PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1R78D7F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1R78D7F
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 57 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 356
Class IB PI3K non-lipid kinase events 287
Signaling events mediated by Stem cell factor receptor (c-Kit) 276
Signaling mediated by p38-alpha and p38-beta 273
Reelin signaling pathway 219
EGFR-dependent Endothelin signaling events 199
Aurora B signaling 191
FOXA2 and FOXA3 transcription factor networks 186
PLK1 signaling events 173
Angiopoietin receptor Tie2-mediated signaling 162
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 1093 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXM1 transcription factor network 0.3257 356 18205 51 -0.053 0.69 1000 -1000 -0.041 -1000
Class IB PI3K non-lipid kinase events 0.2626 287 861 3 -0.13 -1000 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2525 276 21579 78 -0.57 0.18 1000 -1000 -0.056 -1000
Signaling mediated by p38-alpha and p38-beta 0.2498 273 12024 44 -0.32 0.024 1000 -1000 -0.02 -1000
Reelin signaling pathway 0.2004 219 12270 56 -0.32 0.054 1000 -1000 -0.032 -1000
EGFR-dependent Endothelin signaling events 0.1821 199 4191 21 -0.21 0.034 1000 -1000 -0.037 -1000
Aurora B signaling 0.1747 191 12841 67 -0.21 0.27 1000 -1000 -0.038 -1000
FOXA2 and FOXA3 transcription factor networks 0.1702 186 8579 46 -1.1 0.034 1000 -1000 -0.047 -1000
PLK1 signaling events 0.1583 173 14722 85 -0.063 0.23 1000 -1000 -0.041 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1482 162 14337 88 -0.32 0.11 1000 -1000 -0.064 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1391 152 10337 68 -0.34 0.15 1000 -1000 -0.045 -1000
EPHB forward signaling 0.1382 151 12891 85 -0.2 0.14 1000 -1000 -0.059 -1000
Glucocorticoid receptor regulatory network 0.1363 149 17004 114 -0.72 0.28 1000 -1000 -0.053 -1000
Endothelins 0.1345 147 14206 96 -0.34 0.17 1000 -1000 -0.04 -1000
HIF-1-alpha transcription factor network 0.1299 142 10853 76 -0.48 0.035 1000 -1000 -0.044 -1000
p75(NTR)-mediated signaling 0.1290 141 17695 125 -0.22 0.096 1000 -1000 -0.057 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1153 126 6856 54 -0.32 0.054 1000 -1000 -0.035 -1000
Ephrin B reverse signaling 0.1125 123 5924 48 -0.2 0.089 1000 -1000 -0.023 -1000
Noncanonical Wnt signaling pathway 0.1107 121 3149 26 -0.097 0.024 1000 -1000 -0.029 -1000
IL23-mediated signaling events 0.1107 121 7285 60 -0.3 0.084 1000 -1000 -0.031 -1000
IL4-mediated signaling events 0.1089 119 10869 91 -0.66 0.25 1000 -1000 -0.071 -1000
Wnt signaling 0.1089 119 836 7 -0.097 0.017 1000 -1000 -0.006 -1000
IGF1 pathway 0.1025 112 6409 57 -0.11 0.044 1000 -1000 -0.032 -1000
Arf6 signaling events 0.0988 108 6727 62 -0.21 0.05 1000 -1000 -0.025 -1000
Nongenotropic Androgen signaling 0.0942 103 5364 52 -0.25 0.13 1000 -1000 -0.027 -1000
Plasma membrane estrogen receptor signaling 0.0942 103 8936 86 -0.12 0.11 1000 -1000 -0.05 -1000
BMP receptor signaling 0.0897 98 7985 81 -0.38 0.1 1000 -1000 -0.037 -1000
ErbB2/ErbB3 signaling events 0.0878 96 6271 65 -0.26 0.034 1000 -1000 -0.064 -1000
Signaling events regulated by Ret tyrosine kinase 0.0878 96 7918 82 -0.07 0.097 1000 -1000 -0.054 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0860 94 8067 85 -0.24 0.024 1000 -1000 -0.041 -1000
Calcium signaling in the CD4+ TCR pathway 0.0842 92 2860 31 -0.19 0.027 1000 -1000 -0.031 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0823 90 10905 120 -0.35 0.17 1000 -1000 -0.046 -1000
Visual signal transduction: Rods 0.0814 89 4638 52 -0.33 0.055 1000 -1000 -0.017 -1000
ErbB4 signaling events 0.0805 88 6072 69 -0.27 0.06 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 0.0787 86 6606 76 -0.44 0.082 1000 -1000 -0.028 -1000
S1P1 pathway 0.0778 85 3089 36 -0.33 0.024 1000 -1000 -0.028 -1000
Aurora C signaling 0.0769 84 588 7 0 0.14 1000 -1000 -0.013 -1000
Effects of Botulinum toxin 0.0732 80 2086 26 -0.003 0.1 1000 -1000 -0.004 -1000
Glypican 1 network 0.0723 79 3799 48 -0.2 0.045 1000 -1000 -0.023 -1000
amb2 Integrin signaling 0.0723 79 6490 82 -0.33 0.12 1000 -1000 -0.02 -1000
LPA receptor mediated events 0.0714 78 7964 102 -0.19 0.12 1000 -1000 -0.071 -1000
Integrins in angiogenesis 0.0704 77 6538 84 -0.2 0.11 1000 -1000 -0.04 -1000
TCR signaling in naïve CD8+ T cells 0.0695 76 7160 93 -0.089 0.084 1000 -1000 -0.038 -1000
Syndecan-1-mediated signaling events 0.0686 75 2573 34 -0.073 0.18 1000 -1000 -0.028 -1000
Signaling events mediated by the Hedgehog family 0.0659 72 3771 52 -0.12 0.028 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.0659 72 5427 75 -0.18 0.053 1000 -1000 -0.029 -1000
IL12-mediated signaling events 0.0640 70 6100 87 -0.32 0.072 1000 -1000 -0.056 -1000
Ephrin A reverse signaling 0.0622 68 481 7 -0.028 0.023 1000 -1000 -0.008 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0604 66 2264 34 -0.024 0.058 1000 -1000 -0.02 -1000
Fc-epsilon receptor I signaling in mast cells 0.0567 62 6068 97 -0.14 0.033 1000 -1000 -0.057 -1000
PDGFR-alpha signaling pathway 0.0567 62 2745 44 -0.3 0.036 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 0.0567 62 2688 43 -0.19 0.033 1000 -1000 -0.025 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0558 61 3214 52 -0.12 0.071 1000 -1000 -0.023 -1000
Visual signal transduction: Cones 0.0531 58 2234 38 -0.024 0.16 1000 -1000 -0.009 -1000
Canonical Wnt signaling pathway 0.0531 58 2987 51 -0.28 0.12 1000 -1000 -0.042 -1000
Syndecan-3-mediated signaling events 0.0522 57 2029 35 -0.23 0.054 1000 -1000 -0.018 -1000
Presenilin action in Notch and Wnt signaling 0.0503 55 3364 61 -0.27 0.12 1000 -1000 -0.047 -1000
Syndecan-2-mediated signaling events 0.0494 54 3778 69 -0.12 0.11 1000 -1000 -0.033 -1000
Nectin adhesion pathway 0.0494 54 3416 63 -0.056 0.047 1000 -1000 -0.045 -1000
FAS signaling pathway (CD95) 0.0485 53 2537 47 -0.43 0.039 1000 -1000 -0.024 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0485 53 1755 33 -0.38 0.059 1000 -1000 -0.029 -1000
Glypican 2 network 0.0467 51 207 4 0.033 0.058 1000 -1000 0.012 -1000
Rapid glucocorticoid signaling 0.0467 51 1030 20 -0.11 0.026 1000 -1000 -0.004 -1000
Signaling events mediated by HDAC Class III 0.0430 47 1884 40 -0.32 0.045 1000 -1000 -0.019 -1000
TCGA08_rtk_signaling 0.0421 46 1200 26 -0.19 0.037 1000 -1000 -0.011 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0421 46 3446 74 -0.19 0.049 1000 -1000 -0.055 -1000
LPA4-mediated signaling events 0.0412 45 541 12 -0.11 0.006 1000 -1000 -0.022 -1000
Syndecan-4-mediated signaling events 0.0393 43 2934 67 -0.2 0.12 1000 -1000 -0.034 -1000
Regulation of Androgen receptor activity 0.0393 43 3044 70 -0.16 0.11 1000 -1000 -0.041 -1000
Aurora A signaling 0.0384 42 2554 60 -0.079 0.18 1000 -1000 -0.018 -1000
Ras signaling in the CD4+ TCR pathway 0.0384 42 716 17 -0.056 0.025 1000 -1000 -0.023 -1000
Coregulation of Androgen receptor activity 0.0375 41 3158 76 -0.14 0.063 1000 -1000 -0.014 -1000
Insulin Pathway 0.0366 40 2960 74 -0.12 0.06 1000 -1000 -0.041 -1000
Regulation of p38-alpha and p38-beta 0.0348 38 2062 54 -0.24 0.052 1000 -1000 -0.047 -1000
TCGA08_retinoblastoma 0.0348 38 311 8 -0.018 0.06 1000 -1000 -0.004 -1000
BCR signaling pathway 0.0348 38 3852 99 -0.077 0.056 1000 -1000 -0.05 -1000
Thromboxane A2 receptor signaling 0.0339 37 3940 105 -0.19 0.036 1000 -1000 -0.038 -1000
IL27-mediated signaling events 0.0339 37 1897 51 -0.18 0.075 1000 -1000 -0.043 -1000
Regulation of Telomerase 0.0339 37 3851 102 -0.2 0.14 1000 -1000 -0.036 -1000
IL2 signaling events mediated by STAT5 0.0311 34 765 22 0.006 0.11 1000 -1000 -0.031 -1000
Osteopontin-mediated events 0.0302 33 1282 38 -0.14 0.086 1000 -1000 -0.023 -1000
Regulation of nuclear SMAD2/3 signaling 0.0274 30 4195 136 -0.19 0.077 1000 -1000 -0.024 -1000
TCGA08_p53 0.0265 29 207 7 -0.011 0.02 1000 -1000 -0.004 -1000
Ceramide signaling pathway 0.0229 25 1911 76 -0.1 0.063 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 0.0229 25 851 34 -0.12 0.035 1000 -1000 -0.042 -1000
Caspase cascade in apoptosis 0.0220 24 1811 74 -0.025 0.057 1000 -1000 -0.032 -1000
S1P5 pathway 0.0220 24 414 17 -0.007 0.033 1000 -1000 -0.008 -1000
HIF-2-alpha transcription factor network 0.0210 23 1031 43 -0.15 0.16 1000 -1000 -0.039 -1000
S1P4 pathway 0.0201 22 571 25 -0.012 0.044 1000 -1000 -0.019 -1000
Cellular roles of Anthrax toxin 0.0192 21 819 39 -0.079 0.027 1000 -1000 -0.02 -1000
IL2 signaling events mediated by PI3K 0.0192 21 1246 58 -0.001 0.065 1000 -1000 -0.027 -1000
BARD1 signaling events 0.0183 20 1174 57 -0.046 0.1 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 0.0183 20 1354 65 -0.087 0.056 1000 -1000 -0.033 -1000
JNK signaling in the CD4+ TCR pathway 0.0174 19 326 17 0.002 0.064 1000 -1000 -0.023 -1000
mTOR signaling pathway 0.0174 19 1026 53 -0.022 0.029 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 0.0174 19 1342 68 -0.16 0.043 1000 -1000 -0.03 -1000
FoxO family signaling 0.0165 18 1184 64 -0.016 0.23 1000 -1000 -0.03 -1000
a4b1 and a4b7 Integrin signaling 0.0156 17 89 5 0.024 0.041 1000 -1000 0.016 -1000
ceramide signaling pathway 0.0156 17 834 49 -0.001 0.036 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0156 17 1029 58 -0.051 0.051 1000 -1000 -0.021 -1000
S1P3 pathway 0.0156 17 729 42 -0.014 0.042 1000 -1000 -0.037 -1000
IL1-mediated signaling events 0.0146 16 1013 62 -0.015 0.061 1000 -1000 -0.026 -1000
Signaling mediated by p38-gamma and p38-delta 0.0146 16 246 15 -0.026 0.024 1000 -1000 -0.023 -1000
E-cadherin signaling in the nascent adherens junction 0.0137 15 1183 76 -0.023 0.054 1000 -1000 -0.051 -1000
PLK2 and PLK4 events 0.0128 14 44 3 0.016 0.033 1000 -1000 -0.005 -1000
TRAIL signaling pathway 0.0128 14 692 48 -0.015 0.043 1000 -1000 -0.028 -1000
Arf6 trafficking events 0.0128 14 1018 71 -0.27 0.042 1000 -1000 -0.023 -1000
p38 MAPK signaling pathway 0.0119 13 608 44 -0.018 0.067 1000 -1000 -0.02 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0110 12 359 28 -0.007 0.051 1000 -1000 -0.013 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0110 12 459 37 -0.009 0.067 1000 -1000 -0.024 -1000
Class I PI3K signaling events 0.0110 12 911 73 -0.018 0.051 1000 -1000 -0.036 -1000
PDGFR-beta signaling pathway 0.0110 12 1186 97 -0.024 0.056 1000 -1000 -0.056 -1000
IFN-gamma pathway 0.0101 11 783 68 -0.006 0.076 1000 -1000 -0.039 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0101 11 525 45 0.003 0.054 1000 -1000 -0.041 -1000
Canonical NF-kappaB pathway 0.0091 10 418 39 0 0.051 1000 -1000 -0.023 -1000
EPO signaling pathway 0.0091 10 595 55 0.014 0.08 1000 -1000 -0.03 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0091 10 875 83 -0.019 0.047 1000 -1000 -0.026 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0091 10 1332 125 -0.1 0.053 1000 -1000 -0.035 -1000
E-cadherin signaling events 0.0091 10 54 5 0.012 0.033 1000 -1000 0.012 -1000
Signaling events mediated by HDAC Class II 0.0082 9 701 75 -0.035 0.062 1000 -1000 -0.03 -1000
Insulin-mediated glucose transport 0.0082 9 306 32 -0.12 0.039 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 0.0055 6 707 104 -0.06 0.057 1000 -1000 -0.027 -1000
VEGFR1 specific signals 0.0055 6 383 56 -0.1 0.052 1000 -1000 -0.04 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0046 5 125 23 -0.004 0.043 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0046 5 206 36 -0.047 0.051 1000 -1000 -0.031 -1000
Atypical NF-kappaB pathway 0.0046 5 168 31 0 0.028 1000 -1000 -0.01 -1000
Circadian rhythm pathway 0.0037 4 97 22 -0.007 0.049 1000 -1000 -0.022 -1000
Arf6 downstream pathway 0.0018 2 125 43 -0.055 0.056 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0009 1 31 27 -0.008 0.056 1000 -1000 -0.034 -1000
Arf1 pathway 0.0009 1 87 54 -0.001 0.045 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0009 1 20 13 0 0.067 1000 -1000 0 -1000
Total NA 8470 500451 7203 -20 -990 131000 -131000 -3.9 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.57 0.39 0.96 416 -1 3 419
PLK1 0.35 0.24 0.6 408 -0.69 2 410
BIRC5 0.37 0.24 0.63 336 -0.89 3 339
HSPA1B 0.57 0.39 0.95 426 -1 3 429
MAP2K1 0.16 0.11 0.32 253 -10000 0 253
BRCA2 0.58 0.4 0.97 417 -0.99 4 421
FOXM1 0.66 0.48 1.1 494 -1.1 4 498
XRCC1 0.57 0.39 0.95 427 -1 3 430
FOXM1B/p19 0.12 0.26 0.78 69 -0.99 5 74
Cyclin D1/CDK4 0.5 0.37 0.85 442 -0.99 3 445
CDC2 0.62 0.43 1 499 -0.98 4 503
TGFA 0.5 0.39 0.84 473 -0.89 9 482
SKP2 0.58 0.39 0.95 440 -1 3 443
CCNE1 0.089 0.094 0.29 179 -10000 0 179
CKS1B 0.57 0.39 0.91 498 -0.94 4 502
RB1 0.29 0.3 0.64 365 -0.6 7 372
FOXM1C/SP1 0.52 0.36 0.87 415 -1 6 421
AURKB 0.29 0.3 0.62 283 -0.81 19 302
CENPF 0.66 0.45 1 514 -0.99 3 517
CDK4 0.08 0.053 0.23 24 -10000 0 24
MYC 0.34 0.36 0.79 308 -0.96 6 314
CHEK2 0.15 0.11 0.31 291 -10000 0 291
ONECUT1 0.53 0.39 0.88 470 -1.1 3 473
CDKN2A -0.053 0.11 0.23 17 -0.23 187 204
LAMA4 0.57 0.4 0.96 425 -1.1 6 431
FOXM1B/HNF6 0.53 0.4 0.92 421 -1.3 3 424
FOS 0.27 0.64 0.98 317 -0.99 75 392
SP1 0.024 0.021 -10000 0 -0.2 5 5
CDC25B 0.58 0.39 0.96 429 -1 3 432
response to radiation 0.11 0.084 0.22 284 -10000 0 284
CENPB 0.57 0.39 0.94 446 -1 3 449
CENPA 0.62 0.43 1 473 -1 3 476
NEK2 0.69 0.44 1.1 529 -0.97 3 532
HIST1H2BA 0.57 0.39 0.94 442 -1 3 445
CCNA2 0.14 0.13 0.3 401 -10000 0 401
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.6 0.42 1 431 -1.2 3 434
CCNB2 0.63 0.43 1 483 -1 3 486
CCNB1 0.63 0.45 1 464 -1.1 3 467
ETV5 0.58 0.4 0.96 427 -1 3 430
ESR1 0.44 0.55 0.98 399 -0.93 25 424
CCND1 0.52 0.41 0.9 468 -1 3 471
GSK3A 0.13 0.089 0.27 176 -10000 0 176
Cyclin A-E1/CDK1-2 0.23 0.16 0.4 426 -10000 0 426
CDK2 0.056 0.028 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.14 0.11 0.26 394 -10000 0 394
FOXM1B/Cbp/p300 0.26 0.29 0.7 143 -0.97 4 147
GAS1 0.52 0.49 0.94 429 -1 40 469
MMP2 0.56 0.41 0.94 442 -1.2 10 452
RB1/FOXM1C 0.46 0.38 0.85 410 -1 3 413
CREBBP 0.023 0.007 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.13 0.26 0.56 287 -10000 0 287
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.56 287 287
PDE3B -0.13 0.26 -10000 0 -0.57 287 287
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.32 4 -0.38 465 469
CRKL -0.17 0.21 0.26 1 -0.4 482 483
HRAS -0.12 0.18 -10000 0 -0.36 317 317
mol:PIP3 -0.14 0.2 0.29 1 -0.37 365 366
SPRED1 0.024 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 489 489
FOXO3 -0.14 0.2 0.53 1 -0.37 333 334
AKT1 -0.16 0.21 0.37 1 -0.39 428 429
BAD -0.15 0.2 0.34 2 -0.37 345 347
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 489 489
GSK3B -0.14 0.2 0.53 1 -0.37 343 344
RAF1 -0.097 0.16 0.25 4 -0.34 77 81
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 486 486
STAT1 -0.44 0.52 -10000 0 -0.99 497 497
HRAS/SPRED1 -0.094 0.16 -10000 0 -0.34 68 68
cell proliferation -0.18 0.22 -10000 0 -0.41 491 491
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.031 -10000 0 -0.57 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 493 493
HRAS/SPRED2 -0.094 0.16 -10000 0 -0.34 82 82
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.4 410 410
MAPK3 -0.066 0.12 0.33 5 -0.28 24 29
STAP1 -0.18 0.22 -10000 0 -0.42 490 490
GRAP2 0.017 0.063 0.26 3 -0.57 12 15
JAK2 -0.37 0.44 -10000 0 -0.84 495 495
STAT1 (dimer) -0.43 0.51 -10000 0 -0.97 498 498
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.15 0.22 -10000 0 -0.4 417 417
actin filament polymerization -0.18 0.22 0.33 1 -0.41 489 490
LYN 0.021 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.59 497 497
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 433 433
PI3K -0.15 0.22 -10000 0 -0.4 460 460
PTEN 0.023 0.019 -10000 0 -0.57 1 1
SCF/KIT/EPO/EPOR -0.51 0.63 -10000 0 -1.2 492 492
MAPK8 -0.19 0.22 -10000 0 -0.42 491 491
STAT3 (dimer) -0.18 0.22 0.27 1 -0.41 486 487
positive regulation of transcription -0.052 0.1 0.24 13 -0.23 20 33
mol:GDP -0.13 0.19 -10000 0 -0.37 333 333
PIK3C2B -0.17 0.21 -10000 0 -0.42 384 384
CBL/CRKL -0.16 0.2 -10000 0 -0.38 472 472
FER -0.18 0.22 -10000 0 -0.42 487 487
SH2B3 -0.18 0.22 -10000 0 -0.42 491 491
PDPK1 -0.12 0.19 0.34 9 -0.35 331 340
SNAI2 -0.18 0.21 0.28 4 -0.42 438 442
positive regulation of cell proliferation -0.32 0.38 -10000 0 -0.73 496 496
KITLG -0.004 0.058 0.25 10 -0.59 5 15
cell motility -0.32 0.38 -10000 0 -0.73 496 496
PTPN6 0.032 0.017 0.27 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -1 14 14
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 497 497
SOCS1 0.025 0.033 0.26 14 -0.57 1 15
cell migration 0.18 0.22 0.42 489 -10000 0 489
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.041 0.091 0.24 169 -10000 0 169
VAV1 0.023 0.033 0.26 2 -0.57 3 5
GRB10 -0.18 0.22 -10000 0 -0.42 488 488
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 495 495
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.13 0.27 11 -0.29 38 49
CBL 0.022 0.007 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 493 493
MAP2K2 -0.075 0.13 0.33 6 -0.29 37 43
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 359 359
STAT5A -0.27 0.33 -10000 0 -0.62 497 497
GRB2 0.023 0.009 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 438 442
SHC/GRAP2 0.024 0.046 -10000 0 -0.29 17 17
PTPRO -0.18 0.22 -10000 0 -0.42 489 489
SH2B2 -0.18 0.22 -10000 0 -0.42 489 489
DOK1 0.025 0.014 0.26 4 -10000 0 4
MATK -0.19 0.22 -10000 0 -0.42 489 489
CREBBP -0.027 0.072 -10000 0 -10000 0 0
BCL2 -0.16 0.32 -10000 0 -1.3 58 58
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.32 0.5 0.42 4 -1 357 361
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.088 0.18 -10000 0 -0.35 327 327
ATF2/c-Jun -0.081 0.16 -10000 0 -0.41 99 99
MAPK11 -0.082 0.18 -10000 0 -0.35 324 324
MITF -0.12 0.22 0.28 1 -0.41 351 352
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 356 356
KRT8 -0.11 0.21 -10000 0 -0.4 333 333
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.52 356 356
CEBPB -0.1 0.2 0.28 1 -0.4 332 333
SLC9A1 -0.11 0.21 -10000 0 -0.41 350 350
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.39 343 343
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.45 325 325
JUN -0.081 0.16 -10000 0 -0.41 99 99
PPARGC1A -0.2 0.33 0.26 1 -0.56 419 420
USF1 -0.1 0.19 0.31 3 -0.38 335 338
RAB5/GDP/GDI1 -0.081 0.16 -10000 0 -0.3 345 345
NOS2 -0.11 0.22 -10000 0 -0.55 93 93
DDIT3 -0.11 0.2 -10000 0 -0.4 351 351
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.094 0.17 0.28 4 -0.33 322 326
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 323 323
CREB1 -0.12 0.22 -10000 0 -0.43 353 353
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.4 322 322
RPS6KA4 -0.11 0.21 -10000 0 -0.4 349 349
PLA2G4A -0.13 0.22 -10000 0 -0.43 346 346
GDI1 -0.11 0.21 -10000 0 -0.4 356 356
TP53 -0.15 0.27 0.28 1 -0.52 337 338
RPS6KA5 -0.12 0.22 -10000 0 -0.41 360 360
ESR1 -0.15 0.24 0.28 1 -0.42 410 411
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 356 356
MEF2A -0.11 0.21 0.28 1 -0.4 351 352
EIF4EBP1 -0.12 0.22 0.28 1 -0.44 335 336
KRT19 -0.11 0.21 0.31 1 -0.41 323 324
ELK4 -0.1 0.19 0.3 3 -0.38 336 339
ATF6 -0.1 0.19 0.31 3 -0.38 337 340
ATF1 -0.12 0.22 -10000 0 -0.43 355 355
p38alpha-beta/MAPKAPK2 -0.095 0.22 -10000 0 -0.41 308 308
p38alpha-beta/MAPKAPK3 -0.1 0.25 -10000 0 -0.45 325 325
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.027 -10000 0 -10000 0 0
VLDLR 0.007 0.096 -10000 0 -0.57 29 29
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
ITGA3 0.022 0.021 0.26 1 -0.57 1 2
RELN/VLDLR/Fyn -0.19 0.21 -10000 0 -0.37 604 604
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.044 -10000 0 -0.32 7 7
AKT1 -0.15 0.14 -10000 0 -0.27 544 544
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.26 61 -10000 0 61
RELN/LRP8/DAB1 -0.16 0.19 0.32 4 -0.32 608 612
LRPAP1/LRP8 0.048 0.047 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.14 0.18 0.31 4 -0.3 592 596
DAB1/alpha3/beta1 Integrin -0.14 0.17 -10000 0 -0.31 445 445
long-term memory -0.18 0.22 0.33 5 -0.36 544 549
DAB1/LIS1 -0.14 0.19 0.3 4 -0.3 594 598
DAB1/CRLK/C3G -0.14 0.18 -10000 0 -0.31 475 475
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.14 0.19 0.3 4 -0.31 522 526
ARHGEF2 0.021 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.033 0.18 0.26 13 -0.57 107 120
CDK5R1 0.028 0.034 0.26 23 -10000 0 23
RELN -0.32 0.29 0.26 2 -0.57 619 621
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RELN/LRP8/Fyn -0.18 0.2 -10000 0 -0.35 596 596
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 0.33 4 -0.35 557 561
MAPK8 0.02 0.051 -10000 0 -0.57 8 8
RELN/VLDLR/DAB1 -0.17 0.19 0.32 2 -0.34 608 610
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.18 0.22 1 -0.32 608 609
RELN/LRP8 -0.18 0.2 -10000 0 -0.35 612 612
GRIN2B/RELN/LRP8/DAB1/Fyn -0.16 0.2 0.36 3 -0.32 614 617
PI3K 0.028 0.049 -10000 0 -0.4 13 13
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.021 -10000 0 -0.25 3 3
RAP1A -0.16 0.15 0.33 4 -0.51 23 27
PAFAH1B1 0.022 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.029 0.26 4 -0.57 2 6
CRLK/C3G 0.033 0.01 -10000 0 -10000 0 0
GRIN2B -0.018 0.14 0.26 1 -0.57 70 71
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.086 0.12 -10000 0 -0.35 76 76
neuron adhesion -0.14 0.15 0.34 6 -0.48 23 29
LRP8 0.046 0.068 0.26 103 -10000 0 103
GSK3B -0.14 0.14 -10000 0 -0.38 79 79
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.31 2 -0.32 594 596
MAP3K11 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.15 0.16 -10000 0 -0.29 559 559
CDK5 0.025 0.015 0.26 4 -10000 0 4
MAPT -0.021 0.2 0.88 21 -0.51 106 127
neuron migration -0.18 0.18 0.28 1 -0.35 448 449
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.087 0.12 -10000 0 -0.36 76 76
RELN/VLDLR -0.17 0.2 -10000 0 -0.33 612 612
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.022 0.26 9 -10000 0 9
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EGF/EGFR -0.16 0.22 -10000 0 -0.36 518 518
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.35 395 395
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.027 0.26 1 -0.57 2 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.082 0.23 0.26 2 -0.57 194 196
EGF/EGFR dimer/SHC -0.15 0.22 -10000 0 -0.4 421 421
mol:GDP -0.12 0.19 -10000 0 -0.35 395 395
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.017 0.15 0.26 1 -0.57 74 75
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.32 394 394
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.11 0.18 -10000 0 -0.33 394 394
FRAP1 -0.14 0.16 0.16 3 -0.33 395 398
EGF/EGFR dimer -0.21 0.25 -10000 0 -0.45 526 526
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
ETA receptor/Endothelin-1 0.002 0.12 -10000 0 -0.42 76 76
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.1 0.099 0.23 313 -0.26 2 315
STMN1 0.078 0.078 0.26 68 -10000 0 68
Aurora B/RasGAP/Survivin 0.19 0.14 0.33 504 -10000 0 504
Chromosomal passenger complex/Cul3 protein complex 0.006 0.14 0.2 91 -0.26 90 181
BIRC5 0.18 0.11 0.26 711 -10000 0 711
DES -0.16 0.32 -10000 0 -0.59 257 257
Aurora C/Aurora B/INCENP 0.11 0.078 0.32 9 -0.3 1 10
Aurora B/TACC1 0.072 0.098 -10000 0 -0.33 25 25
Aurora B/PP2A 0.11 0.082 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.031 0.026 0.14 8 -10000 0 8
mitotic metaphase/anaphase transition -0.006 0.005 -10000 0 -10000 0 0
NDC80 0.14 0.12 0.26 484 -10000 0 484
Cul3 protein complex -0.11 0.2 -10000 0 -0.36 415 415
KIF2C 0.15 0.1 0.24 587 -10000 0 587
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.25 790 -10000 0 790
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.082 -10000 0 -10000 0 0
SEPT1 0.03 0.042 0.26 35 -10000 0 35
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.021 0.26 9 -10000 0 9
NSUN2/NPM1/Nucleolin 0.074 0.19 0.32 26 -0.45 93 119
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.006 -10000 0 -10000 0 0
H3F3B 0.07 0.06 0.23 33 -10000 0 33
AURKB 0.14 0.12 0.25 560 -10000 0 560
AURKC 0.026 0.032 0.26 14 -0.57 1 15
CDCA8 0.11 0.11 0.26 355 -10000 0 355
cytokinesis 0.14 0.14 0.32 307 -0.35 4 311
Aurora B/Septin1 0.18 0.17 0.36 381 -0.33 3 384
AURKA 0.11 0.11 0.25 428 -10000 0 428
INCENP 0.03 0.008 -10000 0 -10000 0 0
KLHL13 -0.21 0.29 -10000 0 -0.57 424 424
BUB1 0.17 0.11 0.25 709 -10000 0 709
hSgo1/Aurora B/Survivin 0.27 0.18 0.41 630 -10000 0 630
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.14 0.35 331 -10000 0 331
SGOL1 0.16 0.11 0.26 656 -10000 0 656
CENPA 0.16 0.14 0.3 493 -0.28 1 494
NCAPG 0.13 0.12 0.26 505 -10000 0 505
Aurora B/HC8 Proteasome 0.11 0.082 0.2 9 -10000 0 9
NCAPD2 0.024 0.009 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.11 0.081 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.11 0.11 0.26 407 -10000 0 407
NPM1 0.067 0.12 0.26 4 -0.5 13 17
RASA1 0.024 0.004 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.081 0.2 4 -10000 0 4
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.2 0.15 0.37 391 -10000 0 391
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 0.073 0.12 0.27 21 -0.45 6 27
MYLK 0.02 0.14 0.23 8 -0.31 128 136
KIF23 0.098 0.11 0.26 319 -10000 0 319
VIM 0.078 0.084 0.37 32 -0.41 2 34
RACGAP1 0.04 0.046 0.27 41 -10000 0 41
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.062 0.14 -10000 0 -0.43 42 42
Chromosomal passenger complex 0.17 0.12 0.28 544 -10000 0 544
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 491 -10000 0 491
TACC1 0.006 0.089 -10000 0 -0.57 25 25
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.24 0.27 0.52 1 -0.71 142 143
PCK1 -0.92 0.63 -10000 0 -1.4 657 657
HNF4A -0.23 0.28 0.66 2 -0.8 74 76
KCNJ11 -0.28 0.29 -10000 0 -0.77 158 158
AKT1 -0.16 0.16 0.37 1 -0.42 76 77
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.44 0.47 -10000 0 -1.1 348 348
NKX2-1 -0.044 0.16 0.39 21 -0.37 48 69
ACADM -0.25 0.27 -10000 0 -0.76 106 106
TAT -1.1 0.63 0.44 1 -1.4 771 772
CEBPB 0.024 0.01 -10000 0 -10000 0 0
CEBPA 0.02 0.058 -10000 0 -0.57 10 10
TTR -0.4 0.29 0.57 1 -0.7 387 388
PKLR -0.22 0.27 0.57 6 -0.7 127 133
APOA1 -0.28 0.31 0.79 1 -0.88 86 87
CPT1C -0.24 0.27 0.58 1 -0.75 110 111
ALAS1 -0.15 0.16 -10000 0 -0.64 11 11
TFRC -0.42 0.26 -10000 0 -0.68 384 384
FOXF1 0.02 0.041 0.26 6 -0.57 4 10
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.032 0.27 8 -10000 0 8
CPT1A -0.23 0.27 0.53 2 -0.73 116 118
HMGCS1 -0.24 0.27 0.62 2 -0.72 124 126
NR3C1 -0.12 0.12 -10000 0 -0.3 164 164
CPT1B -0.24 0.27 0.52 1 -0.74 119 120
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.023 -10000 0 -10000 0 0
GCK -0.27 0.32 0.52 1 -0.84 159 160
CREB1 -0.076 0.093 -10000 0 -0.21 173 173
IGFBP1 -0.41 0.54 0.41 1 -1.4 243 244
PDX1 -0.12 0.15 -10000 0 -0.58 2 2
UCP2 -0.24 0.27 0.52 2 -0.7 143 145
ALDOB -0.28 0.28 0.68 1 -0.76 152 153
AFP -0.56 0.5 0.35 1 -0.89 626 627
BDH1 -0.24 0.26 0.52 1 -0.73 120 121
HADH -0.27 0.28 -10000 0 -0.76 145 145
F2 -0.28 0.3 0.79 1 -0.88 82 83
HNF1A 0.034 0.032 0.27 8 -10000 0 8
G6PC -0.18 0.12 -10000 0 -0.55 10 10
SLC2A2 -0.16 0.17 0.62 1 -0.78 2 3
INS 0.018 0.077 0.23 23 -10000 0 23
FOXA1 -0.22 0.23 0.27 18 -0.36 660 678
FOXA3 -0.36 0.21 0.34 2 -0.46 802 804
FOXA2 -0.32 0.32 0.77 1 -0.8 207 208
ABCC8 -0.32 0.38 0.56 1 -0.95 205 206
ALB -0.76 0.54 0.35 1 -1.1 709 710
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.063 0.048 0.1 9 -0.1 571 580
BUB1B 0.082 0.066 0.15 443 -10000 0 443
PLK1 0.049 0.038 0.094 282 -0.082 1 283
PLK1S1 0.025 0.034 0.13 10 -0.17 18 28
KIF2A 0.041 0.039 0.24 9 -10000 0 9
regulation of mitotic centrosome separation 0.048 0.038 0.093 282 -0.081 1 283
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.23 0.14 0.31 756 -10000 0 756
WEE1 0.043 0.06 0.23 2 -0.28 22 24
cytokinesis 0.12 0.086 0.21 256 -0.37 2 258
PP2A-alpha B56 0.11 0.12 -10000 0 -0.49 13 13
AURKA 0.063 0.052 0.12 436 -0.14 4 440
PICH/PLK1 0.096 0.087 0.21 310 -10000 0 310
CENPE 0.061 0.054 0.16 87 -10000 0 87
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.041 0.038 0.24 9 -10000 0 9
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.078 0.054 0.12 564 -0.14 2 566
PAK1 0.022 0.019 0.25 6 -10000 0 6
SPC24 0.17 0.11 0.26 664 -10000 0 664
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.071 0.069 0.14 353 -0.19 22 375
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 55 -10000 0 55
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.022 0.019 0.053 151 -10000 0 151
G2 phase of mitotic cell cycle 0.001 0.003 0.015 13 -10000 0 13
STAG2 0.024 0.018 -10000 0 -0.57 1 1
GRASP65/GM130/RAB1/GTP 0.011 0.08 -10000 0 -0.5 25 25
spindle elongation 0.048 0.038 0.093 282 -0.081 1 283
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.1 0.13 -10000 0 -0.51 19 19
TPT1 0.013 0.056 0.12 2 -0.17 78 80
CDC25C 0.11 0.067 0.16 481 -0.21 12 493
CDC25B 0.029 0.031 0.26 18 -10000 0 18
SGOL1 0.063 0.048 0.1 571 -0.1 9 580
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.068 0.064 0.31 11 -10000 0 11
CDC14B -0.01 0.075 -10000 0 -0.42 34 34
CDC20 0.14 0.12 0.26 565 -10000 0 565
PLK1/PBIP1 0.036 0.045 0.14 138 -10000 0 138
mitosis -0.004 0.005 0.027 4 -10000 0 4
FBXO5 0.03 0.035 0.15 17 -0.12 1 18
CDC2 0.003 0.004 0.011 201 -10000 0 201
NDC80 0.16 0.12 0.26 619 -10000 0 619
metaphase plate congression 0.028 0.054 0.15 1 -0.2 40 41
ERCC6L 0.087 0.083 0.24 168 -10000 0 168
NLP/gamma Tubulin 0.023 0.024 0.074 34 -0.083 12 46
microtubule cytoskeleton organization 0.013 0.056 0.12 2 -0.17 78 80
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 15 -10000 0 15
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 15 -10000 0 15
PLK1/PRC1-2 0.2 0.12 0.27 758 -10000 0 758
GRASP65/GM130/RAB1/GTP/PLK1 0.069 0.03 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.041 0.035 0.097 163 -10000 0 163
mitotic prometaphase 0.002 0.005 0.022 51 -10000 0 51
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.051 0.2 2 -0.28 4 6
microtubule-based process 0.17 0.089 0.22 783 -10000 0 783
Golgi organization 0.048 0.038 0.093 282 -0.081 1 283
Cohesin/SA2 0.053 0.031 0.16 3 -0.3 1 4
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.26 790 -10000 0 790
APC/C/CDC20 0.14 0.099 0.23 566 -10000 0 566
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.03 0.046 0.14 138 -10000 0 138
PRC1 0.079 0.099 0.26 257 -10000 0 257
ECT2 0.049 0.057 0.26 47 -10000 0 47
C13orf34 0.04 0.033 0.091 163 -10000 0 163
NUDC 0.028 0.054 0.15 1 -0.2 40 41
regulation of attachment of spindle microtubules to kinetochore 0.082 0.066 0.15 443 -10000 0 443
spindle assembly 0.035 0.029 0.084 137 -10000 0 137
spindle stabilization 0.025 0.034 0.13 10 -0.17 18 28
APC/C/HCDH1 0.009 0.067 -10000 0 -0.36 34 34
MKLP2/PLK1 0.17 0.089 0.22 783 -10000 0 783
CCNB1 0.069 0.091 0.26 205 -10000 0 205
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.026 0.086 0.23 1 -0.38 39 40
TUBG1 0.023 0.038 0.13 3 -0.16 33 36
G2/M transition of mitotic cell cycle 0.041 0.043 0.19 12 -10000 0 12
MLF1IP 0.023 0.045 0.14 147 -10000 0 147
INCENP 0.024 0.005 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.16 0.39 -10000 0 -0.86 241 241
NCK1/PAK1/Dok-R -0.096 0.17 -10000 0 -0.41 241 241
NCK1/Dok-R -0.19 0.46 -10000 0 -1 240 240
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.044 0.099 0.24 212 -10000 0 212
RELA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.048 0.11 0.27 213 -10000 0 213
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.17 0.44 -10000 0 -0.97 240 240
FN1 0.11 0.11 0.26 421 -10000 0 421
PLD2 -0.22 0.47 -10000 0 -1.1 240 240
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.011 0.18 0.26 142 -0.57 80 222
ELK1 -0.19 0.42 -10000 0 -0.96 241 241
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 0.023 0.019 0.26 6 -10000 0 6
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.49 -10000 0 -1 240 240
CDKN1A -0.11 0.26 -10000 0 -0.62 172 172
ITGA5 0.024 0.007 0.26 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.19 0.46 -10000 0 -1 240 240
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.11 0.29 -10000 0 -0.64 241 241
PLG -0.22 0.47 -10000 0 -1.1 240 240
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.16 0.36 -10000 0 -0.82 241 241
GRB2 0.023 0.009 0.26 1 -10000 0 1
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
ANGPT2 -0.15 0.28 -10000 0 -0.73 139 139
BMX -0.32 0.51 -10000 0 -1.2 242 242
ANGPT1 -0.23 0.5 -10000 0 -1.2 212 212
tube development -0.13 0.29 -10000 0 -0.68 197 197
ANGPT4 -0.15 0.26 -10000 0 -0.57 305 305
response to hypoxia -0.014 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.22 0.51 -10000 0 -1.1 240 240
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
STAT5A (dimer) -0.15 0.34 -10000 0 -0.79 192 192
mol:L-citrulline -0.11 0.29 -10000 0 -0.64 241 241
AGTR1 -0.097 0.26 0.26 59 -0.57 244 303
MAPK14 -0.21 0.47 -10000 0 -1.1 242 242
Tie2/SHP2 -0.1 0.32 -10000 0 -1.1 90 90
TEK -0.11 0.35 -10000 0 -1.2 90 90
RPS6KB1 -0.14 0.38 -10000 0 -0.82 240 240
Angiotensin II/AT1 -0.071 0.19 0.18 59 -0.41 247 306
Tie2/Ang1/GRB2 -0.21 0.49 -10000 0 -1.1 240 240
MAPK3 -0.19 0.43 -10000 0 -0.98 240 240
MAPK1 -0.2 0.43 -10000 0 -0.99 240 240
Tie2/Ang1/GRB7 -0.22 0.49 -10000 0 -1.1 240 240
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.22 0.48 -10000 0 -1.1 240 240
PI3K -0.19 0.44 -10000 0 -0.99 241 241
FES -0.21 0.47 -10000 0 -1.1 243 243
Crk/Dok-R -0.19 0.46 -10000 0 -1 240 240
Tie2/Ang1/ABIN2 -0.21 0.5 -10000 0 -1.1 240 240
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.14 0.34 -10000 0 -0.77 241 241
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.38 0.47 1 -0.8 238 239
Tie2/Ang2 -0.18 0.4 -10000 0 -0.95 193 193
Tie2/Ang1 -0.23 0.52 -10000 0 -1.2 240 240
FOXO1 -0.14 0.35 -10000 0 -0.78 241 241
ELF1 0.011 0.037 -10000 0 -10000 0 0
ELF2 -0.21 0.47 -10000 0 -1.1 240 240
mol:Choline -0.2 0.45 -10000 0 -1 240 240
cell migration -0.04 0.1 -10000 0 -0.23 241 241
FYN -0.15 0.33 -10000 0 -0.79 193 193
DOK2 0.02 0.03 0.26 4 -0.57 2 6
negative regulation of cell cycle -0.1 0.24 -10000 0 -0.56 172 172
ETS1 -0.023 0.11 -10000 0 -0.27 172 172
PXN -0.1 0.32 0.45 1 -0.67 239 240
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.13 0.33 -10000 0 -0.73 241 241
RAC1 0.024 0.003 -10000 0 -10000 0 0
TNF -0.026 0.13 0.26 20 -0.27 205 225
MAPKKK cascade -0.2 0.45 -10000 0 -1 240 240
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.21 0.48 -10000 0 -1.1 238 238
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.099 0.26 -10000 0 -0.57 241 241
mol:Phosphatidic acid -0.2 0.45 -10000 0 -1 240 240
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.11 0.29 -10000 0 -0.64 241 241
Rac1/GTP -0.14 0.35 -10000 0 -0.77 241 241
MMP2 -0.22 0.48 -10000 0 -1.1 241 241
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.099 0.13 0.3 282 -0.22 2 284
NFATC2 -0.025 0.23 0.52 5 -0.61 91 96
NFATC3 -0.04 0.12 -10000 0 -0.28 169 169
CD40LG -0.29 0.5 0.65 6 -0.98 314 320
ITCH -0.002 0.082 -10000 0 -0.26 96 96
CBLB -0.002 0.083 -10000 0 -0.27 3 3
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.093 0.39 0.59 53 -0.98 94 147
JUNB 0.025 0.01 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.1 -10000 0 -0.3 105 105
T cell anergy -0.026 0.14 0.33 1 -0.42 102 103
TLE4 -0.026 0.19 -10000 0 -0.66 54 54
Jun/NFAT1-c-4/p21SNFT -0.17 0.43 0.67 6 -0.85 254 260
AP-1/NFAT1-c-4 -0.31 0.61 0.74 15 -1.1 306 321
IKZF1 -0.017 0.16 0.47 7 -0.5 56 63
T-helper 2 cell differentiation -0.084 0.28 0.48 1 -0.83 86 87
AP-1/NFAT1 -0.098 0.26 0.45 12 -0.49 247 259
CALM1 0.011 0.063 -10000 0 -10000 0 0
EGR2 -0.25 0.55 0.69 2 -1.4 165 167
EGR3 -0.33 0.62 0.67 2 -1.3 292 294
NFAT1/FOXP3 0.05 0.22 0.46 105 -0.48 65 170
EGR1 -0.16 0.27 -10000 0 -0.56 336 336
JUN 0.015 0.054 0.2 1 -0.57 6 7
EGR4 0.04 0.06 0.26 75 -10000 0 75
mol:Ca2+ -0.01 0.054 -10000 0 -0.18 96 96
GBP3 -0.021 0.17 0.38 3 -0.54 62 65
FOSL1 0.027 0.048 0.26 26 -0.57 3 29
NFAT1-c-4/MAF/IRF4 -0.19 0.45 0.59 7 -0.87 278 285
DGKA -0.017 0.16 0.56 1 -0.54 39 40
CREM 0.023 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.26 0.48 0.6 3 -0.95 294 297
CTLA4 0.038 0.21 0.43 124 -0.51 45 169
NFAT1-c-4 (dimer)/EGR1 -0.28 0.51 0.61 4 -1 312 316
NFAT1-c-4 (dimer)/EGR4 -0.18 0.45 0.59 6 -0.86 278 284
FOS -0.15 0.27 -10000 0 -0.57 310 310
IFNG -0.054 0.27 0.5 11 -0.73 88 99
T cell activation -0.15 0.29 0.62 4 -0.68 170 174
MAF 0.021 0.008 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.33 0.66 265 -0.61 2 267
TNF -0.25 0.44 0.54 4 -0.9 305 309
FASLG -0.32 0.63 0.74 3 -1.2 310 313
TBX21 0.021 0.12 0.35 15 -0.57 36 51
BATF3 0.021 0.015 0.26 3 -10000 0 3
PRKCQ 0.006 0.11 0.28 8 -0.57 39 47
PTPN1 -0.017 0.16 0.47 1 -0.54 40 41
NFAT1-c-4/ICER1 -0.19 0.44 0.55 3 -0.85 278 281
GATA3 0.01 0.11 0.26 28 -0.57 35 63
T-helper 1 cell differentiation -0.052 0.27 0.49 13 -0.72 88 101
IL2RA -0.094 0.37 0.59 47 -0.84 121 168
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.16 -10000 0 -0.52 47 47
E2F1 0.096 0.11 0.26 320 -10000 0 320
PPARG -0.11 0.25 -10000 0 -0.57 252 252
SLC3A2 -0.018 0.16 -10000 0 -0.54 41 41
IRF4 -0.019 0.16 0.26 13 -0.57 83 96
PTGS2 -0.34 0.54 0.63 4 -1 343 347
CSF2 -0.28 0.48 0.66 8 -0.96 307 315
JunB/Fra1/NFAT1-c-4 -0.17 0.43 0.6 4 -0.82 275 279
IL4 -0.089 0.29 0.48 1 -0.88 85 86
IL5 -0.28 0.48 0.6 6 -0.96 305 311
IL2 -0.15 0.3 0.62 4 -0.69 164 168
IL3 -0.05 0.13 -10000 0 -0.82 18 18
RNF128 -0.041 0.2 -10000 0 -0.65 105 105
NFATC1 -0.15 0.34 0.61 2 -0.67 265 267
CDK4 0.12 0.24 0.63 80 -0.57 2 82
PTPRK -0.02 0.17 0.45 2 -0.55 59 61
IL8 -0.28 0.49 0.58 9 -0.97 306 315
POU2F1 0.021 0.012 0.26 1 -10000 0 1
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.002 0.11 -10000 0 -0.36 95 95
cell-cell adhesion 0.13 0.15 0.3 403 -10000 0 403
Ephrin B/EPHB2/RasGAP 0.031 0.11 -10000 0 -0.31 82 82
ITSN1 0.023 0.026 -10000 0 -0.57 2 2
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.12 0.19 -10000 0 -0.36 410 410
HRAS/GDP -0.11 0.18 -10000 0 -0.41 181 181
Ephrin B/EPHB1/GRB7 -0.1 0.2 -10000 0 -0.35 398 398
Endophilin/SYNJ1 -0.027 0.083 0.22 2 -0.29 80 82
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.21 -10000 0 -0.36 411 411
endothelial cell migration 0.04 0.042 -10000 0 -0.32 11 11
GRB2 0.023 0.009 0.26 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PAK1 -0.031 0.099 0.27 5 -0.33 83 88
HRAS 0.026 0.022 0.26 9 -10000 0 9
RRAS -0.027 0.084 0.23 2 -0.3 80 82
DNM1 0.02 0.048 0.26 1 -0.57 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.14 0.18 0.35 2 -0.34 429 431
lamellipodium assembly -0.13 0.15 -10000 0 -0.3 403 403
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.089 0.16 -10000 0 -0.32 311 311
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
EPHB2 0.027 0.031 0.26 19 -10000 0 19
EPHB3 0.025 0.02 0.26 8 -10000 0 8
EPHB1 -0.2 0.29 0.26 1 -0.57 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.11 0.17 -10000 0 -0.42 174 174
Ephrin B/EPHB2 0.021 0.1 -10000 0 -0.31 82 82
Ephrin B/EPHB3 0.02 0.097 -10000 0 -0.31 77 77
JNK cascade -0.12 0.15 0.36 9 -0.31 408 417
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.35 430 430
RAP1/GDP -0.093 0.16 -10000 0 -0.38 154 154
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.023 0.16 -10000 0 -0.57 82 82
EFNB1 0.024 0.001 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.098 0.18 -10000 0 -0.32 411 411
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.19 -10000 0 -0.33 409 409
Rap1/GTP -0.11 0.17 -10000 0 -0.32 325 325
axon guidance -0.003 0.11 -10000 0 -0.36 95 95
MAPK3 -0.084 0.14 -10000 0 -0.39 101 101
MAPK1 -0.089 0.14 -10000 0 -0.39 106 106
Rac1/GDP -0.1 0.16 -10000 0 -0.39 172 172
actin cytoskeleton reorganization -0.11 0.12 -10000 0 -0.34 135 135
CDC42/GDP -0.1 0.16 -10000 0 -0.39 172 172
PI3K 0.045 0.044 -10000 0 -0.32 11 11
EFNA5 -0.028 0.17 0.26 1 -0.57 95 96
Ephrin B2/EPHB4 0.03 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.089 -10000 0 -0.27 85 85
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.16 -10000 0 -0.31 332 332
PTK2 0.14 0.26 0.67 205 -10000 0 205
MAP4K4 -0.12 0.15 0.36 9 -0.31 408 417
SRC 0.023 0.005 -10000 0 -10000 0 0
KALRN 0.014 0.078 -10000 0 -0.57 19 19
Intersectin/N-WASP 0.034 0.021 -10000 0 -0.42 2 2
neuron projection morphogenesis -0.1 0.14 0.29 9 -0.41 88 97
MAP2K1 -0.086 0.15 -10000 0 -0.4 113 113
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.088 0.19 -10000 0 -0.33 409 409
cell migration -0.1 0.18 0.31 5 -0.45 124 129
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.084 0.23 2 -0.3 80 82
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.32 568 570
HRAS/GTP -0.099 0.19 -10000 0 -0.32 404 404
Ephrin B1/EPHB1-2 -0.096 0.18 -10000 0 -0.33 410 410
cell adhesion mediated by integrin 0.011 0.086 0.28 79 -0.21 20 99
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.33 425 425
RAC1-CDC42/GTP -0.13 0.15 -10000 0 -0.31 383 383
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.095 0.16 -10000 0 -0.38 165 165
ruffle organization -0.12 0.16 0.36 5 -0.49 71 76
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.086 0.22 2 -0.3 81 83
Ephrin B/EPHB2/KALRN 0.026 0.12 -10000 0 -0.34 92 92
ROCK1 0.017 0.031 0.19 30 -0.33 1 31
RAS family/GDP -0.1 0.12 -10000 0 -0.34 131 131
Rac1/GTP -0.12 0.17 -10000 0 -0.32 403 403
Ephrin B/EPHB1/Src/Paxillin -0.12 0.18 -10000 0 -0.32 416 416
Glucocorticoid receptor regulatory network

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
PCK2 0.09 0.1 0.42 5 -10000 0 5
SMARCC2 0.024 0.013 -10000 0 -0.19 1 1
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.12 0.21 0.39 6 -0.58 98 104
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.032 0.26 19 -10000 0 19
FKBP4 0.025 0.017 0.26 5 -10000 0 5
FKBP5 0.015 0.078 0.26 5 -0.57 18 23
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.32 106 -0.35 7 113
PRL -0.062 0.12 0.52 3 -0.47 2 5
cortisol/GR alpha (dimer)/TIF2 0.18 0.28 0.52 328 -0.48 17 345
RELA -0.037 0.1 0.28 1 -0.26 34 35
FGG 0.21 0.24 0.48 347 -0.49 3 350
GR beta/TIF2 0.078 0.16 0.32 120 -0.4 41 161
IFNG -0.3 0.36 0.45 3 -0.69 403 406
apoptosis -0.26 0.3 0.85 1 -0.66 283 284
CREB1 0.06 0.053 -10000 0 -10000 0 0
histone acetylation 0.025 0.13 0.36 56 -0.38 21 77
BGLAP -0.08 0.14 0.41 1 -0.5 19 20
GR/PKAc 0.13 0.13 0.36 81 -0.33 3 84
NF kappa B1 p50/RelA -0.062 0.18 0.42 4 -0.34 180 184
SMARCD1 0.024 0.012 -10000 0 -0.15 2 2
MDM2 0.098 0.11 0.22 369 -10000 0 369
GATA3 0.014 0.11 0.25 30 -0.56 35 65
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.024 0.1 0.47 1 -0.54 5 6
GSK3B 0.001 0.023 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.79 1 -0.64 119 120
CSN2 0.16 0.19 0.38 315 -0.46 3 318
BRG1/BAF155/BAF170/BAF60A 0.06 0.041 -10000 0 -0.44 6 6
NFATC1 0.023 0.026 -10000 0 -0.57 2 2
POU2F1 0.023 0.015 0.26 1 -10000 0 1
CDKN1A 0.016 0.086 -10000 0 -1.3 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.007 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.34 72 -0.32 6 78
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.39 0.62 2 -0.83 378 380
JUN -0.25 0.29 0.44 6 -0.55 413 419
IL4 -0.11 0.15 -10000 0 -0.51 25 25
CDK5R1 0.022 0.036 0.25 23 -10000 0 23
PRKACA 0.024 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.48 488 488
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.13 0.32 95 -0.32 7 102
cortisol/GR alpha (monomer) 0.28 0.32 0.6 434 -0.53 4 438
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.6 313 313
AP-1/NFAT1-c-4 -0.42 0.45 0.48 6 -0.81 542 548
AFP -0.53 0.64 0.5 1 -1.4 355 356
SUV420H1 0.023 0.007 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.42 133 -10000 0 133
TP53 0.031 0.027 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.64 0.68 0.45 2 -1.3 485 487
KRT14 -0.69 0.66 -10000 0 -1.3 557 557
TBP 0.028 0.013 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.29 473 -10000 0 473
HDAC1 0.022 0.011 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.43 0.45 0.48 6 -0.82 543 549
MAPK14 0.004 0.022 -10000 0 -10000 0 0
MAPK10 -0.083 0.2 -10000 0 -0.57 158 158
MAPK11 -0.001 0.038 -10000 0 -0.58 3 3
KRT5 -0.72 0.7 -10000 0 -1.4 559 559
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.019 -10000 0 -0.56 1 1
STAT1 0.033 0.032 0.26 19 -10000 0 19
CGA -0.053 0.17 0.45 1 -0.51 12 13
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.36 394 -10000 0 394
MAPK3 0.001 0.022 -10000 0 -10000 0 0
MAPK1 0.003 0.022 -10000 0 -10000 0 0
ICAM1 -0.18 0.24 0.6 3 -0.57 198 201
NFKB1 -0.038 0.1 0.24 3 -0.22 90 93
MAPK8 -0.19 0.22 0.41 4 -0.42 399 403
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.27 0.32 0.86 1 -0.7 284 285
BAX 0.017 0.064 -10000 0 -10000 0 0
POMC -0.16 0.3 -10000 0 -0.9 84 84
EP300 0.14 0.14 0.29 486 -10000 0 486
cortisol/GR alpha (dimer)/p53 0.21 0.26 0.53 351 -0.54 2 353
proteasomal ubiquitin-dependent protein catabolic process 0.077 0.11 0.26 172 -10000 0 172
SGK1 0.19 0.2 0.5 14 -1.1 6 20
IL13 -0.25 0.28 0.51 5 -0.62 230 235
IL6 -0.43 0.52 0.6 1 -1.1 401 402
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.55 2 -0.69 53 55
IL2 -0.33 0.35 0.46 2 -0.7 422 424
CDK5 0.018 0.019 0.25 4 -10000 0 4
PRKACB 0.032 0.06 0.26 47 -0.57 4 51
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.52 4 -0.65 184 188
CDK5R1/CDK5 0.019 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.018 0.15 0.38 3 -0.39 37 40
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 400 -0.5 2 402
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.16 0.36 243 -0.63 1 244
NF kappa B1 p50/RelA/Cbp 0.061 0.19 0.4 77 -0.41 18 95
JUN (dimer) -0.25 0.29 0.44 6 -0.55 412 418
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.2 -10000 0 -0.64 88 88
NR3C1 0.17 0.2 0.42 301 -0.48 3 304
NR4A1 -0.03 0.18 -10000 0 -0.55 112 112
TIF2/SUV420H1 0.008 0.094 -10000 0 -0.42 48 48
MAPKKK cascade -0.26 0.3 0.85 1 -0.66 283 284
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.53 416 -0.5 3 419
PBX1 0.023 0.015 0.26 1 -10000 0 1
POU1F1 0.021 0.015 0.26 2 -10000 0 2
SELE -0.19 0.31 0.55 3 -0.7 192 195
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.36 243 -0.64 1 244
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 400 -0.5 2 402
mol:cortisol 0.16 0.19 0.35 446 -0.28 3 449
MMP1 0.03 0.31 0.41 4 -0.91 86 90
Endothelins

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
AKT1 -0.073 0.14 -10000 0 -0.43 96 96
PTK2B 0.02 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.2 -10000 0 -0.79 50 50
EDN1 -0.073 0.16 -10000 0 -0.53 98 98
EDN3 -0.22 0.29 0.26 3 -0.57 442 445
EDN2 0.073 0.11 0.26 245 -0.57 5 250
HRAS/GDP -0.093 0.2 -10000 0 -0.48 154 154
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.14 -10000 0 -0.4 108 108
ADCY4 -0.13 0.2 0.28 2 -0.42 279 281
ADCY5 -0.21 0.24 -10000 0 -0.45 466 466
ADCY6 -0.12 0.19 0.28 2 -0.4 270 272
ADCY7 -0.12 0.18 0.28 2 -0.4 269 271
ADCY1 -0.12 0.2 0.26 1 -0.41 270 271
ADCY2 -0.14 0.22 0.29 6 -0.45 289 295
ADCY3 -0.12 0.18 0.26 1 -0.4 269 270
ADCY8 -0.1 0.17 0.27 2 -0.4 207 209
ADCY9 -0.11 0.18 0.26 1 -0.4 256 257
arachidonic acid secretion -0.16 0.28 0.31 2 -0.51 347 349
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.35 167 167
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.025 0.022 0.25 9 -10000 0 9
ETA receptor/Endothelin-1/G12/GTP -0.059 0.14 -10000 0 -0.4 96 96
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.42 271 271
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.064 0.16 0.37 10 -0.44 97 107
EDNRB -0.029 0.17 -10000 0 -0.56 100 100
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.078 0.16 -10000 0 -0.5 106 106
CYSLTR1 -0.081 0.16 -10000 0 -0.49 102 102
SLC9A1 -0.045 0.093 -10000 0 -0.29 93 93
mol:GDP -0.1 0.21 0.33 2 -0.5 165 167
SLC9A3 -0.11 0.28 -10000 0 -0.64 190 190
RAF1 -0.14 0.24 0.33 1 -0.47 282 283
JUN -0.05 0.18 -10000 0 -0.75 46 46
JAK2 -0.072 0.14 -10000 0 -0.43 101 101
mol:IP3 -0.075 0.17 -10000 0 -0.44 128 128
ETA receptor/Endothelin-1 -0.083 0.16 -10000 0 -0.49 106 106
PLCB1 -0.019 0.15 -10000 0 -0.57 74 74
PLCB2 0.014 0.026 0.26 1 -0.57 1 2
ETA receptor/Endothelin-3 -0.19 0.21 0.24 1 -0.43 448 449
FOS -0.29 0.44 -10000 0 -0.94 332 332
Gai/GDP -0.1 0.29 -10000 0 -0.75 164 164
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.21 0.27 2 -0.53 149 151
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.42 139 139
GNAQ 0.013 0.036 -10000 0 -0.57 3 3
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNAL -0.11 0.24 -10000 0 -0.57 235 235
Gs family/GDP -0.15 0.24 -10000 0 -0.5 263 263
ETA receptor/Endothelin-1/Gq/GTP -0.047 0.12 -10000 0 -0.39 73 73
MAPK14 -0.066 0.16 -10000 0 -0.41 142 142
TRPC6 -0.057 0.21 -10000 0 -0.88 47 47
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.17 -10000 0 -0.39 171 171
ETB receptor/Endothelin-2 0.022 0.15 0.24 17 -0.38 110 127
ETB receptor/Endothelin-3 -0.19 0.24 0.24 1 -0.44 499 500
ETB receptor/Endothelin-1 -0.078 0.18 -10000 0 -0.46 170 170
MAPK3 -0.25 0.38 -10000 0 -0.8 337 337
MAPK1 -0.26 0.4 -10000 0 -0.81 340 340
Rac1/GDP -0.094 0.19 -10000 0 -0.48 148 148
cAMP biosynthetic process -0.16 0.22 0.55 1 -0.48 253 254
MAPK8 -0.058 0.21 -10000 0 -0.74 66 66
SRC 0.023 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.068 0.17 -10000 0 -0.37 202 202
p130Cas/CRK/Src/PYK2 -0.097 0.22 0.49 1 -0.58 122 123
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.093 0.19 -10000 0 -0.48 147 147
COL1A2 -0.089 0.2 0.37 9 -0.48 154 163
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.021 0.097 0.26 10 -0.38 11 21
mol:DAG -0.075 0.17 -10000 0 -0.44 128 128
MAP2K2 -0.19 0.3 0.34 2 -0.6 341 343
MAP2K1 -0.19 0.3 0.32 2 -0.59 341 343
EDNRA -0.035 0.07 0.28 1 -0.3 25 26
positive regulation of muscle contraction -0.063 0.12 -10000 0 -0.38 94 94
Gq family/GDP -0.059 0.19 -10000 0 -0.49 104 104
HRAS/GTP -0.1 0.2 0.34 1 -0.47 170 171
PRKCH -0.077 0.16 -10000 0 -0.44 126 126
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.073 0.18 0.28 3 -0.46 133 136
PRKCB -0.074 0.18 0.24 1 -0.44 135 136
PRKCE -0.08 0.16 -10000 0 -0.44 128 128
PRKCD -0.076 0.16 -10000 0 -0.44 124 124
PRKCG -0.078 0.17 0.27 1 -0.44 127 128
regulation of vascular smooth muscle contraction -0.34 0.51 -10000 0 -1.1 330 330
PRKCQ -0.084 0.18 -10000 0 -0.47 144 144
PLA2G4A -0.18 0.31 0.33 1 -0.56 347 348
GNA14 0.014 0.067 0.25 19 -0.57 10 29
GNA15 0.022 0.027 0.25 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.037 -10000 0 -0.57 4 4
Rac1/GTP -0.059 0.14 -10000 0 -0.4 96 96
MMP1 0.17 0.13 0.38 85 -10000 0 85
HIF-1-alpha transcription factor network

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
PKM2 -0.26 0.36 -10000 0 -0.79 221 221
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.34 0.66 3 -0.78 133 136
SMAD4 0.024 0.006 -10000 0 -10000 0 0
ID2 -0.24 0.37 -10000 0 -0.84 177 177
AP1 -0.1 0.21 -10000 0 -0.42 307 307
ABCG2 -0.26 0.39 -10000 0 -0.86 196 196
HIF1A -0.048 0.084 -10000 0 -0.28 7 7
TFF3 -0.25 0.41 0.66 5 -0.85 211 216
GATA2 0.009 0.095 0.25 13 -0.57 26 39
AKT1 -0.055 0.094 -10000 0 -0.28 12 12
response to hypoxia -0.062 0.084 0.21 1 -0.22 100 101
MCL1 -0.24 0.35 -10000 0 -0.82 179 179
NDRG1 -0.22 0.36 -10000 0 -0.82 172 172
SERPINE1 -0.24 0.38 0.65 4 -0.79 215 219
FECH -0.24 0.37 -10000 0 -0.84 171 171
FURIN -0.24 0.37 -10000 0 -0.81 194 194
NCOA2 -0.002 0.12 -10000 0 -0.56 48 48
EP300 -0.06 0.13 0.34 2 -0.34 107 109
HMOX1 -0.24 0.37 0.65 1 -0.84 177 178
BHLHE40 -0.24 0.37 -10000 0 -0.83 181 181
BHLHE41 -0.25 0.38 -10000 0 -0.82 211 211
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.019 0.11 -10000 0 -10000 0 0
ENG -0.016 0.11 0.38 3 -10000 0 3
JUN 0.018 0.046 -10000 0 -0.57 6 6
RORA -0.25 0.37 -10000 0 -0.85 172 172
ABCB1 -0.26 0.45 -10000 0 -1.1 220 220
TFRC -0.24 0.37 -10000 0 -0.82 188 188
CXCR4 -0.24 0.37 0.65 1 -0.84 179 180
TF -0.4 0.45 -10000 0 -0.88 397 397
CITED2 -0.25 0.37 -10000 0 -0.82 189 189
HIF1A/ARNT -0.27 0.42 0.75 2 -0.95 169 171
LDHA -0.037 0.12 -10000 0 -0.73 23 23
ETS1 -0.25 0.37 -10000 0 -0.84 178 178
PGK1 -0.24 0.37 -10000 0 -0.84 181 181
NOS2 -0.24 0.37 -10000 0 -0.84 172 172
ITGB2 -0.24 0.37 0.65 1 -0.85 171 172
ALDOA -0.24 0.37 -10000 0 -0.82 184 184
Cbp/p300/CITED2 -0.25 0.39 -10000 0 -0.9 171 171
FOS -0.15 0.27 -10000 0 -0.57 306 306
HK2 -0.24 0.37 -10000 0 -0.85 172 172
SP1 0.002 0.057 -10000 0 -0.18 10 10
GCK -0.12 0.33 0.57 1 -1.3 60 61
HK1 -0.24 0.37 -10000 0 -0.84 175 175
NPM1 -0.24 0.37 -10000 0 -0.83 181 181
EGLN1 -0.24 0.36 -10000 0 -0.79 201 201
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.25 0.37 -10000 0 -0.84 173 173
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.36 -10000 0 -1 132 132
IGFBP1 -0.31 0.42 -10000 0 -0.87 275 275
VEGFA -0.16 0.29 0.56 1 -0.69 116 117
HIF1A/JAB1 -0.009 0.067 -10000 0 -0.27 1 1
CP -0.3 0.45 0.64 2 -0.92 273 275
CXCL12 -0.26 0.4 -10000 0 -0.88 194 194
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.012 -10000 0 -10000 0 0
BNIP3 -0.24 0.37 0.72 1 -0.82 191 192
EGLN3 -0.24 0.38 0.68 2 -0.79 218 220
CA9 -0.21 0.39 0.66 5 -0.85 161 166
TERT -0.23 0.37 0.66 4 -0.85 163 167
ENO1 -0.25 0.37 -10000 0 -0.84 176 176
PFKL -0.24 0.37 -10000 0 -0.84 179 179
NCOA1 0.024 0.019 -10000 0 -0.57 1 1
ADM -0.26 0.4 -10000 0 -0.86 217 217
ARNT -0.035 0.07 -10000 0 -10000 0 0
HNF4A 0.019 0.041 0.26 19 -10000 0 19
ADFP -0.26 0.36 -10000 0 -0.79 221 221
SLC2A1 -0.16 0.29 0.62 3 -0.68 118 121
LEP -0.48 0.41 -10000 0 -0.86 428 428
HIF1A/ARNT/Cbp/p300 -0.2 0.34 0.66 1 -0.79 145 146
EPO -0.11 0.26 0.64 4 -0.73 54 58
CREBBP -0.05 0.12 0.34 2 -0.35 72 74
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 0.72 1 -0.78 130 131
PFKFB3 -0.24 0.37 -10000 0 -0.81 206 206
NT5E -0.25 0.37 -10000 0 -0.85 177 177
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.034 0.016 -10000 0 -0.42 1 1
Necdin/E2F1 0.061 0.11 -10000 0 -0.39 33 33
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.045 0.17 -10000 0 -0.32 289 289
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.24 0.34 1 -0.4 365 366
NT-4/5 (dimer)/p75(NTR) -0.22 0.29 -10000 0 -0.5 494 494
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.081 0.16 0.36 1 -0.32 274 275
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.012 0.16 0.26 24 -0.57 75 99
MGDIs/NGR/p75(NTR)/LINGO1 -0.037 0.2 0.34 7 -0.34 280 287
FURIN 0.024 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.087 0.2 -10000 0 -0.39 317 317
LINGO1 0.077 0.097 0.26 247 -10000 0 247
Sortilin/TRAF6/NRIF 0.024 0.024 -10000 0 -0.55 1 1
proBDNF (dimer) -0.012 0.16 0.26 24 -0.56 75 99
NTRK1 0.024 0.051 0.26 25 -0.57 4 29
RTN4R 0.032 0.044 0.26 40 -10000 0 40
neuron apoptosis -0.077 0.19 0.34 6 -0.52 67 73
IRAK1 0.025 0.014 0.26 4 -10000 0 4
SHC1 -0.079 0.15 -10000 0 -0.37 221 221
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.053 0.18 -10000 0 -0.34 285 285
MAGEH1 0.024 0.018 -10000 0 -0.57 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.063 0.19 -10000 0 -0.36 293 293
Mammalian IAPs/DIABLO 0.057 0.032 -10000 0 -0.33 2 2
proNGF (dimer) 0.017 0.074 0.26 8 -0.56 16 24
MAGED1 0.025 0.01 0.26 2 -10000 0 2
APP 0.024 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.56 363 363
ZNF274 0.024 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.063 0.15 -10000 0 -0.32 276 276
NGF 0.017 0.074 0.26 8 -0.57 16 24
cell cycle arrest -0.072 0.15 0.23 47 -0.29 285 332
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.052 0.12 -10000 0 -0.27 208 208
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.18 0.26 -10000 0 -0.45 464 464
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.067 0.19 -10000 0 -0.36 287 287
PSENEN 0.024 0.011 0.26 2 -10000 0 2
mol:ceramide -0.076 0.16 -10000 0 -0.33 284 284
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.043 0.11 -10000 0 -0.36 30 30
p75(NTR)/beta APP -0.089 0.2 -10000 0 -0.41 286 286
BEX1 -0.016 0.23 0.26 172 -0.57 139 311
mol:GDP -0.1 0.16 -10000 0 -0.36 289 289
NGF (dimer) 0.002 0.14 0.34 1 -0.34 133 134
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.021 0.18 0.34 6 -0.32 266 272
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RAC1/GTP -0.058 0.16 -10000 0 -0.31 285 285
MYD88 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.067 0.19 -10000 0 -0.37 287 287
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.077 0.073 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.56 157 169
TP53 -0.089 0.16 0.35 3 -0.33 303 306
PRDM4 -0.075 0.16 -10000 0 -0.34 285 285
BDNF (dimer) 0.023 0.2 0.33 21 -0.35 192 213
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.018 -10000 0 -0.57 1 1
activation of caspase activity -0.048 0.17 -10000 0 -0.32 289 289
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.18 -10000 0 -0.34 282 282
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.13 0.2 0.29 5 -0.41 287 292
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.076 0.16 -10000 0 -0.33 284 284
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.069 0.18 -10000 0 -0.37 287 287
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.14 0.25 -10000 0 -0.47 371 371
MAPK8 -0.094 0.18 0.29 10 -0.36 261 271
MAPK9 -0.092 0.17 0.28 8 -0.36 259 267
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.061 0.21 0.26 12 -0.57 157 169
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NDN 0.005 0.1 -10000 0 -0.57 34 34
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.041 0.16 -10000 0 -0.3 285 285
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.022 -10000 0 -0.33 1 1
RhoA-B-C/GTP -0.067 0.19 -10000 0 -0.36 287 287
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.059 0.19 -10000 0 -0.34 310 310
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.069 0.2 -10000 0 -0.36 312 312
PRKACB 0.032 0.06 0.26 47 -0.57 4 51
proBDNF (dimer)/p75 ECD 0.007 0.12 -10000 0 -0.42 74 74
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.086 0.17 0.28 14 -0.36 233 247
BAD -0.11 0.18 0.34 8 -0.39 268 276
RIPK2 0.02 0.016 0.26 3 -10000 0 3
NGFR -0.14 0.26 -10000 0 -0.57 286 286
CYCS -0.084 0.15 0.36 2 -0.32 275 277
ADAM17 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.044 0.16 -10000 0 -0.34 208 208
BCL2L11 -0.11 0.18 0.34 8 -0.39 266 274
BDNF (dimer)/p75(NTR) -0.11 0.23 -10000 0 -0.44 325 325
PI3K -0.056 0.18 -10000 0 -0.34 277 277
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.053 0.18 -10000 0 -0.34 285 285
NDNL2 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.094 0.2 -10000 0 -0.42 291 291
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.052 0.18 -10000 0 -0.34 285 285
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
PLG 0.018 0.021 0.26 8 -10000 0 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.1 0.18 -10000 0 -0.37 323 323
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
NGFRAP1 0.023 0.031 -10000 0 -0.57 3 3
CASP3 -0.1 0.17 0.32 8 -0.36 274 282
E2F1 0.092 0.11 0.26 320 -10000 0 320
CASP9 0.023 0.005 -10000 0 -10000 0 0
IKK complex -0.001 0.11 -10000 0 -0.4 18 18
NGF (dimer)/TRKA 0.026 0.066 -10000 0 -0.4 20 20
MMP7 -0.037 0.19 0.26 33 -0.57 121 154
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.042 0.17 -10000 0 -0.32 278 278
MMP3 0.096 0.14 0.26 380 -0.57 14 394
APAF-1/Caspase 9 -0.084 0.11 -10000 0 -0.44 10 10
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.007 0.096 -10000 0 -0.57 29 29
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.18 0.2 -10000 0 -0.35 612 612
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.18 0.17 -10000 0 -0.32 609 609
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.035 0.054 0.26 61 -10000 0 61
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.023 0.066 0.26 23 -0.57 10 33
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.048 0.047 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.028 0.034 0.26 23 -10000 0 23
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.054 0.083 0.26 155 -10000 0 155
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.19 0.21 0.34 2 -0.37 608 610
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.15 0.33 4 -0.32 65 69
MAP1B -0.001 0.045 -10000 0 -0.31 21 21
RAC1 0.011 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.15 0.15 -10000 0 -0.3 498 498
RELN -0.32 0.29 0.26 2 -0.57 619 621
PAFAH/LIS1 0.023 0.045 0.32 2 -0.36 9 11
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.13 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.3 509 509
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.14 0.15 0.33 3 -0.3 246 249
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.051 0.074 0.26 123 -10000 0 123
PAFAH1B2 0.019 0.044 -10000 0 -0.57 6 6
MAP1B/LIS1/Dynein heavy chain 0.014 0.043 -10000 0 -0.31 3 3
NDEL1/Katanin 60/Dynein heavy chain -0.12 0.15 0.34 3 -0.32 44 47
LRP8 0.046 0.068 0.26 103 -10000 0 103
NDEL1/Katanin 60 -0.13 0.15 0.35 3 -0.33 60 63
P39/CDK5 -0.15 0.16 0.34 6 -0.29 573 579
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.18 0.15 0.2 2 -0.3 605 607
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.16 0.19 0.33 1 -0.32 602 603
RELN/VLDLR -0.17 0.2 -10000 0 -0.33 612 612
CDC42 0.01 0.005 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.031 0.26 19 -10000 0 19
EFNB1 0.002 0.036 -10000 0 -0.42 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.077 0.17 -10000 0 -0.3 399 399
Ephrin B2/EPHB1-2 -0.097 0.18 -10000 0 -0.32 411 411
neuron projection morphogenesis -0.083 0.16 -10000 0 -0.28 400 400
Ephrin B1/EPHB1-2/Tiam1 -0.088 0.18 -10000 0 -0.31 407 407
DNM1 0.02 0.048 0.27 1 -0.57 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.021 0.12 -10000 0 -0.56 45 45
YES1 -0.023 0.17 -10000 0 -0.77 50 50
Ephrin B1/EPHB1-2/NCK2 -0.089 0.18 -10000 0 -0.31 410 410
PI3K 0.006 0.13 -10000 0 -0.51 57 57
mol:GDP -0.088 0.18 -10000 0 -0.31 407 407
ITGA2B 0.033 0.06 0.26 54 -0.57 3 57
endothelial cell proliferation 0.029 0.011 -10000 0 -0.14 1 1
FYN -0.024 0.16 -10000 0 -0.76 49 49
MAP3K7 -0.023 0.12 0.23 1 -0.57 48 49
FGR -0.02 0.16 -10000 0 -0.76 49 49
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.008 0.13 -10000 0 -0.52 53 53
LYN -0.021 0.16 -10000 0 -0.75 49 49
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.15 -10000 0 -0.71 50 50
Ephrin B1/EPHB1-2 -0.022 0.13 -10000 0 -0.63 45 45
SRC -0.019 0.16 -10000 0 -0.75 50 50
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
EPHB1 -0.2 0.29 0.26 1 -0.57 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.011 -10000 0 -0.14 1 1
alphaIIb/beta3 Integrin 0.027 0.089 -10000 0 -0.41 36 36
BLK -0.019 0.17 -10000 0 -0.78 47 47
HCK -0.019 0.16 -10000 0 -0.75 50 50
regulation of stress fiber formation 0.089 0.18 0.31 410 -10000 0 410
MAPK8 -0.024 0.12 -10000 0 -0.53 50 50
Ephrin B1/EPHB1-2/RGS3 -0.088 0.18 -10000 0 -0.31 409 409
endothelial cell migration -0.017 0.11 -10000 0 -0.51 42 42
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.68 26 26
regulation of focal adhesion formation 0.089 0.18 0.31 410 -10000 0 410
chemotaxis 0.088 0.18 0.31 409 -10000 0 409
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.08 0.17 -10000 0 -0.29 399 399
angiogenesis -0.023 0.13 -10000 0 -0.62 47 47
LCK -0.02 0.17 -10000 0 -0.77 49 49
Noncanonical Wnt signaling pathway

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
NFATC2 -0.026 0.16 -10000 0 -0.57 88 88
GNB1/GNG2 -0.076 0.21 -10000 0 -0.47 160 160
mol:DAG -0.077 0.18 0.23 2 -0.44 151 153
PLCG1 -0.08 0.19 0.23 2 -0.46 151 153
YES1 -0.095 0.19 0.2 1 -0.37 278 279
FZD3 0.015 0.054 -10000 0 -0.57 9 9
FZD6 0.014 0.054 -10000 0 -0.57 9 9
G protein -0.063 0.2 0.3 2 -0.46 146 148
MAP3K7 -0.071 0.15 0.23 2 -0.41 119 121
mol:Ca2+ -0.074 0.18 0.22 2 -0.43 151 153
mol:IP3 -0.077 0.18 0.23 2 -0.44 151 153
NLK -0.009 0.13 -10000 0 -0.84 24 24
GNB1 0.023 0.005 -10000 0 -10000 0 0
CAMK2A -0.072 0.17 0.23 4 -0.41 145 149
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.097 0.21 0.22 1 -0.39 297 298
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
GNAS -0.09 0.19 0.2 1 -0.38 265 266
GO:0007205 -0.081 0.18 0.22 2 -0.43 152 154
WNT6 -0.076 0.24 0.26 47 -0.57 200 247
WNT4 0.017 0.086 0.26 20 -0.57 20 40
NFAT1/CK1 alpha -0.09 0.2 0.32 2 -0.47 158 160
GNG2 0.017 0.065 -10000 0 -0.57 13 13
WNT5A 0.017 0.073 0.26 9 -0.57 15 24
WNT11 -0.085 0.23 0.26 10 -0.57 199 209
CDC42 -0.083 0.19 -10000 0 -0.47 139 139
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.02 0.48 0.79 48 -1.1 77 125
IL23A -0.031 0.48 0.89 24 -1.1 71 95
NF kappa B1 p50/RelA/I kappa B alpha -0.059 0.44 0.72 11 -0.86 162 173
positive regulation of T cell mediated cytotoxicity -0.023 0.54 0.83 77 -0.94 165 242
ITGA3 -0.016 0.47 0.79 44 -1 80 124
IL17F -0.007 0.36 0.59 73 -0.6 150 223
IL12B 0.084 0.15 0.35 217 -10000 0 217
STAT1 (dimer) -0.037 0.5 0.73 54 -0.91 167 221
CD4 -0.015 0.48 0.79 54 -0.87 134 188
IL23 -0.016 0.48 0.82 48 -1.1 72 120
IL23R 0.047 0.2 0.57 21 -0.89 18 39
IL1B -0.033 0.5 0.82 41 -1.1 78 119
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.018 0.48 0.82 65 -0.99 77 142
TYK2 0.026 0.058 0.23 1 -10000 0 1
STAT4 0.001 0.12 0.26 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.008 0.11 0.27 5 -0.56 35 40
IL12RB1 0.034 0.091 0.37 42 -0.58 2 44
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.087 0.32 40 -0.43 2 42
IL23R/JAK2 0.06 0.22 0.54 34 -0.86 15 49
positive regulation of chronic inflammatory response -0.023 0.54 0.83 77 -0.94 165 242
natural killer cell activation -0.004 0.015 -10000 0 -0.051 35 35
JAK2 0.038 0.081 0.26 30 -10000 0 30
PIK3R1 0.017 0.064 -10000 0 -0.56 13 13
NFKB1 0.026 0.009 -10000 0 -10000 0 0
RELA 0.026 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.01 0.47 0.8 52 -1 72 124
ALOX12B -0.017 0.47 0.82 45 -1 76 121
CXCL1 -0.18 0.69 0.83 46 -1.2 276 322
T cell proliferation -0.023 0.54 0.83 77 -0.94 165 242
NFKBIA 0.026 0.009 -10000 0 -10000 0 0
IL17A 0.02 0.31 0.55 90 -0.53 69 159
PI3K -0.055 0.46 0.66 34 -0.88 163 197
IFNG 0.025 0.067 0.17 136 -0.11 16 152
STAT3 (dimer) -0.056 0.44 0.67 21 -0.85 161 182
IL18R1 0.016 0.078 -10000 0 -0.56 19 19
IL23/IL23R/JAK2/TYK2/SOCS3 0.036 0.34 0.64 87 -0.6 70 157
IL18/IL18R 0.041 0.1 0.28 11 -0.36 52 63
macrophage activation 0 0.029 0.056 102 -0.045 32 134
TNF -0.03 0.49 0.82 44 -1.1 80 124
STAT3/STAT4 -0.054 0.48 0.67 30 -0.91 166 196
STAT4 (dimer) -0.049 0.51 0.73 45 -0.94 170 215
IL18 0.03 0.038 0.26 26 -10000 0 26
IL19 0.022 0.48 0.8 73 -0.88 122 195
STAT5A (dimer) -0.04 0.49 0.71 52 -0.91 169 221
STAT1 0.028 0.031 0.26 19 -10000 0 19
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
CXCL9 0.008 0.5 0.83 77 -1 78 155
MPO -0.045 0.54 0.8 49 -1.1 122 171
positive regulation of humoral immune response -0.023 0.54 0.83 77 -0.94 165 242
IL23/IL23R/JAK2/TYK2 -0.03 0.55 0.84 73 -0.98 165 238
IL6 -0.3 0.74 0.8 31 -1.2 396 427
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
IL2 0.021 0.037 0.3 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.015 -10000 0 -0.051 35 35
CD3E -0.027 0.5 0.81 58 -0.98 125 183
keratinocyte proliferation -0.023 0.54 0.83 77 -0.94 165 242
NOS2 -0.016 0.48 0.78 52 -1 85 137
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.23 0.61 0.82 6 -1.2 184 190
STAT6 (cleaved dimer) -0.3 0.57 -10000 0 -1.2 235 235
IGHG1 -0.025 0.26 0.51 60 -0.52 11 71
IGHG3 -0.23 0.57 0.67 16 -1.1 231 247
AKT1 -0.082 0.34 0.57 23 -0.76 81 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.044 0.29 0.53 27 -0.75 49 76
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.083 0.36 0.57 30 -0.83 69 99
THY1 -0.23 0.61 0.83 7 -1.2 184 191
MYB 0.011 0.086 0.26 1 -0.57 23 24
HMGA1 0.034 0.048 0.26 48 -10000 0 48
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.41 0.63 61 -0.74 160 221
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.075 0.35 0.57 32 -0.82 59 91
SP1 0.034 0.025 -10000 0 -0.18 1 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.014 0.046 -10000 0 -0.54 1 1
STAT6 (dimer)/ETS1 -0.26 0.6 0.69 8 -1.2 214 222
SOCS1 -0.13 0.4 0.64 17 -0.78 148 165
SOCS3 -0.089 0.35 0.63 9 -0.82 67 76
FCER2 -0.37 0.73 0.77 30 -1.3 342 372
PARP14 0.017 0.031 0.26 2 -10000 0 2
CCL17 -0.22 0.62 0.85 40 -1.2 183 223
GRB2 0.023 0.009 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.039 0.29 0.53 30 -0.75 34 64
T cell proliferation -0.25 0.61 0.75 6 -1.3 202 208
IL4R/JAK1 -0.24 0.6 0.76 1 -1.2 191 192
EGR2 -0.34 0.74 0.85 13 -1.4 257 270
JAK2 0.012 0.076 0.26 1 -10000 0 1
JAK3 0.022 0.035 0.27 14 -10000 0 14
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
JAK1 0.017 0.041 -10000 0 -10000 0 0
COL1A2 -0.022 0.27 0.6 5 -1.1 18 23
CCL26 -0.23 0.61 0.89 7 -1.3 184 191
IL4R -0.24 0.66 0.89 23 -1.3 190 213
PTPN6 0.014 0.035 0.21 2 -10000 0 2
IL13RA2 -0.23 0.61 0.87 5 -1.3 182 187
IL13RA1 0.012 0.077 0.26 1 -10000 0 1
IRF4 -0.13 0.49 0.64 6 -1.4 116 122
ARG1 -0.004 0.22 0.57 6 -0.69 4 10
CBL -0.11 0.38 0.58 37 -0.71 156 193
GTF3A 0.055 0.048 0.26 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.025 0.11 0.29 33 -10000 0 33
IRF4/BCL6 -0.11 0.44 0.55 1 -1.3 116 117
CD40LG -0.01 0.13 0.31 12 -0.57 51 63
MAPK14 -0.1 0.38 0.6 31 -0.74 131 162
mitosis -0.075 0.33 0.55 27 -0.72 78 105
STAT6 -0.26 0.76 0.93 51 -1.4 219 270
SPI1 0.027 0.019 0.26 6 -10000 0 6
RPS6KB1 -0.058 0.32 0.55 30 -0.7 70 100
STAT6 (dimer) -0.26 0.76 0.94 50 -1.4 219 269
STAT6 (dimer)/PARP14 -0.29 0.66 0.73 14 -1.3 233 247
mast cell activation 0 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.088 0.35 0.56 35 -0.74 101 136
FRAP1 -0.082 0.34 0.57 23 -0.76 81 104
LTA -0.22 0.62 0.85 38 -1.2 184 222
FES 0.022 0.031 -10000 0 -0.57 3 3
T-helper 1 cell differentiation 0.25 0.72 1.3 220 -0.93 50 270
CCL11 -0.17 0.59 0.76 22 -1.2 182 204
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.069 0.34 0.57 32 -0.77 66 98
IL2RG 0.025 0.071 0.26 46 -0.56 7 53
IL10 -0.2 0.6 0.84 15 -1.2 170 185
IRS1 0.001 0.11 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
IL4 -0.008 0.26 0.62 20 -1.1 20 40
IL5 -0.23 0.61 0.85 6 -1.3 182 188
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.52 0.79 53 -0.93 186 239
COL1A1 0.003 0.36 0.64 52 -0.97 50 102
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.61 -10000 0 -1.3 176 176
IL2R gamma/JAK3 0.037 0.068 0.37 16 -0.42 6 22
TFF3 -0.28 0.7 0.85 25 -1.4 241 266
ALOX15 -0.3 0.69 0.83 15 -1.4 248 263
MYBL1 0.038 0.063 0.26 81 -10000 0 81
T-helper 2 cell differentiation -0.19 0.52 0.71 27 -0.98 213 240
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.079 0.34 0.55 33 -0.77 75 108
mol:PI-3-4-5-P3 -0.081 0.34 0.57 23 -0.76 80 103
PI3K -0.09 0.36 0.58 21 -0.81 84 105
DOK2 0.02 0.03 0.26 4 -0.57 2 6
ETS1 0.003 0.054 -10000 0 -0.53 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.029 0.27 0.51 32 -0.72 25 57
ITGB3 -0.25 0.63 0.85 4 -1.3 196 200
PIGR -0.66 0.8 0.84 13 -1.3 565 578
IGHE -0.015 0.086 0.18 24 -0.22 31 55
MAPKKK cascade -0.028 0.27 0.51 33 -0.7 25 58
BCL6 0.022 0.046 -10000 0 -0.56 6 6
OPRM1 -0.23 0.61 0.9 6 -1.3 183 189
RETNLB -0.23 0.6 0.83 5 -1.3 183 188
SELP -0.35 0.77 0.81 21 -1.4 293 314
AICDA -0.22 0.58 0.77 11 -1.2 181 192
Wnt signaling

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
Noncanonical Wnts/FZD -0.097 0.21 0.22 1 -0.39 297 298
FZD6 0.014 0.054 -10000 0 -0.57 9 9
WNT6 -0.076 0.24 0.26 47 -0.57 200 247
WNT4 0.017 0.086 0.26 20 -0.57 20 40
FZD3 0.015 0.054 -10000 0 -0.57 9 9
WNT5A 0.017 0.073 0.26 9 -0.57 15 24
WNT11 -0.085 0.23 0.26 10 -0.57 199 209
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.067 0.15 -10000 0 -0.33 242 242
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.026 0.022 0.26 9 -10000 0 9
IRS1/Crk -0.061 0.16 -10000 0 -0.34 246 246
IGF-1R heterotetramer/IGF1/PTP1B -0.044 0.17 -10000 0 -0.36 213 213
AKT1 -0.067 0.14 0.25 2 -0.32 184 186
BAD -0.065 0.13 0.24 2 -0.45 48 50
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.16 -10000 0 -0.33 246 246
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.16 -10000 0 -0.34 246 246
RAF1 -0.047 0.13 -10000 0 -0.47 48 48
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.032 0.16 -10000 0 -0.33 214 214
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.062 0.17 -10000 0 -0.36 246 246
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.32 172 174
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.029 0.12 0.3 10 -0.4 43 53
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.13 -10000 0 -0.31 161 161
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.3 158 158
IGF-1R heterotetramer -0.011 0.098 0.25 1 -0.62 20 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.046 0.17 -10000 0 -0.34 243 243
Crk/p130 Cas/Paxillin -0.037 0.16 -10000 0 -0.32 229 229
IGF1R -0.011 0.098 0.25 1 -0.62 20 21
IGF1 -0.11 0.25 -10000 0 -0.59 233 233
IRS2/Crk -0.067 0.17 -10000 0 -0.35 245 245
PI3K -0.036 0.17 -10000 0 -0.33 236 236
apoptosis 0.044 0.11 0.38 37 -0.28 4 41
HRAS/GDP 0.019 0.015 -10000 0 -10000 0 0
PRKCD -0.078 0.17 -10000 0 -0.39 227 227
RAF1/14-3-3 E -0.024 0.13 0.3 1 -0.41 47 48
BAD/14-3-3 -0.046 0.11 0.29 4 -0.4 39 43
PRKCZ -0.067 0.14 0.25 2 -0.32 200 202
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.11 -10000 0 -0.41 39 39
PTPN1 0.024 0.018 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.18 -10000 0 -0.41 232 232
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.14 -10000 0 -0.32 176 176
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.054 0.16 -10000 0 -0.33 243 243
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.34 246 246
IRS1 -0.071 0.17 -10000 0 -0.36 246 246
IRS2 -0.076 0.17 -10000 0 -0.36 256 256
IGF-1R heterotetramer/IGF1 -0.078 0.21 -10000 0 -0.46 239 239
GRB2 0.023 0.009 0.26 1 -10000 0 1
PDPK1 -0.069 0.14 0.28 1 -0.33 206 207
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.19 -10000 0 -0.43 224 224
SHC1 0.02 0.009 -10000 0 -10000 0 0
Arf6 signaling events

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.027 0.029 -10000 0 -0.39 3 3
ARNO/beta Arrestin1-2 -0.063 0.16 -10000 0 -0.55 45 45
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EPHA2 0.02 0.04 -10000 0 -0.57 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.21 0.25 -10000 0 -0.45 526 526
ARRB2 -0.042 0.13 -10000 0 -0.36 146 146
mol:GTP 0.012 0.049 0.16 21 -0.2 21 42
ARRB1 0.021 0.026 -10000 0 -0.57 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR 0.001 0.12 0.26 4 -0.57 42 46
EGF -0.083 0.23 0.26 2 -0.57 194 196
somatostatin receptor activity 0 0 0.001 1 -0.001 275 276
ARAP2 0.021 0.04 -10000 0 -0.57 5 5
mol:GDP -0.12 0.16 -10000 0 -0.33 295 295
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 144 144
ITGA2B 0.033 0.06 0.26 54 -0.57 3 57
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
ADAP1 0.025 0.029 0.26 10 -0.57 1 11
KIF13B 0.019 0.027 -10000 0 -0.57 2 2
HGF/MET -0.066 0.2 -10000 0 -0.44 226 226
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 0.19 1 -0.28 298 299
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.17 0.23 -10000 0 -0.4 514 514
ADRB2 -0.1 0.24 -10000 0 -0.57 229 229
receptor agonist activity 0 0 0 1 0 266 267
actin filament binding 0 0 0 2 -0.001 283 285
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 166 167
ARF6/GDP -0.037 0.15 0.25 2 -0.43 95 97
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.4 223 223
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.079 -10000 0 -0.32 36 36
ACAP1 0.029 0.066 0.26 47 -0.57 6 53
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.055 0.17 -10000 0 -0.48 146 146
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 0.14 0.26 2 -0.57 65 67
CYTH3 0.004 0.018 -10000 0 -0.42 2 2
CYTH2 0.006 0.099 -10000 0 -1 10 10
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 220 221
endosomal lumen acidification 0 0 0.001 5 0 254 259
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.014 0.14 -10000 0 -0.57 69 69
GNAQ/ARNO 0.018 0.095 -10000 0 -0.95 10 10
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 179 179
MET -0.073 0.22 -10000 0 -0.57 177 177
GNA14 0.022 0.065 0.26 19 -0.57 10 29
GNA15 0.024 0.025 0.26 6 -0.57 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 215 216
GNA11 0.021 0.036 -10000 0 -0.57 4 4
LHCGR -0.069 0.2 -10000 0 -0.57 146 146
AGTR1 -0.098 0.26 0.26 59 -0.57 244 303
desensitization of G-protein coupled receptor protein signaling pathway -0.055 0.17 -10000 0 -0.48 146 146
IPCEF1/ARNO -0.13 0.19 -10000 0 -0.59 68 68
alphaIIb/beta3 Integrin 0.027 0.089 -10000 0 -0.41 36 36
Nongenotropic Androgen signaling

Figure 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
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.01 0.13 -10000 0 -0.33 152 152
regulation of S phase of mitotic cell cycle -0.024 0.11 -10000 0 -0.29 135 135
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.025 0.022 0.25 9 -10000 0 9
SHBG/T-DHT 0.015 0.005 -10000 0 -10000 0 0
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.069 0.11 -10000 0 -0.32 125 125
T-DHT/AR -0.042 0.15 0.17 1 -0.42 142 143
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 321 321
GNAI2 0.023 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
mol:GDP -0.063 0.16 -10000 0 -0.46 147 147
cell proliferation -0.14 0.21 0.27 3 -0.44 303 306
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.25 0.38 -10000 0 -0.81 325 325
mol:Ca2+ -0.013 0.028 -10000 0 -0.073 148 148
MAPK3 -0.1 0.16 0.26 4 -0.4 130 134
MAPK1 -0.08 0.14 -10000 0 -0.39 109 109
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 -0.001 0.002 -10000 0 -0.004 318 318
cAMP biosynthetic process 0.004 0.021 -10000 0 -10000 0 0
GNG2 0.017 0.065 -10000 0 -0.57 13 13
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 318 318
HRAS/GTP -0.028 0.12 -10000 0 -0.32 139 139
actin cytoskeleton reorganization 0.029 0.037 -10000 0 -0.3 12 12
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 318 318
PI3K 0.026 0.042 -10000 0 -0.34 13 13
apoptosis 0.13 0.21 0.43 327 -10000 0 327
T-DHT/AR/PELP1 -0.025 0.13 -10000 0 -0.36 141 141
HRAS/GDP -0.052 0.16 -10000 0 -0.45 142 142
CREB1 -0.14 0.23 -10000 0 -0.47 327 327
RAC1-CDC42/GTP 0.037 0.04 -10000 0 -0.3 12 12
AR -0.054 0.2 0.25 1 -0.57 141 142
GNB1 0.023 0.005 -10000 0 -10000 0 0
RAF1 -0.061 0.11 -10000 0 -0.32 134 134
RAC1-CDC42/GDP -0.028 0.16 -10000 0 -0.44 141 141
T-DHT/AR/PELP1/Src -0.022 0.13 -10000 0 -0.34 140 140
MAP2K2 -0.07 0.11 -10000 0 -0.32 127 127
T-DHT/AR/PELP1/Src/PI3K -0.025 0.11 -10000 0 -0.3 135 135
GNAZ 0.017 0.057 -10000 0 -0.57 10 10
SHBG 0.022 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.052 0.16 -10000 0 -0.5 85 85
mol:T-DHT -0.001 0.001 0.002 1 -0.004 86 87
RAC1 0.024 0.003 -10000 0 -10000 0 0
GNRH1 0.001 0.029 -10000 0 -0.42 5 5
Gi family/GTP -0.036 0.1 -10000 0 -0.28 102 102
CDC42 0.023 0.005 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0 0.15 -10000 0 -0.32 176 176
ER alpha/Gai/GDP/Gbeta gamma -0.085 0.22 -10000 0 -0.47 211 211
AKT1 -0.12 0.33 -10000 0 -0.77 206 206
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.33 -10000 0 -0.78 205 205
mol:Ca2+ -0.026 0.1 0.26 2 -0.45 29 31
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
E2/ER alpha (dimer)/Striatin -0.016 0.16 0.18 113 -0.35 174 287
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.11 0.31 0.73 206 -10000 0 206
RhoA/GTP -0.015 0.1 -10000 0 -0.28 123 123
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.067 0.21 0.31 4 -0.46 199 203
regulation of stress fiber formation 0.023 0.1 0.27 24 -0.31 8 32
E2/ERA-ERB (dimer) -0.019 0.16 0.18 104 -0.35 174 278
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.009 0.13 0.16 101 -0.3 156 257
pseudopodium formation -0.023 0.1 0.31 8 -0.27 24 32
E2/ER alpha (dimer)/PELP1 -0.014 0.15 0.18 98 -0.35 153 251
GRB2 0.023 0.009 0.26 1 -10000 0 1
GNG2 0.017 0.065 -10000 0 -0.57 13 13
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
HRAS 0.026 0.022 0.26 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.088 0.23 -10000 0 -0.5 223 223
E2/ER beta (dimer) 0.008 0.063 -10000 0 -0.4 24 24
mol:GDP -0.039 0.16 0.25 13 -0.39 170 183
mol:NADP -0.088 0.23 -10000 0 -0.5 223 223
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 -0.027 0.11 0.27 2 -0.47 28 30
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
PLCB1 -0.025 0.11 0.28 2 -0.45 33 35
PLCB2 -0.005 0.082 -10000 0 -0.49 17 17
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
mol:L-citrulline -0.088 0.23 -10000 0 -0.5 223 223
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.079 0.25 -10000 0 -0.64 157 157
JNK cascade 0.008 0.063 -10000 0 -0.4 24 24
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.011 0.085 -10000 0 -0.57 23 23
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
ESR1 -0.035 0.23 0.26 115 -0.57 151 266
Gq family/GDP/Gbeta gamma -0.01 0.16 -10000 0 -0.74 39 39
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.017 0.13 -10000 0 -0.6 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.059 0.2 0.31 5 -0.46 164 169
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
E2/ER alpha (dimer) -0.028 0.16 0.18 115 -0.41 157 272
STRN 0.013 0.08 -10000 0 -0.57 20 20
GNAL -0.11 0.24 -10000 0 -0.57 235 235
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.057 -10000 0 -0.36 26 26
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
HBEGF -0.056 0.21 0.33 21 -0.54 95 116
cAMP biosynthetic process -0.086 0.18 -10000 0 -0.32 348 348
SRC -0.079 0.21 0.29 7 -0.45 204 211
PI3K 0.028 0.049 -10000 0 -0.4 13 13
GNB1 0.023 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.16 -10000 0 -0.37 154 154
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.43 218 218
Gs family/GTP -0.083 0.18 -10000 0 -0.33 348 348
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.019 -10000 0 -10000 0 0
vasodilation -0.083 0.22 0.24 1 -0.48 223 224
mol:DAG -0.027 0.11 0.27 2 -0.47 28 30
Gs family/GDP/Gbeta gamma -0.09 0.18 -10000 0 -0.35 280 280
MSN -0.026 0.11 0.32 8 -0.29 24 32
Gq family/GTP -0.001 0.087 -10000 0 -0.51 16 16
mol:PI-3-4-5-P3 -0.11 0.32 -10000 0 -0.75 205 205
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.083 0.22 0.48 223 -0.24 1 224
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.16 0.26 10 -0.38 167 177
NOS3 -0.094 0.25 -10000 0 -0.53 223 223
GNA11 0.022 0.036 -10000 0 -0.57 4 4
MAPKKK cascade -0.084 0.25 0.3 3 -0.55 217 220
E2/ER alpha (dimer)/PELP1/Src -0.071 0.22 0.31 8 -0.48 203 211
ruffle organization -0.023 0.1 0.31 8 -0.27 24 32
ROCK2 -0.025 0.12 0.34 8 -0.28 130 138
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.048 0.2 0.35 25 -0.49 114 139
MMP2 -0.07 0.2 0.28 9 -0.43 190 199
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.058 0.16 0.31 7 -0.35 114 121
SMAD6-7/SMURF1 0.046 0.015 -10000 0 -10000 0 0
NOG 0.012 0.095 0.26 19 -0.57 25 44
SMAD9 -0.088 0.25 -10000 0 -0.58 192 192
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.021 0.14 -10000 0 -0.43 69 69
BMP7/USAG1 -0.19 0.25 -10000 0 -0.42 532 532
SMAD5/SKI -0.015 0.15 0.26 3 -0.44 70 73
SMAD1 0.013 0.062 -10000 0 -0.41 8 8
BMP2 -0.074 0.22 0.26 2 -0.57 179 181
SMAD1/SMAD1/SMAD4 0.018 0.069 -10000 0 -0.39 10 10
BMPR1A 0.023 0.026 -10000 0 -0.57 2 2
BMPR1B 0.1 0.15 0.26 425 -0.57 23 448
BMPR1A-1B/BAMBI 0.083 0.12 0.34 9 -0.32 55 64
AHSG 0.021 0.029 0.26 16 -10000 0 16
CER1 0.018 0.013 0.26 3 -10000 0 3
BMP2-4/CER1 -0.046 0.18 -10000 0 -0.39 214 214
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.038 0.16 -10000 0 -0.41 103 103
BMP2-4 (homodimer) -0.066 0.2 -10000 0 -0.45 221 221
RGMB 0.023 0.019 -10000 0 -0.57 1 1
BMP6/BMPR2/BMPR1A-1B 0.07 0.14 -10000 0 -0.31 96 96
RGMA -0.053 0.2 -10000 0 -0.57 139 139
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.036 0.16 -10000 0 -0.41 123 123
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.44 577 577
SMAD6/SMURF1/SMAD5 -0.016 0.15 0.26 2 -0.43 73 75
SOSTDC1 -0.25 0.3 0.26 3 -0.57 507 510
BMP7/BMPR2/BMPR1A-1B 0.068 0.14 0.3 4 -0.32 90 94
SKI 0.023 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.016 0.15 0.26 2 -0.56 72 74
HFE2 0.018 0.023 0.26 9 -10000 0 9
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.043 0.2 -10000 0 -0.4 220 220
SMAD5/SMAD5/SMAD4 -0.016 0.15 0.26 2 -0.44 71 73
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.022 0.15 -10000 0 -0.37 113 113
BMP7 (homodimer) -0.011 0.16 0.26 30 -0.56 73 103
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.001 0.12 -10000 0 -0.42 71 71
SMAD1/SKI 0.02 0.076 -10000 0 -0.42 12 12
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.045 0.18 0.34 1 -0.39 216 217
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.036 0.095 0.26 94 -0.57 14 108
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.085 0.11 -10000 0 -0.41 25 25
CHRDL1 -0.38 0.28 -10000 0 -0.57 729 729
ENDOFIN/SMAD1 0.019 0.078 -10000 0 -0.43 13 13
SMAD6-7/SMURF1/SMAD1 0.036 0.081 -10000 0 -0.42 12 12
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.016 0.11 0.26 39 -0.57 30 69
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.26 -10000 0 -0.45 729 729
BMP2-4/GREM1 -0.037 0.2 -10000 0 -0.4 224 224
SMAD7 0.023 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.08 0.25 -10000 0 -0.57 192 192
SMAD1/SMAD6 0.019 0.078 -10000 0 -0.43 13 13
TAK1/SMAD6 0.033 0.01 -10000 0 -10000 0 0
BMP7 -0.011 0.16 0.26 30 -0.57 73 103
BMP6 -0.016 0.15 0.26 2 -0.57 72 74
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.034 0.17 -10000 0 -0.42 124 124
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.075 -10000 0 -0.41 14 14
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.007 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.047 0.2 0.23 1 -0.48 133 134
CHRD 0.026 0.095 0.26 58 -0.57 19 77
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.05 0.18 -10000 0 -0.48 122 122
BMP4 -0.01 0.14 0.26 1 -0.57 62 63
FST -0.001 0.12 0.26 3 -0.57 45 48
BMP2-4/NOG -0.047 0.19 0.34 1 -0.4 209 210
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.072 0.14 0.3 4 -0.3 90 94
ErbB2/ErbB3 signaling events

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
USP8 -0.008 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.14 0.31 2 -0.3 54 56
NFATC4 -0.063 0.12 0.27 9 -0.25 196 205
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.068 0.15 -10000 0 -0.3 252 252
JUN -0.009 0.096 0.26 9 -0.45 3 12
HRAS 0.026 0.022 0.26 9 -10000 0 9
DOCK7 -0.079 0.14 0.28 2 -0.3 247 249
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.052 0.15 -10000 0 -0.33 206 206
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.006 -10000 0 -10000 0 0
MAPK10 -0.07 0.11 0.2 10 -0.27 138 148
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.073 0.16 -10000 0 -0.33 252 252
RAF1 -0.019 0.14 0.32 15 -0.3 49 64
ErbB2/ErbB3/neuregulin 2 -0.14 0.18 -10000 0 -0.34 437 437
STAT3 -0.001 0.16 -10000 0 -0.86 34 34
cell migration -0.055 0.1 0.23 16 -0.25 86 102
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.044 0.24 0.42 12 -0.51 92 104
FOS -0.1 0.28 0.37 12 -0.49 326 338
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.068 0.15 -10000 0 -0.3 252 252
MAPK3 -0.015 0.2 0.39 13 -0.52 24 37
MAPK1 -0.027 0.21 0.4 13 -0.57 45 58
JAK2 -0.077 0.14 0.26 1 -0.3 243 244
NF2 -0.002 0.057 -10000 0 -0.68 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.053 0.13 0.23 3 -0.29 207 210
NRG1 -0.14 0.26 0.25 4 -0.57 292 296
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.08 0.15 0.25 2 -0.3 255 257
MAPK9 -0.042 0.083 0.2 12 -0.26 3 15
ERBB2 0.001 0.071 0.24 85 -0.44 1 86
ERBB3 0.021 0.041 -10000 0 -0.57 5 5
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
apoptosis 0.019 0.025 -10000 0 -0.17 4 4
STAT3 (dimer) 0 0.15 -10000 0 -0.84 34 34
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.004 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.07 0.093 -10000 0 -0.24 92 92
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.02 -10000 0 -0.38 1 1
CHRNA1 0.017 0.18 0.35 58 -0.4 20 78
myelination -0.058 0.12 0.29 18 -0.25 84 102
PPP3CB -0.074 0.13 0.27 2 -0.28 248 250
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.26 160 160
NRG2 -0.26 0.29 -10000 0 -0.57 509 509
mol:GDP -0.053 0.13 0.23 3 -0.29 207 210
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.017 0.14 0.32 16 -0.31 48 64
SRC 0.023 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.079 0.14 0.28 2 -0.3 251 253
MAP2K1 -0.053 0.22 0.44 3 -0.63 37 40
heart morphogenesis -0.068 0.15 -10000 0 -0.3 252 252
RAS family/GDP -0.021 0.14 0.33 2 -0.37 16 18
GRB2 0.023 0.009 0.25 1 -10000 0 1
PRKACA -0.002 0.067 -10000 0 -0.68 10 10
CHRNE 0.004 0.027 0.13 3 -0.21 3 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.068 0.15 -10000 0 -0.3 252 252
CDC42 0.023 0.005 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

Figure 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
PTK2 -0.002 0.082 -10000 0 -0.44 25 25
Crk/p130 Cas/Paxillin -0.056 0.12 -10000 0 -0.33 139 139
JUN -0.015 0.12 0.25 1 -0.41 27 28
HRAS 0.026 0.022 0.26 9 -10000 0 9
RET51/GFRalpha1/GDNF/GRB10 0.041 0.19 0.34 53 -0.34 177 230
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.042 0.19 0.34 52 -0.34 176 228
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.011 0.15 0.32 5 -0.33 180 185
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.02 0.16 0.28 37 -0.3 177 214
GRB7 0.019 0.032 -10000 0 -0.57 3 3
RET51/GFRalpha1/GDNF 0.04 0.19 0.34 52 -0.34 176 228
MAPKKK cascade 0 0.15 0.28 11 -0.32 131 142
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.024 0.18 0.32 4 -0.38 192 196
lamellipodium assembly -0.033 0.13 -10000 0 -0.31 143 143
RET51/GFRalpha1/GDNF/SHC 0.036 0.18 0.34 43 -0.34 139 182
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.14 0.32 5 -0.33 135 140
RET9/GFRalpha1/GDNF/Shank3 -0.013 0.15 0.32 5 -0.33 180 185
MAPK3 -0.031 0.13 0.24 8 -0.3 141 149
DOK1 0.025 0.014 0.26 4 -10000 0 4
DOK6 0.017 0.07 0.26 7 -0.57 14 21
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.031 0.12 -10000 0 -0.44 21 21
DOK5 0.011 0.087 0.26 5 -0.57 23 28
GFRA1 -0.07 0.24 0.26 53 -0.57 192 245
MAPK8 -0.01 0.13 0.21 4 -0.28 141 145
HRAS/GTP 0.028 0.18 0.29 53 -0.34 169 222
tube development -0.006 0.14 0.34 11 -0.31 171 182
MAPK1 -0.031 0.13 0.26 7 -0.3 141 148
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.11 0.25 1 -0.26 171 172
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.037 0.19 0.33 49 -0.33 182 231
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.027 0.18 0.34 38 -0.34 179 217
RET51/GFRalpha1/GDNF/Dok5 0.024 0.2 0.34 48 -0.35 187 235
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
HRAS/GDP 0.019 0.015 0.18 9 -10000 0 9
CREB1 -0.014 0.13 0.22 11 -0.31 104 115
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.02 0.1 0.25 1 -0.26 122 123
RET51/GFRalpha1/GDNF/Grb7 0.041 0.18 0.33 66 -0.34 145 211
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.097 0.13 0.26 374 -0.57 13 387
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.014 0.12 0.24 1 -0.4 26 27
RET9/GFRalpha1/GDNF/FRS2 -0.012 0.15 0.32 5 -0.33 180 185
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.02 0.1 0.25 1 -0.26 127 128
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.005 0.14 0.24 16 -0.28 140 156
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.002 0.14 0.25 4 -0.29 142 146
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.01 0.13 0.25 15 -0.3 105 120
PI3K -0.029 0.2 0.28 11 -0.47 144 155
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.14 0.31 4 -0.31 171 175
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.005 0.12 0.23 9 -0.26 134 143
RET51/GFRalpha1/GDNF/FRS2 0.038 0.19 0.34 56 -0.34 178 234
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
IRS2 0.003 0.1 -10000 0 -0.57 35 35
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.13 0.25 15 -0.3 105 120
RET51/GFRalpha1/GDNF/PKC alpha 0.024 0.19 0.35 42 -0.34 185 227
GRB2 0.023 0.009 0.26 1 -10000 0 1
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.052 0.26 54 -10000 0 54
RAC1 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.027 0.22 0.34 50 -0.38 191 241
Rac1/GTP -0.022 0.16 0.23 4 -0.37 143 147
RET9/GFRalpha1/GDNF -0.026 0.16 0.32 5 -0.34 195 200
GFRalpha1/GDNF -0.033 0.18 0.36 5 -0.4 197 202
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.041 0.17 -10000 0 -0.41 177 177
CRKL -0.047 0.15 0.31 2 -0.4 91 93
mol:PIP3 0.002 0.059 0.56 1 -0.89 4 5
AKT1 0.01 0.074 0.37 3 -0.79 4 7
PTK2B 0.02 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.14 0.33 2 -0.4 73 75
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.042 0.18 -10000 0 -0.38 214 214
MAP3K5 -0.04 0.15 0.36 1 -0.43 67 68
HGF/MET/CIN85/CBL/ENDOPHILINS -0.03 0.17 -10000 0 -0.35 222 222
AP1 -0.11 0.19 -10000 0 -0.39 307 307
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.24 0.38 -10000 0 -0.77 356 356
STAT3 (dimer) -0.047 0.15 -10000 0 -0.34 178 178
GAB1/CRKL/SHP2/PI3K -0.02 0.15 -10000 0 -0.44 58 58
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.036 0.14 0.34 1 -0.39 83 84
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
ELK1 -0.03 0.096 0.28 33 -0.21 130 163
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.092 -10000 0 -0.28 59 59
PAK1 0.024 0.087 0.38 6 -0.75 4 10
HGF/MET/RANBP10 -0.045 0.18 -10000 0 -0.38 223 223
HRAS -0.11 0.26 -10000 0 -0.64 193 193
DOCK1 -0.046 0.14 0.52 1 -0.4 74 75
GAB1 -0.05 0.15 -10000 0 -0.35 169 169
CRK -0.049 0.15 0.36 1 -0.4 90 91
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.25 -10000 0 -0.57 232 232
JUN 0.02 0.044 -10000 0 -0.57 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.052 0.12 -10000 0 -0.28 226 226
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
cell morphogenesis -0.049 0.16 0.37 6 -0.45 88 94
GRB2/SHC -0.016 0.11 -10000 0 -0.28 123 123
FOS -0.14 0.27 -10000 0 -0.57 306 306
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.03 0.095 0.27 33 -0.21 130 163
HGF/MET/MUC20 -0.055 0.17 -10000 0 -0.38 225 225
cell migration -0.016 0.11 -10000 0 -0.28 123 123
GRB2 0.023 0.009 0.26 1 -10000 0 1
CBL 0.022 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.042 0.17 -10000 0 -0.41 177 177
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.047 0.14 -10000 0 -0.32 187 187
MET/MUC20 -0.055 0.16 -10000 0 -0.4 186 186
RAP1B -0.039 0.14 0.31 5 -0.39 68 73
RAP1A -0.045 0.13 0.32 3 -0.42 49 52
HGF/MET/RANBP9 -0.043 0.18 -10000 0 -0.38 218 218
RAF1 -0.099 0.24 -10000 0 -0.6 193 193
STAT3 -0.048 0.15 -10000 0 -0.34 178 178
cell proliferation -0.042 0.19 0.32 12 -0.42 159 171
RPS6KB1 -0.015 0.063 -10000 0 -0.25 26 26
MAPK3 -0.042 0.093 0.66 7 -10000 0 7
MAPK1 -0.011 0.17 0.67 55 -10000 0 55
RANBP9 0.023 0.005 -10000 0 -10000 0 0
MAPK8 -0.029 0.14 0.43 1 -0.43 55 56
SRC -0.052 0.13 0.2 1 -0.31 175 176
PI3K -0.028 0.13 -10000 0 -0.29 180 180
MET/Glomulin -0.047 0.14 -10000 0 -0.37 179 179
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.091 0.23 0.47 1 -0.55 192 193
MET -0.073 0.22 -10000 0 -0.57 177 177
MAP4K1 -0.042 0.15 0.38 1 -0.42 88 89
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.09 0.23 0.47 1 -0.55 192 193
BAD 0.008 0.071 0.36 3 -0.75 4 7
MAP2K4 -0.037 0.13 0.34 1 -0.4 60 61
SHP2/GRB2/SOS1/GAB1 -0.041 0.17 -10000 0 -0.4 177 177
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.048 0.11 -10000 0 -0.27 209 209
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 0.26 2 -0.57 65 67
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.022 0.13 -10000 0 -0.26 211 211
PDPK1 0.012 0.077 0.42 1 -0.83 4 5
HGF/MET/SHIP -0.043 0.18 -10000 0 -0.38 224 224
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.003 0.039 0.22 2 -0.37 2 4
NFATC2 -0.026 0.11 0.22 2 -0.37 88 90
NFATC3 0.006 0.034 0.22 2 -10000 0 2
CD40LG -0.14 0.29 0.47 17 -0.56 245 262
PTGS2 -0.19 0.33 0.47 13 -0.64 324 337
JUNB 0.024 0.01 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.027 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.027 -10000 0 -10000 0 0
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.013 0.049 -10000 0 -0.57 6 6
mol:Ca2+ -0.003 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.027 0.048 0.26 26 -0.57 3 29
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.005 0.15 0.46 12 -0.42 48 60
FOS -0.15 0.27 -10000 0 -0.57 306 306
IFNG -0.11 0.28 0.46 42 -0.54 219 261
AP-1/NFAT1-c-4 -0.13 0.34 0.52 40 -0.61 253 293
FASLG -0.12 0.26 0.5 24 -0.54 198 222
NFAT1-c-4/ICER1 -0.018 0.12 0.32 5 -0.35 76 81
IL2RA -0.12 0.28 0.47 30 -0.54 233 263
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.27 0.47 20 -0.53 237 257
JunB/Fra1/NFAT1-c-4 -0.007 0.13 0.34 12 -0.34 71 83
IL4 -0.13 0.26 0.46 14 -0.53 233 247
IL2 -0.014 0.15 -10000 0 -0.94 27 27
IL3 -0.017 0.11 -10000 0 -0.71 24 24
FKBP1A 0.024 0.004 -10000 0 -10000 0 0
BATF3 0.021 0.015 0.26 3 -10000 0 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.069 0.11 -10000 0 -0.29 90 90
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.47 436 436
NT3 (dimer)/TRKB -0.29 0.3 -10000 0 -0.52 614 614
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.033 -10000 0 -0.26 8 8
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.012 0.16 0.26 24 -0.57 75 99
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.024 0.051 0.26 25 -0.57 4 29
NTRK2 -0.28 0.3 -10000 0 -0.57 552 552
NTRK3 -0.17 0.28 0.26 5 -0.57 347 352
NT-4/5 (dimer)/TRKB -0.35 0.33 -10000 0 -0.56 690 690
neuron apoptosis 0.17 0.22 0.47 290 -10000 0 290
SHC 2-3/Grb2 -0.18 0.24 -10000 0 -0.52 290 290
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.18 0.25 -10000 0 -0.54 287 287
SHC3 -0.17 0.23 -10000 0 -0.52 281 281
STAT3 (dimer) 0.033 0.043 -10000 0 -0.36 4 4
NT3 (dimer)/TRKA -0.1 0.21 -10000 0 -0.42 294 294
RIN/GDP -0.045 0.12 0.32 3 -0.26 69 72
GIPC1 0.024 0.008 0.26 1 -10000 0 1
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.078 0.15 -10000 0 -0.34 247 247
RIN/GTP 0.014 0.008 0.18 2 -10000 0 2
CCND1 0.025 0.094 0.42 40 -0.82 4 44
MAGED1 0.025 0.01 0.26 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.56 363 363
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.035 0.082 0.34 3 -0.38 29 32
TRKA/NEDD4-2 0.031 0.04 -10000 0 -0.37 5 5
ELMO1 0.024 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.008 -10000 0 -10000 0 0
NGF 0.017 0.074 0.26 8 -0.57 16 24
HRAS 0.026 0.022 0.26 9 -10000 0 9
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.021 0.019 -10000 0 -0.57 1 1
RIT2 0.018 0.011 0.26 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
DNM1 0.02 0.048 0.26 1 -0.57 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.071 0.16 -10000 0 -0.32 274 274
mol:GDP -0.074 0.16 0.4 3 -0.39 79 82
NGF (dimer) 0.017 0.074 0.26 8 -0.56 16 24
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.044 0.11 0.38 2 -0.27 57 59
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
BDNF (dimer)/TRKB -0.18 0.23 -10000 0 -0.39 572 572
KIDINS220/CRKL/C3G 0.033 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.048 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.56 157 169
RAP1/GDP -0.041 0.093 -10000 0 -0.23 59 59
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.012 0.16 0.26 24 -0.56 75 99
ubiquitin-dependent protein catabolic process 0.036 0.061 -10000 0 -0.36 18 18
Schwann cell development -0.048 0.038 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.048 -10000 0 -0.27 8 8
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.28 -10000 0 -0.47 632 632
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.077 0.13 -10000 0 -0.45 56 56
STAT3 0.033 0.043 -10000 0 -0.36 4 4
axon guidance -0.26 0.26 -10000 0 -0.44 635 635
MAPK3 0.024 0.085 0.24 3 -0.35 27 30
MAPK1 0.026 0.088 0.24 4 -0.35 28 32
CDC42/GDP -0.043 0.12 0.29 5 -0.27 61 66
NTF3 -0.061 0.21 0.26 12 -0.57 157 169
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NGF (dimer)/TRKA/FAIM 0.037 0.061 -10000 0 -0.36 18 18
PI3K 0.028 0.049 -10000 0 -0.4 13 13
FRS3 0.024 0.005 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.024 0.004 -10000 0 -10000 0 0
RASGRF1 -0.076 0.16 0.25 3 -0.36 217 220
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.41 425 426
RGS19 0.023 0.01 0.26 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.095 0.39 1 -0.44 8 9
Rac1/GDP -0.044 0.12 0.34 3 -0.27 55 58
NGF (dimer)/TRKA/GRIT 0.024 0.057 -10000 0 -0.34 20 20
neuron projection morphogenesis -0.068 0.21 -10000 0 -0.74 50 50
NGF (dimer)/TRKA/NEDD4-2 0.036 0.061 -10000 0 -0.36 18 18
MAP2K1 0.029 0.085 0.36 17 -10000 0 17
NGFR -0.14 0.26 -10000 0 -0.57 286 286
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.05 -10000 0 -0.29 21 21
RAS family/GTP/PI3K 0.017 0.03 -10000 0 -0.26 9 9
FRS2 family/SHP2/GRB2/SOS1 0.063 0.026 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAPKKK cascade -0.039 0.14 -10000 0 -0.65 41 41
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.039 -10000 0 -0.42 4 4
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.36 566 566
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.062 -10000 0 -0.31 18 18
MATK 0.02 0.086 0.26 30 -0.57 18 48
NEDD4L 0.023 0.019 -10000 0 -0.57 1 1
RAS family/GDP -0.055 0.069 -10000 0 -0.2 70 70
NGF (dimer)/TRKA -0.085 0.16 -10000 0 -0.34 287 287
Rac1/GTP -0.083 0.12 -10000 0 -0.29 203 203
FRS2 family/SHP2/CRK family 0.06 0.029 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.18 14 -10000 0 14
Metarhodopsin II/Arrestin 0.036 0.037 0.32 2 -10000 0 2
PDE6G/GNAT1/GTP 0.035 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.027 0.26 14 -10000 0 14
GRK1 0.019 0.016 0.26 4 -10000 0 4
CNG Channel -0.048 0.16 -10000 0 -0.3 284 284
mol:Na + -0.047 0.16 0.24 2 -0.3 287 289
mol:ADP 0.019 0.016 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 86 87
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.041 0.16 0.28 5 -0.3 285 290
CNGB1 0.03 0.051 0.26 52 -10000 0 52
RDH5 -0.33 0.29 -10000 0 -0.57 641 641
SAG 0.032 0.052 0.26 54 -10000 0 54
mol:Ca2+ -0.08 0.14 0.36 18 -0.3 197 215
Na + (4 Units) -0.05 0.14 -10000 0 -0.29 274 274
RGS9 -0.024 0.16 0.26 11 -0.57 88 99
GNB1/GNGT1 0.054 0.059 -10000 0 -10000 0 0
GNAT1/GDP 0.025 0.11 0.3 5 -0.31 86 91
GUCY2D 0.024 0.044 0.26 19 -0.57 3 22
GNGT1 0.055 0.086 0.26 169 -10000 0 169
GUCY2F 0.018 0.011 0.26 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.02 0.049 0.2 3 -0.31 16 19
mol:11-cis-retinal -0.33 0.29 -10000 0 -0.56 641 641
mol:cGMP 0.042 0.044 -10000 0 -0.32 7 7
GNB1 0.023 0.005 -10000 0 -10000 0 0
Rhodopsin -0.24 0.22 -10000 0 -0.42 634 634
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.14 0.26 0.26 4 -0.57 294 298
Metarhodopsin II 0.026 0.019 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.05 -10000 0 -0.34 7 7
RGS9BP 0.036 0.052 0.26 57 -10000 0 57
Metarhodopsin II/Transducin 0.024 0.031 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.044 0.037 -10000 0 -0.33 4 4
PDE6A/B 0.029 0.064 -10000 0 -0.38 21 21
mol:Pi 0.016 0.12 0.33 1 -0.36 86 87
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.058 0.053 0.32 2 -10000 0 2
PDE6B 0.014 0.077 0.26 3 -0.57 18 21
PDE6A 0.028 0.032 0.26 20 -10000 0 20
PDE6G 0.032 0.045 0.26 42 -10000 0 42
RHO 0.024 0.028 0.26 15 -10000 0 15
PDE6 0.035 0.12 0.3 8 -0.31 97 105
GUCA1A 0.031 0.045 0.26 42 -10000 0 42
GC2/GCAP Family 0.054 0.039 -10000 0 -0.34 4 4
GUCA1C 0.017 0.008 0.26 1 -10000 0 1
GUCA1B 0.022 0.036 -10000 0 -0.57 4 4
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.081 0.28 1 -0.28 7 8
epithelial cell differentiation 0.032 0.08 0.39 1 -0.36 7 8
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.022 0.097 0.46 8 -10000 0 8
FYN 0.022 0.026 -10000 0 -0.57 2 2
EGFR -0.19 0.28 -10000 0 -0.57 390 390
PRL 0.022 0.023 0.26 10 -10000 0 10
neuron projection morphogenesis -0.041 0.14 0.37 13 -0.36 36 49
PTPRZ1 -0.27 0.3 0.26 6 -0.57 541 547
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.14 -10000 0 -0.36 51 51
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.087 0.15 0.23 1 -0.32 286 287
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.007 0.074 0.38 8 -0.3 6 14
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.002 0.11 0.26 7 -0.33 52 59
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.079 0.15 -10000 0 -0.32 243 243
GRIN2B -0.097 0.16 0.24 7 -0.32 274 281
ErbB4/ErbB2/betacellulin 0.013 0.097 -10000 0 -0.32 35 35
STAT1 0.028 0.031 0.26 19 -10000 0 19
HBEGF 0.023 0.026 -10000 0 -0.57 2 2
PRLR 0.021 0.051 0.26 7 -0.57 7 14
E4ICDs/ETO2 0.006 0.087 0.31 2 -0.36 16 18
axon guidance 0.054 0.11 0.3 53 -0.33 5 58
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.031 0.04 -10000 0 -0.39 7 7
CBFA2T3 0.014 0.071 0.26 4 -0.57 15 19
ErbB4/ErbB2/HBEGF 0.03 0.072 -10000 0 -0.34 3 3
MAPK3 -0.047 0.14 0.34 4 -0.36 41 45
STAT1 (dimer) 0.019 0.081 0.26 10 -0.26 5 15
MAPK1 -0.047 0.14 0.36 5 -0.36 42 47
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.071 0.15 0.25 2 -0.32 231 233
NRG1 -0.1 0.19 -10000 0 -0.42 288 288
NRG3 0.001 0.13 0.26 24 -0.57 50 74
NRG2 -0.26 0.29 -10000 0 -0.57 509 509
NRG4 0.026 0.028 0.26 15 -10000 0 15
heart development 0.054 0.11 0.3 53 -0.33 5 58
neural crest cell migration -0.07 0.15 0.25 2 -0.32 231 233
ERBB2 0.035 0.071 0.27 87 -0.41 1 88
WWOX/E4ICDs 0.011 0.075 0.26 5 -0.26 6 11
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.097 0.16 -10000 0 -0.31 296 296
apoptosis 0.012 0.12 0.46 47 -0.26 4 51
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.15 0.17 0.25 1 -0.32 496 497
ErbB4/ErbB2/epiregulin 0.007 0.13 0.34 14 -0.31 80 94
ErbB4/ErbB4/betacellulin/betacellulin -0.004 0.11 0.26 7 -0.32 62 69
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.04 0.087 0.39 1 -0.37 8 9
MDM2 0.008 0.079 0.26 31 -0.26 5 36
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.083 0.14 -10000 0 -0.31 278 278
STAT5A 0.049 0.11 0.29 43 -0.33 7 50
ErbB4/EGFR/neuregulin 1 beta -0.18 0.23 -10000 0 -0.42 445 445
DLG4 0.022 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.01 0.07 -10000 0 -0.24 6 6
STAT5A (dimer) 0.059 0.1 0.45 1 -0.4 6 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.11 0.32 11 -0.32 7 18
LRIG1 0.022 0.031 -10000 0 -0.57 3 3
EREG -0.024 0.2 0.26 77 -0.57 116 193
BTC -0.007 0.13 0.26 2 -0.57 57 59
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.044 0.11 0.31 42 -0.33 5 47
ERBB4 -0.007 0.074 0.38 8 -0.3 6 14
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
YAP1 -0.013 0.11 -10000 0 -0.39 74 74
GRB2 0.023 0.009 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.033 0.071 0.32 1 -0.41 1 2
glial cell differentiation -0.01 0.07 0.24 6 -10000 0 6
WWOX 0.021 0.013 0.26 2 -10000 0 2
cell proliferation -0.038 0.17 0.34 15 -0.44 50 65
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.41 238 239
PTP1B/AKT1 -0.067 0.13 -10000 0 -0.35 119 119
FYN 0.022 0.026 -10000 0 -0.57 2 2
p210 bcr-abl/PTP1B -0.082 0.14 0.22 2 -0.36 150 152
EGFR -0.2 0.28 -10000 0 -0.58 390 390
EGF/EGFR -0.2 0.24 -10000 0 -0.42 524 524
CSF1 0.021 0.044 -10000 0 -0.57 6 6
AKT1 0.023 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.048 0.16 0.25 9 -0.36 137 146
Insulin Receptor/Insulin -0.043 0.12 -10000 0 -0.39 47 47
HCK 0.027 0.026 0.26 13 -10000 0 13
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.078 0.14 0.41 1 -0.37 123 124
EGF -0.099 0.22 0.25 2 -0.58 194 196
YES1 0.023 0.019 -10000 0 -0.57 1 1
CAV1 -0.16 0.21 0.27 2 -0.44 302 304
TXN 0.017 0.017 0.25 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.072 0.15 -10000 0 -0.38 147 147
cell migration 0.082 0.14 0.36 150 -0.22 2 152
STAT3 0.022 0.004 -10000 0 -10000 0 0
PRLR 0.022 0.052 0.25 7 -0.57 7 14
ITGA2B 0.031 0.06 0.25 54 -0.57 3 57
CSF1R 0.024 0.008 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.031 0.043 0.31 1 -0.42 6 7
FGR 0.024 0.009 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.069 0.14 -10000 0 -0.36 137 137
Crk/p130 Cas -0.062 0.14 -10000 0 -0.37 109 109
DOK1 -0.067 0.13 0.25 1 -0.4 82 83
JAK2 -0.047 0.12 -10000 0 -0.46 54 54
Jak2/Leptin Receptor/Leptin -0.26 0.16 -10000 0 -0.4 408 408
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
PTPN1 -0.083 0.14 0.22 2 -0.36 150 152
LYN 0.021 0.008 -10000 0 -10000 0 0
CDH2 0.063 0.092 0.26 187 -0.57 2 189
SRC -0.018 0.098 -10000 0 -0.62 21 21
ITGB3 0.005 0.1 0.25 4 -0.57 33 37
CAT1/PTP1B -0.092 0.19 0.41 2 -0.47 143 145
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.038 0.12 -10000 0 -0.42 43 43
mol:H2O2 -0.004 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.24 0.14 -10000 0 -0.4 228 228
negative regulation of transcription -0.047 0.12 -10000 0 -0.45 54 54
FCGR2A 0.021 0.012 0.26 1 -10000 0 1
FER 0.011 0.058 -10000 0 -0.58 10 10
alphaIIb/beta3 Integrin 0.023 0.09 -10000 0 -0.42 36 36
BLK 0.051 0.087 0.26 151 -0.57 2 153
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.006 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.57 266 266
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.009 0.26 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.041 0.17 0.34 4 -0.45 102 106
PRL 0.007 0.032 0.26 10 -10000 0 10
SOCS3 0.01 0.16 -10000 0 -1.2 16 16
SPRY2 -0.041 0.18 -10000 0 -0.57 106 106
Insulin Receptor/Insulin/IRS1 0.026 0.08 -10000 0 -0.37 41 41
CSF1/CSF1R -0.064 0.14 -10000 0 -0.37 120 120
Ras protein signal transduction 0.051 0.15 0.64 60 -10000 0 60
IRS1 0.001 0.11 -10000 0 -0.57 42 42
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.44 0.24 -10000 0 -0.57 841 841
STAT5B -0.069 0.14 0.21 1 -0.36 131 132
STAT5A -0.07 0.14 0.2 3 -0.36 136 139
GRB2 0.023 0.009 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.073 0.14 -10000 0 -0.37 131 131
CSN2 0.025 0.057 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.009 0.072 -10000 0 -0.55 9 9
YBX1 0.027 0.015 -10000 0 -10000 0 0
LCK 0.026 0.075 0.26 40 -0.57 11 51
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.019 0.036 0.25 10 -0.57 2 12
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.044 -10000 0 -0.39 6 6
PDGFRB 0.018 0.037 -10000 0 -0.57 4 4
SPHK1 -0.018 0.097 -10000 0 -0.75 14 14
mol:S1P -0.021 0.095 0.38 1 -0.66 14 15
S1P1/S1P/Gi -0.13 0.23 0.31 2 -0.44 334 336
GNAO1 0.006 0.092 0.24 32 -0.57 20 52
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.34 3 -0.41 314 317
PLCG1 -0.13 0.22 0.35 2 -0.42 317 319
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.037 -10000 0 -0.57 4 4
GNAI2 0.009 0.023 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.021 0.13 -10000 0 -0.58 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.03 -10000 0 -0.33 6 6
S1P1/S1P -0.034 0.097 0.27 2 -0.45 19 21
negative regulation of cAMP metabolic process -0.13 0.23 0.31 2 -0.42 348 350
MAPK3 -0.18 0.3 0.3 13 -0.58 357 370
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
KDR 0.011 0.044 -10000 0 -0.57 5 5
PLCB2 -0.025 0.097 0.29 7 -0.41 19 26
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.081 -10000 0 -0.39 18 18
receptor internalization -0.035 0.088 -10000 0 -0.42 19 19
PTGS2 -0.33 0.5 0.38 3 -1 367 370
Rac1/GTP -0.032 0.081 -10000 0 -0.39 18 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.25 7 -10000 0 7
negative regulation of T cell proliferation -0.13 0.23 0.31 2 -0.42 348 350
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.06 -10000 0 -0.57 10 10
MAPK1 -0.2 0.33 0.34 2 -0.62 372 374
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.31 4 -0.48 17 21
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Aurora C signaling

Figure 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
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.078 0.31 10 -0.3 1 11
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.019 -10000 0 -0.3 2 2
AURKB 0.14 0.12 0.26 560 -10000 0 560
AURKC 0.026 0.032 0.26 14 -0.57 1 15
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.01 0.024 0.13 40 -10000 0 40
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.031 0.11 -10000 0 -0.41 45 45
STXBP1 0.02 0.048 -10000 0 -0.57 7 7
ACh/CHRNA1 0.072 0.09 0.19 351 -0.16 8 359
RAB3GAP2/RIMS1/UNC13B 0.036 0.087 -10000 0 -0.36 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.14 0.26 117 -0.57 45 162
mol:ACh -0.003 0.036 0.089 12 -0.14 43 55
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.021 0.082 0.23 1 -0.27 40 41
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.072 0.09 0.19 351 -0.15 8 359
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.26 362 -10000 0 362
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.032 0.11 0.2 196 -0.36 43 239
SNAP25 0 0.058 0.094 59 -0.3 34 93
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.046 0.15 0.26 204 -0.57 39 243
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.036 -10000 0 -0.36 7 7
STX1A/SNAP25 fragment 1/VAMP2 0.021 0.082 0.23 1 -0.27 40 41
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.36 330 330
fibroblast growth factor receptor signaling pathway -0.1 0.18 -10000 0 -0.36 330 330
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
PRNP 0.015 0.072 -10000 0 -0.57 16 16
GPC1/SLIT2 -0.015 0.14 -10000 0 -0.42 116 116
SMAD2 -0.001 0.068 0.24 1 -0.33 42 43
GPC1/PrPc/Cu2+ 0.026 0.05 -10000 0 -0.36 17 17
GPC1/Laminin alpha1 -0.011 0.14 -10000 0 -0.42 106 106
TDGF1 0.019 0.048 0.26 1 -0.57 7 8
CRIPTO/GPC1 0.031 0.042 -10000 0 -0.42 8 8
APP/GPC1 0.035 0.02 -10000 0 -0.42 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.006 0.034 -10000 0 -0.36 8 8
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.031 0.082 -10000 0 -0.36 43 43
SERPINC1 0.031 0.05 0.26 50 -10000 0 50
FYN 0.005 0.037 -10000 0 -0.36 10 10
FGR 0.006 0.034 -10000 0 -0.36 8 8
positive regulation of MAPKKK cascade 0.011 0.079 0.28 3 -0.36 23 26
SLIT2 -0.04 0.18 -10000 0 -0.57 115 115
GPC1/NRG -0.11 0.2 -10000 0 -0.42 293 293
NRG1 -0.14 0.26 0.26 4 -0.57 292 296
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.025 -10000 0 -0.36 1 1
LYN 0.006 0.031 -10000 0 -0.36 6 6
mol:Spermine 0.006 0.016 -10000 0 -0.42 1 1
cell growth -0.1 0.18 -10000 0 -0.36 330 330
BMP signaling pathway -0.025 0.025 0.56 1 -0.26 6 7
SRC 0.006 0.034 -10000 0 -0.36 8 8
TGFBR1 0.024 0.008 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.27 0.26 26 -0.57 310 336
GPC1 0.025 0.025 0.26 6 -0.57 1 7
TGFBR1 (dimer) 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 7 -10000 0 7
BLK 0.021 0.062 -10000 0 -0.37 10 10
HCK 0.008 0.037 -10000 0 -0.36 8 8
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 42 42
cell death 0.035 0.02 -10000 0 -0.42 1 1
ATIII/GPC1 0.037 0.04 -10000 0 -0.42 1 1
PLA2G2A/GPC1 -0.098 0.21 -10000 0 -0.42 310 310
LCK 0.007 0.056 -10000 0 -0.36 19 19
neuron differentiation -0.11 0.2 -10000 0 -0.42 293 293
PrPc/Cu2+ 0.011 0.053 -10000 0 -0.42 16 16
APP 0.024 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.001 0.11 -10000 0 -0.56 42 42
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.006 0.07 0.34 1 -0.33 10 11
alphaM/beta2 Integrin/GPIbA 0.01 0.075 0.33 4 -0.4 6 10
alphaM/beta2 Integrin/proMMP-9 0.074 0.11 0.34 17 -0.41 1 18
PLAUR 0.042 0.062 0.26 83 -10000 0 83
HMGB1 -0.003 0.04 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.009 0.063 0.34 1 -10000 0 1
AGER -0.006 0.05 0.26 1 -0.47 3 4
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.025 0.14 0.32 4 -0.36 14 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
CYR61 -0.004 0.12 -10000 0 -0.57 51 51
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.36 36 36
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.092 0.23 -10000 0 -0.56 206 206
MYH2 -0.013 0.14 0.25 20 -0.39 59 79
MST1R 0.022 0.053 0.26 10 -0.57 7 17
leukocyte activation during inflammatory response -0.18 0.17 0.29 1 -0.33 587 588
APOB -0.33 0.29 -10000 0 -0.57 647 647
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.048 0.26 1 -0.57 7 8
JAM3 0.019 0.041 -10000 0 -0.57 5 5
GP1BA 0.024 0.057 0.26 26 -0.57 6 32
alphaM/beta2 Integrin/CTGF 0.004 0.077 0.34 1 -0.39 14 15
alphaM/beta2 Integrin -0.012 0.12 0.2 8 -0.36 50 58
JAM3 homodimer 0.019 0.041 -10000 0 -0.56 5 5
ICAM2 0.019 0.041 -10000 0 -0.57 5 5
ICAM1 0.027 0.027 0.26 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.011 0.12 0.22 6 -0.37 49 55
cell adhesion 0.01 0.075 0.33 4 -0.4 6 10
NFKB1 -0.098 0.2 0.41 5 -0.37 337 342
THY1 0.024 0.021 0.26 8 -10000 0 8
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.21 0.19 -10000 0 -0.36 646 646
alphaM/beta2 Integrin/LRP/tPA 0.008 0.09 0.34 1 -0.35 31 32
IL6 -0.26 0.39 0.37 3 -0.76 391 394
ITGB2 -0.002 0.052 0.26 16 -10000 0 16
elevation of cytosolic calcium ion concentration 0.031 0.085 0.33 20 -10000 0 20
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 0.34 1 -0.38 47 48
JAM2 -0.007 0.13 -10000 0 -0.57 55 55
alphaM/beta2 Integrin/ICAM1 0.024 0.086 0.34 3 -0.33 17 20
alphaM/beta2 Integrin/uPA/Plg 0.019 0.07 0.33 1 -10000 0 1
RhoA/GTP -0.018 0.15 0.24 17 -0.35 102 119
positive regulation of phagocytosis -0.001 0.1 0.3 5 -0.36 19 24
Ron/MSP 0.03 0.061 0.36 1 -0.4 18 19
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.087 0.34 20 -10000 0 20
alphaM/beta2 Integrin/uPAR 0.02 0.079 0.38 4 -10000 0 4
PLAU 0.03 0.036 0.26 26 -10000 0 26
PLAT 0.006 0.091 0.26 1 -0.57 26 27
actin filament polymerization -0.011 0.14 0.26 16 -0.38 54 70
MST1 0.021 0.055 0.26 8 -0.57 8 16
alphaM/beta2 Integrin/lipoprotein(a) -0.18 0.17 0.32 1 -0.33 587 588
TNF -0.098 0.2 0.39 3 -0.76 17 20
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.013 0.068 0.34 1 -0.17 1 2
fibrinolysis 0.017 0.069 0.32 1 -10000 0 1
HCK 0.027 0.026 0.26 13 -10000 0 13
dendritic cell antigen processing and presentation -0.011 0.12 0.22 6 -0.37 49 55
VTN 0.033 0.077 0.26 68 -0.57 8 76
alphaM/beta2 Integrin/CYR61 -0.008 0.1 0.34 1 -0.37 54 55
LPA 0.018 0.017 0.26 5 -10000 0 5
LRP1 0.018 0.062 -10000 0 -0.57 12 12
cell migration 0.043 0.083 0.28 15 -0.36 8 23
FN1 0.11 0.11 0.26 421 -10000 0 421
alphaM/beta2 Integrin/Thy1 0.01 0.063 0.34 1 -10000 0 1
MPO -0.01 0.13 0.26 2 -0.57 58 60
KNG1 0.023 0.032 0.26 20 -10000 0 20
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.012 0.15 0.25 29 -0.38 63 92
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.021 0.26 8 -10000 0 8
CTGF 0.016 0.068 0.26 3 -0.57 14 17
alphaM/beta2 Integrin/Hck 0.011 0.067 0.35 5 -10000 0 5
ITGAM -0.003 0.043 0.24 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.044 0.16 0.34 1 -0.36 188 189
HP -0.07 0.22 0.26 34 -0.57 178 212
leukocyte adhesion -0.039 0.14 0.28 4 -0.37 61 65
SELP -0.093 0.23 -10000 0 -0.57 206 206
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.033 0.077 -10000 0 -0.34 40 40
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.12 0.26 1 -0.3 110 111
AP1 -0.093 0.19 -10000 0 -0.33 392 392
mol:PIP3 -0.13 0.18 -10000 0 -0.33 422 422
AKT1 0.006 0.08 0.31 3 -0.42 13 16
PTK2B -0.027 0.1 -10000 0 -0.31 75 75
RHOA 0.003 0.061 0.26 2 -0.3 27 29
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.11 0.24 8 -0.28 111 119
MAGI3 0.023 0.018 -10000 0 -0.56 1 1
RELA 0.024 0.005 -10000 0 -10000 0 0
apoptosis -0.025 0.12 0.17 1 -0.31 145 146
HRAS/GDP 0.019 0.015 0.18 9 -10000 0 9
positive regulation of microtubule depolymerization -0.05 0.12 0.26 3 -0.31 135 138
NF kappa B1 p50/RelA -0.011 0.12 -10000 0 -0.32 122 122
endothelial cell migration 0.002 0.081 0.26 1 -0.42 33 34
ADCY4 -0.023 0.12 -10000 0 -0.47 50 50
ADCY5 -0.076 0.15 -10000 0 -0.44 99 99
ADCY6 -0.015 0.099 -10000 0 -0.46 35 35
ADCY7 -0.014 0.098 -10000 0 -0.46 36 36
ADCY1 -0.017 0.11 -10000 0 -0.48 40 40
ADCY2 -0.029 0.13 -10000 0 -0.47 57 57
ADCY3 -0.015 0.099 -10000 0 -0.44 37 37
ADCY8 -0.012 0.091 -10000 0 -0.44 31 31
ADCY9 -0.015 0.098 -10000 0 -0.46 35 35
GSK3B -0.026 0.099 0.22 10 -0.33 54 64
arachidonic acid secretion -0.019 0.11 -10000 0 -0.37 69 69
GNG2 0.017 0.065 -10000 0 -0.56 13 13
TRIP6 0.018 0.015 -10000 0 -0.4 1 1
GNAO1 0.002 0.083 -10000 0 -0.36 47 47
HRAS 0.026 0.022 0.26 9 -10000 0 9
NFKBIA -0.02 0.13 0.26 6 -0.33 116 122
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.027 0.12 -10000 0 -0.81 22 22
JUN 0.02 0.044 -10000 0 -0.57 6 6
LPA/LPA2/NHERF2 0.031 0.017 -10000 0 -10000 0 0
TIAM1 0.012 0.14 -10000 0 -0.95 22 22
PIK3R1 0.016 0.065 -10000 0 -0.56 13 13
mol:IP3 -0.013 0.11 0.24 8 -0.28 111 119
PLCB3 0.025 0.045 0.19 14 -10000 0 14
FOS -0.14 0.27 -10000 0 -0.57 306 306
positive regulation of mitosis -0.019 0.11 -10000 0 -0.37 69 69
LPA/LPA1-2-3 0.002 0.14 -10000 0 -0.33 144 144
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
stress fiber formation -0.016 0.1 -10000 0 -0.34 55 55
GNAZ 0.003 0.07 -10000 0 -0.34 40 40
EGFR/PI3K-beta/Gab1 -0.13 0.2 -10000 0 -0.35 423 423
positive regulation of dendritic cell cytokine production 0.001 0.13 -10000 0 -0.33 144 144
LPA/LPA2/MAGI-3 0.033 0.02 -10000 0 -0.35 1 1
ARHGEF1 0.018 0.07 -10000 0 -0.3 25 25
GNAI2 0.006 0.06 -10000 0 -0.33 32 32
GNAI3 0.006 0.06 -10000 0 -0.33 32 32
GNAI1 -0.013 0.11 -10000 0 -0.37 83 83
LPA/LPA3 -0.025 0.14 0.18 39 -0.4 124 163
LPA/LPA2 0.019 0.015 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.071 -10000 0 -0.37 34 34
HB-EGF/EGFR -0.079 0.2 0.27 2 -0.34 362 364
HBEGF 0.066 0.073 0.27 24 -0.42 3 27
mol:DAG -0.013 0.11 0.24 8 -0.28 111 119
cAMP biosynthetic process -0.033 0.11 0.32 2 -0.41 62 64
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.27 25 -0.33 95 120
GNAQ -0.02 0.11 0.18 4 -0.3 125 129
LPAR2 0.025 0.011 0.26 2 -10000 0 2
LPAR3 -0.034 0.19 0.26 39 -0.57 119 158
LPAR1 0.012 0.088 -10000 0 -0.49 29 29
IL8 -0.13 0.23 0.35 30 -0.41 358 388
PTK2 -0.022 0.1 0.24 1 -0.31 102 103
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 0.17 1 -0.32 145 146
EGFR -0.19 0.28 -10000 0 -0.57 390 390
PLCG1 -0.022 0.11 0.2 4 -0.32 120 124
PLD2 -0.027 0.12 0.24 1 -0.31 141 142
G12/G13 0.036 0.061 -10000 0 -0.31 26 26
PI3K-beta 0 0.079 -10000 0 -0.45 15 15
cell migration 0.002 0.063 -10000 0 -0.25 21 21
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
PXN -0.017 0.1 -10000 0 -0.35 55 55
HRAS/GTP -0.02 0.11 -10000 0 -0.38 69 69
RAC1 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
PRKCE 0.024 0.003 -10000 0 -10000 0 0
PRKCD -0.014 0.1 0.3 2 -0.28 100 102
Gi(beta/gamma) -0.014 0.11 -10000 0 -0.44 47 47
mol:LPA 0.001 0.016 -10000 0 -0.16 10 10
TRIP6/p130 Cas/FAK1/Paxillin -0.013 0.12 -10000 0 -0.4 36 36
MAPKKK cascade -0.019 0.11 -10000 0 -0.37 69 69
contractile ring contraction involved in cytokinesis 0.002 0.063 0.26 2 -0.3 27 29
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.02 0.11 0.21 1 -0.31 127 128
GNA15 -0.018 0.1 0.18 5 -0.3 124 129
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.051 0.12 0.26 3 -0.32 135 138
GNA11 -0.02 0.1 0.18 3 -0.31 123 126
Rac1/GTP 0.028 0.13 -10000 0 -0.86 22 22
MMP2 0.002 0.081 0.26 1 -0.43 33 34
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.035 -10000 0 -0.37 6 6
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.38 407 407
PTK2 -0.055 0.15 0.3 4 -0.48 57 61
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.067 0.26 6 -0.57 13 19
SRC 0.023 0.005 -10000 0 -10000 0 0
CDKN1B -0.044 0.12 -10000 0 -0.53 35 35
VEGFA 0.025 0.019 0.26 7 -10000 0 7
ILK -0.042 0.12 -10000 0 -0.5 31 31
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
AKT1 -0.043 0.1 -10000 0 -0.49 27 27
PTK2B -0.013 0.069 0.36 2 -0.33 33 35
alphaV/beta3 Integrin/JAM-A -0.076 0.17 0.3 1 -0.33 296 297
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.032 0.072 -10000 0 -0.36 33 33
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.19 -10000 0 -0.38 246 246
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.013 0.068 -10000 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 0.043 0.081 -10000 0 -0.36 33 33
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.45 359 359
PI4 Kinase 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.068 0.099 0.34 3 -0.35 33 36
RPS6KB1 -0.16 0.22 0.42 3 -0.54 187 190
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.57 351 351
GPR124 0.016 0.048 -10000 0 -0.57 7 7
MAPK1 -0.2 0.29 -10000 0 -0.57 367 367
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
alphaV/beta3 Integrin/Tumstatin -0.031 0.16 -10000 0 -0.37 197 197
cell adhesion 0.023 0.082 0.25 1 -0.36 42 43
ANGPTL3 0.021 0.015 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.032 -10000 0 -0.36 4 4
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.001 0.11 -10000 0 -0.57 42 42
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
RAC1 0.024 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.025 0.077 -10000 0 -0.39 29 29
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.018 -10000 0 -0.57 1 1
alphaV/beta3 Integrin/CD47 0.034 0.072 -10000 0 -0.36 33 33
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.014 0.13 -10000 0 -0.45 72 72
CSF1 0.021 0.044 -10000 0 -0.57 6 6
PIK3C2A -0.04 0.11 -10000 0 -0.49 28 28
PI4 Kinase/Pyk2 -0.076 0.15 -10000 0 -0.3 246 246
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.078 -10000 0 -0.36 33 33
FAK1/Vinculin -0.037 0.13 0.31 6 -0.39 47 53
alphaV beta3/Integrin/ppsTEM5 0.026 0.077 -10000 0 -0.4 29 29
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.033 0.077 0.26 68 -0.57 8 76
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
F11R -0.12 0.19 -10000 0 -0.42 312 312
alphaV/beta3 Integrin/Lactadherin 0.03 0.087 0.34 1 -0.38 42 43
alphaV/beta3 Integrin/TGFBR2 0.02 0.12 -10000 0 -0.45 55 55
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.038 -10000 0 -0.33 6 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.065 -10000 0 -0.33 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.11 0.26 421 -10000 0 421
alphaV/beta3 Integrin/Pyk2 0.027 0.072 -10000 0 -0.33 33 33
SDC1 0.038 0.059 0.26 68 -0.57 1 69
VAV3 -0.011 0.041 -10000 0 -0.31 13 13
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
FAK1/Paxillin -0.037 0.13 0.31 6 -0.39 48 54
cell migration -0.036 0.12 0.28 9 -0.36 43 52
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.066 0.17 -10000 0 -0.32 262 262
SPP1 0.084 0.1 0.26 279 -10000 0 279
KDR 0.021 0.04 -10000 0 -0.57 5 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.074 0.22 0.26 4 -0.57 179 183
angiogenesis -0.19 0.3 0.3 1 -0.58 338 339
Rac1/GTP 0.021 0.038 -10000 0 -0.29 12 12
EDIL3 -0.007 0.14 0.26 15 -0.57 62 77
cell proliferation 0.02 0.12 -10000 0 -0.45 55 55
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.043 0.17 0.3 129 -0.49 47 176
FYN 0.02 0.19 0.32 63 -0.53 67 130
LAT/GRAP2/SLP76 0.026 0.17 0.34 48 -0.51 55 103
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.022 0.15 0.3 83 -0.36 81 164
B2M 0.024 0.008 -10000 0 -10000 0 0
IKBKG 0.016 0.058 0.16 76 -0.13 29 105
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
mol:Ca2+ -0.022 0.032 -10000 0 -0.092 157 157
integrin-mediated signaling pathway 0.026 0.022 -10000 0 -0.36 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.2 0.35 50 -0.52 81 131
TRPV6 -0.089 0.26 1.2 15 -0.57 195 210
CD28 0.024 0.05 0.26 10 -0.57 6 16
SHC1 0.029 0.21 0.31 155 -0.54 68 223
receptor internalization -0.012 0.22 0.35 36 -0.49 130 166
PRF1 -0.011 0.24 0.55 7 -0.97 43 50
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
COT/AKT1 0.031 0.13 0.29 76 -0.32 64 140
LAT 0.012 0.2 0.32 71 -0.49 88 159
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.023 0.095 0.26 49 -0.57 19 68
CD3E 0.023 0.086 0.27 37 -0.58 16 53
CD3G 0.012 0.11 0.26 38 -0.57 33 71
RASGRP2 0 0.05 0.14 15 -0.17 69 84
RASGRP1 0.024 0.15 0.33 53 -0.41 59 112
HLA-A 0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.019 0.033 0.26 1 -0.57 3 4
RAP1A/GTP/RAPL 0.026 0.022 -10000 0 -0.36 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.079 0.17 170 -0.13 27 197
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.055 -10000 0 -0.22 39 39
PRKCA 0.013 0.098 0.23 46 -0.27 52 98
GRAP2 0.017 0.063 0.25 3 -0.57 12 15
mol:IP3 0.014 0.14 0.26 129 -0.38 51 180
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.004 0.17 0.3 36 -0.66 48 84
ORAI1 0.037 0.17 0.64 4 -0.96 15 19
CSK 0.007 0.2 0.36 37 -0.55 71 108
B7 family/CD28 0.062 0.21 0.45 40 -0.61 50 90
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0 0.22 0.38 37 -0.52 109 146
PTPN6 0.003 0.19 0.33 45 -0.55 69 114
VAV1 0.003 0.2 0.35 42 -0.48 98 140
Monovalent TCR/CD3 -0.001 0.14 0.26 38 -0.5 56 94
CBL 0.022 0.007 -10000 0 -10000 0 0
LCK 0.017 0.2 0.32 64 -0.57 64 128
PAG1 0.02 0.2 0.32 68 -0.55 67 135
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.22 0.36 37 -0.51 106 143
CD80 0.084 0.1 0.26 279 -10000 0 279
CD86 0.026 0.018 0.26 6 -10000 0 6
PDK1/CARD11/BCL10/MALT1 -0.005 0.071 0.19 4 -0.25 42 46
HRAS 0.026 0.022 0.26 9 -10000 0 9
GO:0035030 0.021 0.16 0.32 43 -0.49 53 96
CD8A 0.029 0.057 0.27 29 -0.58 5 34
CD8B 0.014 0.11 0.27 30 -0.57 32 62
PTPRC 0.022 0.041 0.26 12 -0.57 3 15
PDK1/PKC theta 0.023 0.18 0.37 78 -0.46 71 149
CSK/PAG1 0.021 0.19 0.31 70 -0.57 57 127
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.01 -10000 0 -10000 0 0
GRAP2/SLP76 0.019 0.2 0.38 35 -0.59 59 94
STIM1 0.025 0.095 1.3 4 -10000 0 4
RAS family/GTP 0.044 0.091 0.21 100 -0.19 37 137
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.23 0.35 36 -0.52 135 171
mol:DAG -0.016 0.096 0.13 17 -0.33 56 73
RAP1A/GDP 0.021 0.038 0.1 77 -10000 0 77
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.017 0.077 0.26 16 -0.57 15 31
cytotoxic T cell degranulation -0.009 0.22 0.54 7 -0.9 43 50
RAP1A/GTP -0.001 0.017 -10000 0 -0.064 66 66
mol:PI-3-4-5-P3 0.017 0.17 0.33 57 -0.43 80 137
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.021 0.17 0.29 117 -0.5 51 168
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.027 0.098 0.26 61 -0.57 20 81
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.006 0.16 0.36 16 -0.5 54 70
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.032 0.11 0.38 20 -0.48 32 52
CARD11 0.027 0.041 0.26 21 -0.57 2 23
PRKCB 0.014 0.1 0.26 50 -0.27 44 94
PRKCE 0.019 0.094 0.22 56 -0.26 44 100
PRKCQ 0.012 0.2 0.35 53 -0.51 78 131
LCP2 0.024 0.008 0.25 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.14 0.29 86 -0.31 79 165
IKK complex 0.035 0.08 0.2 132 -0.11 29 161
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.025 0.11 0.25 77 -0.27 43 120
PDPK1 0.027 0.15 0.34 80 -0.35 74 154
TCR/CD3/MHC I/CD8/Fyn -0.028 0.24 0.39 29 -0.67 84 113
Syndecan-1-mediated signaling events

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
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CCL5 0.029 0.056 0.26 38 -0.57 4 42
SDCBP 0.021 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.063 0.12 0.25 35 -0.39 10 45
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.049 0.12 0.26 4 -0.37 17 21
Syndecan-1/Syntenin 0.051 0.12 0.28 9 -0.38 14 23
MAPK3 0.047 0.11 0.26 9 -0.35 15 24
HGF/MET -0.066 0.2 -10000 0 -0.44 226 226
TGFB1/TGF beta receptor Type II 0.025 0.013 0.26 3 -10000 0 3
BSG 0.024 0.009 0.26 1 -10000 0 1
keratinocyte migration 0.049 0.12 0.26 4 -0.36 17 21
Syndecan-1/RANTES 0.058 0.13 0.31 36 -0.39 19 55
Syndecan-1/CD147 0.063 0.12 0.3 9 -0.36 16 25
Syndecan-1/Syntenin/PIP2 0.047 0.11 0.26 9 -0.37 14 23
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.046 0.11 0.25 8 -0.36 14 22
MMP7 -0.037 0.19 0.26 33 -0.57 121 154
HGF -0.011 0.14 0.26 2 -0.57 65 67
Syndecan-1/CASK 0.042 0.12 0.19 63 -0.35 20 83
Syndecan-1/HGF/MET -0.004 0.2 0.3 7 -0.45 115 122
regulation of cell adhesion 0.041 0.11 0.26 8 -0.4 7 15
HPSE 0.027 0.035 0.26 18 -0.57 1 19
positive regulation of cell migration 0.063 0.12 0.25 35 -0.39 10 45
SDC1 0.065 0.12 0.25 34 -0.3 23 57
Syndecan-1/Collagen 0.063 0.12 0.25 35 -0.39 10 45
PPIB 0.024 0.013 0.26 3 -10000 0 3
MET -0.073 0.22 -10000 0 -0.57 177 177
PRKACA 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 453 -0.57 1 454
MAPK1 0.048 0.11 0.27 8 -0.36 12 20
homophilic cell adhesion 0.061 0.12 0.27 24 -0.37 15 39
MMP1 0.18 0.11 0.26 739 -10000 0 739
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.04 0.22 0.41 5 -0.63 113 118
IHH 0.016 0.082 0.26 31 -0.2 73 104
SHH Np/Cholesterol/GAS1 0 0.075 -10000 0 -0.33 49 49
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0 0.075 0.33 49 -10000 0 49
SMO/beta Arrestin2 -0.019 0.21 -10000 0 -0.61 100 100
SMO -0.042 0.21 0.32 1 -0.64 100 101
AKT1 -0.004 0.13 -10000 0 -0.62 23 23
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.018 0.15 -10000 0 -0.57 76 76
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.041 0.21 0.32 1 -0.63 100 101
STIL 0.006 0.17 0.3 30 -0.47 88 118
DHH N/PTCH2 -0.008 0.14 -10000 0 -0.44 98 98
DHH N/PTCH1 -0.027 0.2 -10000 0 -0.51 144 144
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.008 0.096 0.26 2 -0.57 29 31
PTHLH -0.061 0.3 0.42 14 -0.83 120 134
determination of left/right symmetry -0.041 0.21 0.32 1 -0.63 100 101
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
skeletal system development -0.059 0.29 0.42 14 -0.82 120 134
IHH N/Hhip 0.027 0.056 0.23 2 -0.46 2 4
DHH N/Hhip 0.022 0.077 -10000 0 -0.41 31 31
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.041 0.21 0.32 1 -0.63 100 101
pancreas development 0.023 0.03 0.26 5 -0.56 2 7
HHAT 0.02 0.02 -10000 0 -0.57 1 1
PI3K 0.028 0.049 -10000 0 -0.4 13 13
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.009 0.14 -10000 0 -0.57 61 61
somite specification -0.041 0.21 0.32 1 -0.63 100 101
SHH Np/Cholesterol/PTCH1 -0.024 0.16 0.3 1 -0.49 93 94
SHH Np/Cholesterol/PTCH2 -0.004 0.082 -10000 0 -0.33 59 59
SHH Np/Cholesterol/Megalin -0.06 0.15 0.28 3 -0.33 229 232
SHH 0 0.037 0.34 7 -0.42 1 8
catabolic process -0.033 0.21 0.31 2 -0.56 126 128
SMO/Vitamin D3 -0.009 0.2 0.34 20 -0.57 90 110
SHH Np/Cholesterol/Hhip 0.015 0.028 0.25 3 -0.33 3 6
LRP2 -0.12 0.26 0.26 26 -0.57 277 303
receptor-mediated endocytosis -0.079 0.22 0.3 11 -0.62 101 112
SHH Np/Cholesterol/BOC -0.004 0.083 -10000 0 -0.33 61 61
SHH Np/Cholesterol/CDO 0.013 0.04 -10000 0 -0.33 12 12
mesenchymal cell differentiation -0.015 0.028 0.33 3 -0.24 3 6
mol:Vitamin D3 0.002 0.18 0.34 21 -0.49 93 114
IHH N/PTCH2 -0.006 0.14 -10000 0 -0.46 78 78
CDON 0.015 0.065 -10000 0 -0.57 13 13
IHH N/PTCH1 -0.024 0.21 0.35 4 -0.57 126 130
Megalin/LRPAP1 -0.079 0.2 -10000 0 -0.42 280 280
PTCH2 -0.018 0.15 -10000 0 -0.57 76 76
SHH Np/Cholesterol 0.01 0.013 -10000 0 -0.33 1 1
PTCH1 -0.033 0.21 0.31 2 -0.57 126 128
HHIP 0.023 0.03 0.26 5 -0.57 2 7
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.028 0.22 0.63 2 -0.68 22 24
CRP -0.007 0.24 0.66 7 -0.71 18 25
cell cycle arrest -0.039 0.25 0.56 11 -0.69 43 54
TIMP1 -0.021 0.21 0.61 2 -0.63 21 23
IL6ST -0.037 0.19 -10000 0 -0.56 120 120
Rac1/GDP -0.069 0.2 0.38 2 -0.49 94 96
AP1 -0.073 0.21 0.37 1 -0.53 72 73
GAB2 0.022 0.02 -10000 0 -0.57 1 1
TNFSF11 -0.018 0.24 0.59 12 -0.69 20 32
HSP90B1 0.022 0.11 -10000 0 -0.79 11 11
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.095 0.18 -10000 0 -0.52 92 92
AKT1 0.022 0.066 -10000 0 -0.66 4 4
FOXO1 0.023 0.068 0.43 1 -0.54 5 6
MAP2K6 -0.096 0.18 0.27 2 -0.5 110 112
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.053 0.2 0.39 11 -0.5 77 88
MITF -0.09 0.19 0.31 3 -0.42 172 175
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.004 -10000 0 -10000 0 0
A2M -0.003 0.18 -10000 0 -1.2 25 25
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.018 0.13 -10000 0 -0.51 35 35
STAT3 -0.045 0.26 0.56 10 -0.75 43 53
STAT1 0.012 0.093 -10000 0 -0.83 10 10
CEBPD -0.014 0.23 0.57 9 -0.68 28 37
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.05 -10000 0 -0.4 13 13
JUN 0.02 0.044 -10000 0 -0.57 6 6
PIAS3/MITF -0.072 0.18 0.32 2 -0.49 85 87
MAPK11 -0.095 0.18 -10000 0 -0.54 87 87
STAT3 (dimer)/FOXO1 -0.026 0.22 0.51 13 -0.61 33 46
GRB2/SOS1/GAB family -0.061 0.18 -10000 0 -0.48 78 78
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.19 -10000 0 -0.4 187 187
GRB2 0.023 0.009 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.17 0.46 0.64 11 -0.93 257 268
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.026 0.008 -10000 0 -10000 0 0
MYC -0.004 0.27 0.57 14 -0.97 32 46
FGG -0.026 0.23 0.6 12 -0.69 22 34
macrophage differentiation -0.039 0.25 0.56 11 -0.69 43 54
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.092 0.21 -10000 0 -0.35 360 360
JUNB -0.03 0.22 0.6 2 -0.67 20 22
FOS -0.14 0.27 -10000 0 -0.57 306 306
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.093 0.2 0.29 11 -0.42 181 192
STAT1/PIAS1 -0.061 0.2 0.35 10 -0.46 99 109
GRB2/SOS1/GAB family/SHP2/PI3K 0.023 0.07 -10000 0 -0.52 8 8
STAT3 (dimer) -0.044 0.26 0.56 10 -0.74 43 53
PRKCD -0.037 0.2 0.45 15 -0.53 53 68
IL6R 0.001 0.11 -10000 0 -0.56 38 38
SOCS3 -0.092 0.19 -10000 0 -0.65 50 50
gp130 (dimer)/JAK1/JAK1/LMO4 0.012 0.13 -10000 0 -0.35 120 120
Rac1/GTP -0.064 0.2 0.34 10 -0.49 94 104
HCK 0.026 0.026 0.26 13 -10000 0 13
MAPKKK cascade -0.002 0.14 -10000 0 -0.61 31 31
bone resorption -0.015 0.23 0.59 12 -0.66 20 32
IRF1 -0.031 0.22 0.63 2 -0.66 27 29
mol:GDP -0.084 0.19 0.28 12 -0.4 176 188
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.085 0.2 0.28 12 -0.41 176 188
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.2 -10000 0 -0.58 99 99
PTPN11 0.011 0.081 -10000 0 -0.84 8 8
IL6/IL6RA -0.12 0.22 0.22 1 -0.38 391 392
gp130 (dimer)/TYK2/TYK2/LMO4 0.007 0.13 -10000 0 -0.35 120 120
gp130 (dimer)/JAK2/JAK2/LMO4 0.007 0.13 -10000 0 -0.35 114 114
IL6 -0.18 0.28 0.27 1 -0.56 380 381
PIAS3 0.02 0.009 -10000 0 -10000 0 0
PTPRE 0.008 0.035 -10000 0 -0.57 2 2
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.11 0.19 0.22 2 -0.34 320 322
LMO4 0.028 0.036 0.28 2 -0.56 3 5
STAT3 (dimer)/PIAS3 -0.049 0.24 0.53 10 -0.71 41 51
MCL1 0.053 0.098 0.49 1 -0.55 5 6
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.042 0.14 0.35 67 -0.34 55 122
TBX21 0.014 0.34 0.75 22 -1.2 53 75
B2M 0.025 0.012 -10000 0 -10000 0 0
TYK2 0.024 0.036 -10000 0 -10000 0 0
IL12RB1 0.031 0.071 0.32 41 -0.6 2 43
GADD45B 0.037 0.26 0.66 19 -0.9 31 50
IL12RB2 0.028 0.15 0.27 120 -0.57 42 162
GADD45G 0.055 0.26 0.65 28 -0.85 33 61
natural killer cell activation 0.007 0.025 0.081 53 -0.042 26 79
RELB 0.026 0.022 0.26 10 -10000 0 10
RELA 0.023 0.005 -10000 0 -10000 0 0
IL18 0.034 0.04 0.27 26 -10000 0 26
IL2RA 0.027 0.088 0.26 58 -0.57 15 73
IFNG 0.054 0.08 0.26 146 -10000 0 146
STAT3 (dimer) 0.035 0.24 0.56 39 -0.7 46 85
HLA-DRB5 -0.006 0.011 -10000 0 -0.025 250 250
FASLG 0.049 0.31 0.72 35 -1 43 78
NF kappa B2 p52/RelB 0.022 0.25 0.63 6 -0.76 56 62
CD4 0.009 0.024 -10000 0 -10000 0 0
SOCS1 0.025 0.033 0.26 14 -0.57 1 15
EntrezGene:6955 -0.006 0.016 0.023 57 -0.028 274 331
CD3D 0.009 0.098 0.26 44 -0.58 19 63
CD3E 0.009 0.089 0.26 37 -0.57 16 53
CD3G -0.001 0.12 0.26 38 -0.57 33 71
IL12Rbeta2/JAK2 0.037 0.12 0.31 24 -0.43 42 66
CCL3 0.033 0.28 0.69 21 -0.96 34 55
CCL4 0.035 0.27 0.68 22 -0.93 33 55
HLA-A 0.002 0.008 0.023 73 -0.046 13 86
IL18/IL18R 0.065 0.12 0.38 15 -0.37 52 67
NOS2 0.032 0.28 0.68 23 -0.95 37 60
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.14 0.35 58 -0.34 57 115
IL1R1 0.017 0.31 0.69 21 -1.1 44 65
IL4 -0.011 0.037 -10000 0 -10000 0 0
JAK2 0.023 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.005 0.014 0.023 58 -0.026 248 306
TCR/CD3/MHC I/CD8 -0.024 0.22 0.37 33 -0.78 56 89
RAB7A 0.052 0.24 0.64 19 -0.8 24 43
lysosomal transport 0.053 0.23 0.61 23 -0.75 24 47
FOS -0.32 0.62 0.6 12 -1.2 348 360
STAT4 (dimer) 0.062 0.28 0.58 43 -0.84 48 91
STAT5A (dimer) 0.047 0.28 0.59 55 -0.75 56 111
GZMA 0.025 0.29 0.69 29 -1.1 34 63
GZMB 0.023 0.32 0.69 30 -1.1 45 75
HLX 0.021 0.015 0.26 3 -10000 0 3
LCK 0.028 0.29 0.66 36 -0.84 59 95
TCR/CD3/MHC II/CD4 -0.054 0.17 0.24 27 -0.32 215 242
IL2/IL2R 0.065 0.098 0.41 39 -0.36 21 60
MAPK14 0.048 0.27 0.64 28 -0.86 38 66
CCR5 0.037 0.27 0.69 28 -0.9 32 60
IL1B 0.017 0.078 0.29 3 -0.58 14 17
STAT6 0.039 0.12 0.4 33 -0.6 7 40
STAT4 0.001 0.12 0.26 1 -0.57 43 44
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 0.26 19 -10000 0 19
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.008 0.26 1 -10000 0 1
IL12B 0.072 0.11 0.28 227 -10000 0 227
CD8A 0.029 0.059 0.28 29 -0.57 5 34
CD8B 0.014 0.11 0.27 30 -0.57 32 62
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.042 0.14 0.34 55 -0.35 67 122
IL2RB 0.03 0.05 0.26 38 -0.57 2 40
proteasomal ubiquitin-dependent protein catabolic process 0.066 0.26 0.56 46 -0.76 47 93
IL2RG 0.03 0.067 0.26 46 -0.57 7 53
IL12 0.049 0.15 0.3 93 -0.42 57 150
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
CD247 0.006 0.079 0.26 16 -0.57 15 31
IL2 0.022 0.021 0.26 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.004 0.14 0.29 18 -0.58 57 75
IL12/IL12R/TYK2/JAK2 0.033 0.3 0.67 43 -0.86 56 99
MAP2K3 0.042 0.28 0.63 28 -0.84 46 74
RIPK2 0.02 0.016 0.26 3 -10000 0 3
MAP2K6 0.046 0.27 0.62 31 -0.82 43 74
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.013 -10000 0 -0.028 279 279
IL18RAP 0.012 0.11 0.28 5 -0.57 35 40
IL12Rbeta1/TYK2 0.04 0.068 0.29 32 -0.46 2 34
EOMES -0.021 0.18 -10000 0 -1 30 30
STAT1 (dimer) 0.067 0.26 0.61 65 -0.72 40 105
T cell proliferation 0.049 0.22 0.49 31 -0.64 43 74
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.08 -10000 0 -0.57 19 19
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.012 0.19 0.38 4 -0.71 41 45
ATF2 0.045 0.25 0.6 28 -0.79 39 67
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.005 0.11 -10000 0 -0.36 95 95
EFNA5 -0.028 0.17 0.26 1 -0.57 95 96
FYN -0.023 0.098 -10000 0 -0.33 95 95
neuron projection morphogenesis -0.005 0.11 -10000 0 -0.36 95 95
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.004 0.11 -10000 0 -0.36 95 95
EPHA5 0.023 0.017 0.26 5 -10000 0 5
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.014 0.14 0.41 87 -0.22 12 99
KIRREL -0.024 0.16 -10000 0 -0.57 87 87
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.014 0.14 0.22 12 -0.42 87 99
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.034 0.12 0.27 9 -0.32 84 93
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.008 0.088 0.24 1 -0.28 71 72
FYN 0.013 0.13 0.27 109 -0.3 83 192
mol:Ca2+ 0.031 0.11 0.26 8 -0.32 79 87
mol:DAG 0.032 0.11 0.26 8 -0.32 79 87
NPHS2 0.014 0.032 0.26 5 -10000 0 5
mol:IP3 0.032 0.11 0.26 8 -0.32 79 87
regulation of endocytosis 0.023 0.1 0.24 6 -0.29 83 89
Nephrin/NEPH1/podocin/Cholesterol 0.023 0.11 0.25 9 -0.32 84 93
establishment of cell polarity 0.014 0.14 0.22 12 -0.41 87 99
Nephrin/NEPH1/podocin/NCK1-2 0.043 0.11 0.3 2 -0.3 82 84
Nephrin/NEPH1/beta Arrestin2 0.026 0.11 0.25 6 -0.29 83 89
NPHS1 0.058 0.089 0.26 166 -10000 0 166
Nephrin/NEPH1/podocin 0.024 0.11 0.3 4 -0.31 83 87
TJP1 0.023 0.019 -10000 0 -0.57 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.033 0.12 0.26 8 -0.32 79 87
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.031 0.12 0.28 7 -0.32 81 88
GRB2 0.023 0.009 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.012 0.13 0.27 110 -0.31 89 199
cytoskeleton organization 0.003 0.11 0.27 17 -0.32 79 96
Nephrin/NEPH1 0.016 0.1 0.19 7 -0.3 85 92
Nephrin/NEPH1/ZO-1 0.025 0.12 -10000 0 -0.34 85 85
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.022 0.026 -10000 0 -0.57 2 2
LAT2 -0.02 0.1 -10000 0 -0.36 58 58
AP1 -0.058 0.18 -10000 0 -0.44 122 122
mol:PIP3 0.009 0.17 0.35 46 -0.42 56 102
IKBKB 0.033 0.13 0.28 119 -0.26 32 151
AKT1 0.012 0.17 0.32 146 -0.44 22 168
IKBKG 0.016 0.11 0.27 53 -0.27 32 85
MS4A2 -0.022 0.15 0.25 5 -0.55 82 87
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.12 0.31 21 -0.39 32 53
mol:Ca2+ 0.014 0.14 0.31 52 -0.32 55 107
LYN 0.022 0.012 -10000 0 -10000 0 0
CBLB -0.019 0.1 -10000 0 -0.36 58 58
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0.001 0.12 -10000 0 -0.33 124 124
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.004 0.17 0.33 126 -0.33 137 263
PTPN13 -0.015 0.15 -10000 0 -0.55 43 43
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.012 0.13 0.33 36 -0.34 31 67
SYK 0.025 0.01 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.027 0.13 -10000 0 -0.36 103 103
LAT -0.019 0.1 -10000 0 -0.36 60 60
PAK2 0.012 0.13 0.29 31 -0.42 33 64
NFATC2 -0.049 0.16 -10000 0 -0.6 75 75
HRAS 0.008 0.13 0.26 22 -0.38 56 78
GAB2 0.021 0.019 -10000 0 -0.57 1 1
PLA2G1B 0.002 0.098 -10000 0 -0.84 12 12
Fc epsilon R1 -0.022 0.16 -10000 0 -0.4 144 144
Antigen/IgE/Fc epsilon R1 -0.018 0.14 -10000 0 -0.36 144 144
mol:GDP -0.014 0.12 0.25 1 -0.39 57 58
JUN 0.02 0.044 -10000 0 -0.57 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
FOS -0.14 0.27 -10000 0 -0.57 306 306
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.017 0.11 -10000 0 -0.3 108 108
CHUK 0.015 0.11 0.27 52 -0.27 32 84
KLRG1 -0.018 0.097 -10000 0 -0.27 109 109
VAV1 -0.02 0.1 -10000 0 -0.36 60 60
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.1 -10000 0 -0.36 56 56
negative regulation of mast cell degranulation -0.007 0.098 -10000 0 -0.3 58 58
BTK -0.013 0.11 -10000 0 -0.46 35 35
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.03 0.13 -10000 0 -0.33 142 142
GAB2/PI3K/SHP2 -0.048 0.1 -10000 0 -0.32 112 112
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.11 -10000 0 -0.29 120 120
RAF1 0.002 0.1 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0.001 0.15 -10000 0 -0.35 146 146
FCER1G 0.019 0.017 0.25 1 -10000 0 1
FCER1A -0.044 0.18 -10000 0 -0.57 115 115
Antigen/IgE/Fc epsilon R1/Fyn -0.009 0.14 -10000 0 -0.34 140 140
MAPK3 0.003 0.099 -10000 0 -0.86 12 12
MAPK1 -0.002 0.1 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.18 -10000 0 -0.59 68 68
DUSP1 -0.045 0.19 -10000 0 -0.57 126 126
NF-kappa-B/RelA 0.007 0.058 0.14 5 -0.17 21 26
actin cytoskeleton reorganization -0.008 0.15 -10000 0 -0.57 37 37
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.12 -10000 0 -0.43 37 37
FER -0.021 0.11 -10000 0 -0.37 61 61
RELA 0.023 0.005 -10000 0 -10000 0 0
ITK -0.012 0.091 -10000 0 -0.4 48 48
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.004 0.13 0.28 9 -0.39 58 67
cytokine secretion -0.003 0.035 -10000 0 -0.15 1 1
SPHK1 -0.018 0.1 0.21 2 -0.35 61 63
PTK2 -0.009 0.15 -10000 0 -0.6 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.024 0.14 -10000 0 -0.38 103 103
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.006 0.16 0.33 42 -0.41 61 103
MAP2K2 -0.001 0.098 -10000 0 -0.85 12 12
MAP2K1 0 0.099 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.095 0.2 1 -0.34 36 37
MAP2K4 -0.072 0.29 -10000 0 -0.83 133 133
Fc epsilon R1/FcgammaRIIB -0.008 0.15 -10000 0 -0.37 146 146
mol:Choline -0.004 0.17 0.33 126 -0.32 137 263
SHC/Grb2/SOS1 0.011 0.11 -10000 0 -0.4 32 32
FYN 0.022 0.026 -10000 0 -0.57 2 2
DOK1 0.025 0.014 0.26 4 -10000 0 4
PXN -0.009 0.14 -10000 0 -0.55 36 36
HCLS1 -0.019 0.1 -10000 0 -0.36 58 58
PRKCB 0.013 0.14 0.31 51 -0.32 61 112
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.007 0.1 -10000 0 -0.31 58 58
LCP2 0.024 0.008 0.26 1 -10000 0 1
PLA2G4A -0.045 0.14 -10000 0 -0.36 132 132
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.17 0.33 126 -0.32 137 263
IKK complex 0.031 0.11 0.28 90 -0.21 18 108
WIPF1 0.024 0.003 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.033 0.15 -10000 0 -0.59 66 66
PDGF/PDGFRA/CRKL -0.011 0.11 -10000 0 -0.42 65 65
positive regulation of JUN kinase activity 0.024 0.083 -10000 0 -0.33 47 47
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.014 0.11 -10000 0 -0.42 67 67
AP1 -0.3 0.44 -10000 0 -0.96 323 323
mol:IP3 -0.036 0.11 -10000 0 -0.45 63 63
PLCG1 -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA/alphaV Integrin -0.011 0.11 -10000 0 -0.43 66 66
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.11 -10000 0 -0.45 63 63
CAV3 0.02 0.011 0.26 2 -10000 0 2
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
SHC/Grb2/SOS1 0.026 0.084 -10000 0 -0.33 47 47
PDGF/PDGFRA/Shf -0.011 0.11 -10000 0 -0.42 67 67
FOS -0.3 0.43 -10000 0 -0.94 323 323
JUN -0.038 0.044 -10000 0 -0.44 6 6
oligodendrocyte development -0.011 0.11 -10000 0 -0.42 66 66
GRB2 0.023 0.009 0.26 1 -10000 0 1
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:DAG -0.036 0.11 -10000 0 -0.45 63 63
PDGF/PDGFRA -0.033 0.15 -10000 0 -0.59 66 66
actin cytoskeleton reorganization -0.011 0.11 -10000 0 -0.42 66 66
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.012 0.11 -10000 0 -0.38 71 71
PDGF/PDGFRA/Crk/C3G 0.015 0.098 -10000 0 -0.36 66 66
JAK1 -0.027 0.1 0.23 1 -0.42 67 68
ELK1/SRF -0.035 0.091 0.32 1 -0.35 64 65
SHB 0.024 0.008 0.26 1 -10000 0 1
SHF 0.024 0.021 0.26 2 -0.57 1 3
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.047 0.11 0.22 1 -0.46 66 67
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.083 -10000 0 -0.33 47 47
PDGF/PDGFRA/SHB -0.011 0.11 -10000 0 -0.42 66 66
PDGF/PDGFRA/Caveolin-1 -0.099 0.22 -10000 0 -0.48 256 256
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.053 0.11 0.24 1 -0.43 65 66
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.012 0.11 -10000 0 -0.42 66 66
JAK-STAT cascade -0.027 0.1 0.23 1 -0.42 67 68
cell proliferation -0.011 0.11 -10000 0 -0.42 67 67
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.001 0.064 0.22 2 -0.32 11 13
adherens junction organization -0.013 0.091 0.22 1 -0.34 50 51
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.085 0.15 0.32 4 -0.28 342 346
FMN1 -0.011 0.085 -10000 0 -0.3 55 55
mol:IP3 -0.001 0.053 -10000 0 -0.28 13 13
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.087 -10000 0 -0.32 48 48
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.002 0.063 -10000 0 -0.28 13 13
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.012 0.13 -10000 0 -0.54 35 35
CTNND1 0.024 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.075 -10000 0 -0.3 42 42
VASP -0.009 0.08 -10000 0 -0.3 46 46
ZYX -0.009 0.081 -10000 0 -0.31 44 44
JUB -0.008 0.082 -10000 0 -0.3 48 48
EGFR(dimer) -0.1 0.18 -10000 0 -0.32 375 375
E-cadherin/beta catenin-gamma catenin 0.033 0.055 -10000 0 -0.35 18 18
mol:PI-3-4-5-P3 0.016 0.073 -10000 0 -0.28 19 19
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.016 0.075 -10000 0 -0.28 19 19
FYN -0.003 0.067 0.22 2 -0.32 12 14
mol:Ca2+ -0.001 0.053 -10000 0 -0.27 13 13
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
mol:DAG -0.001 0.053 -10000 0 -0.28 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
RhoA/GDP -0.084 0.15 0.36 2 -0.33 117 119
establishment of polarity of embryonic epithelium -0.009 0.079 -10000 0 -0.3 46 46
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.57 390 390
CASR -0.003 0.055 0.23 2 -0.27 11 13
RhoA/GTP 0.013 0.057 -10000 0 -0.26 10 10
AKT2 0.001 0.063 -10000 0 -0.29 11 11
actin cable formation -0.016 0.086 0.25 2 -0.32 43 45
apoptosis -0.005 0.073 0.28 23 -0.24 8 31
CTNNA1 0.024 0.006 -10000 0 -10000 0 0
mol:GDP -0.097 0.15 -10000 0 -0.3 345 345
PIP5K1A -0.008 0.077 -10000 0 -0.31 42 42
PLCG1 -0.001 0.054 -10000 0 -0.28 13 13
Rac1/GTP -0.092 0.17 -10000 0 -0.3 367 367
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.034 0.1 0.55 7 -10000 0 7
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.025 0.12 -10000 0 -0.32 18 18
RXRs/LXRs/DNA/Oxysterols -0.006 0.12 -10000 0 -0.42 15 15
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.004 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0 0.083 -10000 0 -0.3 62 62
RXRs/NUR77 -0.05 0.18 -10000 0 -0.35 265 265
RXRs/PPAR -0.1 0.17 -10000 0 -0.32 350 350
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.047 0.043 -10000 0 -0.31 12 12
RARA 0.023 0.012 0.26 2 -10000 0 2
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.036 0.041 -10000 0 -0.3 12 12
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.071 0.18 0.61 99 -10000 0 99
RARs/THRs/DNA/SMRT 0.002 0.079 -10000 0 -0.29 60 60
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.028 0.15 -10000 0 -0.32 215 215
NR1H4 0.021 0.026 0.26 13 -10000 0 13
RXRs/LXRs/DNA -0.006 0.15 -10000 0 -0.3 196 196
NR1H2 0.027 0.012 -10000 0 -10000 0 0
NR1H3 0.028 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.021 0.14 -10000 0 -0.3 214 214
NR4A1 -0.028 0.17 -10000 0 -0.57 95 95
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.031 0.1 -10000 0 -0.23 190 190
RXRG -0.098 0.24 0.26 2 -0.56 219 221
RXR alpha/CCPG 0.035 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.012 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB -0.006 0.13 -10000 0 -0.57 55 55
PPARG -0.12 0.25 -10000 0 -0.57 252 252
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.009 0.14 -10000 0 -1 10 10
mol:Oxysterols 0.004 0.009 -10000 0 -0.12 1 1
cholesterol transport -0.005 0.12 -10000 0 -0.42 15 15
PPARA 0.02 0.044 -10000 0 -0.57 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.016 0.067 -10000 0 -0.57 14 14
RXRs/NUR77/BCL2 -0.069 0.15 -10000 0 -0.3 282 282
SREBF1 -0.006 0.11 0.44 1 -0.5 3 4
RXRs/RXRs/DNA/9cRA -0.028 0.15 -10000 0 -0.32 215 215
ABCA1 -0.01 0.13 -10000 0 -0.8 9 9
RARs/THRs 0.04 0.096 -10000 0 -0.33 60 60
RXRs/FXR -0.024 0.16 -10000 0 -0.33 215 215
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Visual signal transduction: Cones

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.021 0.22 3 -10000 0 3
AES 0.022 0.019 0.21 2 -10000 0 2
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.009 0.095 0.26 2 -0.57 28 30
TLE1 0.019 0.048 0.22 1 -0.57 6 7
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.3 40 -0.37 4 44
WIF1 -0.28 0.3 0.26 13 -0.56 544 557
beta catenin/RanBP3 0.02 0.089 0.42 37 -0.4 1 38
KREMEN2 0.12 0.12 0.26 473 -10000 0 473
DKK1 0.026 0.16 0.26 146 -0.57 54 200
beta catenin/beta TrCP1 0.11 0.094 0.3 29 -0.38 2 31
FZD1 0.024 0.004 -10000 0 -10000 0 0
AXIN2 0.016 0.26 0.6 83 -1.3 22 105
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.046 0.076 -10000 0 -0.56 12 12
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.13 0.31 5 -0.59 22 27
Axin1/APC/GSK3 0.047 0.053 0.25 1 -0.31 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.063 0.31 2 -0.4 4 6
HNF1A 0.025 0.028 0.25 10 -10000 0 10
CTBP1 0.021 0.02 0.25 2 -10000 0 2
MYC 0.11 0.33 0.57 258 -1.3 24 282
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.099 0.34 1 -0.33 22 23
NKD1 0.022 0.053 0.26 16 -0.57 6 22
TCF4 0.016 0.062 0.23 2 -0.56 11 13
TCF3 0.022 0.022 0.25 4 -10000 0 4
WNT1/LRP6/FZD1/Axin1 0.057 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.005 0.12 0.45 36 -0.5 15 51
LEF1 0.052 0.082 0.25 140 -0.53 1 141
DVL1 0.055 0.053 0.22 1 -0.36 2 3
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.14 0.3 12 -0.61 27 39
DKK1/LRP6/Kremen 2 0.099 0.14 0.34 80 -0.34 47 127
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.021 0.24 2 -10000 0 2
NLK 0.023 0.014 0.25 2 -10000 0 2
CCND1 0.091 0.26 0.61 181 -1.2 6 187
WNT1 0.024 0.011 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.055 0.29 5 -0.3 9 14
APC 0.016 0.056 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.22 518 -0.24 1 519
CREBBP 0.021 0.018 0.27 1 -10000 0 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.071 0.16 -10000 0 -0.3 280 280
Syndecan-3/Neurocan 0.027 0.073 0.27 18 -0.37 20 38
POMC 0.019 0.093 0.26 30 -0.57 22 52
EGFR -0.19 0.28 -10000 0 -0.57 390 390
Syndecan-3/EGFR -0.088 0.16 -10000 0 -0.3 333 333
AGRP 0.021 0.024 0.26 10 -10000 0 10
NCSTN 0.02 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.011 0.26 2 -10000 0 2
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.055 0.26 64 -10000 0 64
long-term memory 0.035 0.062 -10000 0 -0.35 16 16
Syndecan-3/IL8 0.021 0.081 0.28 9 -0.34 36 45
PSEN1 0.024 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
limb bud formation 0.002 0.055 -10000 0 -0.39 21 21
MC4R 0.023 0.026 0.26 13 -10000 0 13
SRC 0.023 0.005 -10000 0 -10000 0 0
PTN -0.23 0.29 0.26 2 -0.57 455 457
FGFR/FGF/Syndecan-3 0.002 0.056 -10000 0 -0.39 21 21
neuron projection morphogenesis -0.071 0.15 0.33 5 -0.47 23 28
Syndecan-3/AgRP 0.016 0.06 0.26 1 -0.37 21 22
Syndecan-3/AgRP/MC4R 0.038 0.068 0.3 2 -0.36 20 22
Fyn/Cortactin 0.028 0.021 -10000 0 -0.3 2 2
SDC3 0.002 0.056 -10000 0 -0.39 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.02 0.08 0.28 9 -0.33 36 45
IL8 0.025 0.099 0.26 60 -0.57 21 81
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 16 16
Syndecan-3/CASK 0 0.054 -10000 0 -0.37 22 22
alpha-MSH/MC4R 0.029 0.072 0.36 2 -0.41 22 24
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.084 -10000 0 -0.41 30 30
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.028 0.17 -10000 0 -0.57 95 95
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.044 -10000 0 -0.57 6 6
AP1 -0.074 0.15 -10000 0 -0.31 285 285
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.021 0.036 -10000 0 -0.57 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.1 -10000 0 -0.66 17 17
NICD/RBPSUH 0.02 0.081 -10000 0 -0.41 31 31
WIF1 -0.27 0.3 0.26 13 -0.57 544 557
NOTCH1 0.008 0.075 -10000 0 -0.43 29 29
PSENEN 0.024 0.011 0.26 2 -10000 0 2
KREMEN2 0.12 0.12 0.26 473 -10000 0 473
DKK1 0.026 0.16 0.26 146 -0.57 54 200
beta catenin/beta TrCP1 0.009 0.067 -10000 0 -0.36 5 5
APH1B 0.023 0.018 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.061 -10000 0 -0.45 9 9
CtBP/CBP/TCF1/TLE1/AES 0.012 0.038 -10000 0 -0.29 6 6
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 306 306
JUN 0.02 0.044 -10000 0 -0.57 6 6
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 0 0.066 0.25 1 -0.37 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.091 0.099 0.34 1 -0.33 22 23
HNF1A 0.025 0.02 0.25 8 -10000 0 8
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.013 0.21 -10000 0 -1.3 27 27
NKD1 0.022 0.053 0.26 16 -0.57 6 22
FZD1 0.024 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.006 0.12 -10000 0 -0.44 31 31
apoptosis -0.074 0.15 -10000 0 -0.31 285 285
Delta 1/NOTCHprecursor 0.018 0.083 -10000 0 -0.41 30 30
DLL1 0.02 0.041 -10000 0 -0.57 5 5
PPARD 0.015 0.092 -10000 0 -0.82 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.31 1 1
APC 0.004 0.082 0.25 1 -0.45 24 25
DVL1 -0.029 0.077 -10000 0 -0.36 35 35
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.099 0.14 0.34 80 -0.34 47 127
LRP6 0.023 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.009 -10000 0 -10000 0 0
CCND1 0.02 0.1 -10000 0 -1.1 7 7
WNT1 0.023 0.011 0.26 2 -10000 0 2
Axin1/APC/beta catenin 0.013 0.098 0.32 5 -0.43 18 23
DKK2 0.009 0.095 0.26 2 -0.57 28 30
NOTCH1 precursor/DVL1 -0.02 0.11 -10000 0 -0.59 24 24
GSK3B 0.024 0.004 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.003 0.12 -10000 0 -0.45 31 31
PPP2R5D -0.004 0.057 0.29 5 -0.36 16 21
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.19 -10000 0 -0.33 526 526
RBPJ 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Syndecan-2-mediated 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
Syndecan-2/Fibronectin 0.094 0.1 0.21 421 -0.34 2 423
EPHB2 0.027 0.031 0.26 19 -10000 0 19
Syndecan-2/TACI 0.024 0.06 0.2 63 -0.36 12 75
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
Syndecan-2/alpha2 ITGB1 -0.038 0.15 -10000 0 -0.32 201 201
HRAS 0.026 0.022 0.26 9 -10000 0 9
Syndecan-2/CASK 0.005 0.016 -10000 0 -0.35 2 2
ITGA5 0.024 0.007 0.26 1 -10000 0 1
BAX 0.002 0.031 0.45 1 -10000 0 1
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.018 -10000 0 -0.32 2 2
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
EZR 0.023 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.052 0.2 -10000 0 -0.57 138 138
Syndecan-2/MMP2 0.015 0.038 0.18 1 -0.36 9 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.071 -10000 0 -0.39 29 29
dendrite morphogenesis 0.022 0.033 0.32 4 -0.35 2 6
Syndecan-2/GM-CSF 0.022 0.036 0.32 5 -0.36 2 7
determination of left/right symmetry 0.007 0.019 -10000 0 -0.41 2 2
Syndecan-2/PKC delta 0.019 0.021 0.31 1 -0.35 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.073 0.19 172 -0.32 2 174
MAPK1 0.037 0.076 0.19 196 -0.32 2 198
Syndecan-2/RACK1 0.03 0.026 0.26 2 -0.31 2 4
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.019 -10000 0 -0.41 2 2
ITGA2 0.008 0.094 -10000 0 -0.57 28 28
MAPK8 0.005 0.033 0.27 5 -0.35 6 11
Syndecan-2/alpha2/beta1 Integrin 0.004 0.12 -10000 0 -0.35 84 84
Syndecan-2/Kininogen 0.02 0.033 0.21 20 -0.36 2 22
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.069 0.3 9 -0.29 2 11
Syndecan-2/CASK/Protein 4.1 0.017 0.018 -10000 0 -0.32 2 2
extracellular matrix organization 0.02 0.023 0.24 3 -0.35 2 5
actin cytoskeleton reorganization 0.093 0.1 0.21 421 -0.34 2 423
Syndecan-2/Caveolin-2/Ras -0.009 0.11 0.27 2 -0.33 104 106
Syndecan-2/Laminin alpha3 -0.057 0.14 -10000 0 -0.35 190 190
Syndecan-2/RasGAP 0.038 0.03 0.26 2 -0.3 2 4
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.022 0.033 0.32 4 -0.35 2 6
GO:0007205 0.002 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.024 -10000 0 -0.29 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.028 0.084 0.26 63 -0.57 12 75
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.071 -10000 0 -0.39 29 29
Syndecan-2/Synbindin 0.018 0.02 -10000 0 -0.34 2 2
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CASP3 0.042 0.071 0.19 190 -0.32 2 192
FN1 0.11 0.11 0.26 421 -10000 0 421
Syndecan-2/IL8 0.023 0.07 0.31 13 -0.36 19 32
SDC2 0.007 0.019 -10000 0 -0.41 2 2
KNG1 0.023 0.032 0.26 20 -10000 0 20
Syndecan-2/Neurofibromin 0.018 0.02 -10000 0 -0.35 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.026 0.036 0.26 26 -10000 0 26
Syndecan-2/TGFB1 0.02 0.023 0.24 3 -0.35 2 5
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.018 -10000 0 -0.32 2 2
Syndecan-2/Ezrin 0.029 0.025 0.29 1 -0.32 2 3
PRKACA 0.044 0.072 0.19 203 -0.32 2 205
angiogenesis 0.023 0.07 0.31 13 -0.35 19 32
MMP2 0.018 0.048 0.26 1 -0.57 7 8
IL8 0.025 0.099 0.26 60 -0.57 21 81
calcineurin-NFAT signaling pathway 0.024 0.06 0.2 63 -0.35 12 75
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
alphaV beta3 Integrin 0.021 0.079 -10000 0 -0.42 33 33
PTK2 -0.04 0.16 -10000 0 -0.48 91 91
positive regulation of JNK cascade -0.021 0.12 -10000 0 -0.32 120 120
CDC42/GDP -0.018 0.17 0.42 1 -0.43 126 127
Rac1/GDP -0.018 0.17 -10000 0 -0.43 124 124
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.022 0.15 -10000 0 -0.4 118 118
nectin-3/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
RAPGEF1 -0.036 0.17 0.46 1 -0.47 112 113
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.05 0.18 -10000 0 -0.54 113 113
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.56 4 4
TLN1 -0.024 0.071 -10000 0 -0.4 14 14
Rap1/GTP -0.024 0.12 -10000 0 -0.34 103 103
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.039 0.2 0.44 1 -0.53 127 128
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.018 0.13 -10000 0 -0.34 116 116
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.029 -10000 0 -0.42 3 3
positive regulation of lamellipodium assembly -0.02 0.13 -10000 0 -0.34 126 126
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.039 0.18 -10000 0 -0.57 114 114
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
CLDN1 0.007 0.12 0.26 23 -0.57 40 63
JAM-A/CLDN1 0.003 0.13 -10000 0 -0.35 112 112
SRC -0.056 0.21 -10000 0 -0.59 116 116
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.029 -10000 0 -0.42 3 3
FARP2 -0.038 0.2 0.43 1 -0.54 109 110
RAC1 0.024 0.003 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.002 0.13 -10000 0 -0.37 114 114
nectin-1/I-afadin 0.029 0.029 -10000 0 -0.42 3 3
nectin-2/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.001 0.13 -10000 0 -0.36 115 115
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.021 0.12 -10000 0 -0.32 120 120
alphaV/beta3 Integrin/Talin -0.006 0.1 0.26 2 -0.41 40 42
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
PIP5K1C -0.019 0.079 -10000 0 -0.23 112 112
VAV2 -0.038 0.21 0.43 1 -0.54 125 126
RAP1/GDP -0.014 0.16 0.39 1 -0.4 115 116
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.001 0.13 -10000 0 -0.37 114 114
nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.42 115 115
Rac1/GTP -0.022 0.16 -10000 0 -0.41 125 125
PTPRM -0.017 0.088 -10000 0 -0.25 116 116
E-cadherin/beta catenin/alpha catenin 0.047 0.062 -10000 0 -0.32 20 20
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 -0.003 0.04 0.22 27 -10000 0 27
RFC1 -0.003 0.036 0.22 23 -10000 0 23
PRKDC 0.016 0.078 0.23 106 -10000 0 106
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.1 -10000 0 -0.63 22 22
FASLG/FAS/FADD/FAF1 -0.005 0.059 0.22 11 -0.28 15 26
MAP2K4 -0.084 0.18 0.39 2 -0.33 265 267
mol:ceramide -0.023 0.1 -10000 0 -0.38 29 29
GSN -0.006 0.053 0.22 26 -0.35 11 37
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.078 0.28 1 -0.37 17 18
FAS 0.003 0.044 -10000 0 -0.58 4 4
BID -0.018 0.02 -10000 0 -10000 0 0
MAP3K1 -0.047 0.12 0.31 2 -0.4 41 43
MAP3K7 0.011 0.019 -10000 0 -10000 0 0
RB1 -0.003 0.036 0.22 22 -10000 0 22
CFLAR 0.027 0.018 -10000 0 -0.54 1 1
HGF/MET -0.052 0.19 -10000 0 -0.4 233 233
ARHGDIB -0.001 0.042 0.22 33 -10000 0 33
FADD 0.006 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.059 0.35 11 -0.21 26 37
NFKB1 -0.044 0.12 -10000 0 -0.54 21 21
MAPK8 -0.15 0.26 0.56 2 -0.47 394 396
DFFA -0.004 0.036 0.22 22 -10000 0 22
DNA fragmentation during apoptosis -0.006 0.045 0.22 22 -10000 0 22
FAS/FADD/MET -0.038 0.14 -10000 0 -0.38 143 143
CFLAR/RIP1 0.039 0.018 -10000 0 -0.38 1 1
FAIM3 0.026 0.035 0.26 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.046 0.22 36 -10000 0 36
DFFB -0.004 0.037 0.22 22 -10000 0 22
CHUK -0.039 0.11 -10000 0 -0.53 17 17
FASLG 0.006 0.088 0.25 42 -0.58 15 57
FAS/FADD 0.009 0.039 -10000 0 -0.32 4 4
HGF -0.011 0.14 0.26 2 -0.57 65 67
LMNA -0.003 0.053 0.19 38 -10000 0 38
CASP6 -0.003 0.036 0.22 22 -10000 0 22
CASP10 0.004 0.04 -10000 0 -0.58 3 3
CASP3 0 0.042 0.27 22 -10000 0 22
PTPN13 0.01 0.091 -10000 0 -0.57 26 26
CASP8 -0.021 0.024 -10000 0 -10000 0 0
IL6 -0.43 0.62 -10000 0 -1.2 398 398
MET -0.073 0.22 -10000 0 -0.57 177 177
ICAD/CAD -0.006 0.032 0.22 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.024 0.1 -10000 0 -0.38 29 29
activation of caspase activity by cytochrome c -0.018 0.02 -10000 0 -10000 0 0
PAK2 -0.003 0.048 0.22 35 -10000 0 35
BCL2 0.008 0.094 -10000 0 -0.56 28 28
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.38 0.28 -10000 0 -0.57 728 728
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.029 0.049 -10000 0 -0.27 16 16
HIF1A 0.004 0.029 -10000 0 -0.26 12 12
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.037 0.28 1 -10000 0 1
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.059 0.085 0.26 170 -10000 0 170
ARNT/IPAS -0.25 0.2 -10000 0 -0.42 598 598
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.046 -10000 0 -0.28 15 15
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.05 -10000 0 -0.27 17 17
PHD1-3/OS9 0.056 0.048 -10000 0 -0.33 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.042 0.054 0.31 1 -0.27 11 12
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.026 0.049 -10000 0 -0.28 14 14
EGLN3 0.04 0.063 0.26 77 -0.57 1 78
EGLN2 0.025 0.016 0.26 5 -10000 0 5
EGLN1 0.02 0.02 -10000 0 -0.57 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.065 -10000 0 -0.51 13 13
ARNT 0.02 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.052 0.073 0.24 38 -0.27 14 52
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.033 0.044 0.26 40 -10000 0 40
GPC2 0.049 0.081 0.26 126 -0.57 3 129
GPC2/Midkine 0.058 0.069 0.36 16 -0.42 3 19
neuron projection morphogenesis 0.057 0.069 0.36 16 -0.42 3 19
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.042 0.15 -10000 0 -0.32 238 238
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.13 9 -10000 0 9
GNB1/GNG2 0.026 0.043 -10000 0 -0.36 13 13
GNB1 0.023 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.061 0.14 -10000 0 -0.31 251 251
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.02 0.034 0.081 251 -10000 0 251
GNAL -0.11 0.24 -10000 0 -0.57 235 235
GNG2 0.017 0.065 -10000 0 -0.57 13 13
CRH 0.017 0.023 0.26 9 -10000 0 9
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.031 -10000 0 -0.35 8 8
MAPK11 0.005 0.019 -10000 0 -0.35 3 3
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.02 0.07 0.42 1 -0.26 51 52
CDKN1A -0.009 0.033 -10000 0 -0.76 2 2
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
BAX 0.025 0.014 0.26 4 -10000 0 4
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.02 0.041 -10000 0 -0.57 5 5
FOXO4 0.012 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.32 0.3 0.26 26 -0.57 635 661
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.023 -10000 0 -0.42 1 1
PPARGC1A -0.09 0.24 0.26 10 -0.57 210 220
FHL2 0.022 0.041 0.26 1 -0.57 5 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.02 0.07 0.26 51 -0.42 1 52
SIRT1/FOXO3a 0.015 0.026 -10000 0 -0.19 4 4
SIRT1 0.022 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.023 -10000 0 -0.36 1 1
SIRT1/Histone H1b 0.028 0.043 -10000 0 -0.21 6 6
apoptosis -0.044 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A -0.046 0.16 -10000 0 -0.36 208 208
p53/SIRT1 0.027 0.019 0.41 2 -10000 0 2
SIRT1/FOXO4 0.022 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.037 0.041 -10000 0 -0.33 10 10
HIST1H1E 0.021 0.03 0.2 6 -10000 0 6
SIRT1/p300 0.032 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.023 0.36 1 -10000 0 1
TP53 0.02 0.011 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.045 0.016 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.25 0.21 -10000 0 -0.42 635 635
ACSS2 -0.007 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.023 -10000 0 -0.36 1 1
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.012 0.14 -10000 0 -0.57 66 66
HRAS 0.026 0.022 0.26 9 -10000 0 9
EGFR -0.19 0.28 -10000 0 -0.57 390 390
AKT -0.014 0.12 0.29 6 -0.28 90 96
FOXO3 0.022 0.019 -10000 0 -0.57 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.041 -10000 0 -0.57 5 5
AKT3 0.014 0.06 -10000 0 -0.57 11 11
FOXO4 0.024 0.001 -10000 0 -10000 0 0
MET -0.073 0.22 -10000 0 -0.57 177 177
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.016 0.073 0.26 4 -0.57 16 20
PIK3R3 0.024 0.008 0.26 1 -10000 0 1
PIK3R2 0.024 0.004 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.061 0.14 0.21 4 -0.34 162 166
ERBB2 0.02 0.02 -10000 0 -0.57 1 1
proliferation/survival/translation -0.006 0.089 0.32 49 -0.26 1 50
PI3K -0.05 0.14 0.25 13 -0.32 170 183
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.037 0.057 0.26 8 -0.16 2 10
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.012 0.041 -10000 0 -0.26 19 19
epithelial cell differentiation 0.037 0.052 -10000 0 -0.31 18 18
CYFIP2 0.028 0.048 0.26 26 -0.57 3 29
ENAH -0.003 0.059 0.3 11 -10000 0 11
EGFR -0.19 0.28 -10000 0 -0.57 390 390
EPHA2 0.02 0.04 -10000 0 -0.57 5 5
MYO6 -0.011 0.05 0.36 1 -0.3 19 20
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.034 -10000 0 -0.36 3 3
AQP5 -0.18 0.26 0.31 2 -0.5 419 421
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.049 0.36 1 -0.3 18 19
regulation of calcium-dependent cell-cell adhesion -0.022 0.074 0.36 1 -0.29 62 63
EGF -0.082 0.23 0.26 2 -0.57 194 196
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.015 0.12 0.29 1 -0.47 55 56
cortical microtubule organization 0.037 0.052 -10000 0 -0.31 18 18
GO:0000145 -0.011 0.046 0.35 1 -0.28 18 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.041 0.053 -10000 0 -0.31 18 18
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
ARF6/GDP -0.02 0.037 -10000 0 -0.27 19 19
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.038 -10000 0 -0.33 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0 0.048 -10000 0 -0.28 18 18
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.011 0.049 0.36 1 -0.3 18 19
ARF6/GTP 0.049 0.04 -10000 0 -0.31 5 5
CDH1 0.012 0.076 -10000 0 -0.57 18 18
EGFR/EGFR/EGF/EGF -0.14 0.2 -10000 0 -0.33 519 519
RhoA/GDP 0.038 0.051 -10000 0 -0.3 18 18
actin cytoskeleton organization -0.012 0.047 0.34 1 -0.29 19 20
IGF-1R heterotetramer 0.013 0.079 0.26 3 -0.56 19 22
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.013 0.079 0.26 3 -0.57 19 22
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
DIAPH1 0.026 0.1 -10000 0 -0.57 11 11
Wnt receptor signaling pathway -0.037 0.052 0.31 18 -10000 0 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.037 -10000 0 -0.28 18 18
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.013 0.048 0.35 1 -0.3 19 20
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.014 0.052 -10000 0 -0.29 25 25
Ephrin A1/EPHA2 0.026 0.051 -10000 0 -0.29 20 20
SEC6/SEC8 -0.021 0.04 -10000 0 -0.3 19 19
MGAT3 -0.022 0.075 0.36 1 -0.3 62 63
HGF/MET -0.039 0.15 -10000 0 -0.32 232 232
HGF -0.011 0.14 0.26 2 -0.57 65 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.012 0.042 -10000 0 -0.26 19 19
actin cable formation 0.042 0.094 0.31 39 -0.27 2 41
KIAA1543 -0.012 0.053 0.35 1 -0.33 18 19
KIFC3 -0.012 0.047 0.36 1 -0.3 18 19
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.011 0.048 -10000 0 -0.3 18 18
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.037 0.052 -10000 0 -0.31 18 18
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.011 0.047 0.36 1 -0.3 17 18
PIP5K1C -0.011 0.05 0.36 1 -0.3 18 19
LIMA1 0.024 0.018 -10000 0 -0.57 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.017 0.088 0.31 26 -10000 0 26
adherens junction assembly -0.021 0.1 0.3 3 -0.63 16 19
IGF-1R heterotetramer/IGF1 -0.041 0.15 -10000 0 -0.31 236 236
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.3 6 6
MET -0.073 0.22 -10000 0 -0.57 177 177
PLEKHA7 -0.012 0.056 0.36 1 -0.35 18 19
mol:GTP 0.043 0.037 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.007 0.066 0.37 7 -0.51 1 8
cortical actin cytoskeleton stabilization 0.012 0.041 -10000 0 -0.26 19 19
regulation of cell-cell adhesion -0.012 0.047 0.34 1 -0.29 19 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.012 0.042 -10000 0 -0.26 19 19
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.018 0.063 -10000 0 -0.36 36 36
ADCY5 -0.11 0.16 -10000 0 -0.36 328 328
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.009 0.062 -10000 0 -0.36 28 28
ADCY2 -0.03 0.1 0.24 8 -0.36 85 93
ADCY3 -0.007 0.003 -10000 0 -10000 0 0
ADCY8 -0.004 0.023 0.23 6 -10000 0 6
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.085 0.23 16 -0.25 34 50
Syndecan-4-mediated signaling events

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
PTK2 0.083 0.1 0.27 35 -0.57 6 41
Syndecan-4/Syndesmos 0.094 0.1 0.37 7 -0.7 6 13
positive regulation of JNK cascade 0.083 0.13 0.36 8 -0.64 8 16
Syndecan-4/ADAM12 0.1 0.12 0.35 38 -0.72 6 44
CCL5 0.029 0.056 0.26 38 -0.57 4 42
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.007 0.26 1 -10000 0 1
SDCBP 0.021 0.008 -10000 0 -10000 0 0
PLG -0.008 0.034 0.25 8 -10000 0 8
ADAM12 0.036 0.061 0.26 64 -0.57 2 66
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.066 0.15 0.36 7 -0.66 10 17
Syndecan-4/CXCL12/CXCR4 0.087 0.14 0.37 8 -0.69 8 16
Syndecan-4/Laminin alpha3 0.033 0.15 0.37 6 -0.74 7 13
MDK 0.033 0.044 0.26 40 -10000 0 40
Syndecan-4/FZD7 0.094 0.12 0.37 7 -0.69 7 14
Syndecan-4/Midkine 0.1 0.11 0.37 14 -0.69 6 20
FZD7 0.013 0.082 -10000 0 -0.57 21 21
Syndecan-4/FGFR1/FGF -0.01 0.16 0.35 2 -0.54 18 20
THBS1 0.021 0.04 -10000 0 -0.57 5 5
integrin-mediated signaling pathway 0.092 0.12 0.35 12 -0.69 7 19
positive regulation of MAPKKK cascade 0.083 0.13 0.36 8 -0.64 8 16
Syndecan-4/TACI 0.098 0.12 0.36 21 -0.72 6 27
CXCR4 0.029 0.034 0.26 24 -10000 0 24
cell adhesion 0.06 0.083 0.25 84 -0.25 21 105
Syndecan-4/Dynamin 0.098 0.1 0.37 5 -0.73 6 11
Syndecan-4/TSP1 0.097 0.11 0.37 7 -0.72 6 13
Syndecan-4/GIPC 0.098 0.1 0.37 5 -0.73 6 11
Syndecan-4/RANTES 0.099 0.11 0.36 9 -0.72 6 15
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.034 0.18 0.26 3 -0.57 105 108
LAMA3 -0.12 0.25 -10000 0 -0.57 252 252
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.024 0.22 0.7 96 -0.53 22 118
Syndecan-4/alpha-Actinin 0.098 0.1 0.37 6 -0.72 6 12
TFPI -0.005 0.13 0.26 1 -0.57 54 55
F2 0.025 0.034 0.26 13 -10000 0 13
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
positive regulation of cell adhesion 0 0.17 0.36 4 -0.55 32 36
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.092 0.26 11 -0.57 25 36
Syndecan-4/CXCL12 0.076 0.14 0.37 6 -0.68 9 15
FGF6 0.015 0.025 -10000 0 -0.57 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.019 0.15 -10000 0 -0.57 78 78
TNFRSF13B 0.028 0.084 0.26 63 -0.57 12 75
FGF2 -0.2 0.29 -10000 0 -0.57 413 413
FGFR1 0.016 0.048 -10000 0 -0.57 7 7
Syndecan-4/PI-4-5-P2 0.075 0.1 0.31 8 -0.72 6 14
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.25 417 -10000 0 417
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.012 0.025 -10000 0 -10000 0 0
vasculogenesis 0.095 0.1 0.36 7 -0.68 6 13
SDC4 0.087 0.1 0.36 9 -0.78 5 14
Syndecan-4/Tenascin C 0.093 0.12 0.36 12 -0.72 7 19
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.085 0.1 0.36 6 -0.7 6 12
MMP9 0.12 0.12 0.26 453 -0.56 1 454
Rac1/GTP 0.061 0.084 0.25 83 -0.25 21 104
cytoskeleton organization 0.092 0.1 0.36 7 -0.67 6 13
GIPC1 0.024 0.008 0.26 1 -10000 0 1
Syndecan-4/TFPI 0.085 0.13 0.37 6 -0.72 7 13
Regulation of Androgen receptor activity

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
HDAC1 0.008 0.01 -10000 0 -10000 0 0
SMARCC1 0.006 0.027 -10000 0 -0.59 1 1
REL 0.017 0.068 -10000 0 -0.57 14 14
HDAC7 -0.036 0.11 0.37 3 -0.37 57 60
JUN 0.019 0.044 -10000 0 -0.57 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.018 -10000 0 -0.57 1 1
KAT5 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.008 0.065 -10000 0 -0.43 23 23
FOXO1 0.019 0.041 -10000 0 -0.57 5 5
T-DHT/AR -0.023 0.12 0.33 1 -0.37 70 71
MAP2K6 0.002 0.088 0.24 1 -0.57 23 24
BRM/BAF57 0.026 0.027 -10000 0 -10000 0 0
MAP2K4 0.014 0.02 -10000 0 -10000 0 0
SMARCA2 0.018 0.018 -10000 0 -10000 0 0
PDE9A -0.061 0.26 -10000 0 -1.1 59 59
NCOA2 -0.008 0.12 -10000 0 -0.57 48 48
CEBPA 0.019 0.057 -10000 0 -0.57 10 10
EHMT2 0.021 0.012 -10000 0 -10000 0 0
cell proliferation 0.001 0.15 0.36 30 -0.45 25 55
NR0B1 0.027 0.042 0.26 35 -10000 0 35
EGR1 -0.16 0.27 -10000 0 -0.57 336 336
RXRs/9cRA -0.042 0.15 -10000 0 -0.33 215 215
AR/RACK1/Src -0.016 0.11 0.31 7 -0.36 36 43
AR/GR -0.028 0.12 0.26 2 -0.3 131 133
GNB2L1 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.013 14 14
MAPK8 -0.002 0.042 -10000 0 -0.43 8 8
T-DHT/AR/TIF2/CARM1 -0.017 0.12 0.32 1 -0.38 50 51
SRC -0.019 0.068 0.19 30 -0.34 27 57
NR3C1 0.018 0.06 -10000 0 -0.57 11 11
KLK3 -0.14 0.39 0.37 5 -1.1 135 140
APPBP2 0.016 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.015 0.097 0.42 1 -0.39 30 31
TMPRSS2 -0.12 0.36 -10000 0 -1 138 138
RXRG -0.1 0.24 0.26 2 -0.57 219 221
mol:9cRA -0.001 0.002 -10000 0 -0.011 5 5
RXRA 0.023 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.022 0.011 -10000 0 -10000 0 0
NR2C2 0.018 0.057 -10000 0 -0.57 10 10
KLK2 -0.051 0.2 0.31 8 -0.66 85 93
AR -0.04 0.11 -10000 0 -0.3 145 145
SENP1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.016 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 126 -0.023 42 168
GATA2 0.013 0.095 0.26 13 -0.57 26 39
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.25 446 -10000 0 446
T-DHT/AR/RACK1/Src -0.013 0.1 0.34 9 -0.38 31 40
positive regulation of transcription 0.013 0.094 0.26 13 -0.56 26 39
DNAJA1 0.017 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.022 0.029 -10000 0 -0.6 1 1
SPDEF -0.01 0.15 0.26 36 -0.57 68 104
T-DHT/AR/TIF2 -0.005 0.1 0.32 6 -0.38 29 35
T-DHT/AR/Hsp90 -0.016 0.097 0.33 3 -0.38 30 33
GSK3B 0.022 0.01 -10000 0 -10000 0 0
NR2C1 0.025 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.062 0.23 1 -0.35 28 29
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.025 0.016 -10000 0 -10000 0 0
POU2F1 0.009 0.05 -10000 0 -0.18 12 12
T-DHT/AR/DAX-1 -0.015 0.1 0.33 4 -0.39 31 35
CREBBP 0.022 0.007 -10000 0 -10000 0 0
SMARCE1 0.018 0.018 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.044 0.041 -10000 0 -10000 0 0
BIRC5 0.18 0.11 0.26 711 -10000 0 711
NFKBIA 0.024 0.04 0.28 8 -10000 0 8
CPEB1 -0.079 0.22 0.26 1 -0.57 187 188
AKT1 0.023 0.04 0.29 7 -10000 0 7
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.033 0.036 0.2 1 -0.2 1 2
NDEL1/TACC3 0.066 0.067 0.26 17 -10000 0 17
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.001 0.026 -10000 0 -10000 0 0
PAK1/Aurora A 0.04 0.043 0.27 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.09 0.067 0.27 26 -10000 0 26
TP53 0.022 0.051 -10000 0 -10000 0 0
DLG7 0.022 0.03 0.18 1 -10000 0 1
AURKAIP1 0.026 0.024 0.26 11 -10000 0 11
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.069 0.071 0.28 17 -10000 0 17
G2/M transition of mitotic cell cycle 0.031 0.034 0.2 1 -0.2 1 2
AURKA 0.037 0.045 0.24 1 -10000 0 1
AURKB 0.086 0.074 0.17 417 -10000 0 417
CDC25B 0.031 0.039 0.22 3 -10000 0 3
G2/M transition checkpoint 0.019 0.028 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.13 -10000 0 -0.3 177 177
Aurora A/CPEB -0.025 0.13 -10000 0 -0.3 177 177
Aurora A/TACC1/TRAP/chTOG 0.044 0.07 -10000 0 -0.3 22 22
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
centrosome duplication 0.04 0.043 0.27 2 -10000 0 2
regulation of centrosome cycle 0.064 0.066 0.26 17 -10000 0 17
spindle assembly 0.042 0.069 -10000 0 -0.3 22 22
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.087 0.28 29 -10000 0 29
CENPA 0.095 0.081 0.19 430 -0.21 3 433
Aurora A/PP2A 0.043 0.042 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.031 0.04 0.24 1 -10000 0 1
negative regulation of DNA binding 0.018 0.063 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.028 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.045 0.24 1 -10000 0 1
TACC1 0.006 0.089 -10000 0 -0.57 25 25
TACC3 0.058 0.083 0.26 162 -10000 0 162
Aurora A/Antizyme1 0.054 0.043 -10000 0 -10000 0 0
Aurora A/RasGAP 0.043 0.042 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.001 0.027 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.024 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.089 0.067 0.27 26 -10000 0 26
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.094 0.072 0.24 39 -10000 0 39
PAK1 0.023 0.019 0.26 6 -10000 0 6
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.056 0.2 -10000 0 -0.52 65 65
MAP3K8 0.009 0.051 -10000 0 -0.57 7 7
FOS -0.02 0.14 0.3 1 -0.46 46 47
PRKCA -0.002 0.086 0.24 1 -0.57 22 23
PTPN7 0.021 0.059 0.26 43 -10000 0 43
HRAS 0.024 0.022 0.25 9 -10000 0 9
PRKCB 0.006 0.079 0.25 19 -0.57 15 34
NRAS 0.023 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.036 -10000 0 -10000 0 0
MAPK3 0.008 0.09 -10000 0 -0.81 5 5
MAP2K1 -0.012 0.12 -10000 0 -0.49 47 47
ELK1 0.006 0.029 -10000 0 -10000 0 0
BRAF -0.012 0.099 -10000 0 -0.46 43 43
mol:GTP -0.002 0.003 -10000 0 -0.006 323 323
MAPK1 -0.009 0.12 -10000 0 -0.54 28 28
RAF1 -0.011 0.097 -10000 0 -0.46 42 42
KRAS 0.022 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.012 0.04 -10000 0 -0.57 1 1
SVIL 0.01 0.052 -10000 0 -0.57 5 5
ZNF318 0.039 0.054 0.2 16 -10000 0 16
JMJD2C -0.001 0.042 0.11 32 -0.13 78 110
T-DHT/AR/Ubc9 -0.034 0.14 -10000 0 -0.36 148 148
CARM1 0.019 0.015 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.011 -10000 0 -10000 0 0
CTNNB1 0.014 0.029 -10000 0 -10000 0 0
AKT1 0.027 0.018 -10000 0 -10000 0 0
PTK2B 0.012 0.026 -10000 0 -10000 0 0
MED1 0.025 0.02 -10000 0 -10000 0 0
MAK 0.034 0.083 0.27 10 -0.54 11 21
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.01 0.052 -10000 0 -0.57 5 5
GSN 0.006 0.071 -10000 0 -0.57 12 12
NCOA2 -0.01 0.12 -10000 0 -0.57 48 48
NCOA6 0.013 0.033 -10000 0 -10000 0 0
DNA-PK 0.05 0.053 -10000 0 -10000 0 0
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.027 -10000 0 -10000 0 0
cell proliferation 0.004 0.11 0.35 1 -0.57 24 25
XRCC5 0.026 0.015 -10000 0 -10000 0 0
UBE3A 0.009 0.044 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.042 0.15 -10000 0 -0.39 152 152
FHL2 0.002 0.1 -10000 0 -0.86 7 7
RANBP9 0.013 0.033 -10000 0 -10000 0 0
JMJD1A -0.015 0.047 0.12 1 -0.14 131 132
CDK6 0.02 0.058 0.26 2 -0.57 10 12
TGFB1I1 0.01 0.046 -10000 0 -0.57 3 3
T-DHT/AR/CyclinD1 -0.042 0.14 -10000 0 -0.36 148 148
XRCC6 0.025 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.041 0.16 -10000 0 -0.38 150 150
CTDSP1 0.018 0.019 -10000 0 -10000 0 0
CTDSP2 0.034 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.039 -10000 0 -0.57 1 1
TCF4 0.024 0.066 -10000 0 -0.56 11 11
CDKN2A 0.063 0.088 0.26 170 -10000 0 170
SRF 0.032 0.023 -10000 0 -10000 0 0
NKX3-1 -0.047 0.096 -10000 0 -0.21 248 248
KLK3 -0.14 0.46 0.4 1 -1.4 126 127
TMF1 0.018 0.016 -10000 0 -10000 0 0
HNRNPA1 0.028 0.02 -10000 0 -10000 0 0
AOF2 -0.007 0.023 -10000 0 -0.069 126 126
APPL1 0.019 0.032 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.028 0.14 -10000 0 -0.37 139 139
AR -0.067 0.2 0.21 1 -0.58 141 142
UBA3 0.017 0.019 -10000 0 -10000 0 0
PATZ1 0.027 0.021 -10000 0 -10000 0 0
PAWR 0.018 0.024 -10000 0 -0.57 1 1
PRKDC 0.023 0.016 -10000 0 -10000 0 0
PA2G4 0.031 0.027 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.024 0.13 -10000 0 -0.34 130 130
RPS6KA3 0.008 0.062 -10000 0 -0.57 8 8
T-DHT/AR/ARA70 -0.037 0.14 -10000 0 -0.36 150 150
LATS2 0.027 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.022 0.14 -10000 0 -0.34 140 140
Cyclin D3/CDK11 p58 0.019 0.005 -10000 0 -10000 0 0
VAV3 0.014 0.063 0.25 19 -0.57 7 26
KLK2 -0.076 0.27 0.32 2 -0.99 81 83
CASP8 0.026 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.041 0.15 -10000 0 -0.37 149 149
TMPRSS2 -0.13 0.33 -10000 0 -0.98 136 136
CCND1 0.012 0.042 0.26 1 -0.57 4 5
PIAS1 0.01 0.044 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.028 -10000 0 -0.07 169 169
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.003 0.063 -10000 0 -0.19 17 17
T-DHT/AR/CDK6 -0.035 0.14 -10000 0 -0.36 159 159
CMTM2 0.023 0.012 0.25 1 -10000 0 1
SNURF 0.012 0.082 -10000 0 -0.57 21 21
ZMIZ1 0.01 0.039 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.021 -10000 0 -10000 0 0
FKBP4 0.014 0.036 0.26 4 -10000 0 4
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.049 0.16 -10000 0 -0.32 275 275
TC10/GTP -0.039 0.14 -10000 0 -0.29 258 258
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.078 -10000 0 -0.34 41 41
HRAS 0.026 0.022 0.26 9 -10000 0 9
APS homodimer 0.034 0.046 0.26 45 -10000 0 45
GRB14 0.011 0.18 0.26 142 -0.57 80 222
FOXO3 -0.022 0.16 -10000 0 -0.6 73 73
AKT1 -0.02 0.11 0.35 6 -0.45 2 8
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.055 0.046 0.42 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.12 0.26 -10000 0 -0.57 267 267
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.024 -10000 0 -10000 0 0
CAV1 -0.083 0.15 -10000 0 -0.35 239 239
CBL/APS/CAP/Crk-II/C3G -0.028 0.16 -10000 0 -0.31 262 262
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.078 -10000 0 -0.34 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.075 -10000 0 -0.3 49 49
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.014 0.064 -10000 0 -0.4 8 8
RPS6KB1 -0.019 0.096 0.33 6 -0.48 1 7
PARD6A 0.023 0.019 0.26 6 -10000 0 6
CBL 0.022 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.038 -10000 0 -0.55 4 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.007 0.094 -10000 0 -0.36 1 1
HRAS/GTP -0.02 0.044 -10000 0 -0.28 24 24
Insulin Receptor 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.069 -10000 0 -0.32 26 26
PRKCI 0.013 0.059 -10000 0 -0.45 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.005 0.1 -10000 0 -0.29 117 117
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.035 -10000 0 -0.46 4 4
PI3K 0.037 0.079 -10000 0 -0.3 49 49
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.015 -10000 0 -10000 0 0
AKT2 -0.019 0.11 0.31 7 -0.28 94 101
PRKCZ 0.004 0.086 -10000 0 -0.48 17 17
SH2B2 0.034 0.046 0.26 45 -10000 0 45
SHC/SHIP 0.012 0.057 -10000 0 -0.3 28 28
F2RL2 0.046 0.12 0.26 155 -0.57 20 175
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.033 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.039 0.17 -10000 0 -0.32 266 266
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.049 0.027 -10000 0 -10000 0 0
INPP5D -0.019 0.062 -10000 0 -0.31 41 41
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.02 0.14 -10000 0 -0.69 47 47
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 42 42
p62DOK/RasGAP 0.042 0.035 -10000 0 -0.47 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.31 41 41
GRB2 0.023 0.009 0.26 1 -10000 0 1
EIF4EBP1 -0.021 0.089 0.31 3 -0.48 1 4
PTPRA 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.052 -10000 0 -0.27 28 28
Insulin Receptor/Insulin/IRS1 0.029 0.074 -10000 0 -0.33 42 42
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.06 0.073 -10000 0 -0.31 20 20
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.086 0.26 1 -0.57 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.091 0.12 -10000 0 -0.24 418 418
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.039 0.098 -10000 0 -0.34 73 73
PRKG1 -0.014 0.14 -10000 0 -0.57 69 69
DUSP8 0.022 0.031 -10000 0 -0.57 3 3
PGK/cGMP/p38 alpha -0.018 0.13 -10000 0 -0.35 93 93
apoptosis -0.038 0.093 -10000 0 -0.33 72 72
RAL/GTP 0.032 0.006 -10000 0 -10000 0 0
LYN 0.021 0.008 -10000 0 -10000 0 0
DUSP1 -0.045 0.19 -10000 0 -0.57 126 126
PAK1 0.023 0.019 0.26 6 -10000 0 6
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.024 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.008 0.26 1 -10000 0 1
RAC1-CDC42/GTP 0.031 0.008 -10000 0 -10000 0 0
MAPK11 -0.009 0.13 0.27 7 -0.39 60 67
BLK 0.051 0.087 0.26 151 -0.57 2 153
HCK 0.027 0.026 0.26 13 -10000 0 13
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.014 0.26 2 -10000 0 2
TRAF6/MEKK3 0.028 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.004 0.13 0.28 5 -0.39 67 72
positive regulation of innate immune response -0.01 0.15 0.31 6 -0.45 63 69
LCK 0.026 0.075 0.26 40 -0.57 11 51
p38alpha-beta/MKP7 -0.002 0.14 0.33 5 -0.44 56 61
p38alpha-beta/MKP5 -0.003 0.14 0.37 3 -0.46 47 50
PGK/cGMP -0.01 0.11 -10000 0 -0.42 69 69
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.032 0.17 0.37 3 -0.46 85 88
CDC42 0.023 0.005 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.24 0.29 -10000 0 -0.57 478 478
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.025 0.26 2 -0.54 1 3
CDKN2C 0.014 0.028 -10000 0 -0.55 1 1
CDKN2A 0.06 0.085 0.26 170 -10000 0 170
CCND2 -0.016 0.036 0.2 2 -0.21 14 16
RB1 0.015 0.047 0.25 16 -0.23 8 24
CDK4 -0.017 0.037 0.21 2 -0.22 12 14
CDK6 -0.018 0.04 0.22 2 -0.2 24 26
G1/S progression -0.01 0.058 0.19 41 -0.26 16 57
BCR signaling pathway

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
JUN 0.024 0.13 0.28 25 -0.38 41 66
IKBKB 0.024 0.09 0.28 13 -0.3 17 30
AKT1 0.04 0.11 0.27 81 -0.24 21 102
IKBKG 0.028 0.073 0.29 7 -0.31 5 12
CALM1 0.002 0.096 0.25 1 -0.38 29 30
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.025 0.16 0.36 13 -0.52 45 58
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.1 -10000 0 -0.35 47 47
DOK1 0.025 0.014 0.26 4 -10000 0 4
AP-1 -0.021 0.098 0.25 8 -0.25 50 58
LYN 0.021 0.008 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
BCR complex 0.005 0.16 0.36 21 -0.44 95 116
CD22 -0.01 0.13 0.27 23 -0.44 65 88
CAMK2G 0.003 0.094 0.26 7 -0.41 18 25
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.086 -10000 0 -0.33 54 54
GO:0007205 0.002 0.1 -10000 0 -0.36 47 47
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0.002 0.1 0.26 1 -0.36 36 37
NFATC1 0.031 0.13 0.28 36 -0.45 34 70
B-cell antigen/BCR complex 0.005 0.16 0.36 21 -0.44 95 116
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.024 0.048 0.16 13 -0.12 48 61
HRAS 0.012 0.11 0.26 17 -0.34 41 58
NFKBIA 0.024 0.047 0.16 14 -0.12 48 62
NF-kappa-B/RelA/I kappa B beta 0.027 0.042 0.17 10 -10000 0 10
RasGAP/Csk 0.033 0.12 0.32 22 -0.36 68 90
mol:GDP 0.004 0.098 -10000 0 -0.34 41 41
PTEN 0.022 0.019 -10000 0 -0.57 1 1
CD79B 0.012 0.098 0.26 21 -0.57 27 48
NF-kappa-B/RelA/I kappa B alpha 0.028 0.042 0.16 11 -10000 0 11
GRB2 0.023 0.009 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.024 0.16 0.35 11 -0.48 55 66
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.003 0.1 -10000 0 -0.36 47 47
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.077 0.15 -10000 0 -0.43 82 82
CHUK 0.024 0.082 0.28 8 -0.31 18 26
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.019 0.095 -10000 0 -0.4 18 18
PTPN6 -0.012 0.12 0.25 24 -0.42 63 87
RELA 0.024 0.005 -10000 0 -10000 0 0
BCL2A1 0.025 0.035 0.16 10 -10000 0 10
VAV2 0.014 0.14 0.28 11 -0.57 31 42
ubiquitin-dependent protein catabolic process 0.026 0.047 0.16 13 -0.12 48 61
BTK 0.015 0.061 -10000 0 -0.97 4 4
CD19 0.006 0.14 0.27 35 -0.43 63 98
MAP4K1 0.033 0.054 0.26 48 -0.57 2 50
CD72 0.03 0.042 0.26 30 -0.57 1 31
PAG1 0.02 0.014 0.26 2 -10000 0 2
MAPK14 0.027 0.14 0.35 16 -0.44 43 59
SH3BP5 0.023 0.018 -10000 0 -0.57 1 1
PIK3AP1 0.004 0.11 -10000 0 -0.37 48 48
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.13 0.26 3 -0.41 81 84
RAF1 0.011 0.1 0.26 17 -0.36 28 45
RasGAP/p62DOK/SHIP 0.032 0.12 0.3 21 -0.35 68 89
CD79A -0.002 0.17 0.26 85 -0.57 81 166
re-entry into mitotic cell cycle -0.021 0.097 0.25 8 -0.25 47 55
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.097 0.27 26 -0.36 14 40
MAPK1 0.011 0.09 0.26 11 -0.36 17 28
CD72/SHP1 0.03 0.14 0.35 31 -0.54 31 62
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.025 0.14 0.33 19 -0.44 47 66
actin cytoskeleton organization 0.032 0.14 0.31 31 -0.5 30 61
NF-kappa-B/RelA 0.056 0.081 0.29 11 -0.2 3 14
Calcineurin 0.019 0.091 -10000 0 -0.39 16 16
PI3K -0.013 0.095 -10000 0 -0.39 40 40
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.006 0.11 -10000 0 -0.39 51 51
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.014 0.2 0.44 5 -0.7 50 55
DAPP1 -0.015 0.2 -10000 0 -0.79 51 51
cytokine secretion 0.032 0.13 0.27 42 -0.42 34 76
mol:DAG 0.003 0.1 -10000 0 -0.36 47 47
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
MAP2K1 0.011 0.097 0.27 11 -0.4 17 28
B-cell antigen/BCR complex/FcgammaRIIB 0.017 0.13 0.34 21 -0.41 69 90
mol:PI-3-4-5-P3 0.006 0.089 0.22 17 -0.32 25 42
ETS1 0.001 0.089 0.26 5 -0.39 19 24
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.13 0.33 22 -0.36 74 96
B-cell antigen/BCR complex/LYN -0.01 0.13 0.25 20 -0.43 74 94
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.14 0.31 25 -0.54 30 55
B-cell antigen/BCR complex/LYN/SYK 0.016 0.14 0.35 24 -0.44 59 83
CARD11 0.004 0.1 0.28 6 -0.37 36 42
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
PPP3CA 0.024 0.011 0.26 2 -10000 0 2
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 52 -0.14 4 56
PTPRC 0.021 0.041 0.26 12 -0.57 3 15
PDPK1 0.02 0.082 0.22 53 -0.23 20 73
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.009 -10000 0 -10000 0 0
POU2F2 0.021 0.033 0.17 10 -10000 0 10
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.027 0.027 0.26 14 -10000 0 14
GNB1/GNG2 -0.016 0.048 -10000 0 -0.19 64 64
AKT1 0.023 0.092 0.34 12 -0.32 13 25
EGF -0.082 0.23 0.26 2 -0.57 194 196
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.06 0.25 2 -0.35 4 6
mol:Ca2+ 0.021 0.11 0.38 13 -0.3 71 84
LYN 0.013 0.056 0.25 2 -0.4 2 4
RhoA/GTP 0.009 0.045 0.13 3 -0.14 14 17
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.019 0.12 0.39 14 -0.35 63 77
GNG2 0.017 0.065 -10000 0 -0.57 13 13
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.57 40 40
G beta5/gamma2 -0.012 0.067 -10000 0 -0.26 65 65
PRKCH 0.017 0.12 0.41 11 -0.36 63 74
DNM1 0.02 0.048 0.26 1 -0.57 7 8
TXA2/TP beta/beta Arrestin3 0.008 0.031 -10000 0 -0.4 2 2
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.008 0.1 0.26 7 -0.57 32 39
G12 family/GTP 0 0.09 -10000 0 -0.31 58 58
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.02 0.041 -10000 0 -0.57 5 5
RhoA/GTP/ROCK1 0.031 0.014 -10000 0 -0.36 1 1
mol:GDP -0.011 0.099 0.37 33 -0.33 8 41
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 -0.014 0.14 -10000 0 -0.57 69 69
mol:IP3 0.019 0.14 0.44 10 -0.38 74 84
cell morphogenesis 0.031 0.014 -10000 0 -0.36 1 1
PLCB2 0.01 0.17 0.52 7 -0.52 74 81
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.026 0.072 0.25 7 -0.32 5 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.061 0.25 3 -0.37 3 6
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.026 0.021 0.26 9 -10000 0 9
PRKCB1 0.018 0.13 0.43 10 -0.38 64 74
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.014 0.17 0.54 7 -0.54 64 71
LCK 0.016 0.074 0.24 3 -0.37 13 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.25 27 27
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.1 -10000 0 -0.43 49 49
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.24 21 21
MAPK14 0.018 0.089 0.32 18 -0.24 52 70
TGM2/GTP 0.014 0.15 0.48 10 -0.44 61 71
MAPK11 0.017 0.089 0.33 16 -0.24 52 68
ARHGEF1 0.011 0.066 0.27 10 -0.19 38 48
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.02 0.13 0.42 12 -0.39 64 76
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.022 0.1 0.38 13 -0.28 60 73
cAMP biosynthetic process 0.016 0.13 0.42 10 -0.36 68 78
Gq family/GTP/EBP50 0.015 0.043 0.22 5 -0.27 6 11
actin cytoskeleton reorganization 0.031 0.014 -10000 0 -0.36 1 1
SRC 0.013 0.058 0.24 3 -0.37 3 6
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.047 0.1 0.26 2 -0.3 67 69
VCAM1 0.02 0.11 0.37 13 -0.31 62 75
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.57 40 40
platelet activation 0.023 0.12 0.39 16 -0.31 62 78
PGI2/IP 0.019 0.014 0.18 9 -10000 0 9
PRKACA 0.008 0.053 -10000 0 -0.28 32 32
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.48 36 36
TXA2/TP beta/beta Arrestin2 -0.006 0.066 -10000 0 -0.44 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.047 -10000 0 -0.26 30 30
mol:DAG 0.017 0.14 0.47 9 -0.43 66 75
EGFR -0.19 0.28 -10000 0 -0.57 390 390
TXA2/TP alpha 0.014 0.16 0.5 8 -0.49 71 79
Gq family/GTP 0.001 0.049 0.25 1 -0.22 38 39
YES1 0.014 0.061 0.25 2 -0.34 4 6
GNAI2/GTP 0.013 0.052 -10000 0 -0.28 17 17
PGD2/DP 0.005 0.076 0.18 7 -0.4 35 42
SLC9A3R1 0.036 0.054 0.26 60 -10000 0 60
FYN 0.012 0.059 0.24 2 -0.35 6 8
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.025 0.025 0.26 6 -0.57 1 7
PGK/cGMP 0.007 0.096 -10000 0 -0.36 69 69
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.034 0.072 -10000 0 -0.42 12 12
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.021 0.13 0.42 11 -0.38 59 70
PRKCB 0.02 0.13 0.41 11 -0.37 63 74
PRKCE 0.018 0.12 0.43 10 -0.36 61 71
PRKCD 0.017 0.13 0.44 9 -0.39 62 71
PRKCG 0.019 0.13 0.44 10 -0.39 63 73
muscle contraction 0.014 0.16 0.49 9 -0.5 65 74
PRKCZ 0.017 0.12 0.4 12 -0.35 63 75
ARR3 0.021 0.021 0.26 8 -10000 0 8
TXA2/TP beta 0.024 0.06 -10000 0 -0.28 27 27
PRKCQ 0.015 0.14 0.4 15 -0.39 65 80
MAPKKK cascade 0.014 0.15 0.48 8 -0.46 71 79
SELE 0.016 0.12 0.37 13 -0.39 62 75
TP beta/GNAI2/GDP/G beta/gamma 0.034 0.071 -10000 0 -0.43 12 12
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
GNA14 0.023 0.065 0.26 19 -0.57 10 29
chemotaxis 0.012 0.18 0.57 7 -0.61 63 70
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.014 0.26 3 -10000 0 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.012 0.12 0.48 8 -0.5 4 12
IL27/IL27R/JAK1 0.037 0.16 0.73 6 -0.64 10 16
TBX21 -0.001 0.17 0.5 15 -0.5 46 61
IL12B 0.075 0.098 0.26 227 -10000 0 227
IL12A -0.013 0.097 0.14 10 -0.42 57 67
IL6ST -0.041 0.19 -10000 0 -0.56 120 120
IL27RA/JAK1 0.022 0.079 0.51 2 -1.2 3 5
IL27 0.048 0.076 0.26 112 -10000 0 112
TYK2 0.03 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.097 0.16 1.1 1 -0.79 2 3
T-helper 2 cell differentiation -0.012 0.12 0.48 8 -0.5 4 12
T cell proliferation during immune response -0.012 0.12 0.48 8 -0.5 4 12
MAPKKK cascade 0.012 0.12 0.5 4 -0.48 8 12
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.033 0.26 19 -10000 0 19
IL12RB1 0.033 0.053 0.26 41 -0.57 2 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.009 0.18 0.47 32 -0.52 51 83
IL27/IL27R/JAK2/TYK2 0.012 0.12 0.51 4 -0.48 8 12
positive regulation of T cell mediated cytotoxicity 0.012 0.12 0.5 4 -0.48 8 12
STAT1 (dimer) 0.035 0.21 0.67 23 -0.67 18 41
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.024 0.12 0.44 4 -0.46 8 12
T cell proliferation -0.09 0.18 0.37 4 -0.48 74 78
IL12/IL12R/TYK2/JAK2 0.059 0.18 0.45 3 -0.73 27 30
IL17A -0.097 0.16 1.1 1 -0.79 2 3
mast cell activation -0.012 0.12 0.48 8 -0.5 4 12
IFNG 0.021 0.045 0.12 124 -0.095 10 134
T cell differentiation 0 0.006 0.025 3 -0.022 5 8
STAT3 (dimer) 0.023 0.12 0.44 4 -0.46 8 12
STAT5A (dimer) 0.021 0.12 0.44 4 -0.46 13 17
STAT4 (dimer) 0.011 0.14 0.44 4 -0.45 23 27
STAT4 0.001 0.12 0.26 1 -0.57 43 44
T cell activation -0.005 0.011 0.12 3 -0.1 6 9
IL27R/JAK2/TYK2 0.016 0.14 -10000 0 -1.1 3 3
GATA3 -0.023 0.27 0.6 40 -1.3 35 75
IL18 0.009 0.02 0.13 26 -10000 0 26
positive regulation of mast cell cytokine production 0.023 0.11 0.43 4 -0.45 8 12
IL27/EBI3 0.053 0.072 0.26 51 -0.38 6 57
IL27RA 0.01 0.081 0.74 1 -1.3 3 4
IL6 -0.18 0.28 0.26 1 -0.57 380 381
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.041 0.45 3 -0.52 1 4
IL1B 0.001 0.048 0.13 3 -0.42 14 17
EBI3 0.025 0.054 0.26 14 -0.57 6 20
TNF 0.006 0.043 0.14 25 -0.42 9 34
Regulation of Telomerase

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
Telomerase catalytic core complex 0.058 0.13 0.5 6 -0.58 1 7
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.094 0.21 -10000 0 -0.42 305 305
IFNAR2 0.028 0.02 -10000 0 -0.57 1 1
AKT1 -0.003 0.088 -10000 0 -0.25 53 53
ER alpha/Oestrogen -0.026 0.16 0.18 115 -0.4 157 272
NFX1/SIN3/HDAC complex 0.023 0.058 0.24 1 -0.33 15 16
EGF -0.081 0.23 0.26 2 -0.56 194 196
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.055 0.12 0.44 1 -0.52 1 2
SAP18 0.024 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.022 -10000 0 -10000 0 0
WT1 0.14 0.12 0.26 533 -10000 0 533
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.005 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.051 0.1 -10000 0 -0.5 1 1
Mad/Max 0.041 0.014 -10000 0 -10000 0 0
TERT 0.058 0.13 0.52 4 -0.59 1 5
CCND1 0.081 0.16 0.54 20 -1 4 24
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.019 0.26 7 -10000 0 7
RBBP4 0.024 0.019 -10000 0 -0.56 1 1
TERF2 0.021 0.013 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.039 0.05 -10000 0 -0.38 5 5
CDKN1B 0.029 0.049 -10000 0 -0.67 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.015 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.022 0.044 -10000 0 -0.56 6 6
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.56 306 306
IFN-gamma/IRF1 0.064 0.063 0.28 6 -0.32 3 9
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.044 0.067 0.26 97 -10000 0 97
Telomerase 0.03 0.08 0.27 2 -0.6 6 8
IRF1 0.029 0.018 0.26 3 -0.18 3 6
ESR1 -0.034 0.23 0.26 115 -0.56 151 266
KU/TER 0.034 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.056 0.23 1 -0.33 10 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.057 0.23 1 -0.34 10 11
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.012 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.014 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.008 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.06 0.13 0.49 1 -0.61 4 5
NR2F2 0.012 0.037 -10000 0 -0.57 3 3
MAPK3 0.006 0.019 -10000 0 -10000 0 0
MAPK1 0.006 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.022 0.014 0.25 3 -10000 0 3
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.016 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.56 390 390
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.2 0.25 -10000 0 -0.45 525 525
MYC 0.008 0.084 -10000 0 -0.57 22 22
IL2 0.029 0.024 0.26 8 -10000 0 8
KU 0.034 0.009 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.023 0.014 0.25 3 -10000 0 3
TRF2/BLM 0.043 0.045 0.23 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.068 0.12 0.47 3 -0.55 1 4
SP1/HDAC2 0.046 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.049 0.1 -10000 0 -0.49 1 1
Smad3/Myc 0.007 0.054 -10000 0 -0.36 20 20
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.058 0.081 0.26 146 -0.19 3 149
Telomerase/PinX1 0.041 0.097 -10000 0 -0.49 1 1
Telomerase/AKT1/mTOR/p70S6K 0.026 0.1 0.29 6 -0.57 14 20
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.045 0.095 -10000 0 -10000 0 0
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.051 0.1 -10000 0 -0.5 1 1
E2F1 0.097 0.11 0.26 320 -10000 0 320
ZNFX1 0.024 0.006 -10000 0 -10000 0 0
PIF1 0.069 0.092 0.26 211 -10000 0 211
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.01 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.02 -10000 0 -0.57 1 1
ELF1 0.03 0.054 -10000 0 -0.36 12 12
CCNA2 0.11 0.11 0.26 401 -10000 0 401
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.027 0.026 0.26 14 -10000 0 14
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.046 0.1 0.33 11 -0.53 10 21
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.024 0.045 -10000 0 -0.38 12 12
IL2RA 0.02 0.12 0.29 67 -0.76 15 82
IL2RB 0.031 0.05 0.26 38 -0.57 2 40
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.067 0.26 46 -0.57 7 53
G1/S transition of mitotic cell cycle 0.042 0.14 0.34 4 -0.78 18 22
PTPN11 0.025 0.003 -10000 0 -10000 0 0
CCND2 0.006 0.087 0.34 2 -0.8 12 14
LCK 0.027 0.075 0.26 40 -0.57 11 51
GRB2 0.023 0.009 0.26 1 -10000 0 1
IL2 0.022 0.021 0.26 8 -10000 0 8
CDK6 0.019 0.058 0.26 2 -0.57 10 12
CCND3 0.047 0.1 0.44 4 -0.61 4 8
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.043 0.072 0.32 1 -0.3 27 28
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.082 0.36 9 -0.33 2 11
alphaV/beta3 Integrin/Osteopontin/Src 0.081 0.071 0.23 15 -10000 0 15
AP1 -0.036 0.18 -10000 0 -0.54 32 32
ILK 0.03 0.074 0.29 1 -0.32 27 28
bone resorption 0.019 0.088 0.27 1 -0.49 13 14
PTK2B 0.02 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.068 0.092 0.3 8 -0.29 26 34
ITGAV 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.022 0.075 -10000 0 -0.41 31 31
alphaV/beta3 Integrin/Osteopontin 0.077 0.1 0.34 4 -0.34 33 37
MAP3K1 0.029 0.077 0.26 14 -0.32 33 47
JUN 0.021 0.044 -10000 0 -0.57 6 6
MAPK3 0.02 0.069 0.32 3 -0.3 24 27
MAPK1 0.021 0.07 0.27 11 -0.3 23 34
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.015 0.082 0.26 15 -0.36 29 44
ITGB3 0.009 0.1 0.26 4 -0.56 33 37
NFKBIA 0.018 0.068 0.33 3 -0.34 4 7
FOS -0.14 0.27 -10000 0 -0.57 306 306
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.022 0.098 0.45 6 -0.55 2 8
NF kappa B1 p50/RelA 0.063 0.076 0.37 5 -10000 0 5
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.026 0.08 -10000 0 -0.41 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.03 0.075 0.25 14 -0.32 33 47
VAV3 0.017 0.075 0.26 16 -0.3 31 47
MAP3K14 0.031 0.075 0.34 1 -0.32 28 29
ROCK2 0.007 0.099 -10000 0 -0.57 31 31
SPP1 0.086 0.1 0.26 279 -10000 0 279
RAC1 0.024 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.069 0.3 3 -0.28 27 30
MMP2 -0.054 0.14 0.32 4 -0.51 31 35
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.016 0.16 0.3 3 -0.39 148 151
AKT1 0.025 0.01 -10000 0 -10000 0 0
GSC -0.03 0.27 -10000 0 -1.3 41 41
NKX2-5 0.001 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.026 0.066 0.37 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.068 0.065 -10000 0 -0.44 1 1
SMAD4 0.012 0.045 -10000 0 -10000 0 0
CBFB 0.022 0.008 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.099 0.19 0.26 1 -0.36 379 380
SMAD3/SMAD4/VDR 0.055 0.058 -10000 0 -0.34 1 1
MYC 0.005 0.084 -10000 0 -0.57 22 22
CDKN2B -0.042 0.17 -10000 0 -0.86 23 23
AP1 -0.05 0.16 -10000 0 -0.3 247 247
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.01 0.086 -10000 0 -0.35 33 33
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.013 0.058 -10000 0 -0.36 9 9
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.046 0.081 0.26 127 -10000 0 127
SMAD3/SMAD4/GR 0.023 0.072 -10000 0 -0.39 11 11
GATA3 0.013 0.11 0.26 28 -0.55 36 64
SKI/SIN3/HDAC complex/NCoR1 0.005 0.076 -10000 0 -0.35 34 34
MEF2C/TIF2 0.023 0.087 0.32 3 -0.31 23 26
endothelial cell migration -0.029 0.094 0.55 16 -10000 0 16
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.019 0.26 7 -10000 0 7
RBBP4 0.023 0.018 -10000 0 -0.57 1 1
RUNX2 0.027 0.028 0.26 15 -10000 0 15
RUNX3 0.022 0.043 0.26 5 -0.57 5 10
RUNX1 0.023 0.019 -10000 0 -0.57 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.014 0.061 -10000 0 -0.57 11 11
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.016 0.078 -10000 0 -1.1 3 3
KAT2B 0.024 0.019 -10000 0 -0.57 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.078 0.3 1 -0.26 22 23
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.094 -10000 0 -0.55 16 16
SMAD3/SMAD4/ATF2 0.033 0.061 -10000 0 -0.41 3 3
SMAD3/SMAD4/ATF3 -0.011 0.14 -10000 0 -0.4 110 110
SAP30 0.024 0.015 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.041 0.031 -10000 0 -10000 0 0
JUN -0.059 0.15 0.29 1 -0.38 42 43
SMAD3/SMAD4/IRF7 0.052 0.081 0.35 10 -10000 0 10
TFE3 0.028 0.009 -10000 0 -0.2 1 1
COL1A2 0.045 0.094 0.39 4 -0.6 8 12
mesenchymal cell differentiation -0.035 0.058 -10000 0 -10000 0 0
DLX1 0.055 0.1 0.26 168 -0.57 9 177
TCF3 0.024 0.009 0.26 1 -10000 0 1
FOS -0.14 0.27 -10000 0 -0.57 307 307
SMAD3/SMAD4/Max 0.028 0.058 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.044 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.013 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.034 0.055 -10000 0 -10000 0 0
IRF7 0.048 0.072 0.27 102 -10000 0 102
ESR1 -0.04 0.23 0.25 115 -0.57 151 266
HNF4A 0.023 0.032 0.26 20 -10000 0 20
MEF2C 0.047 0.086 0.4 8 -0.44 3 11
SMAD2-3/SMAD4 0.034 0.065 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.36 1 1
IGHV3OR16-13 0.006 0.039 -10000 0 -0.34 12 12
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.023 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.023 0.26 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.043 0.061 -10000 0 -0.45 1 1
MSG1/HSC70 -0.13 0.22 -10000 0 -0.42 400 400
SMAD2 0.022 0.03 -10000 0 -0.16 14 14
SMAD3 0.015 0.04 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.042 -10000 0 -0.37 2 2
SMAD2/SMAD2/SMAD4 0.026 0.058 0.25 9 -0.51 3 12
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
MYOD/E2A 0.032 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.064 -10000 0 -0.41 1 1
IFNB1 0.022 0.071 0.31 38 -10000 0 38
SMAD3/SMAD4/MEF2C 0.065 0.084 0.31 1 -0.42 3 4
CITED1 -0.19 0.29 0.26 15 -0.57 400 415
SMAD2-3/SMAD4/ARC105 0.042 0.066 -10000 0 -10000 0 0
RBL1 0.023 0.027 0.26 1 -0.57 2 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.017 0.065 -10000 0 -0.48 9 9
RUNX1-3/PEBPB2 0.04 0.039 -10000 0 -0.42 5 5
SMAD7 -0.032 0.14 -10000 0 -0.48 10 10
MYC/MIZ-1 0.015 0.065 -10000 0 -0.42 22 22
SMAD3/SMAD4 0.032 0.073 0.3 24 -0.37 3 27
IL10 0.007 0.08 0.34 2 -0.36 27 29
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.021 0.01 -10000 0 -10000 0 0
CDK2 0.025 0.008 -10000 0 -10000 0 0
IL5 0.004 0.083 0.36 1 -0.35 32 33
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.041 0.18 0.26 1 -0.57 112 113
SMAD3/SMAD4/SP1 0.047 0.064 -10000 0 -0.49 1 1
FOXG1 0.017 0.067 0.26 74 -10000 0 74
FOXO3 0.011 0.017 -10000 0 -0.42 1 1
FOXO1 0.009 0.031 -10000 0 -0.42 5 5
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.047 0.086 0.4 8 -0.43 3 11
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.054 0.089 0.29 5 -0.39 9 14
MYOD1 0.021 0.027 0.26 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.033 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.029 0.098 0.35 1 -0.39 36 37
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.023 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.069 -10000 0 -0.4 4 4
SMAD3/SMAD4/SP1-3 0.062 0.062 -10000 0 -0.44 1 1
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.03 0.015 -10000 0 -0.2 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.056 0.074 0.28 1 -0.25 16 17
ITGB5 0.016 0.042 -10000 0 -0.4 1 1
TGIF/SIN3/HDAC complex/CtBP 0.013 0.061 -10000 0 -0.3 24 24
SMAD3/SMAD4/AR -0.019 0.15 -10000 0 -0.39 136 136
AR -0.053 0.2 0.26 1 -0.57 141 142
negative regulation of cell growth 0 0.083 -10000 0 -0.34 18 18
SMAD3/SMAD4/MYOD 0.032 0.057 -10000 0 -10000 0 0
E2F5 0.022 0.021 0.26 7 -10000 0 7
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.073 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.055 -10000 0 -0.37 11 11
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.035 0.17 -10000 0 -0.32 109 109
SMAD3/SMAD4/RUNX2 0.035 0.058 -10000 0 -10000 0 0
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.022 0.031 -10000 0 -0.57 3 3
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.025 0.046 0.13 170 -10000 0 170
TP53 0.009 0.018 -10000 0 -0.19 2 2
Senescence 0.008 0.022 -10000 0 -0.19 2 2
Apoptosis 0.008 0.022 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.011 0.06 0.29 31 -10000 0 31
MDM4 0.02 0.009 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0.004 0.059 -10000 0 -0.28 19 19
BAG4 0.018 0.032 -10000 0 -0.57 3 3
PKC zeta/ceramide -0.001 0.052 -10000 0 -0.25 16 16
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BAX 0.002 0.041 -10000 0 -0.35 11 11
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.068 0.7 10 -10000 0 10
BAD -0.015 0.046 0.19 4 -0.25 14 18
SMPD1 0.015 0.056 0.2 12 -0.23 18 30
RB1 -0.015 0.044 -10000 0 -0.25 13 13
FADD/Caspase 8 0.028 0.086 0.26 12 -0.4 6 18
MAP2K4 -0.016 0.044 0.18 5 -0.3 8 13
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.056 0.19 33 -0.3 7 40
EGF -0.082 0.23 0.26 2 -0.57 194 196
mol:ceramide -0.014 0.048 0.14 1 -0.25 15 16
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.009 -10000 0 -10000 0 0
ASAH1 0.021 0.015 0.26 3 -10000 0 3
negative regulation of cell cycle -0.016 0.044 -10000 0 -0.25 13 13
cell proliferation -0.044 0.12 0.27 1 -0.27 200 201
BID -0.02 0.17 -10000 0 -0.66 60 60
MAP3K1 -0.015 0.047 0.2 3 -0.24 16 19
EIF2A -0.014 0.049 0.24 6 -0.24 7 13
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.006 0.054 0.28 3 -0.3 6 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.059 0.26 4 -0.33 5 9
Cathepsin D/ceramide 0.004 0.057 0.17 31 -0.24 14 45
FADD 0.006 0.059 0.22 12 -0.28 16 28
KSR1 -0.009 0.055 0.2 24 -0.25 13 37
MAPK8 -0.014 0.058 -10000 0 -0.27 21 21
PRKRA -0.015 0.047 0.2 4 -0.24 15 19
PDGFA 0.024 0.008 0.26 1 -10000 0 1
TRAF2 0.025 0.015 0.26 4 -10000 0 4
IGF1 -0.1 0.24 -10000 0 -0.57 233 233
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.047 0.14 1 -0.25 15 16
CTSD 0.031 0.041 0.26 34 -10000 0 34
regulation of nitric oxide biosynthetic process 0.034 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.047 0.13 0.29 1 -0.29 198 199
PRKCD 0.024 0.009 0.26 1 -10000 0 1
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.034 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.018 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.044 -10000 0 -0.31 7 7
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 11 11
mol:Sphingosine-1-phosphate 0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.009 0.055 0.24 5 -0.31 5 10
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
CYCS 0 0.049 0.18 18 -0.24 10 28
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.36 4 4
EIF2AK2 -0.016 0.043 0.19 5 -0.24 11 16
TNF-alpha/TNFR1A/FAN 0.04 0.044 -10000 0 -0.36 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.077 -10000 0 -0.37 29 29
MAP2K2 -0.01 0.055 0.24 5 -0.29 7 12
SMPD3 -0.002 0.098 0.26 4 -0.28 102 106
TNF 0.024 0.065 0.26 25 -0.57 9 34
PKC zeta/PAR4 0.033 0.021 -10000 0 -0.42 2 2
mol:PHOSPHOCHOLINE 0.042 0.097 0.24 195 -0.21 3 198
NF kappa B1/RelA/I kappa B alpha 0.063 0.03 -10000 0 -0.31 2 2
AIFM1 -0.001 0.049 0.18 20 -0.22 12 32
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Signaling events mediated by PRL

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
CCNE1 0.062 0.087 0.26 179 -10000 0 179
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.018 0.057 -10000 0 -0.57 10 10
CDKN1A -0.031 0.093 -10000 0 -0.44 29 29
PRL-3/alpha Tubulin 0.03 0.019 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.075 0.24 44 -0.42 13 57
AGT 0.029 0.089 0.26 73 -0.57 13 86
CCNA2 -0.065 0.14 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.12 0.2 -10000 0 -0.41 336 336
CDK2/Cyclin E1 0.016 0.11 -10000 0 -0.48 17 17
MAPK3 0.01 0.018 0.26 4 -10000 0 4
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.018 0.26 4 -10000 0 4
PTP4A1 -0.093 0.14 -10000 0 -10000 0 0
PTP4A3 0.021 0.02 0.26 6 -10000 0 6
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.017 0.26 3 -10000 0 3
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 -0.016 0.071 -10000 0 -0.55 6 6
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.072 0.15 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.015 -10000 0 -10000 0 0
RHOC -0.019 0.079 -10000 0 -0.42 19 19
RHOA -0.021 0.089 -10000 0 -0.47 24 24
cell motility -0.026 0.1 -10000 0 -0.39 33 33
PRL-1/alpha Tubulin -0.073 0.15 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.041 -10000 0 -0.42 6 6
ROCK1 -0.024 0.098 -10000 0 -0.39 29 29
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.093 0.14 -10000 0 -10000 0 0
ATF5 0.025 0.013 0.26 3 -10000 0 3
Caspase cascade in apoptosis

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
TOP1 0.009 0.11 0.26 2 -0.41 43 45
ACTA1 0.012 0.11 0.26 7 -0.48 32 39
NUMA1 0.004 0.11 0.26 2 -0.39 47 49
SPTAN1 -0.002 0.11 0.27 7 -0.48 32 39
LIMK1 -0.001 0.11 0.26 6 -0.48 32 38
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.014 0.26 4 -10000 0 4
CASP10 -0.011 0.09 0.2 11 -0.44 33 44
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.004 0.12 0.25 3 -0.43 47 50
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.001 0.1 0.27 7 -0.47 32 39
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.006 0.12 0.28 4 -0.47 40 44
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.013 0.13 -10000 0 -0.64 33 33
BID 0.003 0.053 0.18 3 -0.26 32 35
MAP3K1 -0.003 0.093 -10000 0 -0.4 47 47
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.001 0.11 0.26 7 -0.48 31 38
CASP9 0.023 0.005 -10000 0 -10000 0 0
DNA repair -0.016 0.043 0.25 4 -0.21 4 8
neuron apoptosis 0.004 0.12 -10000 0 -0.69 25 25
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.11 0.26 2 -0.47 34 36
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 0 0.15 -10000 0 -0.9 25 25
TRAF2 0.025 0.015 0.26 4 -10000 0 4
ICAD/CAD -0.004 0.1 0.24 2 -0.49 28 30
CASP7 0.002 0.06 0.26 5 -0.34 7 12
KRT18 0.015 0.079 -10000 0 -0.72 9 9
apoptosis 0.002 0.12 0.3 5 -0.44 46 51
DFFA -0.003 0.1 0.25 3 -0.48 32 35
DFFB -0.003 0.1 0.25 3 -0.48 32 35
PARP1 0.016 0.043 0.21 4 -0.25 4 8
actin filament polymerization 0.001 0.1 0.44 34 -0.29 9 43
TNF 0.024 0.065 0.26 25 -0.57 9 34
CYCS 0.005 0.048 0.21 6 -0.22 21 27
SATB1 -0.008 0.15 -10000 0 -0.77 31 31
SLK -0.002 0.1 0.28 4 -0.48 32 36
p15 BID/BAX 0.013 0.062 0.24 2 -0.29 20 22
CASP2 0.003 0.063 0.23 7 -0.29 18 25
JNK cascade 0.002 0.093 0.39 47 -10000 0 47
CASP3 0 0.11 0.26 4 -0.49 34 38
LMNB2 0.001 0.13 0.27 5 -0.49 46 51
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.032 -10000 0 -0.33 2 2
negative regulation of DNA binding 0.014 0.13 -10000 0 -0.63 33 33
stress fiber formation -0.002 0.1 0.28 4 -0.47 32 36
GZMB 0.011 0.1 0.27 11 -0.49 32 43
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.02 0.12 0.29 8 -0.5 29 37
APP 0.004 0.12 -10000 0 -0.7 25 25
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM 0.004 0.12 0.28 6 -0.44 49 55
LMNA 0.009 0.08 0.32 2 -0.37 23 25
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.066 -10000 0 -0.28 27 27
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.001 0.1 0.27 4 -0.48 32 36
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.61 38 38
nuclear fragmentation during apoptosis 0.004 0.1 0.26 2 -0.38 47 49
CFL2 -0.001 0.11 0.29 9 -0.46 34 43
GAS2 -0.025 0.14 0.27 6 -0.38 97 103
positive regulation of apoptosis 0.014 0.11 0.27 8 -0.47 34 42
PRF1 0.016 0.077 0.26 8 -0.57 17 25
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.004 0.09 0.29 47 -10000 0 47
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 -10000 0 -0.28 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
RhoA/GTP -0.003 0.091 -10000 0 -0.29 47 47
negative regulation of cAMP metabolic process -0.004 0.088 -10000 0 -0.27 88 88
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.27 88 88
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.088 -10000 0 -0.64 8 8
oxygen homeostasis 0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.087 0.087 0.36 10 -0.35 3 13
EPO 0.15 0.17 0.52 65 -0.49 4 69
FIH (dimer) 0.032 0.02 -10000 0 -10000 0 0
APEX1 0.033 0.025 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.48 47 -0.49 9 56
FLT1 -0.018 0.17 -10000 0 -0.77 26 26
ADORA2A 0.16 0.17 0.49 66 -0.48 7 73
germ cell development 0.14 0.16 0.52 26 -0.49 6 32
SLC11A2 0.14 0.16 0.51 18 -0.48 8 26
BHLHE40 0.13 0.16 0.51 16 -0.53 6 22
HIF1AN 0.032 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.13 0.4 59 -0.38 3 62
ETS1 0.026 0.039 -10000 0 -0.58 4 4
CITED2 0.015 0.09 -10000 0 -0.57 14 14
KDR -0.017 0.18 -10000 0 -0.74 35 35
PGK1 0.14 0.16 0.51 18 -0.5 6 24
SIRT1 0.025 0.004 -10000 0 -10000 0 0
response to hypoxia 0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.6 17 -0.54 9 26
EPAS1 0.068 0.088 0.28 57 -0.29 12 69
SP1 0.029 0.012 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.52 18 -0.55 43 61
EFNA1 0.11 0.14 0.49 9 -0.47 8 17
FXN 0.15 0.16 0.46 49 -0.48 7 56
POU5F1 0.14 0.16 0.53 26 -0.5 6 32
neuron apoptosis -0.15 0.18 0.52 9 -0.59 17 26
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.047 0.067 0.27 77 -0.58 1 78
EGLN2 0.033 0.026 0.26 5 -10000 0 5
EGLN1 0.027 0.028 -10000 0 -0.58 1 1
VHL/Elongin B/Elongin C 0.041 0.027 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.028 0.024 -10000 0 -10000 0 0
SLC2A1 0.14 0.16 0.47 52 -0.49 6 58
TWIST1 0.13 0.19 0.46 43 -0.55 39 82
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.41 9 -0.38 3 12
VEGFA 0.13 0.16 0.54 16 -0.49 7 23
CREBBP 0.023 0.007 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
CDC42/GTP -0.005 0.096 -10000 0 -0.31 48 48
PLCG1 -0.012 0.087 -10000 0 -0.31 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
cell migration -0.005 0.094 -10000 0 -0.3 48 48
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
S1PR4 0.029 0.062 0.26 38 -0.57 6 44
MAPK3 -0.008 0.082 0.26 1 -0.31 40 41
MAPK1 -0.008 0.084 -10000 0 -0.32 44 44
S1P/S1P5/Gi -0.004 0.088 -10000 0 -0.27 88 88
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.026 -10000 0 -0.28 3 3
RHOA 0.006 0.058 0.24 1 -0.31 6 7
S1P/S1P4/Gi -0.004 0.094 -10000 0 -0.33 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
S1P/S1P4/G12/G13 0.044 0.041 -10000 0 -0.33 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.022 0.037 0.26 1 -0.57 4 5
ANTXR2 0.018 0.06 -10000 0 -0.57 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.009 -10000 0 -0.078 14 14
monocyte activation 0.003 0.085 0.25 2 -0.35 55 57
MAP2K2 0.003 0.082 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.008 -10000 0 -10000 0 0
MAP2K7 -0.004 0.009 0.12 1 -10000 0 1
MAP2K6 -0.01 0.044 -10000 0 -0.3 23 23
CYAA -0.009 0.039 -10000 0 -0.35 13 13
MAP2K4 -0.004 0.008 -10000 0 -0.11 1 1
IL1B -0.008 0.045 0.18 3 -0.27 26 29
Channel 0.025 0.046 -10000 0 -0.37 13 13
NLRP1 -0.007 0.033 -10000 0 -0.3 12 12
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.066 -10000 0 -0.39 29 29
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.009 0.078 14 -10000 0 14
MAPK3 -0.004 0.008 0.085 1 -0.11 1 2
MAPK1 -0.004 0.009 0.12 2 -0.11 2 4
PGR -0.079 0.14 0.2 2 -0.31 281 283
PA/Cellular Receptors 0.027 0.05 -10000 0 -0.4 13 13
apoptosis -0.002 0.009 -10000 0 -0.078 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.044 -10000 0 -0.35 13 13
macrophage activation -0.005 0.01 0.12 3 -10000 0 3
TNF 0.024 0.065 0.26 25 -0.57 9 34
VCAM1 0.003 0.085 0.25 2 -0.35 55 57
platelet activation -0.001 0.066 -10000 0 -0.39 29 29
MAPKKK cascade -0.002 0.026 0.12 3 -0.14 5 8
IL18 -0.003 0.026 0.11 1 -0.22 10 11
negative regulation of macrophage activation -0.002 0.009 -10000 0 -0.078 14 14
LEF -0.002 0.009 -10000 0 -0.079 14 14
CASP1 -0.003 0.027 -10000 0 -0.16 21 21
mol:cAMP -0.001 0.067 -10000 0 -0.39 29 29
necrosis -0.002 0.009 -10000 0 -0.078 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.044 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 0.077 -10000 0 -0.66 3 3
UGCG 0.009 0.12 -10000 0 -0.67 30 30
AKT1/mTOR/p70S6K/Hsp90/TERT 0.048 0.12 0.3 10 -0.43 25 35
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.12 -10000 0 -0.66 30 30
mol:DAG 0.004 0.085 -10000 0 -0.76 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.13 0.3 6 -0.42 52 58
FRAP1 0.031 0.15 0.33 6 -0.48 52 58
FOXO3 0.036 0.14 0.33 12 -0.51 30 42
AKT1 0.037 0.14 0.34 6 -0.53 34 40
GAB2 0.021 0.02 -10000 0 -0.57 1 1
SMPD1 0.01 0.11 -10000 0 -0.64 25 25
SGMS1 0.018 0.065 -10000 0 -0.54 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.039 -10000 0 -0.34 13 13
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.046 0.11 0.29 7 -0.46 24 31
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.05 -10000 0 -0.39 14 14
RPS6KB1 0.012 0.091 -10000 0 -0.84 10 10
mol:sphingomyelin 0.004 0.085 -10000 0 -0.76 12 12
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.027 0.027 0.26 14 -10000 0 14
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.065 0.2 0.41 10 -0.93 27 37
MYB 0.028 0.19 0.48 2 -1.1 24 26
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.036 0.11 0.29 18 -0.48 17 35
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.088 -10000 0 -0.75 10 10
mol:PI-3-4-5-P3 0.04 0.11 0.29 17 -0.47 17 34
Rac1/GDP 0.014 0.039 -10000 0 -0.33 12 12
T cell proliferation 0.04 0.1 0.29 12 -0.49 12 24
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.013 0.1 3 -0.076 23 26
PRKCZ 0.04 0.1 0.3 10 -0.51 12 22
NF kappa B1 p50/RelA 0.048 0.14 0.32 6 -0.44 42 48
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.075 0.29 11 -0.52 8 19
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.023 0.005 -10000 0 -10000 0 0
IL2RA 0.027 0.088 0.26 58 -0.57 15 73
IL2RB 0.031 0.051 0.26 38 -0.57 2 40
TERT 0.054 0.08 0.26 147 -10000 0 147
E2F1 0.051 0.094 0.4 1 -0.41 18 19
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.033 23 -0.05 3 26
PTPN11 0.023 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.26 46 -0.57 7 53
actin cytoskeleton organization 0.04 0.1 0.29 12 -0.49 12 24
GRB2 0.023 0.011 0.26 1 -10000 0 1
IL2 0.021 0.023 0.26 8 -10000 0 8
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.043 -10000 0 -0.31 12 12
LCK 0.027 0.075 0.26 40 -0.57 11 51
BCL2 0.019 0.19 0.42 2 -0.8 43 45
BARD1 signaling events

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
BARD1/CSTF1 0.026 0.057 -10000 0 -0.39 18 18
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.015 0.19 5 -10000 0 5
protein ubiquitination 0.065 0.071 0.3 2 -0.3 18 20
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.022 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.015 0.086 -10000 0 -0.46 15 15
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
CCNE1 0.062 0.087 0.26 179 -10000 0 179
CDK2/Cyclin E1 0.06 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.06 -10000 0 -0.41 19 19
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
FANCA 0.059 0.088 0.26 178 -10000 0 178
DNA repair 0.027 0.085 0.29 5 -0.37 7 12
BRCA1/BARD1/ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BARD1/DNA-PK 0.045 0.052 -10000 0 -0.33 15 15
FANCL 0.024 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.056 0.39 18 -10000 0 18
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.07 -10000 0 -0.27 22 22
BRCA1/BACH1/BARD1/TopBP1 0.039 0.055 -10000 0 -0.36 18 18
BRCA1/BARD1/P53 0.048 0.054 -10000 0 -0.33 18 18
BARD1/CSTF1/BRCA1 0.037 0.053 -10000 0 -0.36 16 16
BRCA1/BACH1 0.023 0.02 0.26 1 -0.56 1 2
BARD1 0.014 0.076 0.26 1 -0.57 18 19
PCNA 0.024 0.011 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.04 0.053 -10000 0 -0.36 17 17
BRCA1/BARD1/UbcH7 0.038 0.054 -10000 0 -0.36 17 17
BRCA1/BARD1/RAD51/PCNA 0.091 0.088 0.31 2 -0.31 17 19
BARD1/DNA-PK/P53 0.05 0.054 -10000 0 -0.31 15 15
BRCA1/BARD1/Ubiquitin 0.027 0.06 -10000 0 -0.41 19 19
BRCA1/BARD1/CTIP 0.028 0.05 -10000 0 -0.33 18 18
FA complex 0.035 0.037 0.24 3 -0.26 1 4
BARD1/EWS 0.026 0.059 0.2 1 -0.42 18 19
RBBP8 0.01 0.005 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.053 0.33 18 -10000 0 18
BRCA1/BARD1 0.071 0.075 0.33 2 -0.3 18 20
CSTF1 0.023 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.056 0.18 1 -0.42 18 19
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.1 0.11 0.26 373 -10000 0 373
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.06 -10000 0 -0.41 19 19
EWSR1 0.023 0.006 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.062 -10000 0 -0.39 20 20
forebrain development -0.043 0.2 0.35 1 -0.53 124 125
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
SMO/beta Arrestin2 0.027 0.045 -10000 0 -0.42 9 9
SMO 0.017 0.055 -10000 0 -0.57 9 9
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.024 0.081 0.32 2 -0.49 11 13
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 0.022 -10000 0 -10000 0 0
GNAI1 -0.008 0.13 -10000 0 -0.57 57 57
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.19 -10000 0 -0.62 67 67
SAP30 0.024 0.015 0.26 4 -10000 0 4
mol:GDP 0.017 0.055 -10000 0 -0.57 9 9
MIM/GLI2A 0.021 0.02 0.26 2 -10000 0 2
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.022 0.009 -10000 0 -10000 0 0
GLI2 0.01 0.066 -10000 0 -0.3 23 23
GLI3 0.013 0.084 0.34 2 -0.47 14 16
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.017 0.065 -10000 0 -0.57 13 13
Gi family/GTP -0.009 0.098 -10000 0 -0.33 62 62
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.017 0.086 -10000 0 -0.45 20 20
GLI2/Su(fu) 0.013 0.081 -10000 0 -0.38 22 22
FOXA2 0.008 0.1 -10000 0 -0.69 15 15
neural tube patterning -0.043 0.2 0.35 1 -0.53 124 125
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.043 -10000 0 -0.37 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.021 0.02 0.26 2 -10000 0 2
embryonic limb morphogenesis -0.043 0.2 0.35 1 -0.53 124 125
SUFU 0.015 0.027 -10000 0 -0.23 10 10
LGALS3 0.016 0.067 -10000 0 -0.57 14 14
catabolic process 0.026 0.1 0.32 2 -0.51 19 21
GLI3A/CBP 0.003 0.089 -10000 0 -0.36 59 59
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.044 0.21 0.35 1 -0.55 121 122
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
IFT172 0.024 0.018 -10000 0 -0.57 1 1
RBBP7 0.026 0.019 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.061 -10000 0 -0.38 15 15
GNAZ 0.016 0.057 -10000 0 -0.57 10 10
RBBP4 0.023 0.019 -10000 0 -0.57 1 1
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.018 0.07 -10000 0 -0.36 15 15
STK36 0.021 0.023 -10000 0 -0.57 1 1
Gi family/GNB1/GNG2/GDP -0.015 0.11 -10000 0 -0.44 42 42
PTCH1 -0.087 0.32 -10000 0 -1.1 88 88
MIM/GLI1 -0.03 0.19 -10000 0 -0.63 63 63
CREBBP 0.003 0.089 -10000 0 -0.36 59 59
Su(fu)/SIN3/HDAC complex 0.007 0.09 -10000 0 -0.41 35 35
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.056 0.07 0.37 14 -0.38 11 25
MAP4K1 0.033 0.054 0.26 48 -0.57 2 50
MAP3K8 0.02 0.048 -10000 0 -0.57 7 7
PRKCB 0.019 0.076 0.26 19 -0.57 15 34
DBNL 0.024 0.003 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.015 0.054 0.25 1 -0.31 16 17
JUN 0.002 0.13 -10000 0 -0.6 42 42
MAP3K7 0.015 0.052 0.23 2 -0.29 14 16
GRAP2 0.017 0.063 0.26 3 -0.57 12 15
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.013 0.066 0.23 2 -0.38 13 15
LAT 0.025 0.038 0.26 15 -0.57 2 17
LCP2 0.024 0.008 0.26 1 -10000 0 1
MAPK8 0.006 0.14 -10000 0 -0.63 42 42
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.022 0.058 0.25 3 -0.31 17 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.064 0.07 0.37 14 -0.37 11 25
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.065 -10000 0 -0.29 51 51
FRAP1 -0.001 0.082 0.4 1 -0.45 25 26
AKT1 -0.011 0.065 0.19 1 -0.28 38 39
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0.023 0.07 0.23 3 -0.26 16 19
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.21 4 4
TSC2 0.023 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.005 0.048 -10000 0 -0.24 15 15
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.077 -10000 0 -0.31 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.015 0.046 -10000 0 -0.24 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.012 0.075 0.33 3 -0.33 14 17
MAP3K5 -0.001 0.046 0.2 10 -0.2 43 53
PIK3R1 0.017 0.065 -10000 0 -0.57 13 13
apoptosis -0.001 0.046 0.2 10 -0.2 44 54
mol:LY294002 0 0 -10000 0 -0.001 52 52
EIF4B 0.011 0.069 0.3 4 -0.3 13 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.029 0.066 -10000 0 -0.28 12 12
eIF4E/eIF4G1/eIF4A1 0.004 0.049 -10000 0 -0.28 21 21
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.081 -10000 0 -0.29 65 65
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.055 0.23 15 -0.2 2 17
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.027 0.061 -10000 0 -0.24 14 14
mol:Amino Acids 0 0 -10000 0 -0.001 52 52
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.06 0.18 2 -0.28 44 46
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.54 59 59
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.048 -10000 0 -0.24 1 1
TSC1/TSC2 0.026 0.075 0.26 4 -0.28 16 20
tumor necrosis factor receptor activity 0 0 0.001 52 -10000 0 52
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.011 0.079 -10000 0 -0.33 60 60
INS 0.016 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.56 1 1
PDK2 -0.018 0.059 0.18 7 -0.27 42 49
EIF4EBP1 -0.022 0.22 -10000 0 -1 46 46
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D 0.001 0.078 0.42 2 -0.42 23 25
peptide biosynthetic process -0.01 0.018 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.005 16 -10000 0 16
EEF2 -0.01 0.018 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.011 0.21 -10000 0 -0.97 46 46
Class I PI3K signaling events mediated by Akt

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 0.011 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.02 0.3 1 -10000 0 1
CDKN1B 0.011 0.056 -10000 0 -0.43 5 5
CDKN1A 0.01 0.061 -10000 0 -0.42 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -0.43 5 5
AKT1 0.006 0.056 -10000 0 -0.36 17 17
BAD 0.024 0.009 0.26 1 -10000 0 1
AKT3 0.006 0.035 -10000 0 -0.35 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.009 0.059 -10000 0 -0.44 7 7
AKT1/ASK1 0.031 0.067 -10000 0 -0.4 7 7
BAD/YWHAZ 0.037 0.022 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.03 0.065 0.39 7 -10000 0 7
TSC1 0.011 0.051 -10000 0 -0.61 2 2
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.036 0.07 -10000 0 -0.43 7 7
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.01 0.059 -10000 0 -0.36 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.054 0.32 1 -0.39 7 8
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.004 0.015 -10000 0 -0.34 2 2
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.075 0.32 16 -0.25 4 20
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.06 -10000 0 -0.62 3 3
CASP9 0.011 0.045 -10000 0 -0.4 3 3
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.072 0.33 4 -0.54 3 7
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.058 0.25 3 -0.48 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.051 -10000 0 -0.32 20 20
CHUK 0.01 0.055 -10000 0 -0.4 6 6
BAD/BCL-XL 0.038 0.066 0.28 2 -0.53 3 5
mTORC2 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.032 0.097 0.31 7 -0.42 18 25
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.012 0.064 0.27 2 -0.44 7 9
MAPKKK cascade -0.036 0.069 0.42 7 -10000 0 7
MDM2/Cbp/p300 0.042 0.072 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.068 0.33 4 -0.59 3 7
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.069 0.32 4 -0.53 3 7
glucose import -0.16 0.15 0.21 2 -0.31 521 523
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.048 -10000 0 -0.41 4 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 -10000 0 -0.31 521 521
GSK3A 0.01 0.059 -10000 0 -0.62 3 3
FOXO1 0.012 0.04 -10000 0 -0.3 1 1
GSK3B 0.01 0.059 -10000 0 -0.44 7 7
SFN 0.021 0.07 0.26 21 -0.57 12 33
G1/S transition of mitotic cell cycle 0.014 0.065 0.33 2 -0.6 3 5
p27Kip1/14-3-3 family 0.021 0.049 0.37 1 -0.48 2 3
PRKACA 0.024 0.004 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.012 0.06 -10000 0 -10000 0 0
PLK1 0.24 0.18 0.55 80 -0.57 1 81
CDKN1B 0.15 0.13 0.38 56 -0.45 5 61
FOXO3 0.2 0.16 0.45 175 -0.5 3 178
KAT2B 0.055 0.033 -10000 0 -0.57 1 1
FOXO1/SIRT1 0.012 0.055 -10000 0 -0.28 9 9
CAT 0.18 0.17 0.64 11 -1.1 4 15
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.056 0.028 -10000 0 -10000 0 0
FOXO1 0.017 0.062 -10000 0 -0.3 9 9
MAPK10 -0.016 0.12 0.2 11 -0.29 156 167
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.034 0.084 0.38 3 -0.42 2 5
response to oxidative stress 0.034 0.026 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.17 0.14 0.43 46 -0.5 3 49
XPO1 0.024 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.062 0.084 -10000 0 -0.69 10 10
FOXO1/SKP2 0.026 0.058 -10000 0 -0.28 9 9
mol:GDP 0.034 0.026 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.13 0.13 0.45 3 -0.51 14 17
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.022 0.12 -10000 0 -0.5 37 37
MST1 0.052 0.059 0.27 8 -0.51 8 16
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.01 0.12 -10000 0 -0.45 46 46
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.037 0.21 10 -0.3 8 18
MAPK9 0.031 0.024 0.21 11 -10000 0 11
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
SIRT1 0.012 0.02 -10000 0 -10000 0 0
SOD2 0.15 0.13 0.46 16 -0.43 2 18
RBL2 0.1 0.25 0.54 2 -0.63 69 71
RAL/GDP 0.056 0.021 -10000 0 -10000 0 0
CHUK 0.055 0.028 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.057 0.021 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.055 0.18 -10000 0 -1.3 17 17
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.006 -10000 0 -10000 0 0
IKBKB 0.046 0.032 -10000 0 -10000 0 0
CCNB1 0.2 0.17 0.52 85 -0.57 1 86
FOXO1-3a-4/beta catenin 0.15 0.12 0.41 43 -0.39 6 49
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.058 -10000 0 -0.28 9 9
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
SGK1 0.051 0.05 -10000 0 -0.55 5 5
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.032 0.075 0.44 1 -0.4 1 2
SFN 0.021 0.07 0.26 21 -0.57 12 33
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.062 0.11 0.32 2 -0.41 18 20
CREBBP 0.022 0.008 -10000 0 -10000 0 0
FBXO32 0.23 0.2 0.6 119 -1.2 3 122
BCL6 0.16 0.16 0.52 3 -0.87 10 13
RALB 0.025 0.003 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
ITGA4 0.026 0.022 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.041 0.039 0.21 36 -0.42 2 38
alpha4/beta1 Integrin 0.036 0.016 0.2 9 -10000 0 9
ceramide signaling pathway

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
MAP4K4 -0.001 0.098 0.26 2 -0.41 31 33
BAG4 0.018 0.032 -10000 0 -0.57 3 3
BAD 0.005 0.038 0.2 4 -0.18 7 11
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.04 0.26 12 -0.57 3 15
BAX 0.005 0.042 0.22 6 -0.19 5 11
EnzymeConsortium:3.1.4.12 0.002 0.026 0.081 5 -0.091 29 34
IKBKB 0.017 0.1 0.28 10 -0.4 22 32
MAP2K2 0.008 0.051 0.23 12 -0.24 2 14
MAP2K1 0.009 0.053 0.23 14 -0.24 2 16
SMPD1 0.002 0.032 0.14 3 -0.15 14 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.11 0.28 20 -0.42 26 46
MAP2K4 0.006 0.034 0.18 5 -0.22 3 8
protein ubiquitination 0.004 0.1 0.34 4 -0.4 28 32
EnzymeConsortium:2.7.1.37 0.008 0.054 0.23 14 -0.25 2 16
response to UV 0 0.001 0.003 18 -0.002 2 20
RAF1 0.009 0.052 0.19 42 -0.22 4 46
CRADD 0.024 0.004 -10000 0 -10000 0 0
mol:ceramide 0.006 0.04 0.13 6 -0.15 21 27
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.009 -10000 0 -10000 0 0
MADD 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.039 0.18 4 -0.2 6 10
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.023 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.052 0.23 12 -0.23 2 14
MAPK1 0.007 0.059 0.23 12 -0.25 5 17
p50/RELA/I-kappa-B-alpha 0.034 0.009 -10000 0 -10000 0 0
FADD 0.024 0.11 0.27 13 -0.42 24 37
KSR1 0.009 0.05 0.18 36 -0.21 5 41
MAPK8 0.002 0.048 0.23 9 -0.28 9 18
TRAF2 0.025 0.015 0.26 4 -10000 0 4
response to radiation 0 0 0.002 10 -10000 0 10
CHUK -0.001 0.093 0.25 1 -0.41 24 25
TNF R/SODD 0.027 0.029 -10000 0 -0.36 4 4
TNF 0.025 0.065 0.26 25 -0.57 9 34
CYCS 0.008 0.045 0.18 14 -0.18 4 18
IKBKG -0.001 0.095 0.43 1 -0.42 24 25
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.002 0.1 -10000 0 -0.43 29 29
RELA 0.023 0.005 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.007 0.044 0.17 13 -0.19 5 18
TNF/TNF R/SODD 0.036 0.051 -10000 0 -0.36 11 11
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 10 -10000 0 10
CASP8 0.003 0.13 -10000 0 -0.62 41 41
NSMAF 0.017 0.11 0.26 11 -0.4 28 39
response to hydrogen peroxide 0 0.001 0.003 18 -0.002 2 20
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.021 -10000 0 -0.36 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.062 -10000 0 -0.35 16 16
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.005 0.067 0.21 2 -0.37 17 19
RAR alpha/9cRA/Cyclin H 0.046 0.074 -10000 0 -0.33 20 20
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.066 -10000 0 -0.34 21 21
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.023 0.064 -10000 0 -0.3 27 27
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.008 0.11 -10000 0 -0.54 23 23
NCOA2 -0.006 0.12 -10000 0 -0.57 48 48
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.023 0.018 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARG 0.025 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.02 0.051 -10000 0 -0.57 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.1 -10000 0 -0.48 24 24
RARA 0.013 0.055 0.2 13 -0.27 27 40
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.079 -10000 0 -0.38 23 23
PRKCA 0.012 0.084 0.26 1 -0.57 22 23
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.12 0.45 1 -0.53 26 27
RXRG -0.051 0.15 0.24 12 -0.35 204 216
RXRA 0.022 0.064 0.34 1 -0.26 28 29
RXRB 0.016 0.061 0.22 17 -0.34 22 39
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.036 0.076 0.26 73 -0.57 7 80
CRBP1/9-cic-RA 0.026 0.053 0.18 73 -0.42 7 80
RARB 0.017 0.067 -10000 0 -0.57 14 14
PRKCG 0.032 0.045 0.26 41 -10000 0 41
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.51 29 29
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.008 0.1 -10000 0 -0.43 30 30
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.08 0.24 14 -0.36 18 32
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.12 0.45 1 -0.53 26 27
positive regulation of DNA binding 0.032 0.064 -10000 0 -0.31 20 20
NRIP1 0.011 0.12 0.54 1 -0.72 11 12
RXRs/RARs 0.009 0.12 -10000 0 -0.5 31 31
RXRs/RXRs/DNA/9cRA -0.013 0.091 -10000 0 -0.49 24 24
PRKACA 0.024 0.004 -10000 0 -10000 0 0
CDK7 0.023 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.051 0.056 -10000 0 -0.31 3 3
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.044 0.015 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.036 -10000 0 -0.57 4 4
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.014 0.096 -10000 0 -0.3 91 91
GNAO1 0.018 0.09 0.26 32 -0.57 20 52
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.091 -10000 0 -0.51 23 23
AKT3 -0.014 0.17 -10000 0 -1.1 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.036 -10000 0 -0.56 4 4
GNAI2 0.023 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.009 -10000 0 -10000 0 0
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.25 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.1 -10000 0 -0.35 56 56
MAPK3 -0.009 0.091 0.27 2 -0.4 29 31
MAPK1 -0.008 0.092 0.27 1 -0.4 31 32
JAK2 -0.01 0.1 -10000 0 -0.39 41 41
CXCR4 -0.011 0.096 -10000 0 -0.4 32 32
FLT1 0.023 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.011 0.094 -10000 0 -0.4 30 30
S1P/S1P3/Gi -0.004 0.1 -10000 0 -0.35 56 56
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.1 -10000 0 -0.38 33 33
VEGFA 0.025 0.021 0.26 6 -10000 0 6
S1P/S1P2/Gi -0.005 0.093 -10000 0 -0.34 48 48
VEGFR1 homodimer/VEGFA homodimer 0.035 0.022 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.019 0.042 -10000 0 -0.28 18 18
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
GNAZ 0.017 0.057 -10000 0 -0.57 10 10
G12/G13 0.033 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
Rac1/GTP -0.004 0.1 -10000 0 -0.39 33 33
IL1-mediated signaling events

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
UBC13/UEV1A 0.018 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.05 -10000 0 -0.32 10 10
IRAK/TOLLIP 0.026 0.009 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.025 0.094 0.36 3 -0.42 40 43
IL1A 0.028 0.03 0.26 18 -10000 0 18
IL1B 0.004 0.053 0.26 1 -0.43 15 16
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.027 -10000 0 -0.3 1 1
IL1R2 0.008 0.12 0.26 29 -0.57 40 69
IL1R1 0.012 0.084 -10000 0 -0.57 22 22
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.062 0.26 4 -0.3 22 26
TOLLIP 0.024 0.004 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.057 0.27 1 -0.37 1 2
JUN -0.015 0.056 0.21 4 -0.27 35 39
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.085 -10000 0 -0.34 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88 0.053 0.061 -10000 0 -0.33 23 23
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.061 0.061 -10000 0 -0.31 23 23
IL1 beta fragment/IL1R1/IL1RAP 0.022 0.073 -10000 0 -0.35 36 36
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.011 0.054 0.17 30 -0.28 28 58
IRAK1 0.012 0.008 -10000 0 -10000 0 0
IL1RN/IL1R1 0.031 0.074 -10000 0 -0.42 24 24
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.4 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.059 -10000 0 -0.28 30 30
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.022 0.073 -10000 0 -0.35 36 36
IL1 beta/IL1R2 0.013 0.093 -10000 0 -0.37 53 53
IRAK/TRAF6/TAK1/TAB1/TAB2 0.032 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.077 -10000 0 -0.32 44 44
IRAK3 0.003 0.11 0.26 1 -0.57 39 40
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.074 -10000 0 -0.32 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.047 -10000 0 -0.27 23 23
IL1 alpha/IL1R1/IL1RAP 0.041 0.063 -10000 0 -0.36 23 23
RELA 0.023 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.038 0.021 -10000 0 -10000 0 0
IL1RAP 0.023 0.018 -10000 0 -0.57 1 1
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.018 0.06 -10000 0 -0.29 34 34
CASP1 0.021 0.019 -10000 0 -0.57 1 1
IL1RN/IL1R2 0.028 0.099 0.36 5 -0.42 42 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.034 0.073 -10000 0 -0.33 36 36
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.071 -10000 0 -0.34 34 34
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.031 0.049 0.26 37 -0.57 2 39
TRAF6/TAK1/TAB1/TAB2 0.033 0.011 -10000 0 -10000 0 0
MAP2K6 -0.008 0.053 0.19 31 -0.29 22 53
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.011 0.23 2 -10000 0 2
SNTA1 0.024 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.034 0.3 8 -10000 0 8
MAPK12 -0.009 0.048 0.21 1 -0.33 22 23
CCND1 0.01 0.047 -10000 0 -0.38 7 7
p38 gamma/SNTA1 0.021 0.07 0.32 2 -0.32 22 24
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint -0.009 0.048 0.21 1 -0.33 22 23
MAP2K6 -0.006 0.051 -10000 0 -0.35 23 23
MAPT -0.026 0.12 0.26 14 -0.32 120 134
MAPK13 0.011 0.011 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.006 0.001 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.019 0.11 -10000 0 -0.41 41 41
KLHL20 0.016 0.064 0.22 13 -0.22 18 31
CYFIP2 0.028 0.048 0.26 26 -0.57 3 29
Rac1/GDP 0.001 0.084 0.26 8 -0.31 16 24
ENAH -0.014 0.1 -10000 0 -0.4 40 40
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.01 0.046 -10000 0 -0.4 1 1
ABI1/Sra1/Nap1 -0.012 0.031 -10000 0 -0.15 16 16
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.047 0.064 -10000 0 -0.33 20 20
RAPGEF1 -0.018 0.1 0.26 1 -0.39 28 29
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.12 -10000 0 -0.4 53 53
CRK -0.015 0.099 -10000 0 -0.41 32 32
E-cadherin/gamma catenin/alpha catenin 0.033 0.057 -10000 0 -0.36 18 18
alphaE/beta7 Integrin 0.036 0.034 -10000 0 -0.42 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
DLG1 -0.023 0.12 -10000 0 -0.4 49 49
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.031 -10000 0 -0.24 2 2
MLLT4 0.021 0.032 0.26 1 -0.57 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.003 0.045 -10000 0 -0.31 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.021 0.062 -10000 0 -0.33 28 28
TIAM1 0.025 0.015 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.041 0.054 -10000 0 -0.31 18 18
AKT1 -0.007 0.035 0.14 1 -0.21 1 2
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
CDH1 0.012 0.076 -10000 0 -0.57 18 18
RhoA/GDP 0.002 0.083 0.26 8 -0.31 16 24
actin cytoskeleton organization 0.015 0.052 0.18 19 -0.16 12 31
CDC42/GDP 0.002 0.082 0.26 8 -0.31 16 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.04 -10000 0 -0.26 18 18
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.045 0.057 -10000 0 -0.33 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin 0.03 0.049 -10000 0 -0.31 18 18
mol:GDP -0.012 0.09 0.27 8 -0.36 17 25
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 0.085 0.26 7 -0.32 16 23
RAC1/GTP/IQGAP1 0.032 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.047 0.18 39 -0.24 4 43
NME1 0.026 0.031 0.26 18 -10000 0 18
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.021 0.11 -10000 0 -0.41 46 46
regulation of cell-cell adhesion 0.004 0.039 -10000 0 -0.35 1 1
WASF2 0.008 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.056 0.24 3 -0.46 1 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.054 0.064 -10000 0 -0.32 19 19
CCND1 0.015 0.054 0.2 38 -0.3 4 42
VAV2 -0.018 0.15 -10000 0 -0.54 38 38
RAP1/GDP 0.008 0.069 0.26 3 -0.35 3 6
adherens junction assembly -0.02 0.11 -10000 0 -0.39 46 46
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.024 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.042 0.061 -10000 0 -0.3 19 19
E-cadherin/beta catenin 0.001 0.057 -10000 0 -0.34 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.022 0.12 -10000 0 -0.39 51 51
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.089 0.25 34 -0.34 25 59
E-cadherin/beta catenin/alpha catenin 0.034 0.057 -10000 0 -0.36 18 18
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.12 -10000 0 -0.41 53 53
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.009 0.26 1 -9999 0 1
PLK4 0.033 0.044 0.26 41 -9999 0 41
regulation of centriole replication 0.016 0.026 0.26 2 -9999 0 2
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.048 -10000 0 -0.57 7 7
positive regulation of NF-kappaB transcription factor activity -0.005 0.11 -10000 0 -0.33 106 106
MAP2K4 0.016 0.046 -10000 0 -0.38 4 4
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.032 -10000 0 -0.57 3 3
SMPD1 0.008 0.029 -10000 0 -0.34 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.015 0.14 0.26 1 -0.57 64 65
TRAIL/TRAILR2 0.026 0.038 -10000 0 -0.37 8 8
TRAIL/TRAILR3 0.027 0.042 -10000 0 -0.42 7 7
TRAIL/TRAILR1 0.024 0.046 -10000 0 -0.33 15 15
TRAIL/TRAILR4 -0.005 0.11 -10000 0 -0.33 106 106
TRAIL/TRAILR1/DAP3/GTP 0.029 0.038 -10000 0 -0.32 7 7
IKK complex 0.011 0.04 -10000 0 -0.41 1 1
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.035 0.25 1 -0.42 7 8
MAP3K1 0.019 0.059 -10000 0 -0.44 7 7
TRAILR4 (trimer) -0.015 0.14 0.26 1 -0.56 64 65
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.032 -10000 0 -0.56 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.044 -10000 0 -0.36 9 9
CFLAR 0.024 0.018 -10000 0 -0.57 1 1
MAPK1 0.008 0.035 0.25 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.046 -10000 0 -0.3 7 7
mol:ceramide 0.008 0.029 -10000 0 -0.34 6 6
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.013 0.062 0.26 1 -0.44 7 8
TRAF2 0.025 0.015 0.26 4 -10000 0 4
TRAILR3 (trimer) 0.022 0.021 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.031 0.041 -10000 0 -0.35 7 7
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.036 0.084 0.28 61 -0.34 3 64
JNK cascade -0.005 0.11 -10000 0 -0.33 106 106
TRAIL (trimer) 0.02 0.048 -10000 0 -0.56 7 7
TNFRSF10C 0.022 0.021 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.039 -10000 0 -0.31 5 5
TRAIL/TRAILR2/FADD 0.032 0.036 -10000 0 -0.35 5 5
cell death 0.008 0.029 -10000 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.041 -10000 0 -0.41 6 6
TRAILR2 (trimer) 0.02 0.009 -10000 0 -10000 0 0
CASP8 0.012 0.05 -10000 0 -0.56 6 6
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.043 0.043 -10000 0 -0.29 5 5
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.27 0.29 -10000 0 -0.57 524 524
CLTC 0.025 0.067 0.28 1 -0.42 13 14
calcium ion-dependent exocytosis 0.009 0.025 -10000 0 -0.26 2 2
Dynamin 2/GTP 0.022 0.013 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.016 0.046 -10000 0 -0.34 10 10
CPE 0.005 0.049 -10000 0 -0.36 19 19
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.019 -10000 0 -10000 0 0
CTNND1 0.008 0.056 0.2 38 -10000 0 38
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.043 0.21 3 -0.33 7 10
TSHR -0.003 0.072 -10000 0 -0.36 42 42
INS -0.001 0.088 -10000 0 -0.48 34 34
BIN1 0.02 0.051 -10000 0 -0.57 8 8
mol:Choline 0.011 0.019 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.017 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.013 -10000 0 -10000 0 0
JUP 0.017 0.039 0.23 1 -0.33 7 8
ASAP2/amphiphysin II 0.042 0.033 -10000 0 -0.33 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.01 0.053 -10000 0 -0.37 9 9
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.028 0.26 16 -10000 0 16
substrate adhesion-dependent cell spreading 0.016 0.039 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.064 0.34 7 -10000 0 7
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.015 0.028 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.043 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.024 0.063 0.29 5 -0.35 12 17
JIP4/KLC1 0.041 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.02 0.033 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.008 0.057 0.2 39 -10000 0 39
NME1 0.013 0.017 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.069 0.28 3 -0.41 13 16
IL2RA 0.019 0.054 -10000 0 -0.32 13 13
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.37 34 34
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.029 -10000 0 -0.29 9 9
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.039 0.19 1 -0.36 6 7
SDC1 0.019 0.043 -10000 0 -0.33 8 8
ARF6/GDP 0.021 0.014 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.04 0.067 -10000 0 -0.36 6 6
mol:Phosphatidic acid 0.011 0.019 -10000 0 -10000 0 0
endocytosis -0.04 0.033 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.037 0.14 0.26 1 -0.39 47 48
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.018 -10000 0 -0.57 1 1
Dynamin 2/GDP 0.026 0.017 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.079 0.15 0.27 2 -0.43 36 38
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.065 0.32 2 -0.35 5 7
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.019 -10000 0 -0.3 3 3
TRAF2/ASK1 0.03 0.024 -10000 0 -0.36 3 3
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.018 0.11 0.27 1 -0.35 58 59
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.098 0.26 1 -0.36 34 35
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.054 0.077 0.26 138 -10000 0 138
TXN 0.007 0.006 0.11 3 -10000 0 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.027 -10000 0 -0.41 3 3
TAK1/TAB family 0 0.019 0.18 2 -0.14 6 8
RAC1/OSM/MEKK3 0.042 0.016 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.26 4 -10000 0 4
RAC1/OSM/MEKK3/MKK3 0 0.091 -10000 0 -0.31 34 34
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.005 0.15 0.26 44 -0.57 69 113
CCM2 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.012 0.1 -10000 0 -0.36 69 69
MAPK11 0.021 0.032 -10000 0 -0.57 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.023 0.1 -10000 0 -0.33 71 71
OSM/MEKK3 0.032 0.013 -10000 0 -10000 0 0
TAOK1 -0.008 0.081 -10000 0 -0.36 54 54
TAOK2 0.011 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.025 -10000 0 -0.34 3 3
GADD45/MTK1/MTK1 0.067 0.047 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.026 0.041 0.26 20 -0.57 2 22
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.019 0.22 1 -0.29 2 3
GNAO1 0.017 0.09 0.26 32 -0.57 20 52
mol:Sphinganine-1-P 0.012 0.026 0.26 1 -0.42 2 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.035 -10000 0 -0.23 3 3
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.02 0.26 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.006 0.023 -10000 0 -0.24 5 5
S1PR5 0.027 0.041 0.26 20 -0.57 2 22
S1PR4 0.029 0.062 0.26 38 -0.57 6 44
GNAI1 -0.007 0.13 -10000 0 -0.57 57 57
S1P/S1P5/G12 0.046 0.041 0.24 4 -0.24 5 9
S1P/S1P3/Gq 0.026 0.063 -10000 0 -0.29 31 31
S1P/S1P4/Gi 0 0.097 -10000 0 -0.33 47 47
GNAQ 0.022 0.031 -10000 0 -0.57 3 3
GNAZ 0.018 0.057 -10000 0 -0.57 10 10
GNA14 0.023 0.065 0.26 19 -0.57 10 29
GNA15 0.025 0.025 0.26 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.036 -10000 0 -0.57 4 4
ABCC1 0.023 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.019 0.023 0.21 5 -0.3 1 6
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.067 0.048 0.35 10 -0.33 2 12
EPO 0.059 0.085 0.26 169 -10000 0 169
alpha4/beta7 Integrin 0.041 0.039 0.21 36 -0.42 2 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.016 0.2 9 -10000 0 9
EPO/EPOR (dimer) 0.059 0.059 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.077 -10000 0 -0.42 23 23
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.4 13 13
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.033 0.03 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
MADCAM1 0.031 0.044 0.26 39 -10000 0 39
cell adhesion 0.064 0.047 0.34 10 -0.33 2 12
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.013 0.043 -10000 0 -0.33 10 10
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.044 0.046 -10000 0 -0.36 11 11
p130Cas/Crk/Dock1 0.026 0.041 0.35 1 -0.28 9 10
VCAM1 0.019 0.062 0.26 6 -0.57 11 17
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.023 -10000 0 -10000 0 0
BCAR1 -0.009 0.042 0.38 1 -0.3 10 11
EPOR 0.024 0.008 0.26 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.079 -10000 0 -0.43 23 23
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.013 0.04 0.3 4 -0.28 1 5
DAPP1 0.017 0.1 0.27 7 -0.35 36 43
Src family/SYK family/BLNK-LAT/BTK-ITK 0.019 0.14 0.28 13 -0.51 33 46
mol:DAG 0.022 0.078 0.23 36 -0.25 10 46
HRAS 0.027 0.022 0.25 9 -10000 0 9
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.059 0.27 1 -0.32 9 10
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.008 0.26 1 -10000 0 1
mol:GTP -0.01 0.037 0.31 5 -0.28 1 6
ARF1/GTP -0.004 0.033 0.26 8 -0.28 1 9
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
RAP1A/GTP -0.011 0.033 0.2 1 -0.27 1 2
ADAP1 -0.011 0.04 0.3 5 -0.28 2 7
ARAP3 -0.01 0.037 0.31 5 -0.28 1 6
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.027 0.033 0.26 21 -10000 0 21
ARHGEF6 0.017 0.067 -10000 0 -0.57 14 14
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.026 -10000 0 -0.57 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
mol:Ca2+ 0.016 0.053 0.22 21 -10000 0 21
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 4 -10000 0 4
ZAP70 0.026 0.098 0.26 61 -0.57 20 81
mol:IP3 0.017 0.066 0.2 60 -0.18 7 67
LYN 0.021 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.057 0.28 2 -0.32 9 11
RhoA/GDP 0.03 0.041 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.02 0.068 0.3 12 -0.35 2 14
SRC 0.023 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.011 0.23 2 -10000 0 2
RAC1 0.024 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.02 -10000 0 -0.54 1 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.038 0.32 4 -10000 0 4
RhoA/GTP -0.012 0.037 0.33 4 -10000 0 4
Src family/SYK family/BLNK-LAT 0.026 0.096 0.25 18 -0.41 18 36
BLK 0.051 0.087 0.26 151 -0.57 2 153
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.037 0.32 4 -10000 0 4
HCK 0.027 0.026 0.26 13 -10000 0 13
CYTH3 -0.012 0.039 0.33 3 -0.28 2 5
CYTH2 -0.011 0.039 0.32 4 -0.26 1 5
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.009 0.053 0.31 1 -0.41 11 12
SGK1 0.005 0.076 -10000 0 -0.35 39 39
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.06 0.28 2 -0.33 10 12
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.044 0.31 6 -10000 0 6
mol:PI-3-4-5-P3 -0.011 0.035 0.28 4 -0.27 1 5
ARAP3/RAP1A/GTP -0.011 0.033 0.2 1 -0.28 1 2
VAV1 0.023 0.033 0.26 2 -0.57 3 5
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.04 0.039 -10000 0 -0.28 1 1
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.059 0.27 1 -0.35 7 8
LAT 0.025 0.038 0.26 15 -0.57 2 17
Rac1/GTP 0.016 0.051 -10000 0 -0.34 11 11
ITK -0.018 0.062 0.32 4 -0.31 29 33
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.021 0.095 0.26 32 -0.33 15 47
LCK 0.026 0.075 0.26 40 -0.57 11 51
BTK -0.011 0.039 0.32 4 -0.26 1 5
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.025 0.073 0.3 4 -0.41 9 13
PDGFB-D/PDGFRB/SLAP 0.028 0.033 -10000 0 -0.42 3 3
PDGFB-D/PDGFRB/APS/CBL 0.048 0.042 -10000 0 -0.35 4 4
AKT1 0.025 0.095 0.34 38 -10000 0 38
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.032 0.084 0.32 6 -0.43 12 18
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.46 33 33
mol:Ca2+ 0.024 0.087 0.31 4 -0.47 13 17
MYC 0.053 0.17 0.37 28 -0.78 26 54
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.3 3 3
LRP1/PDGFRB/PDGFB 0.041 0.054 -10000 0 -0.4 14 14
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.023 0.088 0.31 4 -0.48 13 17
PTEN 0.022 0.019 -10000 0 -0.57 1 1
GRB2 0.023 0.009 0.26 1 -10000 0 1
GRB7 0.019 0.032 -10000 0 -0.57 3 3
PDGFB-D/PDGFRB/SHP2 0.034 0.028 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.028 -10000 0 -0.42 4 4
cell cycle arrest 0.028 0.033 -10000 0 -0.42 3 3
HRAS 0.026 0.022 0.26 9 -10000 0 9
HIF1A 0.019 0.089 0.33 37 -10000 0 37
GAB1 0.026 0.093 0.31 5 -0.43 16 21
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.026 0.086 0.33 8 -0.43 7 15
PDGFB-D/PDGFRB 0.042 0.031 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.026 -10000 0 -0.42 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.023 0.065 0.29 2 -0.47 4 6
positive regulation of MAPKKK cascade 0.034 0.028 -10000 0 -0.42 4 4
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.024 0.088 0.31 4 -0.48 13 17
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.039 -10000 0 -0.42 7 7
SHB 0.024 0.008 0.26 1 -10000 0 1
BLK -0.024 0.16 0.29 5 -0.41 134 139
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.029 -10000 0 -0.41 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.028 0.1 0.34 4 -0.46 17 21
CBL 0.022 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.029 -10000 0 -0.42 4 4
LCK 0.006 0.11 -10000 0 -0.53 30 30
PDGFRB 0.022 0.037 -10000 0 -0.57 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.016 0.06 -10000 0 -0.52 6 6
ABL1 0.021 0.093 0.3 6 -0.4 21 27
PDGFB-D/PDGFRB/CBL 0.021 0.1 0.32 1 -0.49 20 21
PTPN1 0.024 0.019 0.25 6 -10000 0 6
SNX15 0.023 0.005 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 0.26 19 -10000 0 19
cell proliferation 0.054 0.15 0.35 35 -0.68 26 61
SLA 0.021 0.024 0.26 9 -10000 0 9
actin cytoskeleton reorganization 0.034 0.05 0.33 2 -0.31 1 3
SRC 0.012 0.059 -10000 0 -0.52 7 7
PI3K -0.013 0.032 -10000 0 -0.28 9 9
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.038 -10000 0 -0.36 6 6
SH2B2 0.034 0.046 0.26 45 -10000 0 45
PLCgamma1/SPHK1 0.032 0.086 0.32 6 -0.44 12 18
LYN 0.009 0.064 -10000 0 -0.52 8 8
LRP1 0.018 0.062 -10000 0 -0.57 12 12
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.026 -10000 0 -0.57 2 2
STAT5A 0.02 0.044 -10000 0 -0.57 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.3 3 3
SPHK1 0.027 0.041 0.26 20 -0.57 2 22
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.024 0.088 0.31 4 -0.48 13 17
PLCG1 0.024 0.09 0.32 4 -0.49 13 17
NHERF/PDGFRB 0.049 0.045 -10000 0 -0.36 4 4
YES1 0.001 0.11 -10000 0 -0.56 29 29
cell migration 0.048 0.044 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.049 0.041 -10000 0 -0.3 3 3
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
SLC9A3R1 0.036 0.054 0.26 60 -10000 0 60
NHERF1-2/PDGFRB/PTEN 0.056 0.048 0.29 2 -0.33 4 6
FYN -0.003 0.1 -10000 0 -0.42 44 44
DOK1 0.021 0.049 0.33 1 -0.33 3 4
HRAS/GTP 0.019 0.015 0.18 9 -10000 0 9
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.023 0.12 0.34 2 -0.52 27 29
PRKCD 0.022 0.051 0.33 1 -0.33 3 4
FER 0.018 0.059 -10000 0 -0.34 12 12
MAPKKK cascade 0.037 0.096 0.36 34 -0.31 1 35
RASA1 0.021 0.049 -10000 0 -0.33 3 3
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.035 0.043 0.3 1 -0.31 3 4
PDGFB-D/PDGFRB/SHB 0.034 0.03 -10000 0 -0.42 4 4
chemotaxis 0.021 0.091 0.3 6 -0.39 21 27
STAT1-3-5/STAT1-3-5 0.049 0.047 -10000 0 -0.36 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.027 -10000 0 -0.42 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.069 0.051 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.055 0.046 0.33 5 -10000 0 5
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.042 -10000 0 -0.22 1 1
CaM/Ca2+ 0.067 0.046 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.042 0.042 0.28 2 -10000 0 2
AKT1 0.01 0.064 0.29 11 -0.28 10 21
MAP2K1 0.007 0.045 0.29 4 -0.29 1 5
MAP3K11 0.023 0.042 0.24 9 -10000 0 9
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.019 0.095 -10000 0 -0.4 9 9
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.033 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.076 0.054 -10000 0 -10000 0 0
CEBPB 0.028 0.094 0.32 2 -0.49 7 9
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.075 0.094 -10000 0 -0.67 10 10
STAT1 0.026 0.047 0.29 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.054 0.08 0.26 146 -10000 0 146
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.045 0.28 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.028 0.061 0.34 2 -0.33 5 7
mol:Ca2+ 0.065 0.048 -10000 0 -10000 0 0
MAPK3 0.022 0.078 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.058 -10000 0 -10000 0 0
MAPK1 -0.006 0.16 -10000 0 -0.67 58 58
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.031 -10000 0 -0.57 3 3
DAPK1 0.027 0.069 0.3 2 -0.34 2 4
SMAD7 0.017 0.036 0.18 6 -10000 0 6
CBL/CRKL/C3G 0.045 0.038 0.29 4 -10000 0 4
PI3K 0.056 0.056 -10000 0 -0.29 12 12
IFNG 0.054 0.08 0.26 146 -10000 0 146
apoptosis 0.024 0.071 0.28 1 -0.4 10 11
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.032 0.042 0.26 36 -10000 0 36
CAMK2B -0.004 0.15 0.26 44 -0.57 69 113
FRAP1 0.008 0.06 0.28 11 -0.26 10 21
PRKCD 0.011 0.067 0.3 13 -0.28 11 24
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -0.22 1 1
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.022 0.057 0.29 11 -0.32 1 12
STAT1 (dimer)/PIASy 0.038 0.046 0.27 6 -10000 0 6
SOCS1 0.016 0.11 -10000 0 -1 10 10
mol:GDP 0.041 0.036 0.27 4 -10000 0 4
CASP1 0.016 0.039 0.2 7 -0.24 3 10
PTGES2 0.024 0.008 0.26 1 -10000 0 1
IRF9 0.028 0.041 0.24 8 -10000 0 8
mol:PI-3-4-5-P3 0.041 0.047 -10000 0 -0.28 12 12
RAP1/GDP 0.035 0.022 -10000 0 -10000 0 0
CBL 0.021 0.04 0.29 4 -10000 0 4
MAP3K1 0.022 0.042 0.29 4 -0.3 1 5
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.042 -10000 0 -0.22 1 1
PTPN11 0.025 0.044 0.24 10 -10000 0 10
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.032 -10000 0 -0.57 3 3
Caspase 8 (4 units) 0.039 0.062 -10000 0 -0.46 3 3
NEF 0.003 0.024 -10000 0 -0.18 11 11
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.02 0.054 0.26 12 -0.44 7 19
CYCS 0.036 0.077 0.26 25 -0.29 13 38
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.017 0.086 0.29 16 -0.61 15 31
MAP2K7 0.041 0.12 0.42 1 -0.72 16 17
protein ubiquitination 0.015 0.082 0.31 5 -0.37 11 16
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.022 0.036 -10000 0 -0.57 4 4
BID 0.035 0.073 0.21 4 -0.29 16 20
NF-kappa-B/RelA/I kappa B alpha 0.051 0.033 -10000 0 -0.27 5 5
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
CFLAR 0.024 0.018 -10000 0 -0.57 1 1
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.033 -10000 0 -0.27 5 5
MAPK8 0.038 0.12 0.4 5 -0.65 17 22
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.013 0.26 3 -10000 0 3
TRAF2 0.025 0.015 0.26 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.059 0.23 4 -0.3 16 20
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.015 0.091 -10000 0 -0.42 18 18
CHUK 0.014 0.085 0.31 4 -0.4 11 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.054 0.041 -10000 0 -0.33 5 5
TCRz/NEF 0.016 0.08 0.31 9 -0.42 26 35
TNF 0.024 0.065 0.26 25 -0.57 9 34
FASLG 0.011 0.11 0.28 42 -0.57 26 68
NFKB1 0.025 0.011 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 11 11
CASP6 0.052 0.1 0.38 1 -0.52 17 18
CASP7 0.04 0.1 0.35 9 -0.43 14 23
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.38 5 -0.45 11 16
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.36 4 4
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.005 -10000 0 -10000 0 0
MAP3K14 0.016 0.087 0.29 1 -0.42 13 14
APAF-1/Caspase 9 0.033 0.061 0.24 6 -0.37 5 11
BCL2 0.031 0.12 0.42 6 -0.55 22 28
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.11 0.28 16 -0.32 31 47
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.034 0.36 1 -0.42 1 2
NFKBIA 0.012 0.025 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.016 0.26 3 -10000 0 3
IKBKG 0.019 0.03 -10000 0 -10000 0 0
IKK complex/A20 0.021 0.12 -10000 0 -0.39 45 45
NEMO/A20/RIP2 0.02 0.016 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.014 0.12 0.28 1 -0.37 78 79
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.032 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.11 -10000 0 -0.38 44 44
BCL10/MALT1/TRAF6 0.045 0.014 -10000 0 -10000 0 0
NOD2 0.028 0.043 0.26 30 -0.57 1 31
NFKB1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
MALT1 0.023 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.034 0.049 -10000 0 -0.42 9 9
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.024 0.065 0.26 25 -0.57 9 34
NF kappa B1 p50/RelA 0.051 0.015 -10000 0 -10000 0 0
BCL10 0.024 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.025 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.015 0.12 -10000 0 -0.4 45 45
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.41 53 53
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.051 0.081 -10000 0 -0.48 1 1
CRKL 0.025 0.047 0.31 6 -10000 0 6
mol:DAG 0.038 0.051 -10000 0 -10000 0 0
HRAS 0.034 0.078 0.31 18 -10000 0 18
MAPK8 0.04 0.07 0.24 35 -0.34 5 40
RAP1A 0.027 0.048 0.3 8 -10000 0 8
GAB1 0.026 0.046 0.32 5 -10000 0 5
MAPK14 0.042 0.065 0.24 35 -10000 0 35
EPO 0.061 0.085 0.26 169 -10000 0 169
PLCG1 0.038 0.051 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.013 0.26 1 -10000 0 1
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.063 0.061 -10000 0 -0.35 5 5
GAB1/SHC/GRB2/SOS1 0.042 0.041 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.06 0.059 -10000 0 -10000 0 0
IRS2 0.014 0.071 0.28 8 -0.29 35 43
STAT1 0.044 0.064 0.31 4 -10000 0 4
STAT5B 0.04 0.058 -10000 0 -0.34 1 1
cell proliferation 0.022 0.075 0.24 37 -0.32 5 42
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.044 -10000 0 -0.33 1 1
TEC 0.025 0.047 0.29 5 -0.3 1 6
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
STAT1 (dimer) 0.044 0.063 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
EPO/EPOR (dimer)/JAK2 0.08 0.062 0.33 3 -10000 0 3
EPO/EPOR 0.06 0.059 -10000 0 -10000 0 0
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.046 0.28 3 -0.29 1 4
elevation of cytosolic calcium ion concentration 0.026 0.013 0.26 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.061 0.054 -10000 0 -10000 0 0
mol:IP3 0.038 0.051 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.03 0.079 0.29 2 -0.29 37 39
SH2B3 0.026 0.009 -10000 0 -10000 0 0
NFKB1 0.042 0.066 0.24 35 -10000 0 35
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.042 -10000 0 -0.27 2 2
PTPN6 0.023 0.039 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.047 0.048 0.27 4 -0.28 1 5
EPOR 0.026 0.013 0.26 1 -10000 0 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.041 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
CRKL/CBL/C3G 0.046 0.047 0.28 4 -10000 0 4
VAV2 0.027 0.048 0.28 12 -10000 0 12
CBL 0.025 0.047 0.27 10 -10000 0 10
SHC/Grb2/SOS1 0.036 0.037 -10000 0 -10000 0 0
STAT5A 0.038 0.063 -10000 0 -0.33 6 6
GRB2 0.023 0.009 0.26 1 -10000 0 1
STAT5 (dimer) 0.051 0.079 0.34 1 -0.33 13 14
LYN/PLCgamma2 0.027 0.026 -10000 0 -0.42 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.027 0.048 0.3 8 -10000 0 8
BCL2 0.031 0.17 -10000 0 -0.83 35 35
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.021 0.084 0.31 5 -0.43 11 16
NFATC2 -0.005 0.071 0.18 4 -0.25 38 42
NFATC3 0.014 0.016 -10000 0 -0.4 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.094 0.29 2 -0.41 24 26
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.087 0.27 2 -0.46 10 12
BCL2/BAX 0.021 0.074 -10000 0 -0.41 28 28
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.013 -10000 0 -10000 0 0
BAX 0.025 0.014 0.26 4 -10000 0 4
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.009 0.26 1 -10000 0 1
CABIN1/MEF2D 0.019 0.083 -10000 0 -0.43 14 14
Calcineurin A alpha-beta B1/BCL2 0.008 0.094 -10000 0 -0.56 28 28
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.082 0.42 14 -10000 0 14
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 64 -10000 0 64
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
MAP3K8 0.019 0.048 -10000 0 -0.57 7 7
NFAT4/CK1 alpha 0.018 0.028 -10000 0 -0.28 2 2
MEF2D/NFAT1/Cbp/p300 0.008 0.11 -10000 0 -0.3 76 76
CABIN1 0.012 0.093 0.29 2 -0.41 23 25
CALM1 0.02 0.013 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
CAMK4 0.031 0.046 0.26 37 -0.57 1 38
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.041 0.038 -10000 0 -0.42 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.051 -10000 0 -0.57 8 8
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.096 0.3 1 -0.45 12 13
PRKCH 0.023 0.018 -10000 0 -0.57 1 1
CABIN1/Cbp/p300 0.027 0.023 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.009 -10000 0 -10000 0 0
apoptosis 0.011 0.033 -10000 0 -0.35 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.039 -10000 0 -0.28 4 4
PRKCB 0.019 0.076 0.26 19 -0.57 15 34
PRKCE 0.024 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.008 0.059 -10000 0 -0.37 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.021 0.02 -10000 0 -0.57 1 1
PRKCA 0.01 0.084 0.26 1 -0.57 22 23
PRKCG 0.03 0.045 0.26 41 -10000 0 41
PRKCQ 0.004 0.11 0.26 8 -0.57 39 47
FKBP38/BCL2 0.021 0.074 -10000 0 -0.42 28 28
EP300 0.019 0.016 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.086 0.32 1 -0.41 10 11
CaM/Ca2+/FKBP38 0.027 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.034 -10000 0 -0.36 1 1
NFATc/ERK1 0.03 0.082 0.32 1 -0.4 11 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.039 0.093 0.28 1 -0.45 15 16
NR4A1 -0.013 0.17 0.26 1 -0.51 94 95
GSK3B 0.022 0.008 -10000 0 -10000 0 0
positive T cell selection 0.014 0.016 -10000 0 -0.4 1 1
NFAT1/CK1 alpha -0.002 0.056 -10000 0 -0.26 10 10
RCH1/ KPNB1 0.041 0.04 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.034 0.053 0.26 52 -0.57 1 53
MEF2D 0.017 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.082 0.32 1 -0.41 10 11
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.008 0.094 -10000 0 -0.57 28 28
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.021 0.079 -10000 0 -0.42 33 33
AKT1 0.031 0.088 0.37 3 -0.56 8 11
PTK2B 0.003 0.084 0.35 1 -0.38 31 32
VEGFR2 homodimer/Frs2 0.024 0.063 -10000 0 -0.61 9 9
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.038 0.062 -10000 0 -0.57 9 9
endothelial cell proliferation 0.044 0.11 0.35 24 -0.56 9 33
mol:Ca2+ 0.014 0.056 -10000 0 -0.48 10 10
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.05 0.062 -10000 0 -0.52 10 10
RP11-342D11.1 0.004 0.055 -10000 0 -0.5 10 10
CDH5 0.018 0.048 -10000 0 -0.57 7 7
VEGFA homodimer 0.05 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.011 0.086 0.26 1 -0.57 23 24
HRAS/GDP 0.03 0.049 -10000 0 -0.57 4 4
SH2D2A 0.04 0.072 0.26 95 -0.57 2 97
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.086 -10000 0 -0.53 11 11
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.045 0.074 -10000 0 -0.48 11 11
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.059 -10000 0 -0.64 4 4
GRB10 0.014 0.057 -10000 0 -0.63 6 6
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.009 0.26 1 -10000 0 1
PAK1 0.023 0.019 0.26 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.05 0.075 -10000 0 -0.52 13 13
HRAS 0.026 0.022 0.26 9 -10000 0 9
VEGF/Rho/ROCK1/Integrin Complex 0.01 0.073 -10000 0 -0.47 12 12
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.048 0.061 -10000 0 -0.51 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.031 -10000 0 -0.57 3 3
Nck/Pak 0.033 0.017 0.2 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.036 0.066 -10000 0 -0.54 11 11
mol:GDP 0.039 0.054 -10000 0 -0.62 4 4
mol:NADP 0.025 0.083 0.56 1 -0.47 11 12
eNOS/Hsp90 0.037 0.08 0.54 1 -0.45 10 11
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
mol:IP3 0.014 0.056 -10000 0 -0.49 10 10
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.026 0.019 0.26 7 -10000 0 7
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.022 0.1 0.35 1 -0.65 10 11
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.039 0.095 -10000 0 -0.4 37 37
PTPN6 0.024 0.011 0.26 2 -10000 0 2
EPAS1 0.024 0.057 -10000 0 -0.53 10 10
mol:L-citrulline 0.025 0.083 0.56 1 -0.47 11 12
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.048 0.061 -10000 0 -0.52 9 9
VEGFR2 homodimer/VEGFA homodimer 0.041 0.062 -10000 0 -0.54 10 10
VEGFR2/3 heterodimer 0.023 0.07 -10000 0 -0.62 11 11
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.004 0.069 -10000 0 -0.66 7 7
VEGFR2 homodimer 0.011 0.069 -10000 0 -0.66 10 10
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.006 0.073 0.26 7 -0.56 7 14
MAPK1 0.009 0.075 0.26 6 -0.57 7 13
VEGFA145/NRP2 0.035 0.025 -10000 0 -0.32 3 3
VEGFR1/2 heterodimer 0.023 0.064 -10000 0 -0.6 10 10
KDR 0.011 0.069 -10000 0 -0.66 10 10
VEGFA165/NRP1/VEGFR2 homodimer 0.04 0.064 -10000 0 -0.53 10 10
SRC 0.023 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.014 0.082 0.29 6 -0.52 9 15
PI3K 0.025 0.072 -10000 0 -0.73 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.039 0.062 -10000 0 -0.54 10 10
FES 0.013 0.061 -10000 0 -0.46 13 13
GAB1 0.015 0.062 -10000 0 -0.62 6 6
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.061 -10000 0 -0.53 10 10
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.017 0.13 -10000 0 -0.49 22 22
VEGFR2 homodimer/VEGFA homodimer/Yes 0.037 0.063 -10000 0 -0.52 11 11
PI3K/GAB1 0.039 0.082 -10000 0 -0.55 8 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.053 0.063 -10000 0 -0.53 8 8
PRKACA 0.024 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.036 0.068 -10000 0 -0.57 11 11
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.014 0.059 -10000 0 -0.51 10 10
actin cytoskeleton reorganization 0.045 0.074 -10000 0 -0.47 11 11
PTK2 0.005 0.088 -10000 0 -0.7 10 10
EDG1 0.004 0.055 -10000 0 -0.5 10 10
mol:DAG 0.014 0.056 -10000 0 -0.49 10 10
CaM/Ca2+ 0.025 0.054 -10000 0 -0.47 9 9
MAP2K3 -0.006 0.062 -10000 0 -0.62 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.039 0.061 -10000 0 -0.66 6 6
PLCG1 0.014 0.057 -10000 0 -0.5 10 10
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.049 0.061 -10000 0 -0.5 10 10
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.039 0.062 -10000 0 -0.54 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.062 -10000 0 -0.57 9 9
cell migration 0.024 0.093 0.31 2 -0.61 9 11
mol:PI-3-4-5-P3 0.025 0.067 -10000 0 -0.66 6 6
FYN 0.022 0.026 -10000 0 -0.57 2 2
VEGFB/NRP1 0.019 0.055 -10000 0 -0.52 8 8
mol:NO 0.025 0.083 0.56 1 -0.47 11 12
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.044 -10000 0 -0.57 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.032 0.059 -10000 0 -0.66 6 6
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.006 0.1 0.26 4 -0.57 33 37
NOS3 0.025 0.09 0.57 1 -0.54 11 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.03 0.081 -10000 0 -0.39 32 32
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.009 0.073 0.35 1 -0.38 26 27
PRKCB -0.005 0.067 -10000 0 -0.44 14 14
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.022 0.057 -10000 0 -0.5 10 10
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.064 -10000 0 -0.55 10 10
VEGFA165/NRP2 0.035 0.025 -10000 0 -0.32 3 3
MAPKKK cascade 0.05 0.079 0.33 11 -0.58 4 15
NRP2 0.023 0.027 0.26 1 -0.57 2 3
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.018 -10000 0 -0.57 1 1
FAK1/Paxillin 0.023 0.1 0.42 2 -0.65 10 12
MAP3K13 0.012 0.061 -10000 0 -0.47 13 13
PDPK1 0.014 0.06 0.27 1 -0.58 5 6
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.033 0.057 -9999 0 -0.36 18 18
E-cadherin/beta catenin 0.022 0.062 -9999 0 -0.42 18 18
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.012 0.076 -9999 0 -0.57 18 18
Signaling events mediated by HDAC Class II

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

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

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

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.41 68 68
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.004 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.11 0.15 0.4 1 -0.41 81 82
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.008 0.026 -10000 0 -0.42 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.02 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.024 0.024 0.26 11 -10000 0 11
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.01 0.016 0.24 5 -10000 0 5
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.019 0.063 0.26 1 -0.33 11 12
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.12 0.16 0.41 1 -0.46 81 82
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.021 0.07 0.26 21 -0.57 12 33
LNPEP 0.019 0.051 -10000 0 -0.57 8 8
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.05 0.061 -10000 0 -0.37 8 8
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.06 -10000 0 -0.32 11 11
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.021 0.26 7 -10000 0 7
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.053 0.041 -10000 0 -0.4 1 1
YY1/LSF 0.024 0.049 -10000 0 -0.25 16 16
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.03 -10000 0 -0.3 7 7
I kappa B alpha/HDAC1 0.03 0.036 -10000 0 -0.22 7 7
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.02 0.036 -10000 0 -0.3 7 7
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.031 0.036 -10000 0 -0.43 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.28 12 12
NF kappa B1 p50/RelA 0.026 0.064 0.38 1 -0.28 12 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.013 0.095 0.26 13 -0.57 26 39
GATA1 0.026 0.029 0.26 17 -10000 0 17
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.079 -10000 0 -0.36 20 20
RBBP7 0.026 0.019 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.018 -10000 0 -0.57 1 1
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.026 -10000 0 -0.25 7 7
KAT2B 0.024 0.018 -10000 0 -0.57 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.029 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.022 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.015 0.26 4 -10000 0 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.046 -10000 0 -0.35 4 4
YY1/HDAC2 0.025 0.045 -10000 0 -0.24 14 14
YY1/HDAC1 0.025 0.047 -10000 0 -0.24 13 13
NuRD/MBD2 Complex (MeCP1) 0.024 0.054 -10000 0 -0.27 13 13
PPARG -0.06 0.16 -10000 0 -0.34 226 226
HDAC8/hEST1B 0.041 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.036 -10000 0 -0.43 1 1
MBD3L2 0.017 0.011 0.26 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.065 -10000 0 -0.35 14 14
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.019 0.027 -10000 0 -0.24 8 8
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.011 -10000 0 -0.29 1 1
HDAC8 0.024 0.001 -10000 0 -10000 0 0
SMAD7 0.023 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.007 0.26 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.036 0.048 -10000 0 -0.27 7 7
YY1/SAP30/HDAC1 0.036 0.047 -10000 0 -0.25 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.026 -10000 0 -0.24 7 7
histone deacetylation 0.024 0.053 -10000 0 -0.27 13 13
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.035 -10000 0 -0.33 2 2
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GATAD2B 0.02 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.025 0.065 -10000 0 -0.33 23 23
GATA1/HDAC1 0.036 0.02 0.2 15 -10000 0 15
GATA1/HDAC3 0.032 0.041 -10000 0 -0.45 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.049 -10000 0 -0.42 9 9
SIN3/HDAC complex/Mad/Max 0.016 0.052 -10000 0 -0.29 17 17
NuRD Complex 0.025 0.065 -10000 0 -0.38 9 9
positive regulation of chromatin silencing 0.05 0.039 -10000 0 -0.39 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.21 7 7
HDAC complex 0.057 0.022 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.025 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.015 -10000 0 -10000 0 0
TNF 0.024 0.065 0.26 25 -0.57 9 34
negative regulation of cell growth 0.016 0.052 -10000 0 -0.29 17 17
NuRD/MBD2/PRMT5 Complex 0.024 0.054 -10000 0 -0.27 13 13
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NF kappa B/RelA/I kappa B alpha 0.019 0.051 -10000 0 -0.35 8 8
SIN3/HDAC complex/NCoR1 0.007 0.066 -10000 0 -0.32 28 28
TFCP2 0.024 0.018 -10000 0 -0.57 1 1
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.009 0.26 1 -10000 0 1
MBD2 0.023 0.005 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.026 0.018 -10000 0 -0.46 1 1
VEGFR1 homodimer/NRP1 0.01 0.015 -10000 0 -0.48 1 1
mol:DAG 0.013 0.03 -10000 0 -0.38 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.02 -10000 0 -0.44 1 1
CaM/Ca2+ 0.026 0.029 -10000 0 -0.42 1 1
HIF1A 0.028 0.011 -10000 0 -0.31 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.009 0.051 -10000 0 -0.42 1 1
PLCG1 0.013 0.03 -10000 0 -0.38 2 2
NOS3 0.016 0.052 -10000 0 -0.52 2 2
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:NO 0.02 0.061 0.3 1 -0.45 5 6
FLT1 0.014 0.018 -10000 0 -0.55 1 1
PGF 0.024 0.024 0.26 5 -0.57 1 6
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.03 -10000 0 -0.44 2 2
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.032 0.063 -10000 0 -0.43 6 6
endothelial cell proliferation 0.011 0.081 0.34 5 -0.68 3 8
mol:Ca2+ 0.013 0.03 -10000 0 -0.38 2 2
MAPK3 -0.012 0.049 -10000 0 -0.66 1 1
MAPK1 -0.012 0.048 -10000 0 -0.65 1 1
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
PLGF homodimer 0.024 0.024 0.26 5 -0.56 1 6
PRKACA 0.024 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.1 0.24 -10000 0 -0.57 225 225
VEGFA homodimer 0.025 0.019 0.26 7 -10000 0 7
VEGFR1 homodimer/VEGFA homodimer 0.027 0.022 -10000 0 -0.48 1 1
platelet activating factor biosynthetic process -0.013 0.046 -10000 0 -0.63 1 1
PI3K 0.044 0.048 -10000 0 -0.32 14 14
PRKCA -0.011 0.052 0.24 1 -0.69 1 2
PRKCB -0.009 0.048 -10000 0 -0.69 1 1
VEGFR1 homodimer/PLGF homodimer 0.027 0.024 -10000 0 -0.42 2 2
VEGFA 0.025 0.019 0.26 7 -10000 0 7
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.03 -10000 0 -0.38 2 2
RASA1 0.013 0.028 -10000 0 -0.43 1 1
NRP2 0.023 0.027 0.26 1 -0.57 2 3
VEGFR1 homodimer 0.013 0.018 -10000 0 -0.55 1 1
VEGFB homodimer 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.029 0.14 -10000 0 -0.47 17 17
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.047 -10000 0 -0.32 14 14
mol:L-citrulline 0.02 0.061 0.3 1 -0.45 5 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.028 -10000 0 -0.41 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.039 0.023 -10000 0 -0.44 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.052 0.05 -10000 0 -0.4 1 1
PDPK1 -0.005 0.053 -10000 0 -0.4 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.023 -10000 0 -0.44 1 1
mol:NADP 0.02 0.061 0.3 1 -0.45 5 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.027 -10000 0 -0.4 1 1
VEGFR1 homodimer/NRP2 0.026 0.027 -10000 0 -0.44 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.004 0.039 0.21 1 -0.24 9 10
SMAD3 0.022 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.063 -10000 0 -0.46 10 10
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.058 -10000 0 -0.28 1 1
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.28 7 7
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
TRAP-1/SMAD4 0.027 0.056 -10000 0 -0.42 16 16
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.015 0.072 -10000 0 -0.57 16 16
UBE2I 0.023 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.005 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 64 -10000 0 64
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.022 0.26 10 -10000 0 10
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.039 0.21 36 -0.42 2 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.017 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.044 0.035 0.33 4 -0.33 2 6
lamellipodium assembly -0.003 0.088 -10000 0 -0.42 33 33
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.4 13 13
ARF6 0.024 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.004 -10000 0 -10000 0 0
PXN 0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
ARF6/GTP 0.047 0.02 -10000 0 -10000 0 0
cell adhesion 0.05 0.019 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.016 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.03 0.046 0.26 30 -0.57 2 32
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.048 0.043 -10000 0 -0.31 11 11
p130Cas/Crk/Dock1 0.041 0.019 -10000 0 -10000 0 0
VCAM1 0.019 0.062 0.26 6 -0.57 11 17
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.019 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.021 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.047 0.021 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.019 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.097 -10000 0 -0.46 33 33
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.034 0.011 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.043 -10000 0 -0.33 2 2
NFKBIA 0.015 0.037 -10000 0 -0.25 11 11
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.017 0.067 -10000 0 -0.57 14 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.013 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.012 0.25 2 -10000 0 2
PIK3R1 0.016 0.065 -10000 0 -0.57 13 13
NFKB1 0.01 0.011 0.26 2 -10000 0 2
RELA 0.023 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.024 0.046 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.046 -10000 0 -0.33 3 3
SRC 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.049 -10000 0 -0.4 13 13
NF kappa B1 p50/RelA 0.024 0.046 -10000 0 -0.26 10 10
IKBKB 0.02 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.057 -10000 0 -0.29 16 16
cell death 0.024 0.044 -10000 0 -0.32 3 3
NF kappa B1 p105/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
LCK 0.026 0.075 0.26 40 -0.57 11 51
BCL3 0.024 0.011 0.26 2 -10000 0 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.042 0.035 -10000 0 -10000 0 0
CLOCK 0.02 0.06 -10000 0 -0.56 11 11
TIMELESS/CRY2 0.031 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.014 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.017 -10000 0 -10000 0 0
ARNTL 0.026 0.004 -10000 0 -10000 0 0
TIMELESS 0.018 0.024 -10000 0 -10000 0 0
NPAS2 0.023 0.041 0.26 1 -0.56 5 6
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.006 -10000 0 -0.09 6 6
CHEK1 0.027 0.035 0.26 23 -10000 0 23
mol:HEME 0.007 0.006 0.09 6 -10000 0 6
PER1 0.013 0.072 -10000 0 -0.57 16 16
BMAL/CLOCK/NPAS2 0.049 0.052 -10000 0 -0.36 16 16
BMAL1/CLOCK 0.019 0.062 -10000 0 -0.48 1 1
S phase of mitotic cell cycle 0.042 0.035 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.042 0.036 -10000 0 -10000 0 0
mol:NADPH 0.007 0.006 0.09 6 -10000 0 6
PER1/TIMELESS 0.024 0.046 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.018 0.26 6 -10000 0 6
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.04 0.069 -10000 0 -10000 0 0
regulation of axonogenesis -0.011 0.026 0.24 3 -10000 0 3
myoblast fusion -0.026 0.047 -10000 0 -0.22 1 1
mol:GTP 0.023 0.031 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.055 0.044 -10000 0 -0.3 2 2
ARF1/GTP 0.03 0.028 -10000 0 -10000 0 0
mol:GM1 0.012 0.024 -10000 0 -10000 0 0
mol:Choline 0.008 0.038 -10000 0 -0.34 9 9
lamellipodium assembly 0.018 0.058 -10000 0 -0.36 7 7
MAPK3 0.032 0.045 0.21 1 -10000 0 1
ARF6/GTP/NME1/Tiam1 0.056 0.045 0.31 2 -10000 0 2
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.047 0.22 1 -10000 0 1
ARF1/GDP 0.025 0.047 -10000 0 -0.26 2 2
ARF6 0.032 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.015 0.25 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.032 0.044 -10000 0 -10000 0 0
actin filament bundle formation -0.032 0.05 0.26 3 -10000 0 3
KALRN 0.01 0.054 -10000 0 -0.31 20 20
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.033 0.05 -10000 0 -0.26 3 3
NME1 0.028 0.031 0.26 18 -10000 0 18
Rac1/GDP 0.033 0.051 -10000 0 -0.26 3 3
substrate adhesion-dependent cell spreading 0.023 0.031 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.018 0.058 -10000 0 -0.37 7 7
RAC1 0.024 0.003 -10000 0 -10000 0 0
liver development 0.023 0.031 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.031 -10000 0 -10000 0 0
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.046 0.23 1 -10000 0 1
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.029 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.045 -10000 0 -0.39 9 9
RAB11FIP3 0.023 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.018 0.058 -10000 0 -0.36 7 7
ruffle organization 0.011 0.026 -10000 0 -0.24 3 3
regulation of epithelial cell migration 0.023 0.031 -10000 0 -10000 0 0
PLD2 0.02 0.024 -10000 0 -10000 0 0
PIP5K1A 0.011 0.026 -10000 0 -0.24 3 3
mol:Phosphatidic acid 0.008 0.038 -10000 0 -0.34 9 9
Rac1/GTP 0.018 0.058 -10000 0 -0.37 7 7
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.011 -10000 0 -0.26 1 1
MDM2/SUMO1 0.033 0.039 -10000 0 -0.23 4 4
HDAC4 0.023 0.018 -10000 0 -0.57 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.017 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.01 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.035 0.039 -10000 0 -0.23 5 5
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.21 7 7
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.056 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.036 -10000 0 -0.24 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.038 0.25 1 -0.24 4 5
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.032 0.18 3 -10000 0 3
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.047 -10000 0 -0.18 5 5
AP2 0.034 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.01 -10000 0 -10000 0 0
CLTB 0.025 0.015 0.26 4 -10000 0 4
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.01 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.015 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.012 0.2 3 -10000 0 3
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.01 -10000 0 -10000 0 0
DDEF1 0.006 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.02 -10000 0 -0.15 1 1
AP2M1 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.017 -10000 0 -10000 0 0
ARFIP2 0.015 0.018 -10000 0 -10000 0 0
COPA 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.011 0.023 -10000 0 -0.2 3 3
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.041 -10000 0 -0.24 20 20
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.023 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.013 0.048 -10000 0 -0.26 28 28
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.023 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 -10000 0 -10000 0 0
PIP5K1A 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.006 -10000 0 -10000 0 0
GOSR2 0.008 0.028 -10000 0 -0.31 7 7
USO1 0.01 0.02 -10000 0 -0.32 3 3
GBF1 0.009 0.024 -10000 0 -0.31 5 5
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.015 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.067 0.025 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.016 0.2 9 -9999 0 9
RELB 0.026 0.022 0.26 10 -9999 0 10
NFKB2 0.024 0.008 0.26 1 -9999 0 1
NF kappa B2 p52/RelB 0.033 0.016 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.016 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

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

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

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/14525124/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/15076766/GDAC_Gistic2Report_15084472/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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