PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1SX6BJ3
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1SX6BJ3
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 44 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 217
Glypican 2 network 162
Angiopoietin receptor Tie2-mediated signaling 135
HIF-1-alpha transcription factor network 118
Aurora B signaling 114
Signaling events mediated by the Hedgehog family 89
Endothelins 77
PLK1 signaling events 72
Aurora C signaling 65
Signaling mediated by p38-alpha and p38-beta 59
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 468 . 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 ( 468 ).

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 0.4637 217 11067 51 -0.034 0.79 1000 -1000 -0.078 -1000
Glypican 2 network 0.3462 162 648 4 0.091 0.14 1000 -1000 0.02 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2885 135 11931 88 -0.56 0.11 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 0.2521 118 8979 76 -0.063 0.43 1000 -1000 -0.03 -1000
Aurora B signaling 0.2436 114 7701 67 -0.15 0.28 1000 -1000 -0.037 -1000
Signaling events mediated by the Hedgehog family 0.1902 89 4632 52 -0.22 0.1 1000 -1000 -0.029 -1000
Endothelins 0.1645 77 7427 96 -0.31 0.19 1000 -1000 -0.034 -1000
PLK1 signaling events 0.1538 72 6144 85 -0.05 0.2 1000 -1000 -0.017 -1000
Aurora C signaling 0.1389 65 457 7 0 0.17 1000 -1000 -0.004 -1000
Signaling mediated by p38-alpha and p38-beta 0.1261 59 2605 44 -0.1 0.021 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 0.1239 58 2227 38 -0.083 0.12 1000 -1000 -0.018 -1000
FOXA2 and FOXA3 transcription factor networks 0.1197 56 2600 46 -0.21 0.15 1000 -1000 -0.067 -1000
Signaling events regulated by Ret tyrosine kinase 0.1111 52 4331 82 -0.078 0.063 1000 -1000 -0.044 -1000
Osteopontin-mediated events 0.1068 50 1931 38 -0.002 0.24 1000 -1000 -0.016 -1000
IL4-mediated signaling events 0.1047 49 4508 91 -0.62 0.34 1000 -1000 -0.087 -1000
Fc-epsilon receptor I signaling in mast cells 0.1047 49 4841 97 -0.095 0.021 1000 -1000 -0.042 -1000
BMP receptor signaling 0.1026 48 3966 81 -0.18 0.22 1000 -1000 -0.019 -1000
amb2 Integrin signaling 0.1026 48 4003 82 -0.29 0.078 1000 -1000 -0.021 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.1026 48 2526 52 -0.14 0.044 1000 -1000 -0.025 -1000
Visual signal transduction: Rods 0.0897 42 2220 52 -0.083 0.099 1000 -1000 -0.026 -1000
Ephrin B reverse signaling 0.0876 41 1968 48 -0.073 0.075 1000 -1000 -0.026 -1000
Syndecan-1-mediated signaling events 0.0855 40 1378 34 0 0.21 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 0.0812 38 4769 125 -0.15 0.13 1000 -1000 -0.044 -1000
Thromboxane A2 receptor signaling 0.0769 36 3854 105 -0.12 0.072 1000 -1000 -0.036 -1000
Canonical Wnt signaling pathway 0.0769 36 1870 51 -0.21 0.096 1000 -1000 -0.025 -1000
IL23-mediated signaling events 0.0769 36 2185 60 -0.2 0.025 1000 -1000 -0.072 -1000
Arf6 signaling events 0.0705 33 2060 62 -0.11 0.072 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0705 33 2268 68 -0.15 0.065 1000 -1000 -0.064 -1000
Integrins in angiogenesis 0.0684 32 2744 84 -0.075 0.24 1000 -1000 -0.037 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0684 32 3929 120 -0.16 0.14 1000 -1000 -0.049 -1000
LPA4-mediated signaling events 0.0662 31 382 12 -0.071 0 1000 -1000 -0.016 -1000
TCGA08_retinoblastoma 0.0662 31 251 8 -0.023 0.099 1000 -1000 -0.005 -1000
Glucocorticoid receptor regulatory network 0.0641 30 3513 114 -0.26 0.16 1000 -1000 -0.041 -1000
HIF-2-alpha transcription factor network 0.0641 30 1308 43 -0.13 0.14 1000 -1000 -0.035 -1000
Presenilin action in Notch and Wnt signaling 0.0620 29 1827 61 -0.21 0.096 1000 -1000 -0.032 -1000
Reelin signaling pathway 0.0620 29 1656 56 -0.038 0.048 1000 -1000 -0.024 -1000
TCGA08_p53 0.0620 29 204 7 -0.024 0.019 1000 -1000 -0.009 -1000
IL6-mediated signaling events 0.0620 29 2204 75 -0.15 0.054 1000 -1000 -0.039 -1000
Aurora A signaling 0.0577 27 1645 60 -0.028 0.18 1000 -1000 -0.02 -1000
Wnt signaling 0.0577 27 189 7 -0.023 0.038 1000 -1000 -0.008 -1000
Glypican 1 network 0.0556 26 1278 48 -0.061 0.036 1000 -1000 -0.021 -1000
Effects of Botulinum toxin 0.0556 26 677 26 0 0.044 1000 -1000 -0.007 -1000
EGFR-dependent Endothelin signaling events 0.0556 26 563 21 -0.028 0.072 1000 -1000 -0.028 -1000
Noncanonical Wnt signaling pathway 0.0513 24 639 26 -0.045 0.038 1000 -1000 -0.027 -1000
FoxO family signaling 0.0491 23 1498 64 0 0.2 1000 -1000 -0.044 -1000
Nongenotropic Androgen signaling 0.0491 23 1242 52 -0.062 0.045 1000 -1000 -0.021 -1000
Nectin adhesion pathway 0.0470 22 1410 63 -0.044 0.051 1000 -1000 -0.026 -1000
Syndecan-4-mediated signaling events 0.0470 22 1492 67 -0.043 0.12 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0470 22 748 33 -0.074 0.098 1000 -1000 -0.025 -1000
S1P4 pathway 0.0470 22 557 25 -0.026 0.027 1000 -1000 -0.015 -1000
ErbB2/ErbB3 signaling events 0.0449 21 1406 65 -0.05 0.029 1000 -1000 -0.053 -1000
IL1-mediated signaling events 0.0449 21 1302 62 -0.078 0.042 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 0.0449 21 1501 70 -0.14 0.12 1000 -1000 -0.033 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0427 20 701 34 -0.036 0.059 1000 -1000 -0.022 -1000
PDGFR-alpha signaling pathway 0.0427 20 917 44 -0.19 0.038 1000 -1000 -0.029 -1000
EPHB forward signaling 0.0427 20 1742 85 -0.033 0.084 1000 -1000 -0.045 -1000
LPA receptor mediated events 0.0427 20 2090 102 -0.056 0.078 1000 -1000 -0.068 -1000
ErbB4 signaling events 0.0406 19 1344 69 -0.11 0.14 1000 -1000 -0.026 -1000
Syndecan-2-mediated signaling events 0.0406 19 1339 69 -0.044 0.054 1000 -1000 -0.031 -1000
Ceramide signaling pathway 0.0385 18 1380 76 -0.019 0.072 1000 -1000 -0.027 -1000
FAS signaling pathway (CD95) 0.0385 18 850 47 -0.24 0.033 1000 -1000 -0.025 -1000
Class IB PI3K non-lipid kinase events 0.0385 18 54 3 -0.007 0.007 1000 -1000 -0.015 -1000
S1P5 pathway 0.0363 17 295 17 -0.018 0.02 1000 -1000 -0.001 -1000
Calcium signaling in the CD4+ TCR pathway 0.0363 17 552 31 -0.041 0.031 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 0.0342 16 1245 76 -0.058 0.097 1000 -1000 -0.013 -1000
PLK2 and PLK4 events 0.0342 16 50 3 -0.006 0.037 1000 -1000 -0.015 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0342 16 908 54 -0.034 0.1 1000 -1000 -0.03 -1000
Signaling events mediated by PTP1B 0.0342 16 1255 76 -0.053 0.072 1000 -1000 -0.033 -1000
TCR signaling in naïve CD8+ T cells 0.0342 16 1517 93 -0.04 0.034 1000 -1000 -0.036 -1000
IL12-mediated signaling events 0.0321 15 1357 87 -0.13 0.057 1000 -1000 -0.078 -1000
S1P1 pathway 0.0321 15 560 36 -0.094 0.02 1000 -1000 -0.027 -1000
Plasma membrane estrogen receptor signaling 0.0321 15 1371 86 -0.059 0.055 1000 -1000 -0.037 -1000
Caspase cascade in apoptosis 0.0299 14 1074 74 -0.031 0.088 1000 -1000 -0.028 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0299 14 1196 85 -0.06 0.034 1000 -1000 -0.039 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0299 14 1099 78 -0.04 0.022 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class III 0.0278 13 520 40 -0.063 0.062 1000 -1000 -0.028 -1000
Syndecan-3-mediated signaling events 0.0278 13 475 35 -0.11 0.045 1000 -1000 -0.015 -1000
Regulation of p38-alpha and p38-beta 0.0278 13 719 54 -0.036 0.058 1000 -1000 -0.038 -1000
BCR signaling pathway 0.0278 13 1378 99 -0.047 0.078 1000 -1000 -0.047 -1000
BARD1 signaling events 0.0256 12 707 57 -0.045 0.12 1000 -1000 -0.037 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0256 12 1588 125 -0.19 0.041 1000 -1000 -0.038 -1000
IL27-mediated signaling events 0.0214 10 535 51 -0.044 0.03 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0214 10 221 22 -0.025 0.095 1000 -1000 -0.028 -1000
Signaling events mediated by PRL 0.0214 10 372 34 -0.021 0.084 1000 -1000 -0.028 -1000
Class I PI3K signaling events 0.0192 9 663 73 -0.033 0.058 1000 -1000 -0.021 -1000
VEGFR1 specific signals 0.0192 9 532 56 -0.19 0.048 1000 -1000 -0.03 -1000
PDGFR-beta signaling pathway 0.0192 9 895 97 -0.032 0.052 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 0.0171 8 1140 136 -0.17 0.07 1000 -1000 -0.028 -1000
Ephrin A reverse signaling 0.0171 8 56 7 -0.013 0.028 1000 -1000 -0.006 -1000
JNK signaling in the CD4+ TCR pathway 0.0171 8 136 17 -0.011 0.046 1000 -1000 -0.031 -1000
Hedgehog signaling events mediated by Gli proteins 0.0171 8 529 65 -0.13 0.047 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0171 8 633 74 -0.09 0.072 1000 -1000 -0.048 -1000
Insulin Pathway 0.0171 8 644 74 -0.095 0.05 1000 -1000 -0.035 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0150 7 222 28 -0.016 0.033 1000 -1000 -0.016 -1000
Cellular roles of Anthrax toxin 0.0150 7 305 39 -0.032 0.027 1000 -1000 -0.012 -1000
EPO signaling pathway 0.0150 7 385 55 -0.025 0.045 1000 -1000 -0.028 -1000
mTOR signaling pathway 0.0150 7 402 53 -0.057 0.024 1000 -1000 -0.027 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0150 7 582 83 -0.059 0.043 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0150 7 446 58 -0.093 0.044 1000 -1000 -0.036 -1000
Arf6 trafficking events 0.0150 7 524 71 -0.038 0.038 1000 -1000 -0.03 -1000
Regulation of Telomerase 0.0150 7 730 102 -0.02 0.1 1000 -1000 -0.034 -1000
Ras signaling in the CD4+ TCR pathway 0.0150 7 121 17 -0.004 0.031 1000 -1000 -0.017 -1000
IFN-gamma pathway 0.0128 6 461 68 -0.029 0.063 1000 -1000 -0.031 -1000
ceramide signaling pathway 0.0128 6 338 49 -0.007 0.027 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 0.0128 6 92 15 -0.017 0.021 1000 -1000 -0.023 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0128 6 295 45 -0.019 0.05 1000 -1000 -0.031 -1000
IGF1 pathway 0.0128 6 353 57 -0.032 0.046 1000 -1000 -0.03 -1000
p38 MAPK signaling pathway 0.0128 6 276 44 -0.004 0.063 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class I 0.0107 5 589 104 -0.034 0.047 1000 -1000 -0.034 -1000
IL2 signaling events mediated by PI3K 0.0107 5 333 58 -0.014 0.077 1000 -1000 -0.036 -1000
TCGA08_rtk_signaling 0.0107 5 135 26 -0.011 0.047 1000 -1000 -0.008 -1000
E-cadherin signaling in the nascent adherens junction 0.0107 5 455 76 -0.031 0.05 1000 -1000 -0.037 -1000
S1P3 pathway 0.0107 5 234 42 -0.023 0.034 1000 -1000 -0.022 -1000
E-cadherin signaling in keratinocytes 0.0107 5 228 43 -0.013 0.039 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class II 0.0085 4 349 75 -0.02 0.056 1000 -1000 -0.025 -1000
Circadian rhythm pathway 0.0085 4 92 22 -0.004 0.045 1000 -1000 -0.027 -1000
Arf6 downstream pathway 0.0085 4 206 43 -0.047 0.048 1000 -1000 -0.027 -1000
Class I PI3K signaling events mediated by Akt 0.0085 4 306 68 -0.027 0.043 1000 -1000 -0.021 -1000
Canonical NF-kappaB pathway 0.0043 2 93 39 -0.016 0.042 1000 -1000 -0.02 -1000
Insulin-mediated glucose transport 0.0043 2 80 32 -0.015 0.037 1000 -1000 -0.018 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0043 2 97 37 -0.024 0.049 1000 -1000 -0.015 -1000
TRAIL signaling pathway 0.0043 2 129 48 -0.017 0.045 1000 -1000 -0.02 -1000
Rapid glucocorticoid signaling 0.0043 2 46 20 -0.007 0.025 1000 -1000 -0.01 -1000
Arf1 pathway 0.0043 2 135 54 -0.008 0.033 1000 -1000 -0.011 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0021 1 28 23 0 0.035 1000 -1000 -0.017 -1000
a4b1 and a4b7 Integrin signaling 0.0021 1 7 5 0.019 0.029 1000 -1000 0.019 -1000
Paxillin-dependent events mediated by a4b1 0.0021 1 62 36 -0.036 0.038 1000 -1000 -0.028 -1000
Atypical NF-kappaB pathway 0.0021 1 52 31 -0.017 0.028 1000 -1000 -0.019 -1000
E-cadherin signaling events 0.0021 1 6 5 0.019 0.038 1000 -1000 0.019 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 23 27 -0.018 0.044 1000 -1000 -0.029 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.055 1000 -1000 0 -1000
Total NA 3272 193117 7203 -9.6 11 131000 -131000 -3.7 -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 0.64 0.48 1 266 -10000 0 266
PLK1 0.37 0.32 0.68 222 -0.68 2 224
BIRC5 0.4 0.32 0.69 231 -0.71 1 232
HSPA1B 0.64 0.49 1 261 -10000 0 261
MAP2K1 0.19 0.15 0.33 235 -10000 0 235
BRCA2 0.64 0.49 1 255 -10000 0 255
FOXM1 0.79 0.64 1.3 269 -0.8 2 271
XRCC1 0.64 0.49 1 266 -10000 0 266
FOXM1B/p19 0.21 0.35 0.82 103 -0.78 2 105
Cyclin D1/CDK4 0.52 0.43 0.91 239 -0.69 1 240
CDC2 0.71 0.56 1.1 271 -0.73 2 273
TGFA 0.56 0.45 0.94 255 -0.7 1 256
SKP2 0.7 0.54 1.1 267 -10000 0 267
CCNE1 0.15 0.16 0.38 153 -10000 0 153
CKS1B 0.69 0.54 1.1 261 -10000 0 261
RB1 0.38 0.36 0.72 218 -0.61 3 221
FOXM1C/SP1 0.56 0.42 0.92 249 -0.76 2 251
AURKB 0.34 0.37 0.68 215 -0.73 15 230
CENPF 0.72 0.56 1.1 272 -10000 0 272
CDK4 0.086 0.066 0.18 102 -10000 0 102
MYC 0.42 0.42 0.86 203 -0.67 1 204
CHEK2 0.19 0.16 0.34 227 -10000 0 227
ONECUT1 0.6 0.48 1 253 -0.72 1 254
CDKN2A -0.034 0.15 0.25 49 -0.22 133 182
LAMA4 0.63 0.5 1 261 -1.1 5 266
FOXM1B/HNF6 0.61 0.49 1 247 -0.78 1 248
FOS 0.58 0.52 1 237 -0.94 2 239
SP1 0.021 0.005 -10000 0 -10000 0 0
CDC25B 0.64 0.49 1 262 -0.73 1 263
response to radiation 0.13 0.11 0.22 252 -10000 0 252
CENPB 0.64 0.49 1 260 -10000 0 260
CENPA 0.72 0.56 1.2 272 -10000 0 272
NEK2 0.74 0.57 1.2 278 -10000 0 278
HIST1H2BA 0.64 0.49 1 259 -10000 0 259
CCNA2 0.13 0.15 0.39 116 -10000 0 116
EP300 0.02 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.69 0.54 1.1 258 -10000 0 258
CCNB2 0.71 0.56 1.1 268 -10000 0 268
CCNB1 0.73 0.58 1.2 266 -10000 0 266
ETV5 0.62 0.51 1 254 -1.1 2 256
ESR1 0.62 0.51 1 246 -1 4 250
CCND1 0.6 0.48 0.98 259 -0.7 1 260
GSK3A 0.15 0.11 0.26 219 -10000 0 219
Cyclin A-E1/CDK1-2 0.26 0.22 0.44 244 -10000 0 244
CDK2 0.06 0.039 0.16 2 -10000 0 2
G2/M transition of mitotic cell cycle 0.17 0.15 0.28 267 -10000 0 267
FOXM1B/Cbp/p300 0.15 0.25 0.68 54 -0.74 2 56
GAS1 0.61 0.51 1 256 -1 5 261
MMP2 0.64 0.49 1 260 -10000 0 260
RB1/FOXM1C 0.52 0.44 0.9 238 -0.73 1 239
CREBBP 0.02 0.004 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.11 0.14 0.32 139 -9999 0 139
GPC2 0.091 0.13 0.32 111 -9999 0 111
GPC2/Midkine 0.14 0.14 0.28 199 -9999 0 199
neuron projection morphogenesis 0.14 0.14 0.28 199 -9999 0 199
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.44 0.47 -10000 0 -0.94 216 216
NCK1/PAK1/Dok-R -0.21 0.2 -10000 0 -0.42 220 220
NCK1/Dok-R -0.48 0.57 -10000 0 -1.1 216 216
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
mol:beta2-estradiol 0.059 0.095 0.23 106 -10000 0 106
RELA 0.02 0.003 -10000 0 -10000 0 0
SHC1 0.011 0.014 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
F2 0.11 0.16 0.32 148 -10000 0 148
TNIP2 0.02 0.003 -10000 0 -10000 0 0
NF kappa B/RelA -0.44 0.53 -10000 0 -0.98 215 215
FN1 0.018 0.032 -10000 0 -0.32 4 4
PLD2 -0.51 0.59 -10000 0 -1.1 214 214
PTPN11 0.02 0.003 -10000 0 -10000 0 0
GRB14 0.032 0.076 0.32 24 -0.32 5 29
ELK1 -0.46 0.51 -10000 0 -0.98 215 215
GRB7 0.019 0.023 -10000 0 -0.32 2 2
PAK1 0.02 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.46 0.56 -10000 0 -1 215 215
CDKN1A -0.32 0.32 -10000 0 -0.65 215 215
ITGA5 0.02 0.021 0.32 1 -0.32 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.48 0.57 -10000 0 -1.1 215 215
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:NO -0.32 0.34 -10000 0 -0.67 215 215
PLG -0.51 0.59 -10000 0 -1.1 215 215
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.41 0.44 -10000 0 -0.87 217 217
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.012 0.021 -10000 0 -0.33 1 1
ANGPT2 -0.29 0.32 -10000 0 -0.71 138 138
BMX -0.55 0.61 -10000 0 -1.2 214 214
ANGPT1 -0.3 0.47 -10000 0 -1.1 107 107
tube development -0.36 0.36 -10000 0 -0.73 216 216
ANGPT4 -0.16 0.16 -10000 0 -0.33 225 225
response to hypoxia -0.031 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.51 0.62 -10000 0 -1.1 215 215
alpha5/beta1 Integrin 0.03 0.017 0.23 1 -0.23 1 2
FGF2 -0.022 0.11 -10000 0 -0.32 57 57
STAT5A (dimer) -0.41 0.42 -10000 0 -0.85 214 214
mol:L-citrulline -0.32 0.34 -10000 0 -0.67 215 215
AGTR1 -0.082 0.16 -10000 0 -0.32 138 138
MAPK14 -0.56 0.63 -10000 0 -1.2 217 217
Tie2/SHP2 -0.44 0.52 -10000 0 -1 202 202
TEK -0.49 0.57 -10000 0 -1.1 200 200
RPS6KB1 -0.42 0.45 -10000 0 -0.89 217 217
Angiotensin II/AT1 -0.054 0.11 -10000 0 -0.22 138 138
Tie2/Ang1/GRB2 -0.51 0.62 -10000 0 -1.1 215 215
MAPK3 -0.46 0.53 -10000 0 -1 214 214
MAPK1 -0.46 0.52 -10000 0 -1 212 212
Tie2/Ang1/GRB7 -0.52 0.62 -10000 0 -1.1 215 215
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.51 0.59 -10000 0 -1.1 215 215
PI3K -0.52 0.56 -10000 0 -1.1 217 217
FES -0.56 0.63 -10000 0 -1.2 217 217
Crk/Dok-R -0.48 0.57 -10000 0 -1.1 215 215
Tie2/Ang1/ABIN2 -0.52 0.62 -10000 0 -1.1 215 215
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.39 0.41 -10000 0 -0.82 216 216
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.41 0.45 -10000 0 -0.88 217 217
Tie2/Ang2 -0.51 0.52 -10000 0 -1 216 216
Tie2/Ang1 -0.55 0.66 -10000 0 -1.2 215 215
FOXO1 -0.4 0.42 -10000 0 -0.83 216 216
ELF1 -0.033 0.067 -10000 0 -0.13 68 68
ELF2 -0.5 0.59 -10000 0 -1.1 212 212
mol:Choline -0.48 0.55 -10000 0 -1 214 214
cell migration -0.12 0.11 -10000 0 -0.23 220 220
FYN -0.41 0.42 -10000 0 -0.85 216 216
DOK2 -0.004 0.083 -10000 0 -0.32 29 29
negative regulation of cell cycle -0.29 0.28 -10000 0 -0.58 215 215
ETS1 -0.051 0.1 -10000 0 -0.25 98 98
PXN -0.34 0.37 -10000 0 -0.72 217 217
ITGB1 0.02 0.003 -10000 0 -10000 0 0
NOS3 -0.37 0.39 -10000 0 -0.78 214 214
RAC1 0.018 0.007 -10000 0 -10000 0 0
TNF -0.062 0.12 -10000 0 -0.26 113 113
MAPKKK cascade -0.48 0.55 -10000 0 -1 214 214
RASA1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.51 0.61 -10000 0 -1.1 215 215
NCK1 0.02 0.003 -10000 0 -10000 0 0
vasculogenesis -0.28 0.3 -10000 0 -0.6 215 215
mol:Phosphatidic acid -0.48 0.55 -10000 0 -1 214 214
mol:Angiotensin II 0 0.003 -10000 0 -10000 0 0
mol:NADP -0.32 0.34 -10000 0 -0.67 215 215
Rac1/GTP -0.38 0.41 -10000 0 -0.82 217 217
MMP2 -0.51 0.59 -10000 0 -1.1 214 214
HIF-1-alpha transcription factor network

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
PKM2 0.28 0.24 0.54 146 -0.67 4 150
HDAC7 0.031 0.015 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.31 0.31 0.64 167 -0.83 3 170
SMAD4 0.018 0.01 -10000 0 -10000 0 0
ID2 0.29 0.24 0.53 151 -0.67 4 155
AP1 -0.002 0.076 -10000 0 -0.24 35 35
ABCG2 0.26 0.25 0.54 140 -0.62 6 146
HIF1A 0.1 0.091 0.24 91 -0.21 2 93
TFF3 0.32 0.28 0.59 175 -0.7 4 179
GATA2 -0.02 0.1 -10000 0 -0.34 39 39
AKT1 0.098 0.1 0.26 74 -0.24 4 78
response to hypoxia 0.079 0.097 0.2 129 -0.22 8 137
MCL1 0.24 0.24 0.53 119 -0.74 2 121
NDRG1 0.25 0.24 0.54 124 -0.63 4 128
SERPINE1 0.27 0.24 0.54 142 -0.67 4 146
FECH 0.26 0.24 0.54 137 -0.67 4 141
FURIN 0.29 0.24 0.55 153 -0.67 4 157
NCOA2 0.016 0.033 -10000 0 -0.32 4 4
EP300 0.12 0.14 0.28 124 -0.3 12 136
HMOX1 0.28 0.24 0.54 148 -0.63 4 152
BHLHE40 0.28 0.24 0.54 147 -0.67 4 151
BHLHE41 0.26 0.25 0.54 133 -0.65 6 139
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.14 0.36 73 -0.32 1 74
ENG 0.11 0.1 0.27 58 -0.31 3 61
JUN 0.007 0.041 -10000 0 -0.33 4 4
RORA 0.28 0.24 0.54 145 -0.7 4 149
ABCB1 0.007 0.18 0.37 22 -0.73 19 41
TFRC 0.27 0.24 0.53 140 -0.67 4 144
CXCR4 0.28 0.23 0.53 149 -0.67 4 153
TF 0.32 0.29 0.62 165 -0.63 5 170
CITED2 0.27 0.24 0.53 147 -0.67 4 151
HIF1A/ARNT 0.43 0.4 0.85 181 -0.8 3 184
LDHA 0.042 0.11 0.4 13 -0.54 2 15
ETS1 0.28 0.24 0.53 147 -0.6 4 151
PGK1 0.28 0.24 0.54 148 -0.67 4 152
NOS2 0.27 0.26 0.54 149 -0.73 4 153
ITGB2 0.28 0.24 0.53 149 -0.77 4 153
ALDOA 0.28 0.24 0.54 148 -0.67 4 152
Cbp/p300/CITED2 0.28 0.28 0.59 144 -0.87 4 148
FOS -0.011 0.089 -10000 0 -0.34 30 30
HK2 0.28 0.24 0.54 147 -0.69 5 152
SP1 0.014 0.037 -10000 0 -0.15 19 19
GCK 0.16 0.26 0.5 55 -1 12 67
HK1 0.28 0.24 0.53 147 -0.67 4 151
NPM1 0.27 0.24 0.53 147 -0.67 4 151
EGLN1 0.27 0.24 0.54 141 -0.81 2 143
CREB1 0.023 0.009 -10000 0 -10000 0 0
PGM1 0.28 0.24 0.54 146 -0.67 4 150
SMAD3 0.02 0.008 -10000 0 -10000 0 0
EDN1 -0.063 0.41 0.46 4 -0.97 73 77
IGFBP1 0.29 0.27 0.59 150 -0.67 4 154
VEGFA 0.26 0.24 0.5 159 -0.68 3 162
HIF1A/JAB1 0.08 0.067 0.21 38 -0.17 1 39
CP 0.38 0.29 0.62 227 -0.66 4 231
CXCL12 0.27 0.25 0.54 148 -0.77 4 152
COPS5 0.019 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.027 0.014 -10000 0 -10000 0 0
BNIP3 0.28 0.24 0.53 147 -0.67 4 151
EGLN3 0.31 0.28 0.62 166 -0.59 4 170
CA9 0.41 0.29 0.62 260 -0.67 4 264
TERT 0.29 0.29 0.61 167 -0.67 3 170
ENO1 0.28 0.24 0.54 145 -0.67 4 149
PFKL 0.28 0.23 0.53 149 -0.67 4 153
NCOA1 0.021 0.003 -10000 0 -10000 0 0
ADM 0.28 0.24 0.54 146 -0.7 4 150
ARNT 0.091 0.087 0.25 59 -10000 0 59
HNF4A 0.069 0.13 0.32 88 -0.28 13 101
ADFP 0.26 0.24 0.5 172 -0.67 4 176
SLC2A1 0.33 0.28 0.59 201 -0.65 3 204
LEP 0.29 0.26 0.56 155 -0.67 4 159
HIF1A/ARNT/Cbp/p300 0.32 0.33 0.67 168 -0.85 3 171
EPO 0.23 0.23 0.54 91 -0.89 2 93
CREBBP 0.12 0.13 0.28 128 -0.26 12 140
HIF1A/ARNT/Cbp/p300/HDAC7 0.35 0.33 0.7 174 -0.79 3 177
PFKFB3 0.28 0.24 0.53 145 -0.63 5 150
NT5E 0.28 0.25 0.55 148 -0.67 4 152
Aurora B signaling

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
Condensin I complex 0.11 0.12 0.24 204 -0.19 4 208
STMN1 0.071 0.086 0.16 227 -10000 0 227
Aurora B/RasGAP/Survivin 0.22 0.17 0.36 259 -10000 0 259
Chromosomal passenger complex/Cul3 protein complex 0.09 0.1 0.2 165 -0.27 2 167
BIRC5 0.19 0.16 0.33 254 -10000 0 254
DES -0.15 0.28 -10000 0 -0.56 89 89
Aurora C/Aurora B/INCENP 0.12 0.095 0.22 221 -0.15 3 224
Aurora B/TACC1 0.09 0.1 0.21 187 -0.15 15 202
Aurora B/PP2A 0.12 0.1 0.23 214 -10000 0 214
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.035 0.036 0.14 15 -10000 0 15
mitotic metaphase/anaphase transition -0.005 0.006 -10000 0 -10000 0 0
NDC80 0.14 0.15 0.27 253 -10000 0 253
Cul3 protein complex 0.03 0.045 0.22 3 -0.19 14 17
KIF2C 0.16 0.13 0.26 282 -0.32 1 283
PEBP1 0.023 0.005 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 252 -10000 0 252
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.1 0.23 222 -10000 0 222
SEPT1 0.02 0.016 -10000 0 -0.32 1 1
SMC2 0.02 0.004 -10000 0 -10000 0 0
SMC4 0.02 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.1 0.19 0.3 116 -0.44 29 145
PSMA3 0.02 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.075 0.071 0.15 230 -10000 0 230
AURKB 0.17 0.16 0.33 229 -10000 0 229
AURKC 0.018 0.031 0.32 1 -0.32 3 4
CDCA8 0.13 0.15 0.33 158 -10000 0 158
cytokinesis 0.14 0.15 0.3 207 -0.36 2 209
Aurora B/Septin1 0.18 0.18 0.36 207 -0.25 8 215
AURKA 0.054 0.12 0.32 80 -10000 0 80
INCENP 0.027 0.009 -10000 0 -10000 0 0
KLHL13 0.012 0.064 0.32 3 -0.32 14 17
BUB1 0.089 0.14 0.32 124 -10000 0 124
hSgo1/Aurora B/Survivin 0.28 0.24 0.47 267 -10000 0 267
EVI5 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.17 0.16 0.33 175 -0.32 1 176
SGOL1 0.16 0.15 0.32 214 -10000 0 214
CENPA 0.16 0.16 0.3 244 -0.24 6 250
NCAPG 0.15 0.15 0.32 205 -10000 0 205
Aurora B/HC8 Proteasome 0.12 0.1 0.23 221 -10000 0 221
NCAPD2 0.02 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.12 0.1 0.23 223 -10000 0 223
RHOA 0.02 0.004 -10000 0 -10000 0 0
NCAPH 0.15 0.15 0.32 201 -10000 0 201
NPM1 0.072 0.13 0.22 18 -0.35 22 40
RASA1 0.02 0.005 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 0.23 221 -10000 0 221
PPP1CC 0.02 0.003 -10000 0 -10000 0 0
Centraspindlin 0.18 0.18 0.34 208 -0.33 1 209
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
NSUN2 0.089 0.13 0.28 58 -0.3 15 73
MYLK 0.068 0.075 0.14 221 -0.14 10 231
KIF23 0.09 0.13 0.34 99 -10000 0 99
VIM 0.07 0.089 0.16 223 -10000 0 223
RACGAP1 0.03 0.031 0.34 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.076 0.13 0.22 18 -0.3 24 42
Chromosomal passenger complex 0.16 0.15 0.29 243 -0.28 2 245
Chromosomal passenger complex/EVI5 0.28 0.22 0.47 244 -10000 0 244
TACC1 0.007 0.061 -10000 0 -0.32 15 15
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
CUL3 0.021 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.089 0.18 0.32 7 -0.5 41 48
IHH -0.014 0.13 0.27 7 -0.39 40 47
SHH Np/Cholesterol/GAS1 -0.035 0.056 0.11 1 -0.18 58 59
LRPAP1 0.02 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.035 0.056 0.18 58 -0.11 1 59
SMO/beta Arrestin2 -0.14 0.18 0.3 2 -0.33 177 179
SMO -0.15 0.19 0.34 1 -0.34 187 188
AKT1 -0.078 0.14 0.26 1 -0.49 29 30
ARRB2 0.019 0.006 -10000 0 -10000 0 0
BOC 0.02 0.016 -10000 0 -0.32 1 1
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
heart looping -0.14 0.18 0.34 1 -0.33 187 188
STIL -0.082 0.14 0.26 11 -0.32 60 71
DHH N/PTCH2 0.01 0.07 -10000 0 -0.23 37 37
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.36 60 60
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DHH -0.007 0.093 -10000 0 -0.32 37 37
PTHLH -0.12 0.22 0.38 7 -0.56 39 46
determination of left/right symmetry -0.14 0.18 0.34 1 -0.33 187 188
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
skeletal system development -0.12 0.22 0.38 7 -0.56 39 46
IHH N/Hhip -0.22 0.18 0.21 3 -0.31 340 343
DHH N/Hhip -0.12 0.14 -10000 0 -0.25 256 256
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.14 0.18 0.34 1 -0.33 187 188
pancreas development -0.16 0.17 -10000 0 -0.32 250 250
HHAT 0.018 0.023 -10000 0 -0.32 2 2
PI3K 0.028 0.015 -10000 0 -0.23 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.011 0.055 -10000 0 -0.32 12 12
somite specification -0.14 0.18 0.34 1 -0.33 187 188
SHH Np/Cholesterol/PTCH1 -0.095 0.14 0.18 2 -0.33 63 65
SHH Np/Cholesterol/PTCH2 -0.032 0.051 0.11 1 -0.18 52 53
SHH Np/Cholesterol/Megalin -0.067 0.086 0.11 1 -0.19 139 140
SHH -0.038 0.068 0.15 1 -0.23 52 53
catabolic process -0.1 0.16 0.23 3 -0.4 42 45
SMO/Vitamin D3 -0.12 0.17 0.37 2 -0.4 60 62
SHH Np/Cholesterol/Hhip -0.1 0.1 0.11 1 -0.2 231 232
LRP2 -0.07 0.15 0.32 1 -0.32 123 124
receptor-mediated endocytosis -0.16 0.18 0.3 2 -0.41 120 122
SHH Np/Cholesterol/BOC -0.032 0.051 0.11 1 -0.18 51 52
SHH Np/Cholesterol/CDO -0.034 0.055 0.11 1 -0.18 55 56
mesenchymal cell differentiation 0.1 0.099 0.2 231 -0.11 1 232
mol:Vitamin D3 -0.088 0.15 0.36 6 -0.34 61 67
IHH N/PTCH2 -0.094 0.13 0.21 4 -0.21 249 253
CDON 0.013 0.048 -10000 0 -0.32 9 9
IHH N/PTCH1 -0.096 0.17 0.24 29 -0.39 44 73
Megalin/LRPAP1 -0.036 0.11 0.23 1 -0.23 120 121
PTCH2 0.02 0.016 -10000 0 -0.32 1 1
SHH Np/Cholesterol -0.028 0.051 -10000 0 -0.17 52 52
PTCH1 -0.11 0.16 0.23 3 -0.4 42 45
HHIP -0.16 0.17 -10000 0 -0.32 250 250
Endothelins

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
AKT1 -0.079 0.11 0.23 1 -0.32 46 47
PTK2B 0.016 0.018 -10000 0 -0.32 1 1
mol:Ca2+ -0.12 0.27 -10000 0 -0.78 56 56
EDN1 -0.075 0.13 -10000 0 -0.34 76 76
EDN3 -0.071 0.15 0.32 1 -0.32 120 121
EDN2 0.1 0.14 0.32 126 -0.32 2 128
HRAS/GDP -0.15 0.19 -10000 0 -0.42 113 113
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.07 0.13 -10000 0 -0.35 61 61
ADCY4 -0.066 0.11 0.2 7 -0.28 55 62
ADCY5 -0.076 0.13 0.21 11 -0.3 71 82
ADCY6 -0.062 0.1 0.21 10 -0.27 46 56
ADCY7 -0.062 0.1 0.22 6 -0.27 47 53
ADCY1 -0.059 0.1 0.2 6 -0.27 45 51
ADCY2 -0.06 0.11 0.29 5 -0.29 51 56
ADCY3 -0.062 0.1 0.21 11 -0.27 47 58
ADCY8 -0.096 0.12 0.3 4 -0.26 110 114
ADCY9 -0.064 0.11 0.21 11 -0.27 55 66
arachidonic acid secretion -0.12 0.19 -10000 0 -0.5 78 78
ETB receptor/Endothelin-1/Gq/GTP -0.14 0.16 -10000 0 -0.27 244 244
GNAO1 0.02 0.03 0.32 2 -0.32 2 4
HRAS 0.02 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.049 0.12 0.31 1 -0.29 42 43
ETA receptor/Endothelin-1/Gs/GTP -0.052 0.12 0.29 1 -0.28 51 52
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.046 0.16 0.29 30 -0.32 45 75
EDNRB -0.16 0.17 -10000 0 -0.32 245 245
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.085 0.13 0.23 1 -0.36 48 49
CYSLTR1 -0.089 0.13 0.23 1 -0.38 48 49
SLC9A1 -0.049 0.08 0.16 1 -0.22 49 50
mol:GDP -0.16 0.2 -10000 0 -0.43 122 122
SLC9A3 -0.31 0.34 -10000 0 -0.66 169 169
RAF1 -0.15 0.2 -10000 0 -0.48 94 94
JUN -0.1 0.21 -10000 0 -0.65 45 45
JAK2 -0.077 0.11 0.23 1 -0.32 45 46
mol:IP3 -0.12 0.17 -10000 0 -0.38 101 101
ETA receptor/Endothelin-1 -0.08 0.15 0.35 1 -0.35 58 59
PLCB1 0.018 0.017 0.32 1 -10000 0 1
PLCB2 0.009 0.049 -10000 0 -0.33 9 9
ETA receptor/Endothelin-3 -0.074 0.11 0.24 1 -0.24 128 129
FOS -0.15 0.24 -10000 0 -0.71 55 55
Gai/GDP -0.05 0.2 -10000 0 -0.81 26 26
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.19 -10000 0 -0.43 119 119
BCAR1 0.02 0.017 -10000 0 -0.32 1 1
PRKCB1 -0.12 0.16 -10000 0 -0.35 116 116
GNAQ 0.014 0.022 -10000 0 -0.33 1 1
GNAZ -0.009 0.095 -10000 0 -0.32 39 39
GNAL 0.017 0.046 0.32 3 -0.32 6 9
Gs family/GDP -0.14 0.18 -10000 0 -0.4 114 114
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.13 -10000 0 -0.32 66 66
MAPK14 -0.14 0.16 -10000 0 -0.34 131 131
TRPC6 -0.13 0.29 -10000 0 -0.85 55 55
GNAI2 0.02 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.017 -10000 0 -0.32 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.17 -10000 0 -0.3 189 189
ETB receptor/Endothelin-2 -0.079 0.15 0.24 43 -0.2 251 294
ETB receptor/Endothelin-3 -0.16 0.16 0.23 1 -0.27 283 284
ETB receptor/Endothelin-1 -0.16 0.16 0.21 7 -0.29 245 252
MAPK3 -0.16 0.24 -10000 0 -0.67 66 66
MAPK1 -0.17 0.24 -10000 0 -0.66 70 70
Rac1/GDP -0.14 0.18 -10000 0 -0.42 103 103
cAMP biosynthetic process -0.075 0.14 0.3 8 -0.34 58 66
MAPK8 -0.12 0.24 -10000 0 -0.67 60 60
SRC 0.02 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.14 0.14 -10000 0 -0.25 241 241
p130Cas/CRK/Src/PYK2 -0.17 0.23 0.31 1 -0.56 87 88
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.18 -10000 0 -0.41 107 107
COL1A2 -0.16 0.18 0.31 7 -0.37 151 158
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.044 0.12 0.22 116 -0.18 16 132
mol:DAG -0.12 0.17 -10000 0 -0.38 101 101
MAP2K2 -0.16 0.21 -10000 0 -0.55 78 78
MAP2K1 -0.16 0.21 -10000 0 -0.56 77 77
EDNRA -0.034 0.076 0.23 1 -0.24 17 18
positive regulation of muscle contraction -0.054 0.11 0.21 19 -0.28 41 60
Gq family/GDP -0.11 0.18 0.35 1 -0.41 86 87
HRAS/GTP -0.15 0.2 -10000 0 -0.44 102 102
PRKCH -0.12 0.16 -10000 0 -0.38 93 93
RAC1 0.018 0.007 -10000 0 -10000 0 0
PRKCA -0.12 0.16 -10000 0 -0.37 96 96
PRKCB -0.13 0.17 0.19 1 -0.37 114 115
PRKCE -0.13 0.16 -10000 0 -0.37 107 107
PRKCD -0.13 0.16 -10000 0 -0.36 112 112
PRKCG -0.12 0.16 -10000 0 -0.38 90 90
regulation of vascular smooth muscle contraction -0.18 0.28 -10000 0 -0.85 55 55
PRKCQ -0.14 0.18 -10000 0 -0.39 114 114
PLA2G4A -0.14 0.21 -10000 0 -0.54 78 78
GNA14 0.007 0.057 -10000 0 -0.33 12 12
GNA15 0.015 0.015 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.05 0.12 0.31 1 -0.3 41 42
MMP1 0.19 0.17 0.31 280 -0.67 2 282
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 -0.05 0.063 0.12 15 -0.12 214 229
BUB1B 0.072 0.076 0.14 204 -0.12 4 208
PLK1 0.03 0.039 0.093 94 -0.08 2 96
PLK1S1 0.014 0.037 0.11 3 -0.16 13 16
KIF2A 0.024 0.044 0.17 17 -10000 0 17
regulation of mitotic centrosome separation 0.03 0.039 0.093 94 -0.08 2 96
GOLGA2 0.02 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.18 0.17 0.34 223 -10000 0 223
WEE1 0.029 0.059 0.18 2 -0.26 10 12
cytokinesis 0.09 0.094 0.19 154 -0.19 3 157
PP2A-alpha B56 0.079 0.094 -10000 0 -0.46 6 6
AURKA 0.036 0.057 0.14 94 -0.18 5 99
PICH/PLK1 0.078 0.11 0.21 178 -10000 0 178
CENPE 0.034 0.054 0.13 82 -10000 0 82
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.044 0.17 17 -10000 0 17
PPP2CA 0.02 0.004 -10000 0 -10000 0 0
FZR1 0.019 0.005 -10000 0 -10000 0 0
TPX2 0.074 0.069 0.13 254 -0.16 5 259
PAK1 0.019 0.005 -10000 0 -10000 0 0
SPC24 0.1 0.14 0.32 131 -10000 0 131
FBXW11 0.02 0.005 -10000 0 -10000 0 0
CLSPN 0.062 0.075 0.15 173 -0.21 6 179
GORASP1 0.02 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.015 9 -0.011 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.014 0.019 0.053 39 -0.041 2 41
G2 phase of mitotic cell cycle 0 0.003 0.014 11 -10000 0 11
STAG2 0.02 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.002 0.094 -10000 0 -0.51 15 15
spindle elongation 0.03 0.039 0.093 94 -0.08 2 96
ODF2 0.021 0.006 -10000 0 -10000 0 0
BUB1 0.07 0.11 -10000 0 -0.5 6 6
TPT1 0.008 0.045 0.11 2 -0.16 27 29
CDC25C 0.1 0.093 0.16 293 -0.23 13 306
CDC25B 0.022 0.011 -10000 0 -10000 0 0
SGOL1 0.051 0.064 0.12 214 -0.12 15 229
RHOA 0.02 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.075 0.086 0.22 120 -0.13 1 121
CDC14B -0.008 0.004 -10000 0 -10000 0 0
CDC20 0.2 0.15 0.32 270 -10000 0 270
PLK1/PBIP1 0.01 0.041 0.15 34 -10000 0 34
mitosis -0.003 0.006 0.021 7 -0.016 63 70
FBXO5 0.014 0.04 0.1 19 -0.093 9 28
CDC2 0.003 0.005 0.011 123 -0.01 6 129
NDC80 0.16 0.15 0.32 212 -10000 0 212
metaphase plate congression 0.021 0.043 -10000 0 -0.22 10 10
ERCC6L 0.08 0.1 0.21 168 -10000 0 168
NLP/gamma Tubulin 0.016 0.023 0.071 24 -0.085 3 27
microtubule cytoskeleton organization 0.008 0.045 0.11 2 -0.16 27 29
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 2 -10000 0 2
PPP1R12A 0.021 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 0.17 0.15 0.29 248 -10000 0 248
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.031 -10000 0 -10000 0 0
RAB1A 0.021 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.024 0.035 0.083 92 -0.075 1 93
mitotic prometaphase 0.001 0.003 0.019 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.055 0.18 1 -0.25 3 4
microtubule-based process 0.14 0.12 0.25 252 -10000 0 252
Golgi organization 0.03 0.039 0.093 94 -0.08 2 96
Cohesin/SA2 0.036 0.031 0.12 8 -10000 0 8
PPP1CB/MYPT1 0.031 0.007 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 252 -10000 0 252
APC/C/CDC20 0.15 0.12 0.25 271 -10000 0 271
PPP2R1A 0.02 0.004 -10000 0 -10000 0 0
chromosome segregation 0.01 0.041 0.15 34 -10000 0 34
PRC1 0.065 0.11 0.32 69 -10000 0 69
ECT2 0.032 0.06 0.18 44 -10000 0 44
C13orf34 0.024 0.033 0.078 93 -0.067 2 95
NUDC 0.021 0.044 -10000 0 -0.22 10 10
regulation of attachment of spindle microtubules to kinetochore 0.072 0.075 0.14 204 -0.12 4 208
spindle assembly 0.023 0.031 0.088 40 -0.07 2 42
spindle stabilization 0.014 0.037 0.11 3 -0.16 13 16
APC/C/HCDH1 0.015 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.14 0.12 0.25 252 -10000 0 252
CCNB1 0.1 0.14 0.32 130 -10000 0 130
PPP1CB 0.021 0.003 -10000 0 -10000 0 0
BTRC 0.021 0.003 -10000 0 -10000 0 0
ROCK2 0.025 0.039 0.17 2 -0.26 2 4
TUBG1 0.018 0.027 0.13 3 -0.2 3 6
G2/M transition of mitotic cell cycle 0.031 0.057 0.12 115 -0.12 2 117
MLF1IP 0.005 0.044 0.16 33 -10000 0 33
INCENP 0.02 0.004 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.021 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.12 0.093 0.21 221 -0.16 3 224
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.016 0.014 -10000 0 -10000 0 0
AURKB 0.17 0.15 0.32 229 -10000 0 229
AURKC 0.018 0.031 0.32 1 -0.32 3 4
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.091 0.27 -10000 0 -0.86 46 46
MKNK1 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.025 0.12 -10000 0 -0.29 75 75
ATF2/c-Jun -0.037 0.11 -10000 0 -0.37 19 19
MAPK11 -0.025 0.12 -10000 0 -0.31 69 69
MITF -0.048 0.15 -10000 0 -0.36 77 77
MAPKAPK5 -0.042 0.14 -10000 0 -0.35 71 71
KRT8 -0.043 0.14 0.27 2 -0.35 74 76
MAPKAPK3 0.02 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.04 0.18 -10000 0 -0.44 69 69
CEBPB -0.04 0.14 -10000 0 -0.36 66 66
SLC9A1 -0.044 0.14 -10000 0 -0.36 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.042 0.14 0.25 1 -0.35 74 75
p38alpha-beta/MNK1 -0.019 0.15 -10000 0 -0.36 67 67
JUN -0.036 0.11 -10000 0 -0.36 19 19
PPARGC1A -0.1 0.19 -10000 0 -0.34 156 156
USF1 -0.035 0.13 0.31 1 -0.35 63 64
RAB5/GDP/GDI1 -0.029 0.11 -10000 0 -0.26 71 71
NOS2 -0.087 0.27 0.4 2 -0.86 43 45
DDIT3 -0.042 0.14 0.23 1 -0.35 72 73
RAB5A 0.02 0.004 -10000 0 -10000 0 0
HSPB1 -0.041 0.12 0.26 10 -0.3 68 78
p38alpha-beta/HBP1 -0.02 0.15 -10000 0 -0.36 66 66
CREB1 -0.049 0.15 0.23 2 -0.38 75 77
RAB5/GDP 0.015 0.003 -10000 0 -10000 0 0
EIF4E -0.06 0.12 -10000 0 -0.32 65 65
RPS6KA4 -0.045 0.14 -10000 0 -0.35 74 74
PLA2G4A -0.037 0.13 0.19 43 -0.32 62 105
GDI1 -0.042 0.14 0.28 1 -0.35 71 72
TP53 -0.067 0.16 0.26 1 -0.43 70 71
RPS6KA5 -0.042 0.14 0.29 3 -0.35 71 74
ESR1 -0.048 0.15 0.28 1 -0.38 73 74
HBP1 0.02 0.005 -10000 0 -10000 0 0
MEF2C -0.043 0.14 -10000 0 -0.36 71 71
MEF2A -0.043 0.14 -10000 0 -0.35 72 72
EIF4EBP1 -0.051 0.16 0.24 2 -0.4 73 75
KRT19 -0.044 0.14 -10000 0 -0.36 73 73
ELK4 -0.039 0.13 -10000 0 -0.35 67 67
ATF6 -0.036 0.13 0.31 1 -0.35 65 66
ATF1 -0.049 0.15 0.24 3 -0.37 76 79
p38alpha-beta/MAPKAPK2 -0.019 0.14 -10000 0 -0.35 66 66
p38alpha-beta/MAPKAPK3 -0.02 0.15 -10000 0 -0.36 69 69
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.039 0.048 0.2 28 -0.16 7 35
RGS9BP -0.029 0.12 -10000 0 -0.32 66 66
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.034 0.069 0.32 25 -10000 0 25
mol:Na + 0.1 0.11 0.23 180 -10000 0 180
mol:ADP -0.006 0.043 0.16 27 -10000 0 27
GNAT2 0.02 0.015 0.32 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.059 0.12 -10000 0 -0.21 177 177
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.024 0.014 0.21 2 -10000 0 2
GRK7 0.02 0.014 0.32 1 -10000 0 1
CNGB3 0.062 0.11 0.32 70 -10000 0 70
Cone Metarhodopsin II/X-Arrestin 0.014 0.013 0.22 2 -10000 0 2
mol:Ca2+ 0.056 0.091 0.21 95 -10000 0 95
Cone PDE6 -0.041 0.12 -10000 0 -0.19 172 172
Cone Metarhodopsin II 0.032 0.04 0.2 25 -10000 0 25
Na + (4 Units) 0.11 0.11 0.24 186 -10000 0 186
GNAT2/GDP -0.045 0.11 -10000 0 -0.18 177 177
GNB5 0.02 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.015 0.017 0.17 3 -10000 0 3
Cone Transducin 0.042 0.051 0.21 28 -0.18 7 35
SLC24A2 0.042 0.083 0.32 37 -10000 0 37
GNB3/GNGT2 0.036 0.059 0.23 27 -0.23 7 34
GNB3 0.037 0.074 0.32 28 -0.32 1 29
GNAT2/GTP 0.015 0.01 0.22 1 -10000 0 1
CNGA3 0.12 0.14 0.32 152 -10000 0 152
ARR3 0.019 0.02 0.32 2 -10000 0 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.1 0.11 0.23 180 -10000 0 180
mol:Pi -0.059 0.12 -10000 0 -0.21 177 177
Cone CNG Channel 0.091 0.09 0.21 153 -10000 0 153
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.042 0.082 0.32 37 -10000 0 37
RGS9 -0.083 0.16 -10000 0 -0.32 139 139
PDE6C 0.018 0.003 -10000 0 -10000 0 0
GNGT2 0.016 0.039 -10000 0 -0.32 6 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.015 0.32 1 -10000 0 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.027 0.29 0.53 32 -0.62 25 57
PCK1 0.059 0.24 0.58 40 -0.67 1 41
HNF4A -0.1 0.46 0.67 54 -0.77 101 155
KCNJ11 0.013 0.3 0.59 33 -0.74 15 48
AKT1 0.037 0.18 0.41 41 -0.53 2 43
response to starvation -0.027 0.073 0.15 3 -0.18 52 55
DLK1 0.036 0.3 0.58 49 -0.63 11 60
NKX2-1 -0.043 0.33 0.44 15 -1.1 33 48
ACADM -0.029 0.29 0.51 34 -0.61 29 63
TAT 0.052 0.23 0.52 49 -0.46 1 50
CEBPB 0.026 0.019 0.15 2 -10000 0 2
CEBPA 0.015 0.077 0.21 3 -0.32 20 23
TTR 0.068 0.28 0.61 56 -0.7 9 65
PKLR -0.002 0.3 0.58 40 -0.62 26 66
APOA1 -0.21 0.61 0.73 41 -1.1 132 173
CPT1C -0.027 0.29 0.53 35 -0.61 29 64
ALAS1 0.031 0.19 0.48 15 -0.56 1 16
TFRC 0.08 0.29 0.61 60 -0.8 9 69
FOXF1 -0.021 0.13 0.22 20 -0.32 65 85
NF1 0.022 0.003 -10000 0 -10000 0 0
HNF1A (dimer) 0.11 0.16 0.4 94 -0.32 1 95
CPT1A -0.026 0.29 0.52 35 -0.61 28 63
HMGCS1 0.001 0.29 0.57 40 -0.6 29 69
NR3C1 0.045 0.049 0.21 14 -10000 0 14
CPT1B -0.027 0.29 0.54 30 -0.62 26 56
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.042 0.041 0.16 1 -10000 0 1
GCK -0.022 0.31 0.55 36 -0.64 34 70
CREB1 0.036 0.037 0.19 6 -10000 0 6
IGFBP1 0.032 0.21 0.49 42 -0.52 1 43
PDX1 0.098 0.27 0.66 60 -0.54 2 62
UCP2 -0.025 0.29 0.53 33 -0.61 29 62
ALDOB 0.029 0.31 0.65 39 -0.72 12 51
AFP 0.082 0.11 0.32 52 -10000 0 52
BDH1 -0.027 0.29 0.53 33 -0.61 28 61
HADH 0.016 0.28 0.57 34 -0.63 11 45
F2 -0.024 0.42 0.76 50 -0.79 36 86
HNF1A 0.11 0.16 0.4 94 -0.32 1 95
G6PC 0.08 0.13 0.47 21 -10000 0 21
SLC2A2 0.081 0.28 0.66 55 -0.74 2 57
INS -0.033 0.036 -10000 0 -10000 0 0
FOXA1 0.068 0.1 0.3 52 -0.32 1 53
FOXA3 0.15 0.18 0.41 130 -0.29 3 133
FOXA2 0.054 0.38 0.81 51 -0.66 22 73
ABCC8 -0.02 0.36 0.62 35 -0.77 53 88
ALB 0.092 0.12 0.34 61 -10000 0 61
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.006 0.053 -10000 0 -0.33 9 9
Crk/p130 Cas/Paxillin -0.057 0.087 -10000 0 -0.23 78 78
JUN -0.04 0.084 0.16 9 -0.28 8 17
HRAS 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.009 0.11 0.23 37 -0.18 81 118
RAP1A 0.02 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.006 0.11 0.23 39 -0.17 102 141
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.02 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.015 0.088 0.21 5 -0.17 103 108
RHOA 0.02 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.005 0.099 0.19 38 -0.17 87 125
GRB7 0.019 0.023 -10000 0 -0.32 2 2
RET51/GFRalpha1/GDNF 0.005 0.11 0.23 38 -0.18 90 128
MAPKKK cascade -0.033 0.092 0.18 6 -0.2 83 89
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.014 0.089 0.21 6 -0.17 103 109
lamellipodium assembly -0.036 0.088 -10000 0 -0.22 66 66
RET51/GFRalpha1/GDNF/SHC 0.009 0.1 0.23 35 -0.18 73 108
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.009 0.08 0.21 4 -0.17 82 86
RET9/GFRalpha1/GDNF/Shank3 -0.015 0.09 0.21 6 -0.17 104 110
MAPK3 -0.02 0.099 0.17 59 -0.29 1 60
DOK1 0.021 0.002 -10000 0 -10000 0 0
DOK6 -0.008 0.092 -10000 0 -0.32 36 36
PXN 0.02 0.003 -10000 0 -10000 0 0
neurite development -0.028 0.09 0.2 5 -0.23 16 21
DOK5 0.063 0.11 0.32 67 -10000 0 67
GFRA1 -0.078 0.16 0.32 1 -0.32 134 135
MAPK8 -0.039 0.086 0.15 7 -0.19 90 97
HRAS/GTP -0.006 0.12 0.34 2 -0.21 89 91
tube development -0.012 0.087 0.2 14 -0.17 96 110
MAPK1 -0.02 0.094 0.17 53 -0.29 1 54
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.029 0.081 0.15 2 -0.19 91 93
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
PDLIM7 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.003 0.12 0.23 34 -0.2 103 137
SHC1 0.018 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.007 0.11 0.23 38 -0.18 90 128
RET51/GFRalpha1/GDNF/Dok5 0.02 0.12 0.24 66 -0.18 74 140
PRKCA 0.019 0.023 -10000 0 -0.32 2 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
CREB1 -0.024 0.09 0.2 2 -0.22 66 68
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.079 0.16 3 -0.2 76 79
RET51/GFRalpha1/GDNF/Grb7 0.005 0.11 0.23 38 -0.18 90 128
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.057 0.1 0.32 59 -0.32 3 62
DOK4 0.02 0.004 -10000 0 -10000 0 0
JNK cascade -0.033 0.089 0.17 6 -0.28 8 14
RET9/GFRalpha1/GDNF/FRS2 -0.013 0.087 0.21 6 -0.17 98 104
SHANK3 0.017 0.028 -10000 0 -0.32 3 3
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.02 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.075 0.16 2 -0.19 74 76
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.021 0.092 0.18 9 -0.19 86 95
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.024 0.096 0.18 7 -0.2 93 100
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.086 0.19 11 -0.19 66 77
PI3K -0.048 0.13 0.23 5 -0.3 80 85
SOS1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.007 0.089 0.21 6 -0.17 96 102
GRB10 0.019 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.022 0.083 0.16 9 -0.18 83 92
RET51/GFRalpha1/GDNF/FRS2 0.006 0.11 0.23 38 -0.17 101 139
GAB1 0.02 0.016 -10000 0 -0.32 1 1
IRS1 0.02 0.016 -10000 0 -0.32 1 1
IRS2 0.019 0.017 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.014 0.09 0.19 11 -0.2 70 81
RET51/GFRalpha1/GDNF/PKC alpha 0.006 0.11 0.23 38 -0.18 87 125
GRB2 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GDNF 0.02 0.038 0.32 7 -10000 0 7
RAC1 0.018 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.006 0.11 0.23 39 -0.18 103 142
Rac1/GTP -0.033 0.11 0.22 1 -0.25 63 64
RET9/GFRalpha1/GDNF -0.024 0.091 0.21 6 -0.19 103 109
GFRalpha1/GDNF -0.031 0.11 0.23 6 -0.23 103 109
Osteopontin-mediated events

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
IKK alpha homodimer 0.077 0.077 0.2 75 -10000 0 75
NF kappa B1 p50/RelA/I kappa B alpha 0.086 0.093 0.29 31 -0.27 1 32
alphaV/beta3 Integrin/Osteopontin/Src 0.18 0.096 0.24 329 -10000 0 329
AP1 0.078 0.11 0.32 16 -10000 0 16
ILK 0.069 0.069 0.24 22 -10000 0 22
bone resorption 0.045 0.073 0.23 17 -0.28 1 18
PTK2B 0.017 0.018 -10000 0 -0.32 1 1
PYK2/p130Cas 0.14 0.11 0.28 74 -0.17 3 77
ITGAV 0.025 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.026 0.032 -10000 0 -0.23 7 7
alphaV/beta3 Integrin/Osteopontin 0.18 0.11 0.25 322 -0.19 4 326
MAP3K1 0.067 0.068 0.21 32 -0.18 4 36
JUN 0.018 0.032 -10000 0 -0.32 4 4
MAPK3 0.064 0.083 0.22 81 -10000 0 81
MAPK1 0.062 0.081 0.22 77 -10000 0 77
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.047 0.061 0.21 23 -10000 0 23
ITGB3 0.035 0.076 0.33 22 -0.32 5 27
NFKBIA 0.059 0.086 0.23 76 -10000 0 76
FOS -0.002 0.085 -10000 0 -0.32 30 30
CD44 0.014 0.045 -10000 0 -0.32 8 8
CHUK 0.02 0.003 -10000 0 -10000 0 0
PLAU 0.091 0.13 0.35 73 -10000 0 73
NF kappa B1 p50/RelA 0.089 0.1 0.26 81 -10000 0 81
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
RELA 0.02 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.045 0.057 0.26 22 -0.23 5 27
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.067 0.069 0.23 25 -0.18 5 30
VAV3 0.045 0.062 0.2 25 -0.29 2 27
MAP3K14 0.076 0.078 0.21 76 -10000 0 76
ROCK2 0.02 0.016 -10000 0 -0.32 1 1
SPP1 0.24 0.14 0.33 332 -10000 0 332
RAC1 0.018 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.059 0.21 9 -0.26 2 11
MMP2 0.034 0.076 0.3 7 -10000 0 7
IL4-mediated signaling events

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
BCL2L1 -0.3 0.55 0.77 2 -1.2 82 84
STAT6 (cleaved dimer) -0.32 0.55 -10000 0 -1.2 104 104
IGHG1 -0.085 0.23 0.43 11 -0.64 14 25
IGHG3 -0.3 0.53 0.59 2 -1.1 103 105
AKT1 -0.14 0.31 0.54 1 -0.88 35 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.29 0.54 1 -0.9 32 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.32 0.48 3 -0.87 31 34
THY1 -0.3 0.55 0.73 2 -1.2 83 85
MYB 0.02 0.03 0.32 3 -0.32 1 4
HMGA1 0.046 0.085 0.32 40 -10000 0 40
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.16 0.35 0.52 9 -0.74 71 80
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.32 0.48 3 -0.89 31 34
SP1 0.027 0.026 -10000 0 -10000 0 0
INPP5D 0.018 0.028 -10000 0 -0.32 3 3
SOCS5 0.01 0.036 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.31 0.54 0.61 1 -1.2 99 100
SOCS1 -0.19 0.36 0.52 2 -0.74 84 86
SOCS3 -0.14 0.3 0.52 1 -0.8 33 34
FCER2 -0.24 0.49 0.7 6 -1.1 77 83
PARP14 0.022 0.01 -10000 0 -10000 0 0
CCL17 -0.35 0.62 0.72 3 -1.3 101 104
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.26 0.46 5 -0.72 30 35
T cell proliferation -0.31 0.55 0.63 1 -1.2 92 93
IL4R/JAK1 -0.31 0.55 0.63 1 -1.2 97 98
EGR2 -0.32 0.59 0.75 2 -1.3 85 87
JAK2 -0.007 0.062 -10000 0 -0.36 1 1
JAK3 0.02 0.016 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
JAK1 0.003 0.033 -10000 0 -10000 0 0
COL1A2 -0.063 0.22 0.5 2 -1.3 3 5
CCL26 -0.29 0.56 0.7 6 -1.2 90 96
IL4R -0.32 0.59 0.75 5 -1.3 89 94
PTPN6 0.015 0.03 -10000 0 -10000 0 0
IL13RA2 -0.34 0.6 0.68 2 -1.3 102 104
IL13RA1 -0.007 0.063 0.19 1 -10000 0 1
IRF4 -0.06 0.27 0.54 2 -1 23 25
ARG1 -0.092 0.25 0.55 2 -0.7 30 32
CBL -0.16 0.33 0.5 4 -0.7 70 74
GTF3A 0.063 0.059 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.001 0.086 0.24 8 -0.27 1 9
IRF4/BCL6 -0.062 0.24 -10000 0 -0.94 23 23
CD40LG 0.009 0.076 0.17 1 -0.33 21 22
MAPK14 -0.16 0.33 0.5 4 -0.72 62 66
mitosis -0.13 0.3 0.54 1 -0.81 35 36
STAT6 -0.35 0.67 0.79 6 -1.4 102 108
SPI1 0.005 0.076 -10000 0 -0.32 23 23
RPS6KB1 -0.13 0.29 0.52 1 -0.79 33 34
STAT6 (dimer) -0.35 0.67 0.82 5 -1.4 102 107
STAT6 (dimer)/PARP14 -0.33 0.6 0.66 2 -1.3 101 103
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.36 0.47 4 -0.88 56 60
FRAP1 -0.14 0.31 0.54 1 -0.88 35 36
LTA -0.3 0.55 0.73 3 -1.2 88 91
FES 0.02 0.016 -10000 0 -0.32 1 1
T-helper 1 cell differentiation 0.34 0.64 1.3 102 -0.79 6 108
CCL11 -0.32 0.55 -10000 0 -1.2 103 103
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.33 0.47 4 -0.93 35 39
IL2RG 0.016 0.037 -10000 0 -0.3 5 5
IL10 -0.3 0.56 0.76 4 -1.3 82 86
IRS1 0.02 0.016 -10000 0 -0.32 1 1
IRS2 0.019 0.017 -10000 0 -0.32 1 1
IL4 -0.066 0.25 0.5 4 -1 17 21
IL5 -0.31 0.55 0.68 1 -1.2 86 87
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.25 0.49 0.67 7 -0.98 96 103
COL1A1 -0.015 0.29 0.57 12 -0.88 15 27
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.32 0.56 -10000 0 -1.3 86 86
IL2R gamma/JAK3 0.027 0.03 -10000 0 -0.19 5 5
TFF3 -0.31 0.59 0.74 5 -1.3 92 97
ALOX15 -0.62 0.72 0.69 1 -1.3 233 234
MYBL1 0.023 0.037 0.32 7 -10000 0 7
T-helper 2 cell differentiation -0.25 0.46 0.62 4 -0.98 87 91
SHC1 0.018 0.008 -10000 0 -10000 0 0
CEBPB 0.021 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.3 0.47 3 -0.8 33 36
mol:PI-3-4-5-P3 -0.14 0.31 0.55 1 -0.88 35 36
PI3K -0.15 0.33 0.55 1 -0.96 35 36
DOK2 -0.004 0.083 -10000 0 -0.32 29 29
ETS1 0.011 0.038 -10000 0 -0.22 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.091 0.24 0.45 5 -0.65 27 32
ITGB3 -0.3 0.56 0.68 3 -1.2 88 91
PIGR -0.43 0.69 0.79 3 -1.4 138 141
IGHE 0.009 0.073 0.2 21 -0.19 6 27
MAPKKK cascade -0.089 0.24 0.44 5 -0.63 27 32
BCL6 0.017 0.013 -10000 0 -10000 0 0
OPRM1 -0.31 0.55 0.68 1 -1.2 86 87
RETNLB -0.31 0.55 0.68 1 -1.2 88 89
SELP -0.41 0.68 0.77 2 -1.4 128 130
AICDA -0.32 0.56 0.7 2 -1.2 98 100
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.02 0.015 0.32 1 -10000 0 1
LAT2 -0.072 0.13 -10000 0 -0.31 77 77
AP1 -0.08 0.2 -10000 0 -0.45 76 76
mol:PIP3 -0.079 0.17 0.3 18 -0.36 87 105
IKBKB -0.032 0.12 0.25 28 -0.23 54 82
AKT1 -0.039 0.14 0.32 41 -0.27 42 83
IKBKG -0.041 0.11 0.23 22 -0.23 60 82
MS4A2 -0.06 0.14 -10000 0 -0.32 102 102
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.019 0.006 -10000 0 -10000 0 0
MAP3K1 -0.066 0.14 0.22 9 -0.35 63 72
mol:Ca2+ -0.059 0.14 0.26 22 -0.29 71 93
LYN 0.013 0.017 -10000 0 -10000 0 0
CBLB -0.072 0.12 -10000 0 -0.31 79 79
SHC1 0.018 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK 0.017 0.061 -10000 0 -0.17 42 42
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.018 0.028 -10000 0 -0.32 3 3
PLD2 -0.045 0.15 0.29 47 -0.24 99 146
PTPN13 -0.088 0.17 -10000 0 -0.51 28 28
PTPN11 0.011 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.049 0.12 0.29 10 -0.28 41 51
SYK 0.014 0.028 -10000 0 -0.33 2 2
GRB2 0.02 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.084 0.16 -10000 0 -0.35 94 94
LAT -0.073 0.12 -10000 0 -0.31 80 80
PAK2 -0.072 0.16 0.24 8 -0.38 67 75
NFATC2 -0.035 0.097 -10000 0 -0.5 15 15
HRAS -0.073 0.17 0.25 8 -0.41 66 74
GAB2 0.017 0.032 -10000 0 -0.32 4 4
PLA2G1B -0.049 0.17 -10000 0 -0.92 15 15
Fc epsilon R1 -0.054 0.14 0.22 1 -0.26 142 143
Antigen/IgE/Fc epsilon R1 -0.047 0.13 0.2 1 -0.23 140 141
mol:GDP -0.088 0.18 -10000 0 -0.45 68 68
JUN 0.017 0.032 -10000 0 -0.32 4 4
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.017 -10000 0 -0.33 1 1
FOS -0.002 0.085 -10000 0 -0.32 30 30
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.068 0.13 -10000 0 -0.32 82 82
CHUK -0.046 0.11 0.22 20 -0.22 66 86
KLRG1 -0.064 0.11 0.14 1 -0.27 78 79
VAV1 -0.069 0.12 -10000 0 -0.32 72 72
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.07 0.12 -10000 0 -0.31 78 78
negative regulation of mast cell degranulation -0.055 0.12 -10000 0 -0.31 54 54
BTK -0.095 0.2 -10000 0 -0.49 72 72
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.08 0.15 -10000 0 -0.31 112 112
GAB2/PI3K/SHP2 -0.078 0.086 -10000 0 -0.23 95 95
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.065 0.13 -10000 0 -0.27 104 104
RAF1 -0.013 0.18 -10000 0 -0.97 15 15
Fc epsilon R1/FcgammaRIIB/SHIP -0.033 0.14 0.22 1 -0.23 137 138
FCER1G 0.011 0.046 -10000 0 -0.32 7 7
FCER1A -0.067 0.15 0.32 1 -0.34 108 109
Antigen/IgE/Fc epsilon R1/Fyn -0.04 0.12 0.2 1 -0.22 138 139
MAPK3 -0.015 0.16 -10000 0 -0.89 15 15
MAPK1 -0.018 0.17 -10000 0 -0.91 15 15
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.065 0.21 -10000 0 -0.65 45 45
DUSP1 -0.011 0.099 -10000 0 -0.32 42 42
NF-kappa-B/RelA -0.033 0.061 0.13 6 -0.15 45 51
actin cytoskeleton reorganization -0.074 0.16 -10000 0 -0.53 17 17
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.065 0.15 -10000 0 -0.38 60 60
FER -0.071 0.12 -10000 0 -0.31 77 77
RELA 0.02 0.003 -10000 0 -10000 0 0
ITK -0.024 0.067 -10000 0 -0.29 19 19
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG1 -0.087 0.18 0.26 3 -0.44 71 74
cytokine secretion -0.029 0.039 -10000 0 -0.15 4 4
SPHK1 -0.07 0.12 -10000 0 -0.3 77 77
PTK2 -0.077 0.17 -10000 0 -0.57 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.085 0.16 0.22 1 -0.36 95 96
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.076 0.17 0.27 22 -0.37 73 95
MAP2K2 -0.019 0.16 -10000 0 -0.9 15 15
MAP2K1 -0.018 0.17 -10000 0 -0.91 15 15
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.049 0.11 0.17 1 -0.28 54 55
MAP2K4 -0.094 0.32 -10000 0 -0.92 59 59
Fc epsilon R1/FcgammaRIIB -0.04 0.14 0.22 1 -0.24 140 141
mol:Choline -0.044 0.15 0.29 47 -0.24 99 146
SHC/Grb2/SOS1 -0.041 0.13 -10000 0 -0.31 63 63
FYN 0.018 0.017 -10000 0 -0.32 1 1
DOK1 0.021 0.002 -10000 0 -10000 0 0
PXN -0.074 0.16 -10000 0 -0.51 17 17
HCLS1 -0.072 0.13 -10000 0 -0.31 77 77
PRKCB -0.061 0.14 0.26 20 -0.3 70 90
FCGR2B 0.018 0.007 -10000 0 -10000 0 0
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.056 0.12 -10000 0 -0.31 54 54
LCP2 0.018 0.028 -10000 0 -0.32 3 3
PLA2G4A -0.066 0.12 0.19 1 -0.31 73 74
RASA1 0.02 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.044 0.15 0.29 47 -0.24 99 146
IKK complex -0.023 0.099 0.23 29 -0.18 43 72
WIPF1 0.02 0.003 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.022 0.11 0.23 29 -0.19 76 105
SMAD6-7/SMURF1 0.006 0.078 -10000 0 -0.2 58 58
NOG 0.011 0.088 0.32 11 -0.32 22 33
SMAD9 -0.12 0.22 -10000 0 -0.46 127 127
SMAD4 0.019 0.006 -10000 0 -10000 0 0
SMAD5 -0.044 0.1 -10000 0 -0.31 36 36
BMP7/USAG1 -0.12 0.14 0.23 7 -0.24 258 265
SMAD5/SKI -0.033 0.11 0.24 2 -0.31 39 41
SMAD1 -0.003 0.052 -10000 0 -0.29 7 7
BMP2 -0.025 0.12 -10000 0 -0.32 60 60
SMAD1/SMAD1/SMAD4 -0.01 0.074 -10000 0 -0.33 6 6
BMPR1A 0.02 0.003 -10000 0 -10000 0 0
BMPR1B -0.012 0.11 0.32 3 -0.32 46 49
BMPR1A-1B/BAMBI 0.021 0.082 0.22 14 -0.2 48 62
AHSG 0.037 0.074 0.32 29 -10000 0 29
CER1 0.019 0.032 0.32 5 -10000 0 5
BMP2-4/CER1 0.003 0.083 0.22 3 -0.2 65 68
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.034 0.11 -10000 0 -0.32 34 34
BMP2-4 (homodimer) -0.009 0.092 -10000 0 -0.23 66 66
RGMB 0.02 0.004 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.001 0.11 0.22 4 -0.2 97 101
RGMA 0.023 0.041 0.32 6 -0.32 2 8
SMURF1 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.029 0.089 -10000 0 -0.3 23 23
BMP2-4/USAG1 -0.12 0.13 -10000 0 -0.22 266 266
SMAD6/SMURF1/SMAD5 -0.031 0.11 0.24 2 -0.31 36 38
SOSTDC1 -0.18 0.17 -10000 0 -0.32 267 267
BMP7/BMPR2/BMPR1A-1B 0.015 0.096 0.22 15 -0.19 72 87
SKI 0.02 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) -0.028 0.12 0.32 2 -0.32 67 69
HFE2 0.025 0.044 0.32 10 -10000 0 10
ZFYVE16 0.02 0.005 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD 0.011 0.086 0.22 12 -0.19 62 74
SMAD5/SMAD5/SMAD4 -0.032 0.11 0.24 2 -0.32 35 37
MAPK1 0.02 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.015 0.089 -10000 0 -0.27 22 22
BMP7 (homodimer) 0.002 0.11 0.32 16 -0.32 37 53
NUP214 0.02 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.006 0.1 0.23 29 -0.23 62 91
SMAD1/SKI 0.009 0.064 -10000 0 -0.33 6 6
SMAD6 -0.028 0.12 -10000 0 -0.32 65 65
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.015 0.094 0.22 26 -0.19 62 88
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.22 0.14 0.32 309 -10000 0 309
BMPR2 (homodimer) 0.021 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.037 0.02 -10000 0 -0.2 2 2
BMPR1A-1B (homodimer) 0.006 0.079 0.23 3 -0.23 46 49
CHRDL1 -0.1 0.16 -10000 0 -0.32 164 164
ENDOFIN/SMAD1 0.009 0.063 -10000 0 -0.36 4 4
SMAD6-7/SMURF1/SMAD1 -0.002 0.084 -10000 0 -0.39 5 5
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI 0.026 0.063 0.32 14 -0.32 5 19
SMURF2 0.02 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.068 0.14 -10000 0 -0.23 181 181
BMP2-4/GREM1 0.1 0.14 0.22 242 -0.15 65 307
SMAD7 0.018 0.017 -10000 0 -0.32 1 1
SMAD8A/SMAD8A/SMAD4 -0.11 0.21 -10000 0 -0.43 130 130
SMAD1/SMAD6 0.007 0.065 -10000 0 -0.35 5 5
TAK1/SMAD6 0.027 0.011 -10000 0 -10000 0 0
BMP7 0.002 0.11 0.32 16 -0.32 37 53
BMP6 -0.028 0.12 0.32 2 -0.32 67 69
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.033 0.095 -10000 0 -0.32 29 29
PPM1A 0.02 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.007 0.064 0.22 1 -0.33 6 7
SMAD7/SMURF1 0.026 0.016 -10000 0 -0.23 1 1
CTDSPL 0.02 0.004 -10000 0 -10000 0 0
PPP1CA 0.02 0.003 -10000 0 -10000 0 0
XIAP 0.02 0.003 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
PPP1R15A 0.019 0.023 -10000 0 -0.32 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.032 0.1 -10000 0 -0.33 29 29
CHRD 0.03 0.059 0.32 17 -0.32 1 18
BMPR2 0.021 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.034 0.091 -10000 0 -0.31 21 21
BMP4 0.014 0.054 0.32 2 -0.32 10 12
FST 0.025 0.088 0.32 23 -0.32 13 36
BMP2-4/NOG -0.001 0.1 0.22 7 -0.22 74 81
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.024 0.092 0.22 13 -0.18 63 76
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.007 0.076 0.22 1 -0.29 18 19
alphaM/beta2 Integrin/GPIbA 0.004 0.081 0.22 2 -0.27 24 26
alphaM/beta2 Integrin/proMMP-9 0.043 0.11 0.22 86 -0.25 17 103
PLAUR 0.02 0.005 -10000 0 -10000 0 0
HMGB1 0.005 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.007 0.077 -10000 0 -0.29 19 19
AGER -0.29 0.11 -10000 0 -0.34 408 408
RAP1A 0.02 0.004 -10000 0 -10000 0 0
SELPLG 0.009 0.061 -10000 0 -0.32 15 15
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.2 0.12 -10000 0 -0.23 406 406
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.078 0.12 0.32 90 -10000 0 90
CYR61 0.004 0.073 -10000 0 -0.32 22 22
TLN1 0.019 0.017 -10000 0 -0.32 1 1
Rap1/GTP -0.051 0.13 -10000 0 -0.34 50 50
RHOA 0.02 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.05 0.14 -10000 0 -0.32 93 93
MYH2 -0.1 0.16 0.22 2 -0.38 80 82
MST1R 0.019 0.016 -10000 0 -0.32 1 1
leukocyte activation during inflammatory response 0.01 0.085 0.19 22 -0.21 35 57
APOB 0.023 0.1 0.32 26 -0.32 19 45
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.015 0.32 1 -10000 0 1
JAM3 0.018 0.023 -10000 0 -0.32 2 2
GP1BA 0.015 0.047 0.32 2 -0.32 7 9
alphaM/beta2 Integrin/CTGF -0.002 0.088 -10000 0 -0.26 35 35
alphaM/beta2 Integrin -0.067 0.14 0.21 2 -0.37 54 56
JAM3 homodimer 0.018 0.023 -10000 0 -0.32 2 2
ICAM2 0.018 0.028 -10000 0 -0.32 3 3
ICAM1 0.016 0.036 -10000 0 -0.32 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.067 0.14 0.21 2 -0.37 54 56
cell adhesion 0.004 0.08 0.22 2 -0.27 24 26
NFKB1 -0.22 0.16 -10000 0 -0.47 119 119
THY1 0.029 0.052 0.32 14 -10000 0 14
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.026 0.063 0.21 28 -0.19 20 48
alphaM/beta2 Integrin/LRP/tPA 0.033 0.096 0.22 42 -0.28 17 59
IL6 -0.24 0.25 -10000 0 -0.64 114 114
ITGB2 -0.001 0.056 -10000 0 -0.32 10 10
elevation of cytosolic calcium ion concentration 0.044 0.1 0.22 69 -0.27 16 85
alphaM/beta2 Integrin/JAM2/JAM3 -0.003 0.099 -10000 0 -0.24 52 52
JAM2 -0.013 0.1 -10000 0 -0.32 44 44
alphaM/beta2 Integrin/ICAM1 0.023 0.084 0.22 9 -0.25 21 30
alphaM/beta2 Integrin/uPA/Plg 0.047 0.11 0.23 74 -0.26 18 92
RhoA/GTP -0.079 0.16 0.23 2 -0.36 69 71
positive regulation of phagocytosis -0.052 0.13 -10000 0 -0.36 46 46
Ron/MSP 0.035 0.039 0.23 14 -0.23 2 16
alphaM/beta2 Integrin/uPAR/uPA 0.046 0.1 0.23 69 -0.27 16 85
alphaM/beta2 Integrin/uPAR 0.008 0.073 -10000 0 -0.29 16 16
PLAU 0.076 0.12 0.32 86 -10000 0 86
PLAT 0.048 0.094 0.32 48 -0.32 1 49
actin filament polymerization -0.1 0.15 0.21 2 -0.36 79 81
MST1 0.028 0.054 0.32 14 -0.32 1 15
alphaM/beta2 Integrin/lipoprotein(a) 0.014 0.089 0.21 23 -0.21 35 58
TNF -0.22 0.17 -10000 0 -0.48 113 113
RAP1B 0.02 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.041 0.11 0.22 82 -0.28 19 101
fibrinolysis 0.045 0.11 0.22 74 -0.25 18 92
HCK 0.007 0.065 -10000 0 -0.32 17 17
dendritic cell antigen processing and presentation -0.067 0.14 0.21 2 -0.37 54 56
VTN -0.034 0.14 0.32 6 -0.32 79 85
alphaM/beta2 Integrin/CYR61 -0.002 0.089 -10000 0 -0.26 37 37
LPA 0.017 0.026 0.32 2 -0.32 1 3
LRP1 0.017 0.032 -10000 0 -0.32 4 4
cell migration 0.02 0.077 0.24 2 -0.24 16 18
FN1 0.018 0.032 -10000 0 -0.32 4 4
alphaM/beta2 Integrin/Thy1 0.012 0.081 0.22 13 -0.27 19 32
MPO 0.014 0.05 0.32 1 -0.32 9 10
KNG1 0.038 0.076 0.32 31 -10000 0 31
RAP1/GDP 0.026 0.008 -10000 0 -10000 0 0
ROCK1 -0.075 0.15 0.24 4 -0.39 52 56
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.022 0.042 0.32 9 -10000 0 9
CTGF 0.003 0.073 -10000 0 -0.32 22 22
alphaM/beta2 Integrin/Hck 0.002 0.091 -10000 0 -0.33 23 23
ITGAM -0.009 0.074 -10000 0 -0.35 18 18
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.027 0.12 -10000 0 -0.22 96 96
HP -0.043 0.16 0.32 21 -0.32 103 124
leukocyte adhesion -0.19 0.13 -10000 0 -0.34 137 137
SELP -0.05 0.14 -10000 0 -0.32 93 93
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.011 0.094 0.98 3 -10000 0 3
VDR 0.02 0.021 0.32 1 -0.32 1 2
FAM120B 0.019 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.087 0.11 -10000 0 -0.33 26 26
RXRs/LXRs/DNA/Oxysterols -0.088 0.13 -10000 0 -0.44 28 28
MED1 0.02 0.004 -10000 0 -10000 0 0
mol:9cRA -0.001 0.009 -10000 0 -0.093 1 1
RARs/THRs/DNA/Src-1 -0.008 0.066 -10000 0 -0.19 41 41
RXRs/NUR77 -0.096 0.13 -10000 0 -0.21 251 251
RXRs/PPAR -0.11 0.13 -10000 0 -0.22 231 231
NCOR2 0.02 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.015 0.22 1 -0.22 1 2
RARs/VDR/DNA/Vit D3 0.044 0.024 0.21 1 -0.17 3 4
RARA 0.02 0.004 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.02 0.021 0.32 1 -0.32 1 2
RARs/RARs/DNA/9cRA 0.031 0.021 -10000 0 -0.17 2 2
RARG 0.02 0.003 -10000 0 -10000 0 0
RPS6KB1 0.028 0.1 0.63 13 -10000 0 13
RARs/THRs/DNA/SMRT -0.008 0.065 -10000 0 -0.19 43 43
THRA 0.02 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.015 0.22 1 -0.22 1 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.066 0.11 -10000 0 -0.18 212 212
NR1H4 0.04 0.077 0.32 32 -10000 0 32
RXRs/LXRs/DNA -0.056 0.12 -10000 0 -0.27 13 13
NR1H2 0.019 0.015 -10000 0 -10000 0 0
NR1H3 0.019 0.016 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.058 0.1 -10000 0 -0.17 212 212
NR4A1 -0.048 0.14 -10000 0 -0.32 93 93
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.072 0.095 -10000 0 -0.17 200 200
RXRG -0.14 0.17 -10000 0 -0.32 218 218
RXR alpha/CCPG 0.026 0.016 -10000 0 -10000 0 0
RXRA 0.018 0.016 -10000 0 -10000 0 0
RXRB 0.018 0.015 -10000 0 -10000 0 0
THRB -0.011 0.099 -10000 0 -0.32 42 42
PPARG -0.02 0.11 -10000 0 -0.32 54 54
PPARD 0.02 0.004 -10000 0 -10000 0 0
TNF -0.098 0.18 -10000 0 -0.84 20 20
mol:Oxysterols -0.001 0.009 -10000 0 -10000 0 0
cholesterol transport -0.088 0.13 -10000 0 -0.44 28 28
PPARA 0.02 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.023 -10000 0 -0.32 2 2
RXRs/NUR77/BCL2 -0.12 0.13 -10000 0 -0.23 248 248
SREBF1 -0.077 0.12 -10000 0 -0.46 19 19
RXRs/RXRs/DNA/9cRA -0.066 0.11 -10000 0 -0.18 212 212
ABCA1 -0.083 0.13 -10000 0 -0.55 16 16
RARs/THRs 0.037 0.068 -10000 0 -0.18 40 40
RXRs/FXR -0.056 0.12 0.23 12 -0.18 200 212
BCL2 0.019 0.022 0.32 1 -0.32 1 2
Visual signal transduction: Rods

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
mol:K + 0.02 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.028 0.22 9 -10000 0 9
Metarhodopsin II/Arrestin 0.024 0.01 0.21 1 -10000 0 1
PDE6G/GNAT1/GTP 0.027 0.033 0.23 8 -0.17 3 11
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.042 0.32 9 -10000 0 9
GRK1 0.034 0.069 0.32 25 -10000 0 25
CNG Channel 0.043 0.084 0.26 15 -0.18 27 42
mol:Na + 0.08 0.081 0.28 31 -0.17 3 34
mol:ADP 0.034 0.069 0.32 25 -10000 0 25
RGS9-1/Gbeta5/R9AP -0.059 0.12 -10000 0 -0.21 177 177
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.099 0.096 0.33 32 -0.17 3 35
CNGB1 0.07 0.12 0.32 79 -0.32 1 80
RDH5 0.026 0.042 0.32 9 -10000 0 9
SAG 0.018 0.014 0.32 1 -10000 0 1
mol:Ca2+ 0.016 0.09 0.29 30 -10000 0 30
Na + (4 Units) 0.023 0.08 0.14 103 -0.16 3 106
RGS9 -0.083 0.16 -10000 0 -0.32 139 139
GNB1/GNGT1 0.061 0.077 0.23 77 -10000 0 77
GNAT1/GDP -0.043 0.11 0.21 4 -0.18 172 176
GUCY2D 0.019 0.04 0.32 4 -0.32 3 7
GNGT1 0.074 0.12 0.32 85 -10000 0 85
GUCY2F 0.019 0.014 0.32 1 -10000 0 1
GNB5 0.02 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.03 0.048 0.12 8 -0.18 36 44
mol:11-cis-retinal 0.026 0.042 0.32 9 -10000 0 9
mol:cGMP 0.059 0.074 0.21 74 -0.18 4 78
GNB1 0.02 0.004 -10000 0 -10000 0 0
Rhodopsin 0.032 0.028 0.23 9 -10000 0 9
SLC24A1 0.02 0.003 -10000 0 -10000 0 0
CNGA1 0.06 0.1 0.32 61 -10000 0 61
Metarhodopsin II 0.031 0.039 0.2 24 -10000 0 24
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.07 0.076 0.23 77 -0.17 5 82
RGS9BP -0.029 0.12 -10000 0 -0.32 66 66
Metarhodopsin II/Transducin 0.025 0.039 0.16 8 -10000 0 8
GCAP Family/Ca ++ 0.063 0.069 0.21 77 -0.15 2 79
PDE6A/B 0.008 0.072 0.23 1 -0.23 39 40
mol:Pi -0.059 0.12 -10000 0 -0.21 177 177
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.064 0.071 0.22 79 -10000 0 79
PDE6B 0.016 0.036 -10000 0 -0.32 5 5
PDE6A -0.006 0.093 0.32 1 -0.32 36 37
PDE6G 0.019 0.034 0.32 2 -0.32 3 5
RHO 0.018 0.003 -10000 0 -10000 0 0
PDE6 -0.049 0.13 -10000 0 -0.2 176 176
GUCA1A 0.069 0.11 0.32 77 -10000 0 77
GC2/GCAP Family 0.074 0.07 0.22 77 -0.15 2 79
GUCA1C 0.017 0.003 -10000 0 -10000 0 0
GUCA1B 0.021 0.036 0.32 4 -0.32 2 6
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.014 0.045 -10000 0 -0.32 8 8
EPHB2 0.054 0.095 0.32 52 -10000 0 52
EFNB1 -0.012 0.029 0.18 6 -0.23 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.081 0.28 17 -0.24 5 22
Ephrin B2/EPHB1-2 0.066 0.084 0.22 86 -0.16 9 95
neuron projection morphogenesis 0.043 0.063 0.22 16 -0.23 5 21
Ephrin B1/EPHB1-2/Tiam1 0.07 0.088 0.23 83 -0.22 7 90
DNM1 0.024 0.032 0.33 5 -10000 0 5
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.056 0.16 -10000 0 -0.5 49 49
YES1 -0.066 0.23 -10000 0 -0.72 49 49
Ephrin B1/EPHB1-2/NCK2 0.075 0.084 0.23 87 -0.2 4 91
PI3K -0.025 0.17 -10000 0 -0.5 50 50
mol:GDP 0.068 0.086 0.23 83 -0.22 7 90
ITGA2B -0.008 0.1 0.32 4 -0.32 42 46
endothelial cell proliferation 0.021 0.029 -10000 0 -0.19 8 8
FYN -0.07 0.23 -10000 0 -0.73 49 49
MAP3K7 -0.055 0.16 -10000 0 -0.53 48 48
FGR -0.071 0.23 -10000 0 -0.73 49 49
TIAM1 0.016 0.039 -10000 0 -0.32 6 6
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
RGS3 0.02 0.004 -10000 0 -10000 0 0
cell adhesion -0.045 0.17 0.23 1 -0.49 49 50
LYN -0.063 0.22 -10000 0 -0.72 48 48
Ephrin B1/EPHB1-2/Src Family Kinases -0.062 0.2 -10000 0 -0.66 49 49
Ephrin B1/EPHB1-2 -0.054 0.18 -10000 0 -0.57 48 48
SRC -0.062 0.22 -10000 0 -0.72 49 49
ITGB3 0.031 0.074 0.32 22 -0.32 5 27
EPHB1 0.051 0.096 0.32 49 -0.33 2 51
EPHB4 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.021 0.029 -10000 0 -0.19 8 8
alphaIIb/beta3 Integrin 0.015 0.095 0.23 26 -0.23 46 72
BLK -0.062 0.23 -10000 0 -0.72 49 49
HCK -0.068 0.23 -10000 0 -0.73 49 49
regulation of stress fiber formation -0.073 0.082 0.2 4 -0.23 87 91
MAPK8 -0.056 0.15 0.22 2 -0.48 49 51
Ephrin B1/EPHB1-2/RGS3 0.072 0.082 0.23 83 -0.2 4 87
endothelial cell migration -0.04 0.14 0.2 15 -0.44 44 59
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTPN13 -0.024 0.14 -10000 0 -0.44 46 46
regulation of focal adhesion formation -0.073 0.082 0.2 4 -0.23 87 91
chemotaxis -0.07 0.08 0.2 4 -0.22 83 87
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.054 0.073 0.25 17 -0.24 5 22
angiogenesis -0.054 0.18 -10000 0 -0.57 48 48
LCK -0.062 0.22 -10000 0 -0.72 49 49
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.02 0.004 -10000 0 -10000 0 0
CCL5 0.017 0.032 -10000 0 -0.32 4 4
SDCBP 0.019 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.081 0.079 0.23 44 -0.26 2 46
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 0.071 0.088 0.22 33 -0.3 5 38
Syndecan-1/Syntenin 0.071 0.088 0.23 33 -0.3 5 38
MAPK3 0.057 0.086 0.21 38 -0.27 5 43
HGF/MET 0.015 0.075 0.23 10 -0.23 32 42
TGFB1/TGF beta receptor Type II 0.02 0.004 -10000 0 -10000 0 0
BSG 0.019 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.071 0.087 0.22 33 -0.3 5 38
Syndecan-1/RANTES 0.075 0.091 0.23 36 -0.28 7 43
Syndecan-1/CD147 0.083 0.089 0.23 36 -0.28 5 41
Syndecan-1/Syntenin/PIP2 0.066 0.083 0.21 32 -0.29 5 37
LAMA5 0.016 0.032 -10000 0 -0.32 4 4
positive regulation of cell-cell adhesion 0.064 0.081 0.2 31 -0.29 5 36
MMP7 0.065 0.12 0.32 78 -0.32 7 85
HGF 0.008 0.076 0.32 4 -0.32 20 24
Syndecan-1/CASK 0.06 0.083 0.15 132 -0.25 8 140
Syndecan-1/HGF/MET 0.069 0.1 0.24 36 -0.31 8 44
regulation of cell adhesion 0.048 0.079 0.19 38 -0.26 5 43
HPSE 0.022 0.02 0.32 2 -10000 0 2
positive regulation of cell migration 0.081 0.079 0.23 44 -0.26 2 46
SDC1 0.08 0.079 0.23 43 -0.26 2 45
Syndecan-1/Collagen 0.081 0.079 0.23 44 -0.26 2 46
PPIB 0.021 0.014 0.32 1 -10000 0 1
MET 0.013 0.069 0.32 6 -0.32 14 20
PRKACA 0.02 0.005 -10000 0 -10000 0 0
MMP9 0.078 0.12 0.32 90 -10000 0 90
MAPK1 0.057 0.082 0.2 37 -0.26 5 42
homophilic cell adhesion 0.077 0.088 0.24 38 -0.22 4 42
MMP1 0.21 0.15 0.32 296 -0.32 2 298
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.028 0.018 -10000 0 -0.23 2 2
Necdin/E2F1 0.028 0.031 0.23 4 -0.22 4 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.047 0.069 0.22 23 -0.17 26 49
NGF (dimer)/p75(NTR)/BEX1 -0.015 0.12 0.23 30 -0.2 127 157
NT-4/5 (dimer)/p75(NTR) 0.016 0.072 0.26 7 -0.23 30 37
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.018 0.056 0.18 19 -0.17 19 38
IKBKG 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 231 231
MGDIs/NGR/p75(NTR)/LINGO1 0.058 0.072 0.23 59 -0.18 9 68
FURIN 0.029 0.05 0.32 13 -10000 0 13
proBDNF (dimer)/p75(NTR)/Sortilin -0.075 0.12 0.22 5 -0.2 227 232
LINGO1 0.061 0.1 0.32 62 -10000 0 62
Sortilin/TRAF6/NRIF -0.028 0.019 -10000 0 -0.17 2 2
proBDNF (dimer) -0.15 0.17 -10000 0 -0.32 231 231
NTRK1 0.009 0.059 0.32 1 -0.32 13 14
RTN4R 0.019 0.017 -10000 0 -0.32 1 1
neuron apoptosis -0.099 0.14 0.32 4 -0.39 41 45
IRAK1 0.02 0.004 -10000 0 -10000 0 0
SHC1 -0.015 0.041 0.1 23 -0.2 14 37
ARHGDIA 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.045 0.031 -10000 0 -0.17 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.046 0.066 0.22 24 -0.18 23 47
MAGEH1 0.02 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.042 0.07 0.22 23 -0.19 25 48
Mammalian IAPs/DIABLO 0.05 0.027 0.22 4 -0.18 2 6
proNGF (dimer) 0.022 0.084 0.32 19 -0.32 13 32
MAGED1 0.021 0.014 0.32 1 -10000 0 1
APP 0.02 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.076 -10000 0 -0.32 24 24
ZNF274 0.02 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.019 0.045 0.19 1 -0.16 21 22
NGF 0.023 0.084 0.32 19 -0.32 13 32
cell cycle arrest 0.003 0.072 0.22 19 -10000 0 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.054 0.17 6 -0.2 20 26
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.027 0.066 0.24 7 -0.2 30 37
NCSTN 0.018 0.007 -10000 0 -10000 0 0
mol:GTP 0.038 0.065 0.22 25 -0.19 20 45
PSENEN 0.019 0.005 -10000 0 -10000 0 0
mol:ceramide -0.016 0.051 0.19 11 -0.18 17 28
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.003 0.051 0.16 8 -0.28 3 11
p75(NTR)/beta APP 0.027 0.042 0.23 7 -0.22 8 15
BEX1 -0.058 0.17 0.32 16 -0.32 119 135
mol:GDP -0.014 0.046 0.21 1 -0.19 21 22
NGF (dimer) 0.073 0.095 0.23 99 -0.18 16 115
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.066 0.07 0.23 58 -0.18 7 65
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
RAC1/GTP 0.029 0.054 0.2 20 -0.16 20 40
MYD88 0.02 0.004 -10000 0 -10000 0 0
CHUK 0.02 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.038 0.065 0.22 25 -0.19 20 45
RHOB 0.021 0.002 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.029 0.019 0.23 3 -10000 0 3
NT3 (dimer) 0.004 0.077 0.32 2 -0.32 23 25
TP53 -0.082 0.093 0.3 6 -0.29 5 11
PRDM4 -0.018 0.054 0.19 13 -0.18 20 33
BDNF (dimer) -0.007 0.17 0.26 99 -0.16 204 303
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SORT1 0.019 0.023 -10000 0 -0.32 2 2
activation of caspase activity 0.042 0.066 -10000 0 -0.17 26 26
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.046 0.066 0.22 24 -0.18 23 47
RHOC 0.02 0.004 -10000 0 -10000 0 0
XIAP 0.02 0.003 -10000 0 -10000 0 0
MAPK10 -0.076 0.12 0.3 11 -0.32 43 54
DIABLO 0.02 0.003 -10000 0 -10000 0 0
SMPD2 -0.016 0.051 0.2 11 -0.18 17 28
APH1B 0.019 0.023 -10000 0 -0.32 2 2
APH1A 0.017 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.037 0.067 0.22 24 -0.19 23 47
PSEN1 0.02 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.029 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.015 0.074 0.29 7 -0.23 30 37
MAPK8 -0.06 0.11 0.31 10 -0.29 22 32
MAPK9 -0.059 0.1 0.3 10 -0.3 19 29
APAF1 0.02 0.003 -10000 0 -10000 0 0
NTF3 0.004 0.078 0.32 2 -0.32 23 25
NTF4 0.002 0.076 -10000 0 -0.32 24 24
NDN 0.016 0.036 -10000 0 -0.32 5 5
RAC1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.046 0.056 -10000 0 -0.16 19 19
p75 CTF/Sortilin/TRAF6/NRIF 0.048 0.022 -10000 0 -0.18 2 2
RhoA-B-C/GTP 0.037 0.064 0.22 25 -0.19 20 45
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.057 0.12 0.22 3 -0.18 219 222
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.063 0.12 0.22 5 -0.18 224 229
PRKACB 0.021 0.015 0.32 1 -10000 0 1
proBDNF (dimer)/p75 ECD -0.098 0.13 -10000 0 -0.23 229 229
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.021 0.036 0.32 4 -0.32 2 6
BIRC2 0.02 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.009 0.072 0.22 13 -0.2 14 27
BAD -0.07 0.11 0.32 11 -0.32 27 38
RIPK2 0.018 0.007 -10000 0 -10000 0 0
NGFR 0.019 0.058 0.32 7 -0.32 8 15
CYCS -0.02 0.052 0.2 11 -0.17 19 30
ADAM17 0.021 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.041 0.064 0.22 21 -0.18 21 42
BCL2L11 -0.069 0.11 0.32 10 -0.32 27 37
BDNF (dimer)/p75(NTR) -0.096 0.13 0.23 5 -0.23 228 233
PI3K 0.045 0.065 0.22 23 -0.18 21 44
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.045 0.067 0.22 24 -0.18 22 46
NDNL2 0.02 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.028 0.072 0.23 25 -0.23 21 46
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.047 0.066 0.22 24 -0.18 22 46
TRAF6 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.028 -10000 0 -0.32 3 3
PLG 0.022 0.042 0.32 9 -10000 0 9
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.097 0.096 0.14 2 -0.19 220 222
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
NGFRAP1 0.017 0.036 -10000 0 -0.32 5 5
CASP3 -0.066 0.11 0.31 10 -0.3 28 38
E2F1 0.023 0.028 0.32 4 -10000 0 4
CASP9 0.02 0.004 -10000 0 -10000 0 0
IKK complex 0.028 0.07 0.23 3 -0.26 9 12
NGF (dimer)/TRKA 0.021 0.068 0.23 17 -0.22 22 39
MMP7 0.065 0.12 0.32 78 -0.32 7 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.051 0.065 0.22 22 -0.17 21 43
MMP3 0.13 0.15 0.32 175 -10000 0 175
APAF-1/Caspase 9 -0.039 0.035 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 0.017 0.028 -10000 0 -0.33 3 3
GNB1/GNG2 -0.05 0.07 -10000 0 -0.18 92 92
AKT1 -0.039 0.1 0.24 2 -0.25 31 33
EGF 0.072 0.12 0.32 84 -0.32 4 88
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.03 0.059 0.15 2 -0.22 16 18
mol:Ca2+ -0.062 0.14 0.24 1 -0.3 98 99
LYN -0.021 0.04 0.15 1 -0.2 3 4
RhoA/GTP -0.026 0.057 -10000 0 -0.13 77 77
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.15 -10000 0 -0.34 93 93
GNG2 0.018 0.023 -10000 0 -0.32 2 2
ARRB2 0.019 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.034 0.15 -10000 0 -0.62 27 27
G beta5/gamma2 -0.062 0.092 -10000 0 -0.24 88 88
PRKCH -0.072 0.16 0.31 1 -0.35 96 97
DNM1 0.023 0.031 0.32 5 -10000 0 5
TXA2/TP beta/beta Arrestin3 0.007 0.046 -10000 0 -0.53 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.012 0.05 -10000 0 -0.32 10 10
G12 family/GTP -0.062 0.13 -10000 0 -0.3 92 92
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
ADRBK2 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.042 0.11 0.36 27 -10000 0 27
mol:NADP 0.021 0.052 0.32 7 -0.32 5 12
RAB11A 0.02 0.003 -10000 0 -10000 0 0
PRKG1 -0.016 0.11 -10000 0 -0.32 49 49
mol:IP3 -0.079 0.17 -10000 0 -0.38 102 102
cell morphogenesis 0.026 0.007 -10000 0 -10000 0 0
PLCB2 -0.11 0.23 -10000 0 -0.52 103 103
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.004 0.07 0.15 58 -0.19 3 61
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.025 0.05 0.15 2 -0.22 9 11
RHOA 0.02 0.004 -10000 0 -10000 0 0
PTGIR 0.015 0.039 -10000 0 -0.32 6 6
PRKCB1 -0.077 0.16 -10000 0 -0.37 98 98
GNAQ 0.019 0.016 -10000 0 -0.32 1 1
mol:L-citrulline 0.021 0.052 0.32 7 -0.32 5 12
TXA2/TXA2-R family -0.11 0.22 -10000 0 -0.52 93 93
LCK -0.022 0.046 0.15 2 -0.21 5 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.008 0.049 0.18 2 -0.22 7 9
TXA2-R family/G12 family/GDP/G beta/gamma 0.009 0.061 -10000 0 -0.41 8 8
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.011 0.046 -10000 0 -0.2 11 11
MAPK14 -0.046 0.1 0.27 7 -0.23 88 95
TGM2/GTP -0.089 0.18 -10000 0 -0.42 96 96
MAPK11 -0.05 0.099 0.19 1 -0.23 90 91
ARHGEF1 -0.042 0.073 -10000 0 -0.18 80 80
GNAI2 0.02 0.004 -10000 0 -10000 0 0
JNK cascade -0.079 0.17 -10000 0 -0.38 93 93
RAB11/GDP 0.02 0.005 -10000 0 -10000 0 0
ICAM1 -0.057 0.12 0.23 1 -0.29 90 91
cAMP biosynthetic process -0.076 0.16 -10000 0 -0.35 100 100
Gq family/GTP/EBP50 -0.001 0.042 -10000 0 -0.23 9 9
actin cytoskeleton reorganization 0.026 0.007 -10000 0 -10000 0 0
SRC -0.021 0.042 0.15 2 -0.2 3 5
GNB5 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.007 0.076 0.18 14 -0.23 18 32
VCAM1 -0.058 0.13 0.23 1 -0.29 90 91
TP beta/Gq family/GDP/G beta5/gamma2 -0.034 0.15 -10000 0 -0.62 27 27
platelet activation -0.061 0.14 0.3 6 -0.3 92 98
PGI2/IP 0.011 0.027 -10000 0 -0.22 6 6
PRKACA 0.002 0.04 -10000 0 -0.22 14 14
Gq family/GDP/G beta5/gamma2 -0.019 0.12 -10000 0 -0.55 19 19
TXA2/TP beta/beta Arrestin2 -0.005 0.059 -10000 0 -0.37 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.034 -10000 0 -0.2 13 13
mol:DAG -0.087 0.19 -10000 0 -0.42 98 98
EGFR 0.015 0.042 0.32 1 -0.32 6 7
TXA2/TP alpha -0.1 0.21 -10000 0 -0.48 100 100
Gq family/GTP -0.015 0.069 0.22 1 -0.23 38 39
YES1 -0.02 0.044 0.16 1 -0.2 3 4
GNAI2/GTP -0.005 0.042 -10000 0 -0.19 10 10
PGD2/DP 0.01 0.034 -10000 0 -0.22 10 10
SLC9A3R1 0.021 0.015 0.32 1 -10000 0 1
FYN -0.02 0.041 0.15 2 -0.2 3 5
mol:NO 0.021 0.052 0.32 7 -0.32 5 12
GNA15 0.019 0.005 -10000 0 -10000 0 0
PGK/cGMP 0.006 0.073 0.21 7 -0.2 48 55
RhoA/GDP 0.02 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.019 0.051 -10000 0 -0.23 7 7
NOS3 0.021 0.052 0.32 7 -0.32 5 12
RAC1 0.018 0.007 -10000 0 -10000 0 0
PRKCA -0.072 0.16 0.28 3 -0.35 94 97
PRKCB -0.075 0.16 -10000 0 -0.36 94 94
PRKCE -0.073 0.16 0.29 1 -0.36 93 94
PRKCD -0.079 0.16 -10000 0 -0.38 96 96
PRKCG -0.078 0.17 -10000 0 -0.38 97 97
muscle contraction -0.1 0.21 -10000 0 -0.48 98 98
PRKCZ -0.072 0.15 -10000 0 -0.34 93 93
ARR3 0.019 0.02 0.32 2 -10000 0 2
TXA2/TP beta 0.007 0.048 -10000 0 -0.19 11 11
PRKCQ -0.084 0.16 -10000 0 -0.37 99 99
MAPKKK cascade -0.098 0.2 -10000 0 -0.45 99 99
SELE -0.072 0.15 -10000 0 -0.36 90 90
TP beta/GNAI2/GDP/G beta/gamma 0.02 0.05 -10000 0 -0.2 12 12
ROCK1 0.02 0.004 -10000 0 -10000 0 0
GNA14 0.011 0.055 -10000 0 -0.32 12 12
chemotaxis -0.12 0.25 -10000 0 -0.59 92 92
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.005 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.016 0.19 1 -10000 0 1
AES 0.021 0.014 0.16 1 -10000 0 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.028 0.01 -10000 0 -10000 0 0
SMAD4 0.019 0.006 -10000 0 -10000 0 0
DKK2 -0.046 0.14 -10000 0 -0.32 89 89
TLE1 0.022 0.014 0.17 1 -10000 0 1
MACF1 0.018 0.032 -10000 0 -0.32 4 4
CTNNB1 0.081 0.1 0.26 40 -0.31 6 46
WIF1 -0.21 0.16 -10000 0 -0.32 309 309
beta catenin/RanBP3 0.045 0.1 0.44 18 -0.34 2 20
KREMEN2 0.096 0.13 0.32 117 -10000 0 117
DKK1 0.037 0.16 0.32 76 -0.32 44 120
beta catenin/beta TrCP1 0.082 0.097 0.28 24 -0.3 5 29
FZD1 0.02 0.005 -10000 0 -10000 0 0
AXIN2 -0.026 0.25 0.57 17 -1.2 16 33
AXIN1 0.021 0.004 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin 0.027 0.093 -10000 0 -0.66 7 7
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.019 0.17 0.28 1 -0.6 25 26
Axin1/APC/GSK3 0.053 0.071 0.22 28 -0.36 3 31
Axin1/APC/GSK3/beta catenin/Macf1 0.035 0.08 0.26 13 -0.36 7 20
HNF1A 0.078 0.12 0.32 89 -0.32 1 90
CTBP1 0.022 0.015 0.18 1 -10000 0 1
MYC 0.076 0.24 0.56 77 -1.3 2 79
RANBP3 0.02 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.12 0.22 75 -0.17 82 157
NKD1 -0.017 0.11 0.32 4 -0.32 53 57
TCF4 0.019 0.027 0.17 1 -0.32 2 3
TCF3 0.021 0.015 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.05 0.028 0.23 5 -10000 0 5
Ran/GTP 0.016 0.01 0.22 1 -10000 0 1
CtBP/CBP/TCF/TLE1/AES 0.008 0.12 0.41 17 -0.48 8 25
LEF1 0.024 0.025 0.27 3 -10000 0 3
DVL1 0.038 0.052 -10000 0 -0.34 3 3
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.026 0.16 -10000 0 -0.6 21 21
DKK1/LRP6/Kremen 2 0.083 0.13 0.25 143 -0.18 42 185
LRP6 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.015 -10000 0 -10000 0 0
NLK 0.018 0.01 -10000 0 -10000 0 0
CCND1 -0.004 0.19 0.58 18 -1.3 6 24
WNT1 0.025 0.037 0.32 7 -10000 0 7
GSK3A 0.021 0.005 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.02 0.004 -10000 0 -10000 0 0
PPP2R5D 0.048 0.076 0.24 41 -0.25 3 44
APC -0.003 0.059 0.18 40 -10000 0 40
WNT1/LRP6/FZD1 0.096 0.086 0.17 265 -0.18 3 268
CREBBP 0.022 0.015 0.18 1 -10000 0 1
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.1 0.44 0.7 3 -1.1 46 49
IL23A -0.092 0.46 0.72 6 -1.1 51 57
NF kappa B1 p50/RelA/I kappa B alpha -0.094 0.44 0.63 4 -1.1 51 55
positive regulation of T cell mediated cytotoxicity -0.12 0.51 0.74 3 -1.2 59 62
ITGA3 -0.1 0.45 0.72 3 -1.1 48 51
IL17F -0.068 0.3 0.52 8 -0.7 53 61
IL12B 0.018 0.06 0.29 4 -0.34 1 5
STAT1 (dimer) -0.12 0.48 0.63 2 -1.2 59 61
CD4 -0.1 0.45 0.68 4 -1.2 45 49
IL23 -0.084 0.44 0.68 5 -1.1 51 56
IL23R 0.005 0.17 0.44 1 -0.98 9 10
IL1B -0.11 0.49 0.73 3 -1.3 51 54
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.09 0.43 0.7 4 -1.1 44 48
TYK2 0.015 0.042 -10000 0 -10000 0 0
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP 0.008 0.067 -10000 0 -0.32 18 18
IL12RB1 0.007 0.072 0.16 1 -0.36 12 13
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.017 0.067 0.2 1 -0.26 11 12
IL23R/JAK2 0.015 0.18 0.42 1 -0.96 8 9
positive regulation of chronic inflammatory response -0.12 0.51 0.74 3 -1.2 59 62
natural killer cell activation -0.001 0.01 -10000 0 -0.046 2 2
JAK2 0.016 0.053 -10000 0 -0.33 1 1
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
NFKB1 0.013 0.021 -10000 0 -10000 0 0
RELA 0.013 0.021 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.077 0.43 0.68 5 -1 51 56
ALOX12B -0.091 0.44 0.66 5 -1.1 45 50
CXCL1 -0.12 0.46 0.72 3 -1.2 54 57
T cell proliferation -0.12 0.51 0.74 3 -1.2 59 62
NFKBIA 0.011 0.02 -10000 0 -10000 0 0
IL17A -0.022 0.26 0.48 22 -0.55 43 65
PI3K -0.11 0.46 0.6 2 -1.1 59 61
IFNG 0.007 0.046 0.14 24 -0.13 9 33
STAT3 (dimer) -0.1 0.44 0.6 4 -1.1 59 63
IL18R1 0.007 0.069 -10000 0 -0.32 19 19
IL23/IL23R/JAK2/TYK2/SOCS3 -0.062 0.34 0.5 12 -0.85 43 55
IL18/IL18R 0.025 0.085 0.19 1 -0.23 36 37
macrophage activation -0.003 0.024 0.051 28 -0.045 30 58
TNF -0.11 0.48 0.73 4 -1.2 50 54
STAT3/STAT4 -0.11 0.46 0.6 2 -1.1 59 61
STAT4 (dimer) -0.12 0.48 0.63 2 -1.2 59 61
IL18 0.013 0.049 -10000 0 -0.32 9 9
IL19 -0.088 0.43 0.68 4 -1.1 44 48
STAT5A (dimer) -0.12 0.48 0.63 2 -1.2 59 61
STAT1 0.021 0.002 -10000 0 -10000 0 0
SOCS3 0.017 0.032 -10000 0 -0.32 4 4
CXCL9 -0.1 0.46 0.65 9 -1.2 50 59
MPO -0.11 0.45 0.7 3 -1.2 49 52
positive regulation of humoral immune response -0.12 0.51 0.74 3 -1.2 59 62
IL23/IL23R/JAK2/TYK2 -0.14 0.55 0.74 3 -1.3 57 60
IL6 -0.2 0.58 0.66 3 -1.1 108 111
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
IL2 0.013 0.028 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.01 -10000 0 -0.046 2 2
CD3E -0.11 0.44 0.67 2 -1.1 49 51
keratinocyte proliferation -0.12 0.51 0.74 3 -1.2 59 62
NOS2 -0.15 0.5 0.69 4 -1.1 71 75
Arf6 signaling events

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
CENTA1/KIF3B 0.021 0.015 -10000 0 -0.17 1 1
ARNO/beta Arrestin1-2 -0.054 0.17 -10000 0 -0.82 18 18
EGFR 0.015 0.042 0.32 1 -0.32 6 7
EPHA2 0.013 0.048 -10000 0 -0.32 9 9
USP6 0.019 0.006 -10000 0 -10000 0 0
IQSEC1 0.019 0.016 -10000 0 -0.32 1 1
EGFR/EGFR/EGF/EGF 0.053 0.087 0.24 71 -0.24 9 80
ARRB2 0.017 0.037 0.14 38 -10000 0 38
mol:GTP 0.004 0.039 0.13 10 -0.15 8 18
ARRB1 0.018 0.028 -10000 0 -0.32 3 3
FBXO8 0.02 0.004 -10000 0 -10000 0 0
TSHR 0.049 0.09 0.32 46 -10000 0 46
EGF 0.072 0.12 0.32 84 -0.32 4 88
somatostatin receptor activity 0 0 0.001 14 -0.001 70 84
ARAP2 0.01 0.059 -10000 0 -0.32 14 14
mol:GDP -0.061 0.14 0.16 8 -0.28 94 102
mol:PI-3-4-5-P3 0 0 0.001 11 -0.001 35 46
ITGA2B -0.008 0.1 0.32 4 -0.32 42 46
ARF6 0.02 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.039 0.035 -10000 0 -0.18 7 7
ADAP1 0.018 0.017 -10000 0 -0.32 1 1
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET 0.015 0.075 0.23 10 -0.23 32 42
PXN 0.02 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.044 0.12 0.23 12 -0.24 67 79
EGFR/EGFR/EGF/EGF/ARFGEP100 0.056 0.077 0.22 64 -0.19 10 74
ADRB2 -0.11 0.17 -10000 0 -0.32 171 171
receptor agonist activity 0 0 0 6 0 70 76
actin filament binding 0 0 0 11 0 79 90
SRC 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.031 0.074 0.32 22 -0.32 5 27
GNAQ 0.019 0.017 -10000 0 -0.32 1 1
EFA6/PI-4-5-P2 0 0 0.001 15 -0.001 37 52
ARF6/GDP -0.038 0.14 0.33 2 -0.38 49 51
ARF6/GDP/GULP/ACAP1 -0.044 0.14 -10000 0 -0.3 66 66
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.083 0.22 24 -0.18 46 70
ACAP1 0.018 0.017 -10000 0 -0.32 1 1
ACAP2 0.02 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.031 0.071 0.25 40 -10000 0 40
EFNA1 0.017 0.018 -10000 0 -0.32 1 1
HGF 0.008 0.076 0.32 4 -0.32 20 24
CYTH3 -0.007 0.015 0.21 2 -10000 0 2
CYTH2 -0.025 0.19 -10000 0 -0.99 18 18
NCK1 0.02 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 16 0 43 59
endosomal lumen acidification 0 0 0 38 0 28 66
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.02 0.016 -10000 0 -0.32 1 1
GNAQ/ARNO -0.011 0.18 -10000 0 -0.92 18 18
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 9 0 12 21
MET 0.013 0.069 0.32 6 -0.32 14 20
GNA14 0.011 0.055 -10000 0 -0.32 12 12
GNA15 0.019 0.005 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 47 57
GNA11 0.019 0.005 -10000 0 -10000 0 0
LHCGR 0.041 0.087 0.32 40 -10000 0 40
AGTR1 -0.082 0.16 -10000 0 -0.32 138 138
desensitization of G-protein coupled receptor protein signaling pathway 0.031 0.071 0.25 40 -10000 0 40
IPCEF1/ARNO 0.016 0.18 -10000 0 -0.83 18 18
alphaIIb/beta3 Integrin 0.015 0.095 0.23 26 -0.23 46 72
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.069 0.11 0.33 69 -0.22 2 71
NFATC2 0.004 0.14 -10000 0 -0.56 13 13
NFATC3 -0.006 0.084 -10000 0 -0.26 34 34
CD40LG -0.091 0.29 -10000 0 -0.77 58 58
ITCH -0.023 0.075 -10000 0 -0.24 1 1
CBLB -0.026 0.078 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.031 0.25 0.45 13 -0.74 30 43
JUNB 0.017 0.028 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.025 0.098 -10000 0 -0.23 83 83
T cell anergy -0.054 0.14 0.28 4 -0.34 75 79
TLE4 -0.01 0.11 -10000 0 -0.5 12 12
Jun/NFAT1-c-4/p21SNFT -0.037 0.29 0.51 1 -0.78 52 53
AP-1/NFAT1-c-4 -0.053 0.34 0.76 1 -0.86 56 57
IKZF1 -0.006 0.094 -10000 0 -0.43 11 11
T-helper 2 cell differentiation -0.03 0.19 -10000 0 -0.72 20 20
AP-1/NFAT1 0.01 0.13 0.33 3 -0.38 16 19
CALM1 -0.009 0.066 -10000 0 -0.15 83 83
EGR2 -0.086 0.31 -10000 0 -1.1 30 30
EGR3 -0.13 0.4 -10000 0 -1.2 55 55
NFAT1/FOXP3 0.053 0.14 0.4 20 -0.38 11 31
EGR1 0 0.08 -10000 0 -0.32 26 26
JUN 0.011 0.041 -10000 0 -0.33 4 4
EGR4 0.049 0.091 0.32 46 -10000 0 46
mol:Ca2+ -0.023 0.054 -10000 0 -0.14 85 85
GBP3 -0.018 0.13 -10000 0 -0.57 19 19
FOSL1 0.031 0.068 0.32 20 -0.32 3 23
NFAT1-c-4/MAF/IRF4 -0.035 0.28 -10000 0 -0.75 53 53
DGKA -0.007 0.096 0.5 1 -0.4 12 13
CREM 0.02 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.069 0.3 -10000 0 -0.81 56 56
CTLA4 0.013 0.097 0.34 7 -0.31 10 17
NFAT1-c-4 (dimer)/EGR1 -0.06 0.3 -10000 0 -0.82 56 56
NFAT1-c-4 (dimer)/EGR4 -0.034 0.3 -10000 0 -0.78 56 56
FOS -0.008 0.089 -10000 0 -0.33 30 30
IFNG -0.037 0.23 0.36 3 -0.82 23 26
T cell activation -0.037 0.17 -10000 0 -0.74 9 9
MAF 0.019 0.017 -10000 0 -0.32 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.065 0.23 0.67 54 -10000 0 54
TNF -0.08 0.27 0.47 1 -0.76 56 57
FASLG -0.15 0.43 -10000 0 -1.2 59 59
TBX21 0.015 0.076 0.32 2 -0.29 21 23
BATF3 0.02 0.015 0.32 1 -10000 0 1
PRKCQ -0.024 0.12 -10000 0 -0.33 60 60
PTPN1 -0.008 0.096 0.34 1 -0.43 10 11
NFAT1-c-4/ICER1 -0.049 0.28 -10000 0 -0.76 56 56
GATA3 0.02 0.022 0.32 1 -0.32 1 2
T-helper 1 cell differentiation -0.037 0.22 0.36 3 -0.8 23 26
IL2RA -0.019 0.26 0.47 22 -0.72 31 53
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.008 0.093 -10000 0 -0.43 10 10
E2F1 0.024 0.029 0.32 4 -10000 0 4
PPARG -0.02 0.11 -10000 0 -0.32 54 54
SLC3A2 -0.007 0.092 -10000 0 -0.41 11 11
IRF4 0.024 0.056 0.32 11 -0.32 4 15
PTGS2 -0.094 0.29 0.5 1 -0.8 52 53
CSF2 -0.093 0.29 0.46 4 -0.78 57 61
JunB/Fra1/NFAT1-c-4 -0.035 0.28 0.54 1 -0.75 56 57
IL4 -0.032 0.2 -10000 0 -0.75 20 20
IL5 -0.087 0.28 -10000 0 -0.76 56 56
IL2 -0.038 0.17 -10000 0 -0.76 9 9
IL3 -0.024 0.12 -10000 0 -0.6 14 14
RNF128 -0.068 0.17 -10000 0 -0.43 83 83
NFATC1 -0.066 0.24 -10000 0 -0.67 54 54
CDK4 0.047 0.16 0.58 18 -10000 0 18
PTPRK -0.006 0.091 -10000 0 -0.44 9 9
IL8 -0.081 0.29 0.46 6 -0.76 56 62
POU2F1 0.019 0.006 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.024 0.038 -10000 0 -0.23 10 10
alphaV beta3 Integrin 0.018 0.091 0.22 20 -0.2 58 78
PTK2 -0.041 0.13 0.35 10 -0.35 27 37
IGF1R 0.019 0.023 -10000 0 -0.32 2 2
PI4KB 0.017 0.008 -10000 0 -10000 0 0
MFGE8 0.02 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
CDKN1B -0.056 0.16 0.17 5 -0.41 72 77
VEGFA 0.02 0.004 -10000 0 -10000 0 0
ILK -0.059 0.16 0.17 5 -0.41 76 81
ROCK1 0.02 0.004 -10000 0 -10000 0 0
AKT1 -0.064 0.14 -10000 0 -0.39 72 72
PTK2B -0.012 0.055 0.17 25 -0.3 1 26
alphaV/beta3 Integrin/JAM-A -0.003 0.11 0.22 23 -0.2 86 109
CBL 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.053 0.059 0.22 42 -0.19 5 47
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.045 0.041 0.22 1 -0.19 11 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.022 0.081 -10000 0 -0.3 13 13
alphaV/beta3 Integrin/Syndecan-1 0.046 0.047 0.22 22 -0.2 5 27
PI4KA 0.02 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.016 0.089 -10000 0 -0.19 56 56
PI4 Kinase 0.025 0.012 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.17 0.1 0.23 322 -0.18 5 327
RPS6KB1 -0.044 0.072 0.31 3 -0.36 7 10
TLN1 0.019 0.017 -10000 0 -0.32 1 1
MAPK3 -0.057 0.14 0.28 1 -0.44 49 50
GPR124 0.017 0.024 -10000 0 -0.32 2 2
MAPK1 -0.054 0.14 0.28 2 -0.43 49 51
PXN 0.02 0.003 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
alphaV/beta3 Integrin/Tumstatin -0.019 0.12 0.22 18 -0.2 129 147
cell adhesion 0.039 0.054 0.22 22 -0.2 7 29
ANGPTL3 0.033 0.064 0.32 22 -10000 0 22
VEGFR2 homodimer/VEGFA homodimer/Src 0.034 0.034 -10000 0 -0.2 9 9
IGF-1R heterotetramer 0.019 0.023 -10000 0 -0.32 2 2
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.045 -10000 0 -0.32 8 8
ITGB3 0.031 0.074 0.32 22 -0.32 5 27
IGF1 0.014 0.05 0.32 1 -0.32 9 10
RAC1 0.018 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.04 0.051 0.22 20 -0.22 6 26
apoptosis 0.021 0.002 -10000 0 -10000 0 0
CD47 0.019 0.023 -10000 0 -0.32 2 2
alphaV/beta3 Integrin/CD47 0.045 0.05 0.22 22 -0.2 7 29
VCL 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.027 0.081 0.23 19 -0.21 37 56
CSF1 0.018 0.028 -10000 0 -0.32 3 3
PIK3C2A -0.059 0.16 -10000 0 -0.41 76 76
PI4 Kinase/Pyk2 -0.053 0.072 0.11 17 -0.28 16 33
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.059 0.22 22 -0.19 14 36
FAK1/Vinculin -0.033 0.11 0.32 10 -0.3 22 32
alphaV beta3/Integrin/ppsTEM5 0.04 0.051 0.22 20 -0.22 6 26
RHOA 0.02 0.004 -10000 0 -10000 0 0
VTN -0.034 0.14 0.32 6 -0.32 79 85
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
FGF2 -0.022 0.11 -10000 0 -0.32 57 57
F11R -0.034 0.062 -10000 0 -0.23 42 42
alphaV/beta3 Integrin/Lactadherin 0.046 0.047 0.22 22 -0.2 5 27
alphaV/beta3 Integrin/TGFBR2 0.041 0.057 0.22 22 -0.2 13 35
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.045 0.027 -10000 0 -0.18 4 4
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.042 0.046 0.21 21 -0.19 5 26
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.032 -10000 0 -0.32 4 4
alphaV/beta3 Integrin/Pyk2 0.031 0.058 0.21 19 -0.18 13 32
SDC1 0.021 0.002 -10000 0 -10000 0 0
VAV3 -0.019 0.044 0.17 19 -0.32 1 20
PTPN11 0.02 0.003 -10000 0 -10000 0 0
IRS1 0.02 0.016 -10000 0 -0.32 1 1
FAK1/Paxillin -0.034 0.11 0.31 9 -0.3 23 32
cell migration -0.034 0.1 0.29 10 -0.28 22 32
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.004 0.1 0.28 2 -0.2 73 75
SPP1 0.24 0.14 0.32 332 -10000 0 332
KDR 0.013 0.05 -10000 0 -0.32 10 10
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.002 -10000 0 -10000 0 0
COL4A3 -0.075 0.15 -10000 0 -0.32 129 129
angiogenesis -0.055 0.16 0.28 2 -0.45 47 49
Rac1/GTP -0.019 0.041 0.16 17 -0.28 1 18
EDIL3 -0.005 0.092 0.32 1 -0.32 35 36
cell proliferation 0.041 0.057 0.22 22 -0.19 13 35
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.025 0.071 -10000 0 -0.24 24 24
NT3 (dimer)/TRKC -0.029 0.12 0.23 2 -0.25 98 100
NT3 (dimer)/TRKB -0.045 0.13 0.3 7 -0.21 163 170
SHC/Grb2/SOS1/GAB1/PI3K 0.01 0.021 -10000 0 -0.18 5 5
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 231 231
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
NTRK1 0.009 0.059 0.32 1 -0.32 13 14
NTRK2 -0.091 0.16 0.32 3 -0.32 153 156
NTRK3 -0.048 0.14 -10000 0 -0.32 92 92
NT-4/5 (dimer)/TRKB -0.046 0.13 0.28 6 -0.21 167 173
neuron apoptosis 0.14 0.16 0.39 106 -0.21 1 107
SHC 2-3/Grb2 -0.16 0.18 -10000 0 -0.43 106 106
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 -0.11 0.15 -10000 0 -0.42 60 60
SHC3 -0.16 0.21 0.2 1 -0.51 108 109
STAT3 (dimer) 0.018 0.037 -10000 0 -0.3 6 6
NT3 (dimer)/TRKA 0.021 0.072 0.27 7 -0.2 32 39
RIN/GDP -0.019 0.075 0.33 2 -0.22 14 16
GIPC1 0.02 0.005 -10000 0 -10000 0 0
KRAS 0.019 0.006 -10000 0 -10000 0 0
DNAJA3 -0.015 0.055 0.17 3 -0.21 23 26
RIN/GTP 0.013 0.014 0.22 2 -10000 0 2
CCND1 -0.021 0.065 -10000 0 -0.59 6 6
MAGED1 0.021 0.014 0.32 1 -10000 0 1
PTPN11 0.02 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.076 -10000 0 -0.32 24 24
SHC/GRB2/SOS1 0.034 0.017 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.023 0.073 0.22 14 -0.2 34 48
TRKA/NEDD4-2 0.018 0.045 0.23 1 -0.23 13 14
ELMO1 0.018 0.023 -10000 0 -0.32 2 2
RhoG/GTP/ELMO1/DOCK1 0.024 0.017 -10000 0 -0.19 2 2
NGF 0.023 0.084 0.32 19 -0.32 13 32
HRAS 0.02 0.004 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
GAB2 0.017 0.032 -10000 0 -0.32 4 4
RIT2 0.017 0.021 0.32 2 -10000 0 2
RIT1 0.018 0.007 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
DNM1 0.023 0.031 0.32 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.005 0.063 0.18 2 -0.25 13 15
mol:GDP -0.033 0.1 0.4 2 -0.31 17 19
NGF (dimer) 0.022 0.084 0.32 19 -0.32 13 32
RhoG/GDP 0.013 0.016 -10000 0 -0.22 2 2
RIT1/GDP -0.026 0.062 -10000 0 -0.23 10 10
TIAM1 0.016 0.039 -10000 0 -0.32 6 6
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
BDNF (dimer)/TRKB -0.14 0.14 0.22 1 -0.24 299 300
KIDINS220/CRKL/C3G 0.029 0.008 -10000 0 -10000 0 0
SHC/RasGAP 0.025 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2 0.038 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.042 0.024 -10000 0 -0.18 1 1
RIT1/GTP 0.013 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.004 0.077 0.32 2 -0.32 23 25
RAP1/GDP -0.023 0.06 -10000 0 -0.18 16 16
KIDINS220/CRKL 0.02 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.15 0.17 -10000 0 -0.32 231 231
ubiquitin-dependent protein catabolic process 0.027 0.061 0.22 15 -0.19 22 37
Schwann cell development -0.036 0.025 -10000 0 -10000 0 0
EHD4 0.02 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.046 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.044 -10000 0 -0.18 10 10
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.14 -10000 0 -0.24 280 280
ABL1 0.02 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.07 0.095 -10000 0 -0.39 18 18
STAT3 0.018 0.036 -10000 0 -0.3 6 6
axon guidance -0.16 0.12 -10000 0 -0.24 278 278
MAPK3 -0.014 0.073 0.18 34 -0.19 28 62
MAPK1 -0.012 0.072 0.18 35 -0.19 23 58
CDC42/GDP -0.02 0.076 0.34 2 -0.21 16 18
NTF3 0.004 0.078 0.32 2 -0.32 23 25
NTF4 0.002 0.076 -10000 0 -0.32 24 24
NGF (dimer)/TRKA/FAIM 0.031 0.062 0.22 17 -0.19 21 38
PI3K 0.028 0.015 -10000 0 -0.23 1 1
FRS3 0.02 0.004 -10000 0 -10000 0 0
FAIM 0.02 0.003 -10000 0 -10000 0 0
GAB1 0.02 0.016 -10000 0 -0.32 1 1
RASGRF1 -0.059 0.088 0.15 1 -0.27 33 34
SOS1 0.021 0.003 -10000 0 -10000 0 0
MCF2L -0.054 0.083 0.2 2 -0.21 90 92
RGS19 0.019 0.006 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.076 0.27 1 -0.37 5 6
Rac1/GDP -0.022 0.069 -10000 0 -0.22 14 14
NGF (dimer)/TRKA/GRIT 0.02 0.058 0.21 17 -0.18 22 39
neuron projection morphogenesis 0.003 0.1 -10000 0 -0.88 3 3
NGF (dimer)/TRKA/NEDD4-2 0.027 0.062 0.22 15 -0.19 22 37
MAP2K1 0.014 0.093 0.2 84 -0.17 1 85
NGFR 0.019 0.058 0.32 7 -0.32 8 15
NGF (dimer)/TRKA/GIPC/GAIP 0.004 0.057 0.18 4 -0.22 19 23
RAS family/GTP/PI3K 0.009 0.02 -10000 0 -0.17 5 5
FRS2 family/SHP2/GRB2/SOS1 0.053 0.024 -10000 0 -10000 0 0
NRAS 0.02 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.028 -10000 0 -0.32 3 3
MAPKKK cascade -0.066 0.18 -10000 0 -0.56 51 51
RASA1 0.02 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.02 0.044 0.23 1 -0.23 13 14
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.14 0.22 2 -0.22 300 302
NGF (dimer)/TRKA/p62/Atypical PKCs 0.041 0.064 -10000 0 -0.18 21 21
MATK 0.008 0.063 -10000 0 -0.32 16 16
NEDD4L 0.019 0.006 -10000 0 -10000 0 0
RAS family/GDP -0.03 0.045 -10000 0 -0.17 15 15
NGF (dimer)/TRKA -0.001 0.061 0.18 4 -0.21 25 29
Rac1/GTP -0.061 0.07 -10000 0 -0.24 35 35
FRS2 family/SHP2/CRK family 0.049 0.027 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.021 0.039 -10000 0 -0.2 21 21
ADCY5 -0.032 0.061 0.091 7 -0.2 54 61
ADCY6 -0.014 0.016 -10000 0 -0.19 4 4
ADCY7 -0.014 0.017 -10000 0 -0.19 4 4
ADCY1 -0.012 0.029 0.18 5 -0.19 6 11
ADCY2 -0.019 0.05 0.12 10 -0.19 30 40
ADCY3 -0.015 0.016 -10000 0 -0.19 4 4
ADCY8 -0.071 0.086 0.091 1 -0.19 158 159
PRKCE -0.01 0.02 -10000 0 -0.22 4 4
ADCY9 -0.017 0.028 -10000 0 -0.19 12 12
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.004 0.11 0.21 50 -0.26 12 62
TCGA08_retinoblastoma

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
CDKN2B 0.012 0.036 -10000 0 -0.29 5 5
CDKN2C 0 0.031 0.33 1 -10000 0 1
CDKN2A 0.099 0.14 0.32 126 -10000 0 126
CCND2 -0.021 0.042 0.16 3 -0.16 9 12
RB1 0.021 0.047 0.22 5 -0.16 3 8
CDK4 -0.023 0.047 0.17 4 -0.21 4 8
CDK6 -0.023 0.046 0.17 3 -0.21 5 8
G1/S progression 0.006 0.091 0.18 76 -0.25 7 83
Glucocorticoid receptor regulatory network

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
PCK2 0.026 0.082 -10000 0 -0.32 1 1
SMARCC2 0.02 0.009 -10000 0 -0.16 1 1
SMARCC1 0.02 0.007 -10000 0 -10000 0 0
TBX21 -0.041 0.16 0.34 5 -0.5 33 38
SUMO2 0.018 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.022 0.002 -10000 0 -10000 0 0
FKBP4 0.02 0.005 -10000 0 -10000 0 0
FKBP5 0.019 0.016 -10000 0 -0.32 1 1
GR alpha/HSP90/FKBP51/HSP90 0.046 0.11 0.27 33 -10000 0 33
PRL -0.019 0.11 0.36 7 -0.35 7 14
cortisol/GR alpha (dimer)/TIF2 0.062 0.21 0.49 54 -0.36 6 60
RELA -0.038 0.1 -10000 0 -0.21 94 94
FGG 0.027 0.28 0.5 70 -0.4 63 133
GR beta/TIF2 0.035 0.11 0.28 33 -0.24 2 35
IFNG -0.055 0.26 0.42 13 -0.64 43 56
apoptosis 0.008 0.14 0.46 12 -0.47 10 22
CREB1 0.039 0.045 0.19 1 -10000 0 1
histone acetylation -0.073 0.12 -10000 0 -0.31 49 49
BGLAP -0.02 0.11 -10000 0 -0.38 5 5
GR/PKAc 0.05 0.11 0.28 28 -10000 0 28
NF kappa B1 p50/RelA -0.067 0.18 0.29 1 -0.33 128 129
SMARCD1 0.021 0.006 -10000 0 -10000 0 0
MDM2 0.036 0.086 0.22 51 -10000 0 51
GATA3 0.021 0.022 0.32 1 -0.32 1 2
AKT1 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.12 0.26 -10000 0 -0.86 42 42
GSK3B 0.018 0.013 -10000 0 -10000 0 0
NR1I3 0.022 0.14 0.47 9 -0.48 3 12
CSN2 0.055 0.18 0.37 61 -0.31 9 70
BRG1/BAF155/BAF170/BAF60A 0.048 0.027 -10000 0 -0.26 2 2
NFATC1 0.018 0.023 -10000 0 -0.32 2 2
POU2F1 0.022 0.018 -10000 0 -10000 0 0
CDKN1A -0.006 0.069 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 8 -0.32 1 9
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.054 0.1 0.27 28 -10000 0 28
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.016 0.2 0.45 9 -0.69 28 37
JUN -0.015 0.18 0.33 28 -0.38 38 66
IL4 -0.035 0.12 -10000 0 -0.46 11 11
CDK5R1 0.026 0.049 0.32 12 -10000 0 12
PRKACA 0.02 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.041 0.064 0.17 2 -0.24 20 22
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.048 0.1 0.28 25 -10000 0 25
cortisol/GR alpha (monomer) 0.09 0.27 0.58 66 -0.4 9 75
NCOA2 0.016 0.032 -10000 0 -0.32 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.008 0.11 0.23 11 -0.34 21 32
AP-1/NFAT1-c-4 -0.01 0.27 0.42 33 -0.49 54 87
AFP -0.015 0.16 0.4 15 -0.44 7 22
SUV420H1 0.02 0.003 -10000 0 -10000 0 0
IRF1 0.053 0.14 0.38 25 -10000 0 25
TP53 0.021 0.044 -10000 0 -0.92 1 1
PPP5C 0.02 0.005 -10000 0 -10000 0 0
KRT17 -0.062 0.3 0.44 23 -0.75 47 70
KRT14 0.035 0.18 0.4 13 -0.43 3 16
TBP 0.021 0.007 -10000 0 -10000 0 0
CREBBP -0.019 0.069 -10000 0 -0.27 1 1
HDAC1 0.02 0.002 -10000 0 -10000 0 0
HDAC2 0.023 0.022 -10000 0 -10000 0 0
AP-1 -0.01 0.27 0.42 33 -0.49 55 88
MAPK14 0.018 0.013 -10000 0 -10000 0 0
MAPK10 -0.018 0.11 -10000 0 -0.32 51 51
MAPK11 0.016 0.026 -10000 0 -0.32 2 2
KRT5 -0.2 0.45 0.44 16 -0.9 122 138
interleukin-1 receptor activity 0.004 0.02 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
STAT1 0.022 0.002 -10000 0 -10000 0 0
CGA -0.003 0.13 0.34 13 -0.37 9 22
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.005 0.17 0.45 33 -0.34 7 40
MAPK3 0.019 0.013 -10000 0 -10000 0 0
MAPK1 0.018 0.013 -10000 0 -10000 0 0
ICAM1 -0.11 0.22 -10000 0 -0.54 61 61
NFKB1 -0.038 0.1 0.18 1 -0.2 105 106
MAPK8 -0.019 0.16 0.3 13 -0.35 47 60
MAPK9 0.019 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.007 0.14 0.46 12 -0.49 10 22
BAX -0.009 0.06 -10000 0 -10000 0 0
POMC -0.12 0.28 -10000 0 -0.98 30 30
EP300 -0.018 0.07 -10000 0 -0.27 1 1
cortisol/GR alpha (dimer)/p53 0.074 0.22 0.52 52 -0.38 2 54
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.073 0.2 30 -10000 0 30
SGK1 -0.025 0.11 -10000 0 -0.77 3 3
IL13 -0.052 0.19 -10000 0 -0.55 24 24
IL6 -0.2 0.37 -10000 0 -0.79 118 118
PRKACG 0.017 0.004 -10000 0 -10000 0 0
IL5 -0.048 0.17 -10000 0 -0.59 8 8
IL2 -0.06 0.23 0.41 1 -0.6 34 35
CDK5 0.019 0.01 -10000 0 -10000 0 0
PRKACB 0.021 0.015 0.32 1 -10000 0 1
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 -0.095 0.21 0.34 3 -0.53 50 53
CDK5R1/CDK5 0.032 0.035 0.24 11 -10000 0 11
NF kappa B1 p50/RelA/PKAc -0.029 0.15 0.26 1 -0.28 87 88
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.072 0.21 0.48 59 -0.34 5 64
SMARCA4 0.019 0.017 -10000 0 -0.32 1 1
chromatin remodeling 0.044 0.13 0.33 39 -10000 0 39
NF kappa B1 p50/RelA/Cbp -0.072 0.17 0.37 1 -0.34 76 77
JUN (dimer) -0.014 0.18 0.33 28 -0.38 38 66
YWHAH 0.02 0.004 -10000 0 -10000 0 0
VIPR1 -0.26 0.34 -10000 0 -0.68 186 186
NR3C1 0.057 0.17 0.38 57 -0.26 1 58
NR4A1 -0.06 0.16 -10000 0 -0.35 103 103
TIF2/SUV420H1 0.025 0.026 -10000 0 -0.23 4 4
MAPKKK cascade 0.008 0.14 0.46 12 -0.47 10 22
cortisol/GR alpha (dimer)/Src-1 0.081 0.23 0.51 61 -0.36 5 66
PBX1 0.014 0.055 -10000 0 -0.32 11 11
POU1F1 0.021 0.024 0.42 1 -10000 0 1
SELE -0.18 0.35 -10000 0 -0.82 96 96
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.044 0.13 0.33 39 -10000 0 39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.072 0.21 0.48 59 -0.34 5 64
mol:cortisol 0.05 0.15 0.35 64 -0.22 7 71
MMP1 0.16 0.19 0.38 68 -0.69 6 74
HIF-2-alpha transcription factor network

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
MMP14 0.02 0.07 0.42 2 -0.54 5 7
oxygen homeostasis 0.009 0.014 -10000 0 -10000 0 0
TCEB2 0.02 0.003 -10000 0 -10000 0 0
TCEB1 0.019 0.015 0.32 1 -10000 0 1
VHL/Elongin B/Elongin C/HIF2A 0.068 0.1 0.28 12 -0.3 4 16
EPO 0.098 0.15 0.4 51 -0.38 1 52
FIH (dimer) 0.026 0.021 -10000 0 -10000 0 0
APEX1 0.028 0.025 -10000 0 -10000 0 0
SERPINE1 0.1 0.16 0.41 58 -0.4 1 59
FLT1 -0.007 0.13 -10000 0 -0.58 17 17
ADORA2A 0.097 0.15 0.38 55 -0.39 1 56
germ cell development 0.11 0.17 0.4 66 -0.4 4 70
SLC11A2 0.1 0.16 0.4 61 -0.4 1 62
BHLHE40 0.11 0.16 0.42 49 -0.4 1 50
HIF1AN 0.026 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.08 0.12 0.34 32 -0.29 1 33
ETS1 0.019 0.025 -10000 0 -0.36 1 1
CITED2 -0.016 0.14 -10000 0 -0.53 28 28
KDR -0.005 0.15 -10000 0 -0.75 17 17
PGK1 0.11 0.16 0.4 63 -0.4 1 64
SIRT1 0.021 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.13 0.19 0.54 43 -0.44 1 44
EPAS1 0.049 0.099 0.25 42 -0.25 8 50
SP1 0.023 0.01 0.15 2 -10000 0 2
ABCG2 0.094 0.18 0.4 63 -0.42 11 74
EFNA1 0.089 0.15 0.4 48 -0.4 1 49
FXN 0.098 0.15 0.37 62 -0.38 1 63
POU5F1 0.1 0.17 0.41 65 -0.41 4 69
neuron apoptosis -0.13 0.19 0.44 1 -0.53 43 44
EP300 0.02 0.004 -10000 0 -10000 0 0
EGLN3 0.089 0.13 0.34 102 -0.32 1 103
EGLN2 0.026 0.022 -10000 0 -10000 0 0
EGLN1 0.024 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.036 0.018 0.22 1 -10000 0 1
VHL 0.02 0.004 -10000 0 -10000 0 0
ARNT 0.024 0.025 -10000 0 -10000 0 0
SLC2A1 0.14 0.19 0.42 103 -0.39 1 104
TWIST1 0.11 0.18 0.43 77 -10000 0 77
ELK1 0.021 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.086 0.12 0.35 31 -0.29 2 33
VEGFA 0.1 0.16 0.4 61 -0.4 1 62
CREBBP 0.02 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.006 0.097 -10000 0 -0.41 20 20
HDAC1 0.02 0.005 -10000 0 -10000 0 0
AES 0.019 0.006 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
DTX1 0.022 0.02 0.32 2 -10000 0 2
LRP6/FZD1 0.028 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.004 -10000 0 -10000 0 0
AP1 -0.026 0.088 -10000 0 -0.23 62 62
NCSTN 0.018 0.007 -10000 0 -10000 0 0
ADAM10 0.02 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.1 -10000 0 -0.66 8 8
NICD/RBPSUH 0.005 0.097 -10000 0 -0.41 20 20
WIF1 -0.21 0.16 -10000 0 -0.32 309 309
NOTCH1 -0.003 0.087 -10000 0 -0.43 18 18
PSENEN 0.019 0.005 -10000 0 -10000 0 0
KREMEN2 0.096 0.13 0.32 117 -10000 0 117
DKK1 0.037 0.16 0.32 76 -0.32 44 120
beta catenin/beta TrCP1 0.014 0.072 0.3 1 -0.3 3 4
APH1B 0.019 0.023 -10000 0 -0.32 2 2
APH1A 0.017 0.008 -10000 0 -10000 0 0
AXIN1 0.001 0.07 -10000 0 -0.44 6 6
CtBP/CBP/TCF1/TLE1/AES 0.021 0.054 0.2 6 -0.19 1 7
PSEN1 0.02 0.004 -10000 0 -10000 0 0
FOS -0.002 0.085 -10000 0 -0.32 30 30
JUN 0.017 0.032 -10000 0 -0.32 4 4
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
CTNNB1 0.01 0.072 0.27 2 -0.32 3 5
MAPK3 0.021 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.12 0.22 75 -0.17 82 157
HNF1A 0.076 0.12 0.32 88 -0.32 1 89
CTBP1 0.02 0.004 -10000 0 -10000 0 0
MYC 0.008 0.081 -10000 0 -1.2 2 2
NKD1 -0.017 0.11 0.32 4 -0.32 53 57
FZD1 0.02 0.005 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.007 0.096 -10000 0 -0.42 19 19
apoptosis -0.026 0.087 -10000 0 -0.23 62 62
Delta 1/NOTCHprecursor 0.004 0.097 -10000 0 -0.41 20 20
DLL1 0.015 0.039 -10000 0 -0.32 6 6
PPARD 0.015 0.043 -10000 0 -0.84 1 1
Gamma Secretase 0.045 0.031 -10000 0 -0.17 1 1
APC -0.007 0.091 -10000 0 -0.44 13 13
DVL1 -0.032 0.065 -10000 0 -0.27 26 26
CSNK2A1 0.02 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.082 0.13 0.25 143 -0.18 42 185
LRP6 0.019 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.005 -10000 0 -10000 0 0
NLK 0.006 0.005 -10000 0 -10000 0 0
CCND1 -0.001 0.14 -10000 0 -1.1 8 8
WNT1 0.025 0.037 0.32 7 -10000 0 7
Axin1/APC/beta catenin 0.006 0.1 0.29 8 -0.41 11 19
DKK2 -0.046 0.14 -10000 0 -0.32 89 89
NOTCH1 precursor/DVL1 -0.031 0.11 -10000 0 -0.44 20 20
GSK3B 0.02 0.003 -10000 0 -10000 0 0
FRAT1 0.02 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.01 0.097 -10000 0 -0.42 19 19
PPP2R5D 0.011 0.071 0.22 1 -0.32 6 7
MAPK1 0.02 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.094 0.11 0.22 2 -0.18 284 286
RBPJ 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.034 0.032 0.23 11 -10000 0 11
VLDLR 0.013 0.045 -10000 0 -0.32 8 8
CRKL 0.02 0.004 -10000 0 -10000 0 0
LRPAP1 0.02 0.003 -10000 0 -10000 0 0
FYN 0.018 0.017 -10000 0 -0.32 1 1
ITGA3 0.017 0.032 -10000 0 -0.32 4 4
RELN/VLDLR/Fyn 0.005 0.085 0.22 5 -0.2 60 65
MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.029 -10000 0 -0.17 1 1
AKT1 -0.033 0.073 0.2 3 -0.21 54 57
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
DAB1 0.023 0.037 0.32 7 -10000 0 7
RELN/LRP8/DAB1 0.018 0.079 0.22 17 -0.17 56 73
LRPAP1/LRP8 0.033 0.027 0.23 8 -10000 0 8
RELN/LRP8/DAB1/Fyn 0.022 0.079 0.22 16 -0.17 54 70
DAB1/alpha3/beta1 Integrin 0.014 0.077 0.27 1 -0.18 53 54
long-term memory 0.009 0.1 0.25 14 -0.18 78 92
DAB1/LIS1 0.022 0.083 0.35 1 -0.18 53 54
DAB1/CRLK/C3G 0.015 0.076 0.27 1 -0.18 50 51
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.027 0.084 0.35 1 -0.17 53 54
ARHGEF2 0.018 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.009 0.14 0.32 38 -0.32 48 86
CDK5R1 0.028 0.048 0.32 12 -10000 0 12
RELN -0.019 0.12 0.32 5 -0.32 56 61
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
RELN/LRP8/Fyn 0.013 0.085 0.22 13 -0.2 56 69
GRIN2A/RELN/LRP8/DAB1/Fyn 0.02 0.11 0.23 39 -0.18 83 122
MAPK8 0.02 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.01 0.079 0.23 9 -0.18 59 68
ITGB1 0.02 0.003 -10000 0 -10000 0 0
MAP1B -0.028 0.076 0.17 23 -0.19 53 76
RELN/LRP8 0.016 0.083 0.22 12 -0.19 55 67
GRIN2B/RELN/LRP8/DAB1/Fyn 0.03 0.089 0.25 20 -0.17 52 72
PI3K 0.028 0.015 -10000 0 -0.23 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.027 0.025 -10000 0 -0.23 4 4
RAP1A -0.032 0.073 0.23 6 -0.28 3 9
PAFAH1B1 0.019 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.02 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.029 0.008 -10000 0 -10000 0 0
GRIN2B 0.023 0.042 0.32 9 -10000 0 9
NCK2 0.021 0.002 -10000 0 -10000 0 0
neuron differentiation -0.008 0.074 0.21 3 -0.28 11 14
neuron adhesion -0.033 0.083 0.28 9 -0.28 3 12
LRP8 0.026 0.042 0.32 9 -10000 0 9
GSK3B -0.035 0.069 0.18 3 -0.2 54 57
RELN/VLDLR/DAB1/Fyn 0.015 0.079 0.23 8 -0.18 57 65
MAP3K11 0.02 0.016 -10000 0 -0.32 1 1
RELN/VLDLR/DAB1/P13K -0.017 0.079 0.2 1 -0.21 59 60
CDK5 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.005 0.12 0.77 8 -0.29 22 30
neuron migration -0.038 0.099 0.23 11 -0.26 49 60
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.006 0.07 0.24 2 -0.26 9 11
RELN/VLDLR 0.019 0.086 0.22 11 -0.19 59 70
TCGA08_p53

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
CDKN2A 0.04 0.074 0.16 129 -10000 0 129
TP53 0.011 0.037 -10000 0 -0.12 18 18
Senescence 0.011 0.037 -10000 0 -0.12 18 18
Apoptosis 0.011 0.037 -10000 0 -0.12 18 18
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.024 0.073 0.26 18 -0.19 3 21
MDM4 0.019 0.006 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 0.012 0.28 0.57 20 -0.65 8 28
CRP 0.027 0.29 0.6 25 -0.76 5 30
cell cycle arrest 0.001 0.3 0.54 30 -0.62 29 59
TIMP1 0.017 0.26 0.53 22 -0.62 12 34
IL6ST 0.004 0.069 -10000 0 -0.32 17 17
Rac1/GDP -0.002 0.14 0.32 16 -0.31 33 49
AP1 0.054 0.13 0.38 7 -0.44 8 15
GAB2 0.019 0.033 -10000 0 -0.32 4 4
TNFSF11 0.035 0.3 0.58 35 -0.67 8 43
HSP90B1 0.019 0.15 0.45 1 -0.7 12 13
GAB1 0.021 0.017 -10000 0 -0.32 1 1
MAPK14 -0.028 0.1 0.27 4 -0.4 14 18
AKT1 0.012 0.084 0.26 5 -0.52 6 11
FOXO1 0.011 0.082 0.32 2 -0.54 5 7
MAP2K6 -0.018 0.12 0.26 13 -0.29 38 51
mol:GTP 0 0.004 -10000 0 -10000 0 0
MAP2K4 0 0.18 0.35 26 -0.37 29 55
MITF -0.01 0.13 0.28 20 -0.3 37 57
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.005 -10000 0 -10000 0 0
A2M -0.12 0.39 -10000 0 -1.2 53 53
CEBPB 0.024 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.017 0.09 0.28 4 -0.36 9 13
STAT3 -0.005 0.31 0.56 26 -0.65 29 55
STAT1 0.023 0.037 -10000 0 -10000 0 0
CEBPD 0.018 0.29 0.58 25 -0.74 9 34
PIK3CA 0.02 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.015 -10000 0 -0.23 1 1
JUN 0.018 0.032 -10000 0 -0.32 4 4
PIAS3/MITF -0.003 0.13 0.27 14 -0.29 34 48
MAPK11 -0.027 0.1 0.27 3 -0.4 14 17
STAT3 (dimer)/FOXO1 -0.017 0.26 0.49 24 -0.63 15 39
GRB2/SOS1/GAB family 0.005 0.12 0.28 4 -0.26 39 43
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.02 0.11 0.24 4 -0.26 61 65
GRB2 0.021 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.017 -10000 0 -0.32 1 1
LBP 0.049 0.27 0.54 49 -0.6 10 59
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
JAK1 0.013 0.025 -10000 0 -10000 0 0
MYC 0.031 0.29 0.58 29 -0.69 9 38
FGG -0.15 0.51 0.58 29 -0.9 134 163
macrophage differentiation 0.001 0.3 0.54 30 -0.62 29 59
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0 0.098 0.24 2 -0.2 52 54
JUNB 0.001 0.27 0.53 20 -0.68 11 31
FOS -0.002 0.085 -10000 0 -0.32 30 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.14 0.29 23 -0.3 39 62
STAT1/PIAS1 0.013 0.16 0.33 28 -0.31 30 58
GRB2/SOS1/GAB family/SHP2/PI3K 0.016 0.083 -10000 0 -0.47 8 8
STAT3 (dimer) -0.003 0.31 0.55 29 -0.64 29 58
PRKCD 0.019 0.23 0.42 46 -0.44 26 72
IL6R 0.004 0.051 -10000 0 -0.32 9 9
SOCS3 -0.025 0.14 0.34 1 -0.76 7 8
gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.071 0.24 2 -0.19 13 15
Rac1/GTP -0.002 0.16 0.34 16 -0.33 33 49
HCK 0.008 0.064 -10000 0 -0.32 17 17
MAPKKK cascade 0.033 0.11 0.34 1 -0.48 10 11
bone resorption 0.039 0.3 0.57 36 -0.64 8 44
IRF1 0.005 0.28 0.55 19 -0.66 9 28
mol:GDP -0.001 0.13 0.29 20 -0.3 33 53
SOS1 0.023 0.007 -10000 0 -10000 0 0
VAV1 -0.006 0.13 0.27 26 -0.3 33 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.023 0.11 -10000 0 -0.43 19 19
PTPN11 0.011 0.1 -10000 0 -0.71 8 8
IL6/IL6RA -0.017 0.099 0.17 1 -0.23 73 74
gp130 (dimer)/TYK2/TYK2/LMO4 0.026 0.06 0.2 1 -0.18 18 19
gp130 (dimer)/JAK2/JAK2/LMO4 0.025 0.059 0.2 1 -0.18 16 17
IL6 -0.046 0.14 0.14 1 -0.32 88 89
PIAS3 0.02 0.004 -10000 0 -10000 0 0
PTPRE -0.002 0.043 -10000 0 -0.27 3 3
PIAS1 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.018 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.022 0.11 0.24 3 -0.26 59 62
LMO4 0.016 0.035 0.14 1 -0.29 1 2
STAT3 (dimer)/PIAS3 -0.022 0.28 0.5 21 -0.61 30 51
MCL1 0.04 0.11 0.4 5 -0.53 4 9
Aurora A signaling

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.006 0.054 -10000 0 -10000 0 0
BIRC5 0.18 0.15 0.32 254 -10000 0 254
NFKBIA 0.002 0.076 0.28 26 -10000 0 26
CPEB1 -0.025 0.12 0.32 2 -0.32 63 65
AKT1 -0.014 0.045 0.28 3 -10000 0 3
NDEL1 0.019 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.004 0.05 0.24 1 -10000 0 1
NDEL1/TACC3 0.001 0.053 -10000 0 -10000 0 0
GADD45A 0.02 0.003 -10000 0 -10000 0 0
GSK3B -0.016 0.031 -10000 0 -10000 0 0
PAK1/Aurora A -0.006 0.054 -10000 0 -10000 0 0
MDM2 0.02 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.083 0.094 0.16 254 -10000 0 254
TP53 -0.003 0.055 0.21 1 -0.22 18 19
DLG7 -0.011 0.036 0.16 1 -10000 0 1
AURKAIP1 0.019 0.016 -10000 0 -0.32 1 1
ARHGEF7 0.019 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.001 0.056 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.05 0.24 1 -10000 0 1
AURKA -0.005 0.054 0.2 1 -10000 0 1
AURKB 0.096 0.087 0.19 208 -10000 0 208
CDC25B -0.003 0.041 0.15 1 -0.23 3 4
G2/M transition checkpoint -0.013 0.038 -10000 0 -0.13 6 6
mRNA polyadenylation -0.028 0.077 0.35 1 -0.2 47 48
Aurora A/CPEB -0.028 0.078 0.35 1 -0.2 47 48
Aurora A/TACC1/TRAP/chTOG 0.002 0.065 -10000 0 -0.22 6 6
BRCA1 0.021 0.014 0.32 1 -10000 0 1
centrosome duplication -0.006 0.054 -10000 0 -10000 0 0
regulation of centrosome cycle 0 0.052 -10000 0 -10000 0 0
spindle assembly 0.001 0.064 -10000 0 -0.21 6 6
TDRD7 0.02 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.11 0.098 0.24 97 -10000 0 97
CENPA 0.11 0.09 0.2 206 -10000 0 206
Aurora A/PP2A -0.006 0.054 -10000 0 -0.15 3 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.005 0.045 0.18 3 -0.18 2 5
negative regulation of DNA binding -0.003 0.054 0.21 1 -0.22 18 19
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.028 0.009 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.013 0.038 -10000 0 -0.13 6 6
mitotic prometaphase -0.014 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.053 0.2 1 -10000 0 1
TACC1 0.007 0.061 -10000 0 -0.32 15 15
TACC3 0.021 0.014 0.32 1 -10000 0 1
Aurora A/Antizyme1 0.002 0.057 -10000 0 -0.17 1 1
Aurora A/RasGAP -0.005 0.053 -10000 0 -10000 0 0
OAZ1 0.019 0.005 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.015 0.03 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.037 0.014 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.083 0.094 0.16 254 -10000 0 254
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.05 0.081 0.18 83 -10000 0 83
PAK1 0.02 0.004 -10000 0 -10000 0 0
CKAP5 0.02 0.003 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.019 0.094 0.17 2 -0.23 65 67
FZD6 0.017 0.017 -10000 0 -0.32 1 1
WNT6 0.038 0.071 0.32 27 -10000 0 27
WNT4 0.007 0.082 0.32 5 -0.32 23 28
FZD3 0.018 0.016 0.32 1 -10000 0 1
WNT5A 0.017 0.036 -10000 0 -0.32 5 5
WNT11 -0.023 0.12 0.32 1 -0.32 59 60
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.009 0.077 -10000 0 -0.2 54 54
fibroblast growth factor receptor signaling pathway 0.009 0.076 -10000 0 -0.2 54 54
LAMA1 0.025 0.067 0.32 15 -0.32 6 21
PRNP 0.019 0.017 -10000 0 -0.32 1 1
GPC1/SLIT2 -0.032 0.11 -10000 0 -0.23 110 110
SMAD2 -0.022 0.027 0.17 2 -0.18 8 10
GPC1/PrPc/Cu2+ 0.025 0.018 -10000 0 -0.18 3 3
GPC1/Laminin alpha1 0.03 0.05 0.23 14 -0.22 9 23
TDGF1 0.022 0.074 0.32 15 -0.32 10 25
CRIPTO/GPC1 0.029 0.057 0.23 15 -0.23 13 28
APP/GPC1 0.027 0.022 -10000 0 -0.23 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.019 0.034 -10000 0 -0.2 11 11
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.035 0.038 0.22 1 -0.19 11 12
SERPINC1 0.021 0.032 0.32 5 -10000 0 5
FYN -0.019 0.037 -10000 0 -0.21 11 11
FGR -0.031 0.058 0.1 13 -0.21 37 50
positive regulation of MAPKKK cascade -0.018 0.095 0.19 7 -0.32 28 35
SLIT2 -0.061 0.15 -10000 0 -0.32 110 110
GPC1/NRG -0.016 0.096 -10000 0 -0.23 74 74
NRG1 -0.036 0.12 -10000 0 -0.32 73 73
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.036 0.023 -10000 0 -0.2 3 3
LYN -0.017 0.033 0.1 15 -0.2 9 24
mol:Spermine -0.01 0.017 -10000 0 -0.22 3 3
cell growth 0.009 0.076 -10000 0 -0.2 54 54
BMP signaling pathway -0.018 0.028 0.32 3 -10000 0 3
SRC -0.019 0.035 0.1 14 -0.2 11 25
TGFBR1 0.021 0.014 0.32 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.015 0.12 0.32 10 -0.32 56 66
GPC1 0.018 0.028 -10000 0 -0.32 3 3
TGFBR1 (dimer) 0.021 0.014 0.32 1 -10000 0 1
VEGFA 0.02 0.004 -10000 0 -10000 0 0
BLK 0.008 0.072 0.16 75 -0.2 11 86
HCK -0.024 0.046 0.1 14 -0.2 25 39
FGF2 -0.022 0.11 -10000 0 -0.32 57 57
FGFR1 0.017 0.017 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.014 0.045 -10000 0 -0.32 8 8
cell death 0.027 0.022 -10000 0 -0.23 3 3
ATIII/GPC1 0.028 0.031 0.23 5 -0.23 3 8
PLA2G2A/GPC1 0.002 0.092 0.23 10 -0.23 57 67
LCK -0.02 0.039 0.11 16 -0.2 14 30
neuron differentiation -0.016 0.096 -10000 0 -0.23 74 74
PrPc/Cu2+ 0.014 0.011 -10000 0 -0.22 1 1
APP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.014 0.045 -10000 0 -0.32 8 8
Effects of Botulinum toxin

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
STX1A 0.036 0.077 0.16 120 -10000 0 120
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.016 0.072 0.23 12 -0.23 29 41
STXBP1 0.018 0.028 -10000 0 -0.32 3 3
ACh/CHRNA1 0.028 0.068 0.24 32 -0.15 12 44
RAB3GAP2/RIMS1/UNC13B 0.026 0.062 0.22 10 -0.2 26 36
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 0.006 0.1 0.32 14 -0.32 29 43
mol:ACh 0.004 0.031 0.081 27 -0.11 9 36
RAB3GAP2 0.019 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.027 0.066 0.22 2 -0.16 24 26
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.028 0.068 0.24 32 -0.15 12 44
UNC13B 0.02 0.004 -10000 0 -10000 0 0
CHRNA1 0.035 0.089 0.32 31 -0.32 8 39
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.03 0.067 0.25 32 -0.12 8 40
SNAP25 0.004 0.03 0.12 16 -0.22 4 20
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.037 0.087 0.32 32 -0.32 6 38
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.044 0.055 0.13 118 -0.19 3 121
STX1A/SNAP25 fragment 1/VAMP2 0.027 0.066 0.22 2 -0.16 24 26
EGFR-dependent Endothelin signaling events

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
HRAS 0.02 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.042 0.32 1 -0.32 6 7
EGF/EGFR 0.024 0.088 0.18 54 -0.17 50 104
EGF/EGFR dimer/SHC/GRB2/SOS1 0.061 0.072 0.22 54 -0.19 6 60
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.02 0.016 -10000 0 -0.32 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.072 0.12 0.32 84 -0.32 4 88
EGF/EGFR dimer/SHC 0.05 0.073 0.22 55 -0.21 7 62
mol:GDP 0.056 0.067 0.33 1 -0.19 6 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.028 0.12 -10000 0 -0.32 65 65
GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
HRAS/GTP 0.036 0.047 0.22 1 -0.18 6 7
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.049 0.059 0.28 1 -0.2 5 6
FRAP1 -0.012 0.034 0.17 4 -0.18 6 10
EGF/EGFR dimer 0.053 0.087 0.24 71 -0.24 9 80
SOS1 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.007 0.09 -10000 0 -0.23 66 66
Noncanonical Wnt signaling pathway

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
NFATC2 0.008 0.063 -10000 0 -0.32 16 16
GNB1/GNG2 -0.006 0.1 0.23 1 -0.3 23 24
mol:DAG -0.036 0.084 0.18 3 -0.28 22 25
PLCG1 -0.037 0.086 0.18 3 -0.28 22 25
YES1 -0.035 0.087 0.21 4 -0.23 60 64
FZD3 0.018 0.016 0.32 1 -10000 0 1
FZD6 0.017 0.017 -10000 0 -0.32 1 1
G protein -0.005 0.1 0.24 4 -0.29 22 26
MAP3K7 -0.042 0.087 0.2 3 -0.27 32 35
mol:Ca2+ -0.035 0.082 0.18 3 -0.27 22 25
mol:IP3 -0.036 0.084 0.18 3 -0.28 22 25
NLK -0.001 0.084 -10000 0 -0.8 5 5
GNB1 0.02 0.004 -10000 0 -10000 0 0
CAMK2A -0.045 0.094 0.19 3 -0.28 36 39
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.019 0.094 0.17 2 -0.23 65 67
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
GNAS -0.035 0.085 0.16 2 -0.23 60 62
GO:0007205 -0.034 0.084 0.19 2 -0.28 23 25
WNT6 0.038 0.071 0.32 27 -10000 0 27
WNT4 0.007 0.082 0.32 5 -0.32 23 28
NFAT1/CK1 alpha -0.015 0.1 0.26 2 -0.3 23 25
GNG2 0.019 0.023 -10000 0 -0.32 2 2
WNT5A 0.017 0.036 -10000 0 -0.32 5 5
WNT11 -0.023 0.12 0.32 1 -0.32 59 60
CDC42 -0.036 0.084 0.2 5 -0.3 22 27
FoxO family signaling

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
G6PC 0.013 0.064 0.35 1 -10000 0 1
PLK1 0.21 0.26 0.56 134 -10000 0 134
CDKN1B 0.13 0.17 0.36 122 -0.34 6 128
FOXO3 0.19 0.23 0.52 134 -10000 0 134
KAT2B 0.054 0.044 0.17 12 -10000 0 12
FOXO1/SIRT1 0.008 0.042 -10000 0 -0.25 2 2
CAT 0.15 0.25 0.54 60 -0.75 8 68
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.054 0.044 0.16 27 -10000 0 27
FOXO1 0.016 0.057 0.23 12 -0.26 2 14
MAPK10 0.016 0.063 0.2 35 -0.16 12 47
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.033 0.073 0.29 8 -10000 0 8
response to oxidative stress 0.036 0.043 0.12 46 -10000 0 46
FOXO3A/SIRT1 0.16 0.2 0.43 126 -0.43 2 128
XPO1 0.021 0.002 -10000 0 -10000 0 0
EP300 0.022 0.007 -10000 0 -10000 0 0
BCL2L11 0.063 0.062 -10000 0 -10000 0 0
FOXO1/SKP2 0.022 0.041 -10000 0 -10000 0 0
mol:GDP 0.036 0.043 0.12 46 -10000 0 46
RAN 0.021 0.014 0.32 1 -10000 0 1
GADD45A 0.11 0.17 0.45 18 -0.65 6 24
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.12 -10000 0 -0.46 20 20
MST1 0.063 0.068 0.23 41 -10000 0 41
CSNK1D 0.02 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.004 0.089 -10000 0 -0.37 15 15
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.026 0.06 0.2 44 -10000 0 44
MAPK9 0.026 0.061 0.2 43 -10000 0 43
YWHAG 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
SIRT1 0.002 0.024 -10000 0 -10000 0 0
SOD2 0.12 0.18 0.42 61 -0.42 3 64
RBL2 0.14 0.21 0.51 35 -0.67 7 42
RAL/GDP 0.047 0.031 0.17 1 -10000 0 1
CHUK 0.054 0.043 0.17 10 -10000 0 10
Ran/GTP 0.016 0.01 0.22 1 -10000 0 1
CSNK1G2 0.019 0.006 -10000 0 -10000 0 0
RAL/GTP 0.046 0.03 0.19 1 -10000 0 1
CSNK1G1 0.02 0.004 -10000 0 -10000 0 0
FASLG 0.049 0.15 0.44 1 -1.1 6 7
SKP2 0.017 0.016 0.32 1 -10000 0 1
USP7 0.021 0.003 -10000 0 -10000 0 0
IKBKB 0.046 0.042 0.15 23 -10000 0 23
CCNB1 0.19 0.26 0.57 118 -10000 0 118
FOXO1-3a-4/beta catenin 0.12 0.15 0.38 64 -10000 0 64
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.041 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
SGK1 0.053 0.045 0.17 12 -10000 0 12
CSNK1G3 0.02 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.01 0.21 1 -10000 0 1
ZFAND5 0.028 0.067 0.44 1 -10000 0 1
SFN 0.025 0.043 0.32 8 -0.32 1 9
CDK2 0.012 0.02 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.047 0.11 0.26 17 -0.38 10 27
CREBBP 0.011 0.02 -10000 0 -10000 0 0
FBXO32 0.2 0.26 0.62 85 -0.53 1 86
BCL6 0.13 0.22 0.5 38 -0.77 9 47
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.019 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.01 0.073 0.21 1 -0.18 58 59
regulation of S phase of mitotic cell cycle -0.016 0.074 0.15 2 -0.2 59 61
GNAO1 0.02 0.03 0.32 2 -0.32 2 4
HRAS 0.018 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.009 0.19 1 -10000 0 1
PELP1 0.017 0.01 -10000 0 -10000 0 0
AKT1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.039 0.065 0.16 14 -0.26 11 25
T-DHT/AR -0.016 0.08 0.21 1 -0.22 60 61
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 31 31
GNAI2 0.02 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.017 -10000 0 -0.32 1 1
mol:GDP -0.049 0.11 0.19 2 -0.31 63 65
cell proliferation -0.06 0.13 0.27 2 -0.43 38 40
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FOS -0.062 0.19 -10000 0 -0.72 33 33
mol:Ca2+ -0.008 0.019 -10000 0 -0.056 49 49
MAPK3 -0.051 0.098 0.27 3 -0.32 35 38
MAPK1 -0.032 0.096 0.2 1 -0.34 26 27
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 0 0.001 -10000 0 -0.004 30 30
cAMP biosynthetic process 0.001 0.019 0.23 1 -10000 0 1
GNG2 0.019 0.023 -10000 0 -0.32 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 30 30
HRAS/GTP 0.006 0.069 -10000 0 -0.16 57 57
actin cytoskeleton reorganization 0.026 0.016 -10000 0 -0.16 1 1
SRC 0.018 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 30 30
PI3K 0.026 0.013 -10000 0 -0.19 1 1
apoptosis 0.045 0.12 0.44 35 -0.27 1 36
T-DHT/AR/PELP1 -0.004 0.073 0.2 1 -0.19 60 61
HRAS/GDP -0.05 0.1 0.18 2 -0.3 62 64
CREB1 -0.048 0.14 0.27 1 -0.48 35 36
RAC1-CDC42/GTP 0.032 0.019 -10000 0 -0.16 1 1
AR -0.025 0.12 0.32 1 -0.33 60 61
GNB1 0.02 0.004 -10000 0 -10000 0 0
RAF1 -0.034 0.065 0.18 15 -0.24 10 25
RAC1-CDC42/GDP -0.018 0.11 0.2 1 -0.3 54 55
T-DHT/AR/PELP1/Src 0.006 0.072 0.19 1 -0.18 58 59
MAP2K2 -0.039 0.065 0.24 2 -0.26 11 13
T-DHT/AR/PELP1/Src/PI3K -0.017 0.074 0.15 2 -0.2 59 61
GNAZ -0.009 0.095 -10000 0 -0.32 39 39
SHBG 0.019 0.015 0.32 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.023 0.097 -10000 0 -0.33 28 28
mol:T-DHT 0 0 -10000 0 -0.003 4 4
RAC1 0.018 0.007 -10000 0 -10000 0 0
GNRH1 -0.008 0.014 -10000 0 -0.22 2 2
Gi family/GTP -0.026 0.069 -10000 0 -0.2 48 48
CDC42 0.02 0.003 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.036 0.052 0.23 22 -0.23 5 27
PTK2 -0.021 0.11 -10000 0 -0.34 29 29
positive regulation of JNK cascade -0.02 0.11 -10000 0 -0.27 61 61
CDC42/GDP -0.02 0.15 -10000 0 -0.35 65 65
Rac1/GDP -0.022 0.14 -10000 0 -0.35 59 59
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.02 0.13 -10000 0 -0.33 57 57
nectin-3/I-afadin 0.01 0.065 -10000 0 -0.23 32 32
RAPGEF1 -0.037 0.14 0.28 1 -0.37 61 62
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.042 0.15 -10000 0 -0.4 60 60
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
TLN1 -0.025 0.056 -10000 0 -0.33 11 11
Rap1/GTP -0.026 0.11 -10000 0 -0.27 63 63
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.015 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.065 -10000 0 -0.23 32 32
PVR 0.02 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.037 0.17 -10000 0 -0.42 66 66
MLLT4 0.019 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.038 0.059 -10000 0 -0.17 28 28
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.031 0.032 0.23 10 -10000 0 10
positive regulation of lamellipodium assembly -0.022 0.11 -10000 0 -0.28 59 59
PVRL1 0.026 0.044 0.32 10 -10000 0 10
PVRL3 -0.003 0.089 0.32 1 -0.32 32 33
PVRL2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
CDH1 0.019 0.023 -10000 0 -0.32 2 2
CLDN1 0.023 0.057 0.32 10 -0.32 5 15
JAM-A/CLDN1 0.031 0.067 0.22 10 -0.2 27 37
SRC -0.044 0.16 -10000 0 -0.44 64 64
ITGB3 0.031 0.074 0.32 22 -0.32 5 27
nectin-1(dimer)/I-afadin/I-afadin 0.031 0.032 0.23 10 -10000 0 10
FARP2 -0.033 0.17 -10000 0 -0.46 41 41
RAC1 0.018 0.007 -10000 0 -10000 0 0
CTNNA1 0.02 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.021 0.058 -10000 0 -0.19 30 30
nectin-1/I-afadin 0.031 0.032 0.23 10 -10000 0 10
nectin-2/I-afadin 0.027 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.025 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.025 0.062 0.22 8 -0.19 29 37
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.006 -10000 0 -10000 0 0
F11R 0.018 0.017 -10000 0 -0.32 1 1
positive regulation of filopodium formation -0.02 0.11 -10000 0 -0.27 61 61
alphaV/beta3 Integrin/Talin -0.025 0.08 0.2 23 -0.3 14 37
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.027 0.01 -10000 0 -10000 0 0
PIP5K1C -0.02 0.06 -10000 0 -0.35 11 11
VAV2 -0.038 0.18 -10000 0 -0.48 41 41
RAP1/GDP -0.018 0.14 -10000 0 -0.33 63 63
ITGAV 0.021 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.021 0.059 -10000 0 -0.19 31 31
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.065 -10000 0 -0.23 32 32
Rac1/GTP -0.025 0.14 -10000 0 -0.34 56 56
PTPRM -0.013 0.071 -10000 0 -0.22 38 38
E-cadherin/beta catenin/alpha catenin 0.051 0.036 -10000 0 -0.17 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.016 0.097 -10000 0 -0.58 8 8
Syndecan-4/Syndesmos 0.034 0.15 0.3 5 -0.65 15 20
positive regulation of JNK cascade 0.033 0.15 0.3 4 -0.58 16 20
Syndecan-4/ADAM12 0.094 0.19 0.33 82 -0.68 14 96
CCL5 0.017 0.032 -10000 0 -0.32 4 4
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DNM2 0.02 0.005 -10000 0 -10000 0 0
ITGA5 0.02 0.021 0.32 1 -0.32 1 2
SDCBP 0.019 0.006 -10000 0 -10000 0 0
PLG 0.011 0.047 0.32 9 -10000 0 9
ADAM12 0.12 0.14 0.32 160 -10000 0 160
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.02 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.034 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.037 0.15 0.31 10 -0.66 14 24
Syndecan-4/CXCL12/CXCR4 0.034 0.16 0.31 4 -0.63 16 20
Syndecan-4/Laminin alpha3 0.017 0.15 0.33 1 -0.66 16 17
MDK 0.11 0.14 0.32 139 -10000 0 139
Syndecan-4/FZD7 0.035 0.15 0.29 6 -0.68 14 20
Syndecan-4/Midkine 0.088 0.18 0.34 50 -0.67 14 64
FZD7 0.02 0.016 -10000 0 -0.32 1 1
Syndecan-4/FGFR1/FGF 0.021 0.15 0.29 3 -0.62 17 20
THBS1 0.019 0.017 -10000 0 -0.32 1 1
integrin-mediated signaling pathway 0.043 0.15 0.3 14 -0.63 15 29
positive regulation of MAPKKK cascade 0.033 0.15 0.3 4 -0.58 16 20
Syndecan-4/TACI 0.043 0.16 0.32 19 -0.67 14 33
CXCR4 0.021 0.002 -10000 0 -10000 0 0
cell adhesion 0.007 0.038 0.19 9 -0.27 4 13
Syndecan-4/Dynamin 0.034 0.15 0.29 4 -0.67 14 18
Syndecan-4/TSP1 0.032 0.15 0.29 6 -0.63 16 22
Syndecan-4/GIPC 0.034 0.15 0.3 5 -0.65 15 20
Syndecan-4/RANTES 0.034 0.15 0.3 3 -0.64 15 18
ITGB1 0.02 0.003 -10000 0 -10000 0 0
LAMA1 0.025 0.067 0.32 15 -0.32 6 21
LAMA3 -0.043 0.13 -10000 0 -0.32 84 84
RAC1 0.018 0.007 -10000 0 -10000 0 0
PRKCA 0.008 0.15 0.77 17 -0.32 1 18
Syndecan-4/alpha-Actinin 0.033 0.15 0.3 4 -0.66 15 19
TFPI 0.008 0.065 -10000 0 -0.32 17 17
F2 0.06 0.11 0.32 63 -10000 0 63
alpha5/beta1 Integrin 0.03 0.017 0.23 1 -0.23 1 2
positive regulation of cell adhesion 0 0.15 0.25 8 -0.63 16 24
ACTN1 0.02 0.004 -10000 0 -10000 0 0
TNC 0.032 0.083 0.32 27 -0.32 7 34
Syndecan-4/CXCL12 0.03 0.16 0.29 6 -0.65 16 22
FGF6 0.016 0.004 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
CXCL12 -0.001 0.083 -10000 0 -0.32 29 29
TNFRSF13B 0.034 0.082 0.32 29 -0.32 5 34
FGF2 -0.022 0.11 -10000 0 -0.32 57 57
FGFR1 0.017 0.017 -10000 0 -0.32 1 1
Syndecan-4/PI-4-5-P2 0.018 0.15 0.25 13 -0.65 15 28
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.013 0.036 -10000 0 -0.32 4 4
cell migration -0.021 0.012 -10000 0 -10000 0 0
PRKCD 0.015 0.019 -10000 0 -10000 0 0
vasculogenesis 0.033 0.15 0.29 6 -0.6 16 22
SDC4 0.028 0.14 0.27 13 -0.79 10 23
Syndecan-4/Tenascin C 0.043 0.16 0.31 14 -0.67 15 29
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.031 0.15 0.29 6 -0.67 14 20
MMP9 0.078 0.12 0.32 90 -10000 0 90
Rac1/GTP 0.007 0.039 0.19 9 -0.28 4 13
cytoskeleton organization 0.034 0.15 0.29 6 -0.62 15 21
GIPC1 0.02 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.031 0.16 0.3 4 -0.66 15 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.074 0.15 -10000 0 -0.32 126 126
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.02 0.003 -10000 0 -10000 0 0
TCEB1 0.019 0.015 0.32 1 -10000 0 1
HIF1A/p53 0.027 0.051 0.24 1 -0.24 8 9
HIF1A 0.001 0.036 -10000 0 -0.25 8 8
COPS5 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.051 0.026 -10000 0 -10000 0 0
FIH (dimer) 0.02 0.003 -10000 0 -10000 0 0
CDKN2A 0.098 0.14 0.32 126 -10000 0 126
ARNT/IPAS -0.036 0.11 -10000 0 -0.23 109 109
HIF1AN 0.02 0.003 -10000 0 -10000 0 0
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.043 0.24 1 -0.23 5 6
CUL2 0.02 0.004 -10000 0 -10000 0 0
OS9 0.02 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.036 0.018 0.22 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.027 0.05 -10000 0 -0.24 8 8
PHD1-3/OS9 0.073 0.077 0.22 89 -10000 0 89
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.05 0.24 2 -0.24 6 8
VHL 0.02 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.024 0.051 0.24 1 -0.24 8 9
EGLN3 0.084 0.13 0.32 102 -0.32 1 103
EGLN2 0.02 0.004 -10000 0 -10000 0 0
EGLN1 0.019 0.005 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.009 0.1 -10000 0 -0.49 18 18
ARNT 0.017 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.069 0.097 0.21 121 -0.22 6 127
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.03 0.32 2 -0.32 2 4
CDC42/GTP -0.012 0.077 -10000 0 -0.2 32 32
PLCG1 -0.024 0.066 0.27 1 -0.18 58 59
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.02 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
cell migration -0.012 0.076 -10000 0 -0.2 32 32
S1PR5 0 0.082 0.32 1 -0.32 27 28
S1PR4 0.007 0.065 -10000 0 -0.32 17 17
MAPK3 -0.026 0.066 -10000 0 -0.18 61 61
MAPK1 -0.022 0.058 -10000 0 -0.17 54 54
S1P/S1P5/Gi -0.018 0.078 -10000 0 -0.2 65 65
GNAI1 0.019 0.017 -10000 0 -0.32 1 1
CDC42/GDP 0.015 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.013 0.05 0.21 1 -0.19 25 26
RHOA -0.001 0.075 0.2 49 -0.17 14 63
S1P/S1P4/Gi -0.015 0.072 -10000 0 -0.19 61 61
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.009 0.095 -10000 0 -0.32 39 39
S1P/S1P4/G12/G13 0.026 0.04 -10000 0 -0.17 15 15
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.013 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.083 0.21 1 -0.23 6 7
NFATC4 -0.041 0.065 0.22 9 -0.17 6 15
ERBB2IP 0.02 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.02 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.047 0.065 -10000 0 -0.19 59 59
JUN -0.006 0.065 0.27 4 -10000 0 4
HRAS 0.02 0.006 -10000 0 -10000 0 0
DOCK7 -0.05 0.064 -10000 0 -0.19 58 58
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.07 0.19 2 -0.18 55 57
AKT1 -0.008 0.006 -10000 0 -10000 0 0
BAD -0.013 0.005 -10000 0 -10000 0 0
MAPK10 -0.032 0.065 0.17 10 -0.18 20 30
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.05 0.07 -10000 0 -0.21 59 59
RAF1 -0.012 0.096 0.28 13 -0.25 6 19
ErbB2/ErbB3/neuregulin 2 -0.012 0.066 0.19 2 -0.19 49 51
STAT3 0.003 0.13 -10000 0 -0.86 10 10
cell migration -0.024 0.075 0.21 17 -0.2 12 29
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.031 0.18 0.4 5 -0.56 28 33
FOS -0.027 0.16 0.34 6 -0.41 46 52
NRAS 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.047 0.065 -10000 0 -0.19 59 59
MAPK3 -0.019 0.15 0.38 6 -0.49 20 26
MAPK1 -0.027 0.17 0.4 5 -0.55 23 28
JAK2 -0.047 0.065 -10000 0 -0.2 7 7
NF2 -0.026 0.13 -10000 0 -0.61 21 21
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.017 0.07 0.2 3 -0.2 52 55
NRG1 -0.037 0.12 -10000 0 -0.33 73 73
GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
MAPK8 -0.05 0.085 0.19 1 -0.23 52 53
MAPK9 -0.023 0.056 0.17 12 -10000 0 12
ERBB2 -0.019 0.02 0.26 2 -10000 0 2
ERBB3 0.013 0.026 -10000 0 -0.32 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.004 0.13 -10000 0 -0.84 10 10
RNF41 -0.018 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.042 0.044 -10000 0 -0.15 50 50
ErbB2/ErbB2/HSP90 (dimer) -0.02 0.017 0.2 2 -10000 0 2
CHRNA1 -0.007 0.14 0.31 21 -0.47 19 40
myelination -0.032 0.083 0.26 17 -10000 0 17
PPP3CB -0.048 0.06 -10000 0 -0.18 58 58
KRAS 0.019 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.002 0.077 0.22 1 -0.19 46 47
NRG2 -0.018 0.11 -10000 0 -0.32 52 52
mol:GDP -0.017 0.07 0.2 3 -0.2 52 55
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K2 -0.014 0.098 0.28 14 -0.28 6 20
SRC 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.05 0.065 -10000 0 -0.19 58 58
MAP2K1 -0.036 0.17 0.41 3 -0.58 20 23
heart morphogenesis -0.047 0.065 -10000 0 -0.19 59 59
RAS family/GDP 0.003 0.085 0.23 1 -0.22 6 7
GRB2 0.02 0.004 -10000 0 -10000 0 0
PRKACA -0.025 0.14 -10000 0 -0.65 23 23
CHRNE 0.002 0.022 0.16 5 -10000 0 5
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.006 -10000 0 -10000 0 0
nervous system development -0.047 0.065 -10000 0 -0.19 59 59
CDC42 0.02 0.003 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.027 0.013 0.23 1 -10000 0 1
PRKCZ 0.018 0.028 -10000 0 -0.32 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.019 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.06 -10000 0 -0.27 13 13
IRAK/TOLLIP -0.02 0.014 0.18 1 -10000 0 1
IKBKB 0.018 0.007 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.037 0.13 0.23 18 -0.23 135 153
IL1A -0.078 0.16 0.32 2 -0.32 135 137
IL1B -0.029 0.051 -10000 0 -0.23 29 29
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.035 -10000 0 -0.17 2 2
IL1R2 0.029 0.063 0.32 17 -0.32 3 20
IL1R1 0.018 0.028 -10000 0 -0.32 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.052 -10000 0 -0.26 8 8
TOLLIP 0.02 0.004 -10000 0 -10000 0 0
TICAM2 0.018 0.028 -10000 0 -0.32 3 3
MAP3K3 0.019 0.017 -10000 0 -0.32 1 1
TAK1/TAB1/TAB2 0.013 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.002 0.067 0.25 3 -0.36 2 5
JUN -0.018 0.046 0.16 22 -10000 0 22
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.031 0.058 -10000 0 -0.18 27 27
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.016 0.11 0.22 1 -0.18 134 135
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.009 0.11 0.22 1 -0.17 133 134
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.054 -10000 0 -0.19 29 29
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.012 0.049 0.17 24 -10000 0 24
IRAK1 -0.017 0.013 0.2 1 -10000 0 1
IL1RN/IL1R1 0.025 0.038 -10000 0 -0.23 10 10
IRAK4 0.02 0.003 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
TRAF6 0.02 0.003 -10000 0 -10000 0 0
PI3K 0.028 0.015 -10000 0 -0.23 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.061 -10000 0 -0.3 11 11
CHUK 0.02 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.054 -10000 0 -0.19 29 29
IL1 beta/IL1R2 0.015 0.067 0.22 15 -0.2 29 44
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.003 0.024 0.15 1 -10000 0 1
NF kappa B1 p50/RelA 0.022 0.054 -10000 0 -0.18 23 23
IRAK3 0.011 0.055 -10000 0 -0.32 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.031 0.058 -10000 0 -0.18 29 29
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.046 0.1 -10000 0 -0.2 128 128
IL1 alpha/IL1R1/IL1RAP -0.027 0.11 0.22 2 -0.2 134 136
RELA 0.02 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
MYD88 0.02 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.032 0.03 -10000 0 -10000 0 0
IL1RAP 0.02 0.005 -10000 0 -10000 0 0
UBE2N 0.02 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.045 0.033 -10000 0 -10000 0 0
CASP1 0.017 0.032 -10000 0 -0.32 4 4
IL1RN/IL1R2 0.033 0.055 0.23 17 -0.25 9 26
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.025 0.055 -10000 0 -0.18 29 29
TMEM189-UBE2V1 0.018 0.015 0.32 1 -10000 0 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.04 0.097 -10000 0 -0.33 22 22
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL1RN 0.016 0.042 -10000 0 -0.32 7 7
TRAF6/TAK1/TAB1/TAB2 0.033 0.017 0.18 1 -10000 0 1
MAP2K6 -0.006 0.058 0.18 36 -10000 0 36
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.016 0.005 -10000 0 -10000 0 0
SMARCC1 0.002 0.013 -10000 0 -10000 0 0
REL 0.02 0.007 -10000 0 -10000 0 0
HDAC7 -0.035 0.076 0.3 4 -0.26 20 24
JUN 0.017 0.032 -10000 0 -0.32 4 4
EP300 0.02 0.004 -10000 0 -10000 0 0
KAT2B 0.02 0.004 -10000 0 -10000 0 0
KAT5 0.02 0.003 -10000 0 -10000 0 0
MAPK14 -0.011 0.038 0.16 16 -0.24 2 18
FOXO1 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.033 0.077 0.26 2 -0.28 18 20
MAP2K6 0.024 0.061 0.32 15 -0.33 2 17
BRM/BAF57 0.027 0.02 -10000 0 -0.23 2 2
MAP2K4 0.016 0.015 -10000 0 -10000 0 0
SMARCA2 0.017 0.028 -10000 0 -0.32 3 3
PDE9A -0.029 0.15 -10000 0 -0.91 11 11
NCOA2 0.016 0.032 -10000 0 -0.32 4 4
CEBPA 0.004 0.072 -10000 0 -0.32 21 21
EHMT2 0.02 0.004 -10000 0 -10000 0 0
cell proliferation -0.026 0.14 0.35 17 -0.36 25 42
NR0B1 0.076 0.12 0.32 90 -10000 0 90
EGR1 0.001 0.079 -10000 0 -0.32 26 26
RXRs/9cRA -0.064 0.1 -10000 0 -0.17 216 216
AR/RACK1/Src -0.011 0.083 0.25 18 -0.29 2 20
AR/GR -0.013 0.086 0.21 6 -0.22 51 57
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
RCHY1 0.02 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 0.016 1 -10000 0 1
MAPK8 -0.014 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.016 0.069 0.22 6 -0.28 3 9
SRC -0.021 0.032 0.19 4 -0.2 2 6
NR3C1 0.02 0.004 -10000 0 -10000 0 0
KLK3 0.013 0.093 0.33 1 -0.4 2 3
APPBP2 0.016 0.015 -10000 0 -10000 0 0
TRIM24 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.021 0.062 0.18 21 -0.23 5 26
TMPRSS2 -0.077 0.27 -10000 0 -0.92 40 40
RXRG -0.14 0.17 -10000 0 -0.32 218 218
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.02 0.004 -10000 0 -10000 0 0
RXRB 0.02 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.006 -10000 0 -10000 0 0
NR2C2 0.02 0.004 -10000 0 -10000 0 0
KLK2 -0.002 0.087 0.29 25 -10000 0 25
AR -0.027 0.076 0.18 3 -0.23 52 55
SENP1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.019 0.009 -10000 0 -10000 0 0
SRY 0 0.003 -10000 0 -0.027 7 7
GATA2 -0.008 0.096 -10000 0 -0.32 39 39
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.12 0.14 0.32 161 -10000 0 161
T-DHT/AR/RACK1/Src -0.015 0.076 0.29 10 -0.3 2 12
positive regulation of transcription -0.008 0.095 -10000 0 -0.32 39 39
DNAJA1 0.015 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.011 0.17 2 -10000 0 2
NCOA1 0.023 0.014 -10000 0 -10000 0 0
SPDEF 0.11 0.14 0.32 147 -0.32 3 150
T-DHT/AR/TIF2 -0.007 0.074 0.22 10 -0.32 8 18
T-DHT/AR/Hsp90 -0.02 0.061 0.18 20 -0.23 5 25
GSK3B 0.017 0.012 -10000 0 -10000 0 0
NR2C1 0.02 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.021 0.029 0.13 3 -0.21 2 5
SIRT1 0.02 0.003 -10000 0 -10000 0 0
ZMIZ2 0.018 0.01 -10000 0 -10000 0 0
POU2F1 0.009 0.039 -10000 0 -0.16 5 5
T-DHT/AR/DAX-1 0.017 0.1 0.21 77 -0.26 3 80
CREBBP 0.02 0.004 -10000 0 -10000 0 0
SMARCE1 0.02 0.004 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.036 0.059 0.24 6 -0.23 27 33
KIRREL 0.016 0.041 -10000 0 -0.33 6 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.036 0.059 0.23 27 -0.24 6 33
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARRB2 0.019 0.006 -10000 0 -10000 0 0
WASL 0.02 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.05 0.055 0.22 27 -0.18 6 33
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.014 0.04 0.16 2 -0.21 6 8
FYN 0.016 0.084 0.21 61 -0.17 6 67
mol:Ca2+ 0.048 0.054 0.21 27 -0.18 6 33
mol:DAG 0.049 0.055 0.21 27 -0.18 6 33
NPHS2 -0.004 0.023 -10000 0 -10000 0 0
mol:IP3 0.049 0.055 0.21 27 -0.18 6 33
regulation of endocytosis 0.035 0.048 0.2 23 -0.17 6 29
Nephrin/NEPH1/podocin/Cholesterol 0.041 0.052 0.2 27 -0.17 6 33
establishment of cell polarity 0.036 0.059 0.23 27 -0.24 6 33
Nephrin/NEPH1/podocin/NCK1-2 0.059 0.056 0.25 2 -0.16 6 8
Nephrin/NEPH1/beta Arrestin2 0.037 0.049 0.2 23 -0.17 6 29
NPHS1 0.039 0.081 0.33 32 -10000 0 32
Nephrin/NEPH1/podocin 0.038 0.05 0.2 28 -0.17 7 35
TJP1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.02 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.05 0.055 0.22 27 -0.18 6 33
CD2AP 0.02 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.05 0.055 0.22 26 -0.18 6 32
GRB2 0.02 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.005 0.091 0.22 54 -0.18 26 80
cytoskeleton organization -0.003 0.053 0.22 10 -0.22 6 16
Nephrin/NEPH1 0.03 0.046 0.19 27 -0.16 6 33
Nephrin/NEPH1/ZO-1 0.04 0.051 0.21 23 -0.19 6 29
PDGFR-alpha 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
PDGFRA 0.013 0.036 -10000 0 -0.32 4 4
PDGF/PDGFRA/CRKL 0.023 0.028 -10000 0 -0.21 4 4
positive regulation of JUN kinase activity 0.036 0.028 -10000 0 -0.17 1 1
CRKL 0.02 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.032 0.11 -10000 0 -0.23 100 100
AP1 -0.063 0.18 0.27 2 -0.73 31 33
mol:IP3 -0.02 0.025 -10000 0 -0.23 3 3
PLCG1 -0.02 0.025 -10000 0 -0.23 3 3
PDGF/PDGFRA/alphaV Integrin 0.024 0.029 -10000 0 -0.22 4 4
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.025 -10000 0 -0.23 3 3
CAV3 -0.054 0.14 -10000 0 -0.32 98 98
CAV1 -0.19 0.17 -10000 0 -0.32 278 278
SHC/Grb2/SOS1 0.038 0.029 -10000 0 -0.17 1 1
PDGF/PDGFRA/Shf 0.024 0.031 0.23 2 -0.21 4 6
FOS -0.064 0.18 0.31 2 -0.73 30 32
JUN -0.024 0.027 -10000 0 -0.23 4 4
oligodendrocyte development 0.024 0.028 -10000 0 -0.22 4 4
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:DAG -0.02 0.025 -10000 0 -0.23 3 3
PDGF/PDGFRA 0.013 0.036 -10000 0 -0.32 4 4
actin cytoskeleton reorganization 0.023 0.028 -10000 0 -0.21 4 4
SRF -0.013 0.012 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
PI3K 0.032 0.03 -10000 0 -0.18 5 5
PDGF/PDGFRA/Crk/C3G 0.031 0.029 -10000 0 -0.18 4 4
JAK1 -0.017 0.019 -10000 0 -0.21 3 3
ELK1/SRF -0.021 0.037 0.15 15 -0.19 3 18
SHB 0.02 0.005 -10000 0 -10000 0 0
SHF 0.021 0.02 0.32 2 -10000 0 2
CSNK2A1 0.022 0.016 -10000 0 -10000 0 0
GO:0007205 -0.015 0.026 -10000 0 -0.26 3 3
SOS1 0.021 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.036 0.028 -10000 0 -0.17 1 1
PDGF/PDGFRA/SHB 0.023 0.028 -10000 0 -0.21 4 4
PDGF/PDGFRA/Caveolin-1 -0.13 0.13 -10000 0 -0.24 271 271
ITGAV 0.021 0.002 -10000 0 -10000 0 0
ELK1 -0.021 0.029 -10000 0 -0.23 3 3
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.022 0.028 -10000 0 -0.21 4 4
JAK-STAT cascade -0.017 0.019 -10000 0 -0.21 3 3
cell proliferation 0.024 0.031 0.23 2 -0.21 4 6
EPHB forward signaling

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.045 0.063 0.22 50 -0.17 3 53
cell-cell adhesion 0.021 0.037 0.19 10 -10000 0 10
Ephrin B/EPHB2/RasGAP 0.061 0.07 0.22 46 -0.2 11 57
ITSN1 0.02 0.003 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.028 0.03 0.21 8 -0.19 3 11
Ephrin B1/EPHB1 0.044 0.061 0.21 48 -0.23 4 52
HRAS/GDP 0.011 0.074 -10000 0 -0.25 16 16
Ephrin B/EPHB1/GRB7 0.058 0.069 0.22 36 -0.2 13 49
Endophilin/SYNJ1 -0.01 0.051 0.18 16 -0.2 8 24
KRAS 0.019 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.058 0.066 0.22 37 -0.19 11 48
endothelial cell migration 0.033 0.033 -10000 0 -0.17 9 9
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.019 0.023 -10000 0 -0.32 2 2
PAK1 -0.014 0.055 0.19 18 -0.3 2 20
HRAS 0.02 0.004 -10000 0 -10000 0 0
RRAS -0.012 0.052 0.18 14 -0.21 10 24
DNM1 0.023 0.031 0.32 5 -10000 0 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.013 0.053 0.19 15 -0.2 10 25
lamellipodium assembly -0.021 0.037 -10000 0 -0.19 10 10
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.012 0.055 0.18 7 -0.2 13 20
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
EPHB2 0.054 0.095 0.32 52 -10000 0 52
EPHB3 0.025 0.04 0.32 8 -10000 0 8
EPHB1 0.051 0.096 0.32 49 -0.32 2 51
EPHB4 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.009 0.058 0.22 6 -0.3 9 15
Ephrin B/EPHB2 0.053 0.067 0.21 48 -0.19 11 59
Ephrin B/EPHB3 0.038 0.045 0.21 6 -0.19 11 17
JNK cascade -0.003 0.06 0.26 11 -0.21 4 15
Ephrin B/EPHB1 0.049 0.064 0.21 38 -0.19 12 50
RAP1/GDP -0.014 0.082 0.23 16 -0.27 14 30
EFNB2 0.014 0.045 -10000 0 -0.32 8 8
EFNB3 0.018 0.027 0.32 1 -0.32 2 3
EFNB1 0.018 0.028 -10000 0 -0.32 3 3
Ephrin B2/EPHB1-2 0.066 0.084 0.22 86 -0.16 10 96
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.037 0.069 0.2 5 -0.25 10 15
Rap1/GTP -0.02 0.046 0.097 5 -0.19 10 15
axon guidance 0.045 0.062 0.21 50 -0.17 3 53
MAPK3 -0.003 0.048 0.18 9 -0.2 8 17
MAPK1 -0.002 0.044 0.17 9 -0.19 6 15
Rac1/GDP -0.018 0.072 0.22 7 -0.27 15 22
actin cytoskeleton reorganization -0.028 0.046 0.09 4 -0.22 8 12
CDC42/GDP -0.013 0.083 0.23 17 -0.26 16 33
PI3K 0.037 0.034 -10000 0 -0.17 9 9
EFNA5 0.019 0.034 0.32 2 -0.32 3 5
Ephrin B2/EPHB4 0.021 0.029 -10000 0 -0.19 8 8
Ephrin B/EPHB2/Intersectin/N-WASP 0.013 0.059 0.17 4 -0.2 22 26
CDC42 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.023 0.041 -10000 0 -0.19 10 10
PTK2 0.055 0.18 0.53 61 -10000 0 61
MAP4K4 -0.003 0.061 0.26 11 -0.21 4 15
SRC 0.02 0.004 -10000 0 -10000 0 0
KALRN 0.018 0.028 -10000 0 -0.32 3 3
Intersectin/N-WASP 0.029 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis 0 0.087 0.26 27 -0.29 3 30
MAP2K1 0.005 0.05 0.18 9 -0.21 8 17
WASL 0.02 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.084 0.084 0.24 91 -0.22 4 95
cell migration 0.011 0.083 0.26 15 -0.26 6 21
NRAS 0.02 0.004 -10000 0 -10000 0 0
SYNJ1 -0.01 0.052 0.18 16 -0.2 8 24
PXN 0.02 0.003 -10000 0 -10000 0 0
TF 0.006 0.071 0.19 27 -0.18 13 40
HRAS/GTP 0.039 0.053 0.18 5 -0.19 11 16
Ephrin B1/EPHB1-2 0.072 0.082 0.22 91 -0.21 4 95
cell adhesion mediated by integrin 0.015 0.043 0.2 10 -0.19 9 19
RAC1 0.018 0.007 -10000 0 -10000 0 0
mol:GTP 0.046 0.061 0.21 8 -0.19 11 19
RAC1-CDC42/GTP -0.024 0.038 -10000 0 -0.2 10 10
RASA1 0.02 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.018 0.072 0.21 7 -0.27 14 21
ruffle organization 0.006 0.095 0.28 27 -0.26 3 30
NCK1 0.02 0.003 -10000 0 -10000 0 0
receptor internalization -0.014 0.05 0.18 16 -0.2 7 23
Ephrin B/EPHB2/KALRN 0.061 0.074 0.22 48 -0.2 13 61
ROCK1 -0.011 0.033 0.18 10 -0.17 3 13
RAS family/GDP -0.033 0.042 -10000 0 -0.23 8 8
Rac1/GTP -0.018 0.044 0.11 5 -0.2 10 15
Ephrin B/EPHB1/Src/Paxillin 0.01 0.057 -10000 0 -0.2 23 23
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.022 0.18 1 -0.17 2 3
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.11 0.22 4 -0.34 20 24
AP1 0.004 0.072 -10000 0 -0.16 67 67
mol:PIP3 -0.035 0.042 -10000 0 -0.17 34 34
AKT1 -0.01 0.065 0.25 4 -0.31 5 9
PTK2B -0.041 0.12 0.25 1 -0.3 44 45
RHOA -0.005 0.071 0.18 6 -0.36 12 18
PIK3CB 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.028 0.082 0.21 9 -0.23 40 49
MAGI3 0.016 0.036 -10000 0 -0.32 5 5
RELA 0.02 0.003 -10000 0 -10000 0 0
apoptosis -0.01 0.059 0.17 1 -0.19 41 42
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.046 0.11 0.2 9 -0.33 30 39
NF kappa B1 p50/RelA -0.049 0.082 -10000 0 -0.25 45 45
endothelial cell migration -0.009 0.015 0.3 1 -10000 0 1
ADCY4 -0.016 0.05 -10000 0 -0.24 8 8
ADCY5 -0.025 0.067 0.2 1 -0.26 19 20
ADCY6 -0.011 0.042 -10000 0 -0.25 4 4
ADCY7 -0.011 0.039 -10000 0 -0.2 4 4
ADCY1 -0.011 0.044 -10000 0 -0.23 7 7
ADCY2 -0.016 0.054 -10000 0 -0.24 9 9
ADCY3 -0.011 0.039 -10000 0 -0.2 4 4
ADCY8 -0.056 0.08 -10000 0 -0.25 18 18
ADCY9 -0.015 0.048 -10000 0 -0.24 8 8
GSK3B -0.042 0.11 0.19 5 -0.35 30 35
arachidonic acid secretion -0.015 0.046 -10000 0 -0.26 7 7
GNG2 0.018 0.023 -10000 0 -0.32 2 2
TRIP6 0.009 0.026 0.14 1 -0.3 3 4
GNAO1 -0.01 0.018 0.15 3 -0.19 2 5
HRAS 0.02 0.004 -10000 0 -10000 0 0
NFKBIA -0.027 0.11 0.25 5 -0.29 45 50
GAB1 0.02 0.016 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.009 0.19 -10000 0 -0.85 22 22
JUN 0.017 0.032 -10000 0 -0.32 4 4
LPA/LPA2/NHERF2 0.025 0.023 -10000 0 -0.18 5 5
TIAM1 -0.023 0.22 -10000 0 -1 22 22
PIK3R1 0.018 0.017 -10000 0 -0.32 1 1
mol:IP3 -0.022 0.072 0.21 9 -0.21 33 42
PLCB3 -0.013 0.033 0.18 10 -0.17 5 15
FOS -0.002 0.085 -10000 0 -0.32 30 30
positive regulation of mitosis -0.015 0.046 -10000 0 -0.26 7 7
LPA/LPA1-2-3 0.022 0.063 0.21 5 -0.17 41 46
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
stress fiber formation -0.023 0.09 0.23 1 -0.32 21 22
GNAZ -0.025 0.05 0.12 1 -0.19 39 40
EGFR/PI3K-beta/Gab1 -0.034 0.045 -10000 0 -0.17 31 31
positive regulation of dendritic cell cytokine production 0.021 0.062 0.2 5 -0.17 41 46
LPA/LPA2/MAGI-3 0.025 0.024 -10000 0 -0.19 5 5
ARHGEF1 0.007 0.072 0.19 55 -0.16 1 56
GNAI2 -0.01 0.008 0.12 1 -10000 0 1
GNAI3 -0.01 0.008 0.12 1 -10000 0 1
GNAI1 -0.01 0.012 0.12 1 -0.19 1 2
LPA/LPA3 -0.003 0.07 0.22 4 -0.22 41 45
LPA/LPA2 0.015 0.005 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.009 0.18 1 -10000 0 1
HB-EGF/EGFR -0.016 0.088 0.13 71 -0.2 55 126
HBEGF -0.014 0.1 0.15 80 -0.22 65 145
mol:DAG -0.022 0.072 0.21 9 -0.21 33 42
cAMP biosynthetic process -0.019 0.06 0.26 3 -0.22 11 14
NFKB1 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.019 0.007 -10000 0 -10000 0 0
LYN -0.03 0.1 0.28 3 -0.29 44 47
GNAQ -0.01 0.06 0.17 1 -0.2 39 40
LPAR2 0.02 0.005 -10000 0 -10000 0 0
LPAR3 -0.008 0.1 0.32 4 -0.32 41 45
LPAR1 0.021 0.007 -10000 0 -10000 0 0
IL8 -0.021 0.12 0.29 14 -0.38 20 34
PTK2 -0.024 0.048 0.17 7 -0.17 31 38
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
CASP3 -0.01 0.059 0.17 1 -0.19 41 42
EGFR 0.015 0.042 0.32 1 -0.32 6 7
PLCG1 -0.015 0.071 0.15 6 -0.23 38 44
PLD2 -0.023 0.054 0.19 11 -0.17 33 44
G12/G13 0.036 0.018 0.18 1 -10000 0 1
PI3K-beta -0.024 0.046 -10000 0 -0.31 7 7
cell migration -0.008 0.063 -10000 0 -0.25 21 21
SLC9A3R2 0.017 0.036 -10000 0 -0.32 5 5
PXN -0.023 0.091 0.23 1 -0.33 20 21
HRAS/GTP -0.015 0.047 -10000 0 -0.26 7 7
RAC1 0.018 0.007 -10000 0 -10000 0 0
MMP9 0.078 0.12 0.32 90 -10000 0 90
PRKCE 0.017 0.032 -10000 0 -0.32 4 4
PRKCD -0.034 0.081 0.2 8 -0.34 14 22
Gi(beta/gamma) -0.006 0.043 0.14 2 -0.23 3 5
mol:LPA 0.001 0.004 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.081 -10000 0 -0.34 11 11
MAPKKK cascade -0.015 0.046 -10000 0 -0.26 7 7
contractile ring contraction involved in cytokinesis -0.004 0.072 0.18 7 -0.35 13 20
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.014 0.067 0.17 1 -0.21 48 49
GNA15 -0.009 0.056 0.17 1 -0.2 37 38
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.048 0.11 0.2 9 -0.34 32 41
GNA11 -0.009 0.056 0.17 1 -0.2 37 38
Rac1/GTP -0.01 0.2 -10000 0 -0.9 22 22
MMP2 -0.009 0.015 0.3 1 -10000 0 1
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.048 0.1 -10000 0 -0.3 27 27
epithelial cell differentiation -0.027 0.091 -10000 0 -0.33 4 4
ITCH 0.031 0.017 -10000 0 -10000 0 0
WWP1 -0.018 0.073 -10000 0 -10000 0 0
FYN 0.018 0.017 -10000 0 -0.32 1 1
EGFR 0.015 0.042 0.32 1 -0.32 6 7
PRL 0.025 0.046 0.32 11 -10000 0 11
neuron projection morphogenesis -0.028 0.098 0.38 6 -10000 0 6
PTPRZ1 0.034 0.15 0.32 65 -0.32 38 103
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.02 0.081 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.041 0.082 -10000 0 -0.26 30 30
ADAM17 0.033 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.035 0.068 -10000 0 -0.32 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.087 0.12 -10000 0 -0.3 66 66
NCOR1 0.019 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.037 0.084 -10000 0 -0.25 28 28
GRIN2B -0.048 0.078 0.26 3 -0.32 2 5
ErbB4/ErbB2/betacellulin -0.013 0.065 -10000 0 -0.3 1 1
STAT1 0.021 0.002 -10000 0 -10000 0 0
HBEGF -0.035 0.13 -10000 0 -0.32 74 74
PRLR 0.023 0.092 0.32 25 -0.32 14 39
E4ICDs/ETO2 -0.031 0.086 -10000 0 -0.29 11 11
axon guidance -0.028 0.07 -10000 0 -0.36 4 4
NEDD4 0.03 0.023 -10000 0 -0.3 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.03 0.072 0.24 31 -0.22 14 45
CBFA2T3 0 0.081 -10000 0 -0.32 27 27
ErbB4/ErbB2/HBEGF -0.033 0.086 -10000 0 -0.35 1 1
MAPK3 -0.037 0.079 -10000 0 -10000 0 0
STAT1 (dimer) -0.024 0.077 -10000 0 -0.31 2 2
MAPK1 -0.035 0.079 0.24 1 -10000 0 1
JAK2 0.018 0.017 -10000 0 -0.32 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.052 0.074 -10000 0 -0.35 1 1
NRG1 -0.038 0.081 -10000 0 -0.22 72 72
NRG3 -0.11 0.17 0.32 1 -0.32 179 180
NRG2 -0.018 0.11 -10000 0 -0.32 52 52
NRG4 0.035 0.09 0.32 32 -0.32 8 40
heart development -0.028 0.07 -10000 0 -0.36 4 4
neural crest cell migration -0.051 0.074 -10000 0 -0.24 29 29
ERBB2 0.001 0.032 0.29 3 -10000 0 3
WWOX/E4ICDs -0.022 0.075 -10000 0 -0.3 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.004 0.09 0.29 1 -0.28 9 10
apoptosis 0.14 0.2 0.39 155 -10000 0 155
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.041 0.098 -10000 0 -0.29 24 24
ErbB4/ErbB2/epiregulin -0.001 0.11 0.31 4 -0.25 20 24
ErbB4/ErbB4/betacellulin/betacellulin -0.025 0.082 -10000 0 -0.3 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.013 0.11 0.32 1 -0.32 5 6
MDM2 -0.026 0.073 0.24 14 -0.29 1 15
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.032 0.076 -10000 0 -0.3 1 1
STAT5A -0.03 0.071 -10000 0 -0.36 3 3
ErbB4/EGFR/neuregulin 1 beta -0.033 0.08 -10000 0 -0.25 24 24
DLG4 0.019 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.025 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.021 0.069 -10000 0 -0.28 2 2
STAT5A (dimer) -0.024 0.1 -10000 0 -0.37 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.022 0.082 -10000 0 -0.34 5 5
LRIG1 0.019 0.023 -10000 0 -0.32 2 2
EREG 0.013 0.18 0.32 72 -0.32 73 145
BTC 0.013 0.05 -10000 0 -0.32 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.028 0.068 -10000 0 -0.38 3 3
ERBB4 -0.035 0.068 -10000 0 -0.32 1 1
STAT5B 0.02 0.003 -10000 0 -10000 0 0
YAP1 -0.007 0.066 -10000 0 -0.47 8 8
GRB2 0.02 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.001 0.078 -10000 0 -10000 0 0
glial cell differentiation 0.021 0.069 0.27 2 -10000 0 2
WWOX 0.02 0.005 -10000 0 -10000 0 0
cell proliferation -0.06 0.1 0.33 3 -0.39 11 14
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.012 0.029 -10000 0 -0.21 7 7
EPHB2 0.054 0.095 0.32 52 -10000 0 52
Syndecan-2/TACI 0.024 0.058 0.22 29 -0.18 8 37
LAMA1 0.025 0.067 0.32 15 -0.32 6 21
Syndecan-2/alpha2 ITGB1 0.007 0.08 0.24 9 -0.17 63 72
HRAS 0.02 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK -0.006 0.016 -10000 0 -0.18 4 4
ITGA5 0.02 0.021 0.32 1 -0.32 1 2
BAX -0.013 0.014 -10000 0 -10000 0 0
EPB41 0.02 0.003 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.018 -10000 0 -0.17 4 4
LAMA3 -0.043 0.13 -10000 0 -0.32 84 84
EZR 0.019 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.044 0.13 -10000 0 -0.32 86 86
Syndecan-2/MMP2 0.014 0.022 0.22 1 -0.19 4 5
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.038 0.23 12 -0.23 2 14
dendrite morphogenesis 0.037 0.071 0.23 52 -0.19 4 56
Syndecan-2/GM-CSF 0.008 0.055 0.24 7 -0.19 24 31
determination of left/right symmetry -0.008 0.02 -10000 0 -0.22 4 4
Syndecan-2/PKC delta 0.014 0.02 -10000 0 -0.19 4 4
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
MAPK3 -0.002 0.073 0.18 46 -0.18 23 69
MAPK1 0 0.071 0.18 46 -0.18 18 64
Syndecan-2/RACK1 0.023 0.02 -10000 0 -0.16 4 4
NF1 0.02 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.008 0.02 -10000 0 -0.22 4 4
ITGA2 0.026 0.053 0.32 12 -0.32 2 14
MAPK8 -0.011 0.017 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.041 0.06 0.25 23 -0.19 6 29
Syndecan-2/Kininogen 0.026 0.056 0.22 31 -0.18 4 35
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC 0.003 0.061 0.17 52 -0.16 2 54
Syndecan-2/CASK/Protein 4.1 0.013 0.018 -10000 0 -0.17 4 4
extracellular matrix organization 0.014 0.02 -10000 0 -0.19 4 4
actin cytoskeleton reorganization 0.012 0.029 -10000 0 -0.21 7 7
Syndecan-2/Caveolin-2/Ras -0.006 0.072 -10000 0 -0.17 71 71
Syndecan-2/Laminin alpha3 -0.017 0.073 -10000 0 -0.19 71 71
Syndecan-2/RasGAP 0.03 0.023 -10000 0 -0.16 4 4
alpha5/beta1 Integrin 0.03 0.017 0.23 1 -0.23 1 2
PRKCD 0.02 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.038 0.071 0.23 52 -0.19 4 56
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.018 0.023 0.16 5 -10000 0 5
RHOA 0.02 0.004 -10000 0 -10000 0 0
SDCBP 0.019 0.006 -10000 0 -10000 0 0
TNFRSF13B 0.034 0.082 0.32 29 -0.32 5 34
RASA1 0.02 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.038 0.23 12 -0.23 2 14
Syndecan-2/Synbindin 0.014 0.017 -10000 0 -0.18 3 3
TGFB1 0.02 0.004 -10000 0 -10000 0 0
CASP3 0.005 0.064 0.18 51 -0.17 4 55
FN1 0.018 0.032 -10000 0 -0.32 4 4
Syndecan-2/IL8 0.02 0.048 0.23 17 -0.19 7 24
SDC2 -0.008 0.02 -10000 0 -0.22 4 4
KNG1 0.038 0.076 0.32 31 -10000 0 31
Syndecan-2/Neurofibromin 0.014 0.019 -10000 0 -0.18 4 4
TRAPPC4 0.02 0.004 -10000 0 -10000 0 0
CSF2 0.003 0.092 0.32 7 -0.32 29 36
Syndecan-2/TGFB1 0.014 0.02 -10000 0 -0.19 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.018 -10000 0 -0.17 4 4
Syndecan-2/Ezrin 0.022 0.022 -10000 0 -0.17 4 4
PRKACA 0.007 0.063 0.18 53 -0.17 2 55
angiogenesis 0.02 0.048 0.23 17 -0.19 7 24
MMP2 0.021 0.015 0.32 1 -10000 0 1
IL8 0.028 0.066 0.32 17 -0.32 4 21
calcineurin-NFAT signaling pathway 0.024 0.058 0.22 29 -0.18 8 37
Ceramide signaling pathway

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
SPHK2 -0.019 0.032 -10000 0 -0.23 10 10
MAP4K4 -0.008 0.043 0.14 2 -0.26 4 6
BAG4 0.018 0.007 -10000 0 -10000 0 0
PKC zeta/ceramide 0.002 0.064 -10000 0 -0.18 49 49
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.021 0.036 0.32 4 -0.32 2 6
BAX -0.009 0.076 -10000 0 -0.35 19 19
RIPK1 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.005 0.11 0.72 11 -10000 0 11
BAD -0.013 0.06 0.2 2 -0.18 49 51
SMPD1 0.006 0.054 0.2 10 -0.2 4 14
RB1 -0.013 0.058 0.12 1 -0.18 49 50
FADD/Caspase 8 0.001 0.055 0.18 7 -0.29 5 12
MAP2K4 -0.014 0.059 0.17 7 -0.17 47 54
NSMAF 0.019 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.063 0.2 9 -0.17 48 57
EGF 0.072 0.12 0.32 84 -0.32 4 88
mol:ceramide -0.009 0.063 0.12 6 -0.18 49 55
MADD 0.02 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.027 -10000 0 -0.23 7 7
ASAH1 0.017 0.018 -10000 0 -0.32 1 1
negative regulation of cell cycle -0.013 0.058 0.12 1 -0.17 49 50
cell proliferation 0.001 0.067 0.2 5 -0.2 6 11
BID -0.004 0.12 -10000 0 -0.61 14 14
MAP3K1 -0.01 0.063 0.18 8 -0.18 48 56
EIF2A -0.014 0.068 0.21 16 -0.17 44 60
TRADD 0.02 0.004 -10000 0 -10000 0 0
CRADD 0.021 0.014 0.32 1 -10000 0 1
MAPK3 -0.014 0.06 0.19 9 -0.17 36 45
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.063 0.19 9 -0.18 33 42
Cathepsin D/ceramide 0.003 0.064 -10000 0 -0.18 49 49
FADD -0.007 0.041 0.14 2 -0.26 4 6
KSR1 -0.01 0.067 0.22 9 -0.18 49 58
MAPK8 -0.01 0.065 -10000 0 -0.25 6 6
PRKRA -0.011 0.063 0.23 5 -0.18 48 53
PDGFA 0.012 0.048 -10000 0 -0.32 9 9
TRAF2 0.02 0.004 -10000 0 -10000 0 0
IGF1 0.014 0.05 0.32 1 -0.32 9 10
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.063 0.12 6 -0.18 49 55
CTSD 0.02 0.003 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.03 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.002 0.071 0.21 5 -0.22 6 11
PRKCD 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.018 0.028 -10000 0 -0.32 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.027 -10000 0 -0.23 7 7
RelA/NF kappa B1 0.03 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.02 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.001 0.044 0.16 2 -0.28 3 5
TNFR1A/BAG4/TNF-alpha 0.027 0.044 0.22 1 -0.19 15 16
mol:Sphingosine-1-phosphate -0.019 0.032 -10000 0 -0.23 10 10
MAP2K1 -0.016 0.061 0.18 12 -0.17 46 58
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
CYCS 0.004 0.052 0.18 4 -0.18 14 18
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.062 0.2 9 -0.18 44 53
TNF-alpha/TNFR1A/FAN 0.028 0.043 0.22 1 -0.2 14 15
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.045 -10000 0 -0.32 3 3
MAP2K2 -0.017 0.059 0.19 9 -0.17 43 52
SMPD3 0.007 0.055 0.19 5 -0.26 7 12
TNF 0.009 0.065 0.32 1 -0.32 16 17
PKC zeta/PAR4 0.028 0.022 -10000 0 -0.23 3 3
mol:PHOSPHOCHOLINE -0.019 0.062 0.17 9 -0.14 50 59
NF kappa B1/RelA/I kappa B alpha 0.048 0.03 -10000 0 -0.17 2 2
AIFM1 -0.002 0.061 0.16 5 -0.19 14 19
BCL2 0.019 0.022 0.32 1 -0.32 1 2
FAS signaling pathway (CD95)

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
SPTAN1 -0.013 0.034 0.21 1 -0.2 11 12
RFC1 -0.009 0.041 0.22 7 -0.21 9 16
PRKDC 0 0.057 0.22 24 -0.19 8 32
RIPK1 0.022 0.006 -10000 0 -10000 0 0
CASP7 -0.014 0.095 -10000 0 -0.63 9 9
FASLG/FAS/FADD/FAF1 0.004 0.054 0.16 23 -0.26 3 26
MAP2K4 -0.061 0.14 0.23 3 -0.31 92 95
mol:ceramide -0.021 0.078 -10000 0 -0.26 14 14
GSN -0.013 0.032 -10000 0 -0.2 11 11
FASLG/FAS/FADD/FAF1/Caspase 8 -0.004 0.06 0.19 2 -0.29 3 5
FAS 0.006 0.039 -10000 0 -0.33 4 4
BID -0.021 0.029 0.5 1 -0.19 3 4
MAP3K1 -0.031 0.1 0.24 2 -0.43 12 14
MAP3K7 0.011 0.017 -10000 0 -10000 0 0
RB1 -0.012 0.027 -10000 0 -0.19 9 9
CFLAR 0.023 0.005 -10000 0 -10000 0 0
HGF/MET 0.008 0.097 0.22 10 -0.22 60 70
ARHGDIB -0.01 0.038 0.22 5 -0.2 9 14
FADD 0.009 0.022 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.034 0.2 13 -10000 0 13
NFKB1 -0.024 0.1 -10000 0 -0.6 6 6
MAPK8 -0.1 0.2 0.24 1 -0.46 105 106
DFFA -0.012 0.032 0.21 2 -0.19 10 12
DNA fragmentation during apoptosis -0.012 0.037 0.21 4 -0.18 13 17
FAS/FADD/MET 0.016 0.057 0.22 6 -0.2 16 22
CFLAR/RIP1 0.033 0.01 -10000 0 -10000 0 0
FAIM3 0.021 0.03 0.32 3 -0.32 1 4
FAF1 0.008 0.025 -10000 0 -10000 0 0
PARP1 -0.012 0.035 0.22 2 -0.2 11 13
DFFB -0.011 0.035 0.22 4 -0.19 10 14
CHUK -0.029 0.095 -10000 0 -0.56 6 6
FASLG 0.007 0.038 0.32 1 -0.33 3 4
FAS/FADD 0.012 0.038 -10000 0 -0.24 4 4
HGF 0.008 0.076 0.32 4 -0.32 20 24
LMNA -0.009 0.052 0.19 20 -0.24 3 23
CASP6 -0.012 0.034 0.21 2 -0.2 10 12
CASP10 0.007 0.032 -10000 0 -0.33 2 2
CASP3 -0.006 0.024 -10000 0 -0.26 3 3
PTPN13 -0.013 0.1 -10000 0 -0.32 46 46
CASP8 -0.021 0.025 0.29 1 -0.23 4 5
IL6 -0.24 0.47 -10000 0 -1.1 107 107
MET 0.013 0.069 0.32 6 -0.32 14 20
ICAD/CAD -0.013 0.041 0.3 4 -0.18 10 14
FASLG/FAS/FADD/FAF1/Caspase 10 -0.021 0.079 -10000 0 -0.26 14 14
activation of caspase activity by cytochrome c -0.021 0.029 0.5 1 -0.19 3 4
PAK2 -0.009 0.043 0.22 9 -0.2 9 18
BCL2 0.019 0.022 0.32 1 -0.32 1 2
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.007 0.066 0.32 18 -10000 0 18
PI3K Class IB/PDE3B 0.007 0.066 -10000 0 -0.32 18 18
PDE3B 0.007 0.067 -10000 0 -0.32 18 18
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.014 0.08 0.21 33 -10000 0 33
GNAI2 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.013 0.05 0.21 1 -0.19 25 26
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.03 0.32 2 -0.32 2 4
RhoA/GTP -0.014 0.081 -10000 0 -0.22 33 33
negative regulation of cAMP metabolic process -0.018 0.077 -10000 0 -0.19 66 66
GNAZ -0.009 0.095 -10000 0 -0.32 39 39
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
S1PR5 0 0.082 0.32 1 -0.32 27 28
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.018 0.078 -10000 0 -0.2 65 65
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.017 -10000 0 -0.32 1 1
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.009 0.027 0.11 1 -0.22 2 3
NFATC2 -0.015 0.042 0.11 1 -0.2 16 17
NFATC3 -0.01 0.024 0.11 1 -10000 0 1
CD40LG -0.037 0.14 0.29 18 -0.39 29 47
PTGS2 -0.041 0.15 0.29 21 -0.36 47 68
JUNB 0.017 0.028 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.02 -10000 0 -10000 0 0
CALM1 0.013 0.02 -10000 0 -10000 0 0
JUN 0.01 0.038 -10000 0 -0.33 4 4
mol:Ca2+ -0.001 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.011 -10000 0 -10000 0 0
FOSL1 0.031 0.068 0.32 20 -0.32 3 23
CREM 0.02 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.015 0.093 0.27 14 -0.27 10 24
FOS -0.009 0.086 -10000 0 -0.33 30 30
IFNG -0.022 0.15 0.34 30 -0.36 24 54
AP-1/NFAT1-c-4 0.01 0.16 0.46 14 -0.4 22 36
FASLG -0.03 0.13 0.29 18 -0.35 22 40
NFAT1-c-4/ICER1 0.006 0.063 0.26 1 -0.24 6 7
IL2RA -0.019 0.15 0.34 36 -0.36 21 57
FKBP12/FK506 0.015 0.003 -10000 0 -10000 0 0
CSF2 -0.04 0.15 0.32 19 -0.38 38 57
JunB/Fra1/NFAT1-c-4 0.018 0.082 0.3 9 -0.23 9 18
IL4 -0.035 0.12 0.28 16 -0.35 21 37
IL2 0.001 0.1 -10000 0 -0.82 7 7
IL3 -0.011 0.12 -10000 0 -0.62 18 18
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
BATF3 0.02 0.015 0.32 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.006 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.02 0.005 -10000 0 -10000 0 0
SVIL 0.021 0.004 -10000 0 -10000 0 0
ZNF318 0.019 0.01 -10000 0 -10000 0 0
JMJD2C 0.007 0.028 0.13 24 -10000 0 24
T-DHT/AR/Ubc9 0.004 0.086 0.18 4 -0.2 60 64
CARM1 0.02 0.005 -10000 0 -10000 0 0
PRDX1 0.02 0.005 -10000 0 -10000 0 0
PELP1 0.018 0.008 -10000 0 -10000 0 0
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.019 0.008 -10000 0 -10000 0 0
PTK2B 0.017 0.018 -10000 0 -0.32 1 1
MED1 0.019 0.007 -10000 0 -10000 0 0
MAK 0.008 0.061 -10000 0 -0.32 15 15
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.018 0.028 -10000 0 -0.32 3 3
GSN 0.021 0.005 -10000 0 -10000 0 0
NCOA2 0.016 0.032 -10000 0 -0.32 4 4
NCOA6 0.02 0.005 -10000 0 -10000 0 0
DNA-PK 0.035 0.018 -10000 0 -10000 0 0
NCOA4 0.021 0.002 -10000 0 -10000 0 0
PIAS3 0.02 0.005 -10000 0 -10000 0 0
cell proliferation -0.013 0.11 -10000 0 -0.6 16 16
XRCC5 0.02 0.006 -10000 0 -10000 0 0
UBE3A 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.004 0.094 0.17 5 -0.2 76 81
FHL2 0.041 0.11 0.31 49 -10000 0 49
RANBP9 0.021 0.004 -10000 0 -10000 0 0
JMJD1A -0.009 0.037 -10000 0 -0.13 41 41
CDK6 0.019 0.017 -10000 0 -0.32 1 1
TGFB1I1 0.019 0.028 -10000 0 -0.32 3 3
T-DHT/AR/CyclinD1 0.003 0.087 0.18 5 -0.2 60 65
XRCC6 0.019 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.016 0.11 0.31 5 -0.22 50 55
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.019 0.008 -10000 0 -10000 0 0
BRCA1 0.021 0.015 0.32 1 -10000 0 1
TCF4 0.016 0.024 -10000 0 -0.32 2 2
CDKN2A 0.097 0.14 0.32 126 -10000 0 126
SRF 0.039 0.046 0.15 38 -10000 0 38
NKX3-1 -0.029 0.12 -10000 0 -0.48 21 21
KLK3 -0.008 0.06 -10000 0 -10000 0 0
TMF1 0.02 0.004 -10000 0 -10000 0 0
HNRNPA1 0.02 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 -0.016 0.006 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.004 0.087 0.18 4 -0.2 61 65
AR -0.022 0.12 0.32 1 -0.33 59 60
UBA3 0.02 0.004 -10000 0 -10000 0 0
PATZ1 0.019 0.007 -10000 0 -10000 0 0
PAWR 0.02 0.003 -10000 0 -10000 0 0
PRKDC 0.018 0.008 -10000 0 -10000 0 0
PA2G4 0.019 0.007 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.005 0.077 0.17 4 -0.18 58 62
RPS6KA3 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.005 0.086 0.18 5 -0.2 60 65
LATS2 0.019 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.006 0.078 0.17 4 -0.18 59 63
Cyclin D3/CDK11 p58 0.014 0.004 -10000 0 -10000 0 0
VAV3 0.018 0.035 0.32 1 -0.32 4 5
KLK2 0.008 0.081 0.31 19 -0.34 3 22
CASP8 0.019 0.017 -10000 0 -0.32 1 1
T-DHT/AR/TIF2/CARM1 0.013 0.081 0.19 3 -0.18 54 57
TMPRSS2 -0.058 0.22 -10000 0 -0.75 40 40
CCND1 0.016 0.039 -10000 0 -0.32 6 6
PIAS1 0.021 0.005 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.019 0.069 4 -0.059 19 23
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.02 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.005 0.084 0.17 5 -0.2 57 62
CMTM2 -0.045 0.13 -10000 0 -0.32 87 87
SNURF 0.007 0.065 -10000 0 -0.32 17 17
ZMIZ1 0.02 0.027 -10000 0 -10000 0 0
CCND3 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.018 0.008 -10000 0 -10000 0 0
FKBP4 0.02 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.02 0.005 -10000 0 -9999 0 0
PLK4 0.037 0.068 0.32 25 -9999 0 25
regulation of centriole replication -0.006 0.04 0.16 25 -9999 0 25
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.013 0.045 -10000 0 -0.32 8 8
LRPAP1 0.02 0.003 -10000 0 -10000 0 0
NUDC 0.02 0.003 -10000 0 -10000 0 0
RELN/LRP8 0.016 0.083 0.22 12 -0.19 55 67
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.019 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.029 0.067 0.17 18 -0.18 53 71
IQGAP1/CaM 0.029 0.008 -10000 0 -10000 0 0
DAB1 0.023 0.037 0.32 7 -10000 0 7
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
PLA2G7 0.023 0.043 0.32 7 -0.32 2 9
CALM1 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.033 0.027 0.23 8 -10000 0 8
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.02 0.003 -10000 0 -10000 0 0
CDK5R1 0.028 0.048 0.32 12 -10000 0 12
LIS1/Poliovirus Protein 3A -0.012 0.004 -10000 0 -10000 0 0
CDK5R2 0.1 0.14 0.32 128 -10000 0 128
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.009 0.087 0.24 9 -0.2 59 68
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.003 0.09 0.29 17 -0.21 2 19
MAP1B 0.003 0.014 -10000 0 -0.22 1 1
RAC1 0.004 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.029 0.072 0.19 24 -10000 0 24
RELN -0.019 0.12 0.32 5 -0.32 56 61
PAFAH/LIS1 -0.014 0.032 0.22 7 -0.2 2 9
LIS1/CLIP170 -0.017 0.007 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.02 0.061 0.16 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.021 0.09 0.26 2 -0.3 18 20
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.001 0.077 0.22 19 -0.22 1 20
LIS1/IQGAP1 -0.017 0.007 -10000 0 -10000 0 0
RHOA 0.005 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.015 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.057 0.32 17 -10000 0 17
PAFAH1B2 0.02 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.009 0.03 -10000 0 -0.18 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.001 0.091 0.29 16 -0.22 1 17
LRP8 0.026 0.042 0.32 9 -10000 0 9
NDEL1/Katanin 60 0.001 0.091 0.29 18 -0.22 2 20
P39/CDK5 0.017 0.12 0.2 117 -10000 0 117
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.017 0.007 -10000 0 -10000 0 0
CDK5 -0.034 0.058 0.17 11 -0.17 49 60
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.014 0.006 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.01 0.079 0.25 8 -0.18 54 62
RELN/VLDLR 0.019 0.086 0.22 11 -0.19 59 70
CDC42 0.005 0.002 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.005 0.12 0.24 1 -0.34 39 40
PTP1B/AKT1 0.014 0.071 0.2 2 -0.3 9 11
FYN 0.018 0.017 -10000 0 -0.32 1 1
p210 bcr-abl/PTP1B 0.007 0.075 0.22 4 -0.32 9 13
EGFR 0.015 0.043 0.32 1 -0.33 6 7
EGF/EGFR 0.036 0.095 0.22 46 -0.39 5 51
CSF1 0.018 0.028 -10000 0 -0.32 3 3
AKT1 0.018 0.009 -10000 0 -10000 0 0
INSR 0.02 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.033 0.092 0.23 38 -0.31 8 46
Insulin Receptor/Insulin 0.023 0.069 -10000 0 -0.38 4 4
HCK 0.007 0.065 -10000 0 -0.32 17 17
CRK 0.019 0.006 -10000 0 -10000 0 0
TYK2 0.003 0.072 0.29 3 -0.4 5 8
EGF 0.072 0.12 0.32 84 -0.33 4 88
YES1 0.02 0.005 -10000 0 -10000 0 0
CAV1 -0.053 0.1 0.23 5 -0.32 24 29
TXN 0.021 0.015 0.32 1 -10000 0 1
PTP1B/IRS1/GRB2 0.023 0.072 0.25 1 -0.31 7 8
cell migration -0.007 0.075 0.32 9 -0.22 4 13
STAT3 0.021 0.003 -10000 0 -10000 0 0
PRLR 0.023 0.092 0.32 25 -0.32 14 39
ITGA2B -0.008 0.1 0.32 4 -0.33 42 46
CSF1R 0.015 0.042 -10000 0 -0.32 7 7
Prolactin Receptor/Prolactin 0.03 0.072 0.24 31 -0.22 14 45
FGR -0.004 0.089 -10000 0 -0.32 33 33
PTP1B/p130 Cas 0.015 0.073 0.22 3 -0.32 8 11
Crk/p130 Cas 0.022 0.074 0.24 2 -0.35 6 8
DOK1 0.004 0.08 0.23 4 -0.34 11 15
JAK2 -0.004 0.12 0.24 3 -0.34 39 42
Jak2/Leptin Receptor/Leptin 0.026 0.095 0.22 14 -0.32 10 24
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
PTPN1 0.007 0.076 0.22 4 -0.33 9 13
LYN 0.019 0.006 -10000 0 -10000 0 0
CDH2 0.045 0.098 0.32 45 -0.32 5 50
SRC 0.008 0.09 -10000 0 -0.43 15 15
ITGB3 0.028 0.075 0.32 22 -0.33 5 27
CAT1/PTP1B -0.023 0.14 0.3 5 -0.38 37 42
CAPN1 0.02 0.005 -10000 0 -10000 0 0
CSK 0.02 0.003 -10000 0 -10000 0 0
PI3K 0.027 0.066 -10000 0 -0.31 4 4
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.089 0.21 11 -0.28 13 24
negative regulation of transcription -0.004 0.12 0.24 3 -0.33 39 42
FCGR2A 0.015 0.032 -10000 0 -0.32 4 4
FER 0.021 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.015 0.095 0.23 26 -0.24 46 72
BLK 0.058 0.11 0.32 64 -0.32 1 65
Insulin Receptor/Insulin/Shc 0.032 0.017 -10000 0 -10000 0 0
RHOA 0.02 0.005 -10000 0 -10000 0 0
LEPR -0.01 0.098 -10000 0 -0.32 42 42
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
p210 bcr-abl/Grb2 0.02 0.004 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.039 0.16 0.22 3 -0.37 56 59
PRL 0.023 0.048 0.32 11 -10000 0 11
SOCS3 0 0.14 -10000 0 -1.1 7 7
SPRY2 0.019 0.018 -10000 0 -0.33 1 1
Insulin Receptor/Insulin/IRS1 0.037 0.015 -10000 0 -0.18 1 1
CSF1/CSF1R 0.021 0.079 0.22 1 -0.35 9 10
Ras protein signal transduction 0.009 0.12 0.54 19 -10000 0 19
IRS1 0.02 0.016 -10000 0 -0.32 1 1
INS 0.011 0.014 -10000 0 -10000 0 0
LEP 0.048 0.091 0.32 46 -10000 0 46
STAT5B 0.008 0.087 0.22 6 -0.3 18 24
STAT5A 0.008 0.088 0.22 6 -0.29 19 25
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.073 0.22 3 -0.31 9 12
CSN2 0.02 0.064 0.56 1 -10000 0 1
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
LAT 0.014 0.065 -10000 0 -0.38 9 9
YBX1 0.023 0.005 -10000 0 -10000 0 0
LCK 0.02 0.027 0.32 1 -0.32 2 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
NOX4 0.03 0.052 0.32 14 -10000 0 14
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.032 0.1 0.25 31 -0.33 13 44
FYN 0 0.12 0.26 11 -0.39 20 31
LAT/GRAP2/SLP76 0.012 0.1 0.25 4 -0.37 18 22
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.004 0.095 0.24 10 -0.31 23 33
B2M 0.018 0.013 -10000 0 -10000 0 0
IKBKG -0.002 0.034 0.1 10 -0.1 5 15
MAP3K8 0.019 0.016 -10000 0 -0.32 1 1
mol:Ca2+ -0.016 0.014 0.042 8 -0.055 12 20
integrin-mediated signaling pathway 0.024 0.017 -10000 0 -0.19 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.009 0.12 0.24 8 -0.41 24 32
TRPV6 0.007 0.26 1.2 19 -10000 0 19
CD28 0.018 0.018 -10000 0 -0.33 1 1
SHC1 0.016 0.12 0.26 38 -0.38 16 54
receptor internalization -0.007 0.11 0.2 1 -0.4 23 24
PRF1 -0.04 0.24 -10000 0 -0.95 28 28
KRAS 0.019 0.006 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
COT/AKT1 0.005 0.082 0.23 9 -0.27 18 27
LAT -0.004 0.11 0.27 8 -0.36 24 32
EntrezGene:6955 -0.001 0.005 -10000 0 -0.033 2 2
CD3D 0.016 0.031 -10000 0 -0.34 3 3
CD3E 0.015 0.039 -10000 0 -0.34 5 5
CD3G 0.011 0.052 -10000 0 -0.33 10 10
RASGRP2 -0.008 0.038 -10000 0 -0.15 27 27
RASGRP1 -0.014 0.1 0.25 6 -0.33 19 25
HLA-A 0.018 0.012 -10000 0 -10000 0 0
RASSF5 0.018 0.023 -10000 0 -0.32 2 2
RAP1A/GTP/RAPL 0.024 0.017 -10000 0 -0.19 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.049 0.13 31 -0.12 10 41
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.035 -10000 0 -0.15 14 14
PRKCA -0.008 0.052 0.15 5 -0.2 10 15
GRAP2 0.01 0.057 -10000 0 -0.32 13 13
mol:IP3 0.013 0.087 0.17 39 -0.28 18 57
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.011 0.08 0.15 1 -0.34 16 17
ORAI1 -0.025 0.21 0.37 4 -0.98 19 23
CSK -0.003 0.11 0.27 3 -0.37 22 25
B7 family/CD28 0.014 0.12 0.24 1 -0.42 23 24
CHUK 0.02 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.006 0.12 -10000 0 -0.4 24 24
PTPN6 -0.008 0.1 0.22 4 -0.36 21 25
VAV1 -0.007 0.11 0.23 2 -0.38 22 24
Monovalent TCR/CD3 0.001 0.05 -10000 0 -0.26 12 12
CBL 0.02 0.004 -10000 0 -10000 0 0
LCK 0.002 0.11 0.26 9 -0.41 16 25
PAG1 0.004 0.11 0.24 10 -0.36 21 31
RAP1A 0.02 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.007 0.11 0.2 1 -0.4 22 23
CD80 0.012 0.051 -10000 0 -0.33 10 10
CD86 0.013 0.048 -10000 0 -0.33 9 9
PDK1/CARD11/BCL10/MALT1 0.003 0.049 0.13 5 -0.18 11 16
HRAS 0.02 0.004 -10000 0 -10000 0 0
GO:0035030 -0.018 0.1 0.19 5 -0.33 28 33
CD8A 0.016 0.037 0.32 1 -0.33 4 5
CD8B 0.018 0.043 0.32 3 -0.34 4 7
PTPRC 0.012 0.048 -10000 0 -0.33 9 9
PDK1/PKC theta -0.015 0.11 0.29 10 -0.34 27 37
CSK/PAG1 0 0.11 0.23 13 -0.38 16 29
SOS1 0.021 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.026 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 0.015 0.12 0.23 1 -0.39 22 23
STIM1 -0.002 0.071 1.2 1 -10000 0 1
RAS family/GTP 0.011 0.057 0.18 10 -0.16 12 22
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.009 0.12 -10000 0 -0.42 23 23
mol:DAG -0.02 0.063 0.091 6 -0.24 21 27
RAP1A/GDP 0.008 0.023 0.078 9 -0.06 5 14
PLCG1 0.02 0.005 -10000 0 -10000 0 0
CD247 0.016 0.025 -10000 0 -0.32 2 2
cytotoxic T cell degranulation -0.037 0.23 -10000 0 -0.9 28 28
RAP1A/GTP -0.002 0.015 -10000 0 -0.059 27 27
mol:PI-3-4-5-P3 -0.006 0.11 0.22 9 -0.34 24 33
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.017 0.1 0.22 15 -0.36 17 32
NRAS 0.02 0.004 -10000 0 -10000 0 0
ZAP70 0.016 0.039 -10000 0 -0.33 6 6
GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.002 0.097 0.26 2 -0.35 19 21
MALT1 0.019 0.006 -10000 0 -10000 0 0
TRAF6 0.02 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.026 0.048 0.3 3 -0.3 6 9
CARD11 0.034 0.067 0.32 24 -10000 0 24
PRKCB -0.012 0.06 0.14 3 -0.22 19 22
PRKCE -0.01 0.056 0.15 7 -0.21 12 19
PRKCQ -0.017 0.12 0.24 7 -0.38 29 36
LCP2 0.018 0.028 -10000 0 -0.32 3 3
BCL10 0.02 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.002 0.085 0.22 11 -0.27 22 33
IKK complex 0.007 0.051 0.16 21 -0.11 4 25
RAS family/GDP -0.001 0.009 -10000 0 -0.039 3 3
MAP3K14 -0.005 0.062 0.2 8 -0.21 13 21
PDPK1 -0.005 0.094 0.25 13 -0.3 21 34
TCR/CD3/MHC I/CD8/Fyn -0.014 0.12 -10000 0 -0.44 20 20
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.013 0.095 -10000 0 -0.31 28 28
TBX21 -0.099 0.31 -10000 0 -1.1 30 30
B2M 0.019 0.009 -10000 0 -10000 0 0
TYK2 0.01 0.027 -10000 0 -10000 0 0
IL12RB1 0.002 0.062 -10000 0 -0.35 12 12
GADD45B -0.092 0.28 -10000 0 -1 27 27
IL12RB2 0.033 0.092 0.32 37 -0.34 3 40
GADD45G -0.085 0.28 -10000 0 -1 23 23
natural killer cell activation -0.003 0.013 -10000 0 -10000 0 0
RELB 0.02 0.005 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
IL18 0.007 0.051 -10000 0 -0.33 9 9
IL2RA 0.04 0.08 0.32 33 -0.32 1 34
IFNG 0.034 0.087 0.32 30 -0.32 7 37
STAT3 (dimer) -0.073 0.23 -10000 0 -0.76 29 29
HLA-DRB5 -0.016 0.1 -10000 0 -0.33 45 45
FASLG -0.073 0.27 -10000 0 -1 22 22
NF kappa B2 p52/RelB -0.071 0.27 -10000 0 -0.93 25 25
CD4 0.01 0.049 -10000 0 -0.32 9 9
SOCS1 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.014 0.033 -10000 0 -0.34 3 3
CD3E 0.012 0.039 -10000 0 -0.33 5 5
CD3G 0.009 0.053 -10000 0 -0.33 10 10
IL12Rbeta2/JAK2 0.031 0.071 0.24 30 -0.24 4 34
CCL3 -0.083 0.27 -10000 0 -1 20 20
CCL4 -0.084 0.27 -10000 0 -1.1 21 21
HLA-A 0.02 0.009 -10000 0 -10000 0 0
IL18/IL18R 0.015 0.088 -10000 0 -0.25 34 34
NOS2 -0.13 0.39 -10000 0 -1.1 52 52
IL12/IL12R/TYK2/JAK2/SPHK2 -0.014 0.099 -10000 0 -0.31 30 30
IL1R1 -0.084 0.27 -10000 0 -1 21 21
IL4 0.003 0.027 -10000 0 -10000 0 0
JAK2 0.009 0.031 -10000 0 -0.32 1 1
EntrezGene:6957 -0.001 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.018 0.13 -10000 0 -0.87 8 8
RAB7A -0.074 0.23 -10000 0 -0.85 20 20
lysosomal transport -0.069 0.22 -10000 0 -0.79 20 20
FOS -0.11 0.33 -10000 0 -1 49 49
STAT4 (dimer) -0.071 0.26 -10000 0 -0.9 24 24
STAT5A (dimer) -0.064 0.28 -10000 0 -0.89 28 28
GZMA -0.084 0.27 -10000 0 -1.1 20 20
GZMB -0.093 0.3 -10000 0 -1.1 25 25
HLX 0.016 0.032 -10000 0 -0.32 4 4
LCK -0.088 0.29 -10000 0 -1 25 25
TCR/CD3/MHC II/CD4 -0.03 0.12 -10000 0 -0.32 44 44
IL2/IL2R 0.057 0.057 0.22 33 -0.25 4 37
MAPK14 -0.09 0.29 -10000 0 -0.96 29 29
CCR5 -0.081 0.26 -10000 0 -1.1 20 20
IL1B -0.009 0.085 -10000 0 -0.34 26 26
STAT6 -0.009 0.075 -10000 0 -0.31 1 1
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
NFKB2 0.021 0.003 -10000 0 -10000 0 0
IL12B 0.012 0.041 0.3 4 -0.34 1 5
CD8A 0.018 0.037 0.32 1 -0.34 4 5
CD8B 0.019 0.041 0.32 3 -0.33 4 7
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.013 0.095 0.3 28 -10000 0 28
IL2RB 0.018 0.023 -10000 0 -0.32 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.063 0.23 -10000 0 -0.8 24 24
IL2RG 0.017 0.036 -10000 0 -0.32 5 5
IL12 0.018 0.048 0.23 2 -0.25 4 6
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
CD247 0.014 0.027 -10000 0 -0.32 2 2
IL2 0.019 0.003 -10000 0 -10000 0 0
SPHK2 0.019 0.016 -10000 0 -0.32 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.048 0.33 1 -0.34 5 6
IL12/IL12R/TYK2/JAK2 -0.085 0.32 -10000 0 -1.2 24 24
MAP2K3 -0.097 0.29 -10000 0 -0.95 32 32
RIPK2 0.018 0.007 -10000 0 -10000 0 0
MAP2K6 -0.086 0.29 -10000 0 -0.95 30 30
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.002 0.069 -10000 0 -0.32 19 19
IL18RAP 0.001 0.069 -10000 0 -0.33 18 18
IL12Rbeta1/TYK2 0.011 0.054 -10000 0 -0.25 11 11
EOMES -0.013 0.16 -10000 0 -0.68 19 19
STAT1 (dimer) -0.059 0.24 -10000 0 -0.79 25 25
T cell proliferation -0.059 0.2 -10000 0 -0.64 25 25
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.071 -10000 0 -0.33 19 19
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.065 0.22 -10000 0 -0.66 32 32
ATF2 -0.083 0.26 0.45 1 -0.87 29 30
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.019 0.042 -10000 0 -0.23 10 10
PDGFRB 0.014 0.015 -10000 0 -10000 0 0
SPHK1 0.001 0.05 -10000 0 -0.64 2 2
mol:S1P -0.007 0.049 -10000 0 -0.55 2 2
S1P1/S1P/Gi -0.041 0.14 0.2 6 -0.37 51 57
GNAO1 0.016 0.033 0.31 2 -0.33 2 4
PDGFB-D/PDGFRB/PLCgamma1 -0.035 0.13 0.24 5 -0.35 49 54
PLCG1 -0.048 0.13 0.19 7 -0.36 49 56
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.014 0.015 -10000 0 -10000 0 0
GNAI2 0.016 0.015 -10000 0 -10000 0 0
GNAI3 0.016 0.015 -10000 0 -10000 0 0
GNAI1 0.015 0.022 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.028 -10000 0 -0.19 10 10
S1P1/S1P -0.02 0.059 0.21 1 -0.31 5 6
negative regulation of cAMP metabolic process -0.04 0.13 0.2 6 -0.36 51 57
MAPK3 -0.065 0.18 0.26 8 -0.54 49 57
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
KDR 0.009 0.052 -10000 0 -0.33 10 10
PLCB2 -0.015 0.067 0.27 4 -0.27 7 11
RAC1 0.018 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.024 0.046 -10000 0 -0.28 5 5
receptor internalization -0.021 0.052 -10000 0 -0.3 5 5
PTGS2 -0.094 0.29 0.34 3 -0.89 49 52
Rac1/GTP -0.023 0.046 -10000 0 -0.28 5 5
RHOA 0.02 0.004 -10000 0 -10000 0 0
VEGFA 0.016 0.014 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.04 0.13 0.2 6 -0.36 51 57
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.013 0.096 -10000 0 -0.33 39 39
MAPK1 -0.062 0.17 0.24 6 -0.53 47 53
S1P1/S1P/PDGFB-D/PDGFRB -0.01 0.071 0.22 2 -0.31 5 7
ABCC1 0.016 0.015 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.04 0.043 0.21 8 -0.18 10 18
ER alpha/Gai/GDP/Gbeta gamma -0.033 0.14 -10000 0 -0.48 26 26
AKT1 -0.059 0.23 -10000 0 -0.69 51 51
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.055 0.24 -10000 0 -0.7 52 52
mol:Ca2+ -0.021 0.068 -10000 0 -0.33 18 18
IGF1R 0.019 0.023 -10000 0 -0.32 2 2
E2/ER alpha (dimer)/Striatin 0.025 0.041 0.21 10 -0.19 9 19
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis 0.055 0.22 0.66 51 -10000 0 51
RhoA/GTP -0.023 0.024 -10000 0 -0.15 8 8
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.017 0.12 0.24 2 -0.39 26 28
regulation of stress fiber formation 0.014 0.055 0.24 1 -0.25 3 4
E2/ERA-ERB (dimer) 0.024 0.042 0.21 10 -0.19 10 20
KRAS 0.019 0.006 -10000 0 -10000 0 0
G13/GTP 0.024 0.037 0.2 10 -0.17 8 18
pseudopodium formation -0.014 0.055 0.25 3 -0.24 1 4
E2/ER alpha (dimer)/PELP1 0.024 0.04 0.21 9 -0.18 9 18
GRB2 0.02 0.004 -10000 0 -10000 0 0
GNG2 0.019 0.023 -10000 0 -0.32 2 2
GNAO1 0.02 0.03 0.32 2 -0.32 2 4
HRAS 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.038 0.16 0.24 3 -0.42 53 56
E2/ER beta (dimer) 0.014 0.011 -10000 0 -0.22 1 1
mol:GDP -0.001 0.064 0.18 11 -0.27 11 22
mol:NADP -0.038 0.16 0.24 3 -0.42 53 56
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 -0.021 0.071 -10000 0 -0.35 18 18
IGF-1R heterotetramer 0.019 0.023 -10000 0 -0.32 2 2
PLCB1 -0.008 0.067 -10000 0 -0.35 15 15
PLCB2 -0.01 0.071 -10000 0 -0.35 16 16
IGF1 0.014 0.05 0.32 1 -0.32 9 10
mol:L-citrulline -0.038 0.16 0.24 3 -0.42 53 56
RHOA 0.02 0.004 -10000 0 -10000 0 0
Gai/GDP -0.021 0.15 -10000 0 -0.62 23 23
JNK cascade 0.014 0.011 -10000 0 -0.22 1 1
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
ESR2 0.019 0.016 -10000 0 -0.32 1 1
GNAQ 0.019 0.016 -10000 0 -0.32 1 1
ESR1 0.019 0.065 0.32 10 -0.32 9 19
Gq family/GDP/Gbeta gamma -0.044 0.2 -10000 0 -0.73 34 34
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.013 0.058 -10000 0 -0.55 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.015 0.11 0.23 1 -0.38 24 25
GNAZ -0.009 0.095 -10000 0 -0.32 39 39
E2/ER alpha (dimer) 0.014 0.044 0.22 10 -0.22 9 19
STRN 0.02 0.016 -10000 0 -0.32 1 1
GNAL 0.017 0.046 0.32 3 -0.32 6 9
PELP1 0.019 0.006 -10000 0 -10000 0 0
MAPK11 -0.013 0.018 0.22 1 -0.19 3 4
GNAI2 0.02 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.017 -10000 0 -0.32 1 1
HBEGF -0.04 0.15 0.34 10 -0.45 32 42
cAMP biosynthetic process 0.018 0.04 0.14 12 -0.17 14 26
SRC -0.033 0.13 0.28 1 -0.45 25 26
PI3K 0.028 0.015 -10000 0 -0.23 1 1
GNB1 0.02 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.018 0.066 -10000 0 -0.29 7 7
SOS1 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.025 0.09 -10000 0 -0.34 22 22
Gs family/GTP 0.023 0.043 0.17 12 -0.17 14 26
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.014 -10000 0 -10000 0 0
vasodilation -0.036 0.15 0.23 3 -0.4 53 56
mol:DAG -0.021 0.071 -10000 0 -0.35 18 18
Gs family/GDP/Gbeta gamma 0.001 0.063 -10000 0 -0.29 9 9
MSN -0.015 0.057 0.26 3 -0.26 1 4
Gq family/GTP 0 0.074 -10000 0 -0.36 17 17
mol:PI-3-4-5-P3 -0.053 0.23 -10000 0 -0.67 52 52
NRAS 0.02 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.036 0.15 0.4 53 -0.23 3 56
GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.007 0.07 0.19 9 -0.28 9 18
NOS3 -0.041 0.17 0.24 2 -0.45 53 55
GNA11 0.019 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.031 0.16 0.32 3 -0.47 47 50
E2/ER alpha (dimer)/PELP1/Src -0.019 0.13 0.25 6 -0.41 25 31
ruffle organization -0.014 0.055 0.25 3 -0.24 1 4
ROCK2 -0.01 0.06 0.28 3 -10000 0 3
GNA14 0.011 0.055 -10000 0 -0.32 12 12
GNA15 0.019 0.005 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MMP9 -0.023 0.13 0.37 5 -0.43 24 29
MMP2 -0.031 0.13 0.27 8 -0.44 23 31
Caspase cascade in apoptosis

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
TOP1 -0.016 0.096 0.25 1 -0.35 21 22
ACTA1 -0.023 0.086 0.21 1 -0.29 28 29
NUMA1 -0.011 0.081 0.25 1 -0.32 16 17
SPTAN1 -0.027 0.086 0.19 2 -0.29 31 33
LIMK1 -0.022 0.091 0.21 13 -0.29 29 42
BIRC3 0.021 0.036 0.32 4 -0.32 2 6
BIRC2 0.02 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
CASP10 -0.031 0.05 -10000 0 -0.22 29 29
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.02 0.003 -10000 0 -10000 0 0
PTK2 -0.013 0.08 0.22 1 -0.35 14 15
DIABLO 0.02 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.027 0.085 0.19 2 -0.29 31 33
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.021 0.014 0.32 1 -10000 0 1
GSN -0.028 0.086 0.21 1 -0.29 31 32
MADD 0.02 0.003 -10000 0 -10000 0 0
TFAP2A 0.088 0.14 0.38 1 -0.49 19 20
BID -0.012 0.037 -10000 0 -0.16 27 27
MAP3K1 -0.015 0.087 -10000 0 -0.42 17 17
TRADD 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.029 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.025 0.087 0.21 6 -0.29 30 36
CASP9 0.02 0.004 -10000 0 -10000 0 0
DNA repair 0.001 0.037 0.18 3 -0.16 1 4
neuron apoptosis -0.008 0.12 -10000 0 -0.62 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.019 0.089 0.22 1 -0.34 18 19
APAF1 0.02 0.003 -10000 0 -10000 0 0
CASP6 -0.006 0.11 -10000 0 -0.86 6 6
TRAF2 0.02 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.029 0.087 0.29 4 -0.29 29 33
CASP7 -0.004 0.065 0.27 1 -0.28 9 10
KRT18 0.012 0.036 -10000 0 -0.49 1 1
apoptosis -0.024 0.088 -10000 0 -0.39 15 15
DFFA -0.027 0.087 0.19 3 -0.29 31 34
DFFB -0.026 0.087 0.19 4 -0.29 30 34
PARP1 -0.001 0.037 0.16 1 -0.18 3 4
actin filament polymerization 0.004 0.11 0.26 27 -0.31 17 44
TNF 0.009 0.065 0.32 1 -0.32 16 17
CYCS 0 0.042 0.14 9 -0.19 4 13
SATB1 -0.012 0.11 -10000 0 -0.76 7 7
SLK -0.028 0.086 0.21 1 -0.29 31 32
p15 BID/BAX 0.004 0.049 0.18 1 -0.25 5 6
CASP2 -0.004 0.042 -10000 0 -0.25 3 3
JNK cascade 0.015 0.086 0.42 17 -10000 0 17
CASP3 -0.025 0.091 0.23 1 -0.3 31 32
LMNB2 -0.011 0.13 0.21 2 -0.42 29 31
RIPK1 0.02 0.004 -10000 0 -10000 0 0
CASP4 0.02 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.05 0.027 0.22 4 -0.18 2 6
negative regulation of DNA binding 0.088 0.14 0.37 1 -0.48 19 20
stress fiber formation -0.028 0.085 0.21 1 -0.29 31 32
GZMB -0.03 0.06 -10000 0 -0.25 29 29
CASP1 0.005 0.024 -10000 0 -0.25 4 4
LMNB1 0.001 0.11 0.25 4 -0.46 16 20
APP -0.008 0.12 -10000 0 -0.62 16 16
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.01 -10000 0 -0.22 1 1
VIM -0.019 0.089 -10000 0 -0.39 15 15
LMNA 0.005 0.068 0.24 1 -0.36 6 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.001 0.048 -10000 0 -0.26 5 5
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.025 0.088 0.19 5 -0.29 31 36
APAF-1/Caspase 9 0.002 0.094 -10000 0 -0.64 9 9
nuclear fragmentation during apoptosis -0.01 0.08 0.25 1 -0.32 16 17
CFL2 -0.005 0.11 0.31 17 -0.26 27 44
GAS2 -0.029 0.092 0.23 4 -0.29 32 36
positive regulation of apoptosis -0.001 0.11 0.2 4 -0.47 14 18
PRF1 0.004 0.073 -10000 0 -0.32 22 22
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.023 0.049 0.23 6 -0.23 13 19
CRKL -0.002 0.088 0.29 4 -0.39 10 14
mol:PIP3 0.009 0.008 -10000 0 -10000 0 0
AKT1 0.005 0.04 0.22 1 -10000 0 1
PTK2B 0.017 0.018 -10000 0 -0.32 1 1
RAPGEF1 -0.005 0.082 0.27 4 -0.37 9 13
RANBP10 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.027 0.064 0.22 10 -0.19 29 39
MAP3K5 -0.003 0.09 0.26 5 -0.4 10 15
HGF/MET/CIN85/CBL/ENDOPHILINS 0.034 0.065 0.22 9 -0.18 30 39
AP1 -0.023 0.06 -10000 0 -0.2 29 29
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis -0.06 0.24 -10000 0 -0.71 53 53
STAT3 (dimer) -0.011 0.076 0.22 1 -0.28 15 16
GAB1/CRKL/SHP2/PI3K 0.021 0.088 0.29 1 -0.37 10 11
INPP5D 0.018 0.028 -10000 0 -0.32 3 3
CBL/CRK 0.007 0.086 0.35 2 -0.37 9 11
PTPN11 0.02 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.02 0.003 -10000 0 -10000 0 0
ELK1 0.006 0.093 0.3 35 -10000 0 35
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.045 0.14 1 -0.25 5 6
PAK1 0.006 0.054 0.33 3 -10000 0 3
HGF/MET/RANBP10 0.026 0.067 0.22 10 -0.2 30 40
HRAS -0.009 0.12 0.28 1 -0.48 21 22
DOCK1 -0.005 0.085 0.27 5 -0.4 9 14
GAB1 0 0.082 0.22 3 -0.39 8 11
CRK -0.005 0.087 0.37 2 -0.4 9 11
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.12 -10000 0 -0.42 36 36
JUN 0.017 0.032 -10000 0 -0.32 4 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.003 0.051 0.15 4 -0.18 30 34
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
cell morphogenesis -0.013 0.096 0.3 12 -0.31 12 24
GRB2/SHC 0.018 0.052 0.21 1 -0.2 12 13
FOS -0.002 0.085 -10000 0 -0.32 30 30
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.006 0.093 0.3 36 -10000 0 36
HGF/MET/MUC20 0.015 0.063 0.21 10 -0.19 32 42
cell migration 0.018 0.051 0.2 1 -0.2 12 13
GRB2 0.02 0.004 -10000 0 -10000 0 0
CBL 0.02 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.023 0.049 0.23 6 -0.23 13 19
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0 0.06 0.17 1 -0.22 24 25
MET/MUC20 0.01 0.047 0.22 6 -0.22 14 20
RAP1B -0.001 0.085 0.27 7 -0.36 9 16
RAP1A -0.009 0.078 0.25 5 -0.36 9 14
HGF/MET/RANBP9 0.027 0.067 0.22 10 -0.2 30 40
RAF1 -0.009 0.11 0.26 1 -0.46 21 22
STAT3 -0.012 0.076 0.22 1 -0.28 15 16
cell proliferation 0.001 0.11 0.3 17 -0.31 24 41
RPS6KB1 0.003 0.03 -10000 0 -0.25 2 2
MAPK3 -0.003 0.08 0.35 12 -10000 0 12
MAPK1 0.015 0.13 0.5 25 -10000 0 25
RANBP9 0.02 0.004 -10000 0 -10000 0 0
MAPK8 0.001 0.085 0.26 5 -0.35 10 15
SRC -0.021 0.057 0.16 1 -0.28 7 8
PI3K 0.018 0.058 0.21 1 -0.2 19 20
MET/Glomulin 0.01 0.048 0.24 6 -0.19 14 20
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K1 -0.011 0.11 0.25 1 -0.43 21 22
MET 0.013 0.069 0.32 6 -0.32 14 20
MAP4K1 -0.001 0.096 0.28 5 -0.43 10 15
PTK2 0.018 0.007 -10000 0 -10000 0 0
MAP2K2 -0.011 0.1 0.25 1 -0.43 21 22
BAD 0 0.041 0.4 1 -10000 0 1
MAP2K4 -0.006 0.083 0.25 5 -0.36 10 15
SHP2/GRB2/SOS1/GAB1 0.01 0.084 -10000 0 -0.32 17 17
INPPL1 0.02 0.004 -10000 0 -10000 0 0
PXN 0.02 0.003 -10000 0 -10000 0 0
SH3KBP1 0.02 0.004 -10000 0 -10000 0 0
HGS -0.012 0.045 0.14 4 -0.17 28 32
PLCgamma1/PKC 0.015 0.003 -10000 0 -10000 0 0
HGF 0.008 0.076 0.32 4 -0.32 20 24
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.02 0.003 -10000 0 -10000 0 0
PTPRJ 0.02 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.018 0.059 0.21 1 -0.18 29 30
PDPK1 0.006 0.03 0.24 4 -10000 0 4
HGF/MET/SHIP 0.025 0.072 0.22 9 -0.22 31 40
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.012 0.089 0.42 2 -0.37 17 19
CRKL -0.016 0.083 0.48 1 -0.39 18 19
HRAS -0.005 0.076 -10000 0 -0.37 12 12
mol:PIP3 0.005 0.1 0.37 2 -0.4 18 20
SPRED1 0.02 0.005 -10000 0 -10000 0 0
SPRED2 0.021 0.001 -10000 0 -10000 0 0
GAB1 -0.012 0.089 0.32 1 -0.41 19 20
FOXO3 -0.001 0.11 0.32 1 -0.39 23 24
AKT1 0.002 0.12 -10000 0 -0.42 23 23
BAD -0.001 0.11 -10000 0 -0.4 23 23
megakaryocyte differentiation -0.024 0.097 -10000 0 -0.39 24 24
GSK3B -0.001 0.11 0.25 1 -0.4 23 24
RAF1 -0.005 0.072 0.21 2 -0.3 12 14
SHC1 0.018 0.008 -10000 0 -10000 0 0
STAT3 -0.013 0.091 0.32 1 -0.41 20 21
STAT1 -0.038 0.2 0.44 1 -0.92 20 21
HRAS/SPRED1 0.009 0.073 -10000 0 -0.3 12 12
cell proliferation -0.014 0.088 -10000 0 -0.4 20 20
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TEC 0.02 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.001 0.11 0.24 1 -0.42 21 22
HRAS/SPRED2 0.009 0.073 -10000 0 -0.31 12 12
LYN/TEC/p62DOK 0.021 0.094 0.31 1 -0.4 17 18
MAPK3 0.001 0.065 0.21 7 -0.22 11 18
STAP1 -0.016 0.092 0.32 1 -0.41 20 21
GRAP2 0.01 0.057 -10000 0 -0.32 13 13
JAK2 -0.034 0.18 0.42 1 -0.79 20 21
STAT1 (dimer) -0.037 0.2 0.44 1 -0.9 20 21
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.02 0.091 -10000 0 -0.4 15 15
actin filament polymerization -0.011 0.081 0.32 1 -0.39 16 17
LYN 0.019 0.006 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.029 0.13 0.35 1 -0.55 22 23
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
CBL/CRKL/GRB2 0.009 0.081 0.41 2 -0.37 13 15
PI3K 0.017 0.1 -10000 0 -0.42 17 17
PTEN 0.02 0.003 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.019 0.22 -10000 0 -1.1 19 19
MAPK8 -0.014 0.089 -10000 0 -0.4 20 20
STAT3 (dimer) -0.013 0.089 0.32 1 -0.4 20 21
positive regulation of transcription 0.003 0.057 0.19 8 -0.19 6 14
mol:GDP 0.001 0.078 -10000 0 -0.39 12 12
PIK3C2B -0.013 0.093 0.44 2 -0.42 18 20
CBL/CRKL -0.001 0.086 0.42 2 -0.38 15 17
FER -0.013 0.089 0.32 1 -0.4 20 21
SH2B3 -0.013 0.09 0.32 1 -0.41 20 21
PDPK1 0.004 0.1 0.33 4 -0.38 17 21
SNAI2 -0.011 0.087 0.32 1 -0.42 17 18
positive regulation of cell proliferation -0.03 0.16 0.4 1 -0.68 21 22
KITLG 0.014 0.038 -10000 0 -0.35 4 4
cell motility -0.03 0.16 0.4 1 -0.68 21 22
PTPN6 0.019 0.011 -10000 0 -10000 0 0
EPOR -0.018 0.16 -10000 0 -0.62 22 22
STAT5A (dimer) -0.022 0.13 0.38 1 -0.55 22 23
SOCS1 0.02 0.004 -10000 0 -10000 0 0
cell migration 0.018 0.092 0.4 21 -10000 0 21
SOS1 0.021 0.003 -10000 0 -10000 0 0
EPO 0.019 0.027 0.32 3 -10000 0 3
VAV1 0.017 0.028 -10000 0 -0.32 3 3
GRB10 -0.013 0.087 0.33 1 -0.41 17 18
PTPN11 0.019 0.01 -10000 0 -10000 0 0
SCF/KIT -0.009 0.097 0.35 1 -0.42 21 22
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.003 0.064 0.19 8 -0.24 11 19
CBL 0.02 0.004 -10000 0 -10000 0 0
KIT -0.029 0.24 0.46 1 -1 22 23
MAP2K2 -0.002 0.062 0.19 8 -0.24 12 20
SHC/Grb2/SOS1 0.016 0.087 -10000 0 -0.41 13 13
STAT5A -0.021 0.14 0.38 1 -0.57 22 23
GRB2 0.02 0.004 -10000 0 -10000 0 0
response to radiation -0.011 0.085 0.32 1 -0.41 17 18
SHC/GRAP2 0.022 0.029 -10000 0 -0.23 5 5
PTPRO -0.023 0.098 -10000 0 -0.4 23 23
SH2B2 -0.011 0.082 0.32 1 -0.39 16 17
DOK1 0.021 0.002 -10000 0 -10000 0 0
MATK -0.018 0.093 -10000 0 -0.41 21 21
CREBBP 0.02 0.032 0.29 1 -10000 0 1
BCL2 -0.04 0.2 0.47 1 -0.72 21 22
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.004 -10000 0 -10000 0 0
HDAC4 0.02 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.046 -10000 0 -0.17 28 28
CDKN1A -0.011 0.004 -10000 0 -10000 0 0
KAT2B 0.02 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
FOXO3 -0.002 0.002 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
FOXO4 0.006 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
TAT 0.045 0.084 0.32 39 -10000 0 39
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.014 0.15 3 -10000 0 3
PPARGC1A -0.063 0.15 -10000 0 -0.32 113 113
FHL2 0.062 0.1 0.32 64 -10000 0 64
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.012 0.25 1 -10000 0 1
HIST2H4A -0.005 0.046 0.17 28 -10000 0 28
SIRT1/FOXO3a 0.013 0.027 0.24 1 -0.2 3 4
SIRT1 0.02 0.015 0.35 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.035 0.018 0.24 1 -10000 0 1
SIRT1/Histone H1b 0.025 0.041 0.32 1 -0.22 4 5
apoptosis -0.038 0.015 -10000 0 -0.23 1 1
SIRT1/PGC1A -0.025 0.093 0.22 1 -0.19 111 112
p53/SIRT1 0.027 0.026 0.55 1 -10000 0 1
SIRT1/FOXO4 0.016 0.033 0.24 1 -0.22 4 5
FOXO1/FHL2/SIRT1 0.059 0.06 0.21 62 -10000 0 62
HIST1H1E 0.016 0.033 0.23 1 -10000 0 1
SIRT1/p300 0.029 0.012 0.25 1 -10000 0 1
muscle cell differentiation -0.024 0.019 -10000 0 -0.21 4 4
TP53 0.019 0.016 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.039 0.015 0.24 1 -10000 0 1
CREBBP 0.02 0.004 -10000 0 -10000 0 0
MEF2D 0.018 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.045 0.056 0.23 38 -10000 0 38
ACSS2 -0.016 0.017 0.27 1 -0.23 1 2
SIRT1/PCAF/MYOD 0.024 0.019 0.21 4 -10000 0 4
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.027 0.07 -10000 0 -0.27 3 3
Syndecan-3/Neurocan 0.024 0.046 0.23 13 -0.28 3 16
POMC 0.013 0.072 0.32 6 -0.32 16 22
EGFR 0.015 0.042 0.32 1 -0.32 6 7
Syndecan-3/EGFR 0.016 0.036 0.3 1 -0.29 3 4
AGRP -0.11 0.17 -10000 0 -0.32 181 181
NCSTN 0.018 0.007 -10000 0 -10000 0 0
PSENEN 0.019 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.019 0.023 -10000 0 -0.32 2 2
APH1A 0.017 0.008 -10000 0 -10000 0 0
NCAN 0.027 0.05 0.32 13 -10000 0 13
long-term memory 0.037 0.038 -10000 0 -0.29 2 2
Syndecan-3/IL8 0.024 0.051 0.22 17 -0.29 3 20
PSEN1 0.02 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.028 0.009 -10000 0 -10000 0 0
FYN 0.018 0.017 -10000 0 -0.32 1 1
limb bud formation 0.004 0.019 -10000 0 -0.4 1 1
MC4R 0.037 0.075 0.32 30 -10000 0 30
SRC 0.02 0.004 -10000 0 -10000 0 0
PTN -0.021 0.12 0.32 4 -0.32 58 62
FGFR/FGF/Syndecan-3 0.004 0.019 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.012 0.065 0.3 3 -0.37 1 4
Syndecan-3/AgRP -0.034 0.08 -10000 0 -0.31 4 4
Syndecan-3/AgRP/MC4R -0.02 0.1 0.28 3 -0.3 4 7
Fyn/Cortactin 0.027 0.01 -10000 0 -10000 0 0
SDC3 0.004 0.019 -10000 0 -0.41 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.024 0.05 0.22 17 -0.29 3 20
IL8 0.028 0.066 0.32 17 -0.32 4 21
Syndecan-3/Fyn/Cortactin 0.038 0.039 -10000 0 -0.3 2 2
Syndecan-3/CASK 0.003 0.025 -10000 0 -0.29 3 3
alpha-MSH/MC4R 0.032 0.069 0.23 31 -0.21 16 47
Gamma Secretase 0.045 0.031 -10000 0 -0.17 1 1
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.026 0.012 -10000 0 -0.19 1 1
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.02 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.028 0.058 0.32 15 -0.32 2 17
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.03 0.15 7 -0.16 1 8
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.019 0.017 -10000 0 -0.32 1 1
FYN 0.018 0.017 -10000 0 -0.32 1 1
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR -0.004 0.089 -10000 0 -0.32 33 33
p38 alpha/TAB1 -0.036 0.083 -10000 0 -0.28 34 34
PRKG1 -0.016 0.11 -10000 0 -0.32 49 49
DUSP8 0.013 0.05 -10000 0 -0.32 10 10
PGK/cGMP/p38 alpha -0.016 0.12 -10000 0 -0.31 41 41
apoptosis -0.035 0.08 -10000 0 -0.27 34 34
RAL/GTP 0.025 0.009 -10000 0 -10000 0 0
LYN 0.019 0.006 -10000 0 -10000 0 0
DUSP1 -0.011 0.099 -10000 0 -0.32 42 42
PAK1 0.02 0.004 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.042 0.024 -10000 0 -0.16 1 1
TRAF6 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.018 0.007 -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 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.024 0.01 -10000 0 -10000 0 0
MAPK11 -0.002 0.12 0.27 12 -0.3 32 44
BLK 0.058 0.11 0.32 64 -0.32 1 65
HCK 0.007 0.065 -10000 0 -0.32 17 17
MAP2K3 0.019 0.006 -10000 0 -10000 0 0
DUSP16 0.02 0.005 -10000 0 -10000 0 0
DUSP10 0.018 0.023 -10000 0 -0.32 2 2
TRAF6/MEKK3 0.025 0.011 -10000 0 -0.17 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.12 0.23 14 -0.33 27 41
positive regulation of innate immune response -0.003 0.14 0.29 13 -0.36 31 44
LCK 0.02 0.027 0.32 1 -0.32 2 3
p38alpha-beta/MKP7 0.005 0.14 0.3 11 -0.35 31 42
p38alpha-beta/MKP5 0.004 0.13 0.32 8 -0.35 29 37
PGK/cGMP -0.01 0.073 -10000 0 -0.22 49 49
PAK2 0.02 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.003 0.14 0.32 9 -0.35 36 45
CDC42 0.02 0.003 -10000 0 -10000 0 0
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.019 0.006 -10000 0 -10000 0 0
PAK3 0.052 0.1 0.32 53 -0.32 4 57
BCR signaling pathway

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
JUN 0.032 0.11 0.27 20 -0.4 9 29
IKBKB 0.024 0.09 0.25 7 -0.29 13 20
AKT1 0.031 0.075 0.22 31 -0.23 1 32
IKBKG 0.03 0.067 0.26 3 -0.26 5 8
CALM1 0.017 0.083 0.26 6 -0.4 7 13
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 0.039 0.12 0.27 24 -0.45 9 33
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.087 0.22 1 -0.45 7 8
DOK1 0.021 0.002 -10000 0 -10000 0 0
AP-1 0.018 0.075 0.21 15 -0.25 6 21
LYN 0.019 0.006 -10000 0 -10000 0 0
BLNK 0.019 0.023 -10000 0 -0.32 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
BCR complex 0.066 0.093 0.25 82 -0.32 2 84
CD22 0.009 0.067 0.24 10 -0.4 3 13
CAMK2G 0.013 0.079 0.25 6 -0.38 7 13
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
INPP5D 0.018 0.028 -10000 0 -0.32 3 3
SHC/GRB2/SOS1 -0.007 0.046 0.15 7 -10000 0 7
GO:0007205 0.017 0.088 0.22 1 -0.46 7 8
SYK 0.019 0.023 -10000 0 -0.32 2 2
ELK1 0.014 0.085 0.24 2 -0.44 7 9
NFATC1 0.032 0.092 0.25 18 -0.34 7 25
B-cell antigen/BCR complex 0.066 0.093 0.25 82 -0.32 2 84
PAG1/CSK 0.026 0.016 -10000 0 -0.23 1 1
NFKBIB 0.022 0.039 0.14 5 -0.13 7 12
HRAS 0.022 0.077 0.25 10 -0.35 5 15
NFKBIA 0.022 0.039 0.14 5 -0.13 6 11
NF-kappa-B/RelA/I kappa B beta 0.025 0.035 0.14 5 -10000 0 5
RasGAP/Csk 0.076 0.079 0.38 7 -0.15 1 8
mol:GDP 0.017 0.089 0.22 1 -0.43 8 9
PTEN 0.02 0.003 -10000 0 -10000 0 0
CD79B 0.024 0.043 0.32 8 -0.32 1 9
NF-kappa-B/RelA/I kappa B alpha 0.025 0.035 0.14 5 -10000 0 5
GRB2 0.02 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.045 0.12 0.31 9 -0.47 7 16
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 0.019 0.087 0.22 1 -0.46 7 8
CSK 0.02 0.003 -10000 0 -10000 0 0
FOS 0.004 0.089 0.25 6 -0.38 9 15
CHUK 0.026 0.075 0.26 3 -0.27 10 13
IBTK 0.019 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.035 0.076 -10000 0 -0.33 5 5
PTPN6 0.004 0.064 0.22 10 -0.38 4 14
RELA 0.02 0.003 -10000 0 -10000 0 0
BCL2A1 0.016 0.026 0.12 1 -10000 0 1
VAV2 0.044 0.085 0.28 10 -0.44 3 13
ubiquitin-dependent protein catabolic process 0.023 0.039 0.14 5 -0.13 8 13
BTK -0.047 0.26 -10000 0 -0.98 33 33
CD19 0.041 0.084 0.26 19 -0.39 2 21
MAP4K1 0.017 0.032 -10000 0 -0.32 4 4
CD72 0.019 0.017 -10000 0 -0.32 1 1
PAG1 0.018 0.017 -10000 0 -0.32 1 1
MAPK14 0.04 0.12 0.28 33 -0.4 8 41
SH3BP5 0.017 0.032 -10000 0 -0.32 4 4
PIK3AP1 0.019 0.088 0.23 1 -0.48 7 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.013 0.13 -10000 0 -0.63 12 12
RAF1 0.017 0.073 0.24 8 -0.33 5 13
RasGAP/p62DOK/SHIP 0.072 0.073 0.35 7 -0.24 2 9
CD79A 0.07 0.12 0.32 81 -0.32 3 84
re-entry into mitotic cell cycle 0.018 0.075 0.21 13 -0.25 6 19
RASA1 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.069 0.22 10 -0.3 4 14
MAPK1 0.013 0.067 0.23 11 -0.32 3 14
CD72/SHP1 0.02 0.085 0.26 12 -0.35 4 16
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.035 0.11 0.26 26 -0.4 8 34
actin cytoskeleton organization 0.057 0.098 0.28 31 -0.42 2 33
NF-kappa-B/RelA 0.049 0.069 0.25 5 -0.23 2 7
Calcineurin 0.031 0.075 0.32 1 -0.4 4 5
PI3K 0.003 0.063 0.18 6 -0.29 4 10
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.022 0.08 0.25 1 -0.52 5 6
SOS1 0.021 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.034 0.12 -10000 0 -0.6 11 11
DAPP1 0.022 0.13 -10000 0 -0.66 11 11
cytokine secretion 0.032 0.089 0.24 19 -0.32 7 26
mol:DAG 0.019 0.087 0.22 1 -0.46 7 8
PLCG2 0.018 0.028 -10000 0 -0.32 3 3
MAP2K1 0.012 0.07 0.24 8 -0.31 5 13
B-cell antigen/BCR complex/FcgammaRIIB 0.067 0.083 0.24 78 -0.17 2 80
mol:PI-3-4-5-P3 0.014 0.065 0.18 14 -0.25 2 16
ETS1 0.011 0.075 0.24 8 -0.36 5 13
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.078 0.08 0.24 78 -0.24 2 80
B-cell antigen/BCR complex/LYN 0.028 0.063 0.28 7 -0.39 3 10
MALT1 0.019 0.006 -10000 0 -10000 0 0
TRAF6 0.02 0.003 -10000 0 -10000 0 0
RAC1 0.055 0.098 0.29 26 -0.45 2 28
B-cell antigen/BCR complex/LYN/SYK 0.054 0.099 0.35 11 -0.31 4 15
CARD11 0.033 0.096 0.27 12 -0.42 6 18
FCGR2B 0.018 0.007 -10000 0 -10000 0 0
PPP3CA 0.021 0.003 -10000 0 -10000 0 0
BCL10 0.02 0.004 -10000 0 -10000 0 0
IKK complex 0.022 0.047 0.14 24 -0.12 5 29
PTPRC 0.012 0.048 -10000 0 -0.32 9 9
PDPK1 0.019 0.068 0.21 25 -0.21 1 26
PPP3CB 0.021 0.003 -10000 0 -10000 0 0
PPP3CC 0.017 0.008 -10000 0 -10000 0 0
POU2F2 0.019 0.025 0.12 5 -10000 0 5
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.028 0.021 0.23 1 -0.23 2 3
ATM 0.02 0.004 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
ATR 0.02 0.003 -10000 0 -10000 0 0
UBE2L3 0.02 0.004 -10000 0 -10000 0 0
FANCD2 0.011 0.009 -10000 0 -10000 0 0
protein ubiquitination 0.099 0.077 0.34 2 -0.17 1 3
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.035 0.016 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
DNA-PK 0.037 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.001 0.086 -10000 0 -0.45 12 12
FANCF 0.02 0.003 -10000 0 -10000 0 0
BRCA1 0.021 0.014 0.32 1 -10000 0 1
CCNE1 0.12 0.14 0.32 148 -10000 0 148
CDK2/Cyclin E1 0.09 0.095 0.23 143 -10000 0 143
FANCG 0.02 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.03 0.022 0.23 2 -0.23 2 4
FANCE 0.02 0.004 -10000 0 -10000 0 0
FANCC 0.02 0.004 -10000 0 -10000 0 0
NBN 0.018 0.007 -10000 0 -10000 0 0
FANCA 0.031 0.057 0.32 17 -10000 0 17
DNA repair 0.004 0.069 0.22 5 -0.35 6 11
BRCA1/BARD1/ubiquitin 0.03 0.022 0.23 2 -0.23 2 4
BARD1/DNA-PK 0.046 0.023 -10000 0 -0.17 2 2
FANCL 0.021 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.021 0.23 2 -0.23 1 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.039 -10000 0 -0.21 6 6
BRCA1/BACH1/BARD1/TopBP1 0.04 0.022 0.22 2 -0.2 2 4
BRCA1/BARD1/P53 0.047 0.025 0.22 1 -0.18 2 3
BARD1/CSTF1/BRCA1 0.038 0.023 0.22 2 -0.2 2 4
BRCA1/BACH1 0.021 0.014 0.32 1 -10000 0 1
BARD1 0.02 0.027 0.32 1 -0.32 2 3
PCNA 0.02 0.015 0.32 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.04 0.021 0.22 2 -0.2 2 4
BRCA1/BARD1/UbcH7 0.039 0.021 0.22 1 -0.2 2 3
BRCA1/BARD1/RAD51/PCNA 0.076 0.074 0.23 77 -0.16 2 79
BARD1/DNA-PK/P53 0.049 0.029 -10000 0 -0.16 2 2
BRCA1/BARD1/Ubiquitin 0.03 0.022 0.23 2 -0.23 2 4
BRCA1/BARD1/CTIP 0.027 0.021 0.21 2 -0.17 2 4
FA complex 0.01 0.044 0.25 1 -0.27 4 5
BARD1/EWS 0.029 0.021 0.23 1 -0.23 2 3
RBBP8 -0.015 0.005 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
TOPBP1 0.02 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.045 0.024 0.18 2 -0.22 1 3
BRCA1/BARD1 0.11 0.083 0.22 137 -0.17 1 138
CSTF1 0.019 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.015 0.018 0.22 1 -0.22 2 3
CDK2 0.02 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.073 0.12 0.32 82 -10000 0 82
RAD50 0.02 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.03 0.022 0.23 2 -0.23 2 4
EWSR1 0.02 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.036 0.052 0.23 22 -0.23 5 27
AKT1 -0.024 0.1 0.36 5 -0.42 14 19
PTK2B -0.029 0.087 0.33 1 -0.43 11 12
VEGFR2 homodimer/Frs2 -0.012 0.092 -10000 0 -0.47 10 10
CAV1 -0.19 0.17 -10000 0 -0.32 278 278
CALM1 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.001 0.088 -10000 0 -0.44 10 10
endothelial cell proliferation -0.023 0.12 0.4 8 -0.4 20 28
mol:Ca2+ -0.038 0.078 0.17 5 -0.42 10 15
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.008 0.09 -10000 0 -0.45 10 10
RP11-342D11.1 -0.035 0.078 0.16 11 -0.43 10 21
CDH5 -0.021 0.11 -10000 0 -0.32 56 56
VEGFA homodimer 0.041 0.023 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 0.015 0.045 0.32 1 -0.32 7 8
HRAS/GDP 0.005 0.074 -10000 0 -0.35 10 10
SH2D2A 0.019 0.016 0.32 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.02 0.13 -10000 0 -0.43 32 32
VEGFR2 homodimer/VEGFA homodimer/TsAd 0 0.091 -10000 0 -0.47 10 10
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.017 0.084 -10000 0 -0.38 10 10
GRB10 -0.036 0.077 -10000 0 -0.44 10 10
PTPN11 0.02 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
PAK1 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.003 0.12 -10000 0 -0.4 25 25
HRAS 0.02 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.011 0.071 -10000 0 -0.29 17 17
HIF1A 0.02 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.007 0.089 -10000 0 -0.45 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.01 0.057 -10000 0 -0.32 13 13
Nck/Pak 0.029 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.001 0.09 -10000 0 -0.45 10 10
mol:GDP 0.01 0.079 -10000 0 -0.37 10 10
mol:NADP -0.025 0.13 0.38 5 -0.4 34 39
eNOS/Hsp90 -0.017 0.12 0.4 4 -0.38 32 36
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 -0.038 0.079 0.17 5 -0.42 10 15
HIF1A/ARNT 0.025 0.013 -10000 0 -10000 0 0
SHB 0.02 0.005 -10000 0 -10000 0 0
VEGFA 0.02 0.004 -10000 0 -10000 0 0
VEGFC 0.019 0.027 0.32 1 -0.32 2 3
FAK1/Vinculin -0.013 0.12 0.32 7 -0.47 15 22
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.017 0.1 -10000 0 -0.45 11 11
PTPN6 0.02 0.005 -10000 0 -10000 0 0
EPAS1 -0.023 0.12 -10000 0 -0.34 60 60
mol:L-citrulline -0.025 0.13 0.38 5 -0.4 34 39
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.011 0.086 -10000 0 -0.4 10 10
VEGFR2 homodimer/VEGFA homodimer 0.001 0.092 -10000 0 -0.47 10 10
VEGFR2/3 heterodimer -0.017 0.11 -10000 0 -0.49 14 14
VEGFB 0.02 0.003 -10000 0 -10000 0 0
MAPK11 -0.027 0.092 0.34 4 -0.45 10 14
VEGFR2 homodimer -0.046 0.1 -10000 0 -0.58 10 10
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.02 0.016 -10000 0 -0.32 1 1
MAPK3 -0.028 0.093 0.31 7 -0.4 11 18
MAPK1 -0.027 0.089 0.28 7 -0.4 10 17
VEGFA145/NRP2 0.028 0.021 -10000 0 -0.22 3 3
VEGFR1/2 heterodimer -0.013 0.096 -10000 0 -0.5 10 10
KDR -0.046 0.1 -10000 0 -0.58 10 10
VEGFA165/NRP1/VEGFR2 homodimer 0.002 0.087 -10000 0 -0.45 10 10
SRC 0.02 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.025 0.1 0.33 10 -0.4 11 21
PI3K -0.039 0.085 -10000 0 -0.47 10 10
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.001 0.092 -10000 0 -0.47 10 10
FES -0.04 0.08 -10000 0 -0.44 10 10
GAB1 -0.026 0.096 -10000 0 -0.43 13 13
VEGFR2 homodimer/VEGFA homodimer/Src 0 0.091 -10000 0 -0.45 10 10
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
ARNT 0.017 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.088 0.13 -10000 0 -0.45 35 35
VEGFR2 homodimer/VEGFA homodimer/Yes 0.001 0.091 -10000 0 -0.47 10 10
PI3K/GAB1 -0.013 0.099 -10000 0 -0.43 12 12
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.019 0.088 -10000 0 -0.41 10 10
PRKACA 0.02 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.006 0.1 -10000 0 -0.46 14 14
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 -0.038 0.081 0.17 1 -0.45 10 11
actin cytoskeleton reorganization 0 0.09 -10000 0 -0.47 10 10
PTK2 -0.025 0.11 0.38 2 -0.51 15 17
EDG1 -0.035 0.078 0.16 11 -0.43 10 21
mol:DAG -0.038 0.079 0.17 5 -0.42 10 15
CaM/Ca2+ -0.037 0.073 -10000 0 -0.4 10 10
MAP2K3 -0.033 0.079 0.34 1 -0.38 10 11
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.011 0.099 -10000 0 -0.45 10 10
PLCG1 -0.039 0.079 0.17 1 -0.43 10 11
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.01 0.09 -10000 0 -0.43 10 10
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0 0.092 -10000 0 -0.47 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.001 0.09 -10000 0 -0.45 10 10
cell migration -0.023 0.12 0.32 5 -0.46 16 21
mol:PI-3-4-5-P3 -0.037 0.079 -10000 0 -0.44 10 10
FYN 0.018 0.017 -10000 0 -0.32 1 1
VEGFB/NRP1 -0.037 0.075 -10000 0 -0.42 10 10
mol:NO -0.025 0.13 0.38 5 -0.4 34 39
PXN 0.02 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.042 0.06 -10000 0 -0.35 10 10
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.074 -10000 0 -0.45 10 10
VHL 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.031 0.074 0.32 22 -0.32 5 27
NOS3 -0.03 0.14 0.39 5 -0.45 34 39
VEGFR2 homodimer/VEGFA homodimer/Sck -0.003 0.097 -10000 0 -0.45 13 13
RAC1 0.018 0.007 -10000 0 -10000 0 0
PRKCA -0.036 0.078 -10000 0 -0.42 9 9
PRKCB -0.039 0.087 0.33 1 -0.43 11 12
VCL 0.021 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.035 0.078 -10000 0 -0.43 10 10
VEGFR1/2 heterodimer/VEGFA homodimer 0 0.091 -10000 0 -0.47 10 10
VEGFA165/NRP2 0.028 0.021 -10000 0 -0.22 3 3
MAPKKK cascade -0.026 0.086 0.31 2 -0.4 7 9
NRP2 0.018 0.028 -10000 0 -0.32 3 3
VEGFC homodimer 0.019 0.027 0.32 1 -0.32 2 3
NCK1 0.02 0.003 -10000 0 -10000 0 0
ROCK1 0.02 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.014 0.12 0.29 6 -0.48 15 21
MAP3K13 -0.036 0.077 -10000 0 -0.41 10 10
PDPK1 -0.038 0.075 0.24 2 -0.4 10 12
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.018 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.019 0.11 0.43 12 -10000 0 12
IL27/IL27R/JAK1 0.03 0.092 -10000 0 -0.88 1 1
TBX21 -0.023 0.11 0.9 1 -0.56 4 5
IL12B 0.023 0.033 0.32 4 -0.32 1 5
IL12A -0.009 0.024 0.16 1 -0.22 5 6
IL6ST 0.006 0.067 -10000 0 -0.33 17 17
IL27RA/JAK1 0.009 0.059 0.38 1 -1.1 1 2
IL27 0.008 0.057 -10000 0 -0.33 12 12
TYK2 0.02 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.015 0.12 0.43 2 -10000 0 2
T-helper 2 cell differentiation 0.019 0.11 0.43 12 -10000 0 12
T cell proliferation during immune response 0.019 0.11 0.43 12 -10000 0 12
MAPKKK cascade -0.019 0.11 -10000 0 -0.43 12 12
STAT3 0.02 0.003 -10000 0 -10000 0 0
STAT2 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.02 0.009 -10000 0 -10000 0 0
IL12RB1 0.011 0.055 -10000 0 -0.32 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.013 0.11 0.39 9 -0.54 3 12
IL27/IL27R/JAK2/TYK2 -0.019 0.11 -10000 0 -0.43 12 12
positive regulation of T cell mediated cytotoxicity -0.019 0.11 -10000 0 -0.43 12 12
STAT1 (dimer) 0.026 0.12 -10000 0 -0.61 4 4
JAK2 0.019 0.021 -10000 0 -0.32 1 1
JAK1 0.019 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.011 0.12 0.45 1 -0.4 15 16
T cell proliferation -0.042 0.12 0.34 2 -0.44 18 20
IL12/IL12R/TYK2/JAK2 -0.031 0.24 -10000 0 -0.81 35 35
IL17A -0.018 0.12 0.47 1 -10000 0 1
mast cell activation 0.019 0.11 0.43 12 -10000 0 12
IFNG 0.002 0.042 0.11 32 -0.11 19 51
T cell differentiation -0.001 0.005 0.013 7 -0.02 13 20
STAT3 (dimer) -0.011 0.12 0.45 1 -0.4 15 16
STAT5A (dimer) -0.012 0.12 0.45 1 -0.41 15 16
STAT4 (dimer) -0.012 0.12 0.45 1 -0.41 14 15
STAT4 0.021 0.002 -10000 0 -10000 0 0
T cell activation -0.003 0.006 0.11 1 -10000 0 1
IL27R/JAK2/TYK2 0.027 0.077 -10000 0 -0.86 1 1
GATA3 -0.005 0.084 0.59 5 -1.1 1 6
IL18 -0.011 0.03 -10000 0 -0.22 9 9
positive regulation of mast cell cytokine production -0.011 0.12 0.45 1 -0.4 15 16
IL27/EBI3 0.022 0.047 -10000 0 -0.23 13 13
IL27RA 0 0.058 -10000 0 -1.1 1 1
IL6 -0.044 0.14 -10000 0 -0.32 89 89
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.008 0.034 0.42 1 -10000 0 1
IL1B -0.019 0.049 -10000 0 -0.22 26 26
EBI3 0.019 0.022 -10000 0 -0.32 1 1
TNF -0.014 0.04 0.16 1 -0.22 16 17
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0.032 -10000 0 -0.32 4 4
ELF1 0.032 0.04 -10000 0 -10000 0 0
CCNA2 0.095 0.13 0.32 115 -10000 0 115
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
JAK3 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
JAK1 0.02 0.003 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.016 0.071 -10000 0 -0.4 4 4
SHC1 0.018 0.008 -10000 0 -10000 0 0
SP1 0.016 0.045 -10000 0 -0.3 9 9
IL2RA 0.009 0.08 0.3 33 -10000 0 33
IL2RB 0.019 0.023 -10000 0 -0.32 2 2
SOS1 0.021 0.003 -10000 0 -10000 0 0
IL2RG 0.017 0.036 -10000 0 -0.32 5 5
G1/S transition of mitotic cell cycle 0.029 0.11 0.3 20 -0.42 11 31
PTPN11 0.02 0.003 -10000 0 -10000 0 0
CCND2 -0.025 0.079 -10000 0 -0.59 9 9
LCK 0.02 0.027 0.32 1 -0.32 2 3
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL2 0.019 0.003 -10000 0 -10000 0 0
CDK6 0.019 0.017 -10000 0 -0.32 1 1
CCND3 0.019 0.079 0.42 2 -0.39 2 4
Signaling events mediated by PRL

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
CCNE1 0.12 0.14 0.32 148 -10000 0 148
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.017 0.032 -10000 0 -0.32 4 4
CDKN1A 0.004 0.027 -10000 0 -0.32 2 2
PRL-3/alpha Tubulin 0.027 0.015 0.23 1 -10000 0 1
mol:Ca2+ 0.003 0.067 0.17 56 -0.23 5 61
AGT 0.059 0.11 0.32 66 -0.32 4 70
CCNA2 -0.005 0.055 0.31 6 -10000 0 6
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
EGR1 -0.018 0.049 -10000 0 -0.22 26 26
CDK2/Cyclin E1 0.084 0.096 0.33 10 -0.3 3 13
MAPK3 -0.014 0.01 0.15 1 -10000 0 1
PRL-2 /Rab GGTase beta 0.03 0.006 -10000 0 -10000 0 0
MAPK1 -0.014 0.01 0.15 1 -10000 0 1
PTP4A1 -0.021 0.034 -10000 0 -10000 0 0
PTP4A3 0.019 0.016 0.32 1 -10000 0 1
PTP4A2 0.021 0.002 -10000 0 -10000 0 0
ITGB1 -0.014 0.01 0.15 1 -10000 0 1
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.002 0.037 -10000 0 -0.41 3 3
Rab GGTase beta/Rab GGTase alpha 0.029 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.018 0.048 -10000 0 -10000 0 0
RABGGTA 0.02 0.005 -10000 0 -10000 0 0
BCAR1 -0.018 0.016 -10000 0 -0.23 2 2
RHOC 0 0.045 -10000 0 -0.36 6 6
RHOA -0.001 0.048 -10000 0 -0.34 8 8
cell motility 0.004 0.061 0.26 2 -0.31 7 9
PRL-1/alpha Tubulin -0.019 0.047 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.023 0.23 1 -0.23 2 3
ROCK1 0.002 0.049 0.27 1 -0.33 4 5
RABGGTB 0.02 0.004 -10000 0 -10000 0 0
CDK2 0.02 0.003 -10000 0 -10000 0 0
mitosis -0.021 0.034 -10000 0 -10000 0 0
ATF5 0.021 0.015 0.32 1 -10000 0 1
Class I PI3K signaling events

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
ARF5/GTP -0.011 0.06 0.28 2 -10000 0 2
DAPP1 -0.018 0.11 0.21 4 -0.33 34 38
Src family/SYK family/BLNK-LAT/BTK-ITK -0.033 0.16 -10000 0 -0.47 41 41
mol:DAG -0.014 0.072 0.2 8 -0.21 19 27
HRAS 0.02 0.007 -10000 0 -10000 0 0
RAP1A 0.02 0.007 -10000 0 -10000 0 0
ARF5/GDP -0.002 0.09 -10000 0 -0.32 22 22
PLCG2 0.018 0.028 -10000 0 -0.32 3 3
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.004 -10000 0 -10000 0 0
mol:GTP -0.017 0.045 0.22 4 -10000 0 4
ARF1/GTP -0.01 0.042 0.22 4 -0.18 2 6
RHOA 0.02 0.004 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.017 0.045 0.15 27 -10000 0 27
ADAP1 -0.017 0.047 0.28 3 -0.28 1 4
ARAP3 -0.017 0.045 0.22 4 -10000 0 4
INPPL1 0.02 0.004 -10000 0 -10000 0 0
PREX1 0.017 0.032 -10000 0 -0.32 4 4
ARHGEF6 0.008 0.063 -10000 0 -0.32 16 16
ARHGEF7 0.019 0.005 -10000 0 -10000 0 0
ARF1 0.019 0.006 -10000 0 -10000 0 0
NRAS 0.02 0.007 -10000 0 -10000 0 0
FYN 0.018 0.017 -10000 0 -0.32 1 1
ARF6 0.02 0.005 -10000 0 -10000 0 0
FGR -0.004 0.089 -10000 0 -0.32 33 33
mol:Ca2+ -0.01 0.04 0.13 8 -0.12 9 17
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.016 0.039 -10000 0 -0.32 6 6
ZAP70 0.016 0.039 -10000 0 -0.32 6 6
mol:IP3 -0.016 0.053 0.16 8 -0.17 12 20
LYN 0.019 0.006 -10000 0 -10000 0 0
ARF1/GDP 0 0.085 -10000 0 -0.3 21 21
RhoA/GDP -0.009 0.065 0.24 5 -0.25 4 9
PDK1/Src/Hsp90 0.038 0.013 -10000 0 -10000 0 0
BLNK 0.019 0.023 -10000 0 -0.32 2 2
actin cytoskeleton reorganization -0.006 0.085 0.29 7 -0.3 14 21
SRC 0.02 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.007 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
PTEN 0.019 0.013 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.044 0.28 1 -10000 0 1
RhoA/GTP -0.019 0.047 0.24 3 -10000 0 3
Src family/SYK family/BLNK-LAT -0.015 0.11 -10000 0 -0.31 35 35
BLK 0.058 0.11 0.32 64 -0.32 1 65
PDPK1 0.02 0.003 -10000 0 -10000 0 0
CYTH1 -0.019 0.045 0.28 3 -10000 0 3
HCK 0.007 0.065 -10000 0 -0.32 17 17
CYTH3 -0.017 0.046 0.21 6 -10000 0 6
CYTH2 -0.019 0.046 0.28 3 -10000 0 3
KRAS 0.019 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.046 -10000 0 -0.33 5 5
SGK1 -0.014 0.095 -10000 0 -0.33 34 34
INPP5D 0.018 0.028 -10000 0 -0.32 3 3
mol:GDP -0.012 0.091 0.18 2 -0.31 25 27
SOS1 0.021 0.003 -10000 0 -10000 0 0
SYK 0.019 0.023 -10000 0 -0.32 2 2
ARF6/GDP -0.011 0.059 0.22 5 -0.24 3 8
mol:PI-3-4-5-P3 -0.018 0.041 0.19 3 -10000 0 3
ARAP3/RAP1A/GTP -0.017 0.045 0.16 27 -10000 0 27
VAV1 0.017 0.028 -10000 0 -0.32 3 3
mol:PI-3-4-P2 -0.017 0.014 -10000 0 -0.23 2 2
RAS family/GTP/PI3K Class I -0.022 0.032 0.19 2 -10000 0 2
PLEKHA1 -0.02 0.012 -10000 0 -0.2 2 2
Rac1/GDP -0.002 0.086 -10000 0 -0.32 21 21
LAT 0.021 0.014 0.32 1 -10000 0 1
Rac1/GTP -0.002 0.09 0.2 1 -0.37 19 20
ITK -0.024 0.044 0.27 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.023 0.091 0.24 6 -0.29 22 28
LCK 0.02 0.027 0.32 1 -0.32 2 3
BTK -0.028 0.055 0.27 2 -0.28 2 4
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.018 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.011 0.003 -10000 0 -10000 0 0
mol:DAG -0.012 0.036 0.23 6 -10000 0 6
VEGFR1 homodimer/NRP1/VEGFR 121 0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+ -0.017 0.03 0.22 2 -10000 0 2
HIF1A 0.022 0.004 -10000 0 -10000 0 0
GAB1 0.02 0.016 -10000 0 -0.32 1 1
AKT1 -0.013 0.047 0.41 3 -10000 0 3
PLCG1 -0.012 0.036 0.23 6 -10000 0 6
NOS3 -0.008 0.081 0.4 5 -0.35 10 15
CBL 0.02 0.004 -10000 0 -10000 0 0
mol:NO -0.005 0.09 0.43 7 -0.35 11 18
FLT1 -0.014 0.004 -10000 0 -10000 0 0
PGF 0.03 0.055 0.32 16 -10000 0 16
VEGFR1 homodimer/NRP2/VEGFR121 0.028 0.017 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 -0.013 0.089 0.36 5 -0.36 14 19
endothelial cell proliferation -0.006 0.058 0.32 7 -0.24 1 8
mol:Ca2+ -0.012 0.036 0.23 6 -10000 0 6
MAPK3 -0.018 0.042 0.26 9 -10000 0 9
MAPK1 -0.018 0.04 0.27 7 -10000 0 7
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
PLGF homodimer 0.03 0.055 0.32 16 -10000 0 16
PRKACA 0.02 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.19 0.17 -10000 0 -0.32 278 278
VEGFA homodimer 0.02 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.018 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.021 0.041 0.28 6 -10000 0 6
PI3K 0.042 0.037 -10000 0 -10000 0 0
PRKCA -0.017 0.03 0.23 4 -10000 0 4
PRKCB -0.019 0.04 0.22 7 -10000 0 7
VEGFR1 homodimer/PLGF homodimer 0.025 0.037 0.22 16 -10000 0 16
VEGFA 0.02 0.004 -10000 0 -10000 0 0
VEGFB 0.02 0.003 -10000 0 -10000 0 0
mol:IP3 -0.012 0.036 0.23 6 -10000 0 6
RASA1 -0.016 0.028 0.18 9 -10000 0 9
NRP2 0.018 0.028 -10000 0 -0.32 3 3
VEGFR1 homodimer -0.014 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.02 0.003 -10000 0 -10000 0 0
NCK1 0.02 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.09 0.11 0.44 2 -0.37 28 30
PTPN11 0.02 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.036 -10000 0 -10000 0 0
mol:L-citrulline -0.005 0.09 0.43 7 -0.35 11 18
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.037 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.011 -10000 0 -10000 0 0
CD2AP 0.02 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.048 0.039 -10000 0 -10000 0 0
PDPK1 -0.015 0.047 0.33 4 -10000 0 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.011 -10000 0 -10000 0 0
mol:NADP -0.005 0.09 0.43 7 -0.35 11 18
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.017 0.015 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.001 0.073 0.2 2 -0.3 16 18
PDGFB-D/PDGFRB/SLAP 0.021 0.035 -10000 0 -0.23 8 8
PDGFB-D/PDGFRB/APS/CBL 0.037 0.018 -10000 0 -0.2 1 1
AKT1 -0.012 0.08 0.36 10 -10000 0 10
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.091 0.29 5 -0.34 18 23
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FGR -0.03 0.14 0.33 2 -0.47 40 42
mol:Ca2+ -0.001 0.1 0.29 6 -0.38 20 26
MYC 0.036 0.13 0.37 17 -0.48 6 23
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP -0.012 0.041 0.15 25 -10000 0 25
LRP1/PDGFRB/PDGFB 0.035 0.031 -10000 0 -0.19 7 7
GRB10 0.019 0.006 -10000 0 -10000 0 0
PTPN11 0.02 0.003 -10000 0 -10000 0 0
GO:0007205 -0.002 0.1 0.29 6 -0.38 20 26
PTEN 0.02 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.019 0.023 -10000 0 -0.32 2 2
PDGFB-D/PDGFRB/SHP2 0.029 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.027 0.011 -10000 0 -10000 0 0
cell cycle arrest 0.021 0.035 -10000 0 -0.23 8 8
HRAS 0.02 0.004 -10000 0 -10000 0 0
HIF1A -0.015 0.074 0.35 10 -10000 0 10
GAB1 0 0.097 0.37 3 -0.33 20 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.001 0.086 0.28 9 -0.32 10 19
PDGFB-D/PDGFRB 0.037 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.03 0.008 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.054 0.2 1 -0.27 5 6
positive regulation of MAPKKK cascade 0.029 0.008 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 -0.002 0.1 0.29 6 -0.38 20 26
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.018 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.019 -10000 0 -0.23 2 2
SHB 0.02 0.005 -10000 0 -10000 0 0
BLK -0.029 0.17 0.32 3 -0.39 68 71
PTPN2 0.019 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.03 0.008 -10000 0 -10000 0 0
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
VAV2 -0.002 0.1 0.31 5 -0.37 19 24
CBL 0.02 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.008 -10000 0 -10000 0 0
LCK 0.006 0.061 0.33 2 -0.42 4 6
PDGFRB 0.02 0.009 -10000 0 -10000 0 0
ACP1 0.021 0.002 -10000 0 -10000 0 0
HCK -0.015 0.12 0.32 1 -0.54 22 23
ABL1 -0.005 0.098 0.27 7 -0.34 20 27
PDGFB-D/PDGFRB/CBL -0.003 0.11 0.38 2 -0.39 21 23
PTPN1 0.019 0.009 -10000 0 -10000 0 0
SNX15 0.02 0.003 -10000 0 -10000 0 0
STAT3 0.02 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
cell proliferation 0.037 0.12 0.36 17 -0.41 7 24
SLA 0.011 0.048 -10000 0 -0.32 9 9
actin cytoskeleton reorganization -0.014 0.059 0.3 6 -10000 0 6
SRC -0.001 0.092 0.31 1 -0.62 8 9
PI3K -0.032 0.021 -10000 0 -0.17 6 6
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.023 -10000 0 -0.2 2 2
SH2B2 0.019 0.017 -10000 0 -0.32 1 1
PLCgamma1/SPHK1 0.006 0.093 0.31 4 -0.35 18 22
LYN 0.005 0.051 0.31 1 -0.38 3 4
LRP1 0.017 0.032 -10000 0 -0.32 4 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
STAT5B 0.02 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
NCK1-2/p130 Cas 0.052 0.029 -10000 0 -0.17 1 1
SPHK1 0.022 0.029 0.32 4 -10000 0 4
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.002 0.1 0.29 6 -0.38 20 26
PLCG1 -0.002 0.1 0.29 6 -0.39 20 26
NHERF/PDGFRB 0.036 0.029 0.22 1 -0.2 5 6
YES1 -0.009 0.11 0.34 1 -0.57 15 16
cell migration 0.036 0.029 0.22 1 -0.2 5 6
SHC/Grb2/SOS1 0.045 0.031 -10000 0 -10000 0 0
SLC9A3R2 0.017 0.036 -10000 0 -0.32 5 5
SLC9A3R1 0.021 0.015 0.32 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.046 0.03 0.22 1 -0.18 5 6
FYN -0.026 0.13 0.31 1 -0.41 39 40
DOK1 -0.013 0.036 0.16 18 -10000 0 18
HRAS/GTP 0.015 0.003 -10000 0 -10000 0 0
PDGFB 0.017 0.032 -10000 0 -0.32 4 4
RAC1 0.013 0.12 0.35 10 -0.38 14 24
PRKCD -0.011 0.042 0.16 24 -10000 0 24
FER -0.011 0.041 0.17 23 -10000 0 23
MAPKKK cascade 0.016 0.1 0.36 20 -10000 0 20
RASA1 -0.011 0.04 0.17 22 -10000 0 22
NCK1 0.02 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.014 0.042 0.16 26 -10000 0 26
PDGFB-D/PDGFRB/SHB 0.028 0.009 -10000 0 -10000 0 0
chemotaxis -0.004 0.097 0.27 7 -0.33 20 27
STAT1-3-5/STAT1-3-5 0.042 0.025 -10000 0 -0.18 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.006 -10000 0 -10000 0 0
PTPRJ 0.02 0.003 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.015 0.017 -10000 0 -10000 0 0
HSPA8 0.019 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.022 0.062 0.23 7 -0.22 8 15
AKT1 0.013 0.027 -10000 0 -0.12 1 1
GSC 0.042 0.12 0.79 2 -0.47 2 4
NKX2-5 0.036 0.074 0.32 29 -10000 0 29
muscle cell differentiation -0.011 0.072 0.28 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.047 0.064 -10000 0 -10000 0 0
SMAD4 0.016 0.031 -10000 0 -10000 0 0
CBFB 0.02 0.004 -10000 0 -10000 0 0
SAP18 0.019 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.026 0.058 0.22 7 -0.2 20 27
SMAD3/SMAD4/VDR 0.04 0.05 -10000 0 -0.23 1 1
MYC 0.018 0.026 -10000 0 -0.32 2 2
CDKN2B -0.17 0.39 -10000 0 -1.1 51 51
AP1 0.004 0.061 -10000 0 -0.25 11 11
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.02 0.093 -10000 0 -0.32 26 26
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.021 0.097 0.18 1 -0.32 33 34
SP3 0.021 0.003 -10000 0 -10000 0 0
CREB1 0.021 0.003 -10000 0 -10000 0 0
FOXH1 0.048 0.087 0.33 41 -10000 0 41
SMAD3/SMAD4/GR 0.029 0.042 -10000 0 -10000 0 0
GATA3 0.02 0.026 0.32 1 -0.32 1 2
SKI/SIN3/HDAC complex/NCoR1 -0.014 0.074 -10000 0 -0.36 12 12
MEF2C/TIF2 0.01 0.067 0.24 8 -0.23 1 9
endothelial cell migration -0.012 0.077 0.67 4 -10000 0 4
MAX 0.019 0.009 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
RUNX2 0.025 0.037 0.32 7 -10000 0 7
RUNX3 0.019 0.023 -10000 0 -0.32 2 2
RUNX1 0.02 0.004 -10000 0 -10000 0 0
CTBP1 0.02 0.004 -10000 0 -10000 0 0
NR3C1 0.019 0.009 -10000 0 -10000 0 0
VDR 0.02 0.021 0.32 1 -0.32 1 2
CDKN1A -0.001 0.052 -10000 0 -0.84 1 1
KAT2B 0.016 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.058 0.077 0.25 35 -10000 0 35
DCP1A 0.02 0.004 -10000 0 -10000 0 0
SKI 0.02 0.004 -10000 0 -10000 0 0
SERPINE1 0.012 0.078 -10000 0 -0.68 4 4
SMAD3/SMAD4/ATF2 0.03 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.018 0.06 -10000 0 -0.2 18 18
SAP30 0.02 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.032 0.029 -10000 0 -10000 0 0
JUN -0.012 0.058 0.22 1 -0.25 10 11
SMAD3/SMAD4/IRF7 0.032 0.045 0.4 1 -10000 0 1
TFE3 0.021 0.007 -10000 0 -10000 0 0
COL1A2 0.02 0.079 0.3 19 -0.51 4 23
mesenchymal cell differentiation -0.032 0.046 -10000 0 -0.23 5 5
DLX1 0.039 0.074 0.32 30 -10000 0 30
TCF3 0.019 0.005 -10000 0 -10000 0 0
FOS -0.006 0.086 -10000 0 -0.33 29 29
SMAD3/SMAD4/Max 0.029 0.041 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.033 0.024 -10000 0 -10000 0 0
ZBTB17 0.021 0.009 -10000 0 -10000 0 0
LAMC1 -0.012 0.032 0.18 5 -10000 0 5
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.04 -10000 0 -10000 0 0
IRF7 0.022 0.022 0.35 2 -10000 0 2
ESR1 0.015 0.068 0.32 10 -0.32 9 19
HNF4A 0.07 0.13 0.32 89 -0.32 9 98
MEF2C 0.022 0.079 0.26 17 -10000 0 17
SMAD2-3/SMAD4 0.034 0.052 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.033 0.026 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.016 -10000 0 -0.32 1 1
TGIF2/HDAC complex 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.016 0.015 -10000 0 -10000 0 0
SKIL 0.02 0.005 -10000 0 -10000 0 0
HDAC1 0.021 0.002 -10000 0 -10000 0 0
HDAC2 0.019 0.006 -10000 0 -10000 0 0
SNIP1 0.02 0.007 -10000 0 -10000 0 0
GCN5L2 -0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.034 0.042 -10000 0 -10000 0 0
MSG1/HSC70 0.022 0.059 0.23 8 -0.23 20 28
SMAD2 0.018 0.027 -10000 0 -10000 0 0
SMAD3 0.008 0.032 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.043 0.16 1 -0.19 9 10
SMAD2/SMAD2/SMAD4 -0.013 0.072 0.19 2 -0.26 20 22
NCOR1 0.019 0.006 -10000 0 -10000 0 0
NCOA2 0.016 0.032 -10000 0 -0.32 4 4
NCOA1 0.021 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.027 0.012 0.23 1 -10000 0 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.052 0.068 -10000 0 -10000 0 0
IFNB1 -0.014 0.032 0.34 2 -10000 0 2
SMAD3/SMAD4/MEF2C 0.05 0.07 0.26 5 -10000 0 5
CITED1 0.011 0.081 0.32 8 -0.32 20 28
SMAD2-3/SMAD4/ARC105 0.043 0.052 -10000 0 -10000 0 0
RBL1 0.02 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.04 0.15 -10000 0 -0.52 34 34
RUNX1-3/PEBPB2 0.038 0.019 -10000 0 -0.18 2 2
SMAD7 -0.001 0.079 -10000 0 -0.41 6 6
MYC/MIZ-1 0.027 0.024 0.2 1 -0.23 1 2
SMAD3/SMAD4 -0.009 0.067 -10000 0 -0.33 4 4
IL10 -0.015 0.05 0.3 3 -0.33 5 8
PIASy/HDAC complex 0.018 0.013 -10000 0 -10000 0 0
PIAS3 0.016 0.013 -10000 0 -10000 0 0
CDK2 0.016 0.015 -10000 0 -10000 0 0
IL5 -0.017 0.034 -10000 0 -10000 0 0
CDK4 0.015 0.015 -10000 0 -10000 0 0
PIAS4 0.018 0.013 -10000 0 -10000 0 0
ATF3 0.005 0.068 -10000 0 -0.32 19 19
SMAD3/SMAD4/SP1 0.035 0.051 -10000 0 -10000 0 0
FOXG1 0.045 0.089 0.32 43 -10000 0 43
FOXO3 -0.019 0.022 -10000 0 -0.14 2 2
FOXO1 -0.02 0.023 -10000 0 -0.14 1 1
FOXO4 -0.021 0.022 -10000 0 -0.14 1 1
heart looping 0.022 0.079 0.26 18 -10000 0 18
CEBPB 0.014 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.041 0.058 0.24 20 -10000 0 20
MYOD1 0.019 0.025 0.32 3 -10000 0 3
SMAD3/SMAD4/HNF4 0.057 0.091 0.23 68 -0.2 9 77
SMAD3/SMAD4/GATA3 0.03 0.048 -10000 0 -0.21 3 3
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.048 -10000 0 -0.2 1 1
SMAD3/SMAD4/SP1-3 0.044 0.053 -10000 0 -10000 0 0
MED15 0.02 0.004 -10000 0 -10000 0 0
SP1 0.019 0.021 -10000 0 -0.13 2 2
SIN3B 0.02 0.005 -10000 0 -10000 0 0
SIN3A 0.02 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.07 0.088 0.34 16 -10000 0 16
ITGB5 -0.014 0.04 0.2 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP -0.01 0.058 -10000 0 -0.31 8 8
SMAD3/SMAD4/AR 0.001 0.089 -10000 0 -0.22 56 56
AR -0.023 0.12 0.32 1 -0.32 60 61
negative regulation of cell growth -0.006 0.065 -10000 0 -0.26 14 14
SMAD3/SMAD4/MYOD 0.029 0.043 0.24 2 -10000 0 2
E2F5 0.018 0.007 -10000 0 -10000 0 0
E2F4 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.07 0.074 0.29 8 -10000 0 8
SMAD2-3/SMAD4/FOXO1-3a-4 -0.019 0.096 -10000 0 -0.37 30 30
TFDP1 0.019 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.021 0.068 -10000 0 -0.25 11 11
SMAD3/SMAD4/RUNX2 0.032 0.046 0.24 5 -10000 0 5
TGIF2 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.019 0.006 -10000 0 -10000 0 0
ATF2 0.02 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.028 0.03 0.21 9 -0.17 3 12
EFNA5 0.019 0.034 0.32 2 -0.32 3 5
FYN -0.013 0.025 0.18 5 -0.18 2 7
neuron projection morphogenesis 0.028 0.03 0.21 9 -0.17 3 12
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.028 0.03 0.21 9 -0.17 3 12
EPHA5 0.024 0.04 0.32 8 -10000 0 8
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.04 0.048 0.22 1 -0.21 13 14
MAP4K1 0.017 0.032 -10000 0 -0.32 4 4
MAP3K8 0.019 0.016 -10000 0 -0.32 1 1
PRKCB 0.011 0.057 -10000 0 -0.32 13 13
DBNL 0.019 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 0 0.051 -10000 0 -0.27 9 9
JUN -0.011 0.12 -10000 0 -0.55 21 21
MAP3K7 0.001 0.044 -10000 0 -0.24 8 8
GRAP2 0.01 0.057 -10000 0 -0.32 13 13
CRK 0.019 0.006 -10000 0 -10000 0 0
MAP2K4 -0.001 0.064 0.2 2 -0.37 6 8
LAT 0.021 0.014 0.32 1 -10000 0 1
LCP2 0.018 0.028 -10000 0 -0.32 3 3
MAPK8 -0.007 0.13 -10000 0 -0.56 22 22
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.057 -10000 0 -0.26 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55 0.046 0.042 0.22 1 -0.22 6 7
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 0.021 0.002 -10000 0 -10000 0 0
HDAC2 0.019 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.035 0.025 0.22 1 -0.2 3 4
forebrain development -0.034 0.14 -10000 0 -0.52 19 19
GNAO1 0.014 0.034 0.32 2 -0.32 2 4
SMO/beta Arrestin2 0.021 0.029 0.22 3 -0.2 1 4
SMO 0.015 0.033 0.32 3 -0.32 1 4
ARRB2 0.013 0.015 -10000 0 -10000 0 0
GLI3/SPOP 0.003 0.08 -10000 0 -0.32 15 15
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.02 0.003 -10000 0 -10000 0 0
GNAI2 0.014 0.015 -10000 0 -10000 0 0
SIN3/HDAC complex 0.047 0.02 -10000 0 -10000 0 0
GNAI1 0.013 0.022 -10000 0 -0.33 1 1
XPO1 0.013 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.031 0.13 -10000 0 -0.52 18 18
SAP30 0.02 0.004 -10000 0 -10000 0 0
mol:GDP 0.015 0.033 0.32 3 -0.32 1 4
MIM/GLI2A 0.001 0.047 -10000 0 -0.33 1 1
IFT88 0.019 0.006 -10000 0 -10000 0 0
GNAI3 0.014 0.015 -10000 0 -10000 0 0
GLI2 -0.006 0.073 0.19 1 -0.38 10 11
GLI3 -0.008 0.082 0.2 1 -0.32 19 20
CSNK1D 0.02 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.019 0.005 -10000 0 -10000 0 0
GNG2 0.019 0.023 -10000 0 -0.32 2 2
Gi family/GTP -0.014 0.067 -10000 0 -0.2 45 45
SIN3B 0.02 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) -0.006 0.086 -10000 0 -0.35 17 17
GLI2/Su(fu) -0.006 0.084 -10000 0 -0.41 13 13
FOXA2 -0.13 0.34 -10000 0 -0.85 83 83
neural tube patterning -0.034 0.14 -10000 0 -0.52 19 19
SPOP 0.02 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.013 0.037 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
CSNK1G2 0.019 0.006 -10000 0 -10000 0 0
CSNK1G3 0.02 0.004 -10000 0 -10000 0 0
MTSS1 0.001 0.047 -10000 0 -0.33 1 1
embryonic limb morphogenesis -0.034 0.14 -10000 0 -0.52 19 19
SUFU 0.007 0.014 -10000 0 -10000 0 0
LGALS3 0.02 0.005 -10000 0 -10000 0 0
catabolic process -0.002 0.12 -10000 0 -0.42 24 24
GLI3A/CBP 0.007 0.057 -10000 0 -0.33 11 11
KIF3A 0.02 0.004 -10000 0 -10000 0 0
GLI1 -0.035 0.14 -10000 0 -0.53 19 19
RAB23 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
IFT172 0.021 0.002 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.012 0.037 -10000 0 -10000 0 0
GNAZ -0.014 0.095 -10000 0 -0.33 39 39
RBBP4 0.021 0.003 -10000 0 -10000 0 0
CSNK1G1 0.02 0.004 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.001 0.081 -10000 0 -0.4 12 12
STK36 0.013 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.013 0.064 -10000 0 -0.23 18 18
PTCH1 -0.041 0.16 -10000 0 -0.83 12 12
MIM/GLI1 -0.048 0.18 -10000 0 -0.46 64 64
CREBBP 0.007 0.057 -10000 0 -0.33 11 11
Su(fu)/SIN3/HDAC complex -0.001 0.064 -10000 0 -0.28 15 15
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.009 0.023 -10000 0 -0.17 7 7
epithelial cell differentiation 0.041 0.019 -10000 0 -0.17 2 2
CYFIP2 0.016 0.039 -10000 0 -0.32 6 6
ENAH -0.02 0.056 0.41 2 -0.23 1 3
EGFR 0.015 0.042 0.32 1 -0.32 6 7
EPHA2 0.013 0.048 -10000 0 -0.32 9 9
MYO6 -0.018 0.039 0.23 8 -10000 0 8
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.022 -10000 0 -0.2 3 3
AQP5 -0.061 0.16 0.54 2 -0.37 91 93
CTNND1 0.02 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.018 0.04 0.22 9 -10000 0 9
regulation of calcium-dependent cell-cell adhesion -0.089 0.075 0.16 3 -0.3 1 4
EGF 0.072 0.12 0.32 84 -0.32 4 88
NCKAP1 0.021 0.002 -10000 0 -10000 0 0
AQP3 -0.021 0.071 0.24 1 -0.32 22 23
cortical microtubule organization 0.041 0.019 -10000 0 -0.17 2 2
GO:0000145 -0.017 0.038 0.21 9 -0.16 2 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.02 -10000 0 -0.17 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.032 0.024 -10000 0 -0.16 6 6
ARF6 0.02 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.039 0.035 -10000 0 -0.18 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.011 0.04 0.42 2 -0.21 1 3
PVRL2 0.02 0.004 -10000 0 -10000 0 0
ZYX -0.019 0.041 0.22 9 -10000 0 9
ARF6/GTP 0.042 0.035 -10000 0 -0.17 6 6
CDH1 0.019 0.023 -10000 0 -0.32 2 2
EGFR/EGFR/EGF/EGF 0.042 0.054 0.24 1 -0.18 9 10
RhoA/GDP 0.041 0.019 -10000 0 -0.16 2 2
actin cytoskeleton organization -0.02 0.037 0.22 8 -0.17 2 10
IGF-1R heterotetramer 0.019 0.023 -10000 0 -0.32 2 2
GIT1 0.02 0.003 -10000 0 -10000 0 0
IGF1R 0.019 0.023 -10000 0 -0.32 2 2
IGF1 0.014 0.05 0.32 1 -0.32 9 10
DIAPH1 0.018 0.11 -10000 0 -0.56 10 10
Wnt receptor signaling pathway -0.041 0.019 0.17 2 -10000 0 2
RHOA 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.026 -10000 0 -0.18 7 7
CTNNA1 0.02 0.004 -10000 0 -10000 0 0
VCL -0.02 0.038 0.22 8 -0.17 2 10
EFNA1 0.017 0.018 -10000 0 -0.32 1 1
LPP -0.021 0.039 0.21 9 -10000 0 9
Ephrin A1/EPHA2 0.027 0.034 -10000 0 -0.18 9 9
SEC6/SEC8 -0.024 0.018 -10000 0 -0.16 1 1
MGAT3 -0.09 0.076 0.16 3 -0.3 1 4
HGF/MET 0.022 0.055 -10000 0 -0.17 30 30
HGF 0.008 0.076 0.32 4 -0.32 20 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.023 -10000 0 -0.18 7 7
actin cable formation 0.009 0.087 0.3 18 -0.24 3 21
KIAA1543 -0.02 0.028 0.18 7 -0.16 2 9
KIFC3 -0.022 0.022 0.16 4 -10000 0 4
NCK1 0.02 0.003 -10000 0 -10000 0 0
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ACTN1 -0.018 0.039 0.22 9 -10000 0 9
NCK1/GIT1 0.03 0.006 -10000 0 -10000 0 0
mol:GDP 0.041 0.019 -10000 0 -0.17 2 2
EXOC4 0.02 0.005 -10000 0 -10000 0 0
STX4 -0.02 0.03 0.19 7 -10000 0 7
PIP5K1C -0.018 0.04 0.22 9 -10000 0 9
LIMA1 0.021 0.003 -10000 0 -10000 0 0
ABI1 0.02 0.003 -10000 0 -10000 0 0
ROCK1 -0.008 0.078 0.34 8 -0.26 1 9
adherens junction assembly -0.025 0.092 0.36 6 -0.44 10 16
IGF-1R heterotetramer/IGF1 0.03 0.035 -10000 0 -0.16 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.01 -10000 0 -10000 0 0
MET 0.013 0.069 0.32 6 -0.32 14 20
PLEKHA7 -0.021 0.03 0.19 7 -10000 0 7
mol:GTP 0.038 0.034 -10000 0 -0.18 7 7
establishment of epithelial cell apical/basal polarity 0.021 0.096 0.3 17 -10000 0 17
cortical actin cytoskeleton stabilization 0.009 0.023 -10000 0 -0.17 7 7
regulation of cell-cell adhesion -0.02 0.037 0.22 8 -0.17 2 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.023 -10000 0 -0.18 7 7
Insulin Pathway

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
CBL/APS/CAP 0.027 0.045 -10000 0 -0.16 20 20
TC10/GTP 0.023 0.041 -10000 0 -0.16 18 18
Insulin Receptor/Insulin/IRS1/Shp2 0.048 0.02 -10000 0 -0.14 1 1
HRAS 0.02 0.004 -10000 0 -10000 0 0
APS homodimer 0.019 0.017 -10000 0 -0.32 1 1
GRB14 0.032 0.076 0.32 24 -0.32 5 29
FOXO3 -0.045 0.19 -10000 0 -0.62 45 45
AKT1 -0.019 0.053 0.27 6 -10000 0 6
INSR 0.021 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.04 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.006 -10000 0 -10000 0 0
SORBS1 0.003 0.076 -10000 0 -0.32 24 24
CRK 0.019 0.006 -10000 0 -10000 0 0
PTPN1 -0.012 0.02 -10000 0 -10000 0 0
CAV1 -0.095 0.08 -10000 0 -0.17 237 237
CBL/APS/CAP/Crk-II/C3G 0.04 0.052 -10000 0 -0.17 20 20
Insulin Receptor/Insulin/IRS1/NCK2 0.049 0.019 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.02 -10000 0 -0.17 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0 0.071 -10000 0 -0.32 18 18
RPS6KB1 -0.023 0.047 0.24 5 -10000 0 5
PARD6A 0.019 0.016 -10000 0 -0.32 1 1
CBL 0.02 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.011 0.039 -10000 0 -0.57 2 2
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.026 0.041 0.15 2 -10000 0 2
HRAS/GTP -0.027 0.019 -10000 0 -0.16 1 1
Insulin Receptor 0.021 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.047 0.028 -10000 0 -10000 0 0
PRKCI 0.002 0.073 -10000 0 -0.3 22 22
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.032 -10000 0 -0.17 4 4
SHC1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.028 0.04 -10000 0 -0.48 2 2
PI3K 0.045 0.024 -10000 0 -0.17 1 1
NCK2 0.021 0.002 -10000 0 -10000 0 0
RHOQ 0.02 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
AKT2 -0.02 0.052 0.29 5 -10000 0 5
PRKCZ -0.002 0.084 -10000 0 -0.32 24 24
SH2B2 0.019 0.017 -10000 0 -0.32 1 1
SHC/SHIP -0.019 0.022 0.15 2 -0.17 2 4
F2RL2 0.037 0.083 0.32 31 -0.32 4 35
TRIP10 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.031 0.017 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.047 0.028 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.02 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.034 0.05 -10000 0 -0.18 20 20
TC10/GDP 0.015 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.039 0.025 -10000 0 -10000 0 0
INPP5D -0.019 0.02 0.15 2 -0.17 2 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
SGK1 -0.047 0.19 -10000 0 -0.66 40 40
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.02 0.003 -10000 0 -10000 0 0
IRS1 0.02 0.016 -10000 0 -0.32 1 1
p62DOK/RasGAP 0.028 0.041 -10000 0 -0.49 2 2
INS -0.014 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.018 0.02 0.15 2 -0.17 2 4
GRB2 0.02 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.051 0.2 10 -10000 0 10
PTPRA 0.021 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.026 0.008 -10000 0 -10000 0 0
PDPK1 0.02 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.008 0.023 -10000 0 -0.19 1 1
Insulin Receptor/Insulin/IRS1 0.037 0.016 -10000 0 -0.14 1 1
Insulin Receptor/Insulin/IRS3 0.029 0.012 -10000 0 -10000 0 0
Par3/Par6 0.05 0.046 0.21 26 -0.16 4 30
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.019 0.016 -10000 0 -0.32 1 1
SPHK1 0.023 0.028 0.32 4 -10000 0 4
GNAI2 0.02 0.004 -10000 0 -10000 0 0
mol:S1P 0.006 0.015 -10000 0 -0.22 1 1
GNAO1 0.02 0.03 0.32 2 -0.32 2 4
mol:Sphinganine-1-P -0.015 0.019 0.15 4 -0.23 1 5
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.033 0.033 -10000 0 -0.2 2 2
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
S1PR3 0.021 0.015 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.001 0.028 -10000 0 -0.23 3 3
S1PR5 0 0.082 0.32 1 -0.32 27 28
S1PR4 0.007 0.065 -10000 0 -0.32 17 17
GNAI1 0.019 0.017 -10000 0 -0.32 1 1
S1P/S1P5/G12 0.015 0.052 0.21 1 -0.17 23 24
S1P/S1P3/Gq 0.004 0.068 -10000 0 -0.29 20 20
S1P/S1P4/Gi -0.016 0.086 -10000 0 -0.21 59 59
GNAQ 0.019 0.016 -10000 0 -0.32 1 1
GNAZ -0.009 0.095 -10000 0 -0.32 39 39
GNA14 0.011 0.055 -10000 0 -0.32 12 12
GNA15 0.019 0.005 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.005 -10000 0 -10000 0 0
ABCC1 0.02 0.003 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.02 0.016 -10000 0 -0.32 1 1
ANTXR2 0.021 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.002 -10000 0 -0.046 1 1
monocyte activation -0.011 0.1 -10000 0 -0.36 32 32
MAP2K2 -0.028 0.15 -10000 0 -0.57 32 32
MAP2K1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K7 -0.007 0.002 -10000 0 -10000 0 0
MAP2K6 -0.005 0.019 0.07 16 -0.16 2 18
CYAA -0.011 0.007 -10000 0 -0.16 1 1
MAP2K4 -0.007 0.002 -10000 0 -10000 0 0
IL1B -0.013 0.035 0.16 3 -0.16 22 25
Channel 0.026 0.01 -10000 0 -0.17 1 1
NLRP1 -0.007 0.007 -10000 0 -0.16 1 1
CALM1 0.02 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.057 -10000 0 -0.39 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.002 0.046 1 -10000 0 1
MAPK3 -0.008 0.002 -10000 0 -10000 0 0
MAPK1 -0.007 0.002 -10000 0 -10000 0 0
PGR -0.032 0.056 -10000 0 -0.16 78 78
PA/Cellular Receptors 0.027 0.011 -10000 0 -0.19 1 1
apoptosis -0.003 0.002 -10000 0 -0.046 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.009 -10000 0 -0.16 1 1
macrophage activation -0.012 0.003 -10000 0 -10000 0 0
TNF 0.009 0.065 0.32 1 -0.32 16 17
VCAM1 -0.011 0.1 -10000 0 -0.38 30 30
platelet activation -0.002 0.057 -10000 0 -0.39 10 10
MAPKKK cascade 0.003 0.017 -10000 0 -0.071 18 18
IL18 -0.009 0.026 0.14 2 -0.19 7 9
negative regulation of macrophage activation -0.003 0.002 -10000 0 -0.046 1 1
LEF -0.003 0.002 -10000 0 -0.046 1 1
CASP1 -0.004 0.011 -10000 0 -0.13 3 3
mol:cAMP -0.002 0.058 -10000 0 -0.39 10 10
necrosis -0.003 0.002 -10000 0 -0.046 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.009 -10000 0 -0.16 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.058 0.34 2 -10000 0 2
CRKL -0.01 0.047 0.21 10 -10000 0 10
mol:DAG 0.009 0.032 0.24 1 -0.22 1 2
HRAS 0 0.072 0.24 12 -10000 0 12
MAPK8 -0.001 0.058 0.17 47 -10000 0 47
RAP1A -0.009 0.048 0.21 10 -10000 0 10
GAB1 -0.01 0.047 0.22 8 -10000 0 8
MAPK14 -0.001 0.057 0.17 45 -10000 0 45
EPO 0.01 0.032 0.32 3 -10000 0 3
PLCG1 0.009 0.033 0.24 1 -0.23 1 2
EPOR/TRPC2/IP3 Receptors 0.021 0.008 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.036 0.03 0.21 2 -0.2 4 6
GAB1/SHC/GRB2/SOS1 -0.016 0.045 0.24 4 -10000 0 4
EPO/EPOR (dimer) 0.03 0.021 0.23 3 -10000 0 3
IRS2 -0.01 0.047 0.21 10 -10000 0 10
STAT1 0.01 0.036 0.32 1 -0.23 1 2
STAT5B 0.01 0.034 0.28 1 -0.23 1 2
cell proliferation -0.003 0.063 0.18 47 -10000 0 47
GAB1/SHIP/PIK3R1/SHP2/SHC -0.025 0.034 -10000 0 -0.28 1 1
TEC -0.01 0.049 0.21 10 -10000 0 10
SOCS3 0.017 0.032 -10000 0 -0.32 4 4
STAT1 (dimer) 0.01 0.036 0.31 1 -0.22 1 2
JAK2 0.019 0.019 -10000 0 -0.33 1 1
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
EPO/EPOR (dimer)/JAK2 0.045 0.037 0.35 1 -0.16 3 4
EPO/EPOR 0.03 0.021 0.23 3 -10000 0 3
LYN 0.019 0.006 -10000 0 -10000 0 0
TEC/VAV2 -0.013 0.047 0.26 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.021 0.008 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.037 0.024 0.22 3 -10000 0 3
mol:IP3 0.009 0.032 0.24 1 -0.22 1 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.053 0.26 4 -0.29 1 5
SH2B3 0.02 0.024 -10000 0 -0.33 2 2
NFKB1 -0.001 0.059 0.17 48 -10000 0 48
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.044 0.19 2 -0.23 12 14
PTPN6 -0.008 0.043 0.17 5 -0.16 2 7
TEC/VAV2/GRB2 -0.016 0.047 0.25 4 -10000 0 4
EPOR 0.021 0.008 -10000 0 -10000 0 0
INPP5D 0.018 0.028 -10000 0 -0.32 3 3
mol:GDP -0.016 0.045 0.24 4 -10000 0 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.028 -10000 0 -0.32 3 3
CRKL/CBL/C3G -0.016 0.047 0.25 4 -10000 0 4
VAV2 -0.01 0.049 0.21 10 -10000 0 10
CBL -0.009 0.048 0.21 10 -10000 0 10
SHC/Grb2/SOS1 0.023 0.022 -10000 0 -0.16 1 1
STAT5A 0.01 0.038 0.28 1 -0.3 2 3
GRB2 0.02 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.022 0.039 0.37 1 -0.34 1 2
LYN/PLCgamma2 0.025 0.023 -10000 0 -0.23 3 3
PTPN11 0.02 0.003 -10000 0 -10000 0 0
BTK -0.016 0.058 0.22 8 -0.29 2 10
BCL2 0.009 0.074 0.39 2 -10000 0 2
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.021 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.013 0.025 -10000 0 -0.2 7 7
FRAP1 -0.007 0.085 -10000 0 -0.43 16 16
AKT1 -0.01 0.033 0.15 8 -0.22 5 13
INSR 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.007 -10000 0 -10000 0 0
mol:GTP -0.012 0.045 0.24 2 -0.2 3 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.015 0.027 -10000 0 -0.2 5 5
TSC2 0.02 0.003 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.026 -10000 0 -0.19 2 2
TSC1 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.014 0.027 -10000 0 -0.21 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.038 -10000 0 -0.22 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.021 0.002 -10000 0 -10000 0 0
RPS6KB1 0.005 0.061 0.24 3 -0.36 5 8
MAP3K5 -0.01 0.052 0.18 4 -0.18 37 41
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
apoptosis -0.01 0.052 0.18 4 -0.18 37 41
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.003 0.06 0.28 3 -0.32 5 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.02 0.052 0.23 2 -0.3 4 6
eIF4E/eIF4G1/eIF4A1 0.003 0.053 -10000 0 -0.27 15 15
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.031 -10000 0 -0.2 7 7
mTOR/RHEB/GTP/Raptor/GBL -0.004 0.034 0.14 11 -0.15 3 14
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
RHEB/GTP -0.016 0.039 0.2 1 -0.19 2 3
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.018 0.022 -10000 0 -0.19 6 6
EIF4E 0.021 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.028 0.17 -10000 0 -0.52 47 47
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.039 -10000 0 -0.23 11 11
TSC1/TSC2 -0.012 0.049 0.23 3 -0.22 3 6
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.019 0.006 -10000 0 -10000 0 0
PPP5C 0.02 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.028 -10000 0 -0.24 6 6
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.02 0.004 -10000 0 -10000 0 0
PDK2 -0.018 0.025 0.17 1 -0.19 7 8
EIF4EBP1 -0.057 0.29 -10000 0 -1 36 36
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PPP2R5D -0.004 0.084 0.29 1 -0.4 15 16
peptide biosynthetic process -0.016 0.013 0.17 2 -10000 0 2
RHEB 0.02 0.005 -10000 0 -10000 0 0
EIF4A1 0.019 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 16 -0.002 1 17
EEF2 -0.016 0.013 0.17 2 -10000 0 2
eIF4E/4E-BP1 -0.045 0.27 -10000 0 -0.96 36 36
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.02 0.005 -10000 0 -10000 0 0
NFATC1 -0.015 0.1 0.33 2 -0.39 16 18
NFATC2 -0.013 0.059 0.17 4 -0.25 12 16
NFATC3 0.006 0.022 -10000 0 -0.3 2 2
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.019 0.095 0.26 1 -0.36 18 19
Exportin 1/Ran/NUP214 0.039 0.013 0.22 1 -10000 0 1
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.003 0.086 -10000 0 -0.32 17 17
BCL2/BAX 0.027 0.018 0.23 1 -0.23 1 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.015 -10000 0 -10000 0 0
CaM/Ca2+ 0.007 0.015 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.013 0.016 -10000 0 -10000 0 0
BAD 0.02 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.006 0.085 0.24 1 -0.33 16 17
Calcineurin A alpha-beta B1/BCL2 0.019 0.022 0.32 1 -0.32 1 2
FKBP8 0.019 0.017 -10000 0 -0.32 1 1
activation-induced cell death of T cells 0.006 0.084 0.33 16 -0.23 1 17
KPNB1 0.02 0.004 -10000 0 -10000 0 0
KPNA2 0.023 0.031 0.32 5 -10000 0 5
XPO1 0.02 0.002 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 8 -0.32 1 9
MAP3K8 0.012 0.023 -10000 0 -0.32 1 1
NFAT4/CK1 alpha 0.007 0.026 -10000 0 -0.16 2 2
MEF2D/NFAT1/Cbp/p300 -0.019 0.1 -10000 0 -0.23 78 78
CABIN1 -0.02 0.095 0.26 1 -0.36 18 19
CALM1 0.012 0.017 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
CAMK4 0.015 0.044 0.32 1 -0.32 7 8
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.019 -10000 0 -0.23 2 2
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.012 0.016 -10000 0 -10000 0 0
MAPK9 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.017 0.11 0.33 2 -0.39 19 21
PRKCH 0.02 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.016 0.028 -10000 0 -10000 0 0
CASP3 0.013 0.016 -10000 0 -10000 0 0
PIM1 0.02 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.011 -10000 0 -10000 0 0
apoptosis 0.011 0.016 0.15 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.039 -10000 0 -0.31 2 2
PRKCB 0.011 0.057 -10000 0 -0.32 13 13
PRKCE 0.018 0.032 -10000 0 -0.32 4 4
JNK2/NFAT4 0.015 0.037 -10000 0 -0.19 7 7
BAD/BCL-XL 0.029 0.008 -10000 0 -10000 0 0
PRKCD 0.02 0.004 -10000 0 -10000 0 0
NUP214 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.01 0.032 -10000 0 -0.33 3 3
PRKCA 0.019 0.023 -10000 0 -0.32 2 2
PRKCG 0.043 0.082 0.32 37 -10000 0 37
PRKCQ -0.025 0.12 -10000 0 -0.32 60 60
FKBP38/BCL2 0.026 0.022 0.23 1 -0.23 2 3
EP300 0.011 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
NFATc/JNK1 -0.008 0.1 0.32 2 -0.38 15 17
CaM/Ca2+/FKBP38 0.016 0.023 -10000 0 -0.2 1 1
FKBP12/FK506 0.015 0.003 -10000 0 -10000 0 0
CSNK1A1 -0.015 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.014 0.034 0.21 1 -0.19 7 8
NFATc/ERK1 -0.005 0.1 0.32 2 -0.37 16 18
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.001 0.095 -10000 0 -0.32 20 20
NR4A1 -0.059 0.15 0.22 7 -0.35 85 92
GSK3B 0.013 0.016 -10000 0 -10000 0 0
positive T cell selection 0.006 0.022 -10000 0 -0.3 2 2
NFAT1/CK1 alpha -0.011 0.042 0.12 1 -0.2 9 10
RCH1/ KPNB1 0.031 0.022 0.23 5 -10000 0 5
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
PRKACA 0.012 0.016 -10000 0 -10000 0 0
AKAP5 0.019 0.023 -10000 0 -0.32 2 2
MEF2D 0.009 0.019 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha -0.012 0.097 -10000 0 -0.38 15 15
CREBBP 0.011 0.02 -10000 0 -10000 0 0
BCL2 0.019 0.022 0.32 1 -0.32 1 2
Retinoic acid receptors-mediated 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
HDAC1 0.021 0.002 -10000 0 -10000 0 0
HDAC3 0.02 0.004 -10000 0 -10000 0 0
VDR 0.02 0.021 0.32 1 -0.32 1 2
Cbp/p300/PCAF 0.039 0.012 -10000 0 -10000 0 0
EP300 0.02 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.012 0.04 0.16 1 -0.24 5 6
KAT2B 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.044 0.2 3 -0.23 2 5
RAR alpha/9cRA/Cyclin H 0.033 0.048 -10000 0 -0.23 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.054 0.2 1 -0.23 16 17
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.019 0.034 -10000 0 -0.2 4 4
NCOR2 0.02 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.015 0.22 1 -0.22 1 2
RXRs/RARs/NRIP1/9cRA -0.014 0.1 0.35 4 -0.44 12 16
NCOA2 0.016 0.032 -10000 0 -0.32 4 4
NCOA3 0.02 0.005 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.02 0.021 0.32 1 -0.32 1 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.026 0.008 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.011 0.087 0.27 1 -0.38 12 13
RARA 0.015 0.032 0.19 2 -0.2 2 4
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.006 0.049 0.2 1 -0.27 6 7
PRKCA 0.019 0.023 -10000 0 -0.32 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.02 0.11 0.33 3 -0.48 12 15
RXRG -0.093 0.13 0.25 2 -0.25 181 183
RXRA 0.009 0.027 0.17 4 -0.18 2 6
RXRB 0.02 0.041 0.23 2 -0.25 2 4
VDR/Vit D3/DNA 0.015 0.015 0.22 1 -0.22 1 2
RBP1 0.023 0.035 0.32 5 -0.32 1 6
CRBP1/9-cic-RA 0.017 0.024 0.22 5 -0.22 1 6
RARB 0.019 0.023 -10000 0 -0.32 2 2
PRKCG 0.044 0.082 0.32 37 -10000 0 37
MNAT1 0.02 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.017 0.088 0.27 1 -0.41 12 13
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.085 0.29 4 -0.38 11 15
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.078 0.28 3 -0.34 11 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.021 0.11 0.33 3 -0.48 12 15
positive regulation of DNA binding 0.023 0.041 -10000 0 -0.22 3 3
NRIP1 -0.019 0.11 0.46 1 -0.52 8 9
RXRs/RARs -0.023 0.11 0.28 1 -0.48 13 14
RXRs/RXRs/DNA/9cRA -0.021 0.08 0.28 1 -0.37 13 14
PRKACA 0.02 0.005 -10000 0 -10000 0 0
CDK7 0.02 0.004 -10000 0 -10000 0 0
TFIIH 0.039 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.041 0.04 -10000 0 -0.21 1 1
CCNH 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.034 0.017 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.017 0.035 0.32 1 -0.32 4 5
CLTC 0.016 0.061 0.22 3 -0.44 5 8
calcium ion-dependent exocytosis 0.01 0.03 0.19 3 -0.16 3 6
Dynamin 2/GTP -0.003 0.041 0.12 40 -10000 0 40
EXOC4 0.02 0.005 -10000 0 -10000 0 0
CD59 0.011 0.038 -10000 0 -0.31 4 4
CPE -0.005 0.04 0.2 16 -10000 0 16
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
membrane fusion 0.01 0.025 -10000 0 -10000 0 0
CTNND1 -0.001 0.053 0.19 28 -10000 0 28
DNM2 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.046 0.18 6 -0.25 4 10
TSHR 0.006 0.054 0.17 46 -10000 0 46
INS 0.001 0.073 -10000 0 -0.5 9 9
BIN1 0.021 0.001 -10000 0 -10000 0 0
mol:Choline 0.01 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.062 0.18 47 -10000 0 47
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.04 0.12 40 -10000 0 40
JUP 0.011 0.033 -10000 0 -0.3 3 3
ASAP2/amphiphysin II 0.038 0.01 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.003 -10000 0 -10000 0 0
CDH1 0.01 0.038 -10000 0 -0.31 4 4
clathrin-independent pinocytosis 0.015 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.02 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.015 0.003 -10000 0 -10000 0 0
EXOC2 0.02 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.007 0.019 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.02 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.046 0.28 5 -10000 0 5
positive regulation of phagocytosis -0.012 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.026 0.008 -10000 0 -10000 0 0
ACAP1 0.013 0.028 -10000 0 -0.15 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.011 0.063 -10000 0 -0.31 4 4
clathrin heavy chain/ACAP1 0.015 0.052 0.2 12 -0.32 4 16
JIP4/KLC1 0.036 0.012 -10000 0 -10000 0 0
EXOC1 0.02 0.003 -10000 0 -10000 0 0
exocyst 0.007 0.019 -10000 0 -10000 0 0
RALA/GTP 0.014 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.026 0.008 -10000 0 -10000 0 0
receptor recycling 0.015 0.003 -10000 0 -10000 0 0
CTNNA1 -0.001 0.052 0.19 27 -10000 0 27
NME1 0.008 0.062 0.18 47 -10000 0 47
clathrin coat assembly 0.016 0.063 0.22 3 -0.4 6 9
IL2RA 0.014 0.042 -10000 0 -0.33 4 4
VAMP3 -0.012 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.016 0.049 0.2 2 -0.31 5 7
EXOC6 0.02 0.003 -10000 0 -10000 0 0
PLD1 0.005 0.005 -10000 0 -10000 0 0
PLD2 0.005 0.005 -10000 0 -10000 0 0
EXOC5 0.02 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.044 0.17 5 -0.26 4 9
SDC1 0.011 0.039 -10000 0 -0.31 4 4
ARF6/GDP 0.027 0.035 0.13 44 -10000 0 44
EXOC7 0.02 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.049 -10000 0 -0.28 5 5
mol:Phosphatidic acid 0.01 0.025 -10000 0 -10000 0 0
endocytosis -0.036 0.01 -10000 0 -10000 0 0
SCAMP2 0.02 0.003 -10000 0 -10000 0 0
ADRB2 -0.038 0.09 0.21 1 -0.37 9 10
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ASAP2 0.021 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.032 0.046 0.17 43 -10000 0 43
KLC1 0.02 0.005 -10000 0 -10000 0 0
AVPR2 -0.012 0.092 0.28 9 -0.4 6 15
RALA 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.051 0.33 2 -0.28 4 6
Regulation of Telomerase

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
Telomerase catalytic core complex 0.099 0.16 0.4 32 -0.42 2 34
RAD9A 0.02 0.003 -10000 0 -10000 0 0
AP1 0.019 0.068 -10000 0 -0.22 33 33
IFNAR2 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.021 0.035 -10000 0 -0.34 1 1
ER alpha/Oestrogen 0.018 0.045 0.22 10 -0.21 9 19
NFX1/SIN3/HDAC complex 0.011 0.051 -10000 0 -0.29 5 5
EGF 0.075 0.12 0.32 84 -0.32 4 88
SMG5 0.018 0.007 -10000 0 -10000 0 0
SMG6 0.019 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.039 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.091 0.14 0.38 18 -0.39 2 20
SAP18 0.02 0.007 -10000 0 -10000 0 0
MRN complex 0.035 0.016 -10000 0 -10000 0 0
WT1 0.015 0.093 0.34 10 -0.32 25 35
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.031 0.018 -10000 0 -10000 0 0
SP3 0.024 0.008 -10000 0 -10000 0 0
TERF2IP 0.02 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.048 0.098 -10000 0 -0.39 2 2
Mad/Max 0.038 0.016 -10000 0 -10000 0 0
TERT 0.099 0.16 0.4 28 -0.43 1 29
CCND1 0.087 0.18 0.46 11 -0.86 6 17
MAX 0.024 0.008 -10000 0 -10000 0 0
RBBP7 0.021 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.003 -10000 0 -10000 0 0
TERF2 -0.018 0.013 -10000 0 -10000 0 0
PTGES3 0.02 0.004 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
Telomerase/911 0.055 0.061 0.23 4 -0.31 1 5
CDKN1B 0.002 0.039 0.22 2 -0.19 3 5
RAD1 0.017 0.008 -10000 0 -10000 0 0
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
SAP30 0.021 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.028 0.01 -10000 0 -10000 0 0
UBE3A 0.022 0.008 -10000 0 -10000 0 0
JUN 0.02 0.033 -10000 0 -0.32 4 4
E6 0.003 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.014 -10000 0 -10000 0 0
FOS 0.001 0.084 -10000 0 -0.32 30 30
IFN-gamma/IRF1 0.047 0.063 0.24 30 -0.22 7 37
PARP2 0.02 0.005 -10000 0 -10000 0 0
BLM 0.049 0.089 0.32 45 -10000 0 45
Telomerase 0.035 0.083 0.22 10 -0.41 5 15
IRF1 0.024 0.008 -10000 0 -10000 0 0
ESR1 0.021 0.065 0.32 10 -0.32 9 19
KU/TER 0.03 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.029 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.011 0.056 -10000 0 -0.28 7 7
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.012 0.053 -10000 0 -0.28 5 5
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.027 0.017 -10000 0 -10000 0 0
ATM 0.009 0.008 -10000 0 -10000 0 0
SMAD3 -0.02 0.009 -10000 0 -10000 0 0
ABL1 0.02 0.004 -10000 0 -10000 0 0
MXD1 0.024 0.007 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
HUS1 0.019 0.006 -10000 0 -10000 0 0
RPS6KB1 0.02 0.004 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.094 0.14 0.39 10 -0.44 1 11
NR2F2 0.004 0.026 -10000 0 -10000 0 0
MAPK3 -0.004 0.02 -10000 0 -10000 0 0
MAPK1 -0.005 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.02 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
HNRNPC 0.02 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.008 -10000 0 -10000 0 0
NBN 0.018 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.042 0.33 1 -0.32 6 7
mol:Oestrogen 0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.059 0.087 0.24 71 -0.22 9 80
MYC 0.019 0.025 -10000 0 -0.32 2 2
IL2 0.029 0.018 -10000 0 -10000 0 0
KU 0.03 0.007 -10000 0 -10000 0 0
RAD50 0.02 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.008 0.02 -10000 0 -10000 0 0
TRF2/BLM 0.046 0.056 0.22 42 -10000 0 42
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.1 0.14 0.4 12 -10000 0 12
SP1/HDAC2 0.047 0.035 -10000 0 -10000 0 0
PINX1 0.018 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.045 0.097 -10000 0 -0.38 2 2
Smad3/Myc -0.019 0.015 -10000 0 -0.18 2 2
911 complex 0.032 0.019 -10000 0 -10000 0 0
IFNG 0.038 0.087 0.33 30 -0.32 7 37
Telomerase/PinX1 0.041 0.095 -10000 0 -0.38 2 2
Telomerase/AKT1/mTOR/p70S6K 0.049 0.088 0.28 8 -0.42 4 12
SIN3B 0.021 0.006 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1B 0.041 0.091 -10000 0 -0.38 1 1
response to DNA damage stimulus 0.002 0.017 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.025 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.012 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.048 0.098 -10000 0 -0.39 2 2
E2F1 0.03 0.031 0.32 4 -10000 0 4
ZNFX1 0.021 0.006 -10000 0 -10000 0 0
PIF1 0.058 0.1 0.32 59 -10000 0 59
NCL 0.021 0.003 -10000 0 -10000 0 0
DKC1 0.02 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.007 0.11 -9999 0 -0.42 13 13
MAP3K8 0.017 0.019 -9999 0 -0.32 1 1
FOS 0.005 0.084 -9999 0 -0.38 10 10
PRKCA 0.016 0.026 -9999 0 -0.33 2 2
PTPN7 0.015 0.015 -9999 0 -10000 0 0
HRAS 0.018 0.01 -9999 0 -10000 0 0
PRKCB 0.008 0.058 -9999 0 -0.33 13 13
NRAS 0.018 0.01 -9999 0 -10000 0 0
RAS family/GTP 0.031 0.021 -9999 0 -10000 0 0
MAPK3 0.011 0.043 -9999 0 -0.34 1 1
MAP2K1 -0.004 0.078 -9999 0 -0.38 14 14
ELK1 0.017 0.015 -9999 0 -10000 0 0
BRAF -0.002 0.057 -9999 0 -0.35 11 11
mol:GTP 0 0.001 -9999 0 -0.004 31 31
MAPK1 0.001 0.085 -9999 0 -0.45 12 12
RAF1 -0.004 0.065 -9999 0 -0.36 13 13
KRAS 0.017 0.01 -9999 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.057 -10000 0 -0.16 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.009 0.055 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.025 -10000 0 -0.2 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.037 -10000 0 -0.22 2 2
CaM/Ca2+ 0.042 0.052 -10000 0 -0.16 8 8
RAP1A 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.046 -10000 0 -10000 0 0
AKT1 -0.011 0.058 0.29 6 -10000 0 6
MAP2K1 -0.013 0.049 0.2 7 -10000 0 7
MAP3K11 -0.011 0.05 0.21 6 -0.16 1 7
IFNGR1 0.019 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.003 0.12 0.22 4 -0.32 41 45
Rap1/GTP -0.029 0.025 -10000 0 -10000 0 0
CRKL/C3G 0.029 0.008 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.054 0.058 -10000 0 -0.17 6 6
CEBPB -0.004 0.098 0.28 5 -0.41 14 19
STAT3 0.02 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.051 0.08 -10000 0 -0.67 3 3
STAT1 -0.01 0.05 0.27 3 -10000 0 3
CALM1 0.02 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.032 0.088 0.32 30 -0.33 7 37
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.01 0.054 0.27 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.005 0.062 -10000 0 -0.29 10 10
mol:Ca2+ 0.042 0.055 -10000 0 -0.16 8 8
MAPK3 0.002 0.068 -10000 0 -0.48 3 3
STAT1 (dimer) -0.02 0.052 -10000 0 -0.39 1 1
MAPK1 -0.015 0.13 -10000 0 -0.68 14 14
JAK2 0.018 0.02 -10000 0 -0.33 1 1
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
JAK1 0.02 0.01 -10000 0 -10000 0 0
CAMK2D 0.021 0.003 -10000 0 -10000 0 0
DAPK1 -0.006 0.093 0.25 5 -0.5 10 15
SMAD7 -0.002 0.038 0.17 8 -0.16 2 10
CBL/CRKL/C3G -0.012 0.054 0.27 3 -10000 0 3
PI3K 0.039 0.05 -10000 0 -0.16 6 6
IFNG 0.032 0.088 0.32 30 -0.33 7 37
apoptosis -0.004 0.09 0.24 1 -0.42 15 16
CAMK2G 0.021 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.003 -10000 0 -10000 0 0
CAMK2A -0.011 0.1 0.32 1 -0.32 43 44
CAMK2B 0.063 0.11 0.32 68 -10000 0 68
FRAP1 -0.012 0.054 0.28 6 -10000 0 6
PRKCD -0.012 0.06 0.28 7 -10000 0 7
RAP1B 0.02 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.018 0.037 -10000 0 -0.22 2 2
PTPN2 0.02 0.005 -10000 0 -10000 0 0
EP300 0.02 0.004 -10000 0 -10000 0 0
IRF1 -0.011 0.047 0.23 3 -10000 0 3
STAT1 (dimer)/PIASy -0.01 0.054 0.27 3 -10000 0 3
SOCS1 0.012 0.083 -10000 0 -1 3 3
mol:GDP -0.013 0.051 0.25 3 -10000 0 3
CASP1 -0.004 0.041 0.19 6 -0.2 3 9
PTGES2 0.02 0.004 -10000 0 -10000 0 0
IRF9 -0.002 0.033 0.14 2 -0.16 1 3
mol:PI-3-4-5-P3 0.027 0.041 -10000 0 -0.16 7 7
RAP1/GDP -0.026 0.033 -10000 0 -10000 0 0
CBL -0.009 0.049 0.22 5 -10000 0 5
MAP3K1 -0.01 0.049 0.21 6 -10000 0 6
PIAS1 0.02 0.003 -10000 0 -10000 0 0
PIAS4 0.019 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.037 -10000 0 -0.22 2 2
PTPN11 -0.007 0.048 0.22 2 -0.16 6 8
CREBBP 0.02 0.004 -10000 0 -10000 0 0
RAPGEF1 0.02 0.004 -10000 0 -10000 0 0
ceramide 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
MAP4K4 -0.005 0.068 0.2 1 -0.39 6 7
BAG4 0.018 0.007 -10000 0 -10000 0 0
BAD -0.002 0.035 0.3 2 -0.13 4 6
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.021 0.036 0.32 4 -0.32 2 6
BAX -0.001 0.031 0.16 3 -0.13 3 6
EnzymeConsortium:3.1.4.12 0.001 0.02 0.075 5 -0.086 6 11
IKBKB 0.006 0.083 0.28 8 -0.37 6 14
MAP2K2 -0.005 0.036 0.16 10 -10000 0 10
MAP2K1 -0.005 0.04 0.16 13 -0.15 1 14
SMPD1 -0.001 0.025 0.11 2 -0.12 5 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.004 0.072 0.24 3 -0.38 6 9
MAP2K4 -0.002 0.037 0.18 9 -0.15 1 10
protein ubiquitination 0.002 0.079 0.27 6 -0.37 6 12
EnzymeConsortium:2.7.1.37 -0.007 0.043 0.16 11 -0.17 1 12
response to UV 0 0 0.002 11 -0.002 1 12
RAF1 -0.003 0.038 0.17 10 -0.15 1 11
CRADD 0.021 0.014 0.32 1 -10000 0 1
mol:ceramide 0.002 0.032 0.11 6 -0.13 7 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.024 0.011 -10000 0 -10000 0 0
MADD 0.02 0.003 -10000 0 -10000 0 0
MAP3K1 0.001 0.039 0.19 9 -0.14 3 12
TRADD 0.02 0.004 -10000 0 -10000 0 0
RELA/p50 0.02 0.003 -10000 0 -10000 0 0
MAPK3 -0.004 0.039 0.16 10 -10000 0 10
MAPK1 -0.006 0.043 0.16 10 -0.21 2 12
p50/RELA/I-kappa-B-alpha 0.026 0.012 -10000 0 -10000 0 0
FADD -0.001 0.07 0.24 1 -0.39 6 7
KSR1 0 0.04 0.17 11 -0.14 3 14
MAPK8 -0.005 0.041 0.18 13 -10000 0 13
TRAF2 0.02 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 3 -10000 0 3
CHUK -0.006 0.07 0.36 1 -0.37 6 7
TNF R/SODD 0.026 0.012 -10000 0 -10000 0 0
TNF 0.009 0.065 0.32 1 -0.32 16 17
CYCS 0.008 0.042 0.15 9 -0.13 2 11
IKBKG -0.001 0.074 0.28 3 -0.35 6 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0 0.069 -10000 0 -0.4 6 6
RELA 0.02 0.003 -10000 0 -10000 0 0
RIPK1 0.02 0.004 -10000 0 -10000 0 0
AIFM1 0.002 0.038 0.19 3 -0.13 2 5
TNF/TNF R/SODD 0.027 0.044 0.22 1 -0.19 15 16
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.011 0.077 -10000 0 -0.55 8 8
NSMAF 0.008 0.08 0.24 4 -0.38 6 10
response to hydrogen peroxide 0 0 0.002 11 -0.002 1 12
BCL2 0.019 0.022 0.32 1 -0.32 1 2
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.007 -10000 0 -10000 0 0
SNTA1 0.021 0.02 0.32 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.017 0.018 0.2 2 -10000 0 2
MAPK12 -0.008 0.02 0.18 2 -0.17 2 4
CCND1 0 0.054 -10000 0 -0.38 8 8
p38 gamma/SNTA1 -0.007 0.047 0.18 18 -0.28 1 19
MAP2K3 0.019 0.006 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.002 0.039 0.2 15 -0.16 2 17
MAP2K6 -0.003 0.023 0.22 2 -0.18 2 4
MAPT -0.006 0.074 0.22 14 -0.25 22 36
MAPK13 -0.015 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.007 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.021 0.047 -10000 0 -0.25 4 4
NEF -0.001 0.02 -10000 0 -0.17 6 6
NFKBIA 0.018 0.009 -10000 0 -10000 0 0
BIRC3 0.006 0.067 0.29 4 -10000 0 4
CYCS 0.002 0.043 0.15 23 -0.29 2 25
RIPK1 0.02 0.004 -10000 0 -10000 0 0
CD247 0.017 0.027 -10000 0 -0.22 5 5
MAP2K7 -0.019 0.18 -10000 0 -0.65 29 29
protein ubiquitination 0.002 0.067 0.31 3 -0.3 4 7
CRADD 0.021 0.014 0.32 1 -10000 0 1
DAXX 0.02 0.004 -10000 0 -10000 0 0
FAS 0.017 0.032 -10000 0 -0.32 4 4
BID 0.006 0.048 0.16 25 -0.28 3 28
NF-kappa-B/RelA/I kappa B alpha 0.038 0.024 0.22 4 -10000 0 4
TRADD 0.02 0.004 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
CFLAR 0.021 0.002 -10000 0 -10000 0 0
FADD 0.02 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.039 0.024 0.22 4 -10000 0 4
MAPK8 -0.019 0.17 0.35 2 -0.61 29 31
APAF1 0.02 0.003 -10000 0 -10000 0 0
TRAF1 0.02 0.004 -10000 0 -10000 0 0
TRAF2 0.02 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.034 -10000 0 -0.24 5 5
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.002 0.066 -10000 0 -0.38 4 4
CHUK 0 0.07 0.31 3 -0.33 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.05 0.029 -10000 0 -0.15 2 2
TCRz/NEF 0.014 0.027 0.18 1 -0.23 5 6
TNF 0.009 0.065 0.32 1 -0.32 16 17
FASLG -0.013 0.039 0.3 1 -0.33 5 6
NFKB1 0.021 0.011 -10000 0 -0.13 2 2
TNFR1A/BAG4/TNF-alpha 0.027 0.044 0.22 1 -0.19 15 16
CASP6 0.028 0.07 -10000 0 -0.48 4 4
CASP7 0.026 0.092 0.31 15 -0.3 2 17
RELA 0.021 0.011 -10000 0 -0.13 2 2
CASP2 0.02 0.004 -10000 0 -10000 0 0
CASP3 0.023 0.088 0.32 12 -0.29 1 13
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
CASP8 0.02 0.016 -10000 0 -0.32 1 1
CASP9 0.02 0.004 -10000 0 -10000 0 0
MAP3K14 0.003 0.066 -10000 0 -0.36 4 4
APAF-1/Caspase 9 -0.01 0.05 0.17 4 -0.28 1 5
BCL2 -0.017 0.15 0.3 3 -0.55 29 32
IGF1 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
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTK2 0.018 0.007 -10000 0 -10000 0 0
CRKL -0.018 0.027 0.15 1 -0.19 9 10
GRB2/SOS1/SHC 0.034 0.017 -10000 0 -10000 0 0
HRAS 0.02 0.004 -10000 0 -10000 0 0
IRS1/Crk -0.019 0.028 0.11 1 -0.18 11 12
IGF-1R heterotetramer/IGF1/PTP1B 0.033 0.035 0.21 1 -0.19 9 10
AKT1 -0.023 0.039 0.15 10 -0.24 1 11
BAD -0.027 0.037 0.14 10 -0.23 1 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.017 0.028 0.15 1 -0.19 10 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.017 0.036 0.19 3 -0.19 11 14
RAF1 -0.017 0.068 0.26 1 -0.38 12 13
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.04 0.038 0.2 1 -0.19 7 8
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.02 0.036 0.19 1 -0.2 11 12
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.039 0.15 11 -0.24 1 12
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.006 0.067 0.27 5 -0.29 7 12
PXN 0.02 0.003 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.029 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.024 0.018 -10000 0 -0.17 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.046 0.034 -10000 0 -0.16 3 3
IGF-1R heterotetramer 0.018 0.028 -10000 0 -0.34 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.04 0.2 1 -0.19 11 12
Crk/p130 Cas/Paxillin 0.035 0.04 -10000 0 -0.18 11 11
IGF1R 0.018 0.028 -10000 0 -0.34 2 2
IGF1 0.014 0.053 0.33 1 -0.34 9 10
IRS2/Crk -0.021 0.028 0.14 1 -0.18 11 12
PI3K 0.038 0.042 0.2 1 -0.18 11 12
apoptosis 0.023 0.041 0.21 1 -0.27 1 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
PRKCD -0.004 0.042 -10000 0 -0.24 9 9
RAF1/14-3-3 E -0.012 0.073 0.25 3 -0.33 13 16
BAD/14-3-3 -0.024 0.043 0.28 1 -0.22 1 2
PRKCZ -0.025 0.041 0.15 10 -0.24 1 11
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.032 -10000 0 -0.21 1 1
PTPN1 0.019 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.001 0.044 -10000 0 -0.26 8 8
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.037 0.034 0.21 1 -0.17 6 7
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.015 0.037 -10000 0 -0.19 11 11
GRB10 0.019 0.006 -10000 0 -10000 0 0
PTPN11 -0.018 0.03 0.15 2 -0.19 11 13
IRS1 -0.015 0.034 0.11 7 -0.2 11 18
IRS2 -0.018 0.03 0.15 2 -0.19 11 13
IGF-1R heterotetramer/IGF1 0.023 0.045 0.23 1 -0.25 11 12
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.021 0.041 0.16 11 -0.18 9 20
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKD1 -0.007 0.047 -10000 0 -0.31 5 5
SHC1 0.018 0.008 -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 0.013 0.011 -10000 0 -10000 0 0
TRAF2/ASK1 0.025 0.009 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
MAP2K3 -0.004 0.088 0.29 2 -0.3 23 25
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.001 0.079 0.28 2 -0.33 12 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.018 0.038 0.32 2 -0.32 4 6
TXN 0.004 0.011 0.17 2 -10000 0 2
CALM1 0.02 0.004 -10000 0 -10000 0 0
GADD45A 0.02 0.003 -10000 0 -10000 0 0
GADD45B 0.018 0.023 -10000 0 -0.32 2 2
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
MAP3K6 0.02 0.003 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
MAP3K4 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.028 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.001 0.018 0.13 2 -0.13 1 3
RAC1/OSM/MEKK3 0.034 0.017 -10000 0 -0.16 1 1
TRAF2 0.02 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.005 0.071 -10000 0 -0.27 15 15
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.063 0.11 0.32 68 -10000 0 68
CCM2 0.019 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.05 0.064 0.21 65 -10000 0 65
MAPK11 0.018 0.023 -10000 0 -0.32 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.054 0.062 0.21 60 -10000 0 60
OSM/MEKK3 0.027 0.016 -10000 0 -0.23 1 1
TAOK1 0.006 0.012 -10000 0 -0.25 1 1
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAP3K10 0.018 0.028 -10000 0 -0.32 3 3
MAP3K3 0.019 0.017 -10000 0 -0.32 1 1
TRX/ASK1 0.015 0.017 0.15 1 -10000 0 1
GADD45/MTK1/MTK1 0.04 0.032 0.21 2 -0.2 4 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.029 0.065 0.22 1 -0.25 16 17
Ran/GTP/Exportin 1/HDAC1 -0.018 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.008 0.065 -10000 0 -0.28 15 15
SUMO1 0.021 0.003 -10000 0 -10000 0 0
ZFPM1 0.02 0.015 0.32 1 -10000 0 1
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.004 -10000 0 -10000 0 0
Histones 0.034 0.053 -10000 0 -0.3 2 2
YY1/LSF 0.013 0.045 -10000 0 -0.24 7 7
SMG5 0.018 0.007 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
I kappa B alpha/HDAC3 0.005 0.034 -10000 0 -0.2 12 12
I kappa B alpha/HDAC1 0.014 0.041 -10000 0 -0.32 1 1
SAP18 0.019 0.006 -10000 0 -10000 0 0
RELA 0.007 0.047 -10000 0 -0.21 13 13
HDAC1/Smad7 0.035 0.019 -10000 0 -0.2 1 1
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.015 0.049 -10000 0 -0.21 7 7
NuRD/MBD3 Complex -0.006 0.055 -10000 0 -0.3 9 9
NF kappa B1 p50/RelA 0.012 0.069 -10000 0 -0.3 11 11
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.008 0.096 -10000 0 -0.32 39 39
GATA1 -0.016 0.1 -10000 0 -0.32 48 48
Mad/Max 0.03 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.019 0.091 -10000 0 -0.3 26 26
RBBP7 0.02 0.004 -10000 0 -10000 0 0
NPC 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
MAX 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.025 -10000 0 -10000 0 0
KAT2B 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.009 0.051 -10000 0 -0.37 3 3
SIN3 complex 0.046 0.019 -10000 0 -10000 0 0
SMURF1 0.02 0.005 -10000 0 -10000 0 0
CHD3 0.019 0.006 -10000 0 -10000 0 0
SAP30 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.019 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.004 0.049 -10000 0 -0.26 10 10
YY1/HDAC2 0.014 0.042 -10000 0 -0.24 7 7
YY1/HDAC1 0.013 0.045 -10000 0 -0.24 7 7
NuRD/MBD2 Complex (MeCP1) -0.008 0.059 -10000 0 -0.32 9 9
PPARG -0.021 0.1 -10000 0 -0.29 53 53
HDAC8/hEST1B 0.034 0.017 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.016 0.048 -10000 0 -0.21 7 7
MBD3L2 0.016 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.019 -10000 0 -0.19 1 1
CREBBP 0.02 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.077 -10000 0 -0.31 18 18
HDAC1 0.021 0.002 -10000 0 -10000 0 0
HDAC3 0.006 0.029 -10000 0 -0.34 1 1
HDAC2 0.019 0.006 -10000 0 -10000 0 0
YY1 0.007 0.003 -10000 0 -10000 0 0
HDAC8 0.021 0.002 -10000 0 -10000 0 0
SMAD7 0.018 0.017 -10000 0 -0.32 1 1
NCOR2 0.02 0.003 -10000 0 -10000 0 0
MXD1 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.01 0.003 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.045 -10000 0 -0.22 7 7
YY1/SAP30/HDAC1 0.024 0.045 -10000 0 -0.22 7 7
EP300 0.02 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.01 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.025 -10000 0 -10000 0 0
histone deacetylation -0.001 0.063 -10000 0 -0.32 9 9
STAT3 (dimer non-phopshorylated)/HDAC3 0.005 0.039 -10000 0 -0.22 7 7
nuclear export -0.034 0.017 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GATAD2B 0.018 0.008 -10000 0 -10000 0 0
GATAD2A 0.02 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.002 0.068 -10000 0 -0.24 12 12
GATA1/HDAC1 0.003 0.079 -10000 0 -0.23 48 48
GATA1/HDAC3 -0.003 0.073 -10000 0 -0.27 10 10
CHD4 0.02 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.02 0.047 0.23 1 -0.23 15 16
SIN3/HDAC complex/Mad/Max -0.008 0.056 -10000 0 -0.3 8 8
NuRD Complex -0.004 0.076 -10000 0 -0.3 18 18
positive regulation of chromatin silencing 0.032 0.051 -10000 0 -0.29 2 2
SIN3B 0.02 0.005 -10000 0 -10000 0 0
MTA2 0.02 0.003 -10000 0 -10000 0 0
SIN3A 0.02 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.028 0.03 -10000 0 -0.21 3 3
HDAC complex 0.047 0.018 -10000 0 -10000 0 0
GATA1/Fog1 0.002 0.077 -10000 0 -0.22 48 48
FKBP25/HDAC1/HDAC2 0.037 0.015 -10000 0 -10000 0 0
TNF 0.009 0.065 0.32 1 -0.32 16 17
negative regulation of cell growth -0.006 0.057 -10000 0 -0.3 8 8
NuRD/MBD2/PRMT5 Complex -0.008 0.059 -10000 0 -0.32 9 9
Ran/GTP/Exportin 1 0.028 0.029 -10000 0 -0.19 4 4
NF kappa B/RelA/I kappa B alpha -0.002 0.057 -10000 0 -0.28 14 14
SIN3/HDAC complex/NCoR1 -0.012 0.074 -10000 0 -0.36 13 13
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.02 0.003 -10000 0 -10000 0 0
MBD3 0.018 0.023 -10000 0 -0.32 2 2
MBD2 0.019 0.006 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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 0.001 0.061 -10000 0 -0.5 1 1
UGCG 0 0.1 -10000 0 -0.62 12 12
AKT1/mTOR/p70S6K/Hsp90/TERT 0.052 0.084 0.28 7 -0.36 5 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.001 0.1 -10000 0 -0.62 12 12
mol:DAG 0.003 0.076 -10000 0 -0.78 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.079 0.28 2 -0.38 7 9
FRAP1 0.019 0.087 0.31 2 -0.43 7 9
FOXO3 0.015 0.082 0.31 1 -0.44 6 7
AKT1 0.017 0.087 0.32 1 -0.45 7 8
GAB2 0.017 0.032 -10000 0 -0.32 4 4
SMPD1 0.005 0.085 -10000 0 -0.62 8 8
SGMS1 0.011 0.056 -10000 0 -0.56 4 4
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 -0.012 0.009 -10000 0 -0.19 1 1
CALM1 0.02 0.004 -10000 0 -10000 0 0
cell proliferation 0.025 0.083 0.27 2 -0.35 12 14
EIF3A 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.029 0.015 -10000 0 -0.23 1 1
RPS6KB1 0.013 0.061 -10000 0 -0.84 2 2
mol:sphingomyelin 0.003 0.076 -10000 0 -0.78 4 4
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.02 0.006 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
JAK1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MYC 0.041 0.12 0.4 3 -0.61 5 8
MYB 0.003 0.11 -10000 0 -0.99 4 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.016 0.07 -10000 0 -0.36 6 6
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.033 0.06 -10000 0 -0.77 2 2
mol:PI-3-4-5-P3 0.016 0.069 -10000 0 -0.35 6 6
Rac1/GDP -0.014 0.01 -10000 0 -0.17 1 1
T cell proliferation 0.012 0.067 -10000 0 -0.33 4 4
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.009 0.087 3 -0.066 3 6
PRKCZ 0.012 0.066 -10000 0 -0.34 3 3
NF kappa B1 p50/RelA 0.035 0.085 0.3 2 -0.39 7 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.001 0.055 -10000 0 -0.37 5 5
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
IL2RA 0.04 0.08 0.32 33 -0.32 1 34
IL2RB 0.019 0.023 -10000 0 -0.32 2 2
TERT 0.077 0.12 0.32 95 -10000 0 95
E2F1 0.011 0.079 -10000 0 -0.44 11 11
SOS1 0.021 0.004 -10000 0 -10000 0 0
RPS6 0.019 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 3 -0.047 3 6
PTPN11 0.02 0.005 -10000 0 -10000 0 0
IL2RG 0.017 0.036 -10000 0 -0.32 5 5
actin cytoskeleton organization 0.012 0.067 -10000 0 -0.33 4 4
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL2 0.019 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.031 0.019 -10000 0 -0.16 1 1
LCK 0.02 0.027 0.32 1 -0.32 2 3
BCL2 0.016 0.084 0.46 1 -0.49 4 5
TCGA08_rtk_signaling

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
PDGFRA 0.017 0.032 -10000 0 -0.32 4 4
HRAS 0.02 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.042 0.32 1 -0.32 6 7
AKT 0.029 0.063 0.23 10 -0.21 3 13
FOXO3 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
AKT3 0.018 0.023 -10000 0 -0.32 2 2
FOXO4 0.021 0.002 -10000 0 -10000 0 0
MET 0.013 0.069 0.32 6 -0.32 14 20
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PIK3CB 0.02 0.003 -10000 0 -10000 0 0
NRAS 0.02 0.004 -10000 0 -10000 0 0
PIK3CG 0.01 0.057 -10000 0 -0.32 13 13
PIK3R3 0.02 0.016 -10000 0 -0.32 1 1
PIK3R2 0.02 0.005 -10000 0 -10000 0 0
NF1 0.02 0.003 -10000 0 -10000 0 0
RAS 0.008 0.033 0.15 13 -0.12 12 25
ERBB2 0.02 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.011 0.07 0.27 14 -10000 0 14
PI3K 0.02 0.057 0.2 20 -0.21 3 23
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
KRAS 0.019 0.006 -10000 0 -10000 0 0
FOXO 0.047 0.047 0.22 12 -10000 0 12
AKT2 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.02 0.003 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.004 0.065 -10000 0 -0.31 18 18
KLHL20 -0.001 0.05 0.16 1 -0.21 10 11
CYFIP2 0.016 0.039 -10000 0 -0.32 6 6
Rac1/GDP -0.01 0.058 0.32 3 -0.25 8 11
ENAH -0.004 0.065 -10000 0 -0.32 18 18
AP1M1 0.02 0.005 -10000 0 -10000 0 0
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.026 0.022 -10000 0 -0.17 2 2
ABI1/Sra1/Nap1 -0.014 0.025 -10000 0 -0.14 12 12
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.026 -10000 0 -0.18 3 3
RAPGEF1 -0.008 0.054 0.21 1 -0.28 11 12
CTNND1 0.02 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.068 -10000 0 -0.32 20 20
CRK -0.008 0.047 -10000 0 -0.31 9 9
E-cadherin/gamma catenin/alpha catenin 0.038 0.019 -10000 0 -0.2 2 2
alphaE/beta7 Integrin 0.027 0.015 -10000 0 -0.23 1 1
IQGAP1 0.02 0.003 -10000 0 -10000 0 0
NCKAP1 0.021 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.015 -10000 0 -10000 0 0
DLG1 -0.002 0.062 -10000 0 -0.32 16 16
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.025 0.015 -10000 0 -0.13 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.048 0.055 0.21 39 -0.17 5 44
PI3K -0.031 0.019 -10000 0 -0.16 2 2
ARF6 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.028 0.018 -10000 0 -0.23 2 2
TIAM1 0.016 0.039 -10000 0 -0.32 6 6
E-cadherin(dimer)/Ca2+ 0.045 0.02 -10000 0 -0.17 2 2
AKT1 -0.017 0.024 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
CDH1 0.019 0.023 -10000 0 -0.32 2 2
RhoA/GDP -0.01 0.062 0.29 4 -0.24 9 13
actin cytoskeleton organization 0.001 0.04 0.15 3 -0.16 9 12
CDC42/GDP -0.011 0.062 0.29 4 -0.25 9 13
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.009 0.013 -10000 0 -0.19 2 2
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.018 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.048 0.021 -10000 0 -0.18 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.016 -10000 0 -0.16 2 2
mol:GDP -0.011 0.067 0.3 4 -0.28 10 14
CDC42/GTP/IQGAP1 0.027 0.006 -10000 0 -10000 0 0
JUP 0.02 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 0.057 0.2 1 -0.24 6 7
RAC1/GTP/IQGAP1 0.025 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.029 0.008 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.02 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.004 0.037 0.14 11 -0.14 7 18
NME1 0.048 0.088 0.32 43 -10000 0 43
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.001 0.053 -10000 0 -0.31 11 11
regulation of cell-cell adhesion -0.024 0.018 -10000 0 -0.15 2 2
WASF2 -0.003 0.023 -10000 0 -0.093 1 1
Rap1/GTP -0.023 0.03 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.03 -10000 0 -0.17 3 3
CCND1 0.004 0.043 0.15 10 -0.16 8 18
VAV2 -0.006 0.12 -10000 0 -0.57 16 16
RAP1/GDP -0.019 0.043 0.19 1 -0.22 5 6
adherens junction assembly 0.001 0.051 -10000 0 -0.3 11 11
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.02 0.003 -10000 0 -10000 0 0
PIP5K1C 0.019 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.035 0.027 -10000 0 -0.17 3 3
E-cadherin/beta catenin 0.004 0.02 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.004 0.066 -10000 0 -0.31 19 19
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.062 -10000 0 -0.32 12 12
E-cadherin/beta catenin/alpha catenin 0.038 0.019 -10000 0 -0.2 2 2
ITGAE 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.003 0.07 -10000 0 -0.32 20 20
S1P3 pathway

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
mol:S1P 0 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.01 0.062 -10000 0 -0.19 47 47
GNAO1 0.02 0.031 0.32 2 -0.33 2 4
S1P/S1P3/G12/G13 0.034 0.016 -10000 0 -10000 0 0
AKT1 0.005 0.062 -10000 0 -0.4 9 9
AKT3 -0.006 0.097 -10000 0 -0.83 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
GNAI2 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.02 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.017 -10000 0 -0.32 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.021 0.015 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.065 -10000 0 -0.27 6 6
MAPK3 -0.014 0.059 -10000 0 -0.28 4 4
MAPK1 -0.011 0.056 -10000 0 -0.38 2 2
JAK2 -0.023 0.079 0.2 2 -0.3 15 17
CXCR4 -0.014 0.061 -10000 0 -0.31 4 4
FLT1 0.02 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC -0.014 0.063 0.27 2 -0.28 5 7
S1P/S1P3/Gi -0.007 0.066 -10000 0 -0.27 6 6
RAC1 0.018 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.069 -10000 0 -0.33 4 4
VEGFA 0.02 0.006 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.008 0.066 -10000 0 -0.18 49 49
VEGFR1 homodimer/VEGFA homodimer 0.029 0.012 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.006 0.038 -10000 0 -0.22 12 12
GNAQ 0.019 0.016 -10000 0 -0.32 1 1
GNAZ -0.009 0.095 -10000 0 -0.32 39 39
G12/G13 0.027 0.011 -10000 0 -10000 0 0
GNA14 0.011 0.055 -10000 0 -0.32 12 12
GNA15 0.019 0.005 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.067 -10000 0 -0.3 5 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.004 0.042 0.3 2 -0.25 4 6
adherens junction organization -0.004 0.052 -10000 0 -0.37 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.012 0.049 0.18 5 -0.2 2 7
FMN1 -0.01 0.05 -10000 0 -0.26 11 11
mol:IP3 -0.012 0.028 -10000 0 -0.21 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.054 -10000 0 -0.28 12 12
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
AKT1 -0.013 0.037 0.23 1 -0.24 4 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.002 0.1 -10000 0 -0.5 13 13
CTNND1 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.007 0.041 -10000 0 -0.26 9 9
VASP -0.004 0.04 -10000 0 -0.29 6 6
ZYX -0.008 0.049 -10000 0 -0.27 11 11
JUB -0.001 0.051 -10000 0 -0.26 12 12
EGFR(dimer) 0.008 0.057 0.2 2 -0.25 13 15
E-cadherin/beta catenin-gamma catenin 0.039 0.019 -10000 0 -0.18 2 2
mol:PI-3-4-5-P3 0.021 0.048 0.25 1 -0.24 5 6
PIK3CA 0.019 0.009 -10000 0 -10000 0 0
PI3K 0.022 0.048 0.25 1 -0.24 5 6
FYN -0.012 0.06 0.28 2 -0.27 7 9
mol:Ca2+ -0.012 0.028 -10000 0 -0.21 3 3
JUP 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.33 1 1
mol:DAG -0.012 0.028 -10000 0 -0.21 3 3
CDH1 0.019 0.023 -10000 0 -0.32 2 2
RhoA/GDP -0.004 0.061 0.18 5 -0.2 1 6
establishment of polarity of embryonic epithelium -0.004 0.039 -10000 0 -0.28 6 6
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.042 0.32 1 -0.32 6 7
CASR -0.005 0.046 0.27 3 -0.2 3 6
RhoA/GTP 0.011 0.036 -10000 0 -0.19 3 3
AKT2 -0.012 0.037 0.23 1 -0.24 4 5
actin cable formation -0.011 0.043 -10000 0 -0.29 6 6
apoptosis -0.002 0.048 0.27 5 -0.28 4 9
CTNNA1 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.013 0.038 0.15 9 -0.19 3 12
PIP5K1A -0.007 0.041 -10000 0 -0.26 9 9
PLCG1 -0.012 0.029 -10000 0 -0.22 3 3
Rac1/GTP 0.015 0.053 -10000 0 -0.26 8 8
homophilic cell adhesion -0.001 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.047 0.021 -10000 0 -0.18 1 1
HDAC3 0.02 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.017 0.005 -10000 0 -10000 0 0
GATA1/HDAC4 0.003 0.077 -10000 0 -0.23 47 47
GATA1/HDAC5 0.004 0.076 -10000 0 -0.23 45 45
GATA2/HDAC5 0.008 0.071 -10000 0 -0.23 38 38
HDAC5/BCL6/BCoR 0.038 0.013 -10000 0 -10000 0 0
HDAC9 0.019 0.045 0.32 5 -0.32 4 9
Glucocorticoid receptor/Hsp90/HDAC6 0.039 0.012 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.029 0.007 -10000 0 -10000 0 0
HDAC5/YWHAB 0.029 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
GATA2 -0.008 0.096 -10000 0 -0.32 39 39
HDAC4/RFXANK 0.029 0.008 -10000 0 -10000 0 0
BCOR 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.017 -10000 0 -0.32 1 1
HDAC5 0.02 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.019 -10000 0 -0.23 2 2
Histones 0.01 0.048 -10000 0 -0.26 4 4
ADRBK1 0.02 0.003 -10000 0 -10000 0 0
HDAC4 0.02 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.029 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.029 0.007 -10000 0 -10000 0 0
HDAC7 0.02 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.027 0.01 -10000 0 -10000 0 0
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
HDAC6 0.02 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.029 0.008 -10000 0 -10000 0 0
CAMK4 0.015 0.044 0.32 1 -0.32 7 8
Tubulin/HDAC6 0.044 0.031 0.22 12 -10000 0 12
SUMO1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
GATA1 -0.016 0.1 -10000 0 -0.32 48 48
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.02 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.028 0.028 -10000 0 -0.2 3 3
SRF 0.02 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.029 0.008 -10000 0 -10000 0 0
Tubulin 0.035 0.033 0.23 12 -10000 0 12
HDAC4/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.029 0.008 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.039 0.011 -10000 0 -10000 0 0
HDAC4/SRF 0.035 0.032 0.22 1 -0.2 7 8
HDAC4/ER alpha 0.027 0.047 0.23 9 -0.23 9 18
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.01 0.048 -10000 0 -0.25 4 4
cell motility 0.043 0.031 0.22 12 -10000 0 12
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.029 0.007 -10000 0 -10000 0 0
BCL6 0.02 0.004 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.02 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.029 0.008 -10000 0 -10000 0 0
ESR1 0.019 0.065 0.32 10 -0.32 9 19
HDAC6/HDAC11 0.029 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.029 -10000 0 -0.19 4 4
NPC 0.012 0.001 -10000 0 -10000 0 0
MEF2C 0.02 0.005 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
HDAC4/MEF2C 0.056 0.021 -10000 0 -10000 0 0
GNG2 0.019 0.023 -10000 0 -0.32 2 2
NCOR2 0.02 0.003 -10000 0 -10000 0 0
TUBB2A 0.028 0.048 0.32 12 -10000 0 12
HDAC11 0.02 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
ANKRA2 0.02 0.004 -10000 0 -10000 0 0
RFXANK 0.02 0.005 -10000 0 -10000 0 0
nuclear import -0.02 0.009 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.056 0.41 5 -10000 0 5
CLOCK 0.021 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.026 0.031 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.008 -10000 0 -10000 0 0
ATR 0.02 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.024 -10000 0 -10000 0 0
ARNTL 0.021 0.005 -10000 0 -10000 0 0
TIMELESS 0.01 0.038 0.37 2 -10000 0 2
NPAS2 0.023 0.024 0.32 3 -10000 0 3
CRY2 0.02 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.012 -10000 0 -0.1 7 7
CHEK1 0.039 0.073 0.32 29 -10000 0 29
mol:HEME 0.004 0.012 0.1 7 -10000 0 7
PER1 0.006 0.066 -10000 0 -0.32 18 18
BMAL/CLOCK/NPAS2 0.045 0.023 0.23 3 -10000 0 3
BMAL1/CLOCK 0.01 0.042 -10000 0 -0.37 1 1
S phase of mitotic cell cycle 0.044 0.056 0.41 5 -10000 0 5
TIMELESS/CHEK1/ATR 0.045 0.056 0.41 5 -10000 0 5
mol:NADPH 0.004 0.012 0.1 7 -10000 0 7
PER1/TIMELESS 0.018 0.044 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.017 0.004 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.011 0.016 -10000 0 -10000 0 0
regulation of axonogenesis -0.001 0.017 0.25 2 -10000 0 2
myoblast fusion -0.01 0.026 0.32 1 -10000 0 1
mol:GTP 0.015 0.017 -10000 0 -0.16 4 4
regulation of calcium-dependent cell-cell adhesion -0.047 0.058 0.18 5 -0.21 38 43
ARF1/GTP 0.024 0.018 -10000 0 -0.12 3 3
mol:GM1 0.005 0.012 -10000 0 -0.12 3 3
mol:Choline -0.01 0.009 -10000 0 -10000 0 0
lamellipodium assembly 0.004 0.035 -10000 0 -0.38 3 3
MAPK3 0.012 0.012 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.048 0.059 0.22 38 -0.18 5 43
ARF1 0.019 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.01 0.026 -10000 0 -0.32 1 1
ARF1/GDP 0.013 0.031 -10000 0 -0.23 3 3
ARF6 0.025 0.009 -10000 0 -10000 0 0
RAB11A 0.02 0.003 -10000 0 -10000 0 0
TIAM1 0.015 0.039 -10000 0 -0.32 6 6
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.01 -10000 0 -10000 0 0
actin filament bundle formation -0.016 0.031 0.23 3 -10000 0 3
KALRN 0.003 0.021 -10000 0 -0.2 3 3
RAB11FIP3/RAB11A 0.029 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.031 -10000 0 -0.23 3 3
NME1 0.047 0.088 0.32 43 -10000 0 43
Rac1/GDP 0.015 0.03 -10000 0 -0.23 3 3
substrate adhesion-dependent cell spreading 0.015 0.017 -10000 0 -0.16 4 4
cortical actin cytoskeleton organization 0.004 0.035 -10000 0 -0.38 3 3
RAC1 0.018 0.007 -10000 0 -10000 0 0
liver development 0.015 0.017 -10000 0 -0.16 4 4
ARF6/GTP 0.015 0.017 -10000 0 -0.16 4 4
RhoA/GTP 0.025 0.018 -10000 0 -0.12 2 2
mol:GDP 0.004 0.017 -10000 0 -0.21 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.036 0.019 -10000 0 -10000 0 0
RHOA 0.02 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.014 -10000 0 -0.12 4 4
RAB11FIP3 0.02 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.004 0.035 -10000 0 -0.38 3 3
ruffle organization 0.001 0.017 -10000 0 -0.25 2 2
regulation of epithelial cell migration 0.015 0.017 -10000 0 -0.16 4 4
PLD2 0.009 0.012 -10000 0 -0.12 2 2
PIP5K1A 0.001 0.017 -10000 0 -0.25 2 2
mol:Phosphatidic acid -0.01 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.035 -10000 0 -0.38 3 3
Class I PI3K signaling events mediated by Akt

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.015 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.024 0.013 -10000 0 -10000 0 0
CDKN1B 0.007 0.044 -10000 0 -0.29 7 7
CDKN1A 0.007 0.048 -10000 0 -0.29 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
FOXO3 0.007 0.036 -10000 0 -0.29 4 4
AKT1 0 0.04 -10000 0 -0.3 8 8
BAD 0.02 0.003 -10000 0 -10000 0 0
AKT3 0.006 0.012 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.045 -10000 0 -0.29 8 8
AKT1/ASK1 0.023 0.055 -10000 0 -0.27 8 8
BAD/YWHAZ 0.034 0.017 -10000 0 -10000 0 0
RICTOR 0.017 0.008 -10000 0 -10000 0 0
RAF1 0.02 0.004 -10000 0 -10000 0 0
JNK cascade -0.022 0.053 0.26 8 -10000 0 8
TSC1 0.008 0.038 -10000 0 -0.29 5 5
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.027 0.06 0.22 2 -0.28 8 10
EP300 0.02 0.004 -10000 0 -10000 0 0
mol:GDP 0.002 0.04 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.005 0.043 -10000 0 -0.29 8 8
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAPKAP1 0.02 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.016 0.069 0.28 9 -0.22 10 19
YWHAH 0.02 0.004 -10000 0 -10000 0 0
AKT1S1 0.007 0.041 -10000 0 -0.29 6 6
CASP9 0.008 0.042 -10000 0 -0.29 6 6
YWHAB 0.02 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.028 0.065 0.27 7 -0.27 8 15
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.038 0.013 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.009 0.052 0.23 6 -0.25 7 13
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.037 0.18 1 -0.32 4 5
CHUK 0.005 0.044 -10000 0 -0.29 8 8
BAD/BCL-XL 0.025 0.055 -10000 0 -0.27 8 8
mTORC2 0.021 0.011 -10000 0 -10000 0 0
AKT2 0.007 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.018 0.086 0.29 7 -0.39 7 14
PDPK1 0.02 0.003 -10000 0 -10000 0 0
MDM2 0.014 0.056 0.19 2 -0.29 7 9
MAPKKK cascade -0.027 0.059 0.28 8 -0.22 2 10
MDM2/Cbp/p300 0.043 0.07 0.28 7 -0.28 7 14
TSC1/TSC2 0.003 0.05 0.25 6 -0.28 8 14
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.068 0.27 7 -0.27 7 14
glucose import -0.009 0.024 0.2 4 -0.17 4 8
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.039 0.22 1 -0.21 6 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.015 -10000 0 -0.17 4 4
GSK3A 0.008 0.045 -10000 0 -0.29 7 7
FOXO1 0.006 0.039 -10000 0 -0.29 6 6
GSK3B 0.006 0.042 -10000 0 -0.29 7 7
SFN 0.025 0.043 0.32 8 -0.32 1 9
G1/S transition of mitotic cell cycle 0.006 0.054 0.24 4 -0.28 8 12
p27Kip1/14-3-3 family 0.01 0.056 -10000 0 -0.32 8 8
PRKACA 0.02 0.005 -10000 0 -10000 0 0
KPNA1 0.02 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
RHEB 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.02 0.004 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.059 0.21 4 -0.34 4 8
ERC1 0.019 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.016 0.017 0.2 2 -10000 0 2
BIRC2 0.02 0.004 -10000 0 -10000 0 0
IKBKB 0.018 0.007 -10000 0 -10000 0 0
RIPK2 0.018 0.007 -10000 0 -10000 0 0
IKBKG 0.003 0.046 -10000 0 -0.35 6 6
IKK complex/A20 0.027 0.074 -10000 0 -0.38 6 6
NEMO/A20/RIP2 0.018 0.007 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.024 0.071 -10000 0 -0.37 9 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
Exportin 1/RanGTP 0.028 0.01 0.21 1 -10000 0 1
IKK complex/ELKS 0.023 0.065 -10000 0 -0.35 8 8
BCL10/MALT1/TRAF6 0.036 0.015 -10000 0 -10000 0 0
NOD2 0.02 0.004 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
MALT1 0.019 0.006 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.029 0.007 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.02 0.047 0.23 1 -0.23 15 16
TRAF6 0.02 0.003 -10000 0 -10000 0 0
PRKCA 0.019 0.023 -10000 0 -0.32 2 2
CHUK 0.02 0.003 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
TNF 0.009 0.065 0.32 1 -0.32 16 17
NF kappa B1 p50/RelA 0.042 0.012 -10000 0 -10000 0 0
BCL10 0.02 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.017 0.2 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.07 -10000 0 -0.37 8 8
CYLD 0.02 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.031 0.07 -10000 0 -0.37 7 7
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.008 0.1 -10000 0 -0.36 16 16
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
AKT2 0.02 0.005 -10000 0 -10000 0 0
STXBP4 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.009 0.11 0.24 1 -0.38 19 20
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.015 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.037 0.014 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
ASIP 0.019 0.015 0.32 1 -10000 0 1
PRKCI 0.02 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.02 0.003 -10000 0 -10000 0 0
GYS1 -0.005 0.011 0.23 1 -10000 0 1
PRKCZ 0.018 0.028 -10000 0 -0.32 3 3
TRIP10 0.02 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.004 0.05 -10000 0 -0.22 10 10
VAMP2 0.019 0.006 -10000 0 -10000 0 0
SLC2A4 -0.011 0.12 0.24 1 -0.42 19 20
STX4 0.02 0.003 -10000 0 -10000 0 0
GSK3B 0.01 0.003 -10000 0 -10000 0 0
SFN 0.025 0.043 0.32 8 -0.32 1 9
LNPEP 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.017 -10000 0 -0.23 2 2
CRKL 0.02 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.019 0.023 -10000 0 -0.32 2 2
alpha4/beta7 Integrin/MAdCAM1 0.048 0.031 0.22 5 -0.17 3 8
EPO 0.02 0.025 0.32 3 -10000 0 3
alpha4/beta7 Integrin 0.028 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.029 0.013 -10000 0 -0.23 1 1
EPO/EPOR (dimer) 0.028 0.019 0.23 3 -10000 0 3
lamellipodium assembly 0.002 0.052 -10000 0 -0.38 5 5
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.028 0.015 -10000 0 -0.23 1 1
ARF6 0.02 0.005 -10000 0 -10000 0 0
JAK2 0.011 0.018 0.18 1 -0.29 1 2
PXN 0.02 0.003 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
MADCAM1 0.023 0.035 0.32 6 -10000 0 6
cell adhesion 0.046 0.03 0.22 5 -0.17 3 8
CRKL/CBL 0.028 0.009 -10000 0 -10000 0 0
ITGB1 0.02 0.003 -10000 0 -10000 0 0
SRC -0.017 0.033 0.17 12 -0.18 2 14
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.018 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.038 0.023 0.22 1 -0.2 3 4
p130Cas/Crk/Dock1 -0.024 0.036 0.17 11 -10000 0 11
VCAM1 0.019 0.027 0.32 1 -0.32 2 3
RHOA 0.02 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.018 -10000 0 -0.18 1 1
BCAR1 -0.021 0.032 0.17 10 -0.17 3 13
EPOR 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.02 0.004 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.054 -10000 0 -0.39 5 5
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.017 0.032 -10000 0 -0.32 4 4
positive regulation of NF-kappaB transcription factor activity 0.023 0.026 -10000 0 -0.23 4 4
MAP2K4 0.006 0.021 -10000 0 -0.24 1 1
IKBKB 0.018 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.017 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.017 0.008 -10000 0 -10000 0 0
SMPD1 0.004 0.014 -10000 0 -0.14 4 4
IKBKG 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.018 -10000 0 -0.32 1 1
TRAIL/TRAILR2 0.023 0.026 -10000 0 -0.22 4 4
TRAIL/TRAILR3 0.02 0.039 -10000 0 -0.25 8 8
TRAIL/TRAILR1 0.023 0.026 -10000 0 -0.23 4 4
TRAIL/TRAILR4 0.023 0.026 -10000 0 -0.23 4 4
TRAIL/TRAILR1/DAP3/GTP 0.027 0.024 -10000 0 -0.17 3 3
IKK complex 0 0.045 -10000 0 -0.23 1 1
RIPK1 0.02 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.013 0.005 -10000 0 -10000 0 0
MAPK3 -0.017 0.024 0.27 1 -0.23 4 5
MAP3K1 0.013 0.017 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.017 0.018 -10000 0 -0.32 1 1
TRADD 0.02 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.017 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.01 0.023 -10000 0 -0.18 6 6
CFLAR 0.021 0.002 -10000 0 -10000 0 0
MAPK1 -0.016 0.02 0.27 1 -0.23 2 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.045 0.033 -10000 0 -0.17 2 2
mol:ceramide 0.004 0.014 -10000 0 -0.14 4 4
FADD 0.02 0.004 -10000 0 -10000 0 0
MAPK8 -0.006 0.04 -10000 0 -0.26 3 3
TRAF2 0.02 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.013 0.039 -10000 0 -0.32 6 6
CHUK 0.02 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.031 0.027 -10000 0 -0.19 4 4
DAP3 0.018 0.007 -10000 0 -10000 0 0
CASP10 -0.004 0.042 0.16 23 -0.22 3 26
JNK cascade 0.023 0.026 -10000 0 -0.23 4 4
TRAIL (trimer) 0.017 0.032 -10000 0 -0.32 4 4
TNFRSF10C 0.013 0.039 -10000 0 -0.32 6 6
TRAIL/TRAILR1/DAP3/GTP/FADD 0.033 0.028 -10000 0 -0.17 3 3
TRAIL/TRAILR2/FADD 0.031 0.027 -10000 0 -0.19 4 4
cell death 0.004 0.014 -10000 0 -0.14 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.01 0.023 -10000 0 -0.19 2 2
TRAILR2 (trimer) 0.017 0.008 -10000 0 -10000 0 0
CASP8 0.008 0.052 -10000 0 -0.66 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.045 0.033 -10000 0 -0.17 2 2
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0.03 0.03 0.2 3 -0.16 7 10
MAPK9 0.004 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.013 0.16 3 -10000 0 3
GNB1/GNG2 0.025 0.016 -10000 0 -0.19 2 2
GNB1 0.02 0.004 -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 0.004 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.011 0.024 0.18 3 -0.16 6 9
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 0.002 0.005 0.047 6 -10000 0 6
GNAL 0.017 0.046 0.32 3 -0.32 6 9
GNG2 0.019 0.023 -10000 0 -0.32 2 2
CRH 0.018 0.025 0.32 3 -10000 0 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.001 -10000 0 -10000 0 0
MAPK11 0.002 0.016 -10000 0 -0.25 2 2
Arf1 pathway

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
coatomer protein complex 0.008 0.041 0.15 32 -0.2 1 33
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.037 0.12 26 -0.15 3 29
AP2 0.029 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.021 0.016 -10000 0 -10000 0 0
CLTB 0.02 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.006 -10000 0 -10000 0 0
CD4 0.013 0.048 -10000 0 -0.32 9 9
CLTA 0.019 0.005 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.021 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.003 0.01 -10000 0 -10000 0 0
mol:Choline -0.002 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
DDEF1 -0.001 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.017 -10000 0 -0.094 8 8
AP2M1 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.011 -10000 0 -10000 0 0
Rac/GTP 0.015 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.013 -10000 0 -10000 0 0
ARFIP2 0.01 0.02 -10000 0 -10000 0 0
COPA 0.018 0.007 -10000 0 -10000 0 0
RAC1 0.018 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.001 0.033 -10000 0 -0.17 10 10
ARF1/GTP/ARHGAP10 0.012 0.007 -10000 0 -10000 0 0
GGA3 0.02 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0.026 -10000 0 -0.27 3 3
AP2A1 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.001 0.026 -10000 0 -0.16 10 10
ARF1/GDP/Membrin 0.016 0.03 -10000 0 -0.3 3 3
Arfaptin 2/Rac/GDP 0.019 0.018 -10000 0 -10000 0 0
CYTH2 0.023 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.025 0.012 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.004 0.039 -10000 0 -0.21 10 10
PLD2 -0.002 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.002 -10000 0 -10000 0 0
PIP5K1A -0.001 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.007 0.02 -10000 0 -0.13 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.002 -10000 0 -10000 0 0
GOSR2 0.005 0.016 -10000 0 -0.31 1 1
USO1 0.004 0.026 -10000 0 -0.31 3 3
GBF1 0.003 0.03 -10000 0 -0.31 4 4
ARF1/GTP/Arfaptin 2 0.023 0.016 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.033 0.034 -10000 0 -0.19 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.019 0.006 -10000 0 -10000 0 0
SMAD2 0 0.042 0.24 2 -0.22 4 6
SMAD3 0.01 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4 0.023 0.035 0.25 1 -0.48 1 2
SMAD4/Ubc9/PIASy 0.035 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.048 0.23 1 -0.22 2 3
PPM1A 0.02 0.004 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.007 0.041 0.22 1 -0.2 7 8
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.026 0.019 -10000 0 -0.23 2 2
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
NUP214 0.02 0.004 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
CTDSPL 0.02 0.004 -10000 0 -10000 0 0
KPNB1 0.02 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.019 0.023 -10000 0 -0.32 2 2
UBE2I 0.02 0.004 -10000 0 -10000 0 0
NUP153 0.02 0.003 -10000 0 -10000 0 0
KPNA2 0.023 0.031 0.32 5 -10000 0 5
PIAS4 0.019 0.005 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.02 0.003 -9999 0 -10000 0 0
ITGB7 0.02 0.016 -9999 0 -0.32 1 1
ITGA4 0.019 0.023 -9999 0 -0.32 2 2
alpha4/beta7 Integrin 0.028 0.021 -9999 0 -0.23 3 3
alpha4/beta1 Integrin 0.029 0.013 -9999 0 -0.23 1 1
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 0.02 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.01 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.019 0.023 -10000 0 -0.32 2 2
RAC1 0.018 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.028 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.038 0.016 -10000 0 -0.2 1 1
alpha4/beta7 Integrin/Paxillin 0.027 0.019 -10000 0 -0.18 3 3
lamellipodium assembly -0.007 0.08 -10000 0 -0.37 15 15
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.028 0.015 -10000 0 -0.23 1 1
ARF6 0.02 0.005 -10000 0 -10000 0 0
TLN1 0.019 0.017 -10000 0 -0.32 1 1
PXN -0.016 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
ARF6/GTP 0.035 0.019 -10000 0 -0.16 1 1
cell adhesion 0.035 0.02 -10000 0 -0.16 2 2
CRKL/CBL 0.028 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.027 0.014 -10000 0 -0.18 1 1
ITGB1 0.02 0.003 -10000 0 -10000 0 0
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
ARF6/GDP 0.022 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.037 0.024 0.21 1 -0.17 3 4
p130Cas/Crk/Dock1 0.036 0.018 -10000 0 -0.2 1 1
VCAM1 0.019 0.027 0.32 1 -0.32 2 3
alpha4/beta1 Integrin/Paxillin/Talin 0.036 0.02 -10000 0 -0.16 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.037 0.018 -10000 0 -0.17 1 1
BCAR1 0.019 0.017 -10000 0 -0.32 1 1
mol:GDP -0.036 0.017 0.17 1 -10000 0 1
CBL 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.02 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.036 0.02 -10000 0 -0.16 2 2
Rac1/GTP -0.008 0.087 -10000 0 -0.41 15 15
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.028 0.014 -10000 0 -0.23 1 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.017 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.044 0.21 5 -0.18 2 7
NFKBIA 0.001 0.012 -10000 0 -0.17 2 2
MAPK14 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.016 0.008 -10000 0 -10000 0 0
ARRB2 0.007 0.002 -10000 0 -10000 0 0
REL 0.021 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.016 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.017 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.014 0.014 0.24 1 -10000 0 1
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
NFKB1 -0.014 0.006 -10000 0 -10000 0 0
RELA 0.02 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.008 0.035 -10000 0 -0.19 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.017 0.04 -10000 0 -0.19 3 3
SRC 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.028 0.015 -10000 0 -0.23 1 1
NF kappa B1 p50/RelA 0.008 0.034 -10000 0 -0.18 4 4
IKBKB 0.018 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
SYK 0.019 0.023 -10000 0 -0.32 2 2
I kappa B alpha/PIK3R1 0.026 0.053 0.24 10 -0.17 8 18
cell death 0.017 0.039 -10000 0 -0.18 3 3
NF kappa B1 p105/c-Rel -0.017 0.007 -10000 0 -10000 0 0
LCK 0.02 0.027 0.32 1 -0.32 2 3
BCL3 0.019 0.017 -10000 0 -0.32 1 1
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.038 0.019 -9999 0 -0.2 2 2
E-cadherin/beta catenin 0.028 0.018 -9999 0 -0.23 2 2
CTNNB1 0.02 0.004 -9999 0 -10000 0 0
JUP 0.02 0.003 -9999 0 -10000 0 0
CDH1 0.019 0.023 -9999 0 -0.32 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.008 -10000 0 -10000 0 0
MDM2/SUMO1 0.026 0.03 -10000 0 -0.21 3 3
HDAC4 0.02 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.018 0.008 -10000 0 -10000 0 0
SUMO1 0.021 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.005 0.014 -10000 0 -0.16 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.028 0.028 -10000 0 -0.2 3 3
SUMO1/HDAC1 0.028 0.03 -10000 0 -0.21 3 3
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.044 0.021 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.006 0.002 -10000 0 -10000 0 0
Ran/GTP 0.017 0.028 -10000 0 -0.19 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.005 -10000 0 -10000 0 0
UBE2I 0.02 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.014 0.032 0.21 4 -0.19 4 8
NPC 0.012 0.001 -10000 0 -10000 0 0
PIAS2 0.019 0.006 -10000 0 -10000 0 0
PIAS1 0.02 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.03 0.006 -9999 0 -9999 0 0
FBXW11 0.02 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -9999 0 0
CHUK 0.02 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.055 0.021 -9999 0 -9999 0 0
NFKB1 0.021 0.003 -9999 0 -9999 0 0
MAP3K14 0.02 0.003 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.029 0.007 -9999 0 -9999 0 0
RELB 0.02 0.005 -9999 0 -9999 0 0
NFKB2 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.027 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.026 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 466 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MP.A4TK TCGA.MP.A4TI TCGA.MP.A4TC TCGA.MP.A4TA
109_MAP3K5 0.0082 0.0082 0.0082 0.0082
47_PPARGC1A 0.021 0.021 -0.32 0.021
105_BMP4 0.021 0.021 0.021 0.021
105_BMP6 0.021 0.021 -0.32 0.021
105_BMP7 0.021 0.021 0.021 0.021
105_BMP2 0.021 0.021 0.021 -0.32
131_RELN/VLDLR 0.054 0.054 0.054 0.054
30_TGFB1/TGF beta receptor Type II 0.021 0.021 0.021 -0.023
84_STAT5B 0.015 0.015 0.034 0.071
84_STAT5A 0.015 0.015 0.034 0.071
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/LUAD-TP/4402775/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LUAD-TP/4426078/Gistic2_Analysis_4426085/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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