 0.34 2 -0.44 17 19
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.017 0.065 -10000 0 -0.57 13 13
Gi family/GTP -0.009 0.098 -10000 0 -0.29 98 98
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.017 0.086 -10000 0 -0.43 23 23
GLI2/Su(fu) 0.013 0.081 -10000 0 -0.39 20 20
FOXA2 0.008 0.1 -10000 0 -0.69 15 15
neural tube patterning -0.043 0.2 0.35 1 -0.52 128 129
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.043 -10000 0 -0.37 1 1
GNB1 0.023 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 0.021 0.02 0.26 2 -10000 0 2
embryonic limb morphogenesis -0.043 0.2 0.35 1 -0.52 128 129
SUFU 0.015 0.027 -10000 0 -0.23 10 10
LGALS3 0.016 0.067 -10000 0 -0.57 14 14
catabolic process 0.026 0.1 0.32 2 -0.52 18 20
GLI3A/CBP 0.003 0.089 -10000 0 -0.36 59 59
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.044 0.21 0.35 1 -0.54 126 127
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
IFT172 0.024 0.018 -10000 0 -0.57 1 1
RBBP7 0.026 0.019 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.061 -10000 0 -0.38 15 15
GNAZ 0.016 0.057 -10000 0 -0.57 10 10
RBBP4 0.023 0.019 -10000 0 -0.57 1 1
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.018 0.07 -10000 0 -0.36 15 15
STK36 0.021 0.023 -10000 0 -0.57 1 1
Gi family/GNB1/GNG2/GDP -0.015 0.11 -10000 0 -0.41 49 49
PTCH1 -0.087 0.32 -10000 0 -1.1 95 95
MIM/GLI1 -0.03 0.19 -10000 0 -0.61 69 69
CREBBP 0.003 0.089 -10000 0 -0.36 59 59
Su(fu)/SIN3/HDAC complex 0.007 0.09 -10000 0 -0.41 35 35
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.065 0.16 1 -0.29 51 52
FRAP1 -0.001 0.082 0.4 1 -0.45 25 26
AKT1 -0.011 0.065 0.18 4 -0.28 39 43
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0.023 0.07 0.23 5 -0.24 35 40
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.21 4 4
TSC2 0.023 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.005 0.048 -10000 0 -0.24 16 16
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.077 -10000 0 -0.31 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.015 0.046 -10000 0 -0.23 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.012 0.075 0.29 5 -0.31 21 26
MAP3K5 -0.001 0.046 0.2 10 -0.19 46 56
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
apoptosis -0.001 0.046 0.2 10 -0.19 47 57
mol:LY294002 0 0 -10000 0 -0.001 52 52
EIF4B 0.011 0.069 0.3 4 -0.3 13 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.029 0.066 0.22 2 -0.28 12 14
eIF4E/eIF4G1/eIF4A1 0.004 0.049 -10000 0 -0.28 22 22
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.081 -10000 0 -0.29 66 66
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.055 0.22 17 -0.19 3 20
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.027 0.061 -10000 0 -0.24 15 15
mol:Amino Acids 0 0 -10000 0 -0.001 52 52
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.06 0.17 5 -0.27 48 53
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.52 65 65
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.048 -10000 0 -0.24 3 3
TSC1/TSC2 0.026 0.075 0.25 6 -0.25 35 41
tumor necrosis factor receptor activity 0 0 0.001 52 -10000 0 52
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 0.079 -10000 0 -0.33 60 60
INS 0.016 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.56 1 1
PDK2 -0.018 0.059 0.18 8 -0.27 42 50
EIF4EBP1 -0.022 0.22 -10000 0 -1 46 46
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D 0.001 0.078 0.36 3 -0.42 23 26
peptide biosynthetic process -0.01 0.018 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 53 -0.003 3 56
EEF2 -0.01 0.018 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.011 0.21 -10000 0 -0.97 46 46
BARD1 signaling 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
BARD1/CSTF1 0.026 0.057 -10000 0 -0.39 18 18
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -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 0.015 0.19 5 -10000 0 5
protein ubiquitination 0.065 0.071 0.3 2 -0.3 18 20
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.022 -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 0.015 0.086 -10000 0 -0.54 10 10
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
CCNE1 0.062 0.087 0.26 179 -10000 0 179
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 0.027 0.06 -10000 0 -0.41 19 19
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
FANCA 0.059 0.088 0.26 178 -10000 0 178
DNA repair 0.027 0.085 0.3 4 -0.37 6 10
BRCA1/BARD1/ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BARD1/DNA-PK 0.045 0.052 -10000 0 -0.33 15 15
FANCL 0.024 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.056 0.39 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.07 -10000 0 -0.27 22 22
BRCA1/BACH1/BARD1/TopBP1 0.039 0.055 -10000 0 -0.36 18 18
BRCA1/BARD1/P53 0.048 0.054 -10000 0 -0.33 18 18
BARD1/CSTF1/BRCA1 0.037 0.053 -10000 0 -0.36 16 16
BRCA1/BACH1 0.023 0.02 0.26 1 -0.56 1 2
BARD1 0.014 0.076 0.26 1 -0.57 18 19
PCNA 0.024 0.011 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.04 0.053 -10000 0 -0.36 17 17
BRCA1/BARD1/UbcH7 0.038 0.054 -10000 0 -0.36 17 17
BRCA1/BARD1/RAD51/PCNA 0.091 0.088 0.31 2 -0.31 17 19
BARD1/DNA-PK/P53 0.05 0.054 -10000 0 -0.31 15 15
BRCA1/BARD1/Ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BRCA1/BARD1/CTIP 0.028 0.05 -10000 0 -0.33 18 18
FA complex 0.035 0.037 0.25 2 -10000 0 2
BARD1/EWS 0.026 0.059 -10000 0 -0.42 18 18
RBBP8 0.01 0.005 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.053 0.33 18 -10000 0 18
BRCA1/BARD1 0.071 0.075 0.33 2 -0.3 18 20
CSTF1 0.023 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.056 0.18 1 -0.42 18 19
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.1 0.11 0.26 373 -10000 0 373
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.06 -10000 0 -0.41 19 19
EWSR1 0.023 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.022 0.037 0.26 1 -0.57 4 5
ANTXR2 0.018 0.06 -10000 0 -0.57 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.009 -10000 0 -0.078 14 14
monocyte activation 0.003 0.085 0.25 2 -0.35 55 57
MAP2K2 0.003 0.082 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.008 -10000 0 -10000 0 0
MAP2K7 -0.004 0.009 0.12 1 -0.11 2 3
MAP2K6 -0.01 0.044 0.085 1 -0.3 24 25
CYAA -0.009 0.039 -10000 0 -0.35 13 13
MAP2K4 -0.004 0.008 -10000 0 -10000 0 0
IL1B -0.008 0.045 0.22 2 -0.28 25 27
Channel 0.025 0.046 -10000 0 -0.37 13 13
NLRP1 -0.007 0.033 -10000 0 -0.32 11 11
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.066 -10000 0 -0.39 29 29
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.009 0.078 14 -10000 0 14
MAPK3 -0.004 0.008 -10000 0 -0.11 1 1
MAPK1 -0.004 0.009 0.12 2 -10000 0 2
PGR -0.079 0.14 0.2 2 -0.31 281 283
PA/Cellular Receptors 0.027 0.05 -10000 0 -0.4 13 13
apoptosis -0.002 0.009 -10000 0 -0.078 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.044 -10000 0 -0.35 13 13
macrophage activation -0.005 0.01 0.12 3 -10000 0 3
TNF 0.024 0.065 0.26 25 -0.57 9 34
VCAM1 0.003 0.085 0.25 2 -0.35 55 57
platelet activation -0.001 0.066 -10000 0 -0.39 29 29
MAPKKK cascade -0.002 0.026 0.12 3 -0.14 5 8
IL18 -0.003 0.026 -10000 0 -0.22 10 10
negative regulation of macrophage activation -0.002 0.009 -10000 0 -0.078 14 14
LEF -0.002 0.009 -10000 0 -0.079 14 14
CASP1 -0.003 0.027 -10000 0 -0.21 14 14
mol:cAMP -0.001 0.067 -10000 0 -0.39 29 29
necrosis -0.002 0.009 -10000 0 -0.078 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.044 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.011 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.02 0.3 1 -10000 0 1
CDKN1B 0.011 0.056 -10000 0 -0.34 13 13
CDKN1A 0.01 0.061 -10000 0 -0.44 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -0.41 6 6
AKT1 0.006 0.056 -10000 0 -0.36 17 17
BAD 0.024 0.009 0.26 1 -10000 0 1
AKT3 0.006 0.035 -10000 0 -0.35 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.009 0.059 -10000 0 -0.42 8 8
AKT1/ASK1 0.031 0.067 -10000 0 -0.4 7 7
BAD/YWHAZ 0.037 0.022 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.03 0.065 0.39 7 -10000 0 7
TSC1 0.011 0.051 -10000 0 -0.34 12 12
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.036 0.07 -10000 0 -0.46 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.01 0.059 -10000 0 -0.35 19 19
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.054 0.32 1 -0.39 7 8
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.004 0.015 -10000 0 -0.34 2 2
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.075 0.29 22 -0.22 10 32
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.06 -10000 0 -0.42 8 8
CASP9 0.011 0.045 -10000 0 -0.4 3 3
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.072 0.32 5 -0.54 3 8
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.058 0.25 3 -0.48 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.051 -10000 0 -0.32 20 20
CHUK 0.01 0.055 -10000 0 -0.4 6 6
BAD/BCL-XL 0.038 0.066 0.28 2 -0.53 3 5
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 0.097 0.3 9 -0.4 22 31
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.012 0.064 0.27 2 -0.42 8 10
MAPKKK cascade -0.036 0.069 0.42 7 -0.26 1 8
MDM2/Cbp/p300 0.042 0.072 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.068 0.26 35 -0.59 3 38
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.069 0.32 4 -0.53 3 7
glucose import -0.16 0.15 0.21 2 -0.31 521 523
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.048 0.18 2 -0.41 4 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 -10000 0 -0.31 521 521
GSK3A 0.01 0.059 -10000 0 -0.42 8 8
FOXO1 0.012 0.04 -10000 0 -0.3 1 1
GSK3B 0.01 0.059 -10000 0 -0.62 3 3
SFN 0.021 0.07 0.26 21 -0.57 12 33
G1/S transition of mitotic cell cycle 0.014 0.065 0.33 2 -0.6 3 5
p27Kip1/14-3-3 family 0.021 0.049 0.31 2 -0.39 4 6
PRKACA 0.024 0.004 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.27 0.29 -10000 0 -0.57 524 524
CLTC 0.025 0.067 0.28 1 -0.43 12 13
calcium ion-dependent exocytosis 0.009 0.025 -10000 0 -0.26 2 2
Dynamin 2/GTP 0.022 0.013 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.016 0.046 -10000 0 -0.34 10 10
CPE 0.005 0.049 -10000 0 -0.36 19 19
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.019 -10000 0 -10000 0 0
CTNND1 0.008 0.056 0.2 38 -10000 0 38
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.043 0.22 2 -0.38 5 7
TSHR -0.003 0.072 -10000 0 -0.36 42 42
INS -0.001 0.088 -10000 0 -0.48 34 34
BIN1 0.02 0.051 -10000 0 -0.57 8 8
mol:Choline 0.011 0.019 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.017 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.013 -10000 0 -10000 0 0
JUP 0.017 0.039 0.23 1 -0.33 7 8
ASAP2/amphiphysin II 0.042 0.033 -10000 0 -0.33 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.01 0.053 -10000 0 -0.37 9 9
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.028 0.26 16 -10000 0 16
substrate adhesion-dependent cell spreading 0.016 0.039 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.064 0.34 8 -10000 0 8
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.015 0.028 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.043 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.024 0.063 0.29 5 -0.35 12 17
JIP4/KLC1 0.041 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.02 0.033 -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 0.008 0.057 0.2 39 -10000 0 39
NME1 0.013 0.017 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.069 0.28 3 -0.42 12 15
IL2RA 0.019 0.054 -10000 0 -0.32 13 13
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.27 408 408
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.029 -10000 0 -0.29 9 9
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.039 -10000 0 -0.38 5 5
SDC1 0.019 0.043 -10000 0 -0.33 8 8
ARF6/GDP 0.021 0.014 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.04 0.067 -10000 0 -0.35 7 7
mol:Phosphatidic acid 0.011 0.019 -10000 0 -10000 0 0
endocytosis -0.04 0.033 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.037 0.14 0.26 1 -0.43 35 36
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.018 -10000 0 -0.57 1 1
Dynamin 2/GDP 0.026 0.017 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.079 0.15 0.28 1 -0.44 34 35
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.065 0.32 2 -0.35 5 7
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.056 0.07 0.37 14 -0.38 11 25
MAP4K1 0.033 0.054 0.26 48 -0.57 2 50
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
PRKCB 0.019 0.076 0.26 19 -0.57 15 34
DBNL 0.024 0.003 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.015 0.054 0.25 1 -0.35 10 11
JUN 0.002 0.13 -10000 0 -0.6 42 42
MAP3K7 0.015 0.052 0.23 2 -0.35 6 8
GRAP2 0.017 0.063 0.26 3 -0.57 12 15
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.013 0.066 0.24 1 -0.38 13 14
LAT 0.025 0.038 0.26 15 -0.57 2 17
LCP2 0.024 0.008 0.26 1 -10000 0 1
MAPK8 0.006 0.14 -10000 0 -0.63 42 42
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.022 0.058 0.25 3 -0.31 17 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.064 0.07 0.37 14 -0.37 11 25
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.014 0.096 -10000 0 -0.29 93 93
GNAO1 0.018 0.09 0.26 32 -0.57 20 52
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.091 -10000 0 -0.47 29 29
AKT3 -0.014 0.17 -10000 0 -1.1 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.56 4 4
GNAI2 0.023 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.25 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.1 -10000 0 -0.35 56 56
MAPK3 -0.009 0.091 0.27 2 -0.38 33 35
MAPK1 -0.008 0.092 0.27 1 -0.4 31 32
JAK2 -0.01 0.1 -10000 0 -0.39 41 41
CXCR4 -0.011 0.096 0.21 1 -0.4 32 33
FLT1 0.023 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.011 0.094 0.21 1 -0.37 36 37
S1P/S1P3/Gi -0.004 0.1 -10000 0 -0.35 56 56
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.1 -10000 0 -0.38 33 33
VEGFA 0.025 0.021 0.25 7 -10000 0 7
S1P/S1P2/Gi -0.005 0.093 -10000 0 -0.28 92 92
VEGFR1 homodimer/VEGFA homodimer 0.035 0.022 -10000 0 -0.18 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.019 0.042 -10000 0 -0.28 18 18
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
GNAZ 0.017 0.057 -10000 0 -0.57 10 10
G12/G13 0.033 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
Rac1/GTP -0.004 0.1 -10000 0 -0.39 33 33
FoxO family signaling

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
G6PC 0.012 0.06 -10000 0 -10000 0 0
PLK1 0.24 0.18 0.56 75 -0.57 1 76
CDKN1B 0.15 0.13 0.38 59 -0.47 4 63
FOXO3 0.2 0.16 0.45 179 -0.5 3 182
KAT2B 0.055 0.033 -10000 0 -0.57 1 1
FOXO1/SIRT1 0.012 0.055 -10000 0 -0.29 3 3
CAT 0.18 0.17 0.6 16 -1 5 21
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.056 0.028 -10000 0 -10000 0 0
FOXO1 0.017 0.062 -10000 0 -0.31 7 7
MAPK10 -0.016 0.12 0.2 11 -0.29 156 167
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.034 0.084 0.41 2 -0.51 1 3
response to oxidative stress 0.034 0.026 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.17 0.14 0.42 50 -0.5 3 53
XPO1 0.024 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.062 0.084 -10000 0 -0.71 9 9
FOXO1/SKP2 0.026 0.058 -10000 0 -0.3 4 4
mol:GDP 0.034 0.026 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.13 0.13 0.46 2 -0.58 6 8
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.022 0.12 0.25 1 -0.49 38 39
MST1 0.052 0.059 0.27 8 -0.51 8 16
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 0.01 0.12 -10000 0 -0.45 47 47
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.037 0.2 14 -0.3 8 22
MAPK9 0.031 0.024 0.21 11 -10000 0 11
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
SIRT1 0.012 0.02 -10000 0 -10000 0 0
SOD2 0.15 0.13 0.49 10 -10000 0 10
RBL2 0.1 0.25 0.54 2 -0.64 60 62
RAL/GDP 0.056 0.021 -10000 0 -10000 0 0
CHUK 0.055 0.028 -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 0.057 0.021 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.055 0.18 -10000 0 -1.3 16 16
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.006 -10000 0 -10000 0 0
IKBKB 0.046 0.032 -10000 0 -10000 0 0
CCNB1 0.2 0.17 0.56 51 -0.57 1 52
FOXO1-3a-4/beta catenin 0.15 0.12 0.42 39 -0.42 2 41
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.058 -10000 0 -0.3 4 4
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
SGK1 0.051 0.05 -10000 0 -0.55 5 5
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.032 0.075 0.44 1 -0.4 1 2
SFN 0.021 0.07 0.26 21 -0.57 12 33
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.062 0.11 0.3 3 -0.39 21 24
CREBBP 0.022 0.008 -10000 0 -10000 0 0
FBXO32 0.23 0.2 0.59 122 -1.2 3 125
BCL6 0.16 0.16 0.52 3 -0.91 9 12
RALB 0.025 0.003 -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
Retinoic acid receptors-mediated signaling

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.021 -10000 0 -0.36 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.062 -10000 0 -0.38 13 13
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.005 0.067 0.21 2 -0.37 17 19
RAR alpha/9cRA/Cyclin H 0.046 0.074 -10000 0 -0.34 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.066 -10000 0 -0.4 14 14
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.023 0.064 -10000 0 -0.29 30 30
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 -0.56 21 21
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARG 0.025 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.02 0.051 -10000 0 -0.57 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.1 -10000 0 -0.48 24 24
RARA 0.013 0.055 0.2 13 -0.27 27 40
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.079 -10000 0 -0.38 23 23
PRKCA 0.012 0.084 0.26 1 -0.57 22 23
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.12 0.45 1 -0.56 22 23
RXRG -0.051 0.15 0.24 12 -0.35 204 216
RXRA 0.022 0.064 0.34 1 -0.27 27 28
RXRB 0.016 0.061 0.24 11 -0.34 22 33
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.036 0.076 0.26 73 -0.57 7 80
CRBP1/9-cic-RA 0.026 0.053 0.18 73 -0.42 7 80
RARB 0.017 0.067 -10000 0 -0.57 14 14
PRKCG 0.032 0.045 0.26 41 -10000 0 41
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.52 27 27
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.008 0.1 -10000 0 -0.46 25 25
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.08 0.27 6 -0.36 18 24
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.12 0.45 1 -0.56 23 24
positive regulation of DNA binding 0.032 0.064 -10000 0 -0.32 19 19
NRIP1 0.011 0.12 0.54 1 -0.74 10 11
RXRs/RARs 0.009 0.12 -10000 0 -0.52 28 28
RXRs/RXRs/DNA/9cRA -0.013 0.091 -10000 0 -0.49 24 24
PRKACA 0.024 0.004 -10000 0 -10000 0 0
CDK7 0.023 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.051 0.056 -10000 0 -0.29 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 0.044 0.015 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.001 0.098 0.26 2 -0.43 26 28
BAG4 0.018 0.032 -10000 0 -0.57 3 3
BAD 0.005 0.038 0.2 4 -0.19 5 9
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BAX 0.005 0.042 0.22 6 -0.19 5 11
EnzymeConsortium:3.1.4.12 0.002 0.026 0.081 5 -0.094 24 29
IKBKB 0.017 0.1 0.31 5 -0.42 19 24
MAP2K2 0.008 0.051 0.23 12 -0.24 2 14
MAP2K1 0.009 0.053 0.23 15 -0.24 2 17
SMPD1 0.002 0.032 0.14 3 -0.16 13 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.11 0.28 20 -0.42 24 44
MAP2K4 0.006 0.034 0.19 4 -0.23 2 6
protein ubiquitination 0.004 0.1 0.34 4 -0.42 22 26
EnzymeConsortium:2.7.1.37 0.008 0.054 0.23 14 -0.25 2 16
response to UV 0 0.001 0.003 18 -0.002 2 20
RAF1 0.009 0.052 0.19 41 -0.22 4 45
CRADD 0.024 0.004 -10000 0 -10000 0 0
mol:ceramide 0.006 0.04 0.13 6 -0.15 19 25
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.009 -10000 0 -10000 0 0
MADD 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.039 0.18 4 -0.2 6 10
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.023 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.052 0.23 12 -0.23 2 14
MAPK1 0.007 0.059 0.23 12 -0.25 5 17
p50/RELA/I-kappa-B-alpha 0.034 0.009 -10000 0 -10000 0 0
FADD 0.024 0.11 0.28 12 -0.43 22 34
KSR1 0.009 0.05 0.18 36 -0.21 5 41
MAPK8 0.002 0.048 0.24 8 -0.28 8 16
TRAF2 0.025 0.015 0.26 4 -10000 0 4
response to radiation 0 0 0.002 10 -10000 0 10
CHUK -0.001 0.093 -10000 0 -0.42 23 23
TNF R/SODD 0.027 0.029 -10000 0 -0.42 3 3
TNF 0.025 0.065 0.26 25 -0.57 9 34
CYCS 0.008 0.045 0.18 14 -0.2 3 17
IKBKG -0.001 0.095 0.43 1 -0.42 24 25
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.002 0.1 -10000 0 -0.44 27 27
RELA 0.023 0.005 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.007 0.044 0.17 14 -0.2 4 18
TNF/TNF R/SODD 0.036 0.051 -10000 0 -0.36 11 11
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 10 -10000 0 10
CASP8 0.003 0.13 -10000 0 -0.62 41 41
NSMAF 0.017 0.11 0.26 11 -0.42 24 35
response to hydrogen peroxide 0 0.001 0.003 18 -0.002 2 20
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.011 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 0.034 0.3 8 -10000 0 8
MAPK12 -0.009 0.048 0.21 1 -0.33 22 23
CCND1 0.01 0.047 -10000 0 -0.38 7 7
p38 gamma/SNTA1 0.021 0.07 0.32 2 -0.32 22 24
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint -0.009 0.048 0.21 1 -0.33 22 23
MAP2K6 -0.006 0.051 -10000 0 -0.35 23 23
MAPT -0.026 0.12 0.25 15 -0.32 124 139
MAPK13 0.011 0.011 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.006 0.001 -10000 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.024 0.009 0.26 1 -9999 0 1
PLK4 0.033 0.044 0.26 41 -9999 0 41
regulation of centriole replication 0.016 0.026 0.26 2 -9999 0 2
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.048 -10000 0 -0.57 7 7
positive regulation of NF-kappaB transcription factor activity -0.005 0.11 -10000 0 -0.33 106 106
MAP2K4 0.016 0.046 0.22 1 -0.38 4 5
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.032 -10000 0 -0.57 3 3
SMPD1 0.008 0.029 -10000 0 -0.34 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.015 0.14 0.26 1 -0.57 64 65
TRAIL/TRAILR2 0.026 0.038 -10000 0 -0.37 8 8
TRAIL/TRAILR3 0.027 0.042 0.2 7 -0.37 9 16
TRAIL/TRAILR1 0.024 0.046 -10000 0 -0.33 15 15
TRAIL/TRAILR4 -0.005 0.11 -10000 0 -0.33 106 106
TRAIL/TRAILR1/DAP3/GTP 0.029 0.038 -10000 0 -0.32 7 7
IKK complex 0.011 0.04 -10000 0 -0.41 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 0.035 0.25 1 -0.42 7 8
MAP3K1 0.019 0.059 -10000 0 -0.42 8 8
TRAILR4 (trimer) -0.015 0.14 0.26 1 -0.56 64 65
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.032 -10000 0 -0.56 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.044 -10000 0 -0.36 9 9
CFLAR 0.024 0.018 -10000 0 -0.57 1 1
MAPK1 0.008 0.035 0.25 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.046 -10000 0 -0.3 7 7
mol:ceramide 0.008 0.029 -10000 0 -0.34 6 6
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.013 0.062 0.26 1 -0.35 15 16
TRAF2 0.025 0.015 0.26 4 -10000 0 4
TRAILR3 (trimer) 0.022 0.021 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.031 0.041 -10000 0 -0.35 7 7
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.036 0.084 0.28 61 -0.34 3 64
JNK cascade -0.005 0.11 -10000 0 -0.33 106 106
TRAIL (trimer) 0.02 0.048 -10000 0 -0.56 7 7
TNFRSF10C 0.022 0.021 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.039 -10000 0 -0.31 5 5
TRAIL/TRAILR2/FADD 0.032 0.036 -10000 0 -0.35 5 5
cell death 0.008 0.029 -10000 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.041 -10000 0 -0.41 6 6
TRAILR2 (trimer) 0.02 0.009 -10000 0 -10000 0 0
CASP8 0.012 0.05 -10000 0 -0.56 6 6
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.043 0.043 -10000 0 -0.29 5 5
IL1-mediated signaling events

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
UBC13/UEV1A 0.018 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.05 -10000 0 -0.35 8 8
IRAK/TOLLIP 0.026 0.009 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.025 0.094 0.36 3 -0.42 40 43
IL1A 0.028 0.03 0.26 18 -10000 0 18
IL1B 0.004 0.053 0.26 1 -0.43 15 16
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.027 -10000 0 -0.3 1 1
IL1R2 0.008 0.12 0.26 29 -0.57 40 69
IL1R1 0.012 0.084 -10000 0 -0.57 22 22
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.062 0.26 4 -0.3 20 24
TOLLIP 0.024 0.004 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.057 0.27 1 -0.37 1 2
JUN -0.015 0.056 0.23 3 -0.27 35 38
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.085 -10000 0 -0.34 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88 0.053 0.061 -10000 0 -0.33 23 23
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.061 0.061 -10000 0 -0.31 23 23
IL1 beta fragment/IL1R1/IL1RAP 0.022 0.073 -10000 0 -0.35 36 36
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.011 0.054 0.23 3 -0.28 28 31
IRAK1 0.012 0.008 -10000 0 -10000 0 0
IL1RN/IL1R1 0.031 0.074 -10000 0 -0.42 24 24
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 0.028 0.049 -10000 0 -0.38 14 14
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.059 -10000 0 -0.36 10 10
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.022 0.073 -10000 0 -0.35 36 36
IL1 beta/IL1R2 0.013 0.093 -10000 0 -0.37 53 53
IRAK/TRAF6/TAK1/TAB1/TAB2 0.032 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.077 -10000 0 -0.32 44 44
IRAK3 0.003 0.11 0.26 1 -0.57 39 40
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.074 -10000 0 -0.32 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.047 -10000 0 -0.27 23 23
IL1 alpha/IL1R1/IL1RAP 0.041 0.063 -10000 0 -0.36 23 23
RELA 0.023 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.038 0.021 -10000 0 -10000 0 0
IL1RAP 0.023 0.018 -10000 0 -0.57 1 1
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.018 0.06 -10000 0 -0.58 2 2
CASP1 0.021 0.019 -10000 0 -0.57 1 1
IL1RN/IL1R2 0.028 0.099 0.36 5 -0.42 42 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.034 0.073 -10000 0 -0.33 36 36
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.071 -10000 0 -0.34 34 34
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.049 0.26 37 -0.57 2 39
TRAF6/TAK1/TAB1/TAB2 0.033 0.011 -10000 0 -10000 0 0
MAP2K6 -0.008 0.053 0.25 5 -0.29 22 27
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.019 0.11 -10000 0 -0.44 29 29
KLHL20 0.016 0.064 0.24 9 -0.22 12 21
CYFIP2 0.028 0.048 0.26 26 -0.57 3 29
Rac1/GDP 0.001 0.084 0.26 8 -0.31 15 23
ENAH -0.014 0.1 -10000 0 -0.45 24 24
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 0.01 0.046 -10000 0 -0.4 1 1
ABI1/Sra1/Nap1 -0.012 0.031 -10000 0 -0.16 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.047 0.064 -10000 0 -0.33 20 20
RAPGEF1 -0.018 0.1 0.26 2 -0.4 25 27
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.12 -10000 0 -0.41 50 50
CRK -0.015 0.099 -10000 0 -0.42 29 29
E-cadherin/gamma catenin/alpha catenin 0.033 0.057 -10000 0 -0.36 18 18
alphaE/beta7 Integrin 0.036 0.034 -10000 0 -0.42 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 0.04 0.027 -10000 0 -0.33 3 3
DLG1 -0.023 0.12 -10000 0 -0.44 32 32
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.031 -10000 0 -0.28 1 1
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.003 0.045 -10000 0 -0.38 1 1
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.021 0.062 -10000 0 -0.42 18 18
TIAM1 0.025 0.015 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.041 0.054 -10000 0 -0.31 18 18
AKT1 -0.007 0.035 0.14 1 -0.21 1 2
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
RhoA/GDP 0.002 0.083 0.26 8 -0.31 15 23
actin cytoskeleton organization 0.015 0.052 0.18 19 -0.16 11 30
CDC42/GDP 0.002 0.082 0.26 8 -0.31 15 23
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.04 -10000 0 -0.26 18 18
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.045 0.057 -10000 0 -0.33 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin 0.03 0.049 -10000 0 -0.31 18 18
mol:GDP -0.012 0.09 0.27 8 -0.36 16 24
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 0.085 0.26 5 -0.37 3 8
RAC1/GTP/IQGAP1 0.032 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.047 0.18 39 -0.24 4 43
NME1 0.026 0.031 0.26 18 -10000 0 18
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.021 0.11 -10000 0 -0.45 31 31
regulation of cell-cell adhesion 0.004 0.039 -10000 0 -0.35 1 1
WASF2 0.008 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.056 0.24 1 -0.46 1 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.054 0.064 -10000 0 -0.32 19 19
CCND1 0.015 0.054 0.2 38 -0.3 4 42
VAV2 -0.018 0.15 -10000 0 -0.62 23 23
RAP1/GDP 0.008 0.069 0.26 3 -0.45 1 4
adherens junction assembly -0.02 0.11 -10000 0 -0.43 31 31
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 0.042 0.061 -10000 0 -0.3 19 19
E-cadherin/beta catenin 0.001 0.057 -10000 0 -0.34 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.022 0.12 -10000 0 -0.44 32 32
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.089 0.26 33 -0.34 22 55
E-cadherin/beta catenin/alpha catenin 0.034 0.057 -10000 0 -0.36 18 18
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.12 -10000 0 -0.43 43 43
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.025 0.073 0.3 4 -0.38 12 16
PDGFB-D/PDGFRB/SLAP 0.028 0.033 -10000 0 -0.36 4 4
PDGFB-D/PDGFRB/APS/CBL 0.048 0.042 -10000 0 -0.35 4 4
AKT1 0.025 0.095 0.34 38 -10000 0 38
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.032 0.084 0.32 6 -0.41 14 20
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.46 33 33
mol:Ca2+ 0.024 0.087 0.3 6 -0.44 16 22
MYC 0.053 0.17 0.36 35 -0.78 26 61
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.3 3 3
LRP1/PDGFRB/PDGFB 0.041 0.054 -10000 0 -0.4 14 14
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.023 0.088 0.3 6 -0.45 16 22
PTEN 0.022 0.019 -10000 0 -0.57 1 1
GRB2 0.023 0.009 0.26 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PDGFB-D/PDGFRB/SHP2 0.034 0.028 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.028 -10000 0 -0.42 4 4
cell cycle arrest 0.028 0.033 -10000 0 -0.36 4 4
HRAS 0.026 0.022 0.26 9 -10000 0 9
HIF1A 0.019 0.089 0.33 37 -10000 0 37
GAB1 0.026 0.093 0.31 5 -0.42 17 22
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.026 0.086 0.32 10 -0.38 13 23
PDGFB-D/PDGFRB 0.042 0.031 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.026 -10000 0 -0.36 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.023 0.065 0.28 3 -0.38 9 12
positive regulation of MAPKKK cascade 0.034 0.028 -10000 0 -0.42 4 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.024 0.088 0.3 6 -0.45 16 22
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.039 -10000 0 -0.42 7 7
SHB 0.024 0.008 0.26 1 -10000 0 1
BLK -0.024 0.16 0.29 5 -0.4 136 141
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.029 -10000 0 -0.41 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.028 0.1 0.33 5 -0.44 21 26
CBL 0.022 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.029 -10000 0 -0.42 4 4
LCK 0.006 0.11 -10000 0 -0.5 36 36
PDGFRB 0.022 0.037 -10000 0 -0.57 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.016 0.06 -10000 0 -0.52 6 6
ABL1 0.021 0.093 0.3 7 -0.39 23 30
PDGFB-D/PDGFRB/CBL 0.021 0.1 0.3 2 -0.46 24 26
PTPN1 0.024 0.019 0.25 6 -10000 0 6
SNX15 0.023 0.005 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 0.26 19 -10000 0 19
cell proliferation 0.054 0.15 0.34 45 -0.68 26 71
SLA 0.021 0.024 0.26 9 -10000 0 9
actin cytoskeleton reorganization 0.034 0.05 0.33 2 -0.29 3 5
SRC 0.012 0.059 0.28 1 -0.49 8 9
PI3K -0.013 0.032 -10000 0 -0.28 10 10
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.038 -10000 0 -0.36 6 6
SH2B2 0.034 0.046 0.26 45 -10000 0 45
PLCgamma1/SPHK1 0.032 0.086 0.32 6 -0.42 14 20
LYN 0.009 0.064 -10000 0 -0.47 11 11
LRP1 0.018 0.062 -10000 0 -0.57 12 12
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.3 3 3
SPHK1 0.027 0.041 0.26 20 -0.57 2 22
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.024 0.088 0.3 6 -0.45 16 22
PLCG1 0.024 0.09 0.32 4 -0.46 16 20
NHERF/PDGFRB 0.049 0.045 -10000 0 -0.36 4 4
YES1 0.001 0.11 -10000 0 -0.56 30 30
cell migration 0.048 0.044 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.049 0.041 -10000 0 -0.3 3 3
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
SLC9A3R1 0.036 0.054 0.26 60 -10000 0 60
NHERF1-2/PDGFRB/PTEN 0.056 0.048 0.29 2 -0.33 4 6
FYN -0.003 0.1 -10000 0 -0.44 37 37
DOK1 0.021 0.049 0.33 1 -0.33 3 4
HRAS/GTP 0.019 0.015 0.18 9 -10000 0 9
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.023 0.12 0.33 4 -0.51 29 33
PRKCD 0.022 0.051 0.33 1 -0.33 3 4
FER 0.018 0.059 -10000 0 -0.34 12 12
MAPKKK cascade 0.037 0.096 0.36 34 -0.3 3 37
RASA1 0.021 0.049 -10000 0 -0.33 3 3
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.035 0.043 0.3 1 -0.31 3 4
PDGFB-D/PDGFRB/SHB 0.034 0.03 -10000 0 -0.42 4 4
chemotaxis 0.021 0.091 0.29 7 -0.38 23 30
STAT1-3-5/STAT1-3-5 0.049 0.047 -10000 0 -0.36 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.027 -10000 0 -0.42 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
p38 MAPK 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
TRAF6/ASK1 0.017 0.019 -10000 0 -0.3 3 3
TRAF2/ASK1 0.03 0.024 -10000 0 -0.36 3 3
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.018 0.11 0.27 1 -0.35 57 58
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.098 0.26 1 -0.36 34 35
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.054 0.077 0.26 138 -10000 0 138
TXN 0.007 0.006 0.11 3 -10000 0 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.027 -10000 0 -0.41 3 3
TAK1/TAB family 0 0.019 0.18 2 -0.2 1 3
RAC1/OSM/MEKK3 0.042 0.016 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.26 4 -10000 0 4
RAC1/OSM/MEKK3/MKK3 0 0.091 -10000 0 -0.3 38 38
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.005 0.15 0.26 44 -0.57 69 113
CCM2 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.012 0.1 -10000 0 -0.36 69 69
MAPK11 0.021 0.032 -10000 0 -0.57 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.023 0.1 -10000 0 -0.33 71 71
OSM/MEKK3 0.032 0.013 -10000 0 -10000 0 0
TAOK1 -0.008 0.081 -10000 0 -0.36 54 54
TAOK2 0.011 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 0.022 0.032 -10000 0 -0.57 3 3
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.025 -10000 0 -0.34 3 3
GADD45/MTK1/MTK1 0.067 0.047 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.026 0.041 0.26 20 -0.57 2 22
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.019 0.22 1 -0.29 2 3
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
mol:Sphinganine-1-P 0.012 0.026 0.26 1 -0.42 2 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.035 -10000 0 -0.23 3 3
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.02 0.26 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.006 0.023 -10000 0 -0.24 5 5
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
S1PR4 0.029 0.062 0.26 38 -0.57 6 44
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
S1P/S1P5/G12 0.046 0.041 0.24 4 -0.24 5 9
S1P/S1P3/Gq 0.026 0.063 -10000 0 -0.3 26 26
S1P/S1P4/Gi 0 0.097 -10000 0 -0.33 50 50
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
ABCC1 0.023 0.006 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.051 0.081 -10000 0 -0.48 1 1
CRKL 0.025 0.047 0.27 10 -10000 0 10
mol:DAG 0.038 0.051 -10000 0 -10000 0 0
HRAS 0.034 0.078 0.31 18 -10000 0 18
MAPK8 0.04 0.07 0.24 35 -0.34 5 40
RAP1A 0.027 0.048 0.28 12 -10000 0 12
GAB1 0.026 0.046 0.28 8 -10000 0 8
MAPK14 0.042 0.065 0.24 33 -10000 0 33
EPO 0.061 0.085 0.26 169 -10000 0 169
PLCG1 0.038 0.051 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.013 0.26 1 -10000 0 1
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.063 0.061 -10000 0 -0.35 5 5
GAB1/SHC/GRB2/SOS1 0.042 0.041 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.06 0.059 0.22 6 -10000 0 6
IRS2 0.014 0.071 0.28 8 -0.29 35 43
STAT1 0.044 0.064 0.31 4 -10000 0 4
STAT5B 0.04 0.058 -10000 0 -0.34 1 1
cell proliferation 0.022 0.075 0.24 37 -0.32 5 42
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.044 -10000 0 -0.33 1 1
TEC 0.025 0.047 0.26 8 -0.27 2 10
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
STAT1 (dimer) 0.044 0.063 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
EPO/EPOR (dimer)/JAK2 0.08 0.062 0.33 3 -10000 0 3
EPO/EPOR 0.06 0.059 0.22 6 -10000 0 6
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.046 0.28 3 -0.29 1 4
elevation of cytosolic calcium ion concentration 0.026 0.013 0.26 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.061 0.054 -10000 0 -10000 0 0
mol:IP3 0.038 0.051 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.03 0.079 0.29 2 -0.29 37 39
SH2B3 0.026 0.009 -10000 0 -10000 0 0
NFKB1 0.042 0.066 0.24 35 -10000 0 35
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.042 -10000 0 -0.25 3 3
PTPN6 0.023 0.039 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.047 0.048 0.27 4 -0.28 1 5
EPOR 0.026 0.013 0.26 1 -10000 0 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.041 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
CRKL/CBL/C3G 0.046 0.047 0.27 5 -10000 0 5
VAV2 0.027 0.048 0.28 12 -10000 0 12
CBL 0.025 0.047 0.27 10 -10000 0 10
SHC/Grb2/SOS1 0.036 0.037 -10000 0 -10000 0 0
STAT5A 0.038 0.063 -10000 0 -0.33 6 6
GRB2 0.023 0.009 0.26 1 -10000 0 1
STAT5 (dimer) 0.051 0.079 0.34 1 -0.43 2 3
LYN/PLCgamma2 0.027 0.026 -10000 0 -0.42 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.027 0.048 0.28 12 -10000 0 12
BCL2 0.031 0.17 -10000 0 -0.83 35 35
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.069 0.051 -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 0.055 0.046 0.35 3 -10000 0 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.042 -10000 0 -0.22 1 1
CaM/Ca2+ 0.067 0.046 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.042 0.042 0.28 2 -10000 0 2
AKT1 0.01 0.064 0.29 11 -0.28 10 21
MAP2K1 0.007 0.045 0.29 4 -0.29 1 5
MAP3K11 0.023 0.042 0.29 4 -10000 0 4
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.019 0.095 -10000 0 -0.47 5 5
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.033 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.076 0.054 -10000 0 -10000 0 0
CEBPB 0.028 0.094 0.32 2 -0.49 7 9
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.075 0.094 -10000 0 -0.69 9 9
STAT1 0.026 0.047 0.29 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.054 0.08 0.26 146 -10000 0 146
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.045 0.28 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.028 0.061 0.34 2 -0.36 2 4
mol:Ca2+ 0.065 0.048 -10000 0 -10000 0 0
MAPK3 0.022 0.078 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.058 -10000 0 -10000 0 0
MAPK1 -0.006 0.16 -10000 0 -0.67 58 58
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.031 -10000 0 -0.57 3 3
DAPK1 0.027 0.069 0.3 2 -0.34 2 4
SMAD7 0.017 0.036 0.17 8 -10000 0 8
CBL/CRKL/C3G 0.045 0.038 0.29 4 -10000 0 4
PI3K 0.056 0.056 -10000 0 -0.29 12 12
IFNG 0.054 0.08 0.26 146 -10000 0 146
apoptosis 0.024 0.071 0.28 1 -0.4 10 11
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.032 0.042 0.26 36 -10000 0 36
CAMK2B -0.004 0.15 0.26 44 -0.57 69 113
FRAP1 0.008 0.06 0.28 11 -0.26 10 21
PRKCD 0.011 0.067 0.3 13 -0.28 9 22
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -0.22 1 1
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.022 0.057 0.29 10 -10000 0 10
STAT1 (dimer)/PIASy 0.038 0.046 0.27 6 -10000 0 6
SOCS1 0.016 0.11 -10000 0 -1 10 10
mol:GDP 0.041 0.036 0.27 4 -10000 0 4
CASP1 0.016 0.039 0.2 7 -0.24 3 10
PTGES2 0.024 0.008 0.26 1 -10000 0 1
IRF9 0.028 0.041 0.24 8 -10000 0 8
mol:PI-3-4-5-P3 0.041 0.047 -10000 0 -0.28 12 12
RAP1/GDP 0.035 0.022 -10000 0 -10000 0 0
CBL 0.021 0.04 0.29 4 -10000 0 4
MAP3K1 0.022 0.042 0.29 4 -0.3 1 5
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.042 -10000 0 -0.22 1 1
PTPN11 0.025 0.044 0.29 4 -10000 0 4
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.019 0.023 -10000 0 -0.3 1 1
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.067 0.048 0.35 10 -0.33 2 12
EPO 0.059 0.085 0.26 169 -10000 0 169
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.016 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.059 0.059 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.077 -10000 0 -0.42 23 23
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.38 14 14
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.033 0.03 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
MADCAM1 0.031 0.044 0.26 39 -10000 0 39
cell adhesion 0.064 0.047 0.34 10 -0.33 2 12
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.013 0.043 -10000 0 -0.33 10 10
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.044 0.046 -10000 0 -0.36 11 11
p130Cas/Crk/Dock1 0.026 0.041 0.35 1 -0.28 9 10
VCAM1 0.019 0.062 0.26 6 -0.57 11 17
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.023 -10000 0 -10000 0 0
BCAR1 -0.009 0.042 0.38 1 -0.3 10 11
EPOR 0.024 0.008 0.26 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.079 -10000 0 -0.43 23 23
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.032 -10000 0 -0.57 3 3
Caspase 8 (4 units) 0.039 0.062 -10000 0 -0.37 5 5
NEF 0.003 0.024 -10000 0 -0.18 11 11
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.02 0.054 -10000 0 -0.5 5 5
CYCS 0.036 0.077 0.25 26 -0.29 13 39
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.017 0.086 0.29 16 -0.43 26 42
MAP2K7 0.041 0.12 0.37 2 -0.72 16 18
protein ubiquitination 0.015 0.082 0.31 5 -0.37 11 16
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.022 0.036 -10000 0 -0.57 4 4
BID 0.035 0.073 0.23 2 -0.29 16 18
NF-kappa-B/RelA/I kappa B alpha 0.051 0.033 -10000 0 -0.31 3 3
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
CFLAR 0.024 0.018 -10000 0 -0.57 1 1
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.033 -10000 0 -0.31 3 3
MAPK8 0.038 0.12 0.4 5 -0.63 18 23
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.013 0.26 3 -10000 0 3
TRAF2 0.025 0.015 0.26 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.059 0.23 4 -0.3 16 20
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.015 0.091 -10000 0 -0.42 18 18
CHUK 0.014 0.085 0.31 4 -0.4 11 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.054 0.041 -10000 0 -0.33 5 5
TCRz/NEF 0.016 0.08 0.31 9 -0.42 26 35
TNF 0.024 0.065 0.26 25 -0.57 9 34
FASLG 0.011 0.11 0.28 42 -0.57 26 68
NFKB1 0.025 0.011 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 11 11
CASP6 0.052 0.1 0.38 1 -0.52 16 17
CASP7 0.04 0.1 0.38 6 -0.46 11 17
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.38 5 -0.47 10 15
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.42 3 3
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.005 -10000 0 -10000 0 0
MAP3K14 0.016 0.087 0.29 1 -0.42 13 14
APAF-1/Caspase 9 0.033 0.061 0.25 5 -0.41 3 8
BCL2 0.031 0.12 0.42 6 -0.54 23 29
Class I PI3K signaling events

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
ARF5/GTP -0.013 0.04 0.33 3 -0.28 1 4
DAPP1 0.017 0.1 0.27 7 -0.4 23 30
Src family/SYK family/BLNK-LAT/BTK-ITK 0.019 0.14 0.31 1 -0.53 29 30
mol:DAG 0.022 0.078 0.24 32 -0.26 9 41
HRAS 0.027 0.022 0.25 9 -10000 0 9
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.059 0.27 1 -0.35 7 8
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.008 0.26 1 -10000 0 1
mol:GTP -0.01 0.037 0.34 4 -0.28 1 5
ARF1/GTP -0.004 0.033 0.27 7 -0.28 1 8
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
RAP1A/GTP -0.011 0.033 0.2 1 -0.27 1 2
ADAP1 -0.011 0.04 0.32 4 -0.28 2 6
ARAP3 -0.01 0.037 0.34 4 -0.28 1 5
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.027 0.033 0.26 21 -10000 0 21
ARHGEF6 0.017 0.067 -10000 0 -0.57 14 14
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
mol:Ca2+ 0.016 0.053 0.23 19 -10000 0 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 4 -10000 0 4
ZAP70 0.026 0.098 0.26 61 -0.57 20 81
mol:IP3 0.017 0.066 0.2 58 -0.19 6 64
LYN 0.021 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.057 0.28 2 -0.36 6 8
RhoA/GDP 0.03 0.041 0.25 1 -10000 0 1
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.02 0.068 0.39 4 -0.35 2 6
SRC 0.023 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.011 0.23 2 -10000 0 2
RAC1 0.024 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.02 -10000 0 -0.54 1 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.038 0.32 4 -10000 0 4
RhoA/GTP -0.012 0.037 0.33 4 -0.27 1 5
Src family/SYK family/BLNK-LAT 0.026 0.096 0.27 3 -0.46 12 15
BLK 0.051 0.087 0.26 151 -0.57 2 153
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.037 0.32 4 -0.26 1 5
HCK 0.027 0.026 0.26 13 -10000 0 13
CYTH3 -0.012 0.039 0.33 3 -0.27 3 6
CYTH2 -0.011 0.039 0.32 4 -0.26 1 5
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.009 0.053 0.31 1 -0.41 11 12
SGK1 0.005 0.076 -10000 0 -0.35 39 39
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.06 0.28 2 -0.33 10 12
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.044 0.31 6 -10000 0 6
mol:PI-3-4-5-P3 -0.011 0.035 0.28 4 -0.27 1 5
ARAP3/RAP1A/GTP -0.011 0.033 0.2 1 -0.28 1 2
VAV1 0.023 0.033 0.26 2 -0.57 3 5
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.04 0.039 -10000 0 -0.28 1 1
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.059 0.27 1 -0.35 7 8
LAT 0.025 0.038 0.26 15 -0.57 2 17
Rac1/GTP 0.016 0.051 -10000 0 -0.35 9 9
ITK -0.018 0.062 0.32 4 -0.31 29 33
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.021 0.095 0.28 20 -0.36 11 31
LCK 0.026 0.075 0.26 40 -0.57 11 51
BTK -0.011 0.039 0.32 4 -0.26 1 5
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.4 69 69
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.004 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.11 0.15 0.4 1 -0.4 87 88
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.008 0.026 -10000 0 -0.42 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.02 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.024 0.024 0.26 11 -10000 0 11
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 0.01 0.016 0.24 5 -10000 0 5
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.063 0.26 1 -0.3 17 18
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.12 0.16 0.41 1 -0.43 99 100
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
LNPEP 0.019 0.051 -10000 0 -0.57 8 8
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.021 0.084 0.31 5 -0.43 11 16
NFATC2 -0.005 0.071 0.19 2 -0.25 38 40
NFATC3 0.014 0.016 -10000 0 -0.4 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.094 0.26 3 -0.41 24 27
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.087 0.27 2 -0.44 11 13
BCL2/BAX 0.021 0.074 -10000 0 -0.41 28 28
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.013 -10000 0 -10000 0 0
BAX 0.025 0.014 0.26 4 -10000 0 4
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.009 0.26 1 -10000 0 1
CABIN1/MEF2D 0.019 0.083 -10000 0 -0.43 14 14
Calcineurin A alpha-beta B1/BCL2 0.008 0.094 -10000 0 -0.56 28 28
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.082 0.42 14 -10000 0 14
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 64 -10000 0 64
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
MAP3K8 0.019 0.048 -10000 0 -0.57 7 7
NFAT4/CK1 alpha 0.018 0.028 -10000 0 -0.28 2 2
MEF2D/NFAT1/Cbp/p300 0.008 0.11 -10000 0 -0.3 65 65
CABIN1 0.012 0.093 0.26 3 -0.4 24 27
CALM1 0.02 0.013 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
CAMK4 0.031 0.046 0.26 37 -0.57 1 38
mol:Ca2+ -0.001 0.005 -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 0.041 0.038 -10000 0 -0.42 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.051 -10000 0 -0.57 8 8
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.096 0.3 1 -0.45 12 13
PRKCH 0.023 0.018 -10000 0 -0.57 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 0.011 0.033 -10000 0 -0.35 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.039 -10000 0 -0.28 4 4
PRKCB 0.019 0.076 0.26 19 -0.57 15 34
PRKCE 0.024 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.008 0.059 -10000 0 -0.37 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.021 0.02 -10000 0 -0.57 1 1
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
PRKCG 0.03 0.045 0.26 41 -10000 0 41
PRKCQ 0.004 0.11 0.26 8 -0.57 39 47
FKBP38/BCL2 0.021 0.074 -10000 0 -0.42 28 28
EP300 0.019 0.016 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.086 0.32 1 -0.4 11 12
CaM/Ca2+/FKBP38 0.027 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.034 -10000 0 -0.36 1 1
NFATc/ERK1 0.03 0.082 0.32 1 -0.41 10 11
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.039 0.093 0.28 1 -0.43 17 18
NR4A1 -0.013 0.17 -10000 0 -0.52 91 91
GSK3B 0.022 0.008 -10000 0 -10000 0 0
positive T cell selection 0.014 0.016 -10000 0 -0.4 1 1
NFAT1/CK1 alpha -0.002 0.056 -10000 0 -0.24 16 16
RCH1/ KPNB1 0.041 0.04 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.034 0.053 0.26 52 -0.57 1 53
MEF2D 0.017 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.082 0.32 1 -0.41 10 11
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.008 0.094 -10000 0 -0.57 28 28
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.033 0.057 -9999 0 -0.36 18 18
E-cadherin/beta catenin 0.022 0.062 -9999 0 -0.42 18 18
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.012 0.076 -9999 0 -0.57 18 18
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.049 0.045 -10000 0 -0.33 11 11
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.008 -10000 0 -0.28 1 1
GATA1/HDAC4 0.036 0.025 -10000 0 -0.42 1 1
GATA1/HDAC5 0.036 0.022 -10000 0 -10000 0 0
GATA2/HDAC5 0.025 0.072 -10000 0 -0.42 26 26
HDAC5/BCL6/BCoR 0.043 0.037 -10000 0 -0.36 8 8
HDAC9 0.021 0.061 0.26 10 -0.57 10 20
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.043 -10000 0 -0.36 11 11
HDAC4/ANKRA2 0.034 0.016 -10000 0 -0.42 1 1
HDAC5/YWHAB 0.033 0.01 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.26 13 -0.57 26 39
HDAC4/RFXANK 0.035 0.018 -10000 0 -0.42 1 1
BCOR 0.023 0.026 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.012 0.26 2 -10000 0 2
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.05 -10000 0 -0.42 13 13
Histones 0.016 0.049 -10000 0 -0.32 9 9
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.009 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.018 -10000 0 -0.42 1 1
HDAC7 0.024 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.035 0.012 -10000 0 -10000 0 0
CAMK4 0.031 0.046 0.26 37 -0.57 1 38
Tubulin/HDAC6 0.047 0.018 -10000 0 -0.36 1 1
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
GATA1 0.026 0.029 0.26 17 -10000 0 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.018 0.06 -10000 0 -0.57 11 11
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.23 5 5
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.017 -10000 0 -0.42 1 1
Tubulin 0.035 0.017 -10000 0 -0.42 1 1
HDAC4/14-3-3 E 0.032 0.018 -10000 0 -0.42 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.031 0.04 -10000 0 -0.42 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0.046 0.017 -10000 0 -0.36 1 1
HDAC4/SRF 0.05 0.034 -10000 0 -0.36 2 2
HDAC4/ER alpha -0.015 0.17 -10000 0 -0.41 155 155
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.049 -10000 0 -0.32 9 9
cell motility 0.046 0.018 -10000 0 -0.36 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.035 0.006 -10000 0 -10000 0 0
BCL6 0.02 0.044 -10000 0 -0.57 6 6
HDAC4/CaMK II delta B 0.023 0.018 -10000 0 -0.56 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.035 0.23 0.26 115 -0.57 151 266
HDAC6/HDAC11 0.036 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.026 -10000 0 -0.57 2 2
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.062 0.03 -10000 0 -0.31 2 2
GNG2 0.017 0.065 -10000 0 -0.57 13 13
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.023 0.021 0.26 2 -0.57 1 3
HDAC11 0.024 0.011 0.26 2 -10000 0 2
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.025 0.013 0.26 3 -10000 0 3
nuclear import -0.027 0.016 0.33 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
ITGA4 0.026 0.022 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
alpha4/beta1 Integrin 0.036 0.016 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.021 0.079 -10000 0 -0.42 33 33
AKT1 0.031 0.088 0.37 3 -0.56 8 11
PTK2B 0.003 0.084 0.35 1 -0.69 7 8
VEGFR2 homodimer/Frs2 0.024 0.063 -10000 0 -0.61 9 9
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.038 0.062 -10000 0 -0.57 9 9
endothelial cell proliferation 0.044 0.11 0.34 28 -0.56 9 37
mol:Ca2+ 0.014 0.056 -10000 0 -0.5 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.05 0.062 -10000 0 -0.52 10 10
RP11-342D11.1 0.004 0.055 -10000 0 -0.52 9 9
CDH5 0.018 0.048 -10000 0 -0.57 7 7
VEGFA homodimer 0.05 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.011 0.086 0.26 1 -0.57 23 24
HRAS/GDP 0.03 0.049 -10000 0 -0.57 4 4
SH2D2A 0.04 0.072 0.26 95 -0.57 2 97
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.086 -10000 0 -0.54 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.045 0.074 -10000 0 -0.5 10 10
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.059 -10000 0 -0.64 4 4
GRB10 0.014 0.057 -10000 0 -0.63 6 6
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
PAK1 0.023 0.019 0.26 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.05 0.075 -10000 0 -0.59 10 10
HRAS 0.026 0.022 0.26 9 -10000 0 9
VEGF/Rho/ROCK1/Integrin Complex 0.01 0.073 -10000 0 -0.47 12 12
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.048 0.061 -10000 0 -0.51 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.031 -10000 0 -0.57 3 3
Nck/Pak 0.033 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.036 0.066 -10000 0 -0.57 10 10
mol:GDP 0.039 0.054 -10000 0 -0.62 4 4
mol:NADP 0.025 0.083 0.56 1 -0.47 11 12
eNOS/Hsp90 0.037 0.08 0.54 1 -0.44 11 12
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.014 0.056 -10000 0 -0.51 9 9
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.026 0.019 0.26 7 -10000 0 7
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.022 0.1 0.35 1 -0.68 9 10
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 0.039 0.095 -10000 0 -0.4 37 37
PTPN6 0.024 0.011 0.26 2 -10000 0 2
EPAS1 0.024 0.057 -10000 0 -0.53 10 10
mol:L-citrulline 0.025 0.083 0.56 1 -0.47 11 12
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.048 0.061 -10000 0 -0.52 9 9
VEGFR2 homodimer/VEGFA homodimer 0.041 0.062 -10000 0 -0.54 10 10
VEGFR2/3 heterodimer 0.023 0.07 -10000 0 -0.62 11 11
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.004 0.069 -10000 0 -0.66 7 7
VEGFR2 homodimer 0.011 0.069 -10000 0 -0.66 10 10
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.006 0.073 0.26 5 -0.56 7 12
MAPK1 0.009 0.075 0.26 6 -0.57 7 13
VEGFA145/NRP2 0.035 0.025 -10000 0 -0.32 3 3
VEGFR1/2 heterodimer 0.023 0.064 -10000 0 -0.6 10 10
KDR 0.011 0.069 -10000 0 -0.66 10 10
VEGFA165/NRP1/VEGFR2 homodimer 0.04 0.064 -10000 0 -0.56 9 9
SRC 0.023 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.014 0.082 0.33 3 -0.52 9 12
PI3K 0.025 0.072 -10000 0 -0.73 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.039 0.062 -10000 0 -0.54 10 10
FES 0.013 0.061 -10000 0 -0.66 6 6
GAB1 0.015 0.062 -10000 0 -0.67 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.061 -10000 0 -0.53 10 10
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.017 0.13 -10000 0 -0.49 22 22
VEGFR2 homodimer/VEGFA homodimer/Yes 0.037 0.063 -10000 0 -0.52 11 11
PI3K/GAB1 0.039 0.082 -10000 0 -0.55 8 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.053 0.063 -10000 0 -0.57 7 7
PRKACA 0.024 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.036 0.068 -10000 0 -0.57 11 11
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.014 0.059 -10000 0 -0.66 6 6
actin cytoskeleton reorganization 0.045 0.074 -10000 0 -0.49 10 10
PTK2 0.005 0.088 -10000 0 -0.74 9 9
EDG1 0.004 0.055 -10000 0 -0.52 9 9
mol:DAG 0.014 0.056 -10000 0 -0.51 9 9
CaM/Ca2+ 0.025 0.054 -10000 0 -0.57 6 6
MAP2K3 -0.006 0.062 -10000 0 -0.62 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.039 0.061 -10000 0 -0.66 6 6
PLCG1 0.014 0.057 -10000 0 -0.63 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.049 0.061 -10000 0 -0.5 10 10
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.039 0.062 -10000 0 -0.54 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.062 -10000 0 -0.57 9 9
cell migration 0.024 0.093 0.31 2 -0.64 8 10
mol:PI-3-4-5-P3 0.025 0.067 -10000 0 -0.66 6 6
FYN 0.022 0.026 -10000 0 -0.57 2 2
VEGFB/NRP1 0.019 0.055 -10000 0 -0.52 8 8
mol:NO 0.025 0.083 0.56 1 -0.47 11 12
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.044 -10000 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.032 0.059 -10000 0 -0.66 6 6
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
NOS3 0.025 0.09 0.57 1 -0.54 11 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.03 0.081 -10000 0 -0.4 31 31
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.009 0.073 0.35 1 -0.4 21 22
PRKCB -0.005 0.067 -10000 0 -0.63 6 6
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.022 0.057 -10000 0 -0.5 10 10
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.064 -10000 0 -0.55 10 10
VEGFA165/NRP2 0.035 0.025 -10000 0 -0.32 3 3
MAPKKK cascade 0.05 0.079 0.33 11 -0.58 4 15
NRP2 0.023 0.027 0.26 1 -0.57 2 3
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
FAK1/Paxillin 0.023 0.1 0.42 2 -0.68 9 11
MAP3K13 0.012 0.061 -10000 0 -0.52 10 10
PDPK1 0.014 0.06 0.27 1 -0.58 5 6
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.11 0.28 16 -0.33 22 38
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.034 0.36 1 -0.42 1 2
NFKBIA 0.012 0.025 -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 0.016 0.26 3 -10000 0 3
IKBKG 0.019 0.03 -10000 0 -10000 0 0
IKK complex/A20 0.021 0.12 -10000 0 -0.42 30 30
NEMO/A20/RIP2 0.02 0.016 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.014 0.12 -10000 0 -0.4 49 49
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.032 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.11 -10000 0 -0.41 31 31
BCL10/MALT1/TRAF6 0.045 0.014 -10000 0 -10000 0 0
NOD2 0.028 0.043 0.26 30 -0.57 1 31
NFKB1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
MALT1 0.023 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 0.049 -10000 0 -0.42 9 9
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.065 0.26 25 -0.57 9 34
NF kappa B1 p50/RelA 0.051 0.015 -10000 0 -10000 0 0
BCL10 0.024 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.025 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.015 0.12 -10000 0 -0.4 44 44
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.44 40 40
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 0.026 0.018 -10000 0 -0.46 1 1
VEGFR1 homodimer/NRP1 0.01 0.015 -10000 0 -0.48 1 1
mol:DAG 0.013 0.03 -10000 0 -0.38 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.02 -10000 0 -0.44 1 1
CaM/Ca2+ 0.026 0.029 -10000 0 -0.36 2 2
HIF1A 0.028 0.011 -10000 0 -0.31 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.009 0.051 -10000 0 -0.42 1 1
PLCG1 0.013 0.03 -10000 0 -0.38 2 2
NOS3 0.016 0.052 -10000 0 -0.52 2 2
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:NO 0.02 0.061 0.3 1 -0.45 5 6
FLT1 0.014 0.018 -10000 0 -0.55 1 1
PGF 0.024 0.024 0.26 5 -0.57 1 6
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.03 -10000 0 -0.38 3 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.032 0.063 -10000 0 -0.43 6 6
endothelial cell proliferation 0.011 0.081 0.33 6 -0.6 4 10
mol:Ca2+ 0.013 0.03 -10000 0 -0.38 2 2
MAPK3 -0.012 0.049 -10000 0 -0.32 18 18
MAPK1 -0.012 0.048 -10000 0 -0.32 17 17
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
PLGF homodimer 0.024 0.024 0.26 5 -0.56 1 6
PRKACA 0.024 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
VEGFA homodimer 0.025 0.019 0.26 7 -10000 0 7
VEGFR1 homodimer/VEGFA homodimer 0.027 0.022 -10000 0 -0.48 1 1
platelet activating factor biosynthetic process -0.013 0.046 -10000 0 -0.63 1 1
PI3K 0.044 0.048 -10000 0 -0.32 14 14
PRKCA -0.011 0.052 -10000 0 -0.33 19 19
PRKCB -0.009 0.048 -10000 0 -0.34 14 14
VEGFR1 homodimer/PLGF homodimer 0.027 0.024 -10000 0 -0.42 2 2
VEGFA 0.025 0.019 0.26 7 -10000 0 7
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.03 -10000 0 -0.38 2 2
RASA1 0.013 0.028 -10000 0 -0.43 1 1
NRP2 0.023 0.027 0.26 1 -0.57 2 3
VEGFR1 homodimer 0.013 0.018 -10000 0 -0.55 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 -0.029 0.14 -10000 0 -0.43 26 26
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.047 -10000 0 -0.32 14 14
mol:L-citrulline 0.02 0.061 0.3 1 -0.45 5 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.028 -10000 0 -0.41 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.039 0.023 -10000 0 -0.44 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.052 0.05 -10000 0 -0.31 14 14
PDPK1 -0.005 0.053 -10000 0 -0.4 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.023 -10000 0 -0.44 1 1
mol:NADP 0.02 0.061 0.3 1 -0.45 5 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.027 -10000 0 -0.4 1 1
VEGFR1 homodimer/NRP2 0.026 0.027 -10000 0 -0.44 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.004 0.039 0.21 1 -0.28 4 5
SMAD3 0.022 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.063 -10000 0 -0.44 11 11
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.058 -10000 0 -0.28 1 1
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.27 8 8
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
TRAP-1/SMAD4 0.027 0.056 -10000 0 -0.4 17 17
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 0.003 -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 0.015 0.072 -10000 0 -0.57 16 16
UBE2I 0.023 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.005 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 64 -10000 0 64
PIAS4 0.024 0.004 -10000 0 -10000 0 0
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 0.05 0.061 -10000 0 -0.37 8 8
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.06 -10000 0 -0.36 6 6
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.021 0.26 7 -10000 0 7
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.053 0.041 -10000 0 -0.4 1 1
YY1/LSF 0.024 0.049 -10000 0 -0.3 7 7
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 0.03 -10000 0 -0.3 7 7
I kappa B alpha/HDAC1 0.03 0.036 -10000 0 -0.42 1 1
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.02 0.036 -10000 0 -0.3 7 7
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.031 0.036 -10000 0 -0.43 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.28 12 12
NF kappa B1 p50/RelA 0.026 0.064 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.26 13 -0.57 26 39
GATA1 0.026 0.029 0.26 17 -10000 0 17
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.079 -10000 0 -0.36 20 20
RBBP7 0.026 0.019 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.018 -10000 0 -0.57 1 1
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 0.026 -10000 0 -0.47 1 1
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.029 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.022 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.015 0.26 4 -10000 0 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.046 -10000 0 -0.38 3 3
YY1/HDAC2 0.025 0.045 -10000 0 -0.29 5 5
YY1/HDAC1 0.025 0.047 -10000 0 -0.29 6 6
NuRD/MBD2 Complex (MeCP1) 0.024 0.054 -10000 0 -0.27 13 13
PPARG -0.06 0.16 -10000 0 -0.34 226 226
HDAC8/hEST1B 0.041 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -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) 0.031 0.036 -10000 0 -0.43 1 1
MBD3L2 0.017 0.011 0.26 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.065 -10000 0 -0.35 14 14
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.019 0.027 -10000 0 -0.48 1 1
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.011 -10000 0 -0.29 1 1
HDAC8 0.024 0.001 -10000 0 -10000 0 0
SMAD7 0.023 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.007 0.26 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.036 0.048 -10000 0 -0.27 6 6
YY1/SAP30/HDAC1 0.036 0.047 -10000 0 -0.26 5 5
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.026 -10000 0 -0.47 1 1
histone deacetylation 0.024 0.053 -10000 0 -0.27 13 13
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.035 -10000 0 -0.41 1 1
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GATAD2B 0.02 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.025 0.065 -10000 0 -0.33 23 23
GATA1/HDAC1 0.036 0.02 -10000 0 -10000 0 0
GATA1/HDAC3 0.032 0.041 -10000 0 -0.45 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.049 -10000 0 -0.42 9 9
SIN3/HDAC complex/Mad/Max 0.016 0.052 -10000 0 -0.29 17 17
NuRD Complex 0.025 0.065 -10000 0 -0.38 9 9
positive regulation of chromatin silencing 0.05 0.039 -10000 0 -0.39 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 0.038 -10000 0 -0.23 4 4
HDAC complex 0.057 0.022 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.025 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.015 -10000 0 -10000 0 0
TNF 0.024 0.065 0.26 25 -0.57 9 34
negative regulation of cell growth 0.016 0.052 -10000 0 -0.29 17 17
NuRD/MBD2/PRMT5 Complex 0.024 0.054 -10000 0 -0.27 13 13
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NF kappa B/RelA/I kappa B alpha 0.019 0.051 -10000 0 -0.36 7 7
SIN3/HDAC complex/NCoR1 0.007 0.066 -10000 0 -0.32 28 28
TFCP2 0.024 0.018 -10000 0 -0.57 1 1
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.009 0.26 1 -10000 0 1
MBD2 0.023 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.034 0.011 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.043 -10000 0 -0.33 2 2
NFKBIA 0.015 0.037 -10000 0 -0.25 11 11
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 0.017 0.067 -10000 0 -0.57 14 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.013 -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 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.012 0.25 2 -10000 0 2
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
NFKB1 0.01 0.011 0.26 2 -10000 0 2
RELA 0.023 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.024 0.046 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.046 -10000 0 -0.38 2 2
SRC 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.38 14 14
NF kappa B1 p50/RelA 0.024 0.046 -10000 0 -0.26 10 10
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 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.057 -10000 0 -0.29 16 16
cell death 0.024 0.044 -10000 0 -0.36 2 2
NF kappa B1 p105/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
LCK 0.026 0.075 0.26 40 -0.57 11 51
BCL3 0.024 0.011 0.26 2 -10000 0 2
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 0.042 0.035 -10000 0 -10000 0 0
CLOCK 0.02 0.06 -10000 0 -0.56 11 11
TIMELESS/CRY2 0.031 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.014 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.017 -10000 0 -10000 0 0
ARNTL 0.026 0.004 -10000 0 -10000 0 0
TIMELESS 0.018 0.024 -10000 0 -10000 0 0
NPAS2 0.023 0.041 0.26 1 -0.56 5 6
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.006 -10000 0 -0.09 6 6
CHEK1 0.027 0.035 0.26 23 -10000 0 23
mol:HEME 0.007 0.006 0.09 6 -10000 0 6
PER1 0.013 0.072 -10000 0 -0.57 16 16
BMAL/CLOCK/NPAS2 0.049 0.052 -10000 0 -0.36 16 16
BMAL1/CLOCK 0.019 0.062 -10000 0 -0.48 1 1
S phase of mitotic cell cycle 0.042 0.035 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.042 0.036 -10000 0 -10000 0 0
mol:NADPH 0.007 0.006 0.09 6 -10000 0 6
PER1/TIMELESS 0.024 0.046 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.018 0.26 6 -10000 0 6
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 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.26 10 -10000 0 10
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.039 0.36 4 -0.42 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.017 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.044 0.035 0.33 4 -0.33 2 6
lamellipodium assembly -0.003 0.088 -10000 0 -0.41 35 35
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.38 14 14
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 0.016 0.065 -10000 0 -0.57 13 13
ARF6/GTP 0.047 0.02 -10000 0 -10000 0 0
cell adhesion 0.05 0.019 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.016 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.048 0.043 -10000 0 -0.31 11 11
p130Cas/Crk/Dock1 0.041 0.019 -10000 0 -10000 0 0
VCAM1 0.019 0.062 0.26 6 -0.57 11 17
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.019 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.021 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.047 0.021 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.019 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.097 -10000 0 -0.46 35 35
Arf6 downstream 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
PLAUR 0.04 0.069 0.36 1 -10000 0 1
regulation of axonogenesis -0.011 0.026 0.23 6 -10000 0 6
myoblast fusion -0.026 0.047 -10000 0 -0.22 1 1
mol:GTP 0.023 0.031 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.055 0.044 -10000 0 -0.3 2 2
ARF1/GTP 0.03 0.028 -10000 0 -10000 0 0
mol:GM1 0.012 0.024 -10000 0 -10000 0 0
mol:Choline 0.008 0.038 -10000 0 -0.34 9 9
lamellipodium assembly 0.018 0.058 -10000 0 -0.36 7 7
MAPK3 0.032 0.045 0.21 1 -10000 0 1
ARF6/GTP/NME1/Tiam1 0.056 0.045 0.31 2 -10000 0 2
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.047 0.22 1 -10000 0 1
ARF1/GDP 0.025 0.047 -10000 0 -0.28 1 1
ARF6 0.032 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.015 0.25 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.032 0.044 0.21 1 -10000 0 1
actin filament bundle formation -0.032 0.05 0.26 2 -10000 0 2
KALRN 0.01 0.054 -10000 0 -0.31 20 20
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.033 0.05 -10000 0 -0.26 2 2
NME1 0.028 0.031 0.26 18 -10000 0 18
Rac1/GDP 0.033 0.051 -10000 0 -0.26 3 3
substrate adhesion-dependent cell spreading 0.023 0.031 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.018 0.058 -10000 0 -0.37 7 7
RAC1 0.024 0.003 -10000 0 -10000 0 0
liver development 0.023 0.031 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.031 -10000 0 -10000 0 0
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.046 0.23 1 -10000 0 1
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.029 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.045 -10000 0 -0.39 9 9
RAB11FIP3 0.023 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.018 0.058 -10000 0 -0.36 7 7
ruffle organization 0.011 0.026 -10000 0 -0.23 6 6
regulation of epithelial cell migration 0.023 0.031 -10000 0 -10000 0 0
PLD2 0.02 0.024 -10000 0 -10000 0 0
PIP5K1A 0.011 0.026 -10000 0 -0.23 6 6
mol:Phosphatidic acid 0.008 0.038 -10000 0 -0.34 9 9
Rac1/GTP 0.018 0.058 -10000 0 -0.37 7 7
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.011 -10000 0 -0.26 1 1
MDM2/SUMO1 0.033 0.039 -10000 0 -0.23 4 4
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.017 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 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 0.035 0.039 -10000 0 -0.23 5 5
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.23 4 4
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.056 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.036 -10000 0 -0.24 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.038 0.25 1 -0.24 4 5
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
Arf1 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
coatomer protein complex 0.011 0.032 0.18 3 -10000 0 3
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.047 -10000 0 -0.19 4 4
AP2 0.034 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 0.025 0.015 0.26 4 -10000 0 4
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.01 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.006 0.13 2 -10000 0 2
mol:PI-4-5-P2 0.007 0.015 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.012 0.2 3 -10000 0 3
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.01 -10000 0 -10000 0 0
DDEF1 0.006 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.02 -10000 0 -0.15 1 1
AP2M1 0.024 0.005 -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 0.015 0.018 -10000 0 -10000 0 0
COPA 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.011 0.023 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.041 -10000 0 -0.24 20 20
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.023 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.013 0.048 -10000 0 -0.26 28 28
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.023 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 0.13 2 -10000 0 2
PIP5K1A 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.006 0.13 2 -10000 0 2
GOSR2 0.008 0.028 -10000 0 -0.31 7 7
USO1 0.01 0.02 -10000 0 -0.32 3 3
GBF1 0.009 0.024 -10000 0 -0.31 5 5
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.015 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.067 0.025 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.016 -10000 0 -9999 0 0
RELB 0.026 0.022 0.26 10 -9999 0 10
NFKB2 0.024 0.008 0.26 1 -9999 0 1
NF kappa B2 p52/RelB 0.033 0.016 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.016 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1075 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z7.A8R6 TCGA.Z7.A8R5 TCGA.XX.A89A TCGA.XX.A899
109_MAP3K5 -0.33 0.025 0.025 0.025
47_PPARGC1A -0.57 0.024 0.024 0.024
105_BMP4 0.024 0.024 0.024 0.024
105_BMP6 0.024 0.024 0.024 0.024
105_BMP7 0.024 0.024 0.024 0.024
105_BMP2 -0.57 0.024 0.024 0.024
131_RELN/VLDLR -0.33 -0.33 0.063 0.063
30_TGFB1/TGF beta receptor Type II -0.033 0.024 0.018 0.019
84_STAT5B -0.16 -0.06 0.12 0.029
84_STAT5A -0.16 -0.06 0.12 0.029
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/19437968/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/19775038/GDAC_Gistic2Report_19785909/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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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